Query 029905
Match_columns 185
No_of_seqs 113 out of 144
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 05:30:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029905.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029905hhsearch_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 3.5E-05 7.5E-10 47.0 2.6 24 105-128 7-30 (30)
2 PRK01229 N-glycosylase/DNA lya 97.0 0.0048 1E-07 52.6 8.8 72 103-176 112-192 (208)
3 cd00056 ENDO3c endonuclease II 96.5 0.019 4.1E-07 45.1 8.2 57 105-163 79-140 (158)
4 COG0177 Nth Predicted EndoIII- 96.3 0.0046 9.9E-08 53.0 4.1 71 57-130 42-130 (211)
5 TIGR01084 mutY A/G-specific ad 95.9 0.033 7.1E-07 49.1 7.7 38 104-142 100-137 (275)
6 COG0122 AlkA 3-methyladenine D 95.7 0.035 7.7E-07 49.2 7.0 72 55-135 144-226 (285)
7 PRK10702 endonuclease III; Pro 95.4 0.022 4.8E-07 48.3 4.3 38 104-142 104-141 (211)
8 smart00478 ENDO3c endonuclease 95.3 0.13 2.8E-06 40.1 8.0 39 103-142 66-104 (149)
9 PF02371 Transposase_20: Trans 95.1 0.018 3.9E-07 41.9 2.6 37 109-147 2-39 (87)
10 TIGR00588 ogg 8-oxoguanine DNA 94.9 0.024 5.2E-07 50.5 3.4 39 103-143 214-254 (310)
11 TIGR01083 nth endonuclease III 94.9 0.08 1.7E-06 43.7 6.2 39 104-143 101-139 (191)
12 PRK10880 adenine DNA glycosyla 94.9 0.041 8.9E-07 50.2 4.9 29 104-132 104-132 (350)
13 PRK13913 3-methyladenine DNA g 94.8 0.11 2.4E-06 44.6 7.0 39 106-145 118-156 (218)
14 PRK02515 psbU photosystem II c 94.8 0.017 3.8E-07 46.4 1.9 37 106-147 58-94 (132)
15 PRK13910 DNA glycosylase MutY; 94.5 0.054 1.2E-06 48.3 4.6 34 106-140 69-102 (289)
16 TIGR03252 uncharacterized HhH- 94.5 0.03 6.5E-07 46.9 2.8 44 102-147 108-151 (177)
17 PRK10308 3-methyl-adenine DNA 94.5 0.043 9.4E-07 48.4 3.9 36 103-139 201-238 (283)
18 COG1194 MutY A/G-specific DNA 94.3 0.057 1.2E-06 49.4 4.3 56 108-163 112-174 (342)
19 smart00278 HhH1 Helix-hairpin- 92.7 0.09 2E-06 30.4 1.9 19 110-128 2-20 (26)
20 PF11731 Cdd1: Pathogenicity l 91.3 0.15 3.2E-06 38.8 2.1 26 104-129 7-32 (93)
21 PF10391 DNA_pol_lambd_f: Fing 89.5 0.24 5.1E-06 33.6 1.8 22 108-129 1-22 (52)
22 PF14716 HHH_8: Helix-hairpin- 88.8 0.64 1.4E-05 32.4 3.6 32 96-127 33-65 (68)
23 PRK14605 ruvA Holliday junctio 87.6 0.39 8.5E-06 40.3 2.2 31 103-133 67-97 (194)
24 TIGR01259 comE comEA protein. 87.2 0.73 1.6E-05 35.8 3.4 42 105-147 64-105 (120)
25 KOG1921 Endonuclease III [Repl 86.0 1.2 2.6E-05 39.7 4.5 29 103-131 153-181 (286)
26 PRK00116 ruvA Holliday junctio 85.5 0.64 1.4E-05 38.7 2.4 26 106-131 70-95 (192)
27 PF12826 HHH_2: Helix-hairpin- 85.2 2.1 4.6E-05 29.5 4.6 24 106-129 32-55 (64)
28 TIGR00084 ruvA Holliday juncti 84.7 0.64 1.4E-05 38.9 2.1 28 104-131 67-94 (191)
29 PRK13901 ruvA Holliday junctio 84.7 0.61 1.3E-05 39.6 2.0 29 104-132 67-95 (196)
30 PRK14600 ruvA Holliday junctio 84.6 0.61 1.3E-05 39.1 1.9 29 104-132 68-96 (186)
31 PRK00024 hypothetical protein; 84.5 5.1 0.00011 34.3 7.6 60 54-128 22-85 (224)
32 PF14520 HHH_5: Helix-hairpin- 84.4 1 2.2E-05 30.4 2.6 23 107-129 3-25 (60)
33 PRK14601 ruvA Holliday junctio 82.7 0.81 1.8E-05 38.3 1.9 29 104-132 68-96 (183)
34 TIGR00608 radc DNA repair prot 82.4 1.4 3.1E-05 37.7 3.3 61 54-128 12-79 (218)
35 PF14520 HHH_5: Helix-hairpin- 81.5 0.91 2E-05 30.6 1.5 41 88-128 16-57 (60)
36 PRK14601 ruvA Holliday junctio 81.3 2.1 4.6E-05 35.8 3.9 98 54-164 62-166 (183)
37 PRK14606 ruvA Holliday junctio 80.6 2.3 5.1E-05 35.6 3.9 99 54-164 62-167 (188)
38 COG2003 RadC DNA repair protei 80.5 3.3 7.2E-05 36.0 4.9 79 35-129 3-86 (224)
39 PRK14604 ruvA Holliday junctio 79.9 2.5 5.5E-05 35.6 3.9 99 54-164 62-173 (195)
40 KOG2875 8-oxoguanine DNA glyco 79.6 3 6.5E-05 37.9 4.5 57 104-161 213-278 (323)
41 PRK14606 ruvA Holliday junctio 79.4 1.2 2.7E-05 37.2 1.9 31 103-133 67-97 (188)
42 TIGR00426 competence protein C 79.1 2.8 6.1E-05 28.9 3.3 39 108-147 15-54 (69)
43 PRK14603 ruvA Holliday junctio 79.0 2.8 6.1E-05 35.3 3.9 99 54-164 61-176 (197)
44 PRK14602 ruvA Holliday junctio 78.9 1.4 3.1E-05 37.2 2.2 28 105-132 70-97 (203)
45 COG2231 Uncharacterized protei 78.3 4.4 9.6E-05 35.1 4.9 38 107-145 113-150 (215)
46 PRK13901 ruvA Holliday junctio 78.2 3.1 6.7E-05 35.4 3.9 96 54-161 61-165 (196)
47 COG1555 ComEA DNA uptake prote 78.0 1.7 3.7E-05 35.1 2.3 42 105-147 93-134 (149)
48 PF00416 Ribosomal_S13: Riboso 77.3 4 8.7E-05 31.0 4.0 41 105-145 11-54 (107)
49 PRK14603 ruvA Holliday junctio 76.5 1.7 3.6E-05 36.7 1.9 30 104-133 67-96 (197)
50 PRK14602 ruvA Holliday junctio 76.3 3.7 8.1E-05 34.7 3.9 99 54-164 63-179 (203)
51 COG0353 RecR Recombinational D 75.0 2.1 4.5E-05 36.7 2.1 23 102-124 5-27 (198)
52 COG1796 POL4 DNA polymerase IV 74.3 3.6 7.9E-05 37.6 3.5 31 103-133 45-77 (326)
53 smart00279 HhH2 Helix-hairpin- 73.1 2.6 5.5E-05 26.4 1.6 15 113-127 20-34 (36)
54 PRK14604 ruvA Holliday junctio 72.5 2.4 5.2E-05 35.7 1.9 31 103-133 67-97 (195)
55 PRK07945 hypothetical protein; 72.2 7.5 0.00016 35.0 5.1 19 110-128 50-68 (335)
56 COG0099 RpsM Ribosomal protein 71.9 3.6 7.8E-05 32.7 2.6 42 105-146 13-57 (121)
57 TIGR00084 ruvA Holliday juncti 71.5 13 0.00028 31.1 6.0 98 54-164 61-171 (191)
58 COG0632 RuvA Holliday junction 69.4 3.1 6.6E-05 35.5 1.8 31 103-133 67-97 (201)
59 PRK00116 ruvA Holliday junctio 68.7 41 0.00089 27.9 8.4 68 55-131 63-130 (192)
60 TIGR03629 arch_S13P archaeal r 68.1 4 8.7E-05 33.0 2.2 39 107-145 19-60 (144)
61 PRK04053 rps13p 30S ribosomal 67.7 5.5 0.00012 32.5 2.9 58 101-158 17-80 (149)
62 PF12836 HHH_3: Helix-hairpin- 67.3 2.6 5.7E-05 29.0 0.9 41 106-147 11-51 (65)
63 PRK00076 recR recombination pr 66.2 4.7 0.0001 34.3 2.3 22 104-125 6-27 (196)
64 cd00141 NT_POLXc Nucleotidyltr 64.8 5.4 0.00012 35.5 2.6 25 104-128 80-104 (307)
65 PTZ00134 40S ribosomal protein 64.7 3.4 7.3E-05 34.0 1.1 55 100-154 21-81 (154)
66 PRK14605 ruvA Holliday junctio 64.2 10 0.00022 31.8 4.0 99 54-164 62-172 (194)
67 PF11798 IMS_HHH: IMS family H 64.2 4.4 9.5E-05 24.6 1.3 15 111-125 13-27 (32)
68 TIGR00615 recR recombination p 63.9 5.5 0.00012 33.9 2.3 22 104-125 6-27 (195)
69 KOG2457 A/G-specific adenine D 63.5 3.5 7.6E-05 39.2 1.1 57 74-130 153-227 (555)
70 CHL00137 rps13 ribosomal prote 62.7 8.2 0.00018 30.4 3.0 40 106-145 14-56 (122)
71 PRK13844 recombination protein 62.1 6.2 0.00013 33.8 2.3 22 104-125 10-31 (200)
72 PRK14600 ruvA Holliday junctio 60.4 10 0.00022 31.8 3.3 98 54-164 62-169 (186)
73 smart00483 POLXc DNA polymeras 59.2 8.5 0.00018 34.7 2.8 66 103-173 83-163 (334)
74 cd00080 HhH2_motif Helix-hairp 57.9 6.9 0.00015 27.8 1.6 19 111-129 24-42 (75)
75 cd00141 NT_POLXc Nucleotidyltr 57.8 8.2 0.00018 34.3 2.4 21 151-171 137-157 (307)
76 TIGR01339 phycocy_beta phycocy 57.4 14 0.00031 30.7 3.7 51 52-103 13-63 (170)
77 TIGR03631 bact_S13 30S ribosom 57.3 11 0.00023 29.3 2.7 39 108-146 14-55 (113)
78 PRK05179 rpsM 30S ribosomal pr 56.8 11 0.00025 29.6 2.8 39 108-146 16-57 (122)
79 smart00483 POLXc DNA polymeras 55.6 8.4 0.00018 34.7 2.1 36 98-133 37-72 (334)
80 TIGR00426 competence protein C 53.1 43 0.00094 22.8 5.0 22 107-128 45-66 (69)
81 COG3092 Uncharacterized protei 52.2 34 0.00073 27.9 4.8 51 80-131 28-81 (149)
82 PF00502 Phycobilisome: Phycob 50.9 12 0.00026 30.1 2.2 51 52-103 10-60 (157)
83 PRK14976 5'-3' exonuclease; Pr 49.3 10 0.00022 33.5 1.7 16 114-129 196-211 (281)
84 TIGR01259 comE comEA protein. 49.0 40 0.00086 26.1 4.7 20 107-126 96-115 (120)
85 PRK12766 50S ribosomal protein 48.7 13 0.00027 32.7 2.1 43 87-129 13-56 (232)
86 PF04854 DUF624: Protein of un 47.3 36 0.00078 23.6 3.9 48 113-173 17-64 (77)
87 COG5578 Predicted integral mem 45.9 33 0.00071 29.6 4.2 51 114-177 37-87 (208)
88 PRK09672 phage exclusion prote 45.7 40 0.00087 30.8 4.8 32 114-145 216-254 (305)
89 PRK09482 flap endonuclease-lik 45.4 13 0.00029 32.6 1.7 17 114-130 187-203 (256)
90 PRK08609 hypothetical protein; 44.9 24 0.00052 34.1 3.6 20 107-126 86-105 (570)
91 COG0632 RuvA Holliday junction 43.9 35 0.00076 29.1 4.0 64 54-127 62-126 (201)
92 COG1059 Thermostable 8-oxoguan 41.9 1.2E+02 0.0025 26.4 6.8 69 107-175 118-193 (210)
93 CHL00090 apcD allophycocyanin 41.6 35 0.00077 28.0 3.6 51 52-103 14-64 (161)
94 cd00008 53EXOc 5'-3' exonuclea 41.3 17 0.00037 31.1 1.7 16 114-129 188-203 (240)
95 PF01367 5_3_exonuc: 5'-3' exo 40.7 4.6 0.0001 30.8 -1.6 16 114-129 23-38 (101)
96 PF14229 DUF4332: Domain of un 40.6 26 0.00057 27.1 2.6 25 106-130 50-74 (122)
97 PF14579 HHH_6: Helix-hairpin- 40.6 26 0.00056 25.4 2.4 32 111-144 29-60 (90)
98 smart00475 53EXOc 5'-3' exonuc 40.4 18 0.00039 31.6 1.8 17 114-130 191-207 (259)
99 PRK13482 DNA integrity scannin 40.1 30 0.00065 32.1 3.2 31 98-128 307-338 (352)
100 CHL00086 apcA allophycocyanin 40.0 41 0.00089 27.6 3.7 51 52-103 14-64 (161)
101 CHL00170 cpcA phycocyanin alph 39.9 46 0.001 27.6 4.0 51 52-103 15-65 (162)
102 CHL00173 cpeA phycoerythrin al 39.2 38 0.00083 28.0 3.4 51 52-103 15-65 (164)
103 CHL00172 cpeB phycoerythrin be 38.5 41 0.00089 28.3 3.5 51 52-103 15-65 (177)
104 COG1415 Uncharacterized conser 38.1 1.1E+02 0.0023 28.8 6.4 145 31-178 166-356 (373)
105 TIGR01338 phycocy_alpha phycoc 37.8 56 0.0012 27.0 4.2 51 52-103 14-64 (161)
106 PF05766 NinG: Bacteriophage L 37.5 62 0.0013 27.5 4.5 38 137-174 148-187 (189)
107 PRK08609 hypothetical protein; 35.0 23 0.00051 34.2 1.8 32 98-129 110-143 (570)
108 TIGR01954 nusA_Cterm_rpt trans 34.7 38 0.00083 21.2 2.2 42 87-128 3-45 (50)
109 CHL00171 cpcB phycocyanin beta 34.1 46 0.00099 27.7 3.2 51 52-103 15-65 (172)
110 PRK12766 50S ribosomal protein 32.6 23 0.00051 31.0 1.2 20 109-128 3-22 (232)
111 COG3743 Uncharacterized conser 31.6 26 0.00056 28.4 1.2 20 109-128 67-86 (133)
112 TIGR01448 recD_rel helicase, p 30.9 1.3E+02 0.0028 30.0 6.2 21 108-128 81-103 (720)
113 PHA01976 helix-turn-helix prot 29.8 40 0.00087 22.3 1.8 25 53-77 13-43 (67)
114 PF05772 NinB: NinB protein; 29.4 65 0.0014 25.6 3.2 28 148-175 98-125 (127)
115 KOG1918 3-methyladenine DNA gl 28.6 42 0.0009 29.8 2.1 32 104-135 160-193 (254)
116 PF00356 LacI: Bacterial regul 28.2 45 0.00097 21.8 1.7 30 108-142 2-31 (46)
117 PF14394 DUF4423: Domain of un 27.8 2.9E+02 0.0062 22.6 6.8 109 53-172 10-149 (171)
118 PRK03980 flap endonuclease-1; 27.5 36 0.00078 30.3 1.6 13 114-126 194-206 (292)
119 TIGR03674 fen_arch flap struct 25.9 42 0.00091 30.3 1.7 16 113-128 240-255 (338)
120 cd00128 XPG Xeroderma pigmento 24.7 47 0.001 29.2 1.8 19 113-131 227-245 (316)
121 KOG2582 COP9 signalosome, subu 24.7 3.4E+02 0.0073 25.9 7.4 82 78-161 82-186 (422)
122 PRK14669 uvrC excinuclease ABC 23.8 1.2E+02 0.0025 30.2 4.4 21 109-129 552-572 (624)
123 PF06874 FBPase_2: Firmicute f 23.7 31 0.00068 34.4 0.5 52 17-80 82-133 (640)
124 PRK00558 uvrC excinuclease ABC 23.2 82 0.0018 30.9 3.3 22 108-129 542-563 (598)
125 TIGR00194 uvrC excinuclease AB 23.0 1.3E+02 0.0027 29.6 4.5 21 109-129 541-561 (574)
126 PF11517 Nab2: Nuclear abundan 22.8 40 0.00086 26.3 0.8 46 78-123 54-102 (107)
127 CHL00089 apcF allophycocyanin 22.7 97 0.0021 25.7 3.2 51 52-103 15-65 (169)
128 PRK14350 ligA NAD-dependent DN 22.7 90 0.002 31.2 3.5 23 107-129 539-561 (669)
129 PRK14671 uvrC excinuclease ABC 21.9 1.1E+02 0.0024 30.3 3.8 22 108-129 568-589 (621)
130 PRK14668 uvrC excinuclease ABC 21.7 87 0.0019 30.7 3.1 40 108-147 524-564 (577)
131 TIGR01589 A_thal_3526 uncharac 20.9 1.1E+02 0.0023 21.4 2.5 49 89-137 3-51 (57)
132 PF14307 Glyco_tran_WbsX: Glyc 20.7 29 0.00064 31.1 -0.3 41 134-174 145-190 (345)
133 PF05114 DUF692: Protein of un 20.6 95 0.0021 27.6 2.9 50 135-184 89-145 (274)
134 KOG2534 DNA polymerase IV (fam 20.2 78 0.0017 29.4 2.2 46 98-143 45-94 (353)
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=97.68 E-value=3.5e-05 Score=46.97 Aligned_cols=24 Identities=42% Similarity=0.700 Sum_probs=20.1
Q ss_pred HHHHHHhhcccCcChHHHHHHHhh
Q 029905 105 TKAVSELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~ 128 (185)
.+.++.|.+|+||||.||.+|++.
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 446889999999999999999973
No 2
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=96.99 E-value=0.0048 Score=52.62 Aligned_cols=72 Identities=28% Similarity=0.206 Sum_probs=53.0
Q ss_pred cHHHHHHHhh-cccCcChHHHHHHH-hhhCCCCCCcccHHHHHhhh---C--C--CCCCCHHHHHHHHHHHHHHHHhhCc
Q 029905 103 DLTKAVSELT-VLKGVGPATASAVL-AAYAPDLAPFMSDEAMGAAL---G--H--SKDYSLKQYLLFADKLQAKAKVSDI 173 (185)
Q Consensus 103 dv~~al~~L~-~LkGVGPATASaiL-a~~~P~~~pFfSDEa~~~~~---g--~--~ikYt~keY~~~~~~l~~~a~~L~~ 173 (185)
++..+.+.|. +||||||=||+.|| .+.. ..-|.-|--..-++ | . +..-|.+.|.+.-..+.+.++.+|+
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 21344666444333 4 1 2245669999999999999999998
Q ss_pred hhh
Q 029905 174 FFF 176 (185)
Q Consensus 174 ~~~ 176 (185)
...
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=96.49 E-value=0.019 Score=45.13 Aligned_cols=57 Identities=32% Similarity=0.380 Sum_probs=36.9
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhC-CCCCCcccHHHHHhhh---C-CCCCCCHHHHHHHHHH
Q 029905 105 TKAVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEAMGAAL---G-HSKDYSLKQYLLFADK 163 (185)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~~---g-~~ikYt~keY~~~~~~ 163 (185)
..+.+.|++||||||-||+.+|.... ++.+|. |-...-++ | .+.+-|-++..+..+.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~r~~~~~~~~~~~~~~~~~~~~~~~ 140 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVRRVLKRLGLIPKKKTPEELEELLEE 140 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHHHHHHHhCCCCCCCCHHHHHHHHHH
Confidence 67899999999999999999998743 444454 66554343 2 2333344444444433
No 4
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=96.33 E-value=0.0046 Score=53.02 Aligned_cols=71 Identities=23% Similarity=0.245 Sum_probs=46.4
Q ss_pred CHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHH-HH------------hhC-----ccHHHHHHHhhcccCcC
Q 029905 57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------------KSL-----PDLTKAVSELTVLKGVG 118 (185)
Q Consensus 57 tkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~-Af------------~~l-----~dv~~al~~L~~LkGVG 118 (185)
|.|+.+.-+.=+|- +..|+...+...+.+ .+++.++. +| +++ .++...++.|.+|+|||
T Consensus 42 ttD~~vn~at~~Lf--~~~~t~e~l~~a~~~-~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVG 118 (211)
T COG0177 42 TTDEVVNKATPALF--KRYPTPEDLLNADEE-ELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG 118 (211)
T ss_pred CchHHHHHHHHHHH--HHcCCHHHHHcCCHH-HHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence 46777766665554 234566666655544 44444432 22 011 15677899999999999
Q ss_pred hHHHHHHHhhhC
Q 029905 119 PATASAVLAAYA 130 (185)
Q Consensus 119 PATASaiLa~~~ 130 (185)
+-||..+|+...
T Consensus 119 rKTAnvVL~~a~ 130 (211)
T COG0177 119 RKTANVVLSFAF 130 (211)
T ss_pred hHHHHHHHHhhc
Confidence 999999999854
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=95.95 E-value=0.033 Score=49.13 Aligned_cols=38 Identities=29% Similarity=0.395 Sum_probs=28.9
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM 142 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~ 142 (185)
+...++.|++|+||||-||++||+...-...|+ -|--.
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 345689999999999999999999865433454 55544
No 6
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.73 E-value=0.035 Score=49.17 Aligned_cols=72 Identities=28% Similarity=0.270 Sum_probs=52.9
Q ss_pred CCCHHHHHHHHHHHhh-CCCCCchhhhHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhcccCcChHHHHHH
Q 029905 55 HINTTELSKLVRWKLT-RGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV 125 (185)
Q Consensus 55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~--------dv~~al~~L~~LkGVGPATASai 125 (185)
+.|-++|..+=++-|+ -|..+.+ .+.+.++++...+-.+ +...+++.|++||||||=||-.+
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 6888888888888886 5665553 3445555555554322 46779999999999999999999
Q ss_pred Hhh--hCCCCCC
Q 029905 126 LAA--YAPDLAP 135 (185)
Q Consensus 126 La~--~~P~~~p 135 (185)
|-. ..|+.+|
T Consensus 215 llf~lgr~dvfP 226 (285)
T COG0122 215 LLFGLGRPDVFP 226 (285)
T ss_pred HHHcCCCCCCCC
Confidence 876 4676655
No 7
>PRK10702 endonuclease III; Provisional
Probab=95.38 E-value=0.022 Score=48.32 Aligned_cols=38 Identities=26% Similarity=0.290 Sum_probs=28.4
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM 142 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~ 142 (185)
+..+.+.|.+|+||||-||.+||....-. ..|--|--.
T Consensus 104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~~-~~~~VDt~v 141 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTAFGW-PTIAVDTHI 141 (211)
T ss_pred CCchHHHHhcCCcccHHHHHHHHHHHcCC-CcccccchH
Confidence 45689999999999999999999986532 234445433
No 8
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.26 E-value=0.13 Score=40.07 Aligned_cols=39 Identities=31% Similarity=0.307 Sum_probs=28.3
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM 142 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~ 142 (185)
++....+.|++||||||-||+++|...--. .-|-.|--.
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 344678899999999999999999986544 223444433
No 9
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=95.11 E-value=0.018 Score=41.90 Aligned_cols=37 Identities=32% Similarity=0.497 Sum_probs=30.0
Q ss_pred HHhhcccCcChHHHHHHHhhh-CCCCCCcccHHHHHhhhC
Q 029905 109 SELTVLKGVGPATASAVLAAY-APDLAPFMSDEAMGAALG 147 (185)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~-~P~~~pFfSDEa~~~~~g 147 (185)
+.|+.++||||-||..||+.. +|+ -|=+...+...+|
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 10
>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=94.91 E-value=0.024 Score=50.54 Aligned_cols=39 Identities=28% Similarity=0.376 Sum_probs=31.1
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHH
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG 143 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~ 143 (185)
+...+.+.|++||||||-||.+||.. ..|+.+| .|-...
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 35678999999999999999999976 4566667 376553
No 11
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=94.90 E-value=0.08 Score=43.65 Aligned_cols=39 Identities=28% Similarity=0.227 Sum_probs=28.4
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHH
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMG 143 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (185)
+..+.+.|++||||||-||.+||....-.. -|.-|--..
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~ 139 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVF 139 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHH
Confidence 445788999999999999999998764321 245555443
No 12
>PRK10880 adenine DNA glycosylase; Provisional
Probab=94.89 E-value=0.041 Score=50.23 Aligned_cols=29 Identities=31% Similarity=0.472 Sum_probs=25.1
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (185)
+....+.|.+||||||-||++||+...-.
T Consensus 104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~ 132 (350)
T PRK10880 104 FPETFEEVAALPGVGRSTAGAILSLSLGK 132 (350)
T ss_pred chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence 45678999999999999999999987643
No 13
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=94.81 E-value=0.11 Score=44.58 Aligned_cols=39 Identities=21% Similarity=0.130 Sum_probs=28.1
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhh
Q 029905 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA 145 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~ 145 (185)
...+.|.+||||||=||.+||....- +.-|..|.-..-+
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv 156 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLF 156 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHH
Confidence 45688999999999999999987542 3245556544433
No 14
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.77 E-value=0.017 Score=46.38 Aligned_cols=37 Identities=24% Similarity=0.332 Sum_probs=32.3
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (185)
+..+.|..|+||||++|..|. .+.||-|=|-...+.|
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 447789999999999999999 3679999998888887
No 15
>PRK13910 DNA glycosylase MutY; Provisional
Probab=94.54 E-value=0.054 Score=48.25 Aligned_cols=34 Identities=26% Similarity=0.293 Sum_probs=26.3
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHH
Q 029905 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDE 140 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDE 140 (185)
...+.|.+|+||||-||.+||+...-..++ .-|-
T Consensus 69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~~-~VD~ 102 (289)
T PRK13910 69 NDYQSLLKLPGIGAYTANAILCFGFREKSA-CVDA 102 (289)
T ss_pred hhHHHHHhCCCCCHHHHHHHHHHHCCCCcC-cccH
Confidence 358999999999999999999986543333 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=94.53 E-value=0.03 Score=46.90 Aligned_cols=44 Identities=30% Similarity=0.373 Sum_probs=32.7
Q ss_pred ccHHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905 102 PDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147 (185)
Q Consensus 102 ~dv~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (185)
|+-....+.|.+|+||||-||..+|+...-+. -.-||-|....|
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 45556689999999999999999999755432 245677765554
No 17
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=94.47 E-value=0.043 Score=48.41 Aligned_cols=36 Identities=28% Similarity=0.322 Sum_probs=29.4
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccH
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSD 139 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSD 139 (185)
+...+++.|++||||||-||..||-. ..|+..| -.|
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 5787755 444
No 18
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.29 E-value=0.057 Score=49.42 Aligned_cols=56 Identities=27% Similarity=0.346 Sum_probs=37.5
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhh---hC----CCCCCCHHHHHHHHHH
Q 029905 108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA---LG----HSKDYSLKQYLLFADK 163 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~---~g----~~ikYt~keY~~~~~~ 163 (185)
.+.|.+|+||||-||+||||...-...|+..--+...+ .+ .+.+=+-+++.++++.
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 45666799999999999999987766787666555422 22 1223455666655554
No 19
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=92.68 E-value=0.09 Score=30.38 Aligned_cols=19 Identities=47% Similarity=0.763 Sum_probs=16.9
Q ss_pred HhhcccCcChHHHHHHHhh
Q 029905 110 ELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 110 ~L~~LkGVGPATASaiLa~ 128 (185)
.|.+++|||+.+|..|+..
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=91.33 E-value=0.15 Score=38.77 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=22.1
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhh
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~ 129 (185)
..+.+..|+.|+|||||||-=+..++
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LG 32 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLG 32 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence 34578999999999999999887774
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=89.53 E-value=0.24 Score=33.59 Aligned_cols=22 Identities=36% Similarity=0.351 Sum_probs=17.2
Q ss_pred HHHhhcccCcChHHHHHHHhhh
Q 029905 108 VSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~ 129 (185)
|+.+++.-||||+||.-..+.+
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=88.76 E-value=0.64 Score=32.37 Aligned_cols=32 Identities=31% Similarity=0.398 Sum_probs=23.1
Q ss_pred HHHhhCccHHHHHHH-hhcccCcChHHHHHHHh
Q 029905 96 KAFKSLPDLTKAVSE-LTVLKGVGPATASAVLA 127 (185)
Q Consensus 96 ~Af~~l~dv~~al~~-L~~LkGVGPATASaiLa 127 (185)
.+.+.+|..-..++. +.+|+|||+.+|.-|--
T Consensus 33 ~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 33 AAIKALPYPITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred HHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 334567755555675 99999999999987743
No 23
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.59 E-value=0.39 Score=40.28 Aligned_cols=31 Identities=23% Similarity=0.362 Sum_probs=25.3
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (185)
+-+.-...|.+.+||||-||-+||+.+.|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~ 97 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNAEA 97 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCHHH
Confidence 3566788899999999999999999877643
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=87.22 E-value=0.73 Score=35.78 Aligned_cols=42 Identities=29% Similarity=0.462 Sum_probs=33.9
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147 (185)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (185)
.+..+.|..|+||||.+|..|+.-..- +.||-|-|-+..+.|
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 568888777777766
No 25
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=85.99 E-value=1.2 Score=39.71 Aligned_cols=29 Identities=31% Similarity=0.464 Sum_probs=26.4
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCC
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAAYAP 131 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~~~P 131 (185)
|+...++.|..|+||||-+|=+.|++.--
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
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=85.52 E-value=0.64 Score=38.69 Aligned_cols=26 Identities=35% Similarity=0.565 Sum_probs=19.9
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCC
Q 029905 106 KAVSELTVLKGVGPATASAVLAAYAP 131 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P 131 (185)
.....|..++||||.||-.||+.+.+
T Consensus 70 ~~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 70 ELFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 34667888888888888888887554
No 27
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=85.25 E-value=2.1 Score=29.51 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.7
Q ss_pred HHHHHhhcccCcChHHHHHHHhhh
Q 029905 106 KAVSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~ 129 (185)
+..+.|++++||||.+|..|....
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 357899999999999999998764
No 28
>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=84.70 E-value=0.64 Score=38.90 Aligned_cols=28 Identities=36% Similarity=0.557 Sum_probs=19.8
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCC
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P 131 (185)
-+.-...|...+||||-||-+||+...|
T Consensus 67 Er~lF~~L~~V~GIGpK~Al~iL~~~~~ 94 (191)
T TIGR00084 67 ERELFKELIKVNGVGPKLALAILSNMSP 94 (191)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence 4556677777777777777777777555
No 29
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.67 E-value=0.61 Score=39.59 Aligned_cols=29 Identities=28% Similarity=0.406 Sum_probs=20.8
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (185)
-+.-...|.+..||||-||-+|||...|+
T Consensus 67 Er~lF~~LisVsGIGPK~ALaILs~~~~~ 95 (196)
T PRK13901 67 EREVFEELIGVDGIGPRAALRVLSGIKYN 95 (196)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 45566777777778888877777776664
No 30
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.55 E-value=0.61 Score=39.05 Aligned_cols=29 Identities=24% Similarity=0.371 Sum_probs=21.6
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (185)
-+.-...|.+..||||-||-+||+...|+
T Consensus 68 Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 68 EQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 45567777888888888888888876664
No 31
>PRK00024 hypothetical protein; Reviewed
Probab=84.53 E-value=5.1 Score=34.27 Aligned_cols=60 Identities=28% Similarity=0.449 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc---H-HHHHHHhhcccCcChHHHHHHHhh
Q 029905 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD---L-TKAVSELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d---v-~~al~~L~~LkGVGPATASaiLa~ 128 (185)
..|+-.||..++ |..|..|. .|....++-++...+ + ....+.|++++|||||.|..|+++
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 444555544443332 2 234678999999999999999887
No 32
>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=84.44 E-value=1 Score=30.39 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=20.3
Q ss_pred HHHHhhcccCcChHHHHHHHhhh
Q 029905 107 AVSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~ 129 (185)
....|..++||||.+|..+....
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 46788899999999999999984
No 33
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.73 E-value=0.81 Score=38.30 Aligned_cols=29 Identities=28% Similarity=0.323 Sum_probs=19.0
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (185)
-+.-+..|.+..||||-||-+|||...|+
T Consensus 68 Er~lF~~Li~VsGIGpK~Al~ILs~~~~~ 96 (183)
T PRK14601 68 EQKMFEMLLKVNGIGANTAMAVCSSLDVN 96 (183)
T ss_pred HHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 34456666677777777777777766553
No 34
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.43 E-value=1.4 Score=37.67 Aligned_cols=61 Identities=28% Similarity=0.351 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhcccCcChHHHHHHH
Q 029905 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL 126 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~------l~dv-~~al~~L~~LkGVGPATASaiL 126 (185)
..|+-.||..++ |..|.-|.. .|.+.+++-++. +.++ ....+.|++.+|||||.|..|+
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---LRTGTPKGL-----------DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred ccCCHHHHHHHH---HhCCCCCCC-----------CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence 578888966554 566653320 233444433332 3333 3357889999999999999999
Q ss_pred hh
Q 029905 127 AA 128 (185)
Q Consensus 127 a~ 128 (185)
++
T Consensus 78 a~ 79 (218)
T TIGR00608 78 AA 79 (218)
T ss_pred HH
Confidence 98
No 35
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=81.52 E-value=0.91 Score=30.63 Aligned_cols=41 Identities=29% Similarity=0.458 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhh
Q 029905 88 SSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 88 ~~V~~~t~~Af~~l~dv~~-al~~L~~LkGVGPATASaiLa~ 128 (185)
..++.....+|..+.|+.. ..+.|.+++||||.+|.-|...
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 3334444444443333322 4678999999999999988764
No 36
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.34 E-value=2.1 Score=35.80 Aligned_cols=98 Identities=19% Similarity=0.233 Sum_probs=60.1
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCC-
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P- 131 (185)
.+.|++|..-...-.--.| -=| .-+..++..+++.+.++.... =.+.|++++|||+-||.=|+-=.-.
T Consensus 62 GF~~~~Er~lF~~Li~VsG-IGpK~Al~ILs~~~~~el~~aI~~~---------D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 62 GFLDKDEQKMFEMLLKVNG-IGANTAMAVCSSLDVNSFYKALSLG---------DESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 4788888655444433333 334 345566667777776665542 2678999999999999987632111
Q ss_pred -----CCCCcccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 132 -----DLAPFMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 132 -----~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
...+ -.+|+..++.+ ..|+.++=...+..+
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 13678877763 567777766665554
No 37
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.57 E-value=2.3 Score=35.59 Aligned_cols=99 Identities=17% Similarity=0.161 Sum_probs=60.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPD 132 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (185)
.+.|++|..-.-.-.--.| -=| +-+.+++..+++.+.+++... =.+.||+++|||+-||.-|.-=.-..
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~AL~iLs~~~~~el~~aI~~~---------D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 62 GFSNERKKELFLSLTKVSR-LGPKTALKIISNEDAETLVTMIASQ---------DVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 4788888655444433333 234 345666666777776665542 26789999999999999876321110
Q ss_pred ----CC--CcccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 133 ----LA--PFMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 133 ----~~--pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
.. .-..+|+..++. ...|+-++=..-+.++
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 3567777766555554
No 38
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=80.51 E-value=3.3 Score=36.04 Aligned_cols=79 Identities=27% Similarity=0.375 Sum_probs=51.9
Q ss_pred hhhhHHhhhchh-hhccCCCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhC---ccHHH-HHH
Q 029905 35 LDDYYRKELPSL-IHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSL---PDLTK-AVS 109 (185)
Q Consensus 35 LD~w~~~~lp~~-~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l---~dv~~-al~ 109 (185)
+.+|...+.|.- +...+ ...|+-.||.-|+ |+.|..+- .|...++.-++.+ .++.. .++
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 11122 3589999976665 67776433 5666666665533 34444 499
Q ss_pred HhhcccCcChHHHHHHHhhh
Q 029905 110 ELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 110 ~L~~LkGVGPATASaiLa~~ 129 (185)
.||.++|||+|-|.=+.++.
T Consensus 67 el~~v~GiG~aka~~l~a~~ 86 (224)
T COG2003 67 ELSSVKGIGLAKAIQIKAAI 86 (224)
T ss_pred HHhhCCCccHHHHHHHHHHH
Confidence 99999999999999988873
No 39
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.86 E-value=2.5 Score=35.58 Aligned_cols=99 Identities=18% Similarity=0.146 Sum_probs=59.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPD 132 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (185)
.+.|++|..-...-.--.| -=| +-+.+++..+++.+.++.... =.+.|++++||||-||--|..-....
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~Al~iLs~~~~~el~~aI~~~---------D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 62 GFSTPAQRQLFELLIGVSG-VGPKAALNLLSSGTPDELQLAIAGG---------DVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 5788998665554433333 223 345566666777666655442 26789999999999999876532111
Q ss_pred C-----------CC-cccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 133 L-----------AP-FMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 133 ~-----------~p-FfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
. .+ ---+|+..++. ...|+.++=..-+.++
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 3567777766655555
No 40
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=79.58 E-value=3 Score=37.88 Aligned_cols=57 Identities=19% Similarity=0.160 Sum_probs=35.8
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhh--hCCCCCCcccHHHHH-----hhhC-CCCC-CCHHHHHHHH
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEAMG-----AALG-HSKD-YSLKQYLLFA 161 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~-----~~~g-~~ik-Yt~keY~~~~ 161 (185)
.+.|-++||.|+||||-.|-+|+-. +-++.+|. .--+|. +++| ...| -+.|-|.++-
T Consensus 213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPV-DvHi~ria~~y~l~~~~g~k~l~~ki~~ev~ 278 (323)
T KOG2875|consen 213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVPV-DVHIWRIAQDYILPGLSGAKELTPKINGEVS 278 (323)
T ss_pred HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccc-hhhHHHHhhcccCCCccccccCCcchhHHHH
Confidence 5669999999999999999987644 44555662 222332 3344 2222 5666665554
No 41
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.36 E-value=1.2 Score=37.23 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=26.6
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (185)
+-+.-...|.+..||||-||-+||+...|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs~~~~~e 97 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIISNEDAET 97 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHHH
Confidence 3466788999999999999999999988753
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=79.11 E-value=2.8 Score=28.88 Aligned_cols=39 Identities=28% Similarity=0.441 Sum_probs=29.3
Q ss_pred HHHhhc-ccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905 108 VSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147 (185)
Q Consensus 108 l~~L~~-LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (185)
...|.. ++|||+.+|.+|+.-... ..+|-+-+-+..++|
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 336767677766665
No 43
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.98 E-value=2.8 Score=35.33 Aligned_cols=99 Identities=18% Similarity=0.151 Sum_probs=58.5
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhC--
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA-- 130 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~-- 130 (185)
++.|++|..-.-.-.--.| -=| +-+..++..+++.+.+++... =.+.|++++||||-||.-|..=.-
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 4678888654444332233 334 345666667777776665542 267899999999999987763210
Q ss_pred --------------CCCCCcccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 131 --------------PDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 131 --------------P~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
+....--.+|+..++. ...|+-++=...+.++
T Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~ea~~AL~--~LGy~~~ea~~al~~i 176 (197)
T PRK14603 131 VPEHLLAGPAGGGGTKVSSTAAEDAVLALL--ALGFREAQVRSVVAEL 176 (197)
T ss_pred hhhhcccccccccccccCCccHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 0000011366776665 3567777766665555
No 44
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.93 E-value=1.4 Score=37.20 Aligned_cols=28 Identities=32% Similarity=0.506 Sum_probs=18.0
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhCCC
Q 029905 105 TKAVSELTVLKGVGPATASAVLAAYAPD 132 (185)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (185)
+.-...|.+..||||-||-+||+...|+
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 4455666667777777777777765553
No 45
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=78.30 E-value=4.4 Score=35.12 Aligned_cols=38 Identities=29% Similarity=0.350 Sum_probs=27.1
Q ss_pred HHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhh
Q 029905 107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA 145 (185)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~ 145 (185)
.-+.|-++||||+-||=+||--.. ++.-|.-|..-.-+
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~-~rp~FVvD~Yt~R~ 150 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYAL-DRPVFVVDKYTRRL 150 (215)
T ss_pred HHHHHHccCCcchhhHHHHHHHHh-cCcccchhHHHHHH
Confidence 457888999999999999987543 34356666654433
No 46
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.18 E-value=3.1 Score=35.38 Aligned_cols=96 Identities=15% Similarity=0.185 Sum_probs=56.3
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCC-
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P- 131 (185)
++.|++|..-.-.-.--.| -=| .-+..++..+++.+.+++... =.+.||+++|||+-||.=|.-=...
T Consensus 61 GF~t~~Er~lF~~LisVsG-IGPK~ALaILs~~~~~el~~aI~~~---------D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 61 GFLNSSEREVFEELIGVDG-IGPRAALRVLSGIKYNEFRDAIDRE---------DIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHhC---------CHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 4788888665544433333 233 345666777777776665442 2678999999999999977632111
Q ss_pred -------CCCCcccHHHHHhhhCCCCCCCHHHHHHHH
Q 029905 132 -------DLAPFMSDEAMGAALGHSKDYSLKQYLLFA 161 (185)
Q Consensus 132 -------~~~pFfSDEa~~~~~g~~ikYt~keY~~~~ 161 (185)
...+--.+|+..++.. ..|+-++=..-+
T Consensus 131 l~~~~~~~~~~~~~~ea~~AL~~--LGy~~~ea~~al 165 (196)
T PRK13901 131 LVKNDELESSLFKFKELEQSIVN--MGFDRKLVNSAI 165 (196)
T ss_pred hccccccccCcccHHHHHHHHHH--cCCCHHHHHHHH
Confidence 1111113677776652 456555544433
No 47
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=78.00 E-value=1.7 Score=35.10 Aligned_cols=42 Identities=31% Similarity=0.510 Sum_probs=32.3
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147 (185)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (185)
.+..+.|..|+||||+.|-+|.+--.- ..||=|=|=..-+.|
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 345777889999999999999997543 448887776666665
No 48
>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=77.31 E-value=4 Score=30.97 Aligned_cols=41 Identities=22% Similarity=0.284 Sum_probs=30.1
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhh--CCC-CCCcccHHHHHhh
Q 029905 105 TKAVSELTVLKGVGPATASAVLAAY--APD-LAPFMSDEAMGAA 145 (185)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~ 145 (185)
+...-+|++++|||+.+|..|+... +|. .+-..+|+-+..+
T Consensus 11 k~i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l 54 (107)
T PF00416_consen 11 KPIYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKL 54 (107)
T ss_dssp SBHHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHH
T ss_pred cchHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHH
Confidence 3345678999999999999999984 564 3566777766544
No 49
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.51 E-value=1.7 Score=36.67 Aligned_cols=30 Identities=37% Similarity=0.462 Sum_probs=26.0
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (185)
-+.-...|.+..||||-||-+||+...|+.
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~ 96 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSALPPAL 96 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHHH
Confidence 456688999999999999999999988753
No 50
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.32 E-value=3.7 Score=34.69 Aligned_cols=99 Identities=13% Similarity=0.152 Sum_probs=58.6
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhC--
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA-- 130 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~-- 130 (185)
.+.|.+|..-...-.--.| -=| +-+.+++..+++.+.++.... =.+.|++++|||+-||--|..=.-
T Consensus 63 GF~~~~Er~lF~~Li~V~G-IGpK~Al~iLs~~~~~~l~~aI~~~---------D~~~L~~ipGIGkKtAerIilELkdK 132 (203)
T PRK14602 63 GFATWDERQTFIVLISISK-VGAKTALAILSQFRPDDLRRLVAEE---------DVAALTRVSGIGKKTAQHIFLELKYK 132 (203)
T ss_pred CCCCHHHHHHHHHHhCCCC-cCHHHHHHHHhhCCHHHHHHHHHhC---------CHHHHhcCCCcCHHHHHHHHHHHHHh
Confidence 4788888665554443334 223 345666666777666655442 267899999999999998763210
Q ss_pred -------CC------C-CC-cccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 131 -------PD------L-AP-FMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 131 -------P~------~-~p-FfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
+. . .+ -..+|+..++. ...|+.++=..-+.++
T Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~ea~~AL~--~LGy~~~ea~~av~~~ 179 (203)
T PRK14602 133 LKVEGLPAAAVLAGTGAVPGSVFRDALAGLA--NLGYGEEEARPVLKEV 179 (203)
T ss_pred hccccccccccccccccCCCchHHHHHHHHH--HcCCCHHHHHHHHHHH
Confidence 00 0 00 12256776665 3567777666555554
No 51
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=75.03 E-value=2.1 Score=36.68 Aligned_cols=23 Identities=39% Similarity=0.700 Sum_probs=19.5
Q ss_pred ccHHHHHHHhhcccCcChHHHHH
Q 029905 102 PDLTKAVSELTVLKGVGPATASA 124 (185)
Q Consensus 102 ~dv~~al~~L~~LkGVGPATASa 124 (185)
|.+.+-|+.|.+|+||||-||.=
T Consensus 5 ~~i~~LI~~l~kLPGvG~KsA~R 27 (198)
T COG0353 5 PPIEKLIDALKKLPGVGPKSAQR 27 (198)
T ss_pred HHHHHHHHHHhhCCCCChhHHHH
Confidence 35677899999999999999974
No 52
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=74.28 E-value=3.6 Score=37.65 Aligned_cols=31 Identities=26% Similarity=0.318 Sum_probs=24.9
Q ss_pred cHHHHHHH--hhcccCcChHHHHHHHhhhCCCC
Q 029905 103 DLTKAVSE--LTVLKGVGPATASAVLAAYAPDL 133 (185)
Q Consensus 103 dv~~al~~--L~~LkGVGPATASaiLa~~~P~~ 133 (185)
|+....+. +|+|+|||++||+.|--..+-..
T Consensus 45 ~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~ 77 (326)
T COG1796 45 DLEEIEERGRLTELPGIGKGIAEKISEYLDTGE 77 (326)
T ss_pred chHHHHhhcccCCCCCccHHHHHHHHHHHHcCc
Confidence 67777777 99999999999999877654433
No 53
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=73.07 E-value=2.6 Score=26.44 Aligned_cols=15 Identities=47% Similarity=0.729 Sum_probs=13.2
Q ss_pred cccCcChHHHHHHHh
Q 029905 113 VLKGVGPATASAVLA 127 (185)
Q Consensus 113 ~LkGVGPATASaiLa 127 (185)
.++||||.||--+|.
T Consensus 20 Gv~giG~ktA~~ll~ 34 (36)
T smart00279 20 GVKGIGPKTALKLLR 34 (36)
T ss_pred CCCcccHHHHHHHHH
Confidence 589999999998875
No 54
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.50 E-value=2.4 Score=35.71 Aligned_cols=31 Identities=29% Similarity=0.390 Sum_probs=26.4
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (185)
+-+.-...|.+..||||=||-+||+...|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~e 97 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLSSGTPDE 97 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHHH
Confidence 3466788999999999999999999987753
No 55
>PRK07945 hypothetical protein; Provisional
Probab=72.19 E-value=7.5 Score=34.99 Aligned_cols=19 Identities=47% Similarity=0.733 Sum_probs=14.5
Q ss_pred HhhcccCcChHHHHHHHhh
Q 029905 110 ELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 110 ~L~~LkGVGPATASaiLa~ 128 (185)
.|++|+|||..||.-|--.
T Consensus 50 ~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred CcccCCCcCHHHHHHHHHH
Confidence 5778888888888877554
No 56
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=71.88 E-value=3.6 Score=32.75 Aligned_cols=42 Identities=21% Similarity=0.312 Sum_probs=31.7
Q ss_pred HHHHHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhhh
Q 029905 105 TKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAAL 146 (185)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~~ 146 (185)
+.-.=+|+.++|||+++|-+|+... +|+. +=..+||-...+-
T Consensus 13 K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ir 57 (121)
T COG0099 13 KRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLR 57 (121)
T ss_pred ceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHHH
Confidence 3334478899999999999999984 5653 6778888776443
No 57
>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=71.52 E-value=13 Score=31.13 Aligned_cols=98 Identities=21% Similarity=0.188 Sum_probs=55.6
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhC--
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA-- 130 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~-- 130 (185)
.+.|++|..-...-.--.|- =| +-+.+++.-+++.+.++.... =.+.|+++||||+-||.-|+--..
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 47889987665555433331 12 233444444444444433321 134689999999999999873211
Q ss_pred --------CC--CCCcccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 131 --------PD--LAPFMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 131 --------P~--~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
+. ..+ ..+|+..++. ...|+-++=..-+.++
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 10 112 2366666665 3668877776666655
No 58
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=69.37 E-value=3.1 Score=35.53 Aligned_cols=31 Identities=26% Similarity=0.451 Sum_probs=26.2
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (185)
+-+.-...|.+.-||||-||=+|||..+|+.
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~ 97 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPEE 97 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHHH
Confidence 4566788999999999999999999987753
No 59
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=68.67 E-value=41 Score=27.88 Aligned_cols=68 Identities=19% Similarity=0.185 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCC
Q 029905 55 HINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP 131 (185)
Q Consensus 55 ~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P 131 (185)
+.+..|-...-.+.--.|--.=+-+.+++.-..+.+.+...+ +-.+.|++++|||+.||-.|+.-...
T Consensus 63 F~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~---------~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 63 FLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIAN---------GDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred cCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 345665444334443444322233444444443333332222 12567899999999999999976543
No 60
>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=68.09 E-value=4 Score=33.05 Aligned_cols=39 Identities=26% Similarity=0.393 Sum_probs=28.5
Q ss_pred HHHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhh
Q 029905 107 AVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA 145 (185)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~ 145 (185)
..-+|+.++|||+.+|-.|+... +|.. +--.+|+-...+
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l 60 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKL 60 (144)
T ss_pred EEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHH
Confidence 34468999999999999999874 4543 556777765433
No 61
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=67.66 E-value=5.5 Score=32.52 Aligned_cols=58 Identities=22% Similarity=0.351 Sum_probs=38.1
Q ss_pred CccHHHHHHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhhh---CCCCCCCHHHHH
Q 029905 101 LPDLTKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAAL---GHSKDYSLKQYL 158 (185)
Q Consensus 101 l~dv~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~~---g~~ikYt~keY~ 158 (185)
+|+-+...-+|+.+.|||+.+|-.|+... +|.. +--.+++-...+. ..+-+|.+++|.
T Consensus 17 i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~ 80 (149)
T PRK04053 17 LDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWM 80 (149)
T ss_pred CCCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhh
Confidence 34444445578999999999999999874 5543 5667777665332 344455555554
No 62
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=67.30 E-value=2.6 Score=28.97 Aligned_cols=41 Identities=32% Similarity=0.481 Sum_probs=27.6
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhC
Q 029905 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALG 147 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g 147 (185)
+..+.|..|+||||.+|-.|+..-.- .-||-|=|=+..+.|
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 347777666666655
No 63
>PRK00076 recR recombination protein RecR; Reviewed
Probab=66.23 E-value=4.7 Score=34.34 Aligned_cols=22 Identities=32% Similarity=0.641 Sum_probs=18.8
Q ss_pred HHHHHHHhhcccCcChHHHHHH
Q 029905 104 LTKAVSELTVLKGVGPATASAV 125 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASai 125 (185)
+.+-++.|.+|+||||-||.=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRL 27 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5677899999999999999754
No 64
>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=64.81 E-value=5.4 Score=35.47 Aligned_cols=25 Identities=28% Similarity=0.392 Sum_probs=20.4
Q ss_pred HHHHHHHhhcccCcChHHHHHHHhh
Q 029905 104 LTKAVSELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASaiLa~ 128 (185)
...+|..|++++||||.||-.+...
T Consensus 80 ~~~~l~~l~~i~GiGpk~a~~l~~l 104 (307)
T cd00141 80 VPPGLLLLLRVPGVGPKTARKLYEL 104 (307)
T ss_pred chHHHHHHHcCCCCCHHHHHHHHHc
Confidence 4567888889999999999888843
No 65
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=64.68 E-value=3.4 Score=33.97 Aligned_cols=55 Identities=18% Similarity=0.216 Sum_probs=36.5
Q ss_pred hCccHHHHHHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhh---hCCCCCCCH
Q 029905 100 SLPDLTKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA---LGHSKDYSL 154 (185)
Q Consensus 100 ~l~dv~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~---~g~~ikYt~ 154 (185)
-+|+-+...-+|+.++|||+.+|-.|+... +|.. +--.+|+=...+ ...+.+|.+
T Consensus 21 ~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~i 81 (154)
T PTZ00134 21 NVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKI 81 (154)
T ss_pred cCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCC
Confidence 345555566678999999999999999984 5543 455666655433 334445543
No 66
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.23 E-value=10 Score=31.79 Aligned_cols=99 Identities=19% Similarity=0.208 Sum_probs=53.8
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHH------
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL------ 126 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiL------ 126 (185)
++.|++|-.-.-.-.--.|- =| +-+..++.-+++.+.++... .=.+.|++++|||+-||--|.
T Consensus 62 GF~~~~Er~lF~~Li~V~GI-GpK~Al~ILs~~~~~~l~~aI~~---------~D~~~L~~vpGIGkKtAerIilELk~K 131 (194)
T PRK14605 62 GFATTEELSLFETLIDVSGI-GPKLGLAMLSAMNAEALASAIIS---------GNAELLSTIPGIGKKTASRIVLELKDK 131 (194)
T ss_pred CCCCHHHHHHHHHHhCCCCC-CHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 46888886554444333332 22 34555565666654444322 125679999999999999843
Q ss_pred --hhhCCC---CCCcccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 127 --AAYAPD---LAPFMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 127 --a~~~P~---~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
....+. ..+--.+|++.++.+ ..|+.++=...+.++
T Consensus 132 i~~~~~~~~~~~~~~~~~e~~~aL~~--LGy~~~~a~~ai~~~ 172 (194)
T PRK14605 132 IAKNWEAGVLSQVTEANSDILATLTA--LGYSSSEAAKAISSL 172 (194)
T ss_pred HHhhhhccccccccchHHHHHHHHHH--cCCCHHHHHHHHHHh
Confidence 211110 011124677777653 456555554444444
No 67
>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=64.20 E-value=4.4 Score=24.59 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=11.3
Q ss_pred hhcccCcChHHHHHH
Q 029905 111 LTVLKGVGPATASAV 125 (185)
Q Consensus 111 L~~LkGVGPATASai 125 (185)
+.++.|||+.|+--+
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 558999999998654
No 68
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.93 E-value=5.5 Score=33.93 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=18.8
Q ss_pred HHHHHHHhhcccCcChHHHHHH
Q 029905 104 LTKAVSELTVLKGVGPATASAV 125 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASai 125 (185)
+..-++.|.+|+||||-||-=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5667899999999999999754
No 69
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=63.48 E-value=3.5 Score=39.22 Aligned_cols=57 Identities=19% Similarity=0.184 Sum_probs=33.8
Q ss_pred CCchhhhHhhhCCHHHHHHHHH----------------HHHhhCcc-HHHHHHHhhc-ccCcChHHHHHHHhhhC
Q 029905 74 WRPRLLVFVSSLDDSSVKSASE----------------KAFKSLPD-LTKAVSELTV-LKGVGPATASAVLAAYA 130 (185)
Q Consensus 74 fRP~L~~lV~sN~~~~V~~~t~----------------~Af~~l~d-v~~al~~L~~-LkGVGPATASaiLa~~~ 130 (185)
.=|+|.++....=+..|.+.-. .-.+.++. +...-+.|.+ ++||||-||-||+|..-
T Consensus 153 kwPTl~dla~Asl~~eVn~lWaGlGyY~R~rrL~ega~~vv~~~~ge~Prta~~l~kgvpGVG~YTAGAiaSIAf 227 (555)
T KOG2457|consen 153 KWPTLYDLAQASLEKEVNELWAGLGYYRRARRLLEGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIAF 227 (555)
T ss_pred hCchHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHhhCCCCCccchhhhhhhhh
Confidence 3588888876555555554321 11111111 2223345555 99999999999999853
No 70
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=62.66 E-value=8.2 Score=30.39 Aligned_cols=40 Identities=28% Similarity=0.452 Sum_probs=29.6
Q ss_pred HHHHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhh
Q 029905 106 KAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAA 145 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~ 145 (185)
...-+|+.+.|||+.||-.|+... +|.. +--.+|+-+..+
T Consensus 14 ~v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l 56 (122)
T CHL00137 14 RIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISAL 56 (122)
T ss_pred EeeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHH
Confidence 334568999999999999999984 5643 556777766544
No 71
>PRK13844 recombination protein RecR; Provisional
Probab=62.05 E-value=6.2 Score=33.78 Aligned_cols=22 Identities=14% Similarity=0.374 Sum_probs=18.6
Q ss_pred HHHHHHHhhcccCcChHHHHHH
Q 029905 104 LTKAVSELTVLKGVGPATASAV 125 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASai 125 (185)
+.+-++.|.+|+||||-||.=+
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rl 31 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRL 31 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5667899999999999999754
No 72
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=60.43 E-value=10 Score=31.76 Aligned_cols=98 Identities=17% Similarity=0.207 Sum_probs=59.1
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhh---
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY--- 129 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~--- 129 (185)
.+.|++|..-.-.-.--.| -=| +-+.+++..+++.+.++.... | .+.| +++|||+-||.-|+.=.
T Consensus 62 GF~~~~Er~lF~~LisV~G-IGpK~Al~iLs~~~~~~l~~aI~~~-----D----~~~L-~vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 62 GFLNREEQDCLRMLVKVSG-VNYKTAMSILSKLTPEQLFSAIVNE-----D----KAAL-KVNGIGEKLINRIITELQYK 130 (186)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHccCCHHHHHHHHHcC-----C----Hhhe-ECCCCcHHHHHHHHHHHHHH
Confidence 4688888665544433334 223 345666666777666665542 2 3678 89999999999887321
Q ss_pred ----CCCC-CC-cccHHHHHhhhCCCCCCCHHHHHHHHHHH
Q 029905 130 ----APDL-AP-FMSDEAMGAALGHSKDYSLKQYLLFADKL 164 (185)
Q Consensus 130 ----~P~~-~p-FfSDEa~~~~~g~~ikYt~keY~~~~~~l 164 (185)
.+.. .+ --.+|+..++.+ ..|+.+|=..-+.++
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 00 013677777763 668888776666655
No 73
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=59.18 E-value=8.5 Score=34.68 Aligned_cols=66 Identities=18% Similarity=0.155 Sum_probs=41.8
Q ss_pred cHHHHHHHhhcccCcChHHHHHHHhhhC---------CCCCCcccHHHHHhhhC------CCCCCCHHHHHHHHHHHHHH
Q 029905 103 DLTKAVSELTVLKGVGPATASAVLAAYA---------PDLAPFMSDEAMGAALG------HSKDYSLKQYLLFADKLQAK 167 (185)
Q Consensus 103 dv~~al~~L~~LkGVGPATASaiLa~~~---------P~~~pFfSDEa~~~~~g------~~ikYt~keY~~~~~~l~~~ 167 (185)
.+..++..|.+++||||.||-.+-..+- ++. .++.+- ..| -..+....|-..+.+.+.+.
T Consensus 83 ~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~~~--~l~~~q---~~gl~~~~~~~~ri~r~e~~~i~~~i~~~ 157 (334)
T smart00483 83 EVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKEL--KLTKQQ---KAGLKYYEDILKKVSRAEAFAVEYIVKRA 157 (334)
T ss_pred cHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhcccc--cCCHHH---HHHHHHHHHHhCCCCHHHHHHHHHHHHHH
Confidence 4677899999999999999988876421 111 233322 122 13456666767777777766
Q ss_pred HHhhCc
Q 029905 168 AKVSDI 173 (185)
Q Consensus 168 a~~L~~ 173 (185)
.+.+.-
T Consensus 158 l~~~~~ 163 (334)
T smart00483 158 VRKILP 163 (334)
T ss_pred HHhhCC
Confidence 666543
No 74
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=57.94 E-value=6.9 Score=27.82 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=16.0
Q ss_pred hhcccCcChHHHHHHHhhh
Q 029905 111 LTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 111 L~~LkGVGPATASaiLa~~ 129 (185)
+..++||||-||.-+|.-+
T Consensus 24 i~gv~giG~k~A~~ll~~~ 42 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEY 42 (75)
T ss_pred CCCCCcccHHHHHHHHHHh
Confidence 3458999999999999874
No 75
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=57.80 E-value=8.2 Score=34.34 Aligned_cols=21 Identities=10% Similarity=0.116 Sum_probs=10.4
Q ss_pred CCCHHHHHHHHHHHHHHHHhh
Q 029905 151 DYSLKQYLLFADKLQAKAKVS 171 (185)
Q Consensus 151 kYt~keY~~~~~~l~~~a~~L 171 (185)
+....|-..+.+.+.+..+.+
T Consensus 137 ri~r~ea~~~a~~i~~~l~~~ 157 (307)
T cd00141 137 RIPREEALAIAEIIKEALREV 157 (307)
T ss_pred CeEHHHHHHHHHHHHHHHHhC
Confidence 334444445555555555544
No 76
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=57.39 E-value=14 Score=30.74 Aligned_cols=51 Identities=16% Similarity=0.308 Sum_probs=45.8
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||.+|-.. +..|..|...-+.+.+|.+..|.++.++-|...|+
T Consensus 13 ~gRyl~~~eL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~ 63 (170)
T TIGR01339 13 RGEFISSSQIDALSKL-VADGNKRSDAVSRITNNASTIVTNAARSLFAEQPQ 63 (170)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCC
Confidence 4579999999998776 57899999999999999999999999999998885
No 77
>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=57.25 E-value=11 Score=29.30 Aligned_cols=39 Identities=26% Similarity=0.365 Sum_probs=29.4
Q ss_pred HHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhhh
Q 029905 108 VSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAAL 146 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~~ 146 (185)
.-+|+.+.|||+.+|-.|+... +|.. +-..+|+-+..+.
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~ 55 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIR 55 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHH
Confidence 3467999999999999999884 5643 5677777665443
No 78
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=56.85 E-value=11 Score=29.56 Aligned_cols=39 Identities=33% Similarity=0.458 Sum_probs=29.1
Q ss_pred HHHhhcccCcChHHHHHHHhhh--CCCC-CCcccHHHHHhhh
Q 029905 108 VSELTVLKGVGPATASAVLAAY--APDL-APFMSDEAMGAAL 146 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~~ 146 (185)
.-+|+.+.|||+.+|-.|+.-. +|.. +--.+|+-+..+.
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~ 57 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIR 57 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHH
Confidence 4467999999999999999984 5543 5667777665443
No 79
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=55.62 E-value=8.4 Score=34.72 Aligned_cols=36 Identities=22% Similarity=0.306 Sum_probs=25.6
Q ss_pred HhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCCC
Q 029905 98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (185)
Q Consensus 98 f~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (185)
.+.+|..-..+..|++|+|||+++|.-|--...-..
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 345554334456789999999999999987754433
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=53.14 E-value=43 Score=22.82 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=17.3
Q ss_pred HHHHhhcccCcChHHHHHHHhh
Q 029905 107 AVSELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~ 128 (185)
.++.|.+++|||+.||--|+..
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhh
Confidence 4666778899999999887754
No 81
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.16 E-value=34 Score=27.92 Aligned_cols=51 Identities=22% Similarity=0.277 Sum_probs=35.5
Q ss_pred hHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhc---ccCcChHHHHHHHhhhCC
Q 029905 80 VFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTV---LKGVGPATASAVLAAYAP 131 (185)
Q Consensus 80 ~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~---LkGVGPATASaiLa~~~P 131 (185)
+|---=++..|.++|+-|.+.+|-+. .+.++.. =+.+|||.|+|+.++.-|
T Consensus 28 rL~pvFpEnRVikaTrfairfMP~vA-vftl~wQ~~~~~ql~pAv~tAlfal~lp 81 (149)
T COG3092 28 RLAPVFPENRVIKATRFAIRFMPPVA-VFTLCWQIALGGQLGPAVATALFALSLP 81 (149)
T ss_pred hhcccCchhHHHHHHHHHHHhccHHH-HHHHHHHHHHhcccchHHHHHHHHHhcc
Confidence 33344568899999999999888542 2222222 237999999999998544
No 82
>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=50.86 E-value=12 Score=30.14 Aligned_cols=51 Identities=20% Similarity=0.206 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||..|-.+- .+|.-|....+.++.|.+.-|.++.++-|...|+
T Consensus 10 egRyls~~EL~~l~~~~-~~~~~Rl~aa~~L~~~a~~IV~~A~~~l~~~~P~ 60 (157)
T PF00502_consen 10 EGRYLSDGELQALKGYF-QSANARLEAAEKLRDNASEIVDQAAQKLFEKYPD 60 (157)
T ss_dssp TTSECEHHHHHHHHHHH-HTHHHHHHHHHHHHHTHHHHHHHHHHHHHHHSGG
T ss_pred cCCCCCHHHHHHHHHHH-HhHHHHHHHHHHHHHhHHHHHHHHHHHHHHhccc
Confidence 35799999999998875 4577799999999999999999999999988885
No 83
>PRK14976 5'-3' exonuclease; Provisional
Probab=49.34 E-value=10 Score=33.48 Aligned_cols=16 Identities=50% Similarity=0.918 Sum_probs=14.4
Q ss_pred ccCcChHHHHHHHhhh
Q 029905 114 LKGVGPATASAVLAAY 129 (185)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (185)
++||||-||..+|.-+
T Consensus 196 VpGIG~KtA~~LL~~~ 211 (281)
T PRK14976 196 VKGIGPKTAIKLLNKY 211 (281)
T ss_pred CCcccHHHHHHHHHHc
Confidence 7999999999999764
No 84
>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=49.03 E-value=40 Score=26.06 Aligned_cols=20 Identities=25% Similarity=0.494 Sum_probs=16.4
Q ss_pred HHHHhhcccCcChHHHHHHH
Q 029905 107 AVSELTVLKGVGPATASAVL 126 (185)
Q Consensus 107 al~~L~~LkGVGPATASaiL 126 (185)
.++.|.+++||||.|+--|.
T Consensus 96 s~eeL~~V~GIg~k~~~~i~ 115 (120)
T TIGR01259 96 SVDDLTKVSGIGEKSLEKLK 115 (120)
T ss_pred CHHHHHcCCCCCHHHHHHHH
Confidence 46777889999999987764
No 85
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=48.75 E-value=13 Score=32.66 Aligned_cols=43 Identities=33% Similarity=0.443 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhhCccHHHH-HHHhhcccCcChHHHHHHHhhh
Q 029905 87 DSSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 87 ~~~V~~~t~~Af~~l~dv~~a-l~~L~~LkGVGPATASaiLa~~ 129 (185)
+..++..-+.+|..+.++..| .+.|.+++|||+++|--|....
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 86
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=47.28 E-value=36 Score=23.57 Aligned_cols=48 Identities=13% Similarity=0.148 Sum_probs=28.2
Q ss_pred cccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhCCCCCCCHHHHHHHHHHHHHHHHhhCc
Q 029905 113 VLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDI 173 (185)
Q Consensus 113 ~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l~~~a~~L~~ 173 (185)
.+=|+||||+.+.-.+.. +..++...+..++|.+...+=-..+..+|.
T Consensus 17 ~v~tigPA~~Al~~~~~~-------------~~~~~~~~~~~~~f~~~fk~nf~~~~~~~~ 64 (77)
T PF04854_consen 17 PVFTIGPATAALYYVVRK-------------WVRDEEDSYLFRDFWRAFKQNFKQSLLLGL 64 (77)
T ss_pred HHHHHHHHHHHHHHHHHH-------------HHcCCccChHHHHHHHHHHHHHHHHHHHHH
Confidence 356899999988766632 222323566777776665554444444443
No 87
>COG5578 Predicted integral membrane protein [Function unknown]
Probab=45.94 E-value=33 Score=29.61 Aligned_cols=51 Identities=24% Similarity=0.257 Sum_probs=33.8
Q ss_pred ccCcChHHHHHHHhhhCCCCCCcccHHHHHhhhCCCCCCCHHHHHHHHHHHHHHHHhhCchhhh
Q 029905 114 LKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKVSDIFFFL 177 (185)
Q Consensus 114 LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~g~~ikYt~keY~~~~~~l~~~a~~L~~~~~~ 177 (185)
.=|++||||++. ++.. +|..|++.-+..|++-+..++---++.=+|-.+.+
T Consensus 37 VfG~~PAT~Alf-~v~R------------kw~~g~~d~pi~k~f~~~yK~~F~~aNlig~~f~l 87 (208)
T COG5578 37 VFGLMPATAALF-AVIR------------KWLQGDKDVPIFKTFWQTYKQEFVRANLIGLFFVL 87 (208)
T ss_pred HHccchHHHHHH-HHHH------------HHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 569999999753 3321 35667777777777777777666666655555444
No 88
>PRK09672 phage exclusion protein Lit; Provisional
Probab=45.75 E-value=40 Score=30.76 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=24.0
Q ss_pred ccCcChHHHHHHHhhhCCCC-------CCcccHHHHHhh
Q 029905 114 LKGVGPATASAVLAAYAPDL-------APFMSDEAMGAA 145 (185)
Q Consensus 114 LkGVGPATASaiLa~~~P~~-------~pFfSDEa~~~~ 145 (185)
=||||.|+|.++|++.-|++ +|=+.|+....+
T Consensus 216 Kr~vgIaia~l~l~~l~~~~~~~g~~tHP~~~~RI~a~i 254 (305)
T PRK09672 216 KRSVGIAIALLFLQELELENKSCGKGTHPDADQRIFANL 254 (305)
T ss_pred hhhHHHHHHHHHHHHHhccccCCCCCCCCCHHHHHHHhh
Confidence 68999999999999865532 566666666544
No 89
>PRK09482 flap endonuclease-like protein; Provisional
Probab=45.41 E-value=13 Score=32.64 Aligned_cols=17 Identities=29% Similarity=0.778 Sum_probs=15.3
Q ss_pred ccCcChHHHHHHHhhhC
Q 029905 114 LKGVGPATASAVLAAYA 130 (185)
Q Consensus 114 LkGVGPATASaiLa~~~ 130 (185)
.+||||.||.-+|.-+.
T Consensus 187 VpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 187 VAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCcChHHHHHHHHHhC
Confidence 89999999999998854
No 90
>PRK08609 hypothetical protein; Provisional
Probab=44.86 E-value=24 Score=34.14 Aligned_cols=20 Identities=20% Similarity=0.316 Sum_probs=12.7
Q ss_pred HHHHhhcccCcChHHHHHHH
Q 029905 107 AVSELTVLKGVGPATASAVL 126 (185)
Q Consensus 107 al~~L~~LkGVGPATASaiL 126 (185)
++..|++++||||.||-.+-
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHH
Confidence 55666666666666666555
No 91
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=43.93 E-value=35 Score=29.12 Aligned_cols=64 Identities=22% Similarity=0.294 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHh
Q 029905 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLA 127 (185)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa 127 (185)
++.|.+|-.-.-+-=--.| -=| +-+.++++-+++.+.++.... =++.|++++|||+=||=-|+-
T Consensus 62 GF~~~~ER~lF~~LisVnG-IGpK~ALaiLs~~~~~~l~~aI~~~---------d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 62 GFLTEEERELFRLLISVNG-IGPKLALAILSNLDPEELAQAIANE---------DVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred CCCCHHHHHHHHHHHccCC-ccHHHHHHHHcCCCHHHHHHHHHhc---------ChHhhhcCCCCCHHHHHHHHH
Confidence 4667777332222211222 122 223444444555555544432 256899999999999987764
No 92
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=41.93 E-value=1.2e+02 Score=26.39 Aligned_cols=69 Identities=23% Similarity=0.255 Sum_probs=49.0
Q ss_pred HHHHhh-cccCcChHHHHHHHhhhCCCCCCcccHHHHHhhh--C----CCCCCCHHHHHHHHHHHHHHHHhhCchh
Q 029905 107 AVSELT-VLKGVGPATASAVLAAYAPDLAPFMSDEAMGAAL--G----HSKDYSLKQYLLFADKLQAKAKVSDIFF 175 (185)
Q Consensus 107 al~~L~-~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~--g----~~ikYt~keY~~~~~~l~~~a~~L~~~~ 175 (185)
|=+.|. ++||+|=--||=.|-=.-=+.+....--...|+. | .|...|.|-|+..-+.++..|+++|+..
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 566666 8999999999998864221222222222334654 3 3458899999999999999999999754
No 93
>CHL00090 apcD allophycocyanin gamma subunit
Probab=41.61 E-value=35 Score=27.98 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=45.0
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|+|..||..|-.. +..|.-|-..-+.+++|.+.-|.++.++-|...|+
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 3489999999999776 57788899999999999999999999999988874
No 94
>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=41.31 E-value=17 Score=31.10 Aligned_cols=16 Identities=38% Similarity=0.737 Sum_probs=14.5
Q ss_pred ccCcChHHHHHHHhhh
Q 029905 114 LKGVGPATASAVLAAY 129 (185)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (185)
++||||-||.-+|.-+
T Consensus 188 v~GiG~ktA~~Ll~~~ 203 (240)
T cd00008 188 VPGIGEKTAAKLLKEY 203 (240)
T ss_pred CCccCHHHHHHHHHHh
Confidence 8999999999999874
No 95
>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=40.74 E-value=4.6 Score=30.77 Aligned_cols=16 Identities=44% Similarity=0.910 Sum_probs=13.8
Q ss_pred ccCcChHHHHHHHhhh
Q 029905 114 LKGVGPATASAVLAAY 129 (185)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (185)
.+||||-||+-+|.-+
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 96
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=40.59 E-value=26 Score=27.09 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=21.8
Q ss_pred HHHHHhhcccCcChHHHHHHHhhhC
Q 029905 106 KAVSELTVLKGVGPATASAVLAAYA 130 (185)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~ 130 (185)
.++.-|+.++||||..|-++..++-
T Consensus 50 ~~~AdL~ri~gi~~~~a~LL~~AGv 74 (122)
T PF14229_consen 50 VNQADLMRIPGIGPQYAELLEHAGV 74 (122)
T ss_pred HhHHHhhhcCCCCHHHHHHHHHhCc
Confidence 3677888999999999999999964
No 97
>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=40.58 E-value=26 Score=25.41 Aligned_cols=32 Identities=28% Similarity=0.423 Sum_probs=23.6
Q ss_pred hhcccCcChHHHHHHHhhhCCCCCCcccHHHHHh
Q 029905 111 LTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGA 144 (185)
Q Consensus 111 L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~ 144 (185)
|+.+||||..+|-.|+.... .-||-|=+-|..
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 98
>smart00475 53EXOc 5'-3' exonuclease.
Probab=40.43 E-value=18 Score=31.59 Aligned_cols=17 Identities=29% Similarity=0.651 Sum_probs=14.9
Q ss_pred ccCcChHHHHHHHhhhC
Q 029905 114 LKGVGPATASAVLAAYA 130 (185)
Q Consensus 114 LkGVGPATASaiLa~~~ 130 (185)
++||||-||.-+|.=+.
T Consensus 191 V~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 191 VPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCHHHHHHHHHHhC
Confidence 79999999999998643
No 99
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=40.07 E-value=30 Score=32.06 Aligned_cols=31 Identities=29% Similarity=0.539 Sum_probs=21.2
Q ss_pred HhhCccH-HHHHHHhhcccCcChHHHHHHHhh
Q 029905 98 FKSLPDL-TKAVSELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 98 f~~l~dv-~~al~~L~~LkGVGPATASaiLa~ 128 (185)
|..+.++ .+..+.|++.+||||+.|-.|-..
T Consensus 307 FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 307 FGSLQGLLAASIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred cCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHH
Confidence 4444333 334778889999999998886554
No 100
>CHL00086 apcA allophycocyanin alpha subunit
Probab=39.98 E-value=41 Score=27.64 Aligned_cols=51 Identities=20% Similarity=0.385 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|.++.++-|...|+
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 101
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=39.93 E-value=46 Score=27.56 Aligned_cols=51 Identities=12% Similarity=0.155 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||.+|.. -+.+|.-|-..-+.+.+|....|.++.++-|+..|+
T Consensus 15 qgRyls~~eL~~l~~-~~~~g~~RL~aa~~Lt~nA~~IV~~Aa~~lf~~~P~ 65 (162)
T CHL00170 15 QGRFLSNGELQACNG-RFQRAAASLEAARSLTSNAQRLIDGAAQAVYTKFPY 65 (162)
T ss_pred ccCCCCHHHHHHHHH-HHhccHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcC
Confidence 357999999999866 467899999999999999999999999999998885
No 102
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=39.24 E-value=38 Score=28.04 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||..|-. -+.+|.-|...-+.+.+|-++.|.++.+.-|+..|+
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 357999999999754 467899999999999999999999999999998885
No 103
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=38.54 E-value=41 Score=28.34 Aligned_cols=51 Identities=16% Similarity=0.142 Sum_probs=45.5
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++.+||.+|-. -+..|..|-..-+.+.+|...-|.++.++-|...|+
T Consensus 15 qgRYLs~~eL~~L~~-~~~~g~~RL~aa~~L~~NA~~IV~~A~~~l~~~~P~ 65 (177)
T CHL00172 15 KAAYVGGSDLQALKK-FISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPG 65 (177)
T ss_pred ccCCCCHHHHHHHHH-HHHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCC
Confidence 457999999999855 468899999999999999999999999999998885
No 104
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=38.14 E-value=1.1e+02 Score=28.80 Aligned_cols=145 Identities=21% Similarity=0.232 Sum_probs=77.0
Q ss_pred chhhhhhhHHhhhchhhhccCC-CCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHH-----H---HHhhC
Q 029905 31 NLISLDDYYRKELPSLIHQRNP-NPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASE-----K---AFKSL 101 (185)
Q Consensus 31 ~L~~LD~w~~~~lp~~~~~r~~-~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~-----~---Af~~l 101 (185)
+++.-=.|..+.++..+..+.. ...++.+++++++.=- ++ ++|-....+++.+++...+.... + +|..-
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 4444455666655555544321 1236667766666521 11 45666788888888633332211 0 12111
Q ss_pred -------c---cH------HHH-----------HHHhhcccCcChHHHHHHHhh---hCCCCCCcccHHHHHhh-hC---
Q 029905 102 -------P---DL------TKA-----------VSELTVLKGVGPATASAVLAA---YAPDLAPFMSDEAMGAA-LG--- 147 (185)
Q Consensus 102 -------~---dv------~~a-----------l~~L~~LkGVGPATASaiLa~---~~P~~~pFfSDEa~~~~-~g--- 147 (185)
| ++ ..+ .+.|--.|||||-|.=|+-=+ ..- ..|=|.|-+=.++ .|
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 334444799999998765333 121 1266788765433 34
Q ss_pred -CCCCCCHHHHHHHHHHHHHHHHh--hCchhhhh
Q 029905 148 -HSKDYSLKQYLLFADKLQAKAKV--SDIFFFLN 178 (185)
Q Consensus 148 -~~ikYt~keY~~~~~~l~~~a~~--L~~~~~~~ 178 (185)
.|---+.+.|-+.++.+++..++ +|.+.-++
T Consensus 323 gvP~pV~~~~yde~I~~l~~~ve~a~lg~~e~~~ 356 (373)
T COG1415 323 GVPFPVNRKTYDELIEFLEELVEKARLGRQEKLR 356 (373)
T ss_pred CCCCCcchhhHHHHHHHHHHHHHhhccCcHHHHH
Confidence 23344666677776666666664 77776554
No 105
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=37.83 E-value=56 Score=27.01 Aligned_cols=51 Identities=12% Similarity=0.204 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||.+|.. -+.+|..|-..-+.+.+|....|.++.++-|+..|+
T Consensus 14 qgRyls~~eL~~l~~-~~~~g~~RL~aa~~Lt~na~~IV~~Aa~~lf~~~P~ 64 (161)
T TIGR01338 14 QGRFLSNGELQSIFG-RFQRATASLEAAKSLTSNAQRLISGAAQAVYSKFPY 64 (161)
T ss_pred ccCCCCHHHHHHHHH-HHHchHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcC
Confidence 357999999999865 468899999999999999999999999999998885
No 106
>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=37.46 E-value=62 Score=27.49 Aligned_cols=38 Identities=13% Similarity=0.142 Sum_probs=29.8
Q ss_pred ccHHHHHhhhC--CCCCCCHHHHHHHHHHHHHHHHhhCch
Q 029905 137 MSDEAMGAALG--HSKDYSLKQYLLFADKLQAKAKVSDIF 174 (185)
Q Consensus 137 fSDEa~~~~~g--~~ikYt~keY~~~~~~l~~~a~~L~~~ 174 (185)
+..|.+.|+-+ .+.+||..||..+...-+++.++|.-.
T Consensus 148 iG~~~ve~Le~~~~~~k~~~~el~~i~~~y~~~~k~L~k~ 187 (189)
T PF05766_consen 148 IGQERVEWLEGPHEPRKWTIEELKAIIAIYRAKLKELKKE 187 (189)
T ss_pred HhHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 34455666665 578999999999999999999988643
No 107
>PRK08609 hypothetical protein; Provisional
Probab=35.02 E-value=23 Score=34.23 Aligned_cols=32 Identities=25% Similarity=0.360 Sum_probs=24.4
Q ss_pred HhhCccHHHHHH--HhhcccCcChHHHHHHHhhh
Q 029905 98 FKSLPDLTKAVS--ELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 98 f~~l~dv~~al~--~L~~LkGVGPATASaiLa~~ 129 (185)
++.+.++.+|.. .+..++|+|+-|+--||...
T Consensus 110 i~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i 143 (570)
T PRK08609 110 VVDKESLKEACENGKVQALAGFGKKTEEKILEAV 143 (570)
T ss_pred CCCHHHHHHHHHhCChhhccCcchhHHHHHHHHH
Confidence 344567777776 36689999999999998764
No 108
>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=34.67 E-value=38 Score=21.23 Aligned_cols=42 Identities=21% Similarity=0.390 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhhCccHHH-HHHHhhcccCcChHHHHHHHhh
Q 029905 87 DSSVKSASEKAFKSLPDLTK-AVSELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 87 ~~~V~~~t~~Af~~l~dv~~-al~~L~~LkGVGPATASaiLa~ 128 (185)
+..+......+|..+.++.. ..+.|+.++|+++.+|..|...
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 34455555566655555433 4788999999999999888654
No 109
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=34.13 E-value=46 Score=27.72 Aligned_cols=51 Identities=18% Similarity=0.282 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|+++.++-|...|+
T Consensus 15 ~gRyls~~EL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~ 65 (172)
T CHL00171 15 RGEFLSNTQLDALSKM-VAEGNKRLDAVNKINANASTIVTNAARSLFAEQPQ 65 (172)
T ss_pred ccCCCCHHHHHHHHHH-HHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcC
Confidence 3579999999998776 57788898888899999999999999999988885
No 110
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=32.61 E-value=23 Score=31.03 Aligned_cols=20 Identities=45% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHhhcccCcChHHHHHHHhh
Q 029905 109 SELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~ 128 (185)
+.|..++||||.++-.+|..
T Consensus 3 ~~L~~IpGIG~krakkLl~~ 22 (232)
T PRK12766 3 EELEDISGVGPSKAEALREA 22 (232)
T ss_pred cccccCCCcCHHHHHHHHHc
Confidence 46788999999999999998
No 111
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=31.58 E-value=26 Score=28.39 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.1
Q ss_pred HHhhcccCcChHHHHHHHhh
Q 029905 109 SELTVLKGVGPATASAVLAA 128 (185)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~ 128 (185)
+-|+.|.||||..++.+=..
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~ 86 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNEL 86 (133)
T ss_pred ccchhhcccCHHHHHHHHHc
Confidence 68999999999999977544
No 112
>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=30.86 E-value=1.3e+02 Score=30.02 Aligned_cols=21 Identities=33% Similarity=0.536 Sum_probs=14.2
Q ss_pred HHHhhc--ccCcChHHHHHHHhh
Q 029905 108 VSELTV--LKGVGPATASAVLAA 128 (185)
Q Consensus 108 l~~L~~--LkGVGPATASaiLa~ 128 (185)
++-|+. .|||||.||..|...
T Consensus 81 ~~yL~s~~~~GIG~~~A~~iv~~ 103 (720)
T TIGR01448 81 VAYLSSRSIKGVGKKLAQRIVKT 103 (720)
T ss_pred HHHHhcCCCCCcCHHHHHHHHHH
Confidence 444543 788888888877755
No 113
>PHA01976 helix-turn-helix protein
Probab=29.83 E-value=40 Score=22.31 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=16.4
Q ss_pred CCCCCHHHHHHHHH------HHhhCCCCCch
Q 029905 53 NPHINTTELSKLVR------WKLTRGKWRPR 77 (185)
Q Consensus 53 ~~~ltkdEL~~Lve------WKL~rGkfRP~ 77 (185)
...||.+||-+.+. ++.-+|+..|+
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~ 43 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEADKRLPN 43 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Confidence 45788888887765 44456665564
No 114
>PF05772 NinB: NinB protein; InterPro: IPR008711 The ninR region of Bacteriophage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of Escherichia coli, respectively, operate on phage lambda []. Genetic recombination in phage lambda relies on DNA end processing by Exo to expose 3'-tailed strands for annealing and exchange by beta protein. Phage lambda encodes an additional recombinase, NinB (Orf), which participates in the early stages of recombination by supplying a function equivalent to the E. coli RecFOR complex. These host enzymes assist loading of the RecA strand exchange protein onto ssDNA coated with ssDNA-binding protein. NinB has two structural domains with unusual folds, and exists as an intertwined dimer [].; PDB: 1PC6_B.
Probab=29.44 E-value=65 Score=25.60 Aligned_cols=28 Identities=14% Similarity=0.151 Sum_probs=21.2
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhhCchh
Q 029905 148 HSKDYSLKQYLLFADKLQAKAKVSDIFF 175 (185)
Q Consensus 148 ~~ikYt~keY~~~~~~l~~~a~~L~~~~ 175 (185)
+..+.|.++...|++.+.+.+.+.||+|
T Consensus 98 sTskmsv~~m~~lie~i~afga~~GV~f 125 (127)
T PF05772_consen 98 STSKMSVKEMSELIEYIYAFGAEHGVRF 125 (127)
T ss_dssp -TTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred echhhhHHHHHHHHHHHHHHHHHcCCcc
Confidence 4679999999999999999999999987
No 115
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=28.59 E-value=42 Score=29.75 Aligned_cols=32 Identities=28% Similarity=0.461 Sum_probs=25.9
Q ss_pred HHHHHHHhhcccCcChHHHHHH--HhhhCCCCCC
Q 029905 104 LTKAVSELTVLKGVGPATASAV--LAAYAPDLAP 135 (185)
Q Consensus 104 v~~al~~L~~LkGVGPATASai--La~~~P~~~p 135 (185)
-+.=++-||..||||+-|+=.. -+++.|+..|
T Consensus 160 eEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp 193 (254)
T KOG1918|consen 160 EEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMP 193 (254)
T ss_pred HHHHHHHHHhccCccceeeeeeeeeccCCCcccC
Confidence 4556889999999999999754 4678898866
No 116
>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=28.20 E-value=45 Score=21.80 Aligned_cols=30 Identities=30% Similarity=0.413 Sum_probs=22.0
Q ss_pred HHHhhcccCcChHHHHHHHhhhCCCCCCcccHHHH
Q 029905 108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAM 142 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~ 142 (185)
|+.+.++-||.++|.|-+|.=. +-+|+|.-
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~-----~~vs~~tr 31 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP-----PRVSEETR 31 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC-----SSSTHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhCC-----CCCCHHHH
Confidence 4566778899999999998742 44666654
No 117
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=27.85 E-value=2.9e+02 Score=22.58 Aligned_cols=109 Identities=12% Similarity=0.090 Sum_probs=66.7
Q ss_pred CCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHH-HHHHHHHHHHhhCc--cHHHHHHHhhc----------------
Q 029905 53 NPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDS-SVKSASEKAFKSLP--DLTKAVSELTV---------------- 113 (185)
Q Consensus 53 ~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~-~V~~~t~~Af~~l~--dv~~al~~L~~---------------- 113 (185)
...|+.+++.-+=+|+- |.+..++.-.+-+ .+..+.+.-...++ +++.+|+.|.+
T Consensus 10 ~~~l~~~~~~~~~~W~~------~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~ 83 (171)
T PF14394_consen 10 VRVLDEDEFEYYSSWYH------PAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTD 83 (171)
T ss_pred eeeccHHHHHHHhhhHH------HHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEec
Confidence 34577777777777875 5566666665554 55555555433333 57777777765
Q ss_pred --ccCcChHHHHHHHhhhCCCCCCcccHHHHHhhh---CCCC-------CCCHHHHHHHHHHHHHHHHhhC
Q 029905 114 --LKGVGPATASAVLAAYAPDLAPFMSDEAMGAAL---GHSK-------DYSLKQYLLFADKLQAKAKVSD 172 (185)
Q Consensus 114 --LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~---g~~i-------kYt~keY~~~~~~l~~~a~~L~ 172 (185)
|.|-+..+..+|.+.|- .|-+-|..++. .+.. .-+-+.|.++.+.+++..+++.
T Consensus 84 ~~l~~~~~~~~~avr~~h~-----q~~~lA~~al~~~p~~~R~~s~~T~~vs~~~~~ki~~~i~~fRk~i~ 149 (171)
T PF14394_consen 84 KSLTTSSEIPSEAVRSYHK-----QMLELAQEALDRVPPEERDFSGLTMSVSREDYEKIKKEIREFRKKII 149 (171)
T ss_pred ceeeCCCCCcHHHHHHHHH-----HHHHHHHHHHHhCCccccceeeeEEEeCHHHHHHHHHHHHHHHHHHH
Confidence 33445666666666653 24454544443 3323 4477899988888888777653
No 118
>PRK03980 flap endonuclease-1; Provisional
Probab=27.45 E-value=36 Score=30.29 Aligned_cols=13 Identities=46% Similarity=0.935 Sum_probs=0.0
Q ss_pred ccCcChHHHHHHH
Q 029905 114 LKGVGPATASAVL 126 (185)
Q Consensus 114 LkGVGPATASaiL 126 (185)
++||||-||.-++
T Consensus 194 I~GIG~ktA~kLi 206 (292)
T PRK03980 194 IKGIGPKTALKLI 206 (292)
T ss_pred CCCccHHHHHHHH
No 119
>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=25.92 E-value=42 Score=30.33 Aligned_cols=16 Identities=38% Similarity=0.663 Sum_probs=14.4
Q ss_pred cccCcChHHHHHHHhh
Q 029905 113 VLKGVGPATASAVLAA 128 (185)
Q Consensus 113 ~LkGVGPATASaiLa~ 128 (185)
.++||||-||--++.-
T Consensus 240 Gv~GIG~ktA~kli~~ 255 (338)
T TIGR03674 240 GVKGIGPKTALKLIKE 255 (338)
T ss_pred CCCCccHHHHHHHHHH
Confidence 5999999999999966
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=24.74 E-value=47 Score=29.21 Aligned_cols=19 Identities=32% Similarity=0.644 Sum_probs=16.4
Q ss_pred cccCcChHHHHHHHhhhCC
Q 029905 113 VLKGVGPATASAVLAAYAP 131 (185)
Q Consensus 113 ~LkGVGPATASaiLa~~~P 131 (185)
.++||||-||--++.-+..
T Consensus 227 gv~giG~k~A~~li~~~~~ 245 (316)
T cd00128 227 GIPGIGPVTALKLIKKYGD 245 (316)
T ss_pred CCCCccHHHHHHHHHHcCC
Confidence 4999999999999998653
No 121
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=24.67 E-value=3.4e+02 Score=25.91 Aligned_cols=82 Identities=26% Similarity=0.368 Sum_probs=49.4
Q ss_pred hhhHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhh-cccCcChHHHH-----------------HHHhh-----hCCCCC
Q 029905 78 LLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELT-VLKGVGPATAS-----------------AVLAA-----YAPDLA 134 (185)
Q Consensus 78 L~~lV~sN~~~~V~~~t~~Af~~l~dv~~al~~L~-~LkGVGPATAS-----------------aiLa~-----~~P~~~ 134 (185)
+..+|.+|+.+.++-++..=|....++..++-... .++||||-.=+ ++..+ +.+ .-
T Consensus 82 ~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~-~~ 160 (422)
T KOG2582|consen 82 LNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYAS-VL 160 (422)
T ss_pred HHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccc-cC
Confidence 45899999998888888777665555555544444 45666553211 11111 233 35
Q ss_pred CcccHHHHHhhhCCCCCCCHHHHHHHH
Q 029905 135 PFMSDEAMGAALGHSKDYSLKQYLLFA 161 (185)
Q Consensus 135 pFfSDEa~~~~~g~~ikYt~keY~~~~ 161 (185)
||++|.... +|+...-+..|.++.|+
T Consensus 161 p~ld~dive-i~~~n~h~~~k~fL~Y~ 186 (422)
T KOG2582|consen 161 PYLDDDIVE-ICKANPHLDPKYFLLYL 186 (422)
T ss_pred CccchhHHH-HhccCCCCCHHHHHHHH
Confidence 888888776 46655566666666553
No 122
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=23.82 E-value=1.2e+02 Score=30.22 Aligned_cols=21 Identities=38% Similarity=0.591 Sum_probs=18.3
Q ss_pred HHhhcccCcChHHHHHHHhhh
Q 029905 109 SELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~ 129 (185)
..|..++||||.++=++|.-+
T Consensus 552 S~L~~IpGIG~kr~~~LL~~F 572 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHF 572 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHc
Confidence 577799999999999999864
No 123
>PF06874 FBPase_2: Firmicute fructose-1,6-bisphosphatase; InterPro: IPR009164 Fructose 1,6-bisphosphatase catalyses the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate []. This is an essential reaction in the process of gluconeogenesis, the process by which non-carbohydrate precursors are converted to glucose, and hence this enzyme is found almost universally. Enzyme activity can be regulated by a number of different mechanisms including AMP inhibition, cylic AMP-dependent phosphorylation and light-dependent-activation. This entry represents a group of fructose 1,6-bisphosphatases found within the Firmicutes (low GC Gram-positive bacteria) which do not show any significant sequence similarity to the enzymes from other organisms. The Bacillus subtilis enzyme is inhibited by AMP, though this can be overcome by phosphoenolpyruvate, and is dependent on Mn(2+) [, ]. Mutants lacking this enzyme are apparently still able to grow on gluconeogenic growth substrates such as malate and glycerol.; GO: 0042132 fructose 1,6-bisphosphate 1-phosphatase activity, 0006094 gluconeogenesis
Probab=23.68 E-value=31 Score=34.37 Aligned_cols=52 Identities=40% Similarity=0.405 Sum_probs=37.7
Q ss_pred HHhhHHHHHhcCCCchhhhhhhHHhhhchhhhccCCCCCCCHHHHHHHHHHHhhCCCCCchhhh
Q 029905 17 LASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLV 80 (185)
Q Consensus 17 l~~Y~~~l~~~~k~~L~~LD~w~~~~lp~~~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~ 80 (185)
|=-||+-.=..-+.+-..+|+||+.+|...+ +|.+.|-.|.+|.|-|=.|++
T Consensus 82 LIYYP~ekl~~~~~~~~~~~~Wy~~tl~rLi------------~l~k~vssKYTRSKVRKalP~ 133 (640)
T PF06874_consen 82 LIYYPEEKLELLKKEEEDLDEWYRITLYRLI------------ELCKFVSSKYTRSKVRKALPK 133 (640)
T ss_pred HhcCHHHHHHHHHhhhhhHHHHHHHHHHHHH------------HHHHHHhccccHHHHHHhCCH
Confidence 4556665443333356689999999988776 588899999999887765553
No 124
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=23.19 E-value=82 Score=30.87 Aligned_cols=22 Identities=32% Similarity=0.613 Sum_probs=19.4
Q ss_pred HHHhhcccCcChHHHHHHHhhh
Q 029905 108 VSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~ 129 (185)
...|+.++||||.|+-.||..+
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 125
>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=22.99 E-value=1.3e+02 Score=29.58 Aligned_cols=21 Identities=29% Similarity=0.455 Sum_probs=18.1
Q ss_pred HHhhcccCcChHHHHHHHhhh
Q 029905 109 SELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~ 129 (185)
..|-+++||||.+.-++|.-+
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~F 561 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYF 561 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHc
Confidence 477799999999999999753
No 126
>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=22.80 E-value=40 Score=26.30 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=29.4
Q ss_pred hhhHhhhCCHHHHHHHHHHHHhhCccHH---HHHHHhhcccCcChHHHH
Q 029905 78 LLVFVSSLDDSSVKSASEKAFKSLPDLT---KAVSELTVLKGVGPATAS 123 (185)
Q Consensus 78 L~~lV~sN~~~~V~~~t~~Af~~l~dv~---~al~~L~~LkGVGPATAS 123 (185)
|-.|..+-+.+.+.++.+.||..+.-+. ..=.+..||+|+.++.++
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 4456677788888888888887554222 223456689999887664
No 127
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=22.74 E-value=97 Score=25.74 Aligned_cols=51 Identities=14% Similarity=0.309 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhhhHhhhCCHHHHHHHHHHHHhhCcc
Q 029905 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (185)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (185)
..+|++..||..|-. -+..|..|-..-+.+++|.+.-|.++.++-|...|+
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 457999999999855 468899999999999999999999999999988874
No 128
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=22.71 E-value=90 Score=31.18 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=19.9
Q ss_pred HHHHhhcccCcChHHHHHHHhhh
Q 029905 107 AVSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~ 129 (185)
+.+.|.++.||||-+|..|.+..
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHH
Confidence 45679999999999999998774
No 129
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=21.85 E-value=1.1e+02 Score=30.25 Aligned_cols=22 Identities=36% Similarity=0.604 Sum_probs=19.5
Q ss_pred HHHhhcccCcChHHHHHHHhhh
Q 029905 108 VSELTVLKGVGPATASAVLAAY 129 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~ 129 (185)
-..|..++||||.||-+||.-+
T Consensus 568 ~s~L~~I~GIG~k~a~~Ll~~F 589 (621)
T PRK14671 568 QTELTDIAGIGEKTAEKLLEHF 589 (621)
T ss_pred hhhhhcCCCcCHHHHHHHHHHc
Confidence 4577899999999999999986
No 130
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=21.71 E-value=87 Score=30.68 Aligned_cols=40 Identities=25% Similarity=0.309 Sum_probs=28.0
Q ss_pred HHHhhcccCcChHHHHHHHhhh-CCCCCCcccHHHHHhhhC
Q 029905 108 VSELTVLKGVGPATASAVLAAY-APDLAPFMSDEAMGAALG 147 (185)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~-~P~~~pFfSDEa~~~~~g 147 (185)
--.|+.++||||.++-.+|.-+ .++.+---|.|-+..++|
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 444433344555555655
No 131
>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=20.87 E-value=1.1e+02 Score=21.43 Aligned_cols=49 Identities=20% Similarity=0.180 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhhCccHHHHHHHhhcccCcChHHHHHHHhhhCCCCCCcc
Q 029905 89 SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFM 137 (185)
Q Consensus 89 ~V~~~t~~Af~~l~dv~~al~~L~~LkGVGPATASaiLa~~~P~~~pFf 137 (185)
.|+..+.+-+...-+-+..++.|.+..||-|.--|+|.--.--++.-||
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 4666666777766788899999999999999999988766544444444
No 132
>PF14307 Glyco_tran_WbsX: Glycosyltransferase WbsX
Probab=20.67 E-value=29 Score=31.08 Aligned_cols=41 Identities=12% Similarity=0.157 Sum_probs=33.7
Q ss_pred CCcccHHHHHhhhCCCC-----CCCHHHHHHHHHHHHHHHHhhCch
Q 029905 134 APFMSDEAMGAALGHSK-----DYSLKQYLLFADKLQAKAKVSDIF 174 (185)
Q Consensus 134 ~pFfSDEa~~~~~g~~i-----kYt~keY~~~~~~l~~~a~~L~~~ 174 (185)
.|||+|+-|.-+.|.|+ --++.+..++++.+|+.|++.|..
T Consensus 145 ~~~F~D~rYikVdGKPv~~Iy~p~~~pd~~~~~~~wr~~a~~~G~~ 190 (345)
T PF14307_consen 145 LPYFKDPRYIKVDGKPVFLIYRPGDIPDIKEMIERWREEAKEAGLP 190 (345)
T ss_pred HHHhCCCCceeECCEEEEEEECcccccCHHHHHHHHHHHHHHcCCC
Confidence 58999999988888653 235578889999999999999976
No 133
>PF05114 DUF692: Protein of unknown function (DUF692); InterPro: IPR007801 The proteins in this entry are functionally uncharacterised.; PDB: 3BWW_A.
Probab=20.63 E-value=95 Score=27.59 Aligned_cols=50 Identities=16% Similarity=0.270 Sum_probs=23.8
Q ss_pred CcccHHHHHhhh-C-----CCCCCCHHHHHHHHHHHHHHHHhhCchhhh-heeeecc
Q 029905 135 PFMSDEAMGAAL-G-----HSKDYSLKQYLLFADKLQAKAKVSDIFFFL-NICVYFS 184 (185)
Q Consensus 135 pFfSDEa~~~~~-g-----~~ikYt~keY~~~~~~l~~~a~~L~~~~~~-~~~~~~~ 184 (185)
|++||-.-..-. | -|+-||-.....+++.++...+.||.++.+ |+..|+.
T Consensus 89 ~~vSeHL~~~~~~g~~~dLlP~p~t~e~l~~~~~~i~~vQ~~l~~plllEN~s~y~~ 145 (274)
T PF05114_consen 89 PWVSEHLCWSSVGGHLYDLLPLPYTEEALDHVVDRIRRVQDALGRPLLLENPSSYLP 145 (274)
T ss_dssp ---EE-S--------------B---HHHHHHHHHHHHHHHHHHTS--EEE----S-B
T ss_pred CEEEeEEEEecCCCccCCcCCCCCCHHHHHHHHHHHHHHHHHhCCCeEEeCchhhcC
Confidence 667776433222 2 378999988889999999999999988877 7777664
No 134
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=20.16 E-value=78 Score=29.42 Aligned_cols=46 Identities=28% Similarity=0.365 Sum_probs=31.0
Q ss_pred HhhCccHHHHHHHhhcccCcChHHHHHHHhhhC----CCCCCcccHHHHH
Q 029905 98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAYA----PDLAPFMSDEAMG 143 (185)
Q Consensus 98 f~~l~dv~~al~~L~~LkGVGPATASaiLa~~~----P~~~pFfSDEa~~ 143 (185)
.+.+|-.-.+.+.+++|+||||-.|=.|=-..+ ++.--+--||...
T Consensus 45 lk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~ 94 (353)
T KOG2534|consen 45 LKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQ 94 (353)
T ss_pred HHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHH
Confidence 345565555688899999999999988766643 3333455566553
Done!