Query 005869
Match_columns 672
No_of_seqs 279 out of 1572
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 14:57:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005869hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2518 5'-3' exonuclease [Rep 100.0 2E-81 4.3E-86 679.4 24.6 330 1-331 1-340 (556)
2 PTZ00217 flap endonuclease-1; 100.0 7.5E-62 1.6E-66 526.5 28.2 301 1-308 1-312 (393)
3 cd00128 XPG Xeroderma pigmento 100.0 2.1E-60 4.6E-65 501.1 26.0 298 1-302 1-306 (316)
4 TIGR03674 fen_arch flap struct 100.0 5.8E-55 1.3E-59 465.1 26.4 273 1-285 1-287 (338)
5 PRK03980 flap endonuclease-1; 100.0 2.6E-47 5.7E-52 399.1 24.3 247 48-308 4-258 (292)
6 KOG2519 5'-3' exonuclease [Rep 100.0 1.4E-46 3E-51 404.7 18.1 301 1-308 1-308 (449)
7 TIGR00600 rad2 DNA excision re 100.0 7.6E-31 1.6E-35 308.4 14.5 231 119-371 763-1006(1034)
8 smart00475 53EXOc 5'-3' exonuc 100.0 5.8E-29 1.3E-33 257.1 21.2 206 25-258 2-218 (259)
9 COG0258 Exo 5'-3' exonuclease 100.0 1.7E-29 3.8E-34 266.4 17.4 239 16-281 3-250 (310)
10 cd00008 53EXOc 5'-3' exonuclea 100.0 8.1E-29 1.8E-33 253.1 20.9 203 25-258 2-215 (240)
11 PRK14976 5'-3' exonuclease; Pr 100.0 2.8E-27 6E-32 247.2 21.1 207 24-258 3-223 (281)
12 TIGR00593 pola DNA polymerase 99.9 7.9E-25 1.7E-29 258.0 21.9 203 27-258 2-217 (887)
13 PRK05755 DNA polymerase I; Pro 99.9 1.5E-24 3.3E-29 256.5 21.4 204 25-258 3-219 (880)
14 PRK09482 flap endonuclease-lik 99.9 5.1E-23 1.1E-27 212.4 23.4 198 25-257 4-213 (256)
15 KOG2520 5'-3' exonuclease [Rep 99.9 2.6E-24 5.6E-29 247.0 10.6 205 123-350 461-671 (815)
16 PF00752 XPG_N: XPG N-terminal 99.9 4.8E-24 1E-28 189.9 9.8 98 1-98 1-100 (101)
17 smart00485 XPGN Xeroderma pigm 99.9 4.2E-24 9.2E-29 189.9 8.0 98 1-98 1-98 (99)
18 PF00867 XPG_I: XPG I-region; 99.9 1.6E-24 3.5E-29 191.8 4.3 89 138-226 1-94 (94)
19 TIGR00600 rad2 DNA excision re 99.8 1.6E-20 3.4E-25 221.9 8.4 146 1-149 1-151 (1034)
20 PHA00439 exonuclease 99.7 1.4E-16 3.1E-21 166.6 18.4 195 24-260 6-224 (286)
21 smart00484 XPGI Xeroderma pigm 99.7 2.3E-17 4.9E-22 140.8 5.7 71 139-211 2-73 (73)
22 cd00080 HhH2_motif Helix-hairp 99.3 3.6E-12 7.9E-17 109.2 6.5 51 208-258 2-54 (75)
23 PHA02567 rnh RnaseH; Provision 99.3 1E-10 2.2E-15 123.7 17.9 181 23-233 13-207 (304)
24 PF02739 5_3_exonuc_N: 5'-3' e 99.2 4.4E-11 9.6E-16 117.1 11.0 132 25-180 2-143 (169)
25 smart00279 HhH2 Helix-hairpin- 98.7 2.1E-08 4.7E-13 74.8 3.7 33 213-246 1-36 (36)
26 PF04599 Pox_G5: Poxvirus G5 p 98.6 4.9E-07 1.1E-11 99.2 15.5 236 1-258 1-274 (425)
27 PF12813 XPG_I_2: XPG domain c 98.6 9.4E-08 2E-12 99.0 7.6 91 128-221 4-107 (246)
28 PHA03065 Hypothetical protein; 98.6 1.7E-06 3.6E-11 94.6 16.5 238 1-260 1-278 (438)
29 PF01367 5_3_exonuc: 5'-3' exo 98.4 7.4E-09 1.6E-13 93.9 -5.7 48 211-258 1-50 (101)
30 PF03159 XRN_N: XRN 5'-3' exon 98.4 3.7E-06 8E-11 87.0 13.1 174 1-178 1-222 (237)
31 COG5366 Protein involved in pr 97.7 4.8E-06 1E-10 91.7 -2.0 123 132-257 133-259 (531)
32 KOG2045 5'-3' exonuclease XRN1 97.5 0.0025 5.4E-08 75.5 15.8 238 1-243 1-307 (1493)
33 COG5049 XRN1 5'-3' exonuclease 97.2 0.0069 1.5E-07 70.3 14.8 172 1-179 1-227 (953)
34 KOG2044 5'-3' exonuclease HKE1 95.9 0.11 2.4E-06 61.5 13.6 122 56-179 78-241 (931)
35 PF05991 NYN_YacP: YacP-like N 90.4 0.64 1.4E-05 45.8 6.3 35 140-174 66-106 (166)
36 PF12826 HHH_2: Helix-hairpin- 86.9 0.52 1.1E-05 39.3 2.6 26 230-255 7-32 (64)
37 COG2454 Uncharacterized conser 76.1 9.9 0.00022 39.1 7.5 121 15-172 57-183 (211)
38 PRK14605 ruvA Holliday junctio 75.2 4.1 8.9E-05 41.3 4.6 49 202-257 54-103 (194)
39 PRK14603 ruvA Holliday junctio 74.4 3.8 8.3E-05 41.7 4.2 51 202-258 53-103 (197)
40 PF10391 DNA_pol_lambd_f: Fing 72.9 3.3 7.1E-05 33.6 2.7 26 229-254 5-31 (52)
41 TIGR00084 ruvA Holliday juncti 72.8 8.3 0.00018 39.1 6.1 50 202-258 53-103 (191)
42 PRK14602 ruvA Holliday junctio 72.4 9.2 0.0002 39.1 6.4 51 202-259 55-106 (203)
43 PRK14606 ruvA Holliday junctio 70.1 9.3 0.0002 38.7 5.8 50 202-258 54-104 (188)
44 PRK14604 ruvA Holliday junctio 69.6 9.6 0.00021 38.8 5.8 51 202-259 54-105 (195)
45 PRK14600 ruvA Holliday junctio 68.1 11 0.00024 38.1 5.8 51 202-258 54-104 (186)
46 PF14520 HHH_5: Helix-hairpin- 67.5 5.1 0.00011 32.7 2.7 27 229-255 8-35 (60)
47 PRK13901 ruvA Holliday junctio 67.3 12 0.00026 38.3 5.9 50 202-258 53-103 (196)
48 PRK14601 ruvA Holliday junctio 65.5 13 0.00029 37.5 5.8 50 202-258 54-104 (183)
49 PRK14669 uvrC excinuclease ABC 64.3 5.2 0.00011 47.4 3.0 28 228-255 554-581 (624)
50 PF00633 HHH: Helix-hairpin-he 64.1 5.8 0.00013 28.7 2.1 14 230-243 15-28 (30)
51 PRK14667 uvrC excinuclease ABC 61.1 7.2 0.00016 45.8 3.4 28 228-255 516-543 (567)
52 TIGR00194 uvrC excinuclease AB 60.8 6.6 0.00014 46.1 3.0 28 228-255 543-570 (574)
53 PRK14670 uvrC excinuclease ABC 59.7 7.9 0.00017 45.5 3.4 30 227-256 515-544 (574)
54 PF11977 RNase_Zc3h12a: Zc3h12 59.5 42 0.0009 32.5 7.8 47 24-80 2-48 (155)
55 PF02371 Transposase_20: Trans 55.6 10 0.00022 33.3 2.6 26 225-250 1-26 (87)
56 PRK14671 uvrC excinuclease ABC 54.3 10 0.00022 45.1 3.1 28 228-255 571-598 (621)
57 PRK00116 ruvA Holliday junctio 54.2 11 0.00024 38.0 3.0 19 230-248 77-95 (192)
58 smart00278 HhH1 Helix-hairpin- 52.1 11 0.00025 25.9 1.9 17 228-244 3-19 (26)
59 PRK14601 ruvA Holliday junctio 51.7 10 0.00022 38.3 2.3 37 210-247 92-129 (183)
60 PRK14672 uvrC excinuclease ABC 51.5 13 0.00028 44.6 3.4 29 227-255 609-637 (691)
61 PRK14606 ruvA Holliday junctio 49.2 12 0.00026 37.9 2.3 41 206-247 87-129 (188)
62 PRK14668 uvrC excinuclease ABC 49.1 13 0.00029 43.7 3.0 30 227-256 526-555 (577)
63 PRK13901 ruvA Holliday junctio 48.8 12 0.00026 38.3 2.3 37 210-247 91-128 (196)
64 PRK14604 ruvA Holliday junctio 48.4 12 0.00027 38.0 2.3 36 211-247 93-129 (195)
65 PRK12766 50S ribosomal protein 47.5 16 0.00035 38.3 3.0 28 228-255 5-33 (232)
66 PRK00558 uvrC excinuclease ABC 47.1 15 0.00032 43.5 2.9 28 228-255 545-572 (598)
67 PRK02515 psbU photosystem II c 45.9 18 0.0004 34.9 2.9 25 230-254 65-91 (132)
68 PRK14603 ruvA Holliday junctio 45.7 14 0.00031 37.6 2.3 41 206-247 86-128 (197)
69 PRK14600 ruvA Holliday junctio 45.7 18 0.00038 36.7 2.9 35 211-247 93-128 (186)
70 PRK14666 uvrC excinuclease ABC 44.8 17 0.00036 43.8 2.9 29 228-256 639-667 (694)
71 COG1948 MUS81 ERCC4-type nucle 44.8 19 0.00042 38.3 3.1 27 229-255 185-211 (254)
72 PF01927 Mut7-C: Mut7-C RNAse 44.1 29 0.00064 33.4 4.1 48 129-177 8-55 (147)
73 TIGR00596 rad1 DNA repair prot 43.4 12 0.00027 45.7 1.6 30 226-255 757-786 (814)
74 PF11731 Cdd1: Pathogenicity l 43.1 58 0.0013 29.8 5.5 48 229-276 15-72 (93)
75 COG0632 RuvA Holliday junction 42.8 45 0.00098 34.3 5.3 51 202-258 54-104 (201)
76 PRK14602 ruvA Holliday junctio 42.2 17 0.00038 37.1 2.3 36 211-247 94-130 (203)
77 COG0632 RuvA Holliday junction 39.9 31 0.00066 35.5 3.6 76 163-247 48-129 (201)
78 KOG1602 Cis-prenyltransferase 34.7 1.2E+02 0.0027 32.6 7.1 49 130-179 69-142 (271)
79 cd08556 GDPD Glycerophosphodie 34.1 75 0.0016 30.4 5.2 39 131-170 150-188 (189)
80 TIGR00084 ruvA Holliday juncti 30.8 40 0.00087 34.2 2.8 35 211-245 92-126 (191)
81 COG0322 UvrC Nuclease subunit 29.8 43 0.00094 39.6 3.2 29 228-256 532-560 (581)
82 TIGR01259 comE comEA protein. 29.7 45 0.00097 31.3 2.7 18 229-246 71-88 (120)
83 PRK13844 recombination protein 29.3 73 0.0016 32.9 4.3 48 228-289 17-64 (200)
84 KOG4175 Tryptophan synthase al 28.9 3.9E+02 0.0085 28.1 9.3 88 56-160 79-169 (268)
85 TIGR00305 probable toxin-antit 27.3 37 0.00081 30.7 1.7 29 148-176 85-113 (114)
86 TIGR00615 recR recombination p 27.3 86 0.0019 32.3 4.4 48 228-289 13-60 (195)
87 TIGR00575 dnlj DNA ligase, NAD 27.0 53 0.0011 39.4 3.3 26 230-255 502-527 (652)
88 PRK14351 ligA NAD-dependent DN 26.8 54 0.0012 39.6 3.3 26 230-255 532-557 (689)
89 PRK14605 ruvA Holliday junctio 26.3 41 0.00089 34.2 1.9 36 211-247 93-129 (194)
90 PRK00076 recR recombination pr 26.2 92 0.002 32.0 4.4 48 228-289 13-60 (196)
91 smart00483 POLXc DNA polymeras 25.2 60 0.0013 35.6 3.1 27 229-256 92-120 (334)
92 COG2402 Predicted nucleic acid 25.0 4.8E+02 0.01 25.3 8.8 127 27-181 2-131 (135)
93 PRK13766 Hef nuclease; Provisi 24.6 60 0.0013 39.1 3.2 28 228-255 717-744 (773)
94 cd00141 NT_POLXc Nucleotidyltr 24.4 73 0.0016 34.5 3.5 27 229-256 88-116 (307)
95 PF07719 TPR_2: Tetratricopept 23.7 60 0.0013 22.2 1.8 27 101-127 6-32 (34)
96 COG1555 ComEA DNA uptake prote 23.6 80 0.0017 30.9 3.3 26 229-254 100-131 (149)
97 cd01422 MGS Methylglyoxal synt 22.9 1.2E+02 0.0026 28.1 4.2 35 135-169 38-76 (115)
98 cd08568 GDPD_TmGDE_like Glycer 21.5 1.6E+02 0.0035 29.8 5.2 42 131-174 184-225 (226)
99 PF00515 TPR_1: Tetratricopept 21.3 57 0.0012 22.7 1.3 27 101-127 6-32 (34)
100 PF11798 IMS_HHH: IMS family H 21.1 68 0.0015 23.4 1.7 13 230-242 15-27 (32)
No 1
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2e-81 Score=679.44 Aligned_cols=330 Identities=53% Similarity=0.887 Sum_probs=313.6
Q ss_pred CCccccHHHHhhcccccccccccCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEeCC
Q 005869 1 MGIQGLLPLLKSIMIPIHIKELEGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFDGG 80 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG~ 80 (672)
|||+||++++++++++.|+++|+|++||||||+|||||+++|+.+++.|.||.+||+||++++++|+.+||+||+||||+
T Consensus 1 MGI~GLlp~~k~~~~~~hi~~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG~ 80 (556)
T KOG2518|consen 1 MGIQGLLPLLKPALKPIHISEYKGKTVAVDGYCWLHRGALACAEKLAKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDGD 80 (556)
T ss_pred CCcchhHHHHHHHhhhhhHHHhcCceEEEehhhHHhhhHHhHHHHHhcCCChHHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEeccchHHHHHHHHH
Q 005869 81 LLPMKIEQENKRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAPYEADAQMTFLAV 160 (672)
Q Consensus 81 ~lp~K~~Te~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAPYEADAQLAyLa~ 160 (672)
++|.|..|+.+|+.+|+++++.|.+++..|+..+|.++|++|++|||+|++.+|++|+..||+|||||||||||||||++
T Consensus 81 ~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~ 160 (556)
T KOG2518|consen 81 PLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLER 160 (556)
T ss_pred CcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCeEEEEcCCCCeecccCCeEEEecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHH
Q 005869 161 SKQVEAVITEDSDLIPFGCSRIIFKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRAH 240 (672)
Q Consensus 161 ~G~VDaVISeDSDlLlFG~~kVI~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA~ 240 (672)
.|++|+||||||||++|||++||+|||..|+|.++++..+..+.-+. .+|+.++|+.||||+||||+++|||||++||+
T Consensus 161 ~~~i~~IITEDSDLl~fGc~~vifK~d~~G~~le~~~~~l~~~~~l~-~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~ 239 (556)
T KOG2518|consen 161 EGIVDAIITEDSDLLVFGCKKVIFKMDSFGNGLEINRSKLPECKPLG-DKFTEEKFRRMCILSGCDYLSSLPGVGLATAH 239 (556)
T ss_pred cCcceEEEeccccccccCchhheeeccCCCCcccccHhhhhhccccc-cccCHHHHHHHHHhcCCcccccCccccHHHHH
Confidence 99999999999999999999999999999999999887777776665 67999999999999999999999999999999
Q ss_pred HHHHHhCCHHHHHH-HhhhCCCCCCchhHHHHHHHHHHcCCCeeeCCCCCceeecCCCCCCCC-CCchhh--------hh
Q 005869 241 ALISKFKSYDKVIK-HLKYSTVSVPPFYEESFGKAVLTFQHQRVYDPKTEDIVHLSCISDNIG-NDLDFL--------AK 310 (672)
Q Consensus 241 kLIkky~sle~Il~-~L~~~~~~vP~~Y~e~FrkA~~tFkhq~VfdP~~~~lV~L~~~p~~~~-~~ldfl--------a~ 310 (672)
++|.+|.+.+.++. ++...+..||++|+++|.+|..+|+||+||||..++++||+|+|.++. ++++|+ |.
T Consensus 240 k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A~~tF~hQrVydP~~k~~~~L~~~~~~l~~~~~~~~g~~~~~~~av 319 (556)
T KOG2518|consen 240 KLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERANLTFLHQRVYDPIEKKLIHLNPIEDELDNEDLEFLGPLKDPSVAV 319 (556)
T ss_pred HHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHHHHhhhhhheeCchHhhhhcCCchhhhcchhhHhhcccccCcchhh
Confidence 99999999999865 455567899999999999999999999999999999999999999886 455564 88
Q ss_pred hhhcccCCCCCCCCccccCCC
Q 005869 311 GIAIGDLDPFTQLPFQEVSDN 331 (672)
Q Consensus 311 ~IA~G~ldP~T~~~f~~~~~~ 331 (672)
.+|.|+++|+|..-|....+.
T Consensus 320 ~~a~g~~~~~t~~~~~~~~~~ 340 (556)
T KOG2518|consen 320 EIALGNKDPITFKRIDDHKPH 340 (556)
T ss_pred hhhhccCCccchhhhhhcccc
Confidence 899999999999988776554
No 2
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=7.5e-62 Score=526.51 Aligned_cols=301 Identities=26% Similarity=0.370 Sum_probs=268.7
Q ss_pred CCccccHHHHhhc----ccccccccccCCEEEeeHHHHHHHHhccCcc-----cc--cCCCcchhHHHHHHHHHHHHHHc
Q 005869 1 MGIQGLLPLLKSI----MIPIHIKELEGCCVAVDTYSWLHKGALSCSR-----EL--CKGLPTSRHIDYCMHRVNLLRHY 69 (672)
Q Consensus 1 MGIkGL~~~Lk~~----~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~-----el--~~G~pt~~~L~~~~~rI~~Ll~~ 69 (672)
|||+||+++|++. .++.+|+.|+|++|||||++||||++++|.. .+ ..|.++ .||.+|++++.+|+++
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t-~~l~g~~~r~~~Ll~~ 79 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVT-SHISGLFNRTIRLLEA 79 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCcc-HHHHHHHHHHHHHHHC
Confidence 9999999999974 6888999999999999999999999988863 22 346665 8999999999999999
Q ss_pred CCeeEEEEeCCCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEecc
Q 005869 70 GVKPILIFDGGLLPMKIEQENKRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAPY 149 (672)
Q Consensus 70 gI~PIfVFDG~~lp~K~~Te~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAPY 149 (672)
||+|||||||.+++.|.+++.+|+++|+++.+...++++.|+.++|.+++++++.||++|+..++++|+.+||+||+|||
T Consensus 80 gikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~ 159 (393)
T PTZ00217 80 GIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPC 159 (393)
T ss_pred CCCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCc
Confidence 99999999999999999999999999998888888889999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHcCCeEEEEcCCCCeecccCCeEEEecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhCCCCCC
Q 005869 150 EADAQMTFLAVSKQVEAVITEDSDLIPFGCSRIIFKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSGCDYLQ 229 (672)
Q Consensus 150 EADAQLAyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsGcDYlp 229 (672)
|||||||||++.|+||+|+|+|+|+|+||++++|++++..+... ..+..++...+++.+|++++||+|+|+|+||||+|
T Consensus 160 EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~-~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~p 238 (393)
T PTZ00217 160 EAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKK-RPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCD 238 (393)
T ss_pred CHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCC-CCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCC
Confidence 99999999999999999999999999999999999998633210 01234666778899999999999999999999999
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHHhhhCCCCCCchhHHHHHHHHHHcCCCeeeCCCCCceeecCCCCCCCCCCchhh
Q 005869 230 SLPGMGLKRAHALISKFKSYDKVIKHLKYSTVSVPPFYEESFGKAVLTFQHQRVYDPKTEDIVHLSCISDNIGNDLDFL 308 (672)
Q Consensus 230 gIpGIG~KtA~kLIkky~sle~Il~~L~~~~~~vP~~Y~e~FrkA~~tFkhq~VfdP~~~~lV~L~~~p~~~~~~ldfl 308 (672)
||||||+|||++||++|+++|+|++++......+|++|. |.+|+.+|+|+.|+||..- .|.+-++|.....+|+
T Consensus 239 gi~GIG~ktA~~Li~~~gsle~il~~~~~~k~~~p~~~~--~~~~~~~f~~p~V~~~~~~---~l~w~~pD~~~l~~fl 312 (393)
T PTZ00217 239 TIKGIGPKTAYKLIKKYKSIEEILEHLDKTKYPVPENFD--YKEARELFLNPEVTPAEEI---DLKWNEPDEEGLKKFL 312 (393)
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCCC--hHHHHHHhcCCCcCCCCCC---CCCCCCCCHHHHHHHH
Confidence 999999999999999999999999999877778999997 9999999999999998743 3666666655555555
No 3
>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=2.1e-60 Score=501.06 Aligned_cols=298 Identities=36% Similarity=0.565 Sum_probs=265.8
Q ss_pred CCccccHHHHhhcccccccccccCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEeCC
Q 005869 1 MGIQGLLPLLKSIMIPIHIKELEGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFDGG 80 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG~ 80 (672)
|||+|||+||++..++++|++|+|++|||||++||||++++|......+..++.++.++++++.+|+++||+|||||||.
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~gk~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~~~i~pvfVFDG~ 80 (316)
T cd00128 1 MGIKGLWPLLKPVARPVHLEELRGKKVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLELGIKPVFVFDGK 80 (316)
T ss_pred CchhhHHHHHHhhCCCCCHHHhCCcEEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHHCCCEEEEEEcCC
Confidence 99999999999998899999999999999999999999999875543344446899999999999999999999999999
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEeccchHHHHHHHHH
Q 005869 81 LLPMKIEQENKRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAPYEADAQMTFLAV 160 (672)
Q Consensus 81 ~lp~K~~Te~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAPYEADAQLAyLa~ 160 (672)
.++.|.+++.+|+++|.++.+++.+...+|+.+++.++++++..++++++..++++|+.+||+|++||||||||||+|++
T Consensus 81 ~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~ 160 (316)
T cd00128 81 PPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYLAK 160 (316)
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHHHh
Confidence 99999999999999999888888888888999999999999999999999999999999999999999999999999999
Q ss_pred cCCeEEEEcCCCCeecccCCeEEEecccCC-CceEEEeeccccccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHH
Q 005869 161 SKQVEAVITEDSDLIPFGCSRIIFKMDKFG-QGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRA 239 (672)
Q Consensus 161 ~G~VDaVISeDSDlLlFG~~kVI~kLD~~g-~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA 239 (672)
.|.||+|+|+|||+|+||+++|+++++..+ ..+ ..++...+++.+|++++||+++|+|+||||+|||||||+|||
T Consensus 161 ~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~----~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv~giG~k~A 236 (316)
T cd00128 161 KGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPV----EEIDLEKILKELGLTREKLIDLAILLGCDYTEGIPGIGPVTA 236 (316)
T ss_pred CCCeeEEEecCCCeeeecCceEEEecccCCCCce----EEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCCCccHHHH
Confidence 999999999999999999999999998765 122 235566778889999999999999999999999999999999
Q ss_pred HHHHHHhCCHHHHHHHhhhCCCCCC-----chhHHHHH--HHHHHcCCCeeeCCCCCceeecCCCCCCCC
Q 005869 240 HALISKFKSYDKVIKHLKYSTVSVP-----PFYEESFG--KAVLTFQHQRVYDPKTEDIVHLSCISDNIG 302 (672)
Q Consensus 240 ~kLIkky~sle~Il~~L~~~~~~vP-----~~Y~e~Fr--kA~~tFkhq~VfdP~~~~lV~L~~~p~~~~ 302 (672)
++||++|+++++++..++.+...+| ..+.+-|. .+..+|.|+.+++|..+.+++|.+.+.+..
T Consensus 237 ~~li~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~~~~~~p~~~~l~~~~~~~~~~~ 306 (316)
T cd00128 237 LKLIKKYGDIEKDIERLKKKLYRSPEDFPLKEAREFFLNPEVTDDFIDLRWRDPDEEGIIEFLCKEHGFN 306 (316)
T ss_pred HHHHHHcCChHHHHHHHHHhCccCCCcCChHHHHHHHcCCCCCCCCCceeecCCCHHHHHHHccCCCCCC
Confidence 9999999999999999886554443 34456666 456678999999999999999998776554
No 4
>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=5.8e-55 Score=465.08 Aligned_cols=273 Identities=27% Similarity=0.399 Sum_probs=242.8
Q ss_pred CCccccHHHHhhcccccccccccCCEEEeeHHHHHHHHhccCcc------cccCCCcchhHHHHHHHHHHHHHHcCCeeE
Q 005869 1 MGIQGLLPLLKSIMIPIHIKELEGCCVAVDTYSWLHKGALSCSR------ELCKGLPTSRHIDYCMHRVNLLRHYGVKPI 74 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~------el~~G~pt~~~L~~~~~rI~~Ll~~gI~PI 74 (672)
||| |||++|+ .++.+|++|+|++|||||++||||+++++.. ....|.+| .++.++++++..|+++||+||
T Consensus 1 MGi-~l~~~~~--~~~~~l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t-~~l~g~~~~~~~ll~~~i~Pv 76 (338)
T TIGR03674 1 MGV-DLRDLLA--KEEIELEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRIT-SHLSGLFYRTINLLENGIKPV 76 (338)
T ss_pred CCC-ChHHHhc--cCccCHHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCc-HHHHHHHHHHHHHHHCCCeEE
Confidence 999 9999998 6899999999999999999999999887642 12467775 789999999999999999999
Q ss_pred EEEeCCCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEeccchHHH
Q 005869 75 LIFDGGLLPMKIEQENKRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAPYEADAQ 154 (672)
Q Consensus 75 fVFDG~~lp~K~~Te~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAPYEADAQ 154 (672)
|||||.+++.|.++..+|++.|++..+...++.+.|+.++|.++++++..++++|+..++++|+.+||+|++||||||||
T Consensus 77 ~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq 156 (338)
T TIGR03674 77 YVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQ 156 (338)
T ss_pred EEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHH
Confidence 99999999999999999999998877777777788999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCeEEEEcCCCCeecccCCeEEEecccCCCc--------eEEEeeccccccccccCCCCHHHHHHHHHHhCCC
Q 005869 155 MTFLAVSKQVEAVITEDSDLIPFGCSRIIFKMDKFGQG--------VEFQCSMLQKNKDLSFGGFTKQMLLEMCILSGCD 226 (672)
Q Consensus 155 LAyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD~~g~~--------vei~~~~i~~~~~L~~lGlt~dqFidlcILsGcD 226 (672)
||+|++.|.||+|+|+|+|+|+||+++|+++++..++. +++....++...+++.+|++++||+|+|+|+|||
T Consensus 157 ~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~d 236 (338)
T TIGR03674 157 AAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGTD 236 (338)
T ss_pred HHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999998765431 1112334677788999999999999999999999
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhhCCCCCCchhHHHHHHHHHHcCCCeeeC
Q 005869 227 YLQSLPGMGLKRAHALISKFKSYDKVIKHLKYSTVSVPPFYEESFGKAVLTFQHQRVYD 285 (672)
Q Consensus 227 YlpgIpGIG~KtA~kLIkky~sle~Il~~L~~~~~~vP~~Y~e~FrkA~~tFkhq~Vfd 285 (672)
|+|||+|||+|||++||++|+++|+|++++... ++ .|++++..|.++.|-+
T Consensus 237 yn~Gv~GIG~ktA~kli~~~gsie~il~~~~~~---~~-----~~~~~~~~f~~~~v~~ 287 (338)
T TIGR03674 237 YNEGVKGIGPKTALKLIKEHGDLEKVLKARGED---IE-----NYDEIREFFLNPPVTD 287 (338)
T ss_pred CCCCCCCccHHHHHHHHHHcCCHHHHHHhhcCC---CC-----CHHHHHHHhCCCCCCC
Confidence 999999999999999999999999999987532 22 2578899999988754
No 5
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.6e-47 Score=399.15 Aligned_cols=247 Identities=26% Similarity=0.413 Sum_probs=216.7
Q ss_pred CCCcchhHHHHHHHHHHHHHHcCCeeEEEEeCCCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCH
Q 005869 48 KGLPTSRHIDYCMHRVNLLRHYGVKPILIFDGGLLPMKIEQENKRARSRKENLARAIECESEGNSSASYEFYQKAVDISP 127 (672)
Q Consensus 48 ~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG~~lp~K~~Te~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp 127 (672)
.|.+| +|+.+++.++..|+++||+|||||||.+++.|.++..+|+++|+++.+.+.++.+.|+.++|.+++++++.||+
T Consensus 4 ~G~~T-s~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~ 82 (292)
T PRK03980 4 KGRIT-SHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTD 82 (292)
T ss_pred CCcCc-HHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCH
Confidence 57775 79999999999999999999999999999999999999999999888888888889999999999999999999
Q ss_pred HHHHHHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecccCCeEEEecccCCCc--------eEEEeec
Q 005869 128 SIAHELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFGCSRIIFKMDKFGQG--------VEFQCSM 199 (672)
Q Consensus 128 ~ma~~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD~~g~~--------vei~~~~ 199 (672)
+|+..++++|+.+||+|++||||||||||||++.|+||+|+|+|+|+|+||+++||++++..+.. +......
T Consensus 83 ~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~ 162 (292)
T PRK03980 83 EIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPEL 162 (292)
T ss_pred HHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCcccccccccccee
Confidence 99999999999999999999999999999999999999999999999999999999999866431 1112334
Q ss_pred cccccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhhCCCCCCchhHHHHHHHHHHcC
Q 005869 200 LQKNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKYSTVSVPPFYEESFGKAVLTFQ 279 (672)
Q Consensus 200 i~~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~~~~~vP~~Y~e~FrkA~~tFk 279 (672)
++...+++.+|++++||+++|+|+||||+|||||||+|||++||++|+++|+|++.+.. .+| .|.+++..|+
T Consensus 163 ~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~~---~~~-----~~~~~r~~f~ 234 (292)
T PRK03980 163 IELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERGF---EIE-----NYDEIREFFL 234 (292)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhccC---CCC-----CHHHHHHHhc
Confidence 67778899999999999999999999999999999999999999999999999986542 233 4689999999
Q ss_pred CCeeeCCCCCceeecCCCCCCCCCCchhh
Q 005869 280 HQRVYDPKTEDIVHLSCISDNIGNDLDFL 308 (672)
Q Consensus 280 hq~VfdP~~~~lV~L~~~p~~~~~~ldfl 308 (672)
++.|-+ . ..|.+-+++.....+||
T Consensus 235 ~p~v~~-~----~~~~~~~pd~~~l~~fl 258 (292)
T PRK03980 235 NPPVTD-D----YELKWKEPDKEGIIEFL 258 (292)
T ss_pred CCCCCC-C----CCccCCCCCHHHHHHHH
Confidence 999976 2 35677666655445555
No 6
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.4e-46 Score=404.73 Aligned_cols=301 Identities=25% Similarity=0.390 Sum_probs=254.1
Q ss_pred CCccccHHHHhh----cccccccccccCCEEEeeHHHHHHHHhccCcc-cccCCCcchhHHHHHHHHHHHHHHcCCeeEE
Q 005869 1 MGIQGLLPLLKS----IMIPIHIKELEGCCVAVDTYSWLHKGALSCSR-ELCKGLPTSRHIDYCMHRVNLLRHYGVKPIL 75 (672)
Q Consensus 1 MGIkGL~~~Lk~----~~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~-el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIf 75 (672)
|||+||.+.+.. +.++.++..|+|++|||||++|||+...+-.. ....|.+ +.||.++++|...|+++||+|||
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~~~~~~~~-~~HL~g~f~Rt~~l~~~gi~Pv~ 79 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSCRNEAGEP-TSHLMGMFYRTIRLIENGIKPVY 79 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccccccCCCc-hHHHHHHHHHHHHHHHcCCcEEE
Confidence 999999776654 56778999999999999999999997543221 1223333 68999999999999999999999
Q ss_pred EEeCCCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEeccchHHHH
Q 005869 76 IFDGGLLPMKIEQENKRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAPYEADAQM 155 (672)
Q Consensus 76 VFDG~~lp~K~~Te~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAPYEADAQL 155 (672)
||||.+++.|.++..+|..+|.+.-..-...-..|......+++.+-+.+|.++..++..+|..+||+|+.||+||+|||
T Consensus 80 VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EAEAqC 159 (449)
T KOG2519|consen 80 VFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEAEAQC 159 (449)
T ss_pred EECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchHHHHH
Confidence 99999999999999999888865443333444566677778888888999999999999999999999999999999999
Q ss_pred HHHHHcCCeEEEEcCCCCeecccCCeEEEeccc-CCCceEEEeeccccccccccCCCCHHHHHHHHHHhCCCCCCCCCCC
Q 005869 156 TFLAVSKQVEAVITEDSDLIPFGCSRIIFKMDK-FGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGM 234 (672)
Q Consensus 156 AyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD~-~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGI 234 (672)
|+|+++|.|++++|+|||.|.||.+.+++++.. .+.+.. +..++..++++.++++.++|+|+|+|+|||||++|.||
T Consensus 160 A~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~p--v~e~~~~~il~~l~l~~~~fidL~lLlGCDYc~~I~Gi 237 (449)
T KOG2519|consen 160 AALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLP--VSEYDMSRILEGLGLSRESFIDLCLLLGCDYCPTIRGI 237 (449)
T ss_pred HHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCC--eEEeeHHHHHHHhcccHHHHHHHHHHhcCccccccccc
Confidence 999999999999999999999999988877653 233322 23457778899999999999999999999999999999
Q ss_pred cHHHHHHHHHHhCCHHHHHH-HhhhCCCCCCchhHHHHHHHHHHcCCCeeeCCCCCceeecCCCCCCCCCCchhh
Q 005869 235 GLKRAHALISKFKSYDKVIK-HLKYSTVSVPPFYEESFGKAVLTFQHQRVYDPKTEDIVHLSCISDNIGNDLDFL 308 (672)
Q Consensus 235 G~KtA~kLIkky~sle~Il~-~L~~~~~~vP~~Y~e~FrkA~~tFkhq~VfdP~~~~lV~L~~~p~~~~~~ldfl 308 (672)
|+++|++||++|++++++++ ....+...+|.+| .|..|+..|.-..|.++... +-|++..++......|+
T Consensus 238 g~~~al~lir~~~~i~~ile~~~~~~~~~ip~~w--~~~~~r~~f~~p~~~~~~~~--~~i~w~~pd~~~li~fl 308 (449)
T KOG2519|consen 238 GPKKALKLIRQHGDIENILEINSDLKEYPIPEDW--SYKLARKLFLEPEFPNPESI--LDLKWKTPDTEGLIQFL 308 (449)
T ss_pred ChHHHHHHHHHhcCHHHHhhhccchhhcCCCCCc--cHHHHHHHhcCcccCCccce--eecccCCCChHHHHHHH
Confidence 99999999999999999999 6666668999999 47889999999999888754 67788877766555565
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=99.97 E-value=7.6e-31 Score=308.43 Aligned_cols=231 Identities=20% Similarity=0.252 Sum_probs=162.5
Q ss_pred HhhhcCCCHHHHHHHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecccCCeEEEecccCCCceEEEee
Q 005869 119 YQKAVDISPSIAHELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFGCSRIIFKMDKFGQGVEFQCS 198 (672)
Q Consensus 119 f~kai~ITp~ma~~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD~~g~~vei~~~ 198 (672)
-+++..||++|+..++++|+.+|||||+||||||||||+|++.|+||+|+|+|||+|+||+++||+++...+..++
T Consensus 763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~~~~ve---- 838 (1034)
T TIGR00600 763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVE---- 838 (1034)
T ss_pred ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCCCCceE----
Confidence 3457899999999999999999999999999999999999999999999999999999999999999875544443
Q ss_pred ccccccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhC--CHHHHHHHhhhCCCCCCchhHHHHHHHHH
Q 005869 199 MLQKNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFK--SYDKVIKHLKYSTVSVPPFYEESFGKAVL 276 (672)
Q Consensus 199 ~i~~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~--sle~Il~~L~~~~~~vP~~Y~e~FrkA~~ 276 (672)
.+....+++.+||++++|+++|+|+||||++||+|||+|||++||++|+ +++.++....+ ....+....
T Consensus 839 ~~~~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w---------~~~~~~~~~ 909 (1034)
T TIGR00600 839 YYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEW---------WHEAQKDKK 909 (1034)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHH---------HHHhhhccc
Confidence 2445667788999999999999999999999999999999999999999 57887755431 111000000
Q ss_pred HcCCCeeeCCCCCceeecCCCCCCCCCCchhhhhhhhcccCCCCCC---CCccccCCCccccccccCCCCCCCCccccc-
Q 005869 277 TFQHQRVYDPKTEDIVHLSCISDNIGNDLDFLAKGIAIGDLDPFTQ---LPFQEVSDNSHLVVGQNSHLKNFKPESERK- 352 (672)
Q Consensus 277 tFkhq~VfdP~~~~lV~L~~~p~~~~~~ldfla~~IA~G~ldP~T~---~~f~~~~~~~~l~~~~~~~~~~~~~~~~~k- 352 (672)
......+...+.....-.+|+ +|....|...+++|.+- .+|.|+.|+..-++. +......|+...-.
T Consensus 910 --~~~~~~~~~~~~~~~~~~lp~------~FP~~~V~~~yl~P~V~~~~~~f~W~~PD~e~L~~-Fl~~~~gws~eRv~~ 980 (1034)
T TIGR00600 910 --KRENPNDTKVKKKLRLLQLTP------GFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIRE-FCQRYFGWNREKTDE 980 (1034)
T ss_pred --cccccchhhhhhcccccccCC------CCCcHHHHHHhcCCCCCCCcCCCCCCCCCHHHHHH-HHHHccCCCHHHHHH
Confidence 000000000000001112444 56667888889999844 679998877653221 22223344443322
Q ss_pred -------ccccccccccccccccCCC
Q 005869 353 -------KLDLPVQKNLLTKKFTTPR 371 (672)
Q Consensus 353 -------~~~~~~~~~~~~~~f~~~~ 371 (672)
+......+..|+.||+.+-
T Consensus 981 ~l~plikk~~~~~~Q~~ld~FF~~~~ 1006 (1034)
T TIGR00600 981 VLLPVLKKLNAQQTQLRIDSFFRLAQ 1006 (1034)
T ss_pred HHHHHHHHHHccCCccCHHHhhCccc
Confidence 1111223568999997553
No 8
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.96 E-value=5.8e-29 Score=257.10 Aligned_cols=206 Identities=18% Similarity=0.247 Sum_probs=160.1
Q ss_pred CEEEeeHHHHHHHHhccCcc-cccCCCcchhHHHHHHHHHHHHHH-cCC-eeEEEEeCCCCchhhHHHHHHHHHHHHHHH
Q 005869 25 CCVAVDTYSWLHKGALSCSR-ELCKGLPTSRHIDYCMHRVNLLRH-YGV-KPILIFDGGLLPMKIEQENKRARSRKENLA 101 (672)
Q Consensus 25 k~IAIDa~~WLhRg~~sca~-el~~G~pt~~~L~~~~~rI~~Ll~-~gI-~PIfVFDG~~lp~K~~Te~kRr~~R~e~l~ 101 (672)
+.++|||++++||++|+.+. ....|.++ +.+.+|++++..|++ ++- .+++||||....++++
T Consensus 2 ~lllIDg~~~i~R~~~a~~~l~~~~G~~t-~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~-------------- 66 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALPPLKNSKGEPT-NAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHE-------------- 66 (259)
T ss_pred cEEEEeCcHHHHHHHHCCCcccCCCCCcc-cHHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccc--------------
Confidence 36899999999999888643 23467775 788999999888775 332 3489999876655433
Q ss_pred HHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHHc----CCeEEEEcCCCCeec
Q 005869 102 RAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAVS----KQVEAVITEDSDLIP 176 (672)
Q Consensus 102 kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~~----G~VDaVISeDSDlLl 176 (672)
.+..|++++.+.+.++. .++..+.++|+.+||+++.+| ||||++||+|++. |....|+|+|+|+++
T Consensus 67 -l~p~YKa~R~~~pe~L~--------~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~q 137 (259)
T smart00475 67 -LYPEYKANRPKTPDELL--------EQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQ 137 (259)
T ss_pred -hhHHHHhCCCCCCHHHH--------HHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhh
Confidence 23446666654443332 234788999999999999887 7999999999884 778899999999999
Q ss_pred ccCCeEE-EecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHHHH
Q 005869 177 FGCSRII-FKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSYDKVI 253 (672)
Q Consensus 177 FG~~kVI-~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sle~Il 253 (672)
+++++|. ++... +... ...++...+.+.+|++++||+++|+|+| |||+|||||||+|||.+||++|+++|+|+
T Consensus 138 l~~~~v~~~~~~~-~~~~---~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~ 213 (259)
T smart00475 138 LVSDKVSVLDPTK-GIKE---FELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENIL 213 (259)
T ss_pred cCCCCEEEEeccC-CCCc---cEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHH
Confidence 9987664 33322 1110 1125566667789999999999999999 99999999999999999999999999999
Q ss_pred HHhhh
Q 005869 254 KHLKY 258 (672)
Q Consensus 254 ~~L~~ 258 (672)
+++..
T Consensus 214 ~~~~~ 218 (259)
T smart00475 214 ENLDK 218 (259)
T ss_pred HHHHH
Confidence 99864
No 9
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.96 E-value=1.7e-29 Score=266.37 Aligned_cols=239 Identities=19% Similarity=0.240 Sum_probs=185.1
Q ss_pred ccccccccCCEEEeeHHHHHHHHhccCcc--cccCCCcchhHHHHHHHHHHHHH-HcC-CeeEEEEeCCCCchhhHHHHH
Q 005869 16 PIHIKELEGCCVAVDTYSWLHKGALSCSR--ELCKGLPTSRHIDYCMHRVNLLR-HYG-VKPILIFDGGLLPMKIEQENK 91 (672)
Q Consensus 16 ~~~Ls~lkGk~IAIDa~~WLhRg~~sca~--el~~G~pt~~~L~~~~~rI~~Ll-~~g-I~PIfVFDG~~lp~K~~Te~k 91 (672)
...+..++|+.++|||+.|+||++++.+. ....|.++ ..+.+|+..+..++ ... ++|++||||.++++|+++..+
T Consensus 3 ~~~~~~~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~-~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~ 81 (310)
T COG0258 3 EIQLMNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPT-GAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEE 81 (310)
T ss_pred cccchhccCcEEEEechHHHHHHHHhcchhcCCCCCCCc-cHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHH
Confidence 34567788999999999999999887654 23356664 35566666555443 233 999999999999999888776
Q ss_pred HHHHHHHHHHHHHHHHHcCCch-hhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcC
Q 005869 92 RARSRKENLARAIECESEGNSS-ASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITE 170 (672)
Q Consensus 92 Rr~~R~e~l~kA~e~~k~G~~~-eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISe 170 (672)
|+..| .+ .+.++..+...|++.+....+.+|..+|+| +.+|.|+.||+|+ +.|.+++|+|+
T Consensus 82 yK~~R---------------~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~e-add~i~t~A~~a~--~~g~~~~I~S~ 143 (310)
T COG0258 82 YKANR---------------EKEMPDELAPQIPILTELLVALGIPLLELMGIE-ADDPIETLAQKAY--KKGDVVLIISG 143 (310)
T ss_pred HHhCC---------------CccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCC-cchhHHHHHHHHH--hcCCeEEEEeC
Confidence 65444 44 777888888888888888899999999999 8899999999999 88999999999
Q ss_pred CCCeecccCCeEEEecccCCCceEEEeeccccccccccC-CCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 171 DSDLIPFGCSRIIFKMDKFGQGVEFQCSMLQKNKDLSFG-GFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 171 DSDlLlFG~~kVI~kLD~~g~~vei~~~~i~~~~~L~~l-Glt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
|+|+|+|+++++.......+.... .++...+.+.+ |+++.||+|+++|+| |||+|||+|||+|||++||++|+
T Consensus 144 DkD~lql~~~~~~~~~~~~~~~~~----~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~g 219 (310)
T COG0258 144 DKDLLQLVSPNVLVINGKKGEPEK----FLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYG 219 (310)
T ss_pred CcchhhhcCCCcEEEeccCCCCcc----cCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhC
Confidence 999999999986433333222111 24455556667 999999999999999 99999999999999999999999
Q ss_pred CHHHHHHHhhhCCCCCCchhHHH-HHHHHHHcCCC
Q 005869 248 SYDKVIKHLKYSTVSVPPFYEES-FGKAVLTFQHQ 281 (672)
Q Consensus 248 sle~Il~~L~~~~~~vP~~Y~e~-FrkA~~tFkhq 281 (672)
+++.++.++.. ++..+.+. ......+|.+.
T Consensus 220 s~e~i~~~~~~----~~~~~~~~l~~~~~~afl~~ 250 (310)
T COG0258 220 SLEGLYENLDI----IKKKTREKLLEDKEKAFLSK 250 (310)
T ss_pred CHHHHHHhhhh----hcchhhHHHHHHHHHHhcCc
Confidence 99999999862 22222232 44555667774
No 10
>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=99.96 E-value=8.1e-29 Score=253.13 Aligned_cols=203 Identities=18% Similarity=0.226 Sum_probs=159.7
Q ss_pred CEEEeeHHHHHHHHhccCcccc-c-CCCcchhHHHHHHHHHHHHHHcC--CeeEEEEeCCCCchhhHHHHHHHHHHHHHH
Q 005869 25 CCVAVDTYSWLHKGALSCSREL-C-KGLPTSRHIDYCMHRVNLLRHYG--VKPILIFDGGLLPMKIEQENKRARSRKENL 100 (672)
Q Consensus 25 k~IAIDa~~WLhRg~~sca~el-~-~G~pt~~~L~~~~~rI~~Ll~~g--I~PIfVFDG~~lp~K~~Te~kRr~~R~e~l 100 (672)
+.++|||++++||++++..... . .|.++ .++.+++.++..+++.. ..+++||||....+|++..
T Consensus 2 ~~llIDg~~l~yr~~~a~~~~~~~~~g~~t-~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~----------- 69 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALPPLKNSPKGLPT-NAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELY----------- 69 (240)
T ss_pred cEEEEEChHHHHHHHHCCCCcCCCCCCcCc-hHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCccccccc-----------
Confidence 4799999999999988765321 2 57775 78889998888777544 5789999998666655433
Q ss_pred HHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHH----cCCeEEEEcCCCCee
Q 005869 101 ARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAV----SKQVEAVITEDSDLI 175 (672)
Q Consensus 101 ~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~----~G~VDaVISeDSDlL 175 (672)
..|++++.+.+..+. .+...++++|+.+||+++.+| ||||++||+|++ .|...+|+|+|+|++
T Consensus 70 ----p~YK~~R~~~p~~l~--------~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ 137 (240)
T cd00008 70 ----PEYKANRKKMPEELR--------EQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLL 137 (240)
T ss_pred ----HHHHcCCCCCCHHHH--------HHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChh
Confidence 346666554333332 456789999999999999997 799999999986 577889999999999
Q ss_pred cccCCeEEEecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHHHH
Q 005869 176 PFGCSRIIFKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSYDKVI 253 (672)
Q Consensus 176 lFG~~kVI~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sle~Il 253 (672)
++..++|...... +.. .++...+++.+|++++||+++|+|+| |||+|||||||+|||.+||++|+++|+|+
T Consensus 138 ql~~~~v~~~~~~--~~~-----~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~ 210 (240)
T cd00008 138 QLVSDNVKVVSPM--KKK-----LVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGIL 210 (240)
T ss_pred hhCCCCEEEEeCC--Cce-----EEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHH
Confidence 9987766432111 111 24455567789999999999999999 99999999999999999999999999999
Q ss_pred HHhhh
Q 005869 254 KHLKY 258 (672)
Q Consensus 254 ~~L~~ 258 (672)
+++..
T Consensus 211 ~~~~~ 215 (240)
T cd00008 211 ENLDK 215 (240)
T ss_pred HhHHH
Confidence 99874
No 11
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.95 E-value=2.8e-27 Score=247.23 Aligned_cols=207 Identities=19% Similarity=0.280 Sum_probs=159.9
Q ss_pred CCEEEeeHHHHHHHHhccCc-----ccccCCCcchhHHHHHHHHHHHHHH-cC-CeeEEEEeCCCCchhhHHHHHHHHHH
Q 005869 24 GCCVAVDTYSWLHKGALSCS-----RELCKGLPTSRHIDYCMHRVNLLRH-YG-VKPILIFDGGLLPMKIEQENKRARSR 96 (672)
Q Consensus 24 Gk~IAIDa~~WLhRg~~sca-----~el~~G~pt~~~L~~~~~rI~~Ll~-~g-I~PIfVFDG~~lp~K~~Te~kRr~~R 96 (672)
.+.++|||++++||++|+.. .....|.++ ..+.+|++++..+++ ++ -.+++||||....++++.
T Consensus 3 ~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t-~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l-------- 73 (281)
T PRK14976 3 KKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPT-NAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQL-------- 73 (281)
T ss_pred CcEEEEeCcHHHHHHHHccCccCCCccCCCCCCc-hHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccc--------
Confidence 35789999999999988853 123467775 788899999887775 44 468999999766665543
Q ss_pred HHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHHc----CCeEEEEcCC
Q 005869 97 KENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAVS----KQVEAVITED 171 (672)
Q Consensus 97 ~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~~----G~VDaVISeD 171 (672)
+..|+.++...+..+. .+...+.++|+.+||+++.+| ||||++||+|++. |.-..|+|+|
T Consensus 74 -------~p~YKanR~~~p~~l~--------~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~D 138 (281)
T PRK14976 74 -------YDEYKQGRKKTPESLI--------SQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSD 138 (281)
T ss_pred -------cHHHhcCCCCCCHHHH--------HHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence 3446666654333332 346678899999999999999 7999999999874 5556799999
Q ss_pred CCeecccCCeEEEecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH
Q 005869 172 SDLIPFGCSRIIFKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSY 249 (672)
Q Consensus 172 SDlLlFG~~kVI~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sl 249 (672)
+|++++..++|..-....+.. ...++...+.+.+|++++||+++++|+| ||++|||||||+|||.+||++|+++
T Consensus 139 kDl~ql~~~~v~~~~~~~~~~----~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsl 214 (281)
T PRK14976 139 KDLLQLVNENTDVLLKKKGTS----HFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNI 214 (281)
T ss_pred CCcCccCCCCeEEEEecCCCC----cEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCH
Confidence 999999987653211112211 1125566778889999999999999999 9999999999999999999999999
Q ss_pred HHHHHHhhh
Q 005869 250 DKVIKHLKY 258 (672)
Q Consensus 250 e~Il~~L~~ 258 (672)
|+|++++..
T Consensus 215 e~i~~~~~~ 223 (281)
T PRK14976 215 ENIYENIDK 223 (281)
T ss_pred HHHHHhHHH
Confidence 999998863
No 12
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.93 E-value=7.9e-25 Score=257.97 Aligned_cols=203 Identities=19% Similarity=0.221 Sum_probs=159.6
Q ss_pred EEeeHHHHHHHHhccCcc---cccCCCcchhHHHHHHHHHHHHHH-cCC-eeEEEEeCCCCchhhHHHHHHHHHHHHHHH
Q 005869 27 VAVDTYSWLHKGALSCSR---ELCKGLPTSRHIDYCMHRVNLLRH-YGV-KPILIFDGGLLPMKIEQENKRARSRKENLA 101 (672)
Q Consensus 27 IAIDa~~WLhRg~~sca~---el~~G~pt~~~L~~~~~rI~~Ll~-~gI-~PIfVFDG~~lp~K~~Te~kRr~~R~e~l~ 101 (672)
++|||++++||++|+.+. ....|.|| +.+.+|++++..|++ ++- ..++|||+....++++
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t-~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~tfR~~-------------- 66 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPT-NAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHE-------------- 66 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEe-cHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCcchHH--------------
Confidence 689999999999998752 23467776 789999999888775 332 2389999977666543
Q ss_pred HHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHHc----CCeEEEEcCCCCeec
Q 005869 102 RAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAVS----KQVEAVITEDSDLIP 176 (672)
Q Consensus 102 kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~~----G~VDaVISeDSDlLl 176 (672)
.+..|++++...+.++. .++..++++|+.+||+++.+| ||||++||+|++. |+...|+|+|.|+++
T Consensus 67 -~~~~YKa~R~~~Pe~l~--------~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQ 137 (887)
T TIGR00593 67 -AYAEYKANRAPTPEELI--------EQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQ 137 (887)
T ss_pred -HHHHHHhCCCCChHHHH--------HHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhh
Confidence 24456766655443432 246788999999999999888 7999999999884 778899999999999
Q ss_pred ccCCeEE-EecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHHHH
Q 005869 177 FGCSRII-FKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSYDKVI 253 (672)
Q Consensus 177 FG~~kVI-~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sle~Il 253 (672)
+..++|. ++.. .+.. ...++...+++.+|++++||+|+++|+| ||++|||||||+|||.+||++|+++|+|+
T Consensus 138 Lv~~~v~~~~~~-~~~~----~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~ 212 (887)
T TIGR00593 138 LVSDNVKVLIPK-GKTS----FTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIY 212 (887)
T ss_pred cCCCCEEEEecc-CCCC----ceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHH
Confidence 9988763 2221 1111 1125566678889999999999999999 79999999999999999999999999999
Q ss_pred HHhhh
Q 005869 254 KHLKY 258 (672)
Q Consensus 254 ~~L~~ 258 (672)
.++..
T Consensus 213 ~~~~~ 217 (887)
T TIGR00593 213 ENLDQ 217 (887)
T ss_pred HHHHH
Confidence 99864
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=99.92 E-value=1.5e-24 Score=256.52 Aligned_cols=204 Identities=18% Similarity=0.224 Sum_probs=158.8
Q ss_pred CEEEeeHHHHHHHHhccCcc--cccCCCcchhHHHHHHHHHHHHHH-cCC-eeEEEEeCCCCchhhHHHHHHHHHHHHHH
Q 005869 25 CCVAVDTYSWLHKGALSCSR--ELCKGLPTSRHIDYCMHRVNLLRH-YGV-KPILIFDGGLLPMKIEQENKRARSRKENL 100 (672)
Q Consensus 25 k~IAIDa~~WLhRg~~sca~--el~~G~pt~~~L~~~~~rI~~Ll~-~gI-~PIfVFDG~~lp~K~~Te~kRr~~R~e~l 100 (672)
+.++|||++++||++|+... ....|.++ ..+.+|++++..|++ +.. ..++|||+....++++.
T Consensus 3 ~~~liDg~~~~~r~~~a~~~~~~~~~g~~~-~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~~~R~~~------------ 69 (880)
T PRK05755 3 TLLLIDGSSLLFRAFYALLPTLRNSDGLPT-GAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHEL------------ 69 (880)
T ss_pred eEEEEeCcHHHHHHHHCCCCcccCCCCCcc-cHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccc------------
Confidence 46899999999999888632 23467775 788899988887773 333 23899998766555443
Q ss_pred HHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHH----cCCeEEEEcCCCCee
Q 005869 101 ARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAV----SKQVEAVITEDSDLI 175 (672)
Q Consensus 101 ~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~----~G~VDaVISeDSDlL 175 (672)
+..|++++.+.+.++. .++..+.++|+.+||+++.+| ||||++||+|++ .|..+.|+|+|+|++
T Consensus 70 ---~~~YK~~R~~~p~~l~--------~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ 138 (880)
T PRK05755 70 ---YPEYKANRPPMPEDLR--------EQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLL 138 (880)
T ss_pred ---CHHHhCCCCCCcHHHH--------HHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChh
Confidence 3446666654433332 346778899999999999999 799999999985 478889999999999
Q ss_pred cccCCeE--EEecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHH
Q 005869 176 PFGCSRI--IFKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSYDK 251 (672)
Q Consensus 176 lFG~~kV--I~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sle~ 251 (672)
++++++| +..++. .+.. .++...+.+.+|++++||+++|+|+| ||++|||||||+|||.+||++|+++|+
T Consensus 139 ql~~~~v~~~~~~~~-~~~~-----~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~ 212 (880)
T PRK05755 139 QLVDDNVTLLDTMGV-SKNE-----ELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEG 212 (880)
T ss_pred hhCCCCEEEeeccCC-CCCe-----EEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHH
Confidence 9998765 333221 1211 25556667889999999999999999 899999999999999999999999999
Q ss_pred HHHHhhh
Q 005869 252 VIKHLKY 258 (672)
Q Consensus 252 Il~~L~~ 258 (672)
|++++..
T Consensus 213 i~~~~~~ 219 (880)
T PRK05755 213 LYENLDE 219 (880)
T ss_pred HHHhHHH
Confidence 9999863
No 14
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.91 E-value=5.1e-23 Score=212.44 Aligned_cols=198 Identities=17% Similarity=0.222 Sum_probs=154.0
Q ss_pred CEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHH-HcCCe-eEEEEeCCCCc--hhhHHHHHHHHHHHHHH
Q 005869 25 CCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLR-HYGVK-PILIFDGGLLP--MKIEQENKRARSRKENL 100 (672)
Q Consensus 25 k~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll-~~gI~-PIfVFDG~~lp--~K~~Te~kRr~~R~e~l 100 (672)
+.+.|||++++||++++.+. ..|. +..+.+|++.+..++ .++.+ .++|||+.... ++++
T Consensus 4 ~llLiDg~~l~~R~~~a~~~--~~g~--t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~------------- 66 (256)
T PRK09482 4 HLLIIDALNLIRRIHAVQPS--PNDI--NACVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRHQ------------- 66 (256)
T ss_pred eEEEEeCcHHHHHHHhCCCC--CCCc--chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHHH-------------
Confidence 47899999999998887542 3454 577888888877655 56664 56899996443 3222
Q ss_pred HHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHHc----CCeEEEEcCCCCee
Q 005869 101 ARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAVS----KQVEAVITEDSDLI 175 (672)
Q Consensus 101 ~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~~----G~VDaVISeDSDlL 175 (672)
.+..|++++.+.+.++. .++..+.++|..+||+++..| ||||+.||.|+.. |.-..|+|.|.|++
T Consensus 67 --l~p~YKa~R~~~Pe~l~--------~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~ 136 (256)
T PRK09482 67 --LLPDYKAGRKPMPEALQ--------QGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYC 136 (256)
T ss_pred --HhHHHhcCCCCCcHHHH--------HHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCcc
Confidence 34568888766544443 245678999999999999998 7999999999873 55456889999999
Q ss_pred cccCCeEE-EecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHHH
Q 005869 176 PFGCSRII-FKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSYDKV 252 (672)
Q Consensus 176 lFG~~kVI-~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sle~I 252 (672)
+.-.++|. ... .. ...++...+.+.+|++++|++|+++|+| +|++|||||||+|||.+||++|+++|+|
T Consensus 137 Qlv~~~v~~~~~--~~------~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i 208 (256)
T PRK09482 137 QLLSPTIQIRDY--FQ------KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENI 208 (256)
T ss_pred ccCCCCeEEEec--cc------cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHH
Confidence 98766552 222 11 1236667778889999999999999999 9999999999999999999999999999
Q ss_pred HHHhh
Q 005869 253 IKHLK 257 (672)
Q Consensus 253 l~~L~ 257 (672)
++++.
T Consensus 209 ~~~~~ 213 (256)
T PRK09482 209 YESLD 213 (256)
T ss_pred HHhHH
Confidence 99986
No 15
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.90 E-value=2.6e-24 Score=246.98 Aligned_cols=205 Identities=22% Similarity=0.298 Sum_probs=153.2
Q ss_pred cCCCHHHHHHHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecccCCeEEEecccCCCceEEEeecccc
Q 005869 123 VDISPSIAHELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFGCSRIIFKMDKFGQGVEFQCSMLQK 202 (672)
Q Consensus 123 i~ITp~ma~~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD~~g~~vei~~~~i~~ 202 (672)
-.+|++|+.+++++|+.+|||||+||+|||||||.|++.++||+|||+|||.|+||+.+|+++|...++.++. +..
T Consensus 461 ~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~knk~ve~----y~~ 536 (815)
T KOG2520|consen 461 DEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKNKYVEK----YQL 536 (815)
T ss_pred chhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcCcccee----eeh
Confidence 3578999999999999999999999999999999999999999999999999999999999998766665442 444
Q ss_pred ccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHH---HhhhCCCCCCchhHHHHHHHHHHcC
Q 005869 203 NKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIK---HLKYSTVSVPPFYEESFGKAVLTFQ 279 (672)
Q Consensus 203 ~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~---~L~~~~~~vP~~Y~e~FrkA~~tFk 279 (672)
..+...+|+++..++.+|.|+||||+.||+|||+++|+.+|.+|+.-++++. +++..+ ..+..+.....+.. +
T Consensus 537 ~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~-~~~~~~~s~~~~~l---r 612 (815)
T KOG2520|consen 537 DDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTG-PADKEVGSTQQKML---R 612 (815)
T ss_pred HHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhC-ccccccccHHHHHH---H
Confidence 5566789999999999999999999999999999999999999994344322 222111 11111111111110 0
Q ss_pred CCeeeCCCCCceeecCCCCCCCCCCchhhhhhhhcccCCCC---CCCCccccCCCccccccccCCCCCCCCccc
Q 005869 280 HQRVYDPKTEDIVHLSCISDNIGNDLDFLAKGIAIGDLDPF---TQLPFQEVSDNSHLVVGQNSHLKNFKPESE 350 (672)
Q Consensus 280 hq~VfdP~~~~lV~L~~~p~~~~~~ldfla~~IA~G~ldP~---T~~~f~~~~~~~~l~~~~~~~~~~~~~~~~ 350 (672)
++++ ++ .+....+|+...+...+|.|. .++.|.|+.++..+. +.+++....|+...
T Consensus 613 ---------kkl~--n~---~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~pdl~~l-Ref~~~~fgW~~~k 671 (815)
T KOG2520|consen 613 ---------KKLK--NP---KIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGKPDLDIL-REFMKRLFGWPDEK 671 (815)
T ss_pred ---------HHhc--Cc---ccccCcCCCchhHHHHhhCCccCCCcccccCCCCCHHHH-HHHHHHHcCCCccc
Confidence 0000 00 123345788889999999998 789999999876653 34566666776554
No 16
>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=99.90 E-value=4.8e-24 Score=189.86 Aligned_cols=98 Identities=41% Similarity=0.660 Sum_probs=83.2
Q ss_pred CCccccHHHHhhcc--cccccccccCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEe
Q 005869 1 MGIQGLLPLLKSIM--IPIHIKELEGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFD 78 (672)
Q Consensus 1 MGIkGL~~~Lk~~~--~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFD 78 (672)
|||+|||++|++.. ++.++++|+|++|||||++|||+++++|......+...+.|+.++++++..|+.+||+||||||
T Consensus 1 MGI~gL~~~l~~~~~v~~~~~~~l~g~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~gI~PifVFD 80 (101)
T PF00752_consen 1 MGIKGLWQLLKPAAAVRKVSLSELRGKRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRLLEHGIKPIFVFD 80 (101)
T ss_dssp ---TTHHHHCHHHEGEEEEEGGGGTTCEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHHHHTTEEEEEEE-
T ss_pred CCcccHHHHHHhhccCCccCHHHhCCCEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHCCCEEEEEEC
Confidence 99999999999987 8899999999999999999999998888765555444468999999999999999999999999
Q ss_pred CCCCchhhHHHHHHHHHHHH
Q 005869 79 GGLLPMKIEQENKRARSRKE 98 (672)
Q Consensus 79 G~~lp~K~~Te~kRr~~R~e 98 (672)
|.+++.|.+|..+|+++|++
T Consensus 81 G~~~~~K~~~~~~R~~~r~~ 100 (101)
T PF00752_consen 81 GKPPPLKRETIQKRRKRREE 100 (101)
T ss_dssp -STTGGCHHHHHHHHHHHHH
T ss_pred CCCchhhHHHHHHHHHHHhc
Confidence 99999999999999888865
No 17
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.90 E-value=4.2e-24 Score=189.92 Aligned_cols=98 Identities=38% Similarity=0.648 Sum_probs=88.9
Q ss_pred CCccccHHHHhhcccccccccccCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEeCC
Q 005869 1 MGIQGLLPLLKSIMIPIHIKELEGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFDGG 80 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG~ 80 (672)
|||+|||++|++..++.++++|+|++|||||++|||+++++|......+.+...|+.++++++..|+++||+|||||||.
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~g~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l~~~~~rl~~L~~~~I~PifVFDG~ 80 (99)
T smart00485 1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRLLEFGIKPIFVFDGK 80 (99)
T ss_pred CCHhHHHHHHHHhcccCCHHHhCCceEeccHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHCCCeEEEEECCC
Confidence 99999999999999999999999999999999999999888876554444444599999999999999999999999999
Q ss_pred CCchhhHHHHHHHHHHHH
Q 005869 81 LLPMKIEQENKRARSRKE 98 (672)
Q Consensus 81 ~lp~K~~Te~kRr~~R~e 98 (672)
.++.|.+|..+|+++|++
T Consensus 81 ~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 81 PPPLKSETLAKRRERREE 98 (99)
T ss_pred CchhhHHHHHHHHHHHhc
Confidence 999999999999988764
No 18
>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=99.90 E-value=1.6e-24 Score=191.82 Aligned_cols=89 Identities=43% Similarity=0.729 Sum_probs=73.0
Q ss_pred HHcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecccCCeEEEecc-cC-CCc---eEEEeeccccccccccCCCC
Q 005869 138 KQQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFGCSRIIFKMD-KF-GQG---VEFQCSMLQKNKDLSFGGFT 212 (672)
Q Consensus 138 k~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD-~~-g~~---vei~~~~i~~~~~L~~lGlt 212 (672)
+.+||+|++||||||||||||+++|+||+|+|+|||+|+||+++||++++ .. +++ .+..+..++...+++.++|+
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~l~ 80 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILKELGLT 80 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHHHHTTS
T ss_pred CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHHHcCCC
Confidence 57899999999999999999999999999999999999999999999997 43 322 12234557777888899999
Q ss_pred HHHHHHHHHHhCCC
Q 005869 213 KQMLLEMCILSGCD 226 (672)
Q Consensus 213 ~dqFidlcILsGcD 226 (672)
++||+++|+|+|||
T Consensus 81 ~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 81 REQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHHHHHHHET
T ss_pred HHHHHHHheecCCC
Confidence 99999999999998
No 19
>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=99.81 E-value=1.6e-20 Score=221.90 Aligned_cols=146 Identities=25% Similarity=0.367 Sum_probs=110.6
Q ss_pred CCccccHHHHhhcccccccccccCCEEEeeHHHHHHHHhccCcccccCCCc-chhHHHHHHHHHHHHHHcCCeeEEEEeC
Q 005869 1 MGIQGLLPLLKSIMIPIHIKELEGCCVAVDTYSWLHKGALSCSRELCKGLP-TSRHIDYCMHRVNLLRHYGVKPILIFDG 79 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~el~~G~p-t~~~L~~~~~rI~~Ll~~gI~PIfVFDG 79 (672)
|||+|||++|+++.++++|+.|+|++||||||+|||+++.+|... .|.+ ++.||.+||+|+.+|+.+||+|||||||
T Consensus 1 MGI~GLw~ll~~~~r~v~le~l~Gk~vAIDasiWL~q~l~~vr~~--~g~~l~n~hl~g~f~Ri~~Ll~~gI~PVfVFDG 78 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDR--EGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDG 78 (1034)
T ss_pred CChhHHHHHHHHhcccccHHHhCCeEEEechHHHHHHHHHHHHhc--cCCccCCHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence 999999999999999999999999999999999999998777543 2322 4689999999999999999999999999
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHH----HHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEecc
Q 005869 80 GLLPMKIEQENKRARSRKENLARAI----ECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAPY 149 (672)
Q Consensus 80 ~~lp~K~~Te~kRr~~R~e~l~kA~----e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAPY 149 (672)
.+++.|.+|..+|+++|+++.+.+. .++..+-..+|.+.+.++...+++.+..... .+...-.|...|.
T Consensus 79 ~~p~lK~~t~~~R~~rR~~a~~~a~~~~~~ll~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~~~~~d~y~lp~l 151 (1034)
T TIGR00600 79 GAPLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKSTPEALPSVQQ-VPRPQDLYVLPPL 151 (1034)
T ss_pred CCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCccccccccc-ccccCCCccCCCC
Confidence 9999999999999999987665443 4455554556666655544444433222211 1223445555544
No 20
>PHA00439 exonuclease
Probab=99.72 E-value=1.4e-16 Score=166.61 Aligned_cols=195 Identities=14% Similarity=0.173 Sum_probs=136.7
Q ss_pred CCEEEeeHHHHHHHHhccCcc--------cccCCCcchhHHHHHHHHHHHHHHc----CCee-EEEEeCCCCchhhHHHH
Q 005869 24 GCCVAVDTYSWLHKGALSCSR--------ELCKGLPTSRHIDYCMHRVNLLRHY----GVKP-ILIFDGGLLPMKIEQEN 90 (672)
Q Consensus 24 Gk~IAIDa~~WLhRg~~sca~--------el~~G~pt~~~L~~~~~rI~~Ll~~----gI~P-IfVFDG~~lp~K~~Te~ 90 (672)
...+.|||++++||++|+... ....|.++ +.+.+|++.|..+++. +-.+ +++||+ ...++++
T Consensus 6 ~~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t-~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~-~~tfR~e--- 80 (286)
T PHA00439 6 KGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHA-KARQILEDSIKSYKTRKKAWKDAPIVLAFTD-SVNWRKE--- 80 (286)
T ss_pred CcEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeec-cHHHHHHHHHHHHHHhhccCCCCeEEEEECC-CCChHhh---
Confidence 457999999999999998741 23567775 6788888888877643 4444 567995 3333222
Q ss_pred HHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHH----cCC-e
Q 005869 91 KRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAV----SKQ-V 164 (672)
Q Consensus 91 kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~----~G~-V 164 (672)
.+..|++++...... ..+...+.+++..+||+++..| ||||+.|+.|++ .|. -
T Consensus 81 ------------lyp~YKanR~~~p~~---------~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~ 139 (286)
T PHA00439 81 ------------VVPTYKANRKAKRKP---------VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKK 139 (286)
T ss_pred ------------hhhHhcCCCCCCCCc---------hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCe
Confidence 345687777542211 1234566778888999988777 899999999986 354 4
Q ss_pred EEEEcCCCCeecccCCeEEEecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHH
Q 005869 165 EAVITEDSDLIPFGCSRIIFKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHAL 242 (672)
Q Consensus 165 DaVISeDSDlLlFG~~kVI~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kL 242 (672)
..|+|.|.|++++....++.. . .+. + +. ++. -.+++|+++.+|+| +|.+||||||| |||.+|
T Consensus 140 vvIvS~DKDl~QLv~~~~~~~-~-~~~-~-~~---~~~--------~~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kL 203 (286)
T PHA00439 140 AVLVSCDKDFKTIPNCDFLWC-T-TGN-I-LT---QTP--------ETADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAF 203 (286)
T ss_pred EEEEeCCCCHhhcCcceEEEc-c-CCc-e-EE---cCc--------ccHHHHHhhhhcccccccCCCCCCCcC-HHHHHH
Confidence 578999999999864333321 1 111 1 10 111 13899999999999 99999999999 999999
Q ss_pred HHH---hCCHHHHHHHhhhCC
Q 005869 243 ISK---FKSYDKVIKHLKYST 260 (672)
Q Consensus 243 Ikk---y~sle~Il~~L~~~~ 260 (672)
|++ |-.++++++....+|
T Consensus 204 L~~~~~~~~~~~~~~sg~~~~ 224 (286)
T PHA00439 204 LENPYIFEQVEKVLKSGKRKG 224 (286)
T ss_pred HhCccccchhhHHhhcccccc
Confidence 999 667778887765433
No 21
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.69 E-value=2.3e-17 Score=140.75 Aligned_cols=71 Identities=41% Similarity=0.583 Sum_probs=59.6
Q ss_pred HcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecccCCeEEEecccCCC-ceEEEeeccccccccccCCC
Q 005869 139 QQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFGCSRIIFKMDKFGQ-GVEFQCSMLQKNKDLSFGGF 211 (672)
Q Consensus 139 ~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG~~kVI~kLD~~g~-~vei~~~~i~~~~~L~~lGl 211 (672)
.+||+|++||||||||||||+++|+||+|+|+|+|+|+||+++||+++++.++ +.+ +..+++..+++.+|+
T Consensus 2 ~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~--~~~i~~~~vl~~L~l 73 (73)
T smart00484 2 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLE--FRIIDLESVLKELGL 73 (73)
T ss_pred cCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccC--eEEEEHHHHHHHcCC
Confidence 58999999999999999999999999999999999999999999999998764 222 334555666666653
No 22
>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=99.30 E-value=3.6e-12 Score=109.15 Aligned_cols=51 Identities=27% Similarity=0.572 Sum_probs=48.5
Q ss_pred cCCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 208 FGGFTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 208 ~lGlt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
.+|++++||+++|+|+| |||+|||||||+|+|.++|++|+++++++.+++.
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~ 54 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDK 54 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence 47999999999999999 9999999999999999999999999999998863
No 23
>PHA02567 rnh RnaseH; Provisional
Probab=99.29 E-value=1e-10 Score=123.67 Aligned_cols=181 Identities=12% Similarity=0.045 Sum_probs=116.4
Q ss_pred cCCEEEeeHHHHHHHHhccCcccccCCCcchhHH-HHHHHHHHHHHH-cC---CeeEEEEeCCC-CchhhHHHHHHHHHH
Q 005869 23 EGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHI-DYCMHRVNLLRH-YG---VKPILIFDGGL-LPMKIEQENKRARSR 96 (672)
Q Consensus 23 kGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L-~~~~~rI~~Ll~-~g---I~PIfVFDG~~-lp~K~~Te~kRr~~R 96 (672)
+...+.|||++++++.+++. ..-..|.++ ..| ..+++.++.+.. ++ -..+++||+.. ..+ |+
T Consensus 13 ~~~~~LiDgs~i~~~~~~a~-l~~~~~~~~-~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tf-------R~--- 80 (304)
T PHA02567 13 KEGVNLIDFSQIIIATIMAN-FKPKDKINE-AMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYW-------RR--- 80 (304)
T ss_pred CCCEEEEehHHHHHHHHHhh-CCCCCCCcH-HHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCc-------hh---
Confidence 44579999999999998874 211235554 444 346666665432 22 23578999864 222 22
Q ss_pred HHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHH----cCCeEEEEcCC
Q 005869 97 KENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAV----SKQVEAVITED 171 (672)
Q Consensus 97 ~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~----~G~VDaVISeD 171 (672)
+.+..|++++.....++-.+-..+...+-..+.+++..+||+++..| ||||+.+|.|++ .|.-..|+|.|
T Consensus 81 -----elyp~YKAnR~~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~D 155 (304)
T PHA02567 81 -----DIAWYYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSD 155 (304)
T ss_pred -----hhhhHhhcCCCCCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCC
Confidence 24556888876544443211101112222445667788899999877 899999999987 46656889999
Q ss_pred CCeecccC-CeEEEecccCCCceEEEeeccccccccccCCCCHHHHHHHHHHhC--CCCCCCCCC
Q 005869 172 SDLIPFGC-SRIIFKMDKFGQGVEFQCSMLQKNKDLSFGGFTKQMLLEMCILSG--CDYLQSLPG 233 (672)
Q Consensus 172 SDlLlFG~-~kVI~kLD~~g~~vei~~~~i~~~~~L~~lGlt~dqFidlcILsG--cDYlpgIpG 233 (672)
.|++++-. +.|- .++ .+....+...+| .++|++++.+|+| +|.+||||-
T Consensus 156 KDl~QLv~~~~v~-~~~-----------~~~~~~V~~k~G-~P~q~iD~kaL~GDsSDNIPGVp~ 207 (304)
T PHA02567 156 GDFTQLHKYPGVK-QWS-----------PMQKKWVKPKYG-SPEKDLMTKIIKGDKKDGVASIKV 207 (304)
T ss_pred CChhhccCCCCeE-Eee-----------cCCHHHHHHHhC-CHHHHHHHHHhCCcccCCcCCCCC
Confidence 99999953 4331 111 112233445678 5999999999999 899888875
No 24
>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=99.24 E-value=4.4e-11 Score=117.09 Aligned_cols=132 Identities=17% Similarity=0.184 Sum_probs=93.7
Q ss_pred CEEEeeHHHHHHHHhccCcc---cccCCCcchhHHHHHHHHHHHHHH-cCC-eeEEEEeCCCCchhhHHHHHHHHHHHHH
Q 005869 25 CCVAVDTYSWLHKGALSCSR---ELCKGLPTSRHIDYCMHRVNLLRH-YGV-KPILIFDGGLLPMKIEQENKRARSRKEN 99 (672)
Q Consensus 25 k~IAIDa~~WLhRg~~sca~---el~~G~pt~~~L~~~~~rI~~Ll~-~gI-~PIfVFDG~~lp~K~~Te~kRr~~R~e~ 99 (672)
+.+.|||++.+||++|+++. ....|.|+ ..+.++++.|..|+. ++- ..++|||+....++++.
T Consensus 2 ~llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t-~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l----------- 69 (169)
T PF02739_consen 2 KLLLIDGNSLLFRAYYALPKDPLRNSDGEPT-NAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKEL----------- 69 (169)
T ss_dssp EEEEEEHHHHHHHCCCCCTTST-BETTSEB--HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHC-----------
T ss_pred eEEEEechHHHHHHHHhhccCCCcCCCCCCh-HHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHH-----------
Confidence 46899999999999998872 34577776 678888888877654 443 56899999765443332
Q ss_pred HHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEEEec-cchHHHHHHHHH----cCCeEEEEcCCCCe
Q 005869 100 LARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYIVAP-YEADAQMTFLAV----SKQVEAVITEDSDL 174 (672)
Q Consensus 100 l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yIVAP-YEADAQLAyLa~----~G~VDaVISeDSDl 174 (672)
+..|++++.....++. .++..+.++|..+||+++..| ||||+.+|.|++ .|.-..|+|.|.|+
T Consensus 70 ----~p~YKanR~~~p~~l~--------~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~ 137 (169)
T PF02739_consen 70 ----YPEYKANRKPMPEELI--------PQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDL 137 (169)
T ss_dssp ----CTTTTHHHHHHHHHHH--------HHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGG
T ss_pred ----HHHHHhCCCCCCHHHH--------HHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCH
Confidence 2223333322222222 235678889999999999888 999999999988 45666888999999
Q ss_pred ecccCC
Q 005869 175 IPFGCS 180 (672)
Q Consensus 175 LlFG~~ 180 (672)
+++-.+
T Consensus 138 ~QLv~~ 143 (169)
T PF02739_consen 138 LQLVDE 143 (169)
T ss_dssp GGGTCS
T ss_pred HHhcCC
Confidence 999887
No 25
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.66 E-value=2.1e-08 Score=74.80 Aligned_cols=33 Identities=36% Similarity=0.684 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCCcHHHHHHHHHHh
Q 005869 213 KQMLLEMCILSGCDYLQ---SLPGMGLKRAHALISKF 246 (672)
Q Consensus 213 ~dqFidlcILsGcDYlp---gIpGIG~KtA~kLIkky 246 (672)
++||+++|+|+| ||.+ ||||||+|+|++||++|
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 26
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=98.65 E-value=4.9e-07 Score=99.16 Aligned_cols=236 Identities=21% Similarity=0.257 Sum_probs=139.0
Q ss_pred CCccccHHHHhhccccccc-ccccCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEeC
Q 005869 1 MGIQGLLPLLKSIMIPIHI-KELEGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFDG 79 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~~L-s~lkGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG 79 (672)
|||+.|-.+|.+...-..+ ...+++-|=||++++..-.+|+|... ......+..+|+.+...+=+.++..|-
T Consensus 1 MGIKNLK~lLl~~gsL~~i~~~~~~~~ifVD~msif~tiAysv~s~-------~eL~~~~~~~i~~w~~~~~~VtlFvDR 73 (425)
T PF04599_consen 1 MGIKNLKALLLETGSLKKIDNIEKNNEIFVDTMSIFMTIAYSVNSL-------DELRNSFEEYIQQWIKNNGKVTLFVDR 73 (425)
T ss_pred CchhHHHHHHHhcCCceeccCCCCCccEEEEcchhhhhhhhhhCCH-------HHHHHHHHHHHHHHHhcCCeEEEEEec
Confidence 9999999999886533332 33455789999999999988988631 345566777888887667777888899
Q ss_pred CCCchhhHHHHHHHHHHHHHHH------HHHHHHHcC-C-chhhHH-------------HHhhhcCCCHHHHHHHHHHHH
Q 005869 80 GLLPMKIEQENKRARSRKENLA------RAIECESEG-N-SSASYE-------------FYQKAVDISPSIAHELIQVLK 138 (672)
Q Consensus 80 ~~lp~K~~Te~kRr~~R~e~l~------kA~e~~k~G-~-~~eA~e-------------~f~kai~ITp~ma~~li~lLk 138 (672)
+..+.|....++|++.-+...+ ++.+....+ + ..+..+ .|+-...-...+-..+..+|.
T Consensus 74 G~I~iK~~lReKRr~a~k~~~~RK~~~i~~l~~~~~~ld~~d~~yeEikt~~~lki~K~~F~~fla~~~n~k~~l~~~L~ 153 (425)
T PF04599_consen 74 GSINIKEPLREKRRKALKNTIKRKREEIENLEDCIKNLDVDDEFYEEIKTDLELKIQKLSFQLFLANSNNLKTILESSLS 153 (425)
T ss_pred CccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHH
Confidence 9999999888887653222111 111111110 1 111111 111111111112222334444
Q ss_pred H--cCceEEEec-cchHHHHHHHHH-----cCCeEEEEcCCCCeecccC----CeEEEecccCCCceEEEeecccccccc
Q 005869 139 Q--QNVSYIVAP-YEADAQMTFLAV-----SKQVEAVITEDSDLIPFGC----SRIIFKMDKFGQGVEFQCSMLQKNKDL 206 (672)
Q Consensus 139 ~--~GV~yIVAP-YEADAQLAyLa~-----~G~VDaVISeDSDlLlFG~----~kVI~kLD~~g~~vei~~~~i~~~~~L 206 (672)
. .+|+.+-+. ..|+=.|-+=++ .|.=-.++|.|-|.|+|.+ +++|..++. . +. +-.+
T Consensus 154 ~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t~~~---~--Y~---~~P~--- 222 (425)
T PF04599_consen 154 RLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKTMNQ---L--YK---FIPC--- 222 (425)
T ss_pred hccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHhHHh---H--ee---ecCC---
Confidence 3 588888765 577777655444 5766688899999999976 234433321 1 11 1111
Q ss_pred ccCCCCHHHHHHHHHHhCCCCCCCCCCCcH--HHHHHHHHHhC--CHHHHHHHhhh
Q 005869 207 SFGGFTKQMLLEMCILSGCDYLQSLPGMGL--KRAHALISKFK--SYDKVIKHLKY 258 (672)
Q Consensus 207 ~~lGlt~dqFidlcILsGcDYlpgIpGIG~--KtA~kLIkky~--sle~Il~~L~~ 258 (672)
..+.-.=...++.-||||.||+-|+-. ++- +-++-|. ++++|++.|..
T Consensus 223 ---~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l-~~i~LF~dFti~Ni~~SL~~ 274 (425)
T PF04599_consen 223 ---SKSRYLSKLTALVNGCDFFPGLYGISITKKSL-NRIKLFEDFTIDNILQSLAI 274 (425)
T ss_pred ---chHHHHHHHHHHHhcccccCCcceeEechhhc-cceeccccccHHHHHHHHhh
Confidence 112222235667779999999999653 332 1133344 56888888763
No 27
>PF12813 XPG_I_2: XPG domain containing
Probab=98.59 E-value=9.4e-08 Score=99.04 Aligned_cols=91 Identities=21% Similarity=0.233 Sum_probs=70.1
Q ss_pred HHHHHHHHHHHHc---CceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecccC--C-eEE--EecccCC-----CceE
Q 005869 128 SIAHELIQVLKQQ---NVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFGC--S-RII--FKMDKFG-----QGVE 194 (672)
Q Consensus 128 ~ma~~li~lLk~~---GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG~--~-kVI--~kLD~~g-----~~ve 194 (672)
-+...++++|++. |++++++|+|||..||.++++..| +|+|+|||||+|+. + .+| ..+.+.. .+..
T Consensus 4 f~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~ 82 (246)
T PF12813_consen 4 FLVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSY 82 (246)
T ss_pred chHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCe
Confidence 4567889999999 999999999999999999998777 99999999999976 2 232 2444433 2233
Q ss_pred EEeeccccccccccCCCCHHHHHHHHH
Q 005869 195 FQCSMLQKNKDLSFGGFTKQMLLEMCI 221 (672)
Q Consensus 195 i~~~~i~~~~~L~~lGlt~dqFidlcI 221 (672)
+....+....+.+.+|+. +|+.+|.
T Consensus 83 i~~~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 83 ISAKVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred eEEEEEcHHHHHHHcCCc--hhHHHHH
Confidence 455567777888889998 6666655
No 28
>PHA03065 Hypothetical protein; Provisional
Probab=98.56 E-value=1.7e-06 Score=94.59 Aligned_cols=238 Identities=21% Similarity=0.254 Sum_probs=135.2
Q ss_pred CCccccHHHHhhccccccccc-c--cCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEE
Q 005869 1 MGIQGLLPLLKSIMIPIHIKE-L--EGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIF 77 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~~Ls~-l--kGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVF 77 (672)
|||++|-.+|.+...-..++. . ...-|=||+++++.-.+|+|... +.....+..+|+.+....=+.++..
T Consensus 1 MGIKNLKtLLL~~gsL~~~~~~~~~~~~~iFVD~ms~fmsiAysv~~~-------~eL~~~~~~~iq~w~~~~gkVtlFv 73 (438)
T PHA03065 1 MGIKNLKTLLLETGSLTKLDNNLKDRFNGIFVDTMSVFMSIAYSVNNL-------DELRSTFEEYVQQWVKKAGKVTLFV 73 (438)
T ss_pred CchhhHHHHHHhcCCcccccccccccCceEEEechhhhhhhhhhhCCH-------HHHHHHHHHHHHHHHhcCCcEEEEE
Confidence 999999999988654333321 1 22579999999999988988631 2344556677888865556667778
Q ss_pred eCCCCchhhHHHHHHHHHHHHHHHH------HHHH-HHcCC-----chhhHHHHh----hh---cCC-CHHHHH-HHHHH
Q 005869 78 DGGLLPMKIEQENKRARSRKENLAR------AIEC-ESEGN-----SSASYEFYQ----KA---VDI-SPSIAH-ELIQV 136 (672)
Q Consensus 78 DG~~lp~K~~Te~kRr~~R~e~l~k------A~e~-~k~G~-----~~eA~e~f~----ka---i~I-Tp~ma~-~li~l 136 (672)
|-+..+.|....++|++.-+...++ +.+. .+.=+ .++.+...+ |. .-+ .+..++ .+-..
T Consensus 74 DRG~I~IK~~lReKRr~a~~~~~kRK~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F~~fLa~~~nlk~~l~~~ 153 (438)
T PHA03065 74 DRGSIPIKQSLREKRRKASKNTIKRKREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSFQLFLANSNNLKRLLESA 153 (438)
T ss_pred ecCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHcchhhHHHHHHHH
Confidence 9889999999888876543221111 1111 11001 112211111 10 001 111222 23344
Q ss_pred HHHc--CceEEEec-cchHHHHHHHHH-----cCCeEEEEcCCCCeecccC----CeEEEecccCCCceEEEeecccccc
Q 005869 137 LKQQ--NVSYIVAP-YEADAQMTFLAV-----SKQVEAVITEDSDLIPFGC----SRIIFKMDKFGQGVEFQCSMLQKNK 204 (672)
Q Consensus 137 Lk~~--GV~yIVAP-YEADAQLAyLa~-----~G~VDaVISeDSDlLlFG~----~kVI~kLD~~g~~vei~~~~i~~~~ 204 (672)
|... +|+.+-+. -.|+=.|-.=++ .|.=-.+||.|-|.|+|.+ +++|+.++. . +. +-.+
T Consensus 154 L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~KiI~t~~~---~--Y~---~~P~- 224 (438)
T PHA03065 154 LARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKIIKTANQ---L--YK---FIPC- 224 (438)
T ss_pred HHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHHHHhHHH---H--he---eCCC-
Confidence 6666 88888765 466655444333 5776688899999999975 344433321 1 00 1011
Q ss_pred ccccCCCCHHHHHHHHHHhCCCCCCCCCCCcH--HH--HHHHHHHhCCHHHHHHHhhhCC
Q 005869 205 DLSFGGFTKQMLLEMCILSGCDYLQSLPGMGL--KR--AHALISKFKSYDKVIKHLKYST 260 (672)
Q Consensus 205 ~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~--Kt--A~kLIkky~sle~Il~~L~~~~ 260 (672)
..+.-.=...++.-||||.||+-|+.. ++ -++|...| +.++|++.|....
T Consensus 225 -----~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dF-t~~Nv~~SL~~kn 278 (438)
T PHA03065 225 -----AKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDF-TIDNVVRSLAIKN 278 (438)
T ss_pred -----hhHHHHHHHHHHHhcccccCccceEEechhhccceechhhh-hHHHHHHHHHhhh
Confidence 012222234566679999999999653 33 22333332 4688888886443
No 29
>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=98.40 E-value=7.4e-09 Score=93.88 Aligned_cols=48 Identities=23% Similarity=0.488 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 211 FTKQMLLEMCILSG--CDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 211 lt~dqFidlcILsG--cDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++++|++|+..|+| +|.+|||||||+|||.+||++|+|+|+|+.++..
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~ 50 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDE 50 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SS
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHh
Confidence 46899999999999 9999999999999999999999999999988763
No 30
>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=98.39 E-value=3.7e-06 Score=86.98 Aligned_cols=174 Identities=21% Similarity=0.237 Sum_probs=85.9
Q ss_pred CCccccHHHHhhccccc--cccc-c---cCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCee-
Q 005869 1 MGIQGLLPLLKSIMIPI--HIKE-L---EGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKP- 73 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~~~--~Ls~-l---kGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~P- 73 (672)
|||.||+.||....-.. .+.+ . .=--+-||..+.+|..+..+... ........+..++..|..|.. -|+|
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~~~~~~D~LYiDmN~IIH~~~~~~~~~--~~~~~~~~~~~i~~~id~l~~-~v~P~ 77 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENSIPSEFDNLYIDMNGIIHNCIHPNDSS--IPKTEEEIFQRIFNYIDRLVR-IVRPR 77 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTTSEE-ESEEEEETHHHHHHHHS-SSS------SHHHHHHHHHHHHHHHHH-HH-ES
T ss_pred CCHHHHHHHHHHhCCcceeeccccCCCCcCCEEEEEcchhhhHhcCCcccC--CCccHHHHHHHHHHHHHHhhe-eecCc
Confidence 99999999998732111 1111 1 01148899999999975544320 001113456667777777764 3444
Q ss_pred ---EEEEeCCCCchhhHHHHHHHHHHHHHHHHHHHHH--------HcCCchhh---HHHHhhhcCCCH---HHH---HHH
Q 005869 74 ---ILIFDGGLLPMKIEQENKRARSRKENLARAIECE--------SEGNSSAS---YEFYQKAVDISP---SIA---HEL 133 (672)
Q Consensus 74 ---IfVFDG~~lp~K~~Te~kRr~~R~e~l~kA~e~~--------k~G~~~eA---~e~f~kai~ITp---~ma---~~l 133 (672)
++.+||..|-+|..+..+||-+............ .+|..... ...|. ...||| -|. ..|
T Consensus 78 k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fd-sn~ITPGT~FM~~l~~~L 156 (237)
T PF03159_consen 78 KLLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFD-SNCITPGTEFMEKLSDAL 156 (237)
T ss_dssp SEEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS-----GGGSSTTSHHHHHHHHHH
T ss_pred eEEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhccccccccccccccc-cceeccCCHHHHHHHHHH
Confidence 6889999998998776666544332222111111 11111000 01222 233555 222 122
Q ss_pred HHHHH----H----cCceEEEe----ccchHHHHHHHHHc---------CCeEEEEcCCCCeeccc
Q 005869 134 IQVLK----Q----QNVSYIVA----PYEADAQMTFLAVS---------KQVEAVITEDSDLIPFG 178 (672)
Q Consensus 134 i~lLk----~----~GV~yIVA----PYEADAQLAyLa~~---------G~VDaVISeDSDlLlFG 178 (672)
...++ . .++.++++ |+|++--+..+.+. ....+|+|.|+||++++
T Consensus 157 ~~~~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 157 RYYIKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp HHHHHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred HHHHHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 22221 1 26788886 79999987765552 46889999999999987
No 31
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=97.68 E-value=4.8e-06 Score=91.69 Aligned_cols=123 Identities=20% Similarity=0.347 Sum_probs=87.6
Q ss_pred HHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeeccc-CCeEEEecccCCCceEEEeeccccccccccCC
Q 005869 132 ELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFG-CSRIIFKMDKFGQGVEFQCSMLQKNKDLSFGG 210 (672)
Q Consensus 132 ~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG-~~kVI~kLD~~g~~vei~~~~i~~~~~L~~lG 210 (672)
..-+++.+.+|.|+++||-|..|||||+...+|+++.+ .+|.+.+. ++++|..|....+. . ....++.-+.++..-
T Consensus 133 ~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~g-p~d~l~ld~vdr~il~m~fg~d~-P-pl~~~~vp~~lem~l 209 (531)
T COG5366 133 VASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAFG-PSDILLLDGVDRIILDMSFGSDK-P-PLDVFHVPRFLEMFL 209 (531)
T ss_pred cccccccccceEEEehhhHHHHHHHHHHHHHHHHhcCC-chHhHHHhhhhhheeecccCCCC-C-CCcccccchHHHhcc
Confidence 34457888999999999999999999999999999986 99999995 58888777643221 0 111233334555556
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHH---hCCHHHHHHHhh
Q 005869 211 FTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISK---FKSYDKVIKHLK 257 (672)
Q Consensus 211 lt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkk---y~sle~Il~~L~ 257 (672)
.+...|...-.|.|||+++.++.+-.-.+..+.+- ++.-|-..+++.
T Consensus 210 ~s~~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd~~~qElfs~ai~ 259 (531)
T COG5366 210 LSSRLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGDMKGQELFSKAIR 259 (531)
T ss_pred cccchhhhhcccccccccccccccccchhHHHHHHHhccccHHHHHHHhc
Confidence 67788999999999999999998543234444333 334455555554
No 32
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=97.47 E-value=0.0025 Score=75.45 Aligned_cols=238 Identities=16% Similarity=0.262 Sum_probs=130.5
Q ss_pred CCccccHHHHhh-------cccccccccccCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCee
Q 005869 1 MGIQGLLPLLKS-------IMIPIHIKELEGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKP 73 (672)
Q Consensus 1 MGIkGL~~~Lk~-------~~~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~P 73 (672)
|||.-...|+.+ ..+...|-+|-+ +-.|..+.||.+-+..-.+...-.+-......++..|..|-. -|+|
T Consensus 1 MGvPKFfR~iSERyP~lseliee~qIPEFDN--LYLDMNgIlHNCsH~nDddvt~rLtEeEif~~IfnYIdhLf~-~IkP 77 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCLSELIEEHQIPEFDN--LYLDMNGILHNCSHPNDDDVTFRLTEEEIFQEIFNYIDHLFY-LIKP 77 (1493)
T ss_pred CCchHHHHHhhhhchHHHHHhhhccCCcccc--eeeecccccccCCCCCCCccCcCCCHHHHHHHHHHHHHHHHH-hhCc
Confidence 899888777765 223444566666 788999999874333222222222212233455666666543 4665
Q ss_pred ----EEEEeCCCCchhhHHHHHHHHHHHHHHHHHH-HHHHcCCchhhHHHHhhhcCCCHH--HHHHHHH----HHHH---
Q 005869 74 ----ILIFDGGLLPMKIEQENKRARSRKENLARAI-ECESEGNSSASYEFYQKAVDISPS--IAHELIQ----VLKQ--- 139 (672)
Q Consensus 74 ----IfVFDG~~lp~K~~Te~kRr~~R~e~l~kA~-e~~k~G~~~eA~e~f~kai~ITp~--ma~~li~----lLk~--- 139 (672)
++.-||..+..|......||-+.....+++. ++.++|+...- +-|. +..|||. ....+.+ .++.
T Consensus 78 qKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~-erFD-SNcITPGTeFM~rl~~~L~yfIktKis 155 (1493)
T KOG2045|consen 78 QKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPH-ERFD-SNCITPGTEFMVRLQEGLRYFIKTKIS 155 (1493)
T ss_pred ceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcc-cccc-cCCCCCcHHHHHHHHHHHHHHHHhccc
Confidence 4568999999998766655543322222222 33456654322 3342 3456663 2222333 3322
Q ss_pred -----cCceEEE----eccchHHHHHHHHHc---------CCeEEEEcCCCCeecccC-C-----eEEEe---cccCCCc
Q 005869 140 -----QNVSYIV----APYEADAQMTFLAVS---------KQVEAVITEDSDLIPFGC-S-----RIIFK---MDKFGQG 192 (672)
Q Consensus 140 -----~GV~yIV----APYEADAQLAyLa~~---------G~VDaVISeDSDlLlFG~-~-----kVI~k---LD~~g~~ 192 (672)
.++.+|. +|+|.+--+.-+-+. ..-+++++=|-||+++|. . .+++. +......
T Consensus 156 tDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~lLREEVtFgrrn~~ 235 (1493)
T KOG2045|consen 156 TDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRRNKR 235 (1493)
T ss_pred cchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceeeeeeeeeccccccc
Confidence 3778886 589999887665542 245678888999999983 2 23332 2111111
Q ss_pred eEEEeecc---ccc--c---------cccc--CCCCH----HHHHHHHHHhCCCCCCCCCCCcHH-HHHHHH
Q 005869 193 VEFQCSML---QKN--K---------DLSF--GGFTK----QMLLEMCILSGCDYLQSLPGMGLK-RAHALI 243 (672)
Q Consensus 193 vei~~~~i---~~~--~---------~L~~--lGlt~----dqFidlcILsGcDYlpgIpGIG~K-tA~kLI 243 (672)
.+..-+.| +.. + +... +.++- +.|+.++.|+|+||+|.+|++.+. .|+-|+
T Consensus 236 k~lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlpll 307 (1493)
T KOG2045|consen 236 KSLEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLL 307 (1493)
T ss_pred chhhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHH
Confidence 11111111 100 0 0001 11222 467788889999999999999874 366665
No 33
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=97.17 E-value=0.0069 Score=70.34 Aligned_cols=172 Identities=21% Similarity=0.287 Sum_probs=93.6
Q ss_pred CCccccHHHHhhccc-ccc-cc---cccCCEEEeeHHHHHHHHhccCcccccCCCc-c-hhHHHHHHHHHHHHHHcCCee
Q 005869 1 MGIQGLLPLLKSIMI-PIH-IK---ELEGCCVAVDTYSWLHKGALSCSRELCKGLP-T-SRHIDYCMHRVNLLRHYGVKP 73 (672)
Q Consensus 1 MGIkGL~~~Lk~~~~-~~~-Ls---~lkGk~IAIDa~~WLhRg~~sca~el~~G~p-t-~~~L~~~~~rI~~Ll~~gI~P 73 (672)
|||..|..||...-. ..+ |. .=.+--+-.|..+.||-+.... + .-.| + ..-...++..+..++. .|+|
T Consensus 1 MGVPsfFRwlS~r~p~ii~~I~e~~~P~~DNLYLDMNgIlH~CtHp~--d--~~~petEeEm~~aVf~Yidhil~-~irP 75 (953)
T COG5049 1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPN--D--GSPPETEEEMYKAVFEYIDHILL-KIRP 75 (953)
T ss_pred CCchHHHHHHHhhhhHhhhhhhccCCCCcceeEEecccccccCCCCC--C--CCCCCCHHHHHHHHHHHHHHHHH-hcCc
Confidence 999999999976211 111 11 1234568899999888643221 1 1111 1 2223345556665553 4544
Q ss_pred ----EEEEeCCCCchhhHHHHHHHHHHH-HHHHHHHHHHHcCC--chhh-------------HHHHhhhcCCC---HHHH
Q 005869 74 ----ILIFDGGLLPMKIEQENKRARSRK-ENLARAIECESEGN--SSAS-------------YEFYQKAVDIS---PSIA 130 (672)
Q Consensus 74 ----IfVFDG~~lp~K~~Te~kRr~~R~-e~l~kA~e~~k~G~--~~eA-------------~e~f~kai~IT---p~ma 130 (672)
++..||..+..|......||-+.. ++-+-++++..+|. .+++ .+.|. +..|| |-|.
T Consensus 76 rKllymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~fD-SNcITPGTpFMe 154 (953)
T COG5049 76 RKLLYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKFD-SNCITPGTPFME 154 (953)
T ss_pred ceEEEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccccCCccchhhhhhcccc-ccCCCCCChHHH
Confidence 567899999888865444443221 11111122221221 1111 01121 22344 4332
Q ss_pred HHHHHHHHH------------cCceEEEe----ccchHHHHHHHHHc---------CCeEEEEcCCCCeecccC
Q 005869 131 HELIQVLKQ------------QNVSYIVA----PYEADAQMTFLAVS---------KQVEAVITEDSDLIPFGC 179 (672)
Q Consensus 131 ~~li~lLk~------------~GV~yIVA----PYEADAQLAyLa~~---------G~VDaVISeDSDlLlFG~ 179 (672)
.+.+.|+- .+|.+|.+ |+|.+--+.-+-++ ...++|++-|-||+.+|-
T Consensus 155 -rLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGL 227 (953)
T COG5049 155 -RLAKVLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGL 227 (953)
T ss_pred -HHHHHHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeec
Confidence 22222221 37888875 89999998887663 357899999999999985
No 34
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=95.87 E-value=0.11 Score=61.53 Aligned_cols=122 Identities=23% Similarity=0.329 Sum_probs=66.2
Q ss_pred HHHHHHHHHHHHHcCCee----EEEEeCCCCchhhHHHHHHHHHH-HHHHHHHHH-------HHHcCCc---hhhHHHHh
Q 005869 56 IDYCMHRVNLLRHYGVKP----ILIFDGGLLPMKIEQENKRARSR-KENLARAIE-------CESEGNS---SASYEFYQ 120 (672)
Q Consensus 56 L~~~~~rI~~Ll~~gI~P----IfVFDG~~lp~K~~Te~kRr~~R-~e~l~kA~e-------~~k~G~~---~eA~e~f~ 120 (672)
...+|..|..|.. -|.| ++..||-.+-.|......||-+. ++..+++.+ ....|.. ++-.+.|.
T Consensus 78 ~~avFeyiDrlf~-mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fD 156 (931)
T KOG2044|consen 78 FVAVFEYIDRLFS-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFD 156 (931)
T ss_pred HHHHHHHHHHHHH-hccchheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhccccc
Confidence 3444555665543 2333 67899999999987655554322 111111111 1223321 11112221
Q ss_pred -hhcCC-CHHHHHHHHHHHHH------------cCceEEEe----ccchHHHHHHHHHc---------CCeEEEEcCCCC
Q 005869 121 -KAVDI-SPSIAHELIQVLKQ------------QNVSYIVA----PYEADAQMTFLAVS---------KQVEAVITEDSD 173 (672)
Q Consensus 121 -kai~I-Tp~ma~~li~lLk~------------~GV~yIVA----PYEADAQLAyLa~~---------G~VDaVISeDSD 173 (672)
.||.. ||-|.. |-..|+- .||.+|.+ |+|.+--|..+.+. ...+++++-|-|
T Consensus 157 SNcITPGTpFM~~-La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDAD 235 (931)
T KOG2044|consen 157 SNCITPGTPFMDR-LAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDAD 235 (931)
T ss_pred cCccCCCChHHHH-HHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCcc
Confidence 12222 444432 2222221 37888864 89999887776552 358899999999
Q ss_pred eecccC
Q 005869 174 LIPFGC 179 (672)
Q Consensus 174 lLlFG~ 179 (672)
|+.+|-
T Consensus 236 LImLgL 241 (931)
T KOG2044|consen 236 LIMLGL 241 (931)
T ss_pred ceeeec
Confidence 999984
No 35
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=90.38 E-value=0.64 Score=45.80 Aligned_cols=35 Identities=17% Similarity=0.248 Sum_probs=24.9
Q ss_pred cCceEEEec--cchHHHHHHHHHc----CCeEEEEcCCCCe
Q 005869 140 QNVSYIVAP--YEADAQMTFLAVS----KQVEAVITEDSDL 174 (672)
Q Consensus 140 ~GV~yIVAP--YEADAQLAyLa~~----G~VDaVISeDSDl 174 (672)
.||.++.++ -.||..|--|+.. +.-..|+|.|..+
T Consensus 66 ~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~i 106 (166)
T PF05991_consen 66 GGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREI 106 (166)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHH
Confidence 577888776 6899998877662 3455788866654
No 36
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=86.93 E-value=0.52 Score=39.34 Aligned_cols=26 Identities=31% Similarity=0.593 Sum_probs=21.2
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 230 SLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 230 gIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
||||||.++|..|.+.|++++++..+
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~a 32 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMNA 32 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC-
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHc
Confidence 89999999999999999999987644
No 37
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=76.08 E-value=9.9 Score=39.13 Aligned_cols=121 Identities=21% Similarity=0.202 Sum_probs=68.3
Q ss_pred cccccccccCCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEeCCCCc-----hhhHHH
Q 005869 15 IPIHIKELEGCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFDGGLLP-----MKIEQE 89 (672)
Q Consensus 15 ~~~~Ls~lkGk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG~~lp-----~K~~Te 89 (672)
+...+..++|+.|.||||..|--. ..|. .| +.++-=||---. .|....
T Consensus 57 k~~~~~~~rg~~l~iDGyNvLItl-------------------------eSl~-~g-~~vlcdDg~iRDl~~~~gkyk~~ 109 (211)
T COG2454 57 KRMKINSLRGQDLVIDGYNVLITL-------------------------ESLL-KG-EAVLCDDGVIRDLRGVQGKYKIN 109 (211)
T ss_pred hhccCCCcccceEEEechhhhhhH-------------------------HHHh-cC-cEEEecCchhhhhhhhccchhhh
Confidence 456788999999999999876431 1111 12 333333333221 122111
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHHcCceEE-EeccchHHHHHHHHHcCCeEEEE
Q 005869 90 NKRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELIQVLKQQNVSYI-VAPYEADAQMTFLAVSKQVEAVI 168 (672)
Q Consensus 90 ~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~~GV~yI-VAPYEADAQLAyLa~~G~VDaVI 168 (672)
+ .-++++....+.++.-+.....=+|.+.++-+-+++..+.+.+++.+|+.- ..---||..|-.+. +|.
T Consensus 110 E----~t~~Al~lil~~lk~~~~k~vi~L~d~~vs~SGel~~~i~~~mK~~~I~g~~~lvk~~D~eLk~~e------~Va 179 (211)
T COG2454 110 E----KTDKALDLLLEFLKDVEPKSVIFLFDAPVSKSGELAGRIEEKMKSLGIPGEASLVKNADFELKELE------VVA 179 (211)
T ss_pred h----HHHHHHHHHHHHHHHcCCceEEEEeCCCCCccHHHHHHHHHHHHhcCCCceeEeccCcCHHHHhcC------cee
Confidence 1 122344444455555555444444555555556778889999999999933 34456788877222 666
Q ss_pred cCCC
Q 005869 169 TEDS 172 (672)
Q Consensus 169 SeDS 172 (672)
|.|+
T Consensus 180 TsD~ 183 (211)
T COG2454 180 TSDS 183 (211)
T ss_pred ecCe
Confidence 7665
No 38
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.23 E-value=4.1 Score=41.31 Aligned_cols=49 Identities=22% Similarity=0.323 Sum_probs=33.6
Q ss_pred cccccccCCCCHH-HHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhh
Q 005869 202 KNKDLSFGGFTKQ-MLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLK 257 (672)
Q Consensus 202 ~~~~L~~lGlt~d-qFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~ 257 (672)
++.....+||... +--.|..| -+|+|||||+|+.++..|+ .+.++..+.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~ILs~~~-~~~l~~aI~ 103 (194)
T PRK14605 54 REDALSLFGFATTEELSLFETL------IDVSGIGPKLGLAMLSAMN-AEALASAII 103 (194)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHHhCC-HHHHHHHHH
Confidence 4445667898433 33333333 4799999999999999875 667666664
No 39
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.43 E-value=3.8 Score=41.70 Aligned_cols=51 Identities=31% Similarity=0.385 Sum_probs=31.5
Q ss_pred cccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 202 KNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 202 ~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++.....+||....=.++..+ +-++.|||||+|+.++..+ ++++++.++..
T Consensus 53 rEd~~~LyGF~~~~Er~lF~~-----L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~ 103 (197)
T PRK14603 53 REDALSLYGFPDEDSLELFEL-----LLGVSGVGPKLALALLSAL-PPALLARALLE 103 (197)
T ss_pred ccCCceeeCcCCHHHHHHHHH-----HhCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence 334456778754333333222 2468889999998888764 56777777654
No 40
>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=72.91 E-value=3.3 Score=33.62 Aligned_cols=26 Identities=23% Similarity=0.388 Sum_probs=18.6
Q ss_pred CCCCCCcHHHHHHHHHH-hCCHHHHHH
Q 005869 229 QSLPGMGLKRAHALISK-FKSYDKVIK 254 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkk-y~sle~Il~ 254 (672)
-+|.|||++||.+++.+ ++|++++-+
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhcccccHHHHHHHHHhCCCCHHHHhh
Confidence 37899999999999976 889999843
No 41
>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=72.80 E-value=8.3 Score=39.05 Aligned_cols=50 Identities=20% Similarity=0.207 Sum_probs=34.0
Q ss_pred cccccccCCCC-HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 202 KNKDLSFGGFT-KQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 202 ~~~~L~~lGlt-~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++..+..+||. .++--.|..| -+|+|||||+|..++..+ ++++++.++..
T Consensus 53 red~~~LyGF~~~~Er~lF~~L------~~V~GIGpK~Al~iL~~~-~~~el~~aI~~ 103 (191)
T TIGR00084 53 REDAELLFGFNTLEERELFKEL------IKVNGVGPKLALAILSNM-SPEEFVYAIET 103 (191)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHhcC-CHHHHHHHHHh
Confidence 34456778984 3333333333 379999999999998764 57777777764
No 42
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.38 E-value=9.2 Score=39.12 Aligned_cols=51 Identities=24% Similarity=0.333 Sum_probs=34.0
Q ss_pred cccccccCCCC-HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhhC
Q 005869 202 KNKDLSFGGFT-KQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKYS 259 (672)
Q Consensus 202 ~~~~L~~lGlt-~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~~ 259 (672)
++..+..+||. .++--.|-.| -++.|||||+|+.++..+ ++++++.++..+
T Consensus 55 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~-~~~~l~~aI~~~ 106 (203)
T PRK14602 55 REDALELFGFATWDERQTFIVL------ISISKVGAKTALAILSQF-RPDDLRRLVAEE 106 (203)
T ss_pred ecCcceeeCCCCHHHHHHHHHH------hCCCCcCHHHHHHHHhhC-CHHHHHHHHHhC
Confidence 34455678884 3343344444 478999999999999875 567777777543
No 43
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.12 E-value=9.3 Score=38.69 Aligned_cols=50 Identities=16% Similarity=0.250 Sum_probs=31.3
Q ss_pred cccccccCCCCHH-HHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 202 KNKDLSFGGFTKQ-MLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 202 ~~~~L~~lGlt~d-qFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++..+..+||... +--.|..| -++.|||||+|+.++..+ +++++..++..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~AL~iLs~~-~~~el~~aI~~ 104 (188)
T PRK14606 54 SQDGITLYGFSNERKKELFLSL------TKVSRLGPKTALKIISNE-DAETLVTMIAS 104 (188)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence 3445567887433 33333333 368888999988888654 56677766654
No 44
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.58 E-value=9.6 Score=38.81 Aligned_cols=51 Identities=22% Similarity=0.264 Sum_probs=32.3
Q ss_pred cccccccCCCCHH-HHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhhC
Q 005869 202 KNKDLSFGGFTKQ-MLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKYS 259 (672)
Q Consensus 202 ~~~~L~~lGlt~d-qFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~~ 259 (672)
++.....+||... +--.|-.| -++.|||||+|+.++..+ ++++++.++..+
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~-~~~el~~aI~~~ 105 (195)
T PRK14604 54 REDALTLYGFSTPAQRQLFELL------IGVSGVGPKAALNLLSSG-TPDELQLAIAGG 105 (195)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHhC
Confidence 3445567887433 33333333 368899999999998754 567777776543
No 45
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.12 E-value=11 Score=38.14 Aligned_cols=51 Identities=16% Similarity=0.293 Sum_probs=31.4
Q ss_pred cccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 202 KNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 202 ~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++.....+||....=.++..+ +-++.|||||+|+.++..+ ++++++.++..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~-----LisV~GIGpK~Al~iLs~~-~~~~l~~aI~~ 104 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRM-----LVKVSGVNYKTAMSILSKL-TPEQLFSAIVN 104 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHH-----HhCcCCcCHHHHHHHHccC-CHHHHHHHHHc
Confidence 344456778743333332222 2478889999998888765 56777766653
No 46
>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=67.46 E-value=5.1 Score=32.66 Aligned_cols=27 Identities=33% Similarity=0.589 Sum_probs=23.4
Q ss_pred CCCCCCcHHHHHHHHHH-hCCHHHHHHH
Q 005869 229 QSLPGMGLKRAHALISK-FKSYDKVIKH 255 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkk-y~sle~Il~~ 255 (672)
..|||||+++|..|+.. |.+++++...
T Consensus 8 ~~I~Gig~~~a~~L~~~G~~t~~~l~~a 35 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLYEAGIKTLEDLANA 35 (60)
T ss_dssp HTSTTCHHHHHHHHHHTTCSSHHHHHTS
T ss_pred ccCCCCCHHHHHHHHhcCCCcHHHHHcC
Confidence 36999999999999998 8999888643
No 47
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.30 E-value=12 Score=38.30 Aligned_cols=50 Identities=18% Similarity=0.290 Sum_probs=30.7
Q ss_pred cccccccCCCC-HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 202 KNKDLSFGGFT-KQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 202 ~~~~L~~lGlt-~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++..+..+||. .++--.|-.| -++.|||||+|+.++..+ +++++..++..
T Consensus 53 rED~~~LYGF~t~~Er~lF~~L------isVsGIGPK~ALaILs~~-~~~el~~aI~~ 103 (196)
T PRK13901 53 REDELKLFGFLNSSEREVFEEL------IGVDGIGPRAALRVLSGI-KYNEFRDAIDR 103 (196)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCC-CHHHHHHHHHh
Confidence 34445677874 3333333333 368888888888888664 46666666653
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.47 E-value=13 Score=37.48 Aligned_cols=50 Identities=22% Similarity=0.281 Sum_probs=30.7
Q ss_pred cccccccCCCCH-HHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 202 KNKDLSFGGFTK-QMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 202 ~~~~L~~lGlt~-dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++.....+||.. ++--.|-.| -++.|||||+|+.++..+ +++++..++..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~L------i~VsGIGpK~Al~ILs~~-~~~el~~aI~~ 104 (183)
T PRK14601 54 KEDSNKLYGFLDKDEQKMFEML------LKVNGIGANTAMAVCSSL-DVNSFYKALSL 104 (183)
T ss_pred ecCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCC-CHHHHHHHHHh
Confidence 334456778743 333333333 368888888888888654 46677766654
No 49
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=64.34 E-value=5.2 Score=47.44 Aligned_cols=28 Identities=32% Similarity=0.609 Sum_probs=25.2
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+.+|||||+|++.+|++.|+|+++|..+
T Consensus 554 L~~IpGIG~kr~~~LL~~FgSi~~I~~A 581 (624)
T PRK14669 554 LLEIPGVGAKTVQRLLKHFGSLERVRAA 581 (624)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 4589999999999999999999988754
No 50
>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=64.15 E-value=5.8 Score=28.70 Aligned_cols=14 Identities=50% Similarity=0.945 Sum_probs=11.2
Q ss_pred CCCCCcHHHHHHHH
Q 005869 230 SLPGMGLKRAHALI 243 (672)
Q Consensus 230 gIpGIG~KtA~kLI 243 (672)
.|||||+++|..++
T Consensus 15 ~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 15 KLPGIGPKTANAIL 28 (30)
T ss_dssp TSTT-SHHHHHHHH
T ss_pred hCCCcCHHHHHHHH
Confidence 68999999998765
No 51
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=61.09 E-value=7.2 Score=45.80 Aligned_cols=28 Identities=21% Similarity=0.450 Sum_probs=25.1
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+.+|||||+|+...|++.|+|+++|-.+
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~A 543 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFKTLYDFLKA 543 (567)
T ss_pred cccCCCCCHHHHHHHHHHhCCHHHHHhC
Confidence 4689999999999999999999988655
No 52
>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=60.82 E-value=6.6 Score=46.15 Aligned_cols=28 Identities=36% Similarity=0.589 Sum_probs=25.0
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+..|||||+|+...|++.|+|+++|-++
T Consensus 543 Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 543 LLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 4589999999999999999999988654
No 53
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=59.72 E-value=7.9 Score=45.54 Aligned_cols=30 Identities=17% Similarity=0.426 Sum_probs=26.2
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHHh
Q 005869 227 YLQSLPGMGLKRAHALISKFKSYDKVIKHL 256 (672)
Q Consensus 227 YlpgIpGIG~KtA~kLIkky~sle~Il~~L 256 (672)
-+..|||||+++...|++.|+|+++|-.+-
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~As 544 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLLN 544 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhCC
Confidence 456899999999999999999999986553
No 54
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=59.47 E-value=42 Score=32.54 Aligned_cols=47 Identities=11% Similarity=0.019 Sum_probs=25.6
Q ss_pred CCEEEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEeCC
Q 005869 24 GCCVAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFDGG 80 (672)
Q Consensus 24 Gk~IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG~ 80 (672)
.+.|+|||..--+.. . . ...+ -+..+..-+..|+..|.++++||+-.
T Consensus 2 ~r~VVIDG~NVA~~~-~-~-----~~~f---~~~~i~~~v~~~~~rG~~~v~v~~~~ 48 (155)
T PF11977_consen 2 LRPVVIDGSNVAYSH-G-N-----QKFF---SVRGIQIAVEYFKSRGHEVVVVFPPN 48 (155)
T ss_dssp B--EEEEHHHHHHHH-T-T-----TTSE---EHHHHHHHHHHHHHTT---EEEEEEG
T ss_pred CCEEEEeCHHHHhhc-C-C-----CCCc---CHHHHHHHHHHHHHcCCCeEEEEcch
Confidence 467999999764421 0 0 0001 23344445777889999999999964
No 55
>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=55.57 E-value=10 Score=33.25 Aligned_cols=26 Identities=27% Similarity=0.544 Sum_probs=21.3
Q ss_pred CCCCCCCCCCcHHHHHHHHHHhCCHH
Q 005869 225 CDYLQSLPGMGLKRAHALISKFKSYD 250 (672)
Q Consensus 225 cDYlpgIpGIG~KtA~kLIkky~sle 250 (672)
|+-+.+|||||+.+|..|+.+.++++
T Consensus 1 ~~~l~sipGig~~~a~~llaeigd~~ 26 (87)
T PF02371_consen 1 AELLTSIPGIGPITAATLLAEIGDIS 26 (87)
T ss_pred CchhcCCCCccHHHHHHHHHHHcCch
Confidence 34567999999999999998876654
No 56
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=54.34 E-value=10 Score=45.08 Aligned_cols=28 Identities=39% Similarity=0.612 Sum_probs=24.5
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+.+|||||+|+|..|++.|+|++++..+
T Consensus 571 L~~I~GIG~k~a~~Ll~~Fgs~~~i~~A 598 (621)
T PRK14671 571 LTDIAGIGEKTAEKLLEHFGSVEKVAKA 598 (621)
T ss_pred hhcCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 3589999999999999999999887543
No 57
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=54.19 E-value=11 Score=37.99 Aligned_cols=19 Identities=37% Similarity=0.527 Sum_probs=17.7
Q ss_pred CCCCCcHHHHHHHHHHhCC
Q 005869 230 SLPGMGLKRAHALISKFKS 248 (672)
Q Consensus 230 gIpGIG~KtA~kLIkky~s 248 (672)
.|||||+|+|.+++..|+.
T Consensus 77 ~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSP 95 (192)
T ss_pred cCCCCCHHHHHHHHHhCCH
Confidence 5999999999999999986
No 58
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=52.08 E-value=11 Score=25.88 Aligned_cols=17 Identities=35% Similarity=0.716 Sum_probs=14.6
Q ss_pred CCCCCCCcHHHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALIS 244 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIk 244 (672)
+..|||||.++|.+++.
T Consensus 3 L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 3 LLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhCCCCCHHHHHHHHH
Confidence 45799999999998875
No 59
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=51.67 E-value=10 Score=38.30 Aligned_cols=37 Identities=22% Similarity=0.454 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 210 GFTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 210 Glt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
.+++++|.. ||..| -..+..+||||.|||-++|-+.+
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 478888765 45555 45567999999999999986543
No 60
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=51.50 E-value=13 Score=44.58 Aligned_cols=29 Identities=31% Similarity=0.568 Sum_probs=25.5
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 227 YLQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 227 YlpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
-+..|||||+|++..|++.|+|+++|-.+
T Consensus 609 ~L~~IpGiG~kr~~~LL~~FgS~~~i~~A 637 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLAHFGSFRSLQSA 637 (691)
T ss_pred ccccCCCCCHHHHHHHHHHhcCHHHHHhC
Confidence 34689999999999999999999988655
No 61
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.25 E-value=12 Score=37.92 Aligned_cols=41 Identities=29% Similarity=0.407 Sum_probs=29.0
Q ss_pred cccC-CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 206 LSFG-GFTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 206 L~~l-Glt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
|..+ ++++++|..+ |..| -..+..+||||.|||-++|-+.+
T Consensus 87 L~iLs~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 87 LKIISNEDAETLVTM-IASQDVEGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 4434 4688887654 4444 45567999999999999986644
No 62
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=49.05 E-value=13 Score=43.69 Aligned_cols=30 Identities=27% Similarity=0.488 Sum_probs=26.6
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHHHHHHHh
Q 005869 227 YLQSLPGMGLKRAHALISKFKSYDKVIKHL 256 (672)
Q Consensus 227 YlpgIpGIG~KtA~kLIkky~sle~Il~~L 256 (672)
-+..|||||++++.+|++.|+|+++|..+-
T Consensus 526 ~L~~IpGIG~kr~~~LL~~FGS~~~I~~As 555 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRFGSVEGVREAS 555 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 356899999999999999999999998654
No 63
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.79 E-value=12 Score=38.29 Aligned_cols=37 Identities=19% Similarity=0.320 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 210 GFTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 210 Glt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
.+++++|..+ |..| -..+..+||||.|||-++|-+.+
T Consensus 91 ~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 91 GIKYNEFRDA-IDREDIELISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 4688877654 4444 45567999999999999986644
No 64
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.43 E-value=12 Score=38.01 Aligned_cols=36 Identities=31% Similarity=0.410 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 211 FTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 211 lt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
+++++|..+ |..| -..+..+||||+|||-+++-+.+
T Consensus 93 ~~~~el~~a-I~~~D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 93 GTPDELQLA-IAGGDVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 678887654 3333 45567999999999999987644
No 65
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=47.52 E-value=16 Score=38.35 Aligned_cols=28 Identities=32% Similarity=0.520 Sum_probs=24.7
Q ss_pred CCCCCCCcHHHHHHHHHH-hCCHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALISK-FKSYDKVIKH 255 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkk-y~sle~Il~~ 255 (672)
+..|||||+++|.+|++. |+|+++|..+
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 457999999999999999 9999988654
No 66
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=47.12 E-value=15 Score=43.52 Aligned_cols=28 Identities=36% Similarity=0.674 Sum_probs=25.1
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+.+|||||++++.+|++.|+|++++..+
T Consensus 545 L~~IpGIG~k~~k~Ll~~FgS~~~i~~A 572 (598)
T PRK00558 545 LDDIPGIGPKRRKALLKHFGSLKAIKEA 572 (598)
T ss_pred HhhCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 4589999999999999999999988754
No 67
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=45.88 E-value=18 Score=34.89 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=21.0
Q ss_pred CCCCCcHHHHHHHHHH--hCCHHHHHH
Q 005869 230 SLPGMGLKRAHALISK--FKSYDKVIK 254 (672)
Q Consensus 230 gIpGIG~KtA~kLIkk--y~sle~Il~ 254 (672)
.+|||||+.|-++|+. |.++|++++
T Consensus 65 ~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 4799999999999974 778888864
No 68
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.75 E-value=14 Score=37.63 Aligned_cols=41 Identities=27% Similarity=0.417 Sum_probs=28.3
Q ss_pred cccCC-CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 206 LSFGG-FTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 206 L~~lG-lt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
|..+. +++++|..+ |..| -..+..+||||+|||-++|-+.+
T Consensus 86 L~iLs~~~~~~l~~a-I~~~D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 86 LALLSALPPALLARA-LLEGDARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred HHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 44344 788887654 3333 34456899999999999986644
No 69
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.70 E-value=18 Score=36.71 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 211 FTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 211 lt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
+++++|..+ |..| -..+ .+||||.|||-+++-+.+
T Consensus 93 ~~~~~l~~a-I~~~D~~~L-~vpGIGkKtAerIilELk 128 (186)
T PRK14600 93 LTPEQLFSA-IVNEDKAAL-KVNGIGEKLINRIITELQ 128 (186)
T ss_pred CCHHHHHHH-HHcCCHhhe-ECCCCcHHHHHHHHHHHH
Confidence 688887654 4445 4567 899999999999986644
No 70
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=44.83 E-value=17 Score=43.77 Aligned_cols=29 Identities=28% Similarity=0.361 Sum_probs=25.7
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHHh
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKHL 256 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~L 256 (672)
+..|||||++++.+|++.|+|+++|..+-
T Consensus 639 L~~IPGIGpkr~k~LL~~FGSle~I~~AS 667 (694)
T PRK14666 639 LQRVEGIGPATARLLWERFGSLQAMAAAG 667 (694)
T ss_pred HhhCCCCCHHHHHHHHHHhCCHHHHHhcC
Confidence 45799999999999999999999987653
No 71
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=44.81 E-value=19 Score=38.27 Aligned_cols=27 Identities=41% Similarity=0.700 Sum_probs=24.7
Q ss_pred CCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 229 QSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
.++||||.+.|..+++.|+|+++++.+
T Consensus 185 ~s~pgig~~~a~~ll~~fgS~~~~~ta 211 (254)
T COG1948 185 ESIPGIGPKLAERLLKKFGSVEDVLTA 211 (254)
T ss_pred HcCCCccHHHHHHHHHHhcCHHHHhhc
Confidence 478999999999999999999998766
No 72
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=44.13 E-value=29 Score=33.43 Aligned_cols=48 Identities=19% Similarity=0.176 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecc
Q 005869 129 IAHELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPF 177 (672)
Q Consensus 129 ma~~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlF 177 (672)
|+..+-+.|+.+|+..+..+...|..+..++++..- .|+|-|.+++--
T Consensus 8 ~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~R-illTrd~~l~~~ 55 (147)
T PF01927_consen 8 MLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGR-ILLTRDRDLLKR 55 (147)
T ss_pred CHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHHHH
Confidence 456788999999999999998899999999886543 678999997654
No 73
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=43.40 E-value=12 Score=45.73 Aligned_cols=30 Identities=37% Similarity=0.483 Sum_probs=26.3
Q ss_pred CCCCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 226 DYLQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 226 DYlpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+|+-+|||||++.|..|+.+|+|+++++.+
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~si~~l~~a 786 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVKSIRELAKL 786 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 455589999999999999999999998764
No 74
>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=43.11 E-value=58 Score=29.76 Aligned_cols=48 Identities=19% Similarity=0.239 Sum_probs=33.7
Q ss_pred CCCCCCcHHHHHHHHHH-hC--------CHHHHHHHhhh-CCCCCCchhHHHHHHHHH
Q 005869 229 QSLPGMGLKRAHALISK-FK--------SYDKVIKHLKY-STVSVPPFYEESFGKAVL 276 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkk-y~--------sle~Il~~L~~-~~~~vP~~Y~e~FrkA~~ 276 (672)
..|||||+.+|.+|+.- +. +.+.++..++. .|..+.+-.++-|+-|..
T Consensus 15 ~~iP~IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~lc~~~G~~~DpCvldvfr~av~ 72 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLLGIRSPADLKGRDPEELYERLCALTGQRHDPCVLDVFRCAVY 72 (93)
T ss_pred hcCCCccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHHHHHcCCcCCcHHHHHHHHHHH
Confidence 47999999999998853 33 44566666663 466667777777877643
No 75
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=42.85 E-value=45 Score=34.34 Aligned_cols=51 Identities=24% Similarity=0.296 Sum_probs=27.4
Q ss_pred cccccccCCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHhhh
Q 005869 202 KNKDLSFGGFTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISKFKSYDKVIKHLKY 258 (672)
Q Consensus 202 ~~~~L~~lGlt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkky~sle~Il~~L~~ 258 (672)
++.....+||...+=+++..+ +-++.|||||+|+.++.. -+++.+.+++..
T Consensus 54 REd~~~LyGF~~~~ER~lF~~-----LisVnGIGpK~ALaiLs~-~~~~~l~~aI~~ 104 (201)
T COG0632 54 REDAHLLYGFLTEEERELFRL-----LISVNGIGPKLALAILSN-LDPEELAQAIAN 104 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHHH-----HHccCCccHHHHHHHHcC-CCHHHHHHHHHh
Confidence 334455677743322222111 235777777777777753 345666666653
No 76
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.23 E-value=17 Score=37.13 Aligned_cols=36 Identities=22% Similarity=0.345 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 211 FTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 211 lt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
+++++|+. +|..| -..+..+||||.|||-++|-+.+
T Consensus 94 ~~~~~l~~-aI~~~D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 94 FRPDDLRR-LVAEEDVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred CCHHHHHH-HHHhCCHHHHhcCCCcCHHHHHHHHHHHH
Confidence 67777765 34445 45567999999999999986644
No 77
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=39.89 E-value=31 Score=35.55 Aligned_cols=76 Identities=20% Similarity=0.308 Sum_probs=43.7
Q ss_pred CeEEEEcCCCCeecccCC----eEEE-ecccCCCceEEEeeccccccccccC-CCCHHHHHHHHHHhCCCCCCCCCCCcH
Q 005869 163 QVEAVITEDSDLIPFGCS----RIIF-KMDKFGQGVEFQCSMLQKNKDLSFG-GFTKQMLLEMCILSGCDYLQSLPGMGL 236 (672)
Q Consensus 163 ~VDaVISeDSDlLlFG~~----kVI~-kLD~~g~~vei~~~~i~~~~~L~~l-Glt~dqFidlcILsGcDYlpgIpGIG~ 236 (672)
++.-++-||. ..+||-. +-+| .|- .+.-+.....|..+ .++++.|..+-..-=-.++..+||||.
T Consensus 48 ~t~~~vREd~-~~LyGF~~~~ER~lF~~Li--------sVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGk 118 (201)
T COG0632 48 FTHLVVREDA-HLLYGFLTEEERELFRLLI--------SVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGK 118 (201)
T ss_pred EEEEeehhhH-HHHcCCCCHHHHHHHHHHH--------ccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCH
Confidence 4567778888 7788752 2221 110 01111111122222 357777766544444566779999999
Q ss_pred HHHHHHHHHhC
Q 005869 237 KRAHALISKFK 247 (672)
Q Consensus 237 KtA~kLIkky~ 247 (672)
|+|-+++-..+
T Consensus 119 KtAerivleLk 129 (201)
T COG0632 119 KTAERIVLELK 129 (201)
T ss_pred HHHHHHHHHHh
Confidence 99999986644
No 78
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=34.66 E-value=1.2e+02 Score=32.55 Aligned_cols=49 Identities=22% Similarity=0.283 Sum_probs=32.5
Q ss_pred HHHHHHHHHHcCceEEEe-----------ccchHHHHHHHH--------------HcCCeEEEEcCCCCeecccC
Q 005869 130 AHELIQVLKQQNVSYIVA-----------PYEADAQMTFLA--------------VSKQVEAVITEDSDLIPFGC 179 (672)
Q Consensus 130 a~~li~lLk~~GV~yIVA-----------PYEADAQLAyLa--------------~~G~VDaVISeDSDlLlFG~ 179 (672)
+..+.+++.+.||++|.+ |+|-|..+.-.. +.|..--|++ |.++|-=..
T Consensus 69 l~~ile~C~~lGI~~vT~fAFSieNFkRs~eEVd~LM~L~~~k~~~~~~~~~~~~~~gvririiG-dlslL~~~l 142 (271)
T KOG1602|consen 69 LKEILELCKELGIKEVTVFAFSIENFKRSPEEVDGLMDLALEKIERLLEQGEKLDKYGVRIRVIG-DLSLLPESL 142 (271)
T ss_pred HHHHHHHHHHcCCcEEEEEEEehhhhCCCHHHHHHHHHHHHHHHHHHHHHhhhhhhcCeEEEEEc-chhhCCHHH
Confidence 457888999999999864 678887755322 2455556665 666665443
No 79
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=34.09 E-value=75 Score=30.39 Aligned_cols=39 Identities=18% Similarity=0.214 Sum_probs=32.7
Q ss_pred HHHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcC
Q 005869 131 HELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITE 170 (672)
Q Consensus 131 ~~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISe 170 (672)
..+++.++..|+++.+-.....+++.++.+.| ||+|+|+
T Consensus 150 ~~~i~~~~~~g~~v~~wtvn~~~~~~~~~~~G-VdgI~TD 188 (189)
T cd08556 150 PELVRAAHAAGLKVYVWTVNDPEDARRLLALG-VDGIITD 188 (189)
T ss_pred HHHHHHHHHcCCEEEEEcCCCHHHHHHHHHCC-CCEEecC
Confidence 56788899999999988777777888888777 8999984
No 80
>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=30.75 E-value=40 Score=34.17 Aligned_cols=35 Identities=20% Similarity=0.306 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHH
Q 005869 211 FTKQMLLEMCILSGCDYLQSLPGMGLKRAHALISK 245 (672)
Q Consensus 211 lt~dqFidlcILsGcDYlpgIpGIG~KtA~kLIkk 245 (672)
++.++|...+.--=-..+..+||||.|||-+++-+
T Consensus 92 ~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 92 MSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 57777766544322344568999999999998844
No 81
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=29.83 E-value=43 Score=39.64 Aligned_cols=29 Identities=34% Similarity=0.606 Sum_probs=25.5
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHHh
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKHL 256 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~L 256 (672)
+..|||||+++...|++.|+|+++|.++.
T Consensus 532 Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As 560 (581)
T COG0322 532 LDDIPGIGPKRRKALLKHFGSLKGIKSAS 560 (581)
T ss_pred cccCCCcCHHHHHHHHHHhhCHHHHHhcC
Confidence 45899999999999999999998887664
No 82
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=29.69 E-value=45 Score=31.32 Aligned_cols=18 Identities=44% Similarity=0.708 Sum_probs=15.5
Q ss_pred CCCCCCcHHHHHHHHHHh
Q 005869 229 QSLPGMGLKRAHALISKF 246 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkky 246 (672)
..+||||+++|.++|..+
T Consensus 71 ~~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYR 88 (120)
T ss_pred hcCCCCCHHHHHHHHHHH
Confidence 368999999999999764
No 83
>PRK13844 recombination protein RecR; Provisional
Probab=29.33 E-value=73 Score=32.87 Aligned_cols=48 Identities=19% Similarity=0.162 Sum_probs=32.5
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHHhhhCCCCCCchhHHHHHHHHHHcCCCeeeCCCCC
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKHLKYSTVSVPPFYEESFGKAVLTFQHQRVYDPKTE 289 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~L~~~~~~vP~~Y~e~FrkA~~tFkhq~VfdP~~~ 289 (672)
+..+||||+|+|.+|.-. -| ..|+++.+.|-+|....+...-+|+.-+
T Consensus 17 l~~LPGIG~KsA~Rla~~---------lL-----~~~~~~~~~la~~i~~~~~~i~~C~~C~ 64 (200)
T PRK13844 17 LRKLPTIGKKSSQRLALY---------LL-----DKSPETAIAIANSLLDATANIKKCVYCQ 64 (200)
T ss_pred HHHCCCCCHHHHHHHHHH---------HH-----cCCHHHHHHHHHHHHHHHHhCCcCCCCC
Confidence 457899999999887532 11 2355666677777777766666676654
No 84
>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=28.86 E-value=3.9e+02 Score=28.12 Aligned_cols=88 Identities=26% Similarity=0.379 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHcCCe-eEEEEeCCCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCchhhHHHHhhhcCCCHHHHHHHH
Q 005869 56 IDYCMHRVNLLRHYGVK-PILIFDGGLLPMKIEQENKRARSRKENLARAIECESEGNSSASYEFYQKAVDISPSIAHELI 134 (672)
Q Consensus 56 L~~~~~rI~~Ll~~gI~-PIfVFDG~~lp~K~~Te~kRr~~R~e~l~kA~e~~k~G~~~eA~e~f~kai~ITp~ma~~li 134 (672)
+..++.+++..+..|++ ||..|-=-.+-...+.+. ..+.|.+ .|-. -+. .+++.|+-+..++
T Consensus 79 l~~i~emvk~ar~~gvt~PIiLmgYYNPIl~yG~e~--------~iq~ak~---aGan----Gfi--ivDlPpEEa~~~R 141 (268)
T KOG4175|consen 79 LNSIIEMVKEARPQGVTCPIILMGYYNPILRYGVEN--------YIQVAKN---AGAN----GFI--IVDLPPEEAETLR 141 (268)
T ss_pred HHHHHHHHHHhcccCcccceeeeecccHHHhhhHHH--------HHHHHHh---cCCC----ceE--eccCChHHHHHHH
Confidence 34556667777778887 777776555544443221 1112221 1210 010 2578899999999
Q ss_pred HHHHHcCceEE--EeccchHHHHHHHHH
Q 005869 135 QVLKQQNVSYI--VAPYEADAQMTFLAV 160 (672)
Q Consensus 135 ~lLk~~GV~yI--VAPYEADAQLAyLa~ 160 (672)
..++..||.++ +||.--|.-|-.|+.
T Consensus 142 ne~~k~gislvpLvaPsTtdeRmell~~ 169 (268)
T KOG4175|consen 142 NEARKHGISLVPLVAPSTTDERMELLVE 169 (268)
T ss_pred HHHHhcCceEEEeeCCCChHHHHHHHHH
Confidence 99999999987 899998988887765
No 85
>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=27.33 E-value=37 Score=30.74 Aligned_cols=29 Identities=28% Similarity=0.343 Sum_probs=24.4
Q ss_pred ccchHHHHHHHHHcCCeEEEEcCCCCeec
Q 005869 148 PYEADAQMTFLAVSKQVEAVITEDSDLIP 176 (672)
Q Consensus 148 PYEADAQLAyLa~~G~VDaVISeDSDlLl 176 (672)
+-..|+-+..++..+.+|+|+|+|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 45667777888889999999999999874
No 86
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.29 E-value=86 Score=32.27 Aligned_cols=48 Identities=25% Similarity=0.243 Sum_probs=31.0
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHHhhhCCCCCCchhHHHHHHHHHHcCCCeeeCCCCC
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKHLKYSTVSVPPFYEESFGKAVLTFQHQRVYDPKTE 289 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~L~~~~~~vP~~Y~e~FrkA~~tFkhq~VfdP~~~ 289 (672)
+..+||||+|+|.+|.-. -| ..|+++.+.+-+|....+....+|+.-+
T Consensus 13 l~~LPGIG~KsA~RlA~~---------ll-----~~~~~~~~~la~ai~~~~~~i~~C~~C~ 60 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLAFH---------LL-----KRDPSEVLRLAQALLEAKENLRTCSVCG 60 (195)
T ss_pred HHHCCCCCHHHHHHHHHH---------HH-----cCCHHHHHHHHHHHHHHHHcCCcCCCCC
Confidence 457899999999887522 11 2345556666666666666666666654
No 87
>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=26.97 E-value=53 Score=39.41 Aligned_cols=26 Identities=23% Similarity=0.319 Sum_probs=21.1
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 230 SLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 230 gIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
||||||.++|..|.+.|++++++..+
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~~l~~A 527 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLDKLKAA 527 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence 68888888888888888888877543
No 88
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.75 E-value=54 Score=39.62 Aligned_cols=26 Identities=19% Similarity=0.549 Sum_probs=21.1
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 230 SLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 230 gIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+|||||.++|..|++.|++++++..+
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~A 557 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMDA 557 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHhC
Confidence 58888888888888888888877543
No 89
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.25 E-value=41 Score=34.19 Aligned_cols=36 Identities=31% Similarity=0.633 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 005869 211 FTKQMLLEMCILSG-CDYLQSLPGMGLKRAHALISKFK 247 (672)
Q Consensus 211 lt~dqFidlcILsG-cDYlpgIpGIG~KtA~kLIkky~ 247 (672)
+++++|+.. +..+ -..+..+||||.|||-++|-+.+
T Consensus 93 ~~~~~l~~a-I~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 93 MNAEALASA-IISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred CCHHHHHHH-HHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 567766543 3333 23345899999999999876533
No 90
>PRK00076 recR recombination protein RecR; Reviewed
Probab=26.23 E-value=92 Score=32.05 Aligned_cols=48 Identities=21% Similarity=0.134 Sum_probs=30.7
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHHhhhCCCCCCchhHHHHHHHHHHcCCCeeeCCCCC
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKHLKYSTVSVPPFYEESFGKAVLTFQHQRVYDPKTE 289 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~L~~~~~~vP~~Y~e~FrkA~~tFkhq~VfdP~~~ 289 (672)
+..+||||+|+|.++.-. -| ..++++.+.+-+|....+....+|+.-+
T Consensus 13 l~~LPGIG~KsA~Rla~~---------ll-----~~~~~~~~~la~~i~~~~~~i~~C~~C~ 60 (196)
T PRK00076 13 LRKLPGIGPKSAQRLAFH---------LL-----QRDREDVLRLAQALEEAKEKIKHCSVCG 60 (196)
T ss_pred HHHCCCCCHHHHHHHHHH---------HH-----cCCHHHHHHHHHHHHHHHHcCCcCCCCC
Confidence 457899999999887532 11 2344555666666666666666666654
No 91
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=25.18 E-value=60 Score=35.60 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=22.3
Q ss_pred CCCCCCcHHHHHHHHHHhC--CHHHHHHHh
Q 005869 229 QSLPGMGLKRAHALISKFK--SYDKVIKHL 256 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkky~--sle~Il~~L 256 (672)
-.|+|||+|||..|.+ .+ |++++.++.
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 4789999999999988 55 888886654
No 92
>COG2402 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=25.04 E-value=4.8e+02 Score=25.33 Aligned_cols=127 Identities=20% Similarity=0.127 Sum_probs=64.5
Q ss_pred EEeeHHHHHHHHhccCcccccCCCcchhHHHHHHHHHHHHHHcCCeeEEEEeCCCCchhhHHHHHHHHHHHHHHHHHHHH
Q 005869 27 VAVDTYSWLHKGALSCSRELCKGLPTSRHIDYCMHRVNLLRHYGVKPILIFDGGLLPMKIEQENKRARSRKENLARAIEC 106 (672)
Q Consensus 27 IAIDa~~WLhRg~~sca~el~~G~pt~~~L~~~~~rI~~Ll~~gI~PIfVFDG~~lp~K~~Te~kRr~~R~e~l~kA~e~ 106 (672)
+.||++.|+=-+ ...+ ..|... ...+..+..+++.-++|+|-... ++..-+.++...+.....+.
T Consensus 2 v~vDT~~~~a~~---~~~d-------~~H~~a-~~~~~~~~~~~~~~~~~~~~v~~----e~~~l~k~r~~~aa~~l~~~ 66 (135)
T COG2402 2 VLVDTSVLLALF---DKRD-------KNHEAA-VQLFVSLADNKFRRLVVSDHVLD----ETLTLLKKRVVDAAAFLLEA 66 (135)
T ss_pred EEEechHHHHHH---hchh-------hhHHHH-HHHHhhcccCccceEEEeeeeHH----HHHHHHHHhhhhHHHHHHHH
Confidence 679999997432 1111 234332 23344445556667888885422 22222221111111122222
Q ss_pred HHcCCchhhHHHHhhhcCCCHHHHHHHHHHHHH---cCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCeecccCCe
Q 005869 107 ESEGNSSASYEFYQKAVDISPSIAHELIQVLKQ---QNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDLIPFGCSR 181 (672)
Q Consensus 107 ~k~G~~~eA~e~f~kai~ITp~ma~~li~lLk~---~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDlLlFG~~k 181 (672)
...|... .....+.+.......++++ .+.. -+||-...|+++--+.-|+|-|+|+..++..+
T Consensus 67 i~~~~~~-------~~~~~t~~~~~~a~~~~k~~d~~~~d------f~Da~~~ala~k~g~~~ilSfD~dFd~~~~~~ 131 (135)
T COG2402 67 LEEGALE-------IFESVTEELEEAAEAVFKRQDDLGLD------FVDATSVALAEKLGILKILSFDSDFDATDFGR 131 (135)
T ss_pred hccCceE-------EEecccHHHHHHHHHHHHhhcccCCC------HHHHHHHHHHHHcCCCcEEEeccccccccccc
Confidence 3333221 1122333444445555553 4443 36888888888766778889999998877543
No 93
>PRK13766 Hef nuclease; Provisional
Probab=24.65 E-value=60 Score=39.06 Aligned_cols=28 Identities=32% Similarity=0.527 Sum_probs=25.0
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHHHHHHH
Q 005869 228 LQSLPGMGLKRAHALISKFKSYDKVIKH 255 (672)
Q Consensus 228 lpgIpGIG~KtA~kLIkky~sle~Il~~ 255 (672)
+.+|||||+++|.+|++.|+++++++.+
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~~i~~a 744 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTA 744 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 4579999999999999999999988754
No 94
>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=24.44 E-value=73 Score=34.51 Aligned_cols=27 Identities=26% Similarity=0.485 Sum_probs=22.3
Q ss_pred CCCCCCcHHHHHHHHHH--hCCHHHHHHHh
Q 005869 229 QSLPGMGLKRAHALISK--FKSYDKVIKHL 256 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkk--y~sle~Il~~L 256 (672)
-+|+|||+|+|.+|. . +.|++++..+.
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 5 45888887764
No 95
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=23.68 E-value=60 Score=22.19 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=20.3
Q ss_pred HHHHHHHHcCCchhhHHHHhhhcCCCH
Q 005869 101 ARAIECESEGNSSASYEFYQKAVDISP 127 (672)
Q Consensus 101 ~kA~e~~k~G~~~eA~e~f~kai~ITp 127 (672)
..+.-++..|+.++|.++|++++.+.|
T Consensus 6 ~lg~~~~~~~~~~~A~~~~~~al~l~p 32 (34)
T PF07719_consen 6 YLGQAYYQLGNYEEAIEYFEKALELDP 32 (34)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHCc
Confidence 346677889999999999998876544
No 96
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=23.61 E-value=80 Score=30.87 Aligned_cols=26 Identities=54% Similarity=0.853 Sum_probs=19.7
Q ss_pred CCCCCCcHHHHHHHHHH------hCCHHHHHH
Q 005869 229 QSLPGMGLKRAHALISK------FKSYDKVIK 254 (672)
Q Consensus 229 pgIpGIG~KtA~kLIkk------y~sle~Il~ 254 (672)
..+||||+++|-.+|.. |.++|++.+
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 35799999999999853 567776643
No 97
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=22.92 E-value=1.2e+02 Score=28.11 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=27.4
Q ss_pred HHHHH-cCceEE---EeccchHHHHHHHHHcCCeEEEEc
Q 005869 135 QVLKQ-QNVSYI---VAPYEADAQMTFLAVSKQVEAVIT 169 (672)
Q Consensus 135 ~lLk~-~GV~yI---VAPYEADAQLAyLa~~G~VDaVIS 169 (672)
+.|++ .||++- +.|.|.+.+++.+.+.|.+|+||.
T Consensus 38 ~~L~~~~Gi~v~~vk~~~~~g~~~i~~~i~~g~i~~VIn 76 (115)
T cd01422 38 LLIQEATGLTVNRMKSGPLGGDQQIGALIAEGEIDAVIF 76 (115)
T ss_pred HHHHHhhCCcEEEEecCCCCchhHHHHHHHcCceeEEEE
Confidence 35666 788764 234799999999999999999974
No 98
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=21.46 E-value=1.6e+02 Score=29.82 Aligned_cols=42 Identities=21% Similarity=0.308 Sum_probs=30.3
Q ss_pred HHHHHHHHHcCceEEEeccchHHHHHHHHHcCCeEEEEcCCCCe
Q 005869 131 HELIQVLKQQNVSYIVAPYEADAQMTFLAVSKQVEAVITEDSDL 174 (672)
Q Consensus 131 ~~li~lLk~~GV~yIVAPYEADAQLAyLa~~G~VDaVISeDSDl 174 (672)
..+.+.+++.|+++.+-----..++..|.. + ||+|+|++-|.
T Consensus 184 ~~~v~~~~~~G~~v~~WTvn~~~~~~~l~~-~-vdgiiTD~p~~ 225 (226)
T cd08568 184 VELLRLLRKLGLKIVLWTVNDPELVPKLKG-L-VDGVITDDVEK 225 (226)
T ss_pred HHHHHHHHHCCCEEEEEcCCCHHHHHHHHh-h-CCEEEccCccc
Confidence 467788999999988865333345556654 6 99999977664
No 99
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=21.26 E-value=57 Score=22.65 Aligned_cols=27 Identities=22% Similarity=0.447 Sum_probs=20.6
Q ss_pred HHHHHHHHcCCchhhHHHHhhhcCCCH
Q 005869 101 ARAIECESEGNSSASYEFYQKAVDISP 127 (672)
Q Consensus 101 ~kA~e~~k~G~~~eA~e~f~kai~ITp 127 (672)
.+|...+..|+.++|.++|++++.+.|
T Consensus 6 ~~g~~~~~~~~~~~A~~~~~~al~~~p 32 (34)
T PF00515_consen 6 NLGNAYFQLGDYEEALEYYQRALELDP 32 (34)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHHhCCchHHHHHHHHHHHHCc
Confidence 456677888999999999999876554
No 100
>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=21.11 E-value=68 Score=23.40 Aligned_cols=13 Identities=38% Similarity=0.521 Sum_probs=10.4
Q ss_pred CCCCCcHHHHHHH
Q 005869 230 SLPGMGLKRAHAL 242 (672)
Q Consensus 230 gIpGIG~KtA~kL 242 (672)
.++|||.+++.+|
T Consensus 15 ~~~GIG~kt~~kL 27 (32)
T PF11798_consen 15 KFWGIGKKTAKKL 27 (32)
T ss_dssp GSTTS-HHHHHHH
T ss_pred hhCCccHHHHHHH
Confidence 6899999999875
Done!