Query 029726
Match_columns 189
No_of_seqs 119 out of 146
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 02:42:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029726.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029726hhsearch_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 97.7 3.1E-05 6.7E-10 47.3 2.5 24 105-128 7-30 (30)
2 PRK01229 N-glycosylase/DNA lya 96.8 0.009 2E-07 51.1 8.6 72 103-176 112-192 (208)
3 cd00056 ENDO3c endonuclease II 96.6 0.012 2.7E-07 46.3 7.7 40 105-146 79-119 (158)
4 COG0177 Nth Predicted EndoIII- 96.2 0.0059 1.3E-07 52.5 4.3 72 57-130 42-130 (211)
5 TIGR01084 mutY A/G-specific ad 96.0 0.034 7.3E-07 49.2 8.2 38 104-142 100-137 (275)
6 PRK10702 endonuclease III; Pro 95.5 0.023 5E-07 48.4 4.8 39 104-143 104-142 (211)
7 smart00478 ENDO3c endonuclease 95.5 0.1 2.2E-06 40.8 8.1 39 103-142 66-104 (149)
8 COG0122 AlkA 3-methyladenine D 95.4 0.035 7.6E-07 49.3 5.9 72 55-135 144-226 (285)
9 TIGR01083 nth endonuclease III 95.2 0.062 1.3E-06 44.5 6.5 41 104-145 101-141 (191)
10 PRK10880 adenine DNA glycosyla 95.0 0.039 8.4E-07 50.5 4.9 29 104-132 104-132 (350)
11 TIGR00588 ogg 8-oxoguanine DNA 94.8 0.026 5.7E-07 50.5 3.3 39 103-143 214-254 (310)
12 PF02371 Transposase_20: Trans 94.7 0.027 5.8E-07 41.1 2.6 37 109-147 2-39 (87)
13 PRK02515 psbU photosystem II c 94.7 0.016 3.5E-07 46.7 1.5 37 106-147 58-94 (132)
14 PRK13913 3-methyladenine DNA g 94.6 0.094 2E-06 45.1 6.1 40 106-146 118-157 (218)
15 PRK13910 DNA glycosylase MutY; 94.6 0.051 1.1E-06 48.5 4.7 34 106-140 69-102 (289)
16 TIGR03252 uncharacterized HhH- 94.5 0.031 6.7E-07 46.9 2.8 44 102-147 108-151 (177)
17 PRK10308 3-methyl-adenine DNA 94.4 0.046 9.9E-07 48.4 3.8 36 103-139 201-238 (283)
18 COG1194 MutY A/G-specific DNA 94.3 0.058 1.3E-06 49.5 4.3 56 108-163 112-174 (342)
19 smart00278 HhH1 Helix-hairpin- 92.6 0.091 2E-06 30.4 1.9 19 110-128 2-20 (26)
20 PF11731 Cdd1: Pathogenicity l 91.1 0.15 3.3E-06 38.7 2.1 26 104-129 7-32 (93)
21 PF10391 DNA_pol_lambd_f: Fing 89.5 0.24 5.1E-06 33.7 1.7 22 108-129 1-22 (52)
22 PF14716 HHH_8: Helix-hairpin- 87.8 0.78 1.7E-05 32.0 3.5 31 97-127 34-65 (68)
23 PRK14605 ruvA Holliday junctio 87.5 0.39 8.5E-06 40.4 2.2 30 103-132 67-96 (194)
24 TIGR01259 comE comEA protein. 86.8 0.77 1.7E-05 35.8 3.4 42 105-147 64-105 (120)
25 KOG1921 Endonuclease III [Repl 86.6 1.1 2.3E-05 40.1 4.5 29 103-131 153-181 (286)
26 PF12826 HHH_2: Helix-hairpin- 85.6 2 4.3E-05 29.8 4.6 24 106-129 32-55 (64)
27 COG2231 Uncharacterized protei 85.3 3.2 7E-05 36.0 6.6 68 107-175 113-194 (215)
28 PRK00116 ruvA Holliday junctio 84.9 0.82 1.8E-05 38.2 2.8 27 105-131 69-95 (192)
29 PRK14600 ruvA Holliday junctio 84.5 0.6 1.3E-05 39.2 1.8 30 103-132 67-96 (186)
30 PF14520 HHH_5: Helix-hairpin- 84.4 1 2.2E-05 30.5 2.6 23 107-129 3-25 (60)
31 PRK13901 ruvA Holliday junctio 84.4 0.62 1.3E-05 39.7 1.9 29 104-132 67-95 (196)
32 TIGR00084 ruvA Holliday juncti 84.4 0.66 1.4E-05 38.9 2.0 28 104-131 67-94 (191)
33 TIGR00608 radc DNA repair prot 82.9 1.7 3.8E-05 37.3 4.0 61 54-128 12-79 (218)
34 PRK14601 ruvA Holliday junctio 82.5 0.82 1.8E-05 38.4 1.8 29 104-132 68-96 (183)
35 PRK00024 hypothetical protein; 81.8 2.3 4.9E-05 36.5 4.4 60 54-128 22-85 (224)
36 PRK13901 ruvA Holliday junctio 81.3 6 0.00013 33.7 6.7 111 54-176 61-180 (196)
37 PF14520 HHH_5: Helix-hairpin- 80.2 0.95 2.1E-05 30.6 1.2 41 88-128 16-57 (60)
38 COG2003 RadC DNA repair protei 79.4 3.7 8.1E-05 35.8 4.9 79 35-129 3-86 (224)
39 PRK14606 ruvA Holliday junctio 79.2 1.2 2.7E-05 37.4 1.8 27 105-131 69-95 (188)
40 PRK14602 ruvA Holliday junctio 78.7 1.4 3.1E-05 37.3 2.1 29 104-132 69-97 (203)
41 PF00416 Ribosomal_S13: Riboso 77.5 3.8 8.3E-05 31.2 4.0 40 106-145 12-54 (107)
42 TIGR00426 competence protein C 77.2 3.4 7.4E-05 28.5 3.3 39 108-147 15-54 (69)
43 PRK14603 ruvA Holliday junctio 76.2 1.7 3.6E-05 36.8 1.8 29 104-132 67-95 (197)
44 COG1555 ComEA DNA uptake prote 76.1 2.6 5.7E-05 34.1 2.9 42 105-147 93-134 (149)
45 PRK14606 ruvA Holliday junctio 74.4 4.2 9E-05 34.2 3.7 99 54-164 62-167 (188)
46 PRK14601 ruvA Holliday junctio 73.6 4.5 9.8E-05 34.0 3.7 98 54-164 62-166 (183)
47 COG0353 RecR Recombinational D 73.6 2.4 5.2E-05 36.4 2.1 23 102-124 5-27 (198)
48 COG0099 RpsM Ribosomal protein 73.5 3.3 7.1E-05 33.1 2.7 40 107-146 15-57 (121)
49 PRK14604 ruvA Holliday junctio 73.2 4.6 0.0001 34.1 3.7 99 54-164 62-173 (195)
50 COG1796 POL4 DNA polymerase IV 72.6 5.1 0.00011 36.8 4.0 33 103-135 45-79 (326)
51 smart00279 HhH2 Helix-hairpin- 72.4 2.7 5.8E-05 26.4 1.6 15 113-127 20-34 (36)
52 PRK14604 ruvA Holliday junctio 72.4 2.4 5.1E-05 35.9 1.8 30 103-132 67-96 (195)
53 PRK07945 hypothetical protein; 69.9 8.8 0.00019 34.6 5.0 19 110-128 50-68 (335)
54 PRK14603 ruvA Holliday junctio 69.8 6.1 0.00013 33.4 3.7 99 54-164 61-176 (197)
55 KOG2875 8-oxoguanine DNA glyco 69.4 3.3 7.2E-05 37.7 2.1 32 104-135 213-246 (323)
56 COG0632 RuvA Holliday junction 68.1 3.9 8.4E-05 35.0 2.2 30 103-132 67-96 (201)
57 PRK04053 rps13p 30S ribosomal 67.9 5.5 0.00012 32.6 3.0 57 102-158 18-80 (149)
58 PRK14602 ruvA Holliday junctio 67.7 7.1 0.00015 33.1 3.7 63 54-126 63-126 (203)
59 PF12836 HHH_3: Helix-hairpin- 67.1 4.1 8.8E-05 28.1 1.8 41 106-147 11-51 (65)
60 PTZ00134 40S ribosomal protein 65.0 3.3 7.1E-05 34.1 1.1 54 101-154 22-81 (154)
61 TIGR00084 ruvA Holliday juncti 64.9 7.4 0.00016 32.6 3.3 98 54-164 61-171 (191)
62 PRK00076 recR recombination pr 64.6 5.2 0.00011 34.1 2.3 23 103-125 5-27 (196)
63 CHL00137 rps13 ribosomal prote 63.8 7.9 0.00017 30.6 3.0 39 107-145 15-56 (122)
64 PF11798 IMS_HHH: IMS family H 63.5 4.5 9.8E-05 24.6 1.3 15 111-125 13-27 (32)
65 cd00141 NT_POLXc Nucleotidyltr 62.6 6.2 0.00013 35.2 2.5 25 104-128 80-104 (307)
66 PRK00116 ruvA Holliday junctio 62.6 16 0.00035 30.4 4.9 24 108-131 107-130 (192)
67 TIGR00615 recR recombination p 62.3 6.1 0.00013 33.7 2.3 22 104-125 6-27 (195)
68 KOG2457 A/G-specific adenine D 62.0 3.9 8.4E-05 39.0 1.2 22 109-130 205-227 (555)
69 TIGR03629 arch_S13P archaeal r 61.2 7.2 0.00016 31.7 2.4 37 108-144 20-59 (144)
70 PRK13844 recombination protein 60.5 6.8 0.00015 33.6 2.3 23 103-125 9-31 (200)
71 TIGR03631 bact_S13 30S ribosom 58.9 9.8 0.00021 29.6 2.8 38 109-146 15-55 (113)
72 PRK05179 rpsM 30S ribosomal pr 58.4 10 0.00023 29.8 2.9 65 108-174 16-84 (122)
73 TIGR01339 phycocy_beta phycocy 58.0 13 0.00029 31.1 3.5 52 52-104 13-64 (170)
74 smart00483 POLXc DNA polymeras 57.6 9.4 0.0002 34.5 2.8 66 103-172 83-162 (334)
75 cd00080 HhH2_motif Helix-hairp 56.2 7.6 0.00016 27.7 1.6 19 111-129 24-42 (75)
76 cd00141 NT_POLXc Nucleotidyltr 56.1 8.9 0.00019 34.2 2.4 15 109-123 45-59 (307)
77 smart00483 POLXc DNA polymeras 53.1 9.6 0.00021 34.4 2.1 36 98-133 37-72 (334)
78 COG3092 Uncharacterized protei 51.7 35 0.00076 27.9 4.9 94 80-175 28-145 (149)
79 PF00502 Phycobilisome: Phycob 51.4 11 0.00024 30.5 2.0 52 52-104 10-61 (157)
80 TIGR00426 competence protein C 51.0 47 0.001 22.7 4.9 22 107-128 45-66 (69)
81 PF05766 NinG: Bacteriophage L 50.1 34 0.00075 29.1 4.9 39 137-175 148-188 (189)
82 PRK14605 ruvA Holliday junctio 49.3 13 0.00029 31.2 2.3 63 54-126 62-125 (194)
83 PRK14976 5'-3' exonuclease; Pr 47.7 11 0.00024 33.4 1.6 17 114-130 196-212 (281)
84 PRK12766 50S ribosomal protein 47.2 14 0.00031 32.4 2.2 43 87-129 13-56 (232)
85 TIGR01259 comE comEA protein. 46.3 45 0.00098 25.8 4.7 21 107-127 96-116 (120)
86 PRK09482 flap endonuclease-lik 43.8 14 0.00031 32.5 1.7 18 113-130 186-203 (256)
87 CHL00172 cpeB phycoerythrin be 42.9 29 0.00063 29.3 3.3 52 52-104 15-66 (177)
88 PRK08609 hypothetical protein; 42.5 27 0.00059 33.9 3.5 21 107-127 86-106 (570)
89 CHL00090 apcD allophycocyanin 42.3 33 0.0007 28.3 3.5 51 52-103 14-64 (161)
90 CHL00170 cpcA phycocyanin alph 42.1 43 0.00092 27.9 4.1 52 52-104 15-66 (162)
91 CHL00086 apcA allophycocyanin 41.2 36 0.00078 28.0 3.6 51 52-103 14-64 (161)
92 CHL00173 cpeA phycoerythrin al 40.1 34 0.00074 28.4 3.3 51 52-103 15-65 (164)
93 PRK13482 DNA integrity scannin 39.8 29 0.00063 32.3 3.1 22 107-128 317-338 (352)
94 TIGR01338 phycocy_alpha phycoc 39.7 48 0.001 27.5 4.1 52 52-104 14-65 (161)
95 cd00008 53EXOc 5'-3' exonuclea 39.6 18 0.0004 31.0 1.7 17 113-129 187-203 (240)
96 PF01367 5_3_exonuc: 5'-3' exo 39.2 5 0.00011 30.7 -1.6 16 114-129 23-38 (101)
97 CHL00171 cpcB phycocyanin beta 39.1 34 0.00074 28.5 3.2 52 52-104 15-66 (172)
98 PF14229 DUF4332: Domain of un 39.1 29 0.00062 27.0 2.6 26 106-131 50-75 (122)
99 smart00475 53EXOc 5'-3' exonuc 38.7 20 0.00042 31.4 1.7 18 113-130 190-207 (259)
100 PRK14600 ruvA Holliday junctio 37.6 22 0.00047 29.9 1.8 98 54-164 62-169 (186)
101 TIGR01954 nusA_Cterm_rpt trans 33.7 37 0.0008 21.4 2.1 42 87-128 3-45 (50)
102 PF14579 HHH_6: Helix-hairpin- 32.8 1.2E+02 0.0026 21.9 4.9 32 111-144 29-60 (90)
103 COG3743 Uncharacterized conser 32.8 24 0.00051 28.7 1.2 20 109-128 67-86 (133)
104 PRK12766 50S ribosomal protein 32.1 24 0.00051 31.1 1.2 20 109-128 3-22 (232)
105 PF04854 DUF624: Protein of un 32.1 21 0.00046 24.8 0.8 17 113-129 17-33 (77)
106 PRK08609 hypothetical protein; 31.7 29 0.00062 33.8 1.8 32 98-129 110-143 (570)
107 KOG1918 3-methyladenine DNA gl 31.1 36 0.00078 30.2 2.1 37 104-141 160-198 (254)
108 PF00356 LacI: Bacterial regul 28.8 43 0.00092 21.9 1.7 31 108-143 2-32 (46)
109 COG1059 Thermostable 8-oxoguan 26.5 3.2E+02 0.0068 23.8 7.0 69 107-175 118-193 (210)
110 COG0632 RuvA Holliday junction 26.5 48 0.001 28.4 2.1 20 108-127 107-126 (201)
111 COG5578 Predicted integral mem 26.4 34 0.00074 29.6 1.2 12 114-125 37-48 (208)
112 PRK03980 flap endonuclease-1; 25.9 39 0.00085 30.2 1.5 17 113-129 193-209 (292)
113 TIGR01448 recD_rel helicase, p 25.9 92 0.002 31.2 4.2 15 114-128 89-103 (720)
114 PRK14350 ligA NAD-dependent DN 25.5 73 0.0016 31.9 3.4 23 107-129 539-561 (669)
115 KOG2582 COP9 signalosome, subu 25.0 3.1E+02 0.0067 26.2 7.2 82 78-160 82-185 (422)
116 TIGR03674 fen_arch flap struct 24.7 45 0.00098 30.2 1.7 17 113-129 240-256 (338)
117 PF11517 Nab2: Nuclear abundan 24.5 41 0.0009 26.2 1.2 46 78-123 54-102 (107)
118 PHA01976 helix-turn-helix prot 23.8 61 0.0013 21.5 1.8 25 53-77 13-43 (67)
119 TIGR01337 apcB allophycocyanin 23.7 78 0.0017 26.2 2.8 51 52-103 14-64 (167)
120 cd00128 XPG Xeroderma pigmento 23.6 50 0.0011 29.1 1.7 44 113-162 227-274 (316)
121 CHL00089 apcF allophycocyanin 22.9 89 0.0019 26.0 3.0 51 52-103 15-65 (169)
122 TIGR01589 A_thal_3526 uncharac 22.4 98 0.0021 21.6 2.6 49 89-137 3-51 (57)
123 PRK00558 uvrC excinuclease ABC 22.2 90 0.0019 30.7 3.3 22 108-129 542-563 (598)
124 PRK14669 uvrC excinuclease ABC 21.9 1.3E+02 0.0028 29.9 4.4 21 109-129 552-572 (624)
125 PF08008 Viral_cys_rich: Viral 21.6 31 0.00067 25.9 0.0 29 17-45 55-83 (85)
126 COG1415 Uncharacterized conser 21.3 2.9E+02 0.0063 26.0 6.2 137 31-170 166-346 (373)
127 TIGR00194 uvrC excinuclease AB 21.1 1.4E+02 0.0031 29.3 4.4 21 109-129 541-561 (574)
128 TIGR03292 PhnH_redo phosphonat 21.1 1.2E+02 0.0025 25.4 3.3 31 114-145 26-60 (174)
129 PRK10703 DNA-binding transcrip 21.1 1.8E+02 0.004 24.7 4.7 34 108-146 4-37 (341)
130 PRK14671 uvrC excinuclease ABC 20.3 1.2E+02 0.0026 30.1 3.7 22 108-129 568-589 (621)
131 PRK14668 uvrC excinuclease ABC 20.3 97 0.0021 30.5 3.1 40 108-147 524-564 (577)
132 COG1031 Uncharacterized Fe-S o 20.2 81 0.0018 30.9 2.5 38 105-147 512-549 (560)
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=97.70 E-value=3.1e-05 Score=47.29 Aligned_cols=24 Identities=42% Similarity=0.700 Sum_probs=20.2
Q ss_pred HHHHHHhhcccCcChHHHHHHHHh
Q 029726 105 TKAVSELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 105 ~~al~~Lt~LkGVGPATASaiLa~ 128 (189)
.+.++.|++|+||||.||.+|++.
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 456889999999999999999974
No 2
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=96.75 E-value=0.009 Score=51.12 Aligned_cols=72 Identities=26% Similarity=0.209 Sum_probs=52.8
Q ss_pred cHHHHHHHhh-cccCcChHHHHHHH-HhhcCCCCCcccHHHHHHhh---C--C--CCCCCHHHHHHHHHHHHHHHHHHhh
Q 029726 103 DLTKAVSELT-VLKGVGPATASAVL-AAYAPGVAPFMSDEAMGAAL---G--H--SKDYSLRQYLLFADKLQAKAKFLKK 173 (189)
Q Consensus 103 d~~~al~~Lt-~LkGVGPATASaiL-a~~~P~~~pFfsDEa~~~~~---g--~--~~kYt~keY~~~~~~~~~~~~~L~~ 173 (189)
++..+.+.|. +||||||=|||.|| .+.. ..-|.-|--..-++ | . +..-|.+.|.+.-..+++.++.+|.
T Consensus 112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~--~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~~ 189 (208)
T PRK01229 112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY--EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELGI 189 (208)
T ss_pred CchHHHHHHHHcCCCCcHHHHHHHHHHccC--CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcCC
Confidence 5678899999 99999999999999 4544 21344666544332 4 1 2245669999999999999999887
Q ss_pred hcc
Q 029726 174 IAS 176 (189)
Q Consensus 174 ~~~ 176 (189)
..+
T Consensus 190 ~~~ 192 (208)
T PRK01229 190 SLG 192 (208)
T ss_pred CHH
Confidence 653
No 3
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=96.57 E-value=0.012 Score=46.31 Aligned_cols=40 Identities=38% Similarity=0.449 Sum_probs=30.1
Q ss_pred HHHHHHhhcccCcChHHHHHHHHhhc-CCCCCcccHHHHHHhh
Q 029726 105 TKAVSELTVLKGVGPATASAVLAAYA-PGVAPFMSDEAMGAAL 146 (189)
Q Consensus 105 ~~al~~Lt~LkGVGPATASaiLa~~~-P~~~pFfsDEa~~~~~ 146 (189)
..+.+.|++||||||-||+.+|.... ++.+|. |-...-++
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~r~~ 119 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVRRVL 119 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHHHHH
Confidence 67899999999999999999998753 444443 66554433
No 4
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=96.24 E-value=0.0059 Score=52.49 Aligned_cols=72 Identities=24% Similarity=0.235 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHH------------hhC-----ccHHHHHHHhhcccCcCh
Q 029726 57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAF------------KSL-----PDLTKAVSELTVLKGVGP 119 (189)
Q Consensus 57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af------------~~l-----~d~~~al~~Lt~LkGVGP 119 (189)
|.|+.++-+-=+|- +..|+...+...+.++..+-+-.-+| +++ .++...++.|.+|+|||+
T Consensus 42 ttD~~vn~at~~Lf--~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVGr 119 (211)
T COG0177 42 TTDEVVNKATPALF--KRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGR 119 (211)
T ss_pred CchHHHHHHHHHHH--HHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcch
Confidence 46777766665554 23456666655554443333222222 011 156778999999999999
Q ss_pred HHHHHHHHhhc
Q 029726 120 ATASAVLAAYA 130 (189)
Q Consensus 120 ATASaiLa~~~ 130 (189)
-||..+|+...
T Consensus 120 KTAnvVL~~a~ 130 (211)
T COG0177 120 KTANVVLSFAF 130 (211)
T ss_pred HHHHHHHHhhc
Confidence 99999999854
No 5
>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=96.02 E-value=0.034 Score=49.22 Aligned_cols=38 Identities=29% Similarity=0.385 Sum_probs=29.0
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHH
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM 142 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~ 142 (189)
+...++.|++|+||||-||++||+...-...|+ -|--.
T Consensus 100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~~v 137 (275)
T TIGR01084 100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDGNV 137 (275)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chHhH
Confidence 345789999999999999999999865443454 55544
No 6
>PRK10702 endonuclease III; Provisional
Probab=95.47 E-value=0.023 Score=48.36 Aligned_cols=39 Identities=26% Similarity=0.249 Sum_probs=29.1
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHH
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~ 143 (189)
+..+.+.|.+|+||||-||.+||....-. ..|.-|--..
T Consensus 104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v~ 142 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHIF 142 (211)
T ss_pred CCchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchHH
Confidence 45688999999999999999999986543 2344554333
No 7
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.47 E-value=0.1 Score=40.82 Aligned_cols=39 Identities=31% Similarity=0.293 Sum_probs=28.6
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHH
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAM 142 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~ 142 (189)
++....+.|++|+||||-||+++|...--. .-|..|--.
T Consensus 66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~-~~~~~D~~v 104 (149)
T smart00478 66 EVPDDREELLKLPGVGRKTANAVLSFALGK-PFIPVDTHV 104 (149)
T ss_pred CccHHHHHHHcCCCCcHHHHHHHHHHHCCC-CCCccchHH
Confidence 344678899999999999999999986554 233444433
No 8
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.40 E-value=0.035 Score=49.33 Aligned_cols=72 Identities=28% Similarity=0.256 Sum_probs=52.5
Q ss_pred CCCHHHHHHHHHHHhh-CCCCCcchhhHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhcccCcChHHHHHH
Q 029726 55 HINTTELSKLVRWKLT-RGKWRPRLLDFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV 125 (189)
Q Consensus 55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~--------d~~~al~~Lt~LkGVGPATASai 125 (189)
+.|-++|..+=++-|+ -|..+.+ .+.++.+++...+-.+ +...+++.|++||||||=||-.+
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 6788888888888876 5665553 3455556655554322 46779999999999999999999
Q ss_pred HHh--hcCCCCC
Q 029726 126 LAA--YAPGVAP 135 (189)
Q Consensus 126 La~--~~P~~~p 135 (189)
|-. ..|+.+|
T Consensus 215 llf~lgr~dvfP 226 (285)
T COG0122 215 LLFGLGRPDVFP 226 (285)
T ss_pred HHHcCCCCCCCC
Confidence 876 4677655
No 9
>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=95.25 E-value=0.062 Score=44.49 Aligned_cols=41 Identities=27% Similarity=0.210 Sum_probs=29.4
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHh
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAA 145 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~ 145 (189)
+..+.+.|++|+||||=||.+||....-.. -|.-|--..-+
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~Ri 141 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVFRV 141 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHHHH
Confidence 445788999999999999999998864322 24555544433
No 10
>PRK10880 adenine DNA glycosylase; Provisional
Probab=94.97 E-value=0.039 Score=50.55 Aligned_cols=29 Identities=31% Similarity=0.454 Sum_probs=25.2
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
+....+.|.+|+||||-||++||+...-.
T Consensus 104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~ 132 (350)
T PRK10880 104 FPETFEEVAALPGVGRSTAGAILSLSLGK 132 (350)
T ss_pred chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence 45678999999999999999999987644
No 11
>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=94.81 E-value=0.026 Score=50.46 Aligned_cols=39 Identities=28% Similarity=0.360 Sum_probs=31.0
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhh--cCCCCCcccHHHHH
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAMG 143 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~--~P~~~pFfsDEa~~ 143 (189)
+...+.+.|++||||||=||.+||... .|+.+| .|-...
T Consensus 214 ~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~P--vD~~v~ 254 (310)
T TIGR00588 214 SYEDAREALCELPGVGPKVADCICLMGLDKPQAVP--VDVHVW 254 (310)
T ss_pred ChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCcee--ecHHHH
Confidence 356789999999999999999999774 566666 375553
No 12
>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=94.70 E-value=0.027 Score=41.15 Aligned_cols=37 Identities=32% Similarity=0.496 Sum_probs=30.0
Q ss_pred HHhhcccCcChHHHHHHHHhh-cCCCCCcccHHHHHHhhC
Q 029726 109 SELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMGAALG 147 (189)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~~~~g 147 (189)
+.|+.++||||-||..||+.. +++ -|=+...+...+|
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 4667888887776
No 13
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.68 E-value=0.016 Score=46.66 Aligned_cols=37 Identities=24% Similarity=0.325 Sum_probs=32.1
Q ss_pred HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (189)
Q Consensus 106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (189)
+.++.|..|+||||++|..|. .+.||-|=|-...+.|
T Consensus 58 A~~~el~~lpGigP~~A~~IV-----~nGpf~sveDL~~V~G 94 (132)
T PRK02515 58 SSVRAFRQFPGMYPTLAGKIV-----KNAPYDSVEDVLNLPG 94 (132)
T ss_pred cCHHHHHHCCCCCHHHHHHHH-----HCCCCCCHHHHHcCCC
Confidence 456789999999999999999 3679999998888887
No 14
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=94.62 E-value=0.094 Score=45.15 Aligned_cols=40 Identities=23% Similarity=0.163 Sum_probs=29.0
Q ss_pred HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhh
Q 029726 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL 146 (189)
Q Consensus 106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~ 146 (189)
...+.|.+|+||||=||.+||....- ..-|..|--..-++
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv~ 157 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLFL 157 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHHH
Confidence 45688999999999999999987543 32456666554443
No 15
>PRK13910 DNA glycosylase MutY; Provisional
Probab=94.60 E-value=0.051 Score=48.54 Aligned_cols=34 Identities=26% Similarity=0.262 Sum_probs=26.5
Q ss_pred HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHH
Q 029726 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDE 140 (189)
Q Consensus 106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDE 140 (189)
...+.|.+|+||||-||.+||+...-..++ .-|-
T Consensus 69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~-~VD~ 102 (289)
T PRK13910 69 NDYQSLLKLPGIGAYTANAILCFGFREKSA-CVDA 102 (289)
T ss_pred hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC-cccH
Confidence 458999999999999999999986544333 4444
No 16
>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=94.48 E-value=0.031 Score=46.95 Aligned_cols=44 Identities=27% Similarity=0.342 Sum_probs=32.7
Q ss_pred ccHHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726 102 PDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (189)
Q Consensus 102 ~d~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (189)
|+-....+.|.+|+||||-||..||+...-+- -.-||-|....|
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 45556689999999999999999999765431 145677766554
No 17
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=94.38 E-value=0.046 Score=48.43 Aligned_cols=36 Identities=28% Similarity=0.294 Sum_probs=29.4
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHh--hcCCCCCcccH
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSD 139 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~pFfsD 139 (189)
+...+++.|++||||||-||..||-. ..|+.+| -.|
T Consensus 201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp-~~D 238 (283)
T PRK10308 201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDD 238 (283)
T ss_pred CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC-ccc
Confidence 56778999999999999999999865 5787655 444
No 18
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.26 E-value=0.058 Score=49.51 Aligned_cols=56 Identities=25% Similarity=0.335 Sum_probs=38.3
Q ss_pred HHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHH---hhC----CCCCCCHHHHHHHHHH
Q 029726 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA---ALG----HSKDYSLRQYLLFADK 163 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~---~~g----~~~kYt~keY~~~~~~ 163 (189)
.+.|.+|+||||-||+||||...-...|+..--+... +.+ .+.+=+-+++..+.+.
T Consensus 112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i~~~~~~~~~~~~~~~~~~~ 174 (342)
T COG1194 112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQ 174 (342)
T ss_pred HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcccccccccchhHHHHHHHHH
Confidence 4567779999999999999998777778766655542 222 1223456666666655
No 19
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=92.64 E-value=0.091 Score=30.42 Aligned_cols=19 Identities=47% Similarity=0.763 Sum_probs=16.9
Q ss_pred HhhcccCcChHHHHHHHHh
Q 029726 110 ELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 110 ~Lt~LkGVGPATASaiLa~ 128 (189)
.|++++|||+.+|..|+..
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=91.12 E-value=0.15 Score=38.73 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=22.2
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhh
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~ 129 (189)
..+.+..|+.|+|||||||-=+..++
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LG 32 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLG 32 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence 34578899999999999999888774
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=89.47 E-value=0.24 Score=33.69 Aligned_cols=22 Identities=36% Similarity=0.351 Sum_probs=17.3
Q ss_pred HHHhhcccCcChHHHHHHHHhh
Q 029726 108 VSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~ 129 (189)
|+.++++-||||.||.-..+..
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
>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=87.81 E-value=0.78 Score=32.01 Aligned_cols=31 Identities=32% Similarity=0.415 Sum_probs=22.5
Q ss_pred HHhhCccHHHHHHH-hhcccCcChHHHHHHHH
Q 029726 97 AFKSLPDLTKAVSE-LTVLKGVGPATASAVLA 127 (189)
Q Consensus 97 Af~~l~d~~~al~~-Lt~LkGVGPATASaiLa 127 (189)
+.+.+|..-..++. +.+|+|||+.+|.-|--
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 34556755555575 99999999999988743
No 23
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.48 E-value=0.39 Score=40.40 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=25.1
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
+-+.-+..|.+..||||-||-+||+.+.|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~ 96 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNAE 96 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCHH
Confidence 346678889999999999999999987764
No 24
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=86.85 E-value=0.77 Score=35.75 Aligned_cols=42 Identities=29% Similarity=0.468 Sum_probs=33.7
Q ss_pred HHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (189)
Q Consensus 105 ~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (189)
.+..+.|..|+||||.+|..|+.-..- ..||-|-|-+..+.|
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~-~g~f~s~eeL~~V~G 105 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYREE-NGAFKSVDDLTKVSG 105 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHcCCC
Confidence 345678999999999999999998653 558888777776765
No 25
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=86.59 E-value=1.1 Score=40.12 Aligned_cols=29 Identities=31% Similarity=0.464 Sum_probs=26.4
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAYAP 131 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~~P 131 (189)
|+-..++.|..|+||||-+|=+.|++.--
T Consensus 153 DIP~~v~dLlsLPGVGPKMa~L~m~~AWn 181 (286)
T KOG1921|consen 153 DIPDTVEDLLSLPGVGPKMAHLTMQVAWN 181 (286)
T ss_pred CCchhHHHHhcCCCCchHHHHHHHHHHhc
Confidence 78889999999999999999999998543
No 26
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=85.62 E-value=2 Score=29.77 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.7
Q ss_pred HHHHHhhcccCcChHHHHHHHHhh
Q 029726 106 KAVSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 106 ~al~~Lt~LkGVGPATASaiLa~~ 129 (189)
+..+.|++++||||.+|..|....
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 357889999999999999998764
No 27
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=85.33 E-value=3.2 Score=36.04 Aligned_cols=68 Identities=22% Similarity=0.278 Sum_probs=42.8
Q ss_pred HHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhh---C-CCC-CCC-HHHHH--------HHHHHHHHHHHHHh
Q 029726 107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL---G-HSK-DYS-LRQYL--------LFADKLQAKAKFLK 172 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~---g-~~~-kYt-~keY~--------~~~~~~~~~~~~L~ 172 (189)
.-+.|-++||||+=||=+||--.. +..-|.-|..-.-+. | ... +|+ +|+.. .+++..+++..+.+
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~-~rp~FVvD~Yt~R~l~rlg~i~~k~ydeik~~fe~~l~~~~~lyqe~HAlIv~~~ 191 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYAL-DRPVFVVDKYTRRLLSRLGGIEEKKYDEIKELFEENLPENLRLYQEFHALIVEHA 191 (215)
T ss_pred HHHHHHccCCcchhhHHHHHHHHh-cCcccchhHHHHHHHHHhcccccccHHHHHHHHHhcchhHHHHHHHHHHHHHHHH
Confidence 357788999999999999987643 344677776554433 3 222 575 33332 24556666666666
Q ss_pred hhc
Q 029726 173 KIA 175 (189)
Q Consensus 173 ~~~ 175 (189)
+..
T Consensus 192 K~f 194 (215)
T COG2231 192 KHF 194 (215)
T ss_pred HHH
Confidence 654
No 28
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=84.87 E-value=0.82 Score=38.17 Aligned_cols=27 Identities=33% Similarity=0.541 Sum_probs=21.0
Q ss_pred HHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726 105 TKAVSELTVLKGVGPATASAVLAAYAP 131 (189)
Q Consensus 105 ~~al~~Lt~LkGVGPATASaiLa~~~P 131 (189)
+.....|..++||||.||-.||+.+.+
T Consensus 69 k~~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 69 RELFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 344678888999999999999887554
No 29
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.47 E-value=0.6 Score=39.21 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=23.2
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
+-+.-+..|.+..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 345567788888888888888888887664
No 30
>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=84.45 E-value=1 Score=30.52 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=20.3
Q ss_pred HHHHhhcccCcChHHHHHHHHhh
Q 029726 107 AVSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa~~ 129 (189)
....|..++||||.+|..|....
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 31
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.39 E-value=0.62 Score=39.67 Aligned_cols=29 Identities=28% Similarity=0.385 Sum_probs=20.3
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
-+.-+..|.+..||||-||-+|||...|+
T Consensus 67 Er~lF~~LisVsGIGPK~ALaILs~~~~~ 95 (196)
T PRK13901 67 EREVFEELIGVDGIGPRAALRVLSGIKYN 95 (196)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 34556677777777777777777776664
No 32
>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=84.36 E-value=0.66 Score=38.94 Aligned_cols=28 Identities=36% Similarity=0.557 Sum_probs=21.6
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P 131 (189)
-+.-+..|.+++||||-||-+||+...|
T Consensus 67 Er~lF~~L~~V~GIGpK~Al~iL~~~~~ 94 (191)
T TIGR00084 67 ERELFKELIKVNGVGPKLALAILSNMSP 94 (191)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence 4556777888888888888888887655
No 33
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.86 E-value=1.7 Score=37.28 Aligned_cols=61 Identities=30% Similarity=0.385 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhcccCcChHHHHHHH
Q 029726 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL 126 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~------l~d~-~~al~~Lt~LkGVGPATASaiL 126 (189)
..|+-.||..++ |.-|.-|- + .|...+++-++. +.++ ....+.|++++|||||.|..|+
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 578888866554 45554332 0 334444433332 3333 3357889999999999999999
Q ss_pred Hh
Q 029726 127 AA 128 (189)
Q Consensus 127 a~ 128 (189)
++
T Consensus 78 a~ 79 (218)
T TIGR00608 78 AA 79 (218)
T ss_pred HH
Confidence 98
No 34
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.50 E-value=0.82 Score=38.40 Aligned_cols=29 Identities=28% Similarity=0.303 Sum_probs=20.6
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
-+.-+..|.+..||||-||-+|||...|+
T Consensus 68 Er~lF~~Li~VsGIGpK~Al~ILs~~~~~ 96 (183)
T PRK14601 68 EQKMFEMLLKVNGIGANTAMAVCSSLDVN 96 (183)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 34556777777777777777777776664
No 35
>PRK00024 hypothetical protein; Reviewed
Probab=81.82 E-value=2.3 Score=36.54 Aligned_cols=60 Identities=28% Similarity=0.449 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH----HHHHHHhhcccCcChHHHHHHHHh
Q 029726 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL----TKAVSELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~----~~al~~Lt~LkGVGPATASaiLa~ 128 (189)
..|+-.||..++ |..|..|. .|....++-++...++ ....+.|++++||||+.|..|+++
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 578888865543 56665443 4555555544433332 234678999999999999999887
No 36
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.34 E-value=6 Score=33.70 Aligned_cols=111 Identities=14% Similarity=0.192 Sum_probs=64.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcC-
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P- 131 (189)
++.|++|..-...-.--.| -=| .-+..++..+++.+.+++.. .=.+.||+++|||+-||.=|.-=...
T Consensus 61 GF~t~~Er~lF~~LisVsG-IGPK~ALaILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 61 GFLNSSEREVFEELIGVDG-IGPRAALRVLSGIKYNEFRDAIDR---------EDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 5788888655444433333 233 34556666677666655533 23568999999999999977632111
Q ss_pred -------CCCCcccHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhhhcc
Q 029726 132 -------GVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKFLKKIAS 176 (189)
Q Consensus 132 -------~~~pFfsDEa~~~~~g~~~kYt~keY~~~~~~~~~~~~~L~~~~~ 176 (189)
...+-..+|+..++.. ..|+-++=...+..+.-.-..|+-+++
T Consensus 131 l~~~~~~~~~~~~~~ea~~AL~~--LGy~~~ea~~al~~v~~~~~~~~~~~~ 180 (196)
T PRK13901 131 LVKNDELESSLFKFKELEQSIVN--MGFDRKLVNSAIKEIMLLDEFLNLKDS 180 (196)
T ss_pred hccccccccCcccHHHHHHHHHH--cCCCHHHHHHHHHHHhcchhhhhhhhh
Confidence 1111113677777653 557666666666555444455555443
No 37
>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=80.15 E-value=0.95 Score=30.62 Aligned_cols=41 Identities=29% Similarity=0.458 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHHh
Q 029726 88 SSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 88 ~~V~~~t~~Af~~l~d~~~-al~~Lt~LkGVGPATASaiLa~ 128 (189)
..++.....+|..+.|+.. ..+.|++++|||+.+|.-|...
T Consensus 16 ~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 16 KRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHH
T ss_pred HHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHH
Confidence 3334443444443333322 4577999999999999988764
No 38
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=79.39 E-value=3.7 Score=35.83 Aligned_cols=79 Identities=27% Similarity=0.375 Sum_probs=51.7
Q ss_pred hhhHHHhhhchh-hhccCCCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhC---ccHHH-HHH
Q 029726 35 LDDYYRKELPSL-IHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSL---PDLTK-AVS 109 (189)
Q Consensus 35 LD~w~~~~lp~~-~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l---~d~~~-al~ 109 (189)
+.+|...+.|.- +...+ ...|+-.||.-|+ |+.|..+- .|...++.-++.+ ..+.. .++
T Consensus 3 i~~~~~~~rPRErll~~G-~~~Lsd~ELLail---LrtG~~~~------------~~~~la~~lL~~fg~L~~l~~a~~~ 66 (224)
T COG2003 3 IKDNPENERPRERLLKLG-AEALSDAELLAIL---LRTGTKGE------------SVLDLAKELLQEFGSLAELLKASVE 66 (224)
T ss_pred ccccccccchHHHHHHhC-hhhcchHHHHHHH---HhcCCCCC------------CHHHHHHHHHHHcccHHHHHhCCHH
Confidence 345555555531 21222 3579999977666 67776433 5666666665543 34444 499
Q ss_pred HhhcccCcChHHHHHHHHhh
Q 029726 110 ELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 110 ~Lt~LkGVGPATASaiLa~~ 129 (189)
.||.++|||+|-|.=+.++.
T Consensus 67 el~~v~GiG~aka~~l~a~~ 86 (224)
T COG2003 67 ELSSVKGIGLAKAIQIKAAI 86 (224)
T ss_pred HHhhCCCccHHHHHHHHHHH
Confidence 99999999999999888873
No 39
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.20 E-value=1.2 Score=37.37 Aligned_cols=27 Identities=22% Similarity=0.322 Sum_probs=16.4
Q ss_pred HHHHHHhhcccCcChHHHHHHHHhhcC
Q 029726 105 TKAVSELTVLKGVGPATASAVLAAYAP 131 (189)
Q Consensus 105 ~~al~~Lt~LkGVGPATASaiLa~~~P 131 (189)
+.-+..|++..||||-||-+||+...|
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs~~~~ 95 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIISNEDA 95 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHcCCCH
Confidence 344556666666666666666666555
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.70 E-value=1.4 Score=37.31 Aligned_cols=29 Identities=28% Similarity=0.403 Sum_probs=21.2
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
-+.-+..|.+..||||-||-+||+...|+
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 34556777788888888888888876664
No 41
>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=77.47 E-value=3.8 Score=31.17 Aligned_cols=40 Identities=23% Similarity=0.279 Sum_probs=30.4
Q ss_pred HHHHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 029726 106 KAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (189)
Q Consensus 106 ~al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (189)
...-+|++++|||+.+|..|+... +|. .+-.++|+-+..+
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 5667888877644
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=77.19 E-value=3.4 Score=28.53 Aligned_cols=39 Identities=28% Similarity=0.432 Sum_probs=29.0
Q ss_pred HHHhhc-ccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726 108 VSELTV-LKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (189)
Q Consensus 108 l~~Lt~-LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (189)
...|.. ++|||+.+|.+|+.-... ..+|-+-+-+..++|
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 999999999999998643 336667666666655
No 43
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.21 E-value=1.7 Score=36.79 Aligned_cols=29 Identities=34% Similarity=0.441 Sum_probs=22.3
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
-+.-+..|.+..||||-||-+||+...|+
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~ 95 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSALPPA 95 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 34566778888888888888888877664
No 44
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=76.08 E-value=2.6 Score=34.13 Aligned_cols=42 Identities=31% Similarity=0.517 Sum_probs=32.2
Q ss_pred HHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (189)
Q Consensus 105 ~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (189)
.+..+.|..|+||||+.|-+|.+--.- ..||=|=|=..-+.|
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~-~G~f~sv~dL~~v~G 134 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREE-NGPFKSVDDLAKVKG 134 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHH-cCCCCcHHHHHhccC
Confidence 345677889999999999999998543 448887776666655
No 45
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.43 E-value=4.2 Score=34.19 Aligned_cols=99 Identities=16% Similarity=0.164 Sum_probs=57.9
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
++.|.+|..-.-.-.--.| -=| +-+.+++..+++.+.++... .=++.||+++|||+-||.-|.-=.-..
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~AL~iLs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 62 GFSNERKKELFLSLTKVSR-LGPKTALKIISNEDAETLVTMIAS---------QDVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 5788888654444433333 233 34556666677666655543 235689999999999999876321110
Q ss_pred ----CC--CcccHHHHHHhhCCCCCCCHHHHHHHHHHH
Q 029726 133 ----VA--PFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (189)
Q Consensus 133 ----~~--pFfsDEa~~~~~g~~~kYt~keY~~~~~~~ 164 (189)
.. .-..+|+..++. ...|+-++=..-+.++
T Consensus 132 ~~~~~~~~~~~~~e~~~AL~--~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 132 FESAGIKDMRIYHESLEALV--SLGYPEKQAREAVKHV 167 (188)
T ss_pred hccccCCCcccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 00 012377887776 3567666655554444
No 46
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.61 E-value=4.5 Score=33.96 Aligned_cols=98 Identities=20% Similarity=0.223 Sum_probs=57.9
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcC-
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P- 131 (189)
++.|++|..-...-.--.| -=| .-+..++..+++.+.++... .=.+.|++++|||+-||.=|+-=.-.
T Consensus 62 GF~~~~Er~lF~~Li~VsG-IGpK~Al~ILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 62 GFLDKDEQKMFEMLLKVNG-IGANTAMAVCSSLDVNSFYKALSL---------GDESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 5788888655444432333 233 23455666677666555443 12568999999999999987632111
Q ss_pred -----CCCCcccHHHHHHhhCCCCCCCHHHHHHHHHHH
Q 029726 132 -----GVAPFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (189)
Q Consensus 132 -----~~~pFfsDEa~~~~~g~~~kYt~keY~~~~~~~ 164 (189)
.... -.+|+..++.+ ..|+.++=...+..+
T Consensus 132 ~~~~~~~~~-~~~ea~~AL~~--LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 132 KTKLENVSD-DKSEALAALLT--LGFKQEKIIKVLASC 166 (183)
T ss_pred hhccCCCCc-cHHHHHHHHHH--cCCCHHHHHHHHHhc
Confidence 1111 23678877763 567777666555544
No 47
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=73.57 E-value=2.4 Score=36.42 Aligned_cols=23 Identities=39% Similarity=0.700 Sum_probs=19.6
Q ss_pred ccHHHHHHHhhcccCcChHHHHH
Q 029726 102 PDLTKAVSELTVLKGVGPATASA 124 (189)
Q Consensus 102 ~d~~~al~~Lt~LkGVGPATASa 124 (189)
|.+.+-|+.|.+|+||||-||.=
T Consensus 5 ~~i~~LI~~l~kLPGvG~KsA~R 27 (198)
T COG0353 5 PPIEKLIDALKKLPGVGPKSAQR 27 (198)
T ss_pred HHHHHHHHHHhhCCCCChhHHHH
Confidence 35677899999999999999974
No 48
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=73.48 E-value=3.3 Score=33.05 Aligned_cols=40 Identities=20% Similarity=0.267 Sum_probs=31.3
Q ss_pred HHHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHhh
Q 029726 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAAL 146 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~~ 146 (189)
-.=+||.++|||+++|-+|+... +|+ .+=..+||-...+-
T Consensus 15 v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir 57 (121)
T COG0099 15 VVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLR 57 (121)
T ss_pred EeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHH
Confidence 34468899999999999999984 555 66778888776543
No 49
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.24 E-value=4.6 Score=34.12 Aligned_cols=99 Identities=18% Similarity=0.151 Sum_probs=56.5
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
++.|++|..-...-.--.| -=| +-+.+++..+++.+.++... .=.+.|++++|||+-||--|..-....
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~Al~iLs~~~~~el~~aI~~---------~D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 62 GFSTPAQRQLFELLIGVSG-VGPKAALNLLSSGTPDELQLAIAG---------GDVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 5788888665544433333 223 23455566666665554443 125689999999999999876532111
Q ss_pred C-----------CC-cccHHHHHHhhCCCCCCCHHHHHHHHHHH
Q 029726 133 V-----------AP-FMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (189)
Q Consensus 133 ~-----------~p-FfsDEa~~~~~g~~~kYt~keY~~~~~~~ 164 (189)
. .+ ---+|+..++. ...|+.++=..-+..+
T Consensus 132 ~~~~~~~~~~~~~~~~~~~e~~~aL~--~LGy~~~ea~~ai~~i 173 (195)
T PRK14604 132 IDVRQLSGSTSPAVSALDRELSEILI--SLGYSAAEAAAAIAAL 173 (195)
T ss_pred hccccccccccccccccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 0 00 01256776665 3567666655555444
No 50
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=72.56 E-value=5.1 Score=36.83 Aligned_cols=33 Identities=27% Similarity=0.368 Sum_probs=26.3
Q ss_pred cHHHHHHH--hhcccCcChHHHHHHHHhhcCCCCC
Q 029726 103 DLTKAVSE--LTVLKGVGPATASAVLAAYAPGVAP 135 (189)
Q Consensus 103 d~~~al~~--Lt~LkGVGPATASaiLa~~~P~~~p 135 (189)
|+....+. +|+|+|||++||+.|--..+-..++
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 9999999999999998776544444
No 51
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=72.42 E-value=2.7 Score=26.40 Aligned_cols=15 Identities=47% Similarity=0.729 Sum_probs=13.3
Q ss_pred cccCcChHHHHHHHH
Q 029726 113 VLKGVGPATASAVLA 127 (189)
Q Consensus 113 ~LkGVGPATASaiLa 127 (189)
.++||||-||--+|.
T Consensus 20 Gv~giG~ktA~~ll~ 34 (36)
T smart00279 20 GVKGIGPKTALKLLR 34 (36)
T ss_pred CCCcccHHHHHHHHH
Confidence 589999999998875
No 52
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.39 E-value=2.4 Score=35.88 Aligned_cols=30 Identities=27% Similarity=0.383 Sum_probs=25.9
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
+-+.-+..|.+..||||=||-+||+...|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 96 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLSSGTPD 96 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 345678899999999999999999987774
No 53
>PRK07945 hypothetical protein; Provisional
Probab=69.86 E-value=8.8 Score=34.65 Aligned_cols=19 Identities=47% Similarity=0.733 Sum_probs=15.0
Q ss_pred HhhcccCcChHHHHHHHHh
Q 029726 110 ELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 110 ~Lt~LkGVGPATASaiLa~ 128 (189)
.|++|+|||..||..|--.
T Consensus 50 ~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred CcccCCCcCHHHHHHHHHH
Confidence 5778888888888877655
No 54
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.78 E-value=6.1 Score=33.38 Aligned_cols=99 Identities=18% Similarity=0.126 Sum_probs=56.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcC-
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P- 131 (189)
++.|.+|..-.-.-.--.| -=| +-+.+++..+++.+.+++... =.+.|++++|||+-||.-|..=.-.
T Consensus 61 GF~~~~Er~lF~~L~~V~G-IGpK~AL~iLs~~~~~~l~~aI~~~---------D~~~L~kvpGIGkKtAerIilELkdK 130 (197)
T PRK14603 61 GFPDEDSLELFELLLGVSG-VGPKLALALLSALPPALLARALLEG---------DARLLTSASGVGKKLAERIALELKGK 130 (197)
T ss_pred CcCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 4788888554443332223 233 345566666776666555431 2467999999999999977632100
Q ss_pred --------------CC-CCcccHHHHHHhhCCCCCCCHHHHHHHHHHH
Q 029726 132 --------------GV-APFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (189)
Q Consensus 132 --------------~~-~pFfsDEa~~~~~g~~~kYt~keY~~~~~~~ 164 (189)
.. ..--.+|+..++. ...|+-++=...+..+
T Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~ea~~AL~--~LGy~~~ea~~al~~i 176 (197)
T PRK14603 131 VPEHLLAGPAGGGGTKVSSTAAEDAVLALL--ALGFREAQVRSVVAEL 176 (197)
T ss_pred hhhhcccccccccccccCCccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 00 0011366776664 3567777665555544
No 55
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=69.43 E-value=3.3 Score=37.70 Aligned_cols=32 Identities=28% Similarity=0.389 Sum_probs=25.5
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHh--hcCCCCC
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAA--YAPGVAP 135 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~--~~P~~~p 135 (189)
.+.|-++||.|+||||-.|-+|+-. .-++.+|
T Consensus 213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP 246 (323)
T KOG2875|consen 213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVP 246 (323)
T ss_pred HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc
Confidence 4669999999999999999987644 4555666
No 56
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=68.15 E-value=3.9 Score=34.98 Aligned_cols=30 Identities=27% Similarity=0.458 Sum_probs=26.0
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhhcCC
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~ 132 (189)
+-+.-+..|.+.-||||-||=+|||..+|+
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~ 96 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPE 96 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHH
Confidence 456678899999999999999999998875
No 57
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=67.87 E-value=5.5 Score=32.57 Aligned_cols=57 Identities=23% Similarity=0.358 Sum_probs=37.2
Q ss_pred ccHHHHHHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHh---hCCCCCCCHHHHH
Q 029726 102 PDLTKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSLRQYL 158 (189)
Q Consensus 102 ~d~~~al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~---~g~~~kYt~keY~ 158 (189)
|+-+.-.-+|+.+.|||+.+|-.|+... +|. .+--.+++-...+ ...+-+|.+++|.
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 3334445568999999999999999884 554 4556777766543 2334455555444
No 58
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.74 E-value=7.1 Score=33.10 Aligned_cols=63 Identities=16% Similarity=0.206 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHH
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiL 126 (189)
++.|.+|..-...-.--.| -=| +-+.+++..+++.+.++... .=.+.|++++|||+-||--|+
T Consensus 63 GF~~~~Er~lF~~Li~V~G-IGpK~Al~iLs~~~~~~l~~aI~~---------~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 63 GFATWDERQTFIVLISISK-VGAKTALAILSQFRPDDLRRLVAE---------EDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred CCCCHHHHHHHHHHhCCCC-cCHHHHHHHHhhCCHHHHHHHHHh---------CCHHHHhcCCCcCHHHHHHHH
Confidence 5788888655544433333 223 33555666666665554443 235689999999999999876
No 59
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=67.08 E-value=4.1 Score=28.09 Aligned_cols=41 Identities=32% Similarity=0.488 Sum_probs=26.2
Q ss_pred HHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (189)
Q Consensus 106 ~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (189)
+..+.|..|+|||+.+|-.|+..-.- .-||-|=|=+..+.|
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 45788999999999999999998532 236666555554444
No 60
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=64.97 E-value=3.3 Score=34.13 Aligned_cols=54 Identities=19% Similarity=0.208 Sum_probs=35.7
Q ss_pred CccHHHHHHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHh---hCCCCCCCH
Q 029726 101 LPDLTKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSL 154 (189)
Q Consensus 101 l~d~~~al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~---~g~~~kYt~ 154 (189)
+|+-+...-+|+.++|||+.+|-.|+... +|. .+--.+|+=...+ ...+.+|.+
T Consensus 22 l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~i 81 (154)
T PTZ00134 22 VDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKI 81 (154)
T ss_pred CCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCC
Confidence 44445556678999999999999999984 554 4445666655433 334445543
No 61
>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=64.86 E-value=7.4 Score=32.65 Aligned_cols=98 Identities=21% Similarity=0.197 Sum_probs=53.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcC-
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P- 131 (189)
++.|++|..-...-.--.|- =| +-+.+++.-+++.+.++...- =.+.|++++|||+-||.-|+--...
T Consensus 61 GF~~~~Er~lF~~L~~V~GI-GpK~Al~iL~~~~~~el~~aI~~~---------d~~~L~~ipGiGkKtAerIileLk~k 130 (191)
T TIGR00084 61 GFNTLEERELFKELIKVNGV-GPKLALAILSNMSPEEFVYAIETE---------EVKALVKIPGVGKKTAERLLLELKGK 130 (191)
T ss_pred CCCCHHHHHHHHHHhCCCCC-CHHHHHHHHhcCCHHHHHHHHHhC---------CHHHHHhCCCCCHHHHHHHHHHHHhh
Confidence 57889886655554333331 12 223334433443333333221 1246899999999999998732110
Q ss_pred --------C---CCCcccHHHHHHhhCCCCCCCHHHHHHHHHHH
Q 029726 132 --------G---VAPFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (189)
Q Consensus 132 --------~---~~pFfsDEa~~~~~g~~~kYt~keY~~~~~~~ 164 (189)
. ..+ ..+|+..++. ...|+-++=...+.++
T Consensus 131 ~~~~~~~~~~~~~~~-~~~e~~~aL~--~LGy~~~e~~~ai~~~ 171 (191)
T TIGR00084 131 LKGNKNLEMFTPTEA-ARDELFEALV--SLGYKPQEIQQALKKI 171 (191)
T ss_pred hcccccccccccccc-hHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 0 112 2366666665 3667777766555554
No 62
>PRK00076 recR recombination protein RecR; Reviewed
Probab=64.59 E-value=5.2 Score=34.15 Aligned_cols=23 Identities=30% Similarity=0.603 Sum_probs=19.2
Q ss_pred cHHHHHHHhhcccCcChHHHHHH
Q 029726 103 DLTKAVSELTVLKGVGPATASAV 125 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASai 125 (189)
.+..-++.|.+|+||||-||.=+
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rl 27 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRL 27 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHH
Confidence 35677899999999999999754
No 63
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=63.77 E-value=7.9 Score=30.58 Aligned_cols=39 Identities=26% Similarity=0.360 Sum_probs=29.6
Q ss_pred HHHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 029726 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (189)
..-.|+.+.|||+.||-.|+... +|. .+--.+|+-+..+
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 565 5566777766544
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=63.47 E-value=4.5 Score=24.58 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=11.4
Q ss_pred hhcccCcChHHHHHH
Q 029726 111 LTVLKGVGPATASAV 125 (189)
Q Consensus 111 Lt~LkGVGPATASai 125 (189)
+.++.|||+.|+--+
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 568999999998654
No 65
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=62.62 E-value=6.2 Score=35.22 Aligned_cols=25 Identities=28% Similarity=0.392 Sum_probs=20.2
Q ss_pred HHHHHHHhhcccCcChHHHHHHHHh
Q 029726 104 LTKAVSELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASaiLa~ 128 (189)
...+|..|++++||||.||-.+...
T Consensus 80 ~~~~l~~l~~i~GiGpk~a~~l~~l 104 (307)
T cd00141 80 VPPGLLLLLRVPGVGPKTARKLYEL 104 (307)
T ss_pred chHHHHHHHcCCCCCHHHHHHHHHc
Confidence 3557788889999999999888843
No 66
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=62.60 E-value=16 Score=30.42 Aligned_cols=24 Identities=29% Similarity=0.444 Sum_probs=20.2
Q ss_pred HHHhhcccCcChHHHHHHHHhhcC
Q 029726 108 VSELTVLKGVGPATASAVLAAYAP 131 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P 131 (189)
.+.|++++|||+.||-.|+.-...
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHH
Confidence 457899999999999999976543
No 67
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.26 E-value=6.1 Score=33.74 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=18.9
Q ss_pred HHHHHHHhhcccCcChHHHHHH
Q 029726 104 LTKAVSELTVLKGVGPATASAV 125 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASai 125 (189)
+..-++.|.+|+||||-||.=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5677899999999999999754
No 68
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=62.01 E-value=3.9 Score=39.00 Aligned_cols=22 Identities=36% Similarity=0.379 Sum_probs=18.3
Q ss_pred HHhhc-ccCcChHHHHHHHHhhc
Q 029726 109 SELTV-LKGVGPATASAVLAAYA 130 (189)
Q Consensus 109 ~~Lt~-LkGVGPATASaiLa~~~ 130 (189)
+.|.+ ++||||-||-||+|+.-
T Consensus 205 ~~l~kgvpGVG~YTAGAiaSIAf 227 (555)
T KOG2457|consen 205 SSLMKGVPGVGQYTAGAIASIAF 227 (555)
T ss_pred HHHHhhCCCCCccchhhhhhhhh
Confidence 44555 99999999999999854
No 69
>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=61.15 E-value=7.2 Score=31.67 Aligned_cols=37 Identities=27% Similarity=0.404 Sum_probs=27.8
Q ss_pred HHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHH
Q 029726 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGA 144 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~ 144 (189)
.-+|+.++|||+.+|-.|+... +|. .+--.+|+-...
T Consensus 20 ~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~ 59 (144)
T TIGR03629 20 EYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEK 59 (144)
T ss_pred EEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHH
Confidence 3468999999999999999884 454 555677775543
No 70
>PRK13844 recombination protein RecR; Provisional
Probab=60.51 E-value=6.8 Score=33.61 Aligned_cols=23 Identities=13% Similarity=0.365 Sum_probs=19.1
Q ss_pred cHHHHHHHhhcccCcChHHHHHH
Q 029726 103 DLTKAVSELTVLKGVGPATASAV 125 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASai 125 (189)
.+..-++.|++|+||||-||.=+
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rl 31 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRL 31 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHH
Confidence 35677899999999999999754
No 71
>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=58.87 E-value=9.8 Score=29.59 Aligned_cols=38 Identities=24% Similarity=0.352 Sum_probs=29.5
Q ss_pred HHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHhh
Q 029726 109 SELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAAL 146 (189)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~~ 146 (189)
-.|+.+.|||+.+|-.|+... +|. .+-.++|+-+..+.
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~ 55 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIR 55 (113)
T ss_pred eeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHH
Confidence 457999999999999999884 555 55678888776543
No 72
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=58.35 E-value=10 Score=29.85 Aligned_cols=65 Identities=26% Similarity=0.358 Sum_probs=39.2
Q ss_pred HHHhhcccCcChHHHHHHHHhh--cCC-CCCcccHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHhhh
Q 029726 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAALGH-SKDYSLRQYLLFADKLQAKAKFLKKI 174 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~~g~-~~kYt~keY~~~~~~~~~~~~~L~~~ 174 (189)
.-.|+.+.|||+.+|-.|+... +|. .+--.+|+-+..+... ...|.+.. .+-..+++-.++|-.-
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i~~~~~i~~--dL~~~~~~dI~rl~~I 84 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDKNYKVEG--DLRREVSMNIKRLMDI 84 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHHHhhccchH--HHHHHHHHHHHHHHHh
Confidence 3467999999999999999984 555 4566777766644320 01143332 3334445555555443
No 73
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=57.96 E-value=13 Score=31.06 Aligned_cols=52 Identities=17% Similarity=0.337 Sum_probs=46.3
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~ 104 (189)
..+||+..||.+|-.. +..|..|...-+.+.+|....|.++.++-|...|++
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 4579999999998776 578999999999999999999999999999988853
No 74
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=57.60 E-value=9.4 Score=34.52 Aligned_cols=66 Identities=17% Similarity=0.142 Sum_probs=40.5
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHHhhcCCC------CC--cccHHHHHHhhC------CCCCCCHHHHHHHHHHHHHHH
Q 029726 103 DLTKAVSELTVLKGVGPATASAVLAAYAPGV------AP--FMSDEAMGAALG------HSKDYSLRQYLLFADKLQAKA 168 (189)
Q Consensus 103 d~~~al~~Lt~LkGVGPATASaiLa~~~P~~------~p--FfsDEa~~~~~g------~~~kYt~keY~~~~~~~~~~~ 168 (189)
.+..+|..|.+++||||.||-.+-..+ -.+ .+ .++.+- ..| -..+....|-..+.+.+.+..
T Consensus 83 ~~p~~l~~l~~i~GiGpk~a~~l~~lG-i~tl~eL~~a~~~~l~~~q---~~gl~~~~~~~~ri~r~e~~~i~~~i~~~l 158 (334)
T smart00483 83 EVYKSLKLFTNVFGVGPKTAAKWYRKG-IRTLEELKKNKELKLTKQQ---KAGLKYYEDILKKVSRAEAFAVEYIVKRAV 158 (334)
T ss_pred cHHHHHHHHHccCCcCHHHHHHHHHhC-CCCHHHHHhcccccCCHHH---HHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence 456799999999999999998887742 111 00 233322 112 123556666666666666666
Q ss_pred HHHh
Q 029726 169 KFLK 172 (189)
Q Consensus 169 ~~L~ 172 (189)
+.+.
T Consensus 159 ~~~~ 162 (334)
T smart00483 159 RKIL 162 (334)
T ss_pred HhhC
Confidence 6553
No 75
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=56.23 E-value=7.6 Score=27.68 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=16.1
Q ss_pred hhcccCcChHHHHHHHHhh
Q 029726 111 LTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 111 Lt~LkGVGPATASaiLa~~ 129 (189)
+..++||||-||.-||.-+
T Consensus 24 i~gv~giG~k~A~~ll~~~ 42 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEY 42 (75)
T ss_pred CCCCCcccHHHHHHHHHHh
Confidence 3458999999999999874
No 76
>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=56.10 E-value=8.9 Score=34.22 Aligned_cols=15 Identities=33% Similarity=0.483 Sum_probs=7.2
Q ss_pred HHhhcccCcChHHHH
Q 029726 109 SELTVLKGVGPATAS 123 (189)
Q Consensus 109 ~~Lt~LkGVGPATAS 123 (189)
..+++|+|||+++|+
T Consensus 45 ~~~~~ipgiG~~ia~ 59 (307)
T cd00141 45 EEAKKLPGIGKKIAE 59 (307)
T ss_pred HHhcCCCCccHHHHH
Confidence 344455555555443
No 77
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=53.09 E-value=9.6 Score=34.45 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=25.7
Q ss_pred HhhCccHHHHHHHhhcccCcChHHHHHHHHhhcCCC
Q 029726 98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGV 133 (189)
Q Consensus 98 f~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P~~ 133 (189)
++.+|..-..+..|++|+|||+++|+-|--+..-..
T Consensus 37 i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~ 72 (334)
T smart00483 37 LKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGK 72 (334)
T ss_pred HHhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCc
Confidence 345553333456789999999999999987765443
No 78
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.70 E-value=35 Score=27.87 Aligned_cols=94 Identities=21% Similarity=0.212 Sum_probs=55.9
Q ss_pred hHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhc---ccCcChHHHHHHHHhhcCCC----------CCcccHHHHHH--
Q 029726 80 DFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTV---LKGVGPATASAVLAAYAPGV----------APFMSDEAMGA-- 144 (189)
Q Consensus 80 ~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~---LkGVGPATASaiLa~~~P~~----------~pFfsDEa~~~-- 144 (189)
.|---=++..|.++|+-|.+.+|-+. .+.++.. =+.+|||.|+|+.++.-|-. .| ..-....|
T Consensus 28 rL~pvFpEnRVikaTrfairfMP~vA-vftl~wQ~~~~~ql~pAv~tAlfal~lplqGl~wlGkraiTp-l~p~la~Wfy 105 (149)
T COG3092 28 RLAPVFPENRVIKATRFAIRFMPPVA-VFTLCWQIALGGQLGPAVATALFALSLPLQGLWWLGKRAITP-LPPQLAVWFY 105 (149)
T ss_pred hhcccCchhHHHHHHHHHHHhccHHH-HHHHHHHHHHhcccchHHHHHHHHHhccccchhhcccccCCC-CChHHHHHHH
Confidence 34444568899999999999888542 3333222 23799999999999854421 11 11111111
Q ss_pred -hh------CC--CCCCCHHHHHHHHHHHHHHHHHHhhhc
Q 029726 145 -AL------GH--SKDYSLRQYLLFADKLQAKAKFLKKIA 175 (189)
Q Consensus 145 -~~------g~--~~kYt~keY~~~~~~~~~~~~~L~~~~ 175 (189)
++ |. +.-=.-..|..+.+-+.+--++|.+..
T Consensus 106 ev~~kl~e~g~al~pv~~kP~Yq~LAdvLkrAf~qLdktf 145 (149)
T COG3092 106 EVREKLKEAGQALAPVEEKPTYQALADVLKRAFKQLDKTF 145 (149)
T ss_pred HHHHHHHHhCCCCCcCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 22 21 111234568888888877777776643
No 79
>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=51.39 E-value=11 Score=30.46 Aligned_cols=52 Identities=21% Similarity=0.257 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~ 104 (189)
..+|++..||..|-.+- ..|.-|....+.++.|.+.-|.++.++-|...|++
T Consensus 10 egRyls~~EL~~l~~~~-~~~~~Rl~aa~~L~~~a~~IV~~A~~~l~~~~P~l 61 (157)
T PF00502_consen 10 EGRYLSDGELQALKGYF-QSANARLEAAEKLRDNASEIVDQAAQKLFEKYPDL 61 (157)
T ss_dssp TTSECEHHHHHHHHHHH-HTHHHHHHHHHHHHHTHHHHHHHHHHHHHHHSGGG
T ss_pred cCCCCCHHHHHHHHHHH-HhHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcccc
Confidence 35799999999998875 45777999999999999999999999999888853
No 80
>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=50.96 E-value=47 Score=22.70 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=17.3
Q ss_pred HHHHhhcccCcChHHHHHHHHh
Q 029726 107 AVSELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa~ 128 (189)
.++.|.+++|||..||--|+..
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhh
Confidence 4566778899999999888754
No 81
>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=50.14 E-value=34 Score=29.10 Aligned_cols=39 Identities=23% Similarity=0.266 Sum_probs=31.1
Q ss_pred ccHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHhhhc
Q 029726 137 MSDEAMGAALG--HSKDYSLRQYLLFADKLQAKAKFLKKIA 175 (189)
Q Consensus 137 fsDEa~~~~~g--~~~kYt~keY~~~~~~~~~~~~~L~~~~ 175 (189)
+..|.+.|+.+ .+.+||..||..+...-+++.++|.++.
T Consensus 148 iG~~~ve~Le~~~~~~k~~~~el~~i~~~y~~~~k~L~k~~ 188 (189)
T PF05766_consen 148 IGQERVEWLEGPHEPRKWTIEELKAIIAIYRAKLKELKKEA 188 (189)
T ss_pred HhHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 34455556655 5689999999999999999999998754
No 82
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.31 E-value=13 Score=31.20 Aligned_cols=63 Identities=25% Similarity=0.287 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHH
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiL 126 (189)
++.|++|-.-.-.-.--.|- =| +-+..++.-+++.+.++... .=.+.|++++|||+-||--|.
T Consensus 62 GF~~~~Er~lF~~Li~V~GI-GpK~Al~ILs~~~~~~l~~aI~~---------~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 62 GFATTEELSLFETLIDVSGI-GPKLGLAMLSAMNAEALASAIIS---------GNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred CCCCHHHHHHHHHHhCCCCC-CHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHH
Confidence 57888885544443323332 22 33455555555554333322 124679999999999999843
No 83
>PRK14976 5'-3' exonuclease; Provisional
Probab=47.72 E-value=11 Score=33.36 Aligned_cols=17 Identities=47% Similarity=0.874 Sum_probs=14.9
Q ss_pred ccCcChHHHHHHHHhhc
Q 029726 114 LKGVGPATASAVLAAYA 130 (189)
Q Consensus 114 LkGVGPATASaiLa~~~ 130 (189)
++||||-||.-+|.-+.
T Consensus 196 VpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 196 VKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCcccHHHHHHHHHHcC
Confidence 79999999999998653
No 84
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=47.19 E-value=14 Score=32.45 Aligned_cols=43 Identities=33% Similarity=0.443 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhhCccHHHH-HHHhhcccCcChHHHHHHHHhh
Q 029726 87 DSSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 87 ~~~V~~~t~~Af~~l~d~~~a-l~~Lt~LkGVGPATASaiLa~~ 129 (189)
+..++..-..+|..+.++..| .+.|.+++|||+++|--|....
T Consensus 13 ~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 13 PSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred HHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 344555555557666677665 8999999999999999999874
No 85
>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=46.27 E-value=45 Score=25.82 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=16.8
Q ss_pred HHHHhhcccCcChHHHHHHHH
Q 029726 107 AVSELTVLKGVGPATASAVLA 127 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa 127 (189)
.++.|.+++||||.|+--|.-
T Consensus 96 s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 96 SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHHcCCCCCHHHHHHHHh
Confidence 467778899999999877653
No 86
>PRK09482 flap endonuclease-like protein; Provisional
Probab=43.83 E-value=14 Score=32.52 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=15.8
Q ss_pred cccCcChHHHHHHHHhhc
Q 029726 113 VLKGVGPATASAVLAAYA 130 (189)
Q Consensus 113 ~LkGVGPATASaiLa~~~ 130 (189)
-.+||||-||.-+|.-+.
T Consensus 186 GVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCcChHHHHHHHHHhC
Confidence 389999999999999864
No 87
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=42.85 E-value=29 Score=29.30 Aligned_cols=52 Identities=17% Similarity=0.193 Sum_probs=46.0
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~ 104 (189)
..+||+.+||.+|-. -+..|..|-..-+.+.+|...-|.++.++-|...|++
T Consensus 15 qgRYLs~~eL~~L~~-~~~~g~~RL~aa~~L~~NA~~IV~~A~~~l~~~~P~l 66 (177)
T CHL00172 15 KAAYVGGSDLQALKK-FISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPGL 66 (177)
T ss_pred ccCCCCHHHHHHHHH-HHHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCCC
Confidence 457999999999855 4688999999999999999999999999999988853
No 88
>PRK08609 hypothetical protein; Provisional
Probab=42.48 E-value=27 Score=33.89 Aligned_cols=21 Identities=19% Similarity=0.295 Sum_probs=14.7
Q ss_pred HHHHhhcccCcChHHHHHHHH
Q 029726 107 AVSELTVLKGVGPATASAVLA 127 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa 127 (189)
++..|++++||||.||-.+--
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~ 106 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYK 106 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHH
Confidence 566677777777777766663
No 89
>CHL00090 apcD allophycocyanin gamma subunit
Probab=42.27 E-value=33 Score=28.28 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (189)
..+|++..||..|-.. +..|.-|-..-..+++|.+.-|.++.++-|...|+
T Consensus 14 ~gRyls~~EL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~ 64 (161)
T CHL00090 14 ELRYPTIGELESIQDY-LKTGEKRIRIATILRDNEKEIIQKASKQLFQIHPE 64 (161)
T ss_pred ccCCCCHHHHHHHHHH-HHhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHCcC
Confidence 3589999999999776 57788899999999999999999999999988874
No 90
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=42.11 E-value=43 Score=27.85 Aligned_cols=52 Identities=12% Similarity=0.155 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~ 104 (189)
..+|++..||.+|.. -+.+|..|-..-+.+.+|...-|.++.++-|...|++
T Consensus 15 qgRyls~~eL~~l~~-~~~~g~~RL~aa~~Lt~nA~~IV~~Aa~~lf~~~P~l 66 (162)
T CHL00170 15 QGRFLSNGELQACNG-RFQRAAASLEAARSLTSNAQRLIDGAAQAVYTKFPYT 66 (162)
T ss_pred ccCCCCHHHHHHHHH-HHhccHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcCc
Confidence 357999999999866 4678999999999999999999999999999988853
No 91
>CHL00086 apcA allophycocyanin alpha subunit
Probab=41.23 E-value=36 Score=28.04 Aligned_cols=51 Identities=20% Similarity=0.401 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (189)
..+|++..||..|-.. +..|..|-..-+.+.+|.+.-|.++.++-|...|+
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 57788899999999999999999999999988885
No 92
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=40.10 E-value=34 Score=28.38 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=45.0
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (189)
..+||+..||..|-. -+.+|.-|...-+.+.+|....|.++.+.-|+..|+
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 457999999999754 457899999999999999999999999999998885
No 93
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=39.79 E-value=29 Score=32.26 Aligned_cols=22 Identities=23% Similarity=0.514 Sum_probs=16.7
Q ss_pred HHHHhhcccCcChHHHHHHHHh
Q 029726 107 AVSELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa~ 128 (189)
..+.|++.+|||++.|-.|-..
T Consensus 317 s~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 317 SIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred CHHHHhhCCCcCHHHHHHHHHH
Confidence 4677888888888888876554
No 94
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=39.68 E-value=48 Score=27.49 Aligned_cols=52 Identities=12% Similarity=0.206 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~ 104 (189)
..+|++..||.+|.. -+..|..|-..-+.+.+|...-|.++.++-|+..|++
T Consensus 14 qgRyls~~eL~~l~~-~~~~g~~RL~aa~~Lt~na~~IV~~Aa~~lf~~~P~~ 65 (161)
T TIGR01338 14 QGRFLSNGELQSIFG-RFQRATASLEAAKSLTSNAQRLISGAAQAVYSKFPYT 65 (161)
T ss_pred ccCCCCHHHHHHHHH-HHHchHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcCc
Confidence 357999999999865 4688999999999999999999999999999988853
No 95
>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=39.56 E-value=18 Score=30.97 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=14.9
Q ss_pred cccCcChHHHHHHHHhh
Q 029726 113 VLKGVGPATASAVLAAY 129 (189)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (189)
-++||||-||.-+|.-+
T Consensus 187 Gv~GiG~ktA~~Ll~~~ 203 (240)
T cd00008 187 GVPGIGEKTAAKLLKEY 203 (240)
T ss_pred CCCccCHHHHHHHHHHh
Confidence 38999999999999875
No 96
>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=39.21 E-value=5 Score=30.66 Aligned_cols=16 Identities=44% Similarity=0.910 Sum_probs=13.8
Q ss_pred ccCcChHHHHHHHHhh
Q 029726 114 LKGVGPATASAVLAAY 129 (189)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (189)
.+||||-||+-+|.-+
T Consensus 23 V~GIG~KtA~~LL~~y 38 (101)
T PF01367_consen 23 VPGIGPKTAAKLLQEY 38 (101)
T ss_dssp -TTSTCHCCCCCHHHH
T ss_pred CCCCCHHHHHHHHHHc
Confidence 7899999999999875
No 97
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=39.09 E-value=34 Score=28.54 Aligned_cols=52 Identities=19% Similarity=0.330 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCccH
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL 104 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~ 104 (189)
..+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|.++.++-|...|++
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 3689999999998776 577888888888999999999999999999988853
No 98
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=39.07 E-value=29 Score=26.97 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=22.1
Q ss_pred HHHHHhhcccCcChHHHHHHHHhhcC
Q 029726 106 KAVSELTVLKGVGPATASAVLAAYAP 131 (189)
Q Consensus 106 ~al~~Lt~LkGVGPATASaiLa~~~P 131 (189)
.++.-|+.++||||..|-++..++-.
T Consensus 50 ~~~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 50 VNQADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HhHHHhhhcCCCCHHHHHHHHHhCcC
Confidence 36777889999999999999999653
No 99
>smart00475 53EXOc 5'-3' exonuclease.
Probab=38.65 E-value=20 Score=31.44 Aligned_cols=18 Identities=28% Similarity=0.554 Sum_probs=15.3
Q ss_pred cccCcChHHHHHHHHhhc
Q 029726 113 VLKGVGPATASAVLAAYA 130 (189)
Q Consensus 113 ~LkGVGPATASaiLa~~~ 130 (189)
-++||||-||.-+|.=+.
T Consensus 190 GV~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 190 GVPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCCHHHHHHHHHHhC
Confidence 379999999999998753
No 100
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.55 E-value=22 Score=29.88 Aligned_cols=98 Identities=17% Similarity=0.210 Sum_probs=56.8
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-chhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhh---
Q 029726 54 PHINTTELSKLVRWKLTRGKWRP-RLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY--- 129 (189)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~--- 129 (189)
++.|++|..-.-.-.--.| -=| +-+.+++..+++.+.++..+ .| .+.| +++|||+-||.-|+.=.
T Consensus 62 GF~~~~Er~lF~~LisV~G-IGpK~Al~iLs~~~~~~l~~aI~~-----~D----~~~L-~vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 62 GFLNREEQDCLRMLVKVSG-VNYKTAMSILSKLTPEQLFSAIVN-----ED----KAAL-KVNGIGEKLINRIITELQYK 130 (186)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHccCCHHHHHHHHHc-----CC----Hhhe-ECCCCcHHHHHHHHHHHHHH
Confidence 4788888655444433333 223 34555666666666555443 12 3568 89999999999887321
Q ss_pred ----cCCC-C-CcccHHHHHHhhCCCCCCCHHHHHHHHHHH
Q 029726 130 ----APGV-A-PFMSDEAMGAALGHSKDYSLRQYLLFADKL 164 (189)
Q Consensus 130 ----~P~~-~-pFfsDEa~~~~~g~~~kYt~keY~~~~~~~ 164 (189)
.+.. . .--.+|+..++.+ ..|+.+|=...+.++
T Consensus 131 ~~~~~~~~~~~~~~~~e~~~aL~~--LGy~~~ea~~al~~v 169 (186)
T PRK14600 131 VSKLEINETNFIIINDDALAALIS--LGYEKTKAFNAIQKI 169 (186)
T ss_pred hhccccccccccccHHHHHHHHHH--cCCCHHHHHHHHHHh
Confidence 1111 0 0013677777763 678887766655555
No 101
>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=33.74 E-value=37 Score=21.38 Aligned_cols=42 Identities=21% Similarity=0.390 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHHh
Q 029726 87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 87 ~~~V~~~t~~Af~~l~d~~~-al~~Lt~LkGVGPATASaiLa~ 128 (189)
+..+......+|..+.++.. ..+.|+.++|++..+|..|...
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 34445555555655545433 4788999999999999888754
No 102
>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=32.83 E-value=1.2e+02 Score=21.87 Aligned_cols=32 Identities=28% Similarity=0.431 Sum_probs=23.3
Q ss_pred hhcccCcChHHHHHHHHhhcCCCCCcccHHHHHH
Q 029726 111 LTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA 144 (189)
Q Consensus 111 Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~ 144 (189)
|+.+||||..+|-.|+.... .-||-|=+-|..
T Consensus 29 l~~Ikglg~~~a~~I~~~R~--~g~f~s~~df~~ 60 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERE--NGPFKSLEDFIQ 60 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHH--CSS-SSHHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHh--cCCCCCHHHHHH
Confidence 67899999999999999976 448877555543
No 103
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=32.82 E-value=24 Score=28.66 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.2
Q ss_pred HHhhcccCcChHHHHHHHHh
Q 029726 109 SELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~ 128 (189)
+-|+.|.||||..++.|=..
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~ 86 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNEL 86 (133)
T ss_pred ccchhhcccCHHHHHHHHHc
Confidence 67999999999999987554
No 104
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=32.12 E-value=24 Score=31.07 Aligned_cols=20 Identities=45% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHhhcccCcChHHHHHHHHh
Q 029726 109 SELTVLKGVGPATASAVLAA 128 (189)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~ 128 (189)
+.|..|+||||.++-.||..
T Consensus 3 ~~L~~IpGIG~krakkLl~~ 22 (232)
T PRK12766 3 EELEDISGVGPSKAEALREA 22 (232)
T ss_pred cccccCCCcCHHHHHHHHHc
Confidence 46788999999999999998
No 105
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=32.11 E-value=21 Score=24.82 Aligned_cols=17 Identities=29% Similarity=0.342 Sum_probs=12.9
Q ss_pred cccCcChHHHHHHHHhh
Q 029726 113 VLKGVGPATASAVLAAY 129 (189)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (189)
.+=|+||||+++.-.+.
T Consensus 17 ~v~tigPA~~Al~~~~~ 33 (77)
T PF04854_consen 17 PVFTIGPATAALYYVVR 33 (77)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35589999998876663
No 106
>PRK08609 hypothetical protein; Provisional
Probab=31.74 E-value=29 Score=33.77 Aligned_cols=32 Identities=25% Similarity=0.357 Sum_probs=24.4
Q ss_pred HhhCccHHHHHHH--hhcccCcChHHHHHHHHhh
Q 029726 98 FKSLPDLTKAVSE--LTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 98 f~~l~d~~~al~~--Lt~LkGVGPATASaiLa~~ 129 (189)
+..+.++..|... +..|+|+|+-|+--||...
T Consensus 110 i~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i 143 (570)
T PRK08609 110 VVDKESLKEACENGKVQALAGFGKKTEEKILEAV 143 (570)
T ss_pred CCCHHHHHHHHHhCChhhccCcchhHHHHHHHHH
Confidence 3445677777763 6689999999999998764
No 107
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=31.05 E-value=36 Score=30.20 Aligned_cols=37 Identities=27% Similarity=0.392 Sum_probs=27.8
Q ss_pred HHHHHHHhhcccCcChHHHHHH--HHhhcCCCCCcccHHH
Q 029726 104 LTKAVSELTVLKGVGPATASAV--LAAYAPGVAPFMSDEA 141 (189)
Q Consensus 104 ~~~al~~Lt~LkGVGPATASai--La~~~P~~~pFfsDEa 141 (189)
-+.=++-||..||||+-|+=.+ -+++.|++.| -.|--
T Consensus 160 eEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp-~dDlg 198 (254)
T KOG1918|consen 160 EEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMP-ADDLG 198 (254)
T ss_pred HHHHHHHHHhccCccceeeeeeeeeccCCCcccC-chhhh
Confidence 4556888999999999999754 4668898877 34433
No 108
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=28.76 E-value=43 Score=21.94 Aligned_cols=31 Identities=29% Similarity=0.392 Sum_probs=22.9
Q ss_pred HHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHH
Q 029726 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~ 143 (189)
|+.+.++-||.++|.|-+|.=. +-+|++.-.
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~-----~~vs~~tr~ 32 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP-----PRVSEETRE 32 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC-----SSSTHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhCC-----CCCCHHHHH
Confidence 5567778899999999998743 456766554
No 109
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=26.50 E-value=3.2e+02 Score=23.83 Aligned_cols=69 Identities=20% Similarity=0.199 Sum_probs=48.3
Q ss_pred HHHHhh-cccCcChHHHHHHHHhhcCCCCCcccHHHHHHhh--C----CCCCCCHHHHHHHHHHHHHHHHHHhhhc
Q 029726 107 AVSELT-VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL--G----HSKDYSLRQYLLFADKLQAKAKFLKKIA 175 (189)
Q Consensus 107 al~~Lt-~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~--g----~~~kYt~keY~~~~~~~~~~~~~L~~~~ 175 (189)
|=+.|. ++||+|=--||=.|-=.-=+.+....--...|+. | .|...|.|-|+..-+.++..++.+|..-
T Consensus 118 aRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~g~s~ 193 (210)
T COG1059 118 ARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEVGISL 193 (210)
T ss_pred HHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHhCCCc
Confidence 556666 8999999999998864221222222222334554 3 3458899999999999999999998753
No 110
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=26.49 E-value=48 Score=28.37 Aligned_cols=20 Identities=30% Similarity=0.551 Sum_probs=17.0
Q ss_pred HHHhhcccCcChHHHHHHHH
Q 029726 108 VSELTVLKGVGPATASAVLA 127 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa 127 (189)
++.|++++|||+=||=-|+-
T Consensus 107 ~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 107 VKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred hHhhhcCCCCCHHHHHHHHH
Confidence 46799999999999987764
No 111
>COG5578 Predicted integral membrane protein [Function unknown]
Probab=26.41 E-value=34 Score=29.57 Aligned_cols=12 Identities=42% Similarity=0.509 Sum_probs=9.8
Q ss_pred ccCcChHHHHHH
Q 029726 114 LKGVGPATASAV 125 (189)
Q Consensus 114 LkGVGPATASai 125 (189)
.=|++||||++.
T Consensus 37 VfG~~PAT~Alf 48 (208)
T COG5578 37 VFGLMPATAALF 48 (208)
T ss_pred HHccchHHHHHH
Confidence 569999999754
No 112
>PRK03980 flap endonuclease-1; Provisional
Probab=25.94 E-value=39 Score=30.15 Aligned_cols=17 Identities=35% Similarity=0.593 Sum_probs=14.9
Q ss_pred cccCcChHHHHHHHHhh
Q 029726 113 VLKGVGPATASAVLAAY 129 (189)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (189)
.++||||-||.-|+.-+
T Consensus 193 GI~GIG~ktA~kLi~~~ 209 (292)
T PRK03980 193 GIKGIGPKTALKLIKKH 209 (292)
T ss_pred CCCCccHHHHHHHHHHC
Confidence 48999999999999764
No 113
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=25.93 E-value=92 Score=31.17 Aligned_cols=15 Identities=33% Similarity=0.609 Sum_probs=9.0
Q ss_pred ccCcChHHHHHHHHh
Q 029726 114 LKGVGPATASAVLAA 128 (189)
Q Consensus 114 LkGVGPATASaiLa~ 128 (189)
.+||||.||..|...
T Consensus 89 ~~GIG~~~A~~iv~~ 103 (720)
T TIGR01448 89 IKGVGKKLAQRIVKT 103 (720)
T ss_pred CCCcCHHHHHHHHHH
Confidence 666666666666544
No 114
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=25.53 E-value=73 Score=31.94 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=20.1
Q ss_pred HHHHhhcccCcChHHHHHHHHhh
Q 029726 107 AVSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 107 al~~Lt~LkGVGPATASaiLa~~ 129 (189)
+++.|.++.||||-+|..|.+.+
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHH
Confidence 45679999999999999998875
No 115
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=25.03 E-value=3.1e+02 Score=26.21 Aligned_cols=82 Identities=26% Similarity=0.361 Sum_probs=46.9
Q ss_pred hhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhh-cccCcChHHHH---------------------HHHHhhcCCCCC
Q 029726 78 LLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELT-VLKGVGPATAS---------------------AVLAAYAPGVAP 135 (189)
Q Consensus 78 L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~Lt-~LkGVGPATAS---------------------aiLa~~~P~~~p 135 (189)
+..+|.+|+.+.++-++..=|...-++..++-... .++||||-.=+ ++.+--.-..-|
T Consensus 82 ~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~~~p 161 (422)
T KOG2582|consen 82 LNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYASVLP 161 (422)
T ss_pred HHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccccCC
Confidence 45899999999888888777765555555554444 46666653221 111111122458
Q ss_pred cccHHHHHHhhCCCCCCCHHHHHHH
Q 029726 136 FMSDEAMGAALGHSKDYSLRQYLLF 160 (189)
Q Consensus 136 FfsDEa~~~~~g~~~kYt~keY~~~ 160 (189)
|++|.... +|+...-+..|.++.|
T Consensus 162 ~ld~dive-i~~~n~h~~~k~fL~Y 185 (422)
T KOG2582|consen 162 YLDDDIVE-ICKANPHLDPKYFLLY 185 (422)
T ss_pred ccchhHHH-HhccCCCCCHHHHHHH
Confidence 88887766 4554444444444443
No 116
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=24.67 E-value=45 Score=30.22 Aligned_cols=17 Identities=35% Similarity=0.581 Sum_probs=14.9
Q ss_pred cccCcChHHHHHHHHhh
Q 029726 113 VLKGVGPATASAVLAAY 129 (189)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (189)
.++||||-||--++.-+
T Consensus 240 Gv~GIG~ktA~kli~~~ 256 (338)
T TIGR03674 240 GVKGIGPKTALKLIKEH 256 (338)
T ss_pred CCCCccHHHHHHHHHHc
Confidence 59999999999999663
No 117
>PF11517 Nab2: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); InterPro: IPR021083 Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 []. The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA []. An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 [].; PDB: 3LCN_B 2V75_A 2JPS_A.
Probab=24.48 E-value=41 Score=26.25 Aligned_cols=46 Identities=17% Similarity=0.318 Sum_probs=29.6
Q ss_pred hhhHhhhCCHHHHHHHHHHHHhhCccHH---HHHHHhhcccCcChHHHH
Q 029726 78 LLDFVSSLDDSSVKSASEKAFKSLPDLT---KAVSELTVLKGVGPATAS 123 (189)
Q Consensus 78 L~~lv~sN~~~~V~~~t~~Af~~l~d~~---~al~~Lt~LkGVGPATAS 123 (189)
|-.|..+-+.+.+.++.+.||..+.-+. ..=.+..||+|+.++.++
T Consensus 54 LssLFD~vs~~~l~~VVQtaF~ale~Lq~Ge~~e~iv~Ki~~~~~~~~~ 102 (107)
T PF11517_consen 54 LSSLFDSVSTEALTDVVQTAFFALEALQQGETVENIVSKIRGMNAQPAG 102 (107)
T ss_dssp HHHH-TTS-HHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHTHT-
T ss_pred HHHHHhccCHHHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHccCCCCcc
Confidence 4456677788888888998987554222 223456789999887764
No 118
>PHA01976 helix-turn-helix protein
Probab=23.78 E-value=61 Score=21.50 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=16.1
Q ss_pred CCCCCHHHHHHHHH------HHhhCCCCCcc
Q 029726 53 NPHINTTELSKLVR------WKLTRGKWRPR 77 (189)
Q Consensus 53 ~~~ltkdEL~~Lve------WKL~rGkfRP~ 77 (189)
...||.+||-+.+. ++.-+|+..|+
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~ 43 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEADKRLPN 43 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Confidence 45788888877765 44455665553
No 119
>TIGR01337 apcB allophycocyanin, beta subunit. The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins. This model describes allophycocyanin beta subunit. Other, homologous phyobiliproteins include allophycocyanin alpha chain and the phycocyanin and phycoerythrin alpha and beta chains.
Probab=23.70 E-value=78 Score=26.20 Aligned_cols=51 Identities=18% Similarity=0.396 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (189)
..+|++..||..|-.- +..|.-|-..-..+++|.+.-|.++.++-|...|+
T Consensus 14 ~gRYls~~eL~~l~~~-~~~~~~Rl~aa~~l~~na~~Iv~~A~~~l~~~~P~ 64 (167)
T TIGR01337 14 TGKYLDDNAVTKLKGY-FQTGELRLRAAAIINANSATIIKEAAAQLFEEYPE 64 (167)
T ss_pred cCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcC
Confidence 4679999999998664 56889999999999999999999999999987774
No 120
>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=23.64 E-value=50 Score=29.13 Aligned_cols=44 Identities=20% Similarity=0.350 Sum_probs=27.2
Q ss_pred cccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC----CCCCCCHHHHHHHHH
Q 029726 113 VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG----HSKDYSLRQYLLFAD 162 (189)
Q Consensus 113 ~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g----~~~kYt~keY~~~~~ 162 (189)
.++||||-||--++.-+..- +..+..+.. .+..+..+++.+++.
T Consensus 227 gv~giG~k~A~~li~~~~~~------~~~~~~l~~~~~~~~~~~~~~~~~~~f~ 274 (316)
T cd00128 227 GIPGIGPVTALKLIKKYGDI------EKDIERLKKKLYRSPEDFPLKEAREFFL 274 (316)
T ss_pred CCCCccHHHHHHHHHHcCCh------HHHHHHHHHhCccCCCcCChHHHHHHHc
Confidence 49999999999999986531 223333321 123555666666554
No 121
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=22.93 E-value=89 Score=26.05 Aligned_cols=51 Identities=14% Similarity=0.339 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029726 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (189)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (189)
..+|++..||..|-. -+..|..|-..-+.+++|.+.-|.++.++-|...|+
T Consensus 15 ~gRYls~~eL~~l~~-~~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~ 65 (169)
T CHL00089 15 TGKYLDKNAITQLNS-YFSSASDRIKIVEIINAQASNIIKEASAQLFEEQPE 65 (169)
T ss_pred cCCCCCHHHHHHHHH-HHHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcC
Confidence 468999999999865 467899999999999999999999999999988874
No 122
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=22.40 E-value=98 Score=21.63 Aligned_cols=49 Identities=20% Similarity=0.162 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHHhhcCCCCCcc
Q 029726 89 SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFM 137 (189)
Q Consensus 89 ~V~~~t~~Af~~l~d~~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFf 137 (189)
.|+..+.+-+...-+-+..++.|.+..||-|.--|+|.--.--++.-||
T Consensus 3 ~Vq~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF 51 (57)
T TIGR01589 3 LVQNRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFF 51 (57)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHH
Confidence 4666667777766788889999999999999999988776555554555
No 123
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=22.16 E-value=90 Score=30.71 Aligned_cols=22 Identities=32% Similarity=0.613 Sum_probs=19.4
Q ss_pred HHHhhcccCcChHHHHHHHHhh
Q 029726 108 VSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~ 129 (189)
...|+.++||||.++-.||..+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F 563 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF 563 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc
Confidence 4678899999999999999875
No 124
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=21.87 E-value=1.3e+02 Score=29.94 Aligned_cols=21 Identities=38% Similarity=0.591 Sum_probs=18.5
Q ss_pred HHhhcccCcChHHHHHHHHhh
Q 029726 109 SELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~ 129 (189)
..|..++||||.++=++|.-+
T Consensus 552 S~L~~IpGIG~kr~~~LL~~F 572 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHF 572 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHc
Confidence 567799999999999999874
No 125
>PF08008 Viral_cys_rich: Viral cysteine rich; InterPro: IPR012641 Members of this family are polydna viral proteins that contain a cysteine rich motif []. Some members of this family have multiple copies of this domain.; PDB: 1XJ1_A 1XI7_A.
Probab=21.57 E-value=31 Score=25.87 Aligned_cols=29 Identities=31% Similarity=0.449 Sum_probs=0.0
Q ss_pred HHHhHHHHHhcCCCchhhhhhHHHhhhch
Q 029726 17 LASYEARVESLNKPNLISLDDYYRKELPS 45 (189)
Q Consensus 17 l~~Y~~~v~~~~~~~L~~LD~w~~~~lp~ 45 (189)
+..|-++|+.++...+.+|-.+|...|+.
T Consensus 55 ~~~y~~Li~~lN~tNf~eL~~~Y~~~l~~ 83 (85)
T PF08008_consen 55 LELYLELIKQLNETNFEELRRQYWKDLQR 83 (85)
T ss_dssp -----------------------------
T ss_pred ccccccccccccccccccccccccccccc
Confidence 67899999999999999999999877653
No 126
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=21.35 E-value=2.9e+02 Score=26.04 Aligned_cols=137 Identities=20% Similarity=0.273 Sum_probs=70.7
Q ss_pred chhhhhhHHHhhhchhhhccCC-CCCCCHHHHHHHHHHHhhCCCCCcchhhHhhhCCHHHHHHHHH--------HHHhhC
Q 029726 31 NLISLDDYYRKELPSLIHQRNP-NPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASE--------KAFKSL 101 (189)
Q Consensus 31 ~L~~LD~w~~~~lp~~~~~r~~-~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~--------~Af~~l 101 (189)
+++.==.|..+.++..+..+.. ...++.+++++|+.=- ++ .+|-....+++.+++...+.... .+|..-
T Consensus 166 k~ARRYHW~~~~~~~~v~~h~gis~~~~~~~vlnl~~~~-s~-~~r~~~ldl~reg~~rv~r~~~~~~a~l~g~~~l~~p 243 (373)
T COG1415 166 KMARRYHWLSEDLDEFVEPHSGISGEIRTSEVLNLVDKE-SR-DNRKLILDLVREGPSRVLRELEEAQAMLKGAATLDMP 243 (373)
T ss_pred hhhheeeecccCCcccccCcccccccccccceeeccchh-hh-hhHHHHHHHHHhCcHHHHHHHHHHHHhccCccccccc
Confidence 4555455666655555544321 1236667776666521 11 46667888888888633332211 112211
Q ss_pred -------c---cH------HHH-----------HHHhhcccCcChHHHHHHHHhh---cCCCCCcccHHHHHHh-hC---
Q 029726 102 -------P---DL------TKA-----------VSELTVLKGVGPATASAVLAAY---APGVAPFMSDEAMGAA-LG--- 147 (189)
Q Consensus 102 -------~---d~------~~a-----------l~~Lt~LkGVGPATASaiLa~~---~P~~~pFfsDEa~~~~-~g--- 147 (189)
| ++ ..+ .+.|--.+||||-|.=|+-=+. .- ..|=|.|-+=.+. .|
T Consensus 244 ~~~~~~~~~~~~l~~~~i~~~~l~~~ye~~p~Df~elLl~~GiGpstvRALalVAEvIyg-~~~s~rDP~~yafA~GGKD 322 (373)
T COG1415 244 MDRGAFYPRYLDLRPKRLNWRRLRRLYELNPDDFEELLLVPGIGPSTVRALALVAEVIYG-EPPSFRDPVKYAFAVGGKD 322 (373)
T ss_pred cccccccccccccccccCcHHHHHhhhhcCcccHHHHHhccCCCHHHHHHHHHHHHHHhC-CCCCcCCchhhhhhhcCCC
Confidence 0 10 112 2344447999999987654331 21 2366778765433 34
Q ss_pred -CCCCCCHHHHHHHHHHHHHHHHH
Q 029726 148 -HSKDYSLRQYLLFADKLQAKAKF 170 (189)
Q Consensus 148 -~~~kYt~keY~~~~~~~~~~~~~ 170 (189)
-|---+.+.|-+++..+++..++
T Consensus 323 gvP~pV~~~~yde~I~~l~~~ve~ 346 (373)
T COG1415 323 GVPFPVNRKTYDELIEFLEELVEK 346 (373)
T ss_pred CCCCCcchhhHHHHHHHHHHHHHh
Confidence 23334556666666666555553
No 127
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=21.11 E-value=1.4e+02 Score=29.28 Aligned_cols=21 Identities=29% Similarity=0.455 Sum_probs=18.2
Q ss_pred HHhhcccCcChHHHHHHHHhh
Q 029726 109 SELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 109 ~~Lt~LkGVGPATASaiLa~~ 129 (189)
..|-+++||||.+.-++|.-+
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~F 561 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYF 561 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHc
Confidence 567799999999999999764
No 128
>TIGR03292 PhnH_redo phosphonate C-P lyase system protein PhnH. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on Pfam model pfam05845.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context.
Probab=21.07 E-value=1.2e+02 Score=25.44 Aligned_cols=31 Identities=19% Similarity=0.163 Sum_probs=22.8
Q ss_pred ccCcChHHHHHHHHhhcCCCCCcc----cHHHHHHh
Q 029726 114 LKGVGPATASAVLAAYAPGVAPFM----SDEAMGAA 145 (189)
Q Consensus 114 LkGVGPATASaiLa~~~P~~~pFf----sDEa~~~~ 145 (189)
-.|.+||+++.+|++.|.+. |++ ++.+-.|+
T Consensus 26 ~~~l~~a~~avlLTL~D~et-~lwL~~~~~~v~~~l 60 (174)
T TIGR03292 26 PLPLSPATAAVLLTLLDHET-PVWLAADDAALRAWL 60 (174)
T ss_pred CCCCCHHHHHHHHHHcCCCC-ceeecCCCHHHHHHH
Confidence 35889999999999999876 553 33344555
No 129
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=21.06 E-value=1.8e+02 Score=24.73 Aligned_cols=34 Identities=24% Similarity=0.394 Sum_probs=25.5
Q ss_pred HHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhh
Q 029726 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL 146 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~ 146 (189)
|+-+.++-||..+|.|-+|. .-+..|+|.-.-+.
T Consensus 4 i~dIA~~agVS~~TVSrvLn-----~~~~vs~~tr~~V~ 37 (341)
T PRK10703 4 IKDVAKRAGVSTTTVSHVIN-----KTRFVAEETRNAVW 37 (341)
T ss_pred HHHHHHHhCCCHHHHHHHHc-----CCCCCCHHHHHHHH
Confidence 55667777999999999995 12678999765443
No 130
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=20.30 E-value=1.2e+02 Score=30.13 Aligned_cols=22 Identities=36% Similarity=0.604 Sum_probs=19.6
Q ss_pred HHHhhcccCcChHHHHHHHHhh
Q 029726 108 VSELTVLKGVGPATASAVLAAY 129 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~ 129 (189)
-..|..++||||.||-+||.-+
T Consensus 568 ~s~L~~I~GIG~k~a~~Ll~~F 589 (621)
T PRK14671 568 QTELTDIAGIGEKTAEKLLEHF 589 (621)
T ss_pred hhhhhcCCCcCHHHHHHHHHHc
Confidence 4677899999999999999986
No 131
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=20.28 E-value=97 Score=30.45 Aligned_cols=40 Identities=25% Similarity=0.289 Sum_probs=27.6
Q ss_pred HHHhhcccCcChHHHHHHHHhh-cCCCCCcccHHHHHHhhC
Q 029726 108 VSELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMGAALG 147 (189)
Q Consensus 108 l~~Lt~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~~~~g 147 (189)
--.|+.++||||.++-.||.-+ +++.+---|.|-...++|
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpG 564 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPG 564 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCC
Confidence 3678899999999999999964 444433334455555555
No 132
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=20.22 E-value=81 Score=30.92 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=32.2
Q ss_pred HHHHHHhhcccCcChHHHHHHHHhhcCCCCCcccHHHHHHhhC
Q 029726 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (189)
Q Consensus 105 ~~al~~Lt~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (189)
+++.+.|..|+|||-.|+.-|++- -||.|-|.|.-..+
T Consensus 512 ~~s~~vl~~ipgig~~~~~~I~~~-----Rp~~s~e~~l~~v~ 549 (560)
T COG1031 512 SASKDVLRAIPGIGKKTLRKILAE-----RPFKSSEEFLKLVP 549 (560)
T ss_pred cccHHHHHhcccchhhhHHHHHhc-----CCccchHHHHhccC
Confidence 345889999999999999999875 39999999986665
Done!