Query 032832
Match_columns 132
No_of_seqs 139 out of 878
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 06:29:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032832hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12286 rpmF 50S ribosomal pr 99.8 1.1E-21 2.5E-26 130.0 3.2 49 81-130 1-50 (57)
2 KOG4080 Mitochondrial ribosoma 99.8 2.7E-21 5.9E-26 152.1 0.6 91 30-132 24-117 (176)
3 COG0333 RpmF Ribosomal protein 99.8 5.9E-21 1.3E-25 127.1 1.8 49 81-130 1-50 (57)
4 PRK01110 rpmF 50S ribosomal pr 99.8 1.6E-20 3.4E-25 125.6 2.9 49 81-130 1-49 (60)
5 PF01783 Ribosomal_L32p: Ribos 99.8 5.4E-20 1.2E-24 120.8 2.0 49 82-131 1-50 (56)
6 TIGR01031 rpmF_bact ribosomal 99.7 1E-18 2.2E-23 114.9 3.2 47 83-130 1-49 (55)
7 CHL00152 rpl32 ribosomal prote 97.8 2.1E-06 4.6E-11 56.7 -2.0 22 81-102 1-22 (53)
8 PRK14892 putative transcriptio 97.7 3.5E-05 7.5E-10 56.3 3.7 26 101-127 15-48 (99)
9 COG1545 Predicted nucleic-acid 85.4 0.56 1.2E-05 35.6 1.8 23 108-130 29-52 (140)
10 PF12172 DUF35_N: Rubredoxin-l 78.3 1.4 3E-05 25.9 1.4 22 107-128 10-32 (37)
11 smart00661 RPOL9 RNA polymeras 78.1 1.4 3.1E-05 27.0 1.5 7 111-117 3-9 (52)
12 PF13248 zf-ribbon_3: zinc-rib 76.1 0.99 2.1E-05 25.1 0.3 19 109-127 3-22 (26)
13 PRK13130 H/ACA RNA-protein com 72.2 2.7 5.8E-05 27.9 1.6 20 107-127 4-23 (56)
14 COG2191 Formylmethanofuran deh 71.7 2 4.3E-05 35.4 1.1 25 107-131 171-203 (206)
15 PRK14890 putative Zn-ribbon RN 71.0 3.1 6.6E-05 28.2 1.7 11 107-117 24-34 (59)
16 PF13240 zinc_ribbon_2: zinc-r 70.5 1.7 3.7E-05 23.8 0.4 9 111-119 2-10 (23)
17 COG2260 Predicted Zn-ribbon RN 69.1 2.5 5.5E-05 28.6 1.0 17 110-127 7-23 (59)
18 PRK00432 30S ribosomal protein 67.4 3.6 7.7E-05 26.4 1.4 21 107-127 19-43 (50)
19 PRK08271 anaerobic ribonucleos 66.5 2.9 6.3E-05 39.0 1.2 23 105-127 563-586 (623)
20 COG4888 Uncharacterized Zn rib 65.4 8.1 0.00017 28.8 3.1 16 105-120 19-34 (104)
21 PF13597 NRDD: Anaerobic ribon 60.7 5.2 0.00011 36.4 1.7 23 105-127 488-510 (546)
22 PRK08579 anaerobic ribonucleos 60.7 4.3 9.3E-05 37.9 1.2 23 105-127 565-588 (625)
23 PF07754 DUF1610: Domain of un 58.8 4.5 9.7E-05 22.8 0.6 10 107-116 15-24 (24)
24 KOG2879 Predicted E3 ubiquitin 57.5 5.1 0.00011 34.6 1.0 24 106-129 237-265 (298)
25 PRK07111 anaerobic ribonucleos 56.3 6.4 0.00014 37.3 1.5 24 104-127 676-699 (735)
26 PRK08270 anaerobic ribonucleos 55.9 5.9 0.00013 37.1 1.3 23 105-127 623-645 (656)
27 TIGR00100 hypA hydrogenase nic 55.4 6.8 0.00015 28.6 1.3 27 101-127 63-92 (115)
28 PRK05978 hypothetical protein; 54.0 6 0.00013 30.8 0.8 19 109-127 34-58 (148)
29 TIGR02827 RNR_anaer_Bdell anae 53.2 7.6 0.00016 36.1 1.5 23 105-127 529-552 (586)
30 TIGR02098 MJ0042_CXXC MJ0042 f 51.3 15 0.00033 21.3 2.1 10 108-117 25-34 (38)
31 PRK00420 hypothetical protein; 51.2 9 0.0002 28.6 1.4 19 109-127 24-46 (112)
32 PRK12380 hydrogenase nickel in 50.4 12 0.00026 27.3 1.9 26 102-127 64-92 (113)
33 COG0675 Transposase and inacti 50.1 11 0.00023 29.7 1.7 23 105-127 306-328 (364)
34 PF10571 UPF0547: Uncharacteri 49.9 8.1 0.00018 21.8 0.7 17 110-126 2-19 (26)
35 PHA00626 hypothetical protein 49.8 12 0.00026 25.3 1.7 7 110-116 2-8 (59)
36 TIGR00515 accD acetyl-CoA carb 49.6 10 0.00023 32.0 1.7 21 107-127 25-51 (285)
37 PF13913 zf-C2HC_2: zinc-finge 48.6 5.5 0.00012 21.9 -0.1 15 107-121 1-15 (25)
38 PF14446 Prok-RING_1: Prokaryo 48.5 14 0.00031 24.5 1.8 23 101-125 14-36 (54)
39 COG1645 Uncharacterized Zn-fin 48.2 9.8 0.00021 29.3 1.2 28 96-128 21-51 (131)
40 PRK03824 hypA hydrogenase nick 47.7 12 0.00026 28.1 1.6 17 102-118 64-80 (135)
41 PF09297 zf-NADH-PPase: NADH p 47.7 8.5 0.00018 22.0 0.6 18 110-127 5-27 (32)
42 COG0777 AccD Acetyl-CoA carbox 46.9 15 0.00032 31.8 2.2 23 106-128 26-54 (294)
43 PF02591 DUF164: Putative zinc 46.9 12 0.00025 23.8 1.2 12 106-117 44-55 (56)
44 PF03833 PolC_DP2: DNA polymer 46.4 6.6 0.00014 38.4 0.0 20 108-127 667-686 (900)
45 PF07282 OrfB_Zn_ribbon: Putat 46.1 12 0.00027 24.1 1.3 12 106-117 44-55 (69)
46 PF14319 Zn_Tnp_IS91: Transpos 45.0 15 0.00033 26.7 1.7 23 106-128 40-67 (111)
47 PRK03681 hypA hydrogenase nick 43.7 16 0.00035 26.7 1.7 26 102-127 64-93 (114)
48 PF14803 Nudix_N_2: Nudix N-te 41.8 9.2 0.0002 22.9 0.1 18 110-127 2-28 (34)
49 PF08209 Sgf11: Sgf11 (transcr 41.2 20 0.00043 21.4 1.5 17 106-122 2-18 (33)
50 PF06677 Auto_anti-p27: Sjogre 41.2 17 0.00036 22.6 1.2 19 109-127 18-40 (41)
51 PF12773 DZR: Double zinc ribb 40.3 16 0.00035 22.2 1.1 19 108-126 29-48 (50)
52 PF12653 DUF3785: Protein of u 39.4 12 0.00027 29.1 0.5 15 105-119 117-131 (138)
53 PRK14704 anaerobic ribonucleos 38.4 18 0.00039 33.8 1.5 23 105-127 556-578 (618)
54 TIGR03826 YvyF flagellar opero 37.7 8.3 0.00018 29.6 -0.6 22 108-129 81-102 (137)
55 PF08792 A2L_zn_ribbon: A2L zi 37.5 22 0.00049 21.0 1.3 20 108-127 3-27 (33)
56 CHL00174 accD acetyl-CoA carbo 37.3 15 0.00033 31.5 0.9 21 107-127 37-63 (296)
57 PF02150 RNA_POL_M_15KD: RNA p 36.6 14 0.0003 21.9 0.4 19 109-127 2-26 (35)
58 PF05876 Terminase_GpA: Phage 35.6 22 0.00048 32.4 1.6 11 108-118 200-210 (557)
59 PRK14714 DNA polymerase II lar 35.5 19 0.00041 36.8 1.3 18 109-127 668-685 (1337)
60 PRK04023 DNA polymerase II lar 34.9 19 0.00042 36.1 1.2 18 110-127 640-657 (1121)
61 PRK09335 30S ribosomal protein 34.3 34 0.00074 25.1 2.1 31 84-120 2-32 (95)
62 PRK00564 hypA hydrogenase nick 34.1 25 0.00055 25.8 1.5 26 102-127 65-94 (117)
63 PRK05654 acetyl-CoA carboxylas 33.8 20 0.00043 30.5 1.0 21 107-127 26-52 (292)
64 PF08271 TF_Zn_Ribbon: TFIIB z 33.6 27 0.00059 21.0 1.3 12 109-120 20-31 (43)
65 PRK09263 anaerobic ribonucleos 32.8 23 0.00049 33.6 1.2 23 105-127 638-665 (711)
66 PF12661 hEGF: Human growth fa 32.2 20 0.00043 17.2 0.4 10 123-132 3-12 (13)
67 smart00834 CxxC_CXXC_SSSS Puta 32.1 21 0.00046 20.6 0.6 12 106-117 24-35 (41)
68 PF06044 DRP: Dam-replacing fa 31.9 20 0.00043 30.5 0.7 19 109-127 32-59 (254)
69 TIGR02487 NrdD anaerobic ribon 31.4 24 0.00053 32.4 1.2 23 105-127 521-544 (579)
70 PF14353 CpXC: CpXC protein 31.2 27 0.00059 25.2 1.2 15 105-119 35-49 (128)
71 cd01675 RNR_III Class III ribo 30.3 26 0.00057 32.0 1.2 22 105-127 516-538 (555)
72 PRK00762 hypA hydrogenase nick 30.2 29 0.00063 25.7 1.2 15 102-117 64-78 (124)
73 cd00729 rubredoxin_SM Rubredox 29.4 38 0.00082 19.9 1.4 8 110-117 4-11 (34)
74 COG4830 RPS26B Ribosomal prote 28.6 38 0.00082 25.4 1.6 31 84-120 2-32 (108)
75 COG3024 Uncharacterized protei 28.5 24 0.00053 24.3 0.5 15 106-120 5-19 (65)
76 PF01155 HypA: Hydrogenase exp 28.3 25 0.00054 25.5 0.6 26 102-127 64-92 (113)
77 PTZ00172 40S ribosomal protein 28.0 45 0.00098 25.0 1.9 30 84-119 2-31 (108)
78 COG1439 Predicted nucleic acid 27.7 31 0.00066 27.8 1.0 46 79-125 122-170 (177)
79 PLN00186 ribosomal protein S26 27.7 47 0.001 25.0 2.0 30 84-119 2-31 (109)
80 PRK07218 replication factor A; 27.6 31 0.00068 30.8 1.2 19 108-127 297-315 (423)
81 PRK02935 hypothetical protein; 27.4 40 0.00087 25.4 1.5 22 106-127 68-92 (110)
82 PHA02942 putative transposase; 27.1 38 0.00082 29.6 1.6 23 107-129 324-351 (383)
83 smart00659 RPOLCX RNA polymera 27.0 35 0.00077 21.2 1.0 14 106-119 17-30 (44)
84 PF13408 Zn_ribbon_recom: Reco 26.7 34 0.00074 20.8 0.9 17 106-122 3-19 (58)
85 COG1885 Uncharacterized protei 26.5 33 0.00071 26.0 0.9 23 101-123 42-64 (115)
86 PF11023 DUF2614: Protein of u 26.3 27 0.0006 26.4 0.5 21 107-127 68-91 (114)
87 PRK01103 formamidopyrimidine/5 26.3 42 0.00091 27.6 1.6 21 109-129 246-273 (274)
88 TIGR02605 CxxC_CxxC_SSSS putat 25.4 32 0.00069 21.1 0.6 11 107-117 25-35 (52)
89 PRK12495 hypothetical protein; 25.3 39 0.00084 28.3 1.3 23 106-128 40-65 (226)
90 PF09986 DUF2225: Uncharacteri 24.7 37 0.00081 27.2 1.0 11 107-117 47-57 (214)
91 PF09723 Zn-ribbon_8: Zinc rib 24.7 34 0.00074 20.7 0.6 12 106-117 24-35 (42)
92 PRK14714 DNA polymerase II lar 24.5 43 0.00094 34.4 1.6 19 109-127 680-698 (1337)
93 PF06827 zf-FPG_IleRS: Zinc fi 24.5 43 0.00093 18.6 1.0 19 110-128 3-28 (30)
94 PRK00398 rpoP DNA-directed RNA 24.3 44 0.00095 20.3 1.1 12 108-119 21-32 (46)
95 PF04475 DUF555: Protein of un 24.2 26 0.00055 26.1 0.0 23 100-122 39-61 (102)
96 PF05129 Elf1: Transcription e 24.1 31 0.00066 24.0 0.4 11 105-115 19-29 (81)
97 COG1579 Zn-ribbon protein, pos 23.8 31 0.00067 28.8 0.4 14 105-118 218-231 (239)
98 COG2888 Predicted Zn-ribbon RN 23.8 36 0.00078 23.2 0.7 24 107-130 26-60 (61)
99 PF01396 zf-C4_Topoisom: Topoi 23.7 37 0.0008 20.4 0.7 10 109-118 2-11 (39)
100 smart00064 FYVE Protein presen 23.6 25 0.00055 22.5 -0.1 11 120-130 55-65 (68)
101 PF14952 zf-tcix: Putative tre 23.5 33 0.00072 22.0 0.4 13 106-118 9-21 (44)
102 PF04135 Nop10p: Nucleolar RNA 23.2 68 0.0015 21.1 1.9 8 110-117 19-26 (53)
103 PRK01343 zinc-binding protein; 23.2 55 0.0012 21.9 1.5 20 107-127 8-27 (57)
104 PF04981 NMD3: NMD3 family ; 22.8 63 0.0014 26.0 2.0 20 102-121 29-48 (236)
105 PF13719 zinc_ribbon_5: zinc-r 22.8 72 0.0016 18.8 1.8 17 102-118 19-35 (37)
106 cd00350 rubredoxin_like Rubred 22.4 34 0.00075 19.7 0.3 11 108-118 17-27 (33)
107 PF12677 DUF3797: Domain of un 22.4 36 0.00079 22.3 0.4 14 106-119 11-24 (49)
108 TIGR03831 YgiT_finger YgiT-typ 22.3 37 0.00079 19.8 0.4 12 107-118 31-42 (46)
109 PF13878 zf-C2H2_3: zinc-finge 21.6 44 0.00095 20.4 0.7 11 107-117 12-22 (41)
110 PF13717 zinc_ribbon_4: zinc-r 21.5 63 0.0014 19.1 1.4 16 102-117 19-34 (36)
111 cd01407 SIR2-fam SIR2 family o 20.8 52 0.0011 25.9 1.1 18 107-124 132-149 (218)
112 PF03884 DUF329: Domain of unk 20.7 54 0.0012 21.8 1.0 12 109-120 3-14 (57)
113 TIGR01206 lysW lysine biosynth 20.5 54 0.0012 21.4 1.0 12 106-117 20-31 (54)
114 cd01413 SIR2_Af2 SIR2_Af2: Arc 20.4 53 0.0012 26.1 1.1 17 108-124 136-152 (222)
115 PF07191 zinc-ribbons_6: zinc- 20.3 50 0.0011 22.9 0.8 19 108-126 30-48 (70)
116 PF05180 zf-DNL: DNL zinc fing 20.3 58 0.0013 22.3 1.1 14 106-119 27-40 (66)
117 PF12230 PRP21_like_P: Pre-mRN 20.2 34 0.00074 27.2 0.0 15 105-119 165-179 (229)
No 1
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=99.84 E-value=1.1e-21 Score=129.96 Aligned_cols=49 Identities=45% Similarity=0.722 Sum_probs=45.8
Q ss_pred eeCCCCCCCccccCCCCCCCCCCCCCCeeecCCCCceecCceeCCCC-ccc
Q 032832 81 MAVPKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKLPHFFCCSG-ERK 130 (132)
Q Consensus 81 MAVPKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~klpH~vC~~g-y~k 130 (132)
|||||+|+|++|+++||+|+.+. +++|+.||+||+++++|+||++| ||+
T Consensus 1 MAvPKrk~S~srr~~RRsh~~l~-~~~l~~C~~CG~~~~~H~vC~~CG~Y~ 50 (57)
T PRK12286 1 MAVPKRKTSKSRKRKRRAHFKLK-APGLVECPNCGEPKLPHRVCPSCGYYK 50 (57)
T ss_pred CCcCcCcCChhhcchhccccccc-CCcceECCCCCCccCCeEECCCCCcCC
Confidence 99999999999999999998886 79999999999999999999995 554
No 2
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=2.7e-21 Score=152.06 Aligned_cols=91 Identities=27% Similarity=0.458 Sum_probs=70.3
Q ss_pred CCCCCchhhhcCCCCCCCCCCccccCCCCCCCCCCCCcCCCcceeCCcceeeeCCCCCCCccccCCCC---CCCCCCCCC
Q 032832 30 LPLPLDTAISSQIPPPPLVLPEFDRNGDTTNYNNNSEFGFPSYSFAGSMELMAVPKKKVSRHKRGIRN---GPKALKPVP 106 (132)
Q Consensus 30 ~~ppl~pala~~~~~P~~~lp~~~~~~~~~~~~~~~~~~~P~~~~~~~~~lMAVPKrK~SksRkr~RR---sh~~lk~~~ 106 (132)
++.||+++|+ +..++. +|++.++- +.+.++ .++.++.+||||||+|+|++++++|+ +.+.|+++.
T Consensus 24 ~s~p~~~~L~--~~~~s~-~~~ls~d~--~~s~e~-------~~l~~n~illAVPK~r~S~eK~~kRk~~~~~k~Lk~k~ 91 (176)
T KOG4080|consen 24 PSIPFAKALG--VFQSST-APKLSQDY--SSSREN-------SMLIDNSILLAVPKKRTSKEKKVKRKFLYTRKLLKPKD 91 (176)
T ss_pred CCCCchhhhc--ccchhh-cccccccc--ccCCcc-------ccccccceEEeccccccchhhhhhhhccCccccccchh
Confidence 3456666666 777755 88886653 333443 33556678999999999999966654 346899999
Q ss_pred CeeecCCCCceecCceeCCCCcccCC
Q 032832 107 VIVRCKSCGRVKLPHFFCCSGERKNH 132 (132)
Q Consensus 107 ~L~~Cp~CGe~klpH~vC~~gy~k~~ 132 (132)
||..||.||++|+.|++|.+||+++|
T Consensus 92 nl~~CP~CGh~k~a~~LC~~Cy~kV~ 117 (176)
T KOG4080|consen 92 NLNTCPACGHIKPAHTLCDYCYAKVH 117 (176)
T ss_pred ccccCcccCccccccccHHHHHHHHH
Confidence 99999999999999999999999875
No 3
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=5.9e-21 Score=127.13 Aligned_cols=49 Identities=45% Similarity=0.789 Sum_probs=45.8
Q ss_pred eeCCCCCCCccccCCCCCCCCCCCCCCeeecCCCCceecCceeCCCC-ccc
Q 032832 81 MAVPKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKLPHFFCCSG-ERK 130 (132)
Q Consensus 81 MAVPKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~klpH~vC~~g-y~k 130 (132)
|||||+|+|++|+++||+|+.++ ++++++|++||+++++|+||..| ||+
T Consensus 1 MAVPkrktSksrr~~RRsh~~l~-~~~~~~c~~cG~~~l~Hrvc~~cg~Y~ 50 (57)
T COG0333 1 MAVPKRKTSKSRRRMRRSHDALK-APTLSVCPNCGEYKLPHRVCLKCGYYK 50 (57)
T ss_pred CCCCcccCChhhhhhhhhhHhhh-CccceeccCCCCcccCceEcCCCCCcc
Confidence 99999999999999999999998 68899999999999999999995 554
No 4
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=99.80 E-value=1.6e-20 Score=125.55 Aligned_cols=49 Identities=39% Similarity=0.548 Sum_probs=45.5
Q ss_pred eeCCCCCCCccccCCCCCCCCCCCCCCeeecCCCCceecCceeCCCCccc
Q 032832 81 MAVPKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKLPHFFCCSGERK 130 (132)
Q Consensus 81 MAVPKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~klpH~vC~~gy~k 130 (132)
|||||+|+|++|+++||+||.++ .++++.|++||+++++|++|+.|||+
T Consensus 1 MAVPKrK~Sksr~~~RRa~~~~~-~~~~~~c~~cg~~~~pH~vc~cG~Y~ 49 (60)
T PRK01110 1 MAVPKRKTSKSKRRMRRSHWKLT-APTLSVDKTTGEYHLPHHVSPKGYYK 49 (60)
T ss_pred CCCCcCccchhhchhhhhhhhcc-CCceeEcCCCCceeccceecCCcccC
Confidence 99999999999999999999887 69999999999999999999955664
No 5
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=99.78 E-value=5.4e-20 Score=120.75 Aligned_cols=49 Identities=43% Similarity=0.750 Sum_probs=40.0
Q ss_pred eCCCCCCCccccCCCCCCCCCCCCCCeeecCCCCceecCceeCCCC-cccC
Q 032832 82 AVPKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKLPHFFCCSG-ERKN 131 (132)
Q Consensus 82 AVPKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~klpH~vC~~g-y~k~ 131 (132)
||||+|+|++|+++||+||+++. ++|+.||+||+++++|+||+.| ||+.
T Consensus 1 AvPKrk~Sksr~~~Rrs~~~l~~-~~l~~c~~cg~~~~~H~vc~~cG~y~~ 50 (56)
T PF01783_consen 1 AVPKRKTSKSRKRMRRSHWKLKA-PNLVKCPNCGEPKLPHRVCPSCGYYKG 50 (56)
T ss_dssp ---SS-SCHHHHHHHTTTTS--T-TSEEESSSSSSEESTTSBCTTTBBSSS
T ss_pred CCCCCcCChhHccchhccccccc-cceeeeccCCCEecccEeeCCCCeECC
Confidence 89999999999999999999984 6999999999999999999997 7753
No 6
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=99.74 E-value=1e-18 Score=114.94 Aligned_cols=47 Identities=40% Similarity=0.723 Sum_probs=42.7
Q ss_pred CCCCCCCccccCCCCCC-CCCCCCCCeeecCCCCceecCceeCCCC-ccc
Q 032832 83 VPKKKVSRHKRGIRNGP-KALKPVPVIVRCKSCGRVKLPHFFCCSG-ERK 130 (132)
Q Consensus 83 VPKrK~SksRkr~RRsh-~~lk~~~~L~~Cp~CGe~klpH~vC~~g-y~k 130 (132)
|||+|+|++|+++||+| ++++ +++|+.|++||+++++|+||+.| ||+
T Consensus 1 vPKrk~Sksr~~~RRah~~kl~-~p~l~~C~~cG~~~~~H~vc~~cG~Y~ 49 (55)
T TIGR01031 1 VPKRKTSKSRKRKRRSHDAKLT-APTLVVCPNCGEFKLPHRVCPSCGYYK 49 (55)
T ss_pred CCCCcCCcccccchhcCccccc-CCcceECCCCCCcccCeeECCccCeEC
Confidence 89999999999999999 5576 79999999999999999999995 554
No 7
>CHL00152 rpl32 ribosomal protein L32; Validated
Probab=97.76 E-value=2.1e-06 Score=56.74 Aligned_cols=22 Identities=45% Similarity=0.570 Sum_probs=19.9
Q ss_pred eeCCCCCCCccccCCCCCCCCC
Q 032832 81 MAVPKKKVSRHKRGIRNGPKAL 102 (132)
Q Consensus 81 MAVPKrK~SksRkr~RRsh~~l 102 (132)
|||||+|+|+++++.|+++|..
T Consensus 1 MAVPKKRtSksKk~~Rk~~Wk~ 22 (53)
T CHL00152 1 MAVPKKRTSKSKKRIRKNIWKR 22 (53)
T ss_pred CCCCCCccchHHHHHHHHHHHH
Confidence 9999999999999999987643
No 8
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=97.73 E-value=3.5e-05 Score=56.27 Aligned_cols=26 Identities=31% Similarity=0.717 Sum_probs=22.7
Q ss_pred CCCCCCCeeecCCCCceecC--------ceeCCCC
Q 032832 101 ALKPVPVIVRCKSCGRVKLP--------HFFCCSG 127 (132)
Q Consensus 101 ~lk~~~~L~~Cp~CGe~klp--------H~vC~~g 127 (132)
.++ .+++..||+||+..++ |++|+.|
T Consensus 15 k~k-lpt~f~CP~Cge~~v~v~~~k~~~h~~C~~C 48 (99)
T PRK14892 15 KPK-LPKIFECPRCGKVSISVKIKKNIAIITCGNC 48 (99)
T ss_pred ccC-CCcEeECCCCCCeEeeeecCCCcceEECCCC
Confidence 344 6899999999999996 9999997
No 9
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=85.38 E-value=0.56 Score=35.56 Aligned_cols=23 Identities=35% Similarity=0.743 Sum_probs=19.4
Q ss_pred eeecCCCCce-ecCceeCCCCccc
Q 032832 108 IVRCKSCGRV-KLPHFFCCSGERK 130 (132)
Q Consensus 108 L~~Cp~CGe~-klpH~vC~~gy~k 130 (132)
-+.|++||.. ..|+..|+.|...
T Consensus 29 g~kC~~CG~v~~PPr~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVYFPPRAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEEcCCcccCCCCCCC
Confidence 4689999998 7889999999654
No 10
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=78.26 E-value=1.4 Score=25.93 Aligned_cols=22 Identities=36% Similarity=0.692 Sum_probs=13.6
Q ss_pred CeeecCCCCce-ecCceeCCCCc
Q 032832 107 VIVRCKSCGRV-KLPHFFCCSGE 128 (132)
Q Consensus 107 ~L~~Cp~CGe~-klpH~vC~~gy 128 (132)
-+..|.+||.+ ..|..+|+.|.
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~ 32 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCG 32 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT
T ss_pred EEEEcCCCCCEecCCCcCCCCcC
Confidence 36789999999 66788999884
No 11
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=78.12 E-value=1.4 Score=27.00 Aligned_cols=7 Identities=43% Similarity=1.474 Sum_probs=3.8
Q ss_pred cCCCCce
Q 032832 111 CKSCGRV 117 (132)
Q Consensus 111 Cp~CGe~ 117 (132)
||+||+.
T Consensus 3 Cp~Cg~~ 9 (52)
T smart00661 3 CPKCGNM 9 (52)
T ss_pred CCCCCCc
Confidence 5555554
No 12
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.13 E-value=0.99 Score=25.08 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=12.3
Q ss_pred eecCCCCce-ecCceeCCCC
Q 032832 109 VRCKSCGRV-KLPHFFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~-klpH~vC~~g 127 (132)
..||+||.. ....+.|++|
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~C 22 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNC 22 (26)
T ss_pred CCCcccCCcCCcccccChhh
Confidence 368888886 3344677765
No 13
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=72.23 E-value=2.7 Score=27.94 Aligned_cols=20 Identities=30% Similarity=0.604 Sum_probs=15.6
Q ss_pred CeeecCCCCceecCceeCCCC
Q 032832 107 VIVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 107 ~L~~Cp~CGe~klpH~vC~~g 127 (132)
.+.+|++||.+.+ --+|+.|
T Consensus 4 ~mr~C~~CgvYTL-k~~CP~C 23 (56)
T PRK13130 4 KIRKCPKCGVYTL-KEICPVC 23 (56)
T ss_pred cceECCCCCCEEc-cccCcCC
Confidence 4668888888888 7778774
No 14
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=71.72 E-value=2 Score=35.38 Aligned_cols=25 Identities=28% Similarity=0.551 Sum_probs=20.9
Q ss_pred CeeecCCCCceecCce--------eCCCCcccC
Q 032832 107 VIVRCKSCGRVKLPHF--------FCCSGERKN 131 (132)
Q Consensus 107 ~L~~Cp~CGe~klpH~--------vC~~gy~k~ 131 (132)
..+.|.+|||+...|+ ||.-||+++
T Consensus 171 ~~v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 171 GSVRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred ceeeccccCcccccchhhhcCCceecccccccc
Confidence 3479999999999985 599998865
No 15
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.04 E-value=3.1 Score=28.16 Aligned_cols=11 Identities=45% Similarity=0.996 Sum_probs=8.4
Q ss_pred CeeecCCCCce
Q 032832 107 VIVRCKSCGRV 117 (132)
Q Consensus 107 ~L~~Cp~CGe~ 117 (132)
..-.||+||+.
T Consensus 24 ~~F~CPnCG~~ 34 (59)
T PRK14890 24 VKFLCPNCGEV 34 (59)
T ss_pred CEeeCCCCCCe
Confidence 34579999987
No 16
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=70.55 E-value=1.7 Score=23.81 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=4.3
Q ss_pred cCCCCceec
Q 032832 111 CKSCGRVKL 119 (132)
Q Consensus 111 Cp~CGe~kl 119 (132)
||+||+...
T Consensus 2 Cp~CG~~~~ 10 (23)
T PF13240_consen 2 CPNCGAEIE 10 (23)
T ss_pred CcccCCCCC
Confidence 455554433
No 17
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=69.06 E-value=2.5 Score=28.62 Aligned_cols=17 Identities=35% Similarity=0.727 Sum_probs=9.1
Q ss_pred ecCCCCceecCceeCCCC
Q 032832 110 RCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 110 ~Cp~CGe~klpH~vC~~g 127 (132)
.|++||.+.+. -.|+.|
T Consensus 7 kC~~cg~YTLk-e~Cp~C 23 (59)
T COG2260 7 KCPKCGRYTLK-EKCPVC 23 (59)
T ss_pred cCcCCCceeec-ccCCCC
Confidence 45555555555 455544
No 18
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=67.42 E-value=3.6 Score=26.43 Aligned_cols=21 Identities=24% Similarity=0.529 Sum_probs=15.5
Q ss_pred CeeecCCCCc-eecCc---eeCCCC
Q 032832 107 VIVRCKSCGR-VKLPH---FFCCSG 127 (132)
Q Consensus 107 ~L~~Cp~CGe-~klpH---~vC~~g 127 (132)
....||+||. ....| ..|+.|
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~C 43 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKC 43 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCc
Confidence 3458999999 65554 788886
No 19
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=66.45 E-value=2.9 Score=39.01 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=20.7
Q ss_pred CCCeeecCCCCce-ecCceeCCCC
Q 032832 105 VPVIVRCKSCGRV-KLPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~-klpH~vC~~g 127 (132)
.+.+..|++||.. ...|..||.|
T Consensus 563 n~~~~iC~~CG~~~~g~~~~CP~C 586 (623)
T PRK08271 563 NVKITICNDCHHIDKRTGKRCPIC 586 (623)
T ss_pred CCCCccCCCCCCcCCCCCcCCcCC
Confidence 4889999999987 7789999998
No 20
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=65.37 E-value=8.1 Score=28.84 Aligned_cols=16 Identities=31% Similarity=0.831 Sum_probs=13.0
Q ss_pred CCCeeecCCCCceecC
Q 032832 105 VPVIVRCKSCGRVKLP 120 (132)
Q Consensus 105 ~~~L~~Cp~CGe~klp 120 (132)
.+..-.||.||+.+..
T Consensus 19 L~k~FtCp~Cghe~vs 34 (104)
T COG4888 19 LPKTFTCPRCGHEKVS 34 (104)
T ss_pred CCceEecCccCCeeee
Confidence 4567899999998776
No 21
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=60.68 E-value=5.2 Score=36.43 Aligned_cols=23 Identities=26% Similarity=0.355 Sum_probs=13.8
Q ss_pred CCCeeecCCCCceecCceeCCCC
Q 032832 105 VPVIVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~klpH~vC~~g 127 (132)
.+.+..|++||..-..|..||.|
T Consensus 488 n~~~~~C~~CG~~~~~~~~CP~C 510 (546)
T PF13597_consen 488 NPPIDICPDCGYIGGEGDKCPKC 510 (546)
T ss_dssp E--EEEETTT---S--EEE-CCC
T ss_pred ecCcccccCCCcCCCCCCCCCCC
Confidence 48899999999997779999998
No 22
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=60.66 E-value=4.3 Score=37.89 Aligned_cols=23 Identities=30% Similarity=0.535 Sum_probs=20.3
Q ss_pred CCCeeecCCCCc-eecCceeCCCC
Q 032832 105 VPVIVRCKSCGR-VKLPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe-~klpH~vC~~g 127 (132)
.+.+..|++||. ..-.|..||.|
T Consensus 565 np~~~~C~~CG~~~~g~~~~CP~C 588 (625)
T PRK08579 565 TPAITVCNKCGRSTTGLYTRCPRC 588 (625)
T ss_pred CCCCccCCCCCCccCCCCCcCcCC
Confidence 488999999998 57789999988
No 23
>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=58.83 E-value=4.5 Score=22.77 Aligned_cols=10 Identities=40% Similarity=0.889 Sum_probs=7.7
Q ss_pred CeeecCCCCc
Q 032832 107 VIVRCKSCGR 116 (132)
Q Consensus 107 ~L~~Cp~CGe 116 (132)
+.-.||+||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4557999996
No 24
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.55 E-value=5.1 Score=34.64 Aligned_cols=24 Identities=25% Similarity=0.594 Sum_probs=18.2
Q ss_pred CCeeecCCCCce-ecCcee--CCC--Ccc
Q 032832 106 PVIVRCKSCGRV-KLPHFF--CCS--GER 129 (132)
Q Consensus 106 ~~L~~Cp~CGe~-klpH~v--C~~--gy~ 129 (132)
..-++||-||++ ..||++ |.+ ||+
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~ 265 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYY 265 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehh
Confidence 345689999998 888876 554 775
No 25
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=56.26 E-value=6.4 Score=37.34 Aligned_cols=24 Identities=21% Similarity=0.312 Sum_probs=20.6
Q ss_pred CCCCeeecCCCCceecCceeCCCC
Q 032832 104 PVPVIVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 104 ~~~~L~~Cp~CGe~klpH~vC~~g 127 (132)
..+.+..|+.||...--|..||.|
T Consensus 676 in~~~~~C~~CG~~~~~~~~CP~C 699 (735)
T PRK07111 676 INHPVDRCPVCGYLGVIEDKCPKC 699 (735)
T ss_pred eCCCCeecCCCCCCCCcCccCcCC
Confidence 358899999999766678999998
No 26
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=55.85 E-value=5.9 Score=37.06 Aligned_cols=23 Identities=26% Similarity=0.469 Sum_probs=20.6
Q ss_pred CCCeeecCCCCceecCceeCCCC
Q 032832 105 VPVIVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~klpH~vC~~g 127 (132)
.+.+..|++||...-.|..||.|
T Consensus 623 n~~~~~C~~CG~~~g~~~~CP~C 645 (656)
T PRK08270 623 TPTFSICPKHGYLSGEHEFCPKC 645 (656)
T ss_pred CCCCcccCCCCCcCCCCCCCcCC
Confidence 48899999999877779999998
No 27
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=55.37 E-value=6.8 Score=28.65 Aligned_cols=27 Identities=22% Similarity=0.540 Sum_probs=19.1
Q ss_pred CCCCCCCeeecCCCCceecC---ceeCCCC
Q 032832 101 ALKPVPVIVRCKSCGRVKLP---HFFCCSG 127 (132)
Q Consensus 101 ~lk~~~~L~~Cp~CGe~klp---H~vC~~g 127 (132)
.+...+....|++||+..-. +..||.|
T Consensus 63 ~I~~~p~~~~C~~Cg~~~~~~~~~~~CP~C 92 (115)
T TIGR00100 63 NIEDEPVECECEDCSEEVSPEIDLYRCPKC 92 (115)
T ss_pred EEEeeCcEEEcccCCCEEecCCcCccCcCC
Confidence 34456777889999887533 5668887
No 28
>PRK05978 hypothetical protein; Provisional
Probab=54.01 E-value=6 Score=30.82 Aligned_cols=19 Identities=42% Similarity=0.840 Sum_probs=13.2
Q ss_pred eecCCCCceec------CceeCCCC
Q 032832 109 VRCKSCGRVKL------PHFFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~kl------pH~vC~~g 127 (132)
-.||+||+-++ -|--|+.|
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~C 58 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAAC 58 (148)
T ss_pred CcCCCCCCCcccccccccCCCcccc
Confidence 37888888766 45566666
No 29
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=53.16 E-value=7.6 Score=36.12 Aligned_cols=23 Identities=17% Similarity=0.297 Sum_probs=18.8
Q ss_pred CCCeeecCCCCceec-CceeCCCC
Q 032832 105 VPVIVRCKSCGRVKL-PHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~kl-pH~vC~~g 127 (132)
.+.++.|++||...- -+..||.|
T Consensus 529 n~~~siC~~CGy~~g~~~~~CP~C 552 (586)
T TIGR02827 529 NIKITICNDCHHIDKRTLHRCPVC 552 (586)
T ss_pred CCCCeecCCCCCcCCCcCCcCcCC
Confidence 489999999998533 45999998
No 30
>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=51.25 E-value=15 Score=21.30 Aligned_cols=10 Identities=60% Similarity=1.285 Sum_probs=5.0
Q ss_pred eeecCCCCce
Q 032832 108 IVRCKSCGRV 117 (132)
Q Consensus 108 L~~Cp~CGe~ 117 (132)
.+.||+||+.
T Consensus 25 ~v~C~~C~~~ 34 (38)
T TIGR02098 25 KVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE
Confidence 3455555543
No 31
>PRK00420 hypothetical protein; Validated
Probab=51.15 E-value=9 Score=28.60 Aligned_cols=19 Identities=21% Similarity=0.384 Sum_probs=14.1
Q ss_pred eecCCCCcee----cCceeCCCC
Q 032832 109 VRCKSCGRVK----LPHFFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~k----lpH~vC~~g 127 (132)
..||.||.+. .-..+||.|
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~C 46 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVH 46 (112)
T ss_pred CCCCCCCCcceecCCCceECCCC
Confidence 4799999763 456888887
No 32
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=50.43 E-value=12 Score=27.32 Aligned_cols=26 Identities=19% Similarity=0.284 Sum_probs=18.3
Q ss_pred CCCCCCeeecCCCCceec---CceeCCCC
Q 032832 102 LKPVPVIVRCKSCGRVKL---PHFFCCSG 127 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~kl---pH~vC~~g 127 (132)
+...+....|++||+... .+..||.|
T Consensus 64 I~~vp~~~~C~~Cg~~~~~~~~~~~CP~C 92 (113)
T PRK12380 64 IVYKPAQAWCWDCSQVVEIHQHDAQCPHC 92 (113)
T ss_pred EEeeCcEEEcccCCCEEecCCcCccCcCC
Confidence 445677888999997643 34568887
No 33
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.06 E-value=11 Score=29.73 Aligned_cols=23 Identities=22% Similarity=0.384 Sum_probs=17.2
Q ss_pred CCCeeecCCCCceecCceeCCCC
Q 032832 105 VPVIVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~klpH~vC~~g 127 (132)
..+-..|+.||+.......|+.|
T Consensus 306 ~~tS~~C~~cg~~~~r~~~C~~c 328 (364)
T COG0675 306 YYTSKTCPCCGHLSGRLFKCPRC 328 (364)
T ss_pred CCCcccccccCCccceeEECCCC
Confidence 34557899999955566789987
No 34
>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=49.95 E-value=8.1 Score=21.80 Aligned_cols=17 Identities=29% Similarity=0.667 Sum_probs=8.6
Q ss_pred ecCCCCceec-CceeCCC
Q 032832 110 RCKSCGRVKL-PHFFCCS 126 (132)
Q Consensus 110 ~Cp~CGe~kl-pH~vC~~ 126 (132)
.||+|++.+. .=..|+.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~ 19 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPH 19 (26)
T ss_pred cCCCCcCCchhhcCcCCC
Confidence 3666665532 2245554
No 35
>PHA00626 hypothetical protein
Probab=49.81 E-value=12 Score=25.34 Aligned_cols=7 Identities=43% Similarity=1.364 Sum_probs=4.9
Q ss_pred ecCCCCc
Q 032832 110 RCKSCGR 116 (132)
Q Consensus 110 ~Cp~CGe 116 (132)
.||+||+
T Consensus 2 ~CP~CGS 8 (59)
T PHA00626 2 SCPKCGS 8 (59)
T ss_pred CCCCCCC
Confidence 4777776
No 36
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=49.64 E-value=10 Score=32.05 Aligned_cols=21 Identities=29% Similarity=0.539 Sum_probs=16.7
Q ss_pred CeeecCCCCcee------cCceeCCCC
Q 032832 107 VIVRCKSCGRVK------LPHFFCCSG 127 (132)
Q Consensus 107 ~L~~Cp~CGe~k------lpH~vC~~g 127 (132)
-.++||+||+.. ....||+.|
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c 51 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKC 51 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCC
Confidence 378999999863 456899998
No 37
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=48.56 E-value=5.5 Score=21.94 Aligned_cols=15 Identities=40% Similarity=0.784 Sum_probs=11.3
Q ss_pred CeeecCCCCceecCc
Q 032832 107 VIVRCKSCGRVKLPH 121 (132)
Q Consensus 107 ~L~~Cp~CGe~klpH 121 (132)
+++.|+.||....+.
T Consensus 1 ~l~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 1 ELVPCPICGRKFNPD 15 (25)
T ss_pred CCCcCCCCCCEECHH
Confidence 367899999876543
No 38
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=48.51 E-value=14 Score=24.45 Aligned_cols=23 Identities=35% Similarity=0.524 Sum_probs=16.7
Q ss_pred CCCCCCCeeecCCCCceecCceeCC
Q 032832 101 ALKPVPVIVRCKSCGRVKLPHFFCC 125 (132)
Q Consensus 101 ~lk~~~~L~~Cp~CGe~klpH~vC~ 125 (132)
.+++...++.||.||.+. ||-|.
T Consensus 14 ~~~~~dDiVvCp~Cgapy--HR~C~ 36 (54)
T PF14446_consen 14 KFKDGDDIVVCPECGAPY--HRDCW 36 (54)
T ss_pred cccCCCCEEECCCCCCcc--cHHHH
Confidence 455567899999999864 66664
No 39
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=48.25 E-value=9.8 Score=29.29 Aligned_cols=28 Identities=29% Similarity=0.581 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCCeeecCCCCceecCc---eeCCCCc
Q 032832 96 RNGPKALKPVPVIVRCKSCGRVKLPH---FFCCSGE 128 (132)
Q Consensus 96 RRsh~~lk~~~~L~~Cp~CGe~klpH---~vC~~gy 128 (132)
+.+++++. ..||.||-+.-.+ .+||.|-
T Consensus 21 l~GAkML~-----~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 21 LQGAKMLA-----KHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred HhhhHHHH-----hhCcccCCcceeeCCeEECCCCC
Confidence 34555554 3799999985555 7999984
No 40
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.70 E-value=12 Score=28.14 Aligned_cols=17 Identities=18% Similarity=0.708 Sum_probs=11.5
Q ss_pred CCCCCCeeecCCCCcee
Q 032832 102 LKPVPVIVRCKSCGRVK 118 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~k 118 (132)
+...+....|++||...
T Consensus 64 i~~~p~~~~C~~CG~~~ 80 (135)
T PRK03824 64 FEEEEAVLKCRNCGNEW 80 (135)
T ss_pred EEecceEEECCCCCCEE
Confidence 33456777888888664
No 41
>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=47.68 E-value=8.5 Score=21.99 Aligned_cols=18 Identities=33% Similarity=0.550 Sum_probs=8.6
Q ss_pred ecCCCCceecCc-----eeCCCC
Q 032832 110 RCKSCGRVKLPH-----FFCCSG 127 (132)
Q Consensus 110 ~Cp~CGe~klpH-----~vC~~g 127 (132)
.|+.||.+..++ ++|+.|
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~C 27 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSC 27 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSS
T ss_pred ccCcCCccccCCCCcCEeECCCC
Confidence 577777775544 556654
No 42
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=46.95 E-value=15 Score=31.84 Aligned_cols=23 Identities=22% Similarity=0.463 Sum_probs=16.7
Q ss_pred CCeeecCCCCceec------CceeCCCCc
Q 032832 106 PVIVRCKSCGRVKL------PHFFCCSGE 128 (132)
Q Consensus 106 ~~L~~Cp~CGe~kl------pH~vC~~gy 128 (132)
.--++||.||+..- .-.||+.|-
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~ 54 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCG 54 (294)
T ss_pred CceeECCCccceeeHHHHHhhhhcccccC
Confidence 44568999998743 357899883
No 43
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=46.87 E-value=12 Score=23.83 Aligned_cols=12 Identities=50% Similarity=1.090 Sum_probs=10.2
Q ss_pred CCeeecCCCCce
Q 032832 106 PVIVRCKSCGRV 117 (132)
Q Consensus 106 ~~L~~Cp~CGe~ 117 (132)
..++.||+||..
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 578899999975
No 44
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=46.36 E-value=6.6 Score=38.41 Aligned_cols=20 Identities=30% Similarity=0.730 Sum_probs=0.0
Q ss_pred eeecCCCCceecCceeCCCC
Q 032832 108 IVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 108 L~~Cp~CGe~klpH~vC~~g 127 (132)
...||.||....++..|+.|
T Consensus 667 ~~~Cp~CG~~T~~~~~Cp~C 686 (900)
T PF03833_consen 667 YNRCPECGSHTEPVYVCPDC 686 (900)
T ss_dssp --------------------
T ss_pred hhcCcccCCccccceecccc
Confidence 34677888888888888887
No 45
>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=46.09 E-value=12 Score=24.15 Aligned_cols=12 Identities=25% Similarity=0.672 Sum_probs=6.1
Q ss_pred CCeeecCCCCce
Q 032832 106 PVIVRCKSCGRV 117 (132)
Q Consensus 106 ~~L~~Cp~CGe~ 117 (132)
.....|++||..
T Consensus 44 ~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 44 GRVFTCPNCGFE 55 (69)
T ss_pred cceEEcCCCCCE
Confidence 344456666543
No 46
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=44.95 E-value=15 Score=26.75 Aligned_cols=23 Identities=30% Similarity=0.566 Sum_probs=17.3
Q ss_pred CCeeecCCCCceec-----CceeCCCCc
Q 032832 106 PVIVRCKSCGRVKL-----PHFFCCSGE 128 (132)
Q Consensus 106 ~~L~~Cp~CGe~kl-----pH~vC~~gy 128 (132)
-....|++||+.+. .|+.||.|-
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R~CP~C~ 67 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNRHCPSCQ 67 (111)
T ss_pred cceeecCCCCceEEecCcccCcCCCCCC
Confidence 45679999999976 356777773
No 47
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.67 E-value=16 Score=26.68 Aligned_cols=26 Identities=15% Similarity=0.247 Sum_probs=18.4
Q ss_pred CCCCCCeeecCCCCceecC---c-eeCCCC
Q 032832 102 LKPVPVIVRCKSCGRVKLP---H-FFCCSG 127 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~klp---H-~vC~~g 127 (132)
+...+....|.+||+.... + ..||.|
T Consensus 64 i~~~p~~~~C~~Cg~~~~~~~~~~~~CP~C 93 (114)
T PRK03681 64 LEEQEAECWCETCQQYVTLLTQRVRRCPQC 93 (114)
T ss_pred EEeeCcEEEcccCCCeeecCCccCCcCcCc
Confidence 4456778889999988533 3 458887
No 48
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=41.85 E-value=9.2 Score=22.86 Aligned_cols=18 Identities=22% Similarity=0.519 Sum_probs=8.3
Q ss_pred ecCCCCceec---------CceeCCCC
Q 032832 110 RCKSCGRVKL---------PHFFCCSG 127 (132)
Q Consensus 110 ~Cp~CGe~kl---------pH~vC~~g 127 (132)
.||+||.+.. ...+|+.|
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~C 28 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPAC 28 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTT
T ss_pred ccccccChhhhhcCCCCCccceECCCC
Confidence 4888887632 24567765
No 49
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=41.21 E-value=20 Score=21.40 Aligned_cols=17 Identities=29% Similarity=0.559 Sum_probs=11.4
Q ss_pred CCeeecCCCCceecCce
Q 032832 106 PVIVRCKSCGRVKLPHF 122 (132)
Q Consensus 106 ~~L~~Cp~CGe~klpH~ 122 (132)
..++.|++|+..+..-+
T Consensus 2 ~~~~~C~nC~R~v~a~R 18 (33)
T PF08209_consen 2 SPYVECPNCGRPVAASR 18 (33)
T ss_dssp S-EEE-TTTSSEEEGGG
T ss_pred CCeEECCCCcCCcchhh
Confidence 35789999999876544
No 50
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=41.16 E-value=17 Score=22.62 Aligned_cols=19 Identities=26% Similarity=0.779 Sum_probs=13.7
Q ss_pred eecCCCCceecC----ceeCCCC
Q 032832 109 VRCKSCGRVKLP----HFFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~klp----H~vC~~g 127 (132)
..||.||-+... ..+|+.|
T Consensus 18 ~~Cp~C~~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKDGKIYCVSC 40 (41)
T ss_pred CccCCCCCeeEEecCCCEECCCC
Confidence 379999988544 5777766
No 51
>PF12773 DZR: Double zinc ribbon
Probab=40.32 E-value=16 Score=22.20 Aligned_cols=19 Identities=32% Similarity=0.728 Sum_probs=9.7
Q ss_pred eeecCCCCceecCc-eeCCC
Q 032832 108 IVRCKSCGRVKLPH-FFCCS 126 (132)
Q Consensus 108 L~~Cp~CGe~klpH-~vC~~ 126 (132)
...|++||+...++ .+|+.
T Consensus 29 ~~~C~~Cg~~~~~~~~fC~~ 48 (50)
T PF12773_consen 29 KKICPNCGAENPPNAKFCPN 48 (50)
T ss_pred CCCCcCCcCCCcCCcCccCc
Confidence 34566666654433 44444
No 52
>PF12653 DUF3785: Protein of unknown function (DUF3785); InterPro: IPR024210 This family of proteins is functionally uncharacterised. Proteins in this family are approximately 140 amino acids in length and share two CXXC motifs suggesting these are zinc binding proteins. In clostridia proteins are found in an operon with three signalling proteins, suggesting that they are involved in DNA-binding transcription regulator downstream of an as yet unknown signalling pathway.
Probab=39.39 E-value=12 Score=29.06 Aligned_cols=15 Identities=27% Similarity=0.831 Sum_probs=12.4
Q ss_pred CCCeeecCCCCceec
Q 032832 105 VPVIVRCKSCGRVKL 119 (132)
Q Consensus 105 ~~~L~~Cp~CGe~kl 119 (132)
.+++++||+||.+..
T Consensus 117 iVsi~VC~nCG~y~i 131 (138)
T PF12653_consen 117 IVSIIVCPNCGNYSI 131 (138)
T ss_pred EEEEEECCCCCceEE
Confidence 468899999999854
No 53
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=38.38 E-value=18 Score=33.81 Aligned_cols=23 Identities=26% Similarity=0.306 Sum_probs=18.2
Q ss_pred CCCeeecCCCCceecCceeCCCC
Q 032832 105 VPVIVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~klpH~vC~~g 127 (132)
-+.+..|++||..-.-+..||.|
T Consensus 556 n~~~~~C~~CGy~g~~~~~CP~C 578 (618)
T PRK14704 556 NHPVDRCKCCSYHGVIGNECPSC 578 (618)
T ss_pred CCCCeecCCCCCCCCcCccCcCC
Confidence 48899999999743444889998
No 54
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=37.67 E-value=8.3 Score=29.59 Aligned_cols=22 Identities=23% Similarity=0.350 Sum_probs=19.1
Q ss_pred eeecCCCCceecCceeCCCCcc
Q 032832 108 IVRCKSCGRVKLPHFFCCSGER 129 (132)
Q Consensus 108 L~~Cp~CGe~klpH~vC~~gy~ 129 (132)
...|..||.+.+.-++|..|..
T Consensus 81 ~~~CE~CG~~I~~Gr~C~~C~~ 102 (137)
T TIGR03826 81 GYPCERCGTSIREGRLCDSCAG 102 (137)
T ss_pred cCcccccCCcCCCCCccHHHHH
Confidence 3579999999999999999853
No 55
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=37.54 E-value=22 Score=20.97 Aligned_cols=20 Identities=20% Similarity=0.517 Sum_probs=10.0
Q ss_pred eeecCCCCceec-----CceeCCCC
Q 032832 108 IVRCKSCGRVKL-----PHFFCCSG 127 (132)
Q Consensus 108 L~~Cp~CGe~kl-----pH~vC~~g 127 (132)
+..|..||...+ ...+|..|
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~C 27 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFC 27 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccC
Confidence 445666655422 34555554
No 56
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=37.26 E-value=15 Score=31.48 Aligned_cols=21 Identities=19% Similarity=0.449 Sum_probs=15.9
Q ss_pred CeeecCCCCcee------cCceeCCCC
Q 032832 107 VIVRCKSCGRVK------LPHFFCCSG 127 (132)
Q Consensus 107 ~L~~Cp~CGe~k------lpH~vC~~g 127 (132)
-.++||+|++.. ....||+.|
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c 63 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQC 63 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCC
Confidence 367899999863 446799987
No 57
>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=36.63 E-value=14 Score=21.92 Aligned_cols=19 Identities=26% Similarity=0.681 Sum_probs=12.5
Q ss_pred eecCCCCceecC------ceeCCCC
Q 032832 109 VRCKSCGRVKLP------HFFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~klp------H~vC~~g 127 (132)
..||+||.+..+ ++.|..|
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C 26 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTC 26 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSS
T ss_pred eeCCCCCccceEcCCCccCcCCCCC
Confidence 579999988543 2357665
No 58
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=35.60 E-value=22 Score=32.42 Aligned_cols=11 Identities=36% Similarity=0.927 Sum_probs=8.5
Q ss_pred eeecCCCCcee
Q 032832 108 IVRCKSCGRVK 118 (132)
Q Consensus 108 L~~Cp~CGe~k 118 (132)
.+.||+||+..
T Consensus 200 ~vpCPhCg~~~ 210 (557)
T PF05876_consen 200 YVPCPHCGEEQ 210 (557)
T ss_pred EccCCCCCCCc
Confidence 45799999864
No 59
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=35.52 E-value=19 Score=36.77 Aligned_cols=18 Identities=33% Similarity=0.593 Sum_probs=10.3
Q ss_pred eecCCCCceecCceeCCCC
Q 032832 109 VRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~klpH~vC~~g 127 (132)
..||+||+.... ..|+.|
T Consensus 668 rkCPkCG~~t~~-~fCP~C 685 (1337)
T PRK14714 668 RRCPSCGTETYE-NRCPDC 685 (1337)
T ss_pred EECCCCCCcccc-ccCccc
Confidence 567777765433 255544
No 60
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.93 E-value=19 Score=36.06 Aligned_cols=18 Identities=33% Similarity=0.735 Sum_probs=7.7
Q ss_pred ecCCCCceecCceeCCCC
Q 032832 110 RCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 110 ~Cp~CGe~klpH~vC~~g 127 (132)
.||+||+...+...|+.|
T Consensus 640 rCP~CG~~Te~i~fCP~C 657 (1121)
T PRK04023 640 RCPFCGTHTEPVYRCPRC 657 (1121)
T ss_pred cCCCCCCCCCcceeCccc
Confidence 344444444444444443
No 61
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=34.29 E-value=34 Score=25.12 Aligned_cols=31 Identities=35% Similarity=0.589 Sum_probs=19.4
Q ss_pred CCCCCCccccCCCCCCCCCCCCCCeeecCCCCceecC
Q 032832 84 PKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKLP 120 (132)
Q Consensus 84 PKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~klp 120 (132)
||+|.+..|...-|+| ...+.|.+||.....
T Consensus 2 ~kKRrn~GR~K~~rGh------v~~V~C~nCgr~vPK 32 (95)
T PRK09335 2 PKKRENRGRRKGDKGH------VGYVQCDNCGRRVPR 32 (95)
T ss_pred CcccccCCCCCCCCCC------CccEEeCCCCCcCcC
Confidence 5666665444433333 456799999987654
No 62
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.13 E-value=25 Score=25.76 Aligned_cols=26 Identities=27% Similarity=0.526 Sum_probs=17.0
Q ss_pred CCCCCCeeecCCCCceecC---cee-CCCC
Q 032832 102 LKPVPVIVRCKSCGRVKLP---HFF-CCSG 127 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~klp---H~v-C~~g 127 (132)
+...+....|.+||+.... +.. ||.|
T Consensus 65 Ie~vp~~~~C~~Cg~~~~~~~~~~~~CP~C 94 (117)
T PRK00564 65 IVDEKVELECKDCSHVFKPNALDYGVCEKC 94 (117)
T ss_pred EEecCCEEEhhhCCCccccCCccCCcCcCC
Confidence 4446777888888876433 233 8876
No 63
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=33.83 E-value=20 Score=30.46 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=16.3
Q ss_pred CeeecCCCCcee------cCceeCCCC
Q 032832 107 VIVRCKSCGRVK------LPHFFCCSG 127 (132)
Q Consensus 107 ~L~~Cp~CGe~k------lpH~vC~~g 127 (132)
-.++||+|++.. ....||+.|
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c 52 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLNVCPKC 52 (292)
T ss_pred CeeECCCccchhhHHHHHhcCCCCCCC
Confidence 378999999863 345799987
No 64
>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=33.56 E-value=27 Score=21.02 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=5.3
Q ss_pred eecCCCCceecC
Q 032832 109 VRCKSCGRVKLP 120 (132)
Q Consensus 109 ~~Cp~CGe~klp 120 (132)
..|++||...-.
T Consensus 20 ~vC~~CG~Vl~e 31 (43)
T PF08271_consen 20 LVCPNCGLVLEE 31 (43)
T ss_dssp EEETTT-BBEE-
T ss_pred EECCCCCCEeec
Confidence 356666655443
No 65
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.77 E-value=23 Score=33.63 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=16.3
Q ss_pred CCCeeecCCCCce-----ecCceeCCCC
Q 032832 105 VPVIVRCKSCGRV-----KLPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~-----klpH~vC~~g 127 (132)
.+.+..|++||.. ...+..||.|
T Consensus 638 n~~~~~C~~CG~~Ge~~~~~~~~~CP~C 665 (711)
T PRK09263 638 NTPIDECYECGFTGEFECTEKGFTCPKC 665 (711)
T ss_pred CCCCcccCCCCCCccccCCCCCCcCcCC
Confidence 3778999999962 1223689988
No 66
>PF12661 hEGF: Human growth factor-like EGF; PDB: 2YGQ_A 2E26_A 3A7Q_A 2YGP_A 2YGO_A 1HRE_A 1HAE_A 1HAF_A 1HRF_A.
Probab=32.24 E-value=20 Score=17.23 Aligned_cols=10 Identities=20% Similarity=0.252 Sum_probs=7.0
Q ss_pred eCCCCcccCC
Q 032832 123 FCCSGERKNH 132 (132)
Q Consensus 123 vC~~gy~k~~ 132 (132)
+|+.||.|.|
T Consensus 3 ~C~~G~~G~~ 12 (13)
T PF12661_consen 3 QCPPGWTGPN 12 (13)
T ss_dssp EE-TTEETTT
T ss_pred cCcCCCcCCC
Confidence 5788998875
No 67
>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=32.12 E-value=21 Score=20.57 Aligned_cols=12 Identities=25% Similarity=0.708 Sum_probs=9.4
Q ss_pred CCeeecCCCCce
Q 032832 106 PVIVRCKSCGRV 117 (132)
Q Consensus 106 ~~L~~Cp~CGe~ 117 (132)
..+..||+||..
T Consensus 24 ~~~~~CP~Cg~~ 35 (41)
T smart00834 24 DPLATCPECGGD 35 (41)
T ss_pred CCCCCCCCCCCc
Confidence 456789999984
No 68
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=31.91 E-value=20 Score=30.46 Aligned_cols=19 Identities=32% Similarity=0.904 Sum_probs=9.6
Q ss_pred eecCCCCceecCc---------eeCCCC
Q 032832 109 VRCKSCGRVKLPH---------FFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~klpH---------~vC~~g 127 (132)
..||+||...+.| +.|+.|
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C 59 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNC 59 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT
T ss_pred CcCCCCCChhHhhccCCCccceeECCCC
Confidence 4799999997666 578888
No 69
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=31.37 E-value=24 Score=32.40 Aligned_cols=23 Identities=22% Similarity=0.329 Sum_probs=17.2
Q ss_pred CCCeeecCCCCceecCc-eeCCCC
Q 032832 105 VPVIVRCKSCGRVKLPH-FFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~klpH-~vC~~g 127 (132)
.+.+..|.+||..-.-+ ..||.|
T Consensus 521 n~~~~~C~~CG~~g~~~~~~CP~C 544 (579)
T TIGR02487 521 NPPVDVCEDCGYTGEGLNDKCPKC 544 (579)
T ss_pred ccCCccCCCCCCCCCCCCCcCcCC
Confidence 48899999999743332 689998
No 70
>PF14353 CpXC: CpXC protein
Probab=31.22 E-value=27 Score=25.21 Aligned_cols=15 Identities=27% Similarity=0.434 Sum_probs=11.4
Q ss_pred CCCeeecCCCCceec
Q 032832 105 VPVIVRCKSCGRVKL 119 (132)
Q Consensus 105 ~~~L~~Cp~CGe~kl 119 (132)
.-+...||+||+...
T Consensus 35 ~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 35 SLFSFTCPSCGHKFR 49 (128)
T ss_pred CcCEEECCCCCCcee
Confidence 345679999998754
No 71
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=30.34 E-value=26 Score=31.97 Aligned_cols=22 Identities=27% Similarity=0.599 Sum_probs=18.1
Q ss_pred CCCeeecCCCCcee-cCceeCCCC
Q 032832 105 VPVIVRCKSCGRVK-LPHFFCCSG 127 (132)
Q Consensus 105 ~~~L~~Cp~CGe~k-lpH~vC~~g 127 (132)
.+.. .|.+||..- ..+..||.|
T Consensus 516 ~p~~-~C~~CG~~~~~~~~~CP~C 538 (555)
T cd01675 516 TPID-ICNDCGYIGEGEGFKCPKC 538 (555)
T ss_pred cCCc-cCCCCCCCCcCCCCCCcCC
Confidence 4556 999999865 789999998
No 72
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.17 E-value=29 Score=25.67 Aligned_cols=15 Identities=33% Similarity=0.924 Sum_probs=11.0
Q ss_pred CCCCCCeeecCCCCce
Q 032832 102 LKPVPVIVRCKSCGRV 117 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~ 117 (132)
+...+....| .||+.
T Consensus 64 I~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 64 VEMIPVEIEC-ECGYE 78 (124)
T ss_pred EEecCeeEEe-eCcCc
Confidence 4456777889 89876
No 73
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=29.37 E-value=38 Score=19.88 Aligned_cols=8 Identities=38% Similarity=1.136 Sum_probs=4.6
Q ss_pred ecCCCCce
Q 032832 110 RCKSCGRV 117 (132)
Q Consensus 110 ~Cp~CGe~ 117 (132)
.|..||..
T Consensus 4 ~C~~CG~i 11 (34)
T cd00729 4 VCPVCGYI 11 (34)
T ss_pred ECCCCCCE
Confidence 45666655
No 74
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=28.57 E-value=38 Score=25.38 Aligned_cols=31 Identities=32% Similarity=0.609 Sum_probs=19.9
Q ss_pred CCCCCCccccCCCCCCCCCCCCCCeeecCCCCceecC
Q 032832 84 PKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKLP 120 (132)
Q Consensus 84 PKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~klp 120 (132)
||+|..+-|+..-|+| ...+.|-+||.....
T Consensus 2 pkkR~N~GR~K~~rGh------v~~v~CdnCg~~vPk 32 (108)
T COG4830 2 PKKRRNRGRNKKGRGH------VKYVRCDNCGKAVPK 32 (108)
T ss_pred cchhhhcCCCCCCCCC------ccceeeccccccCCc
Confidence 6777666555554544 335689999987543
No 75
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.47 E-value=24 Score=24.30 Aligned_cols=15 Identities=27% Similarity=0.680 Sum_probs=11.4
Q ss_pred CCeeecCCCCceecC
Q 032832 106 PVIVRCKSCGRVKLP 120 (132)
Q Consensus 106 ~~L~~Cp~CGe~klp 120 (132)
...+.||.||.++.-
T Consensus 5 ~~~v~CP~Cgkpv~w 19 (65)
T COG3024 5 RITVPCPTCGKPVVW 19 (65)
T ss_pred cccccCCCCCCcccc
Confidence 345789999998653
No 76
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=28.33 E-value=25 Score=25.48 Aligned_cols=26 Identities=31% Similarity=0.634 Sum_probs=15.3
Q ss_pred CCCCCCeeecCCCCcee---cCceeCCCC
Q 032832 102 LKPVPVIVRCKSCGRVK---LPHFFCCSG 127 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~k---lpH~vC~~g 127 (132)
+...+....|..||+.. ..+..||.|
T Consensus 64 Ie~~p~~~~C~~Cg~~~~~~~~~~~CP~C 92 (113)
T PF01155_consen 64 IEEVPARARCRDCGHEFEPDEFDFSCPRC 92 (113)
T ss_dssp EEEE--EEEETTTS-EEECHHCCHH-SSS
T ss_pred EEecCCcEECCCCCCEEecCCCCCCCcCC
Confidence 34457788899999874 344668887
No 77
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=27.99 E-value=45 Score=25.01 Aligned_cols=30 Identities=27% Similarity=0.459 Sum_probs=18.7
Q ss_pred CCCCCCccccCCCCCCCCCCCCCCeeecCCCCceec
Q 032832 84 PKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKL 119 (132)
Q Consensus 84 PKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~kl 119 (132)
||+|.+.-|...-|+| ...+.|.+||....
T Consensus 2 ~kKRrN~GR~K~~rGh------v~~V~C~nCgr~vP 31 (108)
T PTZ00172 2 TSKRRNNGRSKHGRGH------VKPVRCSNCGRCVP 31 (108)
T ss_pred CcccccCCCCCCCCCC------CccEEeCCcccccc
Confidence 5666655444433333 45679999998654
No 78
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=27.71 E-value=31 Score=27.82 Aligned_cols=46 Identities=17% Similarity=0.161 Sum_probs=32.0
Q ss_pred eeee-CCCCCCCccccCCCC--CCCCCCCCCCeeecCCCCceecCceeCC
Q 032832 79 ELMA-VPKKKVSRHKRGIRN--GPKALKPVPVIVRCKSCGRVKLPHFFCC 125 (132)
Q Consensus 79 ~lMA-VPKrK~SksRkr~RR--sh~~lk~~~~L~~Cp~CGe~klpH~vC~ 125 (132)
.+|. .-+++..+.++-+.| +=+.+-+ .....||.||...+.+++|-
T Consensus 122 ~~~~~~~~~~I~~v~~w~~rC~GC~~~f~-~~~~~Cp~CG~~~~~~~~~~ 170 (177)
T COG1439 122 NVRSISYKGKIKKVRKWRLRCHGCKRIFP-EPKDFCPICGSPLKRKRVKS 170 (177)
T ss_pred eEEeeeccCccceEeeeeEEEecCceecC-CCCCcCCCCCCceEEeeech
Confidence 3454 566668877775555 2244442 67889999999988888874
No 79
>PLN00186 ribosomal protein S26; Provisional
Probab=27.70 E-value=47 Score=24.96 Aligned_cols=30 Identities=23% Similarity=0.461 Sum_probs=18.6
Q ss_pred CCCCCCccccCCCCCCCCCCCCCCeeecCCCCceec
Q 032832 84 PKKKVSRHKRGIRNGPKALKPVPVIVRCKSCGRVKL 119 (132)
Q Consensus 84 PKrK~SksRkr~RRsh~~lk~~~~L~~Cp~CGe~kl 119 (132)
||+|.+..|...-|+| ...+.|.+||....
T Consensus 2 ~kKRrN~GR~K~~rGh------v~~V~C~nCgr~vP 31 (109)
T PLN00186 2 TKKRRNGGRNKHGRGH------VKRIRCSNCGKCVP 31 (109)
T ss_pred CcccccCCCCCCCCCC------CcceeeCCCccccc
Confidence 5666555444433333 45679999998754
No 80
>PRK07218 replication factor A; Provisional
Probab=27.60 E-value=31 Score=30.85 Aligned_cols=19 Identities=47% Similarity=0.739 Sum_probs=15.4
Q ss_pred eeecCCCCceecCceeCCCC
Q 032832 108 IVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 108 L~~Cp~CGe~klpH~vC~~g 127 (132)
+..||+|+..... -.|+.|
T Consensus 297 i~rCP~C~r~v~~-~~C~~h 315 (423)
T PRK07218 297 IERCPECGRVIQK-GQCRSH 315 (423)
T ss_pred eecCcCccccccC-CcCCCC
Confidence 4689999998865 788875
No 81
>PRK02935 hypothetical protein; Provisional
Probab=27.42 E-value=40 Score=25.41 Aligned_cols=22 Identities=32% Similarity=0.476 Sum_probs=14.4
Q ss_pred CCeeecCCCCce-ecCc--eeCCCC
Q 032832 106 PVIVRCKSCGRV-KLPH--FFCCSG 127 (132)
Q Consensus 106 ~~L~~Cp~CGe~-klpH--~vC~~g 127 (132)
...+.||+|+++ |.-- -.|.+|
T Consensus 68 avqV~CP~C~K~TKmLGrvD~CM~C 92 (110)
T PRK02935 68 AVQVICPSCEKPTKMLGRVDACMHC 92 (110)
T ss_pred ceeeECCCCCchhhhccceeecCcC
Confidence 344689999988 4433 356666
No 82
>PHA02942 putative transposase; Provisional
Probab=27.08 E-value=38 Score=29.55 Aligned_cols=23 Identities=30% Similarity=0.570 Sum_probs=15.3
Q ss_pred CeeecCCCCceecC----ceeCCCC-cc
Q 032832 107 VIVRCKSCGRVKLP----HFFCCSG-ER 129 (132)
Q Consensus 107 ~L~~Cp~CGe~klp----H~vC~~g-y~ 129 (132)
+-..||.||+.... -+.|+.| |.
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCE
Confidence 44569999976432 3689775 53
No 83
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=26.98 E-value=35 Score=21.24 Aligned_cols=14 Identities=43% Similarity=0.911 Sum_probs=10.8
Q ss_pred CCeeecCCCCceec
Q 032832 106 PVIVRCKSCGRVKL 119 (132)
Q Consensus 106 ~~L~~Cp~CGe~kl 119 (132)
...+.||+||.-.+
T Consensus 17 ~~~irC~~CG~rIl 30 (44)
T smart00659 17 KDVVRCRECGYRIL 30 (44)
T ss_pred CCceECCCCCceEE
Confidence 45679999998654
No 84
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=26.69 E-value=34 Score=20.81 Aligned_cols=17 Identities=24% Similarity=0.520 Sum_probs=12.9
Q ss_pred CCeeecCCCCceecCce
Q 032832 106 PVIVRCKSCGRVKLPHF 122 (132)
Q Consensus 106 ~~L~~Cp~CGe~klpH~ 122 (132)
..++.|+.||.....|.
T Consensus 3 ~g~l~C~~CG~~m~~~~ 19 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRK 19 (58)
T ss_pred CCcEEcccCCcEeEEEE
Confidence 46789999999865543
No 85
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.46 E-value=33 Score=25.96 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=16.3
Q ss_pred CCCCCCCeeecCCCCceecCcee
Q 032832 101 ALKPVPVIVRCKSCGRVKLPHFF 123 (132)
Q Consensus 101 ~lk~~~~L~~Cp~CGe~klpH~v 123 (132)
..........||.||+..-+-++
T Consensus 42 yV~ie~G~t~CP~Cg~~~e~~fv 64 (115)
T COG1885 42 YVEIEVGSTSCPKCGEPFESAFV 64 (115)
T ss_pred eEEEecccccCCCCCCccceeEE
Confidence 34444678899999998765544
No 86
>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=26.31 E-value=27 Score=26.40 Aligned_cols=21 Identities=29% Similarity=0.581 Sum_probs=14.3
Q ss_pred CeeecCCCCcee-cC--ceeCCCC
Q 032832 107 VIVRCKSCGRVK-LP--HFFCCSG 127 (132)
Q Consensus 107 ~L~~Cp~CGe~k-lp--H~vC~~g 127 (132)
..+.||+||+.. .- --.|.+|
T Consensus 68 v~V~CP~C~K~TKmLGr~D~CM~C 91 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRVDACMHC 91 (114)
T ss_pred eeeECCCCCChHhhhchhhccCcC
Confidence 456899999984 21 2367777
No 87
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=26.30 E-value=42 Score=27.64 Aligned_cols=21 Identities=29% Similarity=0.747 Sum_probs=16.1
Q ss_pred eecCCCCceec-------CceeCCCCcc
Q 032832 109 VRCKSCGRVKL-------PHFFCCSGER 129 (132)
Q Consensus 109 ~~Cp~CGe~kl-------pH~vC~~gy~ 129 (132)
..||.||..+. .-+.||.|-.
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 46999998865 5578888853
No 88
>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=25.35 E-value=32 Score=21.10 Aligned_cols=11 Identities=27% Similarity=0.824 Sum_probs=8.6
Q ss_pred CeeecCCCCce
Q 032832 107 VIVRCKSCGRV 117 (132)
Q Consensus 107 ~L~~Cp~CGe~ 117 (132)
....||+||..
T Consensus 25 ~~~~CP~Cg~~ 35 (52)
T TIGR02605 25 PLATCPECGGE 35 (52)
T ss_pred CCCCCCCCCCC
Confidence 45679999984
No 89
>PRK12495 hypothetical protein; Provisional
Probab=25.27 E-value=39 Score=28.30 Aligned_cols=23 Identities=26% Similarity=0.600 Sum_probs=16.6
Q ss_pred CCeeecCCCCceecCc---eeCCCCc
Q 032832 106 PVIVRCKSCGRVKLPH---FFCCSGE 128 (132)
Q Consensus 106 ~~L~~Cp~CGe~klpH---~vC~~gy 128 (132)
.....|+.||.++..+ .+|+.|-
T Consensus 40 msa~hC~~CG~PIpa~pG~~~Cp~CQ 65 (226)
T PRK12495 40 MTNAHCDECGDPIFRHDGQEFCPTCQ 65 (226)
T ss_pred cchhhcccccCcccCCCCeeECCCCC
Confidence 4456799999996544 5688883
No 90
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=24.75 E-value=37 Score=27.19 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=8.8
Q ss_pred CeeecCCCCce
Q 032832 107 VIVRCKSCGRV 117 (132)
Q Consensus 107 ~L~~Cp~CGe~ 117 (132)
.+.+||+||-.
T Consensus 47 ~V~vCP~CgyA 57 (214)
T PF09986_consen 47 EVWVCPHCGYA 57 (214)
T ss_pred eEEECCCCCCc
Confidence 46789999964
No 91
>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=24.72 E-value=34 Score=20.72 Aligned_cols=12 Identities=33% Similarity=0.703 Sum_probs=9.5
Q ss_pred CCeeecCCCCce
Q 032832 106 PVIVRCKSCGRV 117 (132)
Q Consensus 106 ~~L~~Cp~CGe~ 117 (132)
.....||+||..
T Consensus 24 ~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 24 DDPVPCPECGST 35 (42)
T ss_pred CCCCcCCCCCCC
Confidence 456789999983
No 92
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.49 E-value=43 Score=34.37 Aligned_cols=19 Identities=32% Similarity=0.786 Sum_probs=16.8
Q ss_pred eecCCCCceecCceeCCCC
Q 032832 109 VRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 109 ~~Cp~CGe~klpH~vC~~g 127 (132)
..||+||...-+...|+.|
T Consensus 680 ~fCP~CGs~te~vy~CPsC 698 (1337)
T PRK14714 680 NRCPDCGTHTEPVYVCPDC 698 (1337)
T ss_pred ccCcccCCcCCCceeCccC
Confidence 4999999998888889887
No 93
>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=24.45 E-value=43 Score=18.61 Aligned_cols=19 Identities=16% Similarity=0.532 Sum_probs=9.1
Q ss_pred ecCCCCceec-------CceeCCCCc
Q 032832 110 RCKSCGRVKL-------PHFFCCSGE 128 (132)
Q Consensus 110 ~Cp~CGe~kl-------pH~vC~~gy 128 (132)
+|+.|+++.. .-.+|+.|.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 6888888752 236677664
No 94
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.28 E-value=44 Score=20.32 Aligned_cols=12 Identities=50% Similarity=0.800 Sum_probs=9.5
Q ss_pred eeecCCCCceec
Q 032832 108 IVRCKSCGRVKL 119 (132)
Q Consensus 108 L~~Cp~CGe~kl 119 (132)
...||.||....
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 679999998643
No 95
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=24.20 E-value=26 Score=26.12 Aligned_cols=23 Identities=17% Similarity=0.199 Sum_probs=16.6
Q ss_pred CCCCCCCCeeecCCCCceecCce
Q 032832 100 KALKPVPVIVRCKSCGRVKLPHF 122 (132)
Q Consensus 100 ~~lk~~~~L~~Cp~CGe~klpH~ 122 (132)
+........+.||.||+...+=.
T Consensus 39 ~~VeIevG~~~cP~Cge~~~~a~ 61 (102)
T PF04475_consen 39 DYVEIEVGDTICPKCGEELDSAF 61 (102)
T ss_pred CeEEEecCcccCCCCCCccCceE
Confidence 34444577889999999876544
No 96
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=24.13 E-value=31 Score=24.05 Aligned_cols=11 Identities=27% Similarity=0.926 Sum_probs=4.3
Q ss_pred CCCeeecCCCC
Q 032832 105 VPVIVRCKSCG 115 (132)
Q Consensus 105 ~~~L~~Cp~CG 115 (132)
.+..-.||.||
T Consensus 19 l~~~F~CPfC~ 29 (81)
T PF05129_consen 19 LPKVFDCPFCN 29 (81)
T ss_dssp -SS----TTT-
T ss_pred CCceEcCCcCC
Confidence 46778899999
No 97
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=23.83 E-value=31 Score=28.82 Aligned_cols=14 Identities=43% Similarity=0.778 Sum_probs=11.5
Q ss_pred CCCeeecCCCCcee
Q 032832 105 VPVIVRCKSCGRVK 118 (132)
Q Consensus 105 ~~~L~~Cp~CGe~k 118 (132)
...++.||.||...
T Consensus 218 ~d~iv~CP~CgRIL 231 (239)
T COG1579 218 KDEIVFCPYCGRIL 231 (239)
T ss_pred CCCCccCCccchHH
Confidence 57789999999863
No 98
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=23.82 E-value=36 Score=23.21 Aligned_cols=24 Identities=25% Similarity=0.546 Sum_probs=14.6
Q ss_pred CeeecCCCCceec---------C-ceeCCCC-ccc
Q 032832 107 VIVRCKSCGRVKL---------P-HFFCCSG-ERK 130 (132)
Q Consensus 107 ~L~~Cp~CGe~kl---------p-H~vC~~g-y~k 130 (132)
..-.||+|||... . -..|++| |+|
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~G 60 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGFEG 60 (61)
T ss_pred eEeeCCCCCceeeehhhhHHHcCCceECCCcCccC
Confidence 3457999995432 1 2567774 655
No 99
>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=23.70 E-value=37 Score=20.42 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=7.8
Q ss_pred eecCCCCcee
Q 032832 109 VRCKSCGRVK 118 (132)
Q Consensus 109 ~~Cp~CGe~k 118 (132)
..||+||...
T Consensus 2 ~~CP~Cg~~l 11 (39)
T PF01396_consen 2 EKCPKCGGPL 11 (39)
T ss_pred cCCCCCCcee
Confidence 4799999763
No 100
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.51 E-value=33 Score=21.98 Aligned_cols=13 Identities=31% Similarity=0.746 Sum_probs=10.2
Q ss_pred CCeeecCCCCcee
Q 032832 106 PVIVRCKSCGRVK 118 (132)
Q Consensus 106 ~~L~~Cp~CGe~k 118 (132)
-.|-+||+||-+-
T Consensus 9 RGirkCp~CGt~N 21 (44)
T PF14952_consen 9 RGIRKCPKCGTYN 21 (44)
T ss_pred hccccCCcCcCcc
Confidence 4566899999874
No 102
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=23.24 E-value=68 Score=21.08 Aligned_cols=8 Identities=38% Similarity=1.219 Sum_probs=4.7
Q ss_pred ecCCCCce
Q 032832 110 RCKSCGRV 117 (132)
Q Consensus 110 ~Cp~CGe~ 117 (132)
.||.||+.
T Consensus 19 ~cp~cG~~ 26 (53)
T PF04135_consen 19 KCPPCGGP 26 (53)
T ss_dssp BBTTTSSB
T ss_pred ccCCCCCC
Confidence 56666655
No 103
>PRK01343 zinc-binding protein; Provisional
Probab=23.21 E-value=55 Score=21.86 Aligned_cols=20 Identities=15% Similarity=0.301 Sum_probs=13.2
Q ss_pred CeeecCCCCceecCceeCCCC
Q 032832 107 VIVRCKSCGRVKLPHFFCCSG 127 (132)
Q Consensus 107 ~L~~Cp~CGe~klpH~vC~~g 127 (132)
....||.||+....... ++|
T Consensus 8 p~~~CP~C~k~~~~~~r-PFC 27 (57)
T PRK01343 8 PTRPCPECGKPSTREAY-PFC 27 (57)
T ss_pred CCCcCCCCCCcCcCCCC-ccc
Confidence 35689999998654332 444
No 104
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=22.81 E-value=63 Score=25.99 Aligned_cols=20 Identities=20% Similarity=0.516 Sum_probs=15.2
Q ss_pred CCCCCCeeecCCCCceecCc
Q 032832 102 LKPVPVIVRCKSCGRVKLPH 121 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~klpH 121 (132)
+....+++.|+.||.++.+.
T Consensus 29 i~~~i~v~~C~~Cg~~~~~~ 48 (236)
T PF04981_consen 29 IPDRIEVTICPKCGRYRIGG 48 (236)
T ss_pred cCCccCceECCCCCCEECCC
Confidence 33345889999999998763
No 105
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=22.78 E-value=72 Score=18.82 Aligned_cols=17 Identities=41% Similarity=0.639 Sum_probs=11.6
Q ss_pred CCCCCCeeecCCCCcee
Q 032832 102 LKPVPVIVRCKSCGRVK 118 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~k 118 (132)
+......+.|++||+..
T Consensus 19 l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 19 LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred cccCCcEEECCCCCcEe
Confidence 33345678899999763
No 106
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=22.38 E-value=34 Score=19.68 Aligned_cols=11 Identities=36% Similarity=0.655 Sum_probs=8.3
Q ss_pred eeecCCCCcee
Q 032832 108 IVRCKSCGRVK 118 (132)
Q Consensus 108 L~~Cp~CGe~k 118 (132)
-..||.||..+
T Consensus 17 ~~~CP~Cg~~~ 27 (33)
T cd00350 17 PWVCPVCGAPK 27 (33)
T ss_pred CCcCcCCCCcH
Confidence 34899999864
No 107
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=22.35 E-value=36 Score=22.27 Aligned_cols=14 Identities=29% Similarity=0.736 Sum_probs=10.8
Q ss_pred CCeeecCCCCceec
Q 032832 106 PVIVRCKSCGRVKL 119 (132)
Q Consensus 106 ~~L~~Cp~CGe~kl 119 (132)
.-+..||+||.-+.
T Consensus 11 ~kY~~Cp~CGN~~v 24 (49)
T PF12677_consen 11 NKYCKCPKCGNDKV 24 (49)
T ss_pred hhhccCcccCCcEe
Confidence 34778999998664
No 108
>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=22.30 E-value=37 Score=19.78 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=9.0
Q ss_pred CeeecCCCCcee
Q 032832 107 VIVRCKSCGRVK 118 (132)
Q Consensus 107 ~L~~Cp~CGe~k 118 (132)
....|++||+..
T Consensus 31 p~~~C~~CGE~~ 42 (46)
T TIGR03831 31 PALVCPQCGEEY 42 (46)
T ss_pred CccccccCCCEe
Confidence 344799999864
No 109
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=21.63 E-value=44 Score=20.36 Aligned_cols=11 Identities=27% Similarity=0.797 Sum_probs=8.5
Q ss_pred CeeecCCCCce
Q 032832 107 VIVRCKSCGRV 117 (132)
Q Consensus 107 ~L~~Cp~CGe~ 117 (132)
..+.|+.||=.
T Consensus 12 ~~~~C~~CgM~ 22 (41)
T PF13878_consen 12 GATTCPTCGML 22 (41)
T ss_pred CCcCCCCCCCE
Confidence 45799999954
No 110
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=21.47 E-value=63 Score=19.08 Aligned_cols=16 Identities=44% Similarity=0.922 Sum_probs=11.4
Q ss_pred CCCCCCeeecCCCCce
Q 032832 102 LKPVPVIVRCKSCGRV 117 (132)
Q Consensus 102 lk~~~~L~~Cp~CGe~ 117 (132)
+......+.|++||+.
T Consensus 19 ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 19 IPPKGRKVRCSKCGHV 34 (36)
T ss_pred CCCCCcEEECCCCCCE
Confidence 4444556889999975
No 111
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=20.78 E-value=52 Score=25.89 Aligned_cols=18 Identities=28% Similarity=0.687 Sum_probs=14.9
Q ss_pred CeeecCCCCceecCceeC
Q 032832 107 VIVRCKSCGRVKLPHFFC 124 (132)
Q Consensus 107 ~L~~Cp~CGe~klpH~vC 124 (132)
.+-.||.||...+|+.|-
T Consensus 132 ~~p~C~~Cg~~lrP~Vv~ 149 (218)
T cd01407 132 EVPRCPKCGGLLRPDVVF 149 (218)
T ss_pred CCCcCCCCCCccCCCeEE
Confidence 345799999999999883
No 112
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=20.68 E-value=54 Score=21.78 Aligned_cols=12 Identities=33% Similarity=0.686 Sum_probs=6.6
Q ss_pred eecCCCCceecC
Q 032832 109 VRCKSCGRVKLP 120 (132)
Q Consensus 109 ~~Cp~CGe~klp 120 (132)
+.||.||+....
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 689999998665
No 113
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=20.54 E-value=54 Score=21.44 Aligned_cols=12 Identities=33% Similarity=0.780 Sum_probs=9.7
Q ss_pred CCeeecCCCCce
Q 032832 106 PVIVRCKSCGRV 117 (132)
Q Consensus 106 ~~L~~Cp~CGe~ 117 (132)
-.++.||.||..
T Consensus 20 GeiV~Cp~CGae 31 (54)
T TIGR01206 20 GELVICDECGAE 31 (54)
T ss_pred CCEEeCCCCCCE
Confidence 458899999965
No 114
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=20.45 E-value=53 Score=26.13 Aligned_cols=17 Identities=29% Similarity=0.776 Sum_probs=14.6
Q ss_pred eeecCCCCceecCceeC
Q 032832 108 IVRCKSCGRVKLPHFFC 124 (132)
Q Consensus 108 L~~Cp~CGe~klpH~vC 124 (132)
+-.||.||...+|+.|.
T Consensus 136 ~p~C~~Cgg~lrP~Vv~ 152 (222)
T cd01413 136 VPRCPKCGGIIRPDVVL 152 (222)
T ss_pred CCcCCCCCCccCCCEEE
Confidence 45799999999999884
No 115
>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=20.27 E-value=50 Score=22.95 Aligned_cols=19 Identities=21% Similarity=0.349 Sum_probs=12.3
Q ss_pred eeecCCCCceecCceeCCC
Q 032832 108 IVRCKSCGRVKLPHFFCCS 126 (132)
Q Consensus 108 L~~Cp~CGe~klpH~vC~~ 126 (132)
...||+||++...-..|+.
T Consensus 30 ~a~CPdC~~~Le~LkACGA 48 (70)
T PF07191_consen 30 EAFCPDCGQPLEVLKACGA 48 (70)
T ss_dssp EEE-TTT-SB-EEEEETTE
T ss_pred cccCCCcccHHHHHHHhcc
Confidence 4578888888888888874
No 116
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=20.25 E-value=58 Score=22.27 Aligned_cols=14 Identities=43% Similarity=0.835 Sum_probs=8.5
Q ss_pred CCeeecCCCCceec
Q 032832 106 PVIVRCKSCGRVKL 119 (132)
Q Consensus 106 ~~L~~Cp~CGe~kl 119 (132)
.-|+.||.|...++
T Consensus 27 vViv~C~gC~~~Hl 40 (66)
T PF05180_consen 27 VVIVQCPGCKNRHL 40 (66)
T ss_dssp EEEEE-TTS--EEE
T ss_pred eEEEECCCCcceee
Confidence 46899999998753
No 117
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=20.22 E-value=34 Score=27.24 Aligned_cols=15 Identities=13% Similarity=0.270 Sum_probs=0.0
Q ss_pred CCCeeecCCCCceec
Q 032832 105 VPVIVRCKSCGRVKL 119 (132)
Q Consensus 105 ~~~L~~Cp~CGe~kl 119 (132)
...++.||-||+.+.
T Consensus 165 ~~~~~~cPitGe~IP 179 (229)
T PF12230_consen 165 KEKMIICPITGEMIP 179 (229)
T ss_dssp ---------------
T ss_pred ccccccccccccccc
Confidence 467899999999864
Done!