Query 027775
Match_columns 219
No_of_seqs 118 out of 150
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 14:59:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027775.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027775hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00633 HHH: Helix-hairpin-he 97.6 5.8E-05 1.3E-09 47.0 2.7 24 105-128 7-30 (30)
2 PRK01229 N-glycosylase/DNA lya 97.1 0.002 4.4E-08 56.3 7.8 82 103-191 112-202 (208)
3 COG0177 Nth Predicted EndoIII- 96.9 0.0035 7.6E-08 55.1 7.4 71 57-130 42-130 (211)
4 cd00056 ENDO3c endonuclease II 96.0 0.035 7.5E-07 44.9 7.7 37 105-143 79-116 (158)
5 TIGR01084 mutY A/G-specific ad 95.7 0.056 1.2E-06 49.0 8.2 36 104-140 100-135 (275)
6 smart00478 ENDO3c endonuclease 95.2 0.11 2.3E-06 41.7 7.5 30 103-132 66-95 (149)
7 PRK10702 endonuclease III; Pro 94.9 0.046 9.9E-07 47.7 5.0 28 104-131 104-131 (211)
8 PRK10880 adenine DNA glycosyla 94.8 0.044 9.6E-07 51.4 5.1 29 104-132 104-132 (350)
9 COG0122 AlkA 3-methyladenine D 94.7 0.11 2.3E-06 47.4 7.0 72 55-135 144-226 (285)
10 TIGR00588 ogg 8-oxoguanine DNA 94.6 0.099 2.2E-06 47.9 6.8 62 104-167 215-288 (310)
11 PF02371 Transposase_20: Trans 94.4 0.036 7.8E-07 41.4 2.7 37 109-147 2-39 (87)
12 TIGR01083 nth endonuclease III 94.2 0.13 2.8E-06 43.7 6.1 39 104-143 101-139 (191)
13 PRK13910 DNA glycosylase MutY; 94.2 0.071 1.5E-06 48.8 4.7 31 105-135 68-98 (289)
14 COG1194 MutY A/G-specific DNA 93.8 0.047 1E-06 51.2 2.9 36 108-143 112-147 (342)
15 TIGR03252 uncharacterized HhH- 93.5 0.062 1.3E-06 46.2 2.9 44 102-147 108-151 (177)
16 PRK13913 3-methyladenine DNA g 93.5 0.13 2.7E-06 45.4 4.8 40 106-146 118-157 (218)
17 PRK10308 3-methyl-adenine DNA 93.2 0.1 2.2E-06 47.4 3.9 36 103-139 201-238 (283)
18 PRK02515 psbU photosystem II c 93.2 0.097 2.1E-06 43.1 3.4 38 106-148 58-95 (132)
19 smart00278 HhH1 Helix-hairpin- 91.7 0.14 3E-06 30.3 1.9 19 110-128 2-20 (26)
20 PF11731 Cdd1: Pathogenicity l 90.0 0.22 4.9E-06 38.7 2.2 26 104-129 7-32 (93)
21 PF10391 DNA_pol_lambd_f: Fing 88.0 0.35 7.6E-06 33.6 1.8 22 108-129 1-22 (52)
22 TIGR01259 comE comEA protein. 87.7 0.58 1.3E-05 37.3 3.2 42 105-147 64-105 (120)
23 PF14716 HHH_8: Helix-hairpin- 85.9 1.2 2.6E-05 31.8 3.7 30 98-127 35-65 (68)
24 PRK14605 ruvA Holliday junctio 85.4 0.62 1.3E-05 40.2 2.4 31 103-133 67-97 (194)
25 KOG1921 Endonuclease III [Repl 84.3 1.3 2.8E-05 40.4 4.0 30 103-132 153-182 (286)
26 PRK00116 ruvA Holliday junctio 81.9 1.3 2.8E-05 37.9 2.9 28 104-131 68-95 (192)
27 TIGR00084 ruvA Holliday juncti 81.1 1.1 2.3E-05 38.6 2.2 30 103-132 66-95 (191)
28 PF14520 HHH_5: Helix-hairpin- 81.1 1.6 3.4E-05 30.2 2.6 23 107-129 3-25 (60)
29 PRK13901 ruvA Holliday junctio 80.9 1.1 2.3E-05 39.1 2.1 30 103-132 66-95 (196)
30 PRK14600 ruvA Holliday junctio 80.5 1.1 2.3E-05 38.6 1.9 30 103-132 67-96 (186)
31 COG2003 RadC DNA repair protei 79.8 3.5 7.5E-05 36.8 4.9 153 35-208 3-183 (224)
32 PF12826 HHH_2: Helix-hairpin- 79.7 1.7 3.8E-05 30.7 2.5 24 106-129 32-55 (64)
33 COG1555 ComEA DNA uptake prote 79.1 1.6 3.5E-05 36.2 2.5 42 105-147 93-134 (149)
34 COG2231 Uncharacterized protei 78.7 6.5 0.00014 34.9 6.2 37 107-144 113-149 (215)
35 TIGR00426 competence protein C 78.5 3 6.5E-05 29.5 3.4 39 108-147 15-54 (69)
36 PRK14601 ruvA Holliday junctio 78.4 1.4 3E-05 37.9 1.9 30 103-132 67-96 (183)
37 PRK14601 ruvA Holliday junctio 77.0 6.8 0.00015 33.7 5.8 66 54-128 62-127 (183)
38 KOG2875 8-oxoguanine DNA glyco 76.6 2.5 5.3E-05 39.3 3.1 63 104-167 213-284 (323)
39 TIGR00608 radc DNA repair prot 76.4 2.9 6.2E-05 36.8 3.4 62 54-129 12-80 (218)
40 PRK13901 ruvA Holliday junctio 76.0 7.1 0.00015 34.0 5.7 66 54-128 61-126 (196)
41 PRK14604 ruvA Holliday junctio 75.9 7.3 0.00016 33.7 5.7 67 54-129 62-128 (195)
42 PRK14606 ruvA Holliday junctio 75.6 7.4 0.00016 33.5 5.6 66 54-128 62-127 (188)
43 PF14520 HHH_5: Helix-hairpin- 75.6 1.7 3.7E-05 30.1 1.4 22 107-128 36-57 (60)
44 COG1796 POL4 DNA polymerase IV 75.5 4.7 0.0001 37.8 4.7 34 102-135 44-79 (326)
45 PF00416 Ribosomal_S13: Riboso 74.9 5 0.00011 31.3 4.0 39 107-145 13-54 (107)
46 PRK00024 hypothetical protein; 74.4 5 0.00011 35.3 4.4 60 54-128 22-85 (224)
47 PRK14602 ruvA Holliday junctio 74.0 2.4 5.1E-05 36.9 2.2 29 104-132 69-97 (203)
48 PRK14606 ruvA Holliday junctio 73.8 2.2 4.7E-05 36.7 1.9 30 103-132 67-96 (188)
49 KOG2457 A/G-specific adenine D 73.0 3.1 6.7E-05 40.4 2.9 90 109-201 205-300 (555)
50 COG0099 RpsM Ribosomal protein 72.6 3.5 7.5E-05 33.6 2.7 38 108-145 16-56 (121)
51 PRK14603 ruvA Holliday junctio 70.5 2.8 6.2E-05 36.2 1.9 29 104-132 67-95 (197)
52 PTZ00134 40S ribosomal protein 70.0 5.1 0.00011 33.7 3.3 55 101-155 22-82 (154)
53 PRK14602 ruvA Holliday junctio 69.0 13 0.00028 32.3 5.6 67 54-129 63-129 (203)
54 PRK14603 ruvA Holliday junctio 68.5 14 0.0003 32.0 5.7 67 54-129 61-127 (197)
55 PF12836 HHH_3: Helix-hairpin- 67.2 2.1 4.6E-05 30.2 0.4 41 106-147 11-51 (65)
56 TIGR00084 ruvA Holliday juncti 67.0 15 0.00033 31.5 5.7 66 54-128 61-126 (191)
57 smart00279 HhH2 Helix-hairpin- 66.7 4.3 9.4E-05 26.0 1.7 15 113-127 20-34 (36)
58 PRK14604 ruvA Holliday junctio 65.3 4.3 9.2E-05 35.1 1.9 30 103-132 67-96 (195)
59 PRK04053 rps13p 30S ribosomal 64.8 7.3 0.00016 32.6 3.2 54 105-158 21-80 (149)
60 COG3092 Uncharacterized protei 64.4 58 0.0013 27.2 8.3 49 83-132 31-82 (149)
61 PRK00116 ruvA Holliday junctio 63.3 50 0.0011 28.2 8.1 70 54-132 62-131 (192)
62 COG0632 RuvA Holliday junction 62.4 5 0.00011 35.1 1.9 30 103-132 67-96 (201)
63 COG0353 RecR Recombinational D 62.1 5.8 0.00012 34.9 2.2 23 103-125 6-28 (198)
64 CHL00137 rps13 ribosomal prote 60.5 9.6 0.00021 30.8 3.1 39 107-145 15-56 (122)
65 COG1059 Thermostable 8-oxoguan 59.5 54 0.0012 29.0 7.7 82 105-191 116-204 (210)
66 PRK14605 ruvA Holliday junctio 58.1 31 0.00067 29.7 6.0 64 54-126 62-125 (194)
67 cd00141 NT_POLXc Nucleotidyltr 57.8 8.5 0.00018 35.2 2.6 23 105-127 81-103 (307)
68 PRK03980 flap endonuclease-1; 57.6 36 0.00079 31.1 6.7 70 113-190 193-276 (292)
69 PF11798 IMS_HHH: IMS family H 56.8 7.1 0.00015 24.2 1.3 15 111-125 13-27 (32)
70 TIGR03629 arch_S13P archaeal r 55.7 9.9 0.00021 31.6 2.4 37 108-144 20-59 (144)
71 PRK00076 recR recombination pr 54.6 9.8 0.00021 33.2 2.3 22 104-125 6-27 (196)
72 PRK05179 rpsM 30S ribosomal pr 54.2 13 0.00029 29.9 2.9 38 108-145 16-56 (122)
73 TIGR03631 bact_S13 30S ribosom 53.7 13 0.00028 29.6 2.7 37 109-145 15-54 (113)
74 PRK14600 ruvA Holliday junctio 53.7 29 0.00063 29.8 5.1 65 54-128 62-126 (186)
75 TIGR00615 recR recombination p 52.2 11 0.00024 32.9 2.3 22 104-125 6-27 (195)
76 smart00483 POLXc DNA polymeras 51.0 14 0.0003 34.3 2.8 67 103-171 83-161 (334)
77 PRK13844 recombination protein 50.7 12 0.00026 32.8 2.3 22 104-125 10-31 (200)
78 cd00080 HhH2_motif Helix-hairp 50.6 11 0.00024 27.5 1.7 19 111-129 24-42 (75)
79 TIGR00426 competence protein C 48.9 55 0.0012 22.9 5.1 22 107-128 45-66 (69)
80 cd00141 NT_POLXc Nucleotidyltr 48.4 15 0.00032 33.6 2.6 17 107-123 43-59 (307)
81 smart00483 POLXc DNA polymeras 47.9 13 0.00028 34.4 2.2 35 99-133 38-72 (334)
82 cd00128 XPG Xeroderma pigmento 47.2 26 0.00057 31.7 4.0 18 113-130 227-244 (316)
83 PRK07945 hypothetical protein; 45.5 33 0.00071 31.8 4.4 19 110-128 50-68 (335)
84 PRK12766 50S ribosomal protein 42.4 18 0.0004 32.5 2.2 42 88-129 14-56 (232)
85 PRK08609 hypothetical protein; 39.9 28 0.00062 34.6 3.3 21 108-128 47-67 (570)
86 TIGR01339 phycocy_beta phycocy 39.8 41 0.0009 28.8 3.8 51 52-103 13-63 (170)
87 PRK14976 5'-3' exonuclease; Pr 39.6 18 0.00039 32.8 1.7 16 114-129 196-211 (281)
88 PRK14350 ligA NAD-dependent DN 37.4 41 0.0009 34.4 4.0 23 107-129 539-561 (669)
89 PRK09482 flap endonuclease-lik 36.5 23 0.0005 32.0 1.9 18 113-130 186-203 (256)
90 PF14579 HHH_6: Helix-hairpin- 34.9 37 0.0008 25.3 2.5 32 111-144 29-60 (90)
91 TIGR01259 comE comEA protein. 34.8 89 0.0019 24.8 4.8 21 107-127 96-116 (120)
92 cd00008 53EXOc 5'-3' exonuclea 32.4 29 0.00062 30.5 1.8 17 113-129 187-203 (240)
93 PF00502 Phycobilisome: Phycob 32.1 31 0.00066 28.6 1.8 111 52-171 10-136 (157)
94 CHL00172 cpeB phycoerythrin be 31.5 65 0.0014 27.8 3.7 51 52-103 15-65 (177)
95 smart00475 53EXOc 5'-3' exonuc 31.1 31 0.00068 30.9 1.8 17 113-129 190-206 (259)
96 PF14229 DUF4332: Domain of un 30.2 49 0.0011 26.3 2.6 26 106-131 50-75 (122)
97 PRK13482 DNA integrity scannin 30.0 52 0.0011 31.3 3.1 23 106-128 316-338 (352)
98 PF01367 5_3_exonuc: 5'-3' exo 29.8 8.4 0.00018 30.1 -1.8 17 113-129 22-38 (101)
99 CHL00170 cpcA phycocyanin alph 28.1 98 0.0021 26.3 4.2 51 52-103 15-65 (162)
100 COG1223 Predicted ATPase (AAA+ 28.0 1E+02 0.0022 29.1 4.6 84 103-189 234-330 (368)
101 PRK08609 hypothetical protein; 27.6 47 0.001 33.1 2.5 24 104-127 83-106 (570)
102 TIGR00600 rad2 DNA excision re 27.4 1.9E+02 0.0042 31.4 7.1 24 107-130 858-887 (1034)
103 KOG2582 COP9 signalosome, subu 26.7 3.1E+02 0.0066 26.8 7.6 83 78-161 82-186 (422)
104 TIGR01954 nusA_Cterm_rpt trans 26.0 64 0.0014 20.7 2.2 41 88-128 4-45 (50)
105 PRK09672 phage exclusion prote 26.0 2.2E+02 0.0047 26.8 6.4 34 114-147 216-256 (305)
106 COG3743 Uncharacterized conser 25.7 38 0.00081 28.1 1.2 20 109-128 67-86 (133)
107 PRK12766 50S ribosomal protein 25.4 38 0.00082 30.5 1.3 20 109-128 3-22 (232)
108 CHL00090 apcD allophycocyanin 24.7 95 0.0021 26.1 3.5 50 53-103 15-64 (161)
109 TIGR01338 phycocy_alpha phycoc 24.6 1.3E+02 0.0029 25.4 4.4 51 52-103 14-64 (161)
110 CHL00086 apcA allophycocyanin 23.8 1.2E+02 0.0025 25.6 3.9 51 52-103 14-64 (161)
111 COG0632 RuvA Holliday junction 23.7 60 0.0013 28.5 2.2 66 54-128 62-127 (201)
112 CHL00171 cpcB phycocyanin beta 23.6 96 0.0021 26.5 3.4 51 52-103 15-65 (172)
113 TIGR01589 A_thal_3526 uncharac 23.3 87 0.0019 22.4 2.6 49 89-137 3-51 (57)
114 CHL00173 cpeA phycoerythrin al 23.1 99 0.0021 26.3 3.4 51 52-103 15-65 (164)
115 PF05766 NinG: Bacteriophage L 23.1 1.5E+02 0.0033 25.8 4.6 25 148-172 161-185 (189)
116 KOG1918 3-methyladenine DNA gl 22.6 60 0.0013 29.5 2.0 37 104-141 160-198 (254)
117 PF04854 DUF624: Protein of un 22.2 39 0.00085 24.0 0.7 17 113-129 17-33 (77)
118 KOG2376 Signal recognition par 21.7 7E+02 0.015 25.8 9.3 19 177-195 525-543 (652)
119 PF05845 PhnH: Bacterial phosp 21.6 79 0.0017 27.4 2.5 23 114-137 39-61 (192)
120 COG1031 Uncharacterized Fe-S o 20.7 82 0.0018 31.5 2.7 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=97.58 E-value=5.8e-05 Score=46.98 Aligned_cols=24 Identities=42% Similarity=0.700 Sum_probs=20.2
Q ss_pred HHHHHHhhccCCCChHHHHHHHHh
Q 027775 105 TKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~ 128 (219)
.+.++.|++|+||||.||.+|++.
T Consensus 7 pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 7 PASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp TSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCHHHHHhCCCcCHHHHHHHHhC
Confidence 356889999999999999999973
No 2
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=97.11 E-value=0.002 Score=56.31 Aligned_cols=82 Identities=24% Similarity=0.250 Sum_probs=60.9
Q ss_pred cHHHHHHHhh-ccCCCChHHHHHHHH-hhcCCCCCcccHHHHHHh---cCC----CCCCCHHHHHHHHHHHHHHHHHhcc
Q 027775 103 DLTKAVSELT-VLKGVGPATASAVLA-AYAPGVAPFMSDEAMGAA---LGH----SKDYSLRQYLLFADKLQAKAKELVS 173 (219)
Q Consensus 103 d~~~al~~L~-~LkGVGPATASaiLa-~~~P~~~pFfsDEa~~~~---~g~----~~kYt~keY~~~~~~l~~~~~~L~~ 173 (219)
++..+.+.|. +||||||=||+.||. +.. ...|.-|.-..-+ +|- +..-|.+.|.+.-..+++.++.++
T Consensus 112 ~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~--~~~~iVDtHv~Ri~~RlG~~~~~~~~lt~~~y~~~E~~l~~~~~~~~- 188 (208)
T PRK01229 112 DQFEAREFLVKNIKGIGYKEASHFLRNVGY--EDLAILDRHILRFLKRYGLIEEIPKTLSKKRYLEIEEILREIAEELG- 188 (208)
T ss_pred CchHHHHHHHHcCCCCcHHHHHHHHHHccC--CCeeeeeHHHHHHHHHhCCCcccccccCcCCHHHHHHHHHHHHHHcC-
Confidence 5678899999 999999999999994 444 2123355543323 351 224567899999999999999884
Q ss_pred cCCCCCHHHHHHHHHHHH
Q 027775 174 EENCFTPFDVERALWSSA 191 (219)
Q Consensus 174 ~~~~~s~~~VEkalws~~ 191 (219)
+.+..+..++|-..
T Consensus 189 ----~~~~~Ldl~~w~~~ 202 (208)
T PRK01229 189 ----ISLGELDLYIWYKE 202 (208)
T ss_pred ----CCHHHHHHHHHHHH
Confidence 88999999999743
No 3
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=96.91 E-value=0.0035 Score=55.08 Aligned_cols=71 Identities=23% Similarity=0.269 Sum_probs=44.4
Q ss_pred CHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHH-HH------h------hC-----ccHHHHHHHhhccCCCC
Q 027775 57 NTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEK-AF------K------SL-----PDLTKAVSELTVLKGVG 118 (219)
Q Consensus 57 tk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~-Af------~------~l-----~d~~~al~~L~~LkGVG 118 (219)
|.|+.++-+.=+|.. .-|+...+...+.++ +++.++. +| + +| .++...++.|.+|+|||
T Consensus 42 ttD~~vn~at~~Lf~--~~~t~e~l~~a~~~~-l~~~I~~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~LPGVG 118 (211)
T COG0177 42 TTDEVVNKATPALFK--RYPTPEDLLNADEEE-LEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVG 118 (211)
T ss_pred CchHHHHHHHHHHHH--HcCCHHHHHcCCHHH-HHHHHHhcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhCCCcc
Confidence 467777666655542 234555555555443 4333322 22 0 01 14667899999999999
Q ss_pred hHHHHHHHHhhc
Q 027775 119 PATASAVLAAYA 130 (219)
Q Consensus 119 PATASaiLa~~~ 130 (219)
+=||..||+...
T Consensus 119 rKTAnvVL~~a~ 130 (211)
T COG0177 119 RKTANVVLSFAF 130 (211)
T ss_pred hHHHHHHHHhhc
Confidence 999999999854
No 4
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=96.02 E-value=0.035 Score=44.87 Aligned_cols=37 Identities=38% Similarity=0.469 Sum_probs=28.7
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhh-cCCCCCcccHHHHH
Q 027775 105 TKAVSELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMG 143 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~ 143 (219)
..+.+.|++||||||-||+.||... .++.+|. |-...
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~~~~~pv--D~~v~ 116 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALGPDAFPV--DTHVR 116 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCCCCCCcc--chhHH
Confidence 6789999999999999999999874 3445554 55444
No 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=95.65 E-value=0.056 Score=48.96 Aligned_cols=36 Identities=31% Similarity=0.395 Sum_probs=27.8
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHH
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDE 140 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDE 140 (219)
+...++.|++||||||-||++||+...-...|+ -|-
T Consensus 100 ~p~~~~~L~~LpGIG~~TA~~Il~~a~~~~~~~-vD~ 135 (275)
T TIGR01084 100 FPQDFEDLAALPGVGRYTAGAILSFALNKPYPI-LDG 135 (275)
T ss_pred CcHHHHHHHhCCCCCHHHHHHHHHHHCCCCCCc-chH
Confidence 345789999999999999999999865443454 444
No 6
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=95.17 E-value=0.11 Score=41.72 Aligned_cols=30 Identities=37% Similarity=0.386 Sum_probs=25.1
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
++...++.|++||||||-||++||...--.
T Consensus 66 ~~~~~~~~L~~l~GIG~~tA~~~l~~~~~~ 95 (149)
T smart00478 66 EVPDDREELLKLPGVGRKTANAVLSFALGK 95 (149)
T ss_pred CccHHHHHHHcCCCCcHHHHHHHHHHHCCC
Confidence 344678899999999999999999986554
No 7
>PRK10702 endonuclease III; Provisional
Probab=94.91 E-value=0.046 Score=47.65 Aligned_cols=28 Identities=32% Similarity=0.383 Sum_probs=24.4
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcC
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P 131 (219)
+..+++.|.+|+||||-||.+||....-
T Consensus 104 ~p~~~~~Ll~lpGVG~ktA~~ill~a~~ 131 (211)
T PRK10702 104 VPEDRAALEALPGVGRKTANVVLNTAFG 131 (211)
T ss_pred CCchHHHHhcCCcccHHHHHHHHHHHcC
Confidence 4568999999999999999999998653
No 8
>PRK10880 adenine DNA glycosylase; Provisional
Probab=94.84 E-value=0.044 Score=51.36 Aligned_cols=29 Identities=31% Similarity=0.454 Sum_probs=25.1
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+...++.|.+||||||-||++||+...-.
T Consensus 104 ~p~~~~~L~~LpGIG~~TA~aIl~~af~~ 132 (350)
T PRK10880 104 FPETFEEVAALPGVGRSTAGAILSLSLGK 132 (350)
T ss_pred chhhHHHHhcCCCccHHHHHHHHHHHCCC
Confidence 45678999999999999999999987644
No 9
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=94.69 E-value=0.11 Score=47.44 Aligned_cols=72 Identities=28% Similarity=0.252 Sum_probs=51.9
Q ss_pred CCCHHHHHHHHHHHhh-cCCCCcchHHHhhhCCHHHHHHHHHHHHhhCc--------cHHHHHHHhhccCCCChHHHHHH
Q 027775 55 HINTTELSKLVRWKLT-RGKWRPRLLDFVSSLDDSSVKSASEKAFKSLP--------DLTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 55 ~ltk~EL~~Lv~WKL~-rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~--------d~~~al~~L~~LkGVGPATASai 125 (219)
+.|-+.|..+=++-|. -|..+.+. +.++.+++...+-.. +...+++.|+.||||||=||-.+
T Consensus 144 fptpe~l~~~~~~~l~~~g~s~~Ka---------~yi~~~A~~~~~g~~~~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~ 214 (285)
T COG0122 144 FPTPEQLAAADEEALRRCGLSGRKA---------EYIISLARAAAEGELDLSELKPLSDEEAIEELTALKGIGPWTAEMF 214 (285)
T ss_pred CCCHHHHHhcCHHHHHHhCCcHHHH---------HHHHHHHHHHHcCCccHHHhccCCHHHHHHHHHcCCCcCHHHHHHH
Confidence 6788888888888776 55555433 355566655554321 46779999999999999999999
Q ss_pred HHh--hcCCCCC
Q 027775 126 LAA--YAPGVAP 135 (219)
Q Consensus 126 La~--~~P~~~p 135 (219)
|-. ..|+.+|
T Consensus 215 llf~lgr~dvfP 226 (285)
T COG0122 215 LLFGLGRPDVFP 226 (285)
T ss_pred HHHcCCCCCCCC
Confidence 976 4576655
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=94.65 E-value=0.099 Score=47.93 Aligned_cols=62 Identities=19% Similarity=0.164 Sum_probs=41.3
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhh--cCCCCCcccHHHHHH----hcCC--CC----CCCHHHHHHHHHHHHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAY--APGVAPFMSDEAMGA----ALGH--SK----DYSLRQYLLFADKLQAK 167 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~--~P~~~pFfsDEa~~~----~~g~--~~----kYt~keY~~~~~~l~~~ 167 (219)
...+++.|+.||||||=||.+||... .|+.+|. |-.+.- +.|. +. .-+.+.|..+.+..++.
T Consensus 215 ~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d~~Pv--D~~v~r~~~r~y~~~~~~~~~~~~~~~~~~~i~~~~~~~ 288 (310)
T TIGR00588 215 YEDAREALCELPGVGPKVADCICLMGLDKPQAVPV--DVHVWRIANRDYPWHPKTSRAKGPSPFARKELGNFFRSL 288 (310)
T ss_pred hHHHHHHHHhCCCccHHHHHHHHHHhCCCCCceee--cHHHHHHHHHHhcccccccccccCChhHHHHHHHHHHHH
Confidence 56789999999999999999999764 5666673 654432 2331 11 13566777755554443
No 11
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=94.39 E-value=0.036 Score=41.40 Aligned_cols=37 Identities=32% Similarity=0.496 Sum_probs=30.1
Q ss_pred HHhhccCCCChHHHHHHHHhh-cCCCCCcccHHHHHHhcC
Q 027775 109 SELTVLKGVGPATASAVLAAY-APGVAPFMSDEAMGAALG 147 (219)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~-~P~~~pFfsDEa~~~~~g 147 (219)
++|+.+|||||-||..||+.. +|. -|=+...+...+|
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~--rF~~~~~l~~~~G 39 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDIS--RFKSAKQLASYAG 39 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCch--hcccchhhhhccc
Confidence 468899999999999999986 443 4667788887777
No 12
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=94.22 E-value=0.13 Score=43.66 Aligned_cols=39 Identities=28% Similarity=0.225 Sum_probs=27.9
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~ 143 (219)
+..+++.|++||||||=||.+||....-.. .|.-|--+.
T Consensus 101 ~~~~~~~L~~l~GIG~ktA~~ill~~~~~~-~~~vD~~v~ 139 (191)
T TIGR01083 101 VPEDREELVKLPGVGRKTANVVLNVAFGIP-AIAVDTHVF 139 (191)
T ss_pred CchHHHHHHhCCCCcHHHHHHHHHHHcCCC-ccccchhHH
Confidence 445788999999999999999998764322 244444333
No 13
>PRK13910 DNA glycosylase MutY; Provisional
Probab=94.19 E-value=0.071 Score=48.80 Aligned_cols=31 Identities=26% Similarity=0.259 Sum_probs=25.1
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCC
Q 027775 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAP 135 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~p 135 (219)
....+.|.+||||||-||.+||+...-..++
T Consensus 68 P~~~~~L~~LpGIG~kTA~aIl~~af~~~~~ 98 (289)
T PRK13910 68 PNDYQSLLKLPGIGAYTANAILCFGFREKSA 98 (289)
T ss_pred ChhHHHHHhCCCCCHHHHHHHHHHHCCCCcC
Confidence 3468999999999999999999986544333
No 14
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=93.82 E-value=0.047 Score=51.20 Aligned_cols=36 Identities=33% Similarity=0.437 Sum_probs=29.5
Q ss_pred HHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHH
Q 027775 108 VSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMG 143 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~ 143 (219)
.+.|.+|+||||-||+||||...-...|+.+--+..
T Consensus 112 ~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~R 147 (342)
T COG1194 112 EEELAALPGVGPYTAGAILSFAFNQPEPVLDGNVKR 147 (342)
T ss_pred HHHHHhCCCCcHHHHHHHHHHHhCCCCceeecchhe
Confidence 456777999999999999999877777877766654
No 15
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=93.52 E-value=0.062 Score=46.17 Aligned_cols=44 Identities=27% Similarity=0.311 Sum_probs=31.4
Q ss_pred ccHHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027775 102 PDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 102 ~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (219)
|+-...++.|.+||||||-||..||+...-+ =-.-||-|....|
T Consensus 108 p~t~~lre~Ll~LpGVG~KTAnvVL~~l~~~--~~~~~~~~~~~~~ 151 (177)
T TIGR03252 108 PDGKELLRRLKALPGFGKQKAKIFLALLGKQ--LGVTPEGWREAAG 151 (177)
T ss_pred CCcHHHHHHHHcCCCCCHHHHHHHHHHHHHH--hCCCCcchHHhcc
Confidence 3445568899999999999999999975432 1134566665544
No 16
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=93.46 E-value=0.13 Score=45.42 Aligned_cols=40 Identities=23% Similarity=0.163 Sum_probs=28.7
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhc
Q 027775 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL 146 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~ 146 (219)
...+.|.+||||||=||.+||....- +..|.-|--..-++
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLlya~~-rp~fvVDty~~Rv~ 157 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILCYVCA-KEVMVVDKYSYLFL 157 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHHHHcC-CCccccchhHHHHH
Confidence 46788999999999999999987542 32455555444443
No 17
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=93.19 E-value=0.1 Score=47.38 Aligned_cols=36 Identities=28% Similarity=0.294 Sum_probs=29.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHh--hcCCCCCcccH
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSD 139 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsD 139 (219)
+..++++.|+.||||||-||..||-. ..|+.+| -.|
T Consensus 201 ~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~fp-~~D 238 (283)
T PRK10308 201 DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL-PDD 238 (283)
T ss_pred CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCCC-ccc
Confidence 56778999999999999999999865 5777655 344
No 18
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=93.17 E-value=0.097 Score=43.12 Aligned_cols=38 Identities=24% Similarity=0.306 Sum_probs=32.2
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcCC
Q 027775 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGH 148 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~ 148 (219)
+....|..|+||||++|..|+. +.||-|-|-+..+.|-
T Consensus 58 A~~~el~~lpGigP~~A~~IV~-----nGpf~sveDL~~V~GI 95 (132)
T PRK02515 58 SSVRAFRQFPGMYPTLAGKIVK-----NAPYDSVEDVLNLPGL 95 (132)
T ss_pred cCHHHHHHCCCCCHHHHHHHHH-----CCCCCCHHHHHcCCCC
Confidence 4577899999999999999993 6699999988888773
No 19
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.73 E-value=0.14 Score=30.28 Aligned_cols=19 Identities=47% Similarity=0.763 Sum_probs=16.9
Q ss_pred HhhccCCCChHHHHHHHHh
Q 027775 110 ELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 110 ~L~~LkGVGPATASaiLa~ 128 (219)
.|+.++|||+.+|..|+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 4789999999999999974
No 20
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=90.00 E-value=0.22 Score=38.66 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=22.0
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhh
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~ 129 (219)
..+.+..|+.|||||||||-=+..++
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LG 32 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLG 32 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcC
Confidence 34578899999999999999887764
No 21
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=87.95 E-value=0.35 Score=33.55 Aligned_cols=22 Identities=36% Similarity=0.351 Sum_probs=17.1
Q ss_pred HHHhhccCCCChHHHHHHHHhh
Q 027775 108 VSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~ 129 (219)
|+.++.+-||||+||.-..+..
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G 22 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKG 22 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT
T ss_pred CcchhhcccccHHHHHHHHHhC
Confidence 5789999999999999887754
No 22
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=87.69 E-value=0.58 Score=37.31 Aligned_cols=42 Identities=29% Similarity=0.466 Sum_probs=33.3
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027775 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (219)
.+....|..|+||||.+|..|+.-.. ...+|-|-|-+..+.|
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~-~~g~f~s~eeL~~V~G 105 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYRE-ENGAFKSVDDLTKVSG 105 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHH-hcCCcCCHHHHHcCCC
Confidence 34577899999999999999999754 3558888777776665
No 23
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=85.85 E-value=1.2 Score=31.82 Aligned_cols=30 Identities=30% Similarity=0.402 Sum_probs=21.6
Q ss_pred HhhCccHHHHHHH-hhccCCCChHHHHHHHH
Q 027775 98 FKSLPDLTKAVSE-LTVLKGVGPATASAVLA 127 (219)
Q Consensus 98 f~~l~d~~~al~~-L~~LkGVGPATASaiLa 127 (219)
...+|..-..++. +..|+|||+.+|.-|--
T Consensus 35 i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 35 IKALPYPITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHHSSS-HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred HHhCCHhHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 4446654445565 99999999999998743
No 24
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.41 E-value=0.62 Score=40.15 Aligned_cols=31 Identities=23% Similarity=0.338 Sum_probs=26.8
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPGV 133 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
+.+.-+..|.+.+||||-||-+||+.+.|+.
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~ 97 (194)
T PRK14605 67 EELSLFETLIDVSGIGPKLGLAMLSAMNAEA 97 (194)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhCCHHH
Confidence 4567889999999999999999999877753
No 25
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=84.35 E-value=1.3 Score=40.40 Aligned_cols=30 Identities=30% Similarity=0.437 Sum_probs=27.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
|+-..++.|..|+||||-+|=+.|+++.-.
T Consensus 153 DIP~~v~dLlsLPGVGPKMa~L~m~~AWn~ 182 (286)
T KOG1921|consen 153 DIPDTVEDLLSLPGVGPKMAHLTMQVAWNK 182 (286)
T ss_pred CCchhHHHHhcCCCCchHHHHHHHHHHhcc
Confidence 788899999999999999999999986554
No 26
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=81.91 E-value=1.3 Score=37.87 Aligned_cols=28 Identities=32% Similarity=0.489 Sum_probs=23.0
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcC
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P 131 (219)
.+.....|..++||||.||-.||..+.+
T Consensus 68 ek~~f~~L~~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 68 ERELFRLLISVSGVGPKLALAILSGLSP 95 (192)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHhCCH
Confidence 3445778999999999999999987655
No 27
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=81.14 E-value=1.1 Score=38.57 Aligned_cols=30 Identities=33% Similarity=0.541 Sum_probs=25.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+.+.-+..|..++||||-||-+||+...|+
T Consensus 66 ~Er~lF~~L~~V~GIGpK~Al~iL~~~~~~ 95 (191)
T TIGR00084 66 EERELFKELIKVNGVGPKLALAILSNMSPE 95 (191)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHhcCCHH
Confidence 356678889999999999999999987663
No 28
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=81.12 E-value=1.6 Score=30.24 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=20.1
Q ss_pred HHHHhhccCCCChHHHHHHHHhh
Q 027775 107 AVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~ 129 (219)
....|..++||||.+|..+....
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G 25 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAG 25 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTT
T ss_pred HHHhhccCCCCCHHHHHHHHhcC
Confidence 45778899999999999999973
No 29
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.93 E-value=1.1 Score=39.13 Aligned_cols=30 Identities=27% Similarity=0.378 Sum_probs=25.8
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+.+.-+..|....||||-||-+||+...|+
T Consensus 66 ~Er~lF~~LisVsGIGPK~ALaILs~~~~~ 95 (196)
T PRK13901 66 SEREVFEELIGVDGIGPRAALRVLSGIKYN 95 (196)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 456678889999999999999999988775
No 30
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=80.52 E-value=1.1 Score=38.60 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=26.0
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+.+.-+..|.+..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~LisV~GIGpK~Al~iLs~~~~~ 96 (186)
T PRK14600 67 EEQDCLRMLVKVSGVNYKTAMSILSKLTPE 96 (186)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHccCCHH
Confidence 456678899999999999999999987775
No 31
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=79.82 E-value=3.5 Score=36.82 Aligned_cols=153 Identities=21% Similarity=0.248 Sum_probs=83.9
Q ss_pred hhhHHHhhhhhHhhccCCCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhC---ccHH-HHHHH
Q 027775 35 LDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSL---PDLT-KAVSE 110 (219)
Q Consensus 35 LD~w~~~elp~~~~~r~~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l---~d~~-~al~~ 110 (219)
+.+|...+.|.-=--+.....|+-.||..|+ |..|..+- .|..+++.-++.+ ..+. +.++.
T Consensus 3 i~~~~~~~rPRErll~~G~~~Lsd~ELLail---LrtG~~~~------------~~~~la~~lL~~fg~L~~l~~a~~~e 67 (224)
T COG2003 3 IKDNPENERPRERLLKLGAEALSDAELLAIL---LRTGTKGE------------SVLDLAKELLQEFGSLAELLKASVEE 67 (224)
T ss_pred ccccccccchHHHHHHhChhhcchHHHHHHH---HhcCCCCC------------CHHHHHHHHHHHcccHHHHHhCCHHH
Confidence 4456665555321111223589999988776 56665332 4666666665543 3444 45999
Q ss_pred hhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcCCCC-CCCHHHHHHHHH-HHHHHHHH------hccc--------
Q 027775 111 LTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSK-DYSLRQYLLFAD-KLQAKAKE------LVSE-------- 174 (219)
Q Consensus 111 L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~~~-kYt~keY~~~~~-~l~~~~~~------L~~~-------- 174 (219)
||.++|||+|-|.-+.++.. ++-+.+..-.-.+. =-|+....+|+. .|...-++ |+.+
T Consensus 68 l~~v~GiG~aka~~l~a~~E------l~~R~~~~~~~~~~~i~sp~~~~~~l~~~l~~~~~E~f~vL~Ld~qnrlI~~e~ 141 (224)
T COG2003 68 LSSVKGIGLAKAIQIKAAIE------LGKRILAERLREGVVITSPEAVAEYLRAELGGEEREHFVVLYLDSQNRLIATET 141 (224)
T ss_pred HhhCCCccHHHHHHHHHHHH------HHHHHHHHHhccCCccCCHHHHHHHHHHHhhhhHHHHHHHHHhcCcCceeccee
Confidence 99999999999999998842 22222222111111 112233333332 22222111 1111
Q ss_pred -------CCCCCHHHH-HHHHHHHHHhhhhcccCCCCccchh
Q 027775 175 -------ENCFTPFDV-ERALWSSAIGLKLKASKSNQDSEIK 208 (219)
Q Consensus 175 -------~~~~s~~~V-Ekalws~~v~~k~~~~~~~~~~~~~ 208 (219)
...+-|++| .+|+...+.+-.+.---|+|+|..|
T Consensus 142 lf~GTi~~s~V~PREI~k~Al~~nAaavIlaHNHPSGd~~PS 183 (224)
T COG2003 142 LFIGTLNVSEVHPREIFKEALKYNAAAVILAHNHPSGDPTPS 183 (224)
T ss_pred EEeeecccceecHHHHHHHHHHhcchhhheeccCCCCCCCcC
Confidence 126778887 6777776666666666677776655
No 32
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=79.73 E-value=1.7 Score=30.75 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.9
Q ss_pred HHHHHhhccCCCChHHHHHHHHhh
Q 027775 106 KAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~ 129 (219)
+..+.|+.++||||.+|..|....
T Consensus 32 a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 32 ASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp --HHHHCTSTT--HHHHHHHHHHH
T ss_pred cCHHHHhccCCcCHHHHHHHHHHH
Confidence 467899999999999999998764
No 33
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=79.13 E-value=1.6 Score=36.22 Aligned_cols=42 Identities=31% Similarity=0.517 Sum_probs=31.9
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027775 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (219)
.+..+.|..|+||||+.|-+|..--.- ..||=|=|=..-+.|
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~-~G~f~sv~dL~~v~G 134 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREE-NGPFKSVDDLAKVKG 134 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHH-cCCCCcHHHHHhccC
Confidence 345777899999999999999996443 448877776666655
No 34
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=78.74 E-value=6.5 Score=34.94 Aligned_cols=37 Identities=27% Similarity=0.330 Sum_probs=26.9
Q ss_pred HHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHH
Q 027775 107 AVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA 144 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~ 144 (219)
..+.|-++||||+=||=+||--.. ++.-|.-|..-.-
T Consensus 113 ~R~~LL~iKGIG~ETaDsILlYa~-~rp~FVvD~Yt~R 149 (215)
T COG2231 113 LREELLSIKGIGKETADSILLYAL-DRPVFVVDKYTRR 149 (215)
T ss_pred HHHHHHccCCcchhhHHHHHHHHh-cCcccchhHHHHH
Confidence 578899999999999999997533 3435555654443
No 35
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=78.48 E-value=3 Score=29.52 Aligned_cols=39 Identities=28% Similarity=0.432 Sum_probs=28.7
Q ss_pred HHHhhc-cCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027775 108 VSELTV-LKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 108 l~~L~~-LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (219)
...|.. ++|||+.+|.+|+.-... ..+|-+-+.+..+.|
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~-~g~~~s~~dL~~v~g 54 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREE-YGPFKTVEDLKQVPG 54 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHH-cCCcCCHHHHHcCCC
Confidence 346777 999999999999997543 336667666666655
No 36
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.43 E-value=1.4 Score=37.90 Aligned_cols=30 Identities=30% Similarity=0.345 Sum_probs=26.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+.+.-+..|++..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~Li~VsGIGpK~Al~ILs~~~~~ 96 (183)
T PRK14601 67 DEQKMFEMLLKVNGIGANTAMAVCSSLDVN 96 (183)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 456778899999999999999999998875
No 37
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.97 E-value=6.8 Score=33.66 Aligned_cols=66 Identities=23% Similarity=0.222 Sum_probs=44.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|++|..-...-.--.|-=.-.-+..++..+++.+.++... .=.+.|+++||||+-||.=|+.=
T Consensus 62 GF~~~~Er~lF~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIilE 127 (183)
T PRK14601 62 GFLDKDEQKMFEMLLKVNGIGANTAMAVCSSLDVNSFYKALSL---------GDESVLKKVPGIGPKSAKRIIAE 127 (183)
T ss_pred CCCCHHHHHHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHH
Confidence 6889999665555544455333345567777777776655533 22568999999999999988753
No 38
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=76.64 E-value=2.5 Score=39.31 Aligned_cols=63 Identities=17% Similarity=0.181 Sum_probs=40.1
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHh--hcCCCCCcccHHHHH-----HhcCC--CCCCCHHHHHHHHHHHHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAA--YAPGVAPFMSDEAMG-----AALGH--SKDYSLRQYLLFADKLQAK 167 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~--~~P~~~pFfsDEa~~-----~~~g~--~~kYt~keY~~~~~~l~~~ 167 (219)
..+|.++||.|+||||-.|-+|+-. .-+..+|+ +--+|. +++|. ...-+.+-|.++-...+.+
T Consensus 213 yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VPV-DvHi~ria~~y~l~~~~g~k~l~~ki~~ev~~~f~~~ 284 (323)
T KOG2875|consen 213 YEEAREALCSLPGVGPKVADCICLMSLDKLSAVPV-DVHIWRIAQDYILPGLSGAKELTPKINGEVSNFFRSL 284 (323)
T ss_pred HHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcccc-hhhHHHHhhcccCCCccccccCCcchhHHHHHHHHHH
Confidence 4569999999999999999988754 34445552 222332 23441 2236777787776554444
No 39
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.44 E-value=2.9 Score=36.80 Aligned_cols=62 Identities=27% Similarity=0.340 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhh------CccH-HHHHHHhhccCCCChHHHHHHH
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKS------LPDL-TKAVSELTVLKGVGPATASAVL 126 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~------l~d~-~~al~~L~~LkGVGPATASaiL 126 (219)
..|+-.||..++ |.-|.-|.. .|...+++-++. +.++ .+..+.|++++|||+|.|..|+
T Consensus 12 ~~Lsd~ELLail---L~~g~~~~~-----------~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~ 77 (218)
T TIGR00608 12 EALSDYELLAII---LRTGTPKGL-----------DVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLK 77 (218)
T ss_pred ccCCHHHHHHHH---HhCCCCCCC-----------CHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHH
Confidence 588999977765 345543320 333334333332 2333 3458889999999999999999
Q ss_pred Hhh
Q 027775 127 AAY 129 (219)
Q Consensus 127 a~~ 129 (219)
++.
T Consensus 78 a~~ 80 (218)
T TIGR00608 78 AAV 80 (218)
T ss_pred HHH
Confidence 983
No 40
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.01 E-value=7.1 Score=34.03 Aligned_cols=66 Identities=15% Similarity=0.235 Sum_probs=45.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|++|..-...-.--.|-=.-.-+..++..+++.+.++... .=.+.||++||||+-||.=|+.=
T Consensus 61 GF~t~~Er~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAeRIIlE 126 (196)
T PRK13901 61 GFLNSSEREVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDR---------EDIELISKVKGIGNKMAGKIFLK 126 (196)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHH
Confidence 6889999766555544455333345667777777776655533 23568999999999999988754
No 41
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.91 E-value=7.3 Score=33.71 Aligned_cols=67 Identities=16% Similarity=0.126 Sum_probs=45.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~ 129 (219)
++.|++|..-...-.--.|-=--.-+.+++..+++.+..+... .=.+.||++||||+-||--|+.-.
T Consensus 62 GF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~---------~D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 62 GFSTPAQRQLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAG---------GDVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHH
Confidence 6889999766555544455333345567777777666555433 235689999999999999887654
No 42
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.62 E-value=7.4 Score=33.48 Aligned_cols=66 Identities=15% Similarity=0.159 Sum_probs=45.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|.+|..-...-.--.|-=.-+-+.+++..+++.+.++... .=.+.||++||||+-||.=|+-=
T Consensus 62 GF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~---------~D~~~L~~vpGIGkKtAerIilE 127 (188)
T PRK14606 62 GFSNERKKELFLSLTKVSRLGPKTALKIISNEDAETLVTMIAS---------QDVEGLSKLPGISKKTAERIVME 127 (188)
T ss_pred CCCCHHHHHHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHH
Confidence 6889998665555544455333345667777777766655533 23568999999999999988754
No 43
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=75.61 E-value=1.7 Score=30.07 Aligned_cols=22 Identities=32% Similarity=0.531 Sum_probs=19.0
Q ss_pred HHHHhhccCCCChHHHHHHHHh
Q 027775 107 AVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~ 128 (219)
..+.|+.++|||+.+|.-|...
T Consensus 36 ~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 36 DPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHHTSTTSSHHHHHHHHHH
T ss_pred CHHHHhcCCCCCHHHHHHHHHH
Confidence 4677999999999999988764
No 44
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=75.48 E-value=4.7 Score=37.83 Aligned_cols=34 Identities=26% Similarity=0.352 Sum_probs=26.6
Q ss_pred ccHHHHHHH--hhccCCCChHHHHHHHHhhcCCCCC
Q 027775 102 PDLTKAVSE--LTVLKGVGPATASAVLAAYAPGVAP 135 (219)
Q Consensus 102 ~d~~~al~~--L~~LkGVGPATASaiLa~~~P~~~p 135 (219)
.|+....+. +|+|||||++||+.|--..+-..++
T Consensus 44 e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~ 79 (326)
T COG1796 44 EDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVK 79 (326)
T ss_pred cchHHHHhhcccCCCCCccHHHHHHHHHHHHcCccH
Confidence 367777777 9999999999999998775544434
No 45
>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=74.86 E-value=5 Score=31.28 Aligned_cols=39 Identities=23% Similarity=0.291 Sum_probs=29.3
Q ss_pred HHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027775 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (219)
-.-+|+.+.|||+.+|..|+... +|. .+-.++|+-+..+
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l 54 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKL 54 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHH
T ss_pred hHhHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHH
Confidence 45578999999999999999984 564 5566777766543
No 46
>PRK00024 hypothetical protein; Reviewed
Probab=74.44 E-value=5 Score=35.27 Aligned_cols=60 Identities=28% Similarity=0.447 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCc---cH-HHHHHHhhccCCCChHHHHHHHHh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLP---DL-TKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~---d~-~~al~~L~~LkGVGPATASaiLa~ 128 (219)
..|+-.||..++ |..|..|. .|....++-++... ++ .+..+.|++++|||++.|..|+++
T Consensus 22 ~~Lsd~ELLa~l---L~~g~~~~------------~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~ 85 (224)
T PRK00024 22 AALSDAELLAIL---LRTGTKGK------------SVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85 (224)
T ss_pred ccCCHHHHHHHH---HcCCCCCC------------CHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHH
Confidence 588999977654 35554443 44444544443333 22 235778999999999999999887
No 47
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.02 E-value=2.4 Score=36.86 Aligned_cols=29 Identities=28% Similarity=0.403 Sum_probs=23.9
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
.+.-+..|.+..||||-||-+||+...|+
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 97 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAILSQFRPD 97 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHhhCCHH
Confidence 45677888899999999999999987775
No 48
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.81 E-value=2.2 Score=36.75 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=26.3
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+.+.-+..|++..||||-||-+||+...|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~AL~iLs~~~~~ 96 (188)
T PRK14606 67 RKKELFLSLTKVSRLGPKTALKIISNEDAE 96 (188)
T ss_pred HHHHHHHHHhccCCccHHHHHHHHcCCCHH
Confidence 356678899999999999999999988775
No 49
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=73.00 E-value=3.1 Score=40.41 Aligned_cols=90 Identities=20% Similarity=0.062 Sum_probs=47.2
Q ss_pred HHhh-ccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC---CCCCCCHHHHHHHHHHHHHHHHHhcc--cCCCCCHHH
Q 027775 109 SELT-VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG---HSKDYSLRQYLLFADKLQAKAKELVS--EENCFTPFD 182 (219)
Q Consensus 109 ~~L~-~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g---~~~kYt~keY~~~~~~l~~~~~~L~~--~~~~~s~~~ 182 (219)
+.|. .+|||||-||-||+|...-+..-..+-.+...++. ..-+-+- ..+.+.+-.+|.+|-. ..++|+-.-
T Consensus 205 ~~l~kgvpGVG~YTAGAiaSIAf~q~tGiVDGNVirvlsRalAIhsDcSk---gk~~q~~wkLA~qLVDP~RPGDFNQal 281 (555)
T KOG2457|consen 205 SSLMKGVPGVGQYTAGAIASIAFNQVTGIVDGNVIRVLSRALAIHSDCSK---GKFFQSSWKLAAQLVDPSRPGDFNQAL 281 (555)
T ss_pred HHHHhhCCCCCccchhhhhhhhhcCcccccccchHHHhHHhHhhcCCcch---hhHHHHHHHHHHHhcCCCCCCcHHHHH
Confidence 3444 49999999999999986443222233333332221 0001111 1234445556666643 234677777
Q ss_pred HHHHHHHHHHhhhhcccCC
Q 027775 183 VERALWSSAIGLKLKASKS 201 (219)
Q Consensus 183 VEkalws~~v~~k~~~~~~ 201 (219)
+|..+=.++.-+-.|..+|
T Consensus 282 MELGAt~CTpq~P~CS~CP 300 (555)
T KOG2457|consen 282 MELGATLCTPQKPSCSSCP 300 (555)
T ss_pred HHhcCeeccCCCCCcCCCC
Confidence 7766655555444444443
No 50
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=72.62 E-value=3.5 Score=33.62 Aligned_cols=38 Identities=21% Similarity=0.299 Sum_probs=30.0
Q ss_pred HHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027775 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (219)
.=+||.+.|||+++|-+|+... +|+ .+-..+||-+..+
T Consensus 16 ~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 16 VIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred eehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 3468899999999999999984 565 6667888877644
No 51
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.52 E-value=2.8 Score=36.24 Aligned_cols=29 Identities=34% Similarity=0.441 Sum_probs=23.7
Q ss_pred HHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 104 LTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
.+.-+..|....||||-||-+||+...|+
T Consensus 67 Er~lF~~L~~V~GIGpK~AL~iLs~~~~~ 95 (197)
T PRK14603 67 SLELFELLLGVSGVGPKLALALLSALPPA 95 (197)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 45667888899999999999999987774
No 52
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=70.02 E-value=5.1 Score=33.74 Aligned_cols=55 Identities=18% Similarity=0.199 Sum_probs=35.8
Q ss_pred CccHHHHHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh---cCCCCCCCHH
Q 027775 101 LPDLTKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSLR 155 (219)
Q Consensus 101 l~d~~~al~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~---~g~~~kYt~k 155 (219)
+++-+...-+|+.+.|||+.+|-.||... +|. .+--.+|+=...+ ...+..|.++
T Consensus 22 l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP 82 (154)
T PTZ00134 22 VDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIP 82 (154)
T ss_pred CCCCCEEEEeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCC
Confidence 44445555678999999999999999985 554 4444566655433 3344456543
No 53
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.00 E-value=13 Score=32.32 Aligned_cols=67 Identities=15% Similarity=0.170 Sum_probs=46.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~ 129 (219)
++.|.+|..-...-.--.|-=--.-+.+++..+++.+.++... .=.+.|+++||||+-||--|+.=.
T Consensus 63 GF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~---------~D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 63 GFATWDERQTFIVLISISKVGAKTALAILSQFRPDDLRRLVAE---------EDVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CCCCHHHHHHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHh---------CCHHHHhcCCCcCHHHHHHHHHHH
Confidence 6888988766555544555433345667777777766655433 235689999999999999887543
No 54
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.49 E-value=14 Score=32.01 Aligned_cols=67 Identities=18% Similarity=0.082 Sum_probs=44.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~ 129 (219)
++.|.+|..-.-.-.--.|-=.-.-+..++..+++.+.++... .=.+.|+++||||+-||.-|+.-.
T Consensus 61 GF~~~~Er~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~---------~D~~~L~kvpGIGkKtAerIilEL 127 (197)
T PRK14603 61 GFPDEDSLELFELLLGVSGVGPKLALALLSALPPALLARALLE---------GDARLLTSASGVGKKLAERIALEL 127 (197)
T ss_pred CcCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHh---------CCHHHHhhCCCCCHHHHHHHHHHH
Confidence 6888888665544443445333345667777777766655543 125689999999999999887543
No 55
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=67.24 E-value=2.1 Score=30.23 Aligned_cols=41 Identities=32% Similarity=0.488 Sum_probs=26.4
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027775 106 KAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (219)
+..+.|..|+|||+.+|-.|+..-.- .-||-|-+=+..+.|
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R~~-~G~f~s~~dL~~v~g 51 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYREK-NGPFKSLEDLKEVPG 51 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHHHH-H-S-SSGGGGGGSTT
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHh-CcCCCCHHHHhhCCC
Confidence 46788999999999999999997433 236666655555544
No 56
>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=67.00 E-value=15 Score=31.50 Aligned_cols=66 Identities=21% Similarity=0.165 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|++|..-...-.--.|-=.-+-+.+++.-+++.+.++...- =...|+++||||+-||.-|+.-
T Consensus 61 GF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~~~el~~aI~~~---------d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 61 GFNTLEERELFKELIKVNGVGPKLALAILSNMSPEEFVYAIETE---------EVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCCHHHHHHHHHhC---------CHHHHHhCCCCCHHHHHHHHHH
Confidence 68899997766665544553333344455554554444333221 1346899999999999999844
No 57
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=66.66 E-value=4.3 Score=26.00 Aligned_cols=15 Identities=47% Similarity=0.729 Sum_probs=13.2
Q ss_pred ccCCCChHHHHHHHH
Q 027775 113 VLKGVGPATASAVLA 127 (219)
Q Consensus 113 ~LkGVGPATASaiLa 127 (219)
.++||||-||-.+|.
T Consensus 20 Gv~giG~ktA~~ll~ 34 (36)
T smart00279 20 GVKGIGPKTALKLLR 34 (36)
T ss_pred CCCcccHHHHHHHHH
Confidence 588999999998875
No 58
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.29 E-value=4.3 Score=35.14 Aligned_cols=30 Identities=27% Similarity=0.383 Sum_probs=26.1
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+.+.-+..|++..||||=||-+||+...|+
T Consensus 67 ~Er~lF~~Li~V~GIGpK~Al~iLs~~~~~ 96 (195)
T PRK14604 67 AQRQLFELLIGVSGVGPKAALNLLSSGTPD 96 (195)
T ss_pred HHHHHHHHHhCcCCcCHHHHHHHHcCCCHH
Confidence 356678899999999999999999987775
No 59
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=64.81 E-value=7.3 Score=32.59 Aligned_cols=54 Identities=24% Similarity=0.389 Sum_probs=36.9
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh---cCCCCCCCHHHHH
Q 027775 105 TKAVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA---LGHSKDYSLRQYL 158 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~---~g~~~kYt~keY~ 158 (219)
+.-.-+|+.+.|||+.+|-.|+... +|. .+--.+++-+..+ ...+-+|.+++|.
T Consensus 21 k~i~~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP~w~ 80 (149)
T PRK04053 21 KPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEEGIPSWM 80 (149)
T ss_pred CEEeeeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHHhhccccCchhh
Confidence 3444568999999999999999884 555 4556777766543 3344556666554
No 60
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.44 E-value=58 Score=27.16 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=34.6
Q ss_pred hhCCHHHHHHHHHHHHhhCccHHHHHHHhhc--c-CCCChHHHHHHHHhhcCC
Q 027775 83 SSLDDSSVKSASEKAFKSLPDLTKAVSELTV--L-KGVGPATASAVLAAYAPG 132 (219)
Q Consensus 83 ~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~--L-kGVGPATASaiLa~~~P~ 132 (219)
---++..|-++|+-|.+.+|-+ +.+.++.. + ..+|||.|+|+.++.-|.
T Consensus 31 pvFpEnRVikaTrfairfMP~v-Avftl~wQ~~~~~ql~pAv~tAlfal~lpl 82 (149)
T COG3092 31 PVFPENRVIKATRFAIRFMPPV-AVFTLCWQIALGGQLGPAVATALFALSLPL 82 (149)
T ss_pred ccCchhHHHHHHHHHHHhccHH-HHHHHHHHHHHhcccchHHHHHHHHHhccc
Confidence 3446889999999999987743 23333322 2 367999999999986653
No 61
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=63.29 E-value=50 Score=28.16 Aligned_cols=70 Identities=19% Similarity=0.165 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
++.+..|-.....+..-.|--.-+.+.+++.-..+.+.++... +-.+.|++++|||+.||-.|+..+...
T Consensus 62 gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~---------~d~~~L~~v~Gig~k~A~~I~~~l~~~ 131 (192)
T PRK00116 62 GFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQAIAN---------GDVKALTKVPGIGKKTAERIVLELKDK 131 (192)
T ss_pred CcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 3446666544445544555443444455554444333322222 235578999999999999999876543
No 62
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=62.41 E-value=5 Score=35.10 Aligned_cols=30 Identities=27% Similarity=0.458 Sum_probs=26.5
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhhcCC
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAYAPG 132 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~~P~ 132 (219)
+-+.-+..|.++-||||-||=+||+..+|+
T Consensus 67 ~ER~lF~~LisVnGIGpK~ALaiLs~~~~~ 96 (201)
T COG0632 67 EERELFRLLISVNGIGPKLALAILSNLDPE 96 (201)
T ss_pred HHHHHHHHHHccCCccHHHHHHHHcCCCHH
Confidence 466778899999999999999999998775
No 63
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=62.06 E-value=5.8 Score=34.86 Aligned_cols=23 Identities=35% Similarity=0.616 Sum_probs=19.2
Q ss_pred cHHHHHHHhhccCCCChHHHHHH
Q 027775 103 DLTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASai 125 (219)
.+..-|+.|.+||||||-+|.=+
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~ 28 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRL 28 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHH
Confidence 45677899999999999999743
No 64
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=60.54 E-value=9.6 Score=30.78 Aligned_cols=39 Identities=26% Similarity=0.360 Sum_probs=28.5
Q ss_pred HHHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027775 107 AVSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (219)
..-.|+.+.|||+.+|-.|+... +|. .+--++|+-+..+
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l 56 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISAL 56 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHH
Confidence 34468999999999999999984 565 4455666655543
No 65
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=59.52 E-value=54 Score=29.02 Aligned_cols=82 Identities=20% Similarity=0.257 Sum_probs=60.2
Q ss_pred HHHHHHhh-ccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhc--C----CCCCCCHHHHHHHHHHHHHHHHHhcccCCC
Q 027775 105 TKAVSELT-VLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL--G----HSKDYSLRQYLLFADKLQAKAKELVSEENC 177 (219)
Q Consensus 105 ~~al~~L~-~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~--g----~~~kYt~keY~~~~~~l~~~~~~L~~~~~~ 177 (219)
.-|.+.|. .++|+|=--||=.|-=.-=+.++..+--...|+. | .|...|.|-|+..-+.++..+..++
T Consensus 116 ~vaRE~Lv~nikGiGyKEASHFLRNVG~~D~AIlDrHIlr~l~r~g~i~e~~kt~t~K~YLe~E~ilr~iae~~g----- 190 (210)
T COG1059 116 KVARELLVENIKGIGYKEASHFLRNVGFEDLAILDRHILRWLVRYGLIDENPKTLTRKLYLEIEEILRSIAEEVG----- 190 (210)
T ss_pred HHHHHHHHHHcccccHHHHHHHHHhcChhHHHHHHHHHHHHHHHhcccccCcccccHHHHHHHHHHHHHHHHHhC-----
Confidence 33778888 8999999999999864222233333333445653 3 3458889999999999999999995
Q ss_pred CCHHHHHHHHHHHH
Q 027775 178 FTPFDVERALWSSA 191 (219)
Q Consensus 178 ~s~~~VEkalws~~ 191 (219)
.++.+++.-+|-.-
T Consensus 191 ~s~gelDL~IWY~e 204 (210)
T COG1059 191 ISLGELDLYIWYKE 204 (210)
T ss_pred CCcchhHHHHHHHH
Confidence 67888888888643
No 66
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.14 E-value=31 Score=29.70 Aligned_cols=64 Identities=23% Similarity=0.220 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHH
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVL 126 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiL 126 (219)
++.|.+|-.-.-.-.--.|-=--+-+..++..+++.+.++... .=.+.|+++||||+-||--|+
T Consensus 62 GF~~~~Er~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~---------~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 62 GFATTEELSLFETLIDVSGIGPKLGLAMLSAMNAEALASAIIS---------GNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred CCCCHHHHHHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHh---------CCHHHHHhCCCCCHHHHHHHH
Confidence 6889998665555544455433455666676666654443322 124579999999999999954
No 67
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=57.84 E-value=8.5 Score=35.19 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=17.6
Q ss_pred HHHHHHhhccCCCChHHHHHHHH
Q 027775 105 TKAVSELTVLKGVGPATASAVLA 127 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa 127 (219)
..+|..|++++||||.||-.+..
T Consensus 81 ~~~l~~l~~i~GiGpk~a~~l~~ 103 (307)
T cd00141 81 PPGLLLLLRVPGVGPKTARKLYE 103 (307)
T ss_pred hHHHHHHHcCCCCCHHHHHHHHH
Confidence 45677788888888888877773
No 68
>PRK03980 flap endonuclease-1; Provisional
Probab=57.59 E-value=36 Score=31.10 Aligned_cols=70 Identities=21% Similarity=0.153 Sum_probs=43.5
Q ss_pred ccCCCChHHHHHHHHhhcC-------CCCCccc-HHHHHHhcCC------CCCCCHHHHHHHHHHHHHHHHHhcccCCCC
Q 027775 113 VLKGVGPATASAVLAAYAP-------GVAPFMS-DEAMGAALGH------SKDYSLRQYLLFADKLQAKAKELVSEENCF 178 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~~P-------~~~pFfs-DEa~~~~~g~------~~kYt~keY~~~~~~l~~~~~~L~~~~~~~ 178 (219)
.++||||-||.-++.-+-- ....|-. +|+......+ .+++..++...+.+-|+. + .+|
T Consensus 193 GI~GIG~ktA~kLi~~~~sle~i~~~~~~~~~~~~~~r~~f~~p~v~~~~~~~~~~pd~~~l~~fl~~---e-----~~f 264 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHGDLEKVLEERGFEIENYDEIREFFLNPPVTDDYELKWKEPDKEGIIEFLVE---E-----HDF 264 (292)
T ss_pred CCCCccHHHHHHHHHHCCCHHHHHHhccCCCCCHHHHHHHhcCCCCCCCCCccCCCCCHHHHHHHHhc---c-----CCC
Confidence 4899999999999976420 0112223 5666655442 345556666666655533 2 259
Q ss_pred CHHHHHHHHHHH
Q 027775 179 TPFDVERALWSS 190 (219)
Q Consensus 179 s~~~VEkalws~ 190 (219)
+..+|+.++=-+
T Consensus 265 ~~~rv~~~~~~l 276 (292)
T PRK03980 265 SEERVKKALERL 276 (292)
T ss_pred CHHHHHHHHHHH
Confidence 999999886554
No 69
>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=56.78 E-value=7.1 Score=24.23 Aligned_cols=15 Identities=27% Similarity=0.470 Sum_probs=11.3
Q ss_pred hhccCCCChHHHHHH
Q 027775 111 LTVLKGVGPATASAV 125 (219)
Q Consensus 111 L~~LkGVGPATASai 125 (219)
+.++.|||+.|+--+
T Consensus 13 i~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKL 27 (32)
T ss_dssp GGGSTTS-HHHHHHH
T ss_pred HHhhCCccHHHHHHH
Confidence 568999999998653
No 70
>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=55.68 E-value=9.9 Score=31.59 Aligned_cols=37 Identities=27% Similarity=0.404 Sum_probs=27.5
Q ss_pred HHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHH
Q 027775 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGA 144 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~ 144 (219)
.-+|+.+.|||+.+|-.|+... +|. .+--.+++-...
T Consensus 20 ~~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~ 59 (144)
T TIGR03629 20 EYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEK 59 (144)
T ss_pred EEeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHH
Confidence 3468999999999999999884 454 445567775543
No 71
>PRK00076 recR recombination protein RecR; Reviewed
Probab=54.58 E-value=9.8 Score=33.25 Aligned_cols=22 Identities=32% Similarity=0.641 Sum_probs=18.4
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASai 125 (219)
+..-++.|.+||||||-||.=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (196)
T PRK00076 6 IEKLIEALRKLPGIGPKSAQRL 27 (196)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5567889999999999999754
No 72
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=54.24 E-value=13 Score=29.93 Aligned_cols=38 Identities=32% Similarity=0.443 Sum_probs=28.3
Q ss_pred HHHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027775 108 VSELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (219)
.-.|+.+.|||+.+|-.|+... +|. .+--.+|+-+..+
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 56 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKI 56 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 3467999999999999999984 555 4456677766544
No 73
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=53.69 E-value=13 Score=29.56 Aligned_cols=37 Identities=24% Similarity=0.381 Sum_probs=28.3
Q ss_pred HHhhccCCCChHHHHHHHHhh--cCC-CCCcccHHHHHHh
Q 027775 109 SELTVLKGVGPATASAVLAAY--APG-VAPFMSDEAMGAA 145 (219)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~~--~P~-~~pFfsDEa~~~~ 145 (219)
-.|+.+.|||+.+|-.|+... +|. .+-.++|+-+..+
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l 54 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAI 54 (113)
T ss_pred eeeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHH
Confidence 457899999999999999984 565 5566777766544
No 74
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.65 E-value=29 Score=29.79 Aligned_cols=65 Identities=18% Similarity=0.196 Sum_probs=44.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|++|..-.-.-.--.|-=--+-+.+++..+++.+.++... .|+ +.| ++||||+-||.-|+.=
T Consensus 62 GF~~~~Er~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~-----~D~----~~L-~vpGIGkKtAerIilE 126 (186)
T PRK14600 62 GFLNREEQDCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVN-----EDK----AAL-KVNGIGEKLINRIITE 126 (186)
T ss_pred CCCCHHHHHHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHc-----CCH----hhe-ECCCCcHHHHHHHHHH
Confidence 6889998766555554555433355667777677766655543 233 578 8999999999988753
No 75
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.22 E-value=11 Score=32.88 Aligned_cols=22 Identities=32% Similarity=0.673 Sum_probs=18.4
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASai 125 (219)
+..-++.|.+||||||=||-=+
T Consensus 6 ~~~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 6 ISKLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5567889999999999998755
No 76
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=50.96 E-value=14 Score=34.28 Aligned_cols=67 Identities=15% Similarity=0.150 Sum_probs=40.4
Q ss_pred cHHHHHHHhhccCCCChHHHHHHHHhh---------cCCCCCcccHHHHHHh---cCCCCCCCHHHHHHHHHHHHHHHHH
Q 027775 103 DLTKAVSELTVLKGVGPATASAVLAAY---------APGVAPFMSDEAMGAA---LGHSKDYSLRQYLLFADKLQAKAKE 170 (219)
Q Consensus 103 d~~~al~~L~~LkGVGPATASaiLa~~---------~P~~~pFfsDEa~~~~---~g~~~kYt~keY~~~~~~l~~~~~~ 170 (219)
.+..+|..|++++||||.||-.+-... ++.. .++.+-...+ -.-.......+-..+.+.+.+.++.
T Consensus 83 ~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~~~--~l~~~q~~gl~~~~~~~~ri~r~e~~~i~~~i~~~l~~ 160 (334)
T smart00483 83 EVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKEL--KLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRK 160 (334)
T ss_pred cHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhcccc--cCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence 356799999999999999998887632 1111 2333221111 0123355666666666677666666
Q ss_pred h
Q 027775 171 L 171 (219)
Q Consensus 171 L 171 (219)
+
T Consensus 161 ~ 161 (334)
T smart00483 161 I 161 (334)
T ss_pred h
Confidence 5
No 77
>PRK13844 recombination protein RecR; Provisional
Probab=50.67 E-value=12 Score=32.82 Aligned_cols=22 Identities=14% Similarity=0.374 Sum_probs=18.3
Q ss_pred HHHHHHHhhccCCCChHHHHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAV 125 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASai 125 (219)
+..-++.|.+||||||=||.=+
T Consensus 10 ~~~LI~~l~~LPGIG~KsA~Rl 31 (200)
T PRK13844 10 ISAVIESLRKLPTIGKKSSQRL 31 (200)
T ss_pred HHHHHHHHHHCCCCCHHHHHHH
Confidence 5567888999999999998754
No 78
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=50.56 E-value=11 Score=27.50 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=15.8
Q ss_pred hhccCCCChHHHHHHHHhh
Q 027775 111 LTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 111 L~~LkGVGPATASaiLa~~ 129 (219)
+..++||||-||.-||.-+
T Consensus 24 i~gv~giG~k~A~~ll~~~ 42 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEY 42 (75)
T ss_pred CCCCCcccHHHHHHHHHHh
Confidence 3458899999999999864
No 79
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=48.93 E-value=55 Score=22.91 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=17.3
Q ss_pred HHHHhhccCCCChHHHHHHHHh
Q 027775 107 AVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~ 128 (219)
.++.|..++|||..||--|+..
T Consensus 45 s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 45 TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHcCCCCCHHHHHHHHhh
Confidence 4566777899999999888764
No 80
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=48.43 E-value=15 Score=33.64 Aligned_cols=17 Identities=29% Similarity=0.483 Sum_probs=9.5
Q ss_pred HHHHhhccCCCChHHHH
Q 027775 107 AVSELTVLKGVGPATAS 123 (219)
Q Consensus 107 al~~L~~LkGVGPATAS 123 (219)
.+..+++|+|||+++|+
T Consensus 43 ~~~~~~~ipgiG~~ia~ 59 (307)
T cd00141 43 SLEEAKKLPGIGKKIAE 59 (307)
T ss_pred CHHHhcCCCCccHHHHH
Confidence 34445666666666654
No 81
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=47.89 E-value=13 Score=34.45 Aligned_cols=35 Identities=26% Similarity=0.361 Sum_probs=25.0
Q ss_pred hhCccHHHHHHHhhccCCCChHHHHHHHHhhcCCC
Q 027775 99 KSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGV 133 (219)
Q Consensus 99 ~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~ 133 (219)
..++..-..+..|++|+|||+++|.-|--...-..
T Consensus 38 ~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~ 72 (334)
T smart00483 38 KSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGK 72 (334)
T ss_pred HhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCc
Confidence 34443333456789999999999999987765444
No 82
>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=47.21 E-value=26 Score=31.69 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=15.8
Q ss_pred ccCCCChHHHHHHHHhhc
Q 027775 113 VLKGVGPATASAVLAAYA 130 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~~ 130 (219)
.++||||-||--++.-+.
T Consensus 227 gv~giG~k~A~~li~~~~ 244 (316)
T cd00128 227 GIPGIGPVTALKLIKKYG 244 (316)
T ss_pred CCCCccHHHHHHHHHHcC
Confidence 499999999999998854
No 83
>PRK07945 hypothetical protein; Provisional
Probab=45.52 E-value=33 Score=31.79 Aligned_cols=19 Identities=47% Similarity=0.733 Sum_probs=15.6
Q ss_pred HhhccCCCChHHHHHHHHh
Q 027775 110 ELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 110 ~L~~LkGVGPATASaiLa~ 128 (219)
.|++|+|||..||..|--.
T Consensus 50 ~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred CcccCCCcCHHHHHHHHHH
Confidence 5888999999999887655
No 84
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=42.38 E-value=18 Score=32.47 Aligned_cols=42 Identities=33% Similarity=0.459 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhhCccHHHH-HHHhhccCCCChHHHHHHHHhh
Q 027775 88 SSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 88 ~~V~~~t~~Af~~l~d~~~a-l~~L~~LkGVGPATASaiLa~~ 129 (219)
...+..-..+|..+.++..| .+.|.+++|||+++|-.|....
T Consensus 14 krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 14 SKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred HHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 44445544456666666555 8899999999999999998875
No 85
>PRK08609 hypothetical protein; Provisional
Probab=39.95 E-value=28 Score=34.60 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=11.4
Q ss_pred HHHhhccCCCChHHHHHHHHh
Q 027775 108 VSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 108 l~~L~~LkGVGPATASaiLa~ 128 (219)
+..|++|+|||+++|+-|--.
T Consensus 47 ~~~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 47 IDDFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred hhhhccCCCcCHHHHHHHHHH
Confidence 344555666666655555444
No 86
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=39.78 E-value=41 Score=28.76 Aligned_cols=51 Identities=16% Similarity=0.318 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+||+..||.+|-.+ +..|..|...-+.+.+|.+.-|.++.+.-|...|+
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 3579999999999776 57788999999999999999999999999987774
No 87
>PRK14976 5'-3' exonuclease; Provisional
Probab=39.63 E-value=18 Score=32.83 Aligned_cols=16 Identities=50% Similarity=0.918 Sum_probs=14.3
Q ss_pred cCCCChHHHHHHHHhh
Q 027775 114 LKGVGPATASAVLAAY 129 (219)
Q Consensus 114 LkGVGPATASaiLa~~ 129 (219)
++||||-||..+|.-+
T Consensus 196 VpGIG~KtA~~LL~~~ 211 (281)
T PRK14976 196 VKGIGPKTAIKLLNKY 211 (281)
T ss_pred CCcccHHHHHHHHHHc
Confidence 7889999999999864
No 88
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=37.37 E-value=41 Score=34.43 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=19.8
Q ss_pred HHHHhhccCCCChHHHHHHHHhh
Q 027775 107 AVSELTVLKGVGPATASAVLAAY 129 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa~~ 129 (219)
+++.|..++||||-+|..|.+.+
T Consensus 539 ~~e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 539 ALSKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred CHHHHhhCCCccHHHHHHHHHHH
Confidence 45679999999999999998865
No 89
>PRK09482 flap endonuclease-like protein; Provisional
Probab=36.49 E-value=23 Score=31.96 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=15.3
Q ss_pred ccCCCChHHHHHHHHhhc
Q 027775 113 VLKGVGPATASAVLAAYA 130 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~~ 130 (219)
.++||||-||.-+|.-+.
T Consensus 186 GVpGIG~KtA~~LL~~~g 203 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR 203 (256)
T ss_pred CCCCcChHHHHHHHHHhC
Confidence 378889999999999753
No 90
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=34.88 E-value=37 Score=25.25 Aligned_cols=32 Identities=28% Similarity=0.431 Sum_probs=23.2
Q ss_pred hhccCCCChHHHHHHHHhhcCCCCCcccHHHHHH
Q 027775 111 LTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGA 144 (219)
Q Consensus 111 L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~ 144 (219)
|+.+||||..+|-.|+.... .-||-|=+=|..
T Consensus 29 l~~Ikglg~~~a~~I~~~R~--~g~f~s~~df~~ 60 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERE--NGPFKSLEDFIQ 60 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHH--CSS-SSHHHHHH
T ss_pred HhhcCCCCHHHHHHHHHhHh--cCCCCCHHHHHH
Confidence 67899999999999999876 448777555443
No 91
>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=34.84 E-value=89 Score=24.76 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=16.7
Q ss_pred HHHHhhccCCCChHHHHHHHH
Q 027775 107 AVSELTVLKGVGPATASAVLA 127 (219)
Q Consensus 107 al~~L~~LkGVGPATASaiLa 127 (219)
.++.|..++|||+.|+--|.-
T Consensus 96 s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 96 SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHHcCCCCCHHHHHHHHh
Confidence 456778899999999877653
No 92
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=32.41 E-value=29 Score=30.52 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=14.5
Q ss_pred ccCCCChHHHHHHHHhh
Q 027775 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (219)
.++||||-||.-+|.-+
T Consensus 187 Gv~GiG~ktA~~Ll~~~ 203 (240)
T cd00008 187 GVPGIGEKTAAKLLKEY 203 (240)
T ss_pred CCCccCHHHHHHHHHHh
Confidence 37899999999999864
No 93
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=32.08 E-value=31 Score=28.56 Aligned_cols=111 Identities=18% Similarity=0.197 Sum_probs=69.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHH-------------HHHHhh-ccCCC
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTK-------------AVSELT-VLKGV 117 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~-------------al~~L~-~LkGV 117 (219)
..+|++..||..|-.+- ..|.-|....+.++.|.+.-|.++..+-|...|++.. .+.-+. =||=
T Consensus 10 egRyls~~EL~~l~~~~-~~~~~Rl~aa~~L~~~a~~IV~~A~~~l~~~~P~l~~~gg~~y~~~~~~~C~RD~~~~LR~- 87 (157)
T PF00502_consen 10 EGRYLSDGELQALKGYF-QSANARLEAAEKLRDNASEIVDQAAQKLFEKYPDLTQPGGNLYPSRRREACWRDIWHYLRY- 87 (157)
T ss_dssp TTSECEHHHHHHHHHHH-HTHHHHHHHHHHHHHTHHHHHHHHHHHHHHHSGGGGSTTSTTSSHHHHHHHHHHHHHHHHH-
T ss_pred cCCCCCHHHHHHHHHHH-HhHHHHHHHHHHHHHhHHHHHHHHHHHHHHhccccccccccccchHHHHHHHHHHHHHHHH-
Confidence 35799999999998875 4566799999999999999999999999987775321 111110 1221
Q ss_pred ChHHHHHHHHhhcCCCCCcccHHHHHHhcC--CCCCCCHHHHHHHHHHHHHHHHHh
Q 027775 118 GPATASAVLAAYAPGVAPFMSDEAMGAALG--HSKDYSLRQYLLFADKLQAKAKEL 171 (219)
Q Consensus 118 GPATASaiLa~~~P~~~pFfsDEa~~~~~g--~~~kYt~keY~~~~~~l~~~~~~L 171 (219)
.+-+|| +.++ -++.|..+.|+-. .....+..-|..-++.|++.+.+.
T Consensus 88 ---i~ya~l-~gd~---~~l~~~~l~~l~ei~~al~vp~~~~v~al~~lk~~~~~~ 136 (157)
T PF00502_consen 88 ---ITYAML-AGDT---DPLDERGLNGLREIYRALGVPIDAYVEALQCLKEAALQL 136 (157)
T ss_dssp ---HHHHHH-HTSS---HHHHHHTTTTHHHHHHHHT--HHHHHHHHHHHHHHHHHH
T ss_pred ---HHHHHH-hcch---hHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHH
Confidence 122222 2455 3477776655432 223445666777777777766554
No 94
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=31.49 E-value=65 Score=27.84 Aligned_cols=51 Identities=16% Similarity=0.216 Sum_probs=44.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+||+..||.+|-.. +..|..|-..-+.+.+|...-|.++.+.-|+..|+
T Consensus 15 qgRYLs~~eL~~L~~~-~~~g~~RL~aa~~L~~NA~~IV~~A~~~l~~~~P~ 65 (177)
T CHL00172 15 KAAYVGGSDLQALKKF-ISEGNKRLDSVNSIVSNASCIVSDAVSGMICENPG 65 (177)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCCC
Confidence 3579999999998654 67899999999999999999999999999987774
No 95
>smart00475 53EXOc 5'-3' exonuclease.
Probab=31.12 E-value=31 Score=30.91 Aligned_cols=17 Identities=29% Similarity=0.577 Sum_probs=14.5
Q ss_pred ccCCCChHHHHHHHHhh
Q 027775 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (219)
.++||||-||.-+|.=+
T Consensus 190 GV~GIG~KtA~~Ll~~y 206 (259)
T smart00475 190 GVPGIGEKTAAKLLKEF 206 (259)
T ss_pred CCCCCCHHHHHHHHHHh
Confidence 37888999999999864
No 96
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=30.17 E-value=49 Score=26.29 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=22.3
Q ss_pred HHHHHhhccCCCChHHHHHHHHhhcC
Q 027775 106 KAVSELTVLKGVGPATASAVLAAYAP 131 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~~~P 131 (219)
.++.-|+.++||||..|-+++.++--
T Consensus 50 ~~~AdL~ri~gi~~~~a~LL~~AGv~ 75 (122)
T PF14229_consen 50 VNQADLMRIPGIGPQYAELLEHAGVD 75 (122)
T ss_pred HhHHHhhhcCCCCHHHHHHHHHhCcC
Confidence 46778889999999999999998643
No 97
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=30.04 E-value=52 Score=31.34 Aligned_cols=23 Identities=22% Similarity=0.486 Sum_probs=16.5
Q ss_pred HHHHHhhccCCCChHHHHHHHHh
Q 027775 106 KAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 106 ~al~~L~~LkGVGPATASaiLa~ 128 (219)
+..+.|++.+|||++.|-.|-..
T Consensus 316 As~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 316 ASIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred CCHHHHhhCCCcCHHHHHHHHHH
Confidence 34667888888888888776544
No 98
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=29.81 E-value=8.4 Score=30.10 Aligned_cols=17 Identities=41% Similarity=0.792 Sum_probs=13.7
Q ss_pred ccCCCChHHHHHHHHhh
Q 027775 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (219)
..+||||-||+.+|.-+
T Consensus 22 GV~GIG~KtA~~LL~~y 38 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEY 38 (101)
T ss_dssp --TTSTCHCCCCCHHHH
T ss_pred CCCCCCHHHHHHHHHHc
Confidence 47899999999999875
No 99
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=28.09 E-value=98 Score=26.31 Aligned_cols=51 Identities=12% Similarity=0.138 Sum_probs=44.4
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|..- +..|..|-..-+.+.+|...-|.++.+.-|+..|+
T Consensus 15 qgRyls~~eL~~l~~~-~~~g~~RL~aa~~Lt~nA~~IV~~Aa~~lf~~~P~ 65 (162)
T CHL00170 15 QGRFLSNGELQACNGR-FQRAAASLEAARSLTSNAQRLIDGAAQAVYTKFPY 65 (162)
T ss_pred ccCCCCHHHHHHHHHH-HhccHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcC
Confidence 3579999999998764 57899999999999999999999999999987774
No 100
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=28.02 E-value=1e+02 Score=29.11 Aligned_cols=84 Identities=21% Similarity=0.269 Sum_probs=58.4
Q ss_pred cHHHHHHH-hhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHhcc--------
Q 027775 103 DLTKAVSE-LTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKLQAKAKELVS-------- 173 (219)
Q Consensus 103 d~~~al~~-L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g~~~kYt~keY~~~~~~l~~~~~~L~~-------- 173 (219)
|++..+++ ||+|-|+- ---.|++..+-++ |=+=|-+...-+...|.|.++.|.+-...++.-++.+.-
T Consensus 234 DVsEiVNALLTelDgi~--eneGVvtIaaTN~-p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~ 310 (368)
T COG1223 234 DVSEIVNALLTELDGIK--ENEGVVTIAATNR-PELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRY 310 (368)
T ss_pred cHHHHHHHHHHhccCcc--cCCceEEEeecCC-hhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHH
Confidence 67777775 56899883 1122444444444 668888888888888999999999888888777766542
Q ss_pred ---cCCCCCHHHH-HHHHHH
Q 027775 174 ---EENCFTPFDV-ERALWS 189 (219)
Q Consensus 174 ---~~~~~s~~~V-Ekalws 189 (219)
....+|.+|| ||+|=+
T Consensus 311 ~~~~t~g~SgRdikekvlK~ 330 (368)
T COG1223 311 LAAKTKGMSGRDIKEKVLKT 330 (368)
T ss_pred HHHHhCCCCchhHHHHHHHH
Confidence 2246888887 777654
No 101
>PRK08609 hypothetical protein; Provisional
Probab=27.60 E-value=47 Score=33.09 Aligned_cols=24 Identities=17% Similarity=0.301 Sum_probs=19.6
Q ss_pred HHHHHHHhhccCCCChHHHHHHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAVLA 127 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASaiLa 127 (219)
+..++..|++++||||.||-.+--
T Consensus 83 ~p~~~~~l~~i~GiGpk~a~~l~~ 106 (570)
T PRK08609 83 VPEGLLPLLKLPGLGGKKIAKLYK 106 (570)
T ss_pred CcHHHHHHhcCCCCCHHHHHHHHH
Confidence 345788899999999999988753
No 102
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.42 E-value=1.9e+02 Score=31.35 Aligned_cols=24 Identities=25% Similarity=0.457 Sum_probs=19.3
Q ss_pred HHHHhhc------cCCCChHHHHHHHHhhc
Q 027775 107 AVSELTV------LKGVGPATASAVLAAYA 130 (219)
Q Consensus 107 al~~L~~------LkGVGPATASaiLa~~~ 130 (219)
.|.+||. |+||||-||=-||..+.
T Consensus 858 ~laiL~G~DY~~GI~GIGpktAl~li~~~~ 887 (1034)
T TIGR00600 858 NLAYLLGSDYTEGIPTVGPVSAMEILNEFP 887 (1034)
T ss_pred HHHHeeCCCCCCCCCcccHHHHHHHHHHcC
Confidence 4566663 99999999999988765
No 103
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=26.74 E-value=3.1e+02 Score=26.82 Aligned_cols=83 Identities=25% Similarity=0.339 Sum_probs=49.5
Q ss_pred hHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhh-ccCCCChHH---------------------HHHHHHhhcCCCCC
Q 027775 78 LLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELT-VLKGVGPAT---------------------ASAVLAAYAPGVAP 135 (219)
Q Consensus 78 L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~-~LkGVGPAT---------------------ASaiLa~~~P~~~p 135 (219)
+..+|.+|+.+.++-++..=|....++..++-... +++||||-. +.++.+--.-...|
T Consensus 82 ~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~~~p 161 (422)
T KOG2582|consen 82 LNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYASVLP 161 (422)
T ss_pred HHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccccCC
Confidence 45799999998888888776665555544444443 455555432 11111111222558
Q ss_pred cccHHHHHHhcCCCCCCCHHHHHHHH
Q 027775 136 FMSDEAMGAALGHSKDYSLRQYLLFA 161 (219)
Q Consensus 136 FfsDEa~~~~~g~~~kYt~keY~~~~ 161 (219)
|++|.... +|+.+.-+..+.++.|+
T Consensus 162 ~ld~dive-i~~~n~h~~~k~fL~Y~ 186 (422)
T KOG2582|consen 162 YLDDDIVE-ICKANPHLDPKYFLLYL 186 (422)
T ss_pred ccchhHHH-HhccCCCCCHHHHHHHH
Confidence 88888776 46655567777766664
No 104
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=26.02 E-value=64 Score=20.75 Aligned_cols=41 Identities=22% Similarity=0.381 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhhCccHH-HHHHHhhccCCCChHHHHHHHHh
Q 027775 88 SSVKSASEKAFKSLPDLT-KAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 88 ~~V~~~t~~Af~~l~d~~-~al~~L~~LkGVGPATASaiLa~ 128 (219)
..+......+|..+.++. ...+.|+.++|++..+|..|...
T Consensus 4 ~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 4 EIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINR 45 (50)
T ss_pred HHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHH
Confidence 334444455555444433 34788999999999999888764
No 105
>PRK09672 phage exclusion protein Lit; Provisional
Probab=26.01 E-value=2.2e+02 Score=26.76 Aligned_cols=34 Identities=18% Similarity=0.101 Sum_probs=27.0
Q ss_pred cCCCChHHHHHHHHhhcCC-------CCCcccHHHHHHhcC
Q 027775 114 LKGVGPATASAVLAAYAPG-------VAPFMSDEAMGAALG 147 (219)
Q Consensus 114 LkGVGPATASaiLa~~~P~-------~~pFfsDEa~~~~~g 147 (219)
=||||.|+|.++|++.-|+ .+|=++|+....+-+
T Consensus 216 Kr~vgIaia~l~l~~l~~~~~~~g~~tHP~~~~RI~a~is~ 256 (305)
T PRK09672 216 KRSVGIAIALLFLQELELENKSCGKGTHPDADQRIFANLSK 256 (305)
T ss_pred hhhHHHHHHHHHHHHHhccccCCCCCCCCCHHHHHHHhhhc
Confidence 6899999999999986553 567788888876544
No 106
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=25.66 E-value=38 Score=28.11 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.0
Q ss_pred HHhhccCCCChHHHHHHHHh
Q 027775 109 SELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~ 128 (219)
+-|+-|.||||..++.+=..
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~ 86 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNEL 86 (133)
T ss_pred ccchhhcccCHHHHHHHHHc
Confidence 67999999999999977544
No 107
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=25.45 E-value=38 Score=30.50 Aligned_cols=20 Identities=45% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHhhccCCCChHHHHHHHHh
Q 027775 109 SELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 109 ~~L~~LkGVGPATASaiLa~ 128 (219)
+.|..|+|||+.++-.+|..
T Consensus 3 ~~L~~IpGIG~krakkLl~~ 22 (232)
T PRK12766 3 EELEDISGVGPSKAEALREA 22 (232)
T ss_pred cccccCCCcCHHHHHHHHHc
Confidence 46788999999999999997
No 108
>CHL00090 apcD allophycocyanin gamma subunit
Probab=24.70 E-value=95 Score=26.14 Aligned_cols=50 Identities=20% Similarity=0.317 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 53 NPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 53 ~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
.+|+|..||..|-.+ +..|.-|-..-+.+++|.+.-|.++.+.-|...|+
T Consensus 15 gRyls~~EL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~ 64 (161)
T CHL00090 15 LRYPTIGELESIQDY-LKTGEKRIRIATILRDNEKEIIQKASKQLFQIHPE 64 (161)
T ss_pred cCCCCHHHHHHHHHH-HHhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHCcC
Confidence 479999999999776 56788888888999999999999999999987774
No 109
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=24.55 E-value=1.3e+02 Score=25.40 Aligned_cols=51 Identities=12% Similarity=0.190 Sum_probs=44.4
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|..- +..|..|-..-+.+.+|...-|.++.+.-|+..|+
T Consensus 14 qgRyls~~eL~~l~~~-~~~g~~RL~aa~~Lt~na~~IV~~Aa~~lf~~~P~ 64 (161)
T TIGR01338 14 QGRFLSNGELQSIFGR-FQRATASLEAAKSLTSNAQRLISGAAQAVYSKFPY 64 (161)
T ss_pred ccCCCCHHHHHHHHHH-HHchHHHHHHHHHHHhhHHHHHHHHHHHHHHhCcC
Confidence 3579999999998663 67899999999999999999999999999987774
No 110
>CHL00086 apcA allophycocyanin alpha subunit
Probab=23.78 E-value=1.2e+02 Score=25.64 Aligned_cols=51 Identities=20% Similarity=0.401 Sum_probs=44.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|-.. +..|..|-..-+.+.+|.+.-|.++.+.-|...|+
T Consensus 14 ~gRyls~~eL~~l~~~-~~~~~~Rl~aa~~l~~na~~IV~~A~~~l~~~~P~ 64 (161)
T CHL00086 14 EARYLSPGELDRIKSF-VLSGQRRLRIAQILTDNRERIVKQGGQQLFQKRPD 64 (161)
T ss_pred ccCCCCHHHHHHHHHH-HHhhHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcC
Confidence 3579999999998776 56788898899999999999999999999987775
No 111
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=23.68 E-value=60 Score=28.45 Aligned_cols=66 Identities=20% Similarity=0.227 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHh
Q 027775 54 PHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAA 128 (219)
Q Consensus 54 ~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~ 128 (219)
++.|.+|-.-.-.-=--.|-=--+-+..+++-+++.+.++... .=++.|+++||||.=||=-|+.=
T Consensus 62 GF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~---------~d~~~L~k~PGIGkKtAerivle 127 (201)
T COG0632 62 GFLTEEERELFRLLISVNGIGPKLALAILSNLDPEELAQAIAN---------EDVKALSKIPGIGKKTAERIVLE 127 (201)
T ss_pred CCCCHHHHHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHh---------cChHhhhcCCCCCHHHHHHHHHH
Confidence 5777777433322222233211223444555455555444332 12568999999999999888764
No 112
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=23.64 E-value=96 Score=26.48 Aligned_cols=51 Identities=18% Similarity=0.311 Sum_probs=43.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+|++..||..|-.. +..|.-|-..-+.+.+|.+.-|.++.+.-|...|+
T Consensus 15 ~gRyls~~EL~~l~~~-~~~~~~Rl~aa~~L~~na~~IV~~A~~~l~~~~P~ 65 (172)
T CHL00171 15 RGEFLSNTQLDALSKM-VAEGNKRLDAVNKINANASTIVTNAARSLFAEQPQ 65 (172)
T ss_pred ccCCCCHHHHHHHHHH-HHhHHHHHHHHHHHHHhHHHHHHHHHHHHHHHCcC
Confidence 3579999999998776 56788888888899999999999999999987775
No 113
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=23.34 E-value=87 Score=22.37 Aligned_cols=49 Identities=20% Similarity=0.162 Sum_probs=38.7
Q ss_pred HHHHHHHHHHhhCccHHHHHHHhhccCCCChHHHHHHHHhhcCCCCCcc
Q 027775 89 SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFM 137 (219)
Q Consensus 89 ~V~~~t~~Af~~l~d~~~al~~L~~LkGVGPATASaiLa~~~P~~~pFf 137 (219)
.|+..+.+-+....+-...++.|.+.-||-|..-|+|.--.--++.-||
T Consensus 3 ~Vq~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF 51 (57)
T TIGR01589 3 LVQNRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFF 51 (57)
T ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHH
Confidence 4667777777777888999999999999999999988776554454555
No 114
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=23.14 E-value=99 Score=26.26 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=44.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCcchHHHhhhCCHHHHHHHHHHHHhhCcc
Q 027775 52 PNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPD 103 (219)
Q Consensus 52 ~~~~ltk~EL~~Lv~WKL~rGkfRP~L~~lV~sN~~~~V~~~t~~Af~~l~d 103 (219)
..+||+..||..|-. -+.+|..|...-+.+.+|.+..|.++.+.-|+..|+
T Consensus 15 ~gRyls~~eL~~l~~-~~~~a~~rl~aa~~L~~na~~iV~~A~~~l~~~~P~ 65 (164)
T CHL00173 15 AGRFPSSSDLESVQG-NIQRAAARLEAAEKLASNHEAVVKEAGDACFAKYSY 65 (164)
T ss_pred ccCCCCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 357999999999855 356888999999999999999999999999987775
No 115
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=23.09 E-value=1.5e+02 Score=25.78 Aligned_cols=25 Identities=20% Similarity=0.321 Sum_probs=16.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHhc
Q 027775 148 HSKDYSLRQYLLFADKLQAKAKELV 172 (219)
Q Consensus 148 ~~~kYt~keY~~~~~~l~~~~~~L~ 172 (219)
.+.+||..||..+...-++++++|-
T Consensus 161 ~~~k~~~~el~~i~~~y~~~~k~L~ 185 (189)
T PF05766_consen 161 EPRKWTIEELKAIIAIYRAKLKELK 185 (189)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 3557777777777776666666663
No 116
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=22.63 E-value=60 Score=29.47 Aligned_cols=37 Identities=27% Similarity=0.392 Sum_probs=28.1
Q ss_pred HHHHHHHhhccCCCChHHHHHH--HHhhcCCCCCcccHHH
Q 027775 104 LTKAVSELTVLKGVGPATASAV--LAAYAPGVAPFMSDEA 141 (219)
Q Consensus 104 ~~~al~~L~~LkGVGPATASai--La~~~P~~~pFfsDEa 141 (219)
-..=++-||.+||||+-|+=.+ -+++.|+..| -.|--
T Consensus 160 eEeL~~~LT~VKGIg~Wtv~MflIfsL~R~DVmp-~dDlg 198 (254)
T KOG1918|consen 160 EEELIERLTNVKGIGRWTVEMFLIFSLHRPDVMP-ADDLG 198 (254)
T ss_pred HHHHHHHHHhccCccceeeeeeeeeccCCCcccC-chhhh
Confidence 4556889999999999999754 4668898877 34433
No 117
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=22.18 E-value=39 Score=24.04 Aligned_cols=17 Identities=29% Similarity=0.342 Sum_probs=12.5
Q ss_pred ccCCCChHHHHHHHHhh
Q 027775 113 VLKGVGPATASAVLAAY 129 (219)
Q Consensus 113 ~LkGVGPATASaiLa~~ 129 (219)
.+=|+||||+.+.=.+.
T Consensus 17 ~v~tigPA~~Al~~~~~ 33 (77)
T PF04854_consen 17 PVFTIGPATAALYYVVR 33 (77)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45578999998876653
No 118
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.66 E-value=7e+02 Score=25.84 Aligned_cols=19 Identities=5% Similarity=-0.202 Sum_probs=14.3
Q ss_pred CCCHHHHHHHHHHHHHhhh
Q 027775 177 CFTPFDVERALWSSAIGLK 195 (219)
Q Consensus 177 ~~s~~~VEkalws~~v~~k 195 (219)
.++...+|...|+-.....
T Consensus 525 ~vdVd~LE~s~ga~~~~~~ 543 (652)
T KOG2376|consen 525 AVDVDALEKSDGAKYSEAY 543 (652)
T ss_pred hcCchHhhhccCcchhhhh
Confidence 4667788999888777663
No 119
>PF05845 PhnH: Bacterial phosphonate metabolism protein (PhnH); InterPro: IPR008772 This family consists of several bacterial PhnH sequences, which is a component of the C-P lyase system (GenProp0232 from GENPROP) for the catabolism of phosphonate compounds []. The specific function of this component is unknown.; GO: 0015716 phosphonate transport; PDB: 2FSU_A.
Probab=21.64 E-value=79 Score=27.40 Aligned_cols=23 Identities=26% Similarity=0.466 Sum_probs=15.6
Q ss_pred cCCCChHHHHHHHHhhcCCCCCcc
Q 027775 114 LKGVGPATASAVLAAYAPGVAPFM 137 (219)
Q Consensus 114 LkGVGPATASaiLa~~~P~~~pFf 137 (219)
-.|..||++..+|++.|.+. ||+
T Consensus 39 ~~~l~~a~~avllTLlD~et-~lw 61 (192)
T PF05845_consen 39 PAGLSPAAAAVLLTLLDNET-PLW 61 (192)
T ss_dssp STTS-HHHHHHHHHH--TTS--EE
T ss_pred CCCccHHHHHHHHHHcCCCC-cee
Confidence 44779999999999999876 773
No 120
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=20.68 E-value=82 Score=31.53 Aligned_cols=38 Identities=26% Similarity=0.399 Sum_probs=32.4
Q ss_pred HHHHHHhhccCCCChHHHHHHHHhhcCCCCCcccHHHHHHhcC
Q 027775 105 TKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALG 147 (219)
Q Consensus 105 ~~al~~L~~LkGVGPATASaiLa~~~P~~~pFfsDEa~~~~~g 147 (219)
+++.+.|..|+|||-.|+.-|++- -||.|-|.|....+
T Consensus 512 ~~s~~vl~~ipgig~~~~~~I~~~-----Rp~~s~e~~l~~v~ 549 (560)
T COG1031 512 SASKDVLRAIPGIGKKTLRKILAE-----RPFKSSEEFLKLVP 549 (560)
T ss_pred cccHHHHHhcccchhhhHHHHHhc-----CCccchHHHHhccC
Confidence 346899999999999999999984 39999999987665
Done!