Query 031632
Match_columns 156
No_of_seqs 124 out of 224
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:14:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031632.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031632hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02294 cytochrome c oxidase 100.0 8E-61 1.7E-65 385.4 13.2 150 1-150 1-157 (174)
2 cd00924 Cyt_c_Oxidase_Vb Cytoc 100.0 4.6E-47 1E-51 281.4 9.4 95 55-151 2-96 (97)
3 KOG3352 Cytochrome c oxidase, 100.0 1.5E-46 3.3E-51 297.6 9.8 98 52-151 53-150 (153)
4 PF01215 COX5B: Cytochrome c o 100.0 1.6E-46 3.4E-51 293.1 6.6 98 53-151 32-129 (136)
5 PTZ00043 cytochrome c oxidase 100.0 7.9E-31 1.7E-35 220.7 7.6 85 65-149 112-196 (268)
6 PF10276 zf-CHCC: Zinc-finger 97.5 0.00011 2.4E-09 47.2 3.2 39 107-145 1-40 (40)
7 KOG3456 NADH:ubiquinone oxidor 96.3 0.0032 6.9E-08 48.8 2.8 44 103-146 73-116 (120)
8 COG4391 Uncharacterized protei 93.6 0.14 3E-06 36.0 4.2 47 99-147 15-61 (62)
9 PF06397 Desulfoferrod_N: Desu 90.9 0.15 3.3E-06 32.1 1.6 26 130-155 2-29 (36)
10 PF13465 zf-H2C2_2: Zinc-finge 85.0 0.48 1E-05 26.9 1.0 14 132-145 12-25 (26)
11 PRK00398 rpoP DNA-directed RNA 84.6 1.2 2.7E-05 28.2 2.9 20 134-153 21-40 (46)
12 COG5189 SFP1 Putative transcri 84.1 0.45 9.8E-06 43.3 1.0 17 129-145 393-409 (423)
13 PF13912 zf-C2H2_6: C2H2-type 79.7 0.93 2E-05 25.1 0.9 12 134-145 1-12 (27)
14 PF10571 UPF0547: Uncharacteri 79.0 0.73 1.6E-05 26.9 0.3 12 134-145 14-25 (26)
15 smart00834 CxxC_CXXC_SSSS Puta 78.7 1.6 3.4E-05 26.3 1.7 14 135-148 6-19 (41)
16 PF03604 DNA_RNApol_7kD: DNA d 77.8 1.2 2.7E-05 27.2 1.0 17 129-145 12-28 (32)
17 TIGR00319 desulf_FeS4 desulfof 77.3 2.5 5.3E-05 25.3 2.3 25 131-155 4-30 (34)
18 cd00974 DSRD Desulforedoxin (D 75.3 3.3 7.2E-05 24.8 2.5 24 132-155 2-27 (34)
19 PF13719 zinc_ribbon_5: zinc-r 74.9 2 4.4E-05 26.4 1.5 15 131-145 22-36 (37)
20 PHA00616 hypothetical protein 74.7 0.72 1.6E-05 30.2 -0.6 12 134-145 1-12 (44)
21 PLN00128 Succinate dehydrogena 73.7 2.2 4.8E-05 40.4 2.1 21 1-21 1-21 (635)
22 PF08274 PhnA_Zn_Ribbon: PhnA 72.8 2.5 5.4E-05 25.5 1.5 19 136-154 4-22 (30)
23 PF04216 FdhE: Protein involve 70.6 3.1 6.7E-05 35.4 2.1 33 118-150 218-254 (290)
24 PF00096 zf-C2H2: Zinc finger, 70.4 2.2 4.7E-05 22.7 0.8 11 135-145 1-11 (23)
25 smart00659 RPOLCX RNA polymera 68.7 6.5 0.00014 25.3 2.8 20 129-148 14-33 (44)
26 PF09723 Zn-ribbon_8: Zinc rib 68.1 3.6 7.7E-05 25.9 1.5 13 135-147 6-18 (42)
27 PF11781 RRN7: RNA polymerase 66.0 4.5 9.7E-05 25.1 1.6 24 131-154 5-28 (36)
28 PF13894 zf-C2H2_4: C2H2-type 64.1 3.8 8.1E-05 21.1 0.9 11 135-145 1-11 (24)
29 TIGR02605 CxxC_CxxC_SSSS putat 63.5 5.2 0.00011 25.4 1.7 14 135-148 6-19 (52)
30 PRK00432 30S ribosomal protein 62.3 7.1 0.00015 25.8 2.1 31 124-154 6-40 (50)
31 PRK14892 putative transcriptio 59.0 5.3 0.00011 30.0 1.2 35 109-147 20-55 (99)
32 PF08271 TF_Zn_Ribbon: TFIIB z 58.2 7.9 0.00017 24.1 1.8 8 136-143 2-9 (43)
33 TIGR02098 MJ0042_CXXC MJ0042 f 58.0 7.2 0.00016 23.4 1.5 14 135-148 3-16 (38)
34 smart00659 RPOLCX RNA polymera 57.4 7.7 0.00017 25.0 1.6 20 135-154 3-22 (44)
35 COG1998 RPS31 Ribosomal protei 56.3 7.9 0.00017 26.3 1.6 30 125-154 6-40 (51)
36 COG0551 TopA Zn-finger domain 55.9 21 0.00046 27.1 4.1 41 102-144 30-70 (140)
37 PHA02768 hypothetical protein; 55.1 5.4 0.00012 27.3 0.6 12 135-146 6-17 (55)
38 cd00729 rubredoxin_SM Rubredox 54.0 8.2 0.00018 23.4 1.3 10 133-142 17-26 (34)
39 PF14353 CpXC: CpXC protein 52.2 7.1 0.00015 29.1 1.0 15 134-148 38-52 (128)
40 PF13717 zinc_ribbon_4: zinc-r 52.0 8.7 0.00019 23.5 1.2 16 130-145 21-36 (36)
41 PRK03564 formate dehydrogenase 49.8 18 0.00039 32.1 3.2 30 121-150 235-268 (309)
42 PF03966 Trm112p: Trm112p-like 48.5 11 0.00025 25.5 1.4 14 135-148 54-67 (68)
43 PF07754 DUF1610: Domain of un 47.8 10 0.00022 22.0 0.9 12 131-142 13-24 (24)
44 KOG3507 DNA-directed RNA polym 47.6 7.4 0.00016 27.3 0.4 16 128-143 31-46 (62)
45 PF09538 FYDLN_acid: Protein o 46.6 8 0.00017 29.3 0.5 25 122-147 15-39 (108)
46 COG1326 Uncharacterized archae 46.0 13 0.00027 31.6 1.6 31 119-150 16-48 (201)
47 PF09237 GAGA: GAGA factor; I 45.9 6 0.00013 27.2 -0.3 24 122-145 12-35 (54)
48 COG2888 Predicted Zn-ribbon RN 45.1 10 0.00022 26.7 0.7 11 131-141 47-57 (61)
49 PF01599 Ribosomal_S27: Riboso 44.8 23 0.0005 23.5 2.4 30 125-154 4-41 (47)
50 PF14690 zf-ISL3: zinc-finger 43.3 12 0.00026 23.0 0.9 11 133-143 1-11 (47)
51 KOG3993 Transcription factor ( 43.1 9.5 0.00021 35.9 0.5 11 135-145 296-306 (500)
52 PF12172 DUF35_N: Rubredoxin-l 41.9 13 0.00029 22.3 0.9 11 134-144 11-21 (37)
53 smart00355 ZnF_C2H2 zinc finge 41.6 11 0.00024 19.2 0.4 11 135-145 1-11 (26)
54 cd00350 rubredoxin_like Rubred 41.6 15 0.00033 21.9 1.1 10 133-142 16-25 (33)
55 PF14255 Cys_rich_CPXG: Cystei 40.2 21 0.00046 23.9 1.7 11 136-146 2-12 (52)
56 PF13913 zf-C2HC_2: zinc-finge 40.1 20 0.00042 20.3 1.3 16 134-149 2-17 (25)
57 COG0846 SIR2 NAD-dependent pro 39.9 44 0.00096 28.6 4.0 67 71-142 80-154 (250)
58 TIGR01206 lysW lysine biosynth 39.9 28 0.00061 23.5 2.3 21 132-152 20-40 (54)
59 smart00451 ZnF_U1 U1-like zinc 37.7 16 0.00035 20.9 0.7 13 133-145 2-14 (35)
60 TIGR01562 FdhE formate dehydro 37.5 29 0.00064 30.7 2.6 30 121-150 233-268 (305)
61 KOG1088 Uncharacterized conser 36.9 19 0.00041 28.4 1.2 27 125-152 90-117 (124)
62 PF12677 DUF3797: Domain of un 36.1 23 0.00049 23.9 1.3 19 135-153 14-32 (49)
63 COG1592 Rubrerythrin [Energy p 36.0 15 0.00032 30.1 0.5 14 129-142 143-157 (166)
64 PF09889 DUF2116: Uncharacteri 34.4 20 0.00044 24.7 0.9 11 133-143 1-12 (59)
65 COG4647 AcxC Acetone carboxyla 34.0 15 0.00032 29.9 0.2 13 132-145 68-80 (165)
66 PRK03824 hypA hydrogenase nick 34.0 26 0.00056 27.1 1.6 20 133-152 106-126 (135)
67 PHA00733 hypothetical protein 33.7 12 0.00027 28.7 -0.3 14 133-146 98-111 (128)
68 PRK07220 DNA topoisomerase I; 33.4 79 0.0017 30.9 5.1 44 104-150 604-652 (740)
69 TIGR03831 YgiT_finger YgiT-typ 32.7 40 0.00087 20.2 2.0 10 135-144 33-42 (46)
70 PRK00564 hypA hydrogenase nick 32.4 17 0.00036 27.5 0.2 18 135-152 89-107 (117)
71 PRK05654 acetyl-CoA carboxylas 31.6 21 0.00045 31.2 0.7 16 132-147 44-59 (292)
72 PRK14890 putative Zn-ribbon RN 31.4 23 0.0005 24.7 0.8 11 132-142 46-56 (59)
73 PF01927 Mut7-C: Mut7-C RNAse 31.4 25 0.00054 27.1 1.1 12 133-144 123-134 (147)
74 COG1997 RPL43A Ribosomal prote 31.2 35 0.00075 25.6 1.8 24 132-156 33-56 (89)
75 PF08882 Acetone_carb_G: Aceto 30.2 44 0.00096 26.0 2.2 19 125-144 15-33 (112)
76 PRK03681 hypA hydrogenase nick 28.4 33 0.00071 25.8 1.3 16 135-150 88-104 (114)
77 PRK14973 DNA topoisomerase I; 28.2 78 0.0017 32.1 4.1 43 106-150 604-653 (936)
78 PF06347 SH3_4: Bacterial SH3 28.1 78 0.0017 20.0 2.9 29 121-151 14-43 (55)
79 PF00301 Rubredoxin: Rubredoxi 27.8 31 0.00068 22.6 0.9 11 135-145 2-12 (47)
80 PF01155 HypA: Hydrogenase exp 27.4 22 0.00047 26.6 0.1 18 135-152 87-105 (113)
81 cd00730 rubredoxin Rubredoxin; 27.3 34 0.00074 22.6 1.1 12 135-146 2-13 (50)
82 PRK12380 hydrogenase nickel in 26.9 38 0.00081 25.4 1.3 17 135-151 87-104 (113)
83 PRK04860 hypothetical protein; 26.5 43 0.00093 26.9 1.7 18 132-149 141-158 (160)
84 PF05605 zf-Di19: Drought indu 26.4 31 0.00067 22.2 0.7 11 134-144 2-12 (54)
85 PF05191 ADK_lid: Adenylate ki 26.4 23 0.00049 21.9 0.1 14 137-150 4-17 (36)
86 COG1996 RPC10 DNA-directed RNA 26.0 55 0.0012 21.9 1.8 18 129-146 19-36 (49)
87 COG1773 Rubredoxin [Energy pro 25.9 36 0.00077 23.3 1.0 13 134-146 3-15 (55)
88 PF03119 DNA_ligase_ZBD: NAD-d 25.5 62 0.0013 18.8 1.8 8 136-143 1-8 (28)
89 CHL00174 accD acetyl-CoA carbo 25.5 24 0.00052 31.2 0.1 16 132-147 55-70 (296)
90 KOG3623 Homeobox transcription 25.2 18 0.0004 36.4 -0.8 15 134-148 281-295 (1007)
91 COG1545 Predicted nucleic-acid 25.1 36 0.00078 26.5 1.0 24 122-145 13-40 (140)
92 TIGR00240 ATCase_reg aspartate 25.0 50 0.0011 26.7 1.8 26 124-149 119-147 (150)
93 PF14311 DUF4379: Domain of un 24.9 45 0.00097 21.6 1.3 11 136-146 30-40 (55)
94 PF12171 zf-C2H2_jaz: Zinc-fin 24.4 34 0.00075 19.0 0.6 11 135-145 2-12 (27)
95 COG4049 Uncharacterized protei 23.9 22 0.00048 25.0 -0.3 15 131-145 13-28 (65)
96 PF13451 zf-trcl: Probable zin 23.6 53 0.0011 21.9 1.4 16 132-147 2-17 (49)
97 PF06170 DUF983: Protein of un 23.0 32 0.00068 25.0 0.3 18 134-151 8-25 (86)
98 COG1594 RPB9 DNA-directed RNA 23.0 1E+02 0.0023 23.3 3.1 27 119-145 78-111 (113)
99 TIGR00515 accD acetyl-CoA carb 22.8 28 0.00062 30.3 0.0 26 122-147 33-58 (285)
100 TIGR02300 FYDLN_acid conserved 22.5 39 0.00084 26.8 0.7 25 122-147 15-39 (129)
101 PHA00626 hypothetical protein 22.5 48 0.001 23.1 1.1 16 132-147 21-36 (59)
102 PF05876 Terminase_GpA: Phage 22.3 35 0.00075 32.1 0.5 13 135-147 201-213 (557)
103 COG3357 Predicted transcriptio 22.3 35 0.00075 25.9 0.4 15 133-147 57-71 (97)
104 PF01428 zf-AN1: AN1-like Zinc 22.1 42 0.00092 20.9 0.7 16 133-148 12-27 (43)
105 PF14354 Lar_restr_allev: Rest 21.9 66 0.0014 20.8 1.6 18 134-151 3-20 (61)
106 PF07282 OrfB_Zn_ribbon: Putat 21.9 92 0.002 20.6 2.4 16 129-144 41-56 (69)
107 PRK00420 hypothetical protein; 21.8 53 0.0012 25.2 1.3 22 126-148 33-54 (112)
108 TIGR00686 phnA alkylphosphonat 21.1 53 0.0012 25.4 1.2 17 129-145 14-30 (109)
109 PRK14138 NAD-dependent deacety 20.6 78 0.0017 26.5 2.2 69 72-144 78-153 (244)
110 PHA02825 LAP/PHD finger-like p 20.2 50 0.0011 27.2 0.9 22 128-149 42-63 (162)
No 1
>PLN02294 cytochrome c oxidase subunit Vb
Probab=100.00 E-value=8e-61 Score=385.37 Aligned_cols=150 Identities=68% Similarity=1.104 Sum_probs=131.1
Q ss_pred ChhhhhhhhhHHHHHHhhhcCCCCCCcCCcc-----ccccccc-ccccccccccCCC-CCccccccCCCCCccchHHHHH
Q 031632 1 MWRRICSSQLKAQALALAQYSCRSAPVNPSI-----ASRSLIS-RPLFASRHFSADS-GTSVKKRVEDVNPVATGHEREE 73 (156)
Q Consensus 1 m~rr~~~~~l~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~-~~~~~~~~~~~~~-~~~~~~~vpd~~EqATGlER~E 73 (156)
||||++++|||+||++.++.++++.+++.+. .+++.++ ++++|+|+|++.+ +++++++|+|+|||||||||+|
T Consensus 1 MwRr~~ss~L~~la~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~d~~~~ATGLER~E 80 (174)
T PLN02294 1 MWRRIVSSHLKTLAASVVAASPRRTVVATTRPLYLSRSRSSISASSSVFSRYFSSESADTAVKKRVEDVMPIATGHEREE 80 (174)
T ss_pred ChhhHHHHHHHHHHHhhcccCcccccccccccccccccccccCchhhhhhhccccccccccccccCCCchhhccchHHHH
Confidence 9999999999999988755544444321111 2344444 4489999999888 6889999999999999999999
Q ss_pred HHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeecCCCCCCCcceEEEEeecCCccccCCCCcEEEEeccC
Q 031632 74 LEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVVSGGS 150 (156)
Q Consensus 74 Lla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsh~v~Wf~L~kG~p~RC~eCG~~FkL~~~~ 150 (156)
|||+++|+|||||+++++++||||||+||||++++|||||+|+.++|+|+|+||||++|+|+||||||+||||+++.
T Consensus 81 Lla~leG~D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~fkL~~vG 157 (174)
T PLN02294 81 LEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVG 157 (174)
T ss_pred HHHHHcCCCccccccccCCCCCccCCcEeccCCCceEEeeCCCCCCCCceeEEEEecCCCceeCCCCCCEEEEEEeC
Confidence 99999999999999999999999999999999999999999965689999999999999999999999999999875
No 2
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=100.00 E-value=4.6e-47 Score=281.43 Aligned_cols=95 Identities=46% Similarity=0.821 Sum_probs=90.9
Q ss_pred cccccCCCCCccchHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeecCCCCCCCcceEEEEeecCCc
Q 031632 55 VKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKP 134 (156)
Q Consensus 55 ~~~~vpd~~EqATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsh~v~Wf~L~kG~p 134 (156)
..|+||||+||||||||+||+|+++|+|+|+|+++++++||++||+||||++++|||||+|+| |+|+|+||||++|+|
T Consensus 2 ~~g~vp~d~e~aTGlEr~ELl~~~~G~d~f~~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~--~~h~v~W~~l~~g~~ 79 (97)
T cd00924 2 AEGEVPTDLEQATGLERKELLAKLEGIDDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEP--DSHDVIWMWLEKGKP 79 (97)
T ss_pred CCcccCCchHhhhccHHHHHHHHHcCCccccccccccCCCCccCCeEecCCCCCeEEeeeCCC--CCceEEEEEEeCCCc
Confidence 468999999999999999999999999999999999999999999999999999999999965 699999999999999
Q ss_pred cccCCCCcEEEEeccCc
Q 031632 135 HECPVCSQYFVVSGGSN 151 (156)
Q Consensus 135 ~RC~eCG~~FkL~~~~~ 151 (156)
+||++|||||||++++.
T Consensus 80 ~rC~eCG~~fkL~~v~~ 96 (97)
T cd00924 80 KRCPECGHVFKLVDVGP 96 (97)
T ss_pred eeCCCCCcEEEEEECCC
Confidence 99999999999999863
No 3
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=100.00 E-value=1.5e-46 Score=297.56 Aligned_cols=98 Identities=49% Similarity=0.864 Sum_probs=93.1
Q ss_pred CCccccccCCCCCccchHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeecCCCCCCCcceEEEEeec
Q 031632 52 GTSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEK 131 (156)
Q Consensus 52 ~~~~~~~vpd~~EqATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsh~v~Wf~L~k 131 (156)
.....|.||||+||||||||+|||++++|.|||||+.+++++|||++||||||+||+|||||.| ++|+|+|+||||+|
T Consensus 53 ~~~~~g~vpddle~aTGlEk~eLla~l~G~d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c--~eD~~~V~Wmwl~K 130 (153)
T KOG3352|consen 53 PMAKGGGVPDDLEQATGLEKEELLAELEGRDPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGC--EEDSHAVVWMWLEK 130 (153)
T ss_pred ccccCCCCCCchhhhhhHHHHHHHHHhhCCCccccccccCCCCcccCCccccccCCceEEeecc--cCCCcceEEEEEEc
Confidence 3667899999999999999999999999999999999999999999999999999999999977 58999999999999
Q ss_pred CCccccCCCCcEEEEeccCc
Q 031632 132 GKPHECPVCSQYFVVSGGSN 151 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~~~~~ 151 (156)
|+++|||||||||||+.+..
T Consensus 131 ge~~rc~eCG~~fkL~~v~~ 150 (153)
T KOG3352|consen 131 GETQRCPECGHYFKLVPVGP 150 (153)
T ss_pred CCcccCCcccceEEeeecCC
Confidence 99999999999999998753
No 4
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=100.00 E-value=1.6e-46 Score=293.08 Aligned_cols=98 Identities=47% Similarity=0.850 Sum_probs=71.8
Q ss_pred CccccccCCCCCccchHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeecCCCCCCCcceEEEEeecC
Q 031632 53 TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKG 132 (156)
Q Consensus 53 ~~~~~~vpd~~EqATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsh~v~Wf~L~kG 132 (156)
....|+|||++||||||||+||||+++|+|||||+++++++||+||||||||++++|||||+|+| +|+|+|+||||++|
T Consensus 32 ~a~~G~vptd~eqATGlER~Ella~~~G~D~Fd~~~~~~~~GT~e~P~lVpS~~~~RiVGC~g~~-~~sH~v~W~~l~~g 110 (136)
T PF01215_consen 32 GAKPGTVPTDLEQATGLEREELLAKLEGIDPFDMKPLKAPFGTKEDPILVPSYFDERIVGCTGEP-DDSHDVIWFWLHKG 110 (136)
T ss_dssp -----BS--HHHH--HHHHHHHHHHHTT--TT--S--B----SSSS-CEEEESSSCEEEEESSST-T-SSS-EEEEEETT
T ss_pred cccCCCCCChhHhhhHHHHHHHHHHhcCcCcccccCccCCCCCccCCeEccCCCCceEEeeccCC-CCcceeEEEEEeCC
Confidence 44678999999999999999999999999999999999999999999999999999999999987 67899999999999
Q ss_pred CccccCCCCcEEEEeccCc
Q 031632 133 KPHECPVCSQYFVVSGGSN 151 (156)
Q Consensus 133 ~p~RC~eCG~~FkL~~~~~ 151 (156)
+|+|||+||+||||+++.+
T Consensus 111 ~~~RCpeCG~~fkL~~vg~ 129 (136)
T PF01215_consen 111 KPQRCPECGQVFKLKYVGP 129 (136)
T ss_dssp SEEEETTTEEEEEEEE---
T ss_pred CccCCCCCCeEEEEEEcCC
Confidence 9999999999999999864
No 5
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=99.97 E-value=7.9e-31 Score=220.73 Aligned_cols=85 Identities=34% Similarity=0.573 Sum_probs=79.9
Q ss_pred ccchHHHHHHHHHHhCCCCCCCCCCCCCCCCCCCCeeeeccCCceeEeecCCCCCCCcceEEEEeecCCccccCCCCcEE
Q 031632 65 VATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYF 144 (156)
Q Consensus 65 qATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsh~v~Wf~L~kG~p~RC~eCG~~F 144 (156)
|....+.+.|+|.++|.+.+.++++.+|+||+|+|+||||++++|||||+|+++||+|+|+|||+++|+++|||+||+||
T Consensus 112 qi~~~~~~hm~~~le~y~~Lk~~~~~GPfGTkEdPiLVpSy~deRyVGCTGg~~EDeH~VvWFwLrEGkpqRCpECGqVF 191 (268)
T PTZ00043 112 QIVNEPSEHMLGLLELYEYLKSSSFVGPFGTIENPVLVPSVGTERVVGCTGGTGEHEHVPLWFRCREGFLYRCGECDQIF 191 (268)
T ss_pred eecCCchHHHHHHHHHHHhcCcCCCCCCCCCccCCeEeccCCCceEEeccCCCccCCceeEEEEecCCCCccCCCCCcEE
Confidence 34445889999999999999999999999999999999999999999999988899999999999999999999999999
Q ss_pred EEecc
Q 031632 145 VVSGG 149 (156)
Q Consensus 145 kL~~~ 149 (156)
||+++
T Consensus 192 KLVr~ 196 (268)
T PTZ00043 192 MLVRV 196 (268)
T ss_pred EEEEE
Confidence 99983
No 6
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=97.51 E-value=0.00011 Score=47.16 Aligned_cols=39 Identities=38% Similarity=0.758 Sum_probs=33.0
Q ss_pred CceeEeecCCCCCCCcceEEEEeec-CCccccCCCCcEEE
Q 031632 107 DKRIVGCPGGEGEDEHDVVWFWLEK-GKPHECPVCSQYFV 145 (156)
Q Consensus 107 ~~RiVGC~g~p~eDsh~v~Wf~L~k-G~p~RC~eCG~~Fk 145 (156)
+.|+|-|.|..++-.|-.+|+.|.+ +++..||.||.-|+
T Consensus 1 ~~~~v~CdG~~~~lgHPrVyl~l~~~~~~~~CpYCg~~yv 40 (40)
T PF10276_consen 1 DGRRVSCDGGGGALGHPRVYLNLDDEPGPVVCPYCGTRYV 40 (40)
T ss_dssp -SSEEEEEESSTTSCCCCEEEE-TTTTCEEEETTTTEEEE
T ss_pred CCcEEEeCCCCCCCCCCeEEEecCCCCCeEECCCCCCEEC
Confidence 4689999998767799999999999 58899999999885
No 7
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=96.32 E-value=0.0032 Score=48.76 Aligned_cols=44 Identities=36% Similarity=0.602 Sum_probs=38.4
Q ss_pred eccCCceeEeecCCCCCCCcceEEEEeecCCccccCCCCcEEEE
Q 031632 103 KSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVV 146 (156)
Q Consensus 103 pS~~~~RiVGC~g~p~eDsh~v~Wf~L~kG~p~RC~eCG~~FkL 146 (156)
|+.-+.|||.|-|+.++=-|-.+|+.|.|..++-|..||.-|.-
T Consensus 73 p~e~d~RVV~CdGg~~aLGHPkvyInLDk~~~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 73 PIEVDGRVVACDGGTPALGHPKVYINLDKPGPHICGYCGLRFVQ 116 (120)
T ss_pred hhhccceEEEecCCCCCCCCCeEEEEcCCCCCcccccchhhhhh
Confidence 34459999999998877799999999999889999999988753
No 8
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=93.60 E-value=0.14 Score=35.99 Aligned_cols=47 Identities=21% Similarity=0.397 Sum_probs=36.0
Q ss_pred CeeeeccCCceeEeecCCCCCCCcceEEEEeecCCccccCCCCcEEEEe
Q 031632 99 PAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVVS 147 (156)
Q Consensus 99 P~lVpS~~~~RiVGC~g~p~eDsh~v~Wf~L~kG~p~RC~eCG~~FkL~ 147 (156)
++.|....- -+-|.|..++-+|-=+|+-+.+..-.-||.||..|+|.
T Consensus 15 ~~~I~~~~~--~l~C~g~~~p~~HPrV~L~mg~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 15 HETIEIGDL--PLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred ceEEEeCCe--eEEcCCCCCCCCCCEEEEEcCCCCcEecCccccEEEec
Confidence 555544322 25799887778999999999665667799999999985
No 9
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=90.92 E-value=0.15 Score=32.08 Aligned_cols=26 Identities=31% Similarity=0.750 Sum_probs=16.2
Q ss_pred ecCCccccCCCCcEEEEeccCc--ceee
Q 031632 130 EKGKPHECPVCSQYFVVSGGSN--LICC 155 (156)
Q Consensus 130 ~kG~p~RC~eCG~~FkL~~~~~--~~~~ 155 (156)
++++-++|..||+...+.+... |+||
T Consensus 2 ~~~~~YkC~~CGniVev~~~g~g~lvCC 29 (36)
T PF06397_consen 2 KKGEFYKCEHCGNIVEVVHDGGGPLVCC 29 (36)
T ss_dssp -TTEEEE-TTT--EEEEEE--SS-EEET
T ss_pred CcccEEEccCCCCEEEEEECCCCCEEeC
Confidence 3577899999999998877654 7776
No 10
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=84.99 E-value=0.48 Score=26.90 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=12.0
Q ss_pred CCccccCCCCcEEE
Q 031632 132 GKPHECPVCSQYFV 145 (156)
Q Consensus 132 G~p~RC~eCG~~Fk 145 (156)
.+|+.|++||..|.
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 46999999999884
No 11
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.56 E-value=1.2 Score=28.18 Aligned_cols=20 Identities=15% Similarity=0.481 Sum_probs=17.1
Q ss_pred ccccCCCCcEEEEeccCcce
Q 031632 134 PHECPVCSQYFVVSGGSNLI 153 (156)
Q Consensus 134 p~RC~eCG~~FkL~~~~~~~ 153 (156)
..+||.||+-+.++..++++
T Consensus 21 ~~~Cp~CG~~~~~~~~~~~v 40 (46)
T PRK00398 21 GVRCPYCGYRILFKERPPVV 40 (46)
T ss_pred ceECCCCCCeEEEccCCCcc
Confidence 78999999998888887765
No 12
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=84.10 E-value=0.45 Score=43.26 Aligned_cols=17 Identities=35% Similarity=0.778 Sum_probs=15.5
Q ss_pred eecCCccccCCCCcEEE
Q 031632 129 LEKGKPHECPVCSQYFV 145 (156)
Q Consensus 129 L~kG~p~RC~eCG~~Fk 145 (156)
.-|+||+||++||+-||
T Consensus 393 ~~~~KPYrCevC~KRYK 409 (423)
T COG5189 393 SAKDKPYRCEVCDKRYK 409 (423)
T ss_pred cccCCceeccccchhhc
Confidence 77899999999999887
No 13
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=79.67 E-value=0.93 Score=25.09 Aligned_cols=12 Identities=42% Similarity=1.041 Sum_probs=10.6
Q ss_pred ccccCCCCcEEE
Q 031632 134 PHECPVCSQYFV 145 (156)
Q Consensus 134 p~RC~eCG~~Fk 145 (156)
|++|.+|++.|.
T Consensus 1 ~~~C~~C~~~F~ 12 (27)
T PF13912_consen 1 PFECDECGKTFS 12 (27)
T ss_dssp SEEETTTTEEES
T ss_pred CCCCCccCCccC
Confidence 689999999994
No 14
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=78.98 E-value=0.73 Score=26.87 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=10.0
Q ss_pred ccccCCCCcEEE
Q 031632 134 PHECPVCSQYFV 145 (156)
Q Consensus 134 p~RC~eCG~~Fk 145 (156)
-.+||.||+.|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 467999999985
No 15
>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=78.75 E-value=1.6 Score=26.29 Aligned_cols=14 Identities=29% Similarity=0.546 Sum_probs=11.6
Q ss_pred cccCCCCcEEEEec
Q 031632 135 HECPVCSQYFVVSG 148 (156)
Q Consensus 135 ~RC~eCG~~FkL~~ 148 (156)
++|++||+.|.+..
T Consensus 6 y~C~~Cg~~fe~~~ 19 (41)
T smart00834 6 YRCEDCGHTFEVLQ 19 (41)
T ss_pred EEcCCCCCEEEEEE
Confidence 58999999887654
No 16
>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=77.77 E-value=1.2 Score=27.16 Aligned_cols=17 Identities=35% Similarity=0.956 Sum_probs=13.2
Q ss_pred eecCCccccCCCCcEEE
Q 031632 129 LEKGKPHECPVCSQYFV 145 (156)
Q Consensus 129 L~kG~p~RC~eCG~~Fk 145 (156)
+..+.+-||++||+.-.
T Consensus 12 ~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 12 LKPGDPIRCPECGHRIL 28 (32)
T ss_dssp BSTSSTSSBSSSS-SEE
T ss_pred cCCCCcEECCcCCCeEE
Confidence 77788999999998543
No 17
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=77.32 E-value=2.5 Score=25.29 Aligned_cols=25 Identities=36% Similarity=0.915 Sum_probs=18.9
Q ss_pred cCCccccCCCCcEEEEec--cCcceee
Q 031632 131 KGKPHECPVCSQYFVVSG--GSNLICC 155 (156)
Q Consensus 131 kG~p~RC~eCG~~FkL~~--~~~~~~~ 155 (156)
+++-++|..||+...+.+ ..+|.||
T Consensus 4 ~~~~ykC~~Cgniv~v~~~~~~~l~Cc 30 (34)
T TIGR00319 4 EGQVYKCEVCGNIVEVLHAGGGQLVCC 30 (34)
T ss_pred cCcEEEcCCCCcEEEEEECCCcceecc
Confidence 367899999999988665 3357776
No 18
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=75.33 E-value=3.3 Score=24.76 Aligned_cols=24 Identities=29% Similarity=0.798 Sum_probs=17.6
Q ss_pred CCccccCCCCcEEEEec--cCcceee
Q 031632 132 GKPHECPVCSQYFVVSG--GSNLICC 155 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~~--~~~~~~~ 155 (156)
++-++|..||+...+.+ ..++.||
T Consensus 2 ~~~ykC~~CGniv~v~~~~~~~l~Cc 27 (34)
T cd00974 2 LEVYKCEICGNIVEVLNVGGGTLVCC 27 (34)
T ss_pred CcEEEcCCCCcEEEEEECCCcceeec
Confidence 45689999999887665 3357776
No 19
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=74.91 E-value=2 Score=26.38 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=12.8
Q ss_pred cCCccccCCCCcEEE
Q 031632 131 KGKPHECPVCSQYFV 145 (156)
Q Consensus 131 kG~p~RC~eCG~~Fk 145 (156)
+|...||+.||+.|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 467889999999995
No 20
>PHA00616 hypothetical protein
Probab=74.68 E-value=0.72 Score=30.24 Aligned_cols=12 Identities=25% Similarity=0.542 Sum_probs=10.6
Q ss_pred ccccCCCCcEEE
Q 031632 134 PHECPVCSQYFV 145 (156)
Q Consensus 134 p~RC~eCG~~Fk 145 (156)
|++|++||..|.
T Consensus 1 pYqC~~CG~~F~ 12 (44)
T PHA00616 1 MYQCLRCGGIFR 12 (44)
T ss_pred CCccchhhHHHh
Confidence 689999999885
No 21
>PLN00128 Succinate dehydrogenase [ubiquinone] flavoprotein subunit
Probab=73.65 E-value=2.2 Score=40.41 Aligned_cols=21 Identities=38% Similarity=0.521 Sum_probs=17.0
Q ss_pred ChhhhhhhhhHHHHHHhhhcC
Q 031632 1 MWRRICSSQLKAQALALAQYS 21 (156)
Q Consensus 1 m~rr~~~~~l~~~~~~~~~~~ 21 (156)
||||-+..-|+-||+++++++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~ 21 (635)
T PLN00128 1 MWRRCVARGLRLLASSSASSS 21 (635)
T ss_pred CcccchhhHHHHHhhhhcCCC
Confidence 999999999999997664444
No 22
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=72.80 E-value=2.5 Score=25.54 Aligned_cols=19 Identities=32% Similarity=1.020 Sum_probs=8.4
Q ss_pred ccCCCCcEEEEeccCccee
Q 031632 136 ECPVCSQYFVVSGGSNLIC 154 (156)
Q Consensus 136 RC~eCG~~FkL~~~~~~~~ 154 (156)
.||.||.-|.+.+...+||
T Consensus 4 ~Cp~C~se~~y~D~~~~vC 22 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVC 22 (30)
T ss_dssp --TTT-----EE-SSSEEE
T ss_pred CCCCCCCcceeccCCEEeC
Confidence 5777777777777777777
No 23
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=70.55 E-value=3.1 Score=35.40 Aligned_cols=33 Identities=18% Similarity=0.539 Sum_probs=17.0
Q ss_pred CCCCcceEEEE-eecCCccc---cCCCCcEEEEeccC
Q 031632 118 GEDEHDVVWFW-LEKGKPHE---CPVCSQYFVVSGGS 150 (156)
Q Consensus 118 ~eDsh~v~Wf~-L~kG~p~R---C~eCG~~FkL~~~~ 150 (156)
|++++.-.|+. .+....+| |..||.|+|..+.+
T Consensus 218 g~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~ 254 (290)
T PF04216_consen 218 GNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDRE 254 (290)
T ss_dssp ---SS-EEE--------SEEEEEETTTTEEEEEEETT
T ss_pred CCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhh
Confidence 45666655554 44444455 99999999999843
No 24
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=70.43 E-value=2.2 Score=22.67 Aligned_cols=11 Identities=36% Similarity=1.171 Sum_probs=9.5
Q ss_pred cccCCCCcEEE
Q 031632 135 HECPVCSQYFV 145 (156)
Q Consensus 135 ~RC~eCG~~Fk 145 (156)
++|++||..|.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 47999999985
No 25
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=68.67 E-value=6.5 Score=25.33 Aligned_cols=20 Identities=10% Similarity=0.300 Sum_probs=14.3
Q ss_pred eecCCccccCCCCcEEEEec
Q 031632 129 LEKGKPHECPVCSQYFVVSG 148 (156)
Q Consensus 129 L~kG~p~RC~eCG~~FkL~~ 148 (156)
+..+.+.|||+||+--..+.
T Consensus 14 ~~~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 14 IKSKDVVRCRECGYRILYKK 33 (44)
T ss_pred cCCCCceECCCCCceEEEEe
Confidence 44678899999998544443
No 26
>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=68.12 E-value=3.6 Score=25.87 Aligned_cols=13 Identities=31% Similarity=0.618 Sum_probs=10.6
Q ss_pred cccCCCCcEEEEe
Q 031632 135 HECPVCSQYFVVS 147 (156)
Q Consensus 135 ~RC~eCG~~FkL~ 147 (156)
++|..||+.|...
T Consensus 6 y~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 6 YRCEECGHEFEVL 18 (42)
T ss_pred EEeCCCCCEEEEE
Confidence 6899999988743
No 27
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=65.96 E-value=4.5 Score=25.08 Aligned_cols=24 Identities=29% Similarity=0.744 Sum_probs=13.4
Q ss_pred cCCccccCCCCcEEEEeccCccee
Q 031632 131 KGKPHECPVCSQYFVVSGGSNLIC 154 (156)
Q Consensus 131 kG~p~RC~eCG~~FkL~~~~~~~~ 154 (156)
+|...+|++||..+-.....-.+|
T Consensus 5 ~~~~~~C~~C~~~~~~~~dG~~yC 28 (36)
T PF11781_consen 5 RGPNEPCPVCGSRWFYSDDGFYYC 28 (36)
T ss_pred ccCCCcCCCCCCeEeEccCCEEEh
Confidence 455556777776644444444444
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=64.11 E-value=3.8 Score=21.07 Aligned_cols=11 Identities=36% Similarity=1.219 Sum_probs=7.3
Q ss_pred cccCCCCcEEE
Q 031632 135 HECPVCSQYFV 145 (156)
Q Consensus 135 ~RC~eCG~~Fk 145 (156)
+.|+.||..|.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 47999999885
No 29
>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=63.49 E-value=5.2 Score=25.43 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=11.2
Q ss_pred cccCCCCcEEEEec
Q 031632 135 HECPVCSQYFVVSG 148 (156)
Q Consensus 135 ~RC~eCG~~FkL~~ 148 (156)
++|.+||+.|.+..
T Consensus 6 y~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 6 YRCTACGHRFEVLQ 19 (52)
T ss_pred EEeCCCCCEeEEEE
Confidence 57999999888653
No 30
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=62.32 E-value=7.1 Score=25.77 Aligned_cols=31 Identities=23% Similarity=0.504 Sum_probs=20.2
Q ss_pred eEEEEeecCCc----cccCCCCcEEEEeccCccee
Q 031632 124 VVWFWLEKGKP----HECPVCSQYFVVSGGSNLIC 154 (156)
Q Consensus 124 v~Wf~L~kG~p----~RC~eCG~~FkL~~~~~~~~ 154 (156)
..|+.+..|+. ..||.||.-|...+.+.+.|
T Consensus 6 ~~~y~v~~~~v~~~~~fCP~Cg~~~m~~~~~r~~C 40 (50)
T PRK00432 6 REYYEVDGGKVKRKNKFCPRCGSGFMAEHLDRWHC 40 (50)
T ss_pred eeeEEECCCEEEEccCcCcCCCcchheccCCcEEC
Confidence 35667766652 24999988666666666665
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=58.97 E-value=5.3 Score=30.02 Aligned_cols=35 Identities=23% Similarity=0.427 Sum_probs=23.5
Q ss_pred eeEeecCCCCCCCcceEEEEeecCCccc-cCCCCcEEEEe
Q 031632 109 RIVGCPGGEGEDEHDVVWFWLEKGKPHE-CPVCSQYFVVS 147 (156)
Q Consensus 109 RiVGC~g~p~eDsh~v~Wf~L~kG~p~R-C~eCG~~FkL~ 147 (156)
.++=|.-- + +..+=..+.+|++++ |+.||++|.-+
T Consensus 20 t~f~CP~C-g---e~~v~v~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRC-G---KVSISVKIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCC-C---CeEeeeecCCCcceEECCCCCCccCEE
Confidence 56667531 2 244555566788887 99999998753
No 32
>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=58.24 E-value=7.9 Score=24.13 Aligned_cols=8 Identities=38% Similarity=1.169 Sum_probs=4.0
Q ss_pred ccCCCCcE
Q 031632 136 ECPVCSQY 143 (156)
Q Consensus 136 RC~eCG~~ 143 (156)
+||.||.-
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 35555553
No 33
>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=58.00 E-value=7.2 Score=23.39 Aligned_cols=14 Identities=36% Similarity=0.800 Sum_probs=11.9
Q ss_pred cccCCCCcEEEEec
Q 031632 135 HECPVCSQYFVVSG 148 (156)
Q Consensus 135 ~RC~eCG~~FkL~~ 148 (156)
.+||.||..|++..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 46999999999874
No 34
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.38 E-value=7.7 Score=24.98 Aligned_cols=20 Identities=15% Similarity=0.343 Sum_probs=17.2
Q ss_pred cccCCCCcEEEEeccCccee
Q 031632 135 HECPVCSQYFVVSGGSNLIC 154 (156)
Q Consensus 135 ~RC~eCG~~FkL~~~~~~~~ 154 (156)
++|.+||.-|.++..+.+-|
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC 22 (44)
T smart00659 3 YICGECGRENEIKSKDVVRC 22 (44)
T ss_pred EECCCCCCEeecCCCCceEC
Confidence 68999999999997777766
No 35
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=56.26 E-value=7.9 Score=26.29 Aligned_cols=30 Identities=20% Similarity=0.564 Sum_probs=22.0
Q ss_pred EEEEeecCCc----cccCCCCc-EEEEeccCccee
Q 031632 125 VWFWLEKGKP----HECPVCSQ-YFVVSGGSNLIC 154 (156)
Q Consensus 125 ~Wf~L~kG~p----~RC~eCG~-~FkL~~~~~~~~ 154 (156)
.|..+..++. ..||-||- +|...|.+-+.|
T Consensus 6 ~yY~v~~~kv~rk~~~CPrCG~gvfmA~H~dR~~C 40 (51)
T COG1998 6 KYYEVDDEKVKRKNRFCPRCGPGVFMADHKDRWAC 40 (51)
T ss_pred eEEEEcCCcEEEccccCCCCCCcchhhhcCceeEe
Confidence 4555665543 44999997 999988888777
No 36
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=55.92 E-value=21 Score=27.09 Aligned_cols=41 Identities=17% Similarity=0.271 Sum_probs=24.3
Q ss_pred eeccCCceeEeecCCCCCCCcceEEEEeecCCccccCCCCcEE
Q 031632 102 VKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYF 144 (156)
Q Consensus 102 VpS~~~~RiVGC~g~p~eDsh~v~Wf~L~kG~p~RC~eCG~~F 144 (156)
..+.+. +.+||..+|.-|-...- --..++....||+||+-.
T Consensus 30 ~~~~~g-~f~gCs~yP~C~~~~~~-~~~~~~~~~~Cp~C~~~~ 70 (140)
T COG0551 30 KFGKYG-IFLGCSNYPKCDYYEPE-KAIAEKTGVKCPKCGKGL 70 (140)
T ss_pred EEccCC-eEEEeCCCCCCCCCccc-ccccccCceeCCCCCCCc
Confidence 355555 99999999843321111 111224458899999633
No 37
>PHA02768 hypothetical protein; Provisional
Probab=55.15 E-value=5.4 Score=27.25 Aligned_cols=12 Identities=33% Similarity=1.193 Sum_probs=9.8
Q ss_pred cccCCCCcEEEE
Q 031632 135 HECPVCSQYFVV 146 (156)
Q Consensus 135 ~RC~eCG~~FkL 146 (156)
++|++||..|..
T Consensus 6 y~C~~CGK~Fs~ 17 (55)
T PHA02768 6 YECPICGEIYIK 17 (55)
T ss_pred cCcchhCCeecc
Confidence 689999998864
No 38
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.03 E-value=8.2 Score=23.44 Aligned_cols=10 Identities=40% Similarity=1.421 Sum_probs=8.0
Q ss_pred CccccCCCCc
Q 031632 133 KPHECPVCSQ 142 (156)
Q Consensus 133 ~p~RC~eCG~ 142 (156)
.|.+||.||+
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4778999987
No 39
>PF14353 CpXC: CpXC protein
Probab=52.17 E-value=7.1 Score=29.11 Aligned_cols=15 Identities=27% Similarity=0.718 Sum_probs=12.1
Q ss_pred ccccCCCCcEEEEec
Q 031632 134 PHECPVCSQYFVVSG 148 (156)
Q Consensus 134 p~RC~eCG~~FkL~~ 148 (156)
-+.||.||+-|.+.+
T Consensus 38 ~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY 52 (128)
T ss_pred EEECCCCCCceecCC
Confidence 367999999998754
No 40
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=51.96 E-value=8.7 Score=23.55 Aligned_cols=16 Identities=31% Similarity=0.814 Sum_probs=12.7
Q ss_pred ecCCccccCCCCcEEE
Q 031632 130 EKGKPHECPVCSQYFV 145 (156)
Q Consensus 130 ~kG~p~RC~eCG~~Fk 145 (156)
.+|.-.+|+.||+.|.
T Consensus 21 ~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 21 PKGRKVRCSKCGHVFF 36 (36)
T ss_pred CCCcEEECCCCCCEeC
Confidence 3566788999999883
No 41
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=49.76 E-value=18 Score=32.11 Aligned_cols=30 Identities=13% Similarity=0.376 Sum_probs=22.1
Q ss_pred CcceEEEEeecCC-ccc---cCCCCcEEEEeccC
Q 031632 121 EHDVVWFWLEKGK-PHE---CPVCSQYFVVSGGS 150 (156)
Q Consensus 121 sh~v~Wf~L~kG~-p~R---C~eCG~~FkL~~~~ 150 (156)
...+.++.++.++ ..| |..|+.|.|..+.+
T Consensus 235 ~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~ 268 (309)
T PRK03564 235 SGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQE 268 (309)
T ss_pred CCceeeeeecCCCcceEeeecccccccceecccc
Confidence 4467777787653 444 99999999998664
No 42
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=48.54 E-value=11 Score=25.52 Aligned_cols=14 Identities=21% Similarity=0.705 Sum_probs=11.9
Q ss_pred cccCCCCcEEEEec
Q 031632 135 HECPVCSQYFVVSG 148 (156)
Q Consensus 135 ~RC~eCG~~FkL~~ 148 (156)
-.|++||.+|-+.+
T Consensus 54 L~Cp~c~r~YPI~d 67 (68)
T PF03966_consen 54 LICPECGREYPIRD 67 (68)
T ss_dssp EEETTTTEEEEEET
T ss_pred EEcCCCCCEEeCCC
Confidence 56999999998865
No 43
>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=47.80 E-value=10 Score=22.00 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=9.9
Q ss_pred cCCccccCCCCc
Q 031632 131 KGKPHECPVCSQ 142 (156)
Q Consensus 131 kG~p~RC~eCG~ 142 (156)
++.++.||.||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 477899999994
No 44
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=47.59 E-value=7.4 Score=27.35 Aligned_cols=16 Identities=25% Similarity=0.522 Sum_probs=13.9
Q ss_pred EeecCCccccCCCCcE
Q 031632 128 WLEKGKPHECPVCSQY 143 (156)
Q Consensus 128 ~L~kG~p~RC~eCG~~ 143 (156)
.|..|.+.||-|||+-
T Consensus 31 ~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 31 TLKRGDVIRCRECGYR 46 (62)
T ss_pred cccCCCcEehhhcchH
Confidence 4788999999999974
No 45
>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=46.56 E-value=8 Score=29.32 Aligned_cols=25 Identities=28% Similarity=0.574 Sum_probs=19.7
Q ss_pred cceEEEEeecCCccccCCCCcEEEEe
Q 031632 122 HDVVWFWLEKGKPHECPVCSQYFVVS 147 (156)
Q Consensus 122 h~v~Wf~L~kG~p~RC~eCG~~FkL~ 147 (156)
.-..|+-|.| .|..||.||..|.+.
T Consensus 15 CG~kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 15 CGAKFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcchhccCCC-CCccCCCCCCccCcc
Confidence 4557777888 778899999888776
No 46
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=45.99 E-value=13 Score=31.55 Aligned_cols=31 Identities=16% Similarity=0.252 Sum_probs=20.0
Q ss_pred CCCcceEEEEeecCCccccCCCCcEE--EEeccC
Q 031632 119 EDEHDVVWFWLEKGKPHECPVCSQYF--VVSGGS 150 (156)
Q Consensus 119 eDsh~v~Wf~L~kG~p~RC~eCG~~F--kL~~~~ 150 (156)
+-.|.++=..-.. ...||.+||++| .++-.+
T Consensus 16 ev~hEVik~~g~~-~lvrC~eCG~V~~~~i~~~k 48 (201)
T COG1326 16 EVSHEVIKERGRE-PLVRCEECGTVHPAIIKTPK 48 (201)
T ss_pred hhhHHHHHhcCCc-eEEEccCCCcEeeceeeccc
Confidence 4456555543222 778999999999 555443
No 47
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=45.85 E-value=6 Score=27.15 Aligned_cols=24 Identities=17% Similarity=0.360 Sum_probs=11.7
Q ss_pred cceEEEEeecCCccccCCCCcEEE
Q 031632 122 HDVVWFWLEKGKPHECPVCSQYFV 145 (156)
Q Consensus 122 h~v~Wf~L~kG~p~RC~eCG~~Fk 145 (156)
..-.|......+|.-||+||..+.
T Consensus 12 ~~~~k~~~~S~~PatCP~C~a~~~ 35 (54)
T PF09237_consen 12 TKKPKSKSQSEQPATCPICGAVIR 35 (54)
T ss_dssp ----CCCCTTS--EE-TTT--EES
T ss_pred hhHHHHhhccCCCCCCCcchhhcc
Confidence 344566677788999999998753
No 48
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.11 E-value=10 Score=26.66 Aligned_cols=11 Identities=45% Similarity=1.222 Sum_probs=9.7
Q ss_pred cCCccccCCCC
Q 031632 131 KGKPHECPVCS 141 (156)
Q Consensus 131 kG~p~RC~eCG 141 (156)
.|.|++||.||
T Consensus 47 ~g~~Y~Cp~CG 57 (61)
T COG2888 47 LGNPYRCPKCG 57 (61)
T ss_pred cCCceECCCcC
Confidence 38899999998
No 49
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=44.76 E-value=23 Score=23.49 Aligned_cols=30 Identities=23% Similarity=0.671 Sum_probs=19.1
Q ss_pred EEEEeecC-C----ccccC--CCCc-EEEEeccCccee
Q 031632 125 VWFWLEKG-K----PHECP--VCSQ-YFVVSGGSNLIC 154 (156)
Q Consensus 125 ~Wf~L~kG-~----p~RC~--eCG~-~FkL~~~~~~~~ 154 (156)
.|+.+.++ + -..|| +||. +|...+.+...|
T Consensus 4 kyYkvd~~Gkv~r~rk~CP~~~CG~GvFMA~H~dR~~C 41 (47)
T PF01599_consen 4 KYYKVDENGKVKRLRKECPSPRCGAGVFMAEHKDRHYC 41 (47)
T ss_dssp --CEEETTTEEEESSEE-TSTTTTSSSEEEE-SSEEEE
T ss_pred eEEEECCCCcEEEhhhcCCCcccCCceEeeecCCCccC
Confidence 45666654 3 24499 9999 899999887776
No 50
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=43.28 E-value=12 Score=23.03 Aligned_cols=11 Identities=45% Similarity=1.096 Sum_probs=8.9
Q ss_pred CccccCCCCcE
Q 031632 133 KPHECPVCSQY 143 (156)
Q Consensus 133 ~p~RC~eCG~~ 143 (156)
+|.+||.||+-
T Consensus 1 ~~~~Cp~Cg~~ 11 (47)
T PF14690_consen 1 KPPRCPHCGSP 11 (47)
T ss_pred CCccCCCcCCC
Confidence 47899999954
No 51
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=43.13 E-value=9.5 Score=35.92 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=9.9
Q ss_pred cccCCCCcEEE
Q 031632 135 HECPVCSQYFV 145 (156)
Q Consensus 135 ~RC~eCG~~Fk 145 (156)
+|||||+++|-
T Consensus 296 YrCPEC~KVFs 306 (500)
T KOG3993|consen 296 YRCPECDKVFS 306 (500)
T ss_pred ecCCccccccc
Confidence 78999999994
No 52
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=41.86 E-value=13 Score=22.29 Aligned_cols=11 Identities=18% Similarity=0.528 Sum_probs=6.4
Q ss_pred ccccCCCCcEE
Q 031632 134 PHECPVCSQYF 144 (156)
Q Consensus 134 p~RC~eCG~~F 144 (156)
-+||..||.++
T Consensus 11 ~~rC~~Cg~~~ 21 (37)
T PF12172_consen 11 GQRCRDCGRVQ 21 (37)
T ss_dssp EEE-TTT--EE
T ss_pred EEEcCCCCCEe
Confidence 47899999985
No 53
>smart00355 ZnF_C2H2 zinc finger.
Probab=41.65 E-value=11 Score=19.24 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=8.8
Q ss_pred cccCCCCcEEE
Q 031632 135 HECPVCSQYFV 145 (156)
Q Consensus 135 ~RC~eCG~~Fk 145 (156)
++|++|+..|.
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 47999998875
No 54
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=41.62 E-value=15 Score=21.87 Aligned_cols=10 Identities=50% Similarity=1.288 Sum_probs=8.0
Q ss_pred CccccCCCCc
Q 031632 133 KPHECPVCSQ 142 (156)
Q Consensus 133 ~p~RC~eCG~ 142 (156)
.|.+||.||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 5778888886
No 55
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=40.18 E-value=21 Score=23.91 Aligned_cols=11 Identities=27% Similarity=0.981 Sum_probs=9.8
Q ss_pred ccCCCCcEEEE
Q 031632 136 ECPVCSQYFVV 146 (156)
Q Consensus 136 RC~eCG~~FkL 146 (156)
.||.||+.+.+
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 59999999986
No 56
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=40.06 E-value=20 Score=20.30 Aligned_cols=16 Identities=25% Similarity=0.559 Sum_probs=11.9
Q ss_pred ccccCCCCcEEEEecc
Q 031632 134 PHECPVCSQYFVVSGG 149 (156)
Q Consensus 134 p~RC~eCG~~FkL~~~ 149 (156)
...|+.||.-|.-..+
T Consensus 2 l~~C~~CgR~F~~~~l 17 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRL 17 (25)
T ss_pred CCcCCCCCCEECHHHH
Confidence 3579999999965443
No 57
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=39.89 E-value=44 Score=28.64 Aligned_cols=67 Identities=27% Similarity=0.293 Sum_probs=39.7
Q ss_pred HHHHHHHHhCCCC-C-----CCCCCCCCCCCCCCCeeeeccCCceeEeecCCCCCCCcceEEE--EeecCCccccCCCCc
Q 031632 71 REELEAELEGKNI-L-----EIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWF--WLEKGKPHECPVCSQ 142 (156)
Q Consensus 71 R~ELla~~~G~Dp-F-----d~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsh~v~Wf--~L~kG~p~RC~eCG~ 142 (156)
-.+++++++.... + ++|-+....|.+ .||.=+.+..-+-|+--. . ......+ ..+++.+.+|+.||.
T Consensus 80 ~H~~la~le~~~~~~~iiTQNiD~Lhe~AGs~---~Vi~lHGsl~~~~C~~C~-~-~~~~~~~~~~~~~~~~p~C~~Cg~ 154 (250)
T COG0846 80 AHYALAELEDKGKLLRIITQNIDGLHERAGSK---NVIELHGSLKRVRCSKCG-N-QYYDEDVIKFIEDGLIPRCPKCGG 154 (250)
T ss_pred HHHHHHHHhhcCCceEEEecccchHHHHcCCC---cEEEeccceeeeEeCCCc-C-ccchhhhhhhcccCCCCcCccCCC
Confidence 3456777775431 1 223334456777 899888888888887321 1 1111111 234556899999998
No 58
>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=39.86 E-value=28 Score=23.49 Aligned_cols=21 Identities=24% Similarity=0.332 Sum_probs=17.4
Q ss_pred CCccccCCCCcEEEEeccCcc
Q 031632 132 GKPHECPVCSQYFVVSGGSNL 152 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~~~~~~ 152 (156)
|....|++||.-|.++..+.+
T Consensus 20 GeiV~Cp~CGaeleVv~~~p~ 40 (54)
T TIGR01206 20 GELVICDECGAELEVVSLDPL 40 (54)
T ss_pred CCEEeCCCCCCEEEEEeCCCC
Confidence 777889999999998877664
No 59
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=37.74 E-value=16 Score=20.93 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=11.1
Q ss_pred CccccCCCCcEEE
Q 031632 133 KPHECPVCSQYFV 145 (156)
Q Consensus 133 ~p~RC~eCG~~Fk 145 (156)
.++.|..|+.+|.
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 3688999999997
No 60
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=37.46 E-value=29 Score=30.68 Aligned_cols=30 Identities=20% Similarity=0.432 Sum_probs=21.4
Q ss_pred CcceEEEEeec--CC-ccc---cCCCCcEEEEeccC
Q 031632 121 EHDVVWFWLEK--GK-PHE---CPVCSQYFVVSGGS 150 (156)
Q Consensus 121 sh~v~Wf~L~k--G~-p~R---C~eCG~~FkL~~~~ 150 (156)
+..+.++.++. ++ ..| |..|+.|.|..+.+
T Consensus 233 ~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~ 268 (305)
T TIGR01562 233 SKHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQE 268 (305)
T ss_pred CCceeeEeecCCCCCcceEEeeccccccchhhhccc
Confidence 34677777765 32 344 99999999998764
No 61
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.87 E-value=19 Score=28.42 Aligned_cols=27 Identities=22% Similarity=0.350 Sum_probs=18.3
Q ss_pred EEEEeecCCccccCCCCcEEEEec-cCcc
Q 031632 125 VWFWLEKGKPHECPVCSQYFVVSG-GSNL 152 (156)
Q Consensus 125 ~Wf~L~kG~p~RC~eCG~~FkL~~-~~~~ 152 (156)
.=.-+.+|+ -.|||||++|-+.+ ++|+
T Consensus 90 le~~v~EG~-l~CpetG~vfpI~~GIPNM 117 (124)
T KOG1088|consen 90 LEIDVIEGE-LVCPETGRVFPISDGIPNM 117 (124)
T ss_pred hhhhhccce-EecCCCCcEeecccCCccc
Confidence 334456777 56999999998754 4443
No 62
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=36.12 E-value=23 Score=23.91 Aligned_cols=19 Identities=37% Similarity=0.693 Sum_probs=16.7
Q ss_pred cccCCCCcEEEEeccCcce
Q 031632 135 HECPVCSQYFVVSGGSNLI 153 (156)
Q Consensus 135 ~RC~eCG~~FkL~~~~~~~ 153 (156)
-.||.||+-+......+||
T Consensus 14 ~~Cp~CGN~~vGngEG~li 32 (49)
T PF12677_consen 14 CKCPKCGNDKVGNGEGTLI 32 (49)
T ss_pred ccCcccCCcEeecCcceEE
Confidence 4599999999999988887
No 63
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=36.01 E-value=15 Score=30.05 Aligned_cols=14 Identities=36% Similarity=1.144 Sum_probs=9.9
Q ss_pred eecCC-ccccCCCCc
Q 031632 129 LEKGK-PHECPVCSQ 142 (156)
Q Consensus 129 L~kG~-p~RC~eCG~ 142 (156)
+.+|+ |-+||.||.
T Consensus 143 ~~~ge~P~~CPiCga 157 (166)
T COG1592 143 THEGEAPEVCPICGA 157 (166)
T ss_pred cccCCCCCcCCCCCC
Confidence 45555 677999985
No 64
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=34.41 E-value=20 Score=24.67 Aligned_cols=11 Identities=55% Similarity=1.476 Sum_probs=8.4
Q ss_pred Cccc-cCCCCcE
Q 031632 133 KPHE-CPVCSQY 143 (156)
Q Consensus 133 ~p~R-C~eCG~~ 143 (156)
+||+ |+.||.-
T Consensus 1 e~HkHC~~CG~~ 12 (59)
T PF09889_consen 1 EPHKHCPVCGKP 12 (59)
T ss_pred CCCCcCCcCCCc
Confidence 4666 9999964
No 65
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=34.05 E-value=15 Score=29.88 Aligned_cols=13 Identities=23% Similarity=0.577 Sum_probs=10.2
Q ss_pred CCccccCCCCcEEE
Q 031632 132 GKPHECPVCSQYFV 145 (156)
Q Consensus 132 G~p~RC~eCG~~Fk 145 (156)
++..|| +|||-|-
T Consensus 68 ~rv~rc-ecghsf~ 80 (165)
T COG4647 68 KRVIRC-ECGHSFG 80 (165)
T ss_pred ccEEEE-ecccccc
Confidence 457889 7999883
No 66
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.96 E-value=26 Score=27.11 Aligned_cols=20 Identities=25% Similarity=0.625 Sum_probs=13.4
Q ss_pred CccccCCCCcE-EEEeccCcc
Q 031632 133 KPHECPVCSQY-FVVSGGSNL 152 (156)
Q Consensus 133 ~p~RC~eCG~~-FkL~~~~~~ 152 (156)
.-.+||.||.. +.+...+.|
T Consensus 106 ~~~~CP~Cgs~~~~i~~G~el 126 (135)
T PRK03824 106 AFLKCPKCGSRDFEIVKGRGV 126 (135)
T ss_pred cCcCCcCCCCCCcEEecCceE
Confidence 44679999976 666655544
No 67
>PHA00733 hypothetical protein
Probab=33.72 E-value=12 Score=28.66 Aligned_cols=14 Identities=36% Similarity=0.850 Sum_probs=9.8
Q ss_pred CccccCCCCcEEEE
Q 031632 133 KPHECPVCSQYFVV 146 (156)
Q Consensus 133 ~p~RC~eCG~~FkL 146 (156)
.++.|++||.+|..
T Consensus 98 ~~~~C~~CgK~F~~ 111 (128)
T PHA00733 98 HSKVCPVCGKEFRN 111 (128)
T ss_pred cCccCCCCCCccCC
Confidence 46778888877753
No 68
>PRK07220 DNA topoisomerase I; Validated
Probab=33.44 E-value=79 Score=30.87 Aligned_cols=44 Identities=18% Similarity=0.276 Sum_probs=26.4
Q ss_pred ccCCceeEeecCCCCCCCcceEEEEeecCC----ccccCCCCc-EEEEeccC
Q 031632 104 SYYDKRIVGCPGGEGEDEHDVVWFWLEKGK----PHECPVCSQ-YFVVSGGS 150 (156)
Q Consensus 104 S~~~~RiVGC~g~p~eDsh~v~Wf~L~kG~----p~RC~eCG~-~FkL~~~~ 150 (156)
+....+.+||.+.| +-....|+. .+|. -..||+||. .++....+
T Consensus 604 ~r~g~~f~gCs~yp--~C~~~~~l~-~~g~~~~~~~~Cp~Cg~~~~k~~~~g 652 (740)
T PRK07220 604 SKRGSRFIGCEGYP--ECTFSLPLP-KSGQIIVTDKVCEAHGLNHIRIINGG 652 (740)
T ss_pred cCCCceEEEcCCCC--CCCceeeCC-CCCccccCCCCCCCCCCceEEEEecC
Confidence 44456789999876 344555542 1221 246999984 56655433
No 69
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=32.65 E-value=40 Score=20.21 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=8.0
Q ss_pred cccCCCCcEE
Q 031632 135 HECPVCSQYF 144 (156)
Q Consensus 135 ~RC~eCG~~F 144 (156)
..|++||..|
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 4699999866
No 70
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.36 E-value=17 Score=27.52 Aligned_cols=18 Identities=17% Similarity=0.619 Sum_probs=11.4
Q ss_pred cccCCCCcE-EEEeccCcc
Q 031632 135 HECPVCSQY-FVVSGGSNL 152 (156)
Q Consensus 135 ~RC~eCG~~-FkL~~~~~~ 152 (156)
.+||.||.. +++..-+.|
T Consensus 89 ~~CP~Cgs~~~~i~~G~El 107 (117)
T PRK00564 89 GVCEKCHSKNVIITQGNEM 107 (117)
T ss_pred CcCcCCCCCceEEecCCEE
Confidence 469999975 455554443
No 71
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=31.58 E-value=21 Score=31.24 Aligned_cols=16 Identities=25% Similarity=0.656 Sum_probs=13.0
Q ss_pred CCccccCCCCcEEEEe
Q 031632 132 GKPHECPVCSQYFVVS 147 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~ 147 (156)
..-+-||+||++|+|.
T Consensus 44 ~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 44 ANLNVCPKCGHHMRIS 59 (292)
T ss_pred hcCCCCCCCCCCeeCC
Confidence 3456799999999984
No 72
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=31.43 E-value=23 Score=24.65 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=9.2
Q ss_pred CCccccCCCCc
Q 031632 132 GKPHECPVCSQ 142 (156)
Q Consensus 132 G~p~RC~eCG~ 142 (156)
+.+++||.||-
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 78899999983
No 73
>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=31.42 E-value=25 Score=27.13 Aligned_cols=12 Identities=25% Similarity=0.850 Sum_probs=9.9
Q ss_pred CccccCCCCcEE
Q 031632 133 KPHECPVCSQYF 144 (156)
Q Consensus 133 ~p~RC~eCG~~F 144 (156)
+=.+|+.||++|
T Consensus 123 ~f~~C~~C~kiy 134 (147)
T PF01927_consen 123 EFWRCPGCGKIY 134 (147)
T ss_pred eEEECCCCCCEe
Confidence 356799999988
No 74
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=31.19 E-value=35 Score=25.60 Aligned_cols=24 Identities=29% Similarity=0.552 Sum_probs=18.8
Q ss_pred CCccccCCCCcEEEEeccCcceeeC
Q 031632 132 GKPHECPVCSQYFVVSGGSNLICCC 156 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~~~~~~~~~~ 156 (156)
-.+|.||+||.- .++++..-|=.|
T Consensus 33 ~~~~~Cp~C~~~-~VkR~a~GIW~C 56 (89)
T COG1997 33 RAKHVCPFCGRT-TVKRIATGIWKC 56 (89)
T ss_pred hcCCcCCCCCCc-ceeeeccCeEEc
Confidence 357889999998 888888777554
No 75
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=30.18 E-value=44 Score=25.96 Aligned_cols=19 Identities=32% Similarity=0.770 Sum_probs=14.4
Q ss_pred EEEEeecCCccccCCCCcEE
Q 031632 125 VWFWLEKGKPHECPVCSQYF 144 (156)
Q Consensus 125 ~Wf~L~kG~p~RC~eCG~~F 144 (156)
.|.--.+++..+| .|||.|
T Consensus 15 l~i~~~~~k~vkc-~CGh~f 33 (112)
T PF08882_consen 15 LWIVQKKDKVVKC-DCGHEF 33 (112)
T ss_pred EEEEEecCceeec-cCCCee
Confidence 4665556678889 799998
No 76
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.39 E-value=33 Score=25.80 Aligned_cols=16 Identities=19% Similarity=0.611 Sum_probs=10.0
Q ss_pred cccCCCCcE-EEEeccC
Q 031632 135 HECPVCSQY-FVVSGGS 150 (156)
Q Consensus 135 ~RC~eCG~~-FkL~~~~ 150 (156)
.+||.||.. ..+..-+
T Consensus 88 ~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 88 RRCPQCHGDMLRIVADD 104 (114)
T ss_pred CcCcCcCCCCcEEccCC
Confidence 569999875 4444433
No 77
>PRK14973 DNA topoisomerase I; Provisional
Probab=28.24 E-value=78 Score=32.08 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=25.0
Q ss_pred CCceeEeecCCCCCCCcceEEEEee-cCCc----cccCCCCc--EEEEeccC
Q 031632 106 YDKRIVGCPGGEGEDEHDVVWFWLE-KGKP----HECPVCSQ--YFVVSGGS 150 (156)
Q Consensus 106 ~~~RiVGC~g~p~eDsh~v~Wf~L~-kG~p----~RC~eCG~--~FkL~~~~ 150 (156)
...+.+||.++|+ -.....++-. .|+. ..||+||. .-.+.+.+
T Consensus 604 k~gkFigCS~Yp~--Ck~t~~L~~~~~g~~~~~~~~Cp~CG~p~~~~~r~Gr 653 (936)
T PRK14973 604 GSSQFIGCSGYPD--CTFNIGLPGTTWGWAIRTDEVCPIHHLNHVRLIRKGA 653 (936)
T ss_pred cCceeEECCCCCC--CCccccCCccccccCCCCCCCCCCCCCCceEEeecCC
Confidence 3456899999873 3334344322 2443 46999996 55555444
No 78
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=28.10 E-value=78 Score=20.00 Aligned_cols=29 Identities=28% Similarity=0.385 Sum_probs=21.2
Q ss_pred CcceEEEEeecCCccccCCC-CcEEEEeccCc
Q 031632 121 EHDVVWFWLEKGKPHECPVC-SQYFVVSGGSN 151 (156)
Q Consensus 121 sh~v~Wf~L~kG~p~RC~eC-G~~FkL~~~~~ 151 (156)
...++ +.|++|.+.+.-+| |.|.++. .++
T Consensus 14 ~~~vv-~~l~~g~~v~v~~~~~~W~~V~-~~g 43 (55)
T PF06347_consen 14 NSPVV-ARLEPGVPVRVIECRGGWCKVR-ADG 43 (55)
T ss_pred CCCEE-EEECCCCEEEEEEccCCeEEEE-ECC
Confidence 44455 88999998886666 7898887 554
No 79
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=27.83 E-value=31 Score=22.56 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=9.0
Q ss_pred cccCCCCcEEE
Q 031632 135 HECPVCSQYFV 145 (156)
Q Consensus 135 ~RC~eCG~~Fk 145 (156)
++|..||.+|-
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 57999998885
No 80
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=27.39 E-value=22 Score=26.59 Aligned_cols=18 Identities=28% Similarity=0.693 Sum_probs=10.2
Q ss_pred cccCCCCcE-EEEeccCcc
Q 031632 135 HECPVCSQY-FVVSGGSNL 152 (156)
Q Consensus 135 ~RC~eCG~~-FkL~~~~~~ 152 (156)
.+||.||.. +.+...+.|
T Consensus 87 ~~CP~Cgs~~~~i~~G~el 105 (113)
T PF01155_consen 87 FSCPRCGSPDVEIISGREL 105 (113)
T ss_dssp HH-SSSSSS-EEEEESS-E
T ss_pred CCCcCCcCCCcEEccCCeE
Confidence 568888876 356555544
No 81
>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=27.30 E-value=34 Score=22.61 Aligned_cols=12 Identities=25% Similarity=0.694 Sum_probs=9.7
Q ss_pred cccCCCCcEEEE
Q 031632 135 HECPVCSQYFVV 146 (156)
Q Consensus 135 ~RC~eCG~~FkL 146 (156)
++|..||.+|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 579999988864
No 82
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.89 E-value=38 Score=25.44 Aligned_cols=17 Identities=29% Similarity=0.714 Sum_probs=9.9
Q ss_pred cccCCCCcE-EEEeccCc
Q 031632 135 HECPVCSQY-FVVSGGSN 151 (156)
Q Consensus 135 ~RC~eCG~~-FkL~~~~~ 151 (156)
.+||.||.. +++..-+.
T Consensus 87 ~~CP~Cgs~~~~i~~G~E 104 (113)
T PRK12380 87 AQCPHCHGERLRVDTGDS 104 (113)
T ss_pred ccCcCCCCCCcEEccCCe
Confidence 458888864 44544443
No 83
>PRK04860 hypothetical protein; Provisional
Probab=26.52 E-value=43 Score=26.88 Aligned_cols=18 Identities=22% Similarity=0.499 Sum_probs=15.1
Q ss_pred CCccccCCCCcEEEEecc
Q 031632 132 GKPHECPVCSQYFVVSGG 149 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~~~ 149 (156)
.++++|..|++-|++...
T Consensus 141 ~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 141 EAVYRCRRCGETLVFKGE 158 (160)
T ss_pred CccEECCCCCceeEEecc
Confidence 468999999999998754
No 84
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=26.44 E-value=31 Score=22.24 Aligned_cols=11 Identities=36% Similarity=1.047 Sum_probs=7.6
Q ss_pred ccccCCCCcEE
Q 031632 134 PHECPVCSQYF 144 (156)
Q Consensus 134 p~RC~eCG~~F 144 (156)
.++||.||..|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 36788888843
No 85
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=26.35 E-value=23 Score=21.91 Aligned_cols=14 Identities=21% Similarity=0.764 Sum_probs=11.1
Q ss_pred cCCCCcEEEEeccC
Q 031632 137 CPVCSQYFVVSGGS 150 (156)
Q Consensus 137 C~eCG~~FkL~~~~ 150 (156)
|+.||..|-+.+-.
T Consensus 4 C~~Cg~~Yh~~~~p 17 (36)
T PF05191_consen 4 CPKCGRIYHIEFNP 17 (36)
T ss_dssp ETTTTEEEETTTB-
T ss_pred cCCCCCccccccCC
Confidence 99999999886543
No 86
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=26.04 E-value=55 Score=21.92 Aligned_cols=18 Identities=22% Similarity=0.586 Sum_probs=12.9
Q ss_pred eecCCccccCCCCcEEEE
Q 031632 129 LEKGKPHECPVCSQYFVV 146 (156)
Q Consensus 129 L~kG~p~RC~eCG~~FkL 146 (156)
+.++...|||.||+--.+
T Consensus 19 ~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 19 DQETRGIRCPYCGSRILV 36 (49)
T ss_pred hhccCceeCCCCCcEEEE
Confidence 345678899999985443
No 87
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.86 E-value=36 Score=23.34 Aligned_cols=13 Identities=23% Similarity=0.603 Sum_probs=9.6
Q ss_pred ccccCCCCcEEEE
Q 031632 134 PHECPVCSQYFVV 146 (156)
Q Consensus 134 p~RC~eCG~~FkL 146 (156)
-++|..||.+|-=
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 4678888888853
No 88
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=25.46 E-value=62 Score=18.85 Aligned_cols=8 Identities=50% Similarity=1.348 Sum_probs=3.2
Q ss_pred ccCCCCcE
Q 031632 136 ECPVCSQY 143 (156)
Q Consensus 136 RC~eCG~~ 143 (156)
.||+||+-
T Consensus 1 ~CP~C~s~ 8 (28)
T PF03119_consen 1 TCPVCGSK 8 (28)
T ss_dssp B-TTT--B
T ss_pred CcCCCCCE
Confidence 47788763
No 89
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.45 E-value=24 Score=31.24 Aligned_cols=16 Identities=25% Similarity=0.445 Sum_probs=13.0
Q ss_pred CCccccCCCCcEEEEe
Q 031632 132 GKPHECPVCSQYFVVS 147 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~ 147 (156)
..-+-||+||++|+|.
T Consensus 55 ~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 55 SKMNICEQCGYHLKMS 70 (296)
T ss_pred HcCCCCCCCCCCcCCC
Confidence 3456799999999985
No 90
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=25.20 E-value=18 Score=36.40 Aligned_cols=15 Identities=20% Similarity=0.567 Sum_probs=12.9
Q ss_pred ccccCCCCcEEEEec
Q 031632 134 PHECPVCSQYFVVSG 148 (156)
Q Consensus 134 p~RC~eCG~~FkL~~ 148 (156)
-+.|.|||..||.++
T Consensus 281 KFKCtECgKAFKfKH 295 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKH 295 (1007)
T ss_pred cccccccchhhhhHH
Confidence 577999999999875
No 91
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=25.07 E-value=36 Score=26.47 Aligned_cols=24 Identities=25% Similarity=0.635 Sum_probs=16.6
Q ss_pred cceEEEE--eecCCc--cccCCCCcEEE
Q 031632 122 HDVVWFW--LEKGKP--HECPVCSQYFV 145 (156)
Q Consensus 122 h~v~Wf~--L~kG~p--~RC~eCG~~Fk 145 (156)
....||+ |.+|+. .||+.||++|-
T Consensus 13 ~~~~~f~~~l~~~kl~g~kC~~CG~v~~ 40 (140)
T COG1545 13 EARSKFFKGLKEGKLLGTKCKKCGRVYF 40 (140)
T ss_pred chhhHHhhhhhhCcEEEEEcCCCCeEEc
Confidence 3344444 667774 77999999884
No 92
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=24.95 E-value=50 Score=26.72 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=17.7
Q ss_pred eEEEEeecCCc---cccCCCCcEEEEecc
Q 031632 124 VVWFWLEKGKP---HECPVCSQYFVVSGG 149 (156)
Q Consensus 124 v~Wf~L~kG~p---~RC~eCG~~FkL~~~ 149 (156)
..-|.|.+..+ .||..|++.|....+
T Consensus 119 ~~~F~v~~~~~~~~lrC~YCe~~~~~~~i 147 (150)
T TIGR00240 119 SSKFYVRSEEPDIALRCYYCEKEIEHNVV 147 (150)
T ss_pred CcEEEEecCCCceEEEEECCCCEEecceE
Confidence 34455544444 899999999986554
No 93
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.91 E-value=45 Score=21.56 Aligned_cols=11 Identities=27% Similarity=0.939 Sum_probs=9.3
Q ss_pred ccCCCCcEEEE
Q 031632 136 ECPVCSQYFVV 146 (156)
Q Consensus 136 RC~eCG~~FkL 146 (156)
+|+.|||-|+.
T Consensus 30 ~C~~Cgh~w~~ 40 (55)
T PF14311_consen 30 KCPKCGHEWKA 40 (55)
T ss_pred ECCCCCCeeEc
Confidence 69999998875
No 94
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=24.37 E-value=34 Score=18.95 Aligned_cols=11 Identities=36% Similarity=1.071 Sum_probs=9.0
Q ss_pred cccCCCCcEEE
Q 031632 135 HECPVCSQYFV 145 (156)
Q Consensus 135 ~RC~eCG~~Fk 145 (156)
+.|..|+.+|.
T Consensus 2 ~~C~~C~k~f~ 12 (27)
T PF12171_consen 2 FYCDACDKYFS 12 (27)
T ss_dssp CBBTTTTBBBS
T ss_pred CCcccCCCCcC
Confidence 57999998884
No 95
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=23.91 E-value=22 Score=24.99 Aligned_cols=15 Identities=33% Similarity=0.775 Sum_probs=11.9
Q ss_pred cCC-ccccCCCCcEEE
Q 031632 131 KGK-PHECPVCSQYFV 145 (156)
Q Consensus 131 kG~-p~RC~eCG~~Fk 145 (156)
+|+ -.|||-||..|.
T Consensus 13 DGE~~lrCPRC~~~FR 28 (65)
T COG4049 13 DGEEFLRCPRCGMVFR 28 (65)
T ss_pred CCceeeeCCchhHHHH
Confidence 465 478999999885
No 96
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=23.57 E-value=53 Score=21.93 Aligned_cols=16 Identities=31% Similarity=0.634 Sum_probs=12.8
Q ss_pred CCccccCCCCcEEEEe
Q 031632 132 GKPHECPVCSQYFVVS 147 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~ 147 (156)
+++..|..||.-|..-
T Consensus 2 Dk~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFT 17 (49)
T ss_pred CeeEEcccCCCeEEEe
Confidence 5677899999988764
No 97
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=22.98 E-value=32 Score=25.05 Aligned_cols=18 Identities=17% Similarity=0.549 Sum_probs=14.5
Q ss_pred ccccCCCCcEEEEeccCc
Q 031632 134 PHECPVCSQYFVVSGGSN 151 (156)
Q Consensus 134 p~RC~eCG~~FkL~~~~~ 151 (156)
..+|+.||+=|...+.+|
T Consensus 8 ~~~C~~CG~d~~~~~adD 25 (86)
T PF06170_consen 8 APRCPHCGLDYSHARADD 25 (86)
T ss_pred CCcccccCCccccCCcCc
Confidence 457999999988777665
No 98
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.98 E-value=1e+02 Score=23.25 Aligned_cols=27 Identities=15% Similarity=0.477 Sum_probs=18.3
Q ss_pred CCCcceEEEEeec---CCc----cccCCCCcEEE
Q 031632 119 EDEHDVVWFWLEK---GKP----HECPVCSQYFV 145 (156)
Q Consensus 119 eDsh~v~Wf~L~k---G~p----~RC~eCG~~Fk 145 (156)
-+.+.++|+.+.. ++| ++|..||+.|+
T Consensus 78 Cg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 78 CGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred CCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 3456666666653 443 66999999886
No 99
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=22.76 E-value=28 Score=30.32 Aligned_cols=26 Identities=15% Similarity=0.319 Sum_probs=16.8
Q ss_pred cceEEEEeecCCccccCCCCcEEEEe
Q 031632 122 HDVVWFWLEKGKPHECPVCSQYFVVS 147 (156)
Q Consensus 122 h~v~Wf~L~kG~p~RC~eCG~~FkL~ 147 (156)
+.++|-.--+.+-+-||.||++|+|.
T Consensus 33 ~~~~~~~~l~~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 33 GQVLYTKELERNLEVCPKCDHHMRMD 58 (285)
T ss_pred cchhhHHHHHhhCCCCCCCCCcCcCC
Confidence 34444432234447799999999983
No 100
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. 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=22.51 E-value=39 Score=26.84 Aligned_cols=25 Identities=16% Similarity=0.347 Sum_probs=19.3
Q ss_pred cceEEEEeecCCccccCCCCcEEEEe
Q 031632 122 HDVVWFWLEKGKPHECPVCSQYFVVS 147 (156)
Q Consensus 122 h~v~Wf~L~kG~p~RC~eCG~~FkL~ 147 (156)
.-..|+-|.| .|.-||.||..|.+.
T Consensus 15 cg~kFYDLnk-~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 15 TGSKFYDLNR-RPAVSPYTGEQFPPE 39 (129)
T ss_pred cCccccccCC-CCccCCCcCCccCcc
Confidence 4456777777 788899999988765
No 101
>PHA00626 hypothetical protein
Probab=22.45 E-value=48 Score=23.13 Aligned_cols=16 Identities=13% Similarity=0.079 Sum_probs=12.8
Q ss_pred CCccccCCCCcEEEEe
Q 031632 132 GKPHECPVCSQYFVVS 147 (156)
Q Consensus 132 G~p~RC~eCG~~FkL~ 147 (156)
-+.+.|+.||..|.-+
T Consensus 21 snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 21 SDDYVCCDCGYNDSKD 36 (59)
T ss_pred CcceEcCCCCCeechh
Confidence 4678899999998643
No 102
>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=22.33 E-value=35 Score=32.11 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=11.5
Q ss_pred cccCCCCcEEEEe
Q 031632 135 HECPVCSQYFVVS 147 (156)
Q Consensus 135 ~RC~eCG~~FkL~ 147 (156)
..||+||++|.|+
T Consensus 201 vpCPhCg~~~~l~ 213 (557)
T PF05876_consen 201 VPCPHCGEEQVLE 213 (557)
T ss_pred ccCCCCCCCcccc
Confidence 4599999999987
No 103
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.28 E-value=35 Score=25.95 Aligned_cols=15 Identities=27% Similarity=0.629 Sum_probs=11.9
Q ss_pred CccccCCCCcEEEEe
Q 031632 133 KPHECPVCSQYFVVS 147 (156)
Q Consensus 133 ~p~RC~eCG~~FkL~ 147 (156)
+|.+|.-||..|.=.
T Consensus 57 ~Pa~CkkCGfef~~~ 71 (97)
T COG3357 57 RPARCKKCGFEFRDD 71 (97)
T ss_pred cChhhcccCcccccc
Confidence 688898899888653
No 104
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=22.14 E-value=42 Score=20.92 Aligned_cols=16 Identities=25% Similarity=0.719 Sum_probs=10.5
Q ss_pred CccccCCCCcEEEEec
Q 031632 133 KPHECPVCSQYFVVSG 148 (156)
Q Consensus 133 ~p~RC~eCG~~FkL~~ 148 (156)
-|.+|+.||..|=+++
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5889999999996654
No 105
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=21.89 E-value=66 Score=20.81 Aligned_cols=18 Identities=22% Similarity=0.468 Sum_probs=11.8
Q ss_pred ccccCCCCcEEEEeccCc
Q 031632 134 PHECPVCSQYFVVSGGSN 151 (156)
Q Consensus 134 p~RC~eCG~~FkL~~~~~ 151 (156)
.+.||.||.--.+.+..+
T Consensus 3 LkPCPFCG~~~~~~~~~~ 20 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDE 20 (61)
T ss_pred CcCCCCCCCcceEeeccc
Confidence 456888887666655543
No 106
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.89 E-value=92 Score=20.56 Aligned_cols=16 Identities=25% Similarity=0.640 Sum_probs=11.8
Q ss_pred eecCCccccCCCCcEE
Q 031632 129 LEKGKPHECPVCSQYF 144 (156)
Q Consensus 129 L~kG~p~RC~eCG~~F 144 (156)
-..+..+.|+.||..+
T Consensus 41 ~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 41 RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccccceEEcCCCCCEE
Confidence 3456678899999874
No 107
>PRK00420 hypothetical protein; Validated
Probab=21.82 E-value=53 Score=25.23 Aligned_cols=22 Identities=32% Similarity=0.667 Sum_probs=15.6
Q ss_pred EEEeecCCccccCCCCcEEEEec
Q 031632 126 WFWLEKGKPHECPVCSQYFVVSG 148 (156)
Q Consensus 126 Wf~L~kG~p~RC~eCG~~FkL~~ 148 (156)
.|.+++| ...||.||..+...+
T Consensus 33 Lf~lk~g-~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 33 LFELKDG-EVVCPVHGKVYIVKS 54 (112)
T ss_pred ceecCCC-ceECCCCCCeeeecc
Confidence 4556445 588999999777654
No 108
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=21.11 E-value=53 Score=25.40 Aligned_cols=17 Identities=24% Similarity=0.536 Sum_probs=11.1
Q ss_pred eecCCccccCCCCcEEE
Q 031632 129 LEKGKPHECPVCSQYFV 145 (156)
Q Consensus 129 L~kG~p~RC~eCG~~Fk 145 (156)
-+.|...-||||||-+.
T Consensus 14 Y~dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 14 YHDGTQLICPSCLYEWN 30 (109)
T ss_pred EecCCeeECcccccccc
Confidence 34566777777777553
No 109
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=20.65 E-value=78 Score=26.47 Aligned_cols=69 Identities=26% Similarity=0.273 Sum_probs=37.0
Q ss_pred HHHHHHHhCCCCC------CCCCCCCCCCCCCCCeeeeccCCceeEeecCCCCCCCc-ceEEEEeecCCccccCCCCcEE
Q 031632 72 EELEAELEGKNIL------EIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEH-DVVWFWLEKGKPHECPVCSQYF 144 (156)
Q Consensus 72 ~ELla~~~G~DpF------d~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsh-~v~Wf~L~kG~p~RC~eCG~~F 144 (156)
..+++.++.+..+ +++-+....|. ..||.=+.+.+.+-|+-- +.... +..+-.+.++...+||.||..-
T Consensus 78 H~ala~L~~~g~~~~viTQNIDgLh~~aG~---~~VielHG~~~~~~C~~C-~~~~~~~~~~~~~~~~~~p~Cp~Cgg~l 153 (244)
T PRK14138 78 HVLLAKLEEKGLIEAVITQNIDRLHQKAGS---KKVIELHGNVEEYYCVRC-GKRYTVEDVIEKLEKSDVPRCDDCSGLI 153 (244)
T ss_pred HHHHHHHHHcCCceEEEeecccChhhHcCC---CeEEEccCCcCeeEECCC-CCcccHHHHHHHHhcCCCCCCCCCCCeE
Confidence 4555655544332 12323334463 468888888888888752 11110 1111123345677899999654
No 110
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=20.17 E-value=50 Score=27.16 Aligned_cols=22 Identities=18% Similarity=0.745 Sum_probs=17.9
Q ss_pred EeecCCccccCCCCcEEEEecc
Q 031632 128 WLEKGKPHECPVCSQYFVVSGG 149 (156)
Q Consensus 128 ~L~kG~p~RC~eCG~~FkL~~~ 149 (156)
|+.+++..+|+.|++-|.++..
T Consensus 42 Wi~~s~~~~CeiC~~~Y~i~~~ 63 (162)
T PHA02825 42 WINTSKNKSCKICNGPYNIKKN 63 (162)
T ss_pred HHhcCCCCcccccCCeEEEEEe
Confidence 4556778899999999998864
Done!