Query 031107
Match_columns 165
No_of_seqs 128 out of 231
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 09:19:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031107.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031107hhsearch_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 1.7E-68 3.8E-73 433.2 15.1 163 1-163 1-169 (174)
2 PF01215 COX5B: Cytochrome c o 100.0 7E-49 1.5E-53 308.8 7.0 102 54-156 32-133 (136)
3 KOG3352 Cytochrome c oxidase, 100.0 3.1E-48 6.7E-53 309.7 10.6 112 42-155 42-153 (153)
4 cd00924 Cyt_c_Oxidase_Vb Cytoc 100.0 1.9E-47 4.2E-52 285.8 9.9 95 56-152 2-96 (97)
5 PTZ00043 cytochrome c oxidase 100.0 3.8E-34 8.3E-39 242.6 9.0 97 66-162 112-212 (268)
6 PF10276 zf-CHCC: Zinc-finger 97.9 1.7E-05 3.7E-10 51.3 3.3 39 108-146 1-40 (40)
7 KOG3456 NADH:ubiquinone oxidor 96.8 0.00093 2E-08 52.1 2.8 44 104-147 73-116 (120)
8 COG4391 Uncharacterized protei 95.6 0.022 4.8E-07 40.3 4.3 47 100-148 15-61 (62)
9 PF13465 zf-H2C2_2: Zinc-finge 87.0 0.37 8E-06 27.6 1.2 14 133-146 12-25 (26)
10 COG4647 AcxC Acetone carboxyla 87.0 0.42 9.1E-06 38.9 2.0 46 106-154 65-139 (165)
11 COG5189 SFP1 Putative transcri 84.9 0.42 9.2E-06 43.8 1.1 17 130-146 393-409 (423)
12 smart00834 CxxC_CXXC_SSSS Puta 81.2 1.5 3.2E-05 26.7 2.2 14 136-149 6-19 (41)
13 PF13912 zf-C2H2_6: C2H2-type 79.7 1 2.2E-05 25.1 1.1 12 135-146 1-12 (27)
14 smart00659 RPOLCX RNA polymera 79.5 1.3 2.8E-05 28.9 1.6 19 129-147 13-31 (44)
15 PHA00616 hypothetical protein 78.6 0.47 1E-05 31.4 -0.7 12 135-146 1-12 (44)
16 PF10571 UPF0547: Uncharacteri 78.2 0.8 1.7E-05 27.0 0.3 12 135-146 14-25 (26)
17 PF00096 zf-C2H2: Zinc finger, 75.5 1.6 3.4E-05 23.5 1.0 11 136-146 1-11 (23)
18 PF06397 Desulfoferrod_N: Desu 75.4 2.5 5.5E-05 26.8 2.0 23 131-153 2-24 (36)
19 PF13719 zinc_ribbon_5: zinc-r 73.7 2.6 5.7E-05 26.1 1.8 15 132-146 22-36 (37)
20 PF03604 DNA_RNApol_7kD: DNA d 73.5 2.1 4.6E-05 26.3 1.3 17 130-146 12-28 (32)
21 PF09723 Zn-ribbon_8: Zinc rib 69.9 3.5 7.5E-05 26.2 1.8 15 136-150 6-20 (42)
22 COG0551 TopA Zn-finger domain 69.8 12 0.00025 28.8 5.0 48 102-151 29-76 (140)
23 PF13894 zf-C2H2_4: C2H2-type 68.7 3.1 6.7E-05 21.6 1.1 11 136-146 1-11 (24)
24 PRK14892 putative transcriptio 68.1 4.3 9.4E-05 30.8 2.2 39 110-153 20-59 (99)
25 TIGR02605 CxxC_CxxC_SSSS putat 67.3 5 0.00011 25.8 2.1 14 136-149 6-19 (52)
26 PLN00128 Succinate dehydrogena 67.0 3.4 7.4E-05 39.5 1.8 19 1-19 1-19 (635)
27 PF04216 FdhE: Protein involve 66.3 5.3 0.00012 34.3 2.7 31 119-149 218-252 (290)
28 PRK00398 rpoP DNA-directed RNA 63.7 9.7 0.00021 24.2 2.9 15 135-149 21-35 (46)
29 TIGR02098 MJ0042_CXXC MJ0042 f 63.3 5.9 0.00013 24.0 1.8 13 136-148 3-15 (38)
30 PF14353 CpXC: CpXC protein 61.8 3.8 8.2E-05 30.9 0.9 14 135-148 38-51 (128)
31 PHA02768 hypothetical protein; 60.6 3.7 8.1E-05 28.3 0.6 12 136-147 6-17 (55)
32 PF09538 FYDLN_acid: Protein o 59.6 3.8 8.3E-05 31.4 0.6 25 123-148 15-39 (108)
33 PRK03564 formate dehydrogenase 57.4 13 0.00028 33.3 3.6 30 122-151 235-268 (309)
34 PF09237 GAGA: GAGA factor; I 56.0 3.9 8.5E-05 28.3 0.1 22 124-145 13-34 (54)
35 PF08882 Acetone_carb_G: Aceto 54.8 14 0.00029 29.0 2.9 30 124-156 66-95 (112)
36 TIGR00319 desulf_FeS4 desulfof 54.3 18 0.00039 21.7 2.8 20 133-152 5-24 (34)
37 COG1198 PriA Primosomal protei 54.3 8.7 0.00019 38.1 2.2 20 133-153 473-492 (730)
38 PF13717 zinc_ribbon_4: zinc-r 53.2 9.3 0.0002 23.6 1.4 16 131-146 21-36 (36)
39 KOG3993 Transcription factor ( 52.6 5.6 0.00012 37.7 0.6 11 136-146 296-306 (500)
40 PF05191 ADK_lid: Adenylate ki 52.6 3.8 8.3E-05 25.6 -0.4 17 137-153 3-19 (36)
41 PF07754 DUF1610: Domain of un 52.5 8.1 0.00018 22.6 1.0 12 132-143 13-24 (24)
42 cd00729 rubredoxin_SM Rubredox 49.9 9.7 0.00021 23.3 1.1 10 134-143 17-26 (34)
43 COG2888 Predicted Zn-ribbon RN 48.7 9.4 0.0002 27.0 1.1 10 133-142 48-57 (61)
44 COG1326 Uncharacterized archae 47.6 13 0.00028 31.8 1.9 23 120-145 16-40 (201)
45 cd00974 DSRD Desulforedoxin (D 47.2 28 0.00061 20.8 2.9 19 133-151 2-20 (34)
46 PF13913 zf-C2HC_2: zinc-finge 46.7 13 0.00028 21.3 1.3 14 135-148 2-15 (25)
47 PF14255 Cys_rich_CPXG: Cystei 46.2 15 0.00033 24.8 1.7 12 137-148 2-13 (52)
48 smart00355 ZnF_C2H2 zinc finge 45.9 8.2 0.00018 19.9 0.3 11 136-146 1-11 (26)
49 TIGR01562 FdhE formate dehydro 45.2 19 0.00041 32.2 2.7 29 123-151 234-268 (305)
50 PF12172 DUF35_N: Rubredoxin-l 44.8 13 0.00027 22.6 1.1 12 135-146 11-22 (37)
51 PF14690 zf-ISL3: zinc-finger 44.8 11 0.00024 23.5 0.8 11 134-144 1-11 (47)
52 TIGR01206 lysW lysine biosynth 44.6 25 0.00055 23.9 2.6 20 133-152 20-39 (54)
53 KOG3507 DNA-directed RNA polym 44.3 9.9 0.00022 26.9 0.6 16 129-144 31-46 (62)
54 PF03966 Trm112p: Trm112p-like 43.9 15 0.00032 25.2 1.4 13 136-148 54-66 (68)
55 COG1996 RPC10 DNA-directed RNA 42.8 25 0.00053 23.8 2.3 22 130-151 19-40 (49)
56 TIGR02300 FYDLN_acid conserved 40.6 12 0.00026 30.0 0.6 26 124-150 16-41 (129)
57 KOG1088 Uncharacterized conser 40.3 14 0.0003 29.4 1.0 22 126-148 90-111 (124)
58 COG1592 Rubrerythrin [Energy p 40.0 13 0.00028 30.6 0.8 14 130-143 143-157 (166)
59 PF13005 zf-IS66: zinc-finger 39.7 24 0.00052 22.1 1.8 16 135-152 2-17 (47)
60 cd00350 rubredoxin_like Rubred 38.4 21 0.00046 21.4 1.4 12 136-147 2-13 (33)
61 PF01927 Mut7-C: Mut7-C RNAse 38.0 19 0.0004 28.1 1.4 12 134-145 123-134 (147)
62 PRK05654 acetyl-CoA carboxylas 37.6 15 0.00032 32.5 0.8 14 134-147 45-58 (292)
63 smart00451 ZnF_U1 U1-like zinc 37.6 18 0.00039 20.9 1.0 13 134-146 2-14 (35)
64 COG0846 SIR2 NAD-dependent pro 37.5 45 0.00097 28.9 3.7 50 92-146 106-158 (250)
65 COG4049 Uncharacterized protei 37.2 9.4 0.0002 27.1 -0.4 15 132-146 13-28 (65)
66 PHA00733 hypothetical protein 35.0 17 0.00037 28.1 0.7 22 125-146 63-84 (128)
67 PF09889 DUF2116: Uncharacteri 34.8 19 0.00041 25.0 0.8 11 134-144 1-12 (59)
68 PRK14890 putative Zn-ribbon RN 34.4 21 0.00046 25.0 1.0 11 133-143 46-56 (59)
69 TIGR00240 ATCase_reg aspartate 34.3 36 0.00078 27.8 2.5 26 125-150 119-147 (150)
70 PF00301 Rubredoxin: Rubredoxi 33.8 24 0.00052 23.3 1.2 11 136-146 2-12 (47)
71 KOG1973 Chromatin remodeling p 33.2 25 0.00054 30.4 1.5 19 109-131 230-248 (274)
72 TIGR03831 YgiT_finger YgiT-typ 32.8 39 0.00084 20.5 2.0 10 136-145 33-42 (46)
73 PF05605 zf-Di19: Drought indu 32.7 20 0.00044 23.3 0.7 11 135-145 2-12 (54)
74 PHA00626 hypothetical protein 32.2 25 0.00054 24.8 1.1 21 133-153 21-41 (59)
75 TIGR00515 accD acetyl-CoA carb 31.7 17 0.00037 32.0 0.2 24 124-147 34-57 (285)
76 PF04423 Rad50_zn_hook: Rad50 31.6 21 0.00045 23.3 0.6 9 137-145 22-30 (54)
77 COG1545 Predicted nucleic-acid 31.2 26 0.00057 27.5 1.2 23 124-146 14-40 (140)
78 COG1885 Uncharacterized protei 31.0 42 0.00092 26.3 2.3 28 123-151 38-65 (115)
79 PRK04860 hypothetical protein; 31.0 60 0.0013 26.3 3.3 17 133-149 141-157 (160)
80 CHL00174 accD acetyl-CoA carbo 30.8 17 0.00037 32.4 0.1 15 134-148 56-70 (296)
81 cd00730 rubredoxin Rubredoxin; 30.4 27 0.00059 23.3 1.0 12 136-147 2-13 (50)
82 PF12171 zf-C2H2_jaz: Zinc-fin 28.8 25 0.00055 19.7 0.6 11 136-146 2-12 (27)
83 COG1773 Rubredoxin [Energy pro 28.8 31 0.00068 23.8 1.1 12 135-146 3-14 (55)
84 PF05876 Terminase_GpA: Phage 28.2 23 0.00049 33.6 0.5 13 137-149 202-214 (557)
85 PHA00732 hypothetical protein 27.9 25 0.00054 25.3 0.5 10 137-146 29-38 (79)
86 COG5216 Uncharacterized conser 27.8 41 0.00089 24.0 1.6 34 113-149 24-58 (67)
87 PF06957 COPI_C: Coatomer (COP 26.7 25 0.00055 32.8 0.5 24 129-152 373-397 (422)
88 PRK07220 DNA topoisomerase I; 26.4 1.2E+02 0.0026 29.9 5.0 41 105-148 604-649 (740)
89 KOG3623 Homeobox transcription 26.3 23 0.00051 36.0 0.2 13 136-148 282-294 (1007)
90 PF13451 zf-trcl: Probable zin 26.2 49 0.0011 22.3 1.7 16 133-148 2-17 (49)
91 PF02591 DUF164: Putative zinc 26.0 31 0.00067 22.7 0.7 16 129-144 39-55 (56)
92 PF11781 RRN7: RNA polymerase 25.8 47 0.001 20.7 1.4 12 133-144 6-17 (36)
93 PF07282 OrfB_Zn_ribbon: Putat 25.8 76 0.0016 21.2 2.6 17 130-146 41-57 (69)
94 PRK12286 rpmF 50S ribosomal pr 25.7 33 0.00072 23.4 0.8 12 134-145 38-50 (57)
95 PF14311 DUF4379: Domain of un 25.4 46 0.001 21.7 1.4 12 137-148 30-41 (55)
96 COG1656 Uncharacterized conser 25.2 33 0.00071 28.5 0.8 12 134-145 129-140 (165)
97 PF01428 zf-AN1: AN1-like Zinc 25.0 39 0.00085 21.3 1.0 19 134-152 12-30 (43)
98 PF09526 DUF2387: Probable met 24.8 1.1E+02 0.0025 21.7 3.4 39 111-150 6-45 (71)
99 PRK14973 DNA topoisomerase I; 24.6 1E+02 0.0022 31.6 4.2 35 107-143 604-643 (936)
100 COG1997 RPL43A Ribosomal prote 24.5 51 0.0011 24.9 1.7 18 134-152 34-51 (89)
101 PF13878 zf-C2H2_3: zinc-finge 24.5 48 0.001 21.0 1.3 14 135-148 13-26 (41)
102 PF10058 DUF2296: Predicted in 24.2 37 0.00081 22.9 0.8 10 135-144 44-53 (54)
103 COG3677 Transposase and inacti 24.0 47 0.001 25.9 1.5 20 135-154 53-72 (129)
104 PRK03824 hypA hydrogenase nick 23.9 49 0.0011 25.8 1.5 14 135-148 70-83 (135)
105 PF08274 PhnA_Zn_Ribbon: PhnA 23.7 48 0.001 20.1 1.1 15 131-145 15-29 (30)
106 PF10122 Mu-like_Com: Mu-like 23.2 72 0.0016 21.8 2.0 22 136-157 25-46 (51)
107 TIGR00686 phnA alkylphosphonat 23.1 50 0.0011 25.8 1.4 19 130-148 14-32 (109)
108 KOG4124 Putative transcription 22.9 30 0.00065 32.4 0.2 21 128-148 391-411 (442)
109 COG3357 Predicted transcriptio 22.4 32 0.0007 26.3 0.3 18 134-151 57-74 (97)
110 PRK12380 hydrogenase nickel in 22.3 47 0.001 25.2 1.1 14 135-148 70-83 (113)
111 PF06170 DUF983: Protein of un 22.2 31 0.00066 25.4 0.1 19 135-153 8-26 (86)
112 KOG3623 Homeobox transcription 21.6 43 0.00093 34.2 1.0 45 101-147 271-321 (1007)
113 PF07975 C1_4: TFIIH C1-like d 21.4 38 0.00081 22.9 0.4 14 134-147 20-33 (51)
114 PF08271 TF_Zn_Ribbon: TFIIB z 20.9 72 0.0016 19.9 1.6 11 136-146 20-30 (43)
115 PF14354 Lar_restr_allev: Rest 20.8 96 0.0021 20.2 2.3 10 137-146 5-14 (61)
116 PRK00432 30S ribosomal protein 20.7 78 0.0017 21.0 1.8 20 125-144 6-29 (50)
117 PF13240 zinc_ribbon_2: zinc-r 20.4 45 0.00097 18.8 0.5 7 137-143 1-7 (23)
118 PF04606 Ogr_Delta: Ogr/Delta- 20.3 66 0.0014 20.7 1.4 7 138-144 2-8 (47)
119 PRK14138 NAD-dependent deacety 20.2 67 0.0015 27.1 1.8 47 100-147 108-155 (244)
120 COG1579 Zn-ribbon protein, pos 20.1 42 0.00091 29.1 0.5 13 132-144 218-230 (239)
No 1
>PLN02294 cytochrome c oxidase subunit Vb
Probab=100.00 E-value=1.7e-68 Score=433.25 Aligned_cols=163 Identities=74% Similarity=1.223 Sum_probs=142.7
Q ss_pred ChhhHHhhhhHHHHHHHhhhcCCCCCCCcc-----ccccccccc-cccccccccccccCcccccccCCCCcccchHHHHH
Q 031107 1 MWRRICSSQLKAQALALAQYSCRSAPVNPS-----IASRSLISR-PLFASRHFSADSAGTSVKKRVEDVNPVATGHEREE 74 (165)
Q Consensus 1 m~rr~~~~~l~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~vpd~~eqATGlER~E 74 (165)
||||+++|+|||||++.++.+.++++++.+ ..+++.+++ +++|+|+|++.|+++.++|+|+|+|||||||||+|
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 999999999999998864432333232211 123444443 47999999999999999999999999999999999
Q ss_pred HHHHHcCCCCCCCCCCCCCCCCCCCCeeeeccCCceEEeecCCCCCCCcceEEEEeecCCceecCCCCceEEEEEeCCCC
Q 031107 75 LEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVLEVVGPGG 154 (165)
Q Consensus 75 Lla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsH~v~Wf~L~kGkp~RCpeCG~~FkL~~vg~~~ 154 (165)
|||+++|+|||||+++++++|||||||||||++++|||||+|+.++|+|+|+||||++|+|+||||||+||||++||+++
T Consensus 81 Lla~leG~D~Fd~~~~~gp~GTke~P~lVpS~~d~RiVGCtg~~~eDsh~v~Wf~L~kGkp~RCpeCG~~fkL~~vG~~~ 160 (174)
T PLN02294 81 LEAELEGRKLLDIDFPEGPFGTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFELEVVGPGG 160 (174)
T ss_pred HHHHHcCCCccccccccCCCCCccCCcEeccCCCceEEeeCCCCCCCCceeEEEEecCCCceeCCCCCCEEEEEEeCCCC
Confidence 99999999999999999999999999999999999999999965689999999999999999999999999999999999
Q ss_pred CCCCCCCCC
Q 031107 155 PPDGHGDDD 163 (165)
Q Consensus 155 ~p~~~~~~~ 163 (165)
|||+|+|++
T Consensus 161 ~~~~h~d~~ 169 (174)
T PLN02294 161 PPDGHGDDD 169 (174)
T ss_pred CCCCCCCcc
Confidence 999998763
No 2
>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=7e-49 Score=308.84 Aligned_cols=102 Identities=50% Similarity=0.920 Sum_probs=71.9
Q ss_pred cccccccCCCCcccchHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCeeeeccCCceEEeecCCCCCCCcceEEEEeecC
Q 031107 54 TSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKG 133 (165)
Q Consensus 54 ~~~~~~vpd~~eqATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsH~v~Wf~L~kG 133 (165)
+...+.||+++||||||||+|||++++|+|||+|+++++++||+||||||||++++|||||+|+| +|+|+|+||||++|
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 44578999999999999999999999999999999999999999999999999999999999997 67899999999999
Q ss_pred CceecCCCCceEEEEEeCCCCCC
Q 031107 134 KPHECPVCSQYFVLEVVGPGGPP 156 (165)
Q Consensus 134 kp~RCpeCG~~FkL~~vg~~~~p 156 (165)
+|+|||+||+||||++||++++.
T Consensus 111 ~~~RCpeCG~~fkL~~vg~~~~~ 133 (136)
T PF01215_consen 111 KPQRCPECGQVFKLKYVGPEGDH 133 (136)
T ss_dssp SEEEETTTEEEEEEEE-------
T ss_pred CccCCCCCCeEEEEEEcCCCCCC
Confidence 99999999999999999985433
No 3
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=100.00 E-value=3.1e-48 Score=309.66 Aligned_cols=112 Identities=51% Similarity=0.848 Sum_probs=101.7
Q ss_pred cccccccccccCcccccccCCCCcccchHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCeeeeccCCceEEeecCCCCCC
Q 031107 42 FASRHFSADSAGTSVKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGED 121 (165)
Q Consensus 42 ~~~~~~~~~~~~~~~~~~vpd~~eqATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eD 121 (165)
...|...+....++..|.|||++||||||||+|||++++|.|||||+.+++++|||++||||||+||+|||||.| ++|
T Consensus 42 a~~r~~~~~~~~~~~~g~vpddle~aTGlEk~eLla~l~G~d~~d~k~~~~~~GTkedP~lV~S~~d~RiVGC~c--~eD 119 (153)
T KOG3352|consen 42 AAPRRGSAAITPMAKGGGVPDDLEQATGLEKEELLAELEGRDPFDMKVPRGPSGTKEDPNLVPSYYDKRIVGCGC--EED 119 (153)
T ss_pred hccCCCcceeeccccCCCCCCchhhhhhHHHHHHHHHhhCCCccccccccCCCCcccCCccccccCCceEEeecc--cCC
Confidence 344445554455667899999999999999999999999999999999999999999999999999999999977 589
Q ss_pred CcceEEEEeecCCceecCCCCceEEEEEeCCCCC
Q 031107 122 EHDVVWFWLEKGKPHECPVCSQYFVLEVVGPGGP 155 (165)
Q Consensus 122 sH~v~Wf~L~kGkp~RCpeCG~~FkL~~vg~~~~ 155 (165)
+|+|+||||+||+++||||||+||||+.+|++++
T Consensus 120 ~~~V~Wmwl~Kge~~rc~eCG~~fkL~~v~~~~~ 153 (153)
T KOG3352|consen 120 SHAVVWMWLEKGETQRCPECGHYFKLVPVGPVNP 153 (153)
T ss_pred CcceEEEEEEcCCcccCCcccceEEeeecCCCCC
Confidence 9999999999999999999999999999998653
No 4
>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=1.9e-47 Score=285.79 Aligned_cols=95 Identities=51% Similarity=0.890 Sum_probs=91.6
Q ss_pred cccccCCCCcccchHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCeeeeccCCceEEeecCCCCCCCcceEEEEeecCCc
Q 031107 56 VKKRVEDVNPVATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKP 135 (165)
Q Consensus 56 ~~~~vpd~~eqATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsH~v~Wf~L~kGkp 135 (165)
..|+|||++||||||||+||+++++|+|+|+|+++++++||++|||||||++++|||||+|+| |+|+|+||||++|+|
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 468999999999999999999999999999999999999999999999999999999999976 699999999999999
Q ss_pred eecCCCCceEEEEEeCC
Q 031107 136 HECPVCSQYFVLEVVGP 152 (165)
Q Consensus 136 ~RCpeCG~~FkL~~vg~ 152 (165)
+||++||+||||+++|+
T Consensus 80 ~rC~eCG~~fkL~~v~~ 96 (97)
T cd00924 80 KRCPECGHVFKLVDVGP 96 (97)
T ss_pred eeCCCCCcEEEEEECCC
Confidence 99999999999999986
No 5
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=100.00 E-value=3.8e-34 Score=242.62 Aligned_cols=97 Identities=34% Similarity=0.554 Sum_probs=91.5
Q ss_pred ccchHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCeeeeccCCceEEeecCCCCCCCcceEEEEeecCCceecCCCCceE
Q 031107 66 VATGHEREELEAELEGKNILEIDYPTGPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYF 145 (165)
Q Consensus 66 qATGlER~ELla~~~G~DpFd~~~~~~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsH~v~Wf~L~kGkp~RCpeCG~~F 145 (165)
|....+.+.|+|.++|.+.+.++++.+|+||+|+|+||||++++|||||+|+++||+|+|+|||+++|+++|||+||+||
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 33447889999999999999999999999999999999999999999999988899999999999999999999999999
Q ss_pred EEEE----eCCCCCCCCCCCC
Q 031107 146 VLEV----VGPGGPPDGHGDD 162 (165)
Q Consensus 146 kL~~----vg~~~~p~~~~~~ 162 (165)
||++ +|+|+||++.|-+
T Consensus 192 KLVr~~~s~~dg~dp~~~dpd 212 (268)
T PTZ00043 192 MLVRVLYSLPDGEDPFPNDPD 212 (268)
T ss_pred EEEEEEeecCCCCCCCCCCCc
Confidence 9998 9999999998854
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=97.85 E-value=1.7e-05 Score=51.31 Aligned_cols=39 Identities=38% Similarity=0.758 Sum_probs=33.1
Q ss_pred CceEEeecCCCCCCCcceEEEEeec-CCceecCCCCceEE
Q 031107 108 DKRIVGCPGGEGEDEHDVVWFWLEK-GKPHECPVCSQYFV 146 (165)
Q Consensus 108 ~~RiVGC~g~p~eDsH~v~Wf~L~k-Gkp~RCpeCG~~Fk 146 (165)
+.|+|-|.|..++-.|-.+|+.|.+ +++..||.||..|+
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 4689999998777789999999999 47899999999986
No 7
>KOG3456 consensus NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion]
Probab=96.83 E-value=0.00093 Score=52.11 Aligned_cols=44 Identities=36% Similarity=0.601 Sum_probs=38.8
Q ss_pred eccCCceEEeecCCCCCCCcceEEEEeecCCceecCCCCceEEE
Q 031107 104 KSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVL 147 (165)
Q Consensus 104 pS~~~~RiVGC~g~p~eDsH~v~Wf~L~kGkp~RCpeCG~~FkL 147 (165)
|+..++|||-|-|+.++--|..+|+.|.|..++-|.+||.-|.-
T Consensus 73 p~e~d~RVV~CdGg~~aLGHPkvyInLDk~~~~~CgYCGlrf~~ 116 (120)
T KOG3456|consen 73 PIEVDGRVVACDGGTPALGHPKVYINLDKPGPHICGYCGLRFVQ 116 (120)
T ss_pred hhhccceEEEecCCCCCCCCCeEEEEcCCCCCcccccchhhhhh
Confidence 34459999999998888889999999999889999999998864
No 8
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.65 E-value=0.022 Score=40.26 Aligned_cols=47 Identities=23% Similarity=0.425 Sum_probs=35.9
Q ss_pred CeeeeccCCceEEeecCCCCCCCcceEEEEeecCCceecCCCCceEEEE
Q 031107 100 PAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVLE 148 (165)
Q Consensus 100 P~lVpS~~~~RiVGC~g~p~eDsH~v~Wf~L~kGkp~RCpeCG~~FkL~ 148 (165)
++.|.... --+-|.|...+-+|--+|+-+.+..-.-||.||..|+|.
T Consensus 15 ~~~I~~~~--~~l~C~g~~~p~~HPrV~L~mg~~gev~CPYC~t~y~l~ 61 (62)
T COG4391 15 HETIEIGD--LPLMCPGPEPPNDHPRVFLDMGDEGEVVCPYCSTRYRLN 61 (62)
T ss_pred ceEEEeCC--eeEEcCCCCCCCCCCEEEEEcCCCCcEecCccccEEEec
Confidence 44554432 236799987788899999999665567799999999985
No 9
>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=87.01 E-value=0.37 Score=27.63 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=12.0
Q ss_pred CCceecCCCCceEE
Q 031107 133 GKPHECPVCSQYFV 146 (165)
Q Consensus 133 Gkp~RCpeCG~~Fk 146 (165)
.+|+.|++|+..|.
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 36999999999884
No 10
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=86.99 E-value=0.42 Score=38.91 Aligned_cols=46 Identities=28% Similarity=0.605 Sum_probs=32.6
Q ss_pred cCCceEEeecCCCC-----------------------------CCCcceEEEEeecCCceecCCCCceEEEEEeCCCC
Q 031107 106 YYDKRIVGCPGGEG-----------------------------EDEHDVVWFWLEKGKPHECPVCSQYFVLEVVGPGG 154 (165)
Q Consensus 106 ~~~~RiVGC~g~p~-----------------------------eDsH~v~Wf~L~kGkp~RCpeCG~~FkL~~vg~~~ 154 (165)
..++|++-|.|+.. .|..+..||.+++ +-||+||..-..+-..|+-
T Consensus 65 s~~~rv~rcecghsf~d~r~nwkl~a~i~vrdtee~lreiyp~s~ipdp~wme~re---ficpecg~l~eveaaap~y 139 (165)
T COG4647 65 SAQKRVIRCECGHSFGDYRENWKLHANIYVRDTEEKLREIYPKSDIPDPQWMEIRE---FICPECGILHEVEAAAPGY 139 (165)
T ss_pred cccccEEEEeccccccChhhCceeeeEEEEcchHHHHHHhCcccCCCCchHHHHHH---hhCccccceeeeccCCCCC
Confidence 35788999999531 2345667777665 7799999987777665543
No 11
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=84.89 E-value=0.42 Score=43.82 Aligned_cols=17 Identities=35% Similarity=0.778 Sum_probs=15.7
Q ss_pred eecCCceecCCCCceEE
Q 031107 130 LEKGKPHECPVCSQYFV 146 (165)
Q Consensus 130 L~kGkp~RCpeCG~~Fk 146 (165)
.-|+||+||++|+.-||
T Consensus 393 ~~~~KPYrCevC~KRYK 409 (423)
T COG5189 393 SAKDKPYRCEVCDKRYK 409 (423)
T ss_pred cccCCceeccccchhhc
Confidence 66889999999999998
No 12
>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=81.21 E-value=1.5 Score=26.66 Aligned_cols=14 Identities=21% Similarity=0.479 Sum_probs=11.9
Q ss_pred eecCCCCceEEEEE
Q 031107 136 HECPVCSQYFVLEV 149 (165)
Q Consensus 136 ~RCpeCG~~FkL~~ 149 (165)
++|++||+.|.+..
T Consensus 6 y~C~~Cg~~fe~~~ 19 (41)
T smart00834 6 YRCEDCGHTFEVLQ 19 (41)
T ss_pred EEcCCCCCEEEEEE
Confidence 68999999998664
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=79.65 E-value=1 Score=25.13 Aligned_cols=12 Identities=42% Similarity=1.041 Sum_probs=10.6
Q ss_pred ceecCCCCceEE
Q 031107 135 PHECPVCSQYFV 146 (165)
Q Consensus 135 p~RCpeCG~~Fk 146 (165)
|++|.+|++.|.
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
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=79.48 E-value=1.3 Score=28.85 Aligned_cols=19 Identities=11% Similarity=0.277 Sum_probs=14.2
Q ss_pred EeecCCceecCCCCceEEE
Q 031107 129 WLEKGKPHECPVCSQYFVL 147 (165)
Q Consensus 129 ~L~kGkp~RCpeCG~~FkL 147 (165)
.+..+.+.|||+||+--..
T Consensus 13 ~~~~~~~irC~~CG~rIly 31 (44)
T smart00659 13 EIKSKDVVRCRECGYRILY 31 (44)
T ss_pred ecCCCCceECCCCCceEEE
Confidence 3557789999999985433
No 15
>PHA00616 hypothetical protein
Probab=78.65 E-value=0.47 Score=31.38 Aligned_cols=12 Identities=25% Similarity=0.542 Sum_probs=10.6
Q ss_pred ceecCCCCceEE
Q 031107 135 PHECPVCSQYFV 146 (165)
Q Consensus 135 p~RCpeCG~~Fk 146 (165)
|++|++||..|.
T Consensus 1 pYqC~~CG~~F~ 12 (44)
T PHA00616 1 MYQCLRCGGIFR 12 (44)
T ss_pred CCccchhhHHHh
Confidence 689999999885
No 16
>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=78.19 E-value=0.8 Score=26.95 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=9.9
Q ss_pred ceecCCCCceEE
Q 031107 135 PHECPVCSQYFV 146 (165)
Q Consensus 135 p~RCpeCG~~Fk 146 (165)
..+||.||+.|.
T Consensus 14 ~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 14 AKFCPHCGYDFE 25 (26)
T ss_pred cCcCCCCCCCCc
Confidence 467999999885
No 17
>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=75.51 E-value=1.6 Score=23.46 Aligned_cols=11 Identities=36% Similarity=1.171 Sum_probs=9.5
Q ss_pred eecCCCCceEE
Q 031107 136 HECPVCSQYFV 146 (165)
Q Consensus 136 ~RCpeCG~~Fk 146 (165)
++|++||..|.
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 57999999985
No 18
>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=75.38 E-value=2.5 Score=26.80 Aligned_cols=23 Identities=26% Similarity=0.481 Sum_probs=13.5
Q ss_pred ecCCceecCCCCceEEEEEeCCC
Q 031107 131 EKGKPHECPVCSQYFVLEVVGPG 153 (165)
Q Consensus 131 ~kGkp~RCpeCG~~FkL~~vg~~ 153 (165)
++++-++|..||+...+..-|.+
T Consensus 2 ~~~~~YkC~~CGniVev~~~g~g 24 (36)
T PF06397_consen 2 KKGEFYKCEHCGNIVEVVHDGGG 24 (36)
T ss_dssp -TTEEEE-TTT--EEEEEE--SS
T ss_pred CcccEEEccCCCCEEEEEECCCC
Confidence 35678999999999988776653
No 19
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=73.74 E-value=2.6 Score=26.13 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=12.7
Q ss_pred cCCceecCCCCceEE
Q 031107 132 KGKPHECPVCSQYFV 146 (165)
Q Consensus 132 kGkp~RCpeCG~~Fk 146 (165)
+|...||+.|++.|.
T Consensus 22 ~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 22 GGRKVRCPKCGHVFR 36 (37)
T ss_pred CCcEEECCCCCcEee
Confidence 466889999999985
No 20
>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=73.48 E-value=2.1 Score=26.34 Aligned_cols=17 Identities=35% Similarity=0.956 Sum_probs=13.2
Q ss_pred eecCCceecCCCCceEE
Q 031107 130 LEKGKPHECPVCSQYFV 146 (165)
Q Consensus 130 L~kGkp~RCpeCG~~Fk 146 (165)
+..+.+.||++||+.-.
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 21
>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=69.93 E-value=3.5 Score=26.16 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=12.2
Q ss_pred eecCCCCceEEEEEe
Q 031107 136 HECPVCSQYFVLEVV 150 (165)
Q Consensus 136 ~RCpeCG~~FkL~~v 150 (165)
++|..||+.|....-
T Consensus 6 y~C~~Cg~~fe~~~~ 20 (42)
T PF09723_consen 6 YRCEECGHEFEVLQS 20 (42)
T ss_pred EEeCCCCCEEEEEEE
Confidence 789999999986543
No 22
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=69.81 E-value=12 Score=28.80 Aligned_cols=48 Identities=17% Similarity=0.248 Sum_probs=27.9
Q ss_pred eeeccCCceEEeecCCCCCCCcceEEEEeecCCceecCCCCceEEEEEeC
Q 031107 102 VVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKPHECPVCSQYFVLEVVG 151 (165)
Q Consensus 102 lVpS~~~~RiVGC~g~p~eDsH~v~Wf~L~kGkp~RCpeCG~~FkL~~vg 151 (165)
+..+.+. +.+||..+|.-+....- --..++....||+||+...+...+
T Consensus 29 ~~~~~~g-~f~gCs~yP~C~~~~~~-~~~~~~~~~~Cp~C~~~~~~~k~~ 76 (140)
T COG0551 29 KKFGKYG-IFLGCSNYPKCDYYEPE-KAIAEKTGVKCPKCGKGLLVLKKG 76 (140)
T ss_pred EEEccCC-eEEEeCCCCCCCCCccc-ccccccCceeCCCCCCCceEEEec
Confidence 3455555 99999999844321111 111224458899999755444443
No 23
>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=68.65 E-value=3.1 Score=21.61 Aligned_cols=11 Identities=36% Similarity=1.219 Sum_probs=7.3
Q ss_pred eecCCCCceEE
Q 031107 136 HECPVCSQYFV 146 (165)
Q Consensus 136 ~RCpeCG~~Fk 146 (165)
+.|+.||..|.
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 47999999884
No 24
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=68.06 E-value=4.3 Score=30.76 Aligned_cols=39 Identities=26% Similarity=0.419 Sum_probs=26.2
Q ss_pred eEEeecCCCCCCCcceEEEEeecCCcee-cCCCCceEEEEEeCCC
Q 031107 110 RIVGCPGGEGEDEHDVVWFWLEKGKPHE-CPVCSQYFVLEVVGPG 153 (165)
Q Consensus 110 RiVGC~g~p~eDsH~v~Wf~L~kGkp~R-CpeCG~~FkL~~vg~~ 153 (165)
.++=|.-- + +..+=..+.+|++++ |+.||.+|.-+ |.++
T Consensus 20 t~f~CP~C-g---e~~v~v~~~k~~~h~~C~~CG~y~~~~-V~~l 59 (99)
T PRK14892 20 KIFECPRC-G---KVSISVKIKKNIAIITCGNCGLYTEFE-VPSV 59 (99)
T ss_pred cEeECCCC-C---CeEeeeecCCCcceEECCCCCCccCEE-CCcc
Confidence 46667432 2 245555667788888 99999999875 4443
No 25
>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=67.30 E-value=5 Score=25.78 Aligned_cols=14 Identities=21% Similarity=0.567 Sum_probs=11.7
Q ss_pred eecCCCCceEEEEE
Q 031107 136 HECPVCSQYFVLEV 149 (165)
Q Consensus 136 ~RCpeCG~~FkL~~ 149 (165)
++|.+||+.|.+..
T Consensus 6 y~C~~Cg~~fe~~~ 19 (52)
T TIGR02605 6 YRCTACGHRFEVLQ 19 (52)
T ss_pred EEeCCCCCEeEEEE
Confidence 68999999998763
No 26
>PLN00128 Succinate dehydrogenase [ubiquinone] flavoprotein subunit
Probab=67.04 E-value=3.4 Score=39.52 Aligned_cols=19 Identities=37% Similarity=0.571 Sum_probs=15.7
Q ss_pred ChhhHHhhhhHHHHHHHhh
Q 031107 1 MWRRICSSQLKAQALALAQ 19 (165)
Q Consensus 1 m~rr~~~~~l~~~~~~~~~ 19 (165)
||||-+..-|+-|++++++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~ 19 (635)
T PLN00128 1 MWRRCVARGLRLLASSSAS 19 (635)
T ss_pred CcccchhhHHHHHhhhhcC
Confidence 9999999999999866533
No 27
>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=66.29 E-value=5.3 Score=34.29 Aligned_cols=31 Identities=19% Similarity=0.527 Sum_probs=16.3
Q ss_pred CCCCcceEEEE-eecCCcee---cCCCCceEEEEE
Q 031107 119 GEDEHDVVWFW-LEKGKPHE---CPVCSQYFVLEV 149 (165)
Q Consensus 119 ~eDsH~v~Wf~-L~kGkp~R---CpeCG~~FkL~~ 149 (165)
|++++.-+|+. .+....+| |..|+.|+|..+
T Consensus 218 g~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 218 GNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp ---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred CCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 35666666654 44433455 999999999998
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=63.72 E-value=9.7 Score=24.22 Aligned_cols=15 Identities=20% Similarity=0.607 Sum_probs=12.0
Q ss_pred ceecCCCCceEEEEE
Q 031107 135 PHECPVCSQYFVLEV 149 (165)
Q Consensus 135 p~RCpeCG~~FkL~~ 149 (165)
..+||.||+-+.++.
T Consensus 21 ~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 21 GVRCPYCGYRILFKE 35 (46)
T ss_pred ceECCCCCCeEEEcc
Confidence 789999998777653
No 29
>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=63.25 E-value=5.9 Score=23.98 Aligned_cols=13 Identities=31% Similarity=0.795 Sum_probs=11.4
Q ss_pred eecCCCCceEEEE
Q 031107 136 HECPVCSQYFVLE 148 (165)
Q Consensus 136 ~RCpeCG~~FkL~ 148 (165)
.+||.||..|++.
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 4799999999986
No 30
>PF14353 CpXC: CpXC protein
Probab=61.76 E-value=3.8 Score=30.89 Aligned_cols=14 Identities=43% Similarity=0.997 Sum_probs=11.7
Q ss_pred ceecCCCCceEEEE
Q 031107 135 PHECPVCSQYFVLE 148 (165)
Q Consensus 135 p~RCpeCG~~FkL~ 148 (165)
-+.||.||+-|.+.
T Consensus 38 ~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPSCGHKFRLE 51 (128)
T ss_pred EEECCCCCCceecC
Confidence 36799999999874
No 31
>PHA02768 hypothetical protein; Provisional
Probab=60.61 E-value=3.7 Score=28.26 Aligned_cols=12 Identities=33% Similarity=1.182 Sum_probs=10.1
Q ss_pred eecCCCCceEEE
Q 031107 136 HECPVCSQYFVL 147 (165)
Q Consensus 136 ~RCpeCG~~FkL 147 (165)
++|++||..|..
T Consensus 6 y~C~~CGK~Fs~ 17 (55)
T PHA02768 6 YECPICGEIYIK 17 (55)
T ss_pred cCcchhCCeecc
Confidence 689999999864
No 32
>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=59.58 E-value=3.8 Score=31.36 Aligned_cols=25 Identities=32% Similarity=0.613 Sum_probs=21.6
Q ss_pred cceEEEEeecCCceecCCCCceEEEE
Q 031107 123 HDVVWFWLEKGKPHECPVCSQYFVLE 148 (165)
Q Consensus 123 H~v~Wf~L~kGkp~RCpeCG~~FkL~ 148 (165)
.-..|+-|.| .|..||.||..|.+.
T Consensus 15 CG~kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 15 CGAKFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcchhccCCC-CCccCCCCCCccCcc
Confidence 3457888999 889999999999998
No 33
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=57.41 E-value=13 Score=33.34 Aligned_cols=30 Identities=13% Similarity=0.380 Sum_probs=21.8
Q ss_pred CcceEEEEeecCC-cee---cCCCCceEEEEEeC
Q 031107 122 EHDVVWFWLEKGK-PHE---CPVCSQYFVLEVVG 151 (165)
Q Consensus 122 sH~v~Wf~L~kGk-p~R---CpeCG~~FkL~~vg 151 (165)
...+.++.+..+. ..| |..|+.|.|..+..
T Consensus 235 ~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~ 268 (309)
T PRK03564 235 SGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQE 268 (309)
T ss_pred CCceeeeeecCCCcceEeeecccccccceecccc
Confidence 3457777777653 444 99999999998665
No 34
>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=56.01 E-value=3.9 Score=28.29 Aligned_cols=22 Identities=18% Similarity=0.427 Sum_probs=11.4
Q ss_pred ceEEEEeecCCceecCCCCceE
Q 031107 124 DVVWFWLEKGKPHECPVCSQYF 145 (165)
Q Consensus 124 ~v~Wf~L~kGkp~RCpeCG~~F 145 (165)
.-.|......+|.-||+||..+
T Consensus 13 ~~~k~~~~S~~PatCP~C~a~~ 34 (54)
T PF09237_consen 13 KKPKSKSQSEQPATCPICGAVI 34 (54)
T ss_dssp ---CCCCTTS--EE-TTT--EE
T ss_pred hHHHHhhccCCCCCCCcchhhc
Confidence 3456677778899999999876
No 35
>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=54.81 E-value=14 Score=29.02 Aligned_cols=30 Identities=33% Similarity=0.701 Sum_probs=25.2
Q ss_pred ceEEEEeecCCceecCCCCceEEEEEeCCCCCC
Q 031107 124 DVVWFWLEKGKPHECPVCSQYFVLEVVGPGGPP 156 (165)
Q Consensus 124 ~v~Wf~L~kGkp~RCpeCG~~FkL~~vg~~~~p 156 (165)
+..|..+++ +.||.||.--..+++.||-++
T Consensus 66 dp~w~~irE---yyCP~Cgt~levE~~~Pg~P~ 95 (112)
T PF08882_consen 66 DPEWQVIRE---YYCPGCGTQLEVEAPPPGYPP 95 (112)
T ss_pred CCCcEEEEE---EECCCCcceeEEccCCCCCCc
Confidence 467888887 889999999999999987654
No 36
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=54.28 E-value=18 Score=21.67 Aligned_cols=20 Identities=25% Similarity=0.532 Sum_probs=15.8
Q ss_pred CCceecCCCCceEEEEEeCC
Q 031107 133 GKPHECPVCSQYFVLEVVGP 152 (165)
Q Consensus 133 Gkp~RCpeCG~~FkL~~vg~ 152 (165)
++-++|..||+.+.+..-+.
T Consensus 5 ~~~ykC~~Cgniv~v~~~~~ 24 (34)
T TIGR00319 5 GQVYKCEVCGNIVEVLHAGG 24 (34)
T ss_pred CcEEEcCCCCcEEEEEECCC
Confidence 67899999999997775443
No 37
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=54.27 E-value=8.7 Score=38.09 Aligned_cols=20 Identities=45% Similarity=0.976 Sum_probs=16.9
Q ss_pred CCceecCCCCceEEEEEeCCC
Q 031107 133 GKPHECPVCSQYFVLEVVGPG 153 (165)
Q Consensus 133 Gkp~RCpeCG~~FkL~~vg~~ 153 (165)
..|..||+||.- .|++.|.|
T Consensus 473 ~~p~~Cp~Cgs~-~L~~~G~G 492 (730)
T COG1198 473 PIPQSCPECGSE-HLRAVGPG 492 (730)
T ss_pred CCCCCCCCCCCC-eeEEeccc
Confidence 457889999998 99999875
No 38
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=53.17 E-value=9.3 Score=23.64 Aligned_cols=16 Identities=31% Similarity=0.814 Sum_probs=12.7
Q ss_pred ecCCceecCCCCceEE
Q 031107 131 EKGKPHECPVCSQYFV 146 (165)
Q Consensus 131 ~kGkp~RCpeCG~~Fk 146 (165)
.+|.-.+|+.||+.|.
T Consensus 21 ~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 21 PKGRKVRCSKCGHVFF 36 (36)
T ss_pred CCCcEEECCCCCCEeC
Confidence 3566788999999883
No 39
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=52.63 E-value=5.6 Score=37.70 Aligned_cols=11 Identities=36% Similarity=1.023 Sum_probs=10.1
Q ss_pred eecCCCCceEE
Q 031107 136 HECPVCSQYFV 146 (165)
Q Consensus 136 ~RCpeCG~~Fk 146 (165)
+|||||+++|.
T Consensus 296 YrCPEC~KVFs 306 (500)
T KOG3993|consen 296 YRCPECDKVFS 306 (500)
T ss_pred ecCCccccccc
Confidence 88999999995
No 40
>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=52.62 E-value=3.8 Score=25.63 Aligned_cols=17 Identities=29% Similarity=0.778 Sum_probs=13.1
Q ss_pred ecCCCCceEEEEEeCCC
Q 031107 137 ECPVCSQYFVLEVVGPG 153 (165)
Q Consensus 137 RCpeCG~~FkL~~vg~~ 153 (165)
-|+.||..|-+.+-.|.
T Consensus 3 ~C~~Cg~~Yh~~~~pP~ 19 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPK 19 (36)
T ss_dssp EETTTTEEEETTTB--S
T ss_pred CcCCCCCccccccCCCC
Confidence 39999999999988764
No 41
>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=52.46 E-value=8.1 Score=22.58 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=9.8
Q ss_pred cCCceecCCCCc
Q 031107 132 KGKPHECPVCSQ 143 (165)
Q Consensus 132 kGkp~RCpeCG~ 143 (165)
++.++.||.||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 467899999994
No 42
>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=49.92 E-value=9.7 Score=23.32 Aligned_cols=10 Identities=40% Similarity=1.421 Sum_probs=7.3
Q ss_pred CceecCCCCc
Q 031107 134 KPHECPVCSQ 143 (165)
Q Consensus 134 kp~RCpeCG~ 143 (165)
.|.+||.||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 3677888876
No 43
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=48.66 E-value=9.4 Score=27.01 Aligned_cols=10 Identities=50% Similarity=1.414 Sum_probs=9.4
Q ss_pred CCceecCCCC
Q 031107 133 GKPHECPVCS 142 (165)
Q Consensus 133 Gkp~RCpeCG 142 (165)
|.+++||.||
T Consensus 48 g~~Y~Cp~CG 57 (61)
T COG2888 48 GNPYRCPKCG 57 (61)
T ss_pred CCceECCCcC
Confidence 8899999998
No 44
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=47.61 E-value=13 Score=31.77 Aligned_cols=23 Identities=26% Similarity=0.531 Sum_probs=15.9
Q ss_pred CCCcceEEEEeecCC--ceecCCCCceE
Q 031107 120 EDEHDVVWFWLEKGK--PHECPVCSQYF 145 (165)
Q Consensus 120 eDsH~v~Wf~L~kGk--p~RCpeCG~~F 145 (165)
+-.|.++=. +|. ..||.+||++|
T Consensus 16 ev~hEVik~---~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 16 EVSHEVIKE---RGREPLVRCEECGTVH 40 (201)
T ss_pred hhhHHHHHh---cCCceEEEccCCCcEe
Confidence 444665432 344 68999999999
No 45
>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=47.16 E-value=28 Score=20.84 Aligned_cols=19 Identities=21% Similarity=0.440 Sum_probs=14.5
Q ss_pred CCceecCCCCceEEEEEeC
Q 031107 133 GKPHECPVCSQYFVLEVVG 151 (165)
Q Consensus 133 Gkp~RCpeCG~~FkL~~vg 151 (165)
.+-++|..||+...+..-+
T Consensus 2 ~~~ykC~~CGniv~v~~~~ 20 (34)
T cd00974 2 LEVYKCEICGNIVEVLNVG 20 (34)
T ss_pred CcEEEcCCCCcEEEEEECC
Confidence 4568999999999777543
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=46.69 E-value=13 Score=21.26 Aligned_cols=14 Identities=29% Similarity=0.807 Sum_probs=10.9
Q ss_pred ceecCCCCceEEEE
Q 031107 135 PHECPVCSQYFVLE 148 (165)
Q Consensus 135 p~RCpeCG~~FkL~ 148 (165)
...|+.||.-|.-.
T Consensus 2 l~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 2 LVPCPICGRKFNPD 15 (25)
T ss_pred CCcCCCCCCEECHH
Confidence 35699999999644
No 47
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=46.22 E-value=15 Score=24.85 Aligned_cols=12 Identities=25% Similarity=0.814 Sum_probs=10.7
Q ss_pred ecCCCCceEEEE
Q 031107 137 ECPVCSQYFVLE 148 (165)
Q Consensus 137 RCpeCG~~FkL~ 148 (165)
.||.||+.+.+.
T Consensus 2 ~CPyCge~~~~~ 13 (52)
T PF14255_consen 2 QCPYCGEPIEIL 13 (52)
T ss_pred CCCCCCCeeEEE
Confidence 699999999985
No 48
>smart00355 ZnF_C2H2 zinc finger.
Probab=45.87 E-value=8.2 Score=19.92 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=8.8
Q ss_pred eecCCCCceEE
Q 031107 136 HECPVCSQYFV 146 (165)
Q Consensus 136 ~RCpeCG~~Fk 146 (165)
++|++|+..|.
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 47999998875
No 49
>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=45.20 E-value=19 Score=32.17 Aligned_cols=29 Identities=21% Similarity=0.449 Sum_probs=20.9
Q ss_pred cceEEEEeec--CC-cee---cCCCCceEEEEEeC
Q 031107 123 HDVVWFWLEK--GK-PHE---CPVCSQYFVLEVVG 151 (165)
Q Consensus 123 H~v~Wf~L~k--Gk-p~R---CpeCG~~FkL~~vg 151 (165)
..+.++.++. ++ ..| |..|+.|.|..+..
T Consensus 234 ~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~ 268 (305)
T TIGR01562 234 KHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQE 268 (305)
T ss_pred CceeeEeecCCCCCcceEEeeccccccchhhhccc
Confidence 4576777764 32 344 99999999998775
No 50
>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=44.80 E-value=13 Score=22.59 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=6.8
Q ss_pred ceecCCCCceEE
Q 031107 135 PHECPVCSQYFV 146 (165)
Q Consensus 135 p~RCpeCG~~Fk 146 (165)
-+||..||.++-
T Consensus 11 ~~rC~~Cg~~~~ 22 (37)
T PF12172_consen 11 GQRCRDCGRVQF 22 (37)
T ss_dssp EEE-TTT--EEE
T ss_pred EEEcCCCCCEec
Confidence 478999999853
No 51
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=44.78 E-value=11 Score=23.47 Aligned_cols=11 Identities=45% Similarity=1.096 Sum_probs=8.8
Q ss_pred CceecCCCCce
Q 031107 134 KPHECPVCSQY 144 (165)
Q Consensus 134 kp~RCpeCG~~ 144 (165)
+|.+||.||+-
T Consensus 1 ~~~~Cp~Cg~~ 11 (47)
T PF14690_consen 1 KPPRCPHCGSP 11 (47)
T ss_pred CCccCCCcCCC
Confidence 47889999953
No 52
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=44.63 E-value=25 Score=23.93 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=17.0
Q ss_pred CCceecCCCCceEEEEEeCC
Q 031107 133 GKPHECPVCSQYFVLEVVGP 152 (165)
Q Consensus 133 Gkp~RCpeCG~~FkL~~vg~ 152 (165)
|....||+||.-|.++...|
T Consensus 20 GeiV~Cp~CGaeleVv~~~p 39 (54)
T TIGR01206 20 GELVICDECGAELEVVSLDP 39 (54)
T ss_pred CCEEeCCCCCCEEEEEeCCC
Confidence 77889999999999886665
No 53
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=44.32 E-value=9.9 Score=26.95 Aligned_cols=16 Identities=25% Similarity=0.522 Sum_probs=13.9
Q ss_pred EeecCCceecCCCCce
Q 031107 129 WLEKGKPHECPVCSQY 144 (165)
Q Consensus 129 ~L~kGkp~RCpeCG~~ 144 (165)
.|..+.+.||-|||+-
T Consensus 31 ~lk~~D~irCReCG~R 46 (62)
T KOG3507|consen 31 TLKRGDVIRCRECGYR 46 (62)
T ss_pred cccCCCcEehhhcchH
Confidence 4788999999999974
No 54
>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=43.91 E-value=15 Score=25.22 Aligned_cols=13 Identities=23% Similarity=0.764 Sum_probs=11.2
Q ss_pred eecCCCCceEEEE
Q 031107 136 HECPVCSQYFVLE 148 (165)
Q Consensus 136 ~RCpeCG~~FkL~ 148 (165)
-.||+||.+|-+.
T Consensus 54 L~Cp~c~r~YPI~ 66 (68)
T PF03966_consen 54 LICPECGREYPIR 66 (68)
T ss_dssp EEETTTTEEEEEE
T ss_pred EEcCCCCCEEeCC
Confidence 5699999999875
No 55
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=42.85 E-value=25 Score=23.78 Aligned_cols=22 Identities=14% Similarity=0.391 Sum_probs=15.9
Q ss_pred eecCCceecCCCCceEEEEEeC
Q 031107 130 LEKGKPHECPVCSQYFVLEVVG 151 (165)
Q Consensus 130 L~kGkp~RCpeCG~~FkL~~vg 151 (165)
+.++...|||.||+--.++.-.
T Consensus 19 ~~~~~~irCp~Cg~rIl~K~R~ 40 (49)
T COG1996 19 DQETRGIRCPYCGSRILVKERP 40 (49)
T ss_pred hhccCceeCCCCCcEEEEeccC
Confidence 4467789999999976665433
No 56
>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=40.56 E-value=12 Score=29.98 Aligned_cols=26 Identities=19% Similarity=0.351 Sum_probs=21.1
Q ss_pred ceEEEEeecCCceecCCCCceEEEEEe
Q 031107 124 DVVWFWLEKGKPHECPVCSQYFVLEVV 150 (165)
Q Consensus 124 ~v~Wf~L~kGkp~RCpeCG~~FkL~~v 150 (165)
-..|+-|.| .|..||.||..|.+.++
T Consensus 16 g~kFYDLnk-~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 16 GSKFYDLNR-RPAVSPYTGEQFPPEEA 41 (129)
T ss_pred CccccccCC-CCccCCCcCCccCcchh
Confidence 456777888 89999999999987744
No 57
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.35 E-value=14 Score=29.40 Aligned_cols=22 Identities=18% Similarity=0.355 Sum_probs=15.8
Q ss_pred EEEEeecCCceecCCCCceEEEE
Q 031107 126 VWFWLEKGKPHECPVCSQYFVLE 148 (165)
Q Consensus 126 ~Wf~L~kGkp~RCpeCG~~FkL~ 148 (165)
.=.-+.+|+ -.|||||++|-+.
T Consensus 90 le~~v~EG~-l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 90 LEIDVIEGE-LVCPETGRVFPIS 111 (124)
T ss_pred hhhhhccce-EecCCCCcEeecc
Confidence 334455666 5799999999764
No 58
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=39.97 E-value=13 Score=30.62 Aligned_cols=14 Identities=36% Similarity=1.144 Sum_probs=8.7
Q ss_pred eecCC-ceecCCCCc
Q 031107 130 LEKGK-PHECPVCSQ 143 (165)
Q Consensus 130 L~kGk-p~RCpeCG~ 143 (165)
+.+|+ |-+||.||.
T Consensus 143 ~~~ge~P~~CPiCga 157 (166)
T COG1592 143 THEGEAPEVCPICGA 157 (166)
T ss_pred cccCCCCCcCCCCCC
Confidence 34455 566888874
No 59
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=39.67 E-value=24 Score=22.07 Aligned_cols=16 Identities=31% Similarity=0.837 Sum_probs=11.6
Q ss_pred ceecCCCCceEEEEEeCC
Q 031107 135 PHECPVCSQYFVLEVVGP 152 (165)
Q Consensus 135 p~RCpeCG~~FkL~~vg~ 152 (165)
+..|+.||.-++ .+|.
T Consensus 2 ~~~C~~Cg~~l~--~ig~ 17 (47)
T PF13005_consen 2 PRACPDCGGELK--EIGE 17 (47)
T ss_pred CCcCCCCCceee--ECCc
Confidence 567999999544 6664
No 60
>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=38.42 E-value=21 Score=21.39 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=9.2
Q ss_pred eecCCCCceEEE
Q 031107 136 HECPVCSQYFVL 147 (165)
Q Consensus 136 ~RCpeCG~~FkL 147 (165)
++|..||..|.-
T Consensus 2 ~~C~~CGy~y~~ 13 (33)
T cd00350 2 YVCPVCGYIYDG 13 (33)
T ss_pred EECCCCCCEECC
Confidence 579999988753
No 61
>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=37.99 E-value=19 Score=28.12 Aligned_cols=12 Identities=25% Similarity=0.850 Sum_probs=9.9
Q ss_pred CceecCCCCceE
Q 031107 134 KPHECPVCSQYF 145 (165)
Q Consensus 134 kp~RCpeCG~~F 145 (165)
+=.+|+.||++|
T Consensus 123 ~f~~C~~C~kiy 134 (147)
T PF01927_consen 123 EFWRCPGCGKIY 134 (147)
T ss_pred eEEECCCCCCEe
Confidence 356799999988
No 62
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=37.62 E-value=15 Score=32.48 Aligned_cols=14 Identities=21% Similarity=0.679 Sum_probs=12.1
Q ss_pred CceecCCCCceEEE
Q 031107 134 KPHECPVCSQYFVL 147 (165)
Q Consensus 134 kp~RCpeCG~~FkL 147 (165)
.-+-||+||++|+|
T Consensus 45 ~~~vc~~c~~h~rl 58 (292)
T PRK05654 45 NLNVCPKCGHHMRI 58 (292)
T ss_pred cCCCCCCCCCCeeC
Confidence 34679999999998
No 63
>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=37.61 E-value=18 Score=20.90 Aligned_cols=13 Identities=23% Similarity=0.595 Sum_probs=11.0
Q ss_pred CceecCCCCceEE
Q 031107 134 KPHECPVCSQYFV 146 (165)
Q Consensus 134 kp~RCpeCG~~Fk 146 (165)
.++.|..|+.+|.
T Consensus 2 ~~~~C~~C~~~~~ 14 (35)
T smart00451 2 GGFYCKLCNVTFT 14 (35)
T ss_pred cCeEccccCCccC
Confidence 3588999999996
No 64
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=37.47 E-value=45 Score=28.88 Aligned_cols=50 Identities=22% Similarity=0.331 Sum_probs=31.4
Q ss_pred CCCCCCCCCeeeeccCCceEEeecCCCCCCCcceEEE--EeecCCceecCCCCc-eEE
Q 031107 92 GPFGTKDAPAVVKSYYDKRIVGCPGGEGEDEHDVVWF--WLEKGKPHECPVCSQ-YFV 146 (165)
Q Consensus 92 ~~~GTke~P~lVpS~~~~RiVGC~g~p~eDsH~v~Wf--~L~kGkp~RCpeCG~-~Fk 146 (165)
...|.+ +||.=+.+...+-|+-- +. ......+ .++.+.+.+||.||. ..+
T Consensus 106 e~AGs~---~Vi~lHGsl~~~~C~~C-~~-~~~~~~~~~~~~~~~~p~C~~Cg~~~lr 158 (250)
T COG0846 106 ERAGSK---NVIELHGSLKRVRCSKC-GN-QYYDEDVIKFIEDGLIPRCPKCGGPVLR 158 (250)
T ss_pred HHcCCC---cEEEeccceeeeEeCCC-cC-ccchhhhhhhcccCCCCcCccCCCcccc
Confidence 456777 89998888888888732 11 1110111 234456899999999 444
No 65
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=37.17 E-value=9.4 Score=27.08 Aligned_cols=15 Identities=33% Similarity=0.775 Sum_probs=11.9
Q ss_pred cCC-ceecCCCCceEE
Q 031107 132 KGK-PHECPVCSQYFV 146 (165)
Q Consensus 132 kGk-p~RCpeCG~~Fk 146 (165)
.|+ -.|||-||..|.
T Consensus 13 DGE~~lrCPRC~~~FR 28 (65)
T COG4049 13 DGEEFLRCPRCGMVFR 28 (65)
T ss_pred CCceeeeCCchhHHHH
Confidence 465 478999999885
No 66
>PHA00733 hypothetical protein
Probab=35.04 E-value=17 Score=28.13 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=13.8
Q ss_pred eEEEEeecCCceecCCCCceEE
Q 031107 125 VVWFWLEKGKPHECPVCSQYFV 146 (165)
Q Consensus 125 v~Wf~L~kGkp~RCpeCG~~Fk 146 (165)
..++.....+|+.|++||..|.
T Consensus 63 ~~~~~~~~~kPy~C~~Cgk~Fs 84 (128)
T PHA00733 63 YKLLTSKAVSPYVCPLCLMPFS 84 (128)
T ss_pred HhhcccCCCCCccCCCCCCcCC
Confidence 3444455566777777777765
No 67
>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=34.83 E-value=19 Score=25.04 Aligned_cols=11 Identities=55% Similarity=1.476 Sum_probs=8.2
Q ss_pred Ccee-cCCCCce
Q 031107 134 KPHE-CPVCSQY 144 (165)
Q Consensus 134 kp~R-CpeCG~~ 144 (165)
+||+ |+.||.-
T Consensus 1 e~HkHC~~CG~~ 12 (59)
T PF09889_consen 1 EPHKHCPVCGKP 12 (59)
T ss_pred CCCCcCCcCCCc
Confidence 4667 9999963
No 68
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=34.36 E-value=21 Score=25.04 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=9.3
Q ss_pred CCceecCCCCc
Q 031107 133 GKPHECPVCSQ 143 (165)
Q Consensus 133 Gkp~RCpeCG~ 143 (165)
+.+++||.||-
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 78899999983
No 69
>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=34.29 E-value=36 Score=27.78 Aligned_cols=26 Identities=23% Similarity=0.477 Sum_probs=17.8
Q ss_pred eEEEEeecCCc---eecCCCCceEEEEEe
Q 031107 125 VVWFWLEKGKP---HECPVCSQYFVLEVV 150 (165)
Q Consensus 125 v~Wf~L~kGkp---~RCpeCG~~FkL~~v 150 (165)
..-|.|....+ .||-+|++.|..+.+
T Consensus 119 ~~~F~v~~~~~~~~lrC~YCe~~~~~~~i 147 (150)
T TIGR00240 119 SSKFYVRSEEPDIALRCYYCEKEIEHNVV 147 (150)
T ss_pred CcEEEEecCCCceEEEEECCCCEEecceE
Confidence 34455544444 899999999986654
No 70
>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=33.82 E-value=24 Score=23.33 Aligned_cols=11 Identities=36% Similarity=1.008 Sum_probs=9.0
Q ss_pred eecCCCCceEE
Q 031107 136 HECPVCSQYFV 146 (165)
Q Consensus 136 ~RCpeCG~~Fk 146 (165)
++|..||.+|.
T Consensus 2 y~C~~CgyvYd 12 (47)
T PF00301_consen 2 YQCPVCGYVYD 12 (47)
T ss_dssp EEETTTSBEEE
T ss_pred cCCCCCCEEEc
Confidence 68999998774
No 71
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=33.17 E-value=25 Score=30.44 Aligned_cols=19 Identities=21% Similarity=0.789 Sum_probs=9.8
Q ss_pred ceEEeecCCCCCCCcceEEEEee
Q 031107 109 KRIVGCPGGEGEDEHDVVWFWLE 131 (165)
Q Consensus 109 ~RiVGC~g~p~eDsH~v~Wf~L~ 131 (165)
.-+|||-+ +.-.+-||.+.
T Consensus 230 g~Mi~CDn----~~C~~eWFH~~ 248 (274)
T KOG1973|consen 230 GKMIGCDN----PGCPIEWFHFT 248 (274)
T ss_pred ccccccCC----CCCCcceEEEe
Confidence 34566654 24455666554
No 72
>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=32.79 E-value=39 Score=20.46 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=8.0
Q ss_pred eecCCCCceE
Q 031107 136 HECPVCSQYF 145 (165)
Q Consensus 136 ~RCpeCG~~F 145 (165)
..|++||..|
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 4599999876
No 73
>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=32.68 E-value=20 Score=23.34 Aligned_cols=11 Identities=36% Similarity=1.047 Sum_probs=8.0
Q ss_pred ceecCCCCceE
Q 031107 135 PHECPVCSQYF 145 (165)
Q Consensus 135 p~RCpeCG~~F 145 (165)
.++||.||..|
T Consensus 2 ~f~CP~C~~~~ 12 (54)
T PF05605_consen 2 SFTCPYCGKGF 12 (54)
T ss_pred CcCCCCCCCcc
Confidence 36788888844
No 74
>PHA00626 hypothetical protein
Probab=32.16 E-value=25 Score=24.76 Aligned_cols=21 Identities=14% Similarity=0.173 Sum_probs=16.6
Q ss_pred CCceecCCCCceEEEEEeCCC
Q 031107 133 GKPHECPVCSQYFVLEVVGPG 153 (165)
Q Consensus 133 Gkp~RCpeCG~~FkL~~vg~~ 153 (165)
-..+.|+.||..|.-+-.|+.
T Consensus 21 snrYkCkdCGY~ft~~~~~~~ 41 (59)
T PHA00626 21 SDDYVCCDCGYNDSKDAFGER 41 (59)
T ss_pred CcceEcCCCCCeechhhhhhc
Confidence 467889999999987766653
No 75
>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=31.74 E-value=17 Score=32.02 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=15.9
Q ss_pred ceEEEEeecCCceecCCCCceEEE
Q 031107 124 DVVWFWLEKGKPHECPVCSQYFVL 147 (165)
Q Consensus 124 ~v~Wf~L~kGkp~RCpeCG~~FkL 147 (165)
.++|-.--+..-+-||.||++|+|
T Consensus 34 ~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 34 QVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred chhhHHHHHhhCCCCCCCCCcCcC
Confidence 444443222344779999999998
No 76
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=31.57 E-value=21 Score=23.34 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=5.3
Q ss_pred ecCCCCceE
Q 031107 137 ECPVCSQYF 145 (165)
Q Consensus 137 RCpeCG~~F 145 (165)
.||.||.-|
T Consensus 22 ~CPlC~r~l 30 (54)
T PF04423_consen 22 CCPLCGRPL 30 (54)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCCC
Confidence 899999876
No 77
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=31.19 E-value=26 Score=27.49 Aligned_cols=23 Identities=26% Similarity=0.657 Sum_probs=15.6
Q ss_pred ceEEEE--eecCCc--eecCCCCceEE
Q 031107 124 DVVWFW--LEKGKP--HECPVCSQYFV 146 (165)
Q Consensus 124 ~v~Wf~--L~kGkp--~RCpeCG~~Fk 146 (165)
...||+ |.+|+. .||+.||++|-
T Consensus 14 ~~~~f~~~l~~~kl~g~kC~~CG~v~~ 40 (140)
T COG1545 14 ARSKFFKGLKEGKLLGTKCKKCGRVYF 40 (140)
T ss_pred hhhHHhhhhhhCcEEEEEcCCCCeEEc
Confidence 344554 566773 67999999874
No 78
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.04 E-value=42 Score=26.33 Aligned_cols=28 Identities=29% Similarity=0.534 Sum_probs=21.0
Q ss_pred cceEEEEeecCCceecCCCCceEEEEEeC
Q 031107 123 HDVVWFWLEKGKPHECPVCSQYFVLEVVG 151 (165)
Q Consensus 123 H~v~Wf~L~kGkp~RCpeCG~~FkL~~vg 151 (165)
++..|..++-|- ..||.||.-|.-.++-
T Consensus 38 ~~LdyV~ie~G~-t~CP~Cg~~~e~~fvv 65 (115)
T COG1885 38 PDLDYVEIEVGS-TSCPKCGEPFESAFVV 65 (115)
T ss_pred CCCCeEEEeccc-ccCCCCCCccceeEEE
Confidence 456677777765 6799999988876654
No 79
>PRK04860 hypothetical protein; Provisional
Probab=30.99 E-value=60 Score=26.28 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=14.3
Q ss_pred CCceecCCCCceEEEEE
Q 031107 133 GKPHECPVCSQYFVLEV 149 (165)
Q Consensus 133 Gkp~RCpeCG~~FkL~~ 149 (165)
.++++|..|+.-|++..
T Consensus 141 ~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 141 EAVYRCRRCGETLVFKG 157 (160)
T ss_pred CccEECCCCCceeEEec
Confidence 46899999999998763
No 80
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=30.82 E-value=17 Score=32.43 Aligned_cols=15 Identities=20% Similarity=0.447 Sum_probs=12.3
Q ss_pred CceecCCCCceEEEE
Q 031107 134 KPHECPVCSQYFVLE 148 (165)
Q Consensus 134 kp~RCpeCG~~FkL~ 148 (165)
.-+-||+||++|+|.
T Consensus 56 ~~~vcp~c~~h~rlt 70 (296)
T CHL00174 56 KMNICEQCGYHLKMS 70 (296)
T ss_pred cCCCCCCCCCCcCCC
Confidence 346799999999983
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=30.44 E-value=27 Score=23.31 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=9.6
Q ss_pred eecCCCCceEEE
Q 031107 136 HECPVCSQYFVL 147 (165)
Q Consensus 136 ~RCpeCG~~FkL 147 (165)
++|..||.+|.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 689999987753
No 82
>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=28.82 E-value=25 Score=19.71 Aligned_cols=11 Identities=36% Similarity=1.071 Sum_probs=9.2
Q ss_pred eecCCCCceEE
Q 031107 136 HECPVCSQYFV 146 (165)
Q Consensus 136 ~RCpeCG~~Fk 146 (165)
+.|..|+.+|.
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 57999999885
No 83
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.82 E-value=31 Score=23.81 Aligned_cols=12 Identities=25% Similarity=0.703 Sum_probs=9.8
Q ss_pred ceecCCCCceEE
Q 031107 135 PHECPVCSQYFV 146 (165)
Q Consensus 135 p~RCpeCG~~Fk 146 (165)
-+||..||.+|-
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 478999998875
No 84
>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=28.21 E-value=23 Score=33.62 Aligned_cols=13 Identities=46% Similarity=0.854 Sum_probs=11.4
Q ss_pred ecCCCCceEEEEE
Q 031107 137 ECPVCSQYFVLEV 149 (165)
Q Consensus 137 RCpeCG~~FkL~~ 149 (165)
.||.||++|.|++
T Consensus 202 pCPhCg~~~~l~~ 214 (557)
T PF05876_consen 202 PCPHCGEEQVLEW 214 (557)
T ss_pred cCCCCCCCccccc
Confidence 4999999999973
No 85
>PHA00732 hypothetical protein
Probab=27.90 E-value=25 Score=25.30 Aligned_cols=10 Identities=40% Similarity=1.291 Sum_probs=5.4
Q ss_pred ecCCCCceEE
Q 031107 137 ECPVCSQYFV 146 (165)
Q Consensus 137 RCpeCG~~Fk 146 (165)
+|++||..|.
T Consensus 29 ~C~~CgKsF~ 38 (79)
T PHA00732 29 KCPVCNKSYR 38 (79)
T ss_pred ccCCCCCEeC
Confidence 4555555554
No 86
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=27.76 E-value=41 Score=24.04 Aligned_cols=34 Identities=29% Similarity=0.602 Sum_probs=21.2
Q ss_pred eecCCCCCCCcceEEEEeecCC-ceecCCCCceEEEEE
Q 031107 113 GCPGGEGEDEHDVVWFWLEKGK-PHECPVCSQYFVLEV 149 (165)
Q Consensus 113 GC~g~p~eDsH~v~Wf~L~kGk-p~RCpeCG~~FkL~~ 149 (165)
-|+|+ |--.|..=-|..|+ ..|||.|.-.--.+|
T Consensus 24 PCPCG---DRFeIsLeDl~~GE~VArCPSCSLiv~vvy 58 (67)
T COG5216 24 PCPCG---DRFEISLEDLRNGEVVARCPSCSLIVCVVY 58 (67)
T ss_pred cCCCC---CEeEEEHHHhhCCceEEEcCCceEEEEEEe
Confidence 46773 44555555566776 678888876555444
No 87
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=26.73 E-value=25 Score=32.79 Aligned_cols=24 Identities=29% Similarity=0.634 Sum_probs=14.7
Q ss_pred EeecCCcee-cCCCCceEEEEEeCC
Q 031107 129 WLEKGKPHE-CPVCSQYFVLEVVGP 152 (165)
Q Consensus 129 ~L~kGkp~R-CpeCG~~FkL~~vg~ 152 (165)
.+++|+|.- ||.||..|+-++-|.
T Consensus 373 PIY~G~~~v~CP~cgA~y~~~~kG~ 397 (422)
T PF06957_consen 373 PIYRGSPSVKCPYCGAKYHPEYKGQ 397 (422)
T ss_dssp EEETTS-EEE-TTT--EEEGGGTTS
T ss_pred cccCCCCCeeCCCCCCccChhhCCC
Confidence 357898754 999999998766553
No 88
>PRK07220 DNA topoisomerase I; Validated
Probab=26.37 E-value=1.2e+02 Score=29.94 Aligned_cols=41 Identities=17% Similarity=0.226 Sum_probs=24.6
Q ss_pred ccCCceEEeecCCCCCCCcceEEEEeecCC----ceecCCCCc-eEEEE
Q 031107 105 SYYDKRIVGCPGGEGEDEHDVVWFWLEKGK----PHECPVCSQ-YFVLE 148 (165)
Q Consensus 105 S~~~~RiVGC~g~p~eDsH~v~Wf~L~kGk----p~RCpeCG~-~FkL~ 148 (165)
+....+.+||.++| +-....|+. .+|. -..||+||. .++..
T Consensus 604 ~r~g~~f~gCs~yp--~C~~~~~l~-~~g~~~~~~~~Cp~Cg~~~~k~~ 649 (740)
T PRK07220 604 SKRGSRFIGCEGYP--ECTFSLPLP-KSGQIIVTDKVCEAHGLNHIRII 649 (740)
T ss_pred cCCCceEEEcCCCC--CCCceeeCC-CCCccccCCCCCCCCCCceEEEE
Confidence 34456789999987 334566642 1221 246999995 55444
No 89
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=26.35 E-value=23 Score=35.98 Aligned_cols=13 Identities=23% Similarity=0.782 Sum_probs=8.1
Q ss_pred eecCCCCceEEEE
Q 031107 136 HECPVCSQYFVLE 148 (165)
Q Consensus 136 ~RCpeCG~~FkL~ 148 (165)
+.|+|||..||.+
T Consensus 282 FKCtECgKAFKfK 294 (1007)
T KOG3623|consen 282 FKCTECGKAFKFK 294 (1007)
T ss_pred ccccccchhhhhH
Confidence 4566666666654
No 90
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=26.15 E-value=49 Score=22.26 Aligned_cols=16 Identities=31% Similarity=0.640 Sum_probs=13.2
Q ss_pred CCceecCCCCceEEEE
Q 031107 133 GKPHECPVCSQYFVLE 148 (165)
Q Consensus 133 Gkp~RCpeCG~~FkL~ 148 (165)
+++..|..||.-|..-
T Consensus 2 Dk~l~C~dCg~~FvfT 17 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFT 17 (49)
T ss_pred CeeEEcccCCCeEEEe
Confidence 5778899999999864
No 91
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.97 E-value=31 Score=22.69 Aligned_cols=16 Identities=31% Similarity=0.646 Sum_probs=11.5
Q ss_pred EeecC-CceecCCCCce
Q 031107 129 WLEKG-KPHECPVCSQY 144 (165)
Q Consensus 129 ~L~kG-kp~RCpeCG~~ 144 (165)
.|.++ +...||+||..
T Consensus 39 ~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 39 EIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHcCCCeEECcCCCcc
Confidence 34454 68899999964
No 92
>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=25.83 E-value=47 Score=20.66 Aligned_cols=12 Identities=42% Similarity=1.049 Sum_probs=5.4
Q ss_pred CCceecCCCCce
Q 031107 133 GKPHECPVCSQY 144 (165)
Q Consensus 133 Gkp~RCpeCG~~ 144 (165)
|...+|++||..
T Consensus 6 ~~~~~C~~C~~~ 17 (36)
T PF11781_consen 6 GPNEPCPVCGSR 17 (36)
T ss_pred cCCCcCCCCCCe
Confidence 333445555543
No 93
>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=25.77 E-value=76 Score=21.17 Aligned_cols=17 Identities=24% Similarity=0.546 Sum_probs=12.4
Q ss_pred eecCCceecCCCCceEE
Q 031107 130 LEKGKPHECPVCSQYFV 146 (165)
Q Consensus 130 L~kGkp~RCpeCG~~Fk 146 (165)
-..+..+.|+.||..+-
T Consensus 41 ~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 41 RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccccceEEcCCCCCEEC
Confidence 34567788999998753
No 94
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=25.65 E-value=33 Score=23.44 Aligned_cols=12 Identities=50% Similarity=1.240 Sum_probs=8.1
Q ss_pred Ccee-cCCCCceE
Q 031107 134 KPHE-CPVCSQYF 145 (165)
Q Consensus 134 kp~R-CpeCG~~F 145 (165)
.|++ |+.||.|=
T Consensus 38 ~~H~vC~~CG~Y~ 50 (57)
T PRK12286 38 LPHRVCPSCGYYK 50 (57)
T ss_pred CCeEECCCCCcCC
Confidence 3555 99999653
No 95
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=25.35 E-value=46 Score=21.70 Aligned_cols=12 Identities=25% Similarity=0.830 Sum_probs=10.1
Q ss_pred ecCCCCceEEEE
Q 031107 137 ECPVCSQYFVLE 148 (165)
Q Consensus 137 RCpeCG~~FkL~ 148 (165)
+|+.||+-|+..
T Consensus 30 ~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 30 KCPKCGHEWKAS 41 (55)
T ss_pred ECCCCCCeeEcc
Confidence 699999999874
No 96
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=25.24 E-value=33 Score=28.46 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=9.9
Q ss_pred CceecCCCCceE
Q 031107 134 KPHECPVCSQYF 145 (165)
Q Consensus 134 kp~RCpeCG~~F 145 (165)
+-.+||.||+.|
T Consensus 129 ~f~~C~~CgkiY 140 (165)
T COG1656 129 EFYRCPKCGKIY 140 (165)
T ss_pred ceeECCCCcccc
Confidence 457899999987
No 97
>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=25.04 E-value=39 Score=21.26 Aligned_cols=19 Identities=32% Similarity=0.674 Sum_probs=12.5
Q ss_pred CceecCCCCceEEEEEeCC
Q 031107 134 KPHECPVCSQYFVLEVVGP 152 (165)
Q Consensus 134 kp~RCpeCG~~FkL~~vg~ 152 (165)
-|.+|+.|+..|=++..-+
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~ 30 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLP 30 (43)
T ss_dssp SHEE-TTTS-EE-TTTHST
T ss_pred CCeECCCCCcccCccccCc
Confidence 5899989999998775554
No 98
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=24.81 E-value=1.1e+02 Score=21.71 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=24.0
Q ss_pred EEeecCCCCCCCcceEEEEeecCCcee-cCCCCceEEEEEe
Q 031107 111 IVGCPGGEGEDEHDVVWFWLEKGKPHE-CPVCSQYFVLEVV 150 (165)
Q Consensus 111 iVGC~g~p~eDsH~v~Wf~L~kGkp~R-CpeCG~~FkL~~v 150 (165)
|-|-+|.- =.+-+.+=||.++|..++ |-.||+...+...
T Consensus 6 IAGa~CP~-C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 6 IAGAVCPK-CQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ecCccCCC-CcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 33555532 234455555667766655 9999998877544
No 99
>PRK14973 DNA topoisomerase I; Provisional
Probab=24.56 E-value=1e+02 Score=31.56 Aligned_cols=35 Identities=17% Similarity=0.211 Sum_probs=21.4
Q ss_pred CCceEEeecCCCCCCCcceEEEEee-cCCc----eecCCCCc
Q 031107 107 YDKRIVGCPGGEGEDEHDVVWFWLE-KGKP----HECPVCSQ 143 (165)
Q Consensus 107 ~~~RiVGC~g~p~eDsH~v~Wf~L~-kGkp----~RCpeCG~ 143 (165)
...+.+||+++|+ -.....++.. .|+. ..||+||.
T Consensus 604 k~gkFigCS~Yp~--Ck~t~~L~~~~~g~~~~~~~~Cp~CG~ 643 (936)
T PRK14973 604 GSSQFIGCSGYPD--CTFNIGLPGTTWGWAIRTDEVCPIHHL 643 (936)
T ss_pred cCceeEECCCCCC--CCccccCCccccccCCCCCCCCCCCCC
Confidence 3456899999873 2334444322 2433 46999997
No 100
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.54 E-value=51 Score=24.90 Aligned_cols=18 Identities=22% Similarity=0.713 Sum_probs=13.2
Q ss_pred CceecCCCCceEEEEEeCC
Q 031107 134 KPHECPVCSQYFVLEVVGP 152 (165)
Q Consensus 134 kp~RCpeCG~~FkL~~vg~ 152 (165)
..+.||+||.- .+++++-
T Consensus 34 ~~~~Cp~C~~~-~VkR~a~ 51 (89)
T COG1997 34 AKHVCPFCGRT-TVKRIAT 51 (89)
T ss_pred cCCcCCCCCCc-ceeeecc
Confidence 46778888887 7776654
No 101
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=24.51 E-value=48 Score=20.98 Aligned_cols=14 Identities=21% Similarity=0.736 Sum_probs=10.7
Q ss_pred ceecCCCCceEEEE
Q 031107 135 PHECPVCSQYFVLE 148 (165)
Q Consensus 135 p~RCpeCG~~FkL~ 148 (165)
...|++||-.|...
T Consensus 13 ~~~C~~CgM~Y~~~ 26 (41)
T PF13878_consen 13 ATTCPTCGMLYSPG 26 (41)
T ss_pred CcCCCCCCCEECCC
Confidence 46799999888643
No 102
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=24.20 E-value=37 Score=22.90 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=8.0
Q ss_pred ceecCCCCce
Q 031107 135 PHECPVCSQY 144 (165)
Q Consensus 135 p~RCpeCG~~ 144 (165)
.+||+.||.+
T Consensus 44 ~y~C~~Cg~~ 53 (54)
T PF10058_consen 44 QYRCPYCGAL 53 (54)
T ss_pred EEEcCCCCCc
Confidence 4789999974
No 103
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.03 E-value=47 Score=25.88 Aligned_cols=20 Identities=25% Similarity=0.522 Sum_probs=16.4
Q ss_pred ceecCCCCceEEEEEeCCCC
Q 031107 135 PHECPVCSQYFVLEVVGPGG 154 (165)
Q Consensus 135 p~RCpeCG~~FkL~~vg~~~ 154 (165)
-++|+.|+.-|.+.+-.+..
T Consensus 53 RyrC~~C~~tf~~~~~~~~~ 72 (129)
T COG3677 53 RYKCKSCGSTFTVETGSPLS 72 (129)
T ss_pred ccccCCcCcceeeeccCccc
Confidence 46799999999999877654
No 104
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.89 E-value=49 Score=25.82 Aligned_cols=14 Identities=21% Similarity=0.563 Sum_probs=10.8
Q ss_pred ceecCCCCceEEEE
Q 031107 135 PHECPVCSQYFVLE 148 (165)
Q Consensus 135 p~RCpeCG~~FkL~ 148 (165)
..+|+.||+.|.+.
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 36788888888775
No 105
>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=23.72 E-value=48 Score=20.12 Aligned_cols=15 Identities=33% Similarity=0.822 Sum_probs=11.6
Q ss_pred ecCCceecCCCCceE
Q 031107 131 EKGKPHECPVCSQYF 145 (165)
Q Consensus 131 ~kGkp~RCpeCG~~F 145 (165)
..|...-||+||+-+
T Consensus 15 ~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 15 EDGELLVCPECGHEW 29 (30)
T ss_dssp E-SSSEEETTTTEEE
T ss_pred ccCCEEeCCcccccC
Confidence 778889999999743
No 106
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=23.19 E-value=72 Score=21.82 Aligned_cols=22 Identities=23% Similarity=0.499 Sum_probs=18.2
Q ss_pred eecCCCCceEEEEEeCCCCCCC
Q 031107 136 HECPVCSQYFVLEVVGPGGPPD 157 (165)
Q Consensus 136 ~RCpeCG~~FkL~~vg~~~~p~ 157 (165)
..||-||..+.|....+...|.
T Consensus 25 IKCpRC~tiN~~~a~~~~~~p~ 46 (51)
T PF10122_consen 25 IKCPRCKTINHVRATSPEPEPL 46 (51)
T ss_pred EECCCCCccceEeccCCCCCch
Confidence 5699999999999988765554
No 107
>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=23.05 E-value=50 Score=25.77 Aligned_cols=19 Identities=21% Similarity=0.447 Sum_probs=15.2
Q ss_pred eecCCceecCCCCceEEEE
Q 031107 130 LEKGKPHECPVCSQYFVLE 148 (165)
Q Consensus 130 L~kGkp~RCpeCG~~FkL~ 148 (165)
-+.|..+-|||||+-+.-.
T Consensus 14 Y~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 14 YHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred EecCCeeECcccccccccc
Confidence 4568889999999977654
No 108
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=22.87 E-value=30 Score=32.40 Aligned_cols=21 Identities=29% Similarity=0.545 Sum_probs=17.6
Q ss_pred EEeecCCceecCCCCceEEEE
Q 031107 128 FWLEKGKPHECPVCSQYFVLE 148 (165)
Q Consensus 128 f~L~kGkp~RCpeCG~~FkL~ 148 (165)
|.+...||+||+.|.+-||..
T Consensus 391 ~~~~~nk~~r~~i~~~~~k~~ 411 (442)
T KOG4124|consen 391 GFVVENKPYRCEVCSKRYKNL 411 (442)
T ss_pred eeeeccCcccChhhhhhhccC
Confidence 356678999999999999964
No 109
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.43 E-value=32 Score=26.32 Aligned_cols=18 Identities=22% Similarity=0.551 Sum_probs=13.4
Q ss_pred CceecCCCCceEEEEEeC
Q 031107 134 KPHECPVCSQYFVLEVVG 151 (165)
Q Consensus 134 kp~RCpeCG~~FkL~~vg 151 (165)
+|.+|--||..|.=..|.
T Consensus 57 ~Pa~CkkCGfef~~~~ik 74 (97)
T COG3357 57 RPARCKKCGFEFRDDKIK 74 (97)
T ss_pred cChhhcccCccccccccC
Confidence 688898899888754443
No 110
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=22.31 E-value=47 Score=25.15 Aligned_cols=14 Identities=29% Similarity=0.359 Sum_probs=11.3
Q ss_pred ceecCCCCceEEEE
Q 031107 135 PHECPVCSQYFVLE 148 (165)
Q Consensus 135 p~RCpeCG~~FkL~ 148 (165)
..||..||+.|.+.
T Consensus 70 ~~~C~~Cg~~~~~~ 83 (113)
T PRK12380 70 QAWCWDCSQVVEIH 83 (113)
T ss_pred EEEcccCCCEEecC
Confidence 36799999998875
No 111
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=22.24 E-value=31 Score=25.36 Aligned_cols=19 Identities=21% Similarity=0.536 Sum_probs=14.0
Q ss_pred ceecCCCCceEEEEEeCCC
Q 031107 135 PHECPVCSQYFVLEVVGPG 153 (165)
Q Consensus 135 p~RCpeCG~~FkL~~vg~~ 153 (165)
..+|+.||.=|.-..-+++
T Consensus 8 ~~~C~~CG~d~~~~~adDg 26 (86)
T PF06170_consen 8 APRCPHCGLDYSHARADDG 26 (86)
T ss_pred CCcccccCCccccCCcCcc
Confidence 3579999998877665543
No 112
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=21.59 E-value=43 Score=34.21 Aligned_cols=45 Identities=27% Similarity=0.461 Sum_probs=28.7
Q ss_pred eeeeccCCceEEeecCCCCCCC----c-ceEEEEeecC-CceecCCCCceEEE
Q 031107 101 AVVKSYYDKRIVGCPGGEGEDE----H-DVVWFWLEKG-KPHECPVCSQYFVL 147 (165)
Q Consensus 101 ~lVpS~~~~RiVGC~g~p~eDs----H-~v~Wf~L~kG-kp~RCpeCG~~FkL 147 (165)
+-+++..--|-.-|+-- + -. | ----+.++.| ||+.||.|+.-|-.
T Consensus 271 ~sltqsa~lRKFKCtEC-g-KAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSH 321 (1007)
T KOG3623|consen 271 ISLTQSALLRKFKCTEC-G-KAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSH 321 (1007)
T ss_pred ccccchhhhcccccccc-c-hhhhhHHHHHhhheeecCCCCcCCccccccccc
Confidence 45555555666667621 1 11 2 2334778887 59999999999854
No 113
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=21.38 E-value=38 Score=22.93 Aligned_cols=14 Identities=29% Similarity=0.826 Sum_probs=7.2
Q ss_pred CceecCCCCceEEE
Q 031107 134 KPHECPVCSQYFVL 147 (165)
Q Consensus 134 kp~RCpeCG~~FkL 147 (165)
..++||.|++.|=+
T Consensus 20 ~~y~C~~C~~~FC~ 33 (51)
T PF07975_consen 20 SRYRCPKCKNHFCI 33 (51)
T ss_dssp EEE--TTTT--B-H
T ss_pred CeEECCCCCCcccc
Confidence 46889999999854
No 114
>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=20.89 E-value=72 Score=19.87 Aligned_cols=11 Identities=27% Similarity=0.679 Sum_probs=5.7
Q ss_pred eecCCCCceEE
Q 031107 136 HECPVCSQYFV 146 (165)
Q Consensus 136 ~RCpeCG~~Fk 146 (165)
.-|+.||.+-.
T Consensus 20 ~vC~~CG~Vl~ 30 (43)
T PF08271_consen 20 LVCPNCGLVLE 30 (43)
T ss_dssp EEETTT-BBEE
T ss_pred EECCCCCCEee
Confidence 45666666543
No 115
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=20.85 E-value=96 Score=20.20 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=4.3
Q ss_pred ecCCCCceEE
Q 031107 137 ECPVCSQYFV 146 (165)
Q Consensus 137 RCpeCG~~Fk 146 (165)
.||.||.--.
T Consensus 5 PCPFCG~~~~ 14 (61)
T PF14354_consen 5 PCPFCGSADV 14 (61)
T ss_pred CCCCCCCcce
Confidence 3444444333
No 116
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.66 E-value=78 Score=20.97 Aligned_cols=20 Identities=25% Similarity=0.582 Sum_probs=12.8
Q ss_pred eEEEEeecCCc---e-ecCCCCce
Q 031107 125 VVWFWLEKGKP---H-ECPVCSQY 144 (165)
Q Consensus 125 v~Wf~L~kGkp---~-RCpeCG~~ 144 (165)
..|+.|..++. . .||.||.-
T Consensus 6 ~~~y~v~~~~v~~~~~fCP~Cg~~ 29 (50)
T PRK00432 6 REYYEVDGGKVKRKNKFCPRCGSG 29 (50)
T ss_pred eeeEEECCCEEEEccCcCcCCCcc
Confidence 45666766652 2 39999885
No 117
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.42 E-value=45 Score=18.82 Aligned_cols=7 Identities=43% Similarity=1.232 Sum_probs=4.8
Q ss_pred ecCCCCc
Q 031107 137 ECPVCSQ 143 (165)
Q Consensus 137 RCpeCG~ 143 (165)
+||.||+
T Consensus 1 ~Cp~CG~ 7 (23)
T PF13240_consen 1 YCPNCGA 7 (23)
T ss_pred CCcccCC
Confidence 4777775
No 118
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=20.31 E-value=66 Score=20.66 Aligned_cols=7 Identities=43% Similarity=1.288 Sum_probs=3.4
Q ss_pred cCCCCce
Q 031107 138 CPVCSQY 144 (165)
Q Consensus 138 CpeCG~~ 144 (165)
||+||..
T Consensus 2 CP~Cg~~ 8 (47)
T PF04606_consen 2 CPHCGSK 8 (47)
T ss_pred cCCCCCe
Confidence 4555543
No 119
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=20.19 E-value=67 Score=27.13 Aligned_cols=47 Identities=21% Similarity=0.167 Sum_probs=28.3
Q ss_pred CeeeeccCCceEEeecCCCCCCCc-ceEEEEeecCCceecCCCCceEEE
Q 031107 100 PAVVKSYYDKRIVGCPGGEGEDEH-DVVWFWLEKGKPHECPVCSQYFVL 147 (165)
Q Consensus 100 P~lVpS~~~~RiVGC~g~p~eDsH-~v~Wf~L~kGkp~RCpeCG~~FkL 147 (165)
..||.=+.+-+.+-|+-- +.... ...+-.+.++...+||.||..-+-
T Consensus 108 ~~VielHG~~~~~~C~~C-~~~~~~~~~~~~~~~~~~p~Cp~Cgg~lrP 155 (244)
T PRK14138 108 KKVIELHGNVEEYYCVRC-GKRYTVEDVIEKLEKSDVPRCDDCSGLIRP 155 (244)
T ss_pred CeEEEccCCcCeeEECCC-CCcccHHHHHHHHhcCCCCCCCCCCCeECC
Confidence 468888888888888652 12110 011112234556789999987664
No 120
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=20.09 E-value=42 Score=29.14 Aligned_cols=13 Identities=31% Similarity=0.685 Sum_probs=11.1
Q ss_pred cCCceecCCCCce
Q 031107 132 KGKPHECPVCSQY 144 (165)
Q Consensus 132 kGkp~RCpeCG~~ 144 (165)
++.+..||+||..
T Consensus 218 ~d~iv~CP~CgRI 230 (239)
T COG1579 218 KDEIVFCPYCGRI 230 (239)
T ss_pred CCCCccCCccchH
Confidence 6778999999984
Done!