Query 027752
Match_columns 219
No_of_seqs 112 out of 149
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 14:38:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027752.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027752hhsearch_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 6.3E-05 1.4E-09 46.7 2.6 24 105-128 7-30 (30)
2 PRK01229 N-glycosylase/DNA lya 96.9 0.0042 9.2E-08 54.3 7.5 81 103-190 112-201 (208)
3 COG0177 Nth Predicted EndoIII- 96.8 0.0051 1.1E-07 54.0 7.6 71 57-130 42-130 (211)
4 TIGR01084 mutY A/G-specific ad 96.2 0.042 9.1E-07 49.8 9.9 36 104-140 100-135 (275)
5 cd00056 ENDO3c endonuclease II 96.0 0.037 8.1E-07 44.7 7.7 37 105-143 79-116 (158)
6 PRK10702 endonuclease III; Pro 95.0 0.042 9.2E-07 47.8 5.1 28 104-131 104-131 (211)
7 PRK10880 adenine DNA glycosyla 94.7 0.051 1.1E-06 50.9 5.1 29 104-132 104-132 (350)
8 smart00478 ENDO3c endonuclease 94.7 0.21 4.6E-06 40.0 8.0 29 104-132 67-95 (149)
9 PF02371 Transposase_20: Trans 94.6 0.03 6.5E-07 41.8 2.8 37 109-147 2-39 (87)
10 PRK13910 DNA glycosylase MutY; 94.4 0.14 3.1E-06 46.8 7.2 30 106-135 69-98 (289)
11 COG1194 MutY A/G-specific DNA 94.4 0.055 1.2E-06 50.7 4.6 36 108-143 112-147 (342)
12 COG0122 AlkA 3-methyladenine D 94.1 0.12 2.5E-06 47.1 5.9 72 55-135 144-226 (285)
13 TIGR01083 nth endonuclease III 94.1 0.14 3.1E-06 43.4 6.1 27 104-130 101-127 (191)
14 TIGR00588 ogg 8-oxoguanine DNA 93.7 0.061 1.3E-06 49.3 3.4 37 104-142 215-253 (310)
15 TIGR03252 uncharacterized HhH- 93.6 0.059 1.3E-06 46.2 2.9 44 102-147 108-151 (177)
16 PRK02515 psbU photosystem II c 93.4 0.083 1.8E-06 43.4 3.3 39 105-148 57-95 (132)
17 PRK13913 3-methyladenine DNA g 93.3 0.24 5.2E-06 43.6 6.2 39 106-145 118-156 (218)
18 PRK10308 3-methyl-adenine DNA 93.1 0.11 2.3E-06 47.2 3.9 33 103-135 201-235 (283)
19 smart00278 HhH1 Helix-hairpin- 91.7 0.14 3E-06 30.2 1.9 19 110-128 2-20 (26)
20 PF11731 Cdd1: Pathogenicity l 89.8 0.23 5.1E-06 38.5 2.1 26 104-129 7-32 (93)
21 PF10391 DNA_pol_lambd_f: Fing 87.5 0.38 8.3E-06 33.3 1.8 22 108-129 1-22 (52)
22 TIGR01259 comE comEA protein. 87.4 0.61 1.3E-05 37.2 3.1 42 105-147 64-105 (120)
23 PF14716 HHH_8: Helix-hairpin- 85.7 1.2 2.7E-05 31.7 3.7 31 97-127 34-65 (68)
24 PRK14605 ruvA Holliday junctio 85.0 0.66 1.4E-05 39.9 2.3 31 103-133 67-97 (194)
25 KOG1921 Endonuclease III [Repl 83.8 1.7 3.8E-05 39.5 4.5 31 103-133 153-183 (286)
26 KOG2875 8-oxoguanine DNA glyco 81.6 2.3 5E-05 39.4 4.5 61 104-165 213-282 (323)
27 PRK00116 ruvA Holliday junctio 81.3 1.4 3E-05 37.7 2.9 28 104-131 68-95 (192)
28 PF14520 HHH_5: Helix-hairpin- 81.0 1.6 3.4E-05 30.2 2.6 23 107-129 3-25 (60)
29 TIGR00084 ruvA Holliday juncti 80.8 1.1 2.5E-05 38.4 2.2 30 103-132 66-95 (191)
30 PRK13901 ruvA Holliday junctio 80.8 1.1 2.3E-05 39.1 2.0 31 103-133 66-96 (196)
31 COG2003 RadC DNA repair protei 80.4 3.3 7.1E-05 36.9 4.9 153 35-208 3-183 (224)
32 PRK14600 ruvA Holliday junctio 80.2 1.1 2.4E-05 38.4 1.9 31 103-133 67-97 (186)
33 PF12826 HHH_2: Helix-hairpin- 78.4 2 4.4E-05 30.3 2.5 24 106-129 32-55 (64)
34 PRK14601 ruvA Holliday junctio 78.2 6.1 0.00013 33.9 5.8 66 54-128 62-127 (183)
35 COG1555 ComEA DNA uptake prote 78.2 1.7 3.8E-05 36.0 2.4 42 105-147 93-134 (149)
36 PRK14601 ruvA Holliday junctio 77.8 1.5 3.2E-05 37.6 2.0 31 103-133 67-97 (183)
37 PRK14604 ruvA Holliday junctio 76.2 7.2 0.00016 33.7 5.7 67 54-129 62-128 (195)
38 TIGR00608 radc DNA repair prot 76.0 2.8 6.2E-05 36.8 3.2 62 54-129 12-80 (218)
39 PF14520 HHH_5: Helix-hairpin- 75.9 1.7 3.6E-05 30.1 1.4 22 107-128 36-57 (60)
40 PRK13901 ruvA Holliday junctio 75.9 7.3 0.00016 33.9 5.7 66 54-128 61-126 (196)
41 PRK14606 ruvA Holliday junctio 75.6 7.5 0.00016 33.4 5.7 66 54-128 62-127 (188)
42 TIGR00426 competence protein C 75.2 4.1 8.9E-05 28.8 3.4 39 108-147 15-54 (69)
43 KOG2457 A/G-specific adenine D 74.1 2.9 6.2E-05 40.6 3.0 89 109-200 205-299 (555)
44 PRK14602 ruvA Holliday junctio 73.5 2.5 5.3E-05 36.7 2.2 29 104-132 69-97 (203)
45 PRK14606 ruvA Holliday junctio 73.3 2.3 4.9E-05 36.6 1.9 31 103-133 67-97 (188)
46 PF00416 Ribosomal_S13: Riboso 72.8 6.2 0.00014 30.7 4.1 40 106-145 12-54 (107)
47 PRK00024 hypothetical protein; 70.5 21 0.00045 31.3 7.4 60 54-128 22-85 (224)
48 COG1796 POL4 DNA polymerase IV 70.5 5.1 0.00011 37.5 3.7 33 103-135 45-79 (326)
49 PRK14603 ruvA Holliday junctio 69.8 3 6.5E-05 36.1 1.9 30 104-133 67-96 (197)
50 PRK14602 ruvA Holliday junctio 69.1 13 0.00028 32.3 5.7 67 54-129 63-129 (203)
51 PRK14603 ruvA Holliday junctio 68.5 6.8 0.00015 33.9 3.8 66 54-128 61-126 (197)
52 COG2231 Uncharacterized protei 68.3 19 0.00041 32.0 6.5 34 107-141 113-146 (215)
53 TIGR00084 ruvA Holliday juncti 67.1 15 0.00033 31.5 5.7 66 54-128 61-126 (191)
54 PRK07945 hypothetical protein; 67.0 11 0.00024 34.9 5.1 19 110-128 50-68 (335)
55 smart00279 HhH2 Helix-hairpin- 66.6 4.4 9.5E-05 25.9 1.7 15 113-127 20-34 (36)
56 COG0099 RpsM Ribosomal protein 66.5 5.5 0.00012 32.4 2.7 39 107-145 15-56 (121)
57 PF12836 HHH_3: Helix-hairpin- 65.0 4.9 0.00011 28.3 1.9 41 106-147 11-51 (65)
58 PRK14604 ruvA Holliday junctio 64.8 4.4 9.5E-05 35.0 1.9 31 103-133 67-97 (195)
59 COG0353 RecR Recombinational D 63.8 5.1 0.00011 35.1 2.1 23 103-125 6-28 (198)
60 COG0632 RuvA Holliday junction 62.8 5.8 0.00013 34.7 2.3 31 103-133 67-97 (201)
61 PRK00116 ruvA Holliday junctio 60.8 59 0.0013 27.7 8.2 70 54-132 62-131 (192)
62 PRK14605 ruvA Holliday junctio 58.7 30 0.00064 29.8 6.0 64 54-126 62-125 (194)
63 PTZ00134 40S ribosomal protein 58.5 5.2 0.00011 33.7 1.2 56 101-156 22-83 (154)
64 PF11798 IMS_HHH: IMS family H 57.5 6.7 0.00015 24.3 1.3 15 111-125 13-27 (32)
65 PRK04053 rps13p 30S ribosomal 56.5 12 0.00025 31.4 3.0 57 102-158 18-80 (149)
66 cd00141 NT_POLXc Nucleotidyltr 56.5 9.3 0.0002 34.9 2.6 23 105-127 81-103 (307)
67 CHL00137 rps13 ribosomal prote 55.7 13 0.00028 30.0 3.1 39 107-145 15-56 (122)
68 PRK14600 ruvA Holliday junctio 55.2 28 0.0006 29.9 5.2 65 54-128 62-126 (186)
69 PRK00076 recR recombination pr 55.2 9.3 0.0002 33.3 2.3 22 104-125 6-27 (196)
70 TIGR00615 recR recombination p 52.7 11 0.00023 32.9 2.3 22 104-125 6-27 (195)
71 PRK03980 flap endonuclease-1; 52.7 47 0.001 30.4 6.5 72 113-193 193-279 (292)
72 COG1059 Thermostable 8-oxoguan 51.8 94 0.002 27.5 7.9 83 104-191 115-204 (210)
73 PRK13844 recombination protein 50.8 12 0.00026 32.8 2.3 22 104-125 10-31 (200)
74 cd00080 HhH2_motif Helix-hairp 49.8 11 0.00025 27.3 1.7 19 111-129 24-42 (75)
75 PRK05179 rpsM 30S ribosomal pr 49.4 18 0.00039 29.1 3.0 38 108-145 16-56 (122)
76 TIGR03631 bact_S13 30S ribosom 48.9 18 0.00038 28.8 2.8 38 108-145 14-54 (113)
77 smart00483 POLXc DNA polymeras 48.5 16 0.00034 33.9 2.8 26 103-128 83-108 (334)
78 cd00141 NT_POLXc Nucleotidyltr 46.8 16 0.00035 33.4 2.6 25 100-124 36-60 (307)
79 smart00483 POLXc DNA polymeras 46.2 14 0.00031 34.1 2.2 35 99-133 38-72 (334)
80 COG3092 Uncharacterized protei 46.0 46 0.00099 27.7 4.8 51 80-131 28-81 (149)
81 TIGR00426 competence protein C 45.0 70 0.0015 22.3 5.2 43 55-128 24-66 (69)
82 TIGR01339 phycocy_beta phycocy 43.8 33 0.00072 29.3 3.9 52 52-104 13-64 (170)
83 TIGR03629 arch_S13P archaeal r 42.1 13 0.00029 30.8 1.2 37 107-143 19-58 (144)
84 PRK12766 50S ribosomal protein 41.0 20 0.00043 32.2 2.1 42 88-129 14-56 (232)
85 PRK14976 5'-3' exonuclease; Pr 39.6 18 0.00039 32.8 1.7 16 114-129 196-211 (281)
86 PRK08609 hypothetical protein; 38.2 32 0.00069 34.3 3.3 21 108-128 47-67 (570)
87 CHL00172 cpeB phycoerythrin be 36.9 47 0.001 28.6 3.7 51 52-103 15-65 (177)
88 PRK09482 flap endonuclease-lik 36.3 23 0.00049 32.0 1.8 18 113-130 186-203 (256)
89 cd00128 XPG Xeroderma pigmento 35.0 53 0.0012 29.7 4.0 18 113-130 227-244 (316)
90 PF00502 Phycobilisome: Phycob 33.8 26 0.00056 28.9 1.7 111 52-171 10-136 (157)
91 PF14579 HHH_6: Helix-hairpin- 33.8 39 0.00084 25.1 2.5 31 111-143 29-59 (90)
92 TIGR01259 comE comEA protein. 33.8 96 0.0021 24.5 4.9 21 107-127 96-116 (120)
93 cd00008 53EXOc 5'-3' exonuclea 32.2 29 0.00063 30.5 1.8 17 113-129 187-203 (240)
94 COG0632 RuvA Holliday junction 31.7 68 0.0015 28.1 3.9 66 54-128 62-127 (201)
95 CHL00170 cpcA phycocyanin alph 31.2 80 0.0017 26.8 4.2 51 52-103 15-65 (162)
96 smart00475 53EXOc 5'-3' exonuc 31.1 31 0.00068 30.9 1.8 17 113-129 190-206 (259)
97 PRK13482 DNA integrity scannin 29.6 53 0.0012 31.2 3.2 31 98-128 307-338 (352)
98 PF14229 DUF4332: Domain of un 29.1 52 0.0011 26.1 2.6 26 106-131 50-75 (122)
99 CHL00090 apcD allophycocyanin 28.0 76 0.0016 26.7 3.5 50 53-103 15-64 (161)
100 PF01367 5_3_exonuc: 5'-3' exo 27.9 8.7 0.00019 30.0 -2.0 17 113-129 22-38 (101)
101 TIGR01338 phycocy_alpha phycoc 27.5 1.1E+02 0.0024 25.9 4.4 51 52-103 14-64 (161)
102 CHL00086 apcA allophycocyanin 26.8 96 0.0021 26.1 3.9 51 52-103 14-64 (161)
103 PRK08609 hypothetical protein; 26.4 51 0.0011 32.8 2.5 24 104-127 83-106 (570)
104 CHL00171 cpcB phycocyanin beta 26.4 79 0.0017 27.0 3.4 52 52-104 15-66 (172)
105 CHL00173 cpeA phycoerythrin al 26.0 83 0.0018 26.7 3.4 51 52-103 15-65 (164)
106 TIGR01954 nusA_Cterm_rpt trans 25.9 66 0.0014 20.6 2.3 42 87-128 3-45 (50)
107 PRK09672 phage exclusion prote 25.9 2.2E+02 0.0047 26.7 6.3 34 114-147 216-256 (305)
108 PRK12766 50S ribosomal protein 25.5 38 0.00082 30.4 1.3 20 109-128 3-22 (232)
109 COG3743 Uncharacterized conser 24.5 41 0.0009 27.8 1.3 20 109-128 67-86 (133)
110 PF04854 DUF624: Protein of un 24.0 35 0.00076 24.3 0.7 17 113-129 17-33 (77)
111 PF05766 NinG: Bacteriophage L 23.3 1.5E+02 0.0033 25.7 4.6 23 149-171 162-184 (189)
112 KOG2582 COP9 signalosome, subu 22.6 3.7E+02 0.008 26.2 7.4 82 78-161 82-186 (422)
113 KOG2376 Signal recognition par 21.9 8.1E+02 0.017 25.3 9.8 18 177-194 525-542 (652)
114 COG5578 Predicted integral mem 20.8 52 0.0011 29.1 1.2 12 114-125 37-48 (208)
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=97.56 E-value=6.3e-05 Score=46.69 Aligned_cols=24 Identities=42% Similarity=0.700 Sum_probs=20.1
Q ss_pred HHHHHHhhccCCCChHHHHHHHHh
Q 027752 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 346889999999999999999973
No 2
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=96.86 E-value=0.0042 Score=54.28 Aligned_cols=81 Identities=26% Similarity=0.257 Sum_probs=59.2
Q ss_pred cHHHHHHHhh-ccCCCChHHHHHHHH-hhCCCCCCcccHHHHHHh---cCC----CCCCCHHHHHHHHHHHHHHHHHhhc
Q 027752 103 DLTKAVSELT-VLKGVGPATASAVLA-AYAPDLAPFMSDEAMGAA---LGH----SKDYSLKQYLLFADKLQAKAKELVS 173 (219)
Q Consensus 103 d~~~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 2123345433322 351 22456689999999999999887
Q ss_pred cCCCCCHHHHHHHHHHH
Q 027752 174 EENCFTPFDVERALWSS 190 (219)
Q Consensus 174 ~~~~~t~~~VEkalw~~ 190 (219)
.+.+..+.-++|-.
T Consensus 188 ---~~~~~~Ldl~~w~~ 201 (208)
T PRK01229 188 ---GISLGELDLYIWYK 201 (208)
T ss_pred ---CCCHHHHHHHHHHH
Confidence 47899999999964
No 3
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=96.80 E-value=0.0051 Score=53.98 Aligned_cols=71 Identities=21% Similarity=0.228 Sum_probs=45.9
Q ss_pred CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHH-H------h------hC-----ccHHHHHHHhhccCCCC
Q 027752 57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKA-F------K------SL-----PDLTKAVSELTVLKGVG 118 (219)
Q Consensus 57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~A-f------~------~l-----~d~~~al~~L~~LkGVG 118 (219)
|.|+.+.-+.=+|-. .-|+...+...+.+ .+++.++.. | + ++ .++...++.|.+|+|||
T Consensus 42 ttD~~vn~at~~Lf~--~~~t~e~l~~a~~~-~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVG 118 (211)
T COG0177 42 TTDEVVNKATPALFK--RYPTPEDLLNADEE-ELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG 118 (211)
T ss_pred CchHHHHHHHHHHHH--HcCCHHHHHcCCHH-HHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence 467777766666542 23455666665544 444443322 2 0 11 14567899999999999
Q ss_pred hHHHHHHHHhhC
Q 027752 119 PATASAVLAAYA 130 (219)
Q Consensus 119 PATASaiLa~~~ 130 (219)
+=||..||+...
T Consensus 119 rKTAnvVL~~a~ 130 (211)
T COG0177 119 RKTANVVLSFAF 130 (211)
T ss_pred hHHHHHHHHhhc
Confidence 999999999854
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=96.20 E-value=0.042 Score=49.75 Aligned_cols=36 Identities=31% Similarity=0.405 Sum_probs=27.9
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHH
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDE 140 (219)
Q Consensus 104 ~~~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 345689999999999999999999865444454 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=95.99 E-value=0.037 Score=44.71 Aligned_cols=37 Identities=41% Similarity=0.484 Sum_probs=28.4
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhC-CCCCCcccHHHHH
Q 027752 105 TKAVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEAMG 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 67899999999999999999998743 444554 55443
No 6
>PRK10702 endonuclease III; Provisional
Probab=94.99 E-value=0.042 Score=47.81 Aligned_cols=28 Identities=32% Similarity=0.383 Sum_probs=24.5
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhCC
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 104 ~~~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 4568999999999999999999998654
No 7
>PRK10880 adenine DNA glycosylase; Provisional
Probab=94.70 E-value=0.051 Score=50.93 Aligned_cols=29 Identities=31% Similarity=0.472 Sum_probs=25.1
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (219)
Q Consensus 104 ~~~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 45678999999999999999999987654
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=94.66 E-value=0.21 Score=39.97 Aligned_cols=29 Identities=38% Similarity=0.386 Sum_probs=24.7
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+...++.|++|+||||-||++||...--.
T Consensus 67 ~~~~~~~L~~l~GIG~~tA~~~l~~~~~~ 95 (149)
T smart00478 67 VPDDREELLKLPGVGRKTANAVLSFALGK 95 (149)
T ss_pred ccHHHHHHHcCCCCcHHHHHHHHHHHCCC
Confidence 44678899999999999999999987554
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=94.62 E-value=0.03 Score=41.80 Aligned_cols=37 Identities=32% Similarity=0.497 Sum_probs=30.2
Q ss_pred HHhhccCCCChHHHHHHHHhh-CCCCCCcccHHHHHHhcC
Q 027752 109 SELTVLKGVGPATASAVLAAY-APDLAPFMSDEAMGAALG 147 (219)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~~~~g 147 (219)
+.|+.++||||-||..||+.. +|+ -|=+...+...+|
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~--rF~~~~~l~~~~G 39 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDIS--RFKSAKQLASYAG 39 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCch--hcccchhhhhccc
Confidence 468899999999999999986 443 4667888887777
No 10
>PRK13910 DNA glycosylase MutY; Provisional
Probab=94.43 E-value=0.14 Score=46.79 Aligned_cols=30 Identities=27% Similarity=0.300 Sum_probs=24.7
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhCCCCCC
Q 027752 106 KAVSELTVLKGVGPATASAVLAAYAPDLAP 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 358999999999999999999986543333
No 11
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.42 E-value=0.055 Score=50.69 Aligned_cols=36 Identities=33% Similarity=0.450 Sum_probs=29.1
Q ss_pred HHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHH
Q 027752 108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG 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 456667999999999999999887777877755554
No 12
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.10 E-value=0.12 Score=47.13 Aligned_cols=72 Identities=28% Similarity=0.270 Sum_probs=51.4
Q ss_pred CCCHHHHHHHHHHHhh-cCCCCcchHHHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhccCCCChHHHHHH
Q 027752 55 HINTTELSKLVRWKLT-RGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~--------d~~~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 6788888888888776 4555442 3455566655554321 46779999999999999999999
Q ss_pred HHh--hCCCCCC
Q 027752 126 LAA--YAPDLAP 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 976 4566544
No 13
>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=94.08 E-value=0.14 Score=43.35 Aligned_cols=27 Identities=37% Similarity=0.423 Sum_probs=23.5
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhC
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYA 130 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~ 130 (219)
+..+++.|++|+||||=||.+||....
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 345788999999999999999998764
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=93.70 E-value=0.061 Score=49.27 Aligned_cols=37 Identities=30% Similarity=0.426 Sum_probs=29.7
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhh--CCCCCCcccHHHH
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAY--APDLAPFMSDEAM 142 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~--~P~~~pFfsDEa~ 142 (219)
...+++.|++||||||=||.+||... .|+.+|. |-..
T Consensus 215 ~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv--D~~v 253 (310)
T TIGR00588 215 YEDAREALCELPGVGPKVADCICLMGLDKPQAVPV--DVHV 253 (310)
T ss_pred hHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceee--cHHH
Confidence 56789999999999999999999774 5666663 6544
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=93.60 E-value=0.059 Score=46.21 Aligned_cols=44 Identities=30% Similarity=0.373 Sum_probs=32.4
Q ss_pred ccHHHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752 102 PDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147 (219)
Q Consensus 102 ~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (219)
|+-...++.|.+|+||||-||..||+...-+. -.-||-|....|
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~--~~~~~~~~~~~~ 151 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQL--GVTPEGWREAAG 151 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh--CCCCcchHHhcc
Confidence 44455689999999999999999999765432 234677765544
No 16
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=93.43 E-value=0.083 Score=43.42 Aligned_cols=39 Identities=23% Similarity=0.303 Sum_probs=32.4
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcCC
Q 027752 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGH 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 NSSVRAFRQFPGMYPTLAGKIV-----KNAPYDSVEDVLNLPGL 95 (132)
T ss_pred ccCHHHHHHCCCCCHHHHHHHH-----HCCCCCCHHHHHcCCCC
Confidence 3456778999999999999999 36799998888878773
No 17
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=93.26 E-value=0.24 Score=43.60 Aligned_cols=39 Identities=21% Similarity=0.130 Sum_probs=27.8
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHh
Q 027752 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA 145 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~ 145 (219)
...+.|.+|+||||=||.+||....- +..|..|--..-+
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv 156 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLF 156 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHH
Confidence 46688999999999999999987543 3234445544434
No 18
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=93.07 E-value=0.11 Score=47.15 Aligned_cols=33 Identities=27% Similarity=0.323 Sum_probs=27.8
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHh--hCCCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAP 135 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~p 135 (219)
+..++++.|+.||||||-||..||-. ..|+.+|
T Consensus 201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp 235 (283)
T PRK10308 201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL 235 (283)
T ss_pred CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC
Confidence 56778999999999999999999865 5777655
No 19
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.74 E-value=0.14 Score=30.19 Aligned_cols=19 Identities=47% Similarity=0.763 Sum_probs=16.9
Q ss_pred HhhccCCCChHHHHHHHHh
Q 027752 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=89.85 E-value=0.23 Score=38.48 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=22.1
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhh
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 104 ~~~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=87.51 E-value=0.38 Score=33.27 Aligned_cols=22 Identities=36% Similarity=0.351 Sum_probs=17.1
Q ss_pred HHHhhccCCCChHHHHHHHHhh
Q 027752 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=87.42 E-value=0.61 Score=37.16 Aligned_cols=42 Identities=29% Similarity=0.487 Sum_probs=33.4
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 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 AASLEELQALPGIGPAKAKAIIEYRE-ENGAFKSVDDLTKVSG 105 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHH-hcCCcCCHHHHHcCCC
Confidence 34577899999999999999999754 3568888777766665
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=85.71 E-value=1.2 Score=31.68 Aligned_cols=31 Identities=32% Similarity=0.415 Sum_probs=22.1
Q ss_pred HHhhCccHHHHHHH-hhccCCCChHHHHHHHH
Q 027752 97 AFKSLPDLTKAVSE-LTVLKGVGPATASAVLA 127 (219)
Q Consensus 97 Af~~l~d~~~al~~-L~~LkGVGPATASaiLa 127 (219)
+...+|..-..++. +..|+|||+.+|.-|--
T Consensus 34 ~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 34 AIKALPYPITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred HHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 34556654445565 99999999999998743
No 24
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.95 E-value=0.66 Score=39.94 Aligned_cols=31 Identities=23% Similarity=0.362 Sum_probs=27.0
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~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 4577889999999999999999999877754
No 25
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=83.82 E-value=1.7 Score=39.55 Aligned_cols=31 Identities=29% Similarity=0.470 Sum_probs=27.7
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
|+-..++.|..|+||||-+|=+.|+++.-..
T Consensus 153 DIP~~v~dLlsLPGVGPKMa~L~m~~AWn~i 183 (286)
T KOG1921|consen 153 DIPDTVEDLLSLPGVGPKMAHLTMQVAWNKI 183 (286)
T ss_pred CCchhHHHHhcCCCCchHHHHHHHHHHhccc
Confidence 7888999999999999999999999976544
No 26
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=81.64 E-value=2.3 Score=39.39 Aligned_cols=61 Identities=18% Similarity=0.175 Sum_probs=38.3
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHh--hCCCCCCcccHHHHH-----HhcC-CCC-CCCHHHHHHHHHHHH
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG-----AALG-HSK-DYSLKQYLLFADKLQ 165 (219)
Q Consensus 104 ~~~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 34445562 222332 3344 122 367777777553333
No 27
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=81.35 E-value=1.4 Score=37.66 Aligned_cols=28 Identities=32% Similarity=0.489 Sum_probs=23.1
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhCC
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 104 ~~~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 3445778999999999999999987654
No 28
>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=80.95 E-value=1.6 Score=30.17 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=20.2
Q ss_pred HHHHhhccCCCChHHHHHHHHhh
Q 027752 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 29
>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=80.84 E-value=1.1 Score=38.40 Aligned_cols=30 Identities=33% Similarity=0.579 Sum_probs=25.0
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPD 132 (219)
Q Consensus 103 d~~~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 456778889999999999999999987663
No 30
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.78 E-value=1.1 Score=39.05 Aligned_cols=31 Identities=26% Similarity=0.355 Sum_probs=26.7
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
+.+.-+..|....||||-||-+||+...|+.
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs~~~~~e 96 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLSGIKYNE 96 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHHH
Confidence 4567888999999999999999999988754
No 31
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=80.41 E-value=3.3 Score=36.91 Aligned_cols=153 Identities=21% Similarity=0.261 Sum_probs=84.9
Q ss_pred hhhHHHhhhhhHhhccCCCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhC---ccHH-HHHHH
Q 027752 35 LDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSL---PDLT-KAVSE 110 (219)
Q Consensus 35 LD~w~~~elp~~~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l---~d~~-~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 4456665555321111223589999977776 56665332 5666776665543 3444 45999
Q ss_pred hhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcCCCCCC-CHHHHHHHHH-HHHHHHHH------hhccC-------
Q 027752 111 LTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDY-SLKQYLLFAD-KLQAKAKE------LVSEE------- 175 (219)
Q Consensus 111 L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~~~kY-t~keY~~~~~-~l~~~~~~------L~~~~------- 175 (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 22222111 12111
Q ss_pred --------CCCCHHHH-HHHHHHHHhhhhhcccCCCCccchh
Q 027752 176 --------NCFTPFDV-ERALWSSAIGLKLKASKSNQDSEIK 208 (219)
Q Consensus 176 --------~~~t~~~V-Ekalw~~~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 25678876 6777777766666666778877766
No 32
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.16 E-value=1.1 Score=38.44 Aligned_cols=31 Identities=23% Similarity=0.359 Sum_probs=26.8
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
+.+.-+..|.+..||||-||-+||+...|+.
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~~ 97 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPEQ 97 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHccCCHHH
Confidence 4567788999999999999999999887754
No 33
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=78.45 E-value=2 Score=30.34 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.9
Q ss_pred HHHHHhhccCCCChHHHHHHHHhh
Q 027752 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=78.20 E-value=6.1 Score=33.92 Aligned_cols=66 Identities=23% Similarity=0.233 Sum_probs=44.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 GFLDKDEQKMFEMLLKVNGIGANTAMAVCSSLDVNSFYKALSLG---------DESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred CCCCHHHHHHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHH
Confidence 68899997665555444443222345667777777776665431 2468999999999999988743
No 35
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=78.18 E-value=1.7 Score=35.96 Aligned_cols=42 Identities=31% Similarity=0.536 Sum_probs=31.7
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 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 TASAEELQALPGIGPKKAQAIIDYRE-ENGPFKSVDDLAKVKG 134 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHH-HcCCCCcHHHHHhccC
Confidence 34577788999999999999999643 3558887666655555
No 36
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.76 E-value=1.5 Score=37.64 Aligned_cols=31 Identities=29% Similarity=0.331 Sum_probs=27.3
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
+.+.-+..|.+..||||-||-+|||...|+.
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs~~~~~e 97 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCSSLDVNS 97 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHHH
Confidence 4567889999999999999999999988854
No 37
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.17 E-value=7.2 Score=33.71 Aligned_cols=67 Identities=16% Similarity=0.102 Sum_probs=45.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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-----G----DVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh-----C----CHHHHhhCCCCCHHHHHHHHHHH
Confidence 6899999766655544444322244666677777766665543 1 24689999999999999887654
No 38
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.96 E-value=2.8 Score=36.79 Aligned_cols=62 Identities=29% Similarity=0.373 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhccCCCChHHHHHHH
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL 126 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~------l~d~-~~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 588889976655 45554332 0 344444433332 2333 3458889999999999999999
Q ss_pred Hhh
Q 027752 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 39
>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=75.95 E-value=1.7 Score=30.08 Aligned_cols=22 Identities=32% Similarity=0.531 Sum_probs=19.0
Q ss_pred HHHHhhccCCCChHHHHHHHHh
Q 027752 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 4677999999999999988765
No 40
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.93 E-value=7.3 Score=33.92 Aligned_cols=66 Identities=15% Similarity=0.220 Sum_probs=45.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|++|..-...-.--.|-=-=.-+..++..+++.+.+++... =.+.||++||||+-||.=|..=
T Consensus 61 GF~t~~Er~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~~---------D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 61 GFLNSSEREVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDRE---------DIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHH
Confidence 68899997665555444453222456677777887776665331 2568999999999999987743
No 41
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.63 E-value=7.5 Score=33.40 Aligned_cols=66 Identities=15% Similarity=0.139 Sum_probs=45.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 GFSNERKKELFLSLTKVSRLGPKTALKIISNEDAETLVTMIASQ---------DVEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred CCCCHHHHHHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHH
Confidence 68899997665555444453222456677777777776665431 2568999999999999988743
No 42
>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=75.19 E-value=4.1 Score=28.76 Aligned_cols=39 Identities=28% Similarity=0.441 Sum_probs=28.8
Q ss_pred HHHhhc-cCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752 108 VSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 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 446767666665655
No 43
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=74.11 E-value=2.9 Score=40.56 Aligned_cols=89 Identities=19% Similarity=0.068 Sum_probs=46.8
Q ss_pred HHhhc-cCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC---CCCCCCHHHHHHHHHHHHHHHHHhhc--cCCCCCHHH
Q 027752 109 SELTV-LKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG---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 34444 9999999999999986543322233333332221 0001111 1233445566777743 234677777
Q ss_pred HHHHHHHHHhhhhhcccC
Q 027752 183 VERALWSSAIGLKLKASK 200 (219)
Q Consensus 183 VEkalw~~~v~~k~~~~~ 200 (219)
+|.++=.+..-+-.|..+
T Consensus 282 MELGAt~CTpq~P~CS~C 299 (555)
T KOG2457|consen 282 MELGATLCTPQKPSCSSC 299 (555)
T ss_pred HHhcCeeccCCCCCcCCC
Confidence 777665555444444333
No 44
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.54 E-value=2.5 Score=36.71 Aligned_cols=29 Identities=31% Similarity=0.456 Sum_probs=24.9
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (219)
Q Consensus 104 ~~~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 46678888999999999999999987775
No 45
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.27 E-value=2.3 Score=36.58 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=26.9
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
+.+.-+..|++..||||-||-+||+...|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs~~~~~e 97 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIISNEDAET 97 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHHH
Confidence 3567789999999999999999999988754
No 46
>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=72.75 E-value=6.2 Score=30.68 Aligned_cols=40 Identities=23% Similarity=0.291 Sum_probs=29.5
Q ss_pred HHHHHhhccCCCChHHHHHHHHhh--CCC-CCCcccHHHHHHh
Q 027752 106 KAVSELTVLKGVGPATASAVLAAY--APD-LAPFMSDEAMGAA 145 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (219)
...-+|+.+.|||+.+|..|+... +|. .+-.++|+-+..+
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l 54 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKL 54 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHH
T ss_pred chHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHH
Confidence 345678999999999999999984 564 3566777766543
No 47
>PRK00024 hypothetical protein; Reviewed
Probab=70.51 E-value=21 Score=31.34 Aligned_cols=60 Identities=28% Similarity=0.449 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc---H-HHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD---L-TKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d---~-~~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 588888966654 45565443 455555554443332 2 335778999999999999999887
No 48
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=70.47 E-value=5.1 Score=37.53 Aligned_cols=33 Identities=24% Similarity=0.293 Sum_probs=25.7
Q ss_pred cHHHHHHH--hhccCCCChHHHHHHHHhhCCCCCC
Q 027752 103 DLTKAVSE--LTVLKGVGPATASAVLAAYAPDLAP 135 (219)
Q Consensus 103 d~~~al~~--L~~LkGVGPATASaiLa~~~P~~~p 135 (219)
|+....+. +|+|+|||++||+.|--..+-..++
T Consensus 45 ~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~ 79 (326)
T COG1796 45 DLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVK 79 (326)
T ss_pred chHHHHhhcccCCCCCccHHHHHHHHHHHHcCccH
Confidence 67777777 9999999999999997765444433
No 49
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.83 E-value=3 Score=36.06 Aligned_cols=30 Identities=37% Similarity=0.462 Sum_probs=25.1
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 104 LTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
.+.-+..|....||||-||-+||+...|+.
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~ 96 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSALPPAL 96 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHHH
Confidence 456788889999999999999999877754
No 50
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.13 E-value=13 Score=32.29 Aligned_cols=67 Identities=15% Similarity=0.166 Sum_probs=46.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 GFATWDERQTFIVLISISKVGAKTALAILSQFRPDDLRRLVAEE---------DVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhC---------CHHHHhcCCCcCHHHHHHHHHHH
Confidence 68899997666555444553222456777777777766655432 25689999999999999887543
No 51
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.47 E-value=6.8 Score=33.86 Aligned_cols=66 Identities=18% Similarity=0.093 Sum_probs=44.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 GFPDEDSLELFELLLGVSGVGPKLALALLSALPPALLARALLEG---------DARLLTSASGVGKKLAERIALE 126 (197)
T ss_pred CcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHH
Confidence 68889986655544433442222446677777777776665432 2468999999999999988754
No 52
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=68.32 E-value=19 Score=31.97 Aligned_cols=34 Identities=32% Similarity=0.424 Sum_probs=25.0
Q ss_pred HHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHH
Q 027752 107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEA 141 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa 141 (219)
..+.|-++||||+=||=+||--+. ++.-|.-|..
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~-~rp~FVvD~Y 146 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYAL-DRPVFVVDKY 146 (215)
T ss_pred HHHHHHccCCcchhhHHHHHHHHh-cCcccchhHH
Confidence 578899999999999999997543 3434444543
No 53
>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=67.14 E-value=15 Score=31.47 Aligned_cols=66 Identities=21% Similarity=0.181 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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-----E----VKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCCHHHHHHHHHhC-----C----HHHHHhCCCCCHHHHHHHHHH
Confidence 68899997776666555553222344555555555554444321 1 246899999999999999843
No 54
>PRK07945 hypothetical protein; Provisional
Probab=66.99 E-value=11 Score=34.89 Aligned_cols=19 Identities=47% Similarity=0.733 Sum_probs=15.3
Q ss_pred HhhccCCCChHHHHHHHHh
Q 027752 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 5788999999998877654
No 55
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=66.60 E-value=4.4 Score=25.89 Aligned_cols=15 Identities=47% Similarity=0.729 Sum_probs=13.1
Q ss_pred ccCCCChHHHHHHHH
Q 027752 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
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=66.47 E-value=5.5 Score=32.37 Aligned_cols=39 Identities=23% Similarity=0.330 Sum_probs=29.9
Q ss_pred HHHHhhccCCCChHHHHHHHHhh--CCCC-CCcccHHHHHHh
Q 027752 107 AVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA 145 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfsDEa~~~~ 145 (219)
-.=+|+.+.|||+++|-+|+... +|+. +-..+||-...+
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred EeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 34468899999999999999984 5543 667788777644
No 57
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=64.98 E-value=4.9 Score=28.32 Aligned_cols=41 Identities=32% Similarity=0.481 Sum_probs=26.4
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhcC
Q 027752 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 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 45788999999999999999997432 347766555554444
No 58
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.76 E-value=4.4 Score=35.03 Aligned_cols=31 Identities=29% Similarity=0.390 Sum_probs=26.8
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
+.+.-+..|++..||||=||-+||+...|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~e 97 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLSSGTPDE 97 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHHH
Confidence 3567789999999999999999999877754
No 59
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=63.77 E-value=5.1 Score=35.13 Aligned_cols=23 Identities=35% Similarity=0.616 Sum_probs=19.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHH
Q 027752 103 DLTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 103 d~~~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 46677899999999999998743
No 60
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=62.76 E-value=5.8 Score=34.68 Aligned_cols=31 Identities=26% Similarity=0.451 Sum_probs=27.3
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
+.+.-+..|.+.-||||-||=+||+..+|+.
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~ 97 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPEE 97 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHHH
Confidence 5677889999999999999999999988754
No 61
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=60.81 E-value=59 Score=27.66 Aligned_cols=70 Identities=19% Similarity=0.174 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhhCCC
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPD 132 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 3456666554445554555433344555555444444333322 134578999999999999999876543
No 62
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.74 E-value=30 Score=29.76 Aligned_cols=64 Identities=23% Similarity=0.222 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHH
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 6889999766555544445333345666666676665444422 124579999999999999854
No 63
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=58.47 E-value=5.2 Score=33.65 Aligned_cols=56 Identities=18% Similarity=0.208 Sum_probs=36.0
Q ss_pred CccHHHHHHHhhccCCCChHHHHHHHHhh--CCCC-CCcccHHHHHHh---cCCCCCCCHHH
Q 027752 101 LPDLTKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA---LGHSKDYSLKQ 156 (219)
Q Consensus 101 l~d~~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfsDEa~~~~---~g~~~kYt~ke 156 (219)
+++-+...-+|+.+.|||+.+|-.||... +|.. +--.+|+=...+ ...+..|.+++
T Consensus 22 l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~ 83 (154)
T PTZ00134 22 VDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIPD 83 (154)
T ss_pred CCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCCh
Confidence 44555566678999999999999999985 4543 444555544433 33344555433
No 64
>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=57.55 E-value=6.7 Score=24.26 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=11.3
Q ss_pred hhccCCCChHHHHHH
Q 027752 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 458999999998654
No 65
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=56.53 E-value=12 Score=31.36 Aligned_cols=57 Identities=23% Similarity=0.373 Sum_probs=37.2
Q ss_pred ccHHHHHHHhhccCCCChHHHHHHHHhh--CCCC-CCcccHHHHHHh---cCCCCCCCHHHHH
Q 027752 102 PDLTKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA---LGHSKDYSLKQYL 158 (219)
Q Consensus 102 ~d~~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfsDEa~~~~---~g~~~kYt~keY~ 158 (219)
++-+.-.-+|+.+.|||+.+|-.|+... +|.. +--.+++-...+ ...+-+|.+++|.
T Consensus 18 ~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~ 80 (149)
T PRK04053 18 DGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWM 80 (149)
T ss_pred CCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhh
Confidence 3334445578999999999999999984 5543 555666655433 3344456666554
No 66
>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=56.50 E-value=9.3 Score=34.90 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=17.7
Q ss_pred HHHHHHhhccCCCChHHHHHHHH
Q 027752 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 45677788888888888877773
No 67
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=55.75 E-value=13 Score=29.96 Aligned_cols=39 Identities=28% Similarity=0.440 Sum_probs=28.3
Q ss_pred HHHHhhccCCCChHHHHHHHHhh--CCCC-CCcccHHHHHHh
Q 027752 107 AVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA 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 5543 455666655533
No 68
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.24 E-value=28 Score=29.91 Aligned_cols=65 Identities=18% Similarity=0.189 Sum_probs=44.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 6889999766655554455322245677777777777666544 233 577 8999999999988743
No 69
>PRK00076 recR recombination protein RecR; Reviewed
Probab=55.20 E-value=9.3 Score=33.32 Aligned_cols=22 Identities=32% Similarity=0.641 Sum_probs=18.4
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027752 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 ~~~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 5667889999999999998754
No 70
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.73 E-value=11 Score=32.93 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=18.3
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027752 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 ~~~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 5567889999999999998754
No 71
>PRK03980 flap endonuclease-1; Provisional
Probab=52.71 E-value=47 Score=30.36 Aligned_cols=72 Identities=21% Similarity=0.114 Sum_probs=43.9
Q ss_pred ccCCCChHHHHHHHHhhC---------CCCCCcccHHHHHHhcCC------CCCCCHHHHHHHHHHHHHHHHHhhccCCC
Q 027752 113 VLKGVGPATASAVLAAYA---------PDLAPFMSDEAMGAALGH------SKDYSLKQYLLFADKLQAKAKELVSEENC 177 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~~---------P~~~pFfsDEa~~~~~g~------~~kYt~keY~~~~~~l~~~~~~L~~~~~~ 177 (219)
.++||||-||.-|+.-+- +..+| -.+|+......+ .+++...+...+.+-+.. ..+
T Consensus 193 GI~GIG~ktA~kLi~~~~sle~i~~~~~~~~~-~~~~~r~~f~~p~v~~~~~~~~~~pd~~~l~~fl~~--------e~~ 263 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHGDLEKVLEERGFEIE-NYDEIREFFLNPPVTDDYELKWKEPDKEGIIEFLVE--------EHD 263 (292)
T ss_pred CCCCccHHHHHHHHHHCCCHHHHHHhccCCCC-CHHHHHHHhcCCCCCCCCCccCCCCCHHHHHHHHhc--------cCC
Confidence 489999999999997642 11222 115666655442 345555566654444432 236
Q ss_pred CCHHHHHHHHHHHHhh
Q 027752 178 FTPFDVERALWSSAIG 193 (219)
Q Consensus 178 ~t~~~VEkalw~~~v~ 193 (219)
|+..+|++++=-+.-.
T Consensus 264 f~~~rv~~~~~~l~~~ 279 (292)
T PRK03980 264 FSEERVKKALERLEKA 279 (292)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 9999999987665443
No 72
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.78 E-value=94 Score=27.49 Aligned_cols=83 Identities=20% Similarity=0.254 Sum_probs=60.1
Q ss_pred HHHHHHHhh-ccCCCChHHHHHHHHhhCCCCCCcccHHHHHHhc--C----CCCCCCHHHHHHHHHHHHHHHHHhhccCC
Q 027752 104 LTKAVSELT-VLKGVGPATASAVLAAYAPDLAPFMSDEAMGAAL--G----HSKDYSLKQYLLFADKLQAKAKELVSEEN 176 (219)
Q Consensus 104 ~~~al~~L~-~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~--g----~~~kYt~keY~~~~~~l~~~~~~L~~~~~ 176 (219)
.+-|.+.|. +++|+|=--||=.|-=.-=+.++..+--...|+. | .|...|.|-|++.-+.++..+..++
T Consensus 115 ~~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~g---- 190 (210)
T COG1059 115 EKVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEVG---- 190 (210)
T ss_pred hHHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHhC----
Confidence 344788888 8999999999999863222222333333445664 3 3447889999999999999999984
Q ss_pred CCCHHHHHHHHHHHH
Q 027752 177 CFTPFDVERALWSSA 191 (219)
Q Consensus 177 ~~t~~~VEkalw~~~ 191 (219)
.++.+++.-+|-.-
T Consensus 191 -~s~gelDL~IWY~e 204 (210)
T COG1059 191 -ISLGELDLYIWYKE 204 (210)
T ss_pred -CCcchhHHHHHHHH
Confidence 67888888888643
No 73
>PRK13844 recombination protein RecR; Provisional
Probab=50.82 E-value=12 Score=32.81 Aligned_cols=22 Identities=14% Similarity=0.374 Sum_probs=18.3
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027752 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 ~~~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 5667889999999999998754
No 74
>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=49.82 E-value=11 Score=27.34 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=15.8
Q ss_pred hhccCCCChHHHHHHHHhh
Q 027752 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 3458999999999999864
No 75
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=49.43 E-value=18 Score=29.10 Aligned_cols=38 Identities=34% Similarity=0.489 Sum_probs=28.0
Q ss_pred HHHhhccCCCChHHHHHHHHhh--CCCC-CCcccHHHHHHh
Q 027752 108 VSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA 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 5543 555666665543
No 76
>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=48.94 E-value=18 Score=28.76 Aligned_cols=38 Identities=26% Similarity=0.394 Sum_probs=28.4
Q ss_pred HHHhhccCCCChHHHHHHHHhh--CCCC-CCcccHHHHHHh
Q 027752 108 VSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA 145 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~--~P~~-~pFfsDEa~~~~ 145 (219)
.-+|+.+.|||+.+|-.|+... +|.. +-.++|+-+..+
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 54 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAI 54 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 3467899999999999999984 5543 566777766544
No 77
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=48.49 E-value=16 Score=33.86 Aligned_cols=26 Identities=31% Similarity=0.419 Sum_probs=22.4
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 103 DLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 103 d~~~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 45679999999999999999888763
No 78
>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=46.79 E-value=16 Score=33.36 Aligned_cols=25 Identities=32% Similarity=0.521 Sum_probs=13.4
Q ss_pred hCccHHHHHHHhhccCCCChHHHHH
Q 027752 100 SLPDLTKAVSELTVLKGVGPATASA 124 (219)
Q Consensus 100 ~l~d~~~al~~L~~LkGVGPATASa 124 (219)
.++..-..+..+++|+|||+++|+.
T Consensus 36 ~l~~~i~~~~~~~~ipgiG~~ia~k 60 (307)
T cd00141 36 SLPEPIESLEEAKKLPGIGKKIAEK 60 (307)
T ss_pred hCCcccCCHHHhcCCCCccHHHHHH
Confidence 3343333444556777777766653
No 79
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=46.20 E-value=14 Score=34.14 Aligned_cols=35 Identities=23% Similarity=0.296 Sum_probs=24.7
Q ss_pred hhCccHHHHHHHhhccCCCChHHHHHHHHhhCCCC
Q 027752 99 KSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (219)
Q Consensus 99 ~~l~d~~~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 34543333456788999999999999987755443
No 80
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.01 E-value=46 Score=27.68 Aligned_cols=51 Identities=24% Similarity=0.331 Sum_probs=35.6
Q ss_pred HHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhc--c-CCCChHHHHHHHHhhCC
Q 027752 80 VFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTV--L-KGVGPATASAVLAAYAP 131 (219)
Q Consensus 80 ~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~--L-kGVGPATASaiLa~~~P 131 (219)
.|----++..|-.+|+-|.+.+|-+- .+.++.. + ..+|||.|+|+.++.-|
T Consensus 28 rL~pvFpEnRVikaTrfairfMP~vA-vftl~wQ~~~~~ql~pAv~tAlfal~lp 81 (149)
T COG3092 28 RLAPVFPENRVIKATRFAIRFMPPVA-VFTLCWQIALGGQLGPAVATALFALSLP 81 (149)
T ss_pred hhcccCchhHHHHHHHHHHHhccHHH-HHHHHHHHHHhcccchHHHHHHHHHhcc
Confidence 34444568899999999999887542 2332221 2 26799999999998655
No 81
>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=45.04 E-value=70 Score=22.34 Aligned_cols=43 Identities=19% Similarity=0.398 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 55 HINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 55 ~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~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 566666667777666555443 4566777889999999888764
No 82
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=43.78 E-value=33 Score=29.28 Aligned_cols=52 Identities=17% Similarity=0.328 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccH
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDL 104 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~ 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 3579999999999776 577899999999999999999999999999877753
No 83
>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=42.12 E-value=13 Score=30.78 Aligned_cols=37 Identities=27% Similarity=0.429 Sum_probs=27.1
Q ss_pred HHHHhhccCCCChHHHHHHHHhh--CCCC-CCcccHHHHH
Q 027752 107 AVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMG 143 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfsDEa~~ 143 (219)
..-+|+.+.|||+.+|-.|+... +|.. +--.+|+-..
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~ 58 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIE 58 (144)
T ss_pred EEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHH
Confidence 34468999999999999999985 4443 5556666554
No 84
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=41.05 E-value=20 Score=32.20 Aligned_cols=42 Identities=33% Similarity=0.459 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhhCccHHHH-HHHhhccCCCChHHHHHHHHhh
Q 027752 88 SSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 88 ~~V~~~t~~Af~~l~d~~~a-l~~L~~LkGVGPATASaiLa~~ 129 (219)
..++..-..+|..+.++..| .+.|.+++|||+++|--|....
T Consensus 14 krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 14 SKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred HHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 34444444446666666555 8899999999999999998875
No 85
>PRK14976 5'-3' exonuclease; Provisional
Probab=39.65 E-value=18 Score=32.78 Aligned_cols=16 Identities=50% Similarity=0.918 Sum_probs=14.2
Q ss_pred cCCCChHHHHHHHHhh
Q 027752 114 LKGVGPATASAVLAAY 129 (219)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (219)
++||||-||..+|.-+
T Consensus 196 VpGIG~KtA~~LL~~~ 211 (281)
T PRK14976 196 VKGIGPKTAIKLLNKY 211 (281)
T ss_pred CCcccHHHHHHHHHHc
Confidence 7889999999999864
No 86
>PRK08609 hypothetical protein; Provisional
Probab=38.20 E-value=32 Score=34.26 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=11.5
Q ss_pred HHHhhccCCCChHHHHHHHHh
Q 027752 108 VSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~ 128 (219)
+..|++|+|||+++|+-|--.
T Consensus 47 ~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 47 IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred hhhhccCCCcCHHHHHHHHHH
Confidence 344555666666666555444
No 87
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=36.88 E-value=47 Score=28.64 Aligned_cols=51 Identities=16% Similarity=0.187 Sum_probs=44.8
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~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 3579999999998664 67899999999999999999999999999987775
No 88
>PRK09482 flap endonuclease-like protein; Provisional
Probab=36.30 E-value=23 Score=31.97 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=15.3
Q ss_pred ccCCCChHHHHHHHHhhC
Q 027752 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
>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=35.02 E-value=53 Score=29.69 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=15.8
Q ss_pred ccCCCChHHHHHHHHhhC
Q 027752 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 90
>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=33.82 E-value=26 Score=28.94 Aligned_cols=111 Identities=17% Similarity=0.165 Sum_probs=68.8
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHH-------------HHHHHhh-ccCCC
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLT-------------KAVSELT-VLKGV 117 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~-------------~al~~L~-~LkGV 117 (219)
..+|++..||..|-.+- ..|.-|....+.++.|.+.-|.++..+-|...|++. +.+.-+. =||=
T Consensus 10 egRyls~~EL~~l~~~~-~~~~~Rl~aa~~L~~~a~~IV~~A~~~l~~~~P~l~~~gg~~y~~~~~~~C~RD~~~~LR~- 87 (157)
T PF00502_consen 10 EGRYLSDGELQALKGYF-QSANARLEAAEKLRDNASEIVDQAAQKLFEKYPDLTQPGGNLYPSRRREACWRDIWHYLRY- 87 (157)
T ss_dssp TTSECEHHHHHHHHHHH-HTHHHHHHHHHHHHHTHHHHHHHHHHHHHHHSGGGGSTTSTTSSHHHHHHHHHHHHHHHHH-
T ss_pred cCCCCCHHHHHHHHHHH-HhHHHHHHHHHHHHHhHHHHHHHHHHHHHHhccccccccccccchHHHHHHHHHHHHHHHH-
Confidence 35799999999998875 456679999999999999999999999998877532 1111110 1221
Q ss_pred ChHHHHHHHHhhCCCCCCcccHHHHHHhcC--CCCCCCHHHHHHHHHHHHHHHHHh
Q 027752 118 GPATASAVLAAYAPDLAPFMSDEAMGAALG--HSKDYSLKQYLLFADKLQAKAKEL 171 (219)
Q Consensus 118 GPATASaiLa~~~P~~~pFfsDEa~~~~~g--~~~kYt~keY~~~~~~l~~~~~~L 171 (219)
.+-+| .+.++ -++.|....|+-. ........-|.+-++.|++.+.+.
T Consensus 88 ---i~ya~-l~gd~---~~l~~~~l~~l~ei~~al~vp~~~~v~al~~lk~~~~~~ 136 (157)
T PF00502_consen 88 ---ITYAM-LAGDT---DPLDERGLNGLREIYRALGVPIDAYVEALQCLKEAALQL 136 (157)
T ss_dssp ---HHHHH-HHTSS---HHHHHHTTTTHHHHHHHHT--HHHHHHHHHHHHHHHHHH
T ss_pred ---HHHHH-Hhcch---hHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHH
Confidence 11222 23455 3466666655432 122344555666666677666554
No 91
>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=33.81 E-value=39 Score=25.11 Aligned_cols=31 Identities=29% Similarity=0.439 Sum_probs=22.9
Q ss_pred hhccCCCChHHHHHHHHhhCCCCCCcccHHHHH
Q 027752 111 LTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG 143 (219)
Q Consensus 111 L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~ 143 (219)
|+.++|||..+|-.|+..-. .-||-|=+-|.
T Consensus 29 l~~Ikglg~~~a~~I~~~R~--~g~f~s~~df~ 59 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERE--NGPFKSLEDFI 59 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHH--CSS-SSHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHh--cCCCCCHHHHH
Confidence 67899999999999999876 45887755444
No 92
>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=33.80 E-value=96 Score=24.53 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=16.5
Q ss_pred HHHHhhccCCCChHHHHHHHH
Q 027752 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 93
>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=32.24 E-value=29 Score=30.46 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=14.5
Q ss_pred ccCCCChHHHHHHHHhh
Q 027752 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 94
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=31.66 E-value=68 Score=28.06 Aligned_cols=66 Identities=20% Similarity=0.223 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027752 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|.+|-.-.-+-=--.|-=-=+-+.++++-+++.+.++.... =++.|+++||||+=||=-|+.=
T Consensus 62 GF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~---------d~~~L~k~PGIGkKtAerivle 127 (201)
T COG0632 62 GFLTEEERELFRLLISVNGIGPKLALAILSNLDPEELAQAIANE---------DVKALSKIPGIGKKTAERIVLE 127 (201)
T ss_pred CCCCHHHHHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhc---------ChHhhhcCCCCCHHHHHHHHHH
Confidence 57788875443333223332111234555555666665555331 2468999999999999888764
No 95
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=31.17 E-value=80 Score=26.78 Aligned_cols=51 Identities=12% Similarity=0.127 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~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 57899999999999999999999999999987775
No 96
>smart00475 53EXOc 5'-3' exonuclease.
Probab=31.06 E-value=31 Score=30.85 Aligned_cols=17 Identities=29% Similarity=0.577 Sum_probs=14.4
Q ss_pred ccCCCChHHHHHHHHhh
Q 027752 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 97
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=29.55 E-value=53 Score=31.18 Aligned_cols=31 Identities=29% Similarity=0.539 Sum_probs=19.7
Q ss_pred HhhCccH-HHHHHHhhccCCCChHHHHHHHHh
Q 027752 98 FKSLPDL-TKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 98 f~~l~d~-~~al~~L~~LkGVGPATASaiLa~ 128 (219)
|..+..+ .+..+.|++.+|||++.|-.|-..
T Consensus 307 FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 307 FGSLQGLLAASIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred cCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHH
Confidence 4433333 334667888888888888776554
No 98
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=29.08 E-value=52 Score=26.10 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=22.4
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhCC
Q 027752 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 46778889999999999999998643
No 99
>CHL00090 apcD allophycocyanin gamma subunit
Probab=28.03 E-value=76 Score=26.69 Aligned_cols=50 Identities=20% Similarity=0.317 Sum_probs=44.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027752 53 NPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 53 ~~~ltkdEL~~LveWKL~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 100
>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=27.85 E-value=8.7 Score=29.97 Aligned_cols=17 Identities=41% Similarity=0.792 Sum_probs=13.6
Q ss_pred ccCCCChHHHHHHHHhh
Q 027752 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 101
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=27.47 E-value=1.1e+02 Score=25.89 Aligned_cols=51 Identities=12% Similarity=0.176 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~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 3579999999998664 67899999999999999999999999999987775
No 102
>CHL00086 apcA allophycocyanin alpha subunit
Probab=26.77 E-value=96 Score=26.11 Aligned_cols=51 Identities=20% Similarity=0.385 Sum_probs=45.0
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~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 57788899999999999999999999999988776
No 103
>PRK08609 hypothetical protein; Provisional
Probab=26.40 E-value=51 Score=32.84 Aligned_cols=24 Identities=17% Similarity=0.301 Sum_probs=19.5
Q ss_pred HHHHHHHhhccCCCChHHHHHHHH
Q 027752 104 LTKAVSELTVLKGVGPATASAVLA 127 (219)
Q Consensus 104 ~~~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 104
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=26.38 E-value=79 Score=26.95 Aligned_cols=52 Identities=19% Similarity=0.302 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccH
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDL 104 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~ 104 (219)
..+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|.++.+.-|...|+.
T Consensus 15 ~gRyls~~EL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~l 66 (172)
T CHL00171 15 RGEFLSNTQLDALSKM-VAEGNKRLDAVNKINANASTIVTNAARSLFAEQPQL 66 (172)
T ss_pred ccCCCCHHHHHHHHHH-HHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcCc
Confidence 3579999999998776 567888888888999999999999999999887753
No 105
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=26.00 E-value=83 Score=26.69 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=44.4
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027752 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~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 356889999999999999999999999999988775
No 106
>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=25.91 E-value=66 Score=20.65 Aligned_cols=42 Identities=21% Similarity=0.393 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhhCccHH-HHHHHhhccCCCChHHHHHHHHh
Q 027752 87 DSSVKSASEKAFKSLPDLT-KAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 87 ~~~V~~~t~~Af~~l~d~~-~al~~L~~LkGVGPATASaiLa~ 128 (219)
+..+......+|..+.++. ...+.|+.++|++..+|..|...
T Consensus 3 ~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 3 EEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINR 45 (50)
T ss_pred HHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence 3344445555555544443 35788999999999999888764
No 107
>PRK09672 phage exclusion protein Lit; Provisional
Probab=25.90 E-value=2.2e+02 Score=26.72 Aligned_cols=34 Identities=18% Similarity=0.106 Sum_probs=26.4
Q ss_pred cCCCChHHHHHHHHhhCCCC-------CCcccHHHHHHhcC
Q 027752 114 LKGVGPATASAVLAAYAPDL-------APFMSDEAMGAALG 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 68999999999999875543 57777887776543
No 108
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=25.49 E-value=38 Score=30.42 Aligned_cols=20 Identities=45% Similarity=0.669 Sum_probs=18.0
Q ss_pred HHhhccCCCChHHHHHHHHh
Q 027752 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
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=24.45 E-value=41 Score=27.80 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.1
Q ss_pred HHhhccCCCChHHHHHHHHh
Q 027752 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 68999999999999977554
No 110
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=23.99 E-value=35 Score=24.28 Aligned_cols=17 Identities=29% Similarity=0.342 Sum_probs=12.8
Q ss_pred ccCCCChHHHHHHHHhh
Q 027752 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 45678999998876663
No 111
>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=23.34 E-value=1.5e+02 Score=25.71 Aligned_cols=23 Identities=22% Similarity=0.379 Sum_probs=13.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHh
Q 027752 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 44666666666655555555555
No 112
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=22.63 E-value=3.7e+02 Score=26.20 Aligned_cols=82 Identities=27% Similarity=0.368 Sum_probs=48.9
Q ss_pred hHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhh-ccCCCChHHH---------------------HHHHHh-hCCCCC
Q 027752 78 LLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELT-VLKGVGPATA---------------------SAVLAA-YAPDLA 134 (219)
Q Consensus 78 L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~-~LkGVGPATA---------------------SaiLa~-~~P~~~ 134 (219)
+..+|.+|+.+.++-++-.=|....++..++-... +++||||-.= .++.+- +.+ ..
T Consensus 82 ~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~-~~ 160 (422)
T KOG2582|consen 82 LNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYAS-VL 160 (422)
T ss_pred HHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccc-cC
Confidence 45789999998888888776665555555544444 4555555321 111111 233 35
Q ss_pred CcccHHHHHHhcCCCCCCCHHHHHHHH
Q 027752 135 PFMSDEAMGAALGHSKDYSLKQYLLFA 161 (219)
Q Consensus 135 pFfsDEa~~~~~g~~~kYt~keY~~~~ 161 (219)
||++|.... +|+...-+..+.++.|+
T Consensus 161 p~ld~dive-i~~~n~h~~~k~fL~Y~ 186 (422)
T KOG2582|consen 161 PYLDDDIVE-ICKANPHLDPKYFLLYL 186 (422)
T ss_pred CccchhHHH-HhccCCCCCHHHHHHHH
Confidence 888887776 35555556666666553
No 113
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.95 E-value=8.1e+02 Score=25.34 Aligned_cols=18 Identities=6% Similarity=-0.175 Sum_probs=14.4
Q ss_pred CCCHHHHHHHHHHHHhhh
Q 027752 177 CFTPFDVERALWSSAIGL 194 (219)
Q Consensus 177 ~~t~~~VEkalw~~~v~~ 194 (219)
.++...+|...|+.....
T Consensus 525 ~vdVd~LE~s~ga~~~~~ 542 (652)
T KOG2376|consen 525 AVDVDALEKSDGAKYSEA 542 (652)
T ss_pred hcCchHhhhccCcchhhh
Confidence 467788899999887776
No 114
>COG5578 Predicted integral membrane protein [Function unknown]
Probab=20.83 E-value=52 Score=29.07 Aligned_cols=12 Identities=42% Similarity=0.509 Sum_probs=9.7
Q ss_pred cCCCChHHHHHH
Q 027752 114 LKGVGPATASAV 125 (219)
Q Consensus 114 LkGVGPATASai 125 (219)
.=|++||||++.
T Consensus 37 VfG~~PAT~Alf 48 (208)
T COG5578 37 VFGLMPATAALF 48 (208)
T ss_pred HHccchHHHHHH
Confidence 569999999754
Done!