Query 030389
Match_columns 178
No_of_seqs 112 out of 146
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 13:00:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030389.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030389hhsearch_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 3.4E-05 7.3E-10 47.0 2.5 25 104-128 6-30 (30)
2 COG0177 Nth Predicted EndoIII- 96.3 0.0054 1.2E-07 52.4 4.2 71 57-130 42-130 (211)
3 cd00056 ENDO3c endonuclease II 96.2 0.0084 1.8E-07 46.8 4.9 39 105-145 79-118 (158)
4 smart00478 ENDO3c endonuclease 95.9 0.017 3.6E-07 44.8 5.1 36 103-140 66-101 (149)
5 TIGR01084 mutY A/G-specific ad 95.9 0.018 4E-07 50.5 5.8 40 104-144 100-139 (275)
6 COG0122 AlkA 3-methyladenine D 95.5 0.032 7E-07 49.2 5.9 72 55-135 144-226 (285)
7 PRK10702 endonuclease III; Pro 95.3 0.023 5.1E-07 47.9 4.3 28 104-131 104-131 (211)
8 PRK10880 adenine DNA glycosyla 95.2 0.02 4.4E-07 52.0 3.8 38 104-143 104-142 (350)
9 TIGR01083 nth endonuclease III 95.0 0.045 9.8E-07 44.9 5.1 39 104-143 101-139 (191)
10 TIGR00588 ogg 8-oxoguanine DNA 94.9 0.024 5.1E-07 50.3 3.4 40 103-144 214-255 (310)
11 PRK02515 psbU photosystem II c 94.8 0.028 6.1E-07 45.1 3.1 41 105-150 57-97 (132)
12 PRK13910 DNA glycosylase MutY; 94.8 0.029 6.3E-07 49.7 3.6 37 106-143 69-105 (289)
13 COG1194 MutY A/G-specific DNA 94.6 0.048 1E-06 49.8 4.5 33 108-140 112-144 (342)
14 PRK10308 3-methyl-adenine DNA 94.6 0.04 8.6E-07 48.4 3.8 33 103-135 201-235 (283)
15 TIGR03252 uncharacterized HhH- 94.4 0.032 7E-07 46.6 2.8 41 102-144 108-148 (177)
16 PRK01229 N-glycosylase/DNA lya 94.2 0.12 2.6E-06 43.9 5.8 28 103-130 112-141 (208)
17 PF02371 Transposase_20: Trans 93.3 0.072 1.6E-06 38.5 2.5 40 109-149 2-41 (87)
18 PRK13913 3-methyladenine DNA g 92.8 0.21 4.5E-06 42.7 5.0 37 106-143 118-154 (218)
19 TIGR01259 comE comEA protein. 92.8 0.1 2.2E-06 40.4 2.8 46 105-151 64-109 (120)
20 smart00278 HhH1 Helix-hairpin- 92.6 0.079 1.7E-06 30.6 1.6 19 110-128 2-20 (26)
21 PF11731 Cdd1: Pathogenicity l 91.0 0.16 3.5E-06 38.4 2.1 26 104-129 7-32 (93)
22 PF10391 DNA_pol_lambd_f: Fing 89.2 0.26 5.6E-06 33.3 1.7 23 108-130 1-23 (52)
23 PF14716 HHH_8: Helix-hairpin- 88.9 0.61 1.3E-05 32.3 3.5 32 96-127 33-65 (68)
24 PF14520 HHH_5: Helix-hairpin- 87.7 0.28 6E-06 33.1 1.1 23 107-129 3-25 (60)
25 PRK13901 ruvA Holliday junctio 87.4 0.27 5.8E-06 41.6 1.1 28 105-132 68-95 (196)
26 PRK14605 ruvA Holliday junctio 87.2 0.42 9.2E-06 39.9 2.2 31 103-133 67-97 (194)
27 KOG1921 Endonuclease III [Repl 86.2 1.2 2.5E-05 39.8 4.5 28 103-130 153-180 (286)
28 PRK14601 ruvA Holliday junctio 86.0 0.35 7.5E-06 40.3 1.1 19 109-127 108-126 (183)
29 PRK00116 ruvA Holliday junctio 85.0 0.7 1.5E-05 38.3 2.4 27 105-131 69-95 (192)
30 PRK14600 ruvA Holliday junctio 84.2 0.65 1.4E-05 38.7 1.9 30 103-132 67-96 (186)
31 TIGR00084 ruvA Holliday juncti 84.1 0.71 1.5E-05 38.5 2.1 29 103-131 66-94 (191)
32 PRK14606 ruvA Holliday junctio 84.0 0.49 1.1E-05 39.5 1.1 42 108-149 107-154 (188)
33 TIGR00426 competence protein C 83.6 1.6 3.4E-05 30.0 3.4 41 108-149 15-56 (69)
34 TIGR00608 radc DNA repair prot 83.4 1.3 2.8E-05 37.8 3.4 61 54-128 12-79 (218)
35 PRK14603 ruvA Holliday junctio 83.2 0.55 1.2E-05 39.4 1.0 46 104-149 67-116 (197)
36 PRK14602 ruvA Holliday junctio 82.9 0.63 1.4E-05 39.2 1.3 29 104-132 69-97 (203)
37 COG1555 ComEA DNA uptake prote 82.0 1.2 2.6E-05 35.9 2.5 46 105-151 93-138 (149)
38 PRK00024 hypothetical protein; 81.7 2.4 5.3E-05 36.1 4.4 60 54-128 22-85 (224)
39 PF12826 HHH_2: Helix-hairpin- 81.4 1.4 2.9E-05 30.4 2.3 24 106-129 32-55 (64)
40 PF14520 HHH_5: Helix-hairpin- 80.8 0.88 1.9E-05 30.6 1.2 22 107-128 36-57 (60)
41 KOG2875 8-oxoguanine DNA glyco 80.6 2.6 5.7E-05 38.2 4.4 32 104-135 213-246 (323)
42 COG2003 RadC DNA repair protei 79.7 3.7 8E-05 35.7 4.9 79 35-129 3-86 (224)
43 PF00416 Ribosomal_S13: Riboso 78.2 3.2 7E-05 31.4 3.7 41 105-145 11-54 (107)
44 PF12836 HHH_3: Helix-hairpin- 77.4 1.2 2.6E-05 30.6 1.1 44 106-150 11-54 (65)
45 PRK14606 ruvA Holliday junctio 76.8 3.4 7.4E-05 34.5 3.8 62 54-116 62-130 (188)
46 COG1796 POL4 DNA polymerase IV 76.3 2.4 5.2E-05 38.7 2.9 27 103-129 45-73 (326)
47 PRK14604 ruvA Holliday junctio 75.9 3.7 8E-05 34.4 3.8 64 54-127 62-126 (195)
48 PRK14601 ruvA Holliday junctio 75.9 3.7 8.1E-05 34.2 3.8 85 54-149 62-153 (183)
49 COG0099 RpsM Ribosomal protein 75.7 2.4 5.2E-05 33.7 2.4 41 105-145 13-56 (121)
50 cd00141 NT_POLXc Nucleotidyltr 75.4 4 8.7E-05 36.1 4.0 38 103-145 79-116 (307)
51 PRK13901 ruvA Holliday junctio 73.6 4.6 0.0001 34.2 3.8 86 54-149 61-155 (196)
52 PRK14603 ruvA Holliday junctio 72.7 5 0.00011 33.7 3.8 63 54-126 61-124 (197)
53 COG0353 RecR Recombinational D 72.3 2.7 5.8E-05 36.0 2.1 23 102-124 5-27 (198)
54 PRK14604 ruvA Holliday junctio 71.9 2.5 5.5E-05 35.4 1.8 48 103-150 67-118 (195)
55 smart00279 HhH2 Helix-hairpin- 71.4 2.9 6.3E-05 26.1 1.6 15 113-127 20-34 (36)
56 PRK14602 ruvA Holliday junctio 71.1 5.7 0.00012 33.4 3.8 63 54-126 63-126 (203)
57 TIGR03629 arch_S13P archaeal r 70.1 3.3 7.1E-05 33.5 2.1 38 107-144 19-59 (144)
58 COG0632 RuvA Holliday junction 69.1 3.2 6.8E-05 35.3 1.8 47 103-149 67-117 (201)
59 TIGR00084 ruvA Holliday juncti 67.8 6.2 0.00013 32.9 3.3 63 54-126 61-124 (191)
60 cd00141 NT_POLXc Nucleotidyltr 66.3 4.9 0.00011 35.6 2.5 37 97-133 33-69 (307)
61 PTZ00134 40S ribosomal protein 64.7 3.4 7.3E-05 33.9 1.1 45 100-144 21-68 (154)
62 PRK00076 recR recombination pr 64.6 5.3 0.00011 33.9 2.3 23 103-125 5-27 (196)
63 PRK04053 rps13p 30S ribosomal 64.4 5.8 0.00012 32.3 2.4 44 102-145 18-64 (149)
64 CHL00137 rps13 ribosomal prote 64.4 6.7 0.00014 30.8 2.7 40 106-145 14-56 (122)
65 PRK00116 ruvA Holliday junctio 63.7 26 0.00056 28.9 6.2 86 55-149 63-160 (192)
66 KOG2457 A/G-specific adenine D 63.3 3.5 7.6E-05 39.2 1.1 56 74-129 153-226 (555)
67 TIGR00615 recR recombination p 62.2 6.2 0.00014 33.5 2.3 22 104-125 6-27 (195)
68 PF11798 IMS_HHH: IMS family H 62.1 5 0.00011 24.3 1.3 15 111-125 13-27 (32)
69 TIGR01339 phycocy_beta phycocy 61.1 12 0.00026 31.1 3.8 51 52-103 13-63 (170)
70 COG2231 Uncharacterized protei 60.6 7.9 0.00017 33.5 2.7 37 107-144 113-149 (215)
71 TIGR03631 bact_S13 30S ribosom 60.5 7.9 0.00017 29.9 2.5 38 108-145 14-54 (113)
72 PRK13844 recombination protein 60.4 6.9 0.00015 33.4 2.3 23 103-125 9-31 (200)
73 PRK05179 rpsM 30S ribosomal pr 59.1 9 0.00019 30.0 2.6 39 107-145 15-56 (122)
74 smart00483 POLXc DNA polymeras 59.1 8.7 0.00019 34.4 2.8 26 103-128 83-108 (334)
75 smart00483 POLXc DNA polymeras 57.6 7.4 0.00016 34.8 2.1 36 98-133 37-72 (334)
76 cd00080 HhH2_motif Helix-hairp 56.0 7.8 0.00017 27.5 1.6 19 111-129 24-42 (75)
77 PF00502 Phycobilisome: Phycob 54.5 10 0.00022 30.4 2.3 51 52-103 10-60 (157)
78 TIGR00426 competence protein C 54.4 40 0.00087 22.9 5.0 22 107-128 45-66 (69)
79 PRK07945 hypothetical protein; 52.4 15 0.00033 32.8 3.3 19 110-128 50-68 (335)
80 PRK14605 ruvA Holliday junctio 51.1 12 0.00026 31.2 2.3 87 54-149 62-159 (194)
81 PRK12766 50S ribosomal protein 50.1 11 0.00024 32.9 2.0 43 87-129 13-56 (232)
82 TIGR01259 comE comEA protein. 49.2 40 0.00086 26.0 4.7 21 107-127 96-116 (120)
83 COG3092 Uncharacterized protei 48.3 44 0.00095 27.3 4.9 51 80-131 28-81 (149)
84 CHL00170 cpcA phycocyanin alph 48.0 34 0.00073 28.3 4.4 51 52-103 15-65 (162)
85 PRK14976 5'-3' exonuclease; Pr 47.6 11 0.00024 33.1 1.6 17 114-130 196-212 (281)
86 PRK14600 ruvA Holliday junctio 47.4 21 0.00046 29.7 3.2 85 54-149 62-156 (186)
87 PRK08609 hypothetical protein; 46.3 22 0.00048 34.2 3.5 19 109-127 48-66 (570)
88 CHL00090 apcD allophycocyanin 46.0 29 0.00063 28.4 3.7 51 52-103 14-64 (161)
89 PRK13482 DNA integrity scannin 45.1 22 0.00048 32.8 3.1 33 96-128 305-338 (352)
90 TIGR01338 phycocy_alpha phycoc 44.7 40 0.00087 27.8 4.3 51 52-103 14-64 (161)
91 CHL00172 cpeB phycoerythrin be 44.2 31 0.00067 29.0 3.6 51 52-103 15-65 (177)
92 CHL00086 apcA allophycocyanin 43.8 34 0.00074 28.0 3.8 51 52-103 14-64 (161)
93 CHL00173 cpeA phycoerythrin al 43.5 31 0.00067 28.5 3.5 51 52-103 15-65 (164)
94 PRK09482 flap endonuclease-lik 43.3 15 0.00032 32.2 1.7 17 114-130 187-203 (256)
95 PF14579 HHH_6: Helix-hairpin- 41.9 23 0.0005 25.6 2.3 33 111-145 29-62 (90)
96 PRK12766 50S ribosomal protein 41.8 16 0.00035 31.9 1.7 42 109-150 3-46 (232)
97 PF14229 DUF4332: Domain of un 40.8 26 0.00057 27.0 2.6 26 106-131 50-75 (122)
98 cd00008 53EXOc 5'-3' exonuclea 39.5 19 0.0004 30.7 1.7 16 114-129 188-203 (240)
99 smart00475 53EXOc 5'-3' exonuc 38.6 20 0.00043 31.2 1.7 17 114-130 191-207 (259)
100 PF01367 5_3_exonuc: 5'-3' exo 38.2 5.1 0.00011 30.4 -1.7 16 114-129 23-38 (101)
101 PRK00558 uvrC excinuclease ABC 38.1 26 0.00057 34.1 2.7 43 108-150 542-585 (598)
102 CHL00171 cpcB phycocyanin beta 37.8 39 0.00084 28.0 3.3 51 52-103 15-65 (172)
103 PRK08609 hypothetical protein; 36.1 22 0.00047 34.2 1.8 22 105-126 84-105 (570)
104 PRK14668 uvrC excinuclease ABC 35.5 31 0.00067 33.6 2.7 43 108-150 524-567 (577)
105 PF04854 DUF624: Protein of un 35.5 18 0.00039 25.0 0.8 17 113-129 17-33 (77)
106 PF00356 LacI: Bacterial regul 35.4 22 0.00048 23.2 1.2 34 108-146 2-35 (46)
107 COG1948 MUS81 ERCC4-type nucle 34.8 55 0.0012 29.0 3.9 68 105-173 178-246 (254)
108 TIGR01954 nusA_Cterm_rpt trans 34.4 36 0.00078 21.3 2.1 42 87-128 3-45 (50)
109 COG0632 RuvA Holliday junction 33.6 61 0.0013 27.6 3.9 64 54-127 62-126 (201)
110 COG3743 Uncharacterized conser 32.1 25 0.00054 28.4 1.2 20 109-128 67-86 (133)
111 KOG1918 3-methyladenine DNA gl 30.1 38 0.00082 30.0 2.1 33 103-135 159-193 (254)
112 COG5578 Predicted integral mem 28.9 30 0.00064 29.8 1.2 12 114-125 37-48 (208)
113 CHL00089 apcF allophycocyanin 26.2 88 0.0019 25.9 3.5 51 52-103 15-65 (169)
114 PRK03980 flap endonuclease-1; 25.9 40 0.00086 29.9 1.5 13 114-126 194-206 (292)
115 PHA01976 helix-turn-helix prot 25.8 54 0.0012 21.6 1.9 25 53-77 13-43 (67)
116 PRK14669 uvrC excinuclease ABC 25.0 1.1E+02 0.0023 30.3 4.4 39 109-147 552-591 (624)
117 PF05559 DUF763: Protein of un 24.8 1E+02 0.0022 28.3 3.9 45 108-153 268-316 (319)
118 TIGR03674 fen_arch flap struct 24.7 46 0.00099 29.9 1.7 17 113-129 240-256 (338)
119 PF11517 Nab2: Nuclear abundan 24.2 42 0.00091 26.2 1.2 46 78-123 54-102 (107)
120 TIGR00194 uvrC excinuclease AB 23.8 1.2E+02 0.0026 29.6 4.5 21 109-129 541-561 (574)
121 cd00128 XPG Xeroderma pigmento 23.6 51 0.0011 28.8 1.8 18 113-130 227-244 (316)
122 PRK14671 uvrC excinuclease ABC 23.1 97 0.0021 30.5 3.7 23 107-129 567-589 (621)
123 PRK14350 ligA NAD-dependent DN 23.0 88 0.0019 31.1 3.4 23 107-129 539-561 (669)
124 PF00514 Arm: Armadillo/beta-c 22.9 88 0.0019 18.8 2.3 20 76-95 15-34 (41)
125 KOG2534 DNA polymerase IV (fam 21.9 67 0.0015 29.8 2.2 47 98-144 45-95 (353)
126 smart00185 ARM Armadillo/beta- 21.1 1.1E+02 0.0023 17.6 2.3 19 76-94 15-33 (41)
127 TIGR01337 apcB allophycocyanin 21.0 1.1E+02 0.0023 25.2 3.1 50 52-102 14-63 (167)
128 COG1031 Uncharacterized Fe-S o 20.1 76 0.0016 31.0 2.3 38 105-147 512-549 (560)
No 1
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=97.68 E-value=3.4e-05 Score=46.99 Aligned_cols=25 Identities=40% Similarity=0.709 Sum_probs=20.6
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhh
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~ 128 (178)
+.+.++.|++|+||||.||.+|++.
T Consensus 6 ~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 6 IPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 3456899999999999999999973
No 2
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=96.26 E-value=0.0054 Score=52.36 Aligned_cols=71 Identities=20% Similarity=0.203 Sum_probs=45.3
Q ss_pred CHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHH-HH------------hh-----CccHHHHHHHhhcccCcc
Q 030389 57 NTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEK-AF------------KS-----LPDLTKAVSELTVLKGVG 118 (178)
Q Consensus 57 tkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~-Af------------~~-----l~d~~~al~~L~~LkGVG 118 (178)
|.|+.+.-+-=+|-. .-|+...+...+.+ .+++.++. +| ++ -.++..+++.|.+|+|||
T Consensus 42 ttD~~vn~at~~Lf~--~~~t~e~l~~a~~~-~l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVG 118 (211)
T COG0177 42 TTDEVVNKATPALFK--RYPTPEDLLNADEE-ELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG 118 (211)
T ss_pred CchHHHHHHHHHHHH--HcCCHHHHHcCCHH-HHHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence 467777666655542 33455666555544 34433332 22 01 115678899999999999
Q ss_pred hHHHHHHHhhhC
Q 030389 119 PATASAVLAAYA 130 (178)
Q Consensus 119 PATASaiLa~~~ 130 (178)
+-||..+|+...
T Consensus 119 rKTAnvVL~~a~ 130 (211)
T COG0177 119 RKTANVVLSFAF 130 (211)
T ss_pred hHHHHHHHHhhc
Confidence 999999999853
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=96.25 E-value=0.0084 Score=46.77 Aligned_cols=39 Identities=38% Similarity=0.389 Sum_probs=29.9
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhhC-CCCCCccchhHHhhh
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAYA-PDLAPFMSDEVCFCS 145 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~-P~~~pFfSDEa~~~~ 145 (178)
..+.+.|++||||||-||+.+|.... ++.+|- |-...-+
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~r~ 118 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVRRV 118 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHHHH
Confidence 67899999999999999999998753 333444 6665543
No 4
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.91 E-value=0.017 Score=44.78 Aligned_cols=36 Identities=36% Similarity=0.496 Sum_probs=28.2
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchh
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDE 140 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDE 140 (178)
++....+.|++|+||||-||+.+|...--. +++..+
T Consensus 66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~--~~~~~D 101 (149)
T smart00478 66 EVPDDREELLKLPGVGRKTANAVLSFALGK--PFIPVD 101 (149)
T ss_pred CccHHHHHHHcCCCCcHHHHHHHHHHHCCC--CCCccc
Confidence 345678999999999999999999987554 555544
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=95.87 E-value=0.018 Score=50.46 Aligned_cols=40 Identities=28% Similarity=0.301 Sum_probs=30.0
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFC 144 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~ 144 (178)
+...++.|++|+||||-||++||+...-...|+ -|--+.-
T Consensus 100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~~v~R 139 (275)
T TIGR01084 100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDGNVKR 139 (275)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chHhHHH
Confidence 345789999999999999999999865433444 5655443
No 6
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=95.49 E-value=0.032 Score=49.16 Aligned_cols=72 Identities=28% Similarity=0.270 Sum_probs=51.2
Q ss_pred CCCHHHHHHHHHHHhh-CCCCCchhHHHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhcccCcchHHHHHH
Q 030389 55 HINTTELSKLVRWKLT-RGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV 125 (178)
Q Consensus 55 ~ltkdEL~~LveWKL~-rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~--------d~~~al~~L~~LkGVGPATASai 125 (178)
+.|-++|..+=++-|+ -|..+.+ .+.+..+++...+-.+ +...+++.|++||||||=||-.+
T Consensus 144 fptpe~l~~~~~~~l~~~g~s~~K---------a~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~ 214 (285)
T COG0122 144 FPTPEQLAAADEEALRRCGLSGRK---------AEYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMF 214 (285)
T ss_pred CCCHHHHHhcCHHHHHHhCCcHHH---------HHHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHH
Confidence 6788888888888776 4555443 3455556655544321 46789999999999999999999
Q ss_pred Hhh--hCCCCCC
Q 030389 126 LAA--YAPDLAP 135 (178)
Q Consensus 126 La~--~~P~~~p 135 (178)
|-. ..|+.+|
T Consensus 215 llf~lgr~dvfP 226 (285)
T COG0122 215 LLFGLGRPDVFP 226 (285)
T ss_pred HHHcCCCCCCCC
Confidence 876 4565533
No 7
>PRK10702 endonuclease III; Provisional
Probab=95.34 E-value=0.023 Score=47.90 Aligned_cols=28 Identities=32% Similarity=0.383 Sum_probs=24.5
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhhhCC
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P 131 (178)
+..+.+.|.+|+||||-||.+||....-
T Consensus 104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~ 131 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTAFG 131 (211)
T ss_pred CCchHHHHhcCCcccHHHHHHHHHHHcC
Confidence 5568999999999999999999988643
No 8
>PRK10880 adenine DNA glycosylase; Provisional
Probab=95.21 E-value=0.02 Score=51.97 Aligned_cols=38 Identities=29% Similarity=0.362 Sum_probs=29.2
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccc-hhHHh
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMS-DEVCF 143 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfS-DEa~~ 143 (178)
+....+.|.+|+||||-||++||+...-. ||+- |=-..
T Consensus 104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~--~~~iVD~nV~ 142 (350)
T PRK10880 104 FPETFEEVAALPGVGRSTAGAILSLSLGK--HFPILDGNVK 142 (350)
T ss_pred chhhHHHHhcCCCccHHHHHHHHHHHCCC--CeecccHHHH
Confidence 45778999999999999999999987643 4554 54433
No 9
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=95.04 E-value=0.045 Score=44.85 Aligned_cols=39 Identities=31% Similarity=0.307 Sum_probs=28.2
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF 143 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (178)
+..+.+.|++|+||||-||.+||....-.. -|.-|--+.
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 456789999999999999999998864322 244454443
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=94.94 E-value=0.024 Score=50.29 Aligned_cols=40 Identities=28% Similarity=0.388 Sum_probs=31.8
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCCccchhHHhh
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAPFMSDEVCFC 144 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfSDEa~~~ 144 (178)
+...+.+.|++||||||-||..||.. ..|+.+| .|-.+.-
T Consensus 214 ~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~P--vD~~v~r 255 (310)
T TIGR00588 214 SYEDAREALCELPGVGPKVADCICLMGLDKPQAVP--VDVHVWR 255 (310)
T ss_pred ChHHHHHHHHhCCCccHHHHHHHHHHhCCCCCcee--ecHHHHH
Confidence 36678999999999999999999976 4566666 3866554
No 11
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.81 E-value=0.028 Score=45.11 Aligned_cols=41 Identities=20% Similarity=0.225 Sum_probs=33.6
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF 150 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~ 150 (178)
.+.++.|..|+||||++|..|. ++.||-|=|-+..++|+.+
T Consensus 57 ~A~~~el~~lpGigP~~A~~IV-----~nGpf~sveDL~~V~GIge 97 (132)
T PRK02515 57 NSSVRAFRQFPGMYPTLAGKIV-----KNAPYDSVEDVLNLPGLSE 97 (132)
T ss_pred ccCHHHHHHCCCCCHHHHHHHH-----HCCCCCCHHHHHcCCCCCH
Confidence 3457789999999999999999 3679999776777888764
No 12
>PRK13910 DNA glycosylase MutY; Provisional
Probab=94.79 E-value=0.029 Score=49.70 Aligned_cols=37 Identities=24% Similarity=0.187 Sum_probs=27.5
Q ss_pred HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF 143 (178)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (178)
...+.|.+|+||||-||.+||+...-..+ |.-|-=+.
T Consensus 69 ~~~~~L~~LpGIG~kTA~aIl~~af~~~~-~~VD~nV~ 105 (289)
T PRK13910 69 NDYQSLLKLPGIGAYTANAILCFGFREKS-ACVDANIK 105 (289)
T ss_pred hhHHHHHhCCCCCHHHHHHHHHHHCCCCc-CcccHHHH
Confidence 46899999999999999999998654322 23454433
No 13
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.58 E-value=0.048 Score=49.75 Aligned_cols=33 Identities=36% Similarity=0.514 Sum_probs=25.3
Q ss_pred HHHhhcccCcchHHHHHHHhhhCCCCCCccchh
Q 030389 108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDE 140 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDE 140 (178)
.+.|.+|+||||-||+||||...-...|+..=-
T Consensus 112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgN 144 (342)
T COG1194 112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGN 144 (342)
T ss_pred HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecc
Confidence 456677999999999999999766555655433
No 14
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=94.57 E-value=0.04 Score=48.38 Aligned_cols=33 Identities=27% Similarity=0.323 Sum_probs=27.5
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhh--hCCCCCC
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPDLAP 135 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~p 135 (178)
+...+++.|++||||||-||..||-. ..|+..|
T Consensus 201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp 235 (283)
T PRK10308 201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL 235 (283)
T ss_pred CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC
Confidence 56778999999999999999999865 5776544
No 15
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=94.45 E-value=0.032 Score=46.57 Aligned_cols=41 Identities=27% Similarity=0.264 Sum_probs=29.2
Q ss_pred ccHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389 102 PDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFC 144 (178)
Q Consensus 102 ~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~ 144 (178)
|+-....+.|.+|+||||-||..+|+...-+. -.-||-|.-
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~~--~~~~~~~~~ 148 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQL--GVTPEGWRE 148 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHHh--CCCCcchHH
Confidence 44556689999999999999999999753321 123555554
No 16
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=94.21 E-value=0.12 Score=43.94 Aligned_cols=28 Identities=32% Similarity=0.249 Sum_probs=24.1
Q ss_pred cHHHHHHHhh-cccCcchHHHHHHH-hhhC
Q 030389 103 DLTKAVSELT-VLKGVGPATASAVL-AAYA 130 (178)
Q Consensus 103 d~~~al~~L~-~LkGVGPATASaiL-a~~~ 130 (178)
++..+.+.|. +||||||=||+.|| .+..
T Consensus 112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~ 141 (208)
T PRK01229 112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY 141 (208)
T ss_pred CchHHHHHHHHcCCCCcHHHHHHHHHHccC
Confidence 5678899999 99999999999999 4543
No 17
>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=93.29 E-value=0.072 Score=38.52 Aligned_cols=40 Identities=30% Similarity=0.415 Sum_probs=30.6
Q ss_pred HHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCc
Q 030389 109 SELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFK 149 (178)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~ 149 (178)
+.|+.++||||-||..||+.. .+.--|=+...+....|+-
T Consensus 2 ~~l~sipGig~~~a~~llaei-gd~~rF~~~~~l~~~~Gl~ 41 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEI-GDISRFKSAKQLASYAGLA 41 (87)
T ss_pred chhcCCCCccHHHHHHHHHHH-cCchhcccchhhhhccccc
Confidence 468899999999999999986 2223477888888765543
No 18
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=92.80 E-value=0.21 Score=42.73 Aligned_cols=37 Identities=22% Similarity=0.273 Sum_probs=27.1
Q ss_pred HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHh
Q 030389 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCF 143 (178)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~ 143 (178)
...+.|.+|+||||=||.+||....- +.-|--|-=..
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~ 154 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSY 154 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHH
Confidence 46688999999999999999987543 32355555444
No 19
>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=92.77 E-value=0.1 Score=40.42 Aligned_cols=46 Identities=24% Similarity=0.261 Sum_probs=37.2
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCccc
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFT 151 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~~ 151 (178)
.+..+.|..|+||||.+|..|+.-..- ..||-|-|-+..++|+.++
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~-~g~f~s~eeL~~V~GIg~k 109 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYREE-NGAFKSVDDLTKVSGIGEK 109 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHHh-cCCcCCHHHHHcCCCCCHH
Confidence 345778999999999999999998653 5689897777778887543
No 20
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=92.62 E-value=0.079 Score=30.57 Aligned_cols=19 Identities=47% Similarity=0.763 Sum_probs=16.9
Q ss_pred HhhcccCcchHHHHHHHhh
Q 030389 110 ELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 110 ~L~~LkGVGPATASaiLa~ 128 (178)
.|++++|||+.+|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 4789999999999999974
No 21
>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=91.01 E-value=0.16 Score=38.43 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=22.2
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhhh
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~ 129 (178)
..+.+..|+.|+|||||||-=+..++
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LG 32 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLG 32 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence 35678899999999999999887774
No 22
>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=89.20 E-value=0.26 Score=33.34 Aligned_cols=23 Identities=35% Similarity=0.325 Sum_probs=17.6
Q ss_pred HHHhhcccCcchHHHHHHHhhhC
Q 030389 108 VSELTVLKGVGPATASAVLAAYA 130 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~ 130 (178)
|+.+++.-||||+||.-..+.+.
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~ 23 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGI 23 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT-
T ss_pred CcchhhcccccHHHHHHHHHhCC
Confidence 57899999999999999888653
No 23
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=88.91 E-value=0.61 Score=32.33 Aligned_cols=32 Identities=31% Similarity=0.398 Sum_probs=23.2
Q ss_pred HHHhhCccHHHHHHH-hhcccCcchHHHHHHHh
Q 030389 96 KAFKSLPDLTKAVSE-LTVLKGVGPATASAVLA 127 (178)
Q Consensus 96 ~Af~~l~d~~~al~~-L~~LkGVGPATASaiLa 127 (178)
.+.+.+|..-..++. +.+|+|||+.+|.-|--
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 345567755555675 99999999999988743
No 24
>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=87.69 E-value=0.28 Score=33.06 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=19.2
Q ss_pred HHHHhhcccCcchHHHHHHHhhh
Q 030389 107 AVSELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~ 129 (178)
....|..++||||.+|..+....
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 45678889999999999998884
No 25
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.40 E-value=0.27 Score=41.61 Aligned_cols=28 Identities=29% Similarity=0.453 Sum_probs=14.8
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhhCCC
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAYAPD 132 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (178)
+.-+..|....||||-||-+|||...|+
T Consensus 68 r~lF~~LisVsGIGPK~ALaILs~~~~~ 95 (196)
T PRK13901 68 REVFEELIGVDGIGPRAALRVLSGIKYN 95 (196)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 3445555555555555555555554443
No 26
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.22 E-value=0.42 Score=39.89 Aligned_cols=31 Identities=23% Similarity=0.362 Sum_probs=24.8
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhCCCC
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (178)
+-+.-+..|.+..||||-||-+||+...|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~ 97 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNAEA 97 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCHHH
Confidence 4566788888899999999999998877754
No 27
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=86.23 E-value=1.2 Score=39.76 Aligned_cols=28 Identities=32% Similarity=0.491 Sum_probs=25.9
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhC
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYA 130 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~ 130 (178)
|+-..++.|..|+||||-+|=+.|+++-
T Consensus 153 DIP~~v~dLlsLPGVGPKMa~L~m~~AW 180 (286)
T KOG1921|consen 153 DIPDTVEDLLSLPGVGPKMAHLTMQVAW 180 (286)
T ss_pred CCchhHHHHhcCCCCchHHHHHHHHHHh
Confidence 7889999999999999999999999853
No 28
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.03 E-value=0.35 Score=40.33 Aligned_cols=19 Identities=37% Similarity=0.686 Sum_probs=11.2
Q ss_pred HHhhcccCcchHHHHHHHh
Q 030389 109 SELTVLKGVGPATASAVLA 127 (178)
Q Consensus 109 ~~L~~LkGVGPATASaiLa 127 (178)
+.|++++|||+-||.=|+-
T Consensus 108 ~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 4566666666666665543
No 29
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=85.03 E-value=0.7 Score=38.27 Aligned_cols=27 Identities=33% Similarity=0.541 Sum_probs=20.2
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhhCC
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAYAP 131 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P 131 (178)
+.....|..++||||.||-.||+.+.+
T Consensus 69 k~~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 69 RELFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 344667788888888888888887654
No 30
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.19 E-value=0.65 Score=38.74 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=22.1
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhCCC
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYAPD 132 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (178)
+-+.-+..|.+..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 345567777788888888888888876664
No 31
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=84.10 E-value=0.71 Score=38.47 Aligned_cols=29 Identities=34% Similarity=0.568 Sum_probs=21.5
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhCC
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYAP 131 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P 131 (178)
+-+.-+..|...+||||-||-+||+...|
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL~~~~~ 94 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAILSNMSP 94 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHhcCCH
Confidence 34566777778888888888888877666
No 32
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.98 E-value=0.49 Score=39.47 Aligned_cols=42 Identities=19% Similarity=0.213 Sum_probs=23.2
Q ss_pred HHHhhcccCcchHHHHHHHhhhCCCC----CC--ccchhHHhhhhcCc
Q 030389 108 VSELTVLKGVGPATASAVLAAYAPDL----AP--FMSDEVCFCSFSFK 149 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~P~~----~p--FfSDEa~~~~~~~~ 149 (178)
.+.||+++|||+-||.-|.-=.-... .+ -..||+..++.+++
T Consensus 107 ~~~L~~vpGIGkKtAerIilELkdK~~~~~~~~~~~~~e~~~AL~~LG 154 (188)
T PRK14606 107 VEGLSKLPGISKKTAERIVMELKDEFESAGIKDMRIYHESLEALVSLG 154 (188)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHHhhccccCCCcccHHHHHHHHHHcC
Confidence 45677778888888876654322211 10 12266777665554
No 33
>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=83.60 E-value=1.6 Score=29.99 Aligned_cols=41 Identities=24% Similarity=0.256 Sum_probs=31.7
Q ss_pred HHHhhc-ccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCc
Q 030389 108 VSELTV-LKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFK 149 (178)
Q Consensus 108 l~~L~~-LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~ 149 (178)
.+.|.. ++|||+.+|.+|+.-... ..+|-+-+.+..++|+.
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~-~g~~~s~~dL~~v~gi~ 56 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREE-YGPFKTVEDLKQVPGIG 56 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHH-cCCcCCHHHHHcCCCCC
Confidence 446777 999999999999998643 33777867777777764
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=83.35 E-value=1.3 Score=37.78 Aligned_cols=61 Identities=31% Similarity=0.402 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHh------hCccH-HHHHHHhhcccCcchHHHHHHH
Q 030389 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFK------SLPDL-TKAVSELTVLKGVGPATASAVL 126 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~------~l~d~-~~al~~L~~LkGVGPATASaiL 126 (178)
..|+-.||..++ |..|.-|- + .|.+.+++-++ .+.++ .+..+.|++.+|||||.|..|+
T Consensus 12 ~~Lsd~ELLail---L~~g~~~~--------~---~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 12 EALSDYELLAII---LRTGTPKG--------L---DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred ccCCHHHHHHHH---HhCCCCCC--------C---CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence 578888966654 46665442 0 23333333332 23333 3458899999999999999999
Q ss_pred hh
Q 030389 127 AA 128 (178)
Q Consensus 127 a~ 128 (178)
++
T Consensus 78 a~ 79 (218)
T TIGR00608 78 AA 79 (218)
T ss_pred HH
Confidence 98
No 35
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.19 E-value=0.55 Score=39.41 Aligned_cols=46 Identities=28% Similarity=0.309 Sum_probs=27.5
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhhhCCCC---CCccchhHHhh-hhcCc
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAAYAPDL---APFMSDEVCFC-SFSFK 149 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFfSDEa~~~-~~~~~ 149 (178)
-+.-+..|....||||-||-+||+...|+. +.--.|..... +||++
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIG 116 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVG 116 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCC
Confidence 345566777777777777777777766643 22333444443 56654
No 36
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.91 E-value=0.63 Score=39.16 Aligned_cols=29 Identities=31% Similarity=0.456 Sum_probs=19.7
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhhhCCC
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAAYAPD 132 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (178)
-+.-+..|.+..||||-||-+||+...|+
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 34556667777777777777777766664
No 37
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=82.01 E-value=1.2 Score=35.91 Aligned_cols=46 Identities=26% Similarity=0.290 Sum_probs=35.4
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCccc
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFT 151 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~~ 151 (178)
.+..+.|..|+||||+.|-+|.+-..- ..||=|=|=..-++|+.+.
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~-~G~f~sv~dL~~v~GiG~~ 138 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREE-NGPFKSVDDLAKVKGIGPK 138 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHH-cCCCCcHHHHHhccCCCHH
Confidence 455778899999999999999998644 4488885656667777653
No 38
>PRK00024 hypothetical protein; Reviewed
Probab=81.68 E-value=2.4 Score=36.07 Aligned_cols=60 Identities=28% Similarity=0.447 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCc---cH-HHHHHHhhcccCcchHHHHHHHhh
Q 030389 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP---DL-TKAVSELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~---d~-~~al~~L~~LkGVGPATASaiLa~ 128 (178)
..|+-.||..++ |..|..|. .|...+++-++... ++ .+..+.|++++|||||.|..|+++
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 44444444443333 22 335778999999999999999887
No 39
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=81.38 E-value=1.4 Score=30.40 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.5
Q ss_pred HHHHHhhcccCcchHHHHHHHhhh
Q 030389 106 KAVSELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~ 129 (178)
+..+.|++++||||.+|..|....
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 467899999999999999988753
No 40
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=80.76 E-value=0.88 Score=30.57 Aligned_cols=22 Identities=32% Similarity=0.531 Sum_probs=18.8
Q ss_pred HHHHhhcccCcchHHHHHHHhh
Q 030389 107 AVSELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~ 128 (178)
..+.|++++||||.+|.-|...
T Consensus 36 ~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 36 DPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHHTSTTSSHHHHHHHHHH
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 4678999999999999988764
No 41
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=80.62 E-value=2.6 Score=38.17 Aligned_cols=32 Identities=28% Similarity=0.376 Sum_probs=24.5
Q ss_pred HHHHHHHhhcccCcchHHHHHHHhh--hCCCCCC
Q 030389 104 LTKAVSELTVLKGVGPATASAVLAA--YAPDLAP 135 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~--~~P~~~p 135 (178)
..+|-++||.|+||||-.|-.|+-. +-+..+|
T Consensus 213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP 246 (323)
T KOG2875|consen 213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVP 246 (323)
T ss_pred HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc
Confidence 4669999999999999999987644 3444444
No 42
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=79.74 E-value=3.7 Score=35.66 Aligned_cols=79 Identities=28% Similarity=0.386 Sum_probs=51.4
Q ss_pred hhhHHHhhhchh-hhccCCCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhh---CccHHH-HHH
Q 030389 35 LDDYYRKELPSL-IHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKS---LPDLTK-AVS 109 (178)
Q Consensus 35 LD~w~~~~lp~~-~~~r~~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~---l~d~~~-al~ 109 (178)
+.+|...+.|.- +...+ ...|+-.||.-|+ |+.|..+ ..|...++.-++. |..+.. .++
T Consensus 3 i~~~~~~~rPRErll~~G-~~~Lsd~ELLail---LrtG~~~------------~~~~~la~~lL~~fg~L~~l~~a~~~ 66 (224)
T COG2003 3 IKDNPENERPRERLLKLG-AEALSDAELLAIL---LRTGTKG------------ESVLDLAKELLQEFGSLAELLKASVE 66 (224)
T ss_pred ccccccccchHHHHHHhC-hhhcchHHHHHHH---HhcCCCC------------CCHHHHHHHHHHHcccHHHHHhCCHH
Confidence 345555555531 11112 3589999977766 6777644 3556666666553 334444 499
Q ss_pred HhhcccCcchHHHHHHHhhh
Q 030389 110 ELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 110 ~L~~LkGVGPATASaiLa~~ 129 (178)
.||.++|||+|-|.=+.++.
T Consensus 67 el~~v~GiG~aka~~l~a~~ 86 (224)
T COG2003 67 ELSSVKGIGLAKAIQIKAAI 86 (224)
T ss_pred HHhhCCCccHHHHHHHHHHH
Confidence 99999999999999888873
No 43
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=78.21 E-value=3.2 Score=31.36 Aligned_cols=41 Identities=22% Similarity=0.181 Sum_probs=30.9
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhh--CCC-CCCccchhHHhhh
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAY--APD-LAPFMSDEVCFCS 145 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~--~P~-~~pFfSDEa~~~~ 145 (178)
+...-+|++++|||+.+|..|+... +|. .+=..+||-+..+
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 664 3677888777653
No 44
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=77.45 E-value=1.2 Score=30.58 Aligned_cols=44 Identities=27% Similarity=0.261 Sum_probs=30.4
Q ss_pred HHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhcCcc
Q 030389 106 KAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKF 150 (178)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~~~~ 150 (178)
+..+.|..|+|||+.+|-.|+..-.- .-||-|=|=+..++|+.+
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R~~-~G~f~s~~dL~~v~gi~~ 54 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYREK-NGPFKSLEDLKEVPGIGP 54 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHHHH-H-S-SSGGGGGGSTT--H
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHh-CcCCCCHHHHhhCCCCCH
Confidence 46788999999999999999998543 358988777777888643
No 45
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.77 E-value=3.4 Score=34.45 Aligned_cols=62 Identities=16% Similarity=0.190 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHH----HHhhCccH--HHHHHHhhcccC
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEK----AFKSLPDL--TKAVSELTVLKG 116 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~----Af~~l~d~--~~al~~L~~LkG 116 (178)
++.|++|..-...-.--.| -=| +-+.+++..+++.+.++... ++..+|.+ +.|=.++.+||+
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkd 130 (188)
T PRK14606 62 GFSNERKKELFLSLTKVSR-LGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKD 130 (188)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 5788888655444433333 233 34666767677777766654 35556643 334444444443
No 46
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=76.26 E-value=2.4 Score=38.70 Aligned_cols=27 Identities=30% Similarity=0.400 Sum_probs=23.1
Q ss_pred cHHHHHHH--hhcccCcchHHHHHHHhhh
Q 030389 103 DLTKAVSE--LTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 103 d~~~al~~--L~~LkGVGPATASaiLa~~ 129 (178)
|+....+. +|+|+|||++||+.|--..
T Consensus 45 ~~~ei~e~~~~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 45 DLEEIEERGRLTELPGIGKGIAEKISEYL 73 (326)
T ss_pred chHHHHhhcccCCCCCccHHHHHHHHHHH
Confidence 67777777 9999999999999987664
No 47
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.91 E-value=3.7 Score=34.44 Aligned_cols=64 Identities=19% Similarity=0.167 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHHh
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLA 127 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa 127 (178)
++.|++|..-...-.--.| -=| +-+.+++..+++.+.++... .=.+.||+++|||+-||--|..
T Consensus 62 GF~~~~Er~lF~~Li~V~G-IGpK~Al~iLs~~~~~el~~aI~~---------~D~~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 62 GFSTPAQRQLFELLIGVSG-VGPKAALNLLSSGTPDELQLAIAG---------GDVARLARVPGIGKKTAERIVL 126 (195)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHH
Confidence 5789998665554433333 223 34556666667666655543 2356899999999999998764
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.88 E-value=3.7 Score=34.20 Aligned_cols=85 Identities=15% Similarity=0.106 Sum_probs=49.9
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHH----HHhhCccH--HHHHHHhhcccCcchHHHHHHH
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEK----AFKSLPDL--TKAVSELTVLKGVGPATASAVL 126 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~----Af~~l~d~--~~al~~L~~LkGVGPATASaiL 126 (178)
++.|++|..-...-.--.| -=| .-+..++..+++.+.++... ++..+|.+ +.|=+++.+|||==+ +
T Consensus 62 GF~~~~Er~lF~~Li~VsG-IGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK~~---~--- 134 (183)
T PRK14601 62 GFLDKDEQKMFEMLLKVNG-IGANTAMAVCSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDAKT---K--- 134 (183)
T ss_pred CCCCHHHHHHHHHHhccCC-ccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHhh---c---
Confidence 5788988665554433333 334 34667777788887777654 46667754 556666667776410 0
Q ss_pred hhhCCCCCCccchhHHhhhhcCc
Q 030389 127 AAYAPDLAPFMSDEVCFCSFSFK 149 (178)
Q Consensus 127 a~~~P~~~pFfSDEa~~~~~~~~ 149 (178)
. .+.. . -.+|+..++.+++
T Consensus 135 -~-~~~~-~-~~~ea~~AL~~LG 153 (183)
T PRK14601 135 -L-ENVS-D-DKSEALAALLTLG 153 (183)
T ss_pred -c-CCCC-c-cHHHHHHHHHHcC
Confidence 0 0111 1 1378888877665
No 49
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=75.65 E-value=2.4 Score=33.72 Aligned_cols=41 Identities=22% Similarity=0.247 Sum_probs=32.4
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhhh
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFCS 145 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~ 145 (178)
+...=+||.++|||+++|-+|+... +|+. +=..+||-+..+
T Consensus 13 K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 13 KRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred ceEeehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 3334478999999999999999984 6654 788899888764
No 50
>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=75.37 E-value=4 Score=36.09 Aligned_cols=38 Identities=24% Similarity=0.314 Sum_probs=28.3
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhh
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCS 145 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~ 145 (178)
+...+|..|++++||||.||-.+...+.-.. ||...++
T Consensus 79 ~~~~~l~~l~~i~GiGpk~a~~l~~lGi~sl-----~dL~~a~ 116 (307)
T cd00141 79 DVPPGLLLLLRVPGVGPKTARKLYELGIRTL-----EDLRKAA 116 (307)
T ss_pred cchHHHHHHHcCCCCCHHHHHHHHHcCCCCH-----HHHHHHh
Confidence 3567899999999999999999885443322 6666655
No 51
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.56 E-value=4.6 Score=34.19 Aligned_cols=86 Identities=15% Similarity=0.223 Sum_probs=52.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHHhhhCC-
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAP- 131 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P- 131 (178)
++.|++|..-...-.--.| -=| .-+..++..+++.+.+++.. .=.+.||+++|||+-||.=|.-=...
T Consensus 61 GF~t~~Er~lF~~LisVsG-IGPK~ALaILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 61 GFLNSSEREVFEELIGVDG-IGPRAALRVLSGIKYNEFRDAIDR---------EDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 5788998665544433333 233 34566666777766665533 23578999999999999977632111
Q ss_pred -------CCCCccchhHHhhhhcCc
Q 030389 132 -------DLAPFMSDEVCFCSFSFK 149 (178)
Q Consensus 132 -------~~~pFfSDEa~~~~~~~~ 149 (178)
...+--.+|+..++.+++
T Consensus 131 l~~~~~~~~~~~~~~ea~~AL~~LG 155 (196)
T PRK13901 131 LVKNDELESSLFKFKELEQSIVNMG 155 (196)
T ss_pred hccccccccCcccHHHHHHHHHHcC
Confidence 011111378888876655
No 52
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.68 E-value=5 Score=33.68 Aligned_cols=63 Identities=21% Similarity=0.154 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHH
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiL 126 (178)
++.|++|..-.-.-.--.| -=| +-+.+++..+++.+.+++.. .=.+.|++++||||-||.-|.
T Consensus 61 GF~~~~Er~lF~~L~~V~G-IGpK~AL~iLs~~~~~~l~~aI~~---------~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 61 GFPDEDSLELFELLLGVSG-VGPKLALALLSALPPALLARALLE---------GDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred CcCCHHHHHHHHHHhCcCC-cCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHH
Confidence 5788888654444332233 233 34566666777766665543 235689999999999998776
No 53
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=72.28 E-value=2.7 Score=35.96 Aligned_cols=23 Identities=39% Similarity=0.700 Sum_probs=19.5
Q ss_pred ccHHHHHHHhhcccCcchHHHHH
Q 030389 102 PDLTKAVSELTVLKGVGPATASA 124 (178)
Q Consensus 102 ~d~~~al~~L~~LkGVGPATASa 124 (178)
+.+.+-|+.|.+|+||||-||.=
T Consensus 5 ~~i~~LI~~l~kLPGvG~KsA~R 27 (198)
T COG0353 5 PPIEKLIDALKKLPGVGPKSAQR 27 (198)
T ss_pred HHHHHHHHHHhhCCCCChhHHHH
Confidence 35677899999999999999873
No 54
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.88 E-value=2.5 Score=35.42 Aligned_cols=48 Identities=23% Similarity=0.182 Sum_probs=34.8
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhCCCC---CCccchhHHhh-hhcCcc
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL---APFMSDEVCFC-SFSFKF 150 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFfSDEa~~~-~~~~~~ 150 (178)
+-+.-+..|++..||||-||-+||+...|+. +.--.|..... +||++.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGk 118 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGK 118 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCH
Confidence 4567788999999999999999999987754 22223444443 677654
No 55
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=71.39 E-value=2.9 Score=26.14 Aligned_cols=15 Identities=47% Similarity=0.729 Sum_probs=13.1
Q ss_pred cccCcchHHHHHHHh
Q 030389 113 VLKGVGPATASAVLA 127 (178)
Q Consensus 113 ~LkGVGPATASaiLa 127 (178)
-++||||.||--+|.
T Consensus 20 Gv~giG~ktA~~ll~ 34 (36)
T smart00279 20 GVKGIGPKTALKLLR 34 (36)
T ss_pred CCCcccHHHHHHHHH
Confidence 589999999998875
No 56
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.06 E-value=5.7 Score=33.44 Aligned_cols=63 Identities=16% Similarity=0.212 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHH
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiL 126 (178)
++.|.+|..-...-.--.|- =| +-+.+++..+++.+.++... .=.+.|++++|||+-||--|+
T Consensus 63 GF~~~~Er~lF~~Li~V~GI-GpK~Al~iLs~~~~~~l~~aI~~---------~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 63 GFATWDERQTFIVLISISKV-GAKTALAILSQFRPDDLRRLVAE---------EDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred CCCCHHHHHHHHHHhCCCCc-CHHHHHHHHhhCCHHHHHHHHHh---------CCHHHHhcCCCcCHHHHHHHH
Confidence 57888886655544333332 23 34566666677766655543 235689999999999999876
No 57
>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=70.13 E-value=3.3 Score=33.46 Aligned_cols=38 Identities=26% Similarity=0.318 Sum_probs=28.7
Q ss_pred HHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhh
Q 030389 107 AVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFC 144 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~ 144 (178)
..-+|+.++|||+.+|-.|+... +|.. +--.+||-...
T Consensus 19 v~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~ 59 (144)
T TIGR03629 19 VEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEK 59 (144)
T ss_pred EEEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHH
Confidence 34468999999999999999874 5543 66677776665
No 58
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=69.08 E-value=3.2 Score=35.31 Aligned_cols=47 Identities=21% Similarity=0.255 Sum_probs=32.0
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhhhCCCC---CCccchhHHhh-hhcCc
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDL---APFMSDEVCFC-SFSFK 149 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~---~pFfSDEa~~~-~~~~~ 149 (178)
+-+.-+..|.+.-||||-||=+|||..+|+. +.==.|..+.. +||.+
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIG 117 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIG 117 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCC
Confidence 5667788888999999999999999887753 11122444443 56654
No 59
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=67.80 E-value=6.2 Score=32.88 Aligned_cols=63 Identities=24% Similarity=0.245 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHH
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiL 126 (178)
++.|++|..-..+-.--.|- =| +-+.+++.-+++.+.++.... =.+.|++++|||+-||.-|+
T Consensus 61 GF~~~~Er~lF~~L~~V~GI-GpK~Al~iL~~~~~~el~~aI~~~---------d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 61 GFNTLEERELFKELIKVNGV-GPKLALAILSNMSPEEFVYAIETE---------EVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred CCCCHHHHHHHHHHhCCCCC-CHHHHHHHHhcCCHHHHHHHHHhC---------CHHHHHhCCCCCHHHHHHHH
Confidence 57899997665555433331 12 223344444444444333221 13468999999999999987
No 60
>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=66.28 E-value=4.9 Score=35.56 Aligned_cols=37 Identities=24% Similarity=0.381 Sum_probs=27.1
Q ss_pred HHhhCccHHHHHHHhhcccCcchHHHHHHHhhhCCCC
Q 030389 97 AFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (178)
Q Consensus 97 Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (178)
+.+.++..-..+..+++|+|||+++|+.|--...-..
T Consensus 33 ~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~tG~ 69 (307)
T cd00141 33 ALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGK 69 (307)
T ss_pred HHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHHcCC
Confidence 3445665455566779999999999999988765433
No 61
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=64.68 E-value=3.4 Score=33.87 Aligned_cols=45 Identities=22% Similarity=0.101 Sum_probs=32.9
Q ss_pred hCccHHHHHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhh
Q 030389 100 SLPDLTKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFC 144 (178)
Q Consensus 100 ~l~d~~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~ 144 (178)
-+|+-+...-+|+.++|||+.+|-.|+... +|+. +-=.+||=...
T Consensus 21 ~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~ 68 (154)
T PTZ00134 21 NVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEK 68 (154)
T ss_pred cCCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHH
Confidence 345555666678999999999999999984 5543 55566666654
No 62
>PRK00076 recR recombination protein RecR; Reviewed
Probab=64.56 E-value=5.3 Score=33.89 Aligned_cols=23 Identities=30% Similarity=0.603 Sum_probs=19.0
Q ss_pred cHHHHHHHhhcccCcchHHHHHH
Q 030389 103 DLTKAVSELTVLKGVGPATASAV 125 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASai 125 (178)
.+.+-++.|.+|+||||-||.=+
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rl 27 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRL 27 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHH
Confidence 35677889999999999999754
No 63
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=64.42 E-value=5.8 Score=32.28 Aligned_cols=44 Identities=27% Similarity=0.292 Sum_probs=31.9
Q ss_pred ccHHHHHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhhh
Q 030389 102 PDLTKAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFCS 145 (178)
Q Consensus 102 ~d~~~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~ 145 (178)
++-+...-+|+.++|||+.+|-.|+... +|.. +--.+||-...+
T Consensus 18 ~~~k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l 64 (149)
T PRK04053 18 DGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKI 64 (149)
T ss_pred CCCCEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHH
Confidence 3444455578999999999999999874 5543 666777766653
No 64
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=64.42 E-value=6.7 Score=30.81 Aligned_cols=40 Identities=25% Similarity=0.361 Sum_probs=30.3
Q ss_pred HHHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhhh
Q 030389 106 KAVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFCS 145 (178)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~ 145 (178)
...-+|+.+.|||+.||-.|+... +|+. +--.+||-+..+
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 344568999999999999999984 6654 667777776653
No 65
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=63.65 E-value=26 Score=28.93 Aligned_cols=86 Identities=19% Similarity=0.171 Sum_probs=46.3
Q ss_pred CCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHHhhhCCCCC
Q 030389 55 HINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLA 134 (178)
Q Consensus 55 ~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~ 134 (178)
+.+..|-.....+.--.|--.=+-+.+++.-..+.+.++..+ +-.+.|++++|||+.||-.|+.-......
T Consensus 63 F~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~---------~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 63 FLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIAN---------GDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred cCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 446665444334443444322233444444443333322222 23567899999999999999976543321
Q ss_pred Cc------------cchhHHhhhhcCc
Q 030389 135 PF------------MSDEVCFCSFSFK 149 (178)
Q Consensus 135 pF------------fSDEa~~~~~~~~ 149 (178)
.+ -.+|++.++.+++
T Consensus 134 ~~~~~~~~~~~~~~~~~ev~~aL~~LG 160 (192)
T PRK00116 134 AAASAAAAAAAASSALEEAVSALVALG 160 (192)
T ss_pred cccccccccccccchHHHHHHHHHHcC
Confidence 11 0267887766654
No 66
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=63.25 E-value=3.5 Score=39.16 Aligned_cols=56 Identities=20% Similarity=0.201 Sum_probs=33.8
Q ss_pred CCchhHHHhhhCCHHHHHHHHH----------------HHHhhCcc-HHHHHHHhhc-ccCcchHHHHHHHhhh
Q 030389 74 WRPRLLVFVSSLDDSSVKSASE----------------KAFKSLPD-LTKAVSELTV-LKGVGPATASAVLAAY 129 (178)
Q Consensus 74 fRP~L~~lv~sN~~~~V~~~t~----------------~Af~~l~d-~~~al~~L~~-LkGVGPATASaiLa~~ 129 (178)
.=|+|.++....=+..|.+.-. .-.+.++. +...-+.|.+ ++||||-||-||+|..
T Consensus 153 kwPTl~dla~Asl~~eVn~lWaGlGyY~R~rrL~ega~~vv~~~~ge~Prta~~l~kgvpGVG~YTAGAiaSIA 226 (555)
T KOG2457|consen 153 KWPTLYDLAQASLEKEVNELWAGLGYYRRARRLLEGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIA 226 (555)
T ss_pred hCchHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHhhCCCCCccchhhhhhhh
Confidence 3588888876655555554321 11111111 2223345555 9999999999999984
No 67
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.23 E-value=6.2 Score=33.50 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=18.7
Q ss_pred HHHHHHHhhcccCcchHHHHHH
Q 030389 104 LTKAVSELTVLKGVGPATASAV 125 (178)
Q Consensus 104 ~~~al~~L~~LkGVGPATASai 125 (178)
+.+-++.|.+|+||||-||-=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5677889999999999999754
No 68
>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=62.08 E-value=5 Score=24.29 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=11.4
Q ss_pred hhcccCcchHHHHHH
Q 030389 111 LTVLKGVGPATASAV 125 (178)
Q Consensus 111 L~~LkGVGPATASai 125 (178)
+.++.|||+.|+--+
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 69
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=61.08 E-value=12 Score=31.15 Aligned_cols=51 Identities=16% Similarity=0.308 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+||+..||.+|-.. +..|..|...-+.+.+|....|.++.++-|...|+
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 4579999999999776 57899999999999999999999999999987773
No 70
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=60.57 E-value=7.9 Score=33.51 Aligned_cols=37 Identities=27% Similarity=0.298 Sum_probs=26.5
Q ss_pred HHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhh
Q 030389 107 AVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFC 144 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~ 144 (178)
.-+.|-++||||+-||=+||--... +.-|.-|.--.-
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~~-rp~FVvD~Yt~R 149 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYALD-RPVFVVDKYTRR 149 (215)
T ss_pred HHHHHHccCCcchhhHHHHHHHHhc-CcccchhHHHHH
Confidence 4577889999999999999876432 435666654443
No 71
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=60.50 E-value=7.9 Score=29.92 Aligned_cols=38 Identities=24% Similarity=0.284 Sum_probs=29.8
Q ss_pred HHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhhh
Q 030389 108 VSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFCS 145 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~ 145 (178)
.-.|+.+.|||+.+|-.|+... +|.. +-..+||-+..+
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 54 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAI 54 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 3467999999999999999874 5654 677888777753
No 72
>PRK13844 recombination protein RecR; Provisional
Probab=60.45 E-value=6.9 Score=33.37 Aligned_cols=23 Identities=13% Similarity=0.365 Sum_probs=18.9
Q ss_pred cHHHHHHHhhcccCcchHHHHHH
Q 030389 103 DLTKAVSELTVLKGVGPATASAV 125 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASai 125 (178)
.+.+-++.|.+|+||||-||.=+
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rl 31 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRL 31 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHH
Confidence 35677889999999999998744
No 73
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=59.14 E-value=9 Score=30.04 Aligned_cols=39 Identities=33% Similarity=0.357 Sum_probs=29.7
Q ss_pred HHHHhhcccCcchHHHHHHHhhh--CCCC-CCccchhHHhhh
Q 030389 107 AVSELTVLKGVGPATASAVLAAY--APDL-APFMSDEVCFCS 145 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~--~P~~-~pFfSDEa~~~~ 145 (178)
..-+|+.+.|||+.+|-.|+... +|.. +--.+||=+..+
T Consensus 15 v~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 56 (122)
T PRK05179 15 VVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKI 56 (122)
T ss_pred EEeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 34468999999999999999874 5654 667777776653
No 74
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=59.10 E-value=8.7 Score=34.42 Aligned_cols=26 Identities=31% Similarity=0.419 Sum_probs=22.9
Q ss_pred cHHHHHHHhhcccCcchHHHHHHHhh
Q 030389 103 DLTKAVSELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~ 128 (178)
.+..++..|++++||||.||-.+-..
T Consensus 83 ~~p~~l~~l~~i~GiGpk~a~~l~~l 108 (334)
T smart00483 83 EVYKSLKLFTNVFGVGPKTAAKWYRK 108 (334)
T ss_pred cHHHHHHHHHccCCcCHHHHHHHHHh
Confidence 46779999999999999999988774
No 75
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=57.58 E-value=7.4 Score=34.85 Aligned_cols=36 Identities=22% Similarity=0.306 Sum_probs=25.9
Q ss_pred HhhCccHHHHHHHhhcccCcchHHHHHHHhhhCCCC
Q 030389 98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDL 133 (178)
Q Consensus 98 f~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (178)
++.+|..-..+..|++|+|||+++|.-|--...-..
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 445554334456789999999999999987754433
No 76
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=56.02 E-value=7.8 Score=27.45 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=16.1
Q ss_pred hhcccCcchHHHHHHHhhh
Q 030389 111 LTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 111 L~~LkGVGPATASaiLa~~ 129 (178)
+..++||||-||.-+|.-+
T Consensus 24 i~gv~giG~k~A~~ll~~~ 42 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEY 42 (75)
T ss_pred CCCCCcccHHHHHHHHHHh
Confidence 3458999999999999874
No 77
>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=54.46 E-value=10 Score=30.42 Aligned_cols=51 Identities=20% Similarity=0.206 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+|++..||..|-..- .+|.-|....+.+++|.+.-|.++.++-|...|+
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 5577799999999999999999999999988874
No 78
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=54.44 E-value=40 Score=22.91 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=17.2
Q ss_pred HHHHhhcccCcchHHHHHHHhh
Q 030389 107 AVSELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~ 128 (178)
.++.|.+++|||..||--|+..
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhh
Confidence 4566777889999999887754
No 79
>PRK07945 hypothetical protein; Provisional
Probab=52.39 E-value=15 Score=32.84 Aligned_cols=19 Identities=47% Similarity=0.733 Sum_probs=13.7
Q ss_pred HhhcccCcchHHHHHHHhh
Q 030389 110 ELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 110 ~L~~LkGVGPATASaiLa~ 128 (178)
.|++|+|||..||.-|--.
T Consensus 50 ~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred CcccCCCcCHHHHHHHHHH
Confidence 5777888888887766554
No 80
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=51.14 E-value=12 Score=31.19 Aligned_cols=87 Identities=17% Similarity=0.158 Sum_probs=48.2
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHH-------
Q 030389 54 PHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL------- 126 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiL------- 126 (178)
++.|++|-.-.-.-.--.|-===+-+..++.-+++.+.++... .=.+.|++++|||+-||--|.
T Consensus 62 GF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~---------~D~~~L~~vpGIGkKtAerIilELk~Ki 132 (194)
T PRK14605 62 GFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAEALASAIIS---------GNAELLSTIPGIGKKTASRIVLELKDKI 132 (194)
T ss_pred CCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 5788888655444433333211134555555566554443322 234679999999999999843
Q ss_pred -hhhCCC---CCCccchhHHhhhhcCc
Q 030389 127 -AAYAPD---LAPFMSDEVCFCSFSFK 149 (178)
Q Consensus 127 -a~~~P~---~~pFfSDEa~~~~~~~~ 149 (178)
...... ..+--.+|++.++.+++
T Consensus 133 ~~~~~~~~~~~~~~~~~e~~~aL~~LG 159 (194)
T PRK14605 133 AKNWEAGVLSQVTEANSDILATLTALG 159 (194)
T ss_pred HhhhhccccccccchHHHHHHHHHHcC
Confidence 211100 01112478888877665
No 81
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=50.09 E-value=11 Score=32.91 Aligned_cols=43 Identities=33% Similarity=0.443 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHhhCccHHHH-HHHhhcccCcchHHHHHHHhhh
Q 030389 87 DSSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 87 ~~~V~~~t~~Af~~l~d~~~a-l~~L~~LkGVGPATASaiLa~~ 129 (178)
+..++..-..+|..+.++..| .+.|.+++|||+++|--|....
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 344455555557666676665 8999999999999999998874
No 82
>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=49.22 E-value=40 Score=25.97 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=16.8
Q ss_pred HHHHhhcccCcchHHHHHHHh
Q 030389 107 AVSELTVLKGVGPATASAVLA 127 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa 127 (178)
.++.|.+++||||.|+--|.-
T Consensus 96 s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 96 SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHHcCCCCCHHHHHHHHh
Confidence 467778899999999877653
No 83
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.27 E-value=44 Score=27.27 Aligned_cols=51 Identities=22% Similarity=0.270 Sum_probs=35.1
Q ss_pred HHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhc---ccCcchHHHHHHHhhhCC
Q 030389 80 VFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTV---LKGVGPATASAVLAAYAP 131 (178)
Q Consensus 80 ~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~---LkGVGPATASaiLa~~~P 131 (178)
+|---=++..|-++|+-|.+-+|-+ +.+.++.. =+.+|||.|+|+.++.-|
T Consensus 28 rL~pvFpEnRVikaTrfairfMP~v-Avftl~wQ~~~~~ql~pAv~tAlfal~lp 81 (149)
T COG3092 28 RLAPVFPENRVIKATRFAIRFMPPV-AVFTLCWQIALGGQLGPAVATALFALSLP 81 (149)
T ss_pred hhcccCchhHHHHHHHHHHHhccHH-HHHHHHHHHHHhcccchHHHHHHHHHhcc
Confidence 3333456889999999999988743 22222222 237999999999998554
No 84
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=48.00 E-value=34 Score=28.30 Aligned_cols=51 Identities=12% Similarity=0.155 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+|++..||.+|.. -+.+|.-|-..-+.+.+|....|.++.++-|+..|+
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 457999999999866 467899999999999999999999999999998774
No 85
>PRK14976 5'-3' exonuclease; Provisional
Probab=47.65 E-value=11 Score=33.05 Aligned_cols=17 Identities=47% Similarity=0.874 Sum_probs=14.9
Q ss_pred ccCcchHHHHHHHhhhC
Q 030389 114 LKGVGPATASAVLAAYA 130 (178)
Q Consensus 114 LkGVGPATASaiLa~~~ 130 (178)
++||||-||.-+|.-+.
T Consensus 196 VpGIG~KtA~~LL~~~g 212 (281)
T PRK14976 196 VKGIGPKTAIKLLNKYG 212 (281)
T ss_pred CCcccHHHHHHHHHHcC
Confidence 79999999999997643
No 86
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.40 E-value=21 Score=29.74 Aligned_cols=85 Identities=16% Similarity=0.165 Sum_probs=50.5
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHHhhh---
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY--- 129 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~--- 129 (178)
++.|++|..-.-.-.--.| -=| +-+.+++..+++.+.++... .| .+.| +++|||+-||.-|+.=.
T Consensus 62 GF~~~~Er~lF~~LisV~G-IGpK~Al~iLs~~~~~~l~~aI~~-----~D----~~~L-~vpGIGkKtAerIilELk~K 130 (186)
T PRK14600 62 GFLNREEQDCLRMLVKVSG-VNYKTAMSILSKLTPEQLFSAIVN-----ED----KAAL-KVNGIGEKLINRIITELQYK 130 (186)
T ss_pred CCCCHHHHHHHHHHhCcCC-cCHHHHHHHHccCCHHHHHHHHHc-----CC----Hhhe-ECCCCcHHHHHHHHHHHHHH
Confidence 5788888665544433333 223 34566666677766665543 13 3567 89999999999887321
Q ss_pred ----CCCC--CCccchhHHhhhhcCc
Q 030389 130 ----APDL--APFMSDEVCFCSFSFK 149 (178)
Q Consensus 130 ----~P~~--~pFfSDEa~~~~~~~~ 149 (178)
.+.. ..--.||+..++.+++
T Consensus 131 ~~~~~~~~~~~~~~~~e~~~aL~~LG 156 (186)
T PRK14600 131 VSKLEINETNFIIINDDALAALISLG 156 (186)
T ss_pred hhccccccccccccHHHHHHHHHHcC
Confidence 1111 0001378888877665
No 87
>PRK08609 hypothetical protein; Provisional
Probab=46.31 E-value=22 Score=34.18 Aligned_cols=19 Identities=37% Similarity=0.634 Sum_probs=9.2
Q ss_pred HHhhcccCcchHHHHHHHh
Q 030389 109 SELTVLKGVGPATASAVLA 127 (178)
Q Consensus 109 ~~L~~LkGVGPATASaiLa 127 (178)
..|++|+|||+++|+-|--
T Consensus 48 ~~l~~ipgIG~~ia~kI~E 66 (570)
T PRK08609 48 DDFTKLKGIGKGTAEVIQE 66 (570)
T ss_pred hhhccCCCcCHHHHHHHHH
Confidence 3444555555555554433
No 88
>CHL00090 apcD allophycocyanin gamma subunit
Probab=45.96 E-value=29 Score=28.39 Aligned_cols=51 Identities=20% Similarity=0.307 Sum_probs=44.8
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+|+|..||..|-.. +..|.-|-..-+.+++|.+.-|.++.++-|...|+
T Consensus 14 ~gRyls~~EL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~ 64 (161)
T CHL00090 14 ELRYPTIGELESIQDY-LKTGEKRIRIATILRDNEKEIIQKASKQLFQIHPE 64 (161)
T ss_pred ccCCCCHHHHHHHHHH-HHhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHCcC
Confidence 3589999999999776 57788899999999999999999999999987773
No 89
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=45.07 E-value=22 Score=32.82 Aligned_cols=33 Identities=27% Similarity=0.511 Sum_probs=22.2
Q ss_pred HHHhhCccH-HHHHHHhhcccCcchHHHHHHHhh
Q 030389 96 KAFKSLPDL-TKAVSELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 96 ~Af~~l~d~-~~al~~L~~LkGVGPATASaiLa~ 128 (178)
+-|..+..+ .+..+.|++.+|||++.|-.|-..
T Consensus 305 ~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 305 EHFGSLQGLLAASIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred HHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHH
Confidence 334444443 344778899999999998886554
No 90
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=44.68 E-value=40 Score=27.77 Aligned_cols=51 Identities=12% Similarity=0.204 Sum_probs=45.2
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+|++..||.+|.. -+..|..|-..-+.+.+|....|.++.++-|+..|+
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 457999999999865 468899999999999999999999999999998774
No 91
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=44.17 E-value=31 Score=28.98 Aligned_cols=51 Identities=16% Similarity=0.142 Sum_probs=45.4
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+||+.+||.+|-. -+..|..|-..-+.+.+|...-|.++.++-|...|+
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 468899999999999999999999999999998774
No 92
>CHL00086 apcA allophycocyanin alpha subunit
Probab=43.85 E-value=34 Score=28.01 Aligned_cols=51 Identities=20% Similarity=0.385 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+|++..||..|-.. +..|..|-..-+.+.+|.+.-|.++.++-|...|+
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 67889999999999999999999999999987774
No 93
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=43.47 E-value=31 Score=28.47 Aligned_cols=51 Identities=16% Similarity=0.193 Sum_probs=44.9
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+||+..||..|-. -+.+|.-|...-+.+.+|-.+.|.++.+.-|+..|+
T Consensus 15 ~gRyls~~eL~~l~~-~~~~a~~rl~aa~~L~~na~~iV~~A~~~l~~~~P~ 65 (164)
T CHL00173 15 AGRFPSSSDLESVQG-NIQRAAARLEAAEKLASNHEAVVKEAGDACFAKYSY 65 (164)
T ss_pred ccCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 457999999999754 467899999999999999999999999999998774
No 94
>PRK09482 flap endonuclease-like protein; Provisional
Probab=43.34 E-value=15 Score=32.21 Aligned_cols=17 Identities=29% Similarity=0.778 Sum_probs=15.3
Q ss_pred ccCcchHHHHHHHhhhC
Q 030389 114 LKGVGPATASAVLAAYA 130 (178)
Q Consensus 114 LkGVGPATASaiLa~~~ 130 (178)
.+||||.||.-+|.-+.
T Consensus 187 VpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 187 VAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCcChHHHHHHHHHhC
Confidence 89999999999998754
No 95
>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=41.85 E-value=23 Score=25.57 Aligned_cols=33 Identities=24% Similarity=0.423 Sum_probs=23.9
Q ss_pred hhcccCcchHHHHHHHhhhCCCCCCccc-hhHHhhh
Q 030389 111 LTVLKGVGPATASAVLAAYAPDLAPFMS-DEVCFCS 145 (178)
Q Consensus 111 L~~LkGVGPATASaiLa~~~P~~~pFfS-DEa~~~~ 145 (178)
|+.+||||..+|-.|+.... .-||-| +|....+
T Consensus 29 l~~Ikglg~~~a~~I~~~R~--~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERE--NGPFKSLEDFIQRL 62 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHH--CSS-SSHHHHHHHS
T ss_pred HhhcCCCCHHHHHHHHHhHh--cCCCCCHHHHHHHH
Confidence 67899999999999999976 458888 4444444
No 96
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=41.76 E-value=16 Score=31.92 Aligned_cols=42 Identities=21% Similarity=0.104 Sum_probs=29.0
Q ss_pred HHhhcccCcchHHHHHHHhhhCC--CCCCccchhHHhhhhcCcc
Q 030389 109 SELTVLKGVGPATASAVLAAYAP--DLAPFMSDEVCFCSFSFKF 150 (178)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~~P--~~~pFfSDEa~~~~~~~~~ 150 (178)
+.|..++||||+++-.+|..+.. +.+---|.|-+..++|+..
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~ 46 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGN 46 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCH
Confidence 46788999999999999998322 2234444555666777643
No 97
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=40.84 E-value=26 Score=27.00 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=22.4
Q ss_pred HHHHHhhcccCcchHHHHHHHhhhCC
Q 030389 106 KAVSELTVLKGVGPATASAVLAAYAP 131 (178)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P 131 (178)
.++.-|+.++||||..|-++..++..
T Consensus 50 ~~~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 50 VNQADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HhHHHhhhcCCCCHHHHHHHHHhCcC
Confidence 46777889999999999999999754
No 98
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=39.52 E-value=19 Score=30.67 Aligned_cols=16 Identities=38% Similarity=0.737 Sum_probs=14.6
Q ss_pred ccCcchHHHHHHHhhh
Q 030389 114 LKGVGPATASAVLAAY 129 (178)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (178)
++||||.||.-+|.-+
T Consensus 188 v~GiG~ktA~~Ll~~~ 203 (240)
T cd00008 188 VPGIGEKTAAKLLKEY 203 (240)
T ss_pred CCccCHHHHHHHHHHh
Confidence 8999999999999875
No 99
>smart00475 53EXOc 5'-3' exonuclease.
Probab=38.63 E-value=20 Score=31.17 Aligned_cols=17 Identities=29% Similarity=0.651 Sum_probs=14.8
Q ss_pred ccCcchHHHHHHHhhhC
Q 030389 114 LKGVGPATASAVLAAYA 130 (178)
Q Consensus 114 LkGVGPATASaiLa~~~ 130 (178)
++||||-||.-+|.=+.
T Consensus 191 V~GIG~KtA~~Ll~~yg 207 (259)
T smart00475 191 VPGIGEKTAAKLLKEFG 207 (259)
T ss_pred CCCCCHHHHHHHHHHhC
Confidence 79999999999997643
No 100
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=38.19 E-value=5.1 Score=30.42 Aligned_cols=16 Identities=44% Similarity=0.910 Sum_probs=13.9
Q ss_pred ccCcchHHHHHHHhhh
Q 030389 114 LKGVGPATASAVLAAY 129 (178)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (178)
.+||||-||+-+|.-+
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 101
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=38.05 E-value=26 Score=34.05 Aligned_cols=43 Identities=21% Similarity=0.176 Sum_probs=29.7
Q ss_pred HHHhhcccCcchHHHHHHHhhhCC-CCCCccchhHHhhhhcCcc
Q 030389 108 VSELTVLKGVGPATASAVLAAYAP-DLAPFMSDEVCFCSFSFKF 150 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~~~~~ 150 (178)
...|+.++||||.++-.||..+.. +.+---|.|-+..++|+..
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~ 585 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISK 585 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCH
Confidence 467889999999999999997532 2222234555666777654
No 102
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=37.83 E-value=39 Score=28.04 Aligned_cols=51 Identities=18% Similarity=0.282 Sum_probs=44.6
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|+++.++-|...|+
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 3579999999998775 67888898888899999999999999999987774
No 103
>PRK08609 hypothetical protein; Provisional
Probab=36.07 E-value=22 Score=34.24 Aligned_cols=22 Identities=18% Similarity=0.308 Sum_probs=14.3
Q ss_pred HHHHHHhhcccCcchHHHHHHH
Q 030389 105 TKAVSELTVLKGVGPATASAVL 126 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiL 126 (178)
..++..|++++||||.||-.+-
T Consensus 84 p~~~~~l~~i~GiGpk~a~~l~ 105 (570)
T PRK08609 84 PEGLLPLLKLPGLGGKKIAKLY 105 (570)
T ss_pred cHHHHHHhcCCCCCHHHHHHHH
Confidence 3456666777777777776654
No 104
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=35.54 E-value=31 Score=33.58 Aligned_cols=43 Identities=21% Similarity=0.089 Sum_probs=31.4
Q ss_pred HHHhhcccCcchHHHHHHHhhh-CCCCCCccchhHHhhhhcCcc
Q 030389 108 VSELTVLKGVGPATASAVLAAY-APDLAPFMSDEVCFCSFSFKF 150 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~-~P~~~pFfSDEa~~~~~~~~~ 150 (178)
--.|+.++||||.++-.+|.-+ .++.+---|.|-...+||+..
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~~ 567 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGE 567 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCH
Confidence 4678899999999999999964 454444445566677877643
No 105
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=35.49 E-value=18 Score=24.99 Aligned_cols=17 Identities=29% Similarity=0.342 Sum_probs=13.7
Q ss_pred cccCcchHHHHHHHhhh
Q 030389 113 VLKGVGPATASAVLAAY 129 (178)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (178)
.+=|+||||+++.-.+.
T Consensus 17 ~v~tigPA~~Al~~~~~ 33 (77)
T PF04854_consen 17 PVFTIGPATAALYYVVR 33 (77)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45689999999887774
No 106
>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=35.37 E-value=22 Score=23.24 Aligned_cols=34 Identities=26% Similarity=0.297 Sum_probs=25.7
Q ss_pred HHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhh
Q 030389 108 VSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSF 146 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~ 146 (178)
|+.+.++-||.++|.|-+|.=. +-.|+|.-+-+.
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~-----~~vs~~tr~rI~ 35 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP-----PRVSEETRERIL 35 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC-----SSSTHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhCC-----CCCCHHHHHHHH
Confidence 5567778899999999998753 567877766544
No 107
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=34.76 E-value=55 Score=29.00 Aligned_cols=68 Identities=16% Similarity=0.047 Sum_probs=45.6
Q ss_pred HHHHHHhhcccCcchHHHHHHHh-hhCCCCCCccchhHHhhhhcCcccccchhhHHHHHHHHhhhhccCC
Q 030389 105 TKAVSELTVLKGVGPATASAVLA-AYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNGMEGYGG 173 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa-~~~P~~~pFfSDEa~~~~~~~~~~l~ys~~~y~y~~~~~~i~~~g~ 173 (178)
..-+.+|..++|||+.+|.=+|- +...+.+-.-|.+-.+.+.|.+.+.-+- ..++|......+++.|.
T Consensus 178 e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~-I~~~~~t~~~~~~~~~~ 246 (254)
T COG1948 178 ELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKARE-IYRFLRTEYKLIEALET 246 (254)
T ss_pred HHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHH-HHHHHhchhhhhcccCC
Confidence 34577888999999999987774 4566666666677777788875432222 23566666666666554
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=34.42 E-value=36 Score=21.29 Aligned_cols=42 Identities=21% Similarity=0.393 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhhCccHH-HHHHHhhcccCcchHHHHHHHhh
Q 030389 87 DSSVKSASEKAFKSLPDLT-KAVSELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 87 ~~~V~~~t~~Af~~l~d~~-~al~~L~~LkGVGPATASaiLa~ 128 (178)
+..+......+|..+.++. .+.+.|+.++|++..+|..|...
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 3444555555555544443 34788999999999999887654
No 109
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=33.64 E-value=61 Score=27.57 Aligned_cols=64 Identities=22% Similarity=0.300 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHHhhCCCCCc-hhHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhcccCcchHHHHHHHh
Q 030389 54 PHINTTELSKLVRWKLTRGKWRP-RLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLA 127 (178)
Q Consensus 54 ~~ltkdEL~~LveWKL~rGkfRP-~L~~lv~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa 127 (178)
++.|.+|-.-.-+-=--.| -=| +-+.++++-+++.+.++... .=++.||+++|||+-||=-|+-
T Consensus 62 GF~~~~ER~lF~~LisVnG-IGpK~ALaiLs~~~~~~l~~aI~~---------~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 62 GFLTEEERELFRLLISVNG-IGPKLALAILSNLDPEELAQAIAN---------EDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred CCCCHHHHHHHHHHHccCC-ccHHHHHHHHcCCCHHHHHHHHHh---------cChHhhhcCCCCCHHHHHHHHH
Confidence 4677777433222211122 112 22344444455555544432 1256899999999999987764
No 110
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=32.13 E-value=25 Score=28.43 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.3
Q ss_pred HHhhcccCcchHHHHHHHhh
Q 030389 109 SELTVLKGVGPATASAVLAA 128 (178)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~ 128 (178)
+-|+.|.||||..++.+=..
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~ 86 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNEL 86 (133)
T ss_pred ccchhhcccCHHHHHHHHHc
Confidence 78999999999999987554
No 111
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=30.07 E-value=38 Score=29.97 Aligned_cols=33 Identities=27% Similarity=0.453 Sum_probs=25.6
Q ss_pred cHHHHHHHhhcccCcchHHHHHH--HhhhCCCCCC
Q 030389 103 DLTKAVSELTVLKGVGPATASAV--LAAYAPDLAP 135 (178)
Q Consensus 103 d~~~al~~L~~LkGVGPATASai--La~~~P~~~p 135 (178)
+-+.=++-||..||||+-|+=.. -+++.|+..|
T Consensus 159 seEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp 193 (254)
T KOG1918|consen 159 SEEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMP 193 (254)
T ss_pred CHHHHHHHHHhccCccceeeeeeeeeccCCCcccC
Confidence 34566889999999999999754 4668887644
No 112
>COG5578 Predicted integral membrane protein [Function unknown]
Probab=28.87 E-value=30 Score=29.80 Aligned_cols=12 Identities=42% Similarity=0.509 Sum_probs=9.9
Q ss_pred ccCcchHHHHHH
Q 030389 114 LKGVGPATASAV 125 (178)
Q Consensus 114 LkGVGPATASai 125 (178)
.=|++||||++.
T Consensus 37 VfG~~PAT~Alf 48 (208)
T COG5578 37 VFGLMPATAALF 48 (208)
T ss_pred HHccchHHHHHH
Confidence 569999999764
No 113
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=26.19 E-value=88 Score=25.90 Aligned_cols=51 Identities=14% Similarity=0.309 Sum_probs=44.8
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCcc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPD 103 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~d 103 (178)
..+|++..||..|-. -+..|..|-..-+.+++|.+.-|.++.++-|...|+
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 468999999999855 478899999999999999999999999999987773
No 114
>PRK03980 flap endonuclease-1; Provisional
Probab=25.91 E-value=40 Score=29.88 Aligned_cols=13 Identities=46% Similarity=0.935 Sum_probs=0.0
Q ss_pred ccCcchHHHHHHH
Q 030389 114 LKGVGPATASAVL 126 (178)
Q Consensus 114 LkGVGPATASaiL 126 (178)
++||||-||.-++
T Consensus 194 I~GIG~ktA~kLi 206 (292)
T PRK03980 194 IKGIGPKTALKLI 206 (292)
T ss_pred CCCccHHHHHHHH
No 115
>PHA01976 helix-turn-helix protein
Probab=25.84 E-value=54 Score=21.56 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=16.0
Q ss_pred CCCCCHHHHHHHHH------HHhhCCCCCch
Q 030389 53 NPHINTTELSKLVR------WKLTRGKWRPR 77 (178)
Q Consensus 53 ~~~ltkdEL~~Lve------WKL~rGkfRP~ 77 (178)
...||.+||-+.+. .+.-+|+..|+
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~ 43 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEADKRLPN 43 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Confidence 45788888877765 34455665554
No 116
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=24.96 E-value=1.1e+02 Score=30.30 Aligned_cols=39 Identities=21% Similarity=0.289 Sum_probs=25.8
Q ss_pred HHhhcccCcchHHHHHHHhhhCC-CCCCccchhHHhhhhc
Q 030389 109 SELTVLKGVGPATASAVLAAYAP-DLAPFMSDEVCFCSFS 147 (178)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~~P-~~~pFfSDEa~~~~~~ 147 (178)
..|..++||||.++=++|.-+.- +.+.-=|.|-...+.|
T Consensus 552 S~L~~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~~vi~ 591 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHFGSLERVRAATETQLAAVVG 591 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhC
Confidence 57779999999999999987432 2333444444444433
No 117
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=24.80 E-value=1e+02 Score=28.29 Aligned_cols=45 Identities=29% Similarity=0.360 Sum_probs=25.8
Q ss_pred HHHhhcccCcchHHHHHHHhh---hCCCCCCccchhHHhh-hhcCccccc
Q 030389 108 VSELTVLKGVGPATASAVLAA---YAPDLAPFMSDEVCFC-SFSFKFTLL 153 (178)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~---~~P~~~pFfSDEa~~~-~~~~~~~l~ 153 (178)
++.|-.++||||.|-=|+-=+ .+- ..|=|.|-+--+ ..|-+.++.
T Consensus 268 feeLL~~~GvGp~TlRALaLvaelIyg-~p~s~~DPakfsfA~GGKDG~P 316 (319)
T PF05559_consen 268 FEELLLIKGVGPSTLRALALVAELIYG-VPPSFRDPAKFSFAHGGKDGVP 316 (319)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHcC-CCCCccChhHHHHhhcCCCCCC
Confidence 556667999999997554332 221 226677776322 445444433
No 118
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=24.66 E-value=46 Score=29.94 Aligned_cols=17 Identities=35% Similarity=0.581 Sum_probs=14.8
Q ss_pred cccCcchHHHHHHHhhh
Q 030389 113 VLKGVGPATASAVLAAY 129 (178)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (178)
.++||||-||--++.-+
T Consensus 240 Gv~GIG~ktA~kli~~~ 256 (338)
T TIGR03674 240 GVKGIGPKTALKLIKEH 256 (338)
T ss_pred CCCCccHHHHHHHHHHc
Confidence 49999999999999663
No 119
>PF11517 Nab2: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); InterPro: IPR021083 Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 []. The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA []. An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 [].; PDB: 3LCN_B 2V75_A 2JPS_A.
Probab=24.25 E-value=42 Score=26.16 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=29.3
Q ss_pred hHHHhhhCCHHHHHHHHHHHHhhCccHH---HHHHHhhcccCcchHHHH
Q 030389 78 LLVFVSSLDDSSVKSASEKAFKSLPDLT---KAVSELTVLKGVGPATAS 123 (178)
Q Consensus 78 L~~lv~sN~~~~V~~~t~~Af~~l~d~~---~al~~L~~LkGVGPATAS 123 (178)
|-.|..+-+.+.+.++.+.||..+.-+. ..=.+..||+|+.++.++
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 233456689999887764
No 120
>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=23.81 E-value=1.2e+02 Score=29.58 Aligned_cols=21 Identities=29% Similarity=0.455 Sum_probs=18.2
Q ss_pred HHhhcccCcchHHHHHHHhhh
Q 030389 109 SELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~ 129 (178)
..|-+++||||.+.-++|.-+
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~F 561 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYF 561 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHc
Confidence 477799999999999999764
No 121
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=23.59 E-value=51 Score=28.82 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=15.9
Q ss_pred cccCcchHHHHHHHhhhC
Q 030389 113 VLKGVGPATASAVLAAYA 130 (178)
Q Consensus 113 ~LkGVGPATASaiLa~~~ 130 (178)
.++||||-||--++.-+.
T Consensus 227 gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 227 GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 399999999999998864
No 122
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=23.05 E-value=97 Score=30.47 Aligned_cols=23 Identities=35% Similarity=0.560 Sum_probs=20.0
Q ss_pred HHHHhhcccCcchHHHHHHHhhh
Q 030389 107 AVSELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~ 129 (178)
--..|..++||||.||-+||.-+
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~~F 589 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLEHF 589 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHHHc
Confidence 34677899999999999999986
No 123
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=22.96 E-value=88 Score=31.13 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=19.9
Q ss_pred HHHHhhcccCcchHHHHHHHhhh
Q 030389 107 AVSELTVLKGVGPATASAVLAAY 129 (178)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~ 129 (178)
+.+.|+++.||||-+|..|.+..
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHH
Confidence 55679999999999999998764
No 124
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=22.90 E-value=88 Score=18.81 Aligned_cols=20 Identities=25% Similarity=0.287 Sum_probs=15.2
Q ss_pred chhHHHhhhCCHHHHHHHHH
Q 030389 76 PRLLVFVSSLDDSSVKSASE 95 (178)
Q Consensus 76 P~L~~lv~sN~~~~V~~~t~ 95 (178)
|.|.+++++.+++.++.++.
T Consensus 15 ~~Lv~ll~~~~~~v~~~a~~ 34 (41)
T PF00514_consen 15 PPLVQLLKSPDPEVQEEAAW 34 (41)
T ss_dssp HHHHHHTTSSSHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 67999999888777766553
No 125
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=21.92 E-value=67 Score=29.76 Aligned_cols=47 Identities=28% Similarity=0.347 Sum_probs=31.4
Q ss_pred HhhCccHHHHHHHhhcccCcchHHHHHHHhhhC----CCCCCccchhHHhh
Q 030389 98 FKSLPDLTKAVSELTVLKGVGPATASAVLAAYA----PDLAPFMSDEVCFC 144 (178)
Q Consensus 98 f~~l~d~~~al~~L~~LkGVGPATASaiLa~~~----P~~~pFfSDEa~~~ 144 (178)
++.+|-.-.+.+.+++|+||||-.|=.|=-..+ ++.--+--||.+..
T Consensus 45 lk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~ 95 (353)
T KOG2534|consen 45 LKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQS 95 (353)
T ss_pred HHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHH
Confidence 345555556788899999999999988766532 33234455666554
No 126
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=21.05 E-value=1.1e+02 Score=17.59 Aligned_cols=19 Identities=37% Similarity=0.546 Sum_probs=12.6
Q ss_pred chhHHHhhhCCHHHHHHHH
Q 030389 76 PRLLVFVSSLDDSSVKSAS 94 (178)
Q Consensus 76 P~L~~lv~sN~~~~V~~~t 94 (178)
|.|.+++++++++.++.++
T Consensus 15 ~~L~~ll~~~~~~i~~~a~ 33 (41)
T smart00185 15 PALVELLKSEDEEVVKEAA 33 (41)
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 4478888877766555544
No 127
>TIGR01337 apcB allophycocyanin, beta subunit. The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins. This model describes allophycocyanin beta subunit. Other, homologous phyobiliproteins include allophycocyanin alpha chain and the phycocyanin and phycoerythrin alpha and beta chains.
Probab=21.02 E-value=1.1e+02 Score=25.22 Aligned_cols=50 Identities=18% Similarity=0.389 Sum_probs=43.9
Q ss_pred CCCCCCHHHHHHHHHHHhhCCCCCchhHHHhhhCCHHHHHHHHHHHHhhCc
Q 030389 52 PNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP 102 (178)
Q Consensus 52 ~~~~ltkdEL~~LveWKL~rGkfRP~L~~lv~sN~~~~V~~~t~~Af~~l~ 102 (178)
..+|++..||..|-.- +..|.-|-..-+.+++|.+.-|+++.++-|...|
T Consensus 14 ~gRYls~~eL~~l~~~-~~~~~~Rl~aa~~l~~na~~Iv~~A~~~l~~~~P 63 (167)
T TIGR01337 14 TGKYLDDNAVTKLKGY-FQTGELRLRAAAIINANSATIIKEAAAQLFEEYP 63 (167)
T ss_pred cCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCc
Confidence 4579999999998664 5689999999999999999999999999998766
No 128
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=20.14 E-value=76 Score=30.98 Aligned_cols=38 Identities=26% Similarity=0.391 Sum_probs=31.3
Q ss_pred HHHHHHhhcccCcchHHHHHHHhhhCCCCCCccchhHHhhhhc
Q 030389 105 TKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFS 147 (178)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfSDEa~~~~~~ 147 (178)
+++.+.|.+|+|||-.|+.-|++- -||.|-|.|.-..+
T Consensus 512 ~~s~~vl~~ipgig~~~~~~I~~~-----Rp~~s~e~~l~~v~ 549 (560)
T COG1031 512 SASKDVLRAIPGIGKKTLRKILAE-----RPFKSSEEFLKLVP 549 (560)
T ss_pred cccHHHHHhcccchhhhHHHHHhc-----CCccchHHHHhccC
Confidence 456899999999999999999875 39999888876443
Done!