Query 044842
Match_columns 602
No_of_seqs 280 out of 1445
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:16:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044842.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044842hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2519 5'-3' exonuclease [Rep 100.0 8.8E-64 1.9E-68 529.8 18.1 429 1-557 1-448 (449)
2 PTZ00217 flap endonuclease-1; 100.0 6.4E-61 1.4E-65 514.8 32.6 308 1-411 1-333 (393)
3 cd00128 XPG Xeroderma pigmento 100.0 2.9E-57 6.2E-62 475.3 30.6 301 1-405 1-314 (316)
4 TIGR03674 fen_arch flap struct 100.0 1.4E-55 3.1E-60 466.2 31.0 297 1-411 1-326 (338)
5 PRK03980 flap endonuclease-1; 100.0 2.7E-50 5.9E-55 417.7 28.9 256 46-412 4-280 (292)
6 KOG2518 5'-3' exonuclease [Rep 100.0 2.8E-44 6.1E-49 384.8 17.9 237 1-241 1-253 (556)
7 KOG2520 5'-3' exonuclease [Rep 100.0 1.5E-42 3.3E-47 391.2 18.0 228 117-422 465-693 (815)
8 TIGR00600 rad2 DNA excision re 100.0 1.8E-41 4E-46 393.5 23.6 215 118-412 772-989 (1034)
9 smart00475 53EXOc 5'-3' exonuc 100.0 2.2E-31 4.7E-36 272.5 23.4 205 26-246 2-219 (259)
10 cd00008 53EXOc 5'-3' exonuclea 100.0 7.8E-30 1.7E-34 258.5 23.7 202 26-247 2-217 (240)
11 PRK14976 5'-3' exonuclease; Pr 100.0 5E-29 1.1E-33 257.8 23.5 206 25-247 3-225 (281)
12 COG0258 Exo 5'-3' exonuclease 100.0 4.8E-28 1E-32 253.9 20.9 209 18-244 4-229 (310)
13 TIGR00593 pola DNA polymerase 99.9 4E-26 8.6E-31 266.8 23.6 203 28-247 2-219 (887)
14 PRK09482 flap endonuclease-lik 99.9 8.1E-26 1.8E-30 230.3 22.5 199 26-246 4-215 (256)
15 PRK05755 DNA polymerase I; Pro 99.9 1.7E-25 3.7E-30 263.3 23.1 203 26-247 3-221 (880)
16 PF00867 XPG_I: XPG I-region; 99.9 2.4E-24 5.2E-29 188.4 7.1 86 128-213 1-94 (94)
17 smart00485 XPGN Xeroderma pigm 99.8 3.3E-21 7.1E-26 169.7 6.8 92 1-94 1-96 (99)
18 PF00752 XPG_N: XPG N-terminal 99.8 4.3E-21 9.2E-26 169.4 7.0 92 1-94 1-98 (101)
19 PHA00439 exonuclease 99.8 1.9E-17 4.2E-22 170.6 17.5 179 24-233 5-206 (286)
20 smart00484 XPGI Xeroderma pigm 99.8 2.3E-18 5E-23 144.0 8.4 70 129-198 2-73 (73)
21 TIGR00600 rad2 DNA excision re 99.7 2.8E-18 6E-23 200.9 6.9 92 1-94 1-95 (1034)
22 PHA02567 rnh RnaseH; Provision 99.5 2.7E-12 5.8E-17 133.4 19.4 173 24-221 13-207 (304)
23 PF02739 5_3_exonuc_N: 5'-3' e 99.5 6.3E-13 1.4E-17 128.5 13.1 154 26-196 2-169 (169)
24 cd00080 HhH2_motif Helix-hairp 99.2 3.7E-11 8E-16 101.2 5.5 51 195-246 2-55 (75)
25 smart00279 HhH2 Helix-hairpin- 98.8 7.1E-09 1.5E-13 75.3 3.8 33 200-234 1-36 (36)
26 PF12813 XPG_I_2: XPG domain c 98.7 3.8E-08 8.3E-13 100.7 9.6 89 120-211 6-110 (246)
27 PF01367 5_3_exonuc: 5'-3' exo 98.5 2.9E-09 6.2E-14 94.7 -5.8 49 198-247 1-52 (101)
28 PF04599 Pox_G5: Poxvirus G5 p 98.0 3.1E-05 6.6E-10 83.9 11.3 230 1-243 1-272 (425)
29 PHA03065 Hypothetical protein; 97.8 0.00015 3.3E-09 78.2 11.9 225 1-243 1-274 (438)
30 PF03159 XRN_N: XRN 5'-3' exon 97.7 6.1E-05 1.3E-09 76.9 7.0 167 1-168 1-222 (237)
31 COG5049 XRN1 5'-3' exonuclease 96.2 0.041 8.8E-07 63.1 12.0 219 1-224 1-328 (953)
32 KOG2045 5'-3' exonuclease XRN1 95.8 0.053 1.1E-06 63.7 10.5 223 1-231 1-307 (1493)
33 COG5366 Protein involved in pr 94.5 0.021 4.5E-07 62.6 2.4 111 123-235 134-246 (531)
34 COG0353 RecR Recombinational D 88.6 0.44 9.5E-06 47.4 3.6 28 427-454 157-185 (198)
35 KOG2044 5'-3' exonuclease HKE1 86.3 4.3 9.3E-05 47.9 10.2 93 131-224 190-352 (931)
36 PF12826 HHH_2: Helix-hairpin- 86.0 0.61 1.3E-05 38.0 2.5 23 218-240 7-30 (64)
37 PF00385 Chromo: Chromo (CHRro 85.2 1.3 2.8E-05 34.5 3.9 51 430-513 1-54 (55)
38 PRK14602 ruvA Holliday junctio 85.1 1.4 3E-05 44.3 5.0 48 191-245 57-105 (203)
39 TIGR00615 recR recombination p 85.0 1.1 2.3E-05 44.9 4.0 18 217-234 14-31 (195)
40 PRK00116 ruvA Holliday junctio 84.5 0.98 2.1E-05 44.8 3.7 28 217-244 76-103 (192)
41 PRK14605 ruvA Holliday junctio 83.7 1.1 2.4E-05 44.7 3.6 47 191-244 56-103 (194)
42 TIGR00084 ruvA Holliday juncti 82.8 1.2 2.6E-05 44.3 3.4 46 193-245 57-103 (191)
43 PRK00076 recR recombination pr 81.7 1.7 3.6E-05 43.5 4.0 18 217-234 14-31 (196)
44 PRK14600 ruvA Holliday junctio 81.3 1.3 2.8E-05 43.9 3.1 49 190-245 55-104 (186)
45 PRK13844 recombination protein 80.6 1.9 4.2E-05 43.2 4.0 18 217-234 18-35 (200)
46 PRK14603 ruvA Holliday junctio 80.0 1.5 3.3E-05 43.7 3.1 48 191-245 55-103 (197)
47 PRK13901 ruvA Holliday junctio 79.5 1.7 3.7E-05 43.4 3.2 48 191-245 55-103 (196)
48 PRK14606 ruvA Holliday junctio 78.9 2.3 4.9E-05 42.3 3.9 49 190-245 55-104 (188)
49 PF00633 HHH: Helix-hairpin-he 78.8 1.6 3.4E-05 30.6 2.0 16 217-232 14-29 (30)
50 PRK14601 ruvA Holliday junctio 78.8 1.8 3.9E-05 42.8 3.2 49 190-245 55-104 (183)
51 PRK14604 ruvA Holliday junctio 77.5 2 4.4E-05 42.9 3.1 48 191-245 56-104 (195)
52 COG2454 Uncharacterized conser 76.3 14 0.00031 37.1 8.5 24 16-39 57-80 (211)
53 PF11977 RNase_Zc3h12a: Zc3h12 75.8 11 0.00023 36.0 7.5 100 25-162 2-110 (155)
54 COG0632 RuvA Holliday junction 75.7 6 0.00013 39.8 5.9 52 187-245 52-104 (201)
55 PF05991 NYN_YacP: YacP-like N 75.4 2.8 6.1E-05 40.6 3.4 34 131-164 67-106 (166)
56 smart00278 HhH1 Helix-hairpin- 67.0 4.3 9.2E-05 27.1 1.8 17 217-233 4-20 (26)
57 smart00298 CHROMO Chromatin or 62.9 18 0.00039 27.4 4.9 24 431-454 3-27 (55)
58 PF14520 HHH_5: Helix-hairpin- 59.2 8 0.00017 30.8 2.4 24 217-240 8-33 (60)
59 PRK14669 uvrC excinuclease ABC 54.6 8.1 0.00018 45.2 2.4 24 217-240 555-579 (624)
60 PF10391 DNA_pol_lambd_f: Fing 53.0 10 0.00023 29.9 2.1 17 217-233 5-21 (52)
61 PRK14671 uvrC excinuclease ABC 52.7 10 0.00023 44.3 2.9 23 217-239 572-595 (621)
62 PRK14667 uvrC excinuclease ABC 52.2 10 0.00022 43.9 2.7 25 216-240 516-541 (567)
63 TIGR00194 uvrC excinuclease AB 50.6 10 0.00022 43.9 2.4 24 217-240 544-568 (574)
64 PRK14601 ruvA Holliday junctio 50.2 9.5 0.00021 37.8 1.8 39 197-236 92-130 (183)
65 PRK14670 uvrC excinuclease ABC 49.7 12 0.00026 43.4 2.7 25 216-240 516-541 (574)
66 KOG2748 Uncharacterized conser 47.6 17 0.00036 39.3 3.1 31 430-460 11-41 (369)
67 COG0632 RuvA Holliday junction 46.3 19 0.00042 36.2 3.3 37 198-236 93-130 (201)
68 cd00024 CHROMO Chromatin organ 46.3 45 0.00099 25.3 4.7 25 430-454 3-29 (55)
69 PRK13901 ruvA Holliday junctio 45.8 12 0.00026 37.5 1.7 38 197-235 91-128 (196)
70 PRK14602 ruvA Holliday junctio 45.3 13 0.00028 37.3 1.9 42 193-235 88-130 (203)
71 PF02371 Transposase_20: Trans 44.4 17 0.00036 31.2 2.2 21 216-236 4-24 (87)
72 PRK14606 ruvA Holliday junctio 42.0 15 0.00033 36.5 1.8 46 189-235 83-129 (188)
73 PRK00558 uvrC excinuclease ABC 41.4 17 0.00037 42.3 2.3 24 217-240 546-570 (598)
74 PRK14672 uvrC excinuclease ABC 40.4 20 0.00044 42.3 2.7 25 216-240 610-635 (691)
75 PRK14604 ruvA Holliday junctio 40.3 17 0.00036 36.4 1.8 42 193-235 87-129 (195)
76 TIGR02765 crypto_DASH cryptoch 40.0 75 0.0016 35.1 7.0 44 117-160 60-103 (429)
77 PF11798 IMS_HHH: IMS family H 39.7 20 0.00044 25.3 1.6 14 217-230 14-27 (32)
78 PRK14600 ruvA Holliday junctio 39.6 22 0.00048 35.3 2.5 47 188-236 82-129 (186)
79 PRK14603 ruvA Holliday junctio 38.8 18 0.00038 36.2 1.7 47 189-236 82-129 (197)
80 PRK14668 uvrC excinuclease ABC 38.2 21 0.00045 41.5 2.4 26 216-241 527-553 (577)
81 PF01927 Mut7-C: Mut7-C RNAse 36.8 40 0.00087 31.9 3.7 44 120-165 9-53 (147)
82 PRK12766 50S ribosomal protein 36.7 26 0.00057 36.0 2.5 25 216-240 5-31 (232)
83 TIGR02766 crypt_chrom_pln cryp 34.3 92 0.002 35.0 6.7 31 380-411 327-357 (475)
84 TIGR00591 phr2 photolyase PhrI 34.2 1.2E+02 0.0026 33.9 7.5 41 119-159 79-119 (454)
85 PRK10674 deoxyribodipyrimidine 32.9 1.1E+02 0.0024 34.5 7.0 42 118-159 57-102 (472)
86 PRK14666 uvrC excinuclease ABC 32.8 28 0.00062 41.2 2.3 25 217-241 640-665 (694)
87 TIGR03556 photolyase_8HDF deox 32.5 1.1E+02 0.0024 34.4 7.0 42 118-159 55-96 (471)
88 TIGR01448 recD_rel helicase, p 31.1 42 0.0009 40.1 3.4 33 197-236 74-106 (720)
89 cd08556 GDPD Glycerophosphodie 30.9 78 0.0017 29.9 4.7 40 121-161 150-189 (189)
90 TIGR00084 ruvA Holliday juncti 30.2 52 0.0011 32.7 3.4 44 190-234 83-127 (191)
91 TIGR00305 probable toxin-antit 29.7 34 0.00073 30.5 1.8 29 138-166 85-113 (114)
92 KOG1911 Heterochromatin-associ 29.2 35 0.00076 35.6 2.1 52 432-517 51-102 (270)
93 COG1948 MUS81 ERCC4-type nucle 26.8 48 0.001 34.6 2.5 25 217-241 185-210 (254)
94 TIGR00114 lumazine-synth 6,7-d 26.8 1.4E+02 0.0031 28.2 5.5 43 117-159 16-65 (138)
95 PRK02515 psbU photosystem II c 25.7 58 0.0013 30.7 2.6 16 217-232 64-79 (132)
96 PF00885 DMRL_synthase: 6,7-di 25.4 1.7E+02 0.0037 27.8 5.8 43 117-159 19-68 (144)
97 PRK14605 ruvA Holliday junctio 25.3 32 0.00069 34.3 0.9 37 198-235 93-129 (194)
98 PF12826 HHH_2: Helix-hairpin- 24.9 64 0.0014 26.2 2.5 20 217-236 38-57 (64)
99 TIGR00269 conserved hypothetic 24.9 2.2E+02 0.0047 25.4 6.1 17 198-214 10-26 (104)
100 smart00483 POLXc DNA polymeras 23.6 59 0.0013 35.1 2.6 24 217-241 92-118 (334)
101 KOG1710 MYND Zn-finger and ank 23.0 19 0.00042 38.2 -1.1 30 273-309 315-344 (396)
102 COG4277 Predicted DNA-binding 22.7 1.5E+02 0.0033 31.9 5.3 51 185-235 276-351 (404)
103 TIGR00288 conserved hypothetic 22.1 94 0.002 30.3 3.4 45 123-167 71-121 (160)
104 cd00141 NT_POLXc Nucleotidyltr 22.0 77 0.0017 33.8 3.1 25 217-242 88-115 (307)
105 PF08940 DUF1918: Domain of un 22.0 65 0.0014 26.2 1.9 23 434-456 24-46 (58)
106 PRK12419 riboflavin synthase s 21.9 1.7E+02 0.0036 28.5 5.1 43 117-159 26-75 (158)
107 PHA02942 putative transposase; 21.9 51 0.0011 36.3 1.7 27 276-302 324-350 (383)
108 TIGR01259 comE comEA protein. 21.8 53 0.0011 30.2 1.6 19 217-235 71-89 (120)
109 TIGR00575 dnlj DNA ligase, NAD 21.6 71 0.0015 37.7 3.0 19 218-236 502-520 (652)
110 PRK14351 ligA NAD-dependent DN 21.3 74 0.0016 37.9 3.0 19 218-236 532-550 (689)
111 COG0322 UvrC Nuclease subunit 20.5 71 0.0015 37.2 2.6 23 217-239 533-556 (581)
112 PRK08609 hypothetical protein; 20.1 97 0.0021 36.0 3.6 27 217-243 91-120 (570)
113 PF13240 zinc_ribbon_2: zinc-r 20.0 61 0.0013 21.3 1.1 20 280-302 2-21 (23)
No 1
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=8.8e-64 Score=529.84 Aligned_cols=429 Identities=31% Similarity=0.425 Sum_probs=334.9
Q ss_pred CCCCCcCh----hhhcccccccCccccCCCEEEEeHHHHHHHHhccccC----CCCCChHHHHHHHHHHHHHHhCCCeEE
Q 044842 1 MGVGGKFW----DLLKPYARFEGLDFLRDKRVAVDLSYWIVQHETAIKK----NSVPKPHLRLTFFRTINLFAKFGAFPV 72 (602)
Q Consensus 1 MGV~G~Lw----~~Lkp~~~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~----~g~~~~~Lr~~f~r~l~lL~~~gI~PV 72 (602)
|||+| |. ....+..+..++..|+|++||||||+||||++.+++. .|++++||+++|+|+++++ .+||+||
T Consensus 1 MGIkg-L~~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~~~~~~~~~~HL~g~f~Rt~~l~-~~gi~Pv 78 (449)
T KOG2519|consen 1 MGIKG-LSKVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSCRNEAGEPTSHLMGMFYRTIRLI-ENGIKPV 78 (449)
T ss_pred CCchh-HHHHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhccccccCCCchHHHHHHHHHHHHHH-HcCCcEE
Confidence 99999 93 5555566778999999999999999999999999874 6789999999999999988 7999999
Q ss_pred EEEcCCCCcchhHHHHHhhhcc-ccccccchHHHhccchhhhHHHHH-------hHHHHHHHHHHcCCCEEeccCcHHHH
Q 044842 73 FVVDGTPSPLKSQARLARFYRS-TIDASTLPVAEEGILVERNQTFLK-------CVQECVELLELFGMPVLKAKGEAEAL 144 (602)
Q Consensus 73 fVFDG~~p~~K~~t~~kR~~R~-~~~~~~~~~~k~g~~~e~~~~f~~-------~i~~~~~lL~~~GI~~i~AP~EADAq 144 (602)
|||||.+|.+|.++.++|..|+ +......+....|........+.+ +..+|+.||.+|||||+.||+|||||
T Consensus 79 ~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EAEAq 158 (449)
T KOG2519|consen 79 YVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEAEAQ 158 (449)
T ss_pred EEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchHHHH
Confidence 9999999999999999998876 333233333333333333333333 34599999999999999999999999
Q ss_pred HHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecC--CCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCcc
Q 044842 145 CAQLNSEGYVDACITADSDAFLFGAKCVVKCIR--PNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGI 222 (602)
Q Consensus 145 cA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~--~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G~DY~~~GipGI 222 (602)
||+|++.|.|++++|+|||+|.||++.+++++. ...+.|+.+|+++.|.+.|+|++++||+||+|+||||| ++|.||
T Consensus 159 CA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGCDYc-~~I~Gi 237 (449)
T KOG2519|consen 159 CAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGCDYC-PTIRGI 237 (449)
T ss_pred HHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcCccc-cccccc
Confidence 999999999999999999999999999999875 34567999999999999999999999999999999998 899999
Q ss_pred cHHHHHHHHHhcCh-HHHHHHHHhhCCCCCCCCcCCccchhhhhcCCCCCCccccCCCCccCCCCCCccccccccccccc
Q 044842 223 GLDTALQFVQNFSE-DEILNILHKIGNGDIPQYWGDIKSTEEAVSHSDESMPMIKSSHCSFCGHPGTKRAHFKFSCEYCI 301 (602)
Q Consensus 223 G~ktA~~Li~~~~~-e~iL~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~Cs~C~h~gs~k~h~k~gc~~C~ 301 (602)
|+++|++||++|++ ++||+-...
T Consensus 238 g~~~al~lir~~~~i~~ile~~~~-------------------------------------------------------- 261 (449)
T KOG2519|consen 238 GPKKALKLIRQHGDIENILEINSD-------------------------------------------------------- 261 (449)
T ss_pred ChHHHHHHHHHhcCHHHHhhhccc--------------------------------------------------------
Confidence 99999999999994 666652000
Q ss_pred cCCCCCCCCCCCCCccccccchhhhhHHHHhhhhhhhHhhhcccccCCCCCCHHHHHHHhccCCCCCCCCCCCCcccCCC
Q 044842 302 NDNNEGCLKKPDGFKCNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTATDGPSISWGSP 381 (602)
Q Consensus 302 ~~~~~gc~~~~~~~~c~c~~~~~~r~~k~~~~~~~~~~~~~~k~~~~~~FP~~~Vi~~yl~p~v~~~~~~~~~~~~W~~P 381 (602)
+++.+..++|+.+.++++++.|.||+++++ ..+.|..|
T Consensus 262 --------------------------~~~~~ip~~w~~~~~r~~f~~p~~~~~~~~----------------~~i~w~~p 299 (449)
T KOG2519|consen 262 --------------------------LKEYPIPEDWSYKLARKLFLEPEFPNPESI----------------LDLKWKTP 299 (449)
T ss_pred --------------------------hhhcCCCCCccHHHHHHHhcCcccCCccce----------------eecccCCC
Confidence 011112234555555555555555544222 47999999
Q ss_pred CHHHHHHHHhhhCCCChhHHhhhHhhHHHhHHHhhhcCCCccccccCcccceeEEEeeecCceeeEEEEEeecccccccc
Q 044842 382 MTEMLVDFLVYHQPWQPSYIRQKMLPMLSTIYLREMATNPVQTLLCGQYEFDSIRRVKIRYGHQSYVVKWKKAASAISGV 461 (602)
Q Consensus 382 dl~~L~~f~~~~~~W~~~~~~e~llPll~~~~l~~~~~~~~~~~~~~~~~~~~i~k~r~~~g~~~~ei~W~~~~~~~~~~ 461 (602)
|.++|++|+....+|+.+|++..+.++++++++...+. ..+-..++..|.|.-.-+|-++-.....
T Consensus 300 d~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgr-------------l~~f~~~~~~~~~~~~~~~~~~~~~~~e- 365 (449)
T KOG2519|consen 300 DTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGR-------------LDSFFKRIPKGSPVRKLKLIDAKGKAEE- 365 (449)
T ss_pred ChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccc-------------hhhhhcccCCCCCcchhHHHHHHhhhhh-
Confidence 99999999999999999999999999999997644222 1223347777777777777777544443
Q ss_pred ccCCCCCcchhhhhcccCCccccCCCcceeeehhhhhHHHhhchHHHHHHHHhhhhhHHhhhccCcccccccCCcccCCC
Q 044842 462 KYTAPVDSDLHLEEFMEYPQIHVDGDCWFLLTDENMKLVHSAFPKKVDHFLQENERRELKRKRTSSLRSEESNGKLESPK 541 (602)
Q Consensus 462 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~e~~~l~~~ayp~~v~~f~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~ 541 (602)
.++.. +..+.|++..+.++.|++|+|+..++..|||.++.+|+..|+....|.+.-+. .. .++|...
T Consensus 366 --~~~~~------~~~~~~~~~~~~~~r~~~t~~~l~~l~~~~p~~~~~~l~~k~~~~~~~~~~~~-le----~~~~~~~ 432 (449)
T KOG2519|consen 366 --VIKAL------NKKEKPKGQTGKIKRFKTTDKPLTMLPSATPLFTFIFLIPKEYPHLKTKRYLD-LE----KEVPRIF 432 (449)
T ss_pred --ccCcc------hhhhhhccCCCccccceeecchHhhcccCCccHHHHHhhhhhcccccccchhh-hh----hccchhh
Confidence 22322 23455788889999999999999999999999999999999886554444332 11 2334666
Q ss_pred CccccchhHHHHhhhh
Q 044842 542 SKGVQLSITEFYRSAK 557 (602)
Q Consensus 542 ~~~~~~~~~~~~~~~~ 557 (602)
+.+.|.+++.++.|.+
T Consensus 433 ~~~~~~~~~~~~~~~~ 448 (449)
T KOG2519|consen 433 NVQIEKLDAKTPWSKK 448 (449)
T ss_pred cccccccccccccccc
Confidence 6677888887777654
No 2
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=6.4e-61 Score=514.83 Aligned_cols=308 Identities=29% Similarity=0.421 Sum_probs=259.6
Q ss_pred CCCCCcChhhhccc----ccccCccccCCCEEEEeHHHHHHHHhccccC----------CCCCChHHHHHHHHHHHHHHh
Q 044842 1 MGVGGKFWDLLKPY----ARFEGLDFLRDKRVAVDLSYWIVQHETAIKK----------NSVPKPHLRLTFFRTINLFAK 66 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~----~~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~----------~g~~~~~Lr~~f~r~l~lL~~ 66 (602)
|||+| ||++|++. .++.+|+.|+|++|||||++||||++++++. .|.+++||.++|.|+++++ +
T Consensus 1 MGI~g-L~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll-~ 78 (393)
T PTZ00217 1 MGIKG-LSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLL-E 78 (393)
T ss_pred CChhh-HHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHH-H
Confidence 99998 99999976 4778999999999999999999999988762 4778899999999988876 5
Q ss_pred CCCeEEEEEcCCCCcchhHHHHHhhhccccccccch-HHHhccchhhhHHH-------HHhHHHHHHHHHHcCCCEEecc
Q 044842 67 FGAFPVFVVDGTPSPLKSQARLARFYRSTIDASTLP-VAEEGILVERNQTF-------LKCVQECVELLELFGMPVLKAK 138 (602)
Q Consensus 67 ~gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~~~~~~-~~k~g~~~e~~~~f-------~~~i~~~~~lL~~~GI~~i~AP 138 (602)
+||+|||||||.+|++|..+..+|..++......+. ..+.|...+....+ ..++..++++|+.||||||+||
T Consensus 79 ~gikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP 158 (393)
T PTZ00217 79 AGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAP 158 (393)
T ss_pred CCCCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECC
Confidence 899999999999999999998888765532222121 22333322222222 3578899999999999999999
Q ss_pred CcHHHHHHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecCC--CCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCC
Q 044842 139 GEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRP--NTKEPFECYCISDIEAGLGLKRKHLIAMSLLIGNDHDL 216 (602)
Q Consensus 139 ~EADAqcA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~~--~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G~DY~~ 216 (602)
||||||||+|++.|+||+|+|+|+|+|+||++.||++++. +.+.++++|+++.+.+.+|++++||+++|+|+||||+
T Consensus 159 ~EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~- 237 (393)
T PTZ00217 159 CEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYC- 237 (393)
T ss_pred cCHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCC-
Confidence 9999999999999999999999999999999999999874 2334678999999999999999999999999999997
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHHHHHHHhhCCCCCCCCcCCccchhhhhcCCCCCCccccCCCCccCCCCCCccccccc
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEILNILHKIGNGDIPQYWGDIKSTEEAVSHSDESMPMIKSSHCSFCGHPGTKRAHFKF 295 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~Cs~C~h~gs~k~h~k~ 295 (602)
+||||||+|||++||++|++ ++|++.++..
T Consensus 238 pgi~GIG~ktA~~Li~~~gsle~il~~~~~~------------------------------------------------- 268 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKKYKSIEEILEHLDKT------------------------------------------------- 268 (393)
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHHHHhc-------------------------------------------------
Confidence 99999999999999999996 8887664321
Q ss_pred cccccccCCCCCCCCCCCCCccccccchhhhhHHHHhhhhhhhHhhhcccccCCCCCCHHHHHHHhccCCCCCCCCCCCC
Q 044842 296 SCEYCINDNNEGCLKKPDGFKCNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTATDGPS 375 (602)
Q Consensus 296 gc~~C~~~~~~gc~~~~~~~~c~c~~~~~~r~~k~~~~~~~~~~~~~~k~~~~~~FP~~~Vi~~yl~p~v~~~~~~~~~~ 375 (602)
+..+|++||+.++++.|++|.|. +.....
T Consensus 269 ------------------------------------------------k~~~p~~~~~~~~~~~f~~p~V~---~~~~~~ 297 (393)
T PTZ00217 269 ------------------------------------------------KYPVPENFDYKEARELFLNPEVT---PAEEID 297 (393)
T ss_pred ------------------------------------------------CCCCCCCCChHHHHHHhcCCCcC---CCCCCC
Confidence 11248899999999999999983 222347
Q ss_pred cccCCCCHHHHHHHHhhhCCCChhHHhhhHhhHHHh
Q 044842 376 ISWGSPMTEMLVDFLVYHQPWQPSYIRQKMLPMLST 411 (602)
Q Consensus 376 ~~W~~Pdl~~L~~f~~~~~~W~~~~~~e~llPll~~ 411 (602)
|.|+.||.++|++||++.++|+++++++.+-+|.+.
T Consensus 298 l~w~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~~ 333 (393)
T PTZ00217 298 LKWNEPDEEGLKKFLVKEKNFNEERVEKYIERLKKA 333 (393)
T ss_pred CCCCCCCHHHHHHHHHhccCCCHHHHHHHHHHHHHH
Confidence 999999999999999999999999999998776553
No 3
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=100.00 E-value=2.9e-57 Score=475.29 Aligned_cols=301 Identities=34% Similarity=0.546 Sum_probs=249.7
Q ss_pred CCCCCcChhhhcccccccCccccCCCEEEEeHHHHHHHHhccccC----CCCCChHHHHHHHHHHHHHHhCCCeEEEEEc
Q 044842 1 MGVGGKFWDLLKPYARFEGLDFLRDKRVAVDLSYWIVQHETAIKK----NSVPKPHLRLTFFRTINLFAKFGAFPVFVVD 76 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~----~g~~~~~Lr~~f~r~l~lL~~~gI~PVfVFD 76 (602)
|||+| ||+||+++++..+|++|+|++|||||++||||++++++. +|.+++++.++|.++..+ .++||+||||||
T Consensus 1 MGI~g-L~~~l~~~~~~~~i~~l~gk~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L-~~~~i~pvfVFD 78 (316)
T cd00128 1 MGIKG-LWPLLKPVARPVHLEELRGKKVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRL-LELGIKPVFVFD 78 (316)
T ss_pred Cchhh-HHHHHHhhCCCCCHHHhCCcEEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHH-HHCCCEEEEEEc
Confidence 99998 999999999999999999999999999999999998764 577889998877776655 468999999999
Q ss_pred CCCCcchhHHHHHhhhcccccccc-chHHHhccchhhhH-------HHHHhHHHHHHHHHHcCCCEEeccCcHHHHHHHH
Q 044842 77 GTPSPLKSQARLARFYRSTIDAST-LPVAEEGILVERNQ-------TFLKCVQECVELLELFGMPVLKAKGEAEALCAQL 148 (602)
Q Consensus 77 G~~p~~K~~t~~kR~~R~~~~~~~-~~~~k~g~~~e~~~-------~f~~~i~~~~~lL~~~GI~~i~AP~EADAqcA~L 148 (602)
|.+++.|..+..+|..++....+. ......|...+... .+..++..++++|+.|||||++||||||||||+|
T Consensus 79 G~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l 158 (316)
T cd00128 79 GKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYL 158 (316)
T ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHH
Confidence 999999999988887654221111 11122232222111 2346788999999999999999999999999999
Q ss_pred HHcCCeeEEEcCCCCeEeeCCeEEEEecCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCcccHHHHH
Q 044842 149 NSEGYVDACITADSDAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTAL 228 (602)
Q Consensus 149 ~~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G~DY~~~GipGIG~ktA~ 228 (602)
++.|.||+|+|+|||+|+||++.||++++..+...+++|+.+++.+.+||+++||+++|+|+||||+ +||||||+|||+
T Consensus 159 ~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~-~gv~giG~k~A~ 237 (316)
T cd00128 159 AKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLGCDYT-EGIPGIGPVTAL 237 (316)
T ss_pred HhCCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCC-CCCCCccHHHHH
Confidence 9999999999999999999999999998764323678999999999999999999999999999997 899999999999
Q ss_pred HHHHhcCh-HHHHHHHHhhCCCCCCCCcCCccchhhhhcCCCCCCccccCCCCccCCCCCCccccccccccccccCCCCC
Q 044842 229 QFVQNFSE-DEILNILHKIGNGDIPQYWGDIKSTEEAVSHSDESMPMIKSSHCSFCGHPGTKRAHFKFSCEYCINDNNEG 307 (602)
Q Consensus 229 ~Li~~~~~-e~iL~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~Cs~C~h~gs~k~h~k~gc~~C~~~~~~g 307 (602)
+||++|++ +.++++++.-
T Consensus 238 ~li~~~~~~~~~~~~l~~~------------------------------------------------------------- 256 (316)
T cd00128 238 KLIKKYGDIEKDIERLKKK------------------------------------------------------------- 256 (316)
T ss_pred HHHHHcCChHHHHHHHHHh-------------------------------------------------------------
Confidence 99999995 5555443310
Q ss_pred CCCCCCCCccccccchhhhhHHHHhhhhhhhHhhhcccccCCCCCCHHHHHHHhccCCCCCCCCCCCCcccCCCCHHHHH
Q 044842 308 CLKKPDGFKCNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTATDGPSISWGSPMTEMLV 387 (602)
Q Consensus 308 c~~~~~~~~c~c~~~~~~r~~k~~~~~~~~~~~~~~k~~~~~~FP~~~Vi~~yl~p~v~~~~~~~~~~~~W~~Pdl~~L~ 387 (602)
+...|++||+.++.+.|++|.+. .....+.|..||.+.|+
T Consensus 257 ------------------------------------~~~~~~~~~~~~~~~~f~~p~~~----~~~~~~~~~~p~~~~l~ 296 (316)
T cd00128 257 ------------------------------------LYRSPEDFPLKEAREFFLNPEVT----DDFIDLRWRDPDEEGII 296 (316)
T ss_pred ------------------------------------CccCCCcCChHHHHHHHcCCCCC----CCCCceeecCCCHHHHH
Confidence 01235899999999999999872 23468999999999999
Q ss_pred HHHhhhCCCChhHHhhhH
Q 044842 388 DFLVYHQPWQPSYIRQKM 405 (602)
Q Consensus 388 ~f~~~~~~W~~~~~~e~l 405 (602)
.|+....+|+++++...+
T Consensus 297 ~~~~~~~~~~~~rv~~~~ 314 (316)
T cd00128 297 EFLCKEHGFNEDRVLKPL 314 (316)
T ss_pred HHccCCCCCCHHHHHhhh
Confidence 999999999988877644
No 4
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=1.4e-55 Score=466.25 Aligned_cols=297 Identities=30% Similarity=0.448 Sum_probs=248.4
Q ss_pred CCCCCcChhhhcccccccCccccCCCEEEEeHHHHHHHHhccccC---------CCCCChHHHHHHHHHHHHHHhCCCeE
Q 044842 1 MGVGGKFWDLLKPYARFEGLDFLRDKRVAVDLSYWIVQHETAIKK---------NSVPKPHLRLTFFRTINLFAKFGAFP 71 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~---------~g~~~~~Lr~~f~r~l~lL~~~gI~P 71 (602)
||| | ||++|+ .++.+++.|+|++|||||++||||++++++. .|.+++||+++|.++++++ ++||+|
T Consensus 1 MGi-~-l~~~~~--~~~~~l~~~~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll-~~~i~P 75 (338)
T TIGR03674 1 MGV-D-LRDLLA--KEEIELEDLSGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLL-ENGIKP 75 (338)
T ss_pred CCC-C-hHHHhc--cCccCHHHhCCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHH-HCCCeE
Confidence 999 8 999999 6889999999999999999999999988751 6888999999999999876 589999
Q ss_pred EEEEcCCCCcchhHHHHHhhhccccccccch-HHHhccchhhhHHH-------HHhHHHHHHHHHHcCCCEEeccCcHHH
Q 044842 72 VFVVDGTPSPLKSQARLARFYRSTIDASTLP-VAEEGILVERNQTF-------LKCVQECVELLELFGMPVLKAKGEAEA 143 (602)
Q Consensus 72 VfVFDG~~p~~K~~t~~kR~~R~~~~~~~~~-~~k~g~~~e~~~~f-------~~~i~~~~~lL~~~GI~~i~AP~EADA 143 (602)
||||||.+|++|..+..+|..++......+. ..++|...++...+ ..+++.++++|+.|||||++|||||||
T Consensus 76 v~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAea 155 (338)
T TIGR03674 76 VYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEA 155 (338)
T ss_pred EEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHH
Confidence 9999999999999998888765422111111 12233322222111 347889999999999999999999999
Q ss_pred HHHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecCCCCCC-----------CeEEEeHHHHHHHhCCCHHHHHHHHHHcCC
Q 044842 144 LCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNTKE-----------PFECYCISDIEAGLGLKRKHLIAMSLLIGN 212 (602)
Q Consensus 144 qcA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k~-----------~~~~y~~~~i~~~lgL~~~qli~laiL~G~ 212 (602)
|||+|++.|.||+|+|+|+|+|+||+++|+++++..++. ..++|+.+.+.+.+|++++||+++|+|+||
T Consensus 156 q~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~ 235 (338)
T TIGR03674 156 QAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGT 235 (338)
T ss_pred HHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCC
Confidence 999999999999999999999999999999998754321 346799999999999999999999999999
Q ss_pred CCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhhCCCCCCCCcCCccchhhhhcCCCCCCccccCCCCccCCCCCCccc
Q 044842 213 DHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKIGNGDIPQYWGDIKSTEEAVSHSDESMPMIKSSHCSFCGHPGTKRA 291 (602)
Q Consensus 213 DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~Cs~C~h~gs~k~ 291 (602)
||+ +||||||+|||++||++|++ ++|++++. .
T Consensus 236 dyn-~Gv~GIG~ktA~kli~~~gsie~il~~~~------------------~---------------------------- 268 (338)
T TIGR03674 236 DYN-EGVKGIGPKTALKLIKEHGDLEKVLKARG------------------E---------------------------- 268 (338)
T ss_pred CCC-CCCCCccHHHHHHHHHHcCCHHHHHHhhc------------------C----------------------------
Confidence 998 99999999999999999995 77775421 0
Q ss_pred cccccccccccCCCCCCCCCCCCCccccccchhhhhHHHHhhhhhhhHhhhcccccCCCCCCHHHHHHHhccCCCCCCCC
Q 044842 292 HFKFSCEYCINDNNEGCLKKPDGFKCNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPNDEIVTMYLCENNGTFTAT 371 (602)
Q Consensus 292 h~k~gc~~C~~~~~~gc~~~~~~~~c~c~~~~~~r~~k~~~~~~~~~~~~~~k~~~~~~FP~~~Vi~~yl~p~v~~~~~~ 371 (602)
. + + +..++++.|++|.+.
T Consensus 269 ----------------------------------------------------~--~-~--~~~~~~~~f~~~~v~----- 286 (338)
T TIGR03674 269 ----------------------------------------------------D--I-E--NYDEIREFFLNPPVT----- 286 (338)
T ss_pred ----------------------------------------------------C--C-C--CHHHHHHHhCCCCCC-----
Confidence 0 0 1 126899999999872
Q ss_pred CCCCcccCCCCHHHHHHHHhhhCCCChhHHhhhHhhHHHh
Q 044842 372 DGPSISWGSPMTEMLVDFLVYHQPWQPSYIRQKMLPMLST 411 (602)
Q Consensus 372 ~~~~~~W~~Pdl~~L~~f~~~~~~W~~~~~~e~llPll~~ 411 (602)
....+.|+.||.++|++|+.+.++|++++++..+-+|.+.
T Consensus 287 ~~~~~~~~~pd~e~l~~fl~~e~~~~~~rv~~~~~~l~~~ 326 (338)
T TIGR03674 287 DDYELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAA 326 (338)
T ss_pred CCCCccCCCCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHh
Confidence 2368999999999999999999999999999999999664
No 5
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.7e-50 Score=417.66 Aligned_cols=256 Identities=29% Similarity=0.457 Sum_probs=214.9
Q ss_pred CCCCChHHHHHHHHHHHHHHhCCCeEEEEEcCCCCcchhHHHHHhhhccccccccch-HHHhccchhhhHHH-------H
Q 044842 46 NSVPKPHLRLTFFRTINLFAKFGAFPVFVVDGTPSPLKSQARLARFYRSTIDASTLP-VAEEGILVERNQTF-------L 117 (602)
Q Consensus 46 ~g~~~~~Lr~~f~r~l~lL~~~gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~~~~~~-~~k~g~~~e~~~~f-------~ 117 (602)
.|.+|+||.++|+|+++++ ++||+|||||||.+|++|..+..+|..++......+. ..++|...++...+ .
T Consensus 4 ~G~~Ts~l~g~~~r~~~ll-~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~ 82 (292)
T PRK03980 4 KGRITSHLSGIFYRTINLL-ENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTD 82 (292)
T ss_pred CCcCcHHHHHHHHHHHHHH-HCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCH
Confidence 6899999999999999987 5899999999999999999999888765532222122 22333332222222 3
Q ss_pred HhHHHHHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecCCCCC-----------CCeEE
Q 044842 118 KCVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNTK-----------EPFEC 186 (602)
Q Consensus 118 ~~i~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k-----------~~~~~ 186 (602)
.++..++++|+.|||||++||||||||||+|++.|+||+|+|+|+|+|+||+++|++++...++ ...++
T Consensus 83 ~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~ 162 (292)
T PRK03980 83 EIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPEL 162 (292)
T ss_pred HHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCcccccccccccee
Confidence 4889999999999999999999999999999999999999999999999999999999865432 13468
Q ss_pred EeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhhCCCCCCCCcCCccchhhhh
Q 044842 187 YCISDIEAGLGLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKIGNGDIPQYWGDIKSTEEAV 265 (602)
Q Consensus 187 y~~~~i~~~lgL~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~~~~~~~~~~~~~~~~~~~ 265 (602)
|+++.+.+.+|++++||+++|+|+||||+ +||||||+|||++||++|++ ++|++.+
T Consensus 163 ~~~~~vl~~lgl~~~q~id~~iL~G~Dy~-~GI~GIG~ktA~kLi~~~~sle~i~~~~---------------------- 219 (292)
T PRK03980 163 IELEEVLKELGITREQLIDIAILVGTDYN-PGIKGIGPKTALKLIKKHGDLEKVLEER---------------------- 219 (292)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHhcCCCCC-CCCCCccHHHHHHHHHHCCCHHHHHHhc----------------------
Confidence 99999999999999999999999999997 89999999999999999995 7666420
Q ss_pred cCCCCCCccccCCCCccCCCCCCccccccccccccccCCCCCCCCCCCCCccccccchhhhhHHHHhhhhhhhHhhhccc
Q 044842 266 SHSDESMPMIKSSHCSFCGHPGTKRAHFKFSCEYCINDNNEGCLKKPDGFKCNCSLCNKNRKEKEQKKHENWWIKVCSKI 345 (602)
Q Consensus 266 ~~~~~~~~~~k~~~Cs~C~h~gs~k~h~k~gc~~C~~~~~~gc~~~~~~~~c~c~~~~~~r~~k~~~~~~~~~~~~~~k~ 345 (602)
T Consensus 220 -------------------------------------------------------------------------------- 219 (292)
T PRK03980 220 -------------------------------------------------------------------------------- 219 (292)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred ccCCCCCC-HHHHHHHhccCCCCCCCCCCCCcccCCCCHHHHHHHHhhhCCCChhHHhhhHhhHHHhH
Q 044842 346 ALETNFPN-DEIVTMYLCENNGTFTATDGPSISWGSPMTEMLVDFLVYHQPWQPSYIRQKMLPMLSTI 412 (602)
Q Consensus 346 ~~~~~FP~-~~Vi~~yl~p~v~~~~~~~~~~~~W~~Pdl~~L~~f~~~~~~W~~~~~~e~llPll~~~ 412 (602)
..+||+ .+|++.|++|.|. +...|+|+.||+++|++||++..+|++++++..+-+|.+.+
T Consensus 220 --~~~~~~~~~~r~~f~~p~v~-----~~~~~~~~~pd~~~l~~fl~~e~~f~~~rv~~~~~~l~~~~ 280 (292)
T PRK03980 220 --GFEIENYDEIREFFLNPPVT-----DDYELKWKEPDKEGIIEFLVEEHDFSEERVKKALERLEKAV 280 (292)
T ss_pred --cCCCCCHHHHHHHhcCCCCC-----CCCCccCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHHh
Confidence 123444 8999999999982 25789999999999999999999999999999999998764
No 6
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=2.8e-44 Score=384.77 Aligned_cols=237 Identities=26% Similarity=0.369 Sum_probs=200.1
Q ss_pred CCCCCcChhhhcccccccCccccCCCEEEEeHHHHHHHHhccccC---CCCCChHHHHHHHHHHHHHHhCCCeEEEEEcC
Q 044842 1 MGVGGKFWDLLKPYARFEGLDFLRDKRVAVDLSYWIVQHETAIKK---NSVPKPHLRLTFFRTINLFAKFGAFPVFVVDG 77 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~---~g~~~~~Lr~~f~r~l~lL~~~gI~PVfVFDG 77 (602)
|||+| |.+++++..++.++++++|++||||+++|||++..+|.. .|.+|.-...+|...++||+.+||.||+||||
T Consensus 1 MGI~G-Llp~~k~~~~~~hi~~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT~ryi~y~ik~v~lL~~~gikPilVFDG 79 (556)
T KOG2518|consen 1 MGIQG-LLPLLKPALKPIHISEYKGKTVAVDGYCWLHRGALACAEKLAKGKPTDRYIQFFIKRVKLLLSYGIKPILVFDG 79 (556)
T ss_pred CCcch-hHHHHHHHhhhhhHHHhcCceEEEehhhHHhhhHHhHHHHHhcCCChHHHHHHHHHHHHHHHhcCCeEEEEecC
Confidence 99999 999999999999999999999999999999999887765 46666544456888899999999999999999
Q ss_pred CCCcchhHHHHHhhhcccccc-ccchHHHhccchhhhHHHHH-------hHHHHHHHHHHcCCCEEeccCcHHHHHHHHH
Q 044842 78 TPSPLKSQARLARFYRSTIDA-STLPVAEEGILVERNQTFLK-------CVQECVELLELFGMPVLKAKGEAEALCAQLN 149 (602)
Q Consensus 78 ~~p~~K~~t~~kR~~R~~~~~-~~~~~~k~g~~~e~~~~f~~-------~i~~~~~lL~~~GI~~i~AP~EADAqcA~L~ 149 (602)
.+.|.|..|..+|+.++.... .+...+.+|...++.+.|.+ |...++++|+..||+||+||||||||+|||+
T Consensus 80 ~~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~ 159 (556)
T KOG2518|consen 80 DPLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLE 159 (556)
T ss_pred CCcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHHH
Confidence 999999998887776552221 22223457777777788865 5567899999999999999999999999999
Q ss_pred HcCCeeEEEcCCCCeEeeCCeEEEEecCCCCCCCeEEEeHHHHHHHh----CCCHHHHHHHHHHcCCCCCCCCCCcccHH
Q 044842 150 SEGYVDACITADSDAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGL----GLKRKHLIAMSLLIGNDHDLNGVQGIGLD 225 (602)
Q Consensus 150 ~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~l----gL~~~qli~laiL~G~DY~~~GipGIG~k 225 (602)
+.|+||||||+|||+++||++.||..|+..+. ...++...+.... +++.++|..+|+|+||||+ .||||||.+
T Consensus 160 ~~~~i~~IITEDSDLl~fGc~~vifK~d~~G~--~le~~~~~l~~~~~l~~~~~~ekfr~mciLSGCDYl-~slpGvGl~ 236 (556)
T KOG2518|consen 160 REGIVDAIITEDSDLLVFGCKKVIFKMDSFGN--GLEINRSKLPECKPLGDKFTEEKFRRMCILSGCDYL-SSLPGVGLA 236 (556)
T ss_pred hcCcceEEEeccccccccCchhheeeccCCCC--cccccHhhhhhccccccccCHHHHHHHHHhcCCccc-ccCccccHH
Confidence 99999999999999999999999999876443 3456776665543 4568999999999999996 999999999
Q ss_pred HHHHHHHhcCh-HHHHH
Q 044842 226 TALQFVQNFSE-DEILN 241 (602)
Q Consensus 226 tA~~Li~~~~~-e~iL~ 241 (602)
||+++|+.|.. +.++.
T Consensus 237 tA~k~l~k~~~~d~vi~ 253 (556)
T KOG2518|consen 237 TAHKLLSKYNTPDRVII 253 (556)
T ss_pred HHHHHHHhcCcHHHHHH
Confidence 99999999996 55543
No 7
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.5e-42 Score=391.25 Aligned_cols=228 Identities=32% Similarity=0.512 Sum_probs=192.0
Q ss_pred HHhHHHHHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecCCCCCCCeEEEeHHHHHHHh
Q 044842 117 LKCVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGL 196 (602)
Q Consensus 117 ~~~i~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~l 196 (602)
..|+.+|++||+.||||||+||+|||||||.|.+.++||||||+|||+|+||+.+||+||+.+. ..++.|.+.+|+..|
T Consensus 465 ~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~kn-k~ve~y~~~di~kel 543 (815)
T KOG2520|consen 465 SDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKN-KYVEKYQLDDIEKEL 543 (815)
T ss_pred HHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcC-ccceeeehHHHHHHH
Confidence 4688999999999999999999999999999999999999999999999999999999998764 467999999999999
Q ss_pred CCCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHhhCCCCCCCCcCCccchhhhhcCCCCCCcccc
Q 044842 197 GLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHKIGNGDIPQYWGDIKSTEEAVSHSDESMPMIK 276 (602)
Q Consensus 197 gL~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k 276 (602)
||+|..||-+|.|+|+||| .||+|||+++|+++|.+|++++-|..|++|..-.. +..+
T Consensus 544 ~l~R~~lI~lA~LlGsDYt-~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~~~---------------------~~~~ 601 (815)
T KOG2520|consen 544 GLDRPNLISLAQLLGSDYT-EGLKGIGPVSALEILAEFPGDENLLKFKKWVQQTG---------------------PADK 601 (815)
T ss_pred ccCchhhHHHHHhcccccc-cCCCcccchHHHHHHHHcCCcchhHHHHHHHHHhC---------------------cccc
Confidence 9999999999999999998 99999999999999999997666888998853100 0000
Q ss_pred CCCCccCCCCCCccccccccccccccCCCCCCCCCCCCCccccccchhhhhHHHHhhhhhhhHhhhc-ccccCCCCCCHH
Q 044842 277 SSHCSFCGHPGTKRAHFKFSCEYCINDNNEGCLKKPDGFKCNCSLCNKNRKEKEQKKHENWWIKVCS-KIALETNFPNDE 355 (602)
Q Consensus 277 ~~~Cs~C~h~gs~k~h~k~gc~~C~~~~~~gc~~~~~~~~c~c~~~~~~r~~k~~~~~~~~~~~~~~-k~~~~~~FP~~~ 355 (602)
..|++ ++ .+.++ ++.. ++.++.+||++.
T Consensus 602 --------~~~s~-----------------------------------~~-~~lrk-------kl~n~~~~l~~~fP~~~ 630 (815)
T KOG2520|consen 602 --------EVGST-----------------------------------QQ-KMLRK-------KLKNPKIILPSDFPNPN 630 (815)
T ss_pred --------ccccH-----------------------------------HH-HHHHH-------HhcCcccccCcCCCchh
Confidence 00100 00 11111 2222 478899999999
Q ss_pred HHHHHhccCCCCCCCCCCCCcccCCCCHHHHHHHHhhhCCCChhHHhhhHhhHHHhHHHhhhcCCCc
Q 044842 356 IVTMYLCENNGTFTATDGPSISWGSPMTEMLVDFLVYHQPWQPSYIRQKMLPMLSTIYLREMATNPV 422 (602)
Q Consensus 356 Vi~~yl~p~v~~~~~~~~~~~~W~~Pdl~~L~~f~~~~~~W~~~~~~e~llPll~~~~l~~~~~~~~ 422 (602)
|++|||+|.| +.+...|.||.||++.|++||...|||+..++++.|+|++++++-++....+.
T Consensus 631 v~~AYLrP~V----D~sk~~f~WG~pdl~~lRef~~~~fgW~~~kT~~~l~p~~~~~~~~~~~~~~~ 693 (815)
T KOG2520|consen 631 VIEAYLRPEV----DDSKEKFRWGKPDLDILREFMKRLFGWPDEKTDEELIPVIKRLEKKKTQLKQD 693 (815)
T ss_pred HHHHhhCCcc----CCCcccccCCCCCHHHHHHHHHHHcCCCccccchhhhhhHHHHHHHhhhhccc
Confidence 9999999998 35678999999999999999999999999999999999999998666444333
No 8
>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=1.8e-41 Score=393.48 Aligned_cols=215 Identities=29% Similarity=0.481 Sum_probs=178.2
Q ss_pred HhHHHHHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecCCCCCCCeEEEeHHHHHHHhC
Q 044842 118 KCVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGLG 197 (602)
Q Consensus 118 ~~i~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~lg 197 (602)
.++.+|++||++||||||+||||||||||+|++.|+||||+|+|||+|+||+++||+||+.. +.++++|.+.+|.+.+|
T Consensus 772 ~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~-~~~ve~~~~~~i~~~lg 850 (1034)
T TIGR00600 772 QMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQ-NKFVEYYQYVDIHNQLG 850 (1034)
T ss_pred HHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCC-CCceEEeeHHHHHHHhC
Confidence 57889999999999999999999999999999999999999999999999999999998753 45789999999999999
Q ss_pred CCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcCh---HHHHHHHHhhCCCCCCCCcCCccchhhhhcCCCCCCcc
Q 044842 198 LKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSE---DEILNILHKIGNGDIPQYWGDIKSTEEAVSHSDESMPM 274 (602)
Q Consensus 198 L~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~---e~iL~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 (602)
|++++||+||+|+||||+ +||+|||++||++||+.|+. +.+ -.|+.|...... +. . .
T Consensus 851 lt~~qli~laiL~G~DY~-~GI~GIGpktAl~li~~~~~~~le~L-~~f~~w~~~~~~---------~~----~----~- 910 (1034)
T TIGR00600 851 LDRNKLINLAYLLGSDYT-EGIPTVGPVSAMEILNEFPGDGLEPL-LKFKEWWHEAQK---------DK----K----K- 910 (1034)
T ss_pred CCHHHHHHHHHeeCCCCC-CCCCcccHHHHHHHHHHcCCCCHHHH-HHHHHHHHHhhh---------cc----c----c-
Confidence 999999999999999998 99999999999999999994 444 456666431100 00 0 0
Q ss_pred ccCCCCccCCCCCCccccccccccccccCCCCCCCCCCCCCccccccchhhhhHHHHhhhhhhhHhhhcccccCCCCCCH
Q 044842 275 IKSSHCSFCGHPGTKRAHFKFSCEYCINDNNEGCLKKPDGFKCNCSLCNKNRKEKEQKKHENWWIKVCSKIALETNFPND 354 (602)
Q Consensus 275 ~k~~~Cs~C~h~gs~k~h~k~gc~~C~~~~~~gc~~~~~~~~c~c~~~~~~r~~k~~~~~~~~~~~~~~k~~~~~~FP~~ 354 (602)
.. .+.+| + .+++ .+++.+|++||+.
T Consensus 911 ------------------------------~~----~~~~~----------~---~~~~--------~~~~~lp~~FP~~ 935 (1034)
T TIGR00600 911 ------------------------------RE----NPNDT----------K---VKKK--------LRLLQLTPGFPNP 935 (1034)
T ss_pred ------------------------------cc----ccchh----------h---hhhc--------ccccccCCCCCcH
Confidence 00 00011 0 0000 1245689999999
Q ss_pred HHHHHHhccCCCCCCCCCCCCcccCCCCHHHHHHHHhhhCCCChhHHhhhHhhHHHhH
Q 044842 355 EIVTMYLCENNGTFTATDGPSISWGSPMTEMLVDFLVYHQPWQPSYIRQKMLPMLSTI 412 (602)
Q Consensus 355 ~Vi~~yl~p~v~~~~~~~~~~~~W~~Pdl~~L~~f~~~~~~W~~~~~~e~llPll~~~ 412 (602)
+|+++|++|.|. .+...|+|+.||+++|+.||++.++|++.++++.|.||+++.
T Consensus 936 ~V~~~yl~P~V~----~~~~~f~W~~PD~e~L~~Fl~~~~gws~eRv~~~l~plikk~ 989 (1034)
T TIGR00600 936 AVADAYLRPVVD----DSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKL 989 (1034)
T ss_pred HHHHHhcCCCCC----CCcCCCCCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHH
Confidence 999999999983 334789999999999999999999999999999999999854
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=2.2e-31 Score=272.51 Aligned_cols=205 Identities=24% Similarity=0.345 Sum_probs=167.5
Q ss_pred CEEEEeHHHHHHHHhccccC----CCCCChHHHHHHHHHHHHHHhC-CCeEEEEEcCCCCcchhHHHHHhhhcccccccc
Q 044842 26 KRVAVDLSYWIVQHETAIKK----NSVPKPHLRLTFFRTINLFAKF-GAFPVFVVDGTPSPLKSQARLARFYRSTIDAST 100 (602)
Q Consensus 26 k~IAIDas~wL~r~~~a~~~----~g~~~~~Lr~~f~r~l~lL~~~-gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~~~~ 100 (602)
+.++|||++++||++++.+. +|.+++++.+++..+.+++... +-++++||||..+.++++.
T Consensus 2 ~lllIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~l-------------- 67 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHEL-------------- 67 (259)
T ss_pred cEEEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccch--------------
Confidence 46899999999999998643 6888999999888877777654 4567999999877664432
Q ss_pred chHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHHc----CCeeEEEcCCCCeEeeCCeEEEEe
Q 044842 101 LPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNSE----GYVDACITADSDAFLFGAKCVVKC 175 (602)
Q Consensus 101 ~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~~----g~vd~ViT~DSD~llfG~~~Vi~~ 175 (602)
++.+|+++. +.++.+..++..++++|+.+|||++.+|+ |||++||+|++. |....|+|.|+|+++++++.|...
T Consensus 68 ~p~YKa~R~-~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~ 146 (259)
T smart00475 68 YPEYKANRP-KTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVL 146 (259)
T ss_pred hHHHHhCCC-CCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEE
Confidence 233444432 45677888889999999999999999996 999999999874 778899999999999988765332
Q ss_pred cCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhh
Q 044842 176 IRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKI 246 (602)
Q Consensus 176 ~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~ 246 (602)
...++....+.++.+.+.+.+|++++||+++++|+| +||. |||||||+|||.+||++||+ ++|++++.++
T Consensus 147 ~~~~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDni-pGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~ 219 (259)
T smart00475 147 DPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNI-PGVPGIGEKTAAKLLKEFGSLENILENLDKL 219 (259)
T ss_pred eccCCCCccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCC-CCCCCCCHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 122211234689999999999999999999999999 8995 99999999999999999996 9999998876
No 10
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=99.97 E-value=7.8e-30 Score=258.53 Aligned_cols=202 Identities=21% Similarity=0.313 Sum_probs=166.9
Q ss_pred CEEEEeHHHHHHHHhccccC-----CCCCChHHHHHHHHHHHHHHhC-CCeEEEEEcCCCCcchhHHHHHhhhccccccc
Q 044842 26 KRVAVDLSYWIVQHETAIKK-----NSVPKPHLRLTFFRTINLFAKF-GAFPVFVVDGTPSPLKSQARLARFYRSTIDAS 99 (602)
Q Consensus 26 k~IAIDas~wL~r~~~a~~~-----~g~~~~~Lr~~f~r~l~lL~~~-gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~~~ 99 (602)
+.++|||++++||++++.+. .|.++.++.+++.++.+++.+. ..++++||||..+.++++.
T Consensus 2 ~~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l------------- 68 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHEL------------- 68 (240)
T ss_pred cEEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccc-------------
Confidence 47999999999999998753 4778889998887777777654 5789999999877765532
Q ss_pred cchHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHH----cCCeeEEEcCCCCeEeeCCeEEEE
Q 044842 100 TLPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNS----EGYVDACITADSDAFLFGAKCVVK 174 (602)
Q Consensus 100 ~~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~----~g~vd~ViT~DSD~llfG~~~Vi~ 174 (602)
++.+|+++. +.++.+..++..++++|+.+|||++.+|+ |||++||+|++ .|....|+|.|+|+++++...|..
T Consensus 69 -~p~YK~~R~-~~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~ 146 (240)
T cd00008 69 -YPEYKANRK-KMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKV 146 (240)
T ss_pred -cHHHHcCCC-CCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEE
Confidence 233444332 35678889999999999999999999996 99999999985 577779999999999997766533
Q ss_pred ecCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhhC
Q 044842 175 CIRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKIG 247 (602)
Q Consensus 175 ~~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~ 247 (602)
.... ....++.+.+.+.+|++++|++++++|+| |||. |||||||+|||.+||++|++ ++|+++++..+
T Consensus 147 ~~~~----~~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDni-pGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~ 217 (240)
T cd00008 147 VSPM----KKKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNI-PGVPGIGEKTAAKLLKEYGSLEGILENLDKIK 217 (240)
T ss_pred EeCC----CceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCC-CCCCccCHHHHHHHHHHhCCHHHHHHhHHHHh
Confidence 2111 12578999999999999999999999999 8995 99999999999999999996 99999988763
No 11
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.97 E-value=5e-29 Score=257.84 Aligned_cols=206 Identities=17% Similarity=0.284 Sum_probs=166.8
Q ss_pred CCEEEEeHHHHHHHHhccc----c----CCCCCChHHHHHHHHHHHHHHhC-CCeEEEEEcCCCCcchhHHHHHhhhccc
Q 044842 25 DKRVAVDLSYWIVQHETAI----K----KNSVPKPHLRLTFFRTINLFAKF-GAFPVFVVDGTPSPLKSQARLARFYRST 95 (602)
Q Consensus 25 gk~IAIDas~wL~r~~~a~----~----~~g~~~~~Lr~~f~r~l~lL~~~-gI~PVfVFDG~~p~~K~~t~~kR~~R~~ 95 (602)
.+.++|||++++||++++. . .+|.++.++.+++.++++++... +.++++|||+..+.++++.
T Consensus 3 ~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l--------- 73 (281)
T PRK14976 3 KKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQL--------- 73 (281)
T ss_pred CcEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccc---------
Confidence 4588999999999998885 1 16888999998777777777654 4689999999877765432
Q ss_pred cccccchHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHHc----CCeeEEEcCCCCeEeeCCe
Q 044842 96 IDASTLPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNSE----GYVDACITADSDAFLFGAK 170 (602)
Q Consensus 96 ~~~~~~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~~----g~vd~ViT~DSD~llfG~~ 170 (602)
++.+|+++ .+.++.+..+++.++++|+.+|||++.+|+ |||++||+|++. |.-..|+|.|.|++++.++
T Consensus 74 -----~p~YKanR-~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~ 147 (281)
T PRK14976 74 -----YDEYKQGR-KKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNE 147 (281)
T ss_pred -----cHHHhcCC-CCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCC
Confidence 23344443 245677888999999999999999999996 999999999864 5555799999999999987
Q ss_pred EEEEecCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhhC
Q 044842 171 CVVKCIRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKIG 247 (602)
Q Consensus 171 ~Vi~~~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~ 247 (602)
+|........ .....++.+.+.+.+|++++||+++++|+| +|| +|||||||+|||.+||++||+ ++|++++.++.
T Consensus 148 ~v~~~~~~~~-~~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDn-ipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~ 225 (281)
T PRK14976 148 NTDVLLKKKG-TSHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDN-IKGVKGIGPKTAIKLLNKYGNIENIYENIDKIK 225 (281)
T ss_pred CeEEEEecCC-CCcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCC-CCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHh
Confidence 6533222222 125689999999999999999999999999 899 599999999999999999996 99999988763
No 12
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.96 E-value=4.8e-28 Score=253.93 Aligned_cols=209 Identities=25% Similarity=0.336 Sum_probs=153.0
Q ss_pred cCccccCCCEEEEeHHHHHHHHhccccC-----CCCCChHHHH---HHHHHHHHHHhCCCeEEEEEcCCCCcchhHHHHH
Q 044842 18 EGLDFLRDKRVAVDLSYWIVQHETAIKK-----NSVPKPHLRL---TFFRTINLFAKFGAFPVFVVDGTPSPLKSQARLA 89 (602)
Q Consensus 18 ~~Ls~L~gk~IAIDas~wL~r~~~a~~~-----~g~~~~~Lr~---~f~r~l~lL~~~gI~PVfVFDG~~p~~K~~t~~k 89 (602)
..+...+|+.++|||++|+||+++|.+. .|.+++.+.+ ++.++++.+ .+++|++||||.++++|+++...
T Consensus 4 ~~~~~~~~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~--~~~~~~~vFD~~~~tfR~~~~~~ 81 (310)
T COG0258 4 IQLMNKSGKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLL--EPTHPVVVFDGKPPTFRHELLEE 81 (310)
T ss_pred ccchhccCcEEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhc--CCCcEEEEEcCCCCcchHHHHHH
Confidence 3456678999999999999999999853 4555554444 344444433 35999999999888898887666
Q ss_pred hhhccccccccchHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHH----HcCCeeEEEcCCCCe
Q 044842 90 RFYRSTIDASTLPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLN----SEGYVDACITADSDA 164 (602)
Q Consensus 90 R~~R~~~~~~~~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~----~~g~vd~ViT~DSD~ 164 (602)
|..+|.. +.+..|..++..+.+++..+|++++..+| ||||.++.++ +.|.+++|+|+|+|+
T Consensus 82 yK~~R~~--------------~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~ 147 (310)
T COG0258 82 YKANREK--------------EMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDL 147 (310)
T ss_pred HHhCCCc--------------cCHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcch
Confidence 5543311 13455655555555555555555555553 4444444443 579999999999999
Q ss_pred EeeCCeEEEEecCCCCCCCeEEEeHHHHHHHh-CCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHH
Q 044842 165 FLFGAKCVVKCIRPNTKEPFECYCISDIEAGL-GLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 165 llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~l-gL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
++|+++++.......+ .+...++...+.+.+ |+++.||+++++|+| |||+ |||+|||+|||++||++||+ +.|+
T Consensus 148 lql~~~~~~~~~~~~~-~~~~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDni-pGV~GIG~ktA~~Ll~~~gs~e~i~ 225 (310)
T COG0258 148 LQLVSPNVLVINGKKG-EPEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNI-PGVKGIGPKTALKLLQEYGSLEGLY 225 (310)
T ss_pred hhhcCCCcEEEeccCC-CCcccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCC-CCCCCcCHHHHHHHHHHhCCHHHHH
Confidence 9999998654333222 121257899999999 999999999999999 9996 99999999999999999996 6777
Q ss_pred HHHH
Q 044842 241 NILH 244 (602)
Q Consensus 241 ~~l~ 244 (602)
+++.
T Consensus 226 ~~~~ 229 (310)
T COG0258 226 ENLD 229 (310)
T ss_pred Hhhh
Confidence 7665
No 13
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.94 E-value=4e-26 Score=266.79 Aligned_cols=203 Identities=21% Similarity=0.327 Sum_probs=166.8
Q ss_pred EEEeHHHHHHHHhccccC------CCCCChHHHHHHHHHHHHHHhC-CCeEEEEEcCCCCcchhHHHHHhhhcccccccc
Q 044842 28 VAVDLSYWIVQHETAIKK------NSVPKPHLRLTFFRTINLFAKF-GAFPVFVVDGTPSPLKSQARLARFYRSTIDAST 100 (602)
Q Consensus 28 IAIDas~wL~r~~~a~~~------~g~~~~~Lr~~f~r~l~lL~~~-gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~~~~ 100 (602)
++|||++++||+++|++. +|.+++++.+++.++++++.+. +-+.+||||+..+.++++ ..
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~tfR~~-~~------------ 68 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHE-AY------------ 68 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCcchHH-HH------------
Confidence 689999999999998851 6889999999877778877654 446699999988777553 22
Q ss_pred chHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHHc----CCeeEEEcCCCCeEeeCCeEEEEe
Q 044842 101 LPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNSE----GYVDACITADSDAFLFGAKCVVKC 175 (602)
Q Consensus 101 ~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~~----g~vd~ViT~DSD~llfG~~~Vi~~ 175 (602)
+.+|+++ .+.++.+..++..++++|+.||||++.+|+ |||++||+|++. |....|+|.|.|+++++.++|...
T Consensus 69 -~~YKa~R-~~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~ 146 (887)
T TIGR00593 69 -AEYKANR-APTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVL 146 (887)
T ss_pred -HHHHhCC-CCChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEE
Confidence 2334333 235778889999999999999999999997 999999999864 777899999999999998765322
Q ss_pred cCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhhC
Q 044842 176 IRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKIG 247 (602)
Q Consensus 176 ~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~ 247 (602)
....+ .....|+.+.+.+.+|++++||+++++|+| ||| +|||||||+|||.+||++||+ |+|++++++.+
T Consensus 147 ~~~~~-~~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDn-IpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~ 219 (887)
T TIGR00593 147 IPKGK-TSFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDN-IPGVKGIGEKTAAKLLQEFGSLENIYENLDQIK 219 (887)
T ss_pred eccCC-CCceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccC-CCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhc
Confidence 11111 134679999999999999999999999999 699 599999999999999999996 99999998874
No 14
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.94 E-value=8.1e-26 Score=230.33 Aligned_cols=199 Identities=19% Similarity=0.240 Sum_probs=159.9
Q ss_pred CEEEEeHHHHHHHHhcccc-CCCCCChHHHHHHHHHHHHHHhCC-CeEEEEEcCCCCc--chhHHHHHhhhccccccccc
Q 044842 26 KRVAVDLSYWIVQHETAIK-KNSVPKPHLRLTFFRTINLFAKFG-AFPVFVVDGTPSP--LKSQARLARFYRSTIDASTL 101 (602)
Q Consensus 26 k~IAIDas~wL~r~~~a~~-~~g~~~~~Lr~~f~r~l~lL~~~g-I~PVfVFDG~~p~--~K~~t~~kR~~R~~~~~~~~ 101 (602)
+.+.|||++++||++++.+ ..|. ++.+.+++..+++++..++ -+.+++||+..+. +++ +. +
T Consensus 4 ~llLiDg~~l~~R~~~a~~~~~g~-t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~-~l-------------~ 68 (256)
T PRK09482 4 HLLIIDALNLIRRIHAVQPSPNDI-NACVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRH-QL-------------L 68 (256)
T ss_pred eEEEEeCcHHHHHHHhCCCCCCCc-chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHH-HH-------------h
Confidence 5789999999999999875 3565 7888886666677776654 4678899997665 433 22 2
Q ss_pred hHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHHc----CCeeEEEcCCCCeEeeCCeEE-EEe
Q 044842 102 PVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNSE----GYVDACITADSDAFLFGAKCV-VKC 175 (602)
Q Consensus 102 ~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~~----g~vd~ViT~DSD~llfG~~~V-i~~ 175 (602)
+.+|+++. +.++.+..++..++++|..+||+++..|+ |||+.||.|+.. |.--.|+|.|.|+++.-...| +++
T Consensus 69 p~YKa~R~-~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~ 147 (256)
T PRK09482 69 PDYKAGRK-PMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRD 147 (256)
T ss_pred HHHhcCCC-CCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEe
Confidence 34444433 45778889999999999999999999997 999999999853 444468999999998866554 333
Q ss_pred cCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhh
Q 044842 176 IRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKI 246 (602)
Q Consensus 176 ~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~ 246 (602)
.. . .++++.+.+.+.+|++++|++++.+|+| +|+ +|||||||+|||.+||++||+ ++|+++++++
T Consensus 148 ~~-~----~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDn-IpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~ 215 (256)
T PRK09482 148 YF-Q----KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSK-IPGVAGIGPKSAAELLNQFRSLENIYESLDAL 215 (256)
T ss_pred cc-c----cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccC-CCCCCCcChHHHHHHHHHhCCHHHHHHhHHHh
Confidence 22 1 1468999999999999999999999999 899 599999999999999999996 9999998776
No 15
>PRK05755 DNA polymerase I; Provisional
Probab=99.94 E-value=1.7e-25 Score=263.33 Aligned_cols=203 Identities=19% Similarity=0.292 Sum_probs=166.5
Q ss_pred CEEEEeHHHHHHHHhccc-cC----CCCCChHHHHHHHHHHHHHHhC-CCeEEEEEcCCCCcchhHHHHHhhhccccccc
Q 044842 26 KRVAVDLSYWIVQHETAI-KK----NSVPKPHLRLTFFRTINLFAKF-GAFPVFVVDGTPSPLKSQARLARFYRSTIDAS 99 (602)
Q Consensus 26 k~IAIDas~wL~r~~~a~-~~----~g~~~~~Lr~~f~r~l~lL~~~-gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~~~ 99 (602)
+.++|||++++||++++. +. +|.+++++.+++.++.+++... +-+.+||||+..+.++++.
T Consensus 3 ~~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~~~R~~~------------- 69 (880)
T PRK05755 3 TLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHEL------------- 69 (880)
T ss_pred eEEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccc-------------
Confidence 578999999999999987 22 6888999999777777777544 4466999999777665432
Q ss_pred cchHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHH----cCCeeEEEcCCCCeEeeCCeEE--
Q 044842 100 TLPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNS----EGYVDACITADSDAFLFGAKCV-- 172 (602)
Q Consensus 100 ~~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~----~g~vd~ViT~DSD~llfG~~~V-- 172 (602)
++.+|+++ .+.++.+..++..++++|+.+||+++.+|+ |||++||+|++ .|....|+|.|+|+++++++.|
T Consensus 70 -~~~YK~~R-~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~ 147 (880)
T PRK05755 70 -YPEYKANR-PPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTL 147 (880)
T ss_pred -CHHHhCCC-CCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEE
Confidence 23344443 245678888999999999999999999996 99999999984 5788899999999999988755
Q ss_pred EEecCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhhC
Q 044842 173 VKCIRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKIG 247 (602)
Q Consensus 173 i~~~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~ 247 (602)
+..+. . .....++.+.+.+.+|++++|++++++|+| +|| +|||||||+|||.+||++||+ |+|+++++.++
T Consensus 148 ~~~~~--~-~~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDn-ipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~ 221 (880)
T PRK05755 148 LDTMG--V-SKNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDN-IPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIK 221 (880)
T ss_pred eeccC--C-CCCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCC-CCCCCCccHHHHHHHHHHcCCHHHHHHhHHHhc
Confidence 33221 1 124679999999999999999999999999 899 599999999999999999996 99999988764
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=2.4e-24 Score=188.42 Aligned_cols=86 Identities=42% Similarity=0.636 Sum_probs=74.7
Q ss_pred HHcCCCEEeccCcHHHHHHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecC-CC-C------CCCeEEEeHHHHHHHhCCC
Q 044842 128 ELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIR-PN-T------KEPFECYCISDIEAGLGLK 199 (602)
Q Consensus 128 ~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~-~~-~------k~~~~~y~~~~i~~~lgL~ 199 (602)
+++||||++||||||||||+|++.|+||+|+|+|||+|+||+++||++++ .. + ...+++|+.+.+.+.++++
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 57999999999999999999999999999999999999999999999997 32 1 1247999999999999999
Q ss_pred HHHHHHHHHHcCCC
Q 044842 200 RKHLIAMSLLIGND 213 (602)
Q Consensus 200 ~~qli~laiL~G~D 213 (602)
+++|+++|+|+|||
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=99.84 E-value=3.3e-21 Score=169.71 Aligned_cols=92 Identities=45% Similarity=0.746 Sum_probs=79.8
Q ss_pred CCCCCcChhhhcccccccCccccCCCEEEEeHHHHHHHHhccccC---CCCC-ChHHHHHHHHHHHHHHhCCCeEEEEEc
Q 044842 1 MGVGGKFWDLLKPYARFEGLDFLRDKRVAVDLSYWIVQHETAIKK---NSVP-KPHLRLTFFRTINLFAKFGAFPVFVVD 76 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~---~g~~-~~~Lr~~f~r~l~lL~~~gI~PVfVFD 76 (602)
|||+| ||+||++..++.+++.|+|++|||||++||||++++++. .+.. .+++.++|+|+..+ ..+||+||||||
T Consensus 1 MGI~g-L~~~l~~~~~~~~i~~l~g~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l~~~~~rl~~L-~~~~I~PifVFD 78 (99)
T smart00485 1 MGIKG-LWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRL-LEFGIKPIFVFD 78 (99)
T ss_pred CCHhH-HHHHHHHhcccCCHHHhCCceEeccHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHH-HHCCCeEEEEEC
Confidence 99998 999999999999999999999999999999999988753 2222 34898888886665 479999999999
Q ss_pred CCCCcchhHHHHHhhhcc
Q 044842 77 GTPSPLKSQARLARFYRS 94 (602)
Q Consensus 77 G~~p~~K~~t~~kR~~R~ 94 (602)
|..++.|..|..+|..++
T Consensus 79 G~~~~~K~~t~~~R~~~r 96 (99)
T smart00485 79 GKPPPLKSETLAKRRERR 96 (99)
T ss_pred CCCchhhHHHHHHHHHHH
Confidence 999999999999987654
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=99.83 E-value=4.3e-21 Score=169.36 Aligned_cols=92 Identities=42% Similarity=0.659 Sum_probs=73.1
Q ss_pred CCCCCcChhhhcccc--cccCccccCCCEEEEeHHHHHHHHhccccC---CCCC-ChHHHHHHHHHHHHHHhCCCeEEEE
Q 044842 1 MGVGGKFWDLLKPYA--RFEGLDFLRDKRVAVDLSYWIVQHETAIKK---NSVP-KPHLRLTFFRTINLFAKFGAFPVFV 74 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~--~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~---~g~~-~~~Lr~~f~r~l~lL~~~gI~PVfV 74 (602)
|||+| ||++|++.. +..++++|+|++|||||++|||++++++.. .+.. ++++.++|.++. .|+.+||+||||
T Consensus 1 MGI~g-L~~~l~~~~~v~~~~~~~l~g~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~-~L~~~gI~PifV 78 (101)
T PF00752_consen 1 MGIKG-LWQLLKPAAAVRKVSLSELRGKRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLC-RLLEHGIKPIFV 78 (101)
T ss_dssp ---TT-HHHHCHHHEGEEEEEGGGGTTCEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHH-HHHHTTEEEEEE
T ss_pred CCccc-HHHHHHhhccCCccCHHHhCCCEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHH-HHHHCCCEEEEE
Confidence 99998 999999998 888999999999999999999999887763 2222 478887776655 456799999999
Q ss_pred EcCCCCcchhHHHHHhhhcc
Q 044842 75 VDGTPSPLKSQARLARFYRS 94 (602)
Q Consensus 75 FDG~~p~~K~~t~~kR~~R~ 94 (602)
|||.+++.|..|..+|..++
T Consensus 79 FDG~~~~~K~~~~~~R~~~r 98 (101)
T PF00752_consen 79 FDGKPPPLKRETIQKRRKRR 98 (101)
T ss_dssp E--STTGGCHHHHHHHHHHH
T ss_pred ECCCCchhhHHHHHHHHHHH
Confidence 99999999999999887654
No 19
>PHA00439 exonuclease
Probab=99.76 E-value=1.9e-17 Score=170.64 Aligned_cols=179 Identities=14% Similarity=0.160 Sum_probs=126.6
Q ss_pred CCCEEEEeHHHHHHHHhcccc-------C----CCCCChHHHHHHHHHHHHHHh---C-CCeEEEEEcCCCCcchhHHHH
Q 044842 24 RDKRVAVDLSYWIVQHETAIK-------K----NSVPKPHLRLTFFRTINLFAK---F-GAFPVFVVDGTPSPLKSQARL 88 (602)
Q Consensus 24 ~gk~IAIDas~wL~r~~~a~~-------~----~g~~~~~Lr~~f~r~l~lL~~---~-gI~PVfVFDG~~p~~K~~t~~ 88 (602)
....++|||++++||+++|.. . .|.++.++.+++..+++++.+ . +-+.+++||+ .+..++ ++.
T Consensus 5 ~~~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD~-~~tfR~-ely 82 (286)
T PHA00439 5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFTD-SVNWRK-EVV 82 (286)
T ss_pred CCcEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEECC-CCChHh-hhh
Confidence 456899999999999999982 1 678888888765555666655 3 4455777994 444432 222
Q ss_pred HhhhccccccccchHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHH----cCC-eeEEEcCCC
Q 044842 89 ARFYRSTIDASTLPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNS----EGY-VDACITADS 162 (602)
Q Consensus 89 kR~~R~~~~~~~~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~----~g~-vd~ViT~DS 162 (602)
+.+|+++.. .+.. ..++..+++++..+||+++..|| |||+.+|.|++ .|. --.|+|.|.
T Consensus 83 -------------p~YKanR~~-~p~~-~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DK 147 (286)
T PHA00439 83 -------------PTYKANRKA-KRKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDK 147 (286)
T ss_pred -------------hHhcCCCCC-CCCc-hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCC
Confidence 333443321 2222 33456678999999999999997 99999999975 354 347999999
Q ss_pred CeEeeCCeEEEEecCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHh
Q 044842 163 DAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQN 233 (602)
Q Consensus 163 D~llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~ 233 (602)
|++++....++.+ .. +..+ .++.+ .+++++++.+|+| +|+ +||||||| |||.+||++
T Consensus 148 Dl~QLv~~~~~~~-~~--~~~~-~~~~~--------~p~~~~d~~AL~GDsSDN-IPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 148 DFKTIPNCDFLWC-TT--GNIL-TQTPE--------TADRWHLFQTIKGDSTDG-YSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred CHhhcCcceEEEc-cC--CceE-EcCcc--------cHHHHHhhhhcccccccC-CCCCCCcC-HHHHHHHhC
Confidence 9999865544432 11 1111 12221 2899999999999 899 69999999 999999999
No 20
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.75 E-value=2.3e-18 Score=144.01 Aligned_cols=70 Identities=41% Similarity=0.551 Sum_probs=64.4
Q ss_pred HcCCCEEeccCcHHHHHHHHHHcCCeeEEEcCCCCeEeeCCeEEEEecCCCCC--CCeEEEeHHHHHHHhCC
Q 044842 129 LFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGAKCVVKCIRPNTK--EPFECYCISDIEAGLGL 198 (602)
Q Consensus 129 ~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k--~~~~~y~~~~i~~~lgL 198 (602)
.+||||++||+|||||||+|++.|+||+|+|+|+|+|+||+++||++++..++ .+++.++...+++.||+
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 68999999999999999999999999999999999999999999999976543 26789999999999885
No 21
>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=99.73 E-value=2.8e-18 Score=200.94 Aligned_cols=92 Identities=36% Similarity=0.559 Sum_probs=84.0
Q ss_pred CCCCCcChhhhcccccccCccccCCCEEEEeHHHHHHHHhccccC-CC--CCChHHHHHHHHHHHHHHhCCCeEEEEEcC
Q 044842 1 MGVGGKFWDLLKPYARFEGLDFLRDKRVAVDLSYWIVQHETAIKK-NS--VPKPHLRLTFFRTINLFAKFGAFPVFVVDG 77 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~Ls~L~gk~IAIDas~wL~r~~~a~~~-~g--~~~~~Lr~~f~r~l~lL~~~gI~PVfVFDG 77 (602)
|||+| ||++|+|++++++|+.|+|++||||||+||||++.+++. .| ..++||+++|+|+++|| .+||+|||||||
T Consensus 1 MGI~G-Lw~ll~~~~r~v~le~l~Gk~vAIDasiWL~q~l~~vr~~~g~~l~n~hl~g~f~Ri~~Ll-~~gI~PVfVFDG 78 (1034)
T TIGR00600 1 MGVQG-LWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDREGNAIKNSHLLTLFHRLCKLL-FFRIRPIFVFDG 78 (1034)
T ss_pred CChhH-HHHHHHHhcccccHHHhCCeEEEechHHHHHHHHHHHHhccCCccCCHHHHHHHHHHHHHH-HCCCeEEEEECC
Confidence 99999 999999999999999999999999999999999998875 23 46889999998988765 699999999999
Q ss_pred CCCcchhHHHHHhhhcc
Q 044842 78 TPSPLKSQARLARFYRS 94 (602)
Q Consensus 78 ~~p~~K~~t~~kR~~R~ 94 (602)
.+|++|++|..+|+.|+
T Consensus 79 ~~p~lK~~t~~~R~~rR 95 (1034)
T TIGR00600 79 GAPLLKRQTLAKRRQRR 95 (1034)
T ss_pred CCchHhHHHHHHHHHHH
Confidence 99999999999998766
No 22
>PHA02567 rnh RnaseH; Provisional
Probab=99.47 E-value=2.7e-12 Score=133.41 Aligned_cols=173 Identities=15% Similarity=0.109 Sum_probs=118.5
Q ss_pred CCCEEEEeHHHHHHHHhcccc-C-CCCCChHHHHHHHHHHHHH-Hh---CCCeEEEEEcCCCCcchhHHHHHhhhccccc
Q 044842 24 RDKRVAVDLSYWIVQHETAIK-K-NSVPKPHLRLTFFRTINLF-AK---FGAFPVFVVDGTPSPLKSQARLARFYRSTID 97 (602)
Q Consensus 24 ~gk~IAIDas~wL~r~~~a~~-~-~g~~~~~Lr~~f~r~l~lL-~~---~gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~ 97 (602)
....+.||+|.+++++++|.- . +|..++.++..|..+++.+ .+ ..-+.+++||+...+..+.+.
T Consensus 13 ~~~~~LiDgs~i~~~~~~a~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~el---------- 82 (304)
T PHA02567 13 KEGVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDI---------- 82 (304)
T ss_pred CCCEEEEehHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhh----------
Confidence 456899999999999998742 2 5777888877777666643 22 334478999997533222222
Q ss_pred cccchHHHhccchhhhHHH-------HHhH-HHHHHHHHHcCCCEEeccC-cHHHHHHHHHH----cCCeeEEEcCCCCe
Q 044842 98 ASTLPVAEEGILVERNQTF-------LKCV-QECVELLELFGMPVLKAKG-EAEALCAQLNS----EGYVDACITADSDA 164 (602)
Q Consensus 98 ~~~~~~~k~g~~~e~~~~f-------~~~i-~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~----~g~vd~ViT~DSD~ 164 (602)
++.+|+++.. .++.+ ..++ ..+.+++..|||+++..|+ |||+.+|.|++ .|.--.|+|.|.|+
T Consensus 83 ---yp~YKAnR~~-~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl 158 (304)
T PHA02567 83 ---AWYYKKNRKK-DREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDF 158 (304)
T ss_pred ---hhHhhcCCCC-CChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCCh
Confidence 2334444322 22222 2222 4567889999999999997 99999999986 35555799999999
Q ss_pred EeeCC-eEEEEecCCCCCCCeEEEeHHHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCc
Q 044842 165 FLFGA-KCVVKCIRPNTKEPFECYCISDIEAGLGLKRKHLIAMSLLIG--NDHDLNGVQG 221 (602)
Q Consensus 165 llfG~-~~Vi~~~~~~~k~~~~~y~~~~i~~~lgL~~~qli~laiL~G--~DY~~~GipG 221 (602)
+++-. +.|... . .++...+.+.+| .+.|++++.+|+| +|. +||||-
T Consensus 159 ~QLv~~~~v~~~-~--------~~~~~~V~~k~G-~P~q~iD~kaL~GDsSDN-IPGVp~ 207 (304)
T PHA02567 159 TQLHKYPGVKQW-S--------PMQKKWVKPKYG-SPEKDLMTKIIKGDKKDG-VASIKV 207 (304)
T ss_pred hhccCCCCeEEe-e--------cCCHHHHHHHhC-CHHHHHHHHHhCCcccCC-cCCCCC
Confidence 98853 333111 1 123466778899 5999999999999 788 588873
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=99.46 E-value=6.3e-13 Score=128.48 Aligned_cols=154 Identities=21% Similarity=0.313 Sum_probs=111.4
Q ss_pred CEEEEeHHHHHHHHhcccc--C----CCCCChHHHHHHHHHHHHHHhCC-CeEEEEEcCCCCcchhHHHHHhhhcccccc
Q 044842 26 KRVAVDLSYWIVQHETAIK--K----NSVPKPHLRLTFFRTINLFAKFG-AFPVFVVDGTPSPLKSQARLARFYRSTIDA 98 (602)
Q Consensus 26 k~IAIDas~wL~r~~~a~~--~----~g~~~~~Lr~~f~r~l~lL~~~g-I~PVfVFDG~~p~~K~~t~~kR~~R~~~~~ 98 (602)
+.+.|||++++||++++.. . .|.++..+.+++....+++.... -++++|||+..+..+++
T Consensus 2 ~llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~------------- 68 (169)
T PF02739_consen 2 KLLLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKE------------- 68 (169)
T ss_dssp EEEEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHH-------------
T ss_pred eEEEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHH-------------
Confidence 4689999999999999887 2 68888899886666666665554 57799999988744321
Q ss_pred ccchHHHhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccC-cHHHHHHHHHH----cCCeeEEEcCCCCeEeeCCe--E
Q 044842 99 STLPVAEEGILVERNQTFLKCVQECVELLELFGMPVLKAKG-EAEALCAQLNS----EGYVDACITADSDAFLFGAK--C 171 (602)
Q Consensus 99 ~~~~~~k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~-EADAqcA~L~~----~g~vd~ViT~DSD~llfG~~--~ 171 (602)
.++.+|+++ .+.++.+..++..++++|+.+||+++..|| |||+.+|.|++ .|.--.|+|.|.|++++... .
T Consensus 69 -l~p~YKanR-~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~ 146 (169)
T PF02739_consen 69 -LYPEYKANR-KPMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDENVN 146 (169)
T ss_dssp -CCTTTTHHH-HHHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TS
T ss_pred -HHHHHHhCC-CCCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCce
Confidence 134445443 345677888899999999999999999996 99999999985 35555799999999999887 5
Q ss_pred EEEecCCCCCCCeEEEeHHHHHHHh
Q 044842 172 VVKCIRPNTKEPFECYCISDIEAGL 196 (602)
Q Consensus 172 Vi~~~~~~~k~~~~~y~~~~i~~~l 196 (602)
|+.- ... ......|+.+.+.+++
T Consensus 147 V~~~-~~~-~~~~~~~~~~~v~eky 169 (169)
T PF02739_consen 147 VYLL-DPG-KKKFKVYDPEEVEEKY 169 (169)
T ss_dssp EEEE-ETT-TTCS-EB-HHHHHHHT
T ss_pred EEEe-ecC-CCCCEEEcHHHHhhcC
Confidence 5432 221 1235789999988764
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=99.16 E-value=3.7e-11 Score=101.20 Aligned_cols=51 Identities=37% Similarity=0.725 Sum_probs=46.7
Q ss_pred HhCCCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhh
Q 044842 195 GLGLKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKI 246 (602)
Q Consensus 195 ~lgL~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~ 246 (602)
.+|++++||+++|+|+| |||. +||||||+|||.+||++|++ +++++.++..
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i-~gv~giG~k~A~~ll~~~~~~~~~~~~~~~~ 55 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNI-PGVPGIGPKTALKLLKEYGSLENLLENLDKI 55 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccC-CCCCcccHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 47999999999999999 9996 89999999999999999996 8888887654
No 25
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.76 E-value=7.1e-09 Score=75.32 Aligned_cols=33 Identities=42% Similarity=0.831 Sum_probs=30.4
Q ss_pred HHHHHHHHHHcCCCCCCC---CCCcccHHHHHHHHHhc
Q 044842 200 RKHLIAMSLLIGNDHDLN---GVQGIGLDTALQFVQNF 234 (602)
Q Consensus 200 ~~qli~laiL~G~DY~~~---GipGIG~ktA~~Li~~~ 234 (602)
++||+++|+|+| ||+ + ||||||+|+|++||++|
T Consensus 1 p~q~~~~~~L~G-D~~-dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVG-DYS-DNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhC-cCC-CCCCCCCcccHHHHHHHHHhC
Confidence 579999999999 886 6 99999999999999986
No 26
>PF12813 XPG_I_2: XPG domain containing
Probab=98.73 E-value=3.8e-08 Score=100.74 Aligned_cols=89 Identities=25% Similarity=0.303 Sum_probs=69.0
Q ss_pred HHHHHHHHHHc---CCCEEeccCcHHHHHHHHHHcCCeeEEEcCCCCeEeeCC----eEEEE-ecCCCC------CCC--
Q 044842 120 VQECVELLELF---GMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGA----KCVVK-CIRPNT------KEP-- 183 (602)
Q Consensus 120 i~~~~~lL~~~---GI~~i~AP~EADAqcA~L~~~g~vd~ViT~DSD~llfG~----~~Vi~-~~~~~~------k~~-- 183 (602)
...+.+.|+.+ |++++++|+|||..||.+++..-+ +|+|+|||+|+|.. ..+.. .+..+. ...
T Consensus 6 ~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i~ 84 (246)
T PF12813_consen 6 VPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYIS 84 (246)
T ss_pred HHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCeeE
Confidence 45577888888 999999999999999999987555 99999999999987 33322 233221 112
Q ss_pred eEEEeHHHHHHHhCCCHHHHHHHHHHcC
Q 044842 184 FECYCISDIEAGLGLKRKHLIAMSLLIG 211 (602)
Q Consensus 184 ~~~y~~~~i~~~lgL~~~qli~laiL~G 211 (602)
..+|+.+.|++.+|+. .|+.||...+
T Consensus 85 ~~~y~~~~i~~~l~l~--~Lp~lA~d~~ 110 (246)
T PF12813_consen 85 AKVYSPDKICKRLGLP--LLPLLAYDYK 110 (246)
T ss_pred EEEEcHHHHHHHcCCc--hhHHHHHHhc
Confidence 3679999999999999 8888887333
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=98.49 E-value=2.9e-09 Score=94.73 Aligned_cols=49 Identities=31% Similarity=0.586 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHcC--CCCCCCCCCcccHHHHHHHHHhcCh-HHHHHHHHhhC
Q 044842 198 LKRKHLIAMSLLIG--NDHDLNGVQGIGLDTALQFVQNFSE-DEILNILHKIG 247 (602)
Q Consensus 198 L~~~qli~laiL~G--~DY~~~GipGIG~ktA~~Li~~~~~-e~iL~~l~~~~ 247 (602)
+.++|++++.+|+| +|+ +|||||||+|||.+||++||+ ++|++++.++.
T Consensus 1 V~P~q~~D~~aL~GD~sDN-IPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~ 52 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDN-IPGVPGIGPKTAAKLLQEYGSLENILANLDEIK 52 (101)
T ss_dssp --GHHHHHHCCCC-CCCCT-B---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-
T ss_pred CCHHHHHHHHHHcCCcccC-CCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhcc
Confidence 46899999999999 899 699999999999999999996 88887665543
No 28
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=98.03 E-value=3.1e-05 Score=83.94 Aligned_cols=230 Identities=20% Similarity=0.227 Sum_probs=134.7
Q ss_pred CCCCCcChhhhcccccccCcc-ccCCCEEEEeHHHHHHHHhccccCCCCCChHHHHHHHHHHHHHHhCCCeEEEEEcCCC
Q 044842 1 MGVGGKFWDLLKPYARFEGLD-FLRDKRVAVDLSYWIVQHETAIKKNSVPKPHLRLTFFRTINLFAKFGAFPVFVVDGTP 79 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~Ls-~L~gk~IAIDas~wL~r~~~a~~~~g~~~~~Lr~~f~r~l~lL~~~gI~PVfVFDG~~ 79 (602)
|||+ +|-++|-....-..++ ..+++-|=||.++..+-..+.+ .....|++.|...++.+...+-+.+++.|-+.
T Consensus 1 MGIK-NLK~lLl~~gsL~~i~~~~~~~~ifVD~msif~tiAysv----~s~~eL~~~~~~~i~~w~~~~~~VtlFvDRG~ 75 (425)
T PF04599_consen 1 MGIK-NLKALLLETGSLKKIDNIEKNNEIFVDTMSIFMTIAYSV----NSLDELRNSFEEYIQQWIKNNGKVTLFVDRGS 75 (425)
T ss_pred Cchh-HHHHHHHhcCCceeccCCCCCccEEEEcchhhhhhhhhh----CCHHHHHHHHHHHHHHHHhcCCeEEEEEecCc
Confidence 9999 5999998765443332 3466889999999877554443 34456788888888888545557888889999
Q ss_pred CcchhHHHHHhhh-------ccccccccchHHHhccc--hh-----------h--hHHHHH------hH-HHHHHHHHHc
Q 044842 80 SPLKSQARLARFY-------RSTIDASTLPVAEEGIL--VE-----------R--NQTFLK------CV-QECVELLELF 130 (602)
Q Consensus 80 p~~K~~t~~kR~~-------R~~~~~~~~~~~k~g~~--~e-----------~--~~~f~~------~i-~~~~~lL~~~ 130 (602)
.+.|...+.+|+. |+....++++.....-+ .+ + ...|.- .+ ..+.++|..+
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 9999988888843 11111111111111000 00 0 011210 11 1244566665
Q ss_pred --CCCEEeccC-cHHHHHHHHH-----HcCCeeEEEcCCCCeEeeCCeEEEEecCCCCCCCeEEEeHHHHHHHhCCCHHH
Q 044842 131 --GMPVLKAKG-EAEALCAQLN-----SEGYVDACITADSDAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGLGLKRKH 202 (602)
Q Consensus 131 --GI~~i~AP~-EADAqcA~L~-----~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~lgL~~~q 202 (602)
+|..+.+.| .||-.+.+=+ +.|.=-.+||.|-|.++|.+..-..++-...+ ++|.+-- -..+.--
T Consensus 156 ~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t~~---~~Y~~~P----~~~s~YL 228 (425)
T PF04599_consen 156 KEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKTMN---QLYKFIP----CSKSRYL 228 (425)
T ss_pred cCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHhHH---hHeeecC----CchHHHH
Confidence 799999987 8887555433 35666689999999999976422111100000 1111100 0011112
Q ss_pred HHHHHHHcCCCCCCCCCCcccH--HH--HHHHHHhcChHHHHHHH
Q 044842 203 LIAMSLLIGNDHDLNGVQGIGL--DT--ALQFVQNFSEDEILNIL 243 (602)
Q Consensus 203 li~laiL~G~DY~~~GipGIG~--kt--A~~Li~~~~~e~iL~~l 243 (602)
=.+.++.-||||- ||+-|+-. ++ -++|...|..++|++.|
T Consensus 229 ~kL~~L~NGCDfF-pGLyG~~it~~~l~~i~LF~dFti~Ni~~SL 272 (425)
T PF04599_consen 229 SKLTALVNGCDFF-PGLYGISITKKSLNRIKLFEDFTIDNILQSL 272 (425)
T ss_pred HHHHHHHhccccc-CCcceeEechhhccceeccccccHHHHHHHH
Confidence 2345677899996 99999653 32 25555566668888766
No 29
>PHA03065 Hypothetical protein; Provisional
Probab=97.82 E-value=0.00015 Score=78.21 Aligned_cols=225 Identities=20% Similarity=0.225 Sum_probs=132.3
Q ss_pred CCCCCcChhhhcccccccCccc---cCCCEEEEeHHHHHHHHhccccCCCCCChHHHHHHHHHHHHHHhCCCeEEEEEcC
Q 044842 1 MGVGGKFWDLLKPYARFEGLDF---LRDKRVAVDLSYWIVQHETAIKKNSVPKPHLRLTFFRTINLFAKFGAFPVFVVDG 77 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~Ls~---L~gk~IAIDas~wL~r~~~a~~~~g~~~~~Lr~~f~r~l~lL~~~gI~PVfVFDG 77 (602)
|||+ +|-++|-....-.+++. -+.+-|=||.++...-..+.+ .....|+..|...++.+....=+.+++.|-
T Consensus 1 MGIK-NLKtLLL~~gsL~~~~~~~~~~~~~iFVD~ms~fmsiAysv----~~~~eL~~~~~~~iq~w~~~~gkVtlFvDR 75 (438)
T PHA03065 1 MGIK-NLKTLLLETGSLTKLDNNLKDRFNGIFVDTMSVFMSIAYSV----NNLDELRSTFEEYVQQWVKKAGKVTLFVDR 75 (438)
T ss_pred Cchh-hHHHHHHhcCCcccccccccccCceEEEechhhhhhhhhhh----CCHHHHHHHHHHHHHHHHhcCCcEEEEEec
Confidence 9999 59999987654444422 234789999999876554443 344567777888888883334477777899
Q ss_pred CCCcchhHHHHHhhh-------ccccccccchHHHhccc--h----h-------h--hHHHH------HhH-HHHHHHHH
Q 044842 78 TPSPLKSQARLARFY-------RSTIDASTLPVAEEGIL--V----E-------R--NQTFL------KCV-QECVELLE 128 (602)
Q Consensus 78 ~~p~~K~~t~~kR~~-------R~~~~~~~~~~~k~g~~--~----e-------~--~~~f~------~~i-~~~~~lL~ 128 (602)
+..+.|...+++|+. |+....+++...-.+-+ . | + .-.|. ..+ ..+.+.|.
T Consensus 76 G~I~IK~~lReKRr~a~~~~~kRK~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F~~fLa~~~nlk~~l~~~L~ 155 (438)
T PHA03065 76 GSIPIKQSLREKRRKASKNTIKRKREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSFQLFLANSNNLKRLLESALA 155 (438)
T ss_pred CccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHcchhhHHHHHHHHHH
Confidence 999999988887754 11111111110000000 0 0 0 01121 011 22445677
Q ss_pred Hc--CCCEEeccC-cHHHHHHHHH-----HcCCeeEEEcCCCCeEeeCCeEEEEecCCCCCCCeEEEeHHHHHHHhCCCH
Q 044842 129 LF--GMPVLKAKG-EAEALCAQLN-----SEGYVDACITADSDAFLFGAKCVVKCIRPNTKEPFECYCISDIEAGLGLKR 200 (602)
Q Consensus 129 ~~--GI~~i~AP~-EADAqcA~L~-----~~g~vd~ViT~DSD~llfG~~~Vi~~~~~~~k~~~~~y~~~~i~~~lgL~~ 200 (602)
.+ +|.++.+.| .||-.+..-+ +.|.=-.+||.|-|.++|.+..-...+ ...+-+.+.+-|
T Consensus 156 ~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki------------I~t~~~~Y~~~P 223 (438)
T PHA03065 156 RLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI------------IKTANQLYKFIP 223 (438)
T ss_pred hccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH------------HHhHHHHheeCC
Confidence 77 899999987 8887544333 357666899999999999663211000 111111222211
Q ss_pred -----HHHHHHHHHcCCCCCCCCCCcccH--H--HHHHHHHhcChHHHHHHH
Q 044842 201 -----KHLIAMSLLIGNDHDLNGVQGIGL--D--TALQFVQNFSEDEILNIL 243 (602)
Q Consensus 201 -----~qli~laiL~G~DY~~~GipGIG~--k--tA~~Li~~~~~e~iL~~l 243 (602)
--=.+.++.-||||- ||+-|+-. + .-++|...|..+++++.|
T Consensus 224 ~~~t~YL~kL~~L~NGCDfF-pGLyG~~it~~~l~r~~LF~dFt~~Nv~~SL 274 (438)
T PHA03065 224 CAKTRYLSKLVALVNGCDFF-PGLYGISITPKSLNRIQLFDDFTIDNVVRSL 274 (438)
T ss_pred ChhHHHHHHHHHHHhccccc-CccceEEechhhccceechhhhhHHHHHHHH
Confidence 122335667799996 99999653 3 234566666667777765
No 30
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=97.74 E-value=6.1e-05 Score=76.93 Aligned_cols=167 Identities=17% Similarity=0.196 Sum_probs=75.3
Q ss_pred CCCCCcChhhhcccccc--cCcccc----CCCEEEEeHHHHHHHHhccccCC-CCCChHHHHHHHHHHHHHHh--CCCeE
Q 044842 1 MGVGGKFWDLLKPYARF--EGLDFL----RDKRVAVDLSYWIVQHETAIKKN-SVPKPHLRLTFFRTINLFAK--FGAFP 71 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~--~~Ls~L----~gk~IAIDas~wL~r~~~a~~~~-g~~~~~Lr~~f~r~l~lL~~--~gI~P 71 (602)
|||+| |+.||...-.. ..+..- .=--+-||.++.||.+....... ......+...++..+..|-. .+-+.
T Consensus 1 MGVp~-f~~wl~~ryp~~~~~~~~~~~~~~~D~LYiDmN~IIH~~~~~~~~~~~~~~~~~~~~i~~~id~l~~~v~P~k~ 79 (237)
T PF03159_consen 1 MGVPG-FFRWLSERYPLIVRPISENSIPSEFDNLYIDMNGIIHNCIHPNDSSIPKTEEEIFQRIFNYIDRLVRIVRPRKL 79 (237)
T ss_dssp --CCH-HHHHHHHHSGGGEEEECTTTSEE-ESEEEEETHHHHHHHHS-SSS----SHHHHHHHHHHHHHHHHHHH-ESSE
T ss_pred CCHHH-HHHHHHHhCCcceeeccccCCCCcCCEEEEEcchhhhHhcCCcccCCCccHHHHHHHHHHHHHHhheeecCceE
Confidence 99998 99999963221 111111 12357899999999986653310 11112222223332332211 23333
Q ss_pred -EEEEcCCCCcchhHHHHHhhhccccccccch-HH--------Hhccch--------------hhhHHHHHhH-HH----
Q 044842 72 -VFVVDGTPSPLKSQARLARFYRSTIDASTLP-VA--------EEGILV--------------ERNQTFLKCV-QE---- 122 (602)
Q Consensus 72 -VfVFDG~~p~~K~~t~~kR~~R~~~~~~~~~-~~--------k~g~~~--------------e~~~~f~~~i-~~---- 122 (602)
++.+||.+|.+|.....+|+.++........ .. ..+... .....|-..+ ..
T Consensus 80 l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn~ITPGT~FM~~l~~~L~~~ 159 (237)
T PF03159_consen 80 LYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFDSNCITPGTEFMEKLSDALRYY 159 (237)
T ss_dssp EEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS----GGGSSTTSHHHHHHHHHHHHH
T ss_pred EEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhccccccccccccccccceeccCCHHHHHHHHHHHHH
Confidence 5779999999998776666554321110000 00 000000 0001221111 11
Q ss_pred HHHHHHH----cCCCEEec----cCcHHHHHHHHHHc---------CCeeEEEcCCCCeEeeC
Q 044842 123 CVELLEL----FGMPVLKA----KGEAEALCAQLNSE---------GYVDACITADSDAFLFG 168 (602)
Q Consensus 123 ~~~lL~~----~GI~~i~A----P~EADAqcA~L~~~---------g~vd~ViT~DSD~llfG 168 (602)
+..-+.. -++.++.+ |||+|--+..+.+. .....|+|.|+|+++++
T Consensus 160 ~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 160 IKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp HHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred HHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 2222221 25667775 78999987765432 46678999999998885
No 31
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=96.22 E-value=0.041 Score=63.10 Aligned_cols=219 Identities=20% Similarity=0.306 Sum_probs=117.9
Q ss_pred CCCCCcChhhhccc-cccc-Cc---cccCCCEEEEeHHHHHHHHhccccCCCCC---ChHHHHHHHHHHHHHHhCCCeE-
Q 044842 1 MGVGGKFWDLLKPY-ARFE-GL---DFLRDKRVAVDLSYWIVQHETAIKKNSVP---KPHLRLTFFRTINLFAKFGAFP- 71 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~-~~~~-~L---s~L~gk~IAIDas~wL~r~~~a~~~~g~~---~~~Lr~~f~r~l~lL~~~gI~P- 71 (602)
|||+. |-.||+.. .... ++ ..-.+--+=.|.++.||-+.+.- ++.+ ...+...++..+..+. .-|+|
T Consensus 1 MGVPs-fFRwlS~r~p~ii~~I~e~~~P~~DNLYLDMNgIlH~CtHp~--d~~~petEeEm~~aVf~Yidhil-~~irPr 76 (953)
T COG5049 1 MGVPS-FFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPN--DGSPPETEEEMYKAVFEYIDHIL-LKIRPR 76 (953)
T ss_pred CCchH-HHHHHHhhhhHhhhhhhccCCCCcceeEEecccccccCCCCC--CCCCCCCHHHHHHHHHHHHHHHH-HhcCcc
Confidence 99995 88888742 1111 11 11345778899999988654321 2211 1112122233333222 12333
Q ss_pred ---EEEEcCCCCcchhHHHHHhhhccccc--cccchHHHhccch--hh----h---------HHHH--------HhHHHH
Q 044842 72 ---VFVVDGTPSPLKSQARLARFYRSTID--ASTLPVAEEGILV--ER----N---------QTFL--------KCVQEC 123 (602)
Q Consensus 72 ---VfVFDG~~p~~K~~t~~kR~~R~~~~--~~~~~~~k~g~~~--e~----~---------~~f~--------~~i~~~ 123 (602)
+...||.+|..|-....+|+.|+..+ .+.++...++... ++ + ..|. ...+.+
T Consensus 77 KllymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~fDSNcITPGTpFMerL 156 (953)
T COG5049 77 KLLYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKFDSNCITPGTPFMERL 156 (953)
T ss_pred eEEEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccccCCccchhhhhhccccccCCCCCChHHHHH
Confidence 44489999999987766677765322 1111111011000 00 0 0010 011111
Q ss_pred HHHHH------------HcCCCEEe----ccCcHHHHHHHHHHc---------CCeeEEEcCCCCeEeeCCe------EE
Q 044842 124 VELLE------------LFGMPVLK----AKGEAEALCAQLNSE---------GYVDACITADSDAFLFGAK------CV 172 (602)
Q Consensus 124 ~~lL~------------~~GI~~i~----AP~EADAqcA~L~~~---------g~vd~ViT~DSD~llfG~~------~V 172 (602)
-..|+ =-++.+|. .|||.|.-+-.+.+. +-...|.+-|.|++++|-. .+
T Consensus 157 ak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~i 236 (953)
T COG5049 157 AKVLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLI 236 (953)
T ss_pred HHHHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEE
Confidence 11111 12556665 489999988877654 3456899999999999852 24
Q ss_pred EE-ecCC-C-----C-------------------CCCeEEEeHHHHHHHh-------------CCCH--HHHHHHHHHcC
Q 044842 173 VK-CIRP-N-----T-------------------KEPFECYCISDIEAGL-------------GLKR--KHLIAMSLLIG 211 (602)
Q Consensus 173 i~-~~~~-~-----~-------------------k~~~~~y~~~~i~~~l-------------gL~~--~qli~laiL~G 211 (602)
+| .++. . . ..+|-+.+++-+.+.| .|.| +.+|.+|-++|
T Consensus 237 LREdVff~~~~~~k~k~~~~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvG 316 (953)
T COG5049 237 LREDVFFGSKSRRKRKCTKCGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVG 316 (953)
T ss_pred eechhccCcccccccccccccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeec
Confidence 55 2221 0 0 1245667777665532 2222 68899999999
Q ss_pred CCCCCCCCCcccH
Q 044842 212 NDHDLNGVQGIGL 224 (602)
Q Consensus 212 ~DY~~~GipGIG~ 224 (602)
+|| +|.+|++-+
T Consensus 317 NDF-LPhLP~Ldi 328 (953)
T COG5049 317 NDF-LPHLPCLDI 328 (953)
T ss_pred ccc-CCCCCcccc
Confidence 999 599998764
No 32
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=95.79 E-value=0.053 Score=63.71 Aligned_cols=223 Identities=18% Similarity=0.254 Sum_probs=114.2
Q ss_pred CCCCCcChhhhcccccccCc-ccc-CC------CEEEEeHHHHHHHHhccccCCCCCCh-----HHHHHHHHHHHHHHhC
Q 044842 1 MGVGGKFWDLLKPYARFEGL-DFL-RD------KRVAVDLSYWIVQHETAIKKNSVPKP-----HLRLTFFRTINLFAKF 67 (602)
Q Consensus 1 MGV~G~Lw~~Lkp~~~~~~L-s~L-~g------k~IAIDas~wL~r~~~a~~~~g~~~~-----~Lr~~f~r~l~lL~~~ 67 (602)
|||+- +..|+. ++.|. ++| ++ --+-.|.++.||-+-+... ...+. .+..-+|..|..| -.
T Consensus 1 MGvPK-FfR~iS---ERyP~lseliee~qIPEFDNLYLDMNgIlHNCsH~nD--ddvt~rLtEeEif~~IfnYIdhL-f~ 73 (1493)
T KOG2045|consen 1 MGVPK-FFRYIS---ERYPCLSELIEEHQIPEFDNLYLDMNGILHNCSHPND--DDVTFRLTEEEIFQEIFNYIDHL-FY 73 (1493)
T ss_pred CCchH-HHHHhh---hhchHHHHHhhhccCCcccceeeecccccccCCCCCC--CccCcCCCHHHHHHHHHHHHHHH-HH
Confidence 99995 766665 33332 221 11 2356899999886644332 22122 1211233333333 13
Q ss_pred CCeE--EE--EEcCCCCcchhHHHHHhhhccccc--cccchHHHhccchhh----------hHHH-HHhHHHHHHHHH--
Q 044842 68 GAFP--VF--VVDGTPSPLKSQARLARFYRSTID--ASTLPVAEEGILVER----------NQTF-LKCVQECVELLE-- 128 (602)
Q Consensus 68 gI~P--Vf--VFDG~~p~~K~~t~~kR~~R~~~~--~~~~~~~k~g~~~e~----------~~~f-~~~i~~~~~lL~-- 128 (602)
-|+| +| ..||.+|..|-....+|++|.... .+..+++..|...+. ...| .++.+.+...++
T Consensus 74 ~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~erFDSNcITPGTeFM~rl~~~L~yfIktK 153 (1493)
T KOG2045|consen 74 LIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPHERFDSNCITPGTEFMVRLQEGLRYFIKTK 153 (1493)
T ss_pred hhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcccccccCCCCCcHHHHHHHHHHHHHHHHhc
Confidence 4444 33 389999999987766677665221 111122233321110 0122 122222222221
Q ss_pred ------HcCCCEEe----ccCcHHHHHHHHHHc---------CCeeEEEcCCCCeEeeCCe------EEEEe---cCC-C
Q 044842 129 ------LFGMPVLK----AKGEAEALCAQLNSE---------GYVDACITADSDAFLFGAK------CVVKC---IRP-N 179 (602)
Q Consensus 129 ------~~GI~~i~----AP~EADAqcA~L~~~---------g~vd~ViT~DSD~llfG~~------~Vi~~---~~~-~ 179 (602)
=.++.+|- +|||.|--+--+.+. +--..+++-|-|++++|-- .++|. |.. +
T Consensus 154 istDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~lLREEVtFgrrn 233 (1493)
T KOG2045|consen 154 ISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRRN 233 (1493)
T ss_pred cccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceeeeeeeeeccccc
Confidence 23666665 699999877655432 1223677889999999853 23442 221 1
Q ss_pred CCC-----CeEEEeHHHHHHH---------------hCCCH--HHHHHHHHHcCCCCCCCCCCcccH-HHHHHHH
Q 044842 180 TKE-----PFECYCISDIEAG---------------LGLKR--KHLIAMSLLIGNDHDLNGVQGIGL-DTALQFV 231 (602)
Q Consensus 180 ~k~-----~~~~y~~~~i~~~---------------lgL~~--~qli~laiL~G~DY~~~GipGIG~-ktA~~Li 231 (602)
... .|-..+++-+.+. +.+.+ +.+|+++.|+|+|| +|.+|++-+ +.|+-|+
T Consensus 234 ~~k~lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDF-LPhLP~LHIn~gAlpll 307 (1493)
T KOG2045|consen 234 KRKSLEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDF-LPHLPCLHINSGALPLL 307 (1493)
T ss_pred ccchhhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhcccc-ccCCCccccCCChHHHH
Confidence 111 1222333333332 22222 57888999999999 599999764 3455544
No 33
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=94.53 E-value=0.021 Score=62.63 Aligned_cols=111 Identities=21% Similarity=0.273 Sum_probs=86.6
Q ss_pred HHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEcCCCCeEeeCC-eEEEEecCC-CCCCCeEEEeHHHHHHHhCCCH
Q 044842 123 CVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITADSDAFLFGA-KCVVKCIRP-NTKEPFECYCISDIEAGLGLKR 200 (602)
Q Consensus 123 ~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~DSD~llfG~-~~Vi~~~~~-~~k~~~~~y~~~~i~~~lgL~~ 200 (602)
+-.++..-||.|+++||-|.+|||||.....++++.. -+|.+++.+ .+++..+.. +.+-|+.+|+.....+-.-.+-
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 4567889999999999999999999999999988775 789988855 566666543 3344678888888777777788
Q ss_pred HHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcC
Q 044842 201 KHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 201 ~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~ 235 (602)
.-|...-.|.|||++ ..++.+-...+..+.+-+|
T Consensus 213 ~lFya~~ll~~c~~~-s~~~~C~~da~f~l~qvig 246 (531)
T COG5366 213 RLFYALGLLLGCDFC-STIPRCATDADFSLNQVIG 246 (531)
T ss_pred chhhhhccccccccc-ccccccccchhHHHHHHHh
Confidence 899999999999996 8888754444555555544
No 34
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=88.65 E-value=0.44 Score=47.39 Aligned_cols=28 Identities=4% Similarity=0.024 Sum_probs=20.6
Q ss_pred cCcccceeEEEeeecCceee-EEEEEeec
Q 044842 427 CGQYEFDSIRRVKIRYGHQS-YVVKWKKA 454 (602)
Q Consensus 427 ~~~~~~~~i~k~r~~~g~~~-~ei~W~~~ 454 (602)
...+++..|+-+|+-.|+|. -+++|-+.
T Consensus 157 ~~~l~~~~ikvtRlA~GiPvGg~lEyvD~ 185 (198)
T COG0353 157 ARLLKPLGLKVTRLAQGVPVGGELEYVDE 185 (198)
T ss_pred HHHHhhcCCeEEEEeecCccCCceecccH
Confidence 34556778888999999998 66666554
No 35
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=86.32 E-value=4.3 Score=47.88 Aligned_cols=93 Identities=22% Similarity=0.369 Sum_probs=61.2
Q ss_pred CCCEEe----ccCcHHHHHHHHHHc---------CCeeEEEcCCCCeEeeCCe------EEEEe-cCCC-----------
Q 044842 131 GMPVLK----AKGEAEALCAQLNSE---------GYVDACITADSDAFLFGAK------CVVKC-IRPN----------- 179 (602)
Q Consensus 131 GI~~i~----AP~EADAqcA~L~~~---------g~vd~ViT~DSD~llfG~~------~Vi~~-~~~~----------- 179 (602)
+|.+|. .|||.|--+-.+.+. +-+..+.+-|-|++++|-- .|+|. |+.+
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 566776 489999988766543 3456899999999999852 24553 2210
Q ss_pred ------------------------CCCCeEEEeHHHHHHHh-------------CCCH--HHHHHHHHHcCCCCCCCCCC
Q 044842 180 ------------------------TKEPFECYCISDIEAGL-------------GLKR--KHLIAMSLLIGNDHDLNGVQ 220 (602)
Q Consensus 180 ------------------------~k~~~~~y~~~~i~~~l-------------gL~~--~qli~laiL~G~DY~~~Gip 220 (602)
.+.++.++++.-+.+.| .|.| +.+|.||-++|+|| +|.+|
T Consensus 270 gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p~lPf~fd~ER~iDDwVF~CFFvGNDF-LPHlP 348 (931)
T KOG2044|consen 270 GHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMPNLPFTFDLERAIDDWVFLCFFVGNDF-LPHLP 348 (931)
T ss_pred CCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCCCCCccccHHhhhcceEEEEeeecCcc-CCCCC
Confidence 01235566666555432 2222 57788999999999 59999
Q ss_pred cccH
Q 044842 221 GIGL 224 (602)
Q Consensus 221 GIG~ 224 (602)
-+-+
T Consensus 349 sLeI 352 (931)
T KOG2044|consen 349 SLEI 352 (931)
T ss_pred chhh
Confidence 7654
No 36
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=86.01 E-value=0.61 Score=38.02 Aligned_cols=23 Identities=26% Similarity=0.658 Sum_probs=18.1
Q ss_pred CCCcccHHHHHHHHHhcCh-HHHH
Q 044842 218 GVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 218 GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
||||||.++|..|++.|++ +++.
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~ 30 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALM 30 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHC
T ss_pred CCCCccHHHHHHHHHHcCCHHHHH
Confidence 9999999999999999996 4443
No 37
>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=85.23 E-value=1.3 Score=34.50 Aligned_cols=51 Identities=27% Similarity=0.451 Sum_probs=38.0
Q ss_pred ccceeEEEeeecCcee---eEEEEEeeccccccccccCCCCCcchhhhhcccCCccccCCCcceeeehhhhhHHHhhchH
Q 044842 430 YEFDSIRRVKIRYGHQ---SYVVKWKKAASAISGVKYTAPVDSDLHLEEFMEYPQIHVDGDCWFLLTDENMKLVHSAFPK 506 (602)
Q Consensus 430 ~~~~~i~k~r~~~g~~---~~ei~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~e~~~l~~~ayp~ 506 (602)
|++.+|.-.|..+|.. -|.|+|+.-.. ++ -|=|+.+.+..++|+
T Consensus 1 ~~Ve~Il~~r~~~~~~~~~~ylVkW~g~~~------------------~~---------------~tWe~~~~l~~~~~~ 47 (55)
T PF00385_consen 1 YEVERILDHRVVKGGNKVYEYLVKWKGYPY------------------SE---------------NTWEPEENLKNCFPE 47 (55)
T ss_dssp EEEEEEEEEEEETTEESEEEEEEEETTSSG------------------GG---------------EEEEEGGGCSSHCHH
T ss_pred CEEEEEEEEEEeCCCcccEEEEEEECCCCC------------------CC---------------CeEeeHHHHhHhhHH
Confidence 4667888888877776 79999986420 11 255777788888999
Q ss_pred HHHHHHH
Q 044842 507 KVDHFLQ 513 (602)
Q Consensus 507 ~v~~f~~ 513 (602)
+++.|++
T Consensus 48 li~~f~~ 54 (55)
T PF00385_consen 48 LIEEFEK 54 (55)
T ss_dssp HHHHHHH
T ss_pred HHHHHhC
Confidence 9999985
No 38
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.07 E-value=1.4 Score=44.29 Aligned_cols=48 Identities=19% Similarity=0.346 Sum_probs=36.9
Q ss_pred HHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 191 DIEAGLGL-KRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 191 ~i~~~lgL-~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
+....||+ +.+..-.|-.| -+|.|||||+|+.++..++.+++.+.+..
T Consensus 57 d~~~LyGF~~~~Er~lF~~L-------i~V~GIGpK~Al~iLs~~~~~~l~~aI~~ 105 (203)
T PRK14602 57 DALELFGFATWDERQTFIVL-------ISISKVGAKTALAILSQFRPDDLRRLVAE 105 (203)
T ss_pred CcceeeCCCCHHHHHHHHHH-------hCCCCcCHHHHHHHHhhCCHHHHHHHHHh
Confidence 33446788 45555555555 48999999999999999999999888763
No 39
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=84.95 E-value=1.1 Score=44.88 Aligned_cols=18 Identities=22% Similarity=0.431 Sum_probs=15.3
Q ss_pred CCCCcccHHHHHHHHHhc
Q 044842 217 NGVQGIGLDTALQFVQNF 234 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~ 234 (602)
.-+||||+|+|.+++-..
T Consensus 14 ~~LPGIG~KsA~RlA~~l 31 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFHL 31 (195)
T ss_pred HHCCCCCHHHHHHHHHHH
Confidence 578999999999997554
No 40
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=84.54 E-value=0.98 Score=44.80 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=24.0
Q ss_pred CCCCcccHHHHHHHHHhcChHHHHHHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSEDEILNILH 244 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~e~iL~~l~ 244 (602)
..||||||++|..++..|+.+.+.+.+.
T Consensus 76 ~~i~GIGpk~A~~il~~fg~~~l~~~i~ 103 (192)
T PRK00116 76 ISVSGVGPKLALAILSGLSPEELVQAIA 103 (192)
T ss_pred hcCCCCCHHHHHHHHHhCCHHHHHHHHH
Confidence 3689999999999999999877776654
No 41
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.74 E-value=1.1 Score=44.67 Aligned_cols=47 Identities=19% Similarity=0.321 Sum_probs=35.5
Q ss_pred HHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHH
Q 044842 191 DIEAGLGLK-RKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILH 244 (602)
Q Consensus 191 ~i~~~lgL~-~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~ 244 (602)
+....||+. .+.--.|-.| -+|+||||++|+.++..|+.+++.+.+.
T Consensus 56 d~~~LyGF~~~~Er~lF~~L-------i~V~GIGpK~Al~ILs~~~~~~l~~aI~ 103 (194)
T PRK14605 56 DALSLFGFATTEELSLFETL-------IDVSGIGPKLGLAMLSAMNAEALASAII 103 (194)
T ss_pred CCceeeCCCCHHHHHHHHHH-------hCCCCCCHHHHHHHHHhCCHHHHHHHHH
Confidence 334457884 4555555555 4899999999999999999988887774
No 42
>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=82.84 E-value=1.2 Score=44.32 Aligned_cols=46 Identities=24% Similarity=0.326 Sum_probs=35.4
Q ss_pred HHHhCC-CHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 193 EAGLGL-KRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 193 ~~~lgL-~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
...||+ +.+.--.|..| -+|+|||||+|+.++..++.+++.+.+.+
T Consensus 57 ~~LyGF~~~~Er~lF~~L-------~~V~GIGpK~Al~iL~~~~~~el~~aI~~ 103 (191)
T TIGR00084 57 ELLFGFNTLEERELFKEL-------IKVNGVGPKLALAILSNMSPEEFVYAIET 103 (191)
T ss_pred ceeeCCCCHHHHHHHHHH-------hCCCCCCHHHHHHHHhcCCHHHHHHHHHh
Confidence 345788 44555555555 48999999999999999998888888763
No 43
>PRK00076 recR recombination protein RecR; Reviewed
Probab=81.67 E-value=1.7 Score=43.52 Aligned_cols=18 Identities=22% Similarity=0.422 Sum_probs=15.6
Q ss_pred CCCCcccHHHHHHHHHhc
Q 044842 217 NGVQGIGLDTALQFVQNF 234 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~ 234 (602)
.-+||||+|+|.+++-..
T Consensus 14 ~~LPGIG~KsA~Rla~~l 31 (196)
T PRK00076 14 RKLPGIGPKSAQRLAFHL 31 (196)
T ss_pred HHCCCCCHHHHHHHHHHH
Confidence 578999999999998665
No 44
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=81.31 E-value=1.3 Score=43.90 Aligned_cols=49 Identities=14% Similarity=0.375 Sum_probs=37.0
Q ss_pred HHHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 190 SDIEAGLGLK-RKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 190 ~~i~~~lgL~-~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
++....||+. .+..-.|-.| -+|.|||||+|+.++..++.+++.+.+.+
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~L-------isV~GIGpK~Al~iLs~~~~~~l~~aI~~ 104 (186)
T PRK14600 55 DNVTQLYGFLNREEQDCLRML-------VKVSGVNYKTAMSILSKLTPEQLFSAIVN 104 (186)
T ss_pred cCCceeeCCCCHHHHHHHHHH-------hCcCCcCHHHHHHHHccCCHHHHHHHHHc
Confidence 4444568884 4444444444 48999999999999999999999988764
No 45
>PRK13844 recombination protein RecR; Provisional
Probab=80.65 E-value=1.9 Score=43.20 Aligned_cols=18 Identities=11% Similarity=0.230 Sum_probs=15.5
Q ss_pred CCCCcccHHHHHHHHHhc
Q 044842 217 NGVQGIGLDTALQFVQNF 234 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~ 234 (602)
.-+||||+|+|.+++-..
T Consensus 18 ~~LPGIG~KsA~Rla~~l 35 (200)
T PRK13844 18 RKLPTIGKKSSQRLALYL 35 (200)
T ss_pred HHCCCCCHHHHHHHHHHH
Confidence 578999999999988654
No 46
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.99 E-value=1.5 Score=43.74 Aligned_cols=48 Identities=25% Similarity=0.348 Sum_probs=35.5
Q ss_pred HHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 191 DIEAGLGLK-RKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 191 ~i~~~lgL~-~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
+....||+. .+.--.|-.| -+|.|||||+|+.++..++.+++.+.+..
T Consensus 55 d~~~LyGF~~~~Er~lF~~L-------~~V~GIGpK~AL~iLs~~~~~~l~~aI~~ 103 (197)
T PRK14603 55 DALSLYGFPDEDSLELFELL-------LGVSGVGPKLALALLSALPPALLARALLE 103 (197)
T ss_pred CCceeeCcCCHHHHHHHHHH-------hCcCCcCHHHHHHHHcCCCHHHHHHHHHh
Confidence 333457884 3444444444 48999999999999999999999888763
No 47
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.46 E-value=1.7 Score=43.45 Aligned_cols=48 Identities=23% Similarity=0.317 Sum_probs=36.4
Q ss_pred HHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 191 DIEAGLGLK-RKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 191 ~i~~~lgL~-~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
+-..-||+. .+..-.|-.| -+|.|||||+|+.++..++.+++.+.+..
T Consensus 55 D~~~LYGF~t~~Er~lF~~L-------isVsGIGPK~ALaILs~~~~~el~~aI~~ 103 (196)
T PRK13901 55 DELKLFGFLNSSEREVFEEL-------IGVDGIGPRAALRVLSGIKYNEFRDAIDR 103 (196)
T ss_pred CCceeeCCCCHHHHHHHHHH-------hCcCCcCHHHHHHHHcCCCHHHHHHHHHh
Confidence 334457884 4555555555 38999999999999999999999888753
No 48
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.95 E-value=2.3 Score=42.28 Aligned_cols=49 Identities=18% Similarity=0.265 Sum_probs=37.0
Q ss_pred HHHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 190 SDIEAGLGLK-RKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 190 ~~i~~~lgL~-~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
++....||+. .+..-.|-.| -+|.|||||+|+.++..++.+++.+.+..
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~L-------i~V~GIGpK~AL~iLs~~~~~el~~aI~~ 104 (188)
T PRK14606 55 QDGITLYGFSNERKKELFLSL-------TKVSRLGPKTALKIISNEDAETLVTMIAS 104 (188)
T ss_pred cCCceeeCCCCHHHHHHHHHH-------hccCCccHHHHHHHHcCCCHHHHHHHHHh
Confidence 3444568884 4555555555 38999999999999999999889888763
No 49
>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=78.84 E-value=1.6 Score=30.57 Aligned_cols=16 Identities=31% Similarity=0.385 Sum_probs=12.5
Q ss_pred CCCCcccHHHHHHHHH
Q 044842 217 NGVQGIGLDTALQFVQ 232 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~ 232 (602)
..+||||++||-.++.
T Consensus 14 ~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 14 MKLPGIGPKTANAILS 29 (30)
T ss_dssp HTSTT-SHHHHHHHHH
T ss_pred HhCCCcCHHHHHHHHh
Confidence 3789999999988764
No 50
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.79 E-value=1.8 Score=42.81 Aligned_cols=49 Identities=20% Similarity=0.315 Sum_probs=36.7
Q ss_pred HHHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 190 SDIEAGLGLK-RKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 190 ~~i~~~lgL~-~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
++...-||+. .+.--.|-.| -+|.|||||+|+.++..++.+++.+.+.+
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~L-------i~VsGIGpK~Al~ILs~~~~~el~~aI~~ 104 (183)
T PRK14601 55 EDSNKLYGFLDKDEQKMFEML-------LKVNGIGANTAMAVCSSLDVNSFYKALSL 104 (183)
T ss_pred cCCceeeCCCCHHHHHHHHHH-------hccCCccHHHHHHHHcCCCHHHHHHHHHh
Confidence 3334457884 4555555555 48999999999999999999999888753
No 51
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.55 E-value=2 Score=42.87 Aligned_cols=48 Identities=25% Similarity=0.330 Sum_probs=35.9
Q ss_pred HHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 191 DIEAGLGLK-RKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 191 ~i~~~lgL~-~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
+....||+. .+..-.|-.| -+|.|||||+|+.++..++.+++.+.+..
T Consensus 56 d~~~LyGF~~~~Er~lF~~L-------i~V~GIGpK~Al~iLs~~~~~el~~aI~~ 104 (195)
T PRK14604 56 DALTLYGFSTPAQRQLFELL-------IGVSGVGPKAALNLLSSGTPDELQLAIAG 104 (195)
T ss_pred CCceeeCCCCHHHHHHHHHH-------hCcCCcCHHHHHHHHcCCCHHHHHHHHHh
Confidence 333457884 4444445555 48999999999999999998889888763
No 52
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=76.31 E-value=14 Score=37.07 Aligned_cols=24 Identities=13% Similarity=0.169 Sum_probs=19.9
Q ss_pred cccCccccCCCEEEEeHHHHHHHH
Q 044842 16 RFEGLDFLRDKRVAVDLSYWIVQH 39 (602)
Q Consensus 16 ~~~~Ls~L~gk~IAIDas~wL~r~ 39 (602)
+..+++.++|+.|.|||++.|--.
T Consensus 57 k~~~~~~~rg~~l~iDGyNvLItl 80 (211)
T COG2454 57 KRMKINSLRGQDLVIDGYNVLITL 80 (211)
T ss_pred hhccCCCcccceEEEechhhhhhH
Confidence 346788999999999999988643
No 53
>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=75.75 E-value=11 Score=35.98 Aligned_cols=100 Identities=16% Similarity=0.094 Sum_probs=49.1
Q ss_pred CCEEEEeHHHHHHHHhccccCCCCCChHHHHHHHHHHHHHHhCCCeEEEEEcCCCCcchhHHHHHhhhccccccccchHH
Q 044842 25 DKRVAVDLSYWIVQHETAIKKNSVPKPHLRLTFFRTINLFAKFGAFPVFVVDGTPSPLKSQARLARFYRSTIDASTLPVA 104 (602)
Q Consensus 25 gk~IAIDas~wL~r~~~a~~~~g~~~~~Lr~~f~r~l~lL~~~gI~PVfVFDG~~p~~K~~t~~kR~~R~~~~~~~~~~~ 104 (602)
.+.|+|||++-.+.... .....+++ +...+..|...|..++.||+-.....+ ..+.
T Consensus 2 ~r~VVIDG~NVA~~~~~------~~~f~~~~-i~~~v~~~~~rG~~~v~v~~~~~~~~~-------~~~~---------- 57 (155)
T PF11977_consen 2 LRPVVIDGSNVAYSHGN------QKFFSVRG-IQIAVEYFKSRGHEVVVVFPPNYRYKK-------LAKK---------- 57 (155)
T ss_dssp B--EEEEHHHHHHHHTT------TTSEEHHH-HHHHHHHHHHTT---EEEEEEGGGGS--------TTS-----------
T ss_pred CCEEEEeCHHHHhhcCC------CCCcCHHH-HHHHHHHHHHcCCCeEEEEcchhhhcc-------ccCC----------
Confidence 46799999998663211 11144444 334566677789999999986431111 0000
Q ss_pred HhccchhhhHHHHHhHHHHHHHHHHcCCCEEeccCc---------HHHHHHHHHHcCCeeEEEcCCC
Q 044842 105 EEGILVERNQTFLKCVQECVELLELFGMPVLKAKGE---------AEALCAQLNSEGYVDACITADS 162 (602)
Q Consensus 105 k~g~~~e~~~~f~~~i~~~~~lL~~~GI~~i~AP~E---------ADAqcA~L~~~g~vd~ViT~DS 162 (602)
. .... ..+-|...|+=+++.++. +|..+.+++...-. .|||+|.
T Consensus 58 --~---~~~~--------~L~~l~~~~~i~~tp~~~~~g~~~~~ydD~~il~~A~~~~a-~IVSND~ 110 (155)
T PF11977_consen 58 --S---DDQE--------ELEKLIRKGIIYFTPSGSNYGSRSRNYDDRYILYYAEEKDA-VIVSNDR 110 (155)
T ss_dssp --E---ESTC--------HHHHHHHTTSEEEE-EEEETTEEEEB-HHHHHHHHHHHTT--EEE-S--
T ss_pred --C---ChHH--------HHHHHHHCCeEEEcCCCCCCCCcccccchHHHHHHHHHcCC-EEEeCch
Confidence 0 0011 122344477755555443 88888888765332 6889884
No 54
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=75.70 E-value=6 Score=39.80 Aligned_cols=52 Identities=23% Similarity=0.309 Sum_probs=38.8
Q ss_pred EeHHHHHHHhCCCH-HHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcChHHHHHHHHh
Q 044842 187 YCISDIEAGLGLKR-KHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSEDEILNILHK 245 (602)
Q Consensus 187 y~~~~i~~~lgL~~-~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~e~iL~~l~~ 245 (602)
+-.++....||+.. +.--.|..| -+|.|||||+|+.++..++.+++.+.+..
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~L-------isVnGIGpK~ALaiLs~~~~~~l~~aI~~ 104 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLL-------ISVNGIGPKLALAILSNLDPEELAQAIAN 104 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHH-------HccCCccHHHHHHHHcCCCHHHHHHHHHh
Confidence 44567777899964 333344444 37999999999999999998888888753
No 55
>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=75.42 E-value=2.8 Score=40.59 Aligned_cols=34 Identities=24% Similarity=0.293 Sum_probs=22.8
Q ss_pred CCCEEecc--CcHHHHHHHHHHc----CCeeEEEcCCCCe
Q 044842 131 GMPVLKAK--GEAEALCAQLNSE----GYVDACITADSDA 164 (602)
Q Consensus 131 GI~~i~AP--~EADAqcA~L~~~----g~vd~ViT~DSD~ 164 (602)
||.++.++ ..||..+-.|... +.--.|+|+|...
T Consensus 67 gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~i 106 (166)
T PF05991_consen 67 GIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREI 106 (166)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHH
Confidence 56677776 4888888877642 3344788877643
No 56
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=66.96 E-value=4.3 Score=27.12 Aligned_cols=17 Identities=35% Similarity=0.438 Sum_probs=15.0
Q ss_pred CCCCcccHHHHHHHHHh
Q 044842 217 NGVQGIGLDTALQFVQN 233 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~ 233 (602)
..|||||+++|..++..
T Consensus 4 ~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 4 LKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhCCCCCHHHHHHHHHh
Confidence 58999999999998864
No 57
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=62.88 E-value=18 Score=27.44 Aligned_cols=24 Identities=33% Similarity=0.599 Sum_probs=19.0
Q ss_pred cceeEEEee-ecCceeeEEEEEeec
Q 044842 431 EFDSIRRVK-IRYGHQSYVVKWKKA 454 (602)
Q Consensus 431 ~~~~i~k~r-~~~g~~~~ei~W~~~ 454 (602)
.+.+|.-.| ..+|...|.|+|+.-
T Consensus 3 ~v~~Il~~r~~~~~~~~ylVkW~g~ 27 (55)
T smart00298 3 EVEKILDHRWKKKGELEYLVKWKGY 27 (55)
T ss_pred chheeeeeeecCCCcEEEEEEECCC
Confidence 456777777 778888999999865
No 58
>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=59.19 E-value=8 Score=30.81 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=19.3
Q ss_pred CCCCcccHHHHHHHHHh-cCh-HHHH
Q 044842 217 NGVQGIGLDTALQFVQN-FSE-DEIL 240 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~-~~~-e~iL 240 (602)
..|||||+++|..|+.. |.+ ++++
T Consensus 8 ~~I~Gig~~~a~~L~~~G~~t~~~l~ 33 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLYEAGIKTLEDLA 33 (60)
T ss_dssp HTSTTCHHHHHHHHHHTTCSSHHHHH
T ss_pred ccCCCCCHHHHHHHHhcCCCcHHHHH
Confidence 47999999999999999 554 5554
No 59
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=54.61 E-value=8.1 Score=45.17 Aligned_cols=24 Identities=17% Similarity=0.491 Sum_probs=21.1
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
.+|||||++++.+|++.||+ ++|.
T Consensus 555 ~~IpGIG~kr~~~LL~~FgSi~~I~ 579 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFGSLERVR 579 (624)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHH
Confidence 69999999999999999996 5554
No 60
>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=53.02 E-value=10 Score=29.87 Aligned_cols=17 Identities=29% Similarity=0.575 Sum_probs=13.4
Q ss_pred CCCCcccHHHHHHHHHh
Q 044842 217 NGVQGIGLDTALQFVQN 233 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~ 233 (602)
.+|.|||++||.+++..
T Consensus 5 ~~I~GVG~~tA~~w~~~ 21 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAK 21 (52)
T ss_dssp HTSTT--HHHHHHHHHT
T ss_pred hhcccccHHHHHHHHHh
Confidence 48999999999999985
No 61
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=52.69 E-value=10 Score=44.29 Aligned_cols=23 Identities=26% Similarity=0.628 Sum_probs=20.3
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEI 239 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~i 239 (602)
.||||||+++|..|++.||+ ++|
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i 595 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKV 595 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHH
Confidence 69999999999999999986 444
No 62
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=52.16 E-value=10 Score=43.86 Aligned_cols=25 Identities=28% Similarity=0.445 Sum_probs=21.5
Q ss_pred CCCCCcccHHHHHHHHHhcCh-HHHH
Q 044842 216 LNGVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 216 ~~GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
+.+|||||+++...|++.||+ ++|.
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fgs~~~ik 541 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFKTLYDFL 541 (567)
T ss_pred cccCCCCCHHHHHHHHHHhCCHHHHH
Confidence 369999999999999999997 5553
No 63
>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=50.65 E-value=10 Score=43.89 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=21.1
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
.+|||||+++...|++.||+ ++|.
T Consensus 544 d~I~GIG~kr~~~LL~~Fgs~~~i~ 568 (574)
T TIGR00194 544 LKIPGVGEKRVQKLLKYFGSLKGIK 568 (574)
T ss_pred hcCCCCCHHHHHHHHHHcCCHHHHH
Confidence 69999999999999999997 5443
No 64
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.17 E-value=9.5 Score=37.77 Aligned_cols=39 Identities=26% Similarity=0.479 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcCh
Q 044842 197 GLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 197 gL~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~ 236 (602)
.+++++|.. |+..|..-.+..+||||+|||-+|+-+...
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilELkd 130 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAELSD 130 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 456666653 555665444679999999999999987653
No 65
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=49.72 E-value=12 Score=43.41 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=21.7
Q ss_pred CCCCCcccHHHHHHHHHhcCh-HHHH
Q 044842 216 LNGVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 216 ~~GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
+..|||||+++..+|++.||+ ++|.
T Consensus 516 L~~I~GiG~kr~~~LL~~Fgs~~~I~ 541 (574)
T PRK14670 516 YTKIKGIGEKKAKKILKSLGTYKDIL 541 (574)
T ss_pred cccCCCCCHHHHHHHHHHhCCHHHHH
Confidence 479999999999999999997 5554
No 66
>KOG2748 consensus Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics]
Probab=47.55 E-value=17 Score=39.34 Aligned_cols=31 Identities=32% Similarity=0.588 Sum_probs=25.0
Q ss_pred ccceeEEEeeecCceeeEEEEEeeccccccc
Q 044842 430 YEFDSIRRVKIRYGHQSYVVKWKKAASAISG 460 (602)
Q Consensus 430 ~~~~~i~k~r~~~g~~~~ei~W~~~~~~~~~ 460 (602)
|..-+|.+.|+|+|.==|.|+|+-=.+.+..
T Consensus 11 fAaEsIlkkRirKGrvEYlVKWkGWs~kyNT 41 (369)
T KOG2748|consen 11 FAAESILKKRIRKGRVEYLVKWKGWSQKYNT 41 (369)
T ss_pred HHHHHHHHHHhhccceEEEEEecccccccCc
Confidence 3455889999999999999999987665544
No 67
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=46.28 E-value=19 Score=36.18 Aligned_cols=37 Identities=24% Similarity=0.346 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHcCC-CCCCCCCCcccHHHHHHHHHhcCh
Q 044842 198 LKRKHLIAMSLLIGN-DHDLNGVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 198 L~~~qli~laiL~G~-DY~~~GipGIG~ktA~~Li~~~~~ 236 (602)
++.+.|+.. +-.+. .+ +..+||||.|||-+|+-+...
T Consensus 93 ~~~~~l~~a-I~~~d~~~-L~k~PGIGkKtAerivleLk~ 130 (201)
T COG0632 93 LDPEELAQA-IANEDVKA-LSKIPGIGKKTAERIVLELKG 130 (201)
T ss_pred CCHHHHHHH-HHhcChHh-hhcCCCCCHHHHHHHHHHHhh
Confidence 355665543 33333 34 579999999999999987643
No 68
>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=46.25 E-value=45 Score=25.25 Aligned_cols=25 Identities=36% Similarity=0.678 Sum_probs=19.6
Q ss_pred ccceeEEEeeecC--ceeeEEEEEeec
Q 044842 430 YEFDSIRRVKIRY--GHQSYVVKWKKA 454 (602)
Q Consensus 430 ~~~~~i~k~r~~~--g~~~~ei~W~~~ 454 (602)
|...+|.-.|... |..-|.|+|+--
T Consensus 3 ~~ve~Il~~r~~~~~~~~~y~VkW~g~ 29 (55)
T cd00024 3 YEVEKILDHRKKKDGGEYEYLVKWKGY 29 (55)
T ss_pred ceEeeeeeeeecCCCCcEEEEEEECCC
Confidence 4556777777776 899999999865
No 69
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.83 E-value=12 Score=37.51 Aligned_cols=38 Identities=18% Similarity=0.230 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcC
Q 044842 197 GLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 197 gL~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~ 235 (602)
.+++++|+. |+..|..-.+..+||||+|||-+||-+..
T Consensus 91 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 91 GIKYNEFRD-AIDREDIELISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 356666654 44555433357999999999999998765
No 70
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.27 E-value=13 Score=37.32 Aligned_cols=42 Identities=24% Similarity=0.225 Sum_probs=29.4
Q ss_pred HHHhC-CCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcC
Q 044842 193 EAGLG-LKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 193 ~~~lg-L~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~ 235 (602)
..-|+ +++++|+. |+..|..-.+..+||||+|||-+|+-+..
T Consensus 88 l~iLs~~~~~~l~~-aI~~~D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 88 LAILSQFRPDDLRR-LVAEEDVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred HHHHhhCCHHHHHH-HHHhCCHHHHhcCCCcCHHHHHHHHHHHH
Confidence 33444 56666553 55566544468999999999999998765
No 71
>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=44.44 E-value=17 Score=31.23 Aligned_cols=21 Identities=29% Similarity=0.496 Sum_probs=18.8
Q ss_pred CCCCCcccHHHHHHHHHhcCh
Q 044842 216 LNGVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 216 ~~GipGIG~ktA~~Li~~~~~ 236 (602)
+..|||||+.+|..|+.+.+.
T Consensus 4 l~sipGig~~~a~~llaeigd 24 (87)
T PF02371_consen 4 LTSIPGIGPITAATLLAEIGD 24 (87)
T ss_pred hcCCCCccHHHHHHHHHHHcC
Confidence 368999999999999999874
No 72
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.04 E-value=15 Score=36.45 Aligned_cols=46 Identities=15% Similarity=0.146 Sum_probs=30.9
Q ss_pred HHHHHHHh-CCCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcC
Q 044842 189 ISDIEAGL-GLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 189 ~~~i~~~l-gL~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~ 235 (602)
.+.-..-| ++++++|+. |+..|..-.+..+||||+|||-+|+-+..
T Consensus 83 pK~AL~iLs~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 83 PKTALKIISNEDAETLVT-MIASQDVEGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HHHHHHHHcCCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 33334444 456666654 45555444468999999999999998765
No 73
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=41.41 E-value=17 Score=42.34 Aligned_cols=24 Identities=21% Similarity=0.473 Sum_probs=21.1
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
.+|||||++++..|++.||+ ++|.
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~~i~ 570 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLKAIK 570 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHHHHH
Confidence 69999999999999999996 5554
No 74
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=40.40 E-value=20 Score=42.26 Aligned_cols=25 Identities=12% Similarity=0.296 Sum_probs=21.3
Q ss_pred CCCCCcccHHHHHHHHHhcCh-HHHH
Q 044842 216 LNGVQGIGLDTALQFVQNFSE-DEIL 240 (602)
Q Consensus 216 ~~GipGIG~ktA~~Li~~~~~-e~iL 240 (602)
+..|||||++++..|++.||+ ++|.
T Consensus 610 L~~IpGiG~kr~~~LL~~FgS~~~i~ 635 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFGSFRSLQ 635 (691)
T ss_pred cccCCCCCHHHHHHHHHHhcCHHHHH
Confidence 369999999999999999997 4443
No 75
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.30 E-value=17 Score=36.36 Aligned_cols=42 Identities=26% Similarity=0.219 Sum_probs=28.6
Q ss_pred HHHhC-CCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcC
Q 044842 193 EAGLG-LKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 193 ~~~lg-L~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~ 235 (602)
..-|+ +++++|+. |+..|..-.+..+||||+|||-+|+-+..
T Consensus 87 l~iLs~~~~~el~~-aI~~~D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 87 LNLLSSGTPDELQL-AIAGGDVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred HHHHcCCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 33444 56666654 44455433357999999999999998765
No 76
>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=40.02 E-value=75 Score=35.12 Aligned_cols=44 Identities=20% Similarity=0.235 Sum_probs=29.7
Q ss_pred HHhHHHHHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEcC
Q 044842 117 LKCVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITA 160 (602)
Q Consensus 117 ~~~i~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~ 160 (602)
.+.+.++.+-|+.+|++.++.-|++...+..|.+.--+..|+++
T Consensus 60 ~esL~~L~~~L~~~g~~L~v~~G~~~~vl~~L~~~~~~~~V~~~ 103 (429)
T TIGR02765 60 LESLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFLH 103 (429)
T ss_pred HHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHhCCCEEEEe
Confidence 34566667777777777777777777777777665445566654
No 77
>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=39.68 E-value=20 Score=25.27 Aligned_cols=14 Identities=36% Similarity=0.442 Sum_probs=11.1
Q ss_pred CCCCcccHHHHHHH
Q 044842 217 NGVQGIGLDTALQF 230 (602)
Q Consensus 217 ~GipGIG~ktA~~L 230 (602)
.-++|||.+|+-+|
T Consensus 14 ~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 14 RKFWGIGKKTAKKL 27 (32)
T ss_dssp GGSTTS-HHHHHHH
T ss_pred HhhCCccHHHHHHH
Confidence 57899999999885
No 78
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.63 E-value=22 Score=35.30 Aligned_cols=47 Identities=17% Similarity=0.243 Sum_probs=32.5
Q ss_pred eHHHHHHHhC-CCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcCh
Q 044842 188 CISDIEAGLG-LKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 188 ~~~~i~~~lg-L~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~ 236 (602)
..+.-..-|+ +++++|+. |+..|..-.+ .+||||+|||-+|+-+...
T Consensus 82 GpK~Al~iLs~~~~~~l~~-aI~~~D~~~L-~vpGIGkKtAerIilELk~ 129 (186)
T PRK14600 82 NYKTAMSILSKLTPEQLFS-AIVNEDKAAL-KVNGIGEKLINRIITELQY 129 (186)
T ss_pred CHHHHHHHHccCCHHHHHH-HHHcCCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence 3443344444 67776664 4556766667 9999999999999987653
No 79
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=38.78 E-value=18 Score=36.23 Aligned_cols=47 Identities=23% Similarity=0.200 Sum_probs=31.5
Q ss_pred HHHHHHHhC-CCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcCh
Q 044842 189 ISDIEAGLG-LKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 189 ~~~i~~~lg-L~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~ 236 (602)
.+.-..-|+ +++++|+. |+..|.--.+..+||||+|||-+|+-+...
T Consensus 82 pK~AL~iLs~~~~~~l~~-aI~~~D~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 82 PKLALALLSALPPALLAR-ALLEGDARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred HHHHHHHHcCCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 333344454 56776654 445554444579999999999999988653
No 80
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=38.18 E-value=21 Score=41.47 Aligned_cols=26 Identities=23% Similarity=0.570 Sum_probs=22.6
Q ss_pred CCCCCcccHHHHHHHHHhcCh-HHHHH
Q 044842 216 LNGVQGIGLDTALQFVQNFSE-DEILN 241 (602)
Q Consensus 216 ~~GipGIG~ktA~~Li~~~~~-e~iL~ 241 (602)
+..|||||++++.+|++.||+ ++|++
T Consensus 527 L~~IpGIG~kr~~~LL~~FGS~~~I~~ 553 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRFGSVEGVRE 553 (577)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHh
Confidence 479999999999999999996 66654
No 81
>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=36.76 E-value=40 Score=31.87 Aligned_cols=44 Identities=23% Similarity=0.317 Sum_probs=36.8
Q ss_pred HHHHHHHHHHcCCCEEeccCcHHHHHHHHHHc-CCeeEEEcCCCCeE
Q 044842 120 VQECVELLELFGMPVLKAKGEAEALCAQLNSE-GYVDACITADSDAF 165 (602)
Q Consensus 120 i~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~-g~vd~ViT~DSD~l 165 (602)
+..+-..|+.+|+.++.++...|..+..++.. |. .++|-|.+++
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 34567889999999999998899999999865 44 5899999875
No 82
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=36.70 E-value=26 Score=36.00 Aligned_cols=25 Identities=20% Similarity=0.500 Sum_probs=20.8
Q ss_pred CCCCCcccHHHHHHHHHh-cCh-HHHH
Q 044842 216 LNGVQGIGLDTALQFVQN-FSE-DEIL 240 (602)
Q Consensus 216 ~~GipGIG~ktA~~Li~~-~~~-e~iL 240 (602)
+..|||||+++|..|++. |++ ++|.
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik 31 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVR 31 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHH
Confidence 368999999999999999 986 5443
No 83
>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=34.30 E-value=92 Score=35.02 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=20.1
Q ss_pred CCCHHHHHHHHhhhCCCChhHHhhhHhhHHHh
Q 044842 380 SPMTEMLVDFLVYHQPWQPSYIRQKMLPMLST 411 (602)
Q Consensus 380 ~Pdl~~L~~f~~~~~~W~~~~~~e~llPll~~ 411 (602)
-|=+++-++-|.+ -||=..+.|..+.-.|++
T Consensus 327 ~P~VDA~MRqL~~-TGwmhnR~Rm~vAsfl~k 357 (475)
T TIGR02766 327 YPLVDAGMRELWA-TGWLHDRIRVVVSSFFVK 357 (475)
T ss_pred CcchhHHHHHHHH-HCCCcHHHHHHHHHHHHc
Confidence 3556666555533 388888888777666664
No 84
>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=34.15 E-value=1.2e+02 Score=33.90 Aligned_cols=41 Identities=17% Similarity=0.131 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEc
Q 044842 119 CVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACIT 159 (602)
Q Consensus 119 ~i~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT 159 (602)
.+.++.+-|+.+|++.++--|++...+..|++.--++.|++
T Consensus 79 sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~i~~V~~ 119 (454)
T TIGR00591 79 GLDEVANECERLIIPFHLLDGPPKELLPYFVDLHAAAAVVT 119 (454)
T ss_pred HHHHHHHHHHHcCCceEEeecChHHHHHHHHHHcCCCEEEE
Confidence 34445555555555555555555555555554433444444
No 85
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=32.93 E-value=1.1e+02 Score=34.51 Aligned_cols=42 Identities=14% Similarity=0.046 Sum_probs=26.0
Q ss_pred HhHHHHHHHHHHcCCCEEeccC----cHHHHHHHHHHcCCeeEEEc
Q 044842 118 KCVQECVELLELFGMPVLKAKG----EAEALCAQLNSEGYVDACIT 159 (602)
Q Consensus 118 ~~i~~~~~lL~~~GI~~i~AP~----EADAqcA~L~~~g~vd~ViT 159 (602)
+.+.++.+-|+.+|++.++.-| +....+..|.+.-.|+.|++
T Consensus 57 esL~~L~~~L~~~g~~L~v~~g~~~g~~~~vl~~l~~~~~i~~v~~ 102 (472)
T PRK10674 57 AQLNALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQQHQVTHLFY 102 (472)
T ss_pred HHHHHHHHHHHHcCCceEEEecCCcCCHHHHHHHHHHHcCCCEEEE
Confidence 4555666667777777776643 56667777765444555554
No 86
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=32.83 E-value=28 Score=41.15 Aligned_cols=25 Identities=28% Similarity=0.420 Sum_probs=21.9
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEILN 241 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~iL~ 241 (602)
..|||||++++..|++.||+ ++|++
T Consensus 640 ~~IPGIGpkr~k~LL~~FGSle~I~~ 665 (694)
T PRK14666 640 QRVEGIGPATARLLWERFGSLQAMAA 665 (694)
T ss_pred hhCCCCCHHHHHHHHHHhCCHHHHHh
Confidence 58999999999999999996 66654
No 87
>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=32.51 E-value=1.1e+02 Score=34.42 Aligned_cols=42 Identities=24% Similarity=0.249 Sum_probs=26.5
Q ss_pred HhHHHHHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEc
Q 044842 118 KCVQECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACIT 159 (602)
Q Consensus 118 ~~i~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT 159 (602)
+.+.++.+-|+.+|++.++.-|+....+..|.+.-.++.|++
T Consensus 55 esL~~L~~~L~~~G~~L~v~~G~p~~vl~~l~~~~~~~~V~~ 96 (471)
T TIGR03556 55 GCLQELQQRYQQAGSQLLILQGDPVQLIPQLAQQLGAKAVYW 96 (471)
T ss_pred HHHHHHHHHHHHCCCCeEEEECCHHHHHHHHHHHcCCCEEEE
Confidence 445556666677777777777777777776665544555554
No 88
>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=31.08 E-value=42 Score=40.05 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=23.6
Q ss_pred CCCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcCh
Q 044842 197 GLKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 197 gL~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~~ 236 (602)
--+.+.++.+.. + .-|+|||+++|-+|+..||.
T Consensus 74 p~~~~~i~~yL~---s----~~~~GIG~~~A~~iv~~fg~ 106 (720)
T TIGR01448 74 PTSKEGIVAYLS---S----RSIKGVGKKLAQRIVKTFGE 106 (720)
T ss_pred CCCHHHHHHHHh---c----CCCCCcCHHHHHHHHHHhCH
Confidence 335566665422 2 24799999999999999984
No 89
>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=30.85 E-value=78 Score=29.89 Aligned_cols=40 Identities=28% Similarity=0.216 Sum_probs=31.6
Q ss_pred HHHHHHHHHcCCCEEeccCcHHHHHHHHHHcCCeeEEEcCC
Q 044842 121 QECVELLELFGMPVLKAKGEAEALCAQLNSEGYVDACITAD 161 (602)
Q Consensus 121 ~~~~~lL~~~GI~~i~AP~EADAqcA~L~~~g~vd~ViT~D 161 (602)
....+.++..|+++++-.-...++..++.+.| ||+|+|++
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 55678888899999887766666777777777 89999963
No 90
>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=30.19 E-value=52 Score=32.73 Aligned_cols=44 Identities=16% Similarity=0.157 Sum_probs=26.6
Q ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhc
Q 044842 190 SDIEAGLGL-KRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNF 234 (602)
Q Consensus 190 ~~i~~~lgL-~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~ 234 (602)
+....-++. +.++|+. |+..|.--.+..+||||+|||-+|+-+.
T Consensus 83 K~Al~iL~~~~~~el~~-aI~~~d~~~L~~ipGiGkKtAerIileL 127 (191)
T TIGR00084 83 KLALAILSNMSPEEFVY-AIETEEVKALVKIPGVGKKTAERLLLEL 127 (191)
T ss_pred HHHHHHHhcCCHHHHHH-HHHhCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 333333443 4555544 3333433335799999999999999554
No 91
>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=29.67 E-value=34 Score=30.47 Aligned_cols=29 Identities=17% Similarity=0.244 Sum_probs=24.7
Q ss_pred cCcHHHHHHHHHHcCCeeEEEcCCCCeEe
Q 044842 138 KGEAEALCAQLNSEGYVDACITADSDAFL 166 (602)
Q Consensus 138 P~EADAqcA~L~~~g~vd~ViT~DSD~ll 166 (602)
+-..|+.+..++..+-+|+++|.|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 55778888888888999999999999763
No 92
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=29.20 E-value=35 Score=35.57 Aligned_cols=52 Identities=23% Similarity=0.380 Sum_probs=34.6
Q ss_pred ceeEEEeeecCceeeEEEEEeeccccccccccCCCCCcchhhhhcccCCccccCCCcceeeehhhhhHHHhhchHHHHHH
Q 044842 432 FDSIRRVKIRYGHQSYVVKWKKAASAISGVKYTAPVDSDLHLEEFMEYPQIHVDGDCWFLLTDENMKLVHSAFPKKVDHF 511 (602)
Q Consensus 432 ~~~i~k~r~~~g~~~~ei~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~e~~~l~~~ayp~~v~~f 511 (602)
=..|.+.|..+|...|.|+|+--. +. | -|=||+.....| |++++.|
T Consensus 51 vEki~~~r~~~g~~eYlvkW~Gy~-----------~~------~----------------ntWEPee~~~~C-~~li~~~ 96 (270)
T KOG1911|consen 51 VEKILKRRKKNGKIEYLVKWKGYP-----------DP------D----------------NTWEPEEHNLDC-PELIDEF 96 (270)
T ss_pred hhhhhhccccCCCceeeeecCCCC-----------Cc------c----------------ccCCchhhcccc-HHHHHHH
Confidence 335677788888888999997431 10 1 233555544444 9999999
Q ss_pred HHhhhh
Q 044842 512 LQENER 517 (602)
Q Consensus 512 ~~~~~~ 517 (602)
.++...
T Consensus 97 ~~~~~~ 102 (270)
T KOG1911|consen 97 EKSQKK 102 (270)
T ss_pred HHHhcc
Confidence 998554
No 93
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=26.76 E-value=48 Score=34.61 Aligned_cols=25 Identities=24% Similarity=0.615 Sum_probs=21.7
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEILN 241 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~iL~ 241 (602)
.++||||++.|..++..||+ ++++.
T Consensus 185 ~s~pgig~~~a~~ll~~fgS~~~~~t 210 (254)
T COG1948 185 ESIPGIGPKLAERLLKKFGSVEDVLT 210 (254)
T ss_pred HcCCCccHHHHHHHHHHhcCHHHHhh
Confidence 68899999999999999996 66654
No 94
>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=26.75 E-value=1.4e+02 Score=28.21 Aligned_cols=43 Identities=23% Similarity=0.307 Sum_probs=34.5
Q ss_pred HHhHHHHHHHHHHcCCC-----EEeccC--cHHHHHHHHHHcCCeeEEEc
Q 044842 117 LKCVQECVELLELFGMP-----VLKAKG--EAEALCAQLNSEGYVDACIT 159 (602)
Q Consensus 117 ~~~i~~~~~lL~~~GI~-----~i~AP~--EADAqcA~L~~~g~vd~ViT 159 (602)
..++.-+.+.|+..|+. ++..|| |-=..+..|.+.|..|+||+
T Consensus 16 ~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~ 65 (138)
T TIGR00114 16 DMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIA 65 (138)
T ss_pred HHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 35677788999999875 777897 77777778888888899886
No 95
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=25.65 E-value=58 Score=30.69 Aligned_cols=16 Identities=19% Similarity=0.129 Sum_probs=14.1
Q ss_pred CCCCcccHHHHHHHHH
Q 044842 217 NGVQGIGLDTALQFVQ 232 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~ 232 (602)
..+|||||+.|-+||+
T Consensus 64 ~~lpGigP~~A~~IV~ 79 (132)
T PRK02515 64 RQFPGMYPTLAGKIVK 79 (132)
T ss_pred HHCCCCCHHHHHHHHH
Confidence 3689999999999996
No 96
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=25.42 E-value=1.7e+02 Score=27.84 Aligned_cols=43 Identities=26% Similarity=0.383 Sum_probs=36.0
Q ss_pred HHhHHHHHHHHHHcCC-----CEEeccC--cHHHHHHHHHHcCCeeEEEc
Q 044842 117 LKCVQECVELLELFGM-----PVLKAKG--EAEALCAQLNSEGYVDACIT 159 (602)
Q Consensus 117 ~~~i~~~~~lL~~~GI-----~~i~AP~--EADAqcA~L~~~g~vd~ViT 159 (602)
..+++.+.+.|...|+ .++..|| |-=..+..|.+.+..|+||+
T Consensus 19 ~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~ 68 (144)
T PF00885_consen 19 DRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIA 68 (144)
T ss_dssp HHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEE
T ss_pred HHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEE
Confidence 4567788899999987 7788897 88888888999999999886
No 97
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.31 E-value=32 Score=34.31 Aligned_cols=37 Identities=27% Similarity=0.465 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHcCCCCCCCCCCcccHHHHHHHHHhcC
Q 044842 198 LKRKHLIAMSLLIGNDHDLNGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 198 L~~~qli~laiL~G~DY~~~GipGIG~ktA~~Li~~~~ 235 (602)
+++++|+. |+..+..-.+..|||||+|||-+|+-+..
T Consensus 93 ~~~~~l~~-aI~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 93 MNAEALAS-AIISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred CCHHHHHH-HHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 45555443 34445433357999999999999997754
No 98
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=24.90 E-value=64 Score=26.15 Aligned_cols=20 Identities=25% Similarity=0.476 Sum_probs=15.3
Q ss_pred CCCCcccHHHHHHHHHhcCh
Q 044842 217 NGVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~ 236 (602)
..|+|||+++|..+..-|..
T Consensus 38 ~~i~gIG~~~A~si~~ff~~ 57 (64)
T PF12826_consen 38 SAIPGIGPKIAQSIYEFFQD 57 (64)
T ss_dssp CTSTT--HHHHHHHHHHHH-
T ss_pred hccCCcCHHHHHHHHHHHCC
Confidence 58999999999999988864
No 99
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=24.88 E-value=2.2e+02 Score=25.35 Aligned_cols=17 Identities=12% Similarity=0.172 Sum_probs=12.2
Q ss_pred CCHHHHHHHHHHcCCCC
Q 044842 198 LKRKHLIAMSLLIGNDH 214 (602)
Q Consensus 198 L~~~qli~laiL~G~DY 214 (602)
++...++.+|.+.|=.|
T Consensus 10 v~E~ei~~ya~~~~lp~ 26 (104)
T TIGR00269 10 IPEKEVVLYAFLNELKV 26 (104)
T ss_pred CCHHHHHHHHHHcCCCc
Confidence 45667788888888444
No 100
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=23.64 E-value=59 Score=35.09 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=19.4
Q ss_pred CCCCcccHHHHHHHHHhcCh---HHHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE---DEILN 241 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~---e~iL~ 241 (602)
-.||||||++|..|.+ .|. +++.+
T Consensus 92 ~~i~GiGpk~a~~l~~-lGi~tl~eL~~ 118 (334)
T smart00483 92 TNVFGVGPKTAAKWYR-KGIRTLEELKK 118 (334)
T ss_pred HccCCcCHHHHHHHHH-hCCCCHHHHHh
Confidence 4899999999999999 884 55543
No 101
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=23.05 E-value=19 Score=38.22 Aligned_cols=30 Identities=37% Similarity=0.807 Sum_probs=21.8
Q ss_pred ccccCCCCccCCCCCCccccccccccccccCCCCCCC
Q 044842 273 PMIKSSHCSFCGHPGTKRAHFKFSCEYCINDNNEGCL 309 (602)
Q Consensus 273 ~~~k~~~Cs~C~h~gs~k~h~k~gc~~C~~~~~~gc~ 309 (602)
+...+..||.|||||-.|. |..|.. ..+|.
T Consensus 315 ~~~d~~fCstCG~~ga~Kr-----Cs~CKa--v~YCd 344 (396)
T KOG1710|consen 315 IAADCQFCSTCGHPGAKKR-----CSQCKA--VAYCD 344 (396)
T ss_pred eEEecccccccCCCCccch-----hhhhHH--HHHHH
Confidence 4455789999999997654 777775 45554
No 102
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=22.67 E-value=1.5e+02 Score=31.88 Aligned_cols=51 Identities=22% Similarity=0.154 Sum_probs=36.4
Q ss_pred EEEeHHHHHHHhCCCHHHHHHH--------------HHHcCCCCCC-----------CCCCcccHHHHHHHHHhcC
Q 044842 185 ECYCISDIEAGLGLKRKHLIAM--------------SLLIGNDHDL-----------NGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 185 ~~y~~~~i~~~lgL~~~qli~l--------------aiL~G~DY~~-----------~GipGIG~ktA~~Li~~~~ 235 (602)
..|..+.+...+|++.+.+.+. ++|--.|..| -.|||||.++|..+|..-.
T Consensus 276 RLYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~Rr 351 (404)
T COG4277 276 RLYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMTRR 351 (404)
T ss_pred HHHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHHhh
Confidence 6788899999999998887653 2222223221 1789999999999987654
No 103
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=22.13 E-value=94 Score=30.25 Aligned_cols=45 Identities=20% Similarity=0.267 Sum_probs=32.2
Q ss_pred HHHHHHHcCCCEEeccCcHHHHHHH--HHH--cCCee--EEEcCCCCeEee
Q 044842 123 CVELLELFGMPVLKAKGEAEALCAQ--LNS--EGYVD--ACITADSDAFLF 167 (602)
Q Consensus 123 ~~~lL~~~GI~~i~AP~EADAqcA~--L~~--~g~vd--~ViT~DSD~llf 167 (602)
+++.|..+|+..+...|-.|-.+|- |.- .+.+| +++|.|+|+-..
T Consensus 71 l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~L 121 (160)
T TIGR00288 71 LIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPV 121 (160)
T ss_pred HHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHH
Confidence 4678999999988888877776663 322 35555 578999997543
No 104
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=21.99 E-value=77 Score=33.77 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=19.6
Q ss_pred CCCCcccHHHHHHHHHhcCh---HHHHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE---DEILNI 242 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~---e~iL~~ 242 (602)
-+|+||||++|.+|. ..|. +++...
T Consensus 88 ~~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 88 LRVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred HcCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 389999999999999 7773 555544
No 105
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=21.96 E-value=65 Score=26.21 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=16.1
Q ss_pred eEEEeeecCceeeEEEEEeeccc
Q 044842 434 SIRRVKIRYGHQSYVVKWKKAAS 456 (602)
Q Consensus 434 ~i~k~r~~~g~~~~ei~W~~~~~ 456 (602)
.|.-+|...|-|=|.|+|.+..|
T Consensus 24 eIveV~g~dG~PPY~VRw~D~Gh 46 (58)
T PF08940_consen 24 EIVEVRGPDGSPPYLVRWDDTGH 46 (58)
T ss_dssp EEEE-S-SSS-S-EEEEETTTTE
T ss_pred EEEEEECCCCCCCEEEEecCCCc
Confidence 67888999999999999998543
No 106
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=21.89 E-value=1.7e+02 Score=28.51 Aligned_cols=43 Identities=16% Similarity=0.201 Sum_probs=34.7
Q ss_pred HHhHHHHHHHHHHcC-----CCEEeccC--cHHHHHHHHHHcCCeeEEEc
Q 044842 117 LKCVQECVELLELFG-----MPVLKAKG--EAEALCAQLNSEGYVDACIT 159 (602)
Q Consensus 117 ~~~i~~~~~lL~~~G-----I~~i~AP~--EADAqcA~L~~~g~vd~ViT 159 (602)
..+++-+.+.|...| |.++..|| |.=..+..|.+.|..|+||.
T Consensus 26 ~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiIa 75 (158)
T PRK12419 26 DQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVA 75 (158)
T ss_pred HHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 356777889999999 57888997 77777778888888898875
No 107
>PHA02942 putative transposase; Provisional
Probab=21.85 E-value=51 Score=36.33 Aligned_cols=27 Identities=37% Similarity=0.656 Sum_probs=16.1
Q ss_pred cCCCCccCCCCCCcccccccccccccc
Q 044842 276 KSSHCSFCGHPGTKRAHFKFSCEYCIN 302 (602)
Q Consensus 276 k~~~Cs~C~h~gs~k~h~k~gc~~C~~ 302 (602)
.+..|+.|||......+...-|..|+.
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCC
Confidence 567899999976422223344555554
No 108
>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=21.77 E-value=53 Score=30.16 Aligned_cols=19 Identities=21% Similarity=0.335 Sum_probs=17.0
Q ss_pred CCCCcccHHHHHHHHHhcC
Q 044842 217 NGVQGIGLDTALQFVQNFS 235 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~ 235 (602)
..+||||+++|.+||..+.
T Consensus 71 ~~lpGIG~~~A~~Ii~~R~ 89 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYRE 89 (120)
T ss_pred hcCCCCCHHHHHHHHHHHH
Confidence 5889999999999999874
No 109
>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=21.61 E-value=71 Score=37.74 Aligned_cols=19 Identities=26% Similarity=0.517 Sum_probs=13.4
Q ss_pred CCCcccHHHHHHHHHhcCh
Q 044842 218 GVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 218 GipGIG~ktA~~Li~~~~~ 236 (602)
||||||+++|..|++.|++
T Consensus 502 gIpgVG~~~ak~L~~~f~s 520 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGT 520 (652)
T ss_pred cCCCcCHHHHHHHHHHhCC
Confidence 6777777777777777764
No 110
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.27 E-value=74 Score=37.88 Aligned_cols=19 Identities=26% Similarity=0.550 Sum_probs=15.3
Q ss_pred CCCcccHHHHHHHHHhcCh
Q 044842 218 GVQGIGLDTALQFVQNFSE 236 (602)
Q Consensus 218 GipGIG~ktA~~Li~~~~~ 236 (602)
||||||.++|..|++.|++
T Consensus 532 gIpgIG~~~ak~L~~~F~s 550 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGT 550 (689)
T ss_pred CCCCcCHHHHHHHHHHhCC
Confidence 6888888888888888875
No 111
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=20.47 E-value=71 Score=37.21 Aligned_cols=23 Identities=22% Similarity=0.512 Sum_probs=20.3
Q ss_pred CCCCcccHHHHHHHHHhcCh-HHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE-DEI 239 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~-e~i 239 (602)
.+|||||+++...|++.||+ ++|
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~~i 556 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLKGI 556 (581)
T ss_pred ccCCCcCHHHHHHHHHHhhCHHHH
Confidence 69999999999999999997 444
No 112
>PRK08609 hypothetical protein; Provisional
Probab=20.10 E-value=97 Score=35.96 Aligned_cols=27 Identities=7% Similarity=0.190 Sum_probs=20.6
Q ss_pred CCCCcccHHHHHHHHHhcCh---HHHHHHH
Q 044842 217 NGVQGIGLDTALQFVQNFSE---DEILNIL 243 (602)
Q Consensus 217 ~GipGIG~ktA~~Li~~~~~---e~iL~~l 243 (602)
-.||||||++|.+|-...|. +++....
T Consensus 91 ~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~ 120 (570)
T PRK08609 91 LKLPGLGGKKIAKLYKELGVVDKESLKEAC 120 (570)
T ss_pred hcCCCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence 37999999999999987763 5555443
No 113
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.05 E-value=61 Score=21.28 Aligned_cols=20 Identities=35% Similarity=0.685 Sum_probs=10.1
Q ss_pred CccCCCCCCcccccccccccccc
Q 044842 280 CSFCGHPGTKRAHFKFSCEYCIN 302 (602)
Q Consensus 280 Cs~C~h~gs~k~h~k~gc~~C~~ 302 (602)
|+.||+.-...+ + -|..|++
T Consensus 2 Cp~CG~~~~~~~--~-fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEIEDDA--K-FCPNCGT 21 (23)
T ss_pred CcccCCCCCCcC--c-chhhhCC
Confidence 666777643222 2 1555554
Done!