Query psy11828
Match_columns 443
No_of_seqs 355 out of 1641
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 20:01:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11828hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03980 flap endonuclease-1; 100.0 8.7E-50 1.9E-54 397.8 20.0 247 15-367 4-264 (292)
2 PTZ00217 flap endonuclease-1; 100.0 1.5E-49 3.2E-54 410.3 20.5 252 16-368 60-319 (393)
3 KOG2518|consensus 100.0 4.6E-48 1E-52 399.7 16.5 244 12-339 46-295 (556)
4 cd00128 XPG Xeroderma pigmento 100.0 7.8E-47 1.7E-51 379.8 20.4 252 15-368 49-306 (316)
5 TIGR03674 fen_arch flap struct 100.0 1.6E-45 3.4E-50 374.2 20.8 247 16-367 52-311 (338)
6 KOG2519|consensus 100.0 5.2E-43 1.1E-47 358.7 11.4 254 16-369 54-316 (449)
7 TIGR00600 rad2 DNA excision re 100.0 2E-34 4.3E-39 322.6 12.2 172 166-370 786-976 (1034)
8 KOG2520|consensus 99.9 2.4E-28 5.2E-33 266.5 8.3 219 141-400 463-701 (815)
9 cd00008 53EXOc 5'-3' exonuclea 99.9 5.9E-23 1.3E-27 199.9 13.9 183 15-299 27-215 (240)
10 smart00475 53EXOc 5'-3' exonuc 99.9 5.4E-23 1.2E-27 202.3 13.4 115 166-299 98-218 (259)
11 COG0258 Exo 5'-3' exonuclease 99.9 1.4E-23 3.1E-28 211.1 8.0 181 18-298 43-229 (310)
12 PRK14976 5'-3' exonuclease; Pr 99.9 9.5E-22 2.1E-26 195.6 14.0 185 15-299 32-223 (281)
13 PF00867 XPG_I: XPG I-region; 99.8 3.1E-22 6.7E-27 168.3 3.4 80 166-265 5-94 (94)
14 PRK05755 DNA polymerase I; Pro 99.8 9.2E-20 2E-24 206.0 13.5 114 166-299 100-219 (880)
15 TIGR00593 pola DNA polymerase 99.8 2.2E-19 4.8E-24 202.0 14.4 115 166-299 98-217 (887)
16 PRK09482 flap endonuclease-lik 99.7 4E-16 8.6E-21 153.4 14.5 108 177-298 101-213 (256)
17 smart00484 XPGI Xeroderma pigm 99.6 4.9E-16 1.1E-20 125.3 4.8 62 166-242 5-70 (73)
18 cd00080 HhH2_motif Helix-hairp 99.4 8.9E-13 1.9E-17 106.8 6.1 49 248-298 3-53 (75)
19 PF00752 XPG_N: XPG N-terminal 99.2 2.1E-11 4.6E-16 103.2 6.9 46 19-64 55-100 (101)
20 smart00485 XPGN Xeroderma pigm 99.2 4E-11 8.7E-16 101.3 6.7 58 7-64 33-98 (99)
21 KOG2518|consensus 99.2 1.1E-11 2.4E-16 130.1 3.2 75 74-149 176-250 (556)
22 TIGR00600 rad2 DNA excision re 99.0 9.2E-10 2E-14 125.2 8.5 59 7-65 33-98 (1034)
23 smart00279 HhH2 Helix-hairpin- 98.9 9.5E-10 2.1E-14 77.1 3.7 33 252-285 1-36 (36)
24 PHA00439 exonuclease 98.9 9E-09 2E-13 102.8 9.5 88 177-284 114-206 (286)
25 PF01367 5_3_exonuc: 5'-3' exo 98.8 4.4E-10 9.6E-15 96.2 -3.2 48 250-299 1-50 (101)
26 cd00080 HhH2_motif Helix-hairp 98.3 7.5E-07 1.6E-11 72.2 5.4 49 108-158 4-54 (75)
27 PRK03980 flap endonuclease-1; 98.0 4.9E-06 1.1E-10 83.8 5.3 56 99-156 164-219 (292)
28 PTZ00217 flap endonuclease-1; 98.0 6.7E-06 1.4E-10 86.1 5.2 56 101-158 212-267 (393)
29 cd00128 XPG Xeroderma pigmento 97.8 1.9E-05 4.2E-10 79.9 5.2 54 104-159 203-256 (316)
30 TIGR03674 fen_arch flap struct 97.7 3.2E-05 7E-10 79.4 4.9 58 98-157 210-267 (338)
31 PF12813 XPG_I_2: XPG domain c 97.7 4.9E-05 1.1E-09 74.9 5.8 69 177-260 24-107 (246)
32 smart00279 HhH2 Helix-hairpin- 97.6 7.9E-05 1.7E-09 52.2 3.3 32 111-143 1-35 (36)
33 PHA02567 rnh RnaseH; Provision 97.4 0.00015 3.3E-09 73.3 4.9 79 177-272 124-207 (304)
34 PF02739 5_3_exonuc_N: 5'-3' e 97.2 0.00082 1.8E-08 62.6 6.7 61 177-241 103-167 (169)
35 smart00475 53EXOc 5'-3' exonuc 97.0 0.001 2.2E-08 66.1 5.2 52 105-158 165-218 (259)
36 cd00008 53EXOc 5'-3' exonuclea 96.9 0.0011 2.5E-08 64.8 5.1 52 105-158 162-215 (240)
37 COG0258 Exo 5'-3' exonuclease 96.8 0.0012 2.6E-08 66.9 4.6 50 106-157 178-229 (310)
38 PF04599 Pox_G5: Poxvirus G5 p 96.8 0.011 2.4E-07 62.2 11.5 46 19-64 47-92 (425)
39 KOG2519|consensus 96.8 0.0012 2.6E-08 69.6 4.2 49 104-154 209-257 (449)
40 PRK14976 5'-3' exonuclease; Pr 96.4 0.0044 9.6E-08 62.3 5.1 59 98-158 163-223 (281)
41 PHA03065 Hypothetical protein; 96.2 0.039 8.5E-07 57.9 10.7 46 19-64 49-94 (438)
42 PF03159 XRN_N: XRN 5'-3' exon 96.0 0.0069 1.5E-07 59.5 4.3 45 19-64 57-105 (237)
43 PF12247 MKT1_N: Temperature d 95.7 0.003 6.6E-08 53.2 0.4 61 355-425 19-86 (90)
44 COG5049 XRN1 5'-3' exonuclease 95.6 0.055 1.2E-06 59.9 9.2 42 177-218 180-227 (953)
45 PRK05755 DNA polymerase I; Pro 95.2 0.022 4.9E-07 65.5 5.1 138 16-156 29-217 (880)
46 KOG2045|consensus 94.5 0.096 2.1E-06 59.6 7.3 56 23-79 62-121 (1493)
47 TIGR00593 pola DNA polymerase 94.1 0.065 1.4E-06 61.9 5.4 139 16-158 27-217 (887)
48 PRK09482 flap endonuclease-lik 94.0 0.093 2E-06 52.2 5.6 52 105-158 161-214 (256)
49 COG5366 Protein involved in pr 92.0 0.03 6.5E-07 59.3 -1.2 90 166-274 143-234 (531)
50 PF12826 HHH_2: Helix-hairpin- 90.5 0.16 3.5E-06 39.7 1.8 26 268-295 6-31 (64)
51 PF01367 5_3_exonuc: 5'-3' exo 86.4 0.22 4.8E-06 42.8 0.1 35 110-144 2-38 (101)
52 PF00633 HHH: Helix-hairpin-he 83.3 0.98 2.1E-05 30.4 2.1 15 269-283 15-29 (30)
53 PF10391 DNA_pol_lambd_f: Fing 81.4 1.6 3.4E-05 33.2 2.8 27 268-295 5-31 (52)
54 PF00867 XPG_I: XPG I-region; 78.6 0.84 1.8E-05 38.2 0.7 24 101-124 71-94 (94)
55 TIGR00084 ruvA Holliday juncti 76.7 2.1 4.6E-05 40.8 2.8 43 248-299 60-103 (191)
56 PRK00116 ruvA Holliday junctio 75.1 1.8 4E-05 41.0 2.0 19 269-287 77-95 (192)
57 PRK14602 ruvA Holliday junctio 73.8 2.7 5.9E-05 40.4 2.8 41 251-300 66-106 (203)
58 PRK14605 ruvA Holliday junctio 72.9 2.9 6.3E-05 39.9 2.8 42 248-298 61-103 (194)
59 PRK14603 ruvA Holliday junctio 72.8 2.5 5.4E-05 40.5 2.3 30 269-301 76-105 (197)
60 PF02371 Transposase_20: Trans 72.7 3.2 6.9E-05 34.2 2.6 22 265-286 2-23 (87)
61 KOG2044|consensus 71.8 16 0.00034 41.9 8.3 44 21-64 77-123 (931)
62 PF14520 HHH_5: Helix-hairpin- 71.1 3.6 7.9E-05 31.4 2.5 25 269-295 9-34 (60)
63 PRK13901 ruvA Holliday junctio 71.0 3 6.5E-05 40.1 2.4 41 251-300 64-104 (196)
64 PRK14600 ruvA Holliday junctio 70.6 3.6 7.7E-05 39.1 2.8 31 268-301 76-106 (186)
65 PRK14606 ruvA Holliday junctio 70.4 3 6.6E-05 39.7 2.3 45 248-301 61-106 (188)
66 PRK14604 ruvA Holliday junctio 70.2 3 6.6E-05 39.9 2.2 29 269-300 77-105 (195)
67 smart00278 HhH1 Helix-hairpin- 70.1 3.5 7.7E-05 26.4 1.8 18 267-284 3-20 (26)
68 KOG2520|consensus 69.0 5.2 0.00011 45.8 4.1 38 110-147 546-583 (815)
69 PRK14669 uvrC excinuclease ABC 68.5 3.8 8.2E-05 45.9 2.8 27 268-296 555-581 (624)
70 PRK14601 ruvA Holliday junctio 68.4 4 8.7E-05 38.7 2.6 17 269-285 77-93 (183)
71 PRK14667 uvrC excinuclease ABC 68.3 4.1 9E-05 45.1 3.1 29 267-297 516-544 (567)
72 PRK14601 ruvA Holliday junctio 68.2 3.7 7.9E-05 39.0 2.3 37 249-286 92-129 (183)
73 PRK14670 uvrC excinuclease ABC 67.2 4.5 9.7E-05 44.9 3.1 29 267-297 516-544 (574)
74 TIGR00194 uvrC excinuclease AB 67.0 4.1 8.9E-05 45.2 2.7 28 267-296 543-570 (574)
75 PHA00439 exonuclease 66.7 4.7 0.0001 40.9 2.8 32 111-143 173-206 (286)
76 PRK13901 ruvA Holliday junctio 64.8 5.2 0.00011 38.4 2.6 37 249-286 91-128 (196)
77 PRK14604 ruvA Holliday junctio 64.7 5.3 0.00011 38.3 2.7 37 249-286 92-129 (195)
78 PRK14606 ruvA Holliday junctio 63.8 5.7 0.00012 37.8 2.7 37 249-286 92-129 (188)
79 PRK14603 ruvA Holliday junctio 62.2 6.3 0.00014 37.8 2.7 37 249-286 91-128 (197)
80 PRK14671 uvrC excinuclease ABC 60.2 6.9 0.00015 43.8 2.9 26 268-295 572-597 (621)
81 PRK14600 ruvA Holliday junctio 59.4 9.1 0.0002 36.4 3.2 36 249-286 92-128 (186)
82 PRK14602 ruvA Holliday junctio 58.7 7.7 0.00017 37.3 2.6 36 250-286 94-130 (203)
83 PRK14672 uvrC excinuclease ABC 58.6 8 0.00017 43.7 3.1 29 267-297 610-638 (691)
84 COG0632 RuvA Holliday junction 57.6 12 0.00025 36.2 3.6 36 250-285 93-128 (201)
85 COG0632 RuvA Holliday junction 56.2 8.9 0.00019 37.0 2.6 31 268-301 76-106 (201)
86 PRK00558 uvrC excinuclease ABC 52.9 10 0.00022 42.3 2.7 27 268-296 546-572 (598)
87 PRK02515 psbU photosystem II c 52.5 13 0.00029 33.5 2.9 27 269-295 65-91 (132)
88 cd00141 NT_POLXc Nucleotidyltr 51.3 14 0.00031 37.5 3.3 29 268-297 88-116 (307)
89 PRK14668 uvrC excinuclease ABC 50.7 12 0.00025 41.7 2.7 29 267-297 527-555 (577)
90 PRK12766 50S ribosomal protein 50.5 13 0.00029 36.6 2.8 28 267-296 5-33 (232)
91 smart00483 POLXc DNA polymeras 50.5 13 0.00029 38.2 3.0 29 268-297 92-120 (334)
92 PF04599 Pox_G5: Poxvirus G5 p 46.0 13 0.00028 39.7 2.0 24 113-136 224-251 (425)
93 TIGR00084 ruvA Holliday juncti 45.9 17 0.00036 34.6 2.7 37 250-286 92-128 (191)
94 PRK14666 uvrC excinuclease ABC 45.7 17 0.00036 41.3 3.0 28 268-297 640-667 (694)
95 PRK14605 ruvA Holliday junctio 44.1 16 0.00034 34.9 2.2 36 250-286 93-129 (194)
96 TIGR01448 recD_rel helicase, p 43.4 24 0.00052 40.2 3.9 40 250-295 75-114 (720)
97 PF11798 IMS_HHH: IMS family H 42.1 18 0.0004 24.4 1.7 14 268-281 14-27 (32)
98 TIGR00596 rad1 DNA repair prot 40.4 14 0.00031 42.7 1.5 28 266-295 758-785 (814)
99 COG1948 MUS81 ERCC4-type nucle 40.3 24 0.00051 35.4 2.8 27 268-296 185-211 (254)
100 PRK08609 hypothetical protein; 39.5 29 0.00063 38.4 3.7 30 269-298 92-121 (570)
101 PHA03065 Hypothetical protein; 37.2 18 0.0004 38.5 1.5 24 113-136 226-253 (438)
102 PF02371 Transposase_20: Trans 37.0 25 0.00055 28.8 2.1 22 123-144 1-22 (87)
103 COG0322 UvrC Nuclease subunit 33.7 32 0.0007 38.3 2.9 28 268-297 533-560 (581)
104 TIGR01259 comE comEA protein. 32.8 43 0.00093 29.5 3.0 18 268-285 71-88 (120)
105 TIGR00575 dnlj DNA ligase, NAD 31.5 39 0.00084 38.2 3.0 25 269-295 502-526 (652)
106 PRK14351 ligA NAD-dependent DN 29.8 44 0.00094 38.1 3.1 25 269-295 532-556 (689)
107 PRK00076 recR recombination pr 28.0 37 0.00081 32.7 1.9 13 270-282 16-28 (196)
108 TIGR00615 recR recombination p 27.5 38 0.00083 32.6 1.9 17 268-284 14-30 (195)
109 COG0353 RecR Recombinational D 27.0 37 0.0008 32.7 1.6 32 267-298 14-48 (198)
110 PF06415 iPGM_N: BPG-independe 26.8 64 0.0014 31.7 3.3 40 15-54 38-80 (223)
111 PRK13766 Hef nuclease; Provisi 26.4 53 0.0011 37.3 3.1 27 267-295 717-743 (773)
112 TIGR00305 probable toxin-antit 25.1 39 0.00085 28.7 1.3 23 190-215 91-113 (114)
113 PRK13844 recombination protein 24.6 47 0.001 32.1 1.9 17 268-284 18-34 (200)
114 TIGR00426 competence protein C 22.7 85 0.0018 24.3 2.7 15 270-284 22-36 (69)
115 TIGR03252 uncharacterized HhH- 22.4 45 0.00097 31.7 1.2 20 267-286 117-136 (177)
116 PF12482 DUF3701: Phage integr 22.3 78 0.0017 27.1 2.6 34 251-284 36-69 (96)
117 PRK07956 ligA NAD-dependent DN 21.3 69 0.0015 36.3 2.7 24 269-294 515-538 (665)
118 PTZ00134 40S ribosomal protein 20.8 1.1E+02 0.0024 28.4 3.4 34 253-286 9-51 (154)
119 PRK04053 rps13p 30S ribosomal 20.7 1.3E+02 0.0029 27.7 3.9 35 252-286 3-46 (149)
120 PF11731 Cdd1: Pathogenicity l 20.0 76 0.0016 27.1 2.0 17 268-284 15-31 (93)
No 1
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=8.7e-50 Score=397.75 Aligned_cols=247 Identities=24% Similarity=0.245 Sum_probs=211.7
Q ss_pred hhhhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccceeee
Q psy11828 15 KLLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMD 94 (443)
Q Consensus 15 ~~~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~~~ 94 (443)
.|..++|+.++++|+..|+++||+|||||||.+|+.|.++.++|+++|++ +.+++.++.++|+.+. +..++++
T Consensus 4 ~G~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~-a~~~~~~~~~~g~~~~------a~k~~~~ 76 (292)
T PRK03980 4 KGRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREE-AEEKYEEAKEEGDLEE------ARKYAQR 76 (292)
T ss_pred CCcCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHH-hHHHHHHHHHcCCHHH------HHHHHhc
Confidence 34567899999999999999999999999999999999999999999999 7778888888998766 7788888
Q ss_pred ccCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccchhc
Q psy11828 95 REKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLT 174 (443)
Q Consensus 95 ~~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f~~ 174 (443)
+.++++++...+.+ +|.++| |||
T Consensus 77 ~~~vt~~~~~~~k~--------lL~~~G-------------------------------------------Ip~------ 99 (292)
T PRK03980 77 SSRLTDEIVEDSKK--------LLDLMG-------------------------------------------IPY------ 99 (292)
T ss_pred cccCCHHHHHHHHH--------HHHHCC-------------------------------------------CCE------
Confidence 99999887654443 366666 999
Q ss_pred CCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCCC-------------eEEeccccccc
Q psy11828 175 SGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGN-------------CCFMDREKLPS 241 (443)
Q Consensus 175 ~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g~-------------~~~i~~~~l~~ 241 (443)
++||+|||| |||+|++. |.||+|+|+|+|+|+||+++|+++++..++ ...|+.+.+.+
T Consensus 100 --i~AP~EAEA----q~A~L~~~---g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~~~~~~vl~ 170 (292)
T PRK03980 100 --VQAPSEGEA----QAAYMAKK---GDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPELIELEEVLK 170 (292)
T ss_pred --EecCchHHH----HHHHHHHC---CCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccceeeeHHHHHH
Confidence 999998888 99999877 999999999999999999999999986542 23577777765
Q ss_pred cccCCCCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhccccccccccCCCCCh-hHHHh
Q psy11828 242 ALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAKVFPLTAILDMKVPA-KWYRR 320 (443)
Q Consensus 242 ~~~l~~~~lt~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~~~~~~~~~~~~~P~-~~~r~ 320 (443)
. +|++++||+|+|+|+||||+|||||||||||++||++|+ +||++++++. ..+|+ ..-|+
T Consensus 171 ~-----lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~--sle~i~~~~~------------~~~~~~~~~r~ 231 (292)
T PRK03980 171 E-----LGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHG--DLEKVLEERG------------FEIENYDEIRE 231 (292)
T ss_pred H-----hCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCC--CHHHHHHhcc------------CCCCCHHHHHH
Confidence 4 689999999999999999999999999999999999998 8999998654 23443 44499
Q ss_pred hhcCCcccccccccccCCCCCCCchhhcccCCcHHHHHHHhhhhhhH
Q psy11828 321 IIGSIEVICGFSMATIPFNMKVPAKWYRRIIGSIEVICGFSMATIPF 367 (443)
Q Consensus 321 l~~~p~v~~~~~~~~vp~~~~~~~~w~~~~v~~l~~l~~fl~~~i~~ 367 (443)
+|++|+|++ ...++| ..|+++.|+.||....+|
T Consensus 232 ~f~~p~v~~-----------~~~~~~---~~pd~~~l~~fl~~e~~f 264 (292)
T PRK03980 232 FFLNPPVTD-----------DYELKW---KEPDKEGIIEFLVEEHDF 264 (292)
T ss_pred HhcCCCCCC-----------CCCccC---CCCCHHHHHHHHhccCCC
Confidence 999999983 335677 899999999999877654
No 2
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.5e-49 Score=410.30 Aligned_cols=252 Identities=23% Similarity=0.272 Sum_probs=218.5
Q ss_pred hhhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccceeeec
Q psy11828 16 LLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMDR 95 (443)
Q Consensus 16 ~~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~~~~ 95 (443)
|..++||.++++|+.+|+++||+|||||||.+|+.|.+|..+|+++|++ +.+.+.++.+.|+.+. +.++++++
T Consensus 60 G~~t~~l~g~~~r~~~Ll~~gikPv~VFDG~~p~~K~~~~~~Rk~~R~~-a~~~l~~a~~~g~~~~------a~k~~~r~ 132 (393)
T PTZ00217 60 GEVTSHISGLFNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERREE-AEEELEKAIEEGDDEE------IKKQSKRT 132 (393)
T ss_pred CCccHHHHHHHHHHHHHHHCCCCEEEEEcCCCchhhHHHHHHHHHHHHH-hHHHHHHHHhcCCHHH------HHHHHhhc
Confidence 4456999999999999999999999999999999999999999999999 7777788888998766 77888889
Q ss_pred cCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccchhcC
Q psy11828 96 EKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTS 175 (443)
Q Consensus 96 ~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f~~~ 175 (443)
.++|+++...+.+ +|.++| |||
T Consensus 133 ~~vt~~~~~~~~~--------lL~~~G-------------------------------------------ip~------- 154 (393)
T PTZ00217 133 VRVTKEQNEDAKK--------LLRLMG-------------------------------------------IPV------- 154 (393)
T ss_pred ccCCHHHHHHHHH--------HHHHcC-------------------------------------------Cce-------
Confidence 9999887654443 366777 999
Q ss_pred CccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCC----CeEEeccccccccccCCCCCCC
Q psy11828 176 GAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSG----NCCFMDREKLPSALKMPLAKFT 251 (443)
Q Consensus 176 ~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g----~~~~i~~~~l~~~~~l~~~~lt 251 (443)
++||||||| |||+|++. |.||+|+|+|+|+|+||+++++++++.++ ...+|+.+.+.+. +|++
T Consensus 155 -i~AP~EAda----q~A~L~~~---g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~-----~gl~ 221 (393)
T PTZ00217 155 -IEAPCEAEA----QCAELVKK---GKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEE-----LGLS 221 (393)
T ss_pred -EECCcCHHH----HHHHHHHC---CCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHH-----hCCC
Confidence 999999999 99999877 99999999999999999999999998522 2457888888764 6899
Q ss_pred HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhccccccccccCCCCChhHH----HhhhcCCcc
Q psy11828 252 DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAKVFPLTAILDMKVPAKWY----RRIIGSIEV 327 (443)
Q Consensus 252 ~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~~~~~~~~~~~~~P~~~~----r~l~~~p~v 327 (443)
++||+|+|+|+||||+|||||||||+|++||++|+ ++|+++++++.. ++.+|++|+ +++|+||+|
T Consensus 222 ~~q~id~~iL~G~Dy~pgi~GIG~ktA~~Li~~~g--sle~il~~~~~~---------k~~~p~~~~~~~~~~~f~~p~V 290 (393)
T PTZ00217 222 MDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKYK--SIEEILEHLDKT---------KYPVPENFDYKEARELFLNPEV 290 (393)
T ss_pred HHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC--CHHHHHHHHHhc---------CCCCCCCCChHHHHHHhcCCCc
Confidence 99999999999999999999999999999999998 899999999833 567899987 999999999
Q ss_pred cccccccccCCCCCCCchhhcccCCcHHHHHHHhhhhhhHH
Q psy11828 328 ICGFSMATIPFNMKVPAKWYRRIIGSIEVICGFSMATIPFI 368 (443)
Q Consensus 328 ~~~~~~~~vp~~~~~~~~w~~~~v~~l~~l~~fl~~~i~~~ 368 (443)
.+.. ...++| ..|+.+.|+.||....+|.
T Consensus 291 ~~~~---------~~~l~w---~~pD~~~l~~fl~~e~~f~ 319 (393)
T PTZ00217 291 TPAE---------EIDLKW---NEPDEEGLKKFLVKEKNFN 319 (393)
T ss_pred CCCC---------CCCCCC---CCCCHHHHHHHHHhccCCC
Confidence 8421 224666 8899999999998776654
No 3
>KOG2518|consensus
Probab=100.00 E-value=4.6e-48 Score=399.71 Aligned_cols=244 Identities=32% Similarity=0.492 Sum_probs=216.1
Q ss_pred hhchhhhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccce
Q psy11828 12 NLKKLLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCC 91 (443)
Q Consensus 12 ~~~~~~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~ 91 (443)
-.+|.+|++||+||++|+++|+.+||+||+||||.++|.|..|+.+||++|++ ++..|+.++..|+... |..+
T Consensus 46 l~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~~LP~K~~te~~Rr~~R~~-n~~~a~~ll~~G~~~~------A~~~ 118 (556)
T KOG2518|consen 46 LAKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGDPLPSKKETERKRRERRKK-NLDAAEQLLAEGKESN------AREC 118 (556)
T ss_pred HhcCCChHHHHHHHHHHHHHHHhcCCeEEEEecCCCcccccccchHHHHHHHH-hHHHHHHHHHcCCHHH------HHHH
Confidence 45688999999999999999999999999999999999999999999999999 9999999999999877 8999
Q ss_pred eeeccCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccc
Q psy11828 92 FMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKE 171 (443)
Q Consensus 92 ~~~~~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~ 171 (443)
++++++||++|...+++. |...| |+|
T Consensus 119 fqr~VdIT~~ma~~lI~~--------~r~~n-------------------------------------------Ve~--- 144 (556)
T KOG2518|consen 119 FQRCVDITPEMAHKLIQY--------LRSQN-------------------------------------------VEY--- 144 (556)
T ss_pred HHHhccCcHHHHHHHHHH--------HHHcC-------------------------------------------Cce---
Confidence 999999999999877765 76666 999
Q ss_pred hhcCCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCCCeEEeccccccccccCCCCCCC
Q psy11828 172 FLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFT 251 (443)
Q Consensus 172 f~~~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g~~~~i~~~~l~~~~~l~~~~lt 251 (443)
|+||||||| |+|||.+. |.||||||||||+++|||++||++|+..|.+.+++...+...+++. .+++
T Consensus 145 -----IVAPyEADA----QlayL~~~---~~i~~IITEDSDLl~fGc~~vifK~d~~G~~le~~~~~l~~~~~l~-~~~~ 211 (556)
T KOG2518|consen 145 -----IVAPYEADA----QLAYLERE---GIVDAIITEDSDLLVFGCKKVIFKMDSFGNGLEINRSKLPECKPLG-DKFT 211 (556)
T ss_pred -----EecCccccc----hhHHHHhc---CcceEEEeccccccccCchhheeeccCCCCcccccHhhhhhccccc-cccC
Confidence 999999999 99999877 9999999999999999999999999999999999999988887654 5799
Q ss_pred HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhccccccccccCCCCChhHH------HhhhcCC
Q psy11828 252 DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAKVFPLTAILDMKVPAKWY------RRIIGSI 325 (443)
Q Consensus 252 ~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~~~~~~~~~~~~~P~~~~------r~l~~~p 325 (443)
.++|..+|||+||||++||||||.+||++++++|. +.+.++..... ..++.+|++|. ...|+|.
T Consensus 212 ~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~--~~d~vi~~~~~--------~~~l~Vpd~y~~~F~~A~~tF~hQ 281 (556)
T KOG2518|consen 212 EEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYN--TPDRVIISHLL--------KKKLTVPDDYIENFERANLTFLHQ 281 (556)
T ss_pred HHHHHHHHHhcCCcccccCccccHHHHHHHHHhcC--cHHHHHHHHHh--------ccCCcCCHHHHHHHHHHHHhhhhh
Confidence 99999999999999999999999999999999997 67777643321 13678999887 4567887
Q ss_pred cccccccccccCCC
Q psy11828 326 EVICGFSMATIPFN 339 (443)
Q Consensus 326 ~v~~~~~~~~vp~~ 339 (443)
.|-+..+-..++.+
T Consensus 282 rVydP~~k~~~~L~ 295 (556)
T KOG2518|consen 282 RVYDPIEKKLIHLN 295 (556)
T ss_pred heeCchHhhhhcCC
Confidence 77665555555443
No 4
>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=100.00 E-value=7.8e-47 Score=379.85 Aligned_cols=252 Identities=27% Similarity=0.303 Sum_probs=210.3
Q ss_pred hhhhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccceeee
Q psy11828 15 KLLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMD 94 (443)
Q Consensus 15 ~~~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~~~ 94 (443)
++.+++|+.++++++.+|+++||+|||||||.+|+.|.+|..+|+++|.+ +++++..+.++|+... +..+.++
T Consensus 49 ~g~~~~~l~~~~~rl~~L~~~~i~pvfVFDG~~~~~K~~~~~~R~~~r~~-~~~~~~~~~~~~~~~~------~~~~~~~ 121 (316)
T cd00128 49 GGETTSHLQGFFYRTCRLLELGIKPVFVFDGKPPPLKAETLAKRRERREE-AEEEAKEALEKGLEEE------AKKLERR 121 (316)
T ss_pred CCCCcHHHHHHHHHHHHHHHCCCEEEEEEcCCCchhhHHHHHHHHHHHHH-HHHHHHHHHHhCCHHH------HHHHHhc
Confidence 46778999999999999999999999999999999999999999999999 7778888888887654 4444455
Q ss_pred ccCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccchhc
Q psy11828 95 REKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLT 174 (443)
Q Consensus 95 ~~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f~~ 174 (443)
...+++.+.. .++.++...| |||
T Consensus 122 ~~~~~~~~~~--------~~~~lL~~~g-------------------------------------------i~~------ 144 (316)
T cd00128 122 AVRVTPQMIE--------EAKELLRLMG-------------------------------------------IPY------ 144 (316)
T ss_pred cCcCCHHHHH--------HHHHHHHHcC-------------------------------------------CCE------
Confidence 5566655432 2333355555 999
Q ss_pred CCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCC--CeEEeccccccccccCCCCCCCH
Q psy11828 175 SGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSG--NCCFMDREKLPSALKMPLAKFTD 252 (443)
Q Consensus 175 ~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g--~~~~i~~~~l~~~~~l~~~~lt~ 252 (443)
++||||||| |||+|++. |.||+|+|+|||+|+||+++|+++++..+ ...+|+.+.+.+. +|+++
T Consensus 145 --i~ap~EAda----q~a~l~~~---g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~-----lgl~~ 210 (316)
T cd00128 145 --IVAPYEAEA----QCAYLAKK---GLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILKE-----LGLTR 210 (316)
T ss_pred --EECCcCHHH----HHHHHHhC---CCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHHH-----cCCCH
Confidence 999999999 99999887 99999999999999999999999998765 6778999988765 68999
Q ss_pred HHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhccccccccccCCCCChhHH----HhhhcCCccc
Q psy11828 253 AKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAKVFPLTAILDMKVPAKWY----RRIIGSIEVI 328 (443)
Q Consensus 253 eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~~~~~~~~~~~~~P~~~~----r~l~~~p~v~ 328 (443)
+||+|+|+|+||||+|||||||||||++||++|+ +++++++++... ...+|++|+ +++|.+|+|.
T Consensus 211 ~q~id~~~L~G~Dy~~gv~giG~k~A~~li~~~~--~~~~~~~~l~~~---------~~~~~~~~~~~~~~~~f~~p~~~ 279 (316)
T cd00128 211 EKLIDLAILLGCDYTEGIPGIGPVTALKLIKKYG--DIEKDIERLKKK---------LYRSPEDFPLKEAREFFLNPEVT 279 (316)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcC--ChHHHHHHHHHh---------CccCCCcCChHHHHHHHcCCCCC
Confidence 9999999999999999999999999999999998 789999988743 234455554 9999999997
Q ss_pred ccccccccCCCCCCCchhhcccCCcHHHHHHHhhhhhhHH
Q psy11828 329 CGFSMATIPFNMKVPAKWYRRIIGSIEVICGFSMATIPFI 368 (443)
Q Consensus 329 ~~~~~~~vp~~~~~~~~w~~~~v~~l~~l~~fl~~~i~~~ 368 (443)
.. ...+.| .-|+.+.++.|+....+|-
T Consensus 280 ~~----------~~~~~~---~~p~~~~l~~~~~~~~~~~ 306 (316)
T cd00128 280 DD----------FIDLRW---RDPDEEGIIEFLCKEHGFN 306 (316)
T ss_pred CC----------CCceee---cCCCHHHHHHHccCCCCCC
Confidence 32 234555 7788899999998877764
No 5
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=1.6e-45 Score=374.22 Aligned_cols=247 Identities=24% Similarity=0.258 Sum_probs=205.9
Q ss_pred hhhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccceeeec
Q psy11828 16 LLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMDR 95 (443)
Q Consensus 16 ~~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~~~~ 95 (443)
|..++|+.++++++..|+++||+|||||||.+|+.|.+|.++|+++|++ +.+++.++.++|+.+. +.++..++
T Consensus 52 G~~t~~l~g~~~~~~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~~~r~~-a~~~~~~~~~~g~~~~------a~~~~~r~ 124 (338)
T TIGR03674 52 GRITSHLSGLFYRTINLLENGIKPVYVFDGKPPELKAETLEERREIREE-AEEKWEEALEKGDLEE------ARKYAQRS 124 (338)
T ss_pred CCCcHHHHHHHHHHHHHHHCCCeEEEEECCCChhhhHhhHHHHHHHHHH-HHHHHHHHHHcCCHHH------HHHHHhhc
Confidence 4456899999999999999999999999999999999999999999999 7778888888888765 67777788
Q ss_pred cCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccchhcC
Q psy11828 96 EKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTS 175 (443)
Q Consensus 96 ~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f~~~ 175 (443)
.++++++...+ +.++.+.| |||
T Consensus 125 ~~~~~~~~~~~--------k~lL~~~G-------------------------------------------ip~------- 146 (338)
T TIGR03674 125 SRLTSEIVESS--------KKLLDLMG-------------------------------------------IPY------- 146 (338)
T ss_pred CCCCHHHHHHH--------HHHHHHcC-------------------------------------------CeE-------
Confidence 88888765433 33466666 999
Q ss_pred CccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCCC-------------eEEecccccccc
Q psy11828 176 GAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGN-------------CCFMDREKLPSA 242 (443)
Q Consensus 176 ~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g~-------------~~~i~~~~l~~~ 242 (443)
++||+|||| |||+|++. |.||+|+|+|+|+|+||+++|+++++..++ ...++.+.+.+.
T Consensus 147 -i~AP~EAea----q~a~L~~~---g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~ 218 (338)
T TIGR03674 147 -VQAPSEGEA----QAAYMAKK---GDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSE 218 (338)
T ss_pred -EECCccHHH----HHHHHHHC---CCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHH
Confidence 999999998 99999877 999999999999999999999999886442 234677666654
Q ss_pred ccCCCCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhccccccccccCCCCChhHHHhhh
Q psy11828 243 LKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAKVFPLTAILDMKVPAKWYRRII 322 (443)
Q Consensus 243 ~~l~~~~lt~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~~~~~~~~~~~~~P~~~~r~l~ 322 (443)
+|++++||+|+|+|+||||++||||||||||+++|++|+ ++|+++++++.. +. +...-+++|
T Consensus 219 -----lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~g--sie~il~~~~~~----------~~-~~~~~~~~f 280 (338)
T TIGR03674 219 -----LGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHG--DLEKVLKARGED----------IE-NYDEIREFF 280 (338)
T ss_pred -----hCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcC--CHHHHHHhhcCC----------CC-CHHHHHHHh
Confidence 689999999999999999999999999999999999998 899999987621 11 112339999
Q ss_pred cCCcccccccccccCCCCCCCchhhcccCCcHHHHHHHhhhhhhH
Q psy11828 323 GSIEVICGFSMATIPFNMKVPAKWYRRIIGSIEVICGFSMATIPF 367 (443)
Q Consensus 323 ~~p~v~~~~~~~~vp~~~~~~~~w~~~~v~~l~~l~~fl~~~i~~ 367 (443)
.+|+|.+. ..+.| ..|+.+.|+.||....+|
T Consensus 281 ~~~~v~~~-----------~~~~~---~~pd~e~l~~fl~~e~~~ 311 (338)
T TIGR03674 281 LNPPVTDD-----------YELKW---RKPDKEGIIEFLCDEHDF 311 (338)
T ss_pred CCCCCCCC-----------CCccC---CCCCHHHHHHHHhhcCCC
Confidence 99999731 24566 788999999988765543
No 6
>KOG2519|consensus
Probab=100.00 E-value=5.2e-43 Score=358.71 Aligned_cols=254 Identities=23% Similarity=0.263 Sum_probs=214.0
Q ss_pred hhhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccceeeec
Q psy11828 16 LLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMDR 95 (443)
Q Consensus 16 ~~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~~~~ 95 (443)
+.+++||.++++|+..|+++||+|||||||.||+.|..+.++|..+|.+ +.+......+.|.... .+.++.+.
T Consensus 54 ~~~~~HL~g~f~Rt~~l~~~gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~-a~~~~~~~~e~~~~~~------~~k~~~r~ 126 (449)
T KOG2519|consen 54 GEPTSHLMGMFYRTIRLIENGIKPVYVFDGKPPDLKSQELAKRSERRSE-ADKELKPAKEAGAKEN------MEKFFSRL 126 (449)
T ss_pred CCchHHHHHHHHHHHHHHHcCCcEEEEECCCCCCcchHHHHHHHHHhhh-hhhhhhhHHHhhhHHH------HHHHHHHH
Confidence 3468999999999999999999999999999999999999999999987 5555555555665544 56777888
Q ss_pred cCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccchhcC
Q psy11828 96 EKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTS 175 (443)
Q Consensus 96 ~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f~~~ 175 (443)
+++|.+++.++.. ++-++| |||
T Consensus 127 vkvtk~~~dEak~--------LL~lmG-------------------------------------------Ip~------- 148 (449)
T KOG2519|consen 127 VKVTKQHNDEAKR--------LLSLMG-------------------------------------------IPV------- 148 (449)
T ss_pred hhhcchhhHHHHH--------HHHHcC-------------------------------------------Cee-------
Confidence 8998888755544 477777 999
Q ss_pred CccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCC---C-CCeEEeccccccccccCCCCCCC
Q psy11828 176 GAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDL---S-GNCCFMDREKLPSALKMPLAKFT 251 (443)
Q Consensus 176 ~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~---~-g~~~~i~~~~l~~~~~l~~~~lt 251 (443)
+.||+||+| |||+|.+. |.|++++|+|||+|.||++.+++++.. + +-..+|+.+.+.+. ++++
T Consensus 149 -i~ap~EAEA----qCA~Lnk~---g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~-----l~l~ 215 (449)
T KOG2519|consen 149 -LDAPGEAEA----QCAALNKA---GKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEG-----LGLS 215 (449)
T ss_pred -ecCCchHHH----HHHHHhhc---CceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHH-----hccc
Confidence 999999888 99999655 999999999999999999999999874 2 23467888888765 6899
Q ss_pred HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHH-hhhhccccccccccCCCCChhHH----HhhhcCCc
Q psy11828 252 DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKE-YVKYAKVFPLTAILDMKVPAKWY----RRIIGSIE 326 (443)
Q Consensus 252 ~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~-~~~~~~~~~~~~~~~~~~P~~~~----r~l~~~p~ 326 (443)
+++|+|+|+|+|||||++|.|||+++|+++|++|+ +++++++ +.+.+ .+.+|++|+ |.+|.+|+
T Consensus 216 ~~~fidL~lLlGCDYc~~I~Gig~~~al~lir~~~--~i~~ile~~~~~~---------~~~ip~~w~~~~~r~~f~~p~ 284 (449)
T KOG2519|consen 216 RESFIDLCLLLGCDYCPTIRGIGPKKALKLIRQHG--DIENILEINSDLK---------EYPIPEDWSYKLARKLFLEPE 284 (449)
T ss_pred HHHHHHHHHHhcCcccccccccChHHHHHHHHHhc--CHHHHhhhccchh---------hcCCCCCccHHHHHHHhcCcc
Confidence 99999999999999999999999999999999999 8999998 55532 679999998 99999999
Q ss_pred ccccccccccCCCCCCCchhhcccCCcHHHHHHHhhhhhhHHh
Q psy11828 327 VICGFSMATIPFNMKVPAKWYRRIIGSIEVICGFSMATIPFIL 369 (443)
Q Consensus 327 v~~~~~~~~vp~~~~~~~~w~~~~v~~l~~l~~fl~~~i~~~L 369 (443)
|...... ...+| .-|+.+++-+||--...|.+
T Consensus 285 ~~~~~~~--------~~i~w---~~pd~~~li~fl~~~~~f~~ 316 (449)
T KOG2519|consen 285 FPNPESI--------LDLKW---KTPDTEGLIQFLVGEKQFNE 316 (449)
T ss_pred cCCccce--------eeccc---CCCChHHHHHHHHhhhccCH
Confidence 9843221 25666 78888888888887777776
No 7
>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=100.00 E-value=2e-34 Score=322.57 Aligned_cols=172 Identities=16% Similarity=0.150 Sum_probs=142.9
Q ss_pred EEeccchhcCCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCCCe-EEecccccccccc
Q psy11828 166 VKITKEFLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNC-CFMDREKLPSALK 244 (443)
Q Consensus 166 v~~~~~f~~~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g~~-~~i~~~~l~~~~~ 244 (443)
||| |+||||||| |||+|++. |+||||+|+|||+|+||+++||||++..+.. ..|+.+++.+.
T Consensus 786 IP~--------i~AP~EAEA----qcA~L~~~---G~vd~V~TeDsD~llFGa~~v~rn~~~~~~~ve~~~~~~i~~~-- 848 (1034)
T TIGR00600 786 IPY--------IVAPMEAEA----QCAILDLL---DQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQ-- 848 (1034)
T ss_pred CCe--------eeCCccHHH----HHHHHHhC---CCeEEEEccccceeccCCceeeecccCCCCceEEeeHHHHHHH--
Confidence 999 999999988 99999887 9999999999999999999999999875554 45778887764
Q ss_pred CCCCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHH---Hhhhhc---cc-------ccc-ccccC
Q psy11828 245 MPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRK---EYVKYA---KV-------FPL-TAILD 310 (443)
Q Consensus 245 l~~~~lt~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~---~~~~~~---~~-------~~~-~~~~~ 310 (443)
+||++++||++|+|+||||++|||||||++|++||++|++.+|++++ +|+... .. +.. .+..+
T Consensus 849 ---lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~~~~~~~~~~~~~~~~~~~~~~ 925 (1034)
T TIGR00600 849 ---LGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRL 925 (1034)
T ss_pred ---hCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhhccccccccchhhhhhcccc
Confidence 68999999999999999999999999999999999999965455554 666431 00 000 12234
Q ss_pred CCCChhHH----HhhhcCCcccccccccccCCCCCCCchhhcccCCcHHHHHHHhhhhhhHHhh
Q psy11828 311 MKVPAKWY----RRIIGSIEVICGFSMATIPFNMKVPAKWYRRIIGSIEVICGFSMATIPFILA 370 (443)
Q Consensus 311 ~~~P~~~~----r~l~~~p~v~~~~~~~~vp~~~~~~~~w~~~~v~~l~~l~~fl~~~i~~~L~ 370 (443)
+.+|++|| +++|++|+|+. ++.++.| +.|+++.|+.||+.+.+|-=.
T Consensus 926 ~~lp~~FP~~~V~~~yl~P~V~~----------~~~~f~W---~~PD~e~L~~Fl~~~~gws~e 976 (1034)
T TIGR00600 926 LQLTPGFPNPAVADAYLRPVVDD----------SKGSFLW---GKPDLDKIREFCQRYFGWNRE 976 (1034)
T ss_pred cccCCCCCcHHHHHHhcCCCCCC----------CcCCCCC---CCCCHHHHHHHHHHccCCCHH
Confidence 67999999 99999999983 3456777 999999999999999998653
No 8
>KOG2520|consensus
Probab=99.95 E-value=2.4e-28 Score=266.54 Aligned_cols=219 Identities=16% Similarity=0.185 Sum_probs=170.1
Q ss_pred HhhccCccHHHHHHHhhhhccccceEEeccchhcCCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCE
Q psy11828 141 VFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKK 220 (443)
Q Consensus 141 V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f~~~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~ 220 (443)
++.-|....+.+|+.++ ||| |+||+|||| |||.|.+. ++||||+|+|||+++||+.+
T Consensus 463 vt~~m~~e~QElL~~fG--------IPy--------I~APmEAEA----QCa~Le~~---~LvdGiITDDSDV~LFGg~~ 519 (815)
T KOG2520|consen 463 VTSDMFKELQELLRLFG--------IPY--------IIAPMEAEA----QCAFLEQL---NLVDGIITDDSDVFLFGGTR 519 (815)
T ss_pred hHHHHHHHHHHHHHHcC--------Cce--------ecccccHHH----HHHHHHHc---CCcceeecccccceeeccch
Confidence 55566667788888887 999 999999998 99999888 99999999999999999999
Q ss_pred EEEecCCCCCe-EEeccccccccccCCCCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCC-CChhhHHHhhh
Q psy11828 221 IIYKLDLSGNC-CFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMD-PDFENRKEYVK 298 (443)
Q Consensus 221 vi~~l~~~g~~-~~i~~~~l~~~~~l~~~~lt~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~-~sle~~~~~~~ 298 (443)
||+||+.++++ ..|...++.+. +|+++..+|-+|.|+||||+.|++||||++|+++|.+|++ .++..+.+|+.
T Consensus 520 VYrn~F~knk~ve~y~~~di~ke-----l~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~ 594 (815)
T KOG2520|consen 520 VYRNFFNKNKYVEKYQLDDIEKE-----LGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQ 594 (815)
T ss_pred hhHHHhhcCccceeeehHHHHHH-----HccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHHHH
Confidence 99999987776 46888888876 6899999999999999999999999999999999999983 24666777775
Q ss_pred hcccccc-----------cccc--CCCCChhHH----HhhhcCCcccccccccccCCCCCCCchhhcccCCcHHHHHHHh
Q psy11828 299 YAKVFPL-----------TAIL--DMKVPAKWY----RRIIGSIEVICGFSMATIPFNMKVPAKWYRRIIGSIEVICGFS 361 (443)
Q Consensus 299 ~~~~~~~-----------~~~~--~~~~P~~~~----r~l~~~p~v~~~~~~~~vp~~~~~~~~w~~~~v~~l~~l~~fl 361 (443)
....-+. ++.. +..+|++|| -++|++|+|+ +.+..|.| |.|+|+.||.|+
T Consensus 595 ~~~~~~~~~~s~~~~~lrkkl~n~~~~l~~~fP~~~v~~AYLrP~VD----------~sk~~f~W---G~pdl~~lRef~ 661 (815)
T KOG2520|consen 595 QTGPADKEVGSTQQKMLRKKLKNPKIILPSDFPNPNVIEAYLRPEVD----------DSKEKFRW---GKPDLDILREFM 661 (815)
T ss_pred HhCccccccccHHHHHHHHHhcCcccccCcCCCchhHHHHhhCCccC----------CCcccccC---CCCCHHHHHHHH
Confidence 2111100 1112 367899998 7888999998 55888888 999999999999
Q ss_pred hhhhhHHhhhhcccccCCchhhH-Hhhhchhhhhhhhhhc
Q psy11828 362 MATIPFILAGKAILDMKVPAKWY-RRIIGSIEVICGFSMA 400 (443)
Q Consensus 362 ~~~i~~~L~~~~~~~~~~ps~~~-rr~~~~~e~~~~l~~~ 400 (443)
+...+|-=..-.-.-+-++-..- +.+.+..+....+..+
T Consensus 662 ~~~fgW~~~kT~~~l~p~~~~~~~~~~~~~~~~~~~~f~~ 701 (815)
T KOG2520|consen 662 KRLFGWPDEKTDEELIPVIKRLEKKKTQLKQDRISQFFED 701 (815)
T ss_pred HHHcCCCccccchhhhhhHHHHHHHhhhhccccHHHHHHh
Confidence 99999964322111122232222 5555666555555544
No 9
>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=99.89 E-value=5.9e-23 Score=199.91 Aligned_cols=183 Identities=16% Similarity=0.163 Sum_probs=135.2
Q ss_pred hhhhhhHHHHHHHHHHHHHhCC--CEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCccccccccccccee
Q psy11828 15 KLLQHLYVNYCMKYINMLLAHK--IKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCF 92 (443)
Q Consensus 15 ~~~~~~~l~~~~~~i~~L~~~g--I~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~ 92 (443)
.+..+..+.++++.+..+++.. .++++||||..+..+.+...+.+..|.. .-
T Consensus 27 ~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~-~p------------------------- 80 (240)
T cd00008 27 KGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKK-MP------------------------- 80 (240)
T ss_pred CCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCC-CC-------------------------
Confidence 3455688999999999999877 7999999998666555555443333222 00
Q ss_pred eeccCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccch
Q psy11828 93 MDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEF 172 (443)
Q Consensus 93 ~~~~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f 172 (443)
.. +. -..+.++.++...| ||+
T Consensus 81 -------~~----l~-~q~~~~~~~l~~~g-------------------------------------------i~~---- 101 (240)
T cd00008 81 -------EE----LR-EQIPLIKELLEALG-------------------------------------------IPV---- 101 (240)
T ss_pred -------HH----HH-HHHHHHHHHHHHCC-------------------------------------------CCE----
Confidence 00 00 00112222333334 888
Q ss_pred hcCCccCC-CccccchhhhHHHhHhhh-hCCCeEEEecCCCceeeeccCEEEEecCCCCCeEEeccccccccccCCCCCC
Q psy11828 173 LTSGAPQP-FGARNEGRSLLSAVTERN-IAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKF 250 (443)
Q Consensus 173 ~~~~i~AP-~EAdaEgEAQ~A~L~~~~-~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g~~~~i~~~~l~~~~~l~~~~l 250 (443)
+.+| +|||+ +||+|++.. ..|....|+|+|+|++++.+++|..... .+..+++.+.+.+. .|+
T Consensus 102 ----i~~~~~EADD----~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~~--~~~~~i~~~~v~~~-----~g~ 166 (240)
T cd00008 102 ----LEIEGYEADD----VIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSP--MKKKLVTEENVIEK-----YGV 166 (240)
T ss_pred ----EecCCcCHHH----HHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEeC--CCceEEeHHHHHHH-----hCc
Confidence 8887 79999 999998764 3488889999999999998776533211 23456888877655 589
Q ss_pred CHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhh
Q psy11828 251 TDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKY 299 (443)
Q Consensus 251 t~eqfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~ 299 (443)
+++||+|+++|+| |||+|||||||||+|.+||++|+ ++|+++++++.
T Consensus 167 ~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~g--sle~i~~~~~~ 215 (240)
T cd00008 167 TPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYG--SLEGILENLDK 215 (240)
T ss_pred CHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhC--CHHHHHHhHHH
Confidence 9999999999999 99999999999999999999998 89999999973
No 10
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.89 E-value=5.4e-23 Score=202.35 Aligned_cols=115 Identities=18% Similarity=0.261 Sum_probs=98.3
Q ss_pred EEeccchhcCCccCC-CccccchhhhHHHhHhhh-hCCCeEEEecCCCceeeeccCEEEE-ecCC-CCCeEEeccccccc
Q psy11828 166 VKITKEFLTSGAPQP-FGARNEGRSLLSAVTERN-IAGYADYVITEDSDLLVFGAKKIIY-KLDL-SGNCCFMDREKLPS 241 (443)
Q Consensus 166 v~~~~~f~~~~i~AP-~EAdaEgEAQ~A~L~~~~-~~g~vd~ViTeDsD~L~fG~~~vi~-~l~~-~g~~~~i~~~~l~~ 241 (443)
||+ +.+| ||||+ +||+|++.. ..|....|+|+|+|+++++++.|.. .... .+....++.+.+.+
T Consensus 98 i~~--------i~~~g~EADD----~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~~v~~ 165 (259)
T smart00475 98 IPV--------LEVEGYEADD----VIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIE 165 (259)
T ss_pred CCE--------EeeCCcCHHH----HHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEEcHHHHHH
Confidence 888 8777 69999 999999864 3478899999999999999887643 3222 22346799998876
Q ss_pred cccCCCCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhh
Q psy11828 242 ALKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKY 299 (443)
Q Consensus 242 ~~~l~~~~lt~eqfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~ 299 (443)
. +|++++||+|+|+|+| |||+|||||||||||.+||++|| ++|+++++++.
T Consensus 166 ~-----~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~yg--sle~i~~~~~~ 218 (259)
T smart00475 166 K-----YGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFG--SLENILENLDK 218 (259)
T ss_pred H-----hCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhC--CHHHHHHHHHH
Confidence 5 5899999999999999 89999999999999999999999 89999999973
No 11
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.89 E-value=1.4e-23 Score=211.09 Aligned_cols=181 Identities=20% Similarity=0.219 Sum_probs=130.2
Q ss_pred hhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCcccccccccccceeeeccC
Q psy11828 18 QHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCFMDREK 97 (443)
Q Consensus 18 ~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~~~~~~ 97 (443)
+.+++..++.++....+. ++|++||||.++..|.++..+|+..|++ . ...++..+ ...
T Consensus 43 ~~~~~~~~l~~~~~~~~~-~~~~~vFD~~~~tfR~~~~~~yK~~R~~-~--~p~~l~~q------------------~~~ 100 (310)
T COG0258 43 AVSGFLGMLYRLIRLLEP-THPVVVFDGKPPTFRHELLEEYKANREK-E--MPDELAPQ------------------IPI 100 (310)
T ss_pred HHHHHHHHHHHHHHhcCC-CcEEEEEcCCCCcchHHHHHHHHhCCCc-c--CHHHHHHH------------------HHH
Confidence 457777777777776666 9999999999999999999999988776 1 11111111 111
Q ss_pred CChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccchhcCCc
Q psy11828 98 LPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSGA 177 (443)
Q Consensus 98 v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f~~~~i 177 (443)
++.. +...| +++ +
T Consensus 101 i~~~----------------~~~~~-------------------------------------------~~~--------l 113 (310)
T COG0258 101 LTEL----------------LVALG-------------------------------------------IPL--------L 113 (310)
T ss_pred HHHH----------------HHHhC-------------------------------------------cHh--------h
Confidence 1111 11111 222 1
Q ss_pred c-CCCcccc--chhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCCCeE-EeccccccccccCCCCCCCHH
Q psy11828 178 P-QPFGARN--EGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCC-FMDREKLPSALKMPLAKFTDA 253 (443)
Q Consensus 178 ~-AP~EAda--EgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g~~~-~i~~~~l~~~~~l~~~~lt~e 253 (443)
. ..+|||| |++||||+ +. |.+++|+|+|+|+|+|+++++.......+... .++...+.+.+ .|++++
T Consensus 114 ~~~G~eadd~i~t~A~~a~--~~---g~~~~I~S~DkD~lql~~~~~~~~~~~~~~~~~~~~~~~~~e~~----~g~~p~ 184 (310)
T COG0258 114 ELMGIEADDPIETLAQKAY--KK---GDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEEKF----KGLTPE 184 (310)
T ss_pred hcCCCCcchhHHHHHHHHH--hc---CCeEEEEeCCcchhhhcCCCcEEEeccCCCCcccCCHHHHHHHH----cCCCHH
Confidence 1 1234444 33447776 44 99999999999999999999554443333333 46777777663 389999
Q ss_pred HHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhh
Q psy11828 254 KFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVK 298 (443)
Q Consensus 254 qfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~ 298 (443)
||+|+++|+| |||+|||||||||||++||++|| +++.++++++
T Consensus 185 qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~g--s~e~i~~~~~ 229 (310)
T COG0258 185 QLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYG--SLEGLYENLD 229 (310)
T ss_pred HHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhC--CHHHHHHhhh
Confidence 9999999999 99999999999999999999999 8999999986
No 12
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.87 E-value=9.5e-22 Score=195.65 Aligned_cols=185 Identities=18% Similarity=0.224 Sum_probs=136.1
Q ss_pred hhhhhhHHHHHHHHHHHHHhCC--CEEEEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCccccccccccccee
Q psy11828 15 KLLQHLYVNYCMKYINMLLAHK--IKVIMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSSIIYKLDLSGNCCF 92 (443)
Q Consensus 15 ~~~~~~~l~~~~~~i~~L~~~g--I~PvfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~~~fKld~~~~~~~ 92 (443)
.|..+..+.++++.+..+++.. -.+++||||..+..+.+....++..|.+ ..+.
T Consensus 32 ~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~-~p~~----------------------- 87 (281)
T PRK14976 32 KGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKK-TPES----------------------- 87 (281)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCCC-CCHH-----------------------
Confidence 3455688899999999998764 5899999998766665555555443332 1000
Q ss_pred eeccCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhhccccceEEeccch
Q psy11828 93 MDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEF 172 (443)
Q Consensus 93 ~~~~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~~k~~~~v~~~~~f 172 (443)
+.. + ....+.++..+| ||+
T Consensus 88 -----l~~-------q--~~~i~~~l~~~g-------------------------------------------i~~---- 106 (281)
T PRK14976 88 -----LIS-------Q--IPLLKKILKLAG-------------------------------------------IKW---- 106 (281)
T ss_pred -----HHH-------H--HHHHHHHHHHCC-------------------------------------------CCE----
Confidence 000 0 011122233334 888
Q ss_pred hcCCccCC-CccccchhhhHHHhHhhh-hCCCeEEEecCCCceeeeccCEEEEecCCCC-CeEEeccccccccccCCCCC
Q psy11828 173 LTSGAPQP-FGARNEGRSLLSAVTERN-IAGYADYVITEDSDLLVFGAKKIIYKLDLSG-NCCFMDREKLPSALKMPLAK 249 (443)
Q Consensus 173 ~~~~i~AP-~EAdaEgEAQ~A~L~~~~-~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g-~~~~i~~~~l~~~~~l~~~~ 249 (443)
+.+| ||||+ +||+|++.. ..|.-..|+|+|+|++++.+++|.......+ ....++.+.+.+. +|
T Consensus 107 ----~~~~g~EADD----viatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~v~~~-----~g 173 (281)
T PRK14976 107 ----EEQPGYEADD----LIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILNTNNFFEL-----YG 173 (281)
T ss_pred ----EecCCcCHHH----HHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEecCCCCcEEEcHHHHHHH-----hC
Confidence 8889 69999 999998875 3466668999999999999876533222222 2457888888765 68
Q ss_pred CCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhh
Q psy11828 250 FTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKY 299 (443)
Q Consensus 250 lt~eqfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~ 299 (443)
++++||+|+++|+| ||++|||||||||||.+||++|| ++++++++++.
T Consensus 174 v~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~g--sle~i~~~~~~ 223 (281)
T PRK14976 174 IEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYG--NIENIYENIDK 223 (281)
T ss_pred cCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcC--CHHHHHHhHHH
Confidence 99999999999999 99999999999999999999999 89999999873
No 13
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=99.85 E-value=3.1e-22 Score=168.30 Aligned_cols=80 Identities=40% Similarity=0.631 Sum_probs=66.8
Q ss_pred EEeccchhcCCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecC-C-CCC--------eEEec
Q psy11828 166 VKITKEFLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLD-L-SGN--------CCFMD 235 (443)
Q Consensus 166 v~~~~~f~~~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~-~-~g~--------~~~i~ 235 (443)
||| ++||||||| |||||++. |.||+|+|+|||+|+||+++||++++ . .++ ...++
T Consensus 5 v~~--------i~AP~EAeA----q~A~L~~~---g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~ 69 (94)
T PF00867_consen 5 VPY--------IVAPYEAEA----QCAYLERN---GLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVID 69 (94)
T ss_dssp -EE--------EE-SS-HHH----HHHHHHHT---TSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEE
T ss_pred CeE--------EEcCchHHH----HHHHHHHh---cceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEE
Confidence 899 999999999 99999888 99999999999999999999999997 3 232 35788
Q ss_pred cccccccccCCCCCCCHHHHHHHHHHhCCC
Q psy11828 236 REKLPSALKMPLAKFTDAKFRYMCILSGCD 265 (443)
Q Consensus 236 ~~~l~~~~~l~~~~lt~eqfidl~iL~G~D 265 (443)
.+.+.+. ++++++||+++|+|+|||
T Consensus 70 ~~~i~~~-----l~l~~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 70 LDDILKE-----LGLTREQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHH-----HTTSHHHHHHHHHHHHET
T ss_pred HHHHHHH-----cCCCHHHHHHHheecCCC
Confidence 8888775 579999999999999998
No 14
>PRK05755 DNA polymerase I; Provisional
Probab=99.81 E-value=9.2e-20 Score=206.01 Aligned_cols=114 Identities=19% Similarity=0.286 Sum_probs=97.5
Q ss_pred EEeccchhcCCccCC-CccccchhhhHHHhHhhh-hCCCeEEEecCCCceeeeccCEE--EEecCCCCCeEEeccccccc
Q psy11828 166 VKITKEFLTSGAPQP-FGARNEGRSLLSAVTERN-IAGYADYVITEDSDLLVFGAKKI--IYKLDLSGNCCFMDREKLPS 241 (443)
Q Consensus 166 v~~~~~f~~~~i~AP-~EAdaEgEAQ~A~L~~~~-~~g~vd~ViTeDsD~L~fG~~~v--i~~l~~~g~~~~i~~~~l~~ 241 (443)
|++ +.+| ||||+ +||+|++.. ..|..+.|+|+|+|++++++++| +..++ .++...++.+.+.+
T Consensus 100 i~~--------~~~~g~EADD----~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~~~~~-~~~~~~~~~~~v~~ 166 (880)
T PRK05755 100 IPL--------LELEGYEADD----VIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTMG-VSKNEELDPEEVVE 166 (880)
T ss_pred CCE--------EeeCCccHHH----HHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEeeccC-CCCCeEEcHHHHHH
Confidence 889 9899 69999 999998754 35889999999999999998765 22222 12455788888876
Q ss_pred cccCCCCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhh
Q psy11828 242 ALKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKY 299 (443)
Q Consensus 242 ~~~l~~~~lt~eqfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~ 299 (443)
. +|++++||+|+++|+| |||+|||||||||||.+||++|| ++|+++++++.
T Consensus 167 ~-----~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~g--sle~i~~~~~~ 219 (880)
T PRK05755 167 K-----YGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYG--SLEGLYENLDE 219 (880)
T ss_pred H-----HCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcC--CHHHHHHhHHH
Confidence 5 5899999999999999 89999999999999999999999 89999999973
No 15
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.80 E-value=2.2e-19 Score=202.05 Aligned_cols=115 Identities=20% Similarity=0.277 Sum_probs=97.0
Q ss_pred EEeccchhcCCccCC-CccccchhhhHHHhHhhh-hCCCeEEEecCCCceeeeccCEEEEecCCCC-CeEEecccccccc
Q psy11828 166 VKITKEFLTSGAPQP-FGARNEGRSLLSAVTERN-IAGYADYVITEDSDLLVFGAKKIIYKLDLSG-NCCFMDREKLPSA 242 (443)
Q Consensus 166 v~~~~~f~~~~i~AP-~EAdaEgEAQ~A~L~~~~-~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g-~~~~i~~~~l~~~ 242 (443)
||+ +.+| ||||+ +||+|++.. ..|....|+|.|.|++++.+++|.......+ +...++.+.+.+.
T Consensus 98 i~~--------i~~~g~EADD----iIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~~~~~~~~~~~~~~v~~~ 165 (887)
T TIGR00593 98 IPI--------LEVEGYEADD----VIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEYVVEK 165 (887)
T ss_pred CcE--------EeeCCccHHH----HHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEeccCCCCceEEcHHHHHHH
Confidence 888 8778 69999 999999875 3588889999999999999887532211212 3456888888765
Q ss_pred ccCCCCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhh
Q psy11828 243 LKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKY 299 (443)
Q Consensus 243 ~~l~~~~lt~eqfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~ 299 (443)
+|++++||+|+++|+| ||++|||||||||||.+||++|| |+|+++++++.
T Consensus 166 -----~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~yg--sle~i~~~~~~ 217 (887)
T TIGR00593 166 -----YGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFG--SLENIYENLDQ 217 (887)
T ss_pred -----hCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcC--CHHHHHHHHHH
Confidence 5899999999999999 79999999999999999999999 89999999873
No 16
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.68 E-value=4e-16 Score=153.36 Aligned_cols=108 Identities=17% Similarity=0.185 Sum_probs=89.6
Q ss_pred ccCC-CccccchhhhHHHhHhhhh-CCCeEEEecCCCceeeeccCEE-EEecCCCCCeEEeccccccccccCCCCCCCHH
Q psy11828 177 APQP-FGARNEGRSLLSAVTERNI-AGYADYVITEDSDLLVFGAKKI-IYKLDLSGNCCFMDREKLPSALKMPLAKFTDA 253 (443)
Q Consensus 177 i~AP-~EAdaEgEAQ~A~L~~~~~-~g~vd~ViTeDsD~L~fG~~~v-i~~l~~~g~~~~i~~~~l~~~~~l~~~~lt~e 253 (443)
+.+| ||||+ .||.|++... .|.-..|+|.|.|+++.-.+.| +.+.. +..+++.+.+.+. +|++++
T Consensus 101 ~~~~g~EADD----vIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~---~~~~~~~~~v~~~-----~Gv~P~ 168 (256)
T PRK09482 101 WHADGNEADD----LIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYF---QKRWLDAPFIEQE-----FGVEPQ 168 (256)
T ss_pred eccCCcCHHH----HHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEecc---ccccCCHHHHHHH-----hCCCHH
Confidence 8888 69999 9999987743 4655678999999998866654 33321 2235777777765 589999
Q ss_pred HHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhh
Q psy11828 254 KFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVK 298 (443)
Q Consensus 254 qfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~ 298 (443)
|++|++.|+| +|++|||||||||||.+|+++|| ++++++++++
T Consensus 169 q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~g--sle~i~~~~~ 213 (256)
T PRK09482 169 QLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFR--SLENIYESLD 213 (256)
T ss_pred HHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhC--CHHHHHHhHH
Confidence 9999999999 89999999999999999999999 8999999987
No 17
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.61 E-value=4.9e-16 Score=125.28 Aligned_cols=62 Identities=32% Similarity=0.501 Sum_probs=55.3
Q ss_pred EEeccchhcCCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeeccCEEEEecCCCCC----eEEeccccccc
Q psy11828 166 VKITKEFLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGN----CCFMDREKLPS 241 (443)
Q Consensus 166 v~~~~~f~~~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~~~vi~~l~~~g~----~~~i~~~~l~~ 241 (443)
||| ++||||||| |||+|++. |+||+|+|+|+|+|+||++++|++++.+++ ...++.+.+.+
T Consensus 5 i~~--------i~AP~eAeA----q~A~L~~~---g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~ 69 (73)
T smart00484 5 IPY--------IVAPYEAEA----QCAYLAKS---GLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLK 69 (73)
T ss_pred CeE--------EEcCCcHHH----HHHHHHhC---CCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHH
Confidence 899 999999888 99999777 999999999999999999999999997553 56788777776
Q ss_pred c
Q psy11828 242 A 242 (443)
Q Consensus 242 ~ 242 (443)
.
T Consensus 70 ~ 70 (73)
T smart00484 70 E 70 (73)
T ss_pred H
Confidence 5
No 18
>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=99.37 E-value=8.9e-13 Score=106.76 Aligned_cols=49 Identities=29% Similarity=0.373 Sum_probs=47.2
Q ss_pred CCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhh
Q psy11828 248 AKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVK 298 (443)
Q Consensus 248 ~~lt~eqfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~ 298 (443)
+|++++||+++|+|+| |||+|||||||+|+|.+++++|+ ++++++++++
T Consensus 3 ~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~--~~~~~~~~~~ 53 (75)
T cd00080 3 LGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYG--SLENLLENLD 53 (75)
T ss_pred CCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhC--CHHHHHHHHH
Confidence 6899999999999999 99999999999999999999998 8999999886
No 19
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=99.22 E-value=2.1e-11 Score=103.16 Aligned_cols=46 Identities=39% Similarity=0.482 Sum_probs=42.2
Q ss_pred hhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHH
Q psy11828 19 HLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEI 64 (443)
Q Consensus 19 ~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~ 64 (443)
++|+.++++++..|+++||+|||||||.+|+.|.+|..+|+++|++
T Consensus 55 ~~~~~~~~~r~~~L~~~gI~PifVFDG~~~~~K~~~~~~R~~~r~~ 100 (101)
T PF00752_consen 55 DSHLRGLFSRLCRLLEHGIKPIFVFDGKPPPLKRETIQKRRKRREE 100 (101)
T ss_dssp -HHHHHHHHHHHHHHHTTEEEEEEE--STTGGCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 6999999999999999999999999999999999999999999987
No 20
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.18 E-value=4e-11 Score=101.30 Aligned_cols=58 Identities=34% Similarity=0.381 Sum_probs=49.6
Q ss_pred hHhHhhhch--------hhhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHH
Q psy11828 7 IWWKTNLKK--------LLQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEI 64 (443)
Q Consensus 7 ~~~~~~~~~--------~~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~ 64 (443)
+|+.+.+.. ..+..|+.++++++..|+++||+|||||||.+|+.|.+|.++|+++|++
T Consensus 33 ~wl~~~~~~~~~~~~~~~~~~~~l~~~~~rl~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 33 IWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREE 98 (99)
T ss_pred HHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHCCCeEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 577665432 2233499999999999999999999999999999999999999999886
No 21
>KOG2518|consensus
Probab=99.17 E-value=1.1e-11 Score=130.12 Aligned_cols=75 Identities=40% Similarity=0.713 Sum_probs=66.2
Q ss_pred hhcCCcccccccccccceeeeccCCChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccH
Q psy11828 74 LHSGSSIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDF 149 (443)
Q Consensus 74 ~~~g~~~~fKld~~~~~~~~~~~~v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~ 149 (443)
..++...+||||..|.+...+...+..+.... .+|+.++||.||||+||||++|+||+|+.||++++.++...+.
T Consensus 176 ~fGc~~vifK~d~~G~~le~~~~~l~~~~~l~-~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~ 250 (556)
T KOG2518|consen 176 VFGCKKVIFKMDSFGNGLEINRSKLPECKPLG-DKFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDR 250 (556)
T ss_pred ccCchhheeeccCCCCcccccHhhhhhccccc-cccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHH
Confidence 35778899999999999999988888888666 7999999999999999999999999999999999998644443
No 22
>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=98.98 E-value=9.2e-10 Score=125.21 Aligned_cols=59 Identities=29% Similarity=0.406 Sum_probs=54.1
Q ss_pred hHhHhhhchh-------hhhhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHHH
Q psy11828 7 IWWKTNLKKL-------LQHLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEIR 65 (443)
Q Consensus 7 ~~~~~~~~~~-------~~~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~~ 65 (443)
||+++.+++. .+++||.+|++|+.+|+.+||+|||||||.+|++|.+|.++|+++|+++
T Consensus 33 iWL~q~l~~vr~~~g~~l~n~hl~g~f~Ri~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~~a 98 (1034)
T TIGR00600 33 IWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGA 98 (1034)
T ss_pred HHHHHHHHHHHhccCCccCCHHHHHHHHHHHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHHHH
Confidence 7999888742 2689999999999999999999999999999999999999999999883
No 23
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.92 E-value=9.5e-10 Score=77.06 Aligned_cols=33 Identities=33% Similarity=0.515 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCCcHHHHHHHHHHc
Q psy11828 252 DAKFRYMCILSGCDYWT---GIKGMGLKKAKDYVFSI 285 (443)
Q Consensus 252 ~eqfidl~iL~G~DY~~---gipGiG~ktA~~li~~~ 285 (443)
++||+++|+|+| ||++ ||||||+|+|.+++++|
T Consensus 1 p~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 479999999999 8887 99999999999999986
No 24
>PHA00439 exonuclease
Probab=98.86 E-value=9e-09 Score=102.76 Aligned_cols=88 Identities=16% Similarity=0.364 Sum_probs=65.4
Q ss_pred ccCC-CccccchhhhHHHhHhhh-hCCC-eEEEecCCCceeeeccCEEEEecCCCCCeEEeccccccccccCCCCCCCHH
Q psy11828 177 APQP-FGARNEGRSLLSAVTERN-IAGY-ADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDA 253 (443)
Q Consensus 177 i~AP-~EAdaEgEAQ~A~L~~~~-~~g~-vd~ViTeDsD~L~fG~~~vi~~l~~~g~~~~i~~~~l~~~~~l~~~~lt~e 253 (443)
+..| ||||+ .+|.|++.. ..|. -..|+|.|.|+++.-...++.. . .+....++ . -.++
T Consensus 114 i~~~G~EADD----vIgtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~~~-~-~~~~~~~~-----~--------~~p~ 174 (286)
T PHA00439 114 ILEPGLEGDD----VMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFLWC-T-TGNILTQT-----P--------ETAD 174 (286)
T ss_pred EeeCCccHHH----HHHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEEEc-c-CCceEEcC-----c--------ccHH
Confidence 5555 89999 999998764 3465 5579999999999864433321 1 11111111 1 1389
Q ss_pred HHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHH
Q psy11828 254 KFRYMCILSG--CDYWTGIKGMGLKKAKDYVFS 284 (443)
Q Consensus 254 qfidl~iL~G--~DY~~gipGiG~ktA~~li~~ 284 (443)
+++|+..|+| +|+.||||||| |||.+||.+
T Consensus 175 ~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 175 RWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred HHHhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 9999999999 99999999999 999999999
No 25
>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=98.75 E-value=4.4e-10 Score=96.15 Aligned_cols=48 Identities=21% Similarity=0.232 Sum_probs=39.3
Q ss_pred CCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhh
Q psy11828 250 FTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKY 299 (443)
Q Consensus 250 lt~eqfidl~iL~G--~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~ 299 (443)
++++|++|+..|+| +|+.|||||||+|||.+|+++|| |+|+++++++.
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~yg--sle~i~~~~~~ 50 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYG--SLENILANLDE 50 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHT--SCHCCCCC-SS
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcC--CHHHHHHhHHh
Confidence 46899999999999 99999999999999999999999 89999999973
No 26
>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=98.34 E-value=7.5e-07 Score=72.19 Aligned_cols=49 Identities=29% Similarity=0.442 Sum_probs=42.7
Q ss_pred ccchHHHHHHHHhcC--CCCCCCccccchhhHHHHHhhccCccHHHHHHHhhh
Q psy11828 108 KFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 158 (443)
Q Consensus 108 ~~t~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~ 158 (443)
++++++|..+|+|+| |||+|+|||||.|+|.+++.+. .+.++++..++.
T Consensus 4 g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~--~~~~~~~~~~~~ 54 (75)
T cd00080 4 GLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEY--GSLENLLENLDK 54 (75)
T ss_pred CcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHh--CCHHHHHHHHHH
Confidence 578999999999999 9999999999999999999884 577777776553
No 27
>PRK03980 flap endonuclease-1; Provisional
Probab=98.05 E-value=4.9e-06 Score=83.80 Aligned_cols=56 Identities=29% Similarity=0.349 Sum_probs=47.3
Q ss_pred ChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHh
Q psy11828 99 PSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 156 (443)
Q Consensus 99 ~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L 156 (443)
+.+...+..++++++|..+|+|+||||.++|||+|.|+|.+++.+. +++++++...
T Consensus 164 ~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~--~sle~i~~~~ 219 (292)
T PRK03980 164 ELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKH--GDLEKVLEER 219 (292)
T ss_pred eHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHC--CCHHHHHHhc
Confidence 3333445667899999999999999999999999999999999985 5788888743
No 28
>PTZ00217 flap endonuclease-1; Provisional
Probab=97.99 E-value=6.7e-06 Score=86.05 Aligned_cols=56 Identities=29% Similarity=0.516 Sum_probs=48.9
Q ss_pred hhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhh
Q psy11828 101 ALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 158 (443)
Q Consensus 101 ~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~ 158 (443)
+...+..++++++|..+|+|.||||+|+|||+|.|+|++++.+. .++++++..+..
T Consensus 212 ~~v~~~~gl~~~q~id~~iL~G~Dy~pgi~GIG~ktA~~Li~~~--gsle~il~~~~~ 267 (393)
T PTZ00217 212 STVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKY--KSIEEILEHLDK 267 (393)
T ss_pred HHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHc--CCHHHHHHHHHh
Confidence 33455668899999999999999999999999999999999985 678899888774
No 29
>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=97.83 E-value=1.9e-05 Score=79.92 Aligned_cols=54 Identities=28% Similarity=0.453 Sum_probs=45.0
Q ss_pred ccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhhhh
Q psy11828 104 MPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVY 159 (443)
Q Consensus 104 ~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~~ 159 (443)
.+-.++++++|..+|+|+||||.|+|||+|.|+|.+++.+. .+.+..+..+...
T Consensus 203 ~~~lgl~~~q~id~~~L~G~Dy~~gv~giG~k~A~~li~~~--~~~~~~~~~l~~~ 256 (316)
T cd00128 203 LKELGLTREKLIDLAILLGCDYTEGIPGIGPVTALKLIKKY--GDIEKDIERLKKK 256 (316)
T ss_pred HHHcCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHc--CChHHHHHHHHHh
Confidence 33457899999999999999999999999999999999985 4556666666543
No 30
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=97.73 E-value=3.2e-05 Score=79.42 Aligned_cols=58 Identities=26% Similarity=0.359 Sum_probs=48.5
Q ss_pred CChhhcccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHHHhh
Q psy11828 98 LPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKIN 157 (443)
Q Consensus 98 v~~~~~~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~ 157 (443)
++.+...+..++++++|..+|+|+||||.++|+|+|.|||.+++.+. +++++++..++
T Consensus 210 ~~~~~v~~~lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~--gsie~il~~~~ 267 (338)
T TIGR03674 210 IELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEH--GDLEKVLKARG 267 (338)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHc--CCHHHHHHhhc
Confidence 34444455667899999999999999999999999999999999995 67888877643
No 31
>PF12813 XPG_I_2: XPG domain containing
Probab=97.72 E-value=4.9e-05 Score=74.88 Aligned_cols=69 Identities=20% Similarity=0.215 Sum_probs=48.9
Q ss_pred ccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeecc--C-EEE--EecCCCC----------CeEEeccccccc
Q psy11828 177 APQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFGA--K-KII--YKLDLSG----------NCCFMDREKLPS 241 (443)
Q Consensus 177 i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG~--~-~vi--~~l~~~g----------~~~~i~~~~l~~ 241 (443)
++.|+|||. .||.+++. .-+ +|+|+|||+++|+. + .++ ..+.... .+..|+.+.+.+
T Consensus 24 ~~~~~EAD~----~~A~~A~~---~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i~~~~y~~~~i~~ 95 (246)
T PF12813_consen 24 VQCPGEADR----ECAALARK---WGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYISAKVYSPDKICK 95 (246)
T ss_pred EEcCccchH----HHHHHHHH---cCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCeeEEEEEcHHHHHH
Confidence 999999999 99999976 334 99999999999987 2 222 2232211 235689999988
Q ss_pred cccCCCCCCCHHHHHHHHH
Q psy11828 242 ALKMPLAKFTDAKFRYMCI 260 (443)
Q Consensus 242 ~~~l~~~~lt~eqfidl~i 260 (443)
.+ |+. .+..||.
T Consensus 96 ~l-----~l~--~Lp~lA~ 107 (246)
T PF12813_consen 96 RL-----GLP--LLPLLAY 107 (246)
T ss_pred Hc-----CCc--hhHHHHH
Confidence 74 555 5555554
No 32
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=97.55 E-value=7.9e-05 Score=52.25 Aligned_cols=32 Identities=34% Similarity=0.520 Sum_probs=28.4
Q ss_pred hHHHHHHHHhcCCCCCC---CccccchhhHHHHHhh
Q psy11828 111 DAKFRYMCILSGCDYWT---GIKGMGLKKAKDYVFS 143 (443)
Q Consensus 111 ~~~f~~~ciL~GCdYl~---~i~g~G~k~A~~~V~~ 143 (443)
+++|..+|+|+| ||.. +|||+|.|+|.+++.+
T Consensus 1 p~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 1 PEQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLRE 35 (36)
T ss_pred CHHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHh
Confidence 467889999999 9999 8999999999988754
No 33
>PHA02567 rnh RnaseH; Provisional
Probab=97.44 E-value=0.00015 Score=73.25 Aligned_cols=79 Identities=15% Similarity=0.140 Sum_probs=56.3
Q ss_pred ccCC-CccccchhhhHHHhHhhhh-CCCeEEEecCCCceeeecc-CEEEEecCCCCCeEEeccccccccccCCCCCCCHH
Q psy11828 177 APQP-FGARNEGRSLLSAVTERNI-AGYADYVITEDSDLLVFGA-KKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDA 253 (443)
Q Consensus 177 i~AP-~EAdaEgEAQ~A~L~~~~~-~g~vd~ViTeDsD~L~fG~-~~vi~~l~~~g~~~~i~~~~l~~~~~l~~~~lt~e 253 (443)
+..| +|||+ .+|.|++... .|.-..|+|.|.|+++.-. +.|-. ++. ++.+.+... .| .++
T Consensus 124 l~~~g~EADD----vIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~-~~~------~~~~~V~~k-----~G-~P~ 186 (304)
T PHA02567 124 MKIDKAEADD----IIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQ-WSP------MQKKWVKPK-----YG-SPE 186 (304)
T ss_pred EEeCCccHHH----HHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeEE-eec------CCHHHHHHH-----hC-CHH
Confidence 5555 89999 9999998753 4666789999999999853 43321 111 122333333 46 599
Q ss_pred HHHHHHHHhC--CCCCCCCCC
Q psy11828 254 KFRYMCILSG--CDYWTGIKG 272 (443)
Q Consensus 254 qfidl~iL~G--~DY~~gipG 272 (443)
|++|+..|+| +|..||||-
T Consensus 187 q~iD~kaL~GDsSDNIPGVp~ 207 (304)
T PHA02567 187 KDLMTKIIKGDKKDGVASIKV 207 (304)
T ss_pred HHHHHHHhCCcccCCcCCCCC
Confidence 9999999999 898888874
No 34
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=97.21 E-value=0.00082 Score=62.58 Aligned_cols=61 Identities=15% Similarity=0.287 Sum_probs=39.2
Q ss_pred ccCC-CccccchhhhHHHhHhhhh-CCCeEEEecCCCceeeeccC--EEEEecCCCCCeEEeccccccc
Q psy11828 177 APQP-FGARNEGRSLLSAVTERNI-AGYADYVITEDSDLLVFGAK--KIIYKLDLSGNCCFMDREKLPS 241 (443)
Q Consensus 177 i~AP-~EAdaEgEAQ~A~L~~~~~-~g~vd~ViTeDsD~L~fG~~--~vi~~l~~~g~~~~i~~~~l~~ 241 (443)
+..| +|||+ .+|.|++... .|.--.|+|.|.|+++.-.+ +|..--....+...++.+.+.+
T Consensus 103 ~~~~g~EADD----vIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~~~~~~~~~~~~~~~~~v~e 167 (169)
T PF02739_consen 103 LEVPGYEADD----VIATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVYLLDPGKKKFKVYDPEEVEE 167 (169)
T ss_dssp EEETTB-HHH----HHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEEEEETTTTCS-EB-HHHHHH
T ss_pred ecCCCCcHHH----HHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEEEeecCCCCCEEEcHHHHhh
Confidence 5555 99999 9999998863 46667899999999999887 4432222223445666665543
No 35
>smart00475 53EXOc 5'-3' exonuclease.
Probab=96.97 E-value=0.001 Score=66.13 Aligned_cols=52 Identities=23% Similarity=0.295 Sum_probs=44.4
Q ss_pred cccccchHHHHHHHHhcC--CCCCCCccccchhhHHHHHhhccCccHHHHHHHhhh
Q psy11828 105 PLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 158 (443)
Q Consensus 105 ~~~~~t~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~ 158 (443)
+.-++++++|..+|+|.| ||+.||+||+|.|||.+++.+. +++++++..+..
T Consensus 165 ~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~y--gsle~i~~~~~~ 218 (259)
T smart00475 165 EKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEF--GSLENILENLDK 218 (259)
T ss_pred HHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHh--CCHHHHHHHHHH
Confidence 334678999999999999 8999999999999999999885 477777776654
No 36
>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=96.92 E-value=0.0011 Score=64.83 Aligned_cols=52 Identities=23% Similarity=0.266 Sum_probs=45.6
Q ss_pred cccccchHHHHHHHHhcC--CCCCCCccccchhhHHHHHhhccCccHHHHHHHhhh
Q psy11828 105 PLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 158 (443)
Q Consensus 105 ~~~~~t~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~ 158 (443)
.-.+.++++|..+|+|.| ||+.|||||+|.|+|.+++.+. +++++++..+..
T Consensus 162 ~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~--gsle~i~~~~~~ 215 (240)
T cd00008 162 EKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEY--GSLEGILENLDK 215 (240)
T ss_pred HHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHh--CCHHHHHHhHHH
Confidence 335678999999999999 9999999999999999999985 688888887764
No 37
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=96.84 E-value=0.0012 Score=66.92 Aligned_cols=50 Identities=22% Similarity=0.336 Sum_probs=43.5
Q ss_pred ccccchHHHHHHHHhcC--CCCCCCccccchhhHHHHHhhccCccHHHHHHHhh
Q psy11828 106 LAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKIN 157 (443)
Q Consensus 106 ~~~~t~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~ 157 (443)
+.+.+++++..+++|+| |||.|||+|+|.|||.+++.+.. +.+.++..+.
T Consensus 178 ~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~g--s~e~i~~~~~ 229 (310)
T COG0258 178 FKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYG--SLEGLYENLD 229 (310)
T ss_pred HcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhC--CHHHHHHhhh
Confidence 44788999999999999 99999999999999999999965 6666666655
No 38
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=96.82 E-value=0.011 Score=62.19 Aligned_cols=46 Identities=26% Similarity=0.282 Sum_probs=38.8
Q ss_pred hhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHH
Q psy11828 19 HLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEI 64 (443)
Q Consensus 19 ~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~ 64 (443)
+...+.+..+++.|.+.+=+.++..|-+..+.|..+.++||+.-..
T Consensus 47 ~eL~~~~~~~i~~w~~~~~~VtlFvDRG~I~iK~~lReKRr~a~k~ 92 (425)
T PF04599_consen 47 DELRNSFEEYIQQWIKNNGKVTLFVDRGSINIKEPLREKRRKALKN 92 (425)
T ss_pred HHHHHHHHHHHHHHHhcCCeEEEEEecCccchhhHHHHHHHHHHHH
Confidence 4677888999999988888888888999999999999999765433
No 39
>KOG2519|consensus
Probab=96.79 E-value=0.0012 Score=69.59 Aligned_cols=49 Identities=35% Similarity=0.590 Sum_probs=43.1
Q ss_pred ccccccchHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCccHHHHHH
Q psy11828 104 MPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALR 154 (443)
Q Consensus 104 ~~~~~~t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~ 154 (443)
.+...++.++|..+|+|.||||.++|.|+|.++|.++++++. |+++++.
T Consensus 209 l~~l~l~~~~fidL~lLlGCDYc~~I~Gig~~~al~lir~~~--~i~~ile 257 (449)
T KOG2519|consen 209 LEGLGLSRESFIDLCLLLGCDYCPTIRGIGPKKALKLIRQHG--DIENILE 257 (449)
T ss_pred HHHhcccHHHHHHHHHHhcCcccccccccChHHHHHHHHHhc--CHHHHhh
Confidence 445567789999999999999999999999999999999986 7777776
No 40
>PRK14976 5'-3' exonuclease; Provisional
Probab=96.38 E-value=0.0044 Score=62.26 Aligned_cols=59 Identities=24% Similarity=0.245 Sum_probs=47.1
Q ss_pred CChhhcccccccchHHHHHHHHhcC--CCCCCCccccchhhHHHHHhhccCccHHHHHHHhhh
Q psy11828 98 LPSALKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 158 (443)
Q Consensus 98 v~~~~~~~~~~~t~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~ 158 (443)
++.+...+--++++++|..+|.|.| ||+.||+||+|.|||.+++.+. +++++++..+..
T Consensus 163 ~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~--gsle~i~~~~~~ 223 (281)
T PRK14976 163 LNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKY--GNIENIYENIDK 223 (281)
T ss_pred EcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHc--CCHHHHHHhHHH
Confidence 3344444445678999999999999 9999999999999999999885 577777766553
No 41
>PHA03065 Hypothetical protein; Provisional
Probab=96.16 E-value=0.039 Score=57.91 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=37.3
Q ss_pred hhHHHHHHHHHHHHHhCCCEEEEEEcCCCCCcchhhHHHHHHHHHH
Q psy11828 19 HLYVNYCMKYINMLLAHKIKVIMVFDGRHLPAKEATEEDRRKRAEI 64 (443)
Q Consensus 19 ~~~l~~~~~~i~~L~~~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~ 64 (443)
+.....+..+++.|.+.+=+.++..|-+..+.|....++||+.-..
T Consensus 49 ~eL~~~~~~~iq~w~~~~gkVtlFvDRG~I~IK~~lReKRr~a~~~ 94 (438)
T PHA03065 49 DELRSTFEEYVQQWVKKAGKVTLFVDRGSIPIKQSLREKRRKASKN 94 (438)
T ss_pred HHHHHHHHHHHHHHHhcCCcEEEEEecCccchhhHHHHHHHHHHHH
Confidence 4566778889999977766777777999999999999999886444
No 42
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=96.04 E-value=0.0069 Score=59.54 Aligned_cols=45 Identities=20% Similarity=0.280 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHHHHHhCCCEE----EEEEcCCCCCcchhhHHHHHHHHHH
Q psy11828 19 HLYVNYCMKYINMLLAHKIKV----IMVFDGRHLPAKEATEEDRRKRAEI 64 (443)
Q Consensus 19 ~~~l~~~~~~i~~L~~~gI~P----vfVFDG~~pp~K~~t~~~R~~~R~~ 64 (443)
...+..++..++.|.. -|+| ++.+||-+|-+|-.+..+||-++..
T Consensus 57 ~~~~~~i~~~id~l~~-~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~ 105 (237)
T PF03159_consen 57 EEIFQRIFNYIDRLVR-IVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAK 105 (237)
T ss_dssp HHHHHHHHHHHHHHHH-HH-ESSEEEEE---S--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhe-eecCceEEEEEcCCCCCchHHHHHHHHHHHHhh
Confidence 4567777888888775 4555 7899999999999999888877655
No 43
>PF12247 MKT1_N: Temperature dependent protein affecting M2 dsRNA replication; InterPro: IPR022040 This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the N-terminal region of MKT1.
Probab=95.75 E-value=0.003 Score=53.17 Aligned_cols=61 Identities=18% Similarity=0.311 Sum_probs=45.7
Q ss_pred HHHHHHhhhhhhHHhhhhcccccCCc-----hhhHHhhhc-hh-hhhhhhhhcccCCcccceeeeecchHHhhhcccc
Q psy11828 355 EVICGFSMATIPFILAGKAILDMKVP-----AKWYRRIIG-SI-EVICGFSMATIPFSTYYLLVCKLDEMILRKNVQY 425 (443)
Q Consensus 355 ~~l~~fl~~~i~~~L~~~~~~~~~~p-----s~~~rr~~~-~~-e~~~~l~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 425 (443)
+..+|.+++.++.+||+|+|.|. .| |+.||+++. ++ +.+|. +..++..+|.+-++.|+|+.
T Consensus 19 yls~GLi~~~ll~~lt~G~~~~~-~PL~~~~S~eYr~lv~~~l~~~r~~---------~l~Ll~~~L~r~y~~K~I~~ 86 (90)
T PF12247_consen 19 YLSIGLISPRLLNALTSGEWIER-PPLDGGDSDEYRKLVTESLLPLRCQ---------ALNLLTQRLHRYYQIKKIKV 86 (90)
T ss_pred HHHccccChHHHhHhccceEecc-CCCCCCCCHHHHHHHHHHHHHHHHH---------HHHHHHHHhhhhhhccceEE
Confidence 46699999999999999999975 46 899999984 33 33332 34556666777788887754
No 44
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=95.56 E-value=0.055 Score=59.94 Aligned_cols=42 Identities=14% Similarity=0.158 Sum_probs=29.6
Q ss_pred ccCCCccccchhhhHHHhHhhhh------CCCeEEEecCCCceeeecc
Q psy11828 177 APQPFGARNEGRSLLSAVTERNI------AGYADYVITEDSDLLVFGA 218 (443)
Q Consensus 177 i~AP~EAdaEgEAQ~A~L~~~~~------~g~vd~ViTeDsD~L~fG~ 218 (443)
|.+.++-..|||--+-.+-+..+ .+....|++-|.|+++.|-
T Consensus 180 I~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGL 227 (953)
T COG5049 180 IFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGL 227 (953)
T ss_pred EEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeec
Confidence 44444444566668877766531 2568899999999999993
No 45
>PRK05755 DNA polymerase I; Provisional
Probab=95.20 E-value=0.022 Score=65.54 Aligned_cols=138 Identities=18% Similarity=0.135 Sum_probs=81.1
Q ss_pred hhhhhHHHHHHHHHHHHHhCCCEE---EEEEcCCCCCcchhhHHHHHHHHHHH------HHHHHHHHhh-----------
Q psy11828 16 LLQHLYVNYCMKYINMLLAHKIKV---IMVFDGRHLPAKEATEEDRRKRAEIR------HKQKAAELLH----------- 75 (443)
Q Consensus 16 ~~~~~~l~~~~~~i~~L~~~gI~P---vfVFDG~~pp~K~~t~~~R~~~R~~~------~~~~a~~~~~----------- 75 (443)
|..+..+.++++.+..++ +..+| ++||||..+..+.+...+++..|.+. ......+++.
T Consensus 29 g~~~~a~~g~~~~l~~~~-~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g 107 (880)
T PRK05755 29 GLPTGAVYGFLNMLLKLL-KEEKPTHVAVAFDAKGKTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEG 107 (880)
T ss_pred CCcccHHHHHHHHHHHHH-HhcCCCEEEEEEECCCCccccccCHHHhCCCCCCcHHHHHHHHHHHHHHHHCCCCEEeeCC
Confidence 444578888998888888 34555 99999987777777666666665321 0011111111
Q ss_pred ----------------cCCc-ccccccccccce-------ee-----eccCCChhhcccccccchHHHHHHHHhcC--CC
Q psy11828 76 ----------------SGSS-IIYKLDLSGNCC-------FM-----DREKLPSALKMPLAKFTDAKFRYMCILSG--CD 124 (443)
Q Consensus 76 ----------------~g~~-~~fKld~~~~~~-------~~-----~~~~v~~~~~~~~~~~t~~~f~~~ciL~G--Cd 124 (443)
.|.. .+.--|..-..+ +. +...++.+....--++++++|..+|+|.| ||
T Consensus 108 ~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~~~~~~~~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sD 187 (880)
T PRK05755 108 YEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEELDPEEVVEKYGVTPEQIIDYLALMGDSSD 187 (880)
T ss_pred ccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEeeccCCCCCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccC
Confidence 1111 111111100000 00 00112222222234667999999999999 79
Q ss_pred CCCCccccchhhHHHHHhhccCccHHHHHHHh
Q psy11828 125 YWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 156 (443)
Q Consensus 125 Yl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L 156 (443)
+.|||||||.|||.+++.+. +++++++..+
T Consensus 188 nipGv~GiG~ktA~~Ll~~~--gsle~i~~~~ 217 (880)
T PRK05755 188 NIPGVPGIGEKTAAKLLQEY--GSLEGLYENL 217 (880)
T ss_pred CCCCCCCccHHHHHHHHHHc--CCHHHHHHhH
Confidence 99999999999999999885 3555555443
No 46
>KOG2045|consensus
Probab=94.46 E-value=0.096 Score=59.60 Aligned_cols=56 Identities=29% Similarity=0.329 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHhCCCEE----EEEEcCCCCCcchhhHHHHHHHHHHHHHHHHHHHhhcCCc
Q psy11828 23 NYCMKYINMLLAHKIKV----IMVFDGRHLPAKEATEEDRRKRAEIRHKQKAAELLHSGSS 79 (443)
Q Consensus 23 ~~~~~~i~~L~~~gI~P----vfVFDG~~pp~K~~t~~~R~~~R~~~~~~~a~~~~~~g~~ 79 (443)
..+++.|..|- +-|+| ++-.||.+|-+|-.....||-+-.+-+.+....+++.|+.
T Consensus 62 ~~IfnYIdhLf-~~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~ 121 (1493)
T KOG2045|consen 62 QEIFNYIDHLF-YLIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGEL 121 (1493)
T ss_pred HHHHHHHHHHH-HhhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhcccc
Confidence 44556666543 34655 4456999999999998888877444232233345666654
No 47
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=94.13 E-value=0.065 Score=61.90 Aligned_cols=139 Identities=18% Similarity=0.151 Sum_probs=83.6
Q ss_pred hhhhhHHHHHHHHHHHHHhCCCEE---EEEEcCCCCCcchhhHHHHHHHHHHHHHHH-------HHHHhh----------
Q psy11828 16 LLQHLYVNYCMKYINMLLAHKIKV---IMVFDGRHLPAKEATEEDRRKRAEIRHKQK-------AAELLH---------- 75 (443)
Q Consensus 16 ~~~~~~l~~~~~~i~~L~~~gI~P---vfVFDG~~pp~K~~t~~~R~~~R~~~~~~~-------a~~~~~---------- 75 (443)
|..+..+.++++++..+++.. +| ++||||..+..+.+...+.+..|... .+. ..+++.
T Consensus 27 G~~t~av~Gf~~~l~~ll~~~-~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~-Pe~l~~Q~~~i~~~l~~~gi~~i~~~ 104 (887)
T TIGR00593 27 GEPTNAVYGFTKMLLKLLKEE-KPTYVAVAFDSGTPTFRHEAYAEYKANRAPT-PEELIEQIPLIKELLDALGIPILEVE 104 (887)
T ss_pred CCEecHHHHHHHHHHHHHHhc-CCCEEEEEEcCCCCcchHHHHHHHHhCCCCC-hHHHHHHHHHHHHHHHHCCCcEEeeC
Confidence 445688899999999888753 44 99999988877777666666665431 111 111111
Q ss_pred -----------------cCCc-ccccccccccce------eeec------cCCChhhcccccccchHHHHHHHHhcC--C
Q psy11828 76 -----------------SGSS-IIYKLDLSGNCC------FMDR------EKLPSALKMPLAKFTDAKFRYMCILSG--C 123 (443)
Q Consensus 76 -----------------~g~~-~~fKld~~~~~~------~~~~------~~v~~~~~~~~~~~t~~~f~~~ciL~G--C 123 (443)
.|.. .+.--|.....+ .... ..++.+...+--++++++|..++.|.| |
T Consensus 105 g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~~~~~~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~s 184 (887)
T TIGR00593 105 GYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEYVVEKYGVTPDQLVDLKALVGDSS 184 (887)
T ss_pred CccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEeccCCCCceEEcHHHHHHHhCCCHHHHHHHHHHcCCcc
Confidence 1110 111111100000 0000 012222222334668999999999999 5
Q ss_pred CCCCCccccchhhHHHHHhhccCccHHHHHHHhhh
Q psy11828 124 DYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 158 (443)
Q Consensus 124 dYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~ 158 (443)
|+.|||||+|.|||.+++.+. +++++++..+..
T Consensus 185 DnIpGVpGIG~KtA~kLL~~y--gsle~i~~~~~~ 217 (887)
T TIGR00593 185 DNIPGVKGIGEKTAAKLLQEF--GSLENIYENLDQ 217 (887)
T ss_pred cCCCCCCCcCHHHHHHHHHHc--CCHHHHHHHHHH
Confidence 999999999999999999885 466666655443
No 48
>PRK09482 flap endonuclease-like protein; Provisional
Probab=94.01 E-value=0.093 Score=52.22 Aligned_cols=52 Identities=17% Similarity=0.256 Sum_probs=43.8
Q ss_pred cccccchHHHHHHHHhcC--CCCCCCccccchhhHHHHHhhccCccHHHHHHHhhh
Q psy11828 105 PLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 158 (443)
Q Consensus 105 ~~~~~t~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~i~~~d~~~ll~~L~~ 158 (443)
.--+++++++..++.|.| .|..||+||+|.|||.+++.+. +++++++..+..
T Consensus 161 ~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~--gsle~i~~~~~~ 214 (256)
T PRK09482 161 QEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQF--RSLENIYESLDA 214 (256)
T ss_pred HHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHh--CCHHHHHHhHHH
Confidence 334677999999999999 8999999999999999999985 577777776653
No 49
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=92.02 E-value=0.03 Score=59.28 Aligned_cols=90 Identities=21% Similarity=0.363 Sum_probs=66.7
Q ss_pred EEeccchhcCCccCCCccccchhhhHHHhHhhhhCCCeEEEecCCCceeeec-cCEEEEecCC-CCCeEEeccccccccc
Q psy11828 166 VKITKEFLTSGAPQPFGARNEGRSLLSAVTERNIAGYADYVITEDSDLLVFG-AKKIIYKLDL-SGNCCFMDREKLPSAL 243 (443)
Q Consensus 166 v~~~~~f~~~~i~AP~EAdaEgEAQ~A~L~~~~~~g~vd~ViTeDsD~L~fG-~~~vi~~l~~-~g~~~~i~~~~l~~~~ 243 (443)
|.| +++||-|.. |||||+.. ..++++.+ .+|++++. .++.|..|.. ++. -.++...+.+.+
T Consensus 143 ~a~--------~i~~ys~~f----q~AYl~~~---~~~~~~~g-p~d~l~ld~vdr~il~m~fg~d~-Ppl~~~~vp~~l 205 (531)
T COG5366 143 VAV--------IIAPYSATF----QCAYLMSA---ETCSYAFG-PSDILLLDGVDRIILDMSFGSDK-PPLDVFHVPRFL 205 (531)
T ss_pred eEE--------EehhhHHHH----HHHHHHHH---HHHHhcCC-chHhHHHhhhhhheeecccCCCC-CCCcccccchHH
Confidence 788 999999999 99999877 89999998 88999995 4888888765 222 122222333322
Q ss_pred cCCCCCCCHHHHHHHHHHhCCCCCCCCCCCc
Q psy11828 244 KMPLAKFTDAKFRYMCILSGCDYWTGIKGMG 274 (443)
Q Consensus 244 ~l~~~~lt~eqfidl~iL~G~DY~~gipGiG 274 (443)
+..-.+..-|...-.+.|||+++.++.+-
T Consensus 206 --em~l~s~~lFya~~ll~~c~~~s~~~~C~ 234 (531)
T COG5366 206 --EMFLLSSRLFYALGLLLGCDFCSTIPRCA 234 (531)
T ss_pred --Hhcccccchhhhhcccccccccccccccc
Confidence 22335667788899999999999998753
No 50
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=90.48 E-value=0.16 Score=39.74 Aligned_cols=26 Identities=31% Similarity=0.294 Sum_probs=20.5
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
-||||||+++|..|.++|+ +++++.+
T Consensus 6 LGI~~VG~~~ak~L~~~f~--sl~~l~~ 31 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFG--SLEALMN 31 (64)
T ss_dssp CTSTT--HHHHHHHHHCCS--CHHHHCC
T ss_pred CCCCCccHHHHHHHHHHcC--CHHHHHH
Confidence 3899999999999999998 7877653
No 51
>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=86.39 E-value=0.22 Score=42.79 Aligned_cols=35 Identities=23% Similarity=0.316 Sum_probs=24.7
Q ss_pred chHHHHHHHHhcC--CCCCCCccccchhhHHHHHhhc
Q psy11828 110 TDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSI 144 (443)
Q Consensus 110 t~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~i 144 (443)
+++++..+..|.| .|-.|+|||+|-|||.+++.+.
T Consensus 2 ~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~y 38 (101)
T PF01367_consen 2 PPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEY 38 (101)
T ss_dssp -GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHH
T ss_pred CHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHc
Confidence 3566666677787 8999999999999999998774
No 52
>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=83.31 E-value=0.98 Score=30.39 Aligned_cols=15 Identities=27% Similarity=0.423 Sum_probs=11.9
Q ss_pred CCCCCcHHHHHHHHH
Q psy11828 269 GIKGMGLKKAKDYVF 283 (443)
Q Consensus 269 gipGiG~ktA~~li~ 283 (443)
.+||||+++|-.++.
T Consensus 15 ~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 15 KLPGIGPKTANAILS 29 (30)
T ss_dssp TSTT-SHHHHHHHHH
T ss_pred hCCCcCHHHHHHHHh
Confidence 689999999987763
No 53
>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=81.44 E-value=1.6 Score=33.15 Aligned_cols=27 Identities=30% Similarity=0.475 Sum_probs=19.3
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
.+|.||||+||.+++.+.- .||+++.+
T Consensus 5 ~~I~GVG~~tA~~w~~~G~-rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGI-RTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHHHTT---SHHHHHH
T ss_pred hhcccccHHHHHHHHHhCC-CCHHHHhh
Confidence 3789999999999999644 58888854
No 54
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=78.63 E-value=0.84 Score=38.20 Aligned_cols=24 Identities=33% Similarity=0.603 Sum_probs=19.3
Q ss_pred hhcccccccchHHHHHHHHhcCCC
Q psy11828 101 ALKMPLAKFTDAKFRYMCILSGCD 124 (443)
Q Consensus 101 ~~~~~~~~~t~~~f~~~ciL~GCd 124 (443)
....+..++|.++|..+|+|+|||
T Consensus 71 ~~i~~~l~l~~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 71 DDILKELGLTREQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHHTTSHHHHHHHHHHHHET
T ss_pred HHHHHHcCCCHHHHHHHheecCCC
Confidence 334445668999999999999998
No 55
>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=76.71 E-value=2.1 Score=40.77 Aligned_cols=43 Identities=19% Similarity=0.094 Sum_probs=30.4
Q ss_pred CCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhh
Q psy11828 248 AKF-TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKY 299 (443)
Q Consensus 248 ~~l-t~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~ 299 (443)
.|+ |.++--.|..| -+|+|||||+|+.++..+ +.+++.+.+..
T Consensus 60 yGF~~~~Er~lF~~L------~~V~GIGpK~Al~iL~~~---~~~el~~aI~~ 103 (191)
T TIGR00084 60 FGFNTLEERELFKEL------IKVNGVGPKLALAILSNM---SPEEFVYAIET 103 (191)
T ss_pred eCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHhcC---CHHHHHHHHHh
Confidence 444 44444455555 389999999999998876 57777777764
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=75.13 E-value=1.8 Score=41.05 Aligned_cols=19 Identities=21% Similarity=0.293 Sum_probs=17.3
Q ss_pred CCCCCcHHHHHHHHHHcCC
Q psy11828 269 GIKGMGLKKAKDYVFSIMD 287 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~ 287 (443)
.|||||||+|.+++..++.
T Consensus 77 ~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSP 95 (192)
T ss_pred cCCCCCHHHHHHHHHhCCH
Confidence 5999999999999999973
No 57
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.84 E-value=2.7 Score=40.40 Aligned_cols=41 Identities=17% Similarity=0.139 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhc
Q psy11828 251 TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYA 300 (443)
Q Consensus 251 t~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~ 300 (443)
|.++--.|-.| -+|+|||||+|+.++..+ +.+++.+.+...
T Consensus 66 ~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~---~~~~l~~aI~~~ 106 (203)
T PRK14602 66 TWDERQTFIVL------ISISKVGAKTALAILSQF---RPDDLRRLVAEE 106 (203)
T ss_pred CHHHHHHHHHH------hCCCCcCHHHHHHHHhhC---CHHHHHHHHHhC
Confidence 44555555555 378999999999999987 477777777643
No 58
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.89 E-value=2.9 Score=39.91 Aligned_cols=42 Identities=17% Similarity=0.192 Sum_probs=29.7
Q ss_pred CCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhh
Q psy11828 248 AKF-TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVK 298 (443)
Q Consensus 248 ~~l-t~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~ 298 (443)
.|+ +.++--.|..| -+|+|||||+|+.++..++ .+++.+.+.
T Consensus 61 yGF~~~~Er~lF~~L------i~V~GIGpK~Al~ILs~~~---~~~l~~aI~ 103 (194)
T PRK14605 61 FGFATTEELSLFETL------IDVSGIGPKLGLAMLSAMN---AEALASAII 103 (194)
T ss_pred eCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHHhCC---HHHHHHHHH
Confidence 444 44444455555 3899999999999999985 566666664
No 59
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.79 E-value=2.5 Score=40.51 Aligned_cols=30 Identities=17% Similarity=0.140 Sum_probs=23.0
Q ss_pred CCCCCcHHHHHHHHHHcCCCChhhHHHhhhhcc
Q psy11828 269 GIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAK 301 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~ 301 (443)
+|.|||||+|+.++..+ +.+++.+.+...+
T Consensus 76 ~V~GIGpK~AL~iLs~~---~~~~l~~aI~~~D 105 (197)
T PRK14603 76 GVSGVGPKLALALLSAL---PPALLARALLEGD 105 (197)
T ss_pred CcCCcCHHHHHHHHcCC---CHHHHHHHHHhCC
Confidence 78899999999998876 4677777776443
No 60
>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=72.71 E-value=3.2 Score=34.16 Aligned_cols=22 Identities=27% Similarity=0.333 Sum_probs=19.5
Q ss_pred CCCCCCCCCcHHHHHHHHHHcC
Q psy11828 265 DYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 265 DY~~gipGiG~ktA~~li~~~~ 286 (443)
+-+.+|||||+.+|..++.+.+
T Consensus 2 ~~l~sipGig~~~a~~llaeig 23 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIG 23 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHc
Confidence 4457899999999999999987
No 61
>KOG2044|consensus
Probab=71.83 E-value=16 Score=41.90 Aligned_cols=44 Identities=27% Similarity=0.334 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHh---CCCEEEEEEcCCCCCcchhhHHHHHHHHHH
Q psy11828 21 YVNYCMKYINMLLA---HKIKVIMVFDGRHLPAKEATEEDRRKRAEI 64 (443)
Q Consensus 21 ~l~~~~~~i~~L~~---~gI~PvfVFDG~~pp~K~~t~~~R~~~R~~ 64 (443)
-...++..|..|.. =-=-.++--||-+|-+|-.....||-|..+
T Consensus 77 m~~avFeyiDrlf~mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaK 123 (931)
T KOG2044|consen 77 MFVAVFEYIDRLFSMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAK 123 (931)
T ss_pred HHHHHHHHHHHHHHhccchheeEEeecccCchhhhhHHHHHHHhhhh
Confidence 34445555555432 233457888999999999998888877544
No 62
>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=71.07 E-value=3.6 Score=31.39 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=20.3
Q ss_pred CCCCCcHHHHHHHHHH-cCCCChhhHHH
Q psy11828 269 GIKGMGLKKAKDYVFS-IMDPDFENRKE 295 (443)
Q Consensus 269 gipGiG~ktA~~li~~-~~~~sle~~~~ 295 (443)
.|||||+++|.+|... +. +++++..
T Consensus 9 ~I~Gig~~~a~~L~~~G~~--t~~~l~~ 34 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIK--TLEDLAN 34 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCS--SHHHHHT
T ss_pred cCCCCCHHHHHHHHhcCCC--cHHHHHc
Confidence 7999999999999988 43 6766654
No 63
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.02 E-value=3 Score=40.07 Aligned_cols=41 Identities=15% Similarity=0.295 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhc
Q psy11828 251 TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYA 300 (443)
Q Consensus 251 t~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~ 300 (443)
|.++--.|-.| -+|+|||||+|+.++..+ +.+++.+.+...
T Consensus 64 t~~Er~lF~~L------isVsGIGPK~ALaILs~~---~~~el~~aI~~~ 104 (196)
T PRK13901 64 NSSEREVFEEL------IGVDGIGPRAALRVLSGI---KYNEFRDAIDRE 104 (196)
T ss_pred CHHHHHHHHHH------hCcCCcCHHHHHHHHcCC---CHHHHHHHHHhC
Confidence 34444444444 378888888888888876 467777777544
No 64
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.61 E-value=3.6 Score=39.14 Aligned_cols=31 Identities=13% Similarity=0.112 Sum_probs=24.3
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhcc
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAK 301 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~ 301 (443)
-++.|||||+|+.++..+ +.+++.+.+...+
T Consensus 76 isV~GIGpK~Al~iLs~~---~~~~l~~aI~~~D 106 (186)
T PRK14600 76 VKVSGVNYKTAMSILSKL---TPEQLFSAIVNED 106 (186)
T ss_pred hCcCCcCHHHHHHHHccC---CHHHHHHHHHcCC
Confidence 378999999999999887 4777777776543
No 65
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.44 E-value=3 Score=39.65 Aligned_cols=45 Identities=20% Similarity=0.186 Sum_probs=31.3
Q ss_pred CCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhcc
Q psy11828 248 AKF-TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAK 301 (443)
Q Consensus 248 ~~l-t~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~ 301 (443)
.|+ |.++--.|..| -+|.|||||+|+.++..+ +.+++.+.+...+
T Consensus 61 yGF~~~~Er~lF~~L------i~V~GIGpK~AL~iLs~~---~~~el~~aI~~~D 106 (188)
T PRK14606 61 YGFSNERKKELFLSL------TKVSRLGPKTALKIISNE---DAETLVTMIASQD 106 (188)
T ss_pred eCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCC---CHHHHHHHHHhCC
Confidence 454 44455555555 378999999999999886 5777777776443
No 66
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.23 E-value=3 Score=39.89 Aligned_cols=29 Identities=21% Similarity=0.204 Sum_probs=22.1
Q ss_pred CCCCCcHHHHHHHHHHcCCCChhhHHHhhhhc
Q psy11828 269 GIKGMGLKKAKDYVFSIMDPDFENRKEYVKYA 300 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~~sle~~~~~~~~~ 300 (443)
+|.|||||+|+.++..+ +.+++.+.+...
T Consensus 77 ~V~GIGpK~Al~iLs~~---~~~el~~aI~~~ 105 (195)
T PRK14604 77 GVSGVGPKAALNLLSSG---TPDELQLAIAGG 105 (195)
T ss_pred CcCCcCHHHHHHHHcCC---CHHHHHHHHHhC
Confidence 68888999998888876 467777777644
No 67
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=70.09 E-value=3.5 Score=26.39 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=15.2
Q ss_pred CCCCCCCcHHHHHHHHHH
Q psy11828 267 WTGIKGMGLKKAKDYVFS 284 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~ 284 (443)
...|||||+++|.+++..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 357999999999998864
No 68
>KOG2520|consensus
Probab=69.03 E-value=5.2 Score=45.84 Aligned_cols=38 Identities=24% Similarity=0.368 Sum_probs=31.7
Q ss_pred chHHHHHHHHhcCCCCCCCccccchhhHHHHHhhccCc
Q psy11828 110 TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDP 147 (443)
Q Consensus 110 t~~~f~~~ciL~GCdYl~~i~g~G~k~A~~~V~~i~~~ 147 (443)
.....-.++.|.||||..+++|+|..+|..++....+.
T Consensus 546 ~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~ 583 (815)
T KOG2520|consen 546 DRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGD 583 (815)
T ss_pred CchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCc
Confidence 34455667889999999999999999999999887633
No 69
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=68.52 E-value=3.8 Score=45.88 Aligned_cols=27 Identities=19% Similarity=0.251 Sum_probs=23.5
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHh
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEY 296 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~ 296 (443)
.+|||||++++.+|++.|| |++++.+.
T Consensus 555 ~~IpGIG~kr~~~LL~~Fg--Si~~I~~A 581 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFG--SLERVRAA 581 (624)
T ss_pred hcCCCCCHHHHHHHHHHcC--CHHHHHhC
Confidence 5899999999999999999 67777653
No 70
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.42 E-value=4 Score=38.72 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=8.5
Q ss_pred CCCCCcHHHHHHHHHHc
Q psy11828 269 GIKGMGLKKAKDYVFSI 285 (443)
Q Consensus 269 gipGiG~ktA~~li~~~ 285 (443)
++.|||||+|+.++..+
T Consensus 77 ~VsGIGpK~Al~ILs~~ 93 (183)
T PRK14601 77 KVNGIGANTAMAVCSSL 93 (183)
T ss_pred ccCCccHHHHHHHHcCC
Confidence 34555555555555444
No 71
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=68.27 E-value=4.1 Score=45.08 Aligned_cols=29 Identities=17% Similarity=0.055 Sum_probs=24.5
Q ss_pred CCCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 267 WTGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
..+|||||+++..+|++.|| |++++.+.-
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fg--s~~~ik~As 544 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFK--TLYDFLKAD 544 (567)
T ss_pred cccCCCCCHHHHHHHHHHhC--CHHHHHhCC
Confidence 35899999999999999999 787776544
No 72
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.21 E-value=3.7 Score=39.00 Aligned_cols=37 Identities=19% Similarity=0.260 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 249 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 249 ~lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
.+++++|.. |+..| ......+||||+|||-+++-+-.
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 467777765 34444 34456899999999999998765
No 73
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=67.25 E-value=4.5 Score=44.87 Aligned_cols=29 Identities=34% Similarity=0.419 Sum_probs=24.9
Q ss_pred CCCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 267 WTGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
...||||||++..+|++.|| |++++.+.-
T Consensus 516 L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As 544 (574)
T PRK14670 516 YTKIKGIGEKKAKKILKSLG--TYKDILLLN 544 (574)
T ss_pred cccCCCCCHHHHHHHHHHhC--CHHHHHhCC
Confidence 45899999999999999999 788876544
No 74
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=67.02 E-value=4.1 Score=45.16 Aligned_cols=28 Identities=18% Similarity=0.220 Sum_probs=24.1
Q ss_pred CCCCCCCcHHHHHHHHHHcCCCChhhHHHh
Q psy11828 267 WTGIKGMGLKKAKDYVFSIMDPDFENRKEY 296 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~~~sle~~~~~ 296 (443)
..+||||||++..+|++.|| |++++.+.
T Consensus 543 Ld~I~GIG~kr~~~LL~~Fg--s~~~i~~A 570 (574)
T TIGR00194 543 LLKIPGVGEKRVQKLLKYFG--SLKGIKKA 570 (574)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhC
Confidence 35899999999999999999 78877653
No 75
>PHA00439 exonuclease
Probab=66.66 E-value=4.7 Score=40.91 Aligned_cols=32 Identities=22% Similarity=0.524 Sum_probs=27.4
Q ss_pred hHHHHHHHHhcC--CCCCCCccccchhhHHHHHhh
Q psy11828 111 DAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFS 143 (443)
Q Consensus 111 ~~~f~~~ciL~G--CdYl~~i~g~G~k~A~~~V~~ 143 (443)
++++..+..|.| .|-.||+||+| |||.+++.+
T Consensus 173 p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 173 ADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred HHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 666766677888 89999999999 999999866
No 76
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.80 E-value=5.2 Score=38.44 Aligned_cols=37 Identities=22% Similarity=0.278 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 249 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 249 ~lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
.+++++|... |..| -.....+||||+|||-++|-+-.
T Consensus 91 ~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 91 GIKYNEFRDA-IDREDIELISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 4688877764 3444 34446899999999999998754
No 77
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.72 E-value=5.3 Score=38.25 Aligned_cols=37 Identities=19% Similarity=0.280 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 249 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 249 ~lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
.+++++|+..- ..| ......+||||+|||-+++-+-.
T Consensus 92 ~~~~~el~~aI-~~~D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 92 SGTPDELQLAI-AGGDVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CCCHHHHHHHH-HhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 36788777643 333 34446899999999999998765
No 78
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=63.79 E-value=5.7 Score=37.82 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 249 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 249 ~lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
++++++|+.. |..| ......+||||+|||-+++-+-.
T Consensus 92 ~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 92 NEDAETLVTM-IASQDVEGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 4688877764 3333 34456899999999999998764
No 79
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.17 E-value=6.3 Score=37.77 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 249 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 249 ~lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
++++++|+.. |..| -.....+||||+|||-+++-+..
T Consensus 91 ~~~~~~l~~a-I~~~D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 91 ALPPALLARA-LLEGDARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 3688877654 3333 23335899999999999998865
No 80
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=60.18 E-value=6.9 Score=43.80 Aligned_cols=26 Identities=27% Similarity=0.328 Sum_probs=22.5
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
.+|||||+++|..|++.|| |++++.+
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fg--s~~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFG--SVEKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcC--CHHHHHh
Confidence 5999999999999999998 6766654
No 81
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.40 E-value=9.1 Score=36.38 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 249 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 249 ~lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
.+++++|+.. |-.| ..-+ .+||||+|||-+++-+-.
T Consensus 92 ~~~~~~l~~a-I~~~D~~~L-~vpGIGkKtAerIilELk 128 (186)
T PRK14600 92 KLTPEQLFSA-IVNEDKAAL-KVNGIGEKLINRIITELQ 128 (186)
T ss_pred cCCHHHHHHH-HHcCCHhhe-ECCCCcHHHHHHHHHHHH
Confidence 3678877764 3344 3445 899999999999998764
No 82
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.68 E-value=7.7 Score=37.31 Aligned_cols=36 Identities=19% Similarity=0.381 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 250 FTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 250 lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
+++++|+.. |..| .+-...+||||+|||-+++-+-.
T Consensus 94 ~~~~~l~~a-I~~~D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 94 FRPDDLRRL-VAEEDVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred CCHHHHHHH-HHhCCHHHHhcCCCcCHHHHHHHHHHHH
Confidence 677777653 3444 34446899999999999998765
No 83
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=58.59 E-value=8 Score=43.70 Aligned_cols=29 Identities=10% Similarity=0.186 Sum_probs=24.3
Q ss_pred CCCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 267 WTGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
...|||||++++.+|++.|| |++++.+.-
T Consensus 610 L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As 638 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFG--SFRSLQSAT 638 (691)
T ss_pred cccCCCCCHHHHHHHHHHhc--CHHHHHhCC
Confidence 35899999999999999999 677776543
No 84
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=57.60 E-value=12 Score=36.22 Aligned_cols=36 Identities=17% Similarity=0.244 Sum_probs=19.6
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHc
Q psy11828 250 FTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSI 285 (443)
Q Consensus 250 lt~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~ 285 (443)
++.+.|...-..-=-.+...+||||.|+|-+++-+-
T Consensus 93 ~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 93 LDPEELAQAIANEDVKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHH
Confidence 455555544333223344567777777776666654
No 85
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=56.25 E-value=8.9 Score=37.01 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=25.5
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHhhhhcc
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEYVKYAK 301 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~~~~~~ 301 (443)
-++.|||||+|+.++... +.+++.+.+...+
T Consensus 76 isVnGIGpK~ALaiLs~~---~~~~l~~aI~~~d 106 (201)
T COG0632 76 ISVNGIGPKLALAILSNL---DPEELAQAIANED 106 (201)
T ss_pred HccCCccHHHHHHHHcCC---CHHHHHHHHHhcC
Confidence 379999999999999986 5788888887543
No 86
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=52.90 E-value=10 Score=42.34 Aligned_cols=27 Identities=26% Similarity=0.329 Sum_probs=23.5
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHh
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEY 296 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~ 296 (443)
.+|||||++++.+|++.|| |++++.+.
T Consensus 546 ~~IpGIG~k~~k~Ll~~Fg--S~~~i~~A 572 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFG--SLKAIKEA 572 (598)
T ss_pred hhCCCcCHHHHHHHHHHcC--CHHHHHhC
Confidence 5899999999999999998 68777653
No 87
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=52.46 E-value=13 Score=33.52 Aligned_cols=27 Identities=19% Similarity=0.010 Sum_probs=19.7
Q ss_pred CCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 269 GIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
.+|||||+.|-++++..+=.++|++++
T Consensus 65 ~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 589999999999996433236666653
No 88
>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=51.29 E-value=14 Score=37.52 Aligned_cols=29 Identities=17% Similarity=0.263 Sum_probs=24.4
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
-+||||||++|.++. +.|=.|++++.+..
T Consensus 88 ~~i~GiGpk~a~~l~-~lGi~sl~dL~~a~ 116 (307)
T cd00141 88 LRVPGVGPKTARKLY-ELGIRTLEDLRKAA 116 (307)
T ss_pred HcCCCCCHHHHHHHH-HcCCCCHHHHHHHh
Confidence 379999999999999 77766888888764
No 89
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=50.70 E-value=12 Score=41.69 Aligned_cols=29 Identities=17% Similarity=0.227 Sum_probs=24.9
Q ss_pred CCCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 267 WTGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
...|||||++++.+|++.|| |++++.+.-
T Consensus 527 L~~IpGIG~kr~~~LL~~FG--S~~~I~~As 555 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRFG--SVEGVREAS 555 (577)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhCC
Confidence 46899999999999999999 788877644
No 90
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=50.54 E-value=13 Score=36.59 Aligned_cols=28 Identities=21% Similarity=0.259 Sum_probs=23.0
Q ss_pred CCCCCCCcHHHHHHHHHH-cCCCChhhHHHh
Q psy11828 267 WTGIKGMGLKKAKDYVFS-IMDPDFENRKEY 296 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~-~~~~sle~~~~~ 296 (443)
+..|||||+++|.+|++. |+ |++++...
T Consensus 5 L~~IpGIG~krakkLl~~GF~--Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFE--SVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCC--CHHHHHhC
Confidence 357999999999999999 87 77776543
No 91
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=50.49 E-value=13 Score=38.24 Aligned_cols=29 Identities=24% Similarity=0.187 Sum_probs=24.3
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
-.||||||++|..+.+ .|=.|++++.+..
T Consensus 92 ~~i~GiGpk~a~~l~~-lGi~tl~eL~~a~ 120 (334)
T smart00483 92 TNVFGVGPKTAAKWYR-KGIRTLEELKKNK 120 (334)
T ss_pred HccCCcCHHHHHHHHH-hCCCCHHHHHhcc
Confidence 4899999999999999 7767888887654
No 92
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=45.96 E-value=13 Score=39.73 Aligned_cols=24 Identities=42% Similarity=1.014 Sum_probs=18.3
Q ss_pred HHHHHHHh----cCCCCCCCccccchhh
Q psy11828 113 KFRYMCIL----SGCDYWTGIKGMGLKK 136 (443)
Q Consensus 113 ~f~~~ciL----~GCdYl~~i~g~G~k~ 136 (443)
.-+.+|+| .||||+||+-|+.+++
T Consensus 224 ~s~YL~kL~~L~NGCDfFpGLyG~~it~ 251 (425)
T PF04599_consen 224 KSRYLSKLTALVNGCDFFPGLYGISITK 251 (425)
T ss_pred hHHHHHHHHHHHhcccccCCcceeEech
Confidence 34455664 4999999999998776
No 93
>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=45.89 E-value=17 Score=34.64 Aligned_cols=37 Identities=19% Similarity=0.313 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 250 FTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 250 lt~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~ 286 (443)
++.+++...+.--=-.-...+||||+|||-+++-+..
T Consensus 92 ~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk 128 (191)
T TIGR00084 92 MSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELK 128 (191)
T ss_pred CCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 5777777655421123345899999999999996543
No 94
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=45.65 E-value=17 Score=41.30 Aligned_cols=28 Identities=11% Similarity=0.057 Sum_probs=24.2
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
..|||||++++.+|++.|| |++++.+.-
T Consensus 640 ~~IPGIGpkr~k~LL~~FG--Sle~I~~AS 667 (694)
T PRK14666 640 QRVEGIGPATARLLWERFG--SLQAMAAAG 667 (694)
T ss_pred hhCCCCCHHHHHHHHHHhC--CHHHHHhcC
Confidence 4799999999999999999 788877643
No 95
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=44.09 E-value=16 Score=34.94 Aligned_cols=36 Identities=22% Similarity=0.394 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHcC
Q psy11828 250 FTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 250 lt~eqfidl~iL~G-~DY~~gipGiG~ktA~~li~~~~ 286 (443)
+++++|+..- ..+ -.-...+||||+|||-+++-+-.
T Consensus 93 ~~~~~l~~aI-~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 93 MNAEALASAI-ISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred CCHHHHHHHH-HhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 6777665432 223 12234799999999999997754
No 96
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=43.41 E-value=24 Score=40.20 Aligned_cols=40 Identities=23% Similarity=0.240 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 250 FTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 250 lt~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
-+.+.++.+.. + ..|||||+++|-+++..||...++-+.+
T Consensus 75 ~~~~~i~~yL~-s-----~~~~GIG~~~A~~iv~~fg~~~~~~i~~ 114 (720)
T TIGR01448 75 TSKEGIVAYLS-S-----RSIKGVGKKLAQRIVKTFGEAAFDVLDD 114 (720)
T ss_pred CCHHHHHHHHh-c-----CCCCCcCHHHHHHHHHHhCHhHHHHHHh
Confidence 46777877643 2 2499999999999999999655544443
No 97
>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=42.10 E-value=18 Score=24.44 Aligned_cols=14 Identities=36% Similarity=0.458 Sum_probs=10.9
Q ss_pred CCCCCCcHHHHHHH
Q psy11828 268 TGIKGMGLKKAKDY 281 (443)
Q Consensus 268 ~gipGiG~ktA~~l 281 (443)
..++|||.+++-+|
T Consensus 14 ~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 14 RKFWGIGKKTAKKL 27 (32)
T ss_dssp GGSTTS-HHHHHHH
T ss_pred HhhCCccHHHHHHH
Confidence 36899999999885
No 98
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=40.41 E-value=14 Score=42.68 Aligned_cols=28 Identities=7% Similarity=0.166 Sum_probs=23.0
Q ss_pred CCCCCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 266 YWTGIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 266 Y~~gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
|.-++||||++.|..|+.+++ |++++..
T Consensus 758 ~L~~lPgI~~~~a~~ll~~f~--si~~l~~ 785 (814)
T TIGR00596 758 FLLKLPGVTKKNYRNLRKKVK--SIRELAK 785 (814)
T ss_pred HHHHCCCCCHHHHHHHHHHcC--CHHHHHh
Confidence 334899999999999999998 6766654
No 99
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=40.30 E-value=24 Score=35.36 Aligned_cols=27 Identities=22% Similarity=0.219 Sum_probs=23.2
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHh
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEY 296 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~ 296 (443)
.++||||++.|.++++.|| |++++...
T Consensus 185 ~s~pgig~~~a~~ll~~fg--S~~~~~ta 211 (254)
T COG1948 185 ESIPGIGPKLAERLLKKFG--SVEDVLTA 211 (254)
T ss_pred HcCCCccHHHHHHHHHHhc--CHHHHhhc
Confidence 4799999999999999999 67777654
No 100
>PRK08609 hypothetical protein; Provisional
Probab=39.48 E-value=29 Score=38.44 Aligned_cols=30 Identities=27% Similarity=0.205 Sum_probs=24.9
Q ss_pred CCCCCcHHHHHHHHHHcCCCChhhHHHhhh
Q psy11828 269 GIKGMGLKKAKDYVFSIMDPDFENRKEYVK 298 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~~sle~~~~~~~ 298 (443)
.|||||||+|.++-++.|=.|++++.+...
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 799999999999998877667777776554
No 101
>PHA03065 Hypothetical protein; Provisional
Probab=37.18 E-value=18 Score=38.54 Aligned_cols=24 Identities=38% Similarity=0.970 Sum_probs=18.4
Q ss_pred HHHHHHHh----cCCCCCCCccccchhh
Q psy11828 113 KFRYMCIL----SGCDYWTGIKGMGLKK 136 (443)
Q Consensus 113 ~f~~~ciL----~GCdYl~~i~g~G~k~ 136 (443)
+-+++|+| .||||+||+-|+.+++
T Consensus 226 ~t~YL~kL~~L~NGCDfFpGLyG~~it~ 253 (438)
T PHA03065 226 KTRYLSKLVALVNGCDFFPGLYGISITP 253 (438)
T ss_pred hHHHHHHHHHHHhcccccCccceEEech
Confidence 44556665 4999999999988766
No 102
>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=37.01 E-value=25 Score=28.77 Aligned_cols=22 Identities=27% Similarity=0.394 Sum_probs=18.7
Q ss_pred CCCCCCccccchhhHHHHHhhc
Q psy11828 123 CDYWTGIKGMGLKKAKDYVFSI 144 (443)
Q Consensus 123 CdYl~~i~g~G~k~A~~~V~~i 144 (443)
|+.+.+|||+|..+|..++..+
T Consensus 1 ~~~l~sipGig~~~a~~llaei 22 (87)
T PF02371_consen 1 AELLTSIPGIGPITAATLLAEI 22 (87)
T ss_pred CchhcCCCCccHHHHHHHHHHH
Confidence 5678899999999998888664
No 103
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=33.68 E-value=32 Score=38.32 Aligned_cols=28 Identities=21% Similarity=0.273 Sum_probs=23.5
Q ss_pred CCCCCCcHHHHHHHHHHcCCCChhhHHHhh
Q psy11828 268 TGIKGMGLKKAKDYVFSIMDPDFENRKEYV 297 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~~~~sle~~~~~~ 297 (443)
.+|||||+++.-+|++.|| |++++.+.-
T Consensus 533 d~I~GiG~~r~~~LL~~Fg--s~~~i~~As 560 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFG--SLKGIKSAS 560 (581)
T ss_pred ccCCCcCHHHHHHHHHHhh--CHHHHHhcC
Confidence 5899999999999999999 676665544
No 104
>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=32.78 E-value=43 Score=29.45 Aligned_cols=18 Identities=28% Similarity=0.342 Sum_probs=16.2
Q ss_pred CCCCCCcHHHHHHHHHHc
Q psy11828 268 TGIKGMGLKKAKDYVFSI 285 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~~ 285 (443)
..+||||+++|.+++..+
T Consensus 71 ~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYR 88 (120)
T ss_pred hcCCCCCHHHHHHHHHHH
Confidence 479999999999999876
No 105
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=31.47 E-value=39 Score=38.22 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=21.3
Q ss_pred CCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 269 GIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
||||||+++|..|.+.|+ +++++..
T Consensus 502 gIpgVG~~~ak~L~~~f~--sl~~l~~ 526 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFG--TLDKLKA 526 (652)
T ss_pred cCCCcCHHHHHHHHHHhC--CHHHHHh
Confidence 799999999999999997 6777654
No 106
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=29.77 E-value=44 Score=38.09 Aligned_cols=25 Identities=24% Similarity=0.353 Sum_probs=21.0
Q ss_pred CCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 269 GIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
||||||+++|..|.+.|+ +++++..
T Consensus 532 gIpgIG~~~ak~L~~~F~--si~~L~~ 556 (689)
T PRK14351 532 GIPEVGPTTARNLAREFG--TFEAIMD 556 (689)
T ss_pred CCCCcCHHHHHHHHHHhC--CHHHHHh
Confidence 799999999999999997 6776654
No 107
>PRK00076 recR recombination protein RecR; Reviewed
Probab=27.98 E-value=37 Score=32.68 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=0.0
Q ss_pred CCCCcHHHHHHHH
Q psy11828 270 IKGMGLKKAKDYV 282 (443)
Q Consensus 270 ipGiG~ktA~~li 282 (443)
+||||+|+|.++.
T Consensus 16 LPGIG~KsA~Rla 28 (196)
T PRK00076 16 LPGIGPKSAQRLA 28 (196)
T ss_pred CCCCCHHHHHHHH
No 108
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.55 E-value=38 Score=32.57 Aligned_cols=17 Identities=29% Similarity=0.557 Sum_probs=14.0
Q ss_pred CCCCCCcHHHHHHHHHH
Q psy11828 268 TGIKGMGLKKAKDYVFS 284 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~ 284 (443)
..+||||+|+|.++.-.
T Consensus 14 ~~LPGIG~KsA~RlA~~ 30 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFH 30 (195)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 57899999999888643
No 109
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=26.98 E-value=37 Score=32.73 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=20.1
Q ss_pred CCCCCCCcHHHHHHHHHHcC---CCChhhHHHhhh
Q psy11828 267 WTGIKGMGLKKAKDYVFSIM---DPDFENRKEYVK 298 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~---~~sle~~~~~~~ 298 (443)
...+||||||+|-++.-.-- ...++++.+++.
T Consensus 14 l~kLPGvG~KsA~R~AfhLL~~~~~~~~~la~al~ 48 (198)
T COG0353 14 LKKLPGVGPKSAQRLAFHLLQRDREDVERLAKALL 48 (198)
T ss_pred HhhCCCCChhHHHHHHHHHHccCHHHHHHHHHHHH
Confidence 45799999999988764321 124455555554
No 110
>PF06415 iPGM_N: BPG-independent PGAM N-terminus (iPGM_N); InterPro: IPR011258 This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (5.4.2.1 from EC). The family is found in conjunction with Metalloenzyme (located in the C-terminal region of the protein). ; GO: 0004619 phosphoglycerate mutase activity, 0030145 manganese ion binding, 0006007 glucose catabolic process, 0005737 cytoplasm; PDB: 1EQJ_A 1EJJ_A 1O99_A 1O98_A 3IGZ_B 3IGY_B 3NVL_A 2IFY_A.
Probab=26.85 E-value=64 Score=31.71 Aligned_cols=40 Identities=23% Similarity=0.265 Sum_probs=28.0
Q ss_pred hhhhhhHHHHHHHHHHHHHhCCCEEEE---EEcCCCCCcchhh
Q psy11828 15 KLLQHLYVNYCMKYINMLLAHKIKVIM---VFDGRHLPAKEAT 54 (443)
Q Consensus 15 ~~~~~~~l~~~~~~i~~L~~~gI~Pvf---VFDG~~pp~K~~t 54 (443)
.+.-++|++.+..-++...++||++|+ +.||+-.+-+...
T Consensus 38 dGGVHSh~~Hl~al~~~a~~~gv~~V~vH~f~DGRDt~P~S~~ 80 (223)
T PF06415_consen 38 DGGVHSHIDHLFALIKLAKKQGVKKVYVHAFTDGRDTPPKSAL 80 (223)
T ss_dssp S-SSS--HHHHHHHHHHHHHTT-SEEEEEEEE-SSSS-TTTHH
T ss_pred CCCccccHHHHHHHHHHHHHcCCCEEEEEEecCCCCCCcchHH
Confidence 355689999999999999999999874 6999976666644
No 111
>PRK13766 Hef nuclease; Provisional
Probab=26.42 E-value=53 Score=37.33 Aligned_cols=27 Identities=11% Similarity=0.064 Sum_probs=23.0
Q ss_pred CCCCCCCcHHHHHHHHHHcCCCChhhHHH
Q psy11828 267 WTGIKGMGLKKAKDYVFSIMDPDFENRKE 295 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~~~sle~~~~ 295 (443)
..++||||+++|.+|+++|+ +++++.+
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~ 743 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMT 743 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHh
Confidence 45799999999999999998 6777654
No 112
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=25.06 E-value=39 Score=28.67 Aligned_cols=23 Identities=35% Similarity=0.368 Sum_probs=17.9
Q ss_pred hHHHhHhhhhCCCeEEEecCCCceee
Q psy11828 190 LLSAVTERNIAGYADYVITEDSDLLV 215 (443)
Q Consensus 190 Q~A~L~~~~~~g~vd~ViTeDsD~L~ 215 (443)
-...++.. +.+|+++|.|.|+|.
T Consensus 91 ~~l~~A~~---~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 91 KFLNTAYA---SKANALITGDTDLLV 113 (114)
T ss_pred HHHHHHHh---cCCCEEEECCHHHhh
Confidence 55556555 889999999999864
No 113
>PRK13844 recombination protein RecR; Provisional
Probab=24.60 E-value=47 Score=32.12 Aligned_cols=17 Identities=12% Similarity=0.249 Sum_probs=14.2
Q ss_pred CCCCCCcHHHHHHHHHH
Q psy11828 268 TGIKGMGLKKAKDYVFS 284 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~ 284 (443)
..+||||+|+|-++.-.
T Consensus 18 ~~LPGIG~KsA~Rla~~ 34 (200)
T PRK13844 18 RKLPTIGKKSSQRLALY 34 (200)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 57999999999887753
No 114
>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=22.69 E-value=85 Score=24.35 Aligned_cols=15 Identities=47% Similarity=0.662 Sum_probs=14.2
Q ss_pred CCCCcHHHHHHHHHH
Q psy11828 270 IKGMGLKKAKDYVFS 284 (443)
Q Consensus 270 ipGiG~ktA~~li~~ 284 (443)
+||+|+++|.+++..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 899999999999987
No 115
>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=22.35 E-value=45 Score=31.66 Aligned_cols=20 Identities=25% Similarity=0.386 Sum_probs=14.8
Q ss_pred CCCCCCCcHHHHHHHHHHcC
Q psy11828 267 WTGIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 267 ~~gipGiG~ktA~~li~~~~ 286 (443)
+-.+||||+|||-=.+...+
T Consensus 117 Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 117 LKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred HHcCCCCCHHHHHHHHHHHH
Confidence 35899999999966555443
No 116
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=22.28 E-value=78 Score=27.12 Aligned_cols=34 Identities=21% Similarity=0.256 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHH
Q psy11828 251 TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFS 284 (443)
Q Consensus 251 t~eqfidl~iL~G~DY~~gipGiG~ktA~~li~~ 284 (443)
|-..+++.+-..|.-.-..|||+|.+.|..+..-
T Consensus 36 TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~aw 69 (96)
T PF12482_consen 36 TLADLVDRINRRGGRWWRAVPGLGAAGARRIEAW 69 (96)
T ss_pred hHHHHHHHHHHccchHHHhCcccchHHHHHHHHH
Confidence 6788999999999888899999999999876543
No 117
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=21.35 E-value=69 Score=36.32 Aligned_cols=24 Identities=29% Similarity=0.361 Sum_probs=16.6
Q ss_pred CCCCCcHHHHHHHHHHcCCCChhhHH
Q psy11828 269 GIKGMGLKKAKDYVFSIMDPDFENRK 294 (443)
Q Consensus 269 gipGiG~ktA~~li~~~~~~sle~~~ 294 (443)
||||||+++|..|.+.|+ +++++.
T Consensus 515 gi~~IG~~~ak~L~~~f~--sl~~l~ 538 (665)
T PRK07956 515 GIRHVGEKAAKALARHFG--SLEALR 538 (665)
T ss_pred hccCcCHHHHHHHHHHcC--CHHHHH
Confidence 577777777777777775 566554
No 118
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=20.79 E-value=1.1e+02 Score=28.41 Aligned_cols=34 Identities=18% Similarity=0.088 Sum_probs=28.4
Q ss_pred HHHHHHHHHhCCCCCC---------CCCCCcHHHHHHHHHHcC
Q psy11828 253 AKFRYMCILSGCDYWT---------GIKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 253 eqfidl~iL~G~DY~~---------gipGiG~ktA~~li~~~~ 286 (443)
++|-.+.-++|+|-.. .|.|||+.+|..++++.+
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 5788888888887543 389999999999999987
No 119
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=20.75 E-value=1.3e+02 Score=27.69 Aligned_cols=35 Identities=26% Similarity=0.503 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhCCCCCCC---------CCCCcHHHHHHHHHHcC
Q psy11828 252 DAKFRYMCILSGCDYWTG---------IKGMGLKKAKDYVFSIM 286 (443)
Q Consensus 252 ~eqfidl~iL~G~DY~~g---------ipGiG~ktA~~li~~~~ 286 (443)
.++|..+.-++|+|-... |.|||+.+|..+.++.|
T Consensus 3 ~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 3 EEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred hhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcC
Confidence 456777777888775443 78999999999999987
No 120
>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=20.05 E-value=76 Score=27.06 Aligned_cols=17 Identities=29% Similarity=0.380 Sum_probs=15.0
Q ss_pred CCCCCCcHHHHHHHHHH
Q psy11828 268 TGIKGMGLKKAKDYVFS 284 (443)
Q Consensus 268 ~gipGiG~ktA~~li~~ 284 (443)
..|||||+.+|..|..-
T Consensus 15 ~~iP~IG~a~a~DL~~L 31 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLL 31 (93)
T ss_pred hcCCCccHHHHHHHHHc
Confidence 47999999999999865
Done!