Query psy10064
Match_columns 257
No_of_seqs 154 out of 369
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 16:57:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10064.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10064hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2990|consensus 100.0 1.7E-91 3.6E-96 634.5 14.0 250 1-250 1-260 (317)
2 PF04502 DUF572: Family of unk 100.0 8.9E-76 1.9E-80 547.2 15.7 212 1-231 1-214 (324)
3 KOG2989|consensus 100.0 1E-50 2.2E-55 362.0 6.6 193 1-211 1-195 (253)
4 COG5134 Uncharacterized conser 100.0 7E-41 1.5E-45 295.2 11.6 214 7-232 1-220 (272)
5 PF05907 DUF866: Eukaryotic pr 91.6 0.2 4.4E-06 43.1 3.6 63 47-112 25-90 (161)
6 PF08271 TF_Zn_Ribbon: TFIIB z 90.3 0.19 4.1E-06 33.7 1.8 25 88-113 1-25 (43)
7 PF10122 Mu-like_Com: Mu-like 87.6 0.48 1E-05 33.8 2.3 34 52-100 4-37 (51)
8 PRK03681 hypA hydrogenase nick 81.2 0.68 1.5E-05 37.6 0.9 32 47-96 65-96 (114)
9 COG4332 Uncharacterized protei 79.8 1.1 2.4E-05 39.8 1.8 41 51-98 16-60 (203)
10 PRK12380 hydrogenase nickel in 79.4 0.96 2.1E-05 36.6 1.2 34 42-95 61-94 (113)
11 smart00834 CxxC_CXXC_SSSS Puta 77.9 2.8 6.1E-05 27.0 2.9 20 82-103 2-21 (41)
12 COG4416 Com Mu-like prophage p 77.8 1 2.3E-05 32.6 0.8 40 52-109 4-46 (60)
13 PF13240 zinc_ribbon_2: zinc-r 77.7 1.1 2.3E-05 26.7 0.7 15 54-68 1-15 (23)
14 PRK00564 hypA hydrogenase nick 77.1 1.2 2.7E-05 36.2 1.2 35 43-96 63-97 (117)
15 COG0375 HybF Zn finger protein 74.0 3 6.5E-05 34.4 2.7 29 48-95 66-94 (115)
16 KOG2990|consensus 72.1 1.8 4E-05 40.8 1.2 14 5-18 74-87 (317)
17 PF11331 DUF3133: Protein of u 69.8 3.8 8.3E-05 28.6 2.1 41 49-100 4-44 (46)
18 TIGR00100 hypA hydrogenase nic 69.7 2.5 5.5E-05 34.2 1.4 35 42-96 61-95 (115)
19 COG2888 Predicted Zn-ribbon RN 68.9 5 0.00011 29.6 2.6 32 52-100 9-40 (61)
20 PF09723 Zn-ribbon_8: Zinc rib 67.9 5.5 0.00012 26.7 2.5 20 82-103 2-21 (42)
21 COG1996 RPC10 DNA-directed RNA 65.4 6.7 0.00014 27.7 2.6 19 87-105 24-42 (49)
22 KOG2272|consensus 65.3 2.7 5.9E-05 39.3 0.8 22 78-99 154-175 (332)
23 TIGR02605 CxxC_CxxC_SSSS putat 63.7 6.1 0.00013 27.0 2.1 18 82-101 2-19 (52)
24 PF07754 DUF1610: Domain of un 62.7 6.3 0.00014 23.9 1.8 10 55-64 1-10 (24)
25 PRK03824 hypA hydrogenase nick 61.1 6 0.00013 33.0 2.0 45 48-96 66-116 (135)
26 PF06107 DUF951: Bacterial pro 60.4 6.1 0.00013 28.8 1.7 33 25-63 10-42 (57)
27 PRK14890 putative Zn-ribbon RN 60.3 9.4 0.0002 28.0 2.7 17 48-64 3-19 (59)
28 PRK00762 hypA hydrogenase nick 59.3 5.1 0.00011 32.9 1.3 18 42-61 61-78 (124)
29 PF10263 SprT-like: SprT-like 58.1 9.2 0.0002 31.5 2.7 34 51-99 122-155 (157)
30 PRK04351 hypothetical protein; 55.9 12 0.00026 31.9 3.0 37 49-100 109-145 (149)
31 PF10058 DUF2296: Predicted in 52.6 12 0.00027 26.6 2.2 34 49-95 19-52 (54)
32 KOG3368|consensus 52.4 17 0.00036 30.9 3.3 32 77-108 62-93 (140)
33 PF01921 tRNA-synt_1f: tRNA sy 51.4 9.1 0.0002 37.2 1.8 41 49-100 171-212 (360)
34 PF13719 zinc_ribbon_5: zinc-r 51.1 19 0.00042 23.4 2.8 36 51-98 1-36 (37)
35 KOG2407|consensus 50.7 5.7 0.00012 40.4 0.3 15 46-60 492-506 (575)
36 PF13717 zinc_ribbon_4: zinc-r 50.2 20 0.00042 23.3 2.7 35 51-97 1-35 (36)
37 KOG3794|consensus 49.9 9.7 0.00021 37.6 1.7 14 5-18 66-81 (453)
38 PRK00398 rpoP DNA-directed RNA 49.8 14 0.00031 24.8 2.1 18 87-104 21-38 (46)
39 PF05876 Terminase_GpA: Phage 49.4 9.3 0.0002 38.9 1.6 36 77-112 190-234 (557)
40 PF07255 Benyvirus_14KDa: Beny 49.1 14 0.0003 30.2 2.2 73 44-121 25-99 (123)
41 COG1405 SUA7 Transcription ini 48.9 8.9 0.00019 36.0 1.3 28 88-116 2-30 (285)
42 COG2956 Predicted N-acetylgluc 48.6 11 0.00024 36.7 1.8 20 82-101 363-382 (389)
43 PF01155 HypA: Hydrogenase exp 47.8 8.1 0.00018 31.1 0.7 18 43-61 62-79 (113)
44 smart00731 SprT SprT homologue 47.3 22 0.00047 29.5 3.3 36 50-99 110-145 (146)
45 smart00132 LIM Zinc-binding do 46.9 13 0.00029 22.8 1.5 36 54-98 1-38 (39)
46 COG3091 SprT Zn-dependent meta 46.1 17 0.00036 31.6 2.4 41 51-103 116-156 (156)
47 PF05876 Terminase_GpA: Phage 46.0 14 0.00031 37.5 2.3 39 51-98 199-240 (557)
48 PF13248 zf-ribbon_3: zinc-rib 42.5 12 0.00026 22.5 0.7 16 52-67 2-17 (26)
49 PF13005 zf-IS66: zinc-finger 42.3 35 0.00076 22.6 3.1 41 54-94 4-47 (47)
50 PF06750 DiS_P_DiS: Bacterial 42.2 4.3 9.4E-05 31.8 -1.6 34 53-99 34-70 (92)
51 PRK04016 DNA-directed RNA poly 42.1 12 0.00026 27.7 0.8 15 50-64 2-16 (62)
52 TIGR01206 lysW lysine biosynth 42.0 18 0.00039 25.9 1.7 15 88-102 3-17 (54)
53 PF09855 DUF2082: Nucleic-acid 41.3 28 0.00061 25.7 2.7 43 54-96 2-45 (64)
54 COG2816 NPY1 NTP pyrophosphohy 40.3 18 0.00038 34.2 1.8 48 54-118 113-166 (279)
55 PF01396 zf-C4_Topoisom: Topoi 39.8 27 0.00059 23.0 2.2 17 89-105 3-19 (39)
56 PF11931 DUF3449: Domain of un 38.7 10 0.00022 33.9 0.0 30 53-82 102-137 (196)
57 TIGR02098 MJ0042_CXXC MJ0042 f 38.0 17 0.00036 23.3 0.9 18 87-104 2-19 (38)
58 COG4481 Uncharacterized protei 37.3 22 0.00048 25.9 1.5 24 42-65 24-47 (60)
59 COG1644 RPB10 DNA-directed RNA 36.7 14 0.00031 27.4 0.5 14 50-63 2-15 (63)
60 PF14255 Cys_rich_CPXG: Cystei 36.6 29 0.00064 24.6 2.1 19 89-107 2-20 (52)
61 PF06044 DRP: Dam-replacing fa 36.6 17 0.00038 33.7 1.1 51 52-116 31-82 (254)
62 COG2093 DNA-directed RNA polym 36.6 20 0.00043 26.8 1.2 20 89-108 20-47 (64)
63 smart00659 RPOLCX RNA polymera 36.5 34 0.00074 23.3 2.3 18 87-104 19-36 (44)
64 COG2051 RPS27A Ribosomal prote 36.5 38 0.00082 25.5 2.7 17 85-101 36-52 (67)
65 PRK00750 lysK lysyl-tRNA synth 35.7 33 0.00073 34.5 3.1 27 49-75 172-199 (510)
66 PF09082 DUF1922: Domain of un 35.5 33 0.00071 25.9 2.3 30 53-101 4-33 (68)
67 PRK11823 DNA repair protein Ra 34.3 26 0.00057 34.6 2.0 28 53-101 8-35 (446)
68 TIGR00467 lysS_arch lysyl-tRNA 33.6 36 0.00077 34.6 2.9 24 49-72 165-188 (515)
69 PF05129 Elf1: Transcription e 33.6 40 0.00086 25.8 2.5 44 47-101 17-60 (81)
70 PF04113 Gpi16: Gpi16 subunit, 33.0 9.3 0.0002 39.2 -1.4 26 46-71 507-533 (564)
71 KOG2846|consensus 32.6 20 0.00043 34.6 0.8 42 51-105 219-260 (328)
72 PF02150 RNA_POL_M_15KD: RNA p 32.1 47 0.001 21.5 2.3 16 90-105 4-19 (35)
73 PRK14704 anaerobic ribonucleos 32.1 30 0.00066 35.9 2.2 38 40-105 548-585 (618)
74 PF05864 Chordopox_RPO7: Chord 32.0 23 0.0005 26.1 0.9 16 49-64 1-16 (63)
75 cd00730 rubredoxin Rubredoxin; 31.7 22 0.00047 25.0 0.7 39 53-95 2-42 (50)
76 PHA02998 RNA polymerase subuni 31.5 11 0.00024 33.6 -1.0 60 49-114 108-178 (195)
77 PF01927 Mut7-C: Mut7-C RNAse 31.4 38 0.00082 28.3 2.3 15 50-64 89-103 (147)
78 PF11793 FANCL_C: FANCL C-term 31.4 27 0.00059 25.8 1.2 16 87-102 55-70 (70)
79 KOG1296|consensus 31.3 20 0.00043 31.0 0.6 61 49-112 27-90 (161)
80 PRK08271 anaerobic ribonucleos 31.2 29 0.00062 36.1 1.8 34 40-95 555-588 (623)
81 PRK00423 tfb transcription ini 30.4 26 0.00056 32.9 1.3 24 88-112 12-35 (310)
82 PRK06260 threonine synthase; V 30.4 35 0.00075 32.9 2.1 35 51-104 2-36 (397)
83 PF01194 RNA_pol_N: RNA polyme 30.4 23 0.00049 26.1 0.7 13 51-63 3-15 (60)
84 TIGR00416 sms DNA repair prote 30.2 31 0.00067 34.2 1.8 28 53-101 8-35 (454)
85 cd02339 ZZ_Mind_bomb Zinc fing 30.0 28 0.00062 23.8 1.1 16 53-68 1-16 (45)
86 PLN00032 DNA-directed RNA poly 29.8 25 0.00054 26.7 0.8 14 51-64 3-16 (71)
87 PRK12496 hypothetical protein; 29.6 32 0.00069 29.6 1.6 11 89-99 145-155 (164)
88 PF13597 NRDD: Anaerobic ribon 29.6 48 0.001 33.7 3.1 33 41-96 481-513 (546)
89 cd02338 ZZ_PCMF_like Zinc fing 29.6 25 0.00054 24.3 0.7 7 53-59 1-7 (49)
90 cd00674 LysRS_core_class_I cat 29.6 48 0.001 32.0 2.9 11 49-59 166-176 (353)
91 COG5134 Uncharacterized conser 29.5 20 0.00043 33.0 0.3 19 77-98 35-53 (272)
92 PRK07111 anaerobic ribonucleos 29.1 37 0.00079 36.0 2.2 33 40-95 669-701 (735)
93 KOG2636|consensus 29.0 17 0.00036 36.6 -0.3 31 52-82 401-437 (497)
94 smart00661 RPOL9 RNA polymeras 28.8 32 0.00069 23.1 1.2 11 54-64 2-12 (52)
95 PRK00464 nrdR transcriptional 28.5 43 0.00094 28.7 2.2 55 53-116 1-58 (154)
96 cd01121 Sms Sms (bacterial rad 27.6 42 0.0009 32.5 2.2 17 86-102 13-29 (372)
97 PHA03082 DNA-dependent RNA pol 27.2 31 0.00067 25.4 0.9 16 49-64 1-16 (63)
98 PF13790 DUF4182: Domain of un 27.1 81 0.0018 21.2 2.8 30 52-94 3-32 (38)
99 PF04606 Ogr_Delta: Ogr/Delta- 26.6 38 0.00082 23.1 1.2 19 89-107 1-19 (47)
100 PF00569 ZZ: Zinc finger, ZZ t 26.5 35 0.00076 23.1 1.0 19 51-69 3-21 (46)
101 PF14353 CpXC: CpXC protein 26.1 38 0.00082 27.3 1.3 40 53-99 2-50 (128)
102 KOG4253|consensus 26.0 2.7E+02 0.0059 24.5 6.6 53 151-203 39-92 (175)
103 PRK11788 tetratricopeptide rep 25.7 45 0.00098 30.5 1.9 14 86-99 367-380 (389)
104 PRK05978 hypothetical protein; 25.6 25 0.00054 30.1 0.2 33 51-100 32-65 (148)
105 PF02146 SIR2: Sir2 family; I 25.4 29 0.00062 29.5 0.5 12 51-62 104-115 (178)
106 PF04828 GFA: Glutathione-depe 25.2 95 0.0021 22.5 3.3 39 74-114 35-74 (92)
107 PF05973 Gp49: Phage derived p 25.1 1.1E+02 0.0023 23.0 3.6 41 78-119 35-76 (91)
108 PF00645 zf-PARP: Poly(ADP-rib 25.1 34 0.00074 25.4 0.8 14 53-66 8-21 (82)
109 PRK03954 ribonuclease P protei 24.7 77 0.0017 26.3 2.9 42 53-100 65-106 (121)
110 TIGR03844 cysteate_syn cysteat 24.7 58 0.0013 31.8 2.6 34 51-104 1-34 (398)
111 PRK04023 DNA polymerase II lar 24.5 38 0.00083 37.3 1.4 19 40-61 617-635 (1121)
112 COG0484 DnaJ DnaJ-class molecu 24.2 1.8E+02 0.0039 28.6 5.8 59 44-105 134-201 (371)
113 TIGR02487 NrdD anaerobic ribon 24.0 53 0.0012 33.7 2.2 35 40-96 513-547 (579)
114 cd02344 ZZ_HERC2 Zinc finger, 23.8 43 0.00094 23.1 1.1 15 53-67 1-15 (45)
115 COG0675 Transposase and inacti 23.5 1.1E+02 0.0024 27.3 4.0 12 49-60 306-317 (364)
116 COG5525 Bacteriophage tail ass 23.5 52 0.0011 34.2 2.0 60 51-116 226-285 (611)
117 PF04810 zf-Sec23_Sec24: Sec23 23.2 86 0.0019 20.6 2.4 35 53-100 3-37 (40)
118 PRK07591 threonine synthase; V 23.2 54 0.0012 32.0 2.1 16 88-103 34-49 (421)
119 PF04690 YABBY: YABBY protein; 23.0 50 0.0011 29.0 1.6 38 52-100 12-49 (170)
120 PF04899 MbeD_MobD: MbeD/MobD 23.0 2.2E+02 0.0047 21.4 4.8 45 160-207 10-54 (70)
121 COG2023 RPR2 RNase P subunit R 23.0 1E+02 0.0022 25.2 3.2 46 46-100 47-95 (105)
122 PF03604 DNA_RNApol_7kD: DNA d 22.7 33 0.00071 22.0 0.3 13 88-100 18-30 (32)
123 PRK00807 50S ribosomal protein 22.6 28 0.00062 24.5 -0.0 43 54-106 3-47 (52)
124 PRK08197 threonine synthase; V 21.6 65 0.0014 31.0 2.2 31 53-103 8-38 (394)
125 COG0846 SIR2 NAD-dependent pro 21.3 45 0.00099 30.7 1.0 17 50-66 120-136 (250)
126 PRK09678 DNA-binding transcrip 21.1 51 0.0011 25.0 1.1 17 88-104 2-18 (72)
127 KOG0006|consensus 21.1 93 0.002 30.4 3.1 49 44-112 126-175 (446)
128 PRK00420 hypothetical protein; 21.1 70 0.0015 26.2 2.0 33 51-101 22-54 (112)
129 smart00531 TFIIE Transcription 21.0 64 0.0014 26.9 1.8 43 50-103 97-139 (147)
130 cd02340 ZZ_NBR1_like Zinc fing 21.0 53 0.0011 22.1 1.0 15 53-68 1-15 (43)
131 TIGR00354 polC DNA polymerase, 20.8 54 0.0012 36.0 1.6 21 53-96 626-646 (1095)
132 PF09538 FYDLN_acid: Protein o 20.8 51 0.0011 26.7 1.1 13 88-100 27-39 (108)
133 PRK05654 acetyl-CoA carboxylas 20.8 35 0.00075 32.2 0.2 33 52-100 27-59 (292)
134 PF08996 zf-DNA_Pol: DNA Polym 20.6 72 0.0016 27.8 2.1 20 85-104 16-35 (188)
135 PRK08351 DNA-directed RNA poly 20.6 57 0.0012 24.0 1.2 8 89-96 17-24 (61)
136 PF01258 zf-dskA_traR: Prokary 20.1 47 0.001 21.2 0.6 14 51-65 3-16 (36)
No 1
>KOG2990|consensus
Probab=100.00 E-value=1.7e-91 Score=634.51 Aligned_cols=250 Identities=51% Similarity=0.944 Sum_probs=241.4
Q ss_pred CCcccCCCcccCCCCCCCCCCCccccCchhhHHHHhhhcCCeeEEEEeceeeeecCCCCccccccceeeeeccccccccc
Q psy10064 1 MGERKGTNKYYPPDYDPSVGGLNKFLGTHALRERARKLHMGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYS 80 (257)
Q Consensus 1 M~ERK~~nkYyPPD~DP~k~~~nk~~~~h~l~~Ra~k~~~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~s 80 (257)
|||||+.||||||||+|.++|+|+|||+||||.||||+++||+||||||||||||.+|.+||++||||||+|++||+||+
T Consensus 1 mgerkg~nkYyPPd~~p~~gsln~~~g~h~lrerarKi~~gilvIRFEMPynIWC~gC~nhIgmGvRyNAeKkkvGnYYt 80 (317)
T KOG2990|consen 1 MGERKGQNKYYPPDFNPKHGSLNKYHGTHALRERARKIDQGILVIRFEMPYNIWCDGCKNHIGMGVRYNAEKKKVGNYYT 80 (317)
T ss_pred CcccccCCcccCCCCCcccCcccccccchhHHHHHHhhccceEEEEEecccchhhccHHHhhhccceechhhhhcccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCceecccCCCcccCCcccccchHhhhcCCCCchhhcccccccchhhhH
Q psy10064 81 TPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARRQENRWNPLENEQIVPETKEVSRKLFDDPMYKLEHGTNDMSSSKS 160 (257)
Q Consensus 81 t~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r~~e~~d~~~~~~~~~~~~e~~~~~~~d~m~~LE~~~~d~~~~~~ 160 (257)
||||+|.||||+|.|+|+|+|||+||+|||+|||+|++++||+.+++++.+.++++++++..|||++|||+..|.+..+.
T Consensus 81 Tpiw~FrmKchlC~n~i~iqTDP~NceYvI~SGaqRKeer~D~~d~Eq~~~t~~e~k~KLa~DamyrLEHqe~D~~k~k~ 160 (317)
T KOG2990|consen 81 TPIWSFRMKCHLCDNYIVIQTDPKNCEYVITSGAQRKEERYDAEDAEQMEPTAEEEKGKLASDAMYRLEHQEVDLKKKKA 160 (317)
T ss_pred CcccchhhcccccCCceeeecCCCCceEEEeccccccccccCchhhhhccchhhhhcccccccHHHHHHhHHHhHhhhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhccChHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhccCCCCCcCCCChhhHHhhhcccccCc----
Q psy10064 161 KASHLNKLLDRQESVWKNDFDANRVLRDSFRKKKKQLKALQDKDNALLSKSSLSLKLVPEHKNDIRLASLYKYQHV---- 236 (257)
Q Consensus 161 ~~~~L~eL~~~~~~~~~ddy~~n~~LR~~fR~~kk~~~~~~~~d~al~~~~~l~i~Ll~e~eeD~~~A~~v~f~~~---- 236 (257)
+.+.|..|++.++++|.|||.+|++||++||++||..+++++.|..|+++.+|+|.|||+|++|+..|.+|+|.+.
T Consensus 161 aep~l~~l~e~~~~rw~Ddf~~ns~LRaqfR~~kK~~~e~~~~D~~l~~r~sl~I~lLPeTe~Dr~~A~llk~~~~~~ke 240 (317)
T KOG2990|consen 161 AEPVLVRLQEVNDARWADDFQANSRLRAQFREEKKLINEQEARDLDLFARASLDILLLPETEEDRKIASLLKFNTKKRKE 240 (317)
T ss_pred cchHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHhhhhhhhhHHHHHhhhcCcccCCCchhhHHHHHHHhhcccchhh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999872
Q ss_pred ------cccccccCCCCCCC
Q psy10064 237 ------KPKLNVKLKAPSSS 250 (257)
Q Consensus 237 ------~~~~~~~~~~~~~~ 250 (257)
+..|+++|--++|.
T Consensus 241 dr~~~~r~~i~srp~~~~S~ 260 (317)
T KOG2990|consen 241 DRENNRRLEIKSRPSRTGST 260 (317)
T ss_pred hHHhhhhhhhccCCCCCCCc
Confidence 46788886655544
No 2
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=100.00 E-value=8.9e-76 Score=547.15 Aligned_cols=212 Identities=47% Similarity=0.766 Sum_probs=192.9
Q ss_pred CCcccCCCcccCCCCCCCCCCCccccCchhhHHHHhhhcCCeeEEEEeceeeeecCCCCccccccceeeeecccccc--c
Q psy10064 1 MGERKGTNKYYPPDYDPSVGGLNKFLGTHALRERARKLHMGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGM--Y 78 (257)
Q Consensus 1 M~ERK~~nkYyPPD~DP~k~~~nk~~~~h~l~~Ra~k~~~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~--Y 78 (257)
||||||+||||||||||++ ||+++|++ +|+++|||||||+|||++|++|||+||||||+|++||+ |
T Consensus 1 M~ERK~~nkYyPPD~d~~k---------~~~~kr~k---~~~~~VRf~~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Y 68 (324)
T PF04502_consen 1 MSERKVLNKYYPPDFDPSK---------HPLRKRAK---QGILTVRFMMPFNIWCNTCGEYIYKGVRFNARKEKVGNEKY 68 (324)
T ss_pred CcccccCCCccCCCCCccc---------ccccccCc---CcceEEEEcCCccCcCCCCccccccceeeeeeeEecCCCcc
Confidence 9999999999999999665 67888877 79999999999999999999999999999999999987 9
Q ss_pred cceeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCceecccCCCcccCCcccccchHhhhcCCCCchhhcccccccchhh
Q psy10064 79 YSTPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARRQENRWNPLENEQIVPETKEVSRKLFDDPMYKLEHGTNDMSSS 158 (257)
Q Consensus 79 ~st~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r~~e~~d~~~~~~~~~~~~e~~~~~~~d~m~~LE~~~~d~~~~ 158 (257)
||||||+||||||.|+++|+|+|||+|+||||++||+|+++.| ...++++...++++++++..|||++||+++.|++++
T Consensus 69 ls~~I~rF~~kC~~C~~~i~~kTDPkn~dY~~~~Ga~R~~~~~-~~~~~~~~~~~~~~~~~~~~d~m~~LE~~~~d~~~~ 147 (324)
T PF04502_consen 69 LSTPIYRFYIKCPRCSNEIEFKTDPKNTDYVVESGARRNFEPD-KEEEEQEEREDKEEEEEEEEDPMKALEKRTEDSKRE 147 (324)
T ss_pred ccceEEEEEEEcCCCCCEEeeecCCCCCCeeeecCeeecCCcc-hhhhhhhhhhhHHHhhhccCCchHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999966554 444555555556666677899999999999999999
Q ss_pred hHHHHHHHHHHHHHhhhccChHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhccCCCCCcCCCChhhHHhhhcc
Q psy10064 159 KSKASHLNKLLDRQESVWKNDFDANRVLRDSFRKKKKQLKALQDKDNALLSKSSLSLKLVPEHKNDIRLASLY 231 (257)
Q Consensus 159 ~~~~~~L~eL~~~~~~~~~ddy~~n~~LR~~fR~~kk~~~~~~~~d~al~~~~~l~i~Ll~e~eeD~~~A~~v 231 (257)
+++.++|++|+++|.+ .|+|+.|++||+.||.++++++.+++.|+++.++++|. |++++|..+|..-
T Consensus 148 ~~~~~~LeeL~~~~~r--~d~~~~n~~Lr~~~r~~~k~~~~~~~~d~~~~~~~~~~----~~~~~~~r~~~~~ 214 (324)
T PF04502_consen 148 MEALERLEELQELNAR--KDDYDANQMLRKRFREEKKERERQEEEDEALKKKISLG----PESEEDKRLAADE 214 (324)
T ss_pred HHHHHHHHHHHHHHhc--cCchhhHHHHHHHHHHHHHHHHHhHHHHHHHHHhhccC----cchhhhhhhhcch
Confidence 9999999999999997 89999999999999999999999999999998888775 8888888887774
No 3
>KOG2989|consensus
Probab=100.00 E-value=1e-50 Score=361.97 Aligned_cols=193 Identities=30% Similarity=0.456 Sum_probs=161.7
Q ss_pred CCcccCCCcccCCCCCCCCCCCccccCchhhHHHHhhhcCCeeEEEEeceeeeecCCCCccccccceeeeecccc-c-cc
Q psy10064 1 MGERKGTNKYYPPDYDPSVGGLNKFLGTHALRERARKLHMGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKV-G-MY 78 (257)
Q Consensus 1 M~ERK~~nkYyPPD~DP~k~~~nk~~~~h~l~~Ra~k~~~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~v-g-~Y 78 (257)
|+||||+|+||||||||++++ |++.....++.||+|+||+|+|++||+|||+|++||++++.| | .|
T Consensus 1 m~Erk~lnkyyppdfDP~ki~------------r~k~~k~~q~~~Rlm~Pf~~rC~tCgeyi~kg~kfN~r~E~~~~e~y 68 (253)
T KOG2989|consen 1 MSERKVLNKYYPPDFDPKKIP------------RAKEPKNRQLKIRLMTPFRLRCNTCGEYIYKGKKFNAREEDVIEETY 68 (253)
T ss_pred CcccccccccCCCCCChhhhh------------hhhccchhhcceeecccceeecccccchhhcCCCcchhHHhhhcccc
Confidence 999999999999999999974 333334456899999999999999999999999999999988 5 69
Q ss_pred cceeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCceecccCCCcccCCcccccchHhhhcCCCCchhhcccccccchhh
Q psy10064 79 YSTPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARRQENRWNPLENEQIVPETKEVSRKLFDDPMYKLEHGTNDMSSS 158 (257)
Q Consensus 79 ~st~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r~~e~~d~~~~~~~~~~~~e~~~~~~~d~m~~LE~~~~d~~~~ 158 (257)
|||+||+|||+|+.|+++|+|+|||+|+|||+++||+|+++.|...+.+.-.. .++ ....|+|..||+++.+++.+
T Consensus 69 Lgiki~Rf~i~Ct~cl~el~~rTDp~N~dY~~E~Ga~r~y~~~~~~eeek~k~--~~~--~d~~d~m~~lekrt~~S~~e 144 (253)
T KOG2989|consen 69 LGIKIFRFYIKCTRCLRELSFRTDPKNSDYVIESGATRNYEPIEEEEEEKRKF--EEE--EDMKDEIKRLEKRTFQSKDE 144 (253)
T ss_pred ccceeeeeeeeccchHhhhhhhcCCcchHHHHHhcchhcccccchhHHHHHHH--Hhh--hhhhhHHHHHHHHhhhhhhH
Confidence 99999999999999999999999999999999999999998876544322111 111 33479999999999999999
Q ss_pred hHHHHHHHHHHHHHhhhccChHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhcc
Q psy10064 159 KSKASHLNKLLDRQESVWKNDFDANRVLRDSFRKKKKQLKALQDKDNALLSKS 211 (257)
Q Consensus 159 ~~~~~~L~eL~~~~~~~~~ddy~~n~~LR~~fR~~kk~~~~~~~~d~al~~~~ 211 (257)
+.....|++|...+.+....|+.. .|....+..++..++.++++++|.+..
T Consensus 145 ~~~~~~ldel~~~k~r~~~id~~~--~l~~~~~~~~k~~~~~eee~~~liks~ 195 (253)
T KOG2989|consen 145 EIIRRALDELKVLKERPAPIDLVS--ELLATNERPRKYAKRKEEEKKVLIKSI 195 (253)
T ss_pred HHHHHHHHHHHHHhcccCcccHHH--HHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 999999999999998877777654 466666667777777777777776544
No 4
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7e-41 Score=295.19 Aligned_cols=214 Identities=31% Similarity=0.568 Sum_probs=165.7
Q ss_pred CCcccCCCCCCCCCCCccccCchhh-HHHHhhhc---CCeeEEEEeceeeeecCCCCccccccceeeeeccccc--cccc
Q psy10064 7 TNKYYPPDYDPSVGGLNKFLGTHAL-RERARKLH---MGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVG--MYYS 80 (257)
Q Consensus 7 ~nkYyPPD~DP~k~~~nk~~~~h~l-~~Ra~k~~---~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg--~Y~s 80 (257)
.|+|||||+.|--.- || +.++.|++ ..-+.||+|.||+|+|+.|++||++|+||||.|+-++ .|||
T Consensus 1 ~~ky~pp~~NrvlAq--------pL~~~~~~KlK~arprglSiRL~TPF~~RCL~C~~YI~K~~rfNavkE~~~dK~y~~ 72 (272)
T COG5134 1 MGKYIPPEGNRVLAQ--------PLAKRKFDKLKNARPRGLSIRLETPFPVRCLNCENYIQKGTRFNAVKEEIGDKSYYT 72 (272)
T ss_pred CCCCcCCCCchhhcc--------hhHHHHHHHhcccCcccceEEeccCcceeecchhhhhhcccchhHHHHHhcccccce
Confidence 489999999986421 12 33444543 3348999999999999999999999999999999996 4889
Q ss_pred eeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCceecccCCCcccCCcccccchHhhhcCCCCchhhcccccccchhhhH
Q psy10064 81 TPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARRQENRWNPLENEQIVPETKEVSRKLFDDPMYKLEHGTNDMSSSKS 160 (257)
Q Consensus 81 t~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r~~e~~d~~~~~~~~~~~~e~~~~~~~d~m~~LE~~~~d~~~~~~ 160 (257)
|.||||+|+||.|++.|.|+|||+|++||+++|++|+.+.-++.+++.. .+ ..+.--..|....+|+...+......
T Consensus 73 ~kiYRf~I~C~~C~n~i~~RTDPkN~~YV~EsGg~R~i~pq~~n~D~~k--~~-~Ve~~~Esd~~~~~eK~~~Q~~~~~~ 149 (272)
T COG5134 73 TKIYRFSIKCHLCSNPIDVRTDPKNTEYVVESGGRRKIEPQDINEDPAK--AE-NVEKVPESDAIEALEKQLTQQKSEKH 149 (272)
T ss_pred eEEEEEEEEccCCCCceeeecCCCCceEEEecCceeecCccccccChhh--hh-hhhcCchhHHHHHHHHHHHHhhcccc
Confidence 9999999999999999999999999999999999998765544332211 00 00111124556677777666555555
Q ss_pred HHHHHHHHHHHHhhhccChHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhccCCCCCcCCCChhhHHhhhccc
Q psy10064 161 KASHLNKLLDRQESVWKNDFDANRVLRDSFRKKKKQLKALQDKDNALLSKSSLSLKLVPEHKNDIRLASLYK 232 (257)
Q Consensus 161 ~~~~L~eL~~~~~~~~~ddy~~n~~LR~~fR~~kk~~~~~~~~d~al~~~~~l~i~Ll~e~eeD~~~A~~v~ 232 (257)
...++..+-.++.+.|.++|...+.+|.+||+.|+-+..|++++-.+..+..++++++|.+- |...|.+++
T Consensus 150 ~ssA~n~~D~L~Krl~~~~~~~~~~~~~~~~~~k~~e~~q~a~~~~~~~~a~~~~~i~~~~~-d~~~~~~~~ 220 (272)
T COG5134 150 NSSAINFIDELNKRLWSDPFVSSQRLRKQFRERKKIEKKQEAKDLSLKNRAALDIDILPSSS-DKDKALLLL 220 (272)
T ss_pred hhhhhhHHHHHHHHhhcCchhhhHHHHHHHHHHhhhHHHHHHHHhhhhhhhhhhhccCCccc-hhhHHHHhh
Confidence 55556666667788999999999999999999999998999999999999999999998654 444454444
No 5
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=91.58 E-value=0.2 Score=43.12 Aligned_cols=63 Identities=29% Similarity=0.490 Sum_probs=35.6
Q ss_pred EeceeeeecCCCCccccccceeeee-cccc-ccccceeeEEEEEEcCCCCceeEEeeCCC-CCCeeecc
Q psy10064 47 FELPYNIWCEGCNNHIGMGVRYNAE-KKKV-GMYYSTPVYQFRMKCHLCDSHFEIKTDPG-NLDYVIVS 112 (257)
Q Consensus 47 fe~Pf~i~C~~C~~~I~kG~rfNA~-K~~v-g~Y~st~I~~F~~kC~~C~~~i~i~TDPk-n~dYv~~~ 112 (257)
|.-.|.|.|..|++--.+.+-+|.. +..+ | |---=.|.+||..|..+.+|.--|. ...|..+.
T Consensus 25 ~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~g---srG~aNfv~KCk~C~re~si~i~~~~~~~~~~e~ 90 (161)
T PF05907_consen 25 FEWFFKVKCTSCGEVHPKWVYINRFEKHEIPG---SRGTANFVMKCKFCKRESSIDIIPGKGKPYTAED 90 (161)
T ss_dssp --EEEEEEETTSS--EEEEEEE-TT-BEE-TT---SS-EESEEE--SSSS--EEEEEE--TTTEEEGGG
T ss_pred CEEEEEEEECCCCCccCcceEeecceEEecCC---CccceEeEecCcCcCCccEEEEEecCcccccccc
Confidence 4577999999999988888888854 3334 3 1112379999999999888855443 45666653
No 6
>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=90.29 E-value=0.19 Score=33.74 Aligned_cols=25 Identities=36% Similarity=0.468 Sum_probs=22.3
Q ss_pred EEcCCCCceeEEeeCCCCCCeeeccC
Q psy10064 88 MKCHLCDSHFEIKTDPGNLDYVIVSG 113 (257)
Q Consensus 88 ~kC~~C~~~i~i~TDPkn~dYv~~~G 113 (257)
|+||.|++.- |-+|+.++++|+..=
T Consensus 1 m~Cp~Cg~~~-~~~D~~~g~~vC~~C 25 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFDPERGELVCPNC 25 (43)
T ss_dssp ESBTTTSSSE-EEEETTTTEEEETTT
T ss_pred CCCcCCcCCc-eEEcCCCCeEECCCC
Confidence 7899999987 899999999998873
No 7
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=87.56 E-value=0.48 Score=33.76 Aligned_cols=34 Identities=24% Similarity=0.632 Sum_probs=25.7
Q ss_pred eeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 52 NIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
.|+|.+|+..++++ |.|- ...||||.|..--.++
T Consensus 4 eiRC~~CnklLa~~----------g~~~-----~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 4 EIRCGHCNKLLAKA----------GEVI-----ELEIKCPRCKTINHVR 37 (51)
T ss_pred ceeccchhHHHhhh----------cCcc-----EEEEECCCCCccceEe
Confidence 58999999999984 2222 4579999998766554
No 8
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=81.22 E-value=0.68 Score=37.57 Aligned_cols=32 Identities=22% Similarity=0.544 Sum_probs=22.2
Q ss_pred EeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCce
Q psy10064 47 FELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSH 96 (257)
Q Consensus 47 fe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~ 96 (257)
-..|-..||..|+.+... +-+ |++.||.|++.
T Consensus 65 ~~~p~~~~C~~Cg~~~~~-----------------~~~-~~~~CP~Cgs~ 96 (114)
T PRK03681 65 EEQEAECWCETCQQYVTL-----------------LTQ-RVRRCPQCHGD 96 (114)
T ss_pred EeeCcEEEcccCCCeeec-----------------CCc-cCCcCcCcCCC
Confidence 478999999999963322 111 33679999874
No 9
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.83 E-value=1.1 Score=39.84 Aligned_cols=41 Identities=27% Similarity=0.536 Sum_probs=30.2
Q ss_pred eeeecCCCCc---cccccc-eeeeeccccccccceeeEEEEEEcCCCCceeE
Q psy10064 51 YNIWCEGCNN---HIGMGV-RYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFE 98 (257)
Q Consensus 51 f~i~C~~C~~---~I~kG~-rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~ 98 (257)
-...|++||- ++.-|. |.||.++.+..++ -| ||+.|.+...
T Consensus 16 ~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWl------IY-kC~~Cd~tWN 60 (203)
T COG4332 16 PAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWL------IY-KCTHCDYTWN 60 (203)
T ss_pred hhhhCcccCCcceeeecCcEEEcCCCcEEEEEE------EE-EeeccCCccc
Confidence 3467999986 777775 8899988887443 33 8999987543
No 10
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=79.36 E-value=0.96 Score=36.64 Aligned_cols=34 Identities=24% Similarity=0.602 Sum_probs=23.2
Q ss_pred eeEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCc
Q psy10064 42 IMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDS 95 (257)
Q Consensus 42 ~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~ 95 (257)
.|.| -+.|-.+||..|+....-. .+.+.||.|++
T Consensus 61 ~L~I-~~vp~~~~C~~Cg~~~~~~-------------------~~~~~CP~Cgs 94 (113)
T PRK12380 61 DLHI-VYKPAQAWCWDCSQVVEIH-------------------QHDAQCPHCHG 94 (113)
T ss_pred EEEE-EeeCcEEEcccCCCEEecC-------------------CcCccCcCCCC
Confidence 3444 4789999999998533221 13456999987
No 11
>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=77.88 E-value=2.8 Score=27.04 Aligned_cols=20 Identities=30% Similarity=0.941 Sum_probs=13.6
Q ss_pred eeEEEEEEcCCCCceeEEeeCC
Q psy10064 82 PVYQFRMKCHLCDSHFEIKTDP 103 (257)
Q Consensus 82 ~I~~F~~kC~~C~~~i~i~TDP 103 (257)
|+|.| +|+.|+..+++...-
T Consensus 2 p~Y~y--~C~~Cg~~fe~~~~~ 21 (41)
T smart00834 2 PIYEY--RCEDCGHTFEVLQKI 21 (41)
T ss_pred CCEEE--EcCCCCCEEEEEEec
Confidence 56665 688888877766543
No 12
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=77.81 E-value=1 Score=32.63 Aligned_cols=40 Identities=30% Similarity=0.621 Sum_probs=26.7
Q ss_pred eeecCCCCccccccceeeeecccccc-ccceeeEEEEEEcCCCC--ceeEEeeCCCCCCee
Q psy10064 52 NIWCEGCNNHIGMGVRYNAEKKKVGM-YYSTPVYQFRMKCHLCD--SHFEIKTDPGNLDYV 109 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~rfNA~K~~vg~-Y~st~I~~F~~kC~~C~--~~i~i~TDPkn~dYv 109 (257)
+|+|.+|+..+.+. -|. || ..|||.|. |+|.|+ -+.+.|+
T Consensus 4 tiRC~~CnKlLa~a---------~~~~yl-------e~KCPrCK~vN~~~~~--~e~~t~~ 46 (60)
T COG4416 4 TIRCAKCNKLLAEA---------EGQAYL-------EKKCPRCKEVNEFYIK--EEATTQI 46 (60)
T ss_pred eeehHHHhHHHHhc---------ccceee-------eecCCccceeeeeecc--cccchhh
Confidence 68999999888762 133 65 67999995 455554 3445554
No 13
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=77.71 E-value=1.1 Score=26.70 Aligned_cols=15 Identities=20% Similarity=0.793 Sum_probs=11.1
Q ss_pred ecCCCCcccccccee
Q psy10064 54 WCEGCNNHIGMGVRY 68 (257)
Q Consensus 54 ~C~~C~~~I~kG~rf 68 (257)
.|..||..|-.+.+|
T Consensus 1 ~Cp~CG~~~~~~~~f 15 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF 15 (23)
T ss_pred CCcccCCCCCCcCcc
Confidence 377888888777665
No 14
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=77.11 E-value=1.2 Score=36.21 Aligned_cols=35 Identities=17% Similarity=0.345 Sum_probs=23.4
Q ss_pred eEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCce
Q psy10064 43 MIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSH 96 (257)
Q Consensus 43 ~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~ 96 (257)
|.| -+.|..++|..|+....-. -+ ++++||.|++.
T Consensus 63 L~I-e~vp~~~~C~~Cg~~~~~~-----------------~~-~~~~CP~Cgs~ 97 (117)
T PRK00564 63 LDI-VDEKVELECKDCSHVFKPN-----------------AL-DYGVCEKCHSK 97 (117)
T ss_pred EEE-EecCCEEEhhhCCCccccC-----------------Cc-cCCcCcCCCCC
Confidence 444 4689999999998543221 11 33579999974
No 15
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=73.97 E-value=3 Score=34.39 Aligned_cols=29 Identities=34% Similarity=0.823 Sum_probs=22.0
Q ss_pred eceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCc
Q psy10064 48 ELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDS 95 (257)
Q Consensus 48 e~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~ 95 (257)
..|-..||..| +.++..-.|.|+ ||.|.+
T Consensus 66 ~~p~~~~C~~C-----------------~~~~~~e~~~~~--CP~C~s 94 (115)
T COG0375 66 EEPAECWCLDC-----------------GQEVELEELDYR--CPKCGS 94 (115)
T ss_pred EeccEEEeccC-----------------CCeecchhheeE--CCCCCC
Confidence 46888999999 344555677777 999985
No 16
>KOG2990|consensus
Probab=72.06 E-value=1.8 Score=40.83 Aligned_cols=14 Identities=29% Similarity=0.261 Sum_probs=11.1
Q ss_pred cCCCcccCCCCCCC
Q psy10064 5 KGTNKYYPPDYDPS 18 (257)
Q Consensus 5 K~~nkYyPPD~DP~ 18 (257)
|+.|+|++|+|.++
T Consensus 74 kvGnYYtTpiw~Fr 87 (317)
T KOG2990|consen 74 KVGNYYTTPIWSFR 87 (317)
T ss_pred hccccccCcccchh
Confidence 67888899988754
No 17
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=69.82 E-value=3.8 Score=28.56 Aligned_cols=41 Identities=17% Similarity=0.618 Sum_probs=25.9
Q ss_pred ceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 49 LPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
.|| |.|.+|.+.+--=..|-..++.+ -.++|-.|+..|.|.
T Consensus 4 APF-v~C~~C~~lLqlP~~~~~~~k~~----------~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 4 APF-VVCSSCFELLQLPAKFSLSKKNQ----------QKLRCGACSEVLSFS 44 (46)
T ss_pred CCE-eECccHHHHHcCCCccCCCccce----------eEEeCCCCceeEEEe
Confidence 477 45999988544333332222222 257899999999875
No 18
>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=69.73 E-value=2.5 Score=34.23 Aligned_cols=35 Identities=20% Similarity=0.395 Sum_probs=23.6
Q ss_pred eeEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCce
Q psy10064 42 IMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSH 96 (257)
Q Consensus 42 ~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~ 96 (257)
.|.| =..|-..+|..|+....-. .+.+.||.|++.
T Consensus 61 ~L~I-~~~p~~~~C~~Cg~~~~~~-------------------~~~~~CP~Cgs~ 95 (115)
T TIGR00100 61 KLNI-EDEPVECECEDCSEEVSPE-------------------IDLYRCPKCHGI 95 (115)
T ss_pred EEEE-EeeCcEEEcccCCCEEecC-------------------CcCccCcCCcCC
Confidence 3444 3678899999998543321 124789999874
No 19
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=68.85 E-value=5 Score=29.60 Aligned_cols=32 Identities=19% Similarity=0.408 Sum_probs=23.2
Q ss_pred eeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 52 NIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
...|.+||..|.-|.++ -.|.||+|+..+.++
T Consensus 9 ~~~CtSCg~~i~p~e~~-----------------v~F~CPnCGe~~I~R 40 (61)
T COG2888 9 PPVCTSCGREIAPGETA-----------------VKFPCPNCGEVEIYR 40 (61)
T ss_pred CceeccCCCEeccCCce-----------------eEeeCCCCCceeeeh
Confidence 57899999988665432 147899998776654
No 20
>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=67.89 E-value=5.5 Score=26.66 Aligned_cols=20 Identities=30% Similarity=0.972 Sum_probs=15.1
Q ss_pred eeEEEEEEcCCCCceeEEeeCC
Q psy10064 82 PVYQFRMKCHLCDSHFEIKTDP 103 (257)
Q Consensus 82 ~I~~F~~kC~~C~~~i~i~TDP 103 (257)
|||.| +|..|++.+++...-
T Consensus 2 P~Yey--~C~~Cg~~fe~~~~~ 21 (42)
T PF09723_consen 2 PIYEY--RCEECGHEFEVLQSI 21 (42)
T ss_pred CCEEE--EeCCCCCEEEEEEEc
Confidence 67765 599999999887643
No 21
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=65.42 E-value=6.7 Score=27.75 Aligned_cols=19 Identities=26% Similarity=0.656 Sum_probs=16.0
Q ss_pred EEEcCCCCceeEEeeCCCC
Q psy10064 87 RMKCHLCDSHFEIKTDPGN 105 (257)
Q Consensus 87 ~~kC~~C~~~i~i~TDPkn 105 (257)
.++|+.|+..|-|+-=|..
T Consensus 24 ~irCp~Cg~rIl~K~R~~~ 42 (49)
T COG1996 24 GIRCPYCGSRILVKERPKV 42 (49)
T ss_pred ceeCCCCCcEEEEeccCCc
Confidence 3799999999999977654
No 22
>KOG2272|consensus
Probab=65.26 E-value=2.7 Score=39.33 Aligned_cols=22 Identities=18% Similarity=0.612 Sum_probs=17.9
Q ss_pred ccceeeEEEEEEcCCCCceeEE
Q psy10064 78 YYSTPVYQFRMKCHLCDSHFEI 99 (257)
Q Consensus 78 Y~st~I~~F~~kC~~C~~~i~i 99 (257)
|-+-|-.-++|+|+.|+++++-
T Consensus 154 fr~d~yH~yHFkCt~C~keL~s 175 (332)
T KOG2272|consen 154 FRGDPYHPYHFKCTTCGKELTS 175 (332)
T ss_pred ccCCCCCccceecccccccccc
Confidence 5567778899999999998753
No 23
>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=63.66 E-value=6.1 Score=27.04 Aligned_cols=18 Identities=33% Similarity=1.139 Sum_probs=13.0
Q ss_pred eeEEEEEEcCCCCceeEEee
Q psy10064 82 PVYQFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 82 ~I~~F~~kC~~C~~~i~i~T 101 (257)
|||.| +|..|+..+++..
T Consensus 2 P~Yey--~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 2 PIYEY--RCTACGHRFEVLQ 19 (52)
T ss_pred CCEEE--EeCCCCCEeEEEE
Confidence 66666 5888888777763
No 24
>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=62.71 E-value=6.3 Score=23.93 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=6.8
Q ss_pred cCCCCccccc
Q psy10064 55 CEGCNNHIGM 64 (257)
Q Consensus 55 C~~C~~~I~k 64 (257)
|.+|+..|.-
T Consensus 1 C~sC~~~i~~ 10 (24)
T PF07754_consen 1 CTSCGRPIAP 10 (24)
T ss_pred CccCCCcccC
Confidence 7778776653
No 25
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.10 E-value=6 Score=32.99 Aligned_cols=45 Identities=22% Similarity=0.400 Sum_probs=24.2
Q ss_pred eceeeeecCCCCccccccceeeeeccccc----c--ccceeeEEEEEEcCCCCce
Q psy10064 48 ELPYNIWCEGCNNHIGMGVRYNAEKKKVG----M--YYSTPVYQFRMKCHLCDSH 96 (257)
Q Consensus 48 e~Pf~i~C~~C~~~I~kG~rfNA~K~~vg----~--Y~st~I~~F~~kC~~C~~~ 96 (257)
..|-..||..||....-. ..++.++ . -|.--...+.++||.|++.
T Consensus 66 ~~p~~~~C~~CG~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLK----EVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecc----cccccccccccccccccccccccCcCCcCCCCC
Confidence 568889999998432110 0122221 0 1111123466889999873
No 26
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=60.44 E-value=6.1 Score=28.79 Aligned_cols=33 Identities=27% Similarity=0.370 Sum_probs=24.8
Q ss_pred ccCchhhHHHHhhhcCCeeEEEEeceeeeecCCCCcccc
Q psy10064 25 FLGTHALRERARKLHMGIMIIRFELPYNIWCEGCNNHIG 63 (257)
Q Consensus 25 ~~~~h~l~~Ra~k~~~g~~~VRfe~Pf~i~C~~C~~~I~ 63 (257)
+...||=|. +-=-++|+=|=|-+.|.+|+..|-
T Consensus 10 mKK~HPCG~------~~Wei~R~GaDikikC~gCg~~im 42 (57)
T PF06107_consen 10 MKKPHPCGS------NEWEIIRIGADIKIKCLGCGRQIM 42 (57)
T ss_pred EcCCCCCCC------CEEEEEEccCcEEEEECCCCCEEE
Confidence 445676553 234699999999999999998764
No 27
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=60.31 E-value=9.4 Score=28.02 Aligned_cols=17 Identities=24% Similarity=0.348 Sum_probs=12.4
Q ss_pred eceeeeecCCCCccccc
Q psy10064 48 ELPYNIWCEGCNNHIGM 64 (257)
Q Consensus 48 e~Pf~i~C~~C~~~I~k 64 (257)
++.-...|.+|+..|.-
T Consensus 3 ~~~~~~~CtSCg~~i~~ 19 (59)
T PRK14890 3 EMMEPPKCTSCGIEIAP 19 (59)
T ss_pred ccccCccccCCCCcccC
Confidence 44455689999998863
No 28
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.27 E-value=5.1 Score=32.91 Aligned_cols=18 Identities=28% Similarity=0.588 Sum_probs=13.5
Q ss_pred eeEEEEeceeeeecCCCCcc
Q psy10064 42 IMIIRFELPYNIWCEGCNNH 61 (257)
Q Consensus 42 ~~~VRfe~Pf~i~C~~C~~~ 61 (257)
.|.| -+.|-..|| .|+.+
T Consensus 61 ~L~I-~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 61 DLIV-EMIPVEIEC-ECGYE 78 (124)
T ss_pred EEEE-EecCeeEEe-eCcCc
Confidence 3444 478999999 99854
No 29
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=58.10 E-value=9.2 Score=31.48 Aligned_cols=34 Identities=18% Similarity=0.417 Sum_probs=22.2
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEE
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEI 99 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i 99 (257)
|...|..|+..+.+=.+.+.. . ..|..|.+.|+.
T Consensus 122 ~~~~C~~C~~~~~r~~~~~~~-----~----------~~C~~C~~~l~~ 155 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRSKRK-----R----------YRCGRCGGPLVQ 155 (157)
T ss_pred eEEEcCCCCCEeeeecccchh-----h----------EECCCCCCEEEE
Confidence 678899998776442222111 1 679999988875
No 30
>PRK04351 hypothetical protein; Provisional
Probab=55.93 E-value=12 Score=31.89 Aligned_cols=37 Identities=22% Similarity=0.458 Sum_probs=28.3
Q ss_pred ceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 49 LPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
-.|.-.|..|+..+.+=.|+|- -...|..|.+.+.+.
T Consensus 109 ~~y~Y~C~~Cg~~~~r~Rr~n~---------------~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 109 KNYLYECQSCGQQYLRKRRINT---------------KRYRCGKCRGKLKLI 145 (149)
T ss_pred ceEEEECCCCCCEeeeeeecCC---------------CcEEeCCCCcEeeec
Confidence 4478899999987776666663 236799999999876
No 31
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=52.59 E-value=12 Score=26.61 Aligned_cols=34 Identities=24% Similarity=0.637 Sum_probs=22.5
Q ss_pred ceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCc
Q psy10064 49 LPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDS 95 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~ 95 (257)
-.+.++|..|..|-|.-- ++.. .| ..++|+.|+.
T Consensus 19 ~r~aLIC~~C~~hNGla~-----~~~~-~~-------i~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAP-----KEEF-EE-------IQYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccc-----cccC-Cc-------eEEEcCCCCC
Confidence 457899999999877731 1111 11 2678999975
No 32
>KOG3368|consensus
Probab=52.43 E-value=17 Score=30.95 Aligned_cols=32 Identities=22% Similarity=0.328 Sum_probs=29.7
Q ss_pred cccceeeEEEEEEcCCCCceeEEeeCCCCCCe
Q psy10064 77 MYYSTPVYQFRMKCHLCDSHFEIKTDPGNLDY 108 (257)
Q Consensus 77 ~Y~st~I~~F~~kC~~C~~~i~i~TDPkn~dY 108 (257)
.||+|.-|+.++-|+--+=+|++-|||+.+++
T Consensus 62 ~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~i 93 (140)
T KOG3368|consen 62 LSYKTSKYKLHFYETPTGLKFVLNTDPKAGSI 93 (140)
T ss_pred eEEeeceeEEEEEEcCCCcEEEEecCCCcccH
Confidence 48899999999999999999999999998775
No 33
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=51.42 E-value=9.1 Score=37.24 Aligned_cols=41 Identities=24% Similarity=0.518 Sum_probs=21.1
Q ss_pred ceeeeecCCCCc-cccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 49 LPYNIWCEGCNN-HIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 49 ~Pf~i~C~~C~~-~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
.||...|..||. .--.=+.||....+| +.+|+.|+.+.++.
T Consensus 171 ~Pf~piC~~cGri~tt~v~~~d~~~~~v-----------~Y~c~~cG~~g~~~ 212 (360)
T PF01921_consen 171 SPFLPICEKCGRIDTTEVTEYDPEGGTV-----------TYRCEECGHEGEVD 212 (360)
T ss_dssp -SEEEEETTTEE--EEEEEEE--SSSEE-----------EEE--TTS---EEE
T ss_pred eeeeeeccccCCcccceeeEeecCCCEE-----------EEEecCCCCEEEEe
Confidence 599999999987 232333444443333 47899999876543
No 34
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=51.13 E-value=19 Score=23.41 Aligned_cols=36 Identities=22% Similarity=0.541 Sum_probs=21.3
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeE
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFE 98 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~ 98 (257)
+.|.|.+|+ ++|+-.-.+++. -.-..+|+.|.+.|.
T Consensus 1 M~i~CP~C~------~~f~v~~~~l~~------~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 1 MIITCPNCQ------TRFRVPDDKLPA------GGRKVRCPKCGHVFR 36 (37)
T ss_pred CEEECCCCC------ceEEcCHHHccc------CCcEEECCCCCcEee
Confidence 357888885 344444444321 111588999988775
No 35
>KOG2407|consensus
Probab=50.73 E-value=5.7 Score=40.38 Aligned_cols=15 Identities=40% Similarity=1.057 Sum_probs=13.1
Q ss_pred EEeceeeeecCCCCc
Q psy10064 46 RFELPYNIWCEGCNN 60 (257)
Q Consensus 46 Rfe~Pf~i~C~~C~~ 60 (257)
=|-|||||+|.+|--
T Consensus 492 DFSMPYNVIcltcTv 506 (575)
T KOG2407|consen 492 DFSMPYNVICLTCTV 506 (575)
T ss_pred CCCCceeEEeeehhh
Confidence 489999999999954
No 36
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=50.15 E-value=20 Score=23.35 Aligned_cols=35 Identities=23% Similarity=0.623 Sum_probs=21.4
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCcee
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHF 97 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i 97 (257)
+.|.|..|+ ++|+-.-++|. -=.-..+|+.|++.|
T Consensus 1 M~i~Cp~C~------~~y~i~d~~ip------~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 1 MIITCPNCQ------AKYEIDDEKIP------PKGRKVRCSKCGHVF 35 (36)
T ss_pred CEEECCCCC------CEEeCCHHHCC------CCCcEEECCCCCCEe
Confidence 357788884 45555555442 111258899998865
No 37
>KOG3794|consensus
Probab=49.87 E-value=9.7 Score=37.60 Aligned_cols=14 Identities=29% Similarity=0.584 Sum_probs=10.7
Q ss_pred cCCCccc--CCCCCCC
Q psy10064 5 KGTNKYY--PPDYDPS 18 (257)
Q Consensus 5 K~~nkYy--PPD~DP~ 18 (257)
.++|+|| ||-+++.
T Consensus 66 ~~~sFMY~~PPG~~KE 81 (453)
T KOG3794|consen 66 NGLSFMYEAPPGAKKE 81 (453)
T ss_pred cccceeecCCCCCCch
Confidence 4678888 7778876
No 38
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=49.77 E-value=14 Score=24.82 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=14.6
Q ss_pred EEEcCCCCceeEEeeCCC
Q psy10064 87 RMKCHLCDSHFEIKTDPG 104 (257)
Q Consensus 87 ~~kC~~C~~~i~i~TDPk 104 (257)
.++|+.|++.+.++..+.
T Consensus 21 ~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 21 GVRCPYCGYRILFKERPP 38 (46)
T ss_pred ceECCCCCCeEEEccCCC
Confidence 489999999999876553
No 39
>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=49.45 E-value=9.3 Score=38.87 Aligned_cols=36 Identities=17% Similarity=0.419 Sum_probs=27.0
Q ss_pred cccceeeEEEEEEcCCCCceeEEe---------eCCCCCCeeecc
Q psy10064 77 MYYSTPVYQFRMKCHLCDSHFEIK---------TDPGNLDYVIVS 112 (257)
Q Consensus 77 ~Y~st~I~~F~~kC~~C~~~i~i~---------TDPkn~dYv~~~ 112 (257)
.|......+|+..||+|+.+..+. .+|+..-|+|.+
T Consensus 190 ~~~~sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~ 234 (557)
T PF05876_consen 190 LYEESDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPH 234 (557)
T ss_pred HHHhCCceEEEccCCCCCCCccccccceeecCCCCccceEEECCC
Confidence 466556668999999998877665 257888888865
No 40
>PF07255 Benyvirus_14KDa: Benyvirus 14KDa protein; InterPro: IPR009884 This family consists of several Benyvirus specific 14 kDa proteins of around 125 residues in length. Members of this family contain 9 conserved cysteine residues. The function of this family is unknown.
Probab=49.09 E-value=14 Score=30.19 Aligned_cols=73 Identities=18% Similarity=0.191 Sum_probs=53.1
Q ss_pred EEEEeceeeeecCCCCc--cccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCceecccCC
Q psy10064 44 IIRFELPYNIWCEGCNN--HIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARRQENRW 121 (257)
Q Consensus 44 ~VRfe~Pf~i~C~~C~~--~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r~~e~~ 121 (257)
.-||-+-|.-||+-=.. --|+| -.+++.+-+ .+--..|.|+|-.|...++++..-+|..=-+..|-.|+...|
T Consensus 25 ~~~FSiK~~~W~LFT~~V~V~YR~---~~~~E~~~K--D~~RLHF~~~CV~C~~K~~~K~~Nk~H~~~~~~G~~R~~RNF 99 (123)
T PF07255_consen 25 CERFSIKFSEWKLFTTAVYVEYRQ---LGEKECSLK--DVCRLHFNMSCVKCCRKLKCKKQNKNHSKHVQNGYLRKVRNF 99 (123)
T ss_pred eEEEEEecCCEEEEeeEEEEEEec---cCCccceeh--eeeeEEEeeehhhhcccceehhcCcchHHHhhcCeEEEecce
Confidence 56899999999986654 12333 224444311 234567999999999999999999998888888888876544
No 41
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=48.94 E-value=8.9 Score=36.03 Aligned_cols=28 Identities=32% Similarity=0.401 Sum_probs=24.1
Q ss_pred EEcCCCCceeEEeeCCCCCCeeecc-Ccee
Q psy10064 88 MKCHLCDSHFEIKTDPGNLDYVIVS-GARR 116 (257)
Q Consensus 88 ~kC~~C~~~i~i~TDPkn~dYv~~~-Ga~r 116 (257)
+.||.|+.. .|-+|++++++||.. |+.=
T Consensus 2 ~~CpeCg~~-~~~~d~~~ge~VC~~CG~Vi 30 (285)
T COG1405 2 MSCPECGST-NIITDYERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCCc-cceeeccCCeEEeccCCEEe
Confidence 579999999 999999999999987 4433
No 42
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=48.56 E-value=11 Score=36.70 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=16.9
Q ss_pred eeEEEEEEcCCCCceeEEee
Q psy10064 82 PVYQFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 82 ~I~~F~~kC~~C~~~i~i~T 101 (257)
..+.||-.||.|..|=+|+.
T Consensus 363 ~a~~l~W~CPsC~~W~TikP 382 (389)
T COG2956 363 TAHTLYWHCPSCRAWETIKP 382 (389)
T ss_pred cceeeeeeCCCcccccccCC
Confidence 35679999999999988874
No 43
>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=47.83 E-value=8.1 Score=31.11 Aligned_cols=18 Identities=28% Similarity=0.637 Sum_probs=11.2
Q ss_pred eEEEEeceeeeecCCCCcc
Q psy10064 43 MIIRFELPYNIWCEGCNNH 61 (257)
Q Consensus 43 ~~VRfe~Pf~i~C~~C~~~ 61 (257)
|.| -..|...+|..|+..
T Consensus 62 L~I-e~~p~~~~C~~Cg~~ 79 (113)
T PF01155_consen 62 LEI-EEVPARARCRDCGHE 79 (113)
T ss_dssp EEE-EEE--EEEETTTS-E
T ss_pred EEE-EecCCcEECCCCCCE
Confidence 444 467999999999864
No 44
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=47.33 E-value=22 Score=29.52 Aligned_cols=36 Identities=25% Similarity=0.506 Sum_probs=26.9
Q ss_pred eeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEE
Q psy10064 50 PYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEI 99 (257)
Q Consensus 50 Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i 99 (257)
.|.-.|..|+..+.+=.|.|.. =...|..|.+.+.+
T Consensus 110 ~~~y~C~~C~~~~~~~rr~~~~--------------~~y~C~~C~g~l~~ 145 (146)
T smart00731 110 KYPYRCTGCGQRYLRVRRSNNV--------------SRYRCGKCGGKLIL 145 (146)
T ss_pred eEEEECCCCCCCCceEccccCc--------------ceEEcCCCCCEEEe
Confidence 5688999999988765555532 23689999999875
No 45
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=46.85 E-value=13 Score=22.75 Aligned_cols=36 Identities=28% Similarity=0.626 Sum_probs=20.8
Q ss_pred ecCCCCcccccc-ceeeeecccccc-ccceeeEEEEEEcCCCCceeE
Q psy10064 54 WCEGCNNHIGMG-VRYNAEKKKVGM-YYSTPVYQFRMKCHLCDSHFE 98 (257)
Q Consensus 54 ~C~~C~~~I~kG-~rfNA~K~~vg~-Y~st~I~~F~~kC~~C~~~i~ 98 (257)
+|..|+..|.-+ ...++ .+. |+.. -|+|..|...|+
T Consensus 1 ~C~~C~~~i~~~~~~~~~----~~~~~H~~-----Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRA----LGKVWHPE-----CFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEe----CCcccccc-----CCCCcccCCcCc
Confidence 488999988776 22221 232 3322 367777777653
No 46
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=46.06 E-value=17 Score=31.58 Aligned_cols=41 Identities=22% Similarity=0.471 Sum_probs=30.1
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCC
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDP 103 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDP 103 (257)
|.-+|. |+++--+=.|+|-.++.- . .+|-.|.+.+.+++++
T Consensus 116 ~~Y~C~-C~q~~l~~RRhn~~~~g~-~----------YrC~~C~gkL~~~~~~ 156 (156)
T COG3091 116 YPYRCQ-CQQHYLRIRRHNTVRRGE-V----------YRCGKCGGKLVFKGQV 156 (156)
T ss_pred eeEEee-cCCccchhhhcccccccc-e----------EEeccCCceEEeccCC
Confidence 345899 999877767777655332 2 5799999999998864
No 47
>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=46.02 E-value=14 Score=37.53 Aligned_cols=39 Identities=18% Similarity=0.446 Sum_probs=25.6
Q ss_pred eeeecCCCCccc---cccceeeeeccccccccceeeEEEEEEcCCCCceeE
Q psy10064 51 YNIWCEGCNNHI---GMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFE 98 (257)
Q Consensus 51 f~i~C~~C~~~I---~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~ 98 (257)
|.+.|.+||++. ..+.+++..- .--.-++.|+.|+..|+
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~---------~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGE---------APETARYVCPHCGCEIE 240 (557)
T ss_pred EEccCCCCCCCccccccceeecCCC---------CccceEEECCCCcCCCC
Confidence 456799999863 3466663211 12335689999999886
No 48
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=42.50 E-value=12 Score=22.49 Aligned_cols=16 Identities=19% Similarity=0.729 Sum_probs=10.6
Q ss_pred eeecCCCCccccccce
Q psy10064 52 NIWCEGCNNHIGMGVR 67 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~r 67 (257)
.+.|..||..|..+-+
T Consensus 2 ~~~Cp~Cg~~~~~~~~ 17 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAK 17 (26)
T ss_pred cCCCcccCCcCCcccc
Confidence 4677788777666533
No 49
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=42.26 E-value=35 Score=22.64 Aligned_cols=41 Identities=15% Similarity=0.290 Sum_probs=27.1
Q ss_pred ecCCCCccccc-cceeeeecccc--ccccceeeEEEEEEcCCCC
Q psy10064 54 WCEGCNNHIGM-GVRYNAEKKKV--GMYYSTPVYQFRMKCHLCD 94 (257)
Q Consensus 54 ~C~~C~~~I~k-G~rfNA~K~~v--g~Y~st~I~~F~~kC~~C~ 94 (257)
-|..||..+.. |..+=.+.-.+ ..+.=+-..++...|+.|+
T Consensus 4 ~C~~Cg~~l~~ig~~~~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 4 ACPDCGGELKEIGEEKVRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred cCCCCCceeeECCceeeEEEEeecccceEEEEEEeceEECCCCC
Confidence 48889886653 44433333222 3566788899999999995
No 50
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=42.18 E-value=4.3 Score=31.77 Aligned_cols=34 Identities=18% Similarity=0.601 Sum_probs=25.4
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEE---EEEcCCCCceeEE
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQF---RMKCHLCDSHFEI 99 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F---~~kC~~C~~~i~i 99 (257)
-.|.+|+..+. -|--+||++| +.||..|...|.+
T Consensus 34 S~C~~C~~~L~-------------~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 34 SHCPHCGHPLS-------------WWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CcCcCCCCcCc-------------ccccchHHHHHHhCCCCcccCCCCCh
Confidence 46999987654 3456888776 5799999998864
No 51
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=42.07 E-value=12 Score=27.73 Aligned_cols=15 Identities=20% Similarity=0.383 Sum_probs=11.9
Q ss_pred eeeeecCCCCccccc
Q psy10064 50 PYNIWCEGCNNHIGM 64 (257)
Q Consensus 50 Pf~i~C~~C~~~I~k 64 (257)
=+.|+|-+||.-|+-
T Consensus 2 iiPvRCFTCGkvi~~ 16 (62)
T PRK04016 2 MIPVRCFTCGKVIAE 16 (62)
T ss_pred CCCeEecCCCCChHH
Confidence 367899999998764
No 52
>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=42.03 E-value=18 Score=25.93 Aligned_cols=15 Identities=20% Similarity=0.682 Sum_probs=7.9
Q ss_pred EEcCCCCceeEEeeC
Q psy10064 88 MKCHLCDSHFEIKTD 102 (257)
Q Consensus 88 ~kC~~C~~~i~i~TD 102 (257)
++|+.|+..|++..+
T Consensus 3 ~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 3 FECPDCGAEIELENP 17 (54)
T ss_pred cCCCCCCCEEecCCC
Confidence 355555555555433
No 53
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=41.28 E-value=28 Score=25.73 Aligned_cols=43 Identities=16% Similarity=0.298 Sum_probs=28.1
Q ss_pred ecCCCCccccccceeeeeccccccccceeeEEEE-EEcCCCCce
Q psy10064 54 WCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFR-MKCHLCDSH 96 (257)
Q Consensus 54 ~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~-~kC~~C~~~ 96 (257)
.|..|++..+.=..+.+.--.+++.+.+..-+|+ +-|++|+-.
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 4999999877766666655444455554444443 469999764
No 54
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=40.33 E-value=18 Score=34.15 Aligned_cols=48 Identities=19% Similarity=0.373 Sum_probs=34.0
Q ss_pred ecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCC------CCCeeeccCceecc
Q psy10064 54 WCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPG------NLDYVIVSGARRQE 118 (257)
Q Consensus 54 ~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPk------n~dYv~~~Ga~r~~ 118 (257)
+|..||...+.. -| ...+.|+.|++.+.=+|||- +.++++--|-.|..
T Consensus 113 FCg~CG~~~~~~---------~~--------g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ilLa~~~~h~ 166 (279)
T COG2816 113 FCGRCGTKTYPR---------EG--------GWARVCPKCGHEHFPRIDPCVIVAVIRGDEILLARHPRHF 166 (279)
T ss_pred CCCCCCCcCccc---------cC--------ceeeeCCCCCCccCCCCCCeEEEEEecCCceeecCCCCCC
Confidence 599998855441 11 23588999999999999996 66666665555543
No 55
>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=39.77 E-value=27 Score=23.02 Aligned_cols=17 Identities=18% Similarity=0.522 Sum_probs=14.9
Q ss_pred EcCCCCceeEEeeCCCC
Q psy10064 89 KCHLCDSHFEIKTDPGN 105 (257)
Q Consensus 89 kC~~C~~~i~i~TDPkn 105 (257)
+|+.|++.+++++....
T Consensus 3 ~CP~Cg~~lv~r~~k~g 19 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKG 19 (39)
T ss_pred CCCCCCceeEEEECCCC
Confidence 69999999999988877
No 56
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=38.66 E-value=10 Score=33.93 Aligned_cols=30 Identities=23% Similarity=0.429 Sum_probs=0.0
Q ss_pred eecCCCCccccccce-----eeeeccccc-ccccee
Q psy10064 53 IWCEGCNNHIGMGVR-----YNAEKKKVG-MYYSTP 82 (257)
Q Consensus 53 i~C~~C~~~I~kG~r-----fNA~K~~vg-~Y~st~ 82 (257)
-.|.=||+++|+|.| |+..+-.-| ..||||
T Consensus 102 y~CEICGN~~Y~GrkaFekHF~E~rH~~GlrcLGI~ 137 (196)
T PF11931_consen 102 YKCEICGNQSYKGRKAFEKHFQEWRHAYGLRCLGIP 137 (196)
T ss_dssp ------------------------------------
T ss_pred eeeEeCCCcceecHHHHHHhcChhHHHccChhcCCC
Confidence 469999999999964 554444444 244444
No 57
>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=38.04 E-value=17 Score=23.30 Aligned_cols=18 Identities=22% Similarity=0.632 Sum_probs=14.4
Q ss_pred EEEcCCCCceeEEeeCCC
Q psy10064 87 RMKCHLCDSHFEIKTDPG 104 (257)
Q Consensus 87 ~~kC~~C~~~i~i~TDPk 104 (257)
.+.|++|...+.|..|+-
T Consensus 2 ~~~CP~C~~~~~v~~~~~ 19 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQL 19 (38)
T ss_pred EEECCCCCCEEEeCHHHc
Confidence 478999999988887754
No 58
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.31 E-value=22 Score=25.92 Aligned_cols=24 Identities=33% Similarity=0.531 Sum_probs=20.5
Q ss_pred eeEEEEeceeeeecCCCCcccccc
Q psy10064 42 IMIIRFELPYNIWCEGCNNHIGMG 65 (257)
Q Consensus 42 ~~~VRfe~Pf~i~C~~C~~~I~kG 65 (257)
--+||+-+-..|.|.+|+..|-.+
T Consensus 24 wkIiRvGaDIkikC~nC~h~vm~p 47 (60)
T COG4481 24 WKIIRVGADIKIKCENCGHSVMMP 47 (60)
T ss_pred EEEEEecCcEEEEecCCCcEEEec
Confidence 358999999999999999977655
No 59
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=36.72 E-value=14 Score=27.37 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=11.1
Q ss_pred eeeeecCCCCcccc
Q psy10064 50 PYNIWCEGCNNHIG 63 (257)
Q Consensus 50 Pf~i~C~~C~~~I~ 63 (257)
=+.|+|-+||.-|+
T Consensus 2 iiPiRCFsCGkvi~ 15 (63)
T COG1644 2 IIPVRCFSCGKVIG 15 (63)
T ss_pred CCceEeecCCCCHH
Confidence 35689999998875
No 60
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=36.65 E-value=29 Score=24.64 Aligned_cols=19 Identities=37% Similarity=0.723 Sum_probs=11.5
Q ss_pred EcCCCCceeEEeeCCCCCC
Q psy10064 89 KCHLCDSHFEIKTDPGNLD 107 (257)
Q Consensus 89 kC~~C~~~i~i~TDPkn~d 107 (257)
.||.|+..|++--|+...+
T Consensus 2 ~CPyCge~~~~~iD~s~~~ 20 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGD 20 (52)
T ss_pred CCCCCCCeeEEEEecCCCC
Confidence 4666666666666665543
No 61
>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=36.58 E-value=17 Score=33.69 Aligned_cols=51 Identities=25% Similarity=0.664 Sum_probs=25.1
Q ss_pred eeecCCCCcc-ccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCcee
Q psy10064 52 NIWCEGCNNH-IGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARR 116 (257)
Q Consensus 52 ~i~C~~C~~~-I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r 116 (257)
++-|..||.. |.+ |.+- .|+=- |.|+.|..+++++.-=++-.=.|.-||-.
T Consensus 31 n~yCP~Cg~~~L~~---f~NN---------~PVaD--F~C~~C~eeyELKSk~~~l~~~I~dGAY~ 82 (254)
T PF06044_consen 31 NMYCPNCGSKPLSK---FENN---------RPVAD--FYCPNCNEEYELKSKKKKLSNKINDGAYH 82 (254)
T ss_dssp H---TTT--SS-EE--------------------E--EE-TTT--EEEEEEEESS--SEEEEEEHH
T ss_pred CCcCCCCCChhHhh---ccCC---------Cccce--eECCCCchHHhhhhhccccCCcccCccHH
Confidence 5789999974 533 3222 23333 55999999999999888888888888843
No 62
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=36.57 E-value=20 Score=26.75 Aligned_cols=20 Identities=30% Similarity=0.605 Sum_probs=15.1
Q ss_pred EcCCCCce--------eEEeeCCCCCCe
Q psy10064 89 KCHLCDSH--------FEIKTDPGNLDY 108 (257)
Q Consensus 89 kC~~C~~~--------i~i~TDPkn~dY 108 (257)
-||.|+++ +.|-+||++++-
T Consensus 20 ~CP~Cgs~~~te~W~G~~iIidpe~SeI 47 (64)
T COG2093 20 ICPVCGSTDLTEEWFGLLIIIDPEKSEI 47 (64)
T ss_pred cCCCCCCcccchhhccEEEEEcCcHHHH
Confidence 38999887 677888887653
No 63
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=36.48 E-value=34 Score=23.34 Aligned_cols=18 Identities=17% Similarity=0.397 Sum_probs=15.3
Q ss_pred EEEcCCCCceeEEeeCCC
Q psy10064 87 RMKCHLCDSHFEIKTDPG 104 (257)
Q Consensus 87 ~~kC~~C~~~i~i~TDPk 104 (257)
.++|+.|++.|.++-=|.
T Consensus 19 ~irC~~CG~rIlyK~R~~ 36 (44)
T smart00659 19 VVRCRECGYRILYKKRTK 36 (44)
T ss_pred ceECCCCCceEEEEeCCC
Confidence 599999999999987654
No 64
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=36.46 E-value=38 Score=25.50 Aligned_cols=17 Identities=18% Similarity=0.473 Sum_probs=12.7
Q ss_pred EEEEEcCCCCceeEEee
Q psy10064 85 QFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 85 ~F~~kC~~C~~~i~i~T 101 (257)
++..+|..|+..|.--|
T Consensus 36 st~V~C~~CG~~l~~PT 52 (67)
T COG2051 36 STVVTCLICGTTLAEPT 52 (67)
T ss_pred ceEEEecccccEEEecC
Confidence 35788999988877655
No 65
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=35.74 E-value=33 Score=34.54 Aligned_cols=27 Identities=30% Similarity=0.550 Sum_probs=19.7
Q ss_pred ceeeeecCCCCccccccc-eeeeecccc
Q psy10064 49 LPYNIWCEGCNNHIGMGV-RYNAEKKKV 75 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~kG~-rfNA~K~~v 75 (257)
.||+..|..||....-.+ -||.+..+|
T Consensus 172 ~P~~pic~~cg~~~~~~~~~~d~~~~~v 199 (510)
T PRK00750 172 SPFLPICPKCGKVLTTPVISYDAEAGTV 199 (510)
T ss_pred eeeeeeCCCCCccceEEEEEEeCCCCEE
Confidence 499999999998765554 566665544
No 66
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=35.51 E-value=33 Score=25.88 Aligned_cols=30 Identities=20% Similarity=0.507 Sum_probs=15.4
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEee
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~T 101 (257)
++| .||.++|-- .+.. +-+| .|+..|-|+.
T Consensus 4 frC-~Cgr~lya~-----------e~~k------TkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 4 FRC-DCGRYLYAK-----------EGAK------TKKC-VCGKTLKVKE 33 (68)
T ss_dssp EEE-TTS--EEEE-----------TT-S------EEEE-TTTEEEE--S
T ss_pred EEe-cCCCEEEec-----------CCcc------eeEe-cCCCeeeeee
Confidence 578 688887741 1112 3578 7888777653
No 67
>PRK11823 DNA repair protein RadA; Provisional
Probab=34.28 E-value=26 Score=34.58 Aligned_cols=28 Identities=14% Similarity=0.408 Sum_probs=22.3
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEee
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~T 101 (257)
-.|..||..-.+ ++-+||.|..|=+|+-
T Consensus 8 y~C~~Cg~~~~~---------------------~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 8 YVCQECGAESPK---------------------WLGRCPECGAWNTLVE 35 (446)
T ss_pred EECCcCCCCCcc---------------------cCeeCcCCCCccceee
Confidence 579999865444 5789999999988876
No 68
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=33.61 E-value=36 Score=34.58 Aligned_cols=24 Identities=25% Similarity=0.643 Sum_probs=17.5
Q ss_pred ceeeeecCCCCccccccceeeeec
Q psy10064 49 LPYNIWCEGCNNHIGMGVRYNAEK 72 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~kG~rfNA~K 72 (257)
.||+..|..||.....=+.+|+..
T Consensus 165 ~P~~pic~~cGrv~~~~~~~~~~~ 188 (515)
T TIGR00467 165 YPISVFCENCGRDTTTVNNYDNEY 188 (515)
T ss_pred eeeeeecCCcCccCceEEEecCCc
Confidence 799999999998755444455544
No 69
>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=33.56 E-value=40 Score=25.84 Aligned_cols=44 Identities=25% Similarity=0.594 Sum_probs=21.2
Q ss_pred EeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEee
Q psy10064 47 FELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 47 fe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~T 101 (257)
--+|=..-|..|+.--.-.++++.. +.+| .+.|..|+..+++..
T Consensus 17 ~~l~~~F~CPfC~~~~sV~v~idkk-~~~~----------~~~C~~Cg~~~~~~i 60 (81)
T PF05129_consen 17 PKLPKVFDCPFCNHEKSVSVKIDKK-EGIG----------ILSCRVCGESFQTKI 60 (81)
T ss_dssp ---SS----TTT--SS-EEEEEETT-TTEE----------EEEESSS--EEEEE-
T ss_pred CCCCceEcCCcCCCCCeEEEEEEcc-CCEE----------EEEecCCCCeEEEcc
Confidence 3456667899999877777777433 3333 589999987776653
No 70
>PF04113 Gpi16: Gpi16 subunit, GPI transamidase component; InterPro: IPR007245 GPI (glycosyl phosphatidyl inositol) transamidase is a multiprotein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase adds glycosylphosphatidylinositols (GPIs) to newly synthesized proteins. Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small C-terminal, cytosolic extension with an ER retrieval motif [].; GO: 0016021 integral to membrane, 0042765 GPI-anchor transamidase complex
Probab=32.97 E-value=9.3 Score=39.16 Aligned_cols=26 Identities=27% Similarity=0.606 Sum_probs=19.5
Q ss_pred EEeceeeeecCCCCc-cccccceeeee
Q psy10064 46 RFELPYNIWCEGCNN-HIGMGVRYNAE 71 (257)
Q Consensus 46 Rfe~Pf~i~C~~C~~-~I~kG~rfNA~ 71 (257)
=|-|||||+|.+|-- -++=|.-||.-
T Consensus 507 DFSMPyNVI~lt~Tv~Al~FG~i~nll 533 (564)
T PF04113_consen 507 DFSMPYNVIILTCTVMALAFGSIFNLL 533 (564)
T ss_pred CCCccchhhHHHHHHHHHHHHHHHHHH
Confidence 478999999999965 35556666653
No 71
>KOG2846|consensus
Probab=32.57 E-value=20 Score=34.55 Aligned_cols=42 Identities=29% Similarity=0.728 Sum_probs=27.7
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCCC
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPGN 105 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPkn 105 (257)
|.++|..|..|-|.- +|+.- .|. .|.|+.|.....=+-+|+|
T Consensus 219 yALIC~~C~~HNGla-----~~ee~-~yi-------~F~C~~Cn~LN~~~k~~e~ 260 (328)
T KOG2846|consen 219 YALICSQCHHHNGLA-----RKEEY-EYI-------TFRCPHCNALNPAKKSPEN 260 (328)
T ss_pred hhhcchhhccccCcC-----Chhhc-Cce-------EEECccccccCCCcCCccc
Confidence 578999999998873 33221 122 4789999987655544443
No 72
>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=32.14 E-value=47 Score=21.46 Aligned_cols=16 Identities=25% Similarity=0.461 Sum_probs=9.3
Q ss_pred cCCCCceeEEeeCCCC
Q psy10064 90 CHLCDSHFEIKTDPGN 105 (257)
Q Consensus 90 C~~C~~~i~i~TDPkn 105 (257)
|+.|++-+..+.|-.+
T Consensus 4 Cp~C~nlL~p~~~~~~ 19 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEK 19 (35)
T ss_dssp ETTTTSBEEEEEETTT
T ss_pred CCCCCccceEcCCCcc
Confidence 5666666665555554
No 73
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.11 E-value=30 Score=35.88 Aligned_cols=38 Identities=26% Similarity=0.565 Sum_probs=27.3
Q ss_pred CCeeEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCCC
Q psy10064 40 MGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPGN 105 (257)
Q Consensus 40 ~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPkn 105 (257)
.|+.-+-|-.||++ |..||- .|. +...||.|++ +||++
T Consensus 548 ~~i~Y~sin~~~~~-C~~CGy---~g~-------------------~~~~CP~CG~-----~d~~~ 585 (618)
T PRK14704 548 HGVGYGSINHPVDR-CKCCSY---HGV-------------------IGNECPSCGN-----EDEAN 585 (618)
T ss_pred cCCceEEeCCCCee-cCCCCC---CCC-------------------cCccCcCCCC-----CCcch
Confidence 46777777888886 999983 442 1278999998 56665
No 74
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 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. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=32.01 E-value=23 Score=26.05 Aligned_cols=16 Identities=13% Similarity=0.655 Sum_probs=12.9
Q ss_pred ceeeeecCCCCccccc
Q psy10064 49 LPYNIWCEGCNNHIGM 64 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~k 64 (257)
|=|.+.|.+||.-|.-
T Consensus 1 MVf~lvCSTCGrDlSe 16 (63)
T PF05864_consen 1 MVFQLVCSTCGRDLSE 16 (63)
T ss_pred CeeeeeecccCCcchH
Confidence 5588999999987654
No 75
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=31.68 E-value=22 Score=25.04 Aligned_cols=39 Identities=18% Similarity=0.340 Sum_probs=21.6
Q ss_pred eecCCCCccccccceeeeecccc-cc-ccceeeEEEEEEcCCCCc
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKV-GM-YYSTPVYQFRMKCHLCDS 95 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~v-g~-Y~st~I~~F~~kC~~C~~ 95 (257)
..|..|| |||-..+-+..--.. |. +-.+|. ..+|+.|+.
T Consensus 2 y~C~~Cg-yiYd~~~Gd~~~~i~pGt~f~~Lp~---~w~CP~C~a 42 (50)
T cd00730 2 YECRICG-YIYDPAEGDPDEGIPPGTPFEDLPD---DWVCPVCGA 42 (50)
T ss_pred cCCCCCC-eEECCCCCCcccCcCCCCCHhHCCC---CCCCCCCCC
Confidence 3699998 887744433322111 32 223332 468999976
No 76
>PHA02998 RNA polymerase subunit; Provisional
Probab=31.50 E-value=11 Score=33.56 Aligned_cols=60 Identities=27% Similarity=0.456 Sum_probs=41.6
Q ss_pred ceeeeecCCCCccccccceeeeecc-cc--ccccceeeEEEEEEcCCCCc----eeEEeeC----CCCCCeeeccCc
Q psy10064 49 LPYNIWCEGCNNHIGMGVRYNAEKK-KV--GMYYSTPVYQFRMKCHLCDS----HFEIKTD----PGNLDYVIVSGA 114 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~kG~rfNA~K~-~v--g~Y~st~I~~F~~kC~~C~~----~i~i~TD----Pkn~dYv~~~Ga 114 (257)
+-|.|.| |.+||-||-+|- .+ +.|+.+--=.-..+|+.|++ .+.++|- |...-|.|..-+
T Consensus 108 ~lfgikc------v~~~veydid~~~d~~y~~yfnvlpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG 178 (195)
T PHA02998 108 LLFGIKC------IKKGVEYDIDKIPDVDYDDYFNVLDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCK 178 (195)
T ss_pred HHHHHHH------HhcCCccchhhcccccchhheeccCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCC
Confidence 4577877 458999999984 35 47887533224589999976 4567776 556778876533
No 77
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=31.39 E-value=38 Score=28.27 Aligned_cols=15 Identities=27% Similarity=0.541 Sum_probs=10.0
Q ss_pred eeeeecCCCCccccc
Q psy10064 50 PYNIWCEGCNNHIGM 64 (257)
Q Consensus 50 Pf~i~C~~C~~~I~k 64 (257)
|+--+|..|+..+-.
T Consensus 89 ~~~sRC~~CN~~L~~ 103 (147)
T PF01927_consen 89 PIFSRCPKCNGPLRP 103 (147)
T ss_pred CCCCccCCCCcEeee
Confidence 445688888875444
No 78
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=31.37 E-value=27 Score=25.78 Aligned_cols=16 Identities=19% Similarity=0.331 Sum_probs=11.4
Q ss_pred EEEcCCCCceeEEeeC
Q psy10064 87 RMKCHLCDSHFEIKTD 102 (257)
Q Consensus 87 ~~kC~~C~~~i~i~TD 102 (257)
...||.|..+|++++|
T Consensus 55 ~G~CP~C~~~i~~~~~ 70 (70)
T PF11793_consen 55 FGECPYCSSPISWSFS 70 (70)
T ss_dssp EEE-TTT-SEEEGGG-
T ss_pred ccCCcCCCCeeeEecC
Confidence 4689999999999876
No 79
>KOG1296|consensus
Probab=31.33 E-value=20 Score=31.01 Aligned_cols=61 Identities=18% Similarity=0.272 Sum_probs=33.0
Q ss_pred ceeeeecCCCCccccccceee--eeccccccccceeeEEEEEEcCCCCceeEEeeCCC-CCCeeecc
Q psy10064 49 LPYNIWCEGCNNHIGMGVRYN--AEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPG-NLDYVIVS 112 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~kG~rfN--A~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPk-n~dYv~~~ 112 (257)
.=|.+.|..||+.--+=+=.| -+-..-|. =|+ -+|-|||..|+.+-+|.-=|. +..|..+.
T Consensus 27 f~~kLkCtnCgE~~dkw~~I~l~E~~~~pg~-Rgt--a~~v~KCK~C~Rensv~iv~~~~~pyt~ed 90 (161)
T KOG1296|consen 27 FYLKLKCTNCGELSDKWQYITLNEEVAMPGS-RGT--ASFVMKCKFCSRENSVTIVAFEDKPYTAED 90 (161)
T ss_pred eEEEeccccccccCCceEEEEeeeeecCCCC-cch--hhHhhhhhhhcccCcEEEecCCCCcccccc
Confidence 346789999999543322211 11111110 122 278999999998877654333 34444443
No 80
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.19 E-value=29 Score=36.15 Aligned_cols=34 Identities=29% Similarity=0.740 Sum_probs=25.6
Q ss_pred CCeeEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCc
Q psy10064 40 MGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDS 95 (257)
Q Consensus 40 ~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~ 95 (257)
.++.=.-+-.||++ |..|| |++.|. ...||.|++
T Consensus 555 ~~i~Yf~in~~~~i-C~~CG-~~~~g~--------------------~~~CP~CGs 588 (623)
T PRK08271 555 TGCNYFAFNVKITI-CNDCH-HIDKRT--------------------GKRCPICGS 588 (623)
T ss_pred cCCceEEeCCCCcc-CCCCC-CcCCCC--------------------CcCCcCCCC
Confidence 46777788888887 99999 554441 278999987
No 81
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=30.44 E-value=26 Score=32.87 Aligned_cols=24 Identities=21% Similarity=0.274 Sum_probs=19.0
Q ss_pred EEcCCCCceeEEeeCCCCCCeeecc
Q psy10064 88 MKCHLCDSHFEIKTDPGNLDYVIVS 112 (257)
Q Consensus 88 ~kC~~C~~~i~i~TDPkn~dYv~~~ 112 (257)
.+||.|++ -.|-+|.+++++||..
T Consensus 12 ~~Cp~Cg~-~~iv~d~~~Ge~vC~~ 35 (310)
T PRK00423 12 LVCPECGS-DKLIYDYERGEIVCAD 35 (310)
T ss_pred CcCcCCCC-CCeeEECCCCeEeecc
Confidence 46999987 4788888888887776
No 82
>PRK06260 threonine synthase; Validated
Probab=30.40 E-value=35 Score=32.90 Aligned_cols=35 Identities=20% Similarity=0.425 Sum_probs=24.4
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCC
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPG 104 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPk 104 (257)
+.+.|..||.... +..+..+|+.|++.+.+.-|..
T Consensus 2 ~~~~C~~cg~~~~-------------------~~~~~~~Cp~cg~~l~~~y~~~ 36 (397)
T PRK06260 2 YWLKCIECGKEYD-------------------PDEIIYTCPECGGLLEVIYDLD 36 (397)
T ss_pred CEEEECCCCCCCC-------------------CCCccccCCCCCCeEEEEecch
Confidence 3478999985422 2223467999999999887754
No 83
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=30.35 E-value=23 Score=26.10 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=9.5
Q ss_pred eeeecCCCCcccc
Q psy10064 51 YNIWCEGCNNHIG 63 (257)
Q Consensus 51 f~i~C~~C~~~I~ 63 (257)
+.|+|-+||..|+
T Consensus 3 iPVRCFTCGkvi~ 15 (60)
T PF01194_consen 3 IPVRCFTCGKVIG 15 (60)
T ss_dssp -SSS-STTTSBTC
T ss_pred CceecCCCCCChh
Confidence 5689999999886
No 84
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=30.19 E-value=31 Score=34.21 Aligned_cols=28 Identities=21% Similarity=0.529 Sum_probs=21.9
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEee
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~T 101 (257)
-.|..||..-.+ ++-+||.|..|=+|.-
T Consensus 8 y~C~~Cg~~~~~---------------------~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 8 FVCQHCGADSPK---------------------WQGKCPACHAWNTITE 35 (454)
T ss_pred EECCcCCCCCcc---------------------ccEECcCCCCccccch
Confidence 579999854333 6789999999988875
No 85
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=29.98 E-value=28 Score=23.81 Aligned_cols=16 Identities=31% Similarity=0.856 Sum_probs=10.3
Q ss_pred eecCCCCcccccccee
Q psy10064 53 IWCEGCNNHIGMGVRY 68 (257)
Q Consensus 53 i~C~~C~~~I~kG~rf 68 (257)
|.|.+|+...-.|+||
T Consensus 1 i~Cd~C~~~~i~G~Ry 16 (45)
T cd02339 1 IICDTCRKQGIIGIRW 16 (45)
T ss_pred CCCCCCCCCCcccCeE
Confidence 5788887655555443
No 86
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=29.75 E-value=25 Score=26.74 Aligned_cols=14 Identities=29% Similarity=0.608 Sum_probs=10.7
Q ss_pred eeeecCCCCccccc
Q psy10064 51 YNIWCEGCNNHIGM 64 (257)
Q Consensus 51 f~i~C~~C~~~I~k 64 (257)
+.|+|=+||..|+-
T Consensus 3 iPVRCFTCGkvig~ 16 (71)
T PLN00032 3 IPVRCFTCGKVIGN 16 (71)
T ss_pred CceeecCCCCCcHH
Confidence 46889999987753
No 87
>PRK12496 hypothetical protein; Provisional
Probab=29.63 E-value=32 Score=29.57 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=7.1
Q ss_pred EcCCCCceeEE
Q psy10064 89 KCHLCDSHFEI 99 (257)
Q Consensus 89 kC~~C~~~i~i 99 (257)
-|+.|++++.-
T Consensus 145 ~C~~CG~~~~r 155 (164)
T PRK12496 145 VCEICGSPVKR 155 (164)
T ss_pred cCCCCCChhhh
Confidence 47777776643
No 88
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=29.59 E-value=48 Score=33.74 Aligned_cols=33 Identities=33% Similarity=0.630 Sum_probs=16.9
Q ss_pred CeeEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCce
Q psy10064 41 GIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSH 96 (257)
Q Consensus 41 g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~ 96 (257)
++.-+.+-.||++ |..||-... + ...||.|+++
T Consensus 481 ~i~Y~~in~~~~~-C~~CG~~~~-------------------~---~~~CP~CGs~ 513 (546)
T PF13597_consen 481 GIPYFTINPPIDI-CPDCGYIGG-------------------E---GDKCPKCGSE 513 (546)
T ss_dssp H-SEEEEE--EEE-ETTT---S------------------------EEE-CCC---
T ss_pred CCCeEEEecCccc-ccCCCcCCC-------------------C---CCCCCCCCCc
Confidence 6777888889987 999984221 1 4679999997
No 89
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=29.58 E-value=25 Score=24.26 Aligned_cols=7 Identities=43% Similarity=1.545 Sum_probs=5.2
Q ss_pred eecCCCC
Q psy10064 53 IWCEGCN 59 (257)
Q Consensus 53 i~C~~C~ 59 (257)
|.|.+|+
T Consensus 1 i~C~~C~ 7 (49)
T cd02338 1 VSCDGCG 7 (49)
T ss_pred CCCCCCc
Confidence 5688886
No 90
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=29.57 E-value=48 Score=32.05 Aligned_cols=11 Identities=36% Similarity=1.147 Sum_probs=10.6
Q ss_pred ceeeeecCCCC
Q psy10064 49 LPYNIWCEGCN 59 (257)
Q Consensus 49 ~Pf~i~C~~C~ 59 (257)
.||+..|..||
T Consensus 166 ~P~~p~c~~cg 176 (353)
T cd00674 166 YPFMPYCEKCG 176 (353)
T ss_pred eeeeeecCCcC
Confidence 79999999999
No 91
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=29.45 E-value=20 Score=32.97 Aligned_cols=19 Identities=26% Similarity=0.765 Sum_probs=15.4
Q ss_pred cccceeeEEEEEEcCCCCceeE
Q psy10064 77 MYYSTPVYQFRMKCHLCDSHFE 98 (257)
Q Consensus 77 ~Y~st~I~~F~~kC~~C~~~i~ 98 (257)
.-|-|| |.|+|-.|.+.|-
T Consensus 35 iRL~TP---F~~RCL~C~~YI~ 53 (272)
T COG5134 35 IRLETP---FPVRCLNCENYIQ 53 (272)
T ss_pred EEeccC---cceeecchhhhhh
Confidence 455666 9999999999883
No 92
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.08 E-value=37 Score=35.99 Aligned_cols=33 Identities=27% Similarity=0.539 Sum_probs=23.6
Q ss_pred CCeeEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCc
Q psy10064 40 MGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDS 95 (257)
Q Consensus 40 ~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~ 95 (257)
.|+.-+-+-.||++ |..|| |++- +...||.|++
T Consensus 669 ~~i~Y~sin~~~~~-C~~CG-~~~~---------------------~~~~CP~CG~ 701 (735)
T PRK07111 669 TNIGYGSINHPVDR-CPVCG-YLGV---------------------IEDKCPKCGS 701 (735)
T ss_pred CCCceEEeCCCCee-cCCCC-CCCC---------------------cCccCcCCCC
Confidence 36666777778876 99998 4332 1278999997
No 93
>KOG2636|consensus
Probab=29.04 E-value=17 Score=36.60 Aligned_cols=31 Identities=29% Similarity=0.528 Sum_probs=23.7
Q ss_pred eeecCCCCccccccce-----eeeecccccc-cccee
Q psy10064 52 NIWCEGCNNHIGMGVR-----YNAEKKKVGM-YYSTP 82 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~r-----fNA~K~~vg~-Y~st~ 82 (257)
.-.|.-||+|.|+|.| ||-.+-.-|. .||||
T Consensus 401 ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLGIp 437 (497)
T KOG2636|consen 401 EYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLGIP 437 (497)
T ss_pred ccceeeccCccccCcHHHHHHhHHHHHhhcceecCCC
Confidence 3579999999999965 7777766673 66665
No 94
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.82 E-value=32 Score=23.14 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=6.7
Q ss_pred ecCCCCccccc
Q psy10064 54 WCEGCNNHIGM 64 (257)
Q Consensus 54 ~C~~C~~~I~k 64 (257)
.|..||+.++.
T Consensus 2 FCp~Cg~~l~~ 12 (52)
T smart00661 2 FCPKCGNMLIP 12 (52)
T ss_pred CCCCCCCcccc
Confidence 36777775543
No 95
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=28.54 E-value=43 Score=28.74 Aligned_cols=55 Identities=18% Similarity=0.292 Sum_probs=29.7
Q ss_pred eecCCCCcc--ccccceeeeeccccccccceeeEEEEEEcCCCCceeE-EeeCCCCCCeeeccCcee
Q psy10064 53 IWCEGCNNH--IGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFE-IKTDPGNLDYVIVSGARR 116 (257)
Q Consensus 53 i~C~~C~~~--I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~-i~TDPkn~dYv~~~Ga~r 116 (257)
|.|..||.. ...-.++++. |--|=+| -.|++|+..+. +.+=-..--+|+-..++.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~--------~~~~~~~-~~c~~c~~~f~~~e~~~~~~i~VIKRDG~~ 58 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED--------GNAIRRR-RECLACGKRFTTFERVELVPLLVIKKDGRR 58 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC--------CCceeee-eeccccCCcceEeEeccCcccEEEecCCcC
Confidence 679999852 2222222222 1135566 78999987653 333333334566655554
No 96
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=27.61 E-value=42 Score=32.50 Aligned_cols=17 Identities=18% Similarity=0.397 Sum_probs=14.3
Q ss_pred EEEEcCCCCceeEEeeC
Q psy10064 86 FRMKCHLCDSHFEIKTD 102 (257)
Q Consensus 86 F~~kC~~C~~~i~i~TD 102 (257)
+.-+||.|..|=+|.-.
T Consensus 13 ~~g~cp~c~~w~~~~e~ 29 (372)
T cd01121 13 WLGKCPECGEWNTLVEE 29 (372)
T ss_pred ccEECcCCCCceeeeeh
Confidence 56899999999888764
No 97
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=27.21 E-value=31 Score=25.42 Aligned_cols=16 Identities=13% Similarity=0.655 Sum_probs=12.7
Q ss_pred ceeeeecCCCCccccc
Q psy10064 49 LPYNIWCEGCNNHIGM 64 (257)
Q Consensus 49 ~Pf~i~C~~C~~~I~k 64 (257)
|=|.+.|.+||.-|.-
T Consensus 1 MVf~lVCsTCGrDlSe 16 (63)
T PHA03082 1 MVFQLVCSTCGRDLSE 16 (63)
T ss_pred CeeeeeecccCcchhH
Confidence 5588999999986653
No 98
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=27.12 E-value=81 Score=21.23 Aligned_cols=30 Identities=30% Similarity=0.698 Sum_probs=19.1
Q ss_pred eeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCC
Q psy10064 52 NIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCD 94 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~ 94 (257)
.|.|.+|+..|.- |- +-++=-||-.|..|.
T Consensus 3 tIvCq~C~~~Id~---~e----------~ekV~~lYg~C~~~e 32 (38)
T PF13790_consen 3 TIVCQHCNETIDH---FE----------TEKVTTLYGKCGKCE 32 (38)
T ss_pred EEEeccccceeee---ec----------CCcEEEEEEECCCCc
Confidence 4789999887754 22 223444667787664
No 99
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=26.61 E-value=38 Score=23.06 Aligned_cols=19 Identities=26% Similarity=0.452 Sum_probs=15.6
Q ss_pred EcCCCCceeEEeeCCCCCC
Q psy10064 89 KCHLCDSHFEIKTDPGNLD 107 (257)
Q Consensus 89 kC~~C~~~i~i~TDPkn~d 107 (257)
+||.|++...|+|-..-+.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~ 19 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSP 19 (47)
T ss_pred CcCCCCCeeEEEEchhhCc
Confidence 5999999999998776543
No 100
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=26.54 E-value=35 Score=23.08 Aligned_cols=19 Identities=37% Similarity=0.819 Sum_probs=10.3
Q ss_pred eeeecCCCCccccccceee
Q psy10064 51 YNIWCEGCNNHIGMGVRYN 69 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfN 69 (257)
..+.|.+|+...-.|+||-
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~ 21 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYH 21 (46)
T ss_dssp SSCE-SSS-SSSEESSEEE
T ss_pred CCeECcCCCCCcCcCCeEE
Confidence 3578999987444455443
No 101
>PF14353 CpXC: CpXC protein
Probab=26.13 E-value=38 Score=27.30 Aligned_cols=40 Identities=28% Similarity=0.686 Sum_probs=25.7
Q ss_pred eecCCCCcccc--ccceeeeec-----ccc--ccccceeeEEEEEEcCCCCceeEE
Q psy10064 53 IWCEGCNNHIG--MGVRYNAEK-----KKV--GMYYSTPVYQFRMKCHLCDSHFEI 99 (257)
Q Consensus 53 i~C~~C~~~I~--kG~rfNA~K-----~~v--g~Y~st~I~~F~~kC~~C~~~i~i 99 (257)
|.|.+|+.... -=+-.|+.. +.| |++ |.+.||.|+..+.+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l-------~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSL-------FSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCc-------CEEECCCCCCceec
Confidence 67999988421 124556543 233 443 46789999998876
No 102
>KOG4253|consensus
Probab=26.00 E-value=2.7e+02 Score=24.47 Aligned_cols=53 Identities=15% Similarity=0.267 Sum_probs=34.2
Q ss_pred ccccchhhhHHHHHHHHHHH-HHhhhccChHHHHHHHHHHHHHHHHHHHHHHHh
Q psy10064 151 GTNDMSSSKSKASHLNKLLD-RQESVWKNDFDANRVLRDSFRKKKKQLKALQDK 203 (257)
Q Consensus 151 ~~~d~~~~~~~~~~L~eL~~-~~~~~~~ddy~~n~~LR~~fR~~kk~~~~~~~~ 203 (257)
..+|.+++.+...+|.++.+ +|.--..|.|+.-++|-+....--++.+-+-+.
T Consensus 39 ~nkdakk~~q~~~ei~dmKqelnavs~qD~fAkwaRlnRKi~kl~~ele~qs~n 92 (175)
T KOG4253|consen 39 GNKDAKKESQKVAEIQDMKQELNAVSMQDNFAKWARLNRKINKLDKELETQSKN 92 (175)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566666667777777754 444455789988888877766555555544443
No 103
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=25.68 E-value=45 Score=30.55 Aligned_cols=14 Identities=21% Similarity=0.487 Sum_probs=10.7
Q ss_pred EEEEcCCCCceeEE
Q psy10064 86 FRMKCHLCDSHFEI 99 (257)
Q Consensus 86 F~~kC~~C~~~i~i 99 (257)
++..||.|+++=++
T Consensus 367 ~~~~c~~c~~~~~~ 380 (389)
T PRK11788 367 LYWHCPSCKAWETI 380 (389)
T ss_pred ceeECcCCCCccCc
Confidence 56789999886554
No 104
>PRK05978 hypothetical protein; Provisional
Probab=25.57 E-value=25 Score=30.13 Aligned_cols=33 Identities=15% Similarity=0.479 Sum_probs=24.5
Q ss_pred eeeecCCCCc-cccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 51 YNIWCEGCNN-HIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 51 f~i~C~~C~~-~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
+..+|-.||+ .+++ .||.+ .-+|+.|+-.+++.
T Consensus 32 l~grCP~CG~G~LF~------------g~Lkv-----~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPACGEGKLFR------------AFLKP-----VDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCCCCCCcccc------------ccccc-----CCCccccCCccccC
Confidence 4578999986 4555 35554 47899999988776
No 105
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=25.44 E-value=29 Score=29.48 Aligned_cols=12 Identities=17% Similarity=0.822 Sum_probs=8.3
Q ss_pred eeeecCCCCccc
Q psy10064 51 YNIWCEGCNNHI 62 (257)
Q Consensus 51 f~i~C~~C~~~I 62 (257)
+.++|..|+...
T Consensus 104 ~~~~C~~C~~~~ 115 (178)
T PF02146_consen 104 FRLRCSKCGKEY 115 (178)
T ss_dssp EEEEETTTSBEE
T ss_pred ceeeecCCCccc
Confidence 457888887743
No 106
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=25.24 E-value=95 Score=22.49 Aligned_cols=39 Identities=26% Similarity=0.308 Sum_probs=21.4
Q ss_pred cccccc-ceeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCc
Q psy10064 74 KVGMYY-STPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGA 114 (257)
Q Consensus 74 ~vg~Y~-st~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga 114 (257)
.+..|- +.+--. +.-|+.|+..|... ++...+++.+..+
T Consensus 35 ~l~~y~~s~~~~~-r~FC~~CGs~l~~~-~~~~~~~~~V~~g 74 (92)
T PF04828_consen 35 NLKEYQFSGKGVE-RYFCPTCGSPLFSE-DERDPDLVGVNAG 74 (92)
T ss_dssp GEEEC--TTSSCE-EEEETTT--EEEEE-ESSTTTEEEEEGG
T ss_pred cceEEEeCCCcCc-CcccCCCCCeeecc-cCCCCCEEEEEeE
Confidence 444565 333333 47899999999988 5555555555443
No 107
>PF05973 Gp49: Phage derived protein Gp49-like (DUF891); InterPro: IPR009241 This entry consists of several hypothetical viral and bacterial proteins some are annotated as addiction module killer proteins.
Probab=25.11 E-value=1.1e+02 Score=23.00 Aligned_cols=41 Identities=15% Similarity=0.176 Sum_probs=34.1
Q ss_pred ccc-eeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCceeccc
Q psy10064 78 YYS-TPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARRQEN 119 (257)
Q Consensus 78 Y~s-t~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r~~e 119 (257)
++. ..||.+++.+.....-+.|-.+..+ .+|+.+|..++.+
T Consensus 35 ~l~~~~i~ElR~~~~~~~~Ri~y~~~~~~-~ivll~~f~Kkt~ 76 (91)
T PF05973_consen 35 HLKGDGIYELRVRGGSNIYRILYFFDGGD-IIVLLHGFIKKTQ 76 (91)
T ss_pred ccCcCCeEEEEEeecCCcceEEEEEcCcc-EEEEEEEEEeCCC
Confidence 344 7899999999998888999998888 7888888888754
No 108
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=25.07 E-value=34 Score=25.41 Aligned_cols=14 Identities=36% Similarity=0.869 Sum_probs=11.1
Q ss_pred eecCCCCccccccc
Q psy10064 53 IWCEGCNNHIGMGV 66 (257)
Q Consensus 53 i~C~~C~~~I~kG~ 66 (257)
-.|.+|+..|.+|.
T Consensus 8 a~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 8 AKCKGCKKKIAKGE 21 (82)
T ss_dssp EBETTTSCBE-TTS
T ss_pred ccCcccCCcCCCCC
Confidence 36999999999984
No 109
>PRK03954 ribonuclease P protein component 4; Validated
Probab=24.70 E-value=77 Score=26.31 Aligned_cols=42 Identities=19% Similarity=0.397 Sum_probs=27.6
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
.+|..|+.++--|+ |+.-+..+.=+ . .+.+.|..|+..--|.
T Consensus 65 ~~CK~C~t~LiPG~--n~~vRi~~~~~---~-~vvitCl~CG~~kR~P 106 (121)
T PRK03954 65 RYCKRCHSFLVPGV--NARVRLRQKRM---P-HVVITCLECGHIMRYP 106 (121)
T ss_pred HHhhcCCCeeecCC--ceEEEEecCCc---c-eEEEECccCCCEEeec
Confidence 47999999988884 55544332101 1 2678999999865543
No 110
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=24.65 E-value=58 Score=31.76 Aligned_cols=34 Identities=18% Similarity=0.497 Sum_probs=23.4
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCC
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPG 104 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPk 104 (257)
|++.|..||.... . - +..+|+.|.+.+.+.-|+.
T Consensus 1 ~~l~C~~Cg~~~~-~-----------------~--~~~~C~~c~g~l~~~y~~~ 34 (398)
T TIGR03844 1 YTLRCPGCGEVLP-D-----------------H--YTLSCPLDCGLLRAEYAER 34 (398)
T ss_pred CEEEeCCCCCccC-C-----------------c--cccCCCCCCCceEEeeccc
Confidence 5688999975322 1 1 2367999989998887753
No 111
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.46 E-value=38 Score=37.33 Aligned_cols=19 Identities=16% Similarity=0.457 Sum_probs=13.1
Q ss_pred CCeeEEEEeceeeeecCCCCcc
Q psy10064 40 MGIMIIRFELPYNIWCEGCNNH 61 (257)
Q Consensus 40 ~g~~~VRfe~Pf~i~C~~C~~~ 61 (257)
.|.+.|....+ .|..||..
T Consensus 617 ~g~~eVEVg~R---fCpsCG~~ 635 (1121)
T PRK04023 617 KGTIEVEIGRR---KCPSCGKE 635 (1121)
T ss_pred CCceeecccCc---cCCCCCCc
Confidence 46666665554 49999887
No 112
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=24.20 E-value=1.8e+02 Score=28.60 Aligned_cols=59 Identities=20% Similarity=0.462 Sum_probs=38.8
Q ss_pred EEEEeceeeeecCCCCccccccceeeeecccc------cccc-c--eeeEEEEEEcCCCCceeEEeeCCCC
Q psy10064 44 IIRFELPYNIWCEGCNNHIGMGVRYNAEKKKV------GMYY-S--TPVYQFRMKCHLCDSHFEIKTDPGN 105 (257)
Q Consensus 44 ~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~v------g~Y~-s--t~I~~F~~kC~~C~~~i~i~TDPkn 105 (257)
++.+.+|-.+-|.+|.-. |.+-.+..++- |... . +-+|.+...|+.|.+.=.+-.||=.
T Consensus 134 ~~~i~~~~~~~C~~C~Gs---Gak~gt~~~tC~tC~G~G~v~~~~~~g~~~~~~~C~~C~G~G~~i~~pC~ 201 (371)
T COG0484 134 KKEIRVTRSVTCSTCHGS---GAKPGTDPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGKIIKDPCG 201 (371)
T ss_pred eeeEecceeeECCcCCCC---CCCCCCCCCcCCCCCCcCeEEEEEeeeEEEEEEECCCCccceeECCCCCC
Confidence 466788999999999754 33333222211 2111 1 1578999999999988888788754
No 113
>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=24.01 E-value=53 Score=33.69 Aligned_cols=35 Identities=37% Similarity=0.776 Sum_probs=25.5
Q ss_pred CCeeEEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCce
Q psy10064 40 MGIMIIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSH 96 (257)
Q Consensus 40 ~g~~~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~ 96 (257)
.|+.-+-+-.|+++ |..|| |++.+. ...||.|++.
T Consensus 513 ~~i~Y~~~n~~~~~-C~~CG-~~g~~~--------------------~~~CP~Cgs~ 547 (579)
T TIGR02487 513 NGIGYFGINPPVDV-CEDCG-YTGEGL--------------------NDKCPKCGSH 547 (579)
T ss_pred cCCceEEeccCCcc-CCCCC-CCCCCC--------------------CCcCcCCCCc
Confidence 46777888888887 99998 354431 1679999973
No 114
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.83 E-value=43 Score=23.06 Aligned_cols=15 Identities=33% Similarity=0.678 Sum_probs=8.7
Q ss_pred eecCCCCccccccce
Q psy10064 53 IWCEGCNNHIGMGVR 67 (257)
Q Consensus 53 i~C~~C~~~I~kG~r 67 (257)
|.|.+|+...-.|.|
T Consensus 1 V~Cd~C~~~pI~G~R 15 (45)
T cd02344 1 VTCDGCQMFPINGPR 15 (45)
T ss_pred CCCCCCCCCCCccCe
Confidence 468888655444433
No 115
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.52 E-value=1.1e+02 Score=27.26 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=9.4
Q ss_pred ceeeeecCCCCc
Q psy10064 49 LPYNIWCEGCNN 60 (257)
Q Consensus 49 ~Pf~i~C~~C~~ 60 (257)
-|=+..|..||.
T Consensus 306 ~~tS~~C~~cg~ 317 (364)
T COG0675 306 YYTSKTCPCCGH 317 (364)
T ss_pred CCCcccccccCC
Confidence 344589999998
No 116
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=23.49 E-value=52 Score=34.20 Aligned_cols=60 Identities=17% Similarity=0.326 Sum_probs=35.5
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCCCCCeeeccCcee
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPGNLDYVIVSGARR 116 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPkn~dYv~~~Ga~r 116 (257)
|-+-|.|||++.+- +|+-.---.|. ..++-=..++.|++|...|.=+ -|+.+|+..-+-+
T Consensus 226 ~yvpCPHCGe~q~l--~~~e~~~~~g~-~~~~~~~~~~~c~h~~~~i~~~---~~~~gv~~~~g~~ 285 (611)
T COG5525 226 FYVPCPHCGEEQQL--KFGEKSGPRGL-KDTPAEAAFIQCEHCGCVIRPK---LNGRGVCLRTGEW 285 (611)
T ss_pred EEeeCCCCCchhhc--cccccCCCcCc-ccchhhhhhhhccccCceeeee---ccCccchhccCCc
Confidence 78899999996443 12111111111 0122233468899999988875 7888887664433
No 117
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=23.24 E-value=86 Score=20.62 Aligned_cols=35 Identities=14% Similarity=0.485 Sum_probs=16.8
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
++|..|+.||--=.+|+-.-+ ..+|..|...-.|.
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~-------------~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGK-------------TWICNFCGTKNPLP 37 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTT-------------EEEETTT--EEE--
T ss_pred cccCCCCCEECCcceEcCCCC-------------EEECcCCCCcCCCC
Confidence 789999999876555543211 36788888755543
No 118
>PRK07591 threonine synthase; Validated
Probab=23.19 E-value=54 Score=32.00 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=13.7
Q ss_pred EEcCCCCceeEEeeCC
Q psy10064 88 MKCHLCDSHFEIKTDP 103 (257)
Q Consensus 88 ~kC~~C~~~i~i~TDP 103 (257)
.+|+.|++.+.+.-|.
T Consensus 34 ~~C~~cg~~l~~~y~~ 49 (421)
T PRK07591 34 HVCEECFGPLEVAYDY 49 (421)
T ss_pred ccCCCCCCeEEEEech
Confidence 6799999999998764
No 119
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=23.04 E-value=50 Score=28.99 Aligned_cols=38 Identities=21% Similarity=0.542 Sum_probs=28.4
Q ss_pred eeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 52 NIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
-|.|+-|+..++-||-.++-=..| +.+|-.|.+-+.+-
T Consensus 12 YVhCnFC~TiLaVsVP~ssL~~~V-----------TVRCGHCtNLLSVN 49 (170)
T PF04690_consen 12 YVHCNFCNTILAVSVPCSSLLKTV-----------TVRCGHCTNLLSVN 49 (170)
T ss_pred EEEcCCcCeEEEEecchhhhhhhh-----------ceeccCccceeeee
Confidence 378999999999887666533333 47899999988854
No 120
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=23.02 E-value=2.2e+02 Score=21.43 Aligned_cols=45 Identities=22% Similarity=0.474 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHhhhccChHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Q psy10064 160 SKASHLNKLLDRQESVWKNDFDANRVLRDSFRKKKKQLKALQDKDNAL 207 (257)
Q Consensus 160 ~~~~~L~eL~~~~~~~~~ddy~~n~~LR~~fR~~kk~~~~~~~~d~al 207 (257)
.+.+.|+.=.......|.+.|.. |+..|-..+++.....+.-..|
T Consensus 10 ~ale~Lq~~y~~q~~~Wq~sy~~---Lq~~~~~t~~~~a~L~~qv~~L 54 (70)
T PF04899_consen 10 SALEELQQSYEKQQQEWQSSYAD---LQHMFEQTSQENAALSEQVNNL 54 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhHHHHHHHHHHHHHH
Confidence 34555555566677789999965 6777766665555444444433
No 121
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=22.97 E-value=1e+02 Score=25.16 Aligned_cols=46 Identities=24% Similarity=0.376 Sum_probs=31.5
Q ss_pred EEeceeee---ecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 46 RFELPYNI---WCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 46 Rfe~Pf~i---~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
+..+|=.+ .|.+|...+.-|+ |++.+-.+.+ -.+.|..|+...-|.
T Consensus 47 rv~lp~~iKR~~CkkC~t~Lvpg~--n~rvR~~~~~-------v~vtC~~CG~~~R~p 95 (105)
T COG2023 47 RVRLPREIKRTICKKCYTPLVPGK--NARVRLRKGR-------VVVTCLECGTIRRYP 95 (105)
T ss_pred ccccCHHHHHHhccccCcccccCc--ceEEEEcCCe-------EEEEecCCCcEEEec
Confidence 34456554 6999999877774 7776666544 457899998866553
No 122
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=22.67 E-value=33 Score=22.02 Aligned_cols=13 Identities=23% Similarity=0.654 Sum_probs=8.6
Q ss_pred EEcCCCCceeEEe
Q psy10064 88 MKCHLCDSHFEIK 100 (257)
Q Consensus 88 ~kC~~C~~~i~i~ 100 (257)
++|+.|+..|-++
T Consensus 18 irC~~CG~RIlyK 30 (32)
T PF03604_consen 18 IRCPECGHRILYK 30 (32)
T ss_dssp SSBSSSS-SEEBE
T ss_pred EECCcCCCeEEEe
Confidence 5788887777665
No 123
>PRK00807 50S ribosomal protein L24e; Validated
Probab=22.58 E-value=28 Score=24.54 Aligned_cols=43 Identities=21% Similarity=0.443 Sum_probs=28.5
Q ss_pred ecCCCCcccccc--ceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCCCCC
Q psy10064 54 WCEGCNNHIGMG--VRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDPGNL 106 (257)
Q Consensus 54 ~C~~C~~~I~kG--~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDPkn~ 106 (257)
.|.-||.-|+-| ..|=.. -| + .|+|-|..|...+-.+.+|..-
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~---Dg-----k--v~~Fcs~KC~~~f~~~~nprk~ 47 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKK---DG-----T--ILYFCSSKCEKNYKLGRVPRKL 47 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEe---CC-----c--EEEEeCHHHHHHHHccCCCCcc
Confidence 599999988854 332110 02 1 3566788999888899888653
No 124
>PRK08197 threonine synthase; Validated
Probab=21.61 E-value=65 Score=31.01 Aligned_cols=31 Identities=19% Similarity=0.454 Sum_probs=22.4
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCC
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDP 103 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDP 103 (257)
.+|..||... ++..+..+| .|++.+.+..|.
T Consensus 8 ~~C~~Cg~~~-------------------~~~~~~~~C-~cg~~l~~~~d~ 38 (394)
T PRK08197 8 LECSKCGETY-------------------DADQVHNLC-KCGKPLLVRYDL 38 (394)
T ss_pred EEECCCCCCC-------------------CCCCcceec-CCCCeeEEEech
Confidence 7899998532 122334679 899999999884
No 125
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=21.29 E-value=45 Score=30.75 Aligned_cols=17 Identities=18% Similarity=0.266 Sum_probs=12.1
Q ss_pred eeeeecCCCCccccccc
Q psy10064 50 PYNIWCEGCNNHIGMGV 66 (257)
Q Consensus 50 Pf~i~C~~C~~~I~kG~ 66 (257)
.+.+.|.+|+.-.+...
T Consensus 120 l~~~~C~~C~~~~~~~~ 136 (250)
T COG0846 120 LKRVRCSKCGNQYYDED 136 (250)
T ss_pred eeeeEeCCCcCccchhh
Confidence 35678999988776543
No 126
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=21.12 E-value=51 Score=24.97 Aligned_cols=17 Identities=24% Similarity=0.513 Sum_probs=13.6
Q ss_pred EEcCCCCceeEEeeCCC
Q psy10064 88 MKCHLCDSHFEIKTDPG 104 (257)
Q Consensus 88 ~kC~~C~~~i~i~TDPk 104 (257)
|+||.|++.-.|+|.=.
T Consensus 2 m~CP~Cg~~a~irtSr~ 18 (72)
T PRK09678 2 FHCPLCQHAAHARTSRY 18 (72)
T ss_pred ccCCCCCCccEEEEChh
Confidence 89999999888776543
No 127
>KOG0006|consensus
Probab=21.09 E-value=93 Score=30.39 Aligned_cols=49 Identities=24% Similarity=0.618 Sum_probs=37.3
Q ss_pred EEEEeceeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCC-CceeEEeeCCCCCCeeecc
Q psy10064 44 IIRFELPYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLC-DSHFEIKTDPGNLDYVIVS 112 (257)
Q Consensus 44 ~VRfe~Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C-~~~i~i~TDPkn~dYv~~~ 112 (257)
-++.-.-|-|||..|... -+| + .+..|..| ++.++++.||++-|=|+.+
T Consensus 126 ~~si~~sFyV~Ck~Cd~v-~~G-----------K--------LRV~C~~C~~~s~tv~~~P~cWdDVLks 175 (446)
T KOG0006|consen 126 GRSILGSFYVWCKNCDDV-KRG-----------K--------LRVYCQKCSSTSVTVKSEPQCWDDVLKS 175 (446)
T ss_pred cceecceeEEEecchhhc-cCC-----------c--------eEEEeecccCceEEEecCccchhhhhhc
Confidence 346677899999999652 222 1 46789999 5679999999998888876
No 128
>PRK00420 hypothetical protein; Validated
Probab=21.09 E-value=70 Score=26.20 Aligned_cols=33 Identities=18% Similarity=0.317 Sum_probs=21.4
Q ss_pred eeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEee
Q psy10064 51 YNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKT 101 (257)
Q Consensus 51 f~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~T 101 (257)
.+--|..||..+++- +-| ...||.|+..+.+..
T Consensus 22 l~~~CP~Cg~pLf~l--------k~g----------~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 22 LSKHCPVCGLPLFEL--------KDG----------EVVCPVHGKVYIVKS 54 (112)
T ss_pred ccCCCCCCCCcceec--------CCC----------ceECCCCCCeeeecc
Confidence 457899998766641 011 367999998666544
No 129
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.01 E-value=64 Score=26.92 Aligned_cols=43 Identities=14% Similarity=0.343 Sum_probs=25.2
Q ss_pred eeeeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEeeCC
Q psy10064 50 PYNIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIKTDP 103 (257)
Q Consensus 50 Pf~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~TDP 103 (257)
.....|..|+. +|...- +..+.+ + .=.|.||.|++.++...+.
T Consensus 97 ~~~Y~Cp~C~~------~y~~~e--a~~~~d-~--~~~f~Cp~Cg~~l~~~dn~ 139 (147)
T smart00531 97 NAYYKCPNCQS------KYTFLE--ANQLLD-M--DGTFTCPRCGEELEEDDNS 139 (147)
T ss_pred CcEEECcCCCC------EeeHHH--HHHhcC-C--CCcEECCCCCCEEEEcCch
Confidence 45678999973 343321 111112 1 1128999999999876553
No 130
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=20.96 E-value=53 Score=22.11 Aligned_cols=15 Identities=53% Similarity=1.369 Sum_probs=9.6
Q ss_pred eecCCCCcccccccee
Q psy10064 53 IWCEGCNNHIGMGVRY 68 (257)
Q Consensus 53 i~C~~C~~~I~kG~rf 68 (257)
|.|.+|+..| .|.||
T Consensus 1 v~Cd~C~~~i-~G~ry 15 (43)
T cd02340 1 VICDGCQGPI-VGVRY 15 (43)
T ss_pred CCCCCCCCcC-cCCeE
Confidence 5788887743 55444
No 131
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized 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.
Probab=20.82 E-value=54 Score=36.04 Aligned_cols=21 Identities=29% Similarity=0.776 Sum_probs=16.8
Q ss_pred eecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCce
Q psy10064 53 IWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSH 96 (257)
Q Consensus 53 i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~ 96 (257)
-+|..||.|. |+.+|+.|+..
T Consensus 626 RKCPkCG~yT-----------------------lk~rCP~CG~~ 646 (1095)
T TIGR00354 626 RKCPQCGKES-----------------------FWLKCPVCGEL 646 (1095)
T ss_pred EECCCCCccc-----------------------ccccCCCCCCc
Confidence 5799998654 55899999995
No 132
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.82 E-value=51 Score=26.72 Aligned_cols=13 Identities=23% Similarity=0.710 Sum_probs=10.9
Q ss_pred EEcCCCCceeEEe
Q psy10064 88 MKCHLCDSHFEIK 100 (257)
Q Consensus 88 ~kC~~C~~~i~i~ 100 (257)
+.||.|+..+.+.
T Consensus 27 ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 27 IVCPKCGTEFPPE 39 (108)
T ss_pred ccCCCCCCccCcc
Confidence 6799999987766
No 133
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.75 E-value=35 Score=32.16 Aligned_cols=33 Identities=18% Similarity=0.366 Sum_probs=23.3
Q ss_pred eeecCCCCccccccceeeeeccccccccceeeEEEEEEcCCCCceeEEe
Q psy10064 52 NIWCEGCNNHIGMGVRYNAEKKKVGMYYSTPVYQFRMKCHLCDSHFEIK 100 (257)
Q Consensus 52 ~i~C~~C~~~I~kG~rfNA~K~~vg~Y~st~I~~F~~kC~~C~~~i~i~ 100 (257)
-+.|..|+..||+- .++.. ..-|+.|+..+.+.
T Consensus 27 ~~~c~~c~~~~~~~--------~l~~~--------~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQVLYRK--------ELEAN--------LNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccchhhHH--------HHHhc--------CCCCCCCCCCeeCC
Confidence 36799999999872 23221 25799999988763
No 134
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=20.58 E-value=72 Score=27.77 Aligned_cols=20 Identities=20% Similarity=0.527 Sum_probs=11.7
Q ss_pred EEEEEcCCCCceeEEeeCCC
Q psy10064 85 QFRMKCHLCDSHFEIKTDPG 104 (257)
Q Consensus 85 ~F~~kC~~C~~~i~i~TDPk 104 (257)
.|.++|+.|++++.|..=-+
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~ 35 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE 35 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS-
T ss_pred ceEeECCCCCCCcccccccc
Confidence 58899999999999965434
No 135
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=20.58 E-value=57 Score=24.03 Aligned_cols=8 Identities=38% Similarity=1.219 Sum_probs=6.2
Q ss_pred EcCCCCce
Q psy10064 89 KCHLCDSH 96 (257)
Q Consensus 89 kC~~C~~~ 96 (257)
.||.|++.
T Consensus 17 ~CP~Cgs~ 24 (61)
T PRK08351 17 RCPVCGSR 24 (61)
T ss_pred cCCCCcCC
Confidence 49999873
No 136
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=20.09 E-value=47 Score=21.20 Aligned_cols=14 Identities=43% Similarity=0.921 Sum_probs=8.8
Q ss_pred eeeecCCCCcccccc
Q psy10064 51 YNIWCEGCNNHIGMG 65 (257)
Q Consensus 51 f~i~C~~C~~~I~kG 65 (257)
|.+ |..||+.|...
T Consensus 3 yg~-C~~CGe~I~~~ 16 (36)
T PF01258_consen 3 YGI-CEDCGEPIPEE 16 (36)
T ss_dssp -SB--TTTSSBEEHH
T ss_pred CCC-ccccCChHHHH
Confidence 344 88999888754
Done!