Query 027792
Match_columns 219
No_of_seqs 113 out of 150
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 15:15:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027792.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027792hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00633 HHH: Helix-hairpin-he 97.6 5.6E-05 1.2E-09 46.9 2.7 24 105-128 7-30 (30)
2 PRK01229 N-glycosylase/DNA lya 97.0 0.0034 7.3E-08 54.9 7.9 82 103-191 112-202 (208)
3 COG0177 Nth Predicted EndoIII- 96.2 0.0059 1.3E-07 53.6 4.1 72 57-130 42-130 (211)
4 TIGR01084 mutY A/G-specific ad 96.2 0.045 9.8E-07 49.5 9.8 36 104-140 100-135 (275)
5 cd00056 ENDO3c endonuclease II 96.1 0.032 7E-07 45.1 7.7 37 105-143 79-116 (158)
6 PRK10702 endonuclease III; Pro 95.0 0.04 8.8E-07 47.9 5.0 28 104-131 104-131 (211)
7 PRK10880 adenine DNA glycosyla 94.9 0.042 9.1E-07 51.5 5.1 29 104-132 104-132 (350)
8 smart00478 ENDO3c endonuclease 94.9 0.091 2E-06 42.1 6.4 30 103-132 66-95 (149)
9 PF02371 Transposase_20: Trans 94.6 0.031 6.7E-07 41.7 2.7 46 109-156 2-49 (87)
10 PRK13910 DNA glycosylase MutY; 94.3 0.066 1.4E-06 48.9 4.7 30 106-135 69-98 (289)
11 TIGR01083 nth endonuclease III 94.1 0.14 3E-06 43.5 6.1 39 104-143 101-139 (191)
12 COG0122 AlkA 3-methyladenine D 94.1 0.11 2.4E-06 47.2 5.9 72 55-135 144-226 (285)
13 COG1194 MutY A/G-specific DNA 93.8 0.048 1E-06 51.1 2.9 36 108-143 112-147 (342)
14 TIGR00588 ogg 8-oxoguanine DNA 93.8 0.058 1.3E-06 49.4 3.4 38 104-143 215-254 (310)
15 TIGR03252 uncharacterized HhH- 93.5 0.063 1.4E-06 46.0 2.9 44 102-147 108-151 (177)
16 PRK02515 psbU photosystem II c 93.4 0.088 1.9E-06 43.3 3.4 39 105-148 57-95 (132)
17 PRK10308 3-methyl-adenine DNA 93.3 0.096 2.1E-06 47.5 3.9 36 103-139 201-238 (283)
18 PRK13913 3-methyladenine DNA g 92.9 0.17 3.7E-06 44.6 4.8 40 106-146 118-157 (218)
19 smart00278 HhH1 Helix-hairpin- 91.9 0.13 2.8E-06 30.3 1.9 19 110-128 2-20 (26)
20 PF11731 Cdd1: Pathogenicity l 90.0 0.22 4.9E-06 38.6 2.2 26 104-129 7-32 (93)
21 PF10391 DNA_pol_lambd_f: Fing 88.2 0.33 7.2E-06 33.6 1.8 22 108-129 1-22 (52)
22 TIGR01259 comE comEA protein. 86.0 0.93 2E-05 36.1 3.5 42 105-147 64-105 (120)
23 PF14716 HHH_8: Helix-hairpin- 85.9 1.2 2.5E-05 31.8 3.7 30 98-127 35-65 (68)
24 PRK14605 ruvA Holliday junctio 85.6 0.6 1.3E-05 40.2 2.4 31 103-133 67-97 (194)
25 KOG1921 Endonuclease III [Repl 83.2 1.6 3.4E-05 39.8 4.0 30 103-132 153-182 (286)
26 KOG2875 8-oxoguanine DNA glyco 82.8 2 4.3E-05 39.8 4.5 61 104-165 213-282 (323)
27 COG2003 RadC DNA repair protei 82.2 2.6 5.7E-05 37.5 5.0 153 35-208 3-183 (224)
28 PRK00116 ruvA Holliday junctio 82.0 1.3 2.8E-05 37.9 2.9 28 104-131 68-95 (192)
29 PF14520 HHH_5: Helix-hairpin- 81.4 1.5 3.3E-05 30.3 2.6 23 107-129 3-25 (60)
30 PRK13901 ruvA Holliday junctio 81.4 1 2.2E-05 39.2 2.1 30 103-132 66-95 (196)
31 TIGR00084 ruvA Holliday juncti 81.3 1.1 2.4E-05 38.5 2.2 30 103-132 66-95 (191)
32 PRK14600 ruvA Holliday junctio 80.9 1 2.2E-05 38.7 1.9 30 103-132 67-96 (186)
33 PF12826 HHH_2: Helix-hairpin- 79.4 1.8 3.9E-05 30.6 2.5 24 106-129 32-55 (64)
34 PRK14601 ruvA Holliday junctio 78.8 1.3 2.9E-05 38.0 1.9 30 103-132 67-96 (183)
35 TIGR00426 competence protein C 78.1 3.1 6.7E-05 29.4 3.4 39 108-147 15-54 (69)
36 PRK14601 ruvA Holliday junctio 77.4 6.6 0.00014 33.7 5.8 66 54-128 62-127 (183)
37 PRK13901 ruvA Holliday junctio 76.6 6.8 0.00015 34.1 5.7 66 54-128 61-126 (196)
38 PRK14604 ruvA Holliday junctio 76.4 7 0.00015 33.8 5.7 67 54-129 62-128 (195)
39 TIGR00608 radc DNA repair prot 76.2 2.9 6.4E-05 36.7 3.4 62 54-129 12-80 (218)
40 PRK14606 ruvA Holliday junctio 76.2 7.1 0.00015 33.5 5.7 66 54-128 62-127 (188)
41 KOG2457 A/G-specific adenine D 75.9 2.4 5.1E-05 41.1 2.9 90 109-201 205-300 (555)
42 PF14520 HHH_5: Helix-hairpin- 75.7 1.7 3.7E-05 30.0 1.4 22 107-128 36-57 (60)
43 PF00416 Ribosomal_S13: Riboso 75.1 4.8 0.00011 31.3 4.0 39 107-145 13-54 (107)
44 COG1555 ComEA DNA uptake prote 75.0 3 6.4E-05 34.6 3.0 42 105-147 93-134 (149)
45 PRK00024 hypothetical protein; 74.5 5 0.00011 35.2 4.4 60 54-128 22-85 (224)
46 PRK14602 ruvA Holliday junctio 74.5 2.3 4.9E-05 36.9 2.2 29 104-132 69-97 (203)
47 PRK14606 ruvA Holliday junctio 74.2 2.1 4.5E-05 36.8 1.9 30 103-132 67-96 (188)
48 COG1796 POL4 DNA polymerase IV 73.9 5.5 0.00012 37.3 4.7 34 102-135 44-79 (326)
49 COG0099 RpsM Ribosomal protein 73.0 3.4 7.3E-05 33.6 2.7 38 108-145 16-56 (121)
50 PRK14603 ruvA Holliday junctio 71.0 2.7 5.9E-05 36.3 1.9 29 104-132 67-95 (197)
51 PRK14602 ruvA Holliday junctio 69.3 13 0.00028 32.3 5.7 67 54-129 63-129 (203)
52 PRK14603 ruvA Holliday junctio 69.0 13 0.00029 32.0 5.8 66 54-128 61-126 (197)
53 COG2231 Uncharacterized protei 68.8 18 0.00039 32.1 6.5 36 107-143 113-148 (215)
54 TIGR00084 ruvA Holliday juncti 67.5 15 0.00032 31.5 5.7 66 54-128 61-126 (191)
55 smart00279 HhH2 Helix-hairpin- 67.0 4.2 9.2E-05 26.0 1.7 15 113-127 20-34 (36)
56 PF12836 HHH_3: Helix-hairpin- 66.8 2.2 4.7E-05 30.1 0.4 41 106-147 11-51 (65)
57 PRK14604 ruvA Holliday junctio 66.0 4 8.8E-05 35.2 1.9 30 103-132 67-96 (195)
58 COG0632 RuvA Holliday junction 63.2 5.6 0.00012 34.8 2.3 30 103-132 67-96 (201)
59 COG0353 RecR Recombinational D 62.3 5.7 0.00012 34.8 2.2 23 103-125 6-28 (198)
60 PRK04053 rps13p 30S ribosomal 61.2 8.6 0.00019 32.1 3.0 56 103-158 19-80 (149)
61 CHL00137 rps13 ribosomal prote 60.8 9.5 0.00021 30.8 3.1 39 107-145 15-56 (122)
62 PRK00116 ruvA Holliday junctio 60.4 60 0.0013 27.6 8.1 70 54-132 62-131 (192)
63 PTZ00134 40S ribosomal protein 60.2 4.6 9.9E-05 34.0 1.2 57 101-157 22-84 (154)
64 PRK14605 ruvA Holliday junctio 57.8 32 0.00069 29.6 6.0 64 54-126 62-125 (194)
65 cd00141 NT_POLXc Nucleotidyltr 57.5 8.7 0.00019 35.1 2.6 23 105-127 81-103 (307)
66 PF11798 IMS_HHH: IMS family H 57.3 6.8 0.00015 24.2 1.3 15 111-125 13-27 (32)
67 PRK00076 recR recombination pr 55.2 9.4 0.0002 33.3 2.3 22 104-125 6-27 (196)
68 PRK05179 rpsM 30S ribosomal pr 54.5 13 0.00028 29.9 2.9 38 108-145 16-56 (122)
69 TIGR03631 bact_S13 30S ribosom 54.0 13 0.00028 29.5 2.7 37 109-145 15-54 (113)
70 PRK14600 ruvA Holliday junctio 53.7 30 0.00064 29.7 5.1 65 54-128 62-126 (186)
71 TIGR00615 recR recombination p 52.9 11 0.00024 32.9 2.3 22 104-125 6-27 (195)
72 PRK03980 flap endonuclease-1; 52.1 50 0.0011 30.2 6.6 73 113-193 193-279 (292)
73 COG1059 Thermostable 8-oxoguan 51.1 96 0.0021 27.4 7.8 82 105-191 116-204 (210)
74 PRK13844 recombination protein 51.1 12 0.00026 32.8 2.3 22 104-125 10-31 (200)
75 cd00080 HhH2_motif Helix-hairp 50.5 11 0.00024 27.4 1.7 19 111-129 24-42 (75)
76 smart00483 POLXc DNA polymeras 50.3 14 0.00031 34.1 2.8 26 103-128 83-108 (334)
77 cd00141 NT_POLXc Nucleotidyltr 48.7 14 0.00031 33.7 2.6 24 101-124 37-60 (307)
78 TIGR00426 competence protein C 48.2 57 0.0012 22.8 5.1 43 55-128 24-66 (69)
79 smart00483 POLXc DNA polymeras 47.4 13 0.00029 34.3 2.2 35 99-133 38-72 (334)
80 PRK07945 hypothetical protein; 46.4 21 0.00046 33.0 3.4 19 110-128 50-68 (335)
81 COG3092 Uncharacterized protei 46.3 46 0.00099 27.7 4.8 52 80-132 28-82 (149)
82 TIGR03629 arch_S13P archaeal r 44.0 24 0.00051 29.3 2.9 50 108-158 20-75 (144)
83 PRK12766 50S ribosomal protein 42.3 18 0.0004 32.4 2.2 43 88-130 14-57 (232)
84 TIGR01339 phycocy_beta phycocy 41.7 37 0.0008 29.0 3.8 52 52-104 13-64 (170)
85 cd00128 XPG Xeroderma pigmento 40.3 39 0.00085 30.6 4.0 18 113-130 227-244 (316)
86 PRK14976 5'-3' exonuclease; Pr 39.7 18 0.00039 32.8 1.7 17 114-130 196-212 (281)
87 PRK08609 hypothetical protein; 39.6 29 0.00063 34.5 3.3 23 107-129 46-68 (570)
88 PRK09482 flap endonuclease-lik 36.5 22 0.00049 32.0 1.8 18 113-130 186-203 (256)
89 TIGR01259 comE comEA protein. 35.1 87 0.0019 24.8 4.8 21 107-127 96-116 (120)
90 PF14579 HHH_6: Helix-hairpin- 34.6 38 0.00081 25.2 2.5 32 111-144 29-60 (90)
91 CHL00172 cpeB phycoerythrin be 33.2 58 0.0013 28.1 3.7 51 52-103 15-65 (177)
92 cd00008 53EXOc 5'-3' exonuclea 32.4 29 0.00062 30.5 1.8 17 113-129 187-203 (240)
93 PF00502 Phycobilisome: Phycob 32.0 31 0.00066 28.5 1.8 51 52-103 10-60 (157)
94 smart00475 53EXOc 5'-3' exonuc 31.1 31 0.00068 30.9 1.8 17 113-129 190-206 (259)
95 TIGR00600 rad2 DNA excision re 31.0 1.3E+02 0.0029 32.5 6.6 24 107-130 858-887 (1034)
96 PRK13482 DNA integrity scannin 30.3 51 0.0011 31.3 3.1 32 97-128 306-338 (352)
97 PF01367 5_3_exonuc: 5'-3' exo 29.8 8.4 0.00018 30.0 -1.8 17 113-129 22-38 (101)
98 PF14229 DUF4332: Domain of un 29.8 50 0.0011 26.2 2.6 26 106-131 50-75 (122)
99 CHL00170 cpcA phycocyanin alph 29.5 90 0.0019 26.5 4.2 51 52-103 15-65 (162)
100 KOG2582 COP9 signalosome, subu 28.0 2.8E+02 0.0061 27.0 7.6 83 78-161 82-186 (422)
101 PRK08609 hypothetical protein; 27.7 47 0.001 33.1 2.5 24 104-127 83-106 (570)
102 TIGR01954 nusA_Cterm_rpt trans 26.4 62 0.0013 20.8 2.2 41 88-128 4-45 (50)
103 PF09660 DUF2397: Protein of u 26.4 6.3E+02 0.014 24.8 10.2 42 159-201 197-238 (486)
104 COG3743 Uncharacterized conser 26.0 37 0.00079 28.1 1.2 20 109-128 67-86 (133)
105 TIGR01589 A_thal_3526 uncharac 26.0 73 0.0016 22.7 2.6 49 89-137 3-51 (57)
106 TIGR01338 phycocy_alpha phycoc 25.9 1.2E+02 0.0027 25.6 4.4 51 52-103 14-64 (161)
107 CHL00090 apcD allophycocyanin 25.7 89 0.0019 26.3 3.5 50 53-103 15-64 (161)
108 PRK12766 50S ribosomal protein 25.6 37 0.00081 30.5 1.3 20 109-128 3-22 (232)
109 CHL00086 apcA allophycocyanin 24.3 1.1E+02 0.0024 25.7 3.9 51 52-103 14-64 (161)
110 KOG2376 Signal recognition par 24.1 6.8E+02 0.015 25.9 9.8 19 177-195 525-543 (652)
111 CHL00173 cpeA phycoerythrin al 23.9 93 0.002 26.4 3.3 51 52-103 15-65 (164)
112 COG0632 RuvA Holliday junction 23.6 60 0.0013 28.4 2.2 66 54-128 62-127 (201)
113 PF05766 NinG: Bacteriophage L 23.6 1.5E+02 0.0032 25.8 4.6 23 149-171 162-184 (189)
114 CHL00171 cpcB phycocyanin beta 23.3 98 0.0021 26.4 3.4 50 53-103 16-65 (172)
115 PF04854 DUF624: Protein of un 23.1 37 0.0008 24.2 0.7 17 113-129 17-33 (77)
116 PF05845 PhnH: Bacterial phosp 22.8 72 0.0016 27.6 2.5 23 114-137 39-61 (192)
117 KOG1918 3-methyladenine DNA gl 21.6 64 0.0014 29.2 2.0 39 103-142 159-199 (254)
118 COG1031 Uncharacterized Fe-S o 20.8 76 0.0016 31.7 2.4 38 105-147 512-549 (560)
119 PRK09672 phage exclusion prote 20.8 3.1E+02 0.0068 25.7 6.3 34 114-147 216-256 (305)
120 PF09713 A_thal_3526: Plant pr 20.3 96 0.0021 21.8 2.3 47 91-137 2-48 (54)
No 1
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=97.59 E-value=5.6e-05 Score=46.91 Aligned_cols=24 Identities=42% Similarity=0.700 Sum_probs=20.2
Q ss_pred HHHHHHhhccCCCChHHHHHHHHh
Q 027792 105 TKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaILa~ 128 (219)
.+.++.|++|+||||.||.+|++.
T Consensus 7 pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 7 PASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCHHHHHhCCCcCHHHHHHHHhC
Confidence 356889999999999999999973
No 2
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=96.98 E-value=0.0034 Score=54.90 Aligned_cols=82 Identities=26% Similarity=0.257 Sum_probs=59.9
Q ss_pred cHHHHHHHhh-ccCCCChHHHHHHHH-hhcCCCCCcccHHHHHHh---cCC----CCCCCHHHHHHHHHHHHHHHHHhhc
Q 027792 103 DLTKAVSELT-VLKGVGPATASAVLA-AYAPGVAPFMSDEAMGAA---LGH----SKDYSLKQYLLFADKLQAKAKELVS 173 (219)
Q Consensus 103 dv~~al~~L~-~LkGVGPATASaILa-~~~P~~~pFfsDEa~~~~---~g~----~~kYt~keY~~~~~~l~~~~~~L~~ 173 (219)
++..+.+.|. +||||||=||+.||. +.. ...|.-|.-..-+ .|- +..-|.+.|.+.-..+.+.+..+
T Consensus 112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~--~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~-- 187 (208)
T PRK01229 112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY--EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEEL-- 187 (208)
T ss_pred CchHHHHHHHHcCCCCcHHHHHHHHHHccC--CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHc--
Confidence 5678899999 999999999999994 444 2123355543323 351 22456689999988999988887
Q ss_pred cCCCCCHHHHHHHHHHHH
Q 027792 174 EENCFTPFDVERALWSSA 191 (219)
Q Consensus 174 ~~~~~t~~~VEkalws~~ 191 (219)
++.+..+.-++|-..
T Consensus 188 ---~~~~~~Ldl~~w~~~ 202 (208)
T PRK01229 188 ---GISLGELDLYIWYKE 202 (208)
T ss_pred ---CCCHHHHHHHHHHHH
Confidence 478999999999643
No 3
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=96.18 E-value=0.0059 Score=53.59 Aligned_cols=72 Identities=22% Similarity=0.224 Sum_probs=45.0
Q ss_pred CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHH------h------hC-----ccHHHHHHHhhccCCCCh
Q 027792 57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAF------K------SL-----PDLTKAVSELTVLKGVGP 119 (219)
Q Consensus 57 tkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af------~------~l-----~dv~~al~~L~~LkGVGP 119 (219)
|.|+.+.-+.=+|.. .-|+...+...+.++..+-|-.-+| + +| .++...++.|.+|+|||+
T Consensus 42 ttD~~vn~at~~Lf~--~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGr 119 (211)
T COG0177 42 TTDEVVNKATPALFK--RYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGR 119 (211)
T ss_pred CchHHHHHHHHHHHH--HcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcch
Confidence 467777666655542 2345566666554443332222222 0 01 145678999999999999
Q ss_pred HHHHHHHHhhc
Q 027792 120 ATASAVLAAYA 130 (219)
Q Consensus 120 ATASaILa~~~ 130 (219)
=||..||+...
T Consensus 120 KTAnvVL~~a~ 130 (211)
T COG0177 120 KTANVVLSFAF 130 (211)
T ss_pred HHHHHHHHhhc
Confidence 99999999854
No 4
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=96.16 E-value=0.045 Score=49.53 Aligned_cols=36 Identities=31% Similarity=0.395 Sum_probs=27.8
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHH
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDE 140 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDE 140 (219)
+...++.|++|+||||-||++||+...-...|+ -|-
T Consensus 100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~ 135 (275)
T TIGR01084 100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDG 135 (275)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chH
Confidence 345789999999999999999999865443454 444
No 5
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=96.05 E-value=0.032 Score=45.06 Aligned_cols=37 Identities=38% Similarity=0.469 Sum_probs=28.6
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhh-cCCCCCcccHHHHH
Q 027792 105 TKAVSELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMG 143 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaILa~~-~P~~~pFfsDEa~~ 143 (219)
..+.+.|++||||||-||+.||... .++.+|. |-...
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~ 116 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVR 116 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHH
Confidence 6789999999999999999999874 3445554 55444
No 6
>PRK10702 endonuclease III; Provisional
Probab=95.03 E-value=0.04 Score=47.94 Aligned_cols=28 Identities=32% Similarity=0.383 Sum_probs=24.4
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcC
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~~P 131 (219)
+..+++.|.+|+||||-||.+||....-
T Consensus 104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~ 131 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTAFG 131 (211)
T ss_pred CCchHHHHhcCCcccHHHHHHHHHHHcC
Confidence 4568899999999999999999998654
No 7
>PRK10880 adenine DNA glycosylase; Provisional
Probab=94.90 E-value=0.042 Score=51.48 Aligned_cols=29 Identities=31% Similarity=0.454 Sum_probs=25.0
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+...++.|.+||||||-||++||+...-.
T Consensus 104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~ 132 (350)
T PRK10880 104 FPETFEEVAALPGVGRSTAGAILSLSLGK 132 (350)
T ss_pred chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence 45678999999999999999999987644
No 8
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=94.88 E-value=0.091 Score=42.11 Aligned_cols=30 Identities=37% Similarity=0.386 Sum_probs=25.1
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
++...++.|++|+||||-||++||...--.
T Consensus 66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~ 95 (149)
T smart00478 66 EVPDDREELLKLPGVGRKTANAVLSFALGK 95 (149)
T ss_pred CccHHHHHHHcCCCCcHHHHHHHHHHHCCC
Confidence 344678899999999999999999986554
No 9
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.57 E-value=0.031 Score=41.71 Aligned_cols=46 Identities=28% Similarity=0.457 Sum_probs=33.8
Q ss_pred HHhhccCCCChHHHHHHHHhh-cCCCCCcccHHHHHHhcC-CCCCCCHHH
Q 027792 109 SELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMGAALG-HSKDYSLKQ 156 (219)
Q Consensus 109 ~~L~~LkGVGPATASaILa~~-~P~~~pFfsDEa~~~~~g-~~~kYt~ke 156 (219)
++|+.++||||-||..||+.. +|. -|=+...+...+| .|..|....
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~--rF~~~~~l~~~~Gl~P~~~~SG~ 49 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDIS--RFKSAKQLASYAGLAPRPYQSGK 49 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCch--hcccchhhhhccccccccccccc
Confidence 468899999999999999986 443 4668888887877 344443333
No 10
>PRK13910 DNA glycosylase MutY; Provisional
Probab=94.27 E-value=0.066 Score=48.92 Aligned_cols=30 Identities=27% Similarity=0.266 Sum_probs=24.7
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcCCCCC
Q 027792 106 KAVSELTVLKGVGPATASAVLAAYAPGVAP 135 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaILa~~~P~~~p 135 (219)
...+.|.+|+||||-||.+||+...-..++
T Consensus 69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~ 98 (289)
T PRK13910 69 NDYQSLLKLPGIGAYTANAILCFGFREKSA 98 (289)
T ss_pred hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC
Confidence 468999999999999999999986544333
No 11
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=94.13 E-value=0.14 Score=43.46 Aligned_cols=39 Identities=28% Similarity=0.225 Sum_probs=27.9
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHH
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~ 143 (219)
+..+++.|++||||||=||.+||....-.. .|.-|--+.
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~ 139 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVF 139 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHH
Confidence 345788999999999999999998764322 244444433
No 12
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.12 E-value=0.11 Score=47.20 Aligned_cols=72 Identities=28% Similarity=0.256 Sum_probs=50.7
Q ss_pred CCCHHHHHHHHHHHhh-cCCCCcchHHHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhccCCCChHHHHHH
Q 027792 55 HINTTELSKLVRWKLT-RGKWRPRLLDFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 55 ~ltkdEL~~Lv~WKL~-rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~--------dv~~al~~L~~LkGVGPATASaI 125 (219)
+.|-+.|..+=++-|. -|..+.+ .+.+..+++...+-.+ +...+++.|++||||||=||-.+
T Consensus 144 fptpe~l~~~~~~~l~~~g~s~~K---------a~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~ 214 (285)
T COG0122 144 FPTPEQLAAADEEALRRCGLSGRK---------AEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMF 214 (285)
T ss_pred CCCHHHHHhcCHHHHHHhCCcHHH---------HHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHH
Confidence 6778888877777775 4554442 3455566655554321 46789999999999999999999
Q ss_pred HHh--hcCCCCC
Q 027792 126 LAA--YAPGVAP 135 (219)
Q Consensus 126 La~--~~P~~~p 135 (219)
|-. ..|+.+|
T Consensus 215 llf~lgr~dvfP 226 (285)
T COG0122 215 LLFGLGRPDVFP 226 (285)
T ss_pred HHHcCCCCCCCC
Confidence 876 4576655
No 13
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=93.82 E-value=0.048 Score=51.12 Aligned_cols=36 Identities=33% Similarity=0.437 Sum_probs=29.6
Q ss_pred HHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHH
Q 027792 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (219)
Q Consensus 108 l~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~ 143 (219)
.+.|.+|+||||-||+||||...-...|+.+--+..
T Consensus 112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~R 147 (342)
T COG1194 112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKR 147 (342)
T ss_pred HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchhe
Confidence 456777999999999999999877777877766654
No 14
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=93.79 E-value=0.058 Score=49.43 Aligned_cols=38 Identities=29% Similarity=0.375 Sum_probs=30.3
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhh--cCCCCCcccHHHHH
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAMG 143 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~--~P~~~pFfsDEa~~ 143 (219)
...+++.|++||||||=||.+||... .|+.+|. |-.+.
T Consensus 215 ~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv--D~~v~ 254 (310)
T TIGR00588 215 YEDAREALCELPGVGPKVADCICLMGLDKPQAVPV--DVHVW 254 (310)
T ss_pred hHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceee--cHHHH
Confidence 56789999999999999999999764 5666663 65443
No 15
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=93.47 E-value=0.063 Score=46.02 Aligned_cols=44 Identities=27% Similarity=0.311 Sum_probs=31.6
Q ss_pred ccHHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027792 102 PDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 102 ~dv~~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g 147 (219)
|+-...++.|.+||||||-||..||+...-+ =-.-||-|....|
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~--~~~~~~~~~~~~~ 151 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQ--LGVTPEGWREAAG 151 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHH--hCCCCcchHHhcc
Confidence 3445568899999999999999999975433 1134666765544
No 16
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=93.35 E-value=0.088 Score=43.26 Aligned_cols=39 Identities=23% Similarity=0.302 Sum_probs=32.8
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcCC
Q 027792 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGH 148 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g~ 148 (219)
.+....|..|+||||++|..|+. +.||-|=|-+..+.|.
T Consensus 57 ~A~~~el~~lpGigP~~A~~IV~-----nGpf~sveDL~~V~GI 95 (132)
T PRK02515 57 NSSVRAFRQFPGMYPTLAGKIVK-----NAPYDSVEDVLNLPGL 95 (132)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHH-----CCCCCCHHHHHcCCCC
Confidence 34577899999999999999993 6699999988888773
No 17
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=93.28 E-value=0.096 Score=47.48 Aligned_cols=36 Identities=28% Similarity=0.294 Sum_probs=29.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHh--hcCCCCCcccH
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSD 139 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~--~~P~~~pFfsD 139 (219)
+..++++.|+.||||||-||..||-. ..|+.+| -.|
T Consensus 201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp-~~D 238 (283)
T PRK10308 201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDD 238 (283)
T ss_pred CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC-ccc
Confidence 56778999999999999999999865 5787655 344
No 18
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=92.93 E-value=0.17 Score=44.56 Aligned_cols=40 Identities=23% Similarity=0.163 Sum_probs=28.6
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhc
Q 027792 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL 146 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~ 146 (219)
...+.|.+||||||=||.+||....- +..|..|--..-++
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv~ 157 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLFL 157 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHHH
Confidence 46688999999999999999987543 32455555444443
No 19
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.89 E-value=0.13 Score=30.31 Aligned_cols=19 Identities=47% Similarity=0.763 Sum_probs=16.9
Q ss_pred HhhccCCCChHHHHHHHHh
Q 027792 110 ELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 110 ~L~~LkGVGPATASaILa~ 128 (219)
.|+.++|||+.+|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 4789999999999999974
No 20
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=90.01 E-value=0.22 Score=38.57 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=22.0
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhh
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~ 129 (219)
..+.+..|+.|+|||||||-=+..++
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LG 32 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLG 32 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence 34578899999999999999887764
No 21
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=88.18 E-value=0.33 Score=33.58 Aligned_cols=22 Identities=36% Similarity=0.351 Sum_probs=17.2
Q ss_pred HHHhhccCCCChHHHHHHHHhh
Q 027792 108 VSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 108 l~~L~~LkGVGPATASaILa~~ 129 (219)
|+.++.+-||||+||.-..+..
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G 22 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKG 22 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT
T ss_pred CcchhhcccccHHHHHHHHHhC
Confidence 5789999999999999888764
No 22
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=86.04 E-value=0.93 Score=36.09 Aligned_cols=42 Identities=29% Similarity=0.468 Sum_probs=33.5
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027792 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g 147 (219)
.+....|..|+||||.+|..|+.-..- ..+|-|-|-+..+.|
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~-~g~f~s~eeL~~V~G 105 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYREE-NGAFKSVDDLTKVSG 105 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHcCCC
Confidence 345778999999999999999997543 558888777776765
No 23
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=85.93 E-value=1.2 Score=31.80 Aligned_cols=30 Identities=30% Similarity=0.402 Sum_probs=21.7
Q ss_pred HhhCccHHHHHHH-hhccCCCChHHHHHHHH
Q 027792 98 FKSLPDLTKAVSE-LTVLKGVGPATASAVLA 127 (219)
Q Consensus 98 f~~l~dv~~al~~-L~~LkGVGPATASaILa 127 (219)
...+|..-..++. +.+|+|||+.+|.-|--
T Consensus 35 i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 35 IKALPYPITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHHSSS-HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred HHhCCHhHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 4456654445565 99999999999998743
No 24
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.59 E-value=0.6 Score=40.20 Aligned_cols=31 Identities=23% Similarity=0.338 Sum_probs=26.9
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPGV 133 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~~ 133 (219)
+.+.-+..|.+.+||||-||-+||+.+.|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~ 97 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNAEA 97 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCHHH
Confidence 4567889999999999999999999887753
No 25
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=83.25 E-value=1.6 Score=39.83 Aligned_cols=30 Identities=30% Similarity=0.437 Sum_probs=27.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
|+-..++.|..|+||||-+|=+.|+++.-.
T Consensus 153 DIP~~v~dLlsLPGVGPKMa~L~m~~AWn~ 182 (286)
T KOG1921|consen 153 DIPDTVEDLLSLPGVGPKMAHLTMQVAWNK 182 (286)
T ss_pred CCchhHHHHhcCCCCchHHHHHHHHHHhcc
Confidence 788899999999999999999999986554
No 26
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=82.79 E-value=2 Score=39.81 Aligned_cols=61 Identities=20% Similarity=0.205 Sum_probs=38.0
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHh--hcCCCCCcccHHHHH-----HhcC-C-CCCCCHHHHHHHHHHHH
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSDEAMG-----AALG-H-SKDYSLKQYLLFADKLQ 165 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~--~~P~~~pFfsDEa~~-----~~~g-~-~~kYt~keY~~~~~~l~ 165 (219)
..+|.++||.|+||||-.|-+|+-. .-+..+|+ +--+|. +++| . ...-+.+-|.++-...+
T Consensus 213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPV-DvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~ 282 (323)
T KOG2875|consen 213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVPV-DVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFR 282 (323)
T ss_pred HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccc-hhhHHHHhhcccCCCccccccCCcchhHHHHHHHH
Confidence 4569999999999999999988754 34455552 222332 2344 1 22367777776543333
No 27
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=82.24 E-value=2.6 Score=37.49 Aligned_cols=153 Identities=21% Similarity=0.257 Sum_probs=85.4
Q ss_pred hhhHHHhhhhhHhhccCCCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhC---ccHH-HHHHH
Q 027792 35 LDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSL---PDLT-KAVSE 110 (219)
Q Consensus 35 LD~w~~~elp~~~~~r~~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l---~dv~-~al~~ 110 (219)
+.+|...+.|.-=--+.....|+-.||..|+ |..|..+- .|..+++.-++.+ ..+. +.++.
T Consensus 3 i~~~~~~~rPRErll~~G~~~Lsd~ELLail---LrtG~~~~------------~~~~la~~lL~~fg~L~~l~~a~~~e 67 (224)
T COG2003 3 IKDNPENERPRERLLKLGAEALSDAELLAIL---LRTGTKGE------------SVLDLAKELLQEFGSLAELLKASVEE 67 (224)
T ss_pred ccccccccchHHHHHHhChhhcchHHHHHHH---HhcCCCCC------------CHHHHHHHHHHHcccHHHHHhCCHHH
Confidence 4456665555321111223589999987777 56665333 5667777766543 3444 45999
Q ss_pred hhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcCCCCCC-CHHHHHHHHH-HHHHHHHH------hhcc--------
Q 027792 111 LTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDY-SLKQYLLFAD-KLQAKAKE------LVSE-------- 174 (219)
Q Consensus 111 L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g~~~kY-t~keY~~~~~-~l~~~~~~------L~~~-------- 174 (219)
||.++|||+|-|.-+.++.. ++-+.+..-.-.+... |.....+|+. .|...-++ |+.+
T Consensus 68 l~~v~GiG~aka~~l~a~~E------l~~R~~~~~~~~~~~i~sp~~~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~ 141 (224)
T COG2003 68 LSSVKGIGLAKAIQIKAAIE------LGKRILAERLREGVVITSPEAVAEYLRAELGGEEREHFVVLYLDSQNRLIATET 141 (224)
T ss_pred HhhCCCccHHHHHHHHHHHH------HHHHHHHHHhccCCccCCHHHHHHHHHHHhhhhHHHHHHHHHhcCcCceeccee
Confidence 99999999999999998842 2222222111111111 2222333322 22221111 1111
Q ss_pred ---C----CCCCHHHH-HHHHHHHHHhhhhcccCCCCccchh
Q 027792 175 ---E----NCFTPFDV-ERALWSSAIGLKLKASKSNQDSEIK 208 (219)
Q Consensus 175 ---~----~~~t~~~V-Ekalws~~v~~k~~~~~~~~~~~~~ 208 (219)
| ..+-|++| .+|+..-+.+=.+.---|+|+|..|
T Consensus 142 lf~GTi~~s~V~PREI~k~Al~~nAaavIlaHNHPSGd~~PS 183 (224)
T COG2003 142 LFIGTLNVSEVHPREIFKEALKYNAAAVILAHNHPSGDPTPS 183 (224)
T ss_pred EEeeecccceecHHHHHHHHHHhcchhhheeccCCCCCCCcC
Confidence 1 25678887 6777777777677667778887766
No 28
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=82.03 E-value=1.3 Score=37.89 Aligned_cols=28 Identities=32% Similarity=0.489 Sum_probs=23.1
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcC
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~~P 131 (219)
.+.....|..++||||.||-.||+.+.+
T Consensus 68 ek~~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 68 ERELFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 3445778999999999999999987655
No 29
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=81.43 E-value=1.5 Score=30.28 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=20.2
Q ss_pred HHHHhhccCCCChHHHHHHHHhh
Q 027792 107 AVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 107 al~~L~~LkGVGPATASaILa~~ 129 (219)
....|..++||||.+|..+....
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G 25 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAG 25 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTT
T ss_pred HHHhhccCCCCCHHHHHHHHhcC
Confidence 45778899999999999999984
No 30
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.35 E-value=1 Score=39.21 Aligned_cols=30 Identities=27% Similarity=0.378 Sum_probs=25.9
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+.+.-+..|....||||-||-+||+...|+
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs~~~~~ 95 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLSGIKYN 95 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 456778899999999999999999988875
No 31
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=81.29 E-value=1.1 Score=38.52 Aligned_cols=30 Identities=33% Similarity=0.541 Sum_probs=24.8
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+.+.-+..|..++||||-||-+||+...|+
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL~~~~~~ 95 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAILSNMSPE 95 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHhcCCHH
Confidence 456678889999999999999999987663
No 32
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.90 E-value=1 Score=38.67 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=26.1
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+.+.-+..|.+..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 456678899999999999999999987775
No 33
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=79.41 E-value=1.8 Score=30.61 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.9
Q ss_pred HHHHHhhccCCCChHHHHHHHHhh
Q 027792 106 KAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaILa~~ 129 (219)
+..+.|+.++||||.+|..|....
T Consensus 32 a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 32 ASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp --HHHHCTSTT--HHHHHHHHHHH
T ss_pred cCHHHHhccCCcCHHHHHHHHHHH
Confidence 467899999999999999998764
No 34
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.85 E-value=1.3 Score=37.97 Aligned_cols=30 Identities=30% Similarity=0.345 Sum_probs=26.4
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+.+.-+..|++..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs~~~~~ 96 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCSSLDVN 96 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 456778999999999999999999998885
No 35
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=78.09 E-value=3.1 Score=29.38 Aligned_cols=39 Identities=28% Similarity=0.432 Sum_probs=28.7
Q ss_pred HHHhhc-cCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027792 108 VSELTV-LKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 108 l~~L~~-LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g 147 (219)
...|.. ++|||+.+|.+|+.-... ..+|-+-+.+..++|
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~-~g~~~s~~dL~~v~g 54 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREE-YGPFKTVEDLKQVPG 54 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHH-cCCcCCHHHHHcCCC
Confidence 346777 999999999999997543 336667666666655
No 36
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.38 E-value=6.6 Score=33.69 Aligned_cols=66 Identities=23% Similarity=0.222 Sum_probs=45.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
++.|++|..-...-.--.|-=--.-+..++..+++.+.++... .=.+.|+++||||+-||.=|+.=
T Consensus 62 GF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 62 GFLDKDEQKMFEMLLKVNGIGANTAMAVCSSLDVNSFYKALSL---------GDESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred CCCCHHHHHHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHH
Confidence 6889998665555544445433345667777777776665543 23568999999999999988743
No 37
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.56 E-value=6.8 Score=34.09 Aligned_cols=66 Identities=15% Similarity=0.235 Sum_probs=45.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
++.|++|..-...-.--.|-=--.-+..++..+++.+.++... .=.+.||++||||+-||.=|+.=
T Consensus 61 GF~t~~Er~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 61 GFLNSSEREVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR---------EDIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHH
Confidence 6889999766555544455433345677777777776665533 23568999999999999988743
No 38
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.44 E-value=7 Score=33.78 Aligned_cols=67 Identities=16% Similarity=0.126 Sum_probs=45.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~~ 129 (219)
++.|++|..-...-.--.|-=--+-+.+++..+++.+..+... .=.+.||++||||+-||--|+.-.
T Consensus 62 GF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~---------~D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 62 GFSTPAQRQLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAG---------GDVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHH
Confidence 6889999766555544455433345666777777766655533 235689999999999999887654
No 39
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.20 E-value=2.9 Score=36.68 Aligned_cols=62 Identities=29% Similarity=0.373 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhccCCCChHHHHHHH
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL 126 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~------l~dv-~~al~~L~~LkGVGPATASaIL 126 (219)
..|+-.||..++ |.-|.-|. + .|....++-++. +.++ .+..+.|++++|||+|.|..|+
T Consensus 12 ~~Lsd~ELLail---L~~g~~~~--------~---~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 12 EALSDYELLAII---LRTGTPKG--------L---DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred ccCCHHHHHHHH---HhCCCCCC--------C---CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence 588899977665 45554332 0 334444433332 2332 3457889999999999999999
Q ss_pred Hhh
Q 027792 127 AAY 129 (219)
Q Consensus 127 a~~ 129 (219)
++.
T Consensus 78 a~~ 80 (218)
T TIGR00608 78 AAV 80 (218)
T ss_pred HHH
Confidence 983
No 40
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.15 E-value=7.1 Score=33.54 Aligned_cols=66 Identities=15% Similarity=0.159 Sum_probs=45.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
++.|.+|..-...-.--.|-=--+-+.+++..+++.+.++... .=.+.||++||||+-||.=|.-=
T Consensus 62 GF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 62 GFSNERKKELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS---------QDVEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred CCCCHHHHHHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHH
Confidence 6888988665555544455433345677777777766665543 23568999999999999988753
No 41
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=75.90 E-value=2.4 Score=41.09 Aligned_cols=90 Identities=20% Similarity=0.062 Sum_probs=49.0
Q ss_pred HHhh-ccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC---CCCCCCHHHHHHHHHHHHHHHHHhhc--cCCCCCHHH
Q 027792 109 SELT-VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG---HSKDYSLKQYLLFADKLQAKAKELVS--EENCFTPFD 182 (219)
Q Consensus 109 ~~L~-~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g---~~~kYt~keY~~~~~~l~~~~~~L~~--~~~~~t~~~ 182 (219)
..|. .++||||-||-||+|...-+..-..+-.+...++. ..-+-+- ..+.+.+-.++.+|-. ..++++-.-
T Consensus 205 ~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSk---gk~~q~~wkLA~qLVDP~RPGDFNQal 281 (555)
T KOG2457|consen 205 SSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSK---GKFFQSSWKLAAQLVDPSRPGDFNQAL 281 (555)
T ss_pred HHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcch---hhHHHHHHHHHHHhcCCCCCCcHHHHH
Confidence 3444 49999999999999986443222233333333221 0001111 1233456667777743 235677777
Q ss_pred HHHHHHHHHHhhhhcccCC
Q 027792 183 VERALWSSAIGLKLKASKS 201 (219)
Q Consensus 183 VEkalws~~v~~k~~~~~~ 201 (219)
+|..+=.+..-+-.|..+|
T Consensus 282 MELGAt~CTpq~P~CS~CP 300 (555)
T KOG2457|consen 282 MELGATLCTPQKPSCSSCP 300 (555)
T ss_pred HHhcCeeccCCCCCcCCCC
Confidence 7777666555554444443
No 42
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=75.65 E-value=1.7 Score=30.03 Aligned_cols=22 Identities=32% Similarity=0.531 Sum_probs=19.0
Q ss_pred HHHHhhccCCCChHHHHHHHHh
Q 027792 107 AVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 107 al~~L~~LkGVGPATASaILa~ 128 (219)
..+.|++++|||+.+|.-|...
T Consensus 36 ~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 36 DPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHHTSTTSSHHHHHHHHHH
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 4577999999999999988765
No 43
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=75.12 E-value=4.8 Score=31.30 Aligned_cols=39 Identities=23% Similarity=0.291 Sum_probs=29.4
Q ss_pred HHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027792 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 107 al~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~ 145 (219)
-.-+|+.+.|||+.+|..|+... +|. .+-.++|+-+..+
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l 54 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKL 54 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHH
T ss_pred hHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHH
Confidence 45678999999999999999984 564 5566777766543
No 44
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=75.02 E-value=3 Score=34.57 Aligned_cols=42 Identities=31% Similarity=0.517 Sum_probs=32.2
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027792 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g 147 (219)
.+..+.|..|+||||+.|-+|..--.- ..||=|=|=..-+.|
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~-~G~f~sv~dL~~v~G 134 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREE-NGPFKSVDDLAKVKG 134 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHH-cCCCCcHHHHHhccC
Confidence 355677889999999999999996543 348877776666655
No 45
>PRK00024 hypothetical protein; Reviewed
Probab=74.49 E-value=5 Score=35.24 Aligned_cols=60 Identities=28% Similarity=0.449 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc---H-HHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD---L-TKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d---v-~~al~~L~~LkGVGPATASaILa~ 128 (219)
..|+-.||..++ |..|..|. .|....++-++...+ + .+..+.|++++|||+|.|..|+++
T Consensus 22 ~~Lsd~ELLa~l---L~~g~~~~------------~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~ 85 (224)
T PRK00024 22 AALSDAELLAIL---LRTGTKGK------------SVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85 (224)
T ss_pred ccCCHHHHHHHH---HcCCCCCC------------CHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHH
Confidence 588888976654 45565443 455555554443332 2 235678999999999999999887
No 46
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.46 E-value=2.3 Score=36.93 Aligned_cols=29 Identities=28% Similarity=0.403 Sum_probs=24.3
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
.+.-+..|.+..||||-||-+||+...|+
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 45677888999999999999999987775
No 47
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.21 E-value=2.1 Score=36.80 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=26.4
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+.+.-+..|++..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs~~~~~ 96 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIISNEDAE 96 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 356678999999999999999999988875
No 48
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=73.85 E-value=5.5 Score=37.32 Aligned_cols=34 Identities=26% Similarity=0.352 Sum_probs=26.7
Q ss_pred ccHHHHHHH--hhccCCCChHHHHHHHHhhcCCCCC
Q 027792 102 PDLTKAVSE--LTVLKGVGPATASAVLAAYAPGVAP 135 (219)
Q Consensus 102 ~dv~~al~~--L~~LkGVGPATASaILa~~~P~~~p 135 (219)
.|+....+. +|+|+|||++||+.|--..+-..++
T Consensus 44 e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~ 79 (326)
T COG1796 44 EDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVK 79 (326)
T ss_pred cchHHHHhhcccCCCCCccHHHHHHHHHHHHcCccH
Confidence 367777777 9999999999999998776554444
No 49
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=72.98 E-value=3.4 Score=33.60 Aligned_cols=38 Identities=21% Similarity=0.299 Sum_probs=30.2
Q ss_pred HHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027792 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 108 l~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~ 145 (219)
.=+|+.+.|||+++|-+|+... +|+ .+-..+||-+..+
T Consensus 16 ~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 16 VIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred eehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 3468899999999999999984 565 6667888877644
No 50
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.02 E-value=2.7 Score=36.30 Aligned_cols=29 Identities=34% Similarity=0.441 Sum_probs=24.3
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
.+.-+..|.+..||||-||-+||+...|+
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~ 95 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSALPPA 95 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 45667888899999999999999987775
No 51
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.25 E-value=13 Score=32.29 Aligned_cols=67 Identities=15% Similarity=0.170 Sum_probs=46.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~~ 129 (219)
++.|.+|..-...-.--.|-=--+-+.+++..+++.+.++... .=.+.|++++|||+-||--|+.=.
T Consensus 63 GF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~---------~D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 63 GFATWDERQTFIVLISISKVGAKTALAILSQFRPDDLRRLVAE---------EDVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHh---------CCHHHHhcCCCcCHHHHHHHHHHH
Confidence 6888888666555544455433345677777777766655543 235689999999999999887543
No 52
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.01 E-value=13 Score=32.04 Aligned_cols=66 Identities=18% Similarity=0.083 Sum_probs=44.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
++.|.+|..-...-.--.|-=--+-+..++..+++.+.++... .=.+.|++++|||+-||.-|+.-
T Consensus 61 GF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~---------~D~~~L~kvpGIGkKtAerIilE 126 (197)
T PRK14603 61 GFPDEDSLELFELLLGVSGVGPKLALALLSALPPALLARALLE---------GDARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred CcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHH
Confidence 5888888665544443444433345677777777766665543 12568999999999999988754
No 53
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=68.78 E-value=18 Score=32.12 Aligned_cols=36 Identities=28% Similarity=0.345 Sum_probs=26.1
Q ss_pred HHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHH
Q 027792 107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (219)
Q Consensus 107 al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~ 143 (219)
..+.|-++||||+=||=+||--.. ++.-|.-|..-.
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~-~rp~FVvD~Yt~ 148 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYAL-DRPVFVVDKYTR 148 (215)
T ss_pred HHHHHHccCCcchhhHHHHHHHHh-cCcccchhHHHH
Confidence 578899999999999999997543 343455555433
No 54
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=67.52 E-value=15 Score=31.53 Aligned_cols=66 Identities=21% Similarity=0.165 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
++.|++|..-...-.--.|-=.-+-+.+++.-+++.+.++...- =...|+++||||+-||.-|+.-
T Consensus 61 GF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~~~el~~aI~~~---------d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 61 GFNTLEERELFKELIKVNGVGPKLALAILSNMSPEEFVYAIETE---------EVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCCHHHHHHHHHhC---------CHHHHHhCCCCCHHHHHHHHHH
Confidence 68899997766665555554333445555555554444443321 1346899999999999999843
No 55
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=66.95 E-value=4.2 Score=25.96 Aligned_cols=15 Identities=47% Similarity=0.729 Sum_probs=13.2
Q ss_pred ccCCCChHHHHHHHH
Q 027792 113 VLKGVGPATASAVLA 127 (219)
Q Consensus 113 ~LkGVGPATASaILa 127 (219)
.++||||-||-.+|.
T Consensus 20 Gv~giG~ktA~~ll~ 34 (36)
T smart00279 20 GVKGIGPKTALKLLR 34 (36)
T ss_pred CCCcccHHHHHHHHH
Confidence 588999999998875
No 56
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=66.79 E-value=2.2 Score=30.11 Aligned_cols=41 Identities=32% Similarity=0.488 Sum_probs=26.7
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027792 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g 147 (219)
+..+.|..|+|||+.+|-.|+..-.- .-||-|=|=+..+.|
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R~~-~G~f~s~~dL~~v~g 51 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYREK-NGPFKSLEDLKEVPG 51 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHHHH-H-S-SSGGGGGGSTT
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHh-CcCCCCHHHHhhCCC
Confidence 46788999999999999999997533 236666665555544
No 57
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.03 E-value=4 Score=35.23 Aligned_cols=30 Identities=27% Similarity=0.383 Sum_probs=26.3
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+.+.-+..|++..||||=||-+||+...|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 96 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLSSGTPD 96 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 356778999999999999999999987775
No 58
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=63.22 E-value=5.6 Score=34.76 Aligned_cols=30 Identities=27% Similarity=0.458 Sum_probs=26.7
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
+.+.-+..|.+.-||||-||=+||+..+|+
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~ 96 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPE 96 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHH
Confidence 566778999999999999999999998875
No 59
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=62.35 E-value=5.7 Score=34.83 Aligned_cols=23 Identities=35% Similarity=0.616 Sum_probs=19.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHH
Q 027792 103 DLTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaI 125 (219)
.+..-|..|.+||||||-+|.=+
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~ 28 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRL 28 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHH
Confidence 45677899999999999998743
No 60
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=61.16 E-value=8.6 Score=32.13 Aligned_cols=56 Identities=23% Similarity=0.370 Sum_probs=37.5
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh---cCCCCCCCHHHHH
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSLKQYL 158 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~---~g~~~kYt~keY~ 158 (219)
+-+.-.-+|+.+.|||+.+|-.|+... +|. .+--.+++-+..+ ...+-+|.+++|.
T Consensus 19 ~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~ 80 (149)
T PRK04053 19 GTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWM 80 (149)
T ss_pred CCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhh
Confidence 334445568999999999999999884 555 4556777766543 3344556666554
No 61
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=60.77 E-value=9.5 Score=30.75 Aligned_cols=39 Identities=26% Similarity=0.360 Sum_probs=28.5
Q ss_pred HHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027792 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 107 al~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~ 145 (219)
..-+|+.+.|||+.+|-.|+... +|. .+--.+|+-+..+
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l 56 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISAL 56 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHH
Confidence 34468999999999999999984 555 4455666655543
No 62
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=60.44 E-value=60 Score=27.61 Aligned_cols=70 Identities=19% Similarity=0.165 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~~~P~ 132 (219)
++.+..|-.....+..-.|--.-+-+.+++.-..+.+.++... +-.+.|++++|||+.||-.|+..+...
T Consensus 62 gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~---------~d~~~L~~v~Gig~k~A~~I~~~l~~~ 131 (192)
T PRK00116 62 GFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIAN---------GDVKALTKVPGIGKKTAERIVLELKDK 131 (192)
T ss_pred CcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 3446666544445544555444444555555444443332222 235578999999999999999876543
No 63
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=60.19 E-value=4.6 Score=33.98 Aligned_cols=57 Identities=18% Similarity=0.223 Sum_probs=37.0
Q ss_pred CccHHHHHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh---cCCCCCCCHHHH
Q 027792 101 LPDLTKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSLKQY 157 (219)
Q Consensus 101 l~dv~~al~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~---~g~~~kYt~keY 157 (219)
+++-+...-+|+.+.|||+.+|-.||... +|. .+--.+|+=...+ ...+..|.+++|
T Consensus 22 l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w 84 (154)
T PTZ00134 22 VDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPDW 84 (154)
T ss_pred CCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCChh
Confidence 44445556678999999999999999984 554 4445666655433 334445655433
No 64
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=57.83 E-value=32 Score=29.57 Aligned_cols=64 Identities=23% Similarity=0.220 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHH
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaIL 126 (219)
++.|.+|-.-.-.-.--.|-=--+-+..++.-+++.+.++... .=.+.|++++|||+-||--|+
T Consensus 62 GF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~---------~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 62 GFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAEALASAIIS---------GNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred CCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHH
Confidence 6888988665555544455443455666676666664444322 124679999999999999954
No 65
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=57.45 E-value=8.7 Score=35.09 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=17.4
Q ss_pred HHHHHHhhccCCCChHHHHHHHH
Q 027792 105 TKAVSELTVLKGVGPATASAVLA 127 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaILa 127 (219)
..+|..|++++||||.||-.+..
T Consensus 81 ~~~l~~l~~i~GiGpk~a~~l~~ 103 (307)
T cd00141 81 PPGLLLLLRVPGVGPKTARKLYE 103 (307)
T ss_pred hHHHHHHHcCCCCCHHHHHHHHH
Confidence 45677778888888888877773
No 66
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=57.30 E-value=6.8 Score=24.22 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=11.3
Q ss_pred hhccCCCChHHHHHH
Q 027792 111 LTVLKGVGPATASAV 125 (219)
Q Consensus 111 L~~LkGVGPATASaI 125 (219)
+.++.|||+.|+--+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 568999999998653
No 67
>PRK00076 recR recombination protein RecR; Reviewed
Probab=55.18 E-value=9.4 Score=33.28 Aligned_cols=22 Identities=32% Similarity=0.641 Sum_probs=18.5
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027792 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaI 125 (219)
+..-++.|.+||||||-||.=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRL 27 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5567889999999999999754
No 68
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=54.52 E-value=13 Score=29.92 Aligned_cols=38 Identities=32% Similarity=0.443 Sum_probs=28.3
Q ss_pred HHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027792 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 108 l~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~ 145 (219)
.-+|+.+.|||+.+|-.|+... +|. .+--.+|+-+..+
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 56 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKI 56 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 3467999999999999999984 554 4456677766544
No 69
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=53.98 E-value=13 Score=29.55 Aligned_cols=37 Identities=24% Similarity=0.381 Sum_probs=28.3
Q ss_pred HHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027792 109 SELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 109 ~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~ 145 (219)
-.|+.+.|||+.+|-.|+... +|. .+-.++|+-+..+
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 54 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAI 54 (113)
T ss_pred eeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 457999999999999999984 555 5566777766544
No 70
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.68 E-value=30 Score=29.72 Aligned_cols=65 Identities=18% Similarity=0.196 Sum_probs=44.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
++.|++|..-.-.-.--.|-=--+-+.+++..+++.+.++... .|+ +.| ++||||+-||.-|+.=
T Consensus 62 GF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~-----~D~----~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 62 GFLNREEQDCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVN-----EDK----AAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHc-----CCH----hhe-ECCCCcHHHHHHHHHH
Confidence 6889998766555554455433455677777777766665543 233 578 8999999999988753
No 71
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.87 E-value=11 Score=32.92 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=18.4
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027792 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaI 125 (219)
+..-+..|.+||||||=||-=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5567889999999999998755
No 72
>PRK03980 flap endonuclease-1; Provisional
Probab=52.05 E-value=50 Score=30.17 Aligned_cols=73 Identities=21% Similarity=0.141 Sum_probs=43.7
Q ss_pred ccCCCChHHHHHHHHhhcC-------CCCCccc-HHHHHHhcCC------CCCCCHHHHHHHHHHHHHHHHHhhccCCCC
Q 027792 113 VLKGVGPATASAVLAAYAP-------GVAPFMS-DEAMGAALGH------SKDYSLKQYLLFADKLQAKAKELVSEENCF 178 (219)
Q Consensus 113 ~LkGVGPATASaILa~~~P-------~~~pFfs-DEa~~~~~g~------~~kYt~keY~~~~~~l~~~~~~L~~~~~~~ 178 (219)
.++||||-||.-++.-+-- ....|-. +|+......+ .+++...+...+.+-|+. ..+|
T Consensus 193 GI~GIG~ktA~kLi~~~~sle~i~~~~~~~~~~~~~~r~~f~~p~v~~~~~~~~~~pd~~~l~~fl~~--------e~~f 264 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHGDLEKVLEERGFEIENYDEIREFFLNPPVTDDYELKWKEPDKEGIIEFLVE--------EHDF 264 (292)
T ss_pred CCCCccHHHHHHHHHHCCCHHHHHHhccCCCCCHHHHHHHhcCCCCCCCCCccCCCCCHHHHHHHHhc--------cCCC
Confidence 4899999999999976420 0012223 5666655442 345555566654444432 2369
Q ss_pred CHHHHHHHHHHHHHh
Q 027792 179 TPFDVERALWSSAIG 193 (219)
Q Consensus 179 t~~~VEkalws~~v~ 193 (219)
+..+|++++=-+.-.
T Consensus 265 ~~~rv~~~~~~l~~~ 279 (292)
T PRK03980 265 SEERVKKALERLEKA 279 (292)
T ss_pred CHHHHHHHHHHHHHH
Confidence 999999986655433
No 73
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.14 E-value=96 Score=27.43 Aligned_cols=82 Identities=21% Similarity=0.259 Sum_probs=59.6
Q ss_pred HHHHHHhh-ccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhc--C----CCCCCCHHHHHHHHHHHHHHHHHhhccCCC
Q 027792 105 TKAVSELT-VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL--G----HSKDYSLKQYLLFADKLQAKAKELVSEENC 177 (219)
Q Consensus 105 ~~al~~L~-~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~--g----~~~kYt~keY~~~~~~l~~~~~~L~~~~~~ 177 (219)
+-|.+.|. +++|+|=--||=.|-=.-=+.++..+--...|+. | .|...|.|-|+..-+.++..+.+++
T Consensus 116 ~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~g----- 190 (210)
T COG1059 116 KVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEVG----- 190 (210)
T ss_pred HHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHhC-----
Confidence 33777787 8999999999999864222233333333445653 3 3448889999999999999999984
Q ss_pred CCHHHHHHHHHHHH
Q 027792 178 FTPFDVERALWSSA 191 (219)
Q Consensus 178 ~t~~~VEkalws~~ 191 (219)
.++.+++.-+|-.-
T Consensus 191 ~s~gelDL~IWY~e 204 (210)
T COG1059 191 ISLGELDLYIWYKE 204 (210)
T ss_pred CCcchhHHHHHHHH
Confidence 67888998888643
No 74
>PRK13844 recombination protein RecR; Provisional
Probab=51.12 E-value=12 Score=32.82 Aligned_cols=22 Identities=14% Similarity=0.374 Sum_probs=18.3
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027792 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaI 125 (219)
+..-+..|.+||||||=||.=+
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rl 31 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRL 31 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5567889999999999998754
No 75
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=50.54 E-value=11 Score=27.45 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=15.8
Q ss_pred hhccCCCChHHHHHHHHhh
Q 027792 111 LTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 111 L~~LkGVGPATASaILa~~ 129 (219)
+..++||||-||.-||.-+
T Consensus 24 i~gv~giG~k~A~~ll~~~ 42 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEY 42 (75)
T ss_pred CCCCCcccHHHHHHHHHHh
Confidence 3458899999999999874
No 76
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=50.31 E-value=14 Score=34.15 Aligned_cols=26 Identities=31% Similarity=0.419 Sum_probs=22.4
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 103 DLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
.+-.+|..|++++||||.||-.+-..
T Consensus 83 ~~p~~l~~l~~i~GiGpk~a~~l~~l 108 (334)
T smart00483 83 EVYKSLKLFTNVFGVGPKTAAKWYRK 108 (334)
T ss_pred cHHHHHHHHHccCCcCHHHHHHHHHh
Confidence 35679999999999999999888763
No 77
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=48.72 E-value=14 Score=33.66 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=12.9
Q ss_pred CccHHHHHHHhhccCCCChHHHHH
Q 027792 101 LPDLTKAVSELTVLKGVGPATASA 124 (219)
Q Consensus 101 l~dv~~al~~L~~LkGVGPATASa 124 (219)
++..-..+..+++|+|||+++|+.
T Consensus 37 l~~~i~~~~~~~~ipgiG~~ia~k 60 (307)
T cd00141 37 LPEPIESLEEAKKLPGIGKKIAEK 60 (307)
T ss_pred CCcccCCHHHhcCCCCccHHHHHH
Confidence 343333444556666666666653
No 78
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=48.18 E-value=57 Score=22.78 Aligned_cols=43 Identities=19% Similarity=0.398 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 55 HINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 55 ~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
+|+.....+|+++.-.+|.|+ .++.|..++|||..||--|+..
T Consensus 24 gig~~~a~~Il~~R~~~g~~~-------------------------------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 24 GVGLKKAEAIVSYREEYGPFK-------------------------------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CCCHHHHHHHHHHHHHcCCcC-------------------------------CHHHHHcCCCCCHHHHHHHHhh
Confidence 566666666777665555443 4566777899999999888764
No 79
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=47.36 E-value=13 Score=34.34 Aligned_cols=35 Identities=26% Similarity=0.361 Sum_probs=24.9
Q ss_pred hhCccHHHHHHHhhccCCCChHHHHHHHHhhcCCC
Q 027792 99 KSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGV 133 (219)
Q Consensus 99 ~~l~dv~~al~~L~~LkGVGPATASaILa~~~P~~ 133 (219)
..++..-..+..|++|+|||+++|.-|--...-..
T Consensus 38 ~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~ 72 (334)
T smart00483 38 KSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGK 72 (334)
T ss_pred HhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCc
Confidence 34543333456789999999999999987765444
No 80
>PRK07945 hypothetical protein; Provisional
Probab=46.42 E-value=21 Score=32.96 Aligned_cols=19 Identities=47% Similarity=0.733 Sum_probs=15.6
Q ss_pred HhhccCCCChHHHHHHHHh
Q 027792 110 ELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 110 ~L~~LkGVGPATASaILa~ 128 (219)
.|++|+|||..||..|--.
T Consensus 50 ~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred CcccCCCcCHHHHHHHHHH
Confidence 5889999999999887655
No 81
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.28 E-value=46 Score=27.67 Aligned_cols=52 Identities=23% Similarity=0.301 Sum_probs=35.8
Q ss_pred HHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhc--c-CCCChHHHHHHHHhhcCC
Q 027792 80 DFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTV--L-KGVGPATASAVLAAYAPG 132 (219)
Q Consensus 80 ~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~--L-kGVGPATASaILa~~~P~ 132 (219)
.|----++..|-++|+-|.+.+|-+ +.+.++.. + ..+|||.|+|+.++.-|.
T Consensus 28 rL~pvFpEnRVikaTrfairfMP~v-Avftl~wQ~~~~~ql~pAv~tAlfal~lpl 82 (149)
T COG3092 28 RLAPVFPENRVIKATRFAIRFMPPV-AVFTLCWQIALGGQLGPAVATALFALSLPL 82 (149)
T ss_pred hhcccCchhHHHHHHHHHHHhccHH-HHHHHHHHHHHhcccchHHHHHHHHHhccc
Confidence 3333456889999999999988743 23333322 2 367999999999986653
No 82
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=44.02 E-value=24 Score=29.28 Aligned_cols=50 Identities=24% Similarity=0.404 Sum_probs=32.8
Q ss_pred HHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHhc---CCCCCCCHHHHH
Q 027792 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAAL---GHSKDYSLKQYL 158 (219)
Q Consensus 108 l~~L~~LkGVGPATASaILa~~--~P~-~~pFfsDEa~~~~~---g~~~kYt~keY~ 158 (219)
.-+|+.+.|||+.+|-.|+... +|. .+--.+++-...+. .. -+|.+++|.
T Consensus 20 ~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~-~~~~iP~w~ 75 (144)
T TIGR03629 20 EYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-YEYGIPSWL 75 (144)
T ss_pred EEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHHh-ccccCCHHH
Confidence 3468999999999999999884 454 45556777554332 22 345555444
No 83
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=42.33 E-value=18 Score=32.39 Aligned_cols=43 Identities=33% Similarity=0.452 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhhCccHHHH-HHHhhccCCCChHHHHHHHHhhc
Q 027792 88 SSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAYA 130 (219)
Q Consensus 88 ~~V~~~t~~Af~~l~dv~~a-l~~L~~LkGVGPATASaILa~~~ 130 (219)
..++..-..+|..+.++..| .+.|.+++|||+++|-.|.....
T Consensus 14 krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 14 SKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred HHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 34444444446666666555 88999999999999999998753
No 84
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=41.68 E-value=37 Score=29.00 Aligned_cols=52 Identities=17% Similarity=0.337 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccH
Q 027792 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (219)
Q Consensus 52 ~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv 104 (219)
..+||+..||.+|-.+ +..|..|...-+.+.+|.+..|.++.+.-|...|+.
T Consensus 13 ~gRyl~~~eL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~l 64 (170)
T TIGR01339 13 RGEFISSSQIDALSKL-VADGNKRSDAVSRITNNASTIVTNAARSLFAEQPQL 64 (170)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCCC
Confidence 3579999999998776 578889999999999999999999999999877753
No 85
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=40.35 E-value=39 Score=30.57 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=15.8
Q ss_pred ccCCCChHHHHHHHHhhc
Q 027792 113 VLKGVGPATASAVLAAYA 130 (219)
Q Consensus 113 ~LkGVGPATASaILa~~~ 130 (219)
.++||||-||--++.-+.
T Consensus 227 gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 227 GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 499999999999998854
No 86
>PRK14976 5'-3' exonuclease; Provisional
Probab=39.72 E-value=18 Score=32.81 Aligned_cols=17 Identities=47% Similarity=0.874 Sum_probs=14.6
Q ss_pred cCCCChHHHHHHHHhhc
Q 027792 114 LKGVGPATASAVLAAYA 130 (219)
Q Consensus 114 LkGVGPATASaILa~~~ 130 (219)
++||||-||..+|.-+-
T Consensus 196 VpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 196 VKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCcccHHHHHHHHHHcC
Confidence 78899999999998643
No 87
>PRK08609 hypothetical protein; Provisional
Probab=39.63 E-value=29 Score=34.52 Aligned_cols=23 Identities=30% Similarity=0.511 Sum_probs=13.6
Q ss_pred HHHHhhccCCCChHHHHHHHHhh
Q 027792 107 AVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 107 al~~L~~LkGVGPATASaILa~~ 129 (219)
.+..|++|+|||+++|+-|--..
T Consensus 46 ~~~~l~~ipgIG~~ia~kI~Eil 68 (570)
T PRK08609 46 EIDDFTKLKGIGKGTAEVIQEYR 68 (570)
T ss_pred hhhhhccCCCcCHHHHHHHHHHH
Confidence 34456666666666666655543
No 88
>PRK09482 flap endonuclease-like protein; Provisional
Probab=36.46 E-value=22 Score=32.01 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=15.4
Q ss_pred ccCCCChHHHHHHHHhhc
Q 027792 113 VLKGVGPATASAVLAAYA 130 (219)
Q Consensus 113 ~LkGVGPATASaILa~~~ 130 (219)
.++||||-||.-+|.-+.
T Consensus 186 GVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCcChHHHHHHHHHhC
Confidence 378889999999999753
No 89
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=35.11 E-value=87 Score=24.75 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=16.6
Q ss_pred HHHHhhccCCCChHHHHHHHH
Q 027792 107 AVSELTVLKGVGPATASAVLA 127 (219)
Q Consensus 107 al~~L~~LkGVGPATASaILa 127 (219)
.++.|..++|||+.|+--|.-
T Consensus 96 s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 96 SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHHcCCCCCHHHHHHHHh
Confidence 456778899999999877653
No 90
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=34.60 E-value=38 Score=25.17 Aligned_cols=32 Identities=28% Similarity=0.431 Sum_probs=23.3
Q ss_pred hhccCCCChHHHHHHHHhhcCCCCCcccHHHHHH
Q 027792 111 LTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA 144 (219)
Q Consensus 111 L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~ 144 (219)
|+.+||||..+|-.|+.... .-||-|=+=|..
T Consensus 29 l~~Ikglg~~~a~~I~~~R~--~g~f~s~~df~~ 60 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERE--NGPFKSLEDFIQ 60 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHH--CSS-SSHHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHh--cCCCCCHHHHHH
Confidence 67899999999999999876 448777555543
No 91
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=33.16 E-value=58 Score=28.06 Aligned_cols=51 Identities=16% Similarity=0.216 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+||+..||.+|-.. +..|..|-..-+.+.+|.+.-|.++.+.-|+..|+
T Consensus 15 qgRYLs~~eL~~L~~~-~~~g~~RL~aa~~L~~NA~~IV~~A~~~l~~~~P~ 65 (177)
T CHL00172 15 KAAYVGGSDLQALKKF-ISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPG 65 (177)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCC
Confidence 3579999999998654 67899999999999999999999999999987774
No 92
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=32.36 E-value=29 Score=30.49 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=14.5
Q ss_pred ccCCCChHHHHHHHHhh
Q 027792 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaILa~~ 129 (219)
.++||||-||.-+|.-+
T Consensus 187 Gv~GiG~ktA~~Ll~~~ 203 (240)
T cd00008 187 GVPGIGEKTAAKLLKEY 203 (240)
T ss_pred CCCccCHHHHHHHHHHh
Confidence 37899999999999864
No 93
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=32.01 E-value=31 Score=28.52 Aligned_cols=51 Identities=20% Similarity=0.236 Sum_probs=44.3
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|-.+- ..|.-|....+.++.|.+.-|.++..+-|...|+
T Consensus 10 egRyls~~EL~~l~~~~-~~~~~Rl~aa~~L~~~a~~IV~~A~~~l~~~~P~ 60 (157)
T PF00502_consen 10 EGRYLSDGELQALKGYF-QSANARLEAAEKLRDNASEIVDQAAQKLFEKYPD 60 (157)
T ss_dssp TTSECEHHHHHHHHHHH-HTHHHHHHHHHHHHHTHHHHHHHHHHHHHHHSGG
T ss_pred cCCCCCHHHHHHHHHHH-HhHHHHHHHHHHHHHhHHHHHHHHHHHHHHhccc
Confidence 35799999999998875 4566799999999999999999999999987775
No 94
>smart00475 53EXOc 5'-3' exonuclease.
Probab=31.09 E-value=31 Score=30.87 Aligned_cols=17 Identities=29% Similarity=0.577 Sum_probs=14.5
Q ss_pred ccCCCChHHHHHHHHhh
Q 027792 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaILa~~ 129 (219)
.++||||-||.-+|.=+
T Consensus 190 GV~GIG~KtA~~Ll~~y 206 (259)
T smart00475 190 GVPGIGEKTAAKLLKEF 206 (259)
T ss_pred CCCCCCHHHHHHHHHHh
Confidence 37889999999999864
No 95
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.96 E-value=1.3e+02 Score=32.48 Aligned_cols=24 Identities=25% Similarity=0.457 Sum_probs=19.3
Q ss_pred HHHHhhc------cCCCChHHHHHHHHhhc
Q 027792 107 AVSELTV------LKGVGPATASAVLAAYA 130 (219)
Q Consensus 107 al~~L~~------LkGVGPATASaILa~~~ 130 (219)
.|.+||. |+||||-||=-||..+.
T Consensus 858 ~laiL~G~DY~~GI~GIGpktAl~li~~~~ 887 (1034)
T TIGR00600 858 NLAYLLGSDYTEGIPTVGPVSAMEILNEFP 887 (1034)
T ss_pred HHHHeeCCCCCCCCCcccHHHHHHHHHHcC
Confidence 4566663 99999999999988765
No 96
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=30.27 E-value=51 Score=31.32 Aligned_cols=32 Identities=28% Similarity=0.514 Sum_probs=20.3
Q ss_pred HHhhCccH-HHHHHHhhccCCCChHHHHHHHHh
Q 027792 97 AFKSLPDL-TKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 97 Af~~l~dv-~~al~~L~~LkGVGPATASaILa~ 128 (219)
-|..+..+ .+..+.|++.+|||++.|-.|-..
T Consensus 306 ~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 306 HFGSLQGLLAASIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred HcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHH
Confidence 34444333 334677888888888888776554
No 97
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=29.84 E-value=8.4 Score=30.05 Aligned_cols=17 Identities=41% Similarity=0.792 Sum_probs=13.6
Q ss_pred ccCCCChHHHHHHHHhh
Q 027792 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaILa~~ 129 (219)
..+||||-||+.+|.-+
T Consensus 22 GV~GIG~KtA~~LL~~y 38 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEY 38 (101)
T ss_dssp --TTSTCHCCCCCHHHH
T ss_pred CCCCCCHHHHHHHHHHc
Confidence 47899999999999875
No 98
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=29.83 E-value=50 Score=26.20 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=22.4
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcC
Q 027792 106 KAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaILa~~~P 131 (219)
.++.-|+.++||||..|-+++.++--
T Consensus 50 ~~~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 50 VNQADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HhHHHhhhcCCCCHHHHHHHHHhCcC
Confidence 46778889999999999999999643
No 99
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=29.50 E-value=90 Score=26.49 Aligned_cols=51 Identities=12% Similarity=0.138 Sum_probs=44.3
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|..- +..|.-|-..-+.+.+|....|.++.+.-|+..|+
T Consensus 15 qgRyls~~eL~~l~~~-~~~g~~RL~aa~~Lt~nA~~IV~~Aa~~lf~~~P~ 65 (162)
T CHL00170 15 QGRFLSNGELQACNGR-FQRAAASLEAARSLTSNAQRLIDGAAQAVYTKFPY 65 (162)
T ss_pred ccCCCCHHHHHHHHHH-HhccHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcC
Confidence 3579999999998764 57899999999999999999999999999987774
No 100
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=28.03 E-value=2.8e+02 Score=26.99 Aligned_cols=83 Identities=27% Similarity=0.341 Sum_probs=48.7
Q ss_pred hHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhh-ccCCCChHH---------------------HHHHHHhhcCCCCC
Q 027792 78 LLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELT-VLKGVGPAT---------------------ASAVLAAYAPGVAP 135 (219)
Q Consensus 78 L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~-~LkGVGPAT---------------------ASaILa~~~P~~~p 135 (219)
+..+|.+|+.+.++.++-.=|....++..++-... +++||||-. +.++.+--.-...|
T Consensus 82 ~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~~~p 161 (422)
T KOG2582|consen 82 LNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYASVLP 161 (422)
T ss_pred HHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccccCC
Confidence 45889999988888888766665545444444333 355555422 11111111222558
Q ss_pred cccHHHHHHhcCCCCCCCHHHHHHHH
Q 027792 136 FMSDEAMGAALGHSKDYSLKQYLLFA 161 (219)
Q Consensus 136 FfsDEa~~~~~g~~~kYt~keY~~~~ 161 (219)
|++|.... +|+...-+..+.++.|+
T Consensus 162 ~ld~dive-i~~~n~h~~~k~fL~Y~ 186 (422)
T KOG2582|consen 162 YLDDDIVE-ICKANPHLDPKYFLLYL 186 (422)
T ss_pred ccchhHHH-HhccCCCCCHHHHHHHH
Confidence 88888776 46655566677766654
No 101
>PRK08609 hypothetical protein; Provisional
Probab=27.71 E-value=47 Score=33.09 Aligned_cols=24 Identities=17% Similarity=0.301 Sum_probs=19.6
Q ss_pred HHHHHHHhhccCCCChHHHHHHHH
Q 027792 104 LTKAVSELTVLKGVGPATASAVLA 127 (219)
Q Consensus 104 v~~al~~L~~LkGVGPATASaILa 127 (219)
+..++..|++++||||.||-.+--
T Consensus 83 ~p~~~~~l~~i~GiGpk~a~~l~~ 106 (570)
T PRK08609 83 VPEGLLPLLKLPGLGGKKIAKLYK 106 (570)
T ss_pred CcHHHHHHhcCCCCCHHHHHHHHH
Confidence 345788899999999999988753
No 102
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=26.42 E-value=62 Score=20.77 Aligned_cols=41 Identities=22% Similarity=0.381 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhhCccHH-HHHHHhhccCCCChHHHHHHHHh
Q 027792 88 SSVKSASEKAFKSLPDLT-KAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 88 ~~V~~~t~~Af~~l~dv~-~al~~L~~LkGVGPATASaILa~ 128 (219)
..+......+|..+.++. .....|+.++|++..+|..|...
T Consensus 4 ~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 4 EIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINR 45 (50)
T ss_pred HHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence 344444555555444433 35788999999999999888764
No 103
>PF09660 DUF2397: Protein of unknown function (DUF2397); InterPro: IPR013493 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=26.38 E-value=6.3e+02 Score=24.80 Aligned_cols=42 Identities=19% Similarity=0.124 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhhhhcccCC
Q 027792 159 LFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKASKS 201 (219)
Q Consensus 159 ~~~~~l~~~~~~L~~~~~~~t~~~VEkalws~~v~~k~~~~~~ 201 (219)
+|+..|+..+.++...-..+....+|..+......... ++.+
T Consensus 197 ~Fv~~L~r~~~~I~~~l~~l~~~~~~~ll~~~~~~~~~-~p~~ 238 (486)
T PF09660_consen 197 RFVQDLQRRAPRIAAALRELEDEGIERLLERAAEYELR-IPRP 238 (486)
T ss_pred HHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHhccc-cCcc
Confidence 44556666666654433467788888666665444443 4443
No 104
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=26.04 E-value=37 Score=28.10 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.1
Q ss_pred HHhhccCCCChHHHHHHHHh
Q 027792 109 SELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 109 ~~L~~LkGVGPATASaILa~ 128 (219)
+-|+-|.||||..++.+=..
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~ 86 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNEL 86 (133)
T ss_pred ccchhhcccCHHHHHHHHHc
Confidence 68999999999999977544
No 105
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=25.99 E-value=73 Score=22.69 Aligned_cols=49 Identities=20% Similarity=0.162 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcc
Q 027792 89 SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFM 137 (219)
Q Consensus 89 ~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~~~P~~~pFf 137 (219)
.|+..+.+-+....+-...++.|.+.-||-|..-|+|.--.--++.-||
T Consensus 3 ~Vq~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF 51 (57)
T TIGR01589 3 LVQNRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFF 51 (57)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHH
Confidence 4677777778878888999999999999999999988776554454555
No 106
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=25.89 E-value=1.2e+02 Score=25.59 Aligned_cols=51 Identities=12% Similarity=0.190 Sum_probs=44.4
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|..- +..|..|-..-+.+.+|....|.++.+.-|+..|+
T Consensus 14 qgRyls~~eL~~l~~~-~~~g~~RL~aa~~Lt~na~~IV~~Aa~~lf~~~P~ 64 (161)
T TIGR01338 14 QGRFLSNGELQSIFGR-FQRATASLEAAKSLTSNAQRLISGAAQAVYSKFPY 64 (161)
T ss_pred ccCCCCHHHHHHHHHH-HHchHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcC
Confidence 3579999999998663 67899999999999999999999999999987774
No 107
>CHL00090 apcD allophycocyanin gamma subunit
Probab=25.66 E-value=89 Score=26.28 Aligned_cols=50 Identities=20% Similarity=0.317 Sum_probs=43.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 53 NPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 53 ~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
.+|++..||..|-.+ +..|.-|-..-+.+++|.+.-|.++.+.-|...|+
T Consensus 15 gRyls~~EL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~ 64 (161)
T CHL00090 15 LRYPTIGELESIQDY-LKTGEKRIRIATILRDNEKEIIQKASKQLFQIHPE 64 (161)
T ss_pred cCCCCHHHHHHHHHH-HHhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHCcC
Confidence 479999999999776 56788888889999999999999999999987774
No 108
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=25.55 E-value=37 Score=30.45 Aligned_cols=20 Identities=45% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHhhccCCCChHHHHHHHHh
Q 027792 109 SELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 109 ~~L~~LkGVGPATASaILa~ 128 (219)
+.|..|+|||+.++-.+|..
T Consensus 3 ~~L~~IpGIG~krakkLl~~ 22 (232)
T PRK12766 3 EELEDISGVGPSKAEALREA 22 (232)
T ss_pred cccccCCCcCHHHHHHHHHc
Confidence 46788999999999999997
No 109
>CHL00086 apcA allophycocyanin alpha subunit
Probab=24.26 E-value=1.1e+02 Score=25.70 Aligned_cols=51 Identities=20% Similarity=0.401 Sum_probs=44.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|-.. +..|..|-..-+.+.+|.+.-|.++.+.-|...|+
T Consensus 14 ~gRyls~~eL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~ 64 (161)
T CHL00086 14 EARYLSPGELDRIKSF-VLSGQRRLRIAQILTDNRERIVKQGGQQLFQKRPD 64 (161)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcC
Confidence 3579999999998776 56788899999999999999999999999987775
No 110
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.12 E-value=6.8e+02 Score=25.87 Aligned_cols=19 Identities=5% Similarity=-0.202 Sum_probs=14.8
Q ss_pred CCCHHHHHHHHHHHHHhhh
Q 027792 177 CFTPFDVERALWSSAIGLK 195 (219)
Q Consensus 177 ~~t~~~VEkalws~~v~~k 195 (219)
.++...+|...|+......
T Consensus 525 ~vdVd~LE~s~ga~~~~~~ 543 (652)
T KOG2376|consen 525 AVDVDALEKSDGAKYSEAY 543 (652)
T ss_pred hcCchHhhhccCcchhhhh
Confidence 4677888999998877763
No 111
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=23.93 E-value=93 Score=26.38 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=44.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+||+..||..|-. -+.+|..|...-+.+.+|.+..|.++.+.-|+..|+
T Consensus 15 ~gRyls~~eL~~l~~-~~~~a~~rl~aa~~L~~na~~iV~~A~~~l~~~~P~ 65 (164)
T CHL00173 15 AGRFPSSSDLESVQG-NIQRAAARLEAAEKLASNHEAVVKEAGDACFAKYSY 65 (164)
T ss_pred ccCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 357999999999855 356888999999999999999999999999987775
No 112
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=23.63 E-value=60 Score=28.39 Aligned_cols=66 Identities=20% Similarity=0.227 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027792 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~ 128 (219)
++.|.+|-.-.-.-=--.|-=--+-+.++++-+++.+.++... .=++.||++||||.=||=-|+.=
T Consensus 62 GF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~---------~d~~~L~k~PGIGkKtAerivle 127 (201)
T COG0632 62 GFLTEEERELFRLLISVNGIGPKLALAILSNLDPEELAQAIAN---------EDVKALSKIPGIGKKTAERIVLE 127 (201)
T ss_pred CCCCHHHHHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHh---------cChHhhhcCCCCCHHHHHHHHHH
Confidence 5777777433332222233222233455555465555544432 12568999999999999888764
No 113
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=23.58 E-value=1.5e+02 Score=25.79 Aligned_cols=23 Identities=22% Similarity=0.379 Sum_probs=14.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHh
Q 027792 149 SKDYSLKQYLLFADKLQAKAKEL 171 (219)
Q Consensus 149 ~~kYt~keY~~~~~~l~~~~~~L 171 (219)
+.+||..||..+....+++.++|
T Consensus 162 ~~k~~~~el~~i~~~y~~~~k~L 184 (189)
T PF05766_consen 162 PRKWTIEELKAIIAIYRAKLKEL 184 (189)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHH
Confidence 45666666666666666666665
No 114
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=23.27 E-value=98 Score=26.38 Aligned_cols=50 Identities=18% Similarity=0.323 Sum_probs=43.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027792 53 NPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 53 ~~~ltkdEL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
.+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|.++.+.-|...|+
T Consensus 16 gRyls~~EL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~ 65 (172)
T CHL00171 16 GEFLSNTQLDALSKM-VAEGNKRLDAVNKINANASTIVTNAARSLFAEQPQ 65 (172)
T ss_pred cCCCCHHHHHHHHHH-HHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcC
Confidence 579999999998776 56788888888899999999999999999987775
No 115
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=23.07 E-value=37 Score=24.16 Aligned_cols=17 Identities=29% Similarity=0.342 Sum_probs=12.6
Q ss_pred ccCCCChHHHHHHHHhh
Q 027792 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaILa~~ 129 (219)
.+=|+||||+.+.=++.
T Consensus 17 ~v~tigPA~~Al~~~~~ 33 (77)
T PF04854_consen 17 PVFTIGPATAALYYVVR 33 (77)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45578999998876653
No 116
>PF05845 PhnH: Bacterial phosphonate metabolism protein (PhnH); InterPro: IPR008772 This family consists of several bacterial PhnH sequences, which is a component of the C-P lyase system (GenProp0232 from GENPROP) for the catabolism of phosphonate compounds []. The specific function of this component is unknown.; GO: 0015716 phosphonate transport; PDB: 2FSU_A.
Probab=22.84 E-value=72 Score=27.59 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=15.6
Q ss_pred cCCCChHHHHHHHHhhcCCCCCcc
Q 027792 114 LKGVGPATASAVLAAYAPGVAPFM 137 (219)
Q Consensus 114 LkGVGPATASaILa~~~P~~~pFf 137 (219)
-.|..||++..+|++.|.+. ||+
T Consensus 39 ~~~l~~a~~avllTLlD~et-~lw 61 (192)
T PF05845_consen 39 PAGLSPAAAAVLLTLLDNET-PLW 61 (192)
T ss_dssp STTS-HHHHHHHHHH--TTS--EE
T ss_pred CCCccHHHHHHHHHHcCCCC-cee
Confidence 34779999999999999876 773
No 117
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=21.62 E-value=64 Score=29.18 Aligned_cols=39 Identities=26% Similarity=0.423 Sum_probs=29.1
Q ss_pred cHHHHHHHhhccCCCChHHHHH--HHHhhcCCCCCcccHHHH
Q 027792 103 DLTKAVSELTVLKGVGPATASA--VLAAYAPGVAPFMSDEAM 142 (219)
Q Consensus 103 dv~~al~~L~~LkGVGPATASa--ILa~~~P~~~pFfsDEa~ 142 (219)
+...=++-||..||||+-|+=. |-+++.|+..| -.|--.
T Consensus 159 seEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp-~dDlgi 199 (254)
T KOG1918|consen 159 SEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMP-ADDLGI 199 (254)
T ss_pred CHHHHHHHHHhccCccceeeeeeeeeccCCCcccC-chhhhH
Confidence 3456688999999999999975 45678998877 344433
No 118
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=20.81 E-value=76 Score=31.70 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=32.4
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027792 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaILa~~~P~~~pFfsDEa~~~~~g 147 (219)
.++.+.|..|+|||-.|+.-|++- -||.|-|.|....+
T Consensus 512 ~~s~~vl~~ipgig~~~~~~I~~~-----Rp~~s~e~~l~~v~ 549 (560)
T COG1031 512 SASKDVLRAIPGIGKKTLRKILAE-----RPFKSSEEFLKLVP 549 (560)
T ss_pred cccHHHHHhcccchhhhHHHHHhc-----CCccchHHHHhccC
Confidence 356899999999999999999984 39999999987665
No 119
>PRK09672 phage exclusion protein Lit; Provisional
Probab=20.79 E-value=3.1e+02 Score=25.69 Aligned_cols=34 Identities=18% Similarity=0.101 Sum_probs=27.0
Q ss_pred cCCCChHHHHHHHHhhcCC-------CCCcccHHHHHHhcC
Q 027792 114 LKGVGPATASAVLAAYAPG-------VAPFMSDEAMGAALG 147 (219)
Q Consensus 114 LkGVGPATASaILa~~~P~-------~~pFfsDEa~~~~~g 147 (219)
=||||.|+|.++|++.-|+ .+|=+.|+....+-+
T Consensus 216 Kr~vgIaia~l~l~~l~~~~~~~g~~tHP~~~~RI~a~is~ 256 (305)
T PRK09672 216 KRSVGIAIALLFLQELELENKSCGKGTHPDADQRIFANLSK 256 (305)
T ss_pred hhhHHHHHHHHHHHHHhccccCCCCCCCCCHHHHHHHhhhc
Confidence 6899999999999986553 567788888776544
No 120
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=20.31 E-value=96 Score=21.78 Aligned_cols=47 Identities=15% Similarity=0.195 Sum_probs=35.0
Q ss_pred HHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcc
Q 027792 91 KSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFM 137 (219)
Q Consensus 91 ~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaILa~~~P~~~pFf 137 (219)
+..+.+-++...+-...++.|.+--||-|..-++|..=.--++.-||
T Consensus 2 q~lIErCl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF 48 (54)
T PF09713_consen 2 QNLIERCLQLYMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFF 48 (54)
T ss_pred chHHHHHHHHcCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHH
Confidence 44555566667778889999999999999999998876544444454
Done!