Query 007971
Match_columns 583
No_of_seqs 296 out of 1451
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 17:46:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007971.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007971hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00217 flap endonuclease-1; 100.0 7.1E-61 1.5E-65 512.4 28.7 310 1-351 1-332 (393)
2 cd00128 XPG Xeroderma pigmento 100.0 5.9E-58 1.3E-62 478.6 27.3 302 1-343 1-311 (316)
3 TIGR03674 fen_arch flap struct 100.0 2.1E-55 4.5E-60 463.1 27.0 301 1-352 1-326 (338)
4 KOG2519 5'-3' exonuclease [Rep 100.0 2.3E-54 4.9E-59 456.4 21.3 397 1-441 1-419 (449)
5 PRK03980 flap endonuclease-1; 100.0 4.2E-49 9.2E-54 407.1 24.2 258 48-354 5-281 (292)
6 KOG2518 5'-3' exonuclease [Rep 100.0 2.2E-44 4.7E-49 384.2 16.9 237 1-239 1-249 (556)
7 TIGR00600 rad2 DNA excision re 100.0 1.3E-41 2.7E-46 393.4 20.5 224 111-353 763-989 (1034)
8 KOG2520 5'-3' exonuclease [Rep 100.0 2.8E-41 6.1E-46 379.5 16.9 238 111-364 457-694 (815)
9 smart00475 53EXOc 5'-3' exonuc 100.0 1.1E-32 2.3E-37 280.9 24.1 206 25-247 2-219 (259)
10 cd00008 53EXOc 5'-3' exonuclea 100.0 1.7E-31 3.7E-36 269.5 24.3 201 25-247 2-216 (240)
11 PRK14976 5'-3' exonuclease; Pr 100.0 1.8E-30 4E-35 267.4 24.4 206 24-247 3-224 (281)
12 COG0258 Exo 5'-3' exonuclease 100.0 5.9E-30 1.3E-34 267.2 19.8 216 17-245 4-229 (310)
13 PRK09482 flap endonuclease-lik 100.0 7E-28 1.5E-32 244.4 23.8 206 25-254 4-222 (256)
14 TIGR00593 pola DNA polymerase 100.0 1.1E-27 2.4E-32 278.7 23.3 202 27-247 2-218 (887)
15 PRK05755 DNA polymerase I; Pro 100.0 3.1E-27 6.8E-32 276.9 25.4 203 25-247 3-220 (880)
16 PF00867 XPG_I: XPG I-region; 99.9 3.1E-24 6.8E-29 186.9 7.0 86 130-215 1-94 (94)
17 smart00485 XPGN Xeroderma pigm 99.9 1E-22 2.2E-27 178.5 7.5 96 1-96 1-98 (99)
18 PF00752 XPG_N: XPG N-terminal 99.9 1.2E-22 2.6E-27 178.5 7.4 95 1-95 1-99 (101)
19 PHA00439 exonuclease 99.8 3.3E-19 7.2E-24 182.9 17.6 179 24-234 6-206 (286)
20 TIGR00600 rad2 DNA excision re 99.8 2.2E-19 4.8E-24 209.2 6.9 97 1-97 1-98 (1034)
21 smart00484 XPGI Xeroderma pigm 99.7 5.3E-18 1.2E-22 141.2 8.0 70 131-200 2-73 (73)
22 PHA02567 rnh RnaseH; Provision 99.6 1E-13 2.2E-18 143.3 18.9 181 23-222 13-207 (304)
23 PF02739 5_3_exonuc_N: 5'-3' e 99.5 1E-14 2.2E-19 140.3 8.6 155 25-198 2-169 (169)
24 cd00080 HhH2_motif Helix-hairp 99.2 8.1E-12 1.8E-16 104.7 5.4 50 197-246 2-54 (75)
25 smart00279 HhH2 Helix-hairpin- 98.8 4.6E-09 1E-13 75.9 4.0 33 202-235 1-36 (36)
26 PF12813 XPG_I_2: XPG domain c 98.7 1.1E-07 2.3E-12 97.0 10.3 87 121-210 5-107 (246)
27 PF01367 5_3_exonuc: 5'-3' exo 98.6 8.5E-10 1.8E-14 97.7 -5.4 48 200-247 1-51 (101)
28 PF03159 XRN_N: XRN 5'-3' exon 97.9 7.5E-05 1.6E-09 75.9 10.6 171 1-171 1-223 (237)
29 PF04599 Pox_G5: Poxvirus G5 p 97.6 0.00056 1.2E-08 74.1 12.8 212 1-224 1-248 (425)
30 PHA03065 Hypothetical protein; 97.5 0.00099 2.1E-08 71.8 12.0 229 1-242 1-272 (438)
31 COG5366 Protein involved in pr 97.1 0.00021 4.6E-09 77.3 1.5 112 125-237 134-247 (531)
32 PF00385 Chromo: Chromo (CHRro 96.5 0.0025 5.5E-08 49.7 3.2 50 383-432 3-55 (55)
33 COG5049 XRN1 5'-3' exonuclease 96.2 0.094 2E-06 60.0 14.4 92 133-224 176-327 (953)
34 smart00298 CHROMO Chromatin or 95.6 0.015 3.3E-07 44.7 3.8 50 383-433 4-54 (55)
35 cd00024 CHROMO Chromatin organ 95.0 0.024 5.2E-07 43.6 3.2 49 383-432 5-55 (55)
36 KOG2045 5'-3' exonuclease XRN1 93.7 0.61 1.3E-05 55.1 11.9 230 1-233 1-308 (1493)
37 KOG2044 5'-3' exonuclease HKE1 92.3 1.1 2.3E-05 52.5 11.2 92 133-224 190-351 (931)
38 PF05991 NYN_YacP: YacP-like N 92.3 0.33 7.2E-06 46.8 6.3 99 27-166 1-106 (166)
39 KOG1911 Heterochromatin-associ 89.2 0.29 6.4E-06 50.7 3.0 56 382-438 50-105 (270)
40 PF12826 HHH_2: Helix-hairpin- 89.1 0.33 7.1E-06 39.4 2.6 23 219-241 7-29 (64)
41 PRK14605 ruvA Holliday junctio 88.3 0.81 1.8E-05 45.4 5.3 66 183-254 42-112 (194)
42 PRK14602 ruvA Holliday junctio 88.0 0.79 1.7E-05 45.8 5.1 68 183-256 43-115 (203)
43 TIGR00084 ruvA Holliday juncti 87.0 0.95 2.1E-05 44.8 4.9 65 183-253 41-110 (191)
44 PRK00116 ruvA Holliday junctio 86.0 0.88 1.9E-05 44.9 4.1 31 219-249 77-107 (192)
45 PRK13901 ruvA Holliday junctio 85.8 1.1 2.5E-05 44.5 4.8 68 183-256 41-113 (196)
46 KOG2748 Uncharacterized conser 85.5 0.44 9.6E-06 50.6 1.8 62 383-446 13-77 (369)
47 PRK14603 ruvA Holliday junctio 85.5 1.1 2.3E-05 44.6 4.4 68 183-256 41-113 (197)
48 PRK14601 ruvA Holliday junctio 85.3 1.1 2.4E-05 44.0 4.4 68 183-256 42-114 (183)
49 PRK14606 ruvA Holliday junctio 85.2 1.2 2.6E-05 44.1 4.5 68 183-256 42-114 (188)
50 PRK14604 ruvA Holliday junctio 83.7 1.4 3.1E-05 43.7 4.4 68 183-256 42-114 (195)
51 PF00633 HHH: Helix-hairpin-he 79.8 1.5 3.1E-05 30.6 2.0 15 219-233 15-29 (30)
52 COG0632 RuvA Holliday junction 78.8 5 0.00011 40.2 6.2 62 189-256 52-114 (201)
53 COG2454 Uncharacterized conser 77.5 11 0.00025 37.6 8.2 26 13-38 55-80 (211)
54 PRK14600 ruvA Holliday junctio 76.5 1.6 3.5E-05 43.0 2.1 55 192-252 55-110 (186)
55 PF11977 RNase_Zc3h12a: Zc3h12 67.8 24 0.00053 33.4 7.8 47 24-78 2-48 (155)
56 smart00278 HhH1 Helix-hairpin- 63.9 5.6 0.00012 26.4 1.9 18 217-234 3-20 (26)
57 PF10391 DNA_pol_lambd_f: Fing 62.2 8.7 0.00019 30.2 3.0 21 219-239 6-27 (52)
58 PF02371 Transposase_20: Trans 59.8 7 0.00015 33.4 2.3 23 216-238 3-25 (87)
59 PRK14601 ruvA Holliday junctio 59.6 7.8 0.00017 38.2 2.9 36 199-235 92-128 (183)
60 PRK14671 uvrC excinuclease ABC 53.4 12 0.00025 43.7 3.4 26 218-243 572-597 (621)
61 cd00034 ChSh Chromo Shadow Dom 53.4 26 0.00056 27.6 4.3 38 394-434 14-51 (54)
62 PRK13901 ruvA Holliday junctio 52.3 9.6 0.00021 38.0 2.2 36 199-235 91-127 (196)
63 PRK14604 ruvA Holliday junctio 50.9 10 0.00023 37.6 2.2 39 196-235 88-128 (195)
64 PRK14606 ruvA Holliday junctio 50.8 11 0.00023 37.4 2.2 40 195-235 87-128 (188)
65 PRK14602 ruvA Holliday junctio 49.4 13 0.00029 37.1 2.7 35 200-235 94-129 (203)
66 PRK14669 uvrC excinuclease ABC 49.3 14 0.0003 43.1 3.2 23 218-240 555-577 (624)
67 PRK14603 ruvA Holliday junctio 48.3 12 0.00026 37.3 2.1 40 195-236 86-128 (197)
68 PRK14667 uvrC excinuclease ABC 48.3 16 0.00035 42.0 3.5 23 218-240 517-539 (567)
69 PF14520 HHH_5: Helix-hairpin- 47.3 16 0.00035 28.9 2.4 21 219-239 9-30 (60)
70 COG0632 RuvA Holliday junction 47.2 19 0.00041 36.1 3.3 36 200-235 93-128 (201)
71 PRK14600 ruvA Holliday junctio 47.1 16 0.00034 36.2 2.7 39 195-235 87-127 (186)
72 PRK14670 uvrC excinuclease ABC 45.2 20 0.00043 41.5 3.5 24 217-240 516-539 (574)
73 TIGR00194 uvrC excinuclease AB 44.5 20 0.00043 41.4 3.4 25 218-242 544-568 (574)
74 smart00300 ChSh Chromo Shadow 39.4 39 0.00085 27.2 3.5 40 392-434 18-57 (61)
75 COG0353 RecR Recombinational D 39.4 29 0.00063 34.6 3.2 17 218-234 15-31 (198)
76 PF11798 IMS_HHH: IMS family H 39.3 21 0.00046 25.0 1.7 14 219-232 15-28 (32)
77 PRK14672 uvrC excinuclease ABC 38.1 30 0.00064 40.8 3.5 24 218-241 611-634 (691)
78 COG0258 Exo 5'-3' exonuclease 37.9 27 0.00059 36.8 3.0 48 108-155 82-132 (310)
79 TIGR03090 SASP_tlp small, acid 35.6 6.8 0.00015 32.7 -1.5 53 529-581 1-66 (70)
80 PRK00558 uvrC excinuclease ABC 34.2 35 0.00076 39.6 3.3 22 218-239 546-567 (598)
81 PRK12766 50S ribosomal protein 32.7 41 0.00089 34.4 3.2 22 218-239 6-28 (232)
82 PF01393 Chromo_shadow: Chromo 31.7 85 0.0018 25.1 4.2 46 386-433 8-53 (58)
83 TIGR02765 crypto_DASH cryptoch 30.8 1.1E+02 0.0024 33.7 6.4 41 121-161 62-102 (429)
84 PRK00076 recR recombination pr 30.7 73 0.0016 31.9 4.5 17 218-234 14-30 (196)
85 TIGR00084 ruvA Holliday juncti 30.3 41 0.00089 33.3 2.7 33 201-234 93-126 (191)
86 TIGR00615 recR recombination p 29.8 78 0.0017 31.6 4.5 17 218-234 14-30 (195)
87 TIGR01259 comE comEA protein. 28.3 77 0.0017 28.9 3.9 17 219-235 72-88 (120)
88 TIGR00575 dnlj DNA ligase, NAD 27.5 53 0.0012 38.6 3.4 21 219-239 502-522 (652)
89 PRK14351 ligA NAD-dependent DN 26.8 57 0.0012 38.6 3.5 21 219-239 532-552 (689)
90 TIGR01448 recD_rel helicase, p 25.8 52 0.0011 39.1 2.9 34 199-238 74-107 (720)
91 PRK14668 uvrC excinuclease ABC 25.7 63 0.0014 37.4 3.5 23 217-239 527-549 (577)
92 PRK14666 uvrC excinuclease ABC 25.7 60 0.0013 38.3 3.4 22 218-239 640-661 (694)
93 PRK13844 recombination protein 24.9 1.1E+02 0.0025 30.7 4.7 17 218-234 18-34 (200)
94 PRK10674 deoxyribodipyrimidine 23.5 2.1E+02 0.0045 32.2 7.0 11 68-78 30-40 (472)
95 cd08556 GDPD Glycerophosphodie 23.4 1.1E+02 0.0024 28.7 4.3 40 123-163 150-189 (189)
96 COG1663 LpxK Tetraacyldisaccha 22.6 3.8E+02 0.0081 29.1 8.3 93 46-164 58-150 (336)
97 TIGR03556 photolyase_8HDF deox 22.4 2.2E+02 0.0048 31.9 7.0 39 123-161 58-96 (471)
98 COG1948 MUS81 ERCC4-type nucle 22.4 77 0.0017 33.0 3.0 21 219-239 186-206 (254)
99 TIGR00305 probable toxin-antit 22.1 54 0.0012 29.0 1.7 29 140-168 85-113 (114)
100 TIGR00591 phr2 photolyase PhrI 21.9 2.4E+02 0.0051 31.4 7.1 13 67-79 53-65 (454)
101 COG0322 UvrC Nuclease subunit 21.8 78 0.0017 36.8 3.3 24 218-241 533-556 (581)
102 PF01927 Mut7-C: Mut7-C RNAse 21.2 86 0.0019 29.5 2.9 45 122-167 9-53 (147)
103 TIGR02766 crypt_chrom_pln cryp 21.0 2.3E+02 0.0049 31.8 6.7 11 68-78 24-34 (475)
104 TIGR00114 lumazine-synth 6,7-d 20.8 2.4E+02 0.0052 26.6 5.8 46 116-161 13-65 (138)
105 PRK02515 psbU photosystem II c 20.7 1.2E+02 0.0026 28.5 3.6 27 219-245 65-93 (132)
106 PRK14605 ruvA Holliday junctio 20.6 62 0.0014 32.1 1.9 34 200-235 93-128 (194)
107 TIGR00596 rad1 DNA repair prot 20.3 53 0.0012 39.6 1.6 27 215-241 757-783 (814)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=7.1e-61 Score=512.43 Aligned_cols=310 Identities=20% Similarity=0.326 Sum_probs=267.2
Q ss_pred CCccchHHHHhh----hcccccccccCCCEEEeeHHHHHHHhhcccCC--C------CCCCchhHHHHHHHHHHHHHHcC
Q 007971 1 MGVKNLWDILES----CKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKS--Y------RPQTDKLFLRGLFHRLRALIALN 68 (583)
Q Consensus 1 MGIkgL~~~L~~----~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~--~------~g~~~~~~Lr~lf~rl~~Ll~~g 68 (583)
|||+||+++|++ +.++++|+.|+|++|||||++||||++++++. . ..|.+++||++||+|+.+|+++|
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~g 80 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEAG 80 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHCC
Confidence 999999999986 46889999999999999999999999987653 1 12456799999999999999999
Q ss_pred CEEEEEEcCCCCcchhhhhHhhhhcCcccc------cccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCccc
Q 007971 69 CGLIFVSDGSIPAIKLSTYRRRLNSGSEVT------QDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEE 142 (583)
Q Consensus 69 I~PIFVFDG~~P~~K~~t~~~R~~~r~~a~------~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~E 142 (583)
|+|||||||.+|++|..++.+|++.|.++. .+.++.+.+.++.+....++..++..++++|+.|||||++||||
T Consensus 81 ikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~E 160 (393)
T PTZ00217 81 IKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCE 160 (393)
T ss_pred CCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcC
Confidence 999999999999999999999998886543 23566677777776666788999999999999999999999999
Q ss_pred HHHHHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccC--CCceEEEEeHHHHHHHhCCChHHHHHHHHHhCCCCCCCC
Q 007971 143 AEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLG--ERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGV 220 (583)
Q Consensus 143 ADAqcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~--~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G~DY~pGv 220 (583)
||||||+|++.|+||+|+|+|+|+|+||++.++++++.. ....+++|+++.+.+.+|++++||+++|+|+||||+|||
T Consensus 161 Adaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi 240 (393)
T PTZ00217 161 AEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTI 240 (393)
T ss_pred HHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCC
Confidence 999999999999999999999999999999999998752 234578999999999999999999999999999999999
Q ss_pred CCCCHHHHHHHHHHcCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCCccccccccccccCCCCCCCCCCCcHHHHHH
Q 007971 221 RGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDA 299 (583)
Q Consensus 221 pGiG~ktA~~Li~~~g~~~-il~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~e~~~~~~~~~~~~~fP~~~Vi~~ 299 (583)
||||+|||++||++||+++ ++++++.. +..+|++||+.++.+.
T Consensus 241 ~GIG~ktA~~Li~~~gsle~il~~~~~~------------------------------------k~~~p~~~~~~~~~~~ 284 (393)
T PTZ00217 241 KGIGPKTAYKLIKKYKSIEEILEHLDKT------------------------------------KYPVPENFDYKEAREL 284 (393)
T ss_pred CCccHHHHHHHHHHcCCHHHHHHHHHhc------------------------------------CCCCCCCCChHHHHHH
Confidence 9999999999999999984 66655421 1235779999999999
Q ss_pred hcCCccCCCC-hHHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhhhhHH
Q 007971 300 YSNPKCYSAD-SEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIA 351 (583)
Q Consensus 300 Yl~P~v~~~~-~~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP~l~ 351 (583)
|++|.|..+. .++.| .+.+...|++||.+.++|+.+++++.|-++.+
T Consensus 285 f~~p~V~~~~~~~l~w-----~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~ 332 (393)
T PTZ00217 285 FLNPEVTPAEEIDLKW-----NEPDEEGLKKFLVKEKNFNEERVEKYIERLKK 332 (393)
T ss_pred hcCCCcCCCCCCCCCC-----CCCCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Confidence 9999998643 22222 24578899999999999999999998765543
No 2
>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=5.9e-58 Score=478.55 Aligned_cols=302 Identities=29% Similarity=0.470 Sum_probs=254.5
Q ss_pred CCccchHHHHhhhcccccccccCCCEEEeeHHHHHHHhhcccCCC--CCCCchhHHHHHHHHHHHHHHcCCEEEEEEcCC
Q 007971 1 MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSY--RPQTDKLFLRGLFHRLRALIALNCGLIFVSDGS 78 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~--~g~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~ 78 (583)
|||+|||+||+++.+..+|++|+|++|||||++||||++++.+.. .++.+++++.++++++.+|+++||+|||||||.
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 999999999999988899999999999999999999999886543 346678999999999999999999999999999
Q ss_pred CCcchhhhhHhhhhcCccccc------ccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHHHHHHHHH
Q 007971 79 IPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNL 152 (583)
Q Consensus 79 ~P~~K~~t~~~R~~~r~~a~~------~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~ 152 (583)
.|++|..+..+|++.+.++.. +.++.+++.++.+.....+..++..++++|+.+||||++||||||||||+|++
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 999999998888776654321 23344555555555556778899999999999999999999999999999999
Q ss_pred cCCeeEEecCCCcEEeecCcEEEEEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHH
Q 007971 153 ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIV 232 (583)
Q Consensus 153 ~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li 232 (583)
.|.||+|+|+|+|+|+||+++|+++++......+++|+.+.+.+.+|++++||+++|+|+||||+|||||||+|||++||
T Consensus 161 ~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv~giG~k~A~~li 240 (316)
T cd00128 161 KGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLGCDYTEGIPGIGPVTALKLI 240 (316)
T ss_pred CCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHH
Confidence 99999999999999999999999998753214788999999999999999999999999999999999999999999999
Q ss_pred HHcCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCCccccccccccccCCCCCCCCCCCcHHHHHHhcCCccCCCChH
Q 007971 233 KSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSE 311 (583)
Q Consensus 233 ~~~g~~~-il~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~e~~~~~~~~~~~~~fP~~~Vi~~Yl~P~v~~~~~~ 311 (583)
++||+++ +++++... ....+.+||...+.++|.+|.|+.....
T Consensus 241 ~~~~~~~~~~~~l~~~------------------------------------~~~~~~~~~~~~~~~~f~~p~~~~~~~~ 284 (316)
T cd00128 241 KKYGDIEKDIERLKKK------------------------------------LYRSPEDFPLKEAREFFLNPEVTDDFID 284 (316)
T ss_pred HHcCChHHHHHHHHHh------------------------------------CccCCCcCChHHHHHHHcCCCCCCCCCc
Confidence 9999973 55555421 0123358999999999999998764233
Q ss_pred HHHHHhhhcccChHHHHHHHHHhcCCCccccc
Q 007971 312 AVHRVLAQHLFQHARLHQVCAQFFQWPPEKTD 343 (583)
Q Consensus 312 ~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~ 343 (583)
..|. ..+...|+.|+...++|+.+++.
T Consensus 285 ~~~~-----~p~~~~l~~~~~~~~~~~~~rv~ 311 (316)
T cd00128 285 LRWR-----DPDEEGIIEFLCKEHGFNEDRVL 311 (316)
T ss_pred eeec-----CCCHHHHHHHccCCCCCCHHHHH
Confidence 2222 33567899999999999975543
No 3
>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=2.1e-55 Score=463.12 Aligned_cols=301 Identities=25% Similarity=0.375 Sum_probs=253.5
Q ss_pred CCccchHHHHhhhcccccccccCCCEEEeeHHHHHHHhhcccCCC-------CCCCchhHHHHHHHHHHHHHHcCCEEEE
Q 007971 1 MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSY-------RPQTDKLFLRGLFHRLRALIALNCGLIF 73 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~-------~g~~~~~~Lr~lf~rl~~Ll~~gI~PIF 73 (583)
||| |||++|+ .+++++++|+|++|||||++||||++++.+.. ..|.++++++++|+++.+|+++||+|||
T Consensus 1 MGi-~l~~~~~--~~~~~l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~Pv~ 77 (338)
T TIGR03674 1 MGV-DLRDLLA--KEEIELEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKPVY 77 (338)
T ss_pred CCC-ChHHHhc--cCccCHHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeEEE
Confidence 999 9999998 78899999999999999999999998876421 1245678999999999999999999999
Q ss_pred EEcCCCCcchhhhhHhhhhcCccccc------ccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHHHH
Q 007971 74 VSDGSIPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQC 147 (583)
Q Consensus 74 VFDG~~P~~K~~t~~~R~~~r~~a~~------~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADAqc 147 (583)
||||.+|++|..++.+|++.|.++.. +.++.+++.++.+.....+..+++.++++|+.|||||++|||||||||
T Consensus 78 VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~ 157 (338)
T TIGR03674 78 VFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQA 157 (338)
T ss_pred EECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHHH
Confidence 99999999999999999887765331 345556666665555566788999999999999999999999999999
Q ss_pred HHHHHcCCeeEEecCCCcEEeecCcEEEEEcccCCCc-----------eEEEEeHHHHHHHhCCChHHHHHHHHHhCCCC
Q 007971 148 ALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERG-----------YVVCYEMDDIERKLGFGRNSLITLALLLGSDY 216 (583)
Q Consensus 148 A~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~~-----------~v~~y~~~~i~~~lgL~r~qli~laiL~G~DY 216 (583)
|+|++.|.||+|+|+|+|+|+||+++|++++...... ++++|+.+.+.+.+|++++||+++|+|+||||
T Consensus 158 a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~dy 237 (338)
T TIGR03674 158 AYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGTDY 237 (338)
T ss_pred HHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCC
Confidence 9999999999999999999999999999998653211 35679999999999999999999999999999
Q ss_pred CCCCCCCCHHHHHHHHHHcCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCCccccccccccccCCCCCCCCCCCcHH
Q 007971 217 SQGVRGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQ 295 (583)
Q Consensus 217 ~pGvpGiG~ktA~~Li~~~g~~~-il~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~e~~~~~~~~~~~~~fP~~~ 295 (583)
+|||||||+|||++||++||+++ +++++.. .+ + +..+
T Consensus 238 n~Gv~GIG~ktA~kli~~~gsie~il~~~~~---------------------------------------~~--~-~~~~ 275 (338)
T TIGR03674 238 NEGVKGIGPKTALKLIKEHGDLEKVLKARGE---------------------------------------DI--E-NYDE 275 (338)
T ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHhhcC---------------------------------------CC--C-CHHH
Confidence 99999999999999999999974 6654320 01 1 2368
Q ss_pred HHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhhhhHHH
Q 007971 296 VIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAE 352 (583)
Q Consensus 296 Vi~~Yl~P~v~~~~~~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP~l~e 352 (583)
+++.|++|.|..+ .+..| .+.+..+|++|+.+.++|+.++++..+-++.+.
T Consensus 276 ~~~~f~~~~v~~~-~~~~~-----~~pd~e~l~~fl~~e~~~~~~rv~~~~~~l~~~ 326 (338)
T TIGR03674 276 IREFFLNPPVTDD-YELKW-----RKPDKEGIIEFLCDEHDFSEDRVERALERLEAA 326 (338)
T ss_pred HHHHhCCCCCCCC-CCccC-----CCCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHh
Confidence 9999999998753 22222 245778999999999999999888888887544
No 4
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.3e-54 Score=456.42 Aligned_cols=397 Identities=25% Similarity=0.321 Sum_probs=310.0
Q ss_pred CCccchHHHH----hhhcccccccccCCCEEEeeHHHHHHHhhcccCCC--CCCCchhHHHHHHHHHHHHHHcCCEEEEE
Q 007971 1 MGVKNLWDIL----ESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSY--RPQTDKLFLRGLFHRLRALIALNCGLIFV 74 (583)
Q Consensus 1 MGIkgL~~~L----~~~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~--~g~~~~~~Lr~lf~rl~~Ll~~gI~PIFV 74 (583)
|||+||.+++ .++.++.++..|+|++||||||+||||++.+.++. ..+.++.||+++|+|+.+|+++||+||||
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~~~~~~~~~~HL~g~f~Rt~~l~~~gi~Pv~V 80 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSCRNEAGEPTSHLMGMFYRTIRLIENGIKPVYV 80 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccccccCCCchHHHHHHHHHHHHHHHcCCcEEEE
Confidence 9999996555 46778899999999999999999999999988752 23567899999999999999999999999
Q ss_pred EcCCCCcchhhhhHhhhhcCcccccc------cccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHHHHH
Q 007971 75 SDGSIPAIKLSTYRRRLNSGSEVTQD------DKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCA 148 (583)
Q Consensus 75 FDG~~P~~K~~t~~~R~~~r~~a~~~------~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADAqcA 148 (583)
|||.+|.+|..++.+|...|.++... .+......++.+....++.....+|+.||..|||||++||+|||||||
T Consensus 81 fDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EAEAqCA 160 (449)
T KOG2519|consen 81 FDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEAEAQCA 160 (449)
T ss_pred ECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchHHHHHH
Confidence 99999999999999998877643321 111222333333334456677789999999999999999999999999
Q ss_pred HHHHcCCeeEEecCCCcEEeecCcEEEEEccc--CCCceEEEEeHHHHHHHhCCChHHHHHHHHHhCCCCCCCCCCCCHH
Q 007971 149 LLNLESLCDGCFSSDSDIFLFGARTVYRDIWL--GERGYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPE 226 (583)
Q Consensus 149 ~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~--~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G~DY~pGvpGiG~k 226 (583)
+|++.|.|++++|+|+|+|.||++.+++|+.. +++..|.+|+++.|.+.|+|++++|+++|+|+|||||++|.|||++
T Consensus 161 ~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGCDYc~~I~Gig~~ 240 (449)
T KOG2519|consen 161 ALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGCDYCPTIRGIGPK 240 (449)
T ss_pred HHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcCcccccccccChH
Confidence 99999999999999999999999999999864 3457899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCCccccccccccccCCCCCCCCCCCcHHHHHHhcCCcc
Q 007971 227 SACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKC 305 (583)
Q Consensus 227 tA~~Li~~~g~~~-il~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~e~~~~~~~~~~~~~fP~~~Vi~~Yl~P~v 305 (583)
+|++||++|++.. +|+ +... .++..+|++|+...+...|+.|.+
T Consensus 241 ~al~lir~~~~i~~ile-~~~~----------------------------------~~~~~ip~~w~~~~~r~~f~~p~~ 285 (449)
T KOG2519|consen 241 KALKLIRQHGDIENILE-INSD----------------------------------LKEYPIPEDWSYKLARKLFLEPEF 285 (449)
T ss_pred HHHHHHHHhcCHHHHhh-hccc----------------------------------hhhcCCCCCccHHHHHHHhcCccc
Confidence 9999999999874 443 2110 112356789999999999999999
Q ss_pred CCCCh--HHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhhhhHHHHHHhhhhhhhccccccCCCCCCCCcCCCCcc
Q 007971 306 YSADS--EAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVDLPLQKVPVKCPI 383 (583)
Q Consensus 306 ~~~~~--~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP~l~e~~lr~~~~l~~~~~~~~~~~~~~~~~v~~~~ 383 (583)
..+.+ +.-|. +.+...|.+|+....+|+.+++..-+.+++..++++..+.+ +.|-...|-...+.+...
T Consensus 286 ~~~~~~~~i~w~-----~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl----~~f~~~~~~~~~~~~~~~ 356 (449)
T KOG2519|consen 286 PNPESILDLKWK-----TPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRL----DSFFKRIPKGSPVRKLKL 356 (449)
T ss_pred CCccceeecccC-----CCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccch----hhhhcccCCCCCcchhHH
Confidence 76544 22222 34667899999999999999999999999999988653321 122111111100000000
Q ss_pred cceeecc-----ccCCccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHHHhccCCCCc
Q 007971 384 TGIIKSR-----KLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQPKKS 441 (583)
Q Consensus 384 ~~I~k~R-----~~~g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~~~~~kk~ 441 (583)
...+..+ ..++-.|+.+..+....+.++..|-.++.+|+|.....|...|-.+..+++
T Consensus 357 ~~~~~~~~e~~~~~~~~~~~~~~~~~~~r~~~t~~~l~~l~~~~p~~~~~~l~~k~~~~~~~~ 419 (449)
T KOG2519|consen 357 IDAKGKAEEVIKALNKKEKPKGQTGKIKRFKTTDKPLTMLPSATPLFTFIFLIPKEYPHLKTK 419 (449)
T ss_pred HHHHhhhhhccCcchhhhhhccCCCccccceeecchHhhcccCCccHHHHHhhhhhccccccc
Confidence 0111111 233445666777788888999999999999999999999988877654443
No 5
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=4.2e-49 Score=407.13 Aligned_cols=258 Identities=22% Similarity=0.358 Sum_probs=221.0
Q ss_pred CCchhHHHHHHHHHHHHHHcCCEEEEEEcCCCCcchhhhhHhhhhcCccccc------ccccHHHHHHhhhccchhHHHH
Q 007971 48 QTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCM 121 (583)
Q Consensus 48 ~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~~------~~~~~~~a~k~~R~~~~~~~~~ 121 (583)
|.+++|+.+||+|+.+|+++||+|||||||.+|++|..++.+|+++|.++.. +.++.+++.++.+....+++.+
T Consensus 5 G~~Ts~l~g~~~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~ 84 (292)
T PRK03980 5 GRITSHLSGIFYRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEI 84 (292)
T ss_pred CcCcHHHHHHHHHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHH
Confidence 4578999999999999999999999999999999999999999988866432 3455666666666666778999
Q ss_pred HHHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccCCC-----------ceEEEEe
Q 007971 122 IKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER-----------GYVVCYE 190 (583)
Q Consensus 122 i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~-----------~~v~~y~ 190 (583)
++.++++|+.|||||++||||||||||+|++.|+||+|+|+|+|+|+||+++|++++..... ..+++|+
T Consensus 85 ~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~~~ 164 (292)
T PRK03980 85 VEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPELIE 164 (292)
T ss_pred HHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccceeee
Confidence 99999999999999999999999999999999999999999999999999999999875321 1356899
Q ss_pred HHHHHHHhCCChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCC
Q 007971 191 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNN 269 (583)
Q Consensus 191 ~~~i~~~lgL~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~-il~~~~~~~~~~~~~~~~~~~~~~~~~c~~ 269 (583)
.+.+.+.+|++++||+++|+|+||||+|||||||+|||++||++||+++ +++.+.
T Consensus 165 ~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~------------------------ 220 (292)
T PRK03980 165 LEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG------------------------ 220 (292)
T ss_pred HHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhcc------------------------
Confidence 9999999999999999999999999999999999999999999999974 554211
Q ss_pred ccccccccccccCCCCCCCCCCC-cHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhhh
Q 007971 270 KEESLNQEINVNGTDHSLQRETP-FSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILP 348 (583)
Q Consensus 270 ~~~~~~~e~~~~~~~~~~~~~fP-~~~Vi~~Yl~P~v~~~~~~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP 348 (583)
.++| +.+|+++|++|.|.. +.++.|+ ..+..+|++|+.+..+|+.++++..+-+
T Consensus 221 -------------------~~~~~~~~~r~~f~~p~v~~-~~~~~~~-----~pd~~~l~~fl~~e~~f~~~rv~~~~~~ 275 (292)
T PRK03980 221 -------------------FEIENYDEIREFFLNPPVTD-DYELKWK-----EPDKEGIIEFLVEEHDFSEERVKKALER 275 (292)
T ss_pred -------------------CCCCCHHHHHHHhcCCCCCC-CCCccCC-----CCCHHHHHHHHhccCCCCHHHHHHHHHH
Confidence 1233 489999999999985 3344433 3478899999999999999999999988
Q ss_pred hHHHHH
Q 007971 349 KIAERD 354 (583)
Q Consensus 349 ~l~e~~ 354 (583)
+.+.+.
T Consensus 276 l~~~~~ 281 (292)
T PRK03980 276 LEKAVK 281 (292)
T ss_pred HHHHhc
Confidence 876543
No 6
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.2e-44 Score=384.17 Aligned_cols=237 Identities=19% Similarity=0.262 Sum_probs=206.7
Q ss_pred CCccchHHHHhhhcccccccccCCCEEEeeHHHHHHHhhcccCC--CCCCCchhHHHHHHHHHHHHHHcCCEEEEEEcCC
Q 007971 1 MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKS--YRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGS 78 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~--~~g~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~ 78 (583)
|||+||.++++++.++++++.|+|++||||+++|||++..++.. ..|.++..||..|++++..|+.+||+||+||||.
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 99999999999999999999999999999999999998766532 2345668899999999999999999999999999
Q ss_pred CCcchhhhhHhhhhcCcccc------cccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHHHHHHHHH
Q 007971 79 IPAIKLSTYRRRLNSGSEVT------QDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNL 152 (583)
Q Consensus 79 ~P~~K~~t~~~R~~~r~~a~------~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~ 152 (583)
+.+.|..|..+|+.+|++.. -..|+..+|+.+.|....+++.|...+.+.++..||+||+||||||||+|||++
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 98889888888777765532 135666677777666778999999999999999999999999999999999999
Q ss_pred cCCeeEEecCCCcEEeecCcEEEEEcccCCCceEEEEeHHHHHHHh----CCChHHHHHHHHHhCCCCCCCCCCCCHHHH
Q 007971 153 ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKL----GFGRNSLITLALLLGSDYSQGVRGLGPESA 228 (583)
Q Consensus 153 ~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~~~v~~y~~~~i~~~l----gL~r~qli~laiL~G~DY~pGvpGiG~ktA 228 (583)
.|+||||||+|||+++|||+.||..+.. . +....++...+.+.. +++.++|..+|+|+||||++||||||.+||
T Consensus 161 ~~~i~~IITEDSDLl~fGc~~vifK~d~-~-G~~le~~~~~l~~~~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~tA 238 (556)
T KOG2518|consen 161 EGIVDAIITEDSDLLVFGCKKVIFKMDS-F-GNGLEINRSKLPECKPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLATA 238 (556)
T ss_pred cCcceEEEeccccccccCchhheeeccC-C-CCcccccHhhhhhccccccccCHHHHHHHHHhcCCcccccCccccHHHH
Confidence 9999999999999999999999988763 2 344456776666543 357899999999999999999999999999
Q ss_pred HHHHHHcCCHH
Q 007971 229 CQIVKSVGDNV 239 (583)
Q Consensus 229 ~~Li~~~g~~~ 239 (583)
+++++.|.+.+
T Consensus 239 ~k~l~k~~~~d 249 (556)
T KOG2518|consen 239 HKLLSKYNTPD 249 (556)
T ss_pred HHHHHhcCcHH
Confidence 99999999975
No 7
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.3e-41 Score=393.35 Aligned_cols=224 Identities=33% Similarity=0.508 Sum_probs=184.3
Q ss_pred hhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccCCCceEEEEe
Q 007971 111 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE 190 (583)
Q Consensus 111 ~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~~~v~~y~ 190 (583)
.|....++..|+.+|++||++||||||+||||||||||+|++.|+||||+|+|+|+|+||+++||||++. .+.+|.+|.
T Consensus 763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~-~~~~ve~~~ 841 (1034)
T TIGR00600 763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFN-QNKFVEYYQ 841 (1034)
T ss_pred ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccC-CCCceEEee
Confidence 3445678899999999999999999999999999999999999999999999999999999999999874 557899999
Q ss_pred HHHHHHHhCCChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCC--HHHHHHHHhcChhHHHHhh-hhcccCccccc
Q 007971 191 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGD--NVVLQRIASEGLSFVKRAK-NSKKEGWSFKC 267 (583)
Q Consensus 191 ~~~i~~~lgL~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~--~~il~~~~~~~~~~~~~~~-~~~~~~~~~~c 267 (583)
++++.+.+||++++||+||+|+||||++||+|||++||++||++||+ ++-|..|..| +.... ...........
T Consensus 842 ~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w----~~~~~~~~~~~~~~~~~ 917 (1034)
T TIGR00600 842 YVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEW----WHEAQKDKKKRENPNDT 917 (1034)
T ss_pred HHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHH----HHHhhhccccccccchh
Confidence 99999999999999999999999999999999999999999999995 5556666654 33221 11000000000
Q ss_pred CCccccccccccccCCCCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhh
Q 007971 268 NNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYIL 347 (583)
Q Consensus 268 ~~~~~~~~~e~~~~~~~~~~~~~fP~~~Vi~~Yl~P~v~~~~~~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~ll 347 (583)
. .....+...+|.+||+..|+++|++|.|++++..+.|+ ..+..+|+.||.++|+|+.++++++|.
T Consensus 918 ~---------~~~~~~~~~lp~~FP~~~V~~~yl~P~V~~~~~~f~W~-----~PD~e~L~~Fl~~~~gws~eRv~~~l~ 983 (1034)
T TIGR00600 918 K---------VKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWG-----KPDLDKIREFCQRYFGWNREKTDEVLL 983 (1034)
T ss_pred h---------hhhcccccccCCCCCcHHHHHHhcCCCCCCCcCCCCCC-----CCCHHHHHHHHHHccCCCHHHHHHHHH
Confidence 0 00011224578899999999999999999866666654 247889999999999999999999999
Q ss_pred hhHHHH
Q 007971 348 PKIAER 353 (583)
Q Consensus 348 P~l~e~ 353 (583)
|++..+
T Consensus 984 plikk~ 989 (1034)
T TIGR00600 984 PVLKKL 989 (1034)
T ss_pred HHHHHH
Confidence 999843
No 8
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.8e-41 Score=379.53 Aligned_cols=238 Identities=32% Similarity=0.517 Sum_probs=195.0
Q ss_pred hhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccCCCceEEEEe
Q 007971 111 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE 190 (583)
Q Consensus 111 ~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~~~v~~y~ 190 (583)
.|...+++..|+.+||+||+.||||||+||+|||||||.|.+.++||||||+|||+|+||+++||||+|. ++++|..|.
T Consensus 457 ~r~~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~-knk~ve~y~ 535 (815)
T KOG2520|consen 457 SRGADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFN-KNKYVEKYQ 535 (815)
T ss_pred hccCchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhh-cCccceeee
Confidence 3455678999999999999999999999999999999999999999999999999999999999999986 568899999
Q ss_pred HHHHHHHhCCChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhhhhcccCcccccCCc
Q 007971 191 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNK 270 (583)
Q Consensus 191 ~~~i~~~lgL~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~~~~~~~~~~~c~~~ 270 (583)
+.+|+..|||+|..||-+|.|+|+||+.|++|||+++|+++|.+|++.+-|..|+.| +... +......++.-
T Consensus 536 ~~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~w----~~~~-~~~~~~~~s~~--- 607 (815)
T KOG2520|consen 536 LDDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKKW----VQQT-GPADKEVGSTQ--- 607 (815)
T ss_pred hHHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHHH----HHHh-CccccccccHH---
Confidence 999999999999999999999999999999999999999999999987768888875 3311 00000000000
Q ss_pred cccccccccccCCCCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccchhhhhH
Q 007971 271 EESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKI 350 (583)
Q Consensus 271 ~~~~~~e~~~~~~~~~~~~~fP~~~Vi~~Yl~P~v~~~~~~~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP~l 350 (583)
.....+ .+...+..++.+||.+.|++|||+|.|+++...+.|+. .+.+.||+||++.|+|+.++|++.++|++
T Consensus 608 -~~~lrk-kl~n~~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~-----pdl~~lRef~~~~fgW~~~kT~~~l~p~~ 680 (815)
T KOG2520|consen 608 -QKMLRK-KLKNPKIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGK-----PDLDILREFMKRLFGWPDEKTDEELIPVI 680 (815)
T ss_pred -HHHHHH-HhcCcccccCcCCCchhHHHHhhCCccCCCcccccCCC-----CCHHHHHHHHHHHcCCCccccchhhhhhH
Confidence 000000 11112245678999999999999999998877777774 36788999999999999999999999999
Q ss_pred HHHHHhhhhhhhcc
Q 007971 351 AERDLRRFANLRAN 364 (583)
Q Consensus 351 ~e~~lr~~~~l~~~ 364 (583)
++...+.....+.+
T Consensus 681 ~~~~~~~~~~~~~~ 694 (815)
T KOG2520|consen 681 KRLEKKKTQLKQDR 694 (815)
T ss_pred HHHHHHhhhhcccc
Confidence 99887764333333
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.1e-32 Score=280.92 Aligned_cols=206 Identities=21% Similarity=0.184 Sum_probs=172.5
Q ss_pred CEEEeeHHHHHHHhhcccCCC--CCCCchhHHHHHHHHHHHHHHc--CCEEEEEEcCCCCcchhhhhHhhhhcCcccccc
Q 007971 25 KRVCIDLSCWIVQLQNVNKSY--RPQTDKLFLRGLFHRLRALIAL--NCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQD 100 (583)
Q Consensus 25 k~IaIDas~wL~~~~~a~~~~--~g~~~~~~Lr~lf~rl~~Ll~~--gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~~~ 100 (583)
+.++|||++++||++++.... ..|.+++++.+|+..+.+|++. +-++++||||..+.+++..+..|+++|.+
T Consensus 2 ~lllIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~l~p~YKa~R~~---- 77 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPEYKANRPK---- 77 (259)
T ss_pred cEEEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccchhHHHHhCCCC----
Confidence 468999999999999886431 1245678999999999999873 56779999998889998888888887754
Q ss_pred cccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHHc----CCeeEEecCCCcEEeecCcEEE
Q 007971 101 DKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNLE----SLCDGCFSSDSDIFLFGARTVY 175 (583)
Q Consensus 101 ~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~~----g~vd~ViS~DsD~llfG~~~V~ 175 (583)
++..+..+++.++++|+.+|||++.+| +|||++||+|++. |..+.|+|+|+|+++++++.|.
T Consensus 78 -------------~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~ 144 (259)
T smart00475 78 -------------TPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVS 144 (259)
T ss_pred -------------CCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEE
Confidence 455677888999999999999999988 5999999999874 7888999999999999987553
Q ss_pred EEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCH-HHHHHHHhc
Q 007971 176 RDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 247 (583)
Q Consensus 176 r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~-~il~~~~~~ 247 (583)
.............|+.+.+.+++|++++||+++++|+| |||+|||||||+|||.+||++||++ ++++++...
T Consensus 145 ~~~~~~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~ 219 (259)
T smart00475 145 VLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKL 219 (259)
T ss_pred EEeccCCCCccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 22122211234679999999999999999999999999 8999999999999999999999998 488888763
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=100.00 E-value=1.7e-31 Score=269.49 Aligned_cols=201 Identities=21% Similarity=0.202 Sum_probs=172.1
Q ss_pred CEEEeeHHHHHHHhhcccCCCC---CCCchhHHHHHHHHHHHHHHc--CCEEEEEEcCCCCcchhhhhHhhhhcCccccc
Q 007971 25 KRVCIDLSCWIVQLQNVNKSYR---PQTDKLFLRGLFHRLRALIAL--NCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQ 99 (583)
Q Consensus 25 k~IaIDas~wL~~~~~a~~~~~---g~~~~~~Lr~lf~rl~~Ll~~--gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~~ 99 (583)
+.++|||++++||++++..... .+.+++++.+|+.++.++++. +.++++||||..+.+|+..+..|+++|.+
T Consensus 2 ~~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~--- 78 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKK--- 78 (240)
T ss_pred cEEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCC---
Confidence 4789999999999988875321 245678999999999999874 58899999999889999888888887754
Q ss_pred ccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHH----cCCeeEEecCCCcEEeecCcEE
Q 007971 100 DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTV 174 (583)
Q Consensus 100 ~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~----~g~vd~ViS~DsD~llfG~~~V 174 (583)
++..+..++..++++|+.+|||++.+| +|||++||+|+. .|....|+|.|+|++++++..|
T Consensus 79 --------------~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v 144 (240)
T cd00008 79 --------------MPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNV 144 (240)
T ss_pred --------------CCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCE
Confidence 456678899999999999999999998 699999999985 5778899999999999977655
Q ss_pred E-EEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCH-HHHHHHHhc
Q 007971 175 Y-RDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 247 (583)
Q Consensus 175 ~-r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~-~il~~~~~~ 247 (583)
. .+.. ....++.+.+.+.+|++++|++++++|+| |||+|||||||+|||.+||++||++ +++++++..
T Consensus 145 ~~~~~~-----~~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~ 216 (240)
T cd00008 145 KVVSPM-----KKKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKI 216 (240)
T ss_pred EEEeCC-----CceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHH
Confidence 3 3221 23478999999999999999999999999 8999999999999999999999998 488888764
No 11
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.97 E-value=1.8e-30 Score=267.42 Aligned_cols=206 Identities=15% Similarity=0.159 Sum_probs=171.7
Q ss_pred CCEEEeeHHHHHHHhhcccC----C--CCCCCchhHHHHHHHHHHHHHHc--CCEEEEEEcCCCCcchhhhhHhhhhcCc
Q 007971 24 NKRVCIDLSCWIVQLQNVNK----S--YRPQTDKLFLRGLFHRLRALIAL--NCGLIFVSDGSIPAIKLSTYRRRLNSGS 95 (583)
Q Consensus 24 gk~IaIDas~wL~~~~~a~~----~--~~g~~~~~~Lr~lf~rl~~Ll~~--gI~PIFVFDG~~P~~K~~t~~~R~~~r~ 95 (583)
.+.++|||++++||++++.. . ...|.++.++.+|+..+.++++. +-++++||||..+.+++..+..|+++|.
T Consensus 3 ~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~ 82 (281)
T PRK14976 3 KKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRK 82 (281)
T ss_pred CcEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcCCC
Confidence 35789999999999888741 1 11245678999999999999874 5789999999888999988888888775
Q ss_pred ccccccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHHc----CCeeEEecCCCcEEeec
Q 007971 96 EVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNLE----SLCDGCFSSDSDIFLFG 170 (583)
Q Consensus 96 ~a~~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~~----g~vd~ViS~DsD~llfG 170 (583)
+ ++..+..++..++++|+.+|||++.+| +|||++||+|+.. |.-..|+|.|+|++++.
T Consensus 83 ~-----------------~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~ 145 (281)
T PRK14976 83 K-----------------TPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLV 145 (281)
T ss_pred C-----------------CCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccC
Confidence 4 355677889999999999999999999 5999999999764 66667999999999999
Q ss_pred CcEEEEEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCH-HHHHHHHhc
Q 007971 171 ARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 247 (583)
Q Consensus 171 ~~~V~r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~-~il~~~~~~ 247 (583)
+..|...... ++.....|+.+.+.+++|++++|++++++|+| +||+|||||||+|||.+||++||++ ++++++...
T Consensus 146 ~~~v~~~~~~-~~~~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~ 224 (281)
T PRK14976 146 NENTDVLLKK-KGTSHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKI 224 (281)
T ss_pred CCCeEEEEec-CCCCcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHH
Confidence 8754322112 22224679999999999999999999999999 8999999999999999999999998 588888764
No 12
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.97 E-value=5.9e-30 Score=267.24 Aligned_cols=216 Identities=19% Similarity=0.204 Sum_probs=163.8
Q ss_pred ccccccCCCEEEeeHHHHHHHhhcccCCC---CCCCchhHHHHHHHHHHHHHH--cCCEEEEEEcCCCCcchhhhhHhhh
Q 007971 17 LPLHHLQNKRVCIDLSCWIVQLQNVNKSY---RPQTDKLFLRGLFHRLRALIA--LNCGLIFVSDGSIPAIKLSTYRRRL 91 (583)
Q Consensus 17 v~L~~L~gk~IaIDas~wL~~~~~a~~~~---~g~~~~~~Lr~lf~rl~~Ll~--~gI~PIFVFDG~~P~~K~~t~~~R~ 91 (583)
..+...+|+.++|||++|+||++++.+.. ..+.+++.+.+|...+.+++. .+++|++||||..|++|+.++.+|+
T Consensus 4 ~~~~~~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK 83 (310)
T COG0258 4 IQLMNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYK 83 (310)
T ss_pred ccchhccCcEEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHH
Confidence 44566789999999999999999987531 123344466766666666555 2599999999999999999999999
Q ss_pred hcCcc-cccccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeec
Q 007971 92 NSGSE-VTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFG 170 (583)
Q Consensus 92 ~~r~~-a~~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG 170 (583)
+.|.+ .. ..+....+.....+......+|+.+|+| +++|.|++||||+ +.|.+++|+|+|+|+++|+
T Consensus 84 ~~R~~~~p---------~~l~~q~~~i~~~~~~~~~~~l~~~G~e-add~i~t~A~~a~--~~g~~~~I~S~DkD~lql~ 151 (310)
T COG0258 84 ANREKEMP---------DELAPQIPILTELLVALGIPLLELMGIE-ADDPIETLAQKAY--KKGDVVLIISGDKDLLQLV 151 (310)
T ss_pred hCCCccCH---------HHHHHHHHHHHHHHHHhCcHhhhcCCCC-cchhHHHHHHHHH--hcCCeEEEEeCCcchhhhc
Confidence 88865 21 1222222333444455556666667777 6667777777777 7899999999999999999
Q ss_pred CcEEEEEcccCCCceEEEEeHHHHHHHh-CCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCHH-HHHHHH
Q 007971 171 ARTVYRDIWLGERGYVVCYEMDDIERKL-GFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDNV-VLQRIA 245 (583)
Q Consensus 171 ~~~V~r~~~~~~~~~v~~y~~~~i~~~l-gL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~~-il~~~~ 245 (583)
++++...... .+.....++...+.+.+ |+++.||+|+++|+| |||+|||+|||+|||++||++||+.+ +++++.
T Consensus 152 ~~~~~~~~~~-~~~~~~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~ 229 (310)
T COG0258 152 SPNVLVINGK-KGEPEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLD 229 (310)
T ss_pred CCCcEEEecc-CCCCcccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhh
Confidence 9985433222 21111157899999999 999999999999999 99999999999999999999999985 565554
No 13
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.96 E-value=7e-28 Score=244.40 Aligned_cols=206 Identities=19% Similarity=0.191 Sum_probs=169.0
Q ss_pred CEEEeeHHHHHHHhhcccCCCCCCCchhHHHHHHHHHHHHHHc--CCEEEEEEcCCCCc--chhhhhHhhhhcCcccccc
Q 007971 25 KRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIAL--NCGLIFVSDGSIPA--IKLSTYRRRLNSGSEVTQD 100 (583)
Q Consensus 25 k~IaIDas~wL~~~~~a~~~~~g~~~~~~Lr~lf~rl~~Ll~~--gI~PIFVFDG~~P~--~K~~t~~~R~~~r~~a~~~ 100 (583)
+.+.|||++++||++++.....|. ++.+++|+..+.++++. +-+.++|||+..+. +++..+..+++.|.+
T Consensus 4 ~llLiDg~~l~~R~~~a~~~~~g~--t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~---- 77 (256)
T PRK09482 4 HLLIIDALNLIRRIHAVQPSPNDI--NACVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKP---- 77 (256)
T ss_pred eEEEEeCcHHHHHHHhCCCCCCCc--chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHHHHhHHHhcCCCC----
Confidence 578999999999999886433333 78899999999988863 56789999998776 888888888777653
Q ss_pred cccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHH----cCCeeEEecCCCcEEeecCcEE-
Q 007971 101 DKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTV- 174 (583)
Q Consensus 101 ~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~----~g~vd~ViS~DsD~llfG~~~V- 174 (583)
++..+..++..++++|+.+||+++..| +|||+.||.|+. .|.-..|+|.|.|+++.-...|
T Consensus 78 -------------~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~ 144 (256)
T PRK09482 78 -------------MPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQ 144 (256)
T ss_pred -------------CcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeE
Confidence 466788899999999999999999999 599999999975 3555578999999998876554
Q ss_pred EEEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCH-HHHHHHHhcChhH
Q 007971 175 YRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSF 251 (583)
Q Consensus 175 ~r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~-~il~~~~~~~~~~ 251 (583)
+.+.. . ..+++.+.+.+++|++|+|++++.+|+| +|++|||||||+|||.+||++||++ +++++++.....+
T Consensus 145 ~~~~~--~---~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~ 219 (256)
T PRK09482 145 IRDYF--Q---KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPEKW 219 (256)
T ss_pred EEecc--c---cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhHHH
Confidence 33322 1 2368999999999999999999999999 8999999999999999999999998 5888887643333
Q ss_pred HHH
Q 007971 252 VKR 254 (583)
Q Consensus 252 ~~~ 254 (583)
.++
T Consensus 220 ~~~ 222 (256)
T PRK09482 220 RKK 222 (256)
T ss_pred HHH
Confidence 333
No 14
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.96 E-value=1.1e-27 Score=278.66 Aligned_cols=202 Identities=20% Similarity=0.198 Sum_probs=171.4
Q ss_pred EEeeHHHHHHHhhcccCC--C--CCCCchhHHHHHHHHHHHHHHc--CCEEEEEEcCCCCcchhhhhHhhhhcCcccccc
Q 007971 27 VCIDLSCWIVQLQNVNKS--Y--RPQTDKLFLRGLFHRLRALIAL--NCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQD 100 (583)
Q Consensus 27 IaIDas~wL~~~~~a~~~--~--~g~~~~~~Lr~lf~rl~~Ll~~--gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~~~ 100 (583)
++|||++++||++++.+. . ..|.+++++.+|+.++.+|++. +-+.+||||+..|.+++..+..|++.|..
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~---- 77 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHEAYAEYKANRAP---- 77 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCcchHHHHHHHHhCCCC----
Confidence 689999999999988742 1 1356788999999999999973 56679999999899999888888887754
Q ss_pred cccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHHc----CCeeEEecCCCcEEeecCcEEE
Q 007971 101 DKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNLE----SLCDGCFSSDSDIFLFGARTVY 175 (583)
Q Consensus 101 ~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~~----g~vd~ViS~DsD~llfG~~~V~ 175 (583)
++..+..++..++++|+.+|||++.+| +|||++||+|++. |+.+.|+|.|.|+++++.+.|.
T Consensus 78 -------------~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~ 144 (887)
T TIGR00593 78 -------------TPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVK 144 (887)
T ss_pred -------------ChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEE
Confidence 456678899999999999999999999 5999999999864 7888999999999999987552
Q ss_pred -EEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCH-HHHHHHHhc
Q 007971 176 -RDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 247 (583)
Q Consensus 176 -r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~-~il~~~~~~ 247 (583)
.+.. ++.....|+.+.+.+++|++++||+|+++|+| |||+|||||||+|||.+||++||++ +++++++.-
T Consensus 145 ~~~~~--~~~~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i 218 (887)
T TIGR00593 145 VLIPK--GKTSFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQI 218 (887)
T ss_pred EEecc--CCCCceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 2221 11134579999999999999999999999999 6999999999999999999999998 588887764
No 15
>PRK05755 DNA polymerase I; Provisional
Probab=99.95 E-value=3.1e-27 Score=276.86 Aligned_cols=203 Identities=18% Similarity=0.191 Sum_probs=171.2
Q ss_pred CEEEeeHHHHHHHhhcccC-C--CCCCCchhHHHHHHHHHHHHHH-c-CCEEEEEEcCCCCcchhhhhHhhhhcCccccc
Q 007971 25 KRVCIDLSCWIVQLQNVNK-S--YRPQTDKLFLRGLFHRLRALIA-L-NCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQ 99 (583)
Q Consensus 25 k~IaIDas~wL~~~~~a~~-~--~~g~~~~~~Lr~lf~rl~~Ll~-~-gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~~ 99 (583)
+.++|||++++||++++.. . ...|.+++++.+|+.++.+|++ . +-+.+||||+..+.+|+..+..|+++|.+
T Consensus 3 ~~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~~--- 79 (880)
T PRK05755 3 TLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHELYPEYKANRPP--- 79 (880)
T ss_pred eEEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECCCCccccccCHHHhCCCCC---
Confidence 5789999999999998862 1 1124567899999999999885 2 55679999998889999889998887754
Q ss_pred ccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHH----cCCeeEEecCCCcEEeecCcEE
Q 007971 100 DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTV 174 (583)
Q Consensus 100 ~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~----~g~vd~ViS~DsD~llfG~~~V 174 (583)
++..+..++..++++|+.+||+++.+| +|||++||+|+. .|..+.|+|.|+|+++++++.|
T Consensus 80 --------------~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v 145 (880)
T PRK05755 80 --------------MPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNV 145 (880)
T ss_pred --------------CcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCE
Confidence 356677889999999999999999999 599999999984 5788999999999999988754
Q ss_pred --EEEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCH-HHHHHHHhc
Q 007971 175 --YRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 247 (583)
Q Consensus 175 --~r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~-~il~~~~~~ 247 (583)
+..+ . +.....++.+.+.+++|++++|++++++|+| |||+|||||||+|||.+||++||++ +++++++..
T Consensus 146 ~~~~~~--~-~~~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~ 220 (880)
T PRK05755 146 TLLDTM--G-VSKNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEI 220 (880)
T ss_pred EEeecc--C-CCCCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHHh
Confidence 3321 1 1234579999999999999999999999999 7999999999999999999999998 588888753
No 16
>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=3.1e-24 Score=186.91 Aligned_cols=86 Identities=40% Similarity=0.622 Sum_probs=75.1
Q ss_pred HHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcc-cCC-------CceEEEEeHHHHHHHhCCC
Q 007971 130 LSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIW-LGE-------RGYVVCYEMDDIERKLGFG 201 (583)
Q Consensus 130 ~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~-~~~-------~~~v~~y~~~~i~~~lgL~ 201 (583)
+.+||||++||||||||||||+++|+||+|+|+|||+|+||+++||++++ ... ...+++|+++.+.+.++++
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 47999999999999999999999999999999999999999999999997 322 2468999999999999999
Q ss_pred hHHHHHHHHHhCCC
Q 007971 202 RNSLITLALLLGSD 215 (583)
Q Consensus 202 r~qli~laiL~G~D 215 (583)
+++|+++|+|+|||
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 17
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=99.87 E-value=1e-22 Score=178.55 Aligned_cols=96 Identities=33% Similarity=0.576 Sum_probs=84.9
Q ss_pred CCccchHHHHhhhcccccccccCCCEEEeeHHHHHHHhhcccCCCC--CCCchhHHHHHHHHHHHHHHcCCEEEEEEcCC
Q 007971 1 MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYR--PQTDKLFLRGLFHRLRALIALNCGLIFVSDGS 78 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~~--g~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~ 78 (583)
|||+|||+||+++.++++++.|+|++|||||++|||++++++.... +....+++.++|+++..|+++||+|||||||.
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 9999999999999999999999999999999999999988764322 22334599999999999999999999999999
Q ss_pred CCcchhhhhHhhhhcCcc
Q 007971 79 IPAIKLSTYRRRLNSGSE 96 (583)
Q Consensus 79 ~P~~K~~t~~~R~~~r~~ 96 (583)
.|+.|..|..+|+++|.+
T Consensus 81 ~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 81 PPPLKSETLAKRRERREE 98 (99)
T ss_pred CchhhHHHHHHHHHHHhc
Confidence 999999999999876643
No 18
>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=99.87 E-value=1.2e-22 Score=178.50 Aligned_cols=95 Identities=36% Similarity=0.601 Sum_probs=78.2
Q ss_pred CCccchHHHHhhhc--ccccccccCCCEEEeeHHHHHHHhhcccCCCC--CCCchhHHHHHHHHHHHHHHcCCEEEEEEc
Q 007971 1 MGVKNLWDILESCK--KTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYR--PQTDKLFLRGLFHRLRALIALNCGLIFVSD 76 (583)
Q Consensus 1 MGIkgL~~~L~~~~--~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~~--g~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFD 76 (583)
|||+|||++|+++. +..++++|+|++|||||++|||+++++..... +...+.++.++++++..|+.+||+||||||
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 88999999999999999999999987765322 222358999999999999999999999999
Q ss_pred CCCCcchhhhhHhhhhcCc
Q 007971 77 GSIPAIKLSTYRRRLNSGS 95 (583)
Q Consensus 77 G~~P~~K~~t~~~R~~~r~ 95 (583)
|..|+.|..+..+|+.+|.
T Consensus 81 G~~~~~K~~~~~~R~~~r~ 99 (101)
T PF00752_consen 81 GKPPPLKRETIQKRRKRRE 99 (101)
T ss_dssp -STTGGCHHHHHHHHHHHH
T ss_pred CCCchhhHHHHHHHHHHHh
Confidence 9999999999998877654
No 19
>PHA00439 exonuclease
Probab=99.82 E-value=3.3e-19 Score=182.86 Aligned_cols=179 Identities=9% Similarity=0.019 Sum_probs=137.1
Q ss_pred CCEEEeeHHHHHHHhhcccC-------CC--CCCCchhHHHHHHHHHHHHHHc-----CCEEEEEEcCCCCcchhhhhHh
Q 007971 24 NKRVCIDLSCWIVQLQNVNK-------SY--RPQTDKLFLRGLFHRLRALIAL-----NCGLIFVSDGSIPAIKLSTYRR 89 (583)
Q Consensus 24 gk~IaIDas~wL~~~~~a~~-------~~--~g~~~~~~Lr~lf~rl~~Ll~~-----gI~PIFVFDG~~P~~K~~t~~~ 89 (583)
...++|||++++||++++.. .. ..+.+++.+.+|+..|.++++. +-+.+++||+ .+.+++..+..
T Consensus 6 ~~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~-~~tfR~elyp~ 84 (286)
T PHA00439 6 KGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTD-SVNWRKEVVPT 84 (286)
T ss_pred CcEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEECC-CCChHhhhhhH
Confidence 46899999999999999872 11 1245678899999999888854 5567888994 67888888888
Q ss_pred hhhcCcccccccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHH----cCC-eeEEecCC
Q 007971 90 RLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNL----ESL-CDGCFSSD 163 (583)
Q Consensus 90 R~~~r~~a~~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~----~g~-vd~ViS~D 163 (583)
++++|... +.. ..++..+++++..+||+++..| +|||+.+|.|+. .|. -..|+|.|
T Consensus 85 YKanR~~~-----------------p~~-~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~D 146 (286)
T PHA00439 85 YKANRKAK-----------------RKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCD 146 (286)
T ss_pred hcCCCCCC-----------------CCc-hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCC
Confidence 88877642 222 3356678899999999999988 699999999975 355 55899999
Q ss_pred CcEEeecCcEEEEEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHH
Q 007971 164 SDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKS 234 (583)
Q Consensus 164 sD~llfG~~~V~r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~ 234 (583)
.|++++....++.+- . +.+..++.+ .+++++++.+|+| +|++||||||| |||.+||++
T Consensus 147 KDl~QLv~~~~~~~~---~-~~~~~~~~~--------~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 147 KDFKTIPNCDFLWCT---T-GNILTQTPE--------TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred CCHhhcCcceEEEcc---C-CceEEcCcc--------cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 999998655444321 1 121113322 3899999999999 89999999999 999999999
No 20
>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=99.77 E-value=2.2e-19 Score=209.19 Aligned_cols=97 Identities=31% Similarity=0.513 Sum_probs=88.8
Q ss_pred CCccchHHHHhhhcccccccccCCCEEEeeHHHHHHHhhcccCCCCC-CCchhHHHHHHHHHHHHHHcCCEEEEEEcCCC
Q 007971 1 MGVKNLWDILESCKKTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRP-QTDKLFLRGLFHRLRALIALNCGLIFVSDGSI 79 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~~g-~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~~ 79 (583)
|||+|||++|+++.++++|..|+|++||||+|+||||++.+++...| ..+++||++||+|+++|+.+||+|||||||.+
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~~ 80 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLLFFRIRPIFVFDGGA 80 (1034)
T ss_pred CChhHHHHHHHHhcccccHHHhCCeEEEechHHHHHHHHHHHHhccCCccCCHHHHHHHHHHHHHHHCCCeEEEEECCCC
Confidence 99999999999999999999999999999999999999988765433 34679999999999999999999999999999
Q ss_pred CcchhhhhHhhhhcCccc
Q 007971 80 PAIKLSTYRRRLNSGSEV 97 (583)
Q Consensus 80 P~~K~~t~~~R~~~r~~a 97 (583)
|++|..|+.+|+++|.++
T Consensus 81 p~lK~~t~~~R~~rR~~a 98 (1034)
T TIGR00600 81 PLLKRQTLAKRRQRRDGA 98 (1034)
T ss_pred chHhHHHHHHHHHHHHHH
Confidence 999999999998887653
No 21
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.74 E-value=5.3e-18 Score=141.21 Aligned_cols=70 Identities=33% Similarity=0.635 Sum_probs=64.0
Q ss_pred HhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeecCcEEEEEcccCCC--ceEEEEeHHHHHHHhCC
Q 007971 131 SLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER--GYVVCYEMDDIERKLGF 200 (583)
Q Consensus 131 ~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~--~~v~~y~~~~i~~~lgL 200 (583)
.+||||++||||||||||+|+++|+||+|+|+|+|+|+||+++++++++...+ ..++.++...++++||+
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 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73 (73)
T ss_pred cCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence 58999999999999999999999999999999999999999999999976542 26889999999999885
No 22
>PHA02567 rnh RnaseH; Provisional
Probab=99.57 E-value=1e-13 Score=143.33 Aligned_cols=181 Identities=14% Similarity=0.068 Sum_probs=125.8
Q ss_pred CCCEEEeeHHHHHHHhhcccCCCCCCCchhHHHH-HHHHHHHHHH----cCCEEEEEEcCCC-CcchhhhhHhhhhcCcc
Q 007971 23 QNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRG-LFHRLRALIA----LNCGLIFVSDGSI-PAIKLSTYRRRLNSGSE 96 (583)
Q Consensus 23 ~gk~IaIDas~wL~~~~~a~~~~~g~~~~~~Lr~-lf~rl~~Ll~----~gI~PIFVFDG~~-P~~K~~t~~~R~~~r~~ 96 (583)
....+.||+|.++++.+++.-....+.+++.++. ++..+..+.. ..-+.+++||+.. +.+++..+..++++|.+
T Consensus 13 ~~~~~LiDgs~i~~~~~~a~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~~ 92 (304)
T PHA02567 13 KEGVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRKK 92 (304)
T ss_pred CCCEEEEehHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCCC
Confidence 3468999999999999887532222344566655 5555665554 3445799999975 67888888888888765
Q ss_pred cccccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHH----cCCeeEEecCCCcEEeecC
Q 007971 97 VTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNL----ESLCDGCFSSDSDIFLFGA 171 (583)
Q Consensus 97 a~~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~----~g~vd~ViS~DsD~llfG~ 171 (583)
...+.. ... ...+..+-..+++++..+||+++..| +|||+.+|.|++ .|.-..|+|.|.|++++-.
T Consensus 93 ~Peel~-------~q~--~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~ 163 (304)
T PHA02567 93 DREESP-------WDW--EGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHK 163 (304)
T ss_pred CChHHH-------HHH--HHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccC
Confidence 321100 000 00112222456888899999999998 699999999885 4666689999999999853
Q ss_pred -cEEEEEcccCCCceEEEEeHHHHHHHhCCChHHHHHHHHHhC--CCCCCCCCC
Q 007971 172 -RTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRG 222 (583)
Q Consensus 172 -~~V~r~~~~~~~~~v~~y~~~~i~~~lgL~r~qli~laiL~G--~DY~pGvpG 222 (583)
..|... . .++...+..++| .+.|++++.+|+| +|++||||-
T Consensus 164 ~~~v~~~-~--------~~~~~~V~~k~G-~P~q~iD~kaL~GDsSDNIPGVp~ 207 (304)
T PHA02567 164 YPGVKQW-S--------PMQKKWVKPKYG-SPEKDLMTKIIKGDKKDGVASIKV 207 (304)
T ss_pred CCCeEEe-e--------cCCHHHHHHHhC-CHHHHHHHHHhCCcccCCcCCCCC
Confidence 332110 0 123466778899 5999999999999 799999984
No 23
>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=99.55 E-value=1e-14 Score=140.26 Aligned_cols=155 Identities=20% Similarity=0.156 Sum_probs=116.2
Q ss_pred CEEEeeHHHHHHHhhcccCC-C---CCCCchhHHHHHHHHHHHHHHc--CCEEEEEEcCCCCcchhhhhHhhhhcCcccc
Q 007971 25 KRVCIDLSCWIVQLQNVNKS-Y---RPQTDKLFLRGLFHRLRALIAL--NCGLIFVSDGSIPAIKLSTYRRRLNSGSEVT 98 (583)
Q Consensus 25 k~IaIDas~wL~~~~~a~~~-~---~g~~~~~~Lr~lf~rl~~Ll~~--gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~ 98 (583)
+.++|||++++||++++... . ..|.++..+.+|+..+.+|++. +-++++|||+..+.++...+..++++|..
T Consensus 2 ~llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l~p~YKanR~~-- 79 (169)
T PF02739_consen 2 KLLLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKELYPEYKANRKP-- 79 (169)
T ss_dssp EEEEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHCCTTTTHHHHH--
T ss_pred eEEEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHHHHHHHhCCCC--
Confidence 46899999999999988751 1 2355678999999999888874 45789999998887777766666655432
Q ss_pred cccccHHHHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHH----cCCeeEEecCCCcEEeecCc-
Q 007971 99 QDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNL----ESLCDGCFSSDSDIFLFGAR- 172 (583)
Q Consensus 99 ~~~~~~~~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~----~g~vd~ViS~DsD~llfG~~- 172 (583)
++..+..++..++++++.+||+++..| +|||+.+|.|++ .|.-..|+|.|.|++++...
T Consensus 80 ---------------~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~ 144 (169)
T PF02739_consen 80 ---------------MPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDEN 144 (169)
T ss_dssp ---------------HHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-
T ss_pred ---------------CCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCC
Confidence 345677788999999999999999998 799999999975 46667899999999999888
Q ss_pred -EEEEEcccCCCceEEEEeHHHHHHHh
Q 007971 173 -TVYRDIWLGERGYVVCYEMDDIERKL 198 (583)
Q Consensus 173 -~V~r~~~~~~~~~v~~y~~~~i~~~l 198 (583)
.|+.- .. ......+|+.+.+.+++
T Consensus 145 ~~V~~~-~~-~~~~~~~~~~~~v~eky 169 (169)
T PF02739_consen 145 VNVYLL-DP-GKKKFKVYDPEEVEEKY 169 (169)
T ss_dssp TSEEEE-ET-TTTCS-EB-HHHHHHHT
T ss_pred ceEEEe-ec-CCCCCEEEcHHHHhhcC
Confidence 44431 11 12345689998887764
No 24
>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=99.24 E-value=8.1e-12 Score=104.74 Aligned_cols=50 Identities=38% Similarity=0.689 Sum_probs=45.7
Q ss_pred HhCCChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCHH-HHHHHHh
Q 007971 197 KLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDNV-VLQRIAS 246 (583)
Q Consensus 197 ~lgL~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~~-il~~~~~ 246 (583)
.+|++++||+++|+|+| |||+|||||||+|||.+|+++|++.+ ++++++.
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 99999999999999999999999984 6766654
No 25
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.80 E-value=4.6e-09 Score=75.93 Aligned_cols=33 Identities=42% Similarity=0.913 Sum_probs=30.4
Q ss_pred hHHHHHHHHHhCCCCCC---CCCCCCHHHHHHHHHHc
Q 007971 202 RNSLITLALLLGSDYSQ---GVRGLGPESACQIVKSV 235 (583)
Q Consensus 202 r~qli~laiL~G~DY~p---GvpGiG~ktA~~Li~~~ 235 (583)
++||+++|+|+| ||++ ||||||+|+|++|+++|
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 579999999999 7776 99999999999999986
No 26
>PF12813 XPG_I_2: XPG domain containing
Probab=98.66 E-value=1.1e-07 Score=97.03 Aligned_cols=87 Identities=24% Similarity=0.355 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHh---CCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeecC----cEE-EEEcccCC------Cce-
Q 007971 121 MIKEAKALGLSL---GVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGA----RTV-YRDIWLGE------RGY- 185 (583)
Q Consensus 121 ~i~~~k~LL~~~---GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG~----~~V-~r~~~~~~------~~~- 185 (583)
++..+.+.|+.+ |++++.+|+|||..||.++++.-+ +|+|+|||+|+|+. ..+ +..+.... +.+
T Consensus 5 ~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i 83 (246)
T PF12813_consen 5 LVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYI 83 (246)
T ss_pred hHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCee
Confidence 345567888888 999999999999999999987666 99999999999987 233 22332211 122
Q ss_pred -EEEEeHHHHHHHhCCChHHHHHHHH
Q 007971 186 -VVCYEMDDIERKLGFGRNSLITLAL 210 (583)
Q Consensus 186 -v~~y~~~~i~~~lgL~r~qli~lai 210 (583)
..+|+.+.|++.||+. .|+.||.
T Consensus 84 ~~~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 84 SAKVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred EEEEEcHHHHHHHcCCc--hhHHHHH
Confidence 4679999999999999 8888877
No 27
>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=98.62 E-value=8.5e-10 Score=97.66 Aligned_cols=48 Identities=25% Similarity=0.483 Sum_probs=37.4
Q ss_pred CChHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCHH-HHHHHHhc
Q 007971 200 FGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDNV-VLQRIASE 247 (583)
Q Consensus 200 L~r~qli~laiL~G--~DY~pGvpGiG~ktA~~Li~~~g~~~-il~~~~~~ 247 (583)
+.|+|++|+.+|+| +|++|||||||+|||.+|+++||+++ +++++...
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~ 51 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEI 51 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhc
Confidence 46899999999999 89999999999999999999999975 77777653
No 28
>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=97.89 E-value=7.5e-05 Score=75.92 Aligned_cols=171 Identities=20% Similarity=0.282 Sum_probs=81.3
Q ss_pred CCccchHHHHhhhccc--ccccc-c---CCCEEEeeHHHHHHHhhcccCCCCCCCchhHHHHHHHHHHHHHHc--CCEE-
Q 007971 1 MGVKNLWDILESCKKT--LPLHH-L---QNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIAL--NCGL- 71 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~--v~L~~-L---~gk~IaIDas~wL~~~~~a~~~~~g~~~~~~Lr~lf~rl~~Ll~~--gI~P- 71 (583)
|||+||+.||...-.. ..+.. . .=--+-||.++.+|.+...............+..+|..+..|... +-+.
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~~~~~~D~LYiDmN~IIH~~~~~~~~~~~~~~~~~~~~i~~~id~l~~~v~P~k~l 80 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENSIPSEFDNLYIDMNGIIHNCIHPNDSSIPKTEEEIFQRIFNYIDRLVRIVRPRKLL 80 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTTSEE-ESEEEEETHHHHHHHHS-SSS----SHHHHHHHHHHHHHHHHHHH-ESSEE
T ss_pred CCHHHHHHHHHHhCCcceeeccccCCCCcCCEEEEEcchhhhHhcCCcccCCCccHHHHHHHHHHHHHHhheeecCceEE
Confidence 9999999999852111 11111 1 123688999999999865543211112234566677777777652 4444
Q ss_pred EEEEcCCCCcchhhhhHhhhhcCcc-ccccc-------ccHH----------HHHHhhhc---cchhHHHHH-HH----H
Q 007971 72 IFVSDGSIPAIKLSTYRRRLNSGSE-VTQDD-------KNLD----------KMSSLRRN---MGSEFSCMI-KE----A 125 (583)
Q Consensus 72 IFVFDG~~P~~K~~t~~~R~~~r~~-a~~~~-------~~~~----------~a~k~~R~---~~~~~~~~i-~~----~ 125 (583)
++.+||.+|..|-...++|+-+... ..... .+.. ...++..+ .|..|...+ .. +
T Consensus 81 ~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn~ITPGT~FM~~l~~~L~~~~ 160 (237)
T PF03159_consen 81 YIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFDSNCITPGTEFMEKLSDALRYYI 160 (237)
T ss_dssp EEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS----GGGSSTTSHHHHHHHHHHHHHH
T ss_pred EEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhccccccccccccccccceeccCCHHHHHHHHHHHHHH
Confidence 5779999998887655444322111 00000 0000 00122222 133342222 11 2
Q ss_pred HHHHHH----hCCCeeeC----cccHHHHHHHHHH---------cCCeeEEecCCCcEEeecC
Q 007971 126 KALGLS----LGVPCLEG----VEEAEAQCALLNL---------ESLCDGCFSSDSDIFLFGA 171 (583)
Q Consensus 126 k~LL~~----~GIp~i~A----P~EADAqcA~L~~---------~g~vd~ViS~DsD~llfG~ 171 (583)
+.-+.. -++.++.+ |||+|--+..+.+ ......|+|.|+|+++++-
T Consensus 161 ~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L 223 (237)
T PF03159_consen 161 KKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSL 223 (237)
T ss_dssp HHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHH
T ss_pred HHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHH
Confidence 222211 25566664 7999988765433 2567899999999998874
No 29
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=97.64 E-value=0.00056 Score=74.06 Aligned_cols=212 Identities=16% Similarity=0.109 Sum_probs=115.9
Q ss_pred CCccchHHHHhhhccccccc-ccCCCEEEeeHHHHHHHhhcccCCCCCCCchhHHHHHHHHHHHHHHcCCEEEEEEcCCC
Q 007971 1 MGVKNLWDILESCKKTLPLH-HLQNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSI 79 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~v~L~-~L~gk~IaIDas~wL~~~~~a~~~~~g~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~~ 79 (583)
||||+|-..|-.+..-.++. ..+++-|=||+++..+-..+.+.+ .......+..++..+.+.+=+.++..|-+.
T Consensus 1 MGIKNLK~lLl~~gsL~~i~~~~~~~~ifVD~msif~tiAysv~s-----~~eL~~~~~~~i~~w~~~~~~VtlFvDRG~ 75 (425)
T PF04599_consen 1 MGIKNLKALLLETGSLKKIDNIEKNNEIFVDTMSIFMTIAYSVNS-----LDELRNSFEEYIQQWIKNNGKVTLFVDRGS 75 (425)
T ss_pred CchhHHHHHHHhcCCceeccCCCCCccEEEEcchhhhhhhhhhCC-----HHHHHHHHHHHHHHHHhcCCeEEEEEecCc
Confidence 99999999998765433332 345689999999987765544421 223344566777777677667777778766
Q ss_pred CcchhhhhHhhhhcCccc-cc------------cccc-----HHHH-----HHhhhccchhH---H-HHHHHHHHHHHHh
Q 007971 80 PAIKLSTYRRRLNSGSEV-TQ------------DDKN-----LDKM-----SSLRRNMGSEF---S-CMIKEAKALGLSL 132 (583)
Q Consensus 80 P~~K~~t~~~R~~~r~~a-~~------------~~~~-----~~~a-----~k~~R~~~~~~---~-~~i~~~k~LL~~~ 132 (583)
-..|.....+|+..-+.. .+ +..+ .++. -+..|..-..+ + .+-.-+.++|..+
T Consensus 76 I~iK~~lReKRr~a~k~~~~RK~~~i~~l~~~~~~ld~~d~~yeEikt~~~lki~K~~F~~fla~~~n~k~~l~~~L~~~ 155 (425)
T PF04599_consen 76 INIKEPLREKRRKALKNTIKRKREEIENLEDCIKNLDVDDEFYEEIKTDLELKIQKLSFQLFLANSNNLKTILESSLSRL 155 (425)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHhc
Confidence 567777666654321110 00 0000 0110 01111111100 1 1111234555554
Q ss_pred --CCCeeeCc-ccHHHHHHH-----HHHcCCeeEEecCCCcEEeecCcEEEEEcccCCCceEEEEeHHHHHHHhCCChHH
Q 007971 133 --GVPCLEGV-EEAEAQCAL-----LNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNS 204 (583)
Q Consensus 133 --GIp~i~AP-~EADAqcA~-----L~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~~~v~~y~~~~i~~~lgL~r~q 204 (583)
+|..+.+. ..||=.+.+ ..+.|.=-.++|.|.|.++|.+.....++... ....-.|-... .++--
T Consensus 156 ~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t-~~~~Y~~~P~~------~s~YL 228 (425)
T PF04599_consen 156 KEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKT-MNQLYKFIPCS------KSRYL 228 (425)
T ss_pred cCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHh-HHhHeeecCCc------hHHHH
Confidence 88888876 488855433 23467777899999999999875322221100 00000111110 11112
Q ss_pred HHHHHHHhCCCCCCCCCCCC
Q 007971 205 LITLALLLGSDYSQGVRGLG 224 (583)
Q Consensus 205 li~laiL~G~DY~pGvpGiG 224 (583)
-.+.++.-||||.||+-|+-
T Consensus 229 ~kL~~L~NGCDfFpGLyG~~ 248 (425)
T PF04599_consen 229 SKLTALVNGCDFFPGLYGIS 248 (425)
T ss_pred HHHHHHHhcccccCCcceeE
Confidence 23456777999999999964
No 30
>PHA03065 Hypothetical protein; Provisional
Probab=97.48 E-value=0.00099 Score=71.81 Aligned_cols=229 Identities=18% Similarity=0.159 Sum_probs=117.6
Q ss_pred CCccchHHHHhhhcccccccc-c--CCCEEEeeHHHHHHHhhcccCCCCCCCchhHHH-HHHHHHHHHHHcCCEEEEEEc
Q 007971 1 MGVKNLWDILESCKKTLPLHH-L--QNKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLR-GLFHRLRALIALNCGLIFVSD 76 (583)
Q Consensus 1 MGIkgL~~~L~~~~~~v~L~~-L--~gk~IaIDas~wL~~~~~a~~~~~g~~~~~~Lr-~lf~rl~~Ll~~gI~PIFVFD 76 (583)
||||+|-..|-....-.+++. . ..+-|=||+++...-..+++. ....|+ .+..++..+.+..=+.++..|
T Consensus 1 MGIKNLKtLLL~~gsL~~~~~~~~~~~~~iFVD~ms~fmsiAysv~------~~~eL~~~~~~~iq~w~~~~gkVtlFvD 74 (438)
T PHA03065 1 MGIKNLKTLLLETGSLTKLDNNLKDRFNGIFVDTMSVFMSIAYSVN------NLDELRSTFEEYVQQWVKKAGKVTLFVD 74 (438)
T ss_pred CchhhHHHHHHhcCCcccccccccccCceEEEechhhhhhhhhhhC------CHHHHHHHHHHHHHHHHhcCCcEEEEEe
Confidence 999999999986544334422 2 236899999998766544432 123344 455677777555555555557
Q ss_pred CCCCcchhhhhHhhhhcCccc-cc------------cccc-----HHHH-----HHhhhccchhH---HHHH-HHHHHHH
Q 007971 77 GSIPAIKLSTYRRRLNSGSEV-TQ------------DDKN-----LDKM-----SSLRRNMGSEF---SCMI-KEAKALG 129 (583)
Q Consensus 77 G~~P~~K~~t~~~R~~~r~~a-~~------------~~~~-----~~~a-----~k~~R~~~~~~---~~~i-~~~k~LL 129 (583)
-+.-+.|.....+|++.-... .+ +..+ .++. -+.+|.+-..| +..+ .-+.+.|
T Consensus 75 RG~I~IK~~lReKRr~a~~~~~kRK~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F~~fLa~~~nlk~~l~~~L 154 (438)
T PHA03065 75 RGSIPIKQSLREKRRKASKNTIKRKREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSFQLFLANSNNLKRLLESAL 154 (438)
T ss_pred cCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHcchhhHHHHHHHHH
Confidence 655567777666655421110 00 0000 0111 01122111101 1112 2234456
Q ss_pred HHh--CCCeeeCc-ccHHHHH-HH---H-HHcCCeeEEecCCCcEEeecCcEEEEEcccCCCceEEEEeHHHHHHHhCCC
Q 007971 130 LSL--GVPCLEGV-EEAEAQC-AL---L-NLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFG 201 (583)
Q Consensus 130 ~~~--GIp~i~AP-~EADAqc-A~---L-~~~g~vd~ViS~DsD~llfG~~~V~r~~~~~~~~~v~~y~~~~i~~~lgL~ 201 (583)
..+ +|..+.+. -.||=.+ ++ + .+.|.=-.++|.|.|.++|.+..-...+...- ...-.|-... .+
T Consensus 155 ~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~KiI~t~-~~~Y~~~P~~------~t 227 (438)
T PHA03065 155 ARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKIIKTA-NQLYKFIPCA------KT 227 (438)
T ss_pred HhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHHHHhH-HHHheeCCCh------hH
Confidence 666 88888876 4777553 32 2 34677778999999999997743111110000 0000000000 01
Q ss_pred hHHHHHHHHHhCCCCCCCCCCCC--HHH--HHHHHHHcCCHHHHH
Q 007971 202 RNSLITLALLLGSDYSQGVRGLG--PES--ACQIVKSVGDNVVLQ 242 (583)
Q Consensus 202 r~qli~laiL~G~DY~pGvpGiG--~kt--A~~Li~~~g~~~il~ 242 (583)
+---.+.++.-||||.||+-|+- +++ -.+|...|.-.++++
T Consensus 228 ~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dFt~~Nv~~ 272 (438)
T PHA03065 228 RYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDFTIDNVVR 272 (438)
T ss_pred HHHHHHHHHHhcccccCccceEEechhhccceechhhhhHHHHHH
Confidence 11123446667999999999974 332 234444444344444
No 31
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=97.07 E-value=0.00021 Score=77.33 Aligned_cols=112 Identities=21% Similarity=0.337 Sum_probs=84.8
Q ss_pred HHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEEeecC-cEEEEEcccCCC-ceEEEEeHHHHHHHhCCCh
Q 007971 125 AKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGA-RTVYRDIWLGER-GYVVCYEMDDIERKLGFGR 202 (583)
Q Consensus 125 ~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~llfG~-~~V~r~~~~~~~-~~v~~y~~~~i~~~lgL~r 202 (583)
+-.++..-|+.++++||-|..|||||....+++++.. -+|++++.+ .+.+-.+.++.+ .++.+|......+-.-.+-
T Consensus 134 ~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~g-p~d~l~ld~vdr~il~m~fg~d~Ppl~~~~vp~~lem~l~s~ 212 (531)
T COG5366 134 ASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAFG-PSDILLLDGVDRIILDMSFGSDKPPLDVFHVPRFLEMFLLSS 212 (531)
T ss_pred ccccccccceEEEehhhHHHHHHHHHHHHHHHHhcCC-chHhHHHhhhhhheeecccCCCCCCCcccccchHHHhccccc
Confidence 4556778899999999999999999999999999887 789998865 455555544332 4677888777666666778
Q ss_pred HHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCC
Q 007971 203 NSLITLALLLGSDYSQGVRGLGPESACQIVKSVGD 237 (583)
Q Consensus 203 ~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~ 237 (583)
.-|...-.|.|||+++.++.|-.-.+..+-+-+|+
T Consensus 213 ~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd 247 (531)
T COG5366 213 RLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGD 247 (531)
T ss_pred chhhhhcccccccccccccccccchhHHHHHHHhc
Confidence 88889999999999999988655334444333433
No 32
>PF00385 Chromo: Chromo (CHRromatin Organisation MOdifier) domain; InterPro: IPR023780 The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1. Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro []. The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [].; PDB: 2H1E_B 3MWY_W 2DY8_A 1KNE_A 1KNA_A 1Q3L_A 2EE1_A 1AP0_A 1GUW_A 1X3P_A ....
Probab=96.47 E-value=0.0025 Score=49.66 Aligned_cols=50 Identities=26% Similarity=0.470 Sum_probs=45.1
Q ss_pred ccceeeccccCCcc---ceEEeecCCCCceeccchhhhHhhhcchHHHHHHHH
Q 007971 383 ITGIIKSRKLQGKE---CFEVSWEESYGLKSSVVPADLIESACPEKIVEFEER 432 (583)
Q Consensus 383 ~~~I~k~R~~~g~~---c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~ 432 (583)
|.+|+..|...+.. =|-|.|.+.+.-..||+|++.+...+|++|.+|+++
T Consensus 3 Ve~Il~~r~~~~~~~~~~ylVkW~g~~~~~~tWe~~~~l~~~~~~li~~f~~r 55 (55)
T PF00385_consen 3 VERILDHRVVKGGNKVYEYLVKWKGYPYSENTWEPEENLKNCFPELIEEFEKR 55 (55)
T ss_dssp EEEEEEEEEETTEESEEEEEEEETTSSGGGEEEEEGGGCSSHCHHHHHHHHHH
T ss_pred EEEEEEEEEeCCCcccEEEEEEECCCCCCCCeEeeHHHHhHhhHHHHHHHhCC
Confidence 46788888887777 799999999999999999999999999999999875
No 33
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=96.17 E-value=0.094 Score=60.04 Aligned_cols=92 Identities=15% Similarity=0.262 Sum_probs=63.1
Q ss_pred CCCeee----CcccHHHHHHHHHHc---------CCeeEEecCCCcEEeecCc------EEEE-EcccCCC---------
Q 007971 133 GVPCLE----GVEEAEAQCALLNLE---------SLCDGCFSSDSDIFLFGAR------TVYR-DIWLGER--------- 183 (583)
Q Consensus 133 GIp~i~----AP~EADAqcA~L~~~---------g~vd~ViS~DsD~llfG~~------~V~r-~~~~~~~--------- 183 (583)
++.+|. .|||.|--+-.+.+. +-..+|++-|.|++++|-. .++| +++++.+
T Consensus 176 nl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~ 255 (953)
T COG5049 176 NLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTK 255 (953)
T ss_pred eEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCccccccccccc
Confidence 455554 389999998877653 3567899999999999953 3566 4433210
Q ss_pred ----------------ceEEEEeHHHHHHHh-------CCC--------hHHHHHHHHHhCCCCCCCCCCCC
Q 007971 184 ----------------GYVVCYEMDDIERKL-------GFG--------RNSLITLALLLGSDYSQGVRGLG 224 (583)
Q Consensus 184 ----------------~~v~~y~~~~i~~~l-------gL~--------r~qli~laiL~G~DY~pGvpGiG 224 (583)
.++.+.+.+-+++.| ++. -+.+|.+|-++|+||+|.+|++-
T Consensus 256 ~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ld 327 (953)
T COG5049 256 CGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLD 327 (953)
T ss_pred ccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccc
Confidence 134566666555422 221 26788999999999999999863
No 34
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=95.61 E-value=0.015 Score=44.66 Aligned_cols=50 Identities=18% Similarity=0.424 Sum_probs=44.2
Q ss_pred ccceeecc-ccCCccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHHH
Q 007971 383 ITGIIKSR-KLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 433 (583)
Q Consensus 383 ~~~I~k~R-~~~g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~ 433 (583)
+.+|+..| ...|...|.|.|.+.+.-.-+|+|.+-+.. +|++|.+|.+++
T Consensus 4 v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~~l~~-~~~~v~~~~~~~ 54 (55)
T smart00298 4 VEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEENLLN-CSKKLDNYKKKE 54 (55)
T ss_pred hheeeeeeecCCCcEEEEEEECCCCCccCceeeHHHHHH-HHHHHHHHHHhh
Confidence 45788888 788888999999999888889999999998 999999998864
No 35
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
Probab=94.98 E-value=0.024 Score=43.65 Aligned_cols=49 Identities=24% Similarity=0.409 Sum_probs=43.3
Q ss_pred ccceeeccccC--CccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHH
Q 007971 383 ITGIIKSRKLQ--GKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEER 432 (583)
Q Consensus 383 ~~~I~k~R~~~--g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~ 432 (583)
+.+|+..|... |..-|.|.|.+.+.-.-+|+|++-+..+ |++|.+|+++
T Consensus 5 ve~Il~~r~~~~~~~~~y~VkW~g~~~~~~tWe~~~~l~~~-~~~i~~~~~~ 55 (55)
T cd00024 5 VEKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEENLEDC-KELIDEFKKK 55 (55)
T ss_pred EeeeeeeeecCCCCcEEEEEEECCCCCccCccccHHHhCch-HHHHHHHHhC
Confidence 35788888877 8999999999999888899999999988 9999999863
No 36
>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=93.70 E-value=0.61 Score=55.09 Aligned_cols=230 Identities=16% Similarity=0.258 Sum_probs=110.8
Q ss_pred CCccchHHHHh---hhc----ccccccccCCCEEEeeHHHHHHHhhcccCCCCC--CCchhHHHHHHHHHHHHHHc--CC
Q 007971 1 MGVKNLWDILE---SCK----KTLPLHHLQNKRVCIDLSCWIVQLQNVNKSYRP--QTDKLFLRGLFHRLRALIAL--NC 69 (583)
Q Consensus 1 MGIkgL~~~L~---~~~----~~v~L~~L~gk~IaIDas~wL~~~~~a~~~~~g--~~~~~~Lr~lf~rl~~Ll~~--gI 69 (583)
|||+.+..|+. ||. +.--|-++.| +=.|-++.||.+-+....+-. .........+|..+..|... +-
T Consensus 1 MGvPKFfR~iSERyP~lseliee~qIPEFDN--LYLDMNgIlHNCsH~nDddvt~rLtEeEif~~IfnYIdhLf~~IkPq 78 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCLSELIEEHQIPEFDN--LYLDMNGILHNCSHPNDDDVTFRLTEEEIFQEIFNYIDHLFYLIKPQ 78 (1493)
T ss_pred CCchHHHHHhhhhchHHHHHhhhccCCcccc--eeeecccccccCCCCCCCccCcCCCHHHHHHHHHHHHHHHHHhhCcc
Confidence 99999999997 232 2222223333 556777777765444332211 12222334455555554442 22
Q ss_pred EEEE-EEcCCCCcchhhhhHhhhhcCc-cc-------ccccccHHHHHHhhhcc---chhHH-HHHHHHHHHHHH-----
Q 007971 70 GLIF-VSDGSIPAIKLSTYRRRLNSGS-EV-------TQDDKNLDKMSSLRRNM---GSEFS-CMIKEAKALGLS----- 131 (583)
Q Consensus 70 ~PIF-VFDG~~P~~K~~t~~~R~~~r~-~a-------~~~~~~~~~a~k~~R~~---~~~~~-~~i~~~k~LL~~----- 131 (583)
+..| ..||.+|..|-...+.|+-+-. .| ..++....+ ..+-.+. +..|. .+.+.+...++.
T Consensus 79 KlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~-erFDSNcITPGTeFM~rl~~~L~yfIktKistD 157 (1493)
T KOG2045|consen 79 KLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPH-ERFDSNCITPGTEFMVRLQEGLRYFIKTKISTD 157 (1493)
T ss_pred eEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcc-cccccCCCCCcHHHHHHHHHHHHHHHHhccccc
Confidence 3233 4799998766543333321100 00 000000000 1111111 12221 111222222221
Q ss_pred ---hCCCeee----CcccHHHHHHHHHHc---------CCeeEEecCCCcEEeecCc------EEEEE-cccC-CC--c-
Q 007971 132 ---LGVPCLE----GVEEAEAQCALLNLE---------SLCDGCFSSDSDIFLFGAR------TVYRD-IWLG-ER--G- 184 (583)
Q Consensus 132 ---~GIp~i~----AP~EADAqcA~L~~~---------g~vd~ViS~DsD~llfG~~------~V~r~-~~~~-~~--~- 184 (583)
-++.+|- +|||.|--+--+.+. +--.++++=|-|++++|-- .++|. ..++ .+ +
T Consensus 158 s~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~lLREEVtFgrrn~~k~ 237 (1493)
T KOG2045|consen 158 SLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRRNKRKS 237 (1493)
T ss_pred hhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceeeeeeeeecccccccch
Confidence 2566654 699999887655432 2345788889999999853 24442 1111 11 1
Q ss_pred ----eEEEEeHHHHHHH---------------hCCC--hHHHHHHHHHhCCCCCCCCCCCCH-HHHHHHHH
Q 007971 185 ----YVVCYEMDDIERK---------------LGFG--RNSLITLALLLGSDYSQGVRGLGP-ESACQIVK 233 (583)
Q Consensus 185 ----~v~~y~~~~i~~~---------------lgL~--r~qli~laiL~G~DY~pGvpGiG~-ktA~~Li~ 233 (583)
.+-..+++-+++. +.+. -+.||+++.|+|+||+|.+|++-+ +.|+-|+-
T Consensus 238 lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlplly 308 (1493)
T KOG2045|consen 238 LEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLLY 308 (1493)
T ss_pred hhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHHH
Confidence 1222222222221 1222 266788999999999999999853 23555443
No 37
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=92.32 E-value=1.1 Score=52.45 Aligned_cols=92 Identities=12% Similarity=0.265 Sum_probs=61.4
Q ss_pred CCCeeeC----cccHHHHHHHHHHc---------CCeeEEecCCCcEEeecCc------EEEEEcccC-----------C
Q 007971 133 GVPCLEG----VEEAEAQCALLNLE---------SLCDGCFSSDSDIFLFGAR------TVYRDIWLG-----------E 182 (583)
Q Consensus 133 GIp~i~A----P~EADAqcA~L~~~---------g~vd~ViS~DsD~llfG~~------~V~r~~~~~-----------~ 182 (583)
+|.+|-+ |||.|--+-...+. +-+.++++-|-|++++|-. .++|..++. .
T Consensus 190 NikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~ 269 (931)
T KOG2044|consen 190 NIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLGLATHEPHFSILREEFFPNKPRRCFLCGQT 269 (931)
T ss_pred ceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccceeeeccccCCceEEeeeeecCCCcccchhhccc
Confidence 6666663 89999988665542 3477899999999999954 256654320 0
Q ss_pred --------C-----------------ceEEEEeHHHHHH----HhCC-------C----hHHHHHHHHHhCCCCCCCCCC
Q 007971 183 --------R-----------------GYVVCYEMDDIER----KLGF-------G----RNSLITLALLLGSDYSQGVRG 222 (583)
Q Consensus 183 --------~-----------------~~v~~y~~~~i~~----~lgL-------~----r~qli~laiL~G~DY~pGvpG 222 (583)
| +.+.+++..-+++ +|-+ + -+.+|.+|-++|+||+|.+|-
T Consensus 270 gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPs 349 (931)
T KOG2044|consen 270 GHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMPNLPFTFDLERAIDDWVFLCFFVGNDFLPHLPS 349 (931)
T ss_pred CCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCCCCCccccHHhhhcceEEEEeeecCccCCCCCc
Confidence 0 1344556554444 3322 1 267788999999999999997
Q ss_pred CC
Q 007971 223 LG 224 (583)
Q Consensus 223 iG 224 (583)
+-
T Consensus 350 Le 351 (931)
T KOG2044|consen 350 LE 351 (931)
T ss_pred hh
Confidence 63
No 38
>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=92.25 E-value=0.33 Score=46.80 Aligned_cols=99 Identities=16% Similarity=0.001 Sum_probs=53.7
Q ss_pred EEeeHHHHHHHhhcccCCCCCCCchhHHHHHHHHHHHHHH-cCCEEEEEEcCCCCcchhhhhHhhhhcCcccccccccHH
Q 007971 27 VCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIA-LNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLD 105 (583)
Q Consensus 27 IaIDas~wL~~~~~a~~~~~g~~~~~~Lr~lf~rl~~Ll~-~gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~~~~~~~~ 105 (583)
|.|||++.||..-..............=..|...|..+.. .|++.++||||...+.... . .
T Consensus 1 LlIDGYNli~~~~~l~~~~~~~~l~~aR~~Li~~L~~y~~~~~~~v~VVFDa~~~~~~~~---~-----~---------- 62 (166)
T PF05991_consen 1 LLIDGYNLIHAWPELRSLAERGDLEAARERLIEMLSEYAQFSGYEVIVVFDAYKVPGGSE---E-----R---------- 62 (166)
T ss_pred CeEcchhhhCCCHHHHhhcCcCCHHHHHHHHHHHHHHHhcccCCEEEEEEeCCcCCCCCc---e-----e----------
Confidence 5799999998732111110000111121234444444444 4899999999964221100 0 0
Q ss_pred HHHHhhhccchhHHHHHHHHHHHHHHhCCCeeeCc--ccHHHHHHHHHHc----CCeeEEecCCCcE
Q 007971 106 KMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGV--EEAEAQCALLNLE----SLCDGCFSSDSDI 166 (583)
Q Consensus 106 ~a~k~~R~~~~~~~~~i~~~k~LL~~~GIp~i~AP--~EADAqcA~L~~~----g~vd~ViS~DsD~ 166 (583)
...-||.++-++ ..||..+-.|... +.-..|+|+|...
T Consensus 63 -----------------------~~~~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~i 106 (166)
T PF05991_consen 63 -----------------------EEYGGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREI 106 (166)
T ss_pred -----------------------eeeCceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHH
Confidence 001467777766 6899988776542 4455788877543
No 39
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=89.18 E-value=0.29 Score=50.71 Aligned_cols=56 Identities=29% Similarity=0.417 Sum_probs=47.1
Q ss_pred cccceeeccccCCccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHHHhccCC
Q 007971 382 PITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQP 438 (583)
Q Consensus 382 ~~~~I~k~R~~~g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~~~~~ 438 (583)
++..|.+.|..+|..+|=|.|.+.+.---+|+|.+-. .-||++|.+|.+..+..+.
T Consensus 50 vvEki~~~r~~~g~~eYlvkW~Gy~~~~ntWEPee~~-~~C~~li~~~~~~~~~~k~ 105 (270)
T KOG1911|consen 50 VVEKILKRRKKNGKIEYLVKWKGYPDPDNTWEPEEHN-LDCPELIDEFEKSQKKLKK 105 (270)
T ss_pred hhhhhhhccccCCCceeeeecCCCCCccccCCchhhc-cccHHHHHHHHHHhcccCc
Confidence 4578999999999999999999999999999999622 2249999999998776643
No 40
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.09 E-value=0.33 Score=39.44 Aligned_cols=23 Identities=30% Similarity=0.527 Sum_probs=18.8
Q ss_pred CCCCCCHHHHHHHHHHcCCHHHH
Q 007971 219 GVRGLGPESACQIVKSVGDNVVL 241 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~~g~~~il 241 (583)
||||||+++|..|++.|++.+-+
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l 29 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEAL 29 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHH
T ss_pred CCCCccHHHHHHHHHHcCCHHHH
Confidence 99999999999999999997533
No 41
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.31 E-value=0.81 Score=45.37 Aligned_cols=66 Identities=18% Similarity=0.342 Sum_probs=45.0
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHH
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKR 254 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~ 254 (583)
|..+.+|.. ++....||+ +++.--.|-.|. +|+||||++|+.++..|+...+...+...+.+...+
T Consensus 42 g~~~~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~ 112 (194)
T PRK14605 42 GQRVRVFTHLHVREDALSLFGFATTEELSLFETLI------DVSGIGPKLGLAMLSAMNAEALASAIISGNAELLST 112 (194)
T ss_pred CCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHh
Confidence 344555544 333446787 455555555553 799999999999999999888888886655544433
No 42
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.04 E-value=0.79 Score=45.76 Aligned_cols=68 Identities=19% Similarity=0.329 Sum_probs=47.9
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhh
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 256 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~ 256 (583)
|..+.+|.. ++....||+ +.+..-.|-.|. +|+|||||+|+.++..++..++.+.+.+.+.+...+.+
T Consensus 43 g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ip 115 (203)
T PRK14602 43 GGQVSFFVHTVVREDALELFGFATWDERQTFIVLI------SISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVS 115 (203)
T ss_pred CCeEEEEEEEEEecCcceeeCCCCHHHHHHHHHHh------CCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCC
Confidence 344555544 333456787 566666666663 79999999999999999988888888877665554443
No 43
>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=87.03 E-value=0.95 Score=44.76 Aligned_cols=65 Identities=20% Similarity=0.299 Sum_probs=43.7
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHH
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVK 253 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~ 253 (583)
|..+.+|.. ++-...||+ +++.--.|..|. +|+|||||+|+.++..++..++.+.+.+.+.....
T Consensus 41 g~~v~l~t~~~vred~~~LyGF~~~~Er~lF~~L~------~V~GIGpK~Al~iL~~~~~~el~~aI~~~d~~~L~ 110 (191)
T TIGR00084 41 EQKAQVFTHLVVREDAELLFGFNTLEERELFKELI------KVNGVGPKLALAILSNMSPEEFVYAIETEEVKALV 110 (191)
T ss_pred CCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHhcCCHHHHHHHHHhCCHHHHH
Confidence 345555544 333346787 455555555553 79999999999999988877788888765444443
No 44
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=86.04 E-value=0.88 Score=44.91 Aligned_cols=31 Identities=29% Similarity=0.505 Sum_probs=25.2
Q ss_pred CCCCCCHHHHHHHHHHcCCHHHHHHHHhcCh
Q 007971 219 GVRGLGPESACQIVKSVGDNVVLQRIASEGL 249 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~~g~~~il~~~~~~~~ 249 (583)
.||||||++|..|+..||...+.+.+.....
T Consensus 77 ~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~ 107 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSPEELVQAIANGDV 107 (192)
T ss_pred cCCCCCHHHHHHHHHhCCHHHHHHHHHhCCH
Confidence 4999999999999999998776666655433
No 45
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.82 E-value=1.1 Score=44.49 Aligned_cols=68 Identities=22% Similarity=0.384 Sum_probs=46.8
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhh
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 256 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~ 256 (583)
|..+.+|.. ++-...||+ +.+..-.|-.|. +|.|||||+|+.++..+...++...+.+.+.+...+..
T Consensus 41 g~~v~l~t~~~vrED~~~LYGF~t~~Er~lF~~Li------sVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vp 113 (196)
T PRK13901 41 LEDVEILTYLHTREDELKLFGFLNSSEREVFEELI------GVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVK 113 (196)
T ss_pred CCcEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 344444443 333446787 455555666663 78999999999999999888888888877665555443
No 46
>KOG2748 consensus Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics]
Probab=85.52 E-value=0.44 Score=50.63 Aligned_cols=62 Identities=27% Similarity=0.389 Sum_probs=51.4
Q ss_pred ccceeeccccCCccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHHHhcc---CCCCcCCCch
Q 007971 383 ITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALR---QPKKSKPKSS 446 (583)
Q Consensus 383 ~~~I~k~R~~~g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~~~---~~kk~~~~~~ 446 (583)
+-.|+|.|.+.|+-=|=|.|.+-..=..+|+|.+=| --|-||.+|+++..++ ++||++++..
T Consensus 13 aEsIlkkRirKGrvEYlVKWkGWs~kyNTWEPEENI--LDpRLi~AFe~rErek~~~~~kKrgpkPk 77 (369)
T KOG2748|consen 13 AESILKKRIRKGRVEYLVKWKGWSQKYNTWEPEENI--LDPRLIAAFEQREREKELYGKKKRGPKPK 77 (369)
T ss_pred HHHHHHHHhhccceEEEEEecccccccCccCccccc--cCHHHHHHHHhhhHHHhhhhhhccCCCCc
Confidence 358999999999999999999999999999998755 3488999999988877 4666665443
No 47
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.51 E-value=1.1 Score=44.64 Aligned_cols=68 Identities=22% Similarity=0.337 Sum_probs=46.5
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhh
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 256 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~ 256 (583)
|..+.+|.. ++-...||+ +.+.--.|-.|. +|.|||||+|+.++..++..++...+.+.+.+...+..
T Consensus 41 g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~L~------~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvp 113 (197)
T PRK14603 41 GQEAELHTRLVVREDALSLYGFPDEDSLELFELLL------GVSGVGPKLALALLSALPPALLARALLEGDARLLTSAS 113 (197)
T ss_pred CCeEEEEEEEEEccCCceeeCcCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 344554443 333445787 444445555553 79999999999999999888888888887766655544
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.33 E-value=1.1 Score=44.04 Aligned_cols=68 Identities=19% Similarity=0.323 Sum_probs=47.6
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhh
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 256 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~ 256 (583)
|..+..|.. ++-...||+ +.+.--.|-.|. +|.|||||+|+.++..+...++...+.+.+.+...+..
T Consensus 42 g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vp 114 (183)
T PRK14601 42 GEKHELFITQIIKEDSNKLYGFLDKDEQKMFEMLL------KVNGIGANTAMAVCSSLDVNSFYKALSLGDESVLKKVP 114 (183)
T ss_pred CCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 344554443 333446787 455555566653 78999999999999999888888888887666555444
No 49
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.19 E-value=1.2 Score=44.06 Aligned_cols=68 Identities=21% Similarity=0.248 Sum_probs=47.8
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhh
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 256 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~ 256 (583)
|..+.+|.. ++....||+ +.+.--.|-.|. +|.|||||+|+.++..+...++.+.+...+.+...+.+
T Consensus 42 g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vp 114 (188)
T PRK14606 42 GGECFLHTFLSVSQDGITLYGFSNERKKELFLSLT------KVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLP 114 (188)
T ss_pred CCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 445555543 344456787 455555666663 78999999999999999888888888877666555443
No 50
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.73 E-value=1.4 Score=43.73 Aligned_cols=68 Identities=25% Similarity=0.359 Sum_probs=46.8
Q ss_pred CceEEEEeH----HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhh
Q 007971 183 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 256 (583)
Q Consensus 183 ~~~v~~y~~----~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~ 256 (583)
+..+.+|.. ++....||+ +.+.--.|-.|. +|.|||||+|+.++..+...++...+.+.+.+...+.+
T Consensus 42 g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvp 114 (195)
T PRK14604 42 GDEVFLYTHLIVREDALTLYGFSTPAQRQLFELLI------GVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVP 114 (195)
T ss_pred CCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 344554443 333445787 455555555553 78999999999999998888888888877666555544
No 51
>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=79.85 E-value=1.5 Score=30.60 Aligned_cols=15 Identities=33% Similarity=0.720 Sum_probs=12.2
Q ss_pred CCCCCCHHHHHHHHH
Q 007971 219 GVRGLGPESACQIVK 233 (583)
Q Consensus 219 GvpGiG~ktA~~Li~ 233 (583)
.+||||++||-.++.
T Consensus 15 ~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 15 KLPGIGPKTANAILS 29 (30)
T ss_dssp TSTT-SHHHHHHHHH
T ss_pred hCCCcCHHHHHHHHh
Confidence 689999999998864
No 52
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=78.77 E-value=5 Score=40.17 Aligned_cols=62 Identities=24% Similarity=0.329 Sum_probs=42.7
Q ss_pred EeHHHHHHHhCCC-hHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHHHHhh
Q 007971 189 YEMDDIERKLGFG-RNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 256 (583)
Q Consensus 189 y~~~~i~~~lgL~-r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~~~~~ 256 (583)
+-.++....||+. .+.--.|..| -.|.|||||+|+.++..+.-.++.+.+...+.+...+..
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~L------isVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~P 114 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLL------ISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIP 114 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHH------HccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCC
Confidence 4456777788984 3333444444 268999999999999988877777777766555544443
No 53
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=77.48 E-value=11 Score=37.56 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=21.5
Q ss_pred hcccccccccCCCEEEeeHHHHHHHh
Q 007971 13 CKKTLPLHHLQNKRVCIDLSCWIVQL 38 (583)
Q Consensus 13 ~~~~v~L~~L~gk~IaIDas~wL~~~ 38 (583)
..+..++..++|+.+.|||++.|--.
T Consensus 55 ~rk~~~~~~~rg~~l~iDGyNvLItl 80 (211)
T COG2454 55 VRKRMKINSLRGQDLVIDGYNVLITL 80 (211)
T ss_pred HHhhccCCCcccceEEEechhhhhhH
Confidence 34568899999999999999987654
No 54
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.49 E-value=1.6 Score=43.04 Aligned_cols=55 Identities=22% Similarity=0.385 Sum_probs=40.5
Q ss_pred HHHHHHhCC-ChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCHHHHHHHHhcChhHH
Q 007971 192 DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFV 252 (583)
Q Consensus 192 ~~i~~~lgL-~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~~il~~~~~~~~~~~ 252 (583)
++....||+ +++.--.|-.|. +|.|||||+|+.++..++..++...+.+.+.+..
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li------sV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L 110 (186)
T PRK14600 55 DNVTQLYGFLNREEQDCLRMLV------KVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL 110 (186)
T ss_pred cCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe
Confidence 444456787 455555555553 7899999999999999988888888887666544
No 55
>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=67.76 E-value=24 Score=33.39 Aligned_cols=47 Identities=17% Similarity=0.075 Sum_probs=28.5
Q ss_pred CCEEEeeHHHHHHHhhcccCCCCCCCchhHHHHHHHHHHHHHHcCCEEEEEEcCC
Q 007971 24 NKRVCIDLSCWIVQLQNVNKSYRPQTDKLFLRGLFHRLRALIALNCGLIFVSDGS 78 (583)
Q Consensus 24 gk~IaIDas~wL~~~~~a~~~~~g~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~ 78 (583)
.+.|+|||++-.+..... ...-++++..-+..|.+.|.+++.||+-.
T Consensus 2 ~r~VVIDG~NVA~~~~~~--------~~f~~~~i~~~v~~~~~rG~~~v~v~~~~ 48 (155)
T PF11977_consen 2 LRPVVIDGSNVAYSHGNQ--------KFFSVRGIQIAVEYFKSRGHEVVVVFPPN 48 (155)
T ss_dssp B--EEEEHHHHHHHHTTT--------TSEEHHHHHHHHHHHHHTT---EEEEEEG
T ss_pred CCEEEEeCHHHHhhcCCC--------CCcCHHHHHHHHHHHHHcCCCeEEEEcch
Confidence 368999999986622110 11345666666777889999999999974
No 56
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=63.86 E-value=5.6 Score=26.41 Aligned_cols=18 Identities=33% Similarity=0.612 Sum_probs=15.1
Q ss_pred CCCCCCCCHHHHHHHHHH
Q 007971 217 SQGVRGLGPESACQIVKS 234 (583)
Q Consensus 217 ~pGvpGiG~ktA~~Li~~ 234 (583)
...|||||+++|..++..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 347999999999999863
No 57
>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=62.15 E-value=8.7 Score=30.16 Aligned_cols=21 Identities=24% Similarity=0.463 Sum_probs=14.9
Q ss_pred CCCCCCHHHHHHHHHH-cCCHH
Q 007971 219 GVRGLGPESACQIVKS-VGDNV 239 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~-~g~~~ 239 (583)
+|.|||++||.++... +.+++
T Consensus 6 ~I~GVG~~tA~~w~~~G~rtl~ 27 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAKGIRTLE 27 (52)
T ss_dssp TSTT--HHHHHHHHHTT--SHH
T ss_pred hcccccHHHHHHHHHhCCCCHH
Confidence 7899999999999997 66664
No 58
>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=59.84 E-value=7 Score=33.40 Aligned_cols=23 Identities=26% Similarity=0.606 Sum_probs=20.3
Q ss_pred CCCCCCCCCHHHHHHHHHHcCCH
Q 007971 216 YSQGVRGLGPESACQIVKSVGDN 238 (583)
Q Consensus 216 Y~pGvpGiG~ktA~~Li~~~g~~ 238 (583)
-+..|||||+.+|..|+.+.|+.
T Consensus 3 ~l~sipGig~~~a~~llaeigd~ 25 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDI 25 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCc
Confidence 34689999999999999999876
No 59
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.59 E-value=7.8 Score=38.20 Aligned_cols=36 Identities=36% Similarity=0.559 Sum_probs=25.6
Q ss_pred CCChHHHHHHHHHhCC-CCCCCCCCCCHHHHHHHHHHc
Q 007971 199 GFGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSV 235 (583)
Q Consensus 199 gL~r~qli~laiL~G~-DY~pGvpGiG~ktA~~Li~~~ 235 (583)
.+++++|.. |+..|. .....+||||+|||-+|+-+.
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 467777665 444443 334699999999999999663
No 60
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=53.45 E-value=12 Score=43.70 Aligned_cols=26 Identities=15% Similarity=0.424 Sum_probs=22.3
Q ss_pred CCCCCCCHHHHHHHHHHcCCHHHHHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNVVLQR 243 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~il~~ 243 (583)
.||||||+++|..|++.||+.+.+.+
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHHh
Confidence 59999999999999999999864443
No 61
>cd00034 ChSh Chromo Shadow Domain, found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2)
Probab=53.41 E-value=26 Score=27.63 Aligned_cols=38 Identities=26% Similarity=0.602 Sum_probs=32.4
Q ss_pred CccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHHHh
Q 007971 394 GKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRA 434 (583)
Q Consensus 394 g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~ 434 (583)
|-=-|-+.|.+ + ..++||+.++...||.+|-+|=++..
T Consensus 14 g~l~fl~kwk~-~--~~~lVp~~~~~~k~P~~vI~FYE~~l 51 (54)
T cd00034 14 GELTFLAKWKD-G--QASLVPNKELNVKCPLLVISFYEEHL 51 (54)
T ss_pred CeEEEEEEEeC-C--eEEEEEHHHHHhhCcHHHHHHHHHhc
Confidence 77788899999 5 45589999999999999999977653
No 62
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.30 E-value=9.6 Score=38.01 Aligned_cols=36 Identities=22% Similarity=0.314 Sum_probs=25.1
Q ss_pred CCChHHHHHHHHHhCC-CCCCCCCCCCHHHHHHHHHHc
Q 007971 199 GFGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSV 235 (583)
Q Consensus 199 gL~r~qli~laiL~G~-DY~pGvpGiG~ktA~~Li~~~ 235 (583)
.+++++|+. |+..|. .....+||||+|||-+|+-+.
T Consensus 91 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 91 GIKYNEFRD-AIDREDIELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 356776665 334442 334699999999999999663
No 63
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.89 E-value=10 Score=37.63 Aligned_cols=39 Identities=26% Similarity=0.247 Sum_probs=26.1
Q ss_pred HHhC-CChHHHHHHHHHhCC-CCCCCCCCCCHHHHHHHHHHc
Q 007971 196 RKLG-FGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSV 235 (583)
Q Consensus 196 ~~lg-L~r~qli~laiL~G~-DY~pGvpGiG~ktA~~Li~~~ 235 (583)
.-|+ +++++|+. |+..|. .....+||||+|||-+|+-+.
T Consensus 88 ~iLs~~~~~el~~-aI~~~D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 88 NLLSSGTPDELQL-AIAGGDVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred HHHcCCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 3443 56777665 333332 334699999999999999663
No 64
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.83 E-value=11 Score=37.38 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=27.2
Q ss_pred HHHh-CCChHHHHHHHHHhCC-CCCCCCCCCCHHHHHHHHHHc
Q 007971 195 ERKL-GFGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSV 235 (583)
Q Consensus 195 ~~~l-gL~r~qli~laiL~G~-DY~pGvpGiG~ktA~~Li~~~ 235 (583)
..-+ ++++++|+. |+..|. .....+||||+|||-+|+-+.
T Consensus 87 L~iLs~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 87 LKIISNEDAETLVT-MIASQDVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred HHHHcCCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 3444 457777665 344443 344699999999999999663
No 65
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.37 E-value=13 Score=37.07 Aligned_cols=35 Identities=20% Similarity=0.253 Sum_probs=24.7
Q ss_pred CChHHHHHHHHHhCC-CCCCCCCCCCHHHHHHHHHHc
Q 007971 200 FGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSV 235 (583)
Q Consensus 200 L~r~qli~laiL~G~-DY~pGvpGiG~ktA~~Li~~~ 235 (583)
+++++|+. |+..|+ .-...+||||+|||-+|+-+.
T Consensus 94 ~~~~~l~~-aI~~~D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 94 FRPDDLRR-LVAEEDVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CCHHHHHH-HHHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence 56676655 444443 334699999999999999663
No 66
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=49.34 E-value=14 Score=43.06 Aligned_cols=23 Identities=17% Similarity=0.362 Sum_probs=20.8
Q ss_pred CCCCCCCHHHHHHHHHHcCCHHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNVV 240 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~i 240 (583)
.+|||||++++..|++.||+.+-
T Consensus 555 ~~IpGIG~kr~~~LL~~FgSi~~ 577 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFGSLER 577 (624)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHH
Confidence 48999999999999999999743
No 67
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.31 E-value=12 Score=37.29 Aligned_cols=40 Identities=25% Similarity=0.210 Sum_probs=27.0
Q ss_pred HHHhC-CChHHHHHHHHHhCCCC--CCCCCCCCHHHHHHHHHHcC
Q 007971 195 ERKLG-FGRNSLITLALLLGSDY--SQGVRGLGPESACQIVKSVG 236 (583)
Q Consensus 195 ~~~lg-L~r~qli~laiL~G~DY--~pGvpGiG~ktA~~Li~~~g 236 (583)
..-|+ +++++|+. |+.. .|. ...+||||+|||-+|+-+..
T Consensus 86 L~iLs~~~~~~l~~-aI~~-~D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 86 LALLSALPPALLAR-ALLE-GDARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred HHHHcCCCHHHHHH-HHHh-CCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 34444 67777665 3333 343 35999999999999996643
No 68
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=48.30 E-value=16 Score=42.04 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=20.9
Q ss_pred CCCCCCCHHHHHHHHHHcCCHHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNVV 240 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~i 240 (583)
.+|||||+++...|++.||+.+-
T Consensus 517 d~I~GiG~kr~~~Ll~~Fgs~~~ 539 (567)
T PRK14667 517 DKIKGIGEVKKEIIYRNFKTLYD 539 (567)
T ss_pred ccCCCCCHHHHHHHHHHhCCHHH
Confidence 49999999999999999999753
No 69
>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=47.30 E-value=16 Score=28.89 Aligned_cols=21 Identities=19% Similarity=0.464 Sum_probs=18.7
Q ss_pred CCCCCCHHHHHHHHHH-cCCHH
Q 007971 219 GVRGLGPESACQIVKS-VGDNV 239 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~-~g~~~ 239 (583)
.|||||+++|..|... |++..
T Consensus 9 ~I~Gig~~~a~~L~~~G~~t~~ 30 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIKTLE 30 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCSSHH
T ss_pred cCCCCCHHHHHHHHhcCCCcHH
Confidence 6999999999999999 88763
No 70
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=47.23 E-value=19 Score=36.13 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=23.9
Q ss_pred CChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHc
Q 007971 200 FGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSV 235 (583)
Q Consensus 200 L~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~ 235 (583)
++.+.|+..-..-=-.+...+||||+|||-+|+-+.
T Consensus 93 ~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 93 LDPEELAQAIANEDVKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHH
Confidence 466666553222112445699999999999999653
No 71
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.07 E-value=16 Score=36.18 Aligned_cols=39 Identities=18% Similarity=0.276 Sum_probs=27.2
Q ss_pred HHHhC-CChHHHHHHHHHhCC-CCCCCCCCCCHHHHHHHHHHc
Q 007971 195 ERKLG-FGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSV 235 (583)
Q Consensus 195 ~~~lg-L~r~qli~laiL~G~-DY~pGvpGiG~ktA~~Li~~~ 235 (583)
..-|. +++++|+. |+..|. ..+ .+||||+|||-+|+-+.
T Consensus 87 l~iLs~~~~~~l~~-aI~~~D~~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 87 MSILSKLTPEQLFS-AIVNEDKAAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred HHHHccCCHHHHHH-HHHcCCHhhe-ECCCCcHHHHHHHHHHH
Confidence 34443 67777765 444453 345 89999999999999653
No 72
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=45.18 E-value=20 Score=41.46 Aligned_cols=24 Identities=29% Similarity=0.477 Sum_probs=21.4
Q ss_pred CCCCCCCCHHHHHHHHHHcCCHHH
Q 007971 217 SQGVRGLGPESACQIVKSVGDNVV 240 (583)
Q Consensus 217 ~pGvpGiG~ktA~~Li~~~g~~~i 240 (583)
...|||||+++...|++.||+.+-
T Consensus 516 L~~I~GiG~kr~~~LL~~Fgs~~~ 539 (574)
T PRK14670 516 YTKIKGIGEKKAKKILKSLGTYKD 539 (574)
T ss_pred cccCCCCCHHHHHHHHHHhCCHHH
Confidence 459999999999999999999753
No 73
>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=44.50 E-value=20 Score=41.45 Aligned_cols=25 Identities=16% Similarity=0.316 Sum_probs=21.7
Q ss_pred CCCCCCCHHHHHHHHHHcCCHHHHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNVVLQ 242 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~il~ 242 (583)
.+|||||+++...|++.||+.+-+.
T Consensus 544 d~I~GIG~kr~~~LL~~Fgs~~~i~ 568 (574)
T TIGR00194 544 LKIPGVGEKRVQKLLKYFGSLKGIK 568 (574)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHH
Confidence 4899999999999999999975443
No 74
>smart00300 ChSh Chromo Shadow Domain.
Probab=39.39 E-value=39 Score=27.24 Aligned_cols=40 Identities=28% Similarity=0.614 Sum_probs=33.4
Q ss_pred cCCccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHHHh
Q 007971 392 LQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRA 434 (583)
Q Consensus 392 ~~g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~ 434 (583)
.+|-=-|-+.|.+ + ..++||+.++...||.+|-+|=++..
T Consensus 18 ~~G~l~flikwk~-~--~~~lVp~~~~~~k~P~~vI~FYE~~l 57 (61)
T smart00300 18 DDGELTFLIKWKD-D--AASLVPNKEANVKCPQKVIRFYESHL 57 (61)
T ss_pred CCCeEEEEEEEeC-C--cEEEEEHHHHHHHChHHHHHHHHHhC
Confidence 5666778899999 5 45589999999999999999977653
No 75
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=39.36 E-value=29 Score=34.62 Aligned_cols=17 Identities=29% Similarity=0.554 Sum_probs=14.5
Q ss_pred CCCCCCCHHHHHHHHHH
Q 007971 218 QGVRGLGPESACQIVKS 234 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~ 234 (583)
.-+||||+|+|.+++-.
T Consensus 15 ~kLPGvG~KsA~R~Afh 31 (198)
T COG0353 15 KKLPGVGPKSAQRLAFH 31 (198)
T ss_pred hhCCCCChhHHHHHHHH
Confidence 46899999999999855
No 76
>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=39.34 E-value=21 Score=25.02 Aligned_cols=14 Identities=21% Similarity=0.411 Sum_probs=11.0
Q ss_pred CCCCCCHHHHHHHH
Q 007971 219 GVRGLGPESACQIV 232 (583)
Q Consensus 219 GvpGiG~ktA~~Li 232 (583)
-++|||.+|+-+|-
T Consensus 15 ~~~GIG~kt~~kL~ 28 (32)
T PF11798_consen 15 KFWGIGKKTAKKLN 28 (32)
T ss_dssp GSTTS-HHHHHHHH
T ss_pred hhCCccHHHHHHHH
Confidence 68999999998863
No 77
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=38.10 E-value=30 Score=40.76 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=21.2
Q ss_pred CCCCCCCHHHHHHHHHHcCCHHHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNVVL 241 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~il 241 (583)
..|||||++++..|++.||+..-+
T Consensus 611 ~~IpGiG~kr~~~LL~~FgS~~~i 634 (691)
T PRK14672 611 ERLPHVGKVRAHRLLAHFGSFRSL 634 (691)
T ss_pred ccCCCCCHHHHHHHHHHhcCHHHH
Confidence 489999999999999999997533
No 78
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=37.86 E-value=27 Score=36.82 Aligned_cols=48 Identities=27% Similarity=0.299 Sum_probs=40.4
Q ss_pred HHhhhc--cchhHHHHHHHHHHHHHHhCCCeeeCc-ccHHHHHHHHHHcCC
Q 007971 108 SSLRRN--MGSEFSCMIKEAKALGLSLGVPCLEGV-EEAEAQCALLNLESL 155 (583)
Q Consensus 108 ~k~~R~--~~~~~~~~i~~~k~LL~~~GIp~i~AP-~EADAqcA~L~~~g~ 155 (583)
++..|. ++..+..++..+.+++..+|++++..+ +||||.++.+++.-.
T Consensus 82 yK~~R~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~ 132 (310)
T COG0258 82 YKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY 132 (310)
T ss_pred HHhCCCccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHH
Confidence 444453 466788899999999999999999988 799999999999744
No 79
>TIGR03090 SASP_tlp small, acid-soluble spore protein tlp. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. Although previously designated tlp (thioredoxin-like protein), the B. subtilis protein was shown to be a minor small acid-soluble spore protein SASP, unique to spores. The motif E[VIL]XDE near the C-terminus probably represents at a germination protease cleavage site.
Probab=35.63 E-value=6.8 Score=32.67 Aligned_cols=53 Identities=25% Similarity=0.471 Sum_probs=35.5
Q ss_pred CCcc-cccccccccccCCCCeeeeeCCCC----CCCCChHHHH--------HHHHHHHHHHHhhhh
Q 007971 529 PSPV-QCRNVSRIREMSDQPINTIELSDS----ETEKSPELER--------KARALRMFIASIRDD 581 (583)
Q Consensus 529 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~--------~~~~~~~~~~~~~~~ 581 (583)
|.|- ++++|-|.|++-++.|+=|+..+- -+|+|++.++ +-..|..|=+-|+||
T Consensus 1 ~kPDdRsDNVEkLQ~mi~nTieN~~eAee~l~~~~el~~~~~~~i~eKN~RR~eSi~~~r~EIkDE 66 (70)
T TIGR03090 1 AKPDDRSDNVEKLQQMIDNTIENMEEANEYIEAHAELSEEEKQRIEEKNERREQSIDGFRSEIKDE 66 (70)
T ss_pred CCCCcccchHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhHHHHHHHHHHHHHhH
Confidence 6788 999999999998887775554332 1156776554 334466666666665
No 80
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=34.16 E-value=35 Score=39.65 Aligned_cols=22 Identities=23% Similarity=0.521 Sum_probs=20.3
Q ss_pred CCCCCCCHHHHHHHHHHcCCHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNV 239 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~ 239 (583)
.+|||||++++..|++.||+..
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~ 567 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLK 567 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHH
Confidence 4899999999999999999974
No 81
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=32.68 E-value=41 Score=34.44 Aligned_cols=22 Identities=18% Similarity=0.389 Sum_probs=20.2
Q ss_pred CCCCCCCHHHHHHHHHH-cCCHH
Q 007971 218 QGVRGLGPESACQIVKS-VGDNV 239 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~-~g~~~ 239 (583)
..|||||+++|..|++. |++..
T Consensus 6 ~~IpGIG~krakkLl~~GF~Sve 28 (232)
T PRK12766 6 EDISGVGPSKAEALREAGFESVE 28 (232)
T ss_pred ccCCCcCHHHHHHHHHcCCCCHH
Confidence 48999999999999999 99975
No 82
>PF01393 Chromo_shadow: Chromo shadow domain Web page maintained by Rein Aasland; InterPro: IPR008251 Chromo shadow domain is distantly related to chromo domain. It is always found in association with a chromo domain. The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain [], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2. The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigenand and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.; GO: 0005634 nucleus; PDB: 3Q6S_C 2FMM_B 3P7J_B 1E0B_B 3I3C_A 1DZ1_B 1S4Z_A 3KUP_D.
Probab=31.67 E-value=85 Score=25.14 Aligned_cols=46 Identities=26% Similarity=0.622 Sum_probs=34.7
Q ss_pred eeeccccCCccceEEeecCCCCceeccchhhhHhhhcchHHHHHHHHH
Q 007971 386 IIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 433 (583)
Q Consensus 386 I~k~R~~~g~~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~ 433 (583)
|+..=...|---|=|.|.+.+ ..++||+.++...||.+|-.|-+..
T Consensus 8 Ivg~~d~~G~l~~likwk~~~--~~~~v~~~~~~~k~Pq~vI~FYE~~ 53 (58)
T PF01393_consen 8 IVGATDTNGELMFLIKWKNSG--EKDLVPSKEANEKCPQKVIKFYESH 53 (58)
T ss_dssp EEEEEECTSSEEEEEEETTSS--SEEEEEHHHHHHHSHHHHHHHHHHT
T ss_pred HheeecCCCcEEEEEEECCCC--ceEEeeHHHHHHHCcHHHHHHHHHH
Confidence 343333346556668999877 4678999999999999999997754
No 83
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=30.80 E-value=1.1e+02 Score=33.66 Aligned_cols=41 Identities=20% Similarity=0.055 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEec
Q 007971 121 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFS 161 (583)
Q Consensus 121 ~i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS 161 (583)
-+.++++-|+.+|++.++.-+++...+..|.+.--+..|++
T Consensus 62 sL~~L~~~L~~~g~~L~v~~G~~~~vl~~L~~~~~~~~V~~ 102 (429)
T TIGR02765 62 SLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFL 102 (429)
T ss_pred HHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHhCCCEEEE
Confidence 34455555666777777776777777766666544555555
No 84
>PRK00076 recR recombination protein RecR; Reviewed
Probab=30.73 E-value=73 Score=31.89 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=14.7
Q ss_pred CCCCCCCHHHHHHHHHH
Q 007971 218 QGVRGLGPESACQIVKS 234 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~ 234 (583)
.-+||||+|+|.+++-.
T Consensus 14 ~~LPGIG~KsA~Rla~~ 30 (196)
T PRK00076 14 RKLPGIGPKSAQRLAFH 30 (196)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36899999999999865
No 85
>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=30.32 E-value=41 Score=33.29 Aligned_cols=33 Identities=9% Similarity=0.176 Sum_probs=21.2
Q ss_pred ChHHHHHHHHHhCC-CCCCCCCCCCHHHHHHHHHH
Q 007971 201 GRNSLITLALLLGS-DYSQGVRGLGPESACQIVKS 234 (583)
Q Consensus 201 ~r~qli~laiL~G~-DY~pGvpGiG~ktA~~Li~~ 234 (583)
+.++++.. +..|. .....+||||+|||-+|+-+
T Consensus 93 ~~~el~~a-I~~~d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 93 SPEEFVYA-IETEEVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CHHHHHHH-HHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 55555543 22232 22348999999999999833
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=29.80 E-value=78 Score=31.64 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=14.5
Q ss_pred CCCCCCCHHHHHHHHHH
Q 007971 218 QGVRGLGPESACQIVKS 234 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~ 234 (583)
.-+||||+|+|.+++-.
T Consensus 14 ~~LPGIG~KsA~RlA~~ 30 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFH 30 (195)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36899999999999865
No 87
>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=28.27 E-value=77 Score=28.94 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=15.7
Q ss_pred CCCCCCHHHHHHHHHHc
Q 007971 219 GVRGLGPESACQIVKSV 235 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~~ 235 (583)
.+||||+++|.+|+..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 68999999999999986
No 88
>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=27.51 E-value=53 Score=38.57 Aligned_cols=21 Identities=29% Similarity=0.438 Sum_probs=14.9
Q ss_pred CCCCCCHHHHHHHHHHcCCHH
Q 007971 219 GVRGLGPESACQIVKSVGDNV 239 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~~g~~~ 239 (583)
||||||+++|..|++.|++.+
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~ 522 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLD 522 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHH
Confidence 677777777777777777653
No 89
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.79 E-value=57 Score=38.61 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=16.5
Q ss_pred CCCCCCHHHHHHHHHHcCCHH
Q 007971 219 GVRGLGPESACQIVKSVGDNV 239 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~~g~~~ 239 (583)
||||||+++|..|++.|++.+
T Consensus 532 gIpgIG~~~ak~L~~~F~si~ 552 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFE 552 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHH
Confidence 678888888888888887764
No 90
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=25.83 E-value=52 Score=39.10 Aligned_cols=34 Identities=24% Similarity=0.490 Sum_probs=25.1
Q ss_pred CCChHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCH
Q 007971 199 GFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDN 238 (583)
Q Consensus 199 gL~r~qli~laiL~G~DY~pGvpGiG~ktA~~Li~~~g~~ 238 (583)
--+.+.++.+.. + ..++|||+++|-+|+..||..
T Consensus 74 p~~~~~i~~yL~---s---~~~~GIG~~~A~~iv~~fg~~ 107 (720)
T TIGR01448 74 PTSKEGIVAYLS---S---RSIKGVGKKLAQRIVKTFGEA 107 (720)
T ss_pred CCCHHHHHHHHh---c---CCCCCcCHHHHHHHHHHhCHh
Confidence 335566666532 2 248999999999999999975
No 91
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=25.72 E-value=63 Score=37.45 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=20.9
Q ss_pred CCCCCCCCHHHHHHHHHHcCCHH
Q 007971 217 SQGVRGLGPESACQIVKSVGDNV 239 (583)
Q Consensus 217 ~pGvpGiG~ktA~~Li~~~g~~~ 239 (583)
...|||||++++.+|++.||+..
T Consensus 527 L~~IpGIG~kr~~~LL~~FGS~~ 549 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRFGSVE 549 (577)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHH
Confidence 35899999999999999999974
No 92
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=25.71 E-value=60 Score=38.35 Aligned_cols=22 Identities=32% Similarity=0.502 Sum_probs=20.2
Q ss_pred CCCCCCCHHHHHHHHHHcCCHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNV 239 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~ 239 (583)
..|||||++++..|++.||+.+
T Consensus 640 ~~IPGIGpkr~k~LL~~FGSle 661 (694)
T PRK14666 640 QRVEGIGPATARLLWERFGSLQ 661 (694)
T ss_pred hhCCCCCHHHHHHHHHHhCCHH
Confidence 4899999999999999999974
No 93
>PRK13844 recombination protein RecR; Provisional
Probab=24.89 E-value=1.1e+02 Score=30.65 Aligned_cols=17 Identities=12% Similarity=0.227 Sum_probs=14.6
Q ss_pred CCCCCCCHHHHHHHHHH
Q 007971 218 QGVRGLGPESACQIVKS 234 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~ 234 (583)
.-+||||+|+|.+++-.
T Consensus 18 ~~LPGIG~KsA~Rla~~ 34 (200)
T PRK13844 18 RKLPTIGKKSSQRLALY 34 (200)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36799999999999865
No 94
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=23.48 E-value=2.1e+02 Score=32.18 Aligned_cols=11 Identities=9% Similarity=0.250 Sum_probs=9.5
Q ss_pred CCEEEEEEcCC
Q 007971 68 NCGLIFVSDGS 78 (583)
Q Consensus 68 gI~PIFVFDG~ 78 (583)
.+.||||||..
T Consensus 30 ~vlpvyv~dp~ 40 (472)
T PRK10674 30 RVLALFIATPA 40 (472)
T ss_pred CEEEEEEECch
Confidence 48999999974
No 95
>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=23.40 E-value=1.1e+02 Score=28.67 Aligned_cols=40 Identities=15% Similarity=0.092 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCC
Q 007971 123 KEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSD 163 (583)
Q Consensus 123 ~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~D 163 (583)
....+.++..|+++....-.-.++..++.+.| ||+|+|++
T Consensus 150 ~~~i~~~~~~g~~v~~wtvn~~~~~~~~~~~G-VdgI~TD~ 189 (189)
T cd08556 150 PELVRAAHAAGLKVYVWTVNDPEDARRLLALG-VDGIITDD 189 (189)
T ss_pred HHHHHHHHHcCCEEEEEcCCCHHHHHHHHHCC-CCEEecCC
Confidence 34455666789999887655566777777777 89999963
No 96
>COG1663 LpxK Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]
Probab=22.60 E-value=3.8e+02 Score=29.14 Aligned_cols=93 Identities=22% Similarity=0.186 Sum_probs=56.4
Q ss_pred CCCCchhHHHHHHHHHHHHHHcCCEEEEEEcCCCCcchhhhhHhhhhcCcccccccccHHHHHHhhhccchhHHHHHHHH
Q 007971 46 RPQTDKLFLRGLFHRLRALIALNCGLIFVSDGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEA 125 (583)
Q Consensus 46 ~g~~~~~~Lr~lf~rl~~Ll~~gI~PIFVFDG~~P~~K~~t~~~R~~~r~~a~~~~~~~~~a~k~~R~~~~~~~~~i~~~ 125 (583)
+|.+.|+.+..|. ..|.+.|++|-+|-=|-.-..|..+........ +.+ .+.+ -
T Consensus 58 GGtGKTP~vi~la---~~l~~rG~~~gvvSRGYgg~~~~~~~~~~~~~~---a~~-------------~GDE-------P 111 (336)
T COG1663 58 GGTGKTPVVIWLA---EALQARGVRVGVVSRGYGGKLKVVPLVDNIHTT---AAE-------------VGDE-------P 111 (336)
T ss_pred CCCCcCHHHHHHH---HHHHhcCCeeEEEecCcCCCCccccccccCcCC---hHH-------------cCch-------H
Confidence 3444567766554 457888999999988753212211111100000 000 1111 1
Q ss_pred HHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCC
Q 007971 126 KALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDS 164 (583)
Q Consensus 126 k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~Ds 164 (583)
.-|.+..+.|++++|...++.-+.++.+.-+|.|++||.
T Consensus 112 lLlA~~t~~pv~v~~~R~~~~~~l~~~~~~~diIi~DDG 150 (336)
T COG1663 112 LLLARRTGAPVAVSPDRKDAAKALLAAHLGCDIIVLDDG 150 (336)
T ss_pred HHHhhhcCCcEEEehhHHHHHHHHHhhCCCCCEEEEcCc
Confidence 122333599999999999999998888778999999985
No 97
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=22.44 E-value=2.2e+02 Score=31.95 Aligned_cols=39 Identities=10% Similarity=-0.062 Sum_probs=21.1
Q ss_pred HHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEec
Q 007971 123 KEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFS 161 (583)
Q Consensus 123 ~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS 161 (583)
.++++-|+.+|++.+..-|+....+..|.+.-.++.|++
T Consensus 58 ~~L~~~L~~~G~~L~v~~G~p~~vl~~l~~~~~~~~V~~ 96 (471)
T TIGR03556 58 QELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYW 96 (471)
T ss_pred HHHHHHHHHCCCCeEEEECCHHHHHHHHHHHcCCCEEEE
Confidence 344444555666666666666666655555444444443
No 98
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=22.38 E-value=77 Score=32.98 Aligned_cols=21 Identities=29% Similarity=0.591 Sum_probs=19.6
Q ss_pred CCCCCCHHHHHHHHHHcCCHH
Q 007971 219 GVRGLGPESACQIVKSVGDNV 239 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~~g~~~ 239 (583)
++||||++.|..|++.||+..
T Consensus 186 s~pgig~~~a~~ll~~fgS~~ 206 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVE 206 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHH
Confidence 789999999999999999974
No 99
>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=22.08 E-value=54 Score=29.00 Aligned_cols=29 Identities=10% Similarity=0.243 Sum_probs=23.9
Q ss_pred cccHHHHHHHHHHcCCeeEEecCCCcEEe
Q 007971 140 VEEAEAQCALLNLESLCDGCFSSDSDIFL 168 (583)
Q Consensus 140 P~EADAqcA~L~~~g~vd~ViS~DsD~ll 168 (583)
+-..|+-+..++..+-+|+++|.|.|++.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 45667777788888899999999999763
No 100
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.94 E-value=2.4e+02 Score=31.37 Aligned_cols=13 Identities=15% Similarity=0.033 Sum_probs=10.3
Q ss_pred cCCEEEEEEcCCC
Q 007971 67 LNCGLIFVSDGSI 79 (583)
Q Consensus 67 ~gI~PIFVFDG~~ 79 (583)
.++-||||||-..
T Consensus 53 ~~vl~vyi~dp~~ 65 (454)
T TIGR00591 53 LPLHVCFCLVDFF 65 (454)
T ss_pred CCEEEEEEeCCCc
Confidence 3589999999754
No 101
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=21.79 E-value=78 Score=36.75 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=21.1
Q ss_pred CCCCCCCHHHHHHHHHHcCCHHHH
Q 007971 218 QGVRGLGPESACQIVKSVGDNVVL 241 (583)
Q Consensus 218 pGvpGiG~ktA~~Li~~~g~~~il 241 (583)
.+|||||++....|++.||+..-+
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~~i 556 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLKGI 556 (581)
T ss_pred ccCCCcCHHHHHHHHHHhhCHHHH
Confidence 489999999999999999997533
No 102
>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=21.18 E-value=86 Score=29.49 Aligned_cols=45 Identities=16% Similarity=0.056 Sum_probs=35.9
Q ss_pred HHHHHHHHHHhCCCeeeCcccHHHHHHHHHHcCCeeEEecCCCcEE
Q 007971 122 IKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIF 167 (583)
Q Consensus 122 i~~~k~LL~~~GIp~i~AP~EADAqcA~L~~~g~vd~ViS~DsD~l 167 (583)
+..+-+.|+.+|+.++..+...|.++..++...-- .|+|-|.+++
T Consensus 9 L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~R-illTrd~~l~ 53 (147)
T PF01927_consen 9 LGRLARWLRLLGYDTLYSRDIDDDEILELAREEGR-ILLTRDRDLL 53 (147)
T ss_pred HHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHH
Confidence 34567789999999999998889999988865332 6889998865
No 103
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=20.99 E-value=2.3e+02 Score=31.77 Aligned_cols=11 Identities=18% Similarity=0.026 Sum_probs=9.5
Q ss_pred CCEEEEEEcCC
Q 007971 68 NCGLIFVSDGS 78 (583)
Q Consensus 68 gI~PIFVFDG~ 78 (583)
.+-||||||..
T Consensus 24 ~vlpvyi~dp~ 34 (475)
T TIGR02766 24 PVIPVFVWAPE 34 (475)
T ss_pred CEEEEEEechH
Confidence 68899999974
No 104
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=20.84 E-value=2.4e+02 Score=26.60 Aligned_cols=46 Identities=15% Similarity=0.017 Sum_probs=36.0
Q ss_pred hhHHHHHHHHHHHHHHhCCC-----eeeCcc--cHHHHHHHHHHcCCeeEEec
Q 007971 116 SEFSCMIKEAKALGLSLGVP-----CLEGVE--EAEAQCALLNLESLCDGCFS 161 (583)
Q Consensus 116 ~~~~~~i~~~k~LL~~~GIp-----~i~AP~--EADAqcA~L~~~g~vd~ViS 161 (583)
.++..+++.+.+.|+..|+. .+.-|| |-=-.+..|.+.|..|+|++
T Consensus 13 ~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~ 65 (138)
T TIGR00114 13 DITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIA 65 (138)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 45677888899999999976 566785 66666677888888899886
No 105
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=20.71 E-value=1.2e+02 Score=28.54 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=18.9
Q ss_pred CCCCCCHHHHHHHHHH--cCCHHHHHHHH
Q 007971 219 GVRGLGPESACQIVKS--VGDNVVLQRIA 245 (583)
Q Consensus 219 GvpGiG~ktA~~Li~~--~g~~~il~~~~ 245 (583)
.+|||||+.|-+|++. |.+.+-|.++.
T Consensus 65 ~lpGigP~~A~~IV~nGpf~sveDL~~V~ 93 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDSVEDVLNLP 93 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCCHHHHHcCC
Confidence 4799999999999964 45544333343
No 106
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.60 E-value=62 Score=32.09 Aligned_cols=34 Identities=21% Similarity=0.445 Sum_probs=22.7
Q ss_pred CChHHHHHHHHHhCCCCC--CCCCCCCHHHHHHHHHHc
Q 007971 200 FGRNSLITLALLLGSDYS--QGVRGLGPESACQIVKSV 235 (583)
Q Consensus 200 L~r~qli~laiL~G~DY~--pGvpGiG~ktA~~Li~~~ 235 (583)
+++++|+. ++.. .|.. ..+||||+|||-+|+-+.
T Consensus 93 ~~~~~l~~-aI~~-~D~~~L~~vpGIGkKtAerIilEL 128 (194)
T PRK14605 93 MNAEALAS-AIIS-GNAELLSTIPGIGKKTASRIVLEL 128 (194)
T ss_pred CCHHHHHH-HHHh-CCHHHHHhCCCCCHHHHHHHHHHH
Confidence 45665544 2323 3433 489999999999998663
No 107
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=20.29 E-value=53 Score=39.59 Aligned_cols=27 Identities=19% Similarity=0.190 Sum_probs=22.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHcCCHHHH
Q 007971 215 DYSQGVRGLGPESACQIVKSVGDNVVL 241 (583)
Q Consensus 215 DY~pGvpGiG~ktA~~Li~~~g~~~il 241 (583)
+|+-++||||+++|..|+..||+..-+
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~si~~l 783 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVKSIREL 783 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcCCHHHH
Confidence 344479999999999999999997433
Done!