Query psy14291
Match_columns 538
No_of_seqs 419 out of 1784
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 16:06:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14291hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00217 flap endonuclease-1; 100.0 1.2E-58 2.7E-63 489.8 30.5 325 110-534 1-334 (393)
2 cd00128 XPG Xeroderma pigmento 100.0 5.9E-55 1.3E-59 449.7 29.5 312 110-527 1-314 (316)
3 TIGR03674 fen_arch flap struct 100.0 1.4E-54 2.9E-59 451.6 28.2 314 110-534 1-327 (338)
4 KOG2519|consensus 100.0 1.3E-47 2.9E-52 402.4 20.5 323 110-537 1-333 (449)
5 PRK03980 flap endonuclease-1; 100.0 4E-46 8.7E-51 381.0 27.3 257 201-536 12-282 (292)
6 KOG2518|consensus 100.0 3.9E-47 8.3E-52 402.7 18.5 243 110-435 1-248 (556)
7 TIGR00600 rad2 DNA excision re 100.0 5.8E-42 1.3E-46 392.4 24.4 220 310-536 763-991 (1034)
8 KOG2520|consensus 100.0 1.2E-39 2.5E-44 363.4 18.5 219 310-537 457-686 (815)
9 PRK14976 5'-3' exonuclease; Pr 100.0 4.2E-36 9.1E-41 305.9 21.1 195 307-519 75-281 (281)
10 smart00475 53EXOc 5'-3' exonuc 100.0 1.3E-33 2.8E-38 284.6 15.5 207 276-499 37-257 (259)
11 PRK09482 flap endonuclease-lik 100.0 2E-32 4.3E-37 275.0 14.7 205 276-500 35-254 (256)
12 PRK05755 DNA polymerase I; Pro 100.0 8.4E-32 1.8E-36 310.9 20.7 196 306-520 70-278 (880)
13 TIGR00593 pola DNA polymerase 100.0 3.7E-32 8.1E-37 312.3 17.5 225 278-520 39-277 (887)
14 cd00008 53EXOc 5'-3' exonuclea 100.0 8.9E-32 1.9E-36 268.4 17.0 150 316-485 83-240 (240)
15 COG0258 Exo 5'-3' exonuclease 100.0 2.7E-31 5.9E-36 273.7 15.8 279 124-520 2-292 (310)
16 PF00867 XPG_I: XPG I-region; 99.8 5.6E-22 1.2E-26 171.1 5.4 85 328-412 1-94 (94)
17 smart00485 XPGN Xeroderma pigm 99.8 2.7E-20 5.9E-25 161.4 6.9 96 110-257 1-96 (99)
18 TIGR00600 rad2 DNA excision re 99.8 5.8E-20 1.3E-24 212.1 9.9 108 110-270 1-108 (1034)
19 PF00752 XPG_N: XPG N-terminal 99.8 5.5E-20 1.2E-24 159.8 6.9 97 110-258 1-99 (101)
20 PHA00439 exonuclease 99.8 2.3E-18 4.9E-23 175.4 11.6 127 290-431 68-206 (286)
21 PF01367 5_3_exonuc: 5'-3' exo 99.7 2.6E-20 5.6E-25 163.2 -4.8 99 397-510 1-101 (101)
22 smart00484 XPGI Xeroderma pigm 99.6 4.5E-16 9.8E-21 129.0 6.2 69 329-397 2-73 (73)
23 PHA02567 rnh RnaseH; Provision 99.6 1.8E-14 4E-19 147.7 11.3 119 289-419 66-207 (304)
24 cd00080 HhH2_motif Helix-hairp 99.5 4.5E-14 9.8E-19 117.5 5.4 53 394-451 2-56 (75)
25 PF02739 5_3_exonuc_N: 5'-3' e 99.2 2.8E-12 6E-17 122.3 2.9 116 277-395 40-169 (169)
26 smart00279 HhH2 Helix-hairpin- 99.1 8.5E-11 1.8E-15 84.8 4.1 34 399-432 1-36 (36)
27 PF12813 XPG_I_2: XPG domain c 98.4 1.5E-06 3.2E-11 87.9 9.0 84 321-407 7-107 (246)
28 PF04599 Pox_G5: Poxvirus G5 p 98.0 7.2E-05 1.6E-09 80.2 14.0 225 110-421 1-248 (425)
29 PHA03065 Hypothetical protein; 97.9 0.00019 4.1E-09 76.8 14.1 218 110-421 1-250 (438)
30 PRK03980 flap endonuclease-1; 96.9 0.0012 2.5E-08 68.7 5.0 48 259-306 68-115 (292)
31 PF03159 XRN_N: XRN 5'-3' exon 96.7 0.0055 1.2E-07 61.9 8.3 32 337-368 182-222 (237)
32 smart00475 53EXOc 5'-3' exonuc 96.5 0.008 1.7E-07 61.4 8.0 83 201-306 34-117 (259)
33 cd00128 XPG Xeroderma pigmento 95.6 0.015 3.3E-07 60.6 5.0 47 260-306 114-160 (316)
34 PF12826 HHH_2: Helix-hairpin- 92.6 0.071 1.5E-06 43.0 1.9 20 416-435 7-26 (64)
35 smart00484 XPGI Xeroderma pigm 92.6 0.065 1.4E-06 44.7 1.6 22 285-306 2-23 (73)
36 PF00867 XPG_I: XPG I-region; 91.6 0.11 2.3E-06 45.0 1.9 22 284-305 1-22 (94)
37 TIGR00593 pola DNA polymerase 90.7 0.54 1.2E-05 56.0 7.2 82 201-305 34-116 (887)
38 TIGR03674 fen_arch flap struct 89.5 0.27 5.8E-06 52.2 3.1 47 260-306 116-162 (338)
39 PTZ00217 flap endonuclease-1; 89.3 0.28 6.2E-06 53.1 3.1 48 259-306 123-170 (393)
40 COG5049 XRN1 5'-3' exonuclease 87.5 6 0.00013 45.8 11.9 93 336-428 185-335 (953)
41 KOG2520|consensus 86.6 0.34 7.3E-06 56.6 1.7 54 253-306 445-498 (815)
42 PF00633 HHH: Helix-hairpin-he 85.7 0.6 1.3E-05 32.5 2.0 15 416-430 15-29 (30)
43 COG5366 Protein involved in pr 85.4 0.36 7.8E-06 52.8 1.1 113 322-435 133-248 (531)
44 PRK14605 ruvA Holliday junctio 82.4 1.8 3.9E-05 42.6 4.5 37 392-434 58-95 (194)
45 PRK14602 ruvA Holliday junctio 82.0 1.9 4.2E-05 42.7 4.6 44 392-447 59-103 (203)
46 TIGR00084 ruvA Holliday juncti 81.1 1.9 4.2E-05 42.2 4.2 45 392-448 57-102 (191)
47 PRK00116 ruvA Holliday junctio 79.5 1.9 4E-05 42.2 3.5 19 416-434 77-95 (192)
48 KOG2519|consensus 78.6 0.99 2.1E-05 49.5 1.4 61 258-320 116-176 (449)
49 KOG2045|consensus 78.1 34 0.00073 41.2 13.2 30 400-429 277-307 (1493)
50 PRK14601 ruvA Holliday junctio 78.0 1.4 2.9E-05 43.2 2.0 19 416-434 77-95 (183)
51 PRK14606 ruvA Holliday junctio 76.2 3.1 6.6E-05 40.8 3.9 46 390-447 56-102 (188)
52 PRK14669 uvrC excinuclease ABC 76.1 1.6 3.4E-05 50.2 2.1 26 415-445 555-580 (624)
53 smart00278 HhH1 Helix-hairpin- 76.1 2.1 4.6E-05 28.4 1.9 18 414-431 3-20 (26)
54 PRK14601 ruvA Holliday junctio 75.7 3.1 6.8E-05 40.7 3.8 37 396-433 92-129 (183)
55 PRK13901 ruvA Holliday junctio 75.4 1.7 3.8E-05 42.9 2.0 18 416-433 76-93 (196)
56 PRK14603 ruvA Holliday junctio 75.4 3.2 7E-05 40.9 3.8 44 392-447 57-101 (197)
57 PRK14667 uvrC excinuclease ABC 75.3 1.9 4.1E-05 49.1 2.4 27 414-445 516-542 (567)
58 PRK14600 ruvA Holliday junctio 75.1 3.4 7.3E-05 40.5 3.8 49 388-448 54-103 (186)
59 PRK13901 ruvA Holliday junctio 74.7 3.6 7.9E-05 40.7 4.0 36 397-433 92-128 (196)
60 TIGR00194 uvrC excinuclease AB 73.6 2.2 4.7E-05 48.6 2.4 21 415-435 544-564 (574)
61 PRK14604 ruvA Holliday junctio 73.5 3.8 8.1E-05 40.4 3.8 44 392-447 58-102 (195)
62 PRK14606 ruvA Holliday junctio 73.4 2.1 4.7E-05 41.9 2.0 37 396-433 92-129 (188)
63 PRK14670 uvrC excinuclease ABC 73.4 2.2 4.9E-05 48.5 2.5 28 413-445 515-542 (574)
64 PRK14604 ruvA Holliday junctio 72.1 2.4 5.2E-05 41.8 2.0 36 397-433 93-129 (195)
65 PRK14602 ruvA Holliday junctio 71.7 2.4 5.3E-05 42.0 2.0 36 397-433 94-130 (203)
66 PF14520 HHH_5: Helix-hairpin- 70.9 2.7 5.8E-05 33.2 1.7 20 416-435 9-29 (60)
67 PRK14671 uvrC excinuclease ABC 70.4 3 6.5E-05 48.0 2.6 26 415-445 572-597 (621)
68 PRK14600 ruvA Holliday junctio 70.1 3.6 7.7E-05 40.3 2.7 34 397-432 93-127 (186)
69 PRK14603 ruvA Holliday junctio 69.7 2.8 6.1E-05 41.3 2.0 35 397-433 92-128 (197)
70 KOG2518|consensus 68.2 9.9 0.00021 42.7 5.9 48 259-306 113-160 (556)
71 PF10391 DNA_pol_lambd_f: Fing 67.8 3.7 8E-05 32.1 1.8 20 416-435 6-26 (52)
72 PF02371 Transposase_20: Trans 67.1 5 0.00011 34.0 2.7 23 413-435 3-25 (87)
73 KOG2044|consensus 67.0 43 0.00092 39.6 10.7 99 331-429 190-360 (931)
74 COG0632 RuvA Holliday junction 66.4 13 0.00029 36.9 5.9 42 386-433 52-94 (201)
75 PRK14672 uvrC excinuclease ABC 65.0 4.3 9.3E-05 47.1 2.5 27 414-445 610-636 (691)
76 PRK00558 uvrC excinuclease ABC 62.4 4.9 0.00011 46.1 2.3 26 415-445 546-571 (598)
77 PRK14668 uvrC excinuclease ABC 61.3 5 0.00011 45.8 2.1 28 414-446 527-554 (577)
78 PRK12766 50S ribosomal protein 60.1 6 0.00013 40.1 2.2 22 414-435 5-27 (232)
79 COG0632 RuvA Holliday junction 58.3 10 0.00022 37.7 3.5 36 397-432 93-128 (201)
80 PRK14666 uvrC excinuclease ABC 56.9 7.3 0.00016 45.3 2.5 26 415-445 640-665 (694)
81 TIGR00305 probable toxin-antit 55.3 7.9 0.00017 34.1 1.9 28 338-365 85-112 (114)
82 PF11798 IMS_HHH: IMS family H 54.4 8.9 0.00019 26.9 1.7 17 415-432 14-30 (32)
83 PF04796 RepA_C: Plasmid encod 48.0 6.5 0.00014 37.8 0.2 38 114-151 111-151 (161)
84 TIGR00084 ruvA Holliday juncti 47.5 15 0.00032 36.1 2.6 32 398-430 93-125 (191)
85 COG0322 UvrC Nuclease subunit 47.2 13 0.00028 42.5 2.5 27 415-446 533-559 (581)
86 PRK14605 ruvA Holliday junctio 46.6 13 0.00029 36.5 2.2 35 397-432 93-128 (194)
87 COG1948 MUS81 ERCC4-type nucle 45.5 15 0.00033 37.8 2.4 26 416-446 186-211 (254)
88 TIGR01448 recD_rel helicase, p 45.0 32 0.00068 40.4 5.2 32 398-435 76-107 (720)
89 TIGR00575 dnlj DNA ligase, NAD 44.6 16 0.00034 42.4 2.7 20 416-435 502-521 (652)
90 PRK14351 ligA NAD-dependent DN 44.3 16 0.00036 42.6 2.8 20 416-435 532-551 (689)
91 PRK09482 flap endonuclease-lik 43.5 1.7E+02 0.0037 30.2 9.6 29 276-304 86-115 (256)
92 PF08258 WWamide: WWamide pept 43.1 11 0.00023 18.3 0.4 7 11-17 1-7 (7)
93 PRK00076 recR recombination pr 41.8 24 0.00052 35.0 3.1 39 415-453 14-52 (196)
94 TIGR00615 recR recombination p 41.5 25 0.00055 34.9 3.2 39 415-453 14-52 (195)
95 COG0353 RecR Recombinational D 40.2 24 0.00052 35.1 2.8 39 415-453 15-53 (198)
96 PRK13844 recombination protein 39.9 26 0.00055 35.0 2.9 40 415-454 18-57 (200)
97 TIGR00596 rad1 DNA repair prot 39.1 14 0.00029 44.1 1.1 28 413-445 758-785 (814)
98 PF14520 HHH_5: Helix-hairpin- 37.9 26 0.00057 27.5 2.2 19 414-432 40-58 (60)
99 PRK13766 Hef nuclease; Provisi 36.0 26 0.00056 40.9 2.7 27 414-445 717-743 (773)
100 COG4277 Predicted DNA-binding 33.4 66 0.0014 34.3 4.8 53 383-435 275-355 (404)
101 COG1555 ComEA DNA uptake prote 33.2 37 0.00079 32.1 2.8 15 416-430 101-115 (149)
102 PRK07956 ligA NAD-dependent DN 33.0 28 0.00061 40.5 2.4 20 416-435 515-534 (665)
103 COG1569 Predicted nucleic acid 32.9 74 0.0016 30.1 4.6 46 340-394 91-136 (142)
104 PF11731 Cdd1: Pathogenicity l 32.1 38 0.00082 29.8 2.4 16 415-430 15-30 (93)
105 PRK14168 bifunctional 5,10-met 30.5 4.2E+02 0.009 28.0 10.3 91 322-434 53-157 (297)
106 PRK00116 ruvA Holliday junctio 30.5 45 0.00097 32.6 3.0 21 414-434 110-130 (192)
107 PRK02515 psbU photosystem II c 29.4 40 0.00086 31.5 2.2 15 416-430 65-79 (132)
108 TIGR01259 comE comEA protein. 28.4 36 0.00079 30.9 1.8 18 416-433 72-89 (120)
109 TIGR00028 Mtu_PIN_fam Mycobact 28.3 59 0.0013 28.7 3.2 35 340-375 105-139 (142)
110 TIGR00426 competence protein C 26.8 59 0.0013 26.1 2.6 19 417-435 22-43 (69)
111 PF02739 5_3_exonuc_N: 5'-3' e 25.9 4.4E+02 0.0095 25.2 8.8 22 276-297 88-110 (169)
112 TIGR03252 uncharacterized HhH- 25.9 43 0.00093 32.8 1.9 19 416-434 119-137 (177)
113 PF13052 DUF3913: Protein of u 25.6 36 0.00079 26.4 1.0 26 408-435 14-40 (57)
114 PF14716 HHH_8: Helix-hairpin- 25.3 53 0.0011 26.6 2.1 14 415-428 50-63 (68)
115 PF00875 DNA_photolyase: DNA p 24.9 86 0.0019 29.1 3.7 44 316-359 51-94 (165)
116 smart00483 POLXc DNA polymeras 24.9 47 0.001 35.3 2.2 18 416-434 93-110 (334)
117 PRK01229 N-glycosylase/DNA lya 24.3 53 0.0011 32.9 2.3 26 506-532 178-203 (208)
118 cd00141 NT_POLXc Nucleotidyltr 24.0 52 0.0011 34.5 2.3 17 416-433 89-105 (307)
119 cd00008 53EXOc 5'-3' exonuclea 23.6 90 0.0019 31.5 3.8 82 201-305 35-117 (240)
120 PF01927 Mut7-C: Mut7-C RNAse 22.3 70 0.0015 29.8 2.5 45 320-365 9-53 (147)
121 PRK14187 bifunctional 5,10-met 22.1 6.8E+02 0.015 26.5 10.0 91 322-434 52-156 (294)
122 COG2454 Uncharacterized conser 21.8 3.3E+02 0.0071 27.5 7.1 29 123-151 56-84 (211)
123 TIGR00114 lumazine-synth 6,7-d 21.4 1.6E+02 0.0035 27.6 4.7 45 315-359 13-65 (138)
124 COG1936 Predicted nucleotide k 21.3 63 0.0014 31.8 2.0 22 414-435 5-26 (180)
125 PRK14180 bifunctional 5,10-met 21.3 7.4E+02 0.016 26.0 10.0 90 322-434 51-154 (282)
126 COG0272 Lig NAD-dependent DNA 21.1 52 0.0011 38.3 1.7 20 416-435 515-534 (667)
127 PTZ00134 40S ribosomal protein 20.9 1E+02 0.0022 29.5 3.4 35 400-434 9-52 (154)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.2e-58 Score=489.81 Aligned_cols=325 Identities=26% Similarity=0.413 Sum_probs=261.0
Q ss_pred hchhchHHHhhhc----CcccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHH
Q psy14291 110 MGVNGLWKLLEAS----GKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEE 185 (538)
Q Consensus 110 MGi~GLw~~l~~~----~~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 185 (538)
|||+|||++|++. .++++++.|+|++||||+|+|+|++..+++....+.++.+. .+..++||
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~---------~G~~t~~l----- 66 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYFGRVIAIDASMALYQFLIAIRDDSQGGNLTNE---------AGEVTSHI----- 66 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhCCcEEEEeHHHHHHHHHHHcccccccccchhc---------cCCccHHH-----
Confidence 9999999999976 58999999999999999999999987776531112222221 12333566
Q ss_pred HhcCcchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhh
Q psy14291 186 IAGGKEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQT 265 (538)
Q Consensus 186 ~~~~~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~ 265 (538)
.+||+|+++|+ ..||+| ++||||.+|+.|..++++|+.++++-.+++.
T Consensus 67 ---------------~g~~~r~~~Ll----~~gikP-------------v~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~ 114 (393)
T PTZ00217 67 ---------------SGLFNRTIRLL----EAGIKP-------------VYVFDGKPPELKSGELEKRRERREEAEEELE 114 (393)
T ss_pred ---------------HHHHHHHHHHH----HCCCCE-------------EEEEcCCCchhhHHHHHHHHHHHHHhHHHHH
Confidence 67999976655 456777 9999999999999999998876543322221
Q ss_pred hhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHhH-HHHHHHHHHcCCCcccCcchHHHH
Q psy14291 266 RLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKM-LEAQELLQLFGVPFIVAPGEAEAQ 344 (538)
Q Consensus 266 R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q~-~~ik~lL~~~GIp~i~APgEADaq 344 (538)
+..+.. ...++. ++.++...++.++ ..++++|+.|||||++||||||||
T Consensus 115 ---------------~a~~~g--------~~~~a~-------k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAdaq 164 (393)
T PTZ00217 115 ---------------KAIEEG--------DDEEIK-------KQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQ 164 (393)
T ss_pred ---------------HHHhcC--------CHHHHH-------HHHhhcccCCHHHHHHHHHHHHHcCCceEECCcCHHHH
Confidence 111110 000110 1123445666554 689999999999999999999999
Q ss_pred HHHHHhhcCCCceEecCCceEeecCeEEEEecCC---CCCcEEEEchhHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCCC
Q psy14291 345 CASLELGNHTQGVITDDSDIWLFGARTVYKNFFD---KKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVG 421 (538)
Q Consensus 345 iA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~---~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~GsDyipGVpGIG 421 (538)
||+|++.|.+++|+|+|+|+|+||+++++++++. ....+++|+.+.+.+.+|++++||+|+|+|+||||+|||||||
T Consensus 165 ~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi~GIG 244 (393)
T PTZ00217 165 CAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIG 244 (393)
T ss_pred HHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCcc
Confidence 9999999999999999999999999999998753 2235788999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCc-ccccC
Q psy14291 422 PVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNV-QKLAW 500 (538)
Q Consensus 422 ~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~-~~~~w 500 (538)
+|||++||++||++ ++|+++++..+ ..++.+|+..++..+|++|.|..+. .++.|
T Consensus 245 ~ktA~~Li~~~gsl-----e~il~~~~~~k-------------------~~~p~~~~~~~~~~~f~~p~V~~~~~~~l~w 300 (393)
T PTZ00217 245 PKTAYKLIKKYKSI-----EEILEHLDKTK-------------------YPVPENFDYKEARELFLNPEVTPAEEIDLKW 300 (393)
T ss_pred HHHHHHHHHHcCCH-----HHHHHHHHhcC-------------------CCCCCCCChHHHHHHhcCCCcCCCCCCCCCC
Confidence 99999999999999 99988876431 2358899999999999999998642 27999
Q ss_pred CCCCHHHHHHHHHHhcCCChHhhhhhhHHHHHHh
Q psy14291 501 GTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKI 534 (538)
Q Consensus 501 ~~PD~~~L~~fl~~~~ew~~~kvd~~l~Pll~~~ 534 (538)
..||.++|++||.++++|+.++|++.|.++.+..
T Consensus 301 ~~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~~~ 334 (393)
T PTZ00217 301 NEPDEEGLKKFLVKEKNFNEERVEKYIERLKKAK 334 (393)
T ss_pred CCCCHHHHHHHHHhccCCCHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999998877654
No 2
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=100.00 E-value=5.9e-55 Score=449.66 Aligned_cols=312 Identities=34% Similarity=0.535 Sum_probs=250.0
Q ss_pred hchhchHHHhhhcCcccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHhcC
Q psy14291 110 MGVNGLWKLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGG 189 (538)
Q Consensus 110 MGi~GLw~~l~~~~~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 189 (538)
|||+|||++|++.++++++++|+|++||||+|+|+|+...++.... ...+...+|+
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~gk~laID~~~~l~r~~~a~~~~~---------------~~~g~~~~~l--------- 56 (316)
T cd00128 1 MGIKGLWPLLKPVARPVHLEELRGKKVAIDASIWLYQFLKACRQEL---------------GSGGETTSHL--------- 56 (316)
T ss_pred CchhhHHHHHHhhCCCCCHHHhCCcEEEecHHHHHHHHHHHhhhhc---------------cCCCCCcHHH---------
Confidence 9999999999999999999999999999999999998776653321 0123344555
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhh
Q psy14291 190 KEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLAS 269 (538)
Q Consensus 190 ~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~ 269 (538)
.+||+|+.+|+ ..||+| +|||||..|+.|..+..+|++++.+...+......
T Consensus 57 -----------~~~~~rl~~L~----~~~i~p-------------vfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~ 108 (316)
T cd00128 57 -----------QGFFYRTCRLL----ELGIKP-------------VFVFDGKPPPLKAETLAKRRERREEAEEEAKEALE 108 (316)
T ss_pred -----------HHHHHHHHHHH----HCCCEE-------------EEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888866554 455666 99999999999999999888775443322211110
Q ss_pred cccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcc-hHhHHHHHHHHHHcCCCcccCcchHHHHHHHH
Q psy14291 270 TITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYV-SRKMLEAQELLQLFGVPFIVAPGEAEAQCASL 348 (538)
Q Consensus 270 ~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~l-t~q~~~ik~lL~~~GIp~i~APgEADaqiA~L 348 (538)
.. ...++ + .+.++...+ ..++..++++|+.+||||++||+|||||||+|
T Consensus 109 ---------------~~--------~~~~~-~------~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l 158 (316)
T cd00128 109 ---------------KG--------LEEEA-K------KLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYL 158 (316)
T ss_pred ---------------hC--------CHHHH-H------HHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHH
Confidence 00 00000 0 011222334 45567999999999999999999999999999
Q ss_pred HhhcCCCceEecCCceEeecCeEEEEecCCCC-CcEEEEchhHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q psy14291 349 ELGNHTQGVITDDSDIWLFGARTVYKNFFDKK-SHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALE 427 (538)
Q Consensus 349 a~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~-~~~~~~~~~~i~~~~gl~~~q~idl~~L~GsDyipGVpGIG~KtA~k 427 (538)
++.|.+++|+|+|||+++||+.+++++++... ..+++|+.+++.+.+|++++||+|+|+|+||||+|||||||+|||++
T Consensus 159 ~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv~giG~k~A~~ 238 (316)
T cd00128 159 AKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLGCDYTEGIPGIGPVTALK 238 (316)
T ss_pred HhCCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHH
Confidence 99999999999999999999999999876443 36889999999999999999999999999999999999999999999
Q ss_pred HHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcccccCCCCCHHH
Q psy14291 428 ILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDG 507 (538)
Q Consensus 428 LL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~~~w~~PD~~~ 507 (538)
||++||++ +++++++.+ +. ...+..|++..+.++|.+|.+..+...+.|..||.++
T Consensus 239 li~~~~~~-----~~~~~~l~~-----------------~~--~~~~~~~~~~~~~~~f~~p~~~~~~~~~~~~~p~~~~ 294 (316)
T cd00128 239 LIKKYGDI-----EKDIERLKK-----------------KL--YRSPEDFPLKEAREFFLNPEVTDDFIDLRWRDPDEEG 294 (316)
T ss_pred HHHHcCCh-----HHHHHHHHH-----------------hC--ccCCCcCChHHHHHHHcCCCCCCCCCceeecCCCHHH
Confidence 99999999 777665532 11 1235789999999999999988776678999999999
Q ss_pred HHHHHHHhcCCChHhhhhhh
Q psy14291 508 LRRFAANKFGWSQNRVDQTL 527 (538)
Q Consensus 508 L~~fl~~~~ew~~~kvd~~l 527 (538)
|+.|+...++|+.+++...+
T Consensus 295 l~~~~~~~~~~~~~rv~~~~ 314 (316)
T cd00128 295 IIEFLCKEHGFNEDRVLKPL 314 (316)
T ss_pred HHHHccCCCCCCHHHHHhhh
Confidence 99999999999988887654
No 3
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=1.4e-54 Score=451.61 Aligned_cols=314 Identities=25% Similarity=0.403 Sum_probs=249.2
Q ss_pred hchhchHHHhhhcCcccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHhcC
Q psy14291 110 MGVNGLWKLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGG 189 (538)
Q Consensus 110 MGi~GLw~~l~~~~~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 189 (538)
||| |||++|+ .++++++.|+|+++|||+|+|||++..+++.. ++..+.++ .+..++|+
T Consensus 1 MGi-~l~~~~~--~~~~~l~~~~gk~vaIDas~~L~r~~~a~~~~-~g~~l~~~---------~G~~t~~l--------- 58 (338)
T TIGR03674 1 MGV-DLRDLLA--KEEIELEDLSGKVVAVDAFNALYQFLSSIRQP-DGTPLMDS---------RGRITSHL--------- 58 (338)
T ss_pred CCC-ChHHHhc--cCccCHHHhCCCEEEEeHHHHHHHHHHHHhcc-ccchhhhc---------cCCCcHHH---------
Confidence 999 9999999 89999999999999999999999887766432 12233221 23334566
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhh
Q psy14291 190 KEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLAS 269 (538)
Q Consensus 190 ~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~ 269 (538)
.+||+|+.+| +..||+| ++||||.+|+.|..++++|+.++++-.+++...
T Consensus 59 -----------~g~~~~~~~l----l~~~i~P-------------v~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~-- 108 (338)
T TIGR03674 59 -----------SGLFYRTINL----LENGIKP-------------VYVFDGKPPELKAETLEERREIREEAEEKWEEA-- 108 (338)
T ss_pred -----------HHHHHHHHHH----HHCCCeE-------------EEEECCCChhhhHhhHHHHHHHHHHHHHHHHHH--
Confidence 6788886655 4556677 999999999999999999987754333322211
Q ss_pred cccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHh-HHHHHHHHHHcCCCcccCcchHHHHHHHH
Q psy14291 270 TITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRK-MLEAQELLQLFGVPFIVAPGEAEAQCASL 348 (538)
Q Consensus 270 ~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q-~~~ik~lL~~~GIp~i~APgEADaqiA~L 348 (538)
++. +...++. .+.++...++.+ +..++++|++|||||++||||||||||+|
T Consensus 109 -------------~~~--------g~~~~a~-------~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L 160 (338)
T TIGR03674 109 -------------LEK--------GDLEEAR-------KYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYM 160 (338)
T ss_pred -------------HHc--------CCHHHHH-------HHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHH
Confidence 110 0111111 111233455544 46999999999999999999999999999
Q ss_pred HhhcCCCceEecCCceEeecCeEEEEecCCCCC------------cEEEEchhHHHHHhCCCHHHHHHHHHHcCCCCCCC
Q psy14291 349 ELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS------------HVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPG 416 (538)
Q Consensus 349 a~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~------------~~~~~~~~~i~~~~gl~~~q~idl~~L~GsDyipG 416 (538)
++.|.+|+|+|+|+|+++||+++++++++..++ ..+.|+.+.+.+.+|++++||+|+|+|+||||+||
T Consensus 161 ~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~dyn~G 240 (338)
T TIGR03674 161 AKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGTDYNEG 240 (338)
T ss_pred HHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCC
Confidence 999999999999999999999999988754322 35679999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcc
Q psy14291 417 LQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQ 496 (538)
Q Consensus 417 VpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~ 496 (538)
|||||+|||++||++||++ ++|+++++. .++ +..+++++|++|++..+ .
T Consensus 241 v~GIG~ktA~kli~~~gsi-----e~il~~~~~----------------------~~~---~~~~~~~~f~~~~v~~~-~ 289 (338)
T TIGR03674 241 VKGIGPKTALKLIKEHGDL-----EKVLKARGE----------------------DIE---NYDEIREFFLNPPVTDD-Y 289 (338)
T ss_pred CCCccHHHHHHHHHHcCCH-----HHHHHhhcC----------------------CCC---CHHHHHHHhCCCCCCCC-C
Confidence 9999999999999999999 888876421 012 12699999999999876 5
Q ss_pred cccCCCCCHHHHHHHHHHhcCCChHhhhhhhHHHHHHh
Q psy14291 497 KLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKI 534 (538)
Q Consensus 497 ~~~w~~PD~~~L~~fl~~~~ew~~~kvd~~l~Pll~~~ 534 (538)
++.|..||.++|++|+.++++|+.++|++.+.++.+..
T Consensus 290 ~~~~~~pd~e~l~~fl~~e~~~~~~rv~~~~~~l~~~~ 327 (338)
T TIGR03674 290 ELKWRKPDKEGIIEFLCDEHDFSEDRVERALERLEAAY 327 (338)
T ss_pred CccCCCCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHhh
Confidence 78999999999999887779999999999999997764
No 4
>KOG2519|consensus
Probab=100.00 E-value=1.3e-47 Score=402.36 Aligned_cols=323 Identities=26% Similarity=0.407 Sum_probs=255.3
Q ss_pred hchhchH----HHhhhcCcccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHH
Q psy14291 110 MGVNGLW----KLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEE 185 (538)
Q Consensus 110 MGi~GLw----~~l~~~~~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 185 (538)
|||+||. ....+..|..+++.|+|++||||+|+||++...++...+ + ..+++++||
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~~kkVAID~s~~lyqfl~~v~~~~------~---------~~~~~~~HL----- 60 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFFGKKVAIDASMWLYQFLIVVRSCR------N---------EAGEPTSHL----- 60 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhcCceEEEecceeHhhHhhhhcccc------c---------cCCCchHHH-----
Confidence 9999993 555566688999999999999999999999875553211 0 113455677
Q ss_pred HhcCcchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhh
Q psy14291 186 IAGGKEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQT 265 (538)
Q Consensus 186 ~~~~~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~ 265 (538)
++||+|.+.++ ..||+| |+||||.+|.+|..+++||-.++. +..+-.
T Consensus 61 ---------------~g~f~Rt~~l~----~~gi~P-------------v~VfDG~pP~lKs~e~~kR~~rr~-~a~~~~ 107 (449)
T KOG2519|consen 61 ---------------MGMFYRTIRLI----ENGIKP-------------VYVFDGKPPDLKSQELAKRSERRS-EADKEL 107 (449)
T ss_pred ---------------HHHHHHHHHHH----HcCCcE-------------EEEECCCCCCcchHHHHHHHHHhh-hhhhhh
Confidence 89999966555 556666 999999999999999999876643 111110
Q ss_pred hhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHhH-HHHHHHHHHcCCCcccCcchHHHH
Q psy14291 266 RLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKM-LEAQELLQLFGVPFIVAPGEAEAQ 344 (538)
Q Consensus 266 R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q~-~~ik~lL~~~GIp~i~APgEADaq 344 (538)
.-+ .++ -..+.+ ...-.+-..+|.+. .+++.+|..|||||+.||+||+||
T Consensus 108 ~~~----~e~--~~~~~~-----------------------~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EAEAq 158 (449)
T KOG2519|consen 108 KPA----KEA--GAKENM-----------------------EKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEAEAQ 158 (449)
T ss_pred hhH----HHh--hhHHHH-----------------------HHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchHHHH
Confidence 000 000 000000 01112223455554 589999999999999999999999
Q ss_pred HHHHHhhcCCCceEecCCceEeecCeEEEEecCC---CCCcEEEEchhHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCCC
Q psy14291 345 CASLELGNHTQGVITDDSDIWLFGARTVYKNFFD---KKSHVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVG 421 (538)
Q Consensus 345 iA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~---~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~GsDyipGVpGIG 421 (538)
||+|++.|.+++++|+|+|.++||++.+++++.. ....+.+|+.+.+.+.++++.++|+|+|+|+||||+++|.|||
T Consensus 159 CA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGCDYc~~I~Gig 238 (449)
T KOG2519|consen 159 CAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGCDYCPTIRGIG 238 (449)
T ss_pred HHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcCcccccccccC
Confidence 9999999999999999999999999988887632 2357899999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcc--ccc
Q psy14291 422 PVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQ--KLA 499 (538)
Q Consensus 422 ~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~--~~~ 499 (538)
+++|++||++|+++ ++|++.-.. +.+..+|.+|+...+..++.+|.+..... ++.
T Consensus 239 ~~~al~lir~~~~i-----~~ile~~~~------------------~~~~~ip~~w~~~~~r~~f~~p~~~~~~~~~~i~ 295 (449)
T KOG2519|consen 239 PKKALKLIRQHGDI-----ENILEINSD------------------LKEYPIPEDWSYKLARKLFLEPEFPNPESILDLK 295 (449)
T ss_pred hHHHHHHHHHhcCH-----HHHhhhccc------------------hhhcCCCCCccHHHHHHHhcCcccCCccceeecc
Confidence 99999999999998 888763111 12334688999999999999999887655 899
Q ss_pred CCCCCHHHHHHHHHHhcCCChHhhhhhhHHHHHHhhhc
Q psy14291 500 WGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQR 537 (538)
Q Consensus 500 w~~PD~~~L~~fl~~~~ew~~~kvd~~l~Pll~~~~~~ 537 (538)
|..||.+.+.+|+....+|+.+++...+.|+.++++-.
T Consensus 296 w~~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~ 333 (449)
T KOG2519|consen 296 WKTPDTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLG 333 (449)
T ss_pred cCCCChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccc
Confidence 99999999999999889999999999999999988653
No 5
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=4e-46 Score=380.96 Aligned_cols=257 Identities=26% Similarity=0.435 Sum_probs=209.6
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhhcccHHhHHHHH
Q psy14291 201 REMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTITEQMSREAQ 280 (538)
Q Consensus 201 ~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~~it~~m~~e~~ 280 (538)
.+||.|+.+| +..||+| +|||||.+|+.|..++++|+.++++-.+++..
T Consensus 12 ~g~~~r~~~l----l~~gi~P-------------vfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~-------------- 60 (292)
T PRK03980 12 SGIFYRTINL----LENGIKP-------------VYVFDGKPPELKAEEIEERREVREEAEEKYEE-------------- 60 (292)
T ss_pred HHHHHHHHHH----HHCCCEE-------------EEEECCCCchHHHHHHHHHHHHHHHhHHHHHH--------------
Confidence 6789996665 4556777 99999999999999999988775433322221
Q ss_pred HHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHhH-HHHHHHHHHcCCCcccCcchHHHHHHHHHhhcCCCceEe
Q psy14291 281 ELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKM-LEAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVIT 359 (538)
Q Consensus 281 kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q~-~~ik~lL~~~GIp~i~APgEADaqiA~La~~g~vd~IiS 359 (538)
++.. +..++ + .++.++...+++++ ..++++|++|||||++||||||||||+|++.|.+|+|+|
T Consensus 61 -~~~~---------g~~~~--a----~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S 124 (292)
T PRK03980 61 -AKEE---------GDLEE--A----RKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGS 124 (292)
T ss_pred -HHHc---------CCHHH--H----HHHHhccccCCHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEec
Confidence 1111 11110 0 01223455666654 699999999999999999999999999999999999999
Q ss_pred cCCceEeecCeEEEEecCCCCC------------cEEEEchhHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCCCHHHHHH
Q psy14291 360 DDSDIWLFGARTVYKNFFDKKS------------HVLRYTAPDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALE 427 (538)
Q Consensus 360 ~DsDllLfG~~~Vi~~~~~~~~------------~~~~~~~~~i~~~~gl~~~q~idl~~L~GsDyipGVpGIG~KtA~k 427 (538)
+|+|+|+||+++++++++..+. ..+.|+.+.+.+.+|++++||+|+|+|+||||+|||||||+|||++
T Consensus 125 ~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~k 204 (292)
T PRK03980 125 QDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPELIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALK 204 (292)
T ss_pred CCcCeeeecCCEEEEeecccccccCccccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHH
Confidence 9999999999999998753321 3568999999999999999999999999999999999999999999
Q ss_pred HHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCC-HHHHHhhcCCCCCCCcccccCCCCCHH
Q psy14291 428 ILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPN-VSVIEAYLKPDINTNVQKLAWGTPDLD 506 (538)
Q Consensus 428 LL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps-~~lv~ly~dp~v~~s~~~~~w~~PD~~ 506 (538)
||++||++ ++|++.+ +..+++ .++.++|.+|+|.. ..++.|..||.+
T Consensus 205 Li~~~~sl-----e~i~~~~--------------------------~~~~~~~~~~r~~f~~p~v~~-~~~~~~~~pd~~ 252 (292)
T PRK03980 205 LIKKHGDL-----EKVLEER--------------------------GFEIENYDEIREFFLNPPVTD-DYELKWKEPDKE 252 (292)
T ss_pred HHHHCCCH-----HHHHHhc--------------------------cCCCCCHHHHHHHhcCCCCCC-CCCccCCCCCHH
Confidence 99999999 8887521 223555 78999999999986 457999999999
Q ss_pred HHHHHHHHhcCCChHhhhhhhHHHHHHhhh
Q psy14291 507 GLRRFAANKFGWSQNRVDQTLIPIMKKISQ 536 (538)
Q Consensus 507 ~L~~fl~~~~ew~~~kvd~~l~Pll~~~~~ 536 (538)
+|++|+.++.+|+.++|++.+.++.+.+++
T Consensus 253 ~l~~fl~~e~~f~~~rv~~~~~~l~~~~~~ 282 (292)
T PRK03980 253 GIIEFLVEEHDFSEERVKKALERLEKAVKE 282 (292)
T ss_pred HHHHHHhccCCCCHHHHHHHHHHHHHHhcc
Confidence 999999988999999999999999988764
No 6
>KOG2518|consensus
Probab=100.00 E-value=3.9e-47 Score=402.69 Aligned_cols=243 Identities=28% Similarity=0.348 Sum_probs=203.7
Q ss_pred hchhchHHHhhhcCcccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHhcC
Q psy14291 110 MGVNGLWKLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGG 189 (538)
Q Consensus 110 MGi~GLw~~l~~~~~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 189 (538)
|||+||+++|+++.+++|+++|+|++||||+|||||+++-++++ + +. ++-||..||+|
T Consensus 1 MGI~GLlp~~k~~~~~~hi~~~~g~tvavD~y~WLhrg~~~Ca~------------e-l~--~~~pT~ryi~y------- 58 (556)
T KOG2518|consen 1 MGIQGLLPLLKPALKPIHISEYKGKTVAVDGYCWLHRGALACAE------------K-LA--KGKPTDRYIQF------- 58 (556)
T ss_pred CCcchhHHHHHHHhhhhhHHHhcCceEEEehhhHHhhhHHhHHH------------H-Hh--cCCChHHHHHH-------
Confidence 99999999999999999999999999999999999976644433 1 21 34578888866
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhh
Q psy14291 190 KEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLAS 269 (538)
Q Consensus 190 ~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~ 269 (538)
|++| +.+|..+||+| |.||||++.+.|+.|..+||+++++..
T Consensus 59 -------------~ik~----v~lL~~~gikP-------------ilVFDG~~LP~K~~te~~Rr~~R~~n~-------- 100 (556)
T KOG2518|consen 59 -------------FIKR----VKLLLSYGIKP-------------ILVFDGDPLPSKKETERKRRERRKKNL-------- 100 (556)
T ss_pred -------------HHHH----HHHHHhcCCeE-------------EEEecCCCcccccccchHHHHHHHHhH--------
Confidence 5667 55566778888 999999999999999999998865443
Q ss_pred cccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHhHH-HHHHHHHHcCCCcccCcchHHHHHHHH
Q psy14291 270 TITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASL 348 (538)
Q Consensus 270 ~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q~~-~ik~lL~~~GIp~i~APgEADaqiA~L 348 (538)
.++++||..++ +++|.-. -.+...+|+.|. .+.+.|+..||+||+||||||||+|||
T Consensus 101 -------~~a~~ll~~G~--------~~~A~~~-------fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL 158 (556)
T KOG2518|consen 101 -------DAAEQLLAEGK--------ESNAREC-------FQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYL 158 (556)
T ss_pred -------HHHHHHHHcCC--------HHHHHHH-------HHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHH
Confidence 34555655433 2332221 245688999997 789999999999999999999999999
Q ss_pred HhhcCCCceEecCCceEeecCeEEEEecCCCCCcEEEEchhHHHHHhC----CCHHHHHHHHHHcCCCCCCCCCCCCHHH
Q psy14291 349 ELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYYFE----LTREKLIQLALLVGSDYTPGLQGVGPVT 424 (538)
Q Consensus 349 a~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~~~~~~~~~~i~~~~g----l~~~q~idl~~L~GsDyipGVpGIG~Kt 424 (538)
++.|.+|||||+|||+++|||..||+++.. .+++..++...+...++ ++.++|..||+|+||||++||||||.+|
T Consensus 159 ~~~~~i~~IITEDSDLl~fGc~~vifK~d~-~G~~le~~~~~l~~~~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~t 237 (556)
T KOG2518|consen 159 EREGIVDAIITEDSDLLVFGCKKVIFKMDS-FGNGLEINRSKLPECKPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLAT 237 (556)
T ss_pred HhcCcceEEEeccccccccCchhheeeccC-CCCcccccHhhhhhccccccccCHHHHHHHHHhcCCcccccCccccHHH
Confidence 999999999999999999999999999853 56678888888877654 5689999999999999999999999999
Q ss_pred HHHHHHHcCCC
Q psy14291 425 ALEILAKFSPS 435 (538)
Q Consensus 425 A~kLL~~ygsl 435 (538)
|+++|+.|.+.
T Consensus 238 A~k~l~k~~~~ 248 (556)
T KOG2518|consen 238 AHKLLSKYNTP 248 (556)
T ss_pred HHHHHHhcCcH
Confidence 99999999998
No 7
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=5.8e-42 Score=392.40 Aligned_cols=220 Identities=49% Similarity=0.880 Sum_probs=192.7
Q ss_pred cCCCCcchHhHH-HHHHHHHHcCCCcccCcchHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecCCCCCcEEEEch
Q psy14291 310 KKRRPYVSRKML-EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTA 388 (538)
Q Consensus 310 k~rr~~lt~q~~-~ik~lL~~~GIp~i~APgEADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~~~~~~~~ 388 (538)
.++...+|.+|. .|+++|+.||||||+||||||||||+|++.|.+|+|+|+|+|+|+||+++||++++..+..+.+|+.
T Consensus 763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~~~~ve~~~~ 842 (1034)
T TIGR00600 763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQY 842 (1034)
T ss_pred ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCCCCceEEeeH
Confidence 455678999985 9999999999999999999999999999999999999999999999999999998877777899999
Q ss_pred hHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcC--------CC
Q psy14291 389 PDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKN--------KP 460 (538)
Q Consensus 389 ~~i~~~~gl~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~--------~~ 460 (538)
+++.+.+|++++||+++|+|+||||++||+|||+|||++||++||+. + ++.|.+|+.||.... ..
T Consensus 843 ~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~------~-le~L~~f~~w~~~~~~~~~~~~~~~ 915 (1034)
T TIGR00600 843 VDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGD------G-LEPLLKFKEWWHEAQKDKKKRENPN 915 (1034)
T ss_pred HHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCC------C-HHHHHHHHHHHHHhhhccccccccc
Confidence 99999999999999999999999999999999999999999999962 1 246677888876511 01
Q ss_pred ChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcccccCCCCCHHHHHHHHHHhcCCChHhhhhhhHHHHHHhhh
Q psy14291 461 DTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQ 536 (538)
Q Consensus 461 ~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~~~w~~PD~~~L~~fl~~~~ew~~~kvd~~l~Pll~~~~~ 536 (538)
....+.+.....++.+||+..+..+|++|.|+.+...|.|+.||+++|+.||.++++|+.++|++.|.|++++..+
T Consensus 916 ~~~~~~~~~~~~lp~~FP~~~V~~~yl~P~V~~~~~~f~W~~PD~e~L~~Fl~~~~gws~eRv~~~l~plikk~~~ 991 (1034)
T TIGR00600 916 DTKVKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNA 991 (1034)
T ss_pred hhhhhhcccccccCCCCCcHHHHHHhcCCCCCCCcCCCCCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHc
Confidence 1112222333457999999999999999999988788999999999999999999999999999999999997653
No 8
>KOG2520|consensus
Probab=100.00 E-value=1.2e-39 Score=363.45 Aligned_cols=219 Identities=49% Similarity=0.889 Sum_probs=201.9
Q ss_pred cCCCCcchHhH-HHHHHHHHHcCCCcccCcchHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecCCCCCcEEEEch
Q psy14291 310 KKRRPYVSRKM-LEAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTA 388 (538)
Q Consensus 310 k~rr~~lt~q~-~~ik~lL~~~GIp~i~APgEADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~~~~~~~~ 388 (538)
++...+++.+| .+||++|+.||||||+||+|||||||.|.+.+.+|||||+|||+||||+++||+++|.+++++..|..
T Consensus 457 ~r~~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~knk~ve~y~~ 536 (815)
T KOG2520|consen 457 SRGADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKNKYVEKYQL 536 (815)
T ss_pred hccCchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcCccceeeeh
Confidence 34456688777 59999999999999999999999999999999999999999999999999999999999889999999
Q ss_pred hHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhc--------CCC
Q psy14291 389 PDIRYYFELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKK--------NKP 460 (538)
Q Consensus 389 ~~i~~~~gl~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~--------~~~ 460 (538)
++|...||+++..+|-++.|+||||+.||+|||+++|+++|.+|++- ++|..|+.|++.. +..
T Consensus 537 ~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~---------~~l~~f~~w~~~~~~~~~~~~s~~ 607 (815)
T KOG2520|consen 537 DDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGD---------ENLLKFKKWVQQTGPADKEVGSTQ 607 (815)
T ss_pred HHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCc---------chhHHHHHHHHHhCccccccccHH
Confidence 99999999999999999999999999999999999999999999975 4588999998762 112
Q ss_pred ChhhhHhhhh--ccCCCCCCCHHHHHhhcCCCCCCCcccccCCCCCHHHHHHHHHHhcCCChHhhhhhhHHHHHHhhhc
Q psy14291 461 DTHLTRKLRN--VKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQNRVDQTLIPIMKKISQR 537 (538)
Q Consensus 461 ~~~lr~kL~~--~~i~~~fps~~lv~ly~dp~v~~s~~~~~w~~PD~~~L~~fl~~~~ew~~~kvd~~l~Pll~~~~~~ 537 (538)
...+++|+.+ ..++..||++.++.+|+.|.|+.+.+.|.|+.||++.|++||++.|||+..++++.++|++++++++
T Consensus 608 ~~~lrkkl~n~~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~pdl~~lRef~~~~fgW~~~kT~~~l~p~~~~~~~~ 686 (815)
T KOG2520|consen 608 QKMLRKKLKNPKIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGKPDLDILREFMKRLFGWPDEKTDEELIPVIKRLEKK 686 (815)
T ss_pred HHHHHHHhcCcccccCcCCCchhHHHHhhCCccCCCcccccCCCCCHHHHHHHHHHHcCCCccccchhhhhhHHHHHHH
Confidence 4566778887 5678999999999999999999999999999999999999999999999999999999999999875
No 9
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=4.2e-36 Score=305.85 Aligned_cols=195 Identities=19% Similarity=0.303 Sum_probs=165.2
Q ss_pred ccccCCCCc----chHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHHHhhcCCCc----eEecCCceE-eecCeEEEEec
Q psy14291 307 GTDKKRRPY----VSRKMLEAQELLQLFGVPFIVAPG-EAEAQCASLELGNHTQG----VITDDSDIW-LFGARTVYKNF 376 (538)
Q Consensus 307 ~~~k~rr~~----lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~La~~g~vd~----IiS~DsDll-LfG~~~Vi~~~ 376 (538)
+.||++|.+ +..|++.++++|+++|||++.+|| ||||+||+|+++....+ |+|+|+|++ +.+....+...
T Consensus 75 p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~ 154 (281)
T PRK14976 75 DEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLK 154 (281)
T ss_pred HHHhcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEe
Confidence 344555532 567888999999999999999998 99999999998854433 899999999 55543333322
Q ss_pred CCCCCcEEEEchhHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHH
Q psy14291 377 FDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWL 454 (538)
Q Consensus 377 ~~~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~ 454 (538)
... .....++.+.+.+++|++|+||+|+++|+| |||+|||||||+|||.+||++||++ ++|+++++++++
T Consensus 155 ~~~-~~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsl-----e~i~~~~~~~~~-- 226 (281)
T PRK14976 155 KKG-TSHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNI-----ENIYENIDKIKK-- 226 (281)
T ss_pred cCC-CCcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCH-----HHHHHhHHHHhH--
Confidence 222 225789999999999999999999999999 9999999999999999999999999 999999999864
Q ss_pred hhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcccccCCCCCHHHHHHHHHHhcCCC
Q psy14291 455 AKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWS 519 (538)
Q Consensus 455 ~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~~~w~~PD~~~L~~fl~~~~ew~ 519 (538)
+++++|.+.. +.++.|++|+++.+|.+++.+++++.+.++|.++|+++|++ ++|+
T Consensus 227 --------~~~~~L~~~~-~~~~~s~~L~~l~~d~~l~~~l~~~~~~~~~~~~l~~~~~~-~e~~ 281 (281)
T PRK14976 227 --------KIKNKLSEAK-EKALLSKKLATIKTDVPLDFQIEDIKLKKLDQPELKKIFEE-LELK 281 (281)
T ss_pred --------HHHHHHHHhH-HHHHHhhhhhEEeecCCCCCCHHHhccCCCCHHHHHHHHHH-cCCC
Confidence 3566888874 88899999999999999999988999999999999999998 8874
No 10
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.3e-33 Score=284.63 Aligned_cols=207 Identities=22% Similarity=0.310 Sum_probs=168.3
Q ss_pred HHHHHHHHHhhCC--cEEeCCCchhhhhhhhhhccccCCCCc----chHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHH
Q psy14291 276 SREAQELLQLFGV--PFIVAPGEAEAQCASLELGTDKKRRPY----VSRKMLEAQELLQLFGVPFIVAPG-EAEAQCASL 348 (538)
Q Consensus 276 ~~e~~kLL~~~g~--P~iv~d~Eaeaqca~l~~~~~k~rr~~----lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~L 348 (538)
.....++++.+.+ .+++||+... +=|+..++.||++|.+ +..|++.++++|+++|||++.+|+ ||||+||+|
T Consensus 37 ~~~l~~l~~~~~p~~~~~~fD~~~~-~~R~~l~p~YKa~R~~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatl 115 (259)
T smart00475 37 LRMLLKLIKEEKPTYVAVVFDAKGK-TFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATL 115 (259)
T ss_pred HHHHHHHHHHcCCCeEEEEEeCCCC-ccccchhHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHH
Confidence 3345566666655 5778987532 2388889999999865 667889999999999999999998 999999999
Q ss_pred HhhcCC----CceEecCCceE-eecCeEEEEecCCCCCcEEEEchhHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCCC
Q psy14291 349 ELGNHT----QGVITDDSDIW-LFGARTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVG 421 (538)
Q Consensus 349 a~~g~v----d~IiS~DsDll-LfG~~~Vi~~~~~~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~G--sDyipGVpGIG 421 (538)
++++.. ..|+|+|+|++ +++....++...........++.+.+.++||++|+||+|+++|+| |||+|||||||
T Consensus 116 a~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG 195 (259)
T smart00475 116 AKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIG 195 (259)
T ss_pred HHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCC
Confidence 997443 34999999999 444433333332222335789999999999999999999999999 99999999999
Q ss_pred HHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCccccc
Q psy14291 422 PVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLA 499 (538)
Q Consensus 422 ~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~~~ 499 (538)
+|||.+||++||++ ++|+++++++++ +++++|.++. +.++.|++|+++.++.+++.+++++.
T Consensus 196 ~KtA~~Ll~~ygsl-----e~i~~~~~~~~~----------~~~~~l~~~~-~~~~ls~~L~~l~~d~~l~~~~~~~~ 257 (259)
T smart00475 196 EKTAAKLLKEFGSL-----ENILENLDKLKK----------KLREKLLAHK-EDAKLSRKLATIETDVPLEVDLEDLR 257 (259)
T ss_pred HHHHHHHHHHhCCH-----HHHHHHHHHHHH----------HHHHHHHhcH-HHHHHhhhhheeeeCCCCCCCHHHhc
Confidence 99999999999999 999999999864 3466888874 88999999999999988876655544
No 11
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.98 E-value=2e-32 Score=275.03 Aligned_cols=205 Identities=21% Similarity=0.284 Sum_probs=170.1
Q ss_pred HHHHHHHHHhhCC--cEEeCCCchhh-hhhhhhhccccCCCCc----chHhHHHHHHHHHHcCCCcccCcc-hHHHHHHH
Q psy14291 276 SREAQELLQLFGV--PFIVAPGEAEA-QCASLELGTDKKRRPY----VSRKMLEAQELLQLFGVPFIVAPG-EAEAQCAS 347 (538)
Q Consensus 276 ~~e~~kLL~~~g~--P~iv~d~Eaea-qca~l~~~~~k~rr~~----lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~ 347 (538)
.+...++++.+++ -+++||+.... .-|+..|+.||++|.+ +..|++.++++|.++||+++..|| ||||+||+
T Consensus 35 ~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIat 114 (256)
T PRK09482 35 QHALDKLIRHSQPTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIAT 114 (256)
T ss_pred HHHHHHHHHHcCCCEEEEEEeCCCCCcccHHHHhHHHhcCCCCCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHH
Confidence 3345677777776 45678875431 1388889999999965 567788999999999999999999 99999999
Q ss_pred HHhhcCCCc----eEecCCceE-eecCeEEEEecCCCCCcEEEEchhHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCC
Q psy14291 348 LELGNHTQG----VITDDSDIW-LFGARTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGV 420 (538)
Q Consensus 348 La~~g~vd~----IiS~DsDll-LfG~~~Vi~~~~~~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~G--sDyipGVpGI 420 (538)
|+++....+ |+|.|+|++ |++....+++.. ...+++.+.+.++||++|+|++|+++|+| |||+||||||
T Consensus 115 la~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~----~~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGI 190 (256)
T PRK09482 115 LAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYF----QKRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGI 190 (256)
T ss_pred HHHHHHHCCCeEEEEECCCCccccCCCCeEEEecc----ccccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCc
Confidence 998755443 899999999 887544334332 13468999999999999999999999999 9999999999
Q ss_pred CHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcccccC
Q psy14291 421 GPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAW 500 (538)
Q Consensus 421 G~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~~~w 500 (538)
|+|||.+||++||++ ++|++++++++. +++++|.++. +.++.|++|+++.+|.+++.+++++++
T Consensus 191 G~KtA~~LL~~~gsl-----e~i~~~~~~~~~----------~~~~~L~~~~-~~a~lsr~L~~l~~dv~l~~~l~~l~~ 254 (256)
T PRK09482 191 GPKSAAELLNQFRSL-----ENIYESLDALPE----------KWRKKLEEHK-EMARLCRKLAQLQTDLPLGGNLQQLRL 254 (256)
T ss_pred ChHHHHHHHHHhCCH-----HHHHHhHHHhhH----------HHHHHHHHhH-HHHHHHHhhheEeeCCCCCCCHHHhcc
Confidence 999999999999999 999999999864 3466888874 889999999999999999877766665
No 12
>PRK05755 DNA polymerase I; Provisional
Probab=99.98 E-value=8.4e-32 Score=310.92 Aligned_cols=196 Identities=22% Similarity=0.350 Sum_probs=166.3
Q ss_pred hccccCCCCc----chHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHHHhh----cCCCceEecCCceE-eecC-eEEEE
Q psy14291 306 LGTDKKRRPY----VSRKMLEAQELLQLFGVPFIVAPG-EAEAQCASLELG----NHTQGVITDDSDIW-LFGA-RTVYK 374 (538)
Q Consensus 306 ~~~~k~rr~~----lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~La~~----g~vd~IiS~DsDll-LfG~-~~Vi~ 374 (538)
|+.||++|++ +..|++.++++|+++||+++.+|| ||||+||+|+++ |....|+|+|+|++ +++. ..++.
T Consensus 70 ~~~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~~ 149 (880)
T PRK05755 70 YPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLD 149 (880)
T ss_pred CHHHhCCCCCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEee
Confidence 3445555533 567889999999999999999998 999999999975 33446999999999 5543 34444
Q ss_pred ecCCCCCcEEEEchhHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHH
Q psy14291 375 NFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKN 452 (538)
Q Consensus 375 ~~~~~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~ 452 (538)
.+ . .+....++.+.+.++||++|+|++|+++|+| |||+|||||||+|||.+||++||++ |+|+++++++++
T Consensus 150 ~~-~-~~~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsl-----e~i~~~~~~~~~ 222 (880)
T PRK05755 150 TM-G-VSKNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSL-----EGLYENLDEIKG 222 (880)
T ss_pred cc-C-CCCCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCH-----HHHHHhHHHhch
Confidence 32 1 1245789999999999999999999999999 9999999999999999999999999 999999998864
Q ss_pred HHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcccccCCCCCHHHHHHHHHHhcCCCh
Q psy14291 453 WLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRRFAANKFGWSQ 520 (538)
Q Consensus 453 ~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~~~w~~PD~~~L~~fl~~~~ew~~ 520 (538)
. ++++|.+.. +.+++|++|+++++|++++.+..++.|..||.++|.+||++ ++|+.
T Consensus 223 ~----------~~~~l~~~~-~~~~ls~~l~~l~~d~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~ 278 (880)
T PRK05755 223 K----------KKEKLRENK-EQAFLSRKLATIKTDVPLEVDLEDLELQPPDREKLIALFKE-LEFKS 278 (880)
T ss_pred H----------HHHHHHHhH-HHHHhhhhhheeeeCCCCCCCHHHhccCCCCHHHHHHHHHH-hCcHH
Confidence 3 456787764 88999999999999999998888899999999999999977 99876
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=99.98 E-value=3.7e-32 Score=312.29 Aligned_cols=225 Identities=21% Similarity=0.293 Sum_probs=188.4
Q ss_pred HHHHHHHhhCC--cEEeCCCchhhhhhhhhhccccCCCCc----chHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHHHh
Q psy14291 278 EAQELLQLFGV--PFIVAPGEAEAQCASLELGTDKKRRPY----VSRKMLEAQELLQLFGVPFIVAPG-EAEAQCASLEL 350 (538)
Q Consensus 278 e~~kLL~~~g~--P~iv~d~Eaeaqca~l~~~~~k~rr~~----lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~La~ 350 (538)
...++++..++ .+++||+... .=|+..|+.||++|++ +..|++.++++|+++|||++.+|| ||||+||+|++
T Consensus 39 ~l~~ll~~~~p~~i~v~FD~~~~-tfR~~~~~~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~ 117 (887)
T TIGR00593 39 MLLKLLKEEKPTYVAVAFDSGTP-TFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAK 117 (887)
T ss_pred HHHHHHHhcCCCEEEEEEcCCCC-cchHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHH
Confidence 44566666665 4678887542 2288889999999964 667789999999999999999999 99999999998
Q ss_pred hcC----CCceEecCCceE-eecCeEEEEecCCCCCcEEEEchhHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCCCHH
Q psy14291 351 GNH----TQGVITDDSDIW-LFGARTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPV 423 (538)
Q Consensus 351 ~g~----vd~IiS~DsDll-LfG~~~Vi~~~~~~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~G--sDyipGVpGIG~K 423 (538)
++. ...|+|+|+|++ |++....+.+... +.....|+.+.|.++||++|+||+|+++|+| |||+|||||||+|
T Consensus 118 ~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~~~-~~~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~K 196 (887)
T TIGR00593 118 QAEKEGYEVRIISGDKDLLQLVSDNVKVLIPKG-KTSFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEK 196 (887)
T ss_pred HHHhCCCcEEEEECCCChhhcCCCCEEEEeccC-CCCceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHH
Confidence 744 335999999999 5554333332211 1135679999999999999999999999999 8999999999999
Q ss_pred HHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCcccccCCCC
Q psy14291 424 TALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQKLAWGTP 503 (538)
Q Consensus 424 tA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~~~w~~P 503 (538)
||.+||++|||+ |+|+++++++++. +++++|+++. +.++.|++|+++.+|.+++.+.+++.+..|
T Consensus 197 tA~kLL~~ygsl-----e~i~~~~~~i~~~---------k~~~~L~~~~-e~a~ls~~L~ti~~d~~l~~~~~~~~~~~~ 261 (887)
T TIGR00593 197 TAAKLLQEFGSL-----ENIYENLDQIKSA---------KMREKLIAHK-EDAFLSKELATIVTDVPLEVDLEDLRLSEP 261 (887)
T ss_pred HHHHHHHHcCCH-----HHHHHHHHHhccH---------HHHHHHHHhH-HHHHHHHHhheeecCCCCCCCHHHhccCCC
Confidence 999999999999 9999999998542 3567888874 889999999999999999988888999999
Q ss_pred CHHHHHHHHHHhcCCCh
Q psy14291 504 DLDGLRRFAANKFGWSQ 520 (538)
Q Consensus 504 D~~~L~~fl~~~~ew~~ 520 (538)
|.+++.+||.+ ++|++
T Consensus 262 ~~~~l~~~~~~-lef~~ 277 (887)
T TIGR00593 262 DRERLYALLQE-LEFKS 277 (887)
T ss_pred CHHHHHHHHHH-hCCcc
Confidence 99999999998 99975
No 14
>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=99.98 E-value=8.9e-32 Score=268.41 Aligned_cols=150 Identities=22% Similarity=0.368 Sum_probs=127.5
Q ss_pred chHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHHHhhcCCC----ceEecCCceEee-cCeEEEEecCCCCCcEEEEchh
Q psy14291 316 VSRKMLEAQELLQLFGVPFIVAPG-EAEAQCASLELGNHTQ----GVITDDSDIWLF-GARTVYKNFFDKKSHVLRYTAP 389 (538)
Q Consensus 316 lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~La~~g~vd----~IiS~DsDllLf-G~~~Vi~~~~~~~~~~~~~~~~ 389 (538)
+..|++.++++|+++|||++.+|+ ||||+||+|++++..+ .|+|+|+|++.+ +....+.+.. ....++.+
T Consensus 83 l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~~~----~~~~i~~~ 158 (240)
T cd00008 83 LREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSPM----KKKLVTEE 158 (240)
T ss_pred HHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEeCC----CceEEeHH
Confidence 567788999999999999999998 9999999999865544 499999999955 5544444321 24689999
Q ss_pred HHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHh
Q psy14291 390 DIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRK 467 (538)
Q Consensus 390 ~i~~~~gl~~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~k 467 (538)
.+.+++|++|+|++|+++|+| |||+|||||||+|||.+||++||++ |+|++++++++. +++++
T Consensus 159 ~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsl-----e~i~~~~~~~~~----------~~~~~ 223 (240)
T cd00008 159 NVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSL-----EGILENLDKIKG----------KLREK 223 (240)
T ss_pred HHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCH-----HHHHHhHHHHhH----------HHHHH
Confidence 999999999999999999999 9999999999999999999999999 999999988754 34567
Q ss_pred hhhccCCCCCCCHHHHHh
Q psy14291 468 LRNVKLNDDFPNVSVIEA 485 (538)
Q Consensus 468 L~~~~i~~~fps~~lv~l 485 (538)
|.++. +.++.|++|+++
T Consensus 224 l~~~~-~~~~~s~~L~~l 240 (240)
T cd00008 224 LEEGK-EMAFLSKRLATI 240 (240)
T ss_pred HHHhH-HHHHHHHHhhcC
Confidence 77764 778888888764
No 15
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.97 E-value=2.7e-31 Score=273.68 Aligned_cols=279 Identities=20% Similarity=0.238 Sum_probs=203.3
Q ss_pred cccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHhcCcchhhHHHHHHHHH
Q psy14291 124 KPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGGKEEKTEKIKLTREM 203 (538)
Q Consensus 124 ~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 203 (538)
+.++.....|+.++||++.|++++..++.-.- ++. .+.++. -+.-...|
T Consensus 2 ~~~~~~~~~~~l~~IDg~~~lyr~~~a~~~~~-~~~------------~g~~~~------------------~~~~~~~~ 50 (310)
T COG0258 2 REIQLMNKSGKLLLIDGSSLLYRALHALPQPL-GNP------------LGDPTG------------------AVSGFLGM 50 (310)
T ss_pred CcccchhccCcEEEEechHHHHHHHHhcchhc-CCC------------CCCCcc------------------HHHHHHHH
Confidence 45677889999999999999998776653210 000 000110 11123456
Q ss_pred HHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhhcccHHhHHHHHHHH
Q psy14291 204 LAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTITEQMSREAQELL 283 (538)
Q Consensus 204 ~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~~it~~m~~e~~kLL 283 (538)
|.|+++.. .+ ++| +.||||+++..|.+++.+++.++.+ ++
T Consensus 51 l~~~~~~~----~~-~~~-------------~~vFD~~~~tfR~~~~~~yK~~R~~--------------~~-------- 90 (310)
T COG0258 51 LYRLIRLL----EP-THP-------------VVVFDGKPPTFRHELLEEYKANREK--------------EM-------- 90 (310)
T ss_pred HHHHHHhc----CC-CcE-------------EEEEcCCCCcchHHHHHHHHhCCCc--------------cC--------
Confidence 66644433 33 555 9999999999998888776544211 00
Q ss_pred HhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHHHhhc----CCCceE
Q psy14291 284 QLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKMLEAQELLQLFGVPFIVAPG-EAEAQCASLELGN----HTQGVI 358 (538)
Q Consensus 284 ~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~La~~g----~vd~Ii 358 (538)
..++..|++.+.+++.++|++++..+| ||||.++++|+.. ...+|+
T Consensus 91 -----------------------------p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~ 141 (310)
T COG0258 91 -----------------------------PDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLII 141 (310)
T ss_pred -----------------------------HHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEE
Confidence 023556778899999999999999999 9999999999864 455699
Q ss_pred ecCCceEeecCeEEEEecCCCCCcEE-EEchhHHHHHh-CCCHHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHHcCC
Q psy14291 359 TDDSDIWLFGARTVYKNFFDKKSHVL-RYTAPDIRYYF-ELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 359 S~DsDllLfG~~~Vi~~~~~~~~~~~-~~~~~~i~~~~-gl~~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~ygs 434 (538)
|+|+|++.|++.++....... +... .++...+.++| |++|+||+|+++|+| |||+|||+|||+|||++||++||+
T Consensus 142 S~DkD~lql~~~~~~~~~~~~-~~~~~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs 220 (310)
T COG0258 142 SGDKDLLQLVSPNVLVINGKK-GEPEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGS 220 (310)
T ss_pred eCCcchhhhcCCCcEEEeccC-CCCcccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCC
Confidence 999999977655433211112 1122 58999999999 999999999999999 999999999999999999999999
Q ss_pred CCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCCCCCCCHHHHHhhcCCCCCCCccc-ccCC--CCCHHHHHHH
Q psy14291 435 SDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLNDDFPNVSVIEAYLKPDINTNVQK-LAWG--TPDLDGLRRF 511 (538)
Q Consensus 435 l~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~~~fps~~lv~ly~dp~v~~s~~~-~~w~--~PD~~~L~~f 511 (538)
+ +.++++++.++.. .+.++.+. ++.+|.++.++++++|.++..+..+ +.+. ..|.+++..+
T Consensus 221 ~-----e~i~~~~~~~~~~----------~~~~l~~~-~~~afl~~~l~t~~~d~~l~~~~~~~~~~~~~~~d~~~~~~~ 284 (310)
T COG0258 221 L-----EGLYENLDIIKKK----------TREKLLED-KEKAFLSKPLATIKTDVPLEFDLEDILELLVPEHDFSKLLEE 284 (310)
T ss_pred H-----HHHHHhhhhhcch----------hhHHHHHH-HHHHhcCcccccccccccCCcCccchhhhccCcccHHHHHHH
Confidence 9 9999998855432 34456565 4789999999999999988877666 3444 3488877777
Q ss_pred HHHhcCCCh
Q psy14291 512 AANKFGWSQ 520 (538)
Q Consensus 512 l~~~~ew~~ 520 (538)
+.+ ++|..
T Consensus 285 ~~~-~~~~~ 292 (310)
T COG0258 285 RVE-LGFKR 292 (310)
T ss_pred HHH-HhHHH
Confidence 766 55543
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=99.85 E-value=5.6e-22 Score=171.13 Aligned_cols=85 Identities=47% Similarity=0.681 Sum_probs=74.4
Q ss_pred HHcCCCcccCcchHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecC-CC--------CCcEEEEchhHHHHHhCCC
Q psy14291 328 QLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFF-DK--------KSHVLRYTAPDIRYYFELT 398 (538)
Q Consensus 328 ~~~GIp~i~APgEADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~-~~--------~~~~~~~~~~~i~~~~gl~ 398 (538)
+++||||++||||||||||+|+++|.+|+|+|+|||+|+||+++|+++++ .. ...+.+|+.+++.+.+|++
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 57999999999999999999999999999999999999999999999986 22 1358999999999999999
Q ss_pred HHHHHHHHHHcCCC
Q psy14291 399 REKLIQLALLVGSD 412 (538)
Q Consensus 399 ~~q~idl~~L~GsD 412 (538)
++||+++|+|+|||
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=99.81 E-value=2.7e-20 Score=161.43 Aligned_cols=96 Identities=26% Similarity=0.342 Sum_probs=75.0
Q ss_pred hchhchHHHhhhcCcccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHhcC
Q psy14291 110 MGVNGLWKLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGG 189 (538)
Q Consensus 110 MGi~GLw~~l~~~~~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 189 (538)
|||+|||++|++..+++++++|+|++||||+|+|||+...++.+.. . ...++..|+
T Consensus 1 MGI~gL~~~l~~~~~~~~i~~l~g~~vaIDa~~wl~~~~~~~~~~~------------~---~~~~~~~~l--------- 56 (99)
T smart00485 1 MGIKGLWPLLKPVVREVPLEALRGKTLAIDASIWLYQFLTACREKL------------G---TPLPNSKHL--------- 56 (99)
T ss_pred CCHhHHHHHHHHhcccCCHHHhCCceEeccHHHHHHHHHHHHhhhh------------c---CCCCchHHH---------
Confidence 9999999999999999999999999999999999998765543211 0 001111233
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHH
Q psy14291 190 KEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQL 257 (538)
Q Consensus 190 ~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qL 257 (538)
.++|+|++. |+.+||+| ||||||..|+.|..|.++|++++
T Consensus 57 -----------~~~~~rl~~----L~~~~I~P-------------ifVFDG~~~~~K~~t~~~R~~~r 96 (99)
T smart00485 57 -----------MGLFYRTCR----LLEFGIKP-------------IFVFDGKPPPLKSETLAKRRERR 96 (99)
T ss_pred -----------HHHHHHHHH----HHHCCCeE-------------EEEECCCCchhhHHHHHHHHHHH
Confidence 678888554 55666677 99999999999999999988764
No 18
>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=99.80 E-value=5.8e-20 Score=212.05 Aligned_cols=108 Identities=34% Similarity=0.475 Sum_probs=86.9
Q ss_pred hchhchHHHhhhcCcccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHhcC
Q psy14291 110 MGVNGLWKLLEASGKPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIAGG 189 (538)
Q Consensus 110 MGi~GLw~~l~~~~~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 189 (538)
|||+|||++|+++++++++++|+||+||||+|+|||++++++++.. |+.+ +..||
T Consensus 1 MGI~GLw~ll~~~~r~v~le~l~Gk~vAIDasiWL~q~l~~vr~~~-g~~l---------------~n~hl--------- 55 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVSPETLEGKRLAVDISIWLNQALKGVRDRE-GNAI---------------KNSHL--------- 55 (1034)
T ss_pred CChhHHHHHHHHhcccccHHHhCCeEEEechHHHHHHHHHHHHhcc-CCcc---------------CCHHH---------
Confidence 9999999999999999999999999999999999999888776543 2221 23466
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhh
Q psy14291 190 KEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLAS 269 (538)
Q Consensus 190 ~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~ 269 (538)
.+||+|+++||+ +||+| ||||||++|++|+.|+++|++++++..+...+.+.
T Consensus 56 -----------~g~f~Ri~~Ll~----~gI~P-------------VfVFDG~~p~lK~~t~~~R~~rR~~a~~~a~~~~~ 107 (1034)
T TIGR00600 56 -----------LTLFHRLCKLLF----FRIRP-------------IFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAE 107 (1034)
T ss_pred -----------HHHHHHHHHHHH----CCCeE-------------EEEECCCCchHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 679999666554 56677 99999999999999999999887655554444443
Q ss_pred c
Q psy14291 270 T 270 (538)
Q Consensus 270 ~ 270 (538)
.
T Consensus 108 ~ 108 (1034)
T TIGR00600 108 K 108 (1034)
T ss_pred H
Confidence 3
No 19
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=99.80 E-value=5.5e-20 Score=159.77 Aligned_cols=97 Identities=21% Similarity=0.320 Sum_probs=69.4
Q ss_pred hchhchHHHhhhcC--cccccccccCeEEEeehhhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHh
Q psy14291 110 MGVNGLWKLLEASG--KPVPVETLENKVLAVGILYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIA 187 (538)
Q Consensus 110 MGi~GLw~~l~~~~--~~~~~~~l~G~~laiD~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 187 (538)
|||+|||++|++.. +++++++|+|++||||+|+|+|+...++.... ... .++..|+
T Consensus 1 MGI~gL~~~l~~~~~v~~~~~~~l~g~~vaID~s~wl~~~~~~~~~~~-----~~~----------~~~~~~~------- 58 (101)
T PF00752_consen 1 MGIKGLWQLLKPAAAVRKVSLSELRGKRVAIDASCWLHQFLFSCREEL-----GQG----------VGTDSHL------- 58 (101)
T ss_dssp ---TTHHHHCHHHEGEEEEEGGGGTTCEEEEEHHHHHHHHHHHSBCTT-----SCB-----------BS-HHH-------
T ss_pred CCcccHHHHHHhhccCCccCHHHhCCCEEEEEcHHHHHHHHHHhHHHh-----ccc----------cchHHHH-------
Confidence 99999999999999 99999999999999999999998664443211 000 0111233
Q ss_pred cCcchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHH
Q psy14291 188 GGKEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLL 258 (538)
Q Consensus 188 ~~~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLq 258 (538)
.++++|+ +.|+.+||+| ||||||.+|+.|.+|..+|+++++
T Consensus 59 -------------~~~~~r~----~~L~~~gI~P-------------ifVFDG~~~~~K~~~~~~R~~~r~ 99 (101)
T PF00752_consen 59 -------------RGLFSRL----CRLLEHGIKP-------------IFVFDGKPPPLKRETIQKRRKRRE 99 (101)
T ss_dssp -------------HHHHHHH----HHHHHTTEEE-------------EEEE--STTGGCHHHHHHHHHHHH
T ss_pred -------------HHHHHHH----HHHHHCCCEE-------------EEEECCCCchhhHHHHHHHHHHHh
Confidence 5678884 4556666667 999999999999999999887753
No 20
>PHA00439 exonuclease
Probab=99.76 E-value=2.3e-18 Score=175.38 Aligned_cols=127 Identities=17% Similarity=0.163 Sum_probs=98.8
Q ss_pred EEeCCCchhhhhhhhhhccccCCCCcc---hHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHHHhhcCC----C-ceEec
Q psy14291 290 FIVAPGEAEAQCASLELGTDKKRRPYV---SRKMLEAQELLQLFGVPFIVAPG-EAEAQCASLELGNHT----Q-GVITD 360 (538)
Q Consensus 290 ~iv~d~Eaeaqca~l~~~~~k~rr~~l---t~q~~~ik~lL~~~GIp~i~APg-EADaqiA~La~~g~v----d-~IiS~ 360 (538)
++.||+. ..=|+..|+.||++|++. ..+++.++++++++||+++..|| ||||+||+|+++... + .|+|.
T Consensus 68 ~vaFD~~--~tfR~elyp~YKanR~~~p~~~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~ 145 (286)
T PHA00439 68 VLAFTDS--VNWRKEVVPTYKANRKAKRKPVGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSC 145 (286)
T ss_pred EEEECCC--CChHhhhhhHhcCCCCCCCCchhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeC
Confidence 4467742 223899999999999643 45667899999999999999999 999999999986432 2 38999
Q ss_pred CCceE-eecCeEEEEecCCCCCcEEEEchhHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHH
Q psy14291 361 DSDIW-LFGARTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAK 431 (538)
Q Consensus 361 DsDll-LfG~~~Vi~~~~~~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~ 431 (538)
|+|++ |.+...++.. .+....++.+ .+++++++.+|+| |||+||||||| |||.+||++
T Consensus 146 DKDl~QLv~~~~~~~~----~~~~~~~~~~--------~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 146 DKDFKTIPNCDFLWCT----TGNILTQTPE--------TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred CCCHhhcCcceEEEcc----CCceEEcCcc--------cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 99999 7766333222 1222224432 2899999999999 99999999999 999999998
No 21
>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=99.75 E-value=2.6e-20 Score=163.21 Aligned_cols=99 Identities=24% Similarity=0.415 Sum_probs=63.8
Q ss_pred CCHHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHHhhcCCCChhhhHhhhhccCC
Q psy14291 397 LTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWLAKKNKPDTHLTRKLRNVKLN 474 (538)
Q Consensus 397 l~~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~~~~~~~~~~lr~kL~~~~i~ 474 (538)
|+|+|++||.+|+| |||+|||||||+|||.+||++|||+ |+|++++++++.. +++++|.++. +
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsl-----e~i~~~~~~~~~~---------k~~~~l~~~~-e 65 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSL-----ENILANLDEIKGK---------KIREKLRENK-E 65 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSC-----HCCCCC-SSS-TS---------CCCHHHHTSC-C
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCH-----HHHHHhHHhcccc---------HHHHHHHHHH-H
Confidence 57999999999999 9999999999999999999999999 9999998887641 4567888874 9
Q ss_pred CCCCCHHHHHhhcCCCCCCCcccccCCCCCHHHHHH
Q psy14291 475 DDFPNVSVIEAYLKPDINTNVQKLAWGTPDLDGLRR 510 (538)
Q Consensus 475 ~~fps~~lv~ly~dp~v~~s~~~~~w~~PD~~~L~~ 510 (538)
.++.|++|+++.+|.+++.+++++.+..+|.+++.+
T Consensus 66 ~a~ls~~L~tl~~dv~l~~~l~~l~~~~~d~~~l~~ 101 (101)
T PF01367_consen 66 QALLSRKLATLKTDVPLPFSLEDLRLQPPDREKLIE 101 (101)
T ss_dssp CCCCHHHHH-H-S-----------------HHHH--
T ss_pred HHHHhHHHhhhhcCCCCCCCcchhccCCCCHHHhcC
Confidence 999999999999999999999999999999998753
No 22
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.62 E-value=4.5e-16 Score=128.98 Aligned_cols=69 Identities=41% Similarity=0.629 Sum_probs=63.4
Q ss_pred HcCCCcccCcchHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecCCCCC---cEEEEchhHHHHHhCC
Q psy14291 329 LFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKS---HVLRYTAPDIRYYFEL 397 (538)
Q Consensus 329 ~~GIp~i~APgEADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~---~~~~~~~~~i~~~~gl 397 (538)
.+||||++||+|||||||+|++.|.+|+|+|+|+|+++||+++++++++..++ .+..++.+.+.+.+|+
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 58999999999999999999999999999999999999999999999865544 6889999999998874
No 23
>PHA02567 rnh RnaseH; Provisional
Probab=99.55 E-value=1.8e-14 Score=147.71 Aligned_cols=119 Identities=13% Similarity=0.075 Sum_probs=93.4
Q ss_pred cEEeCCCchhhhh-hhhhhccccCCCCcch----HhH--------HHHHHHHHHcCCCcccCcc-hHHHHHHHHHhhcCC
Q psy14291 289 PFIVAPGEAEAQC-ASLELGTDKKRRPYVS----RKM--------LEAQELLQLFGVPFIVAPG-EAEAQCASLELGNHT 354 (538)
Q Consensus 289 P~iv~d~Eaeaqc-a~l~~~~~k~rr~~lt----~q~--------~~ik~lL~~~GIp~i~APg-EADaqiA~La~~g~v 354 (538)
.++.||+.. ..+ |+..|+.||++|++.. .|+ +.+++++.++||+++..|| ||||+||+|+++...
T Consensus 66 i~vaFD~~~-~~tfR~elyp~YKAnR~~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~ 144 (304)
T PHA02567 66 IVLAFDNSK-SGYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSA 144 (304)
T ss_pred EEEEEeCCC-CCCchhhhhhHhhcCCCCCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHh
Confidence 356777753 234 8889999999997533 332 4678889999999999999 999999999987554
Q ss_pred Cc----eEecCCceE-eec--CeEEEEecCCCCCcEEEEchhHHHHHhCCCHHHHHHHHHHcC--CCCCCCCCC
Q psy14291 355 QG----VITDDSDIW-LFG--ARTVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLALLVG--SDYTPGLQG 419 (538)
Q Consensus 355 d~----IiS~DsDll-LfG--~~~Vi~~~~~~~~~~~~~~~~~i~~~~gl~~~q~idl~~L~G--sDyipGVpG 419 (538)
.+ |+|+|+|++ |+. ...++.. ++.+.+.+++| .|+|++|+.+|+| |||+||||-
T Consensus 145 ~g~~VvIvS~DKDl~QLv~~~~v~~~~~----------~~~~~V~~k~G-~P~q~iD~kaL~GDsSDNIPGVp~ 207 (304)
T PHA02567 145 EGRPVLIVSSDGDFTQLHKYPGVKQWSP----------MQKKWVKPKYG-SPEKDLMTKIIKGDKKDGVASIKV 207 (304)
T ss_pred CCCcEEEEeCCCChhhccCCCCeEEeec----------CCHHHHHHHhC-CHHHHHHHHHhCCcccCCcCCCCC
Confidence 43 899999999 774 3333322 23477888999 5999999999999 999999984
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=99.47 E-value=4.5e-14 Score=117.48 Aligned_cols=53 Identities=42% Similarity=0.769 Sum_probs=50.2
Q ss_pred HhCCCHHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHH
Q psy14291 394 YFELTREKLIQLALLVG--SDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFK 451 (538)
Q Consensus 394 ~~gl~~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k 451 (538)
++|++|+||+++|+|+| |||+|||||||+|||.+||++|+++ ++++++++.++
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~-----~~~~~~~~~~~ 56 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSL-----ENLLENLDKIK 56 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCH-----HHHHHHHHHHh
Confidence 58999999999999999 9999999999999999999999999 99999887763
No 25
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=99.24 E-value=2.8e-12 Score=122.27 Aligned_cols=116 Identities=20% Similarity=0.288 Sum_probs=87.0
Q ss_pred HHHHHHHHhhCC--cEEeCCCchhhhhhhhhhccccCCCCc----chHhHHHHHHHHHHcCCCcccCcc-hHHHHHHHHH
Q psy14291 277 REAQELLQLFGV--PFIVAPGEAEAQCASLELGTDKKRRPY----VSRKMLEAQELLQLFGVPFIVAPG-EAEAQCASLE 349 (538)
Q Consensus 277 ~e~~kLL~~~g~--P~iv~d~Eaeaqca~l~~~~~k~rr~~----lt~q~~~ik~lL~~~GIp~i~APg-EADaqiA~La 349 (538)
....++++.+.+ .+++||+... .-|+..++.||++|.+ +..|++.++++++++||+++..|| ||||+||+|+
T Consensus 40 ~~l~~l~~~~~p~~~vv~fD~~~~-~fR~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla 118 (169)
T PF02739_consen 40 RMLLKLLKDFKPDYVVVAFDSKGP-TFRKELYPEYKANRKPMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLA 118 (169)
T ss_dssp HHHHHHHHHTTEEEEEEEEEBSSC-HHHHHCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHH
T ss_pred HHHHHHHHHcCCceEEEEecCCCc-chHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHH
Confidence 344566777775 5678887654 3388999999999864 566788999999999999999999 9999999999
Q ss_pred hhcCCCc----eEecCCceE-eecC--eEEEEecCCCCCcEEEEchhHHHHHh
Q psy14291 350 LGNHTQG----VITDDSDIW-LFGA--RTVYKNFFDKKSHVLRYTAPDIRYYF 395 (538)
Q Consensus 350 ~~g~vd~----IiS~DsDll-LfG~--~~Vi~~~~~~~~~~~~~~~~~i~~~~ 395 (538)
++....+ |+|+|+|++ |+.. ...+.+. +......|+.+.|.++|
T Consensus 119 ~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~~~~~--~~~~~~~~~~~~v~eky 169 (169)
T PF02739_consen 119 KKASEEGFEVIIVSGDKDLLQLVDENVNVYLLDP--GKKKFKVYDPEEVEEKY 169 (169)
T ss_dssp HHHHHTTCEEEEE-SSGGGGGGTCS-TSEEEEET--TTTCS-EB-HHHHHHHT
T ss_pred hhhccCCCEEEEEcCCCCHHHhcCCCceEEEeec--CCCCCEEEcHHHHhhcC
Confidence 9865553 899999999 8855 3333332 23457899999998876
No 26
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.09 E-value=8.5e-11 Score=84.79 Aligned_cols=34 Identities=56% Similarity=0.993 Sum_probs=31.7
Q ss_pred HHHHHHHHHHcC--CCCCCCCCCCCHHHHHHHHHHc
Q psy14291 399 REKLIQLALLVG--SDYTPGLQGVGPVTALEILAKF 432 (538)
Q Consensus 399 ~~q~idl~~L~G--sDyipGVpGIG~KtA~kLL~~y 432 (538)
|+||+++|+|+| +||+|||||||+|||.+||++|
T Consensus 1 p~q~~~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence 589999999999 7777899999999999999987
No 27
>PF12813 XPG_I_2: XPG domain containing
Probab=98.35 E-value=1.5e-06 Score=87.89 Aligned_cols=84 Identities=27% Similarity=0.300 Sum_probs=65.0
Q ss_pred HHHHHHHHHc---CCCcccCcchHHHHHHHHHhhcCCCceEecCCceEeecC----eEEE-EecCCCC---------CcE
Q psy14291 321 LEAQELLQLF---GVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA----RTVY-KNFFDKK---------SHV 383 (538)
Q Consensus 321 ~~ik~lL~~~---GIp~i~APgEADaqiA~La~~g~vd~IiS~DsDllLfG~----~~Vi-~~~~~~~---------~~~ 383 (538)
+.+.+.|+.+ |++++..|||||..||.+|++..+ .|+|.|||+++|+. ..+. ..+.... -..
T Consensus 7 ~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i~~ 85 (246)
T PF12813_consen 7 PAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYISA 85 (246)
T ss_pred HHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCeeEE
Confidence 3577888888 999999999999999999988665 79999999999954 2222 2211111 135
Q ss_pred EEEchhHHHHHhCCCHHHHHHHHH
Q psy14291 384 LRYTAPDIRYYFELTREKLIQLAL 407 (538)
Q Consensus 384 ~~~~~~~i~~~~gl~~~q~idl~~ 407 (538)
..|+.+.|.+++|+. .|..++.
T Consensus 86 ~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 86 KVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred EEEcHHHHHHHcCCc--hhHHHHH
Confidence 679999999999999 7776666
No 28
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=98.03 E-value=7.2e-05 Score=80.24 Aligned_cols=225 Identities=20% Similarity=0.222 Sum_probs=116.6
Q ss_pred hchhchHHHhhhcCccccc-ccccCeEEEeeh-hhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHHHh
Q psy14291 110 MGVNGLWKLLEASGKPVPV-ETLENKVLAVGI-LYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEEIA 187 (538)
Q Consensus 110 MGi~GLw~~l~~~~~~~~~-~~l~G~~laiD~-s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~ 187 (538)
|||+.|-.+|...|.=..+ ...+++-+=||. |+++- .|.++.+.. ++
T Consensus 1 MGIKNLK~lLl~~gsL~~i~~~~~~~~ifVD~msif~t-iAysv~s~~-----------eL------------------- 49 (425)
T PF04599_consen 1 MGIKNLKALLLETGSLKKIDNIEKNNEIFVDTMSIFMT-IAYSVNSLD-----------EL------------------- 49 (425)
T ss_pred CchhHHHHHHHhcCCceeccCCCCCccEEEEcchhhhh-hhhhhCCHH-----------HH-------------------
Confidence 9999999999999864333 334467788995 55555 343332211 11
Q ss_pred cCcchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHH------
Q psy14291 188 GGKEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLER------ 261 (538)
Q Consensus 188 ~~~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~------ 261 (538)
...|..+++.+.. . +-++....|-|....|...-+|||...+...
T Consensus 50 ------------~~~~~~~i~~w~~----~-------------~~~VtlFvDRG~I~iK~~lReKRr~a~k~~~~RK~~~ 100 (425)
T PF04599_consen 50 ------------RNSFEEYIQQWIK----N-------------NGKVTLFVDRGSINIKEPLREKRRKALKNTIKRKREE 100 (425)
T ss_pred ------------HHHHHHHHHHHHh----c-------------CCeEEEEEecCccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 1234445444332 1 1123444499999999988888876543322
Q ss_pred -hhhhhh--hhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHhHHHHHHHHHHc--CCCccc
Q psy14291 262 -GKQTRL--ASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKMLEAQELLQLF--GVPFIV 336 (538)
Q Consensus 262 -~k~~R~--A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q~~~ik~lL~~~--GIp~i~ 336 (538)
++.... ...+...+.++.+.-+++. .+. +.++-.-.....+.. .+.++|..+ +|..+.
T Consensus 101 i~~l~~~~~~ld~~d~~yeEikt~~~lk------------i~K--~~F~~fla~~~n~k~---~l~~~L~~~~~~V~Ivy 163 (425)
T PF04599_consen 101 IENLEDCIKNLDVDDEFYEEIKTDLELK------------IQK--LSFQLFLANSNNLKT---ILESSLSRLKEDVEIVY 163 (425)
T ss_pred HHHHHHHHhcCCccHHHHHHHHHHHHHH------------HHH--HHHHHHhcchhhHHH---HHHHHHHhccCCceEEE
Confidence 211111 1122333333333222211 000 000000011111222 345555555 888888
Q ss_pred Ccc-hHHHHHHHHHhh-----cCCCceEecCCceEeecCe----EEEEecCCCCCcEEEEchhHHHHHhCCCHHHHHHHH
Q psy14291 337 APG-EAEAQCASLELG-----NHTQGVITDDSDIWLFGAR----TVYKNFFDKKSHVLRYTAPDIRYYFELTREKLIQLA 406 (538)
Q Consensus 337 APg-EADaqiA~La~~-----g~vd~IiS~DsDllLfG~~----~Vi~~~~~~~~~~~~~~~~~i~~~~gl~~~q~idl~ 406 (538)
-.| -||=++.+=|++ |.--.++|.|.|.++|.+. ++++.. ...-.|-+.. .+.---...+
T Consensus 164 CDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t~----~~~Y~~~P~~------~s~YL~kL~~ 233 (425)
T PF04599_consen 164 CDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKTM----NQLYKFIPCS------KSRYLSKLTA 233 (425)
T ss_pred ECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHhH----HhHeeecCCc------hHHHHHHHHH
Confidence 888 899877766654 4444599999999999542 222211 1111111111 1111122335
Q ss_pred HHcCCCCCCCCCCCC
Q psy14291 407 LLVGSDYTPGLQGVG 421 (538)
Q Consensus 407 ~L~GsDyipGVpGIG 421 (538)
..-||||.||+-|+-
T Consensus 234 L~NGCDfFpGLyG~~ 248 (425)
T PF04599_consen 234 LVNGCDFFPGLYGIS 248 (425)
T ss_pred HHhcccccCCcceeE
Confidence 566899999999964
No 29
>PHA03065 Hypothetical protein; Provisional
Probab=97.90 E-value=0.00019 Score=76.79 Aligned_cols=218 Identities=21% Similarity=0.210 Sum_probs=117.1
Q ss_pred hchhchHHHhhhcCccccccccc---CeEEEeeh-hhHHHhhhhhhhhhccccccchhhHHHHHHHHhhhhhhhHHHHHH
Q psy14291 110 MGVNGLWKLLEASGKPVPVETLE---NKVLAVGI-LYFTQGRASALLDRRKEDNIIDAEEKDILEMIRAEEENEIEFEEE 185 (538)
Q Consensus 110 MGi~GLw~~l~~~~~~~~~~~l~---G~~laiD~-s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 185 (538)
|||+.|-.+|...|.=..++.-. ++-+=||. |+++- .|.++.+.. ++ |
T Consensus 1 MGIKNLKtLLL~~gsL~~~~~~~~~~~~~iFVD~ms~fms-iAysv~~~~---------------eL------~------ 52 (438)
T PHA03065 1 MGIKNLKTLLLETGSLTKLDNNLKDRFNGIFVDTMSVFMS-IAYSVNNLD---------------EL------R------ 52 (438)
T ss_pred CchhhHHHHHHhcCCcccccccccccCceEEEechhhhhh-hhhhhCCHH---------------HH------H------
Confidence 99999999999988655553222 35788995 56655 344443311 11 1
Q ss_pred HhcCcchhhHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHH----
Q psy14291 186 IAGGKEEKTEKIKLTREMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLER---- 261 (538)
Q Consensus 186 ~~~~~~~~~~~~~~~~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~---- 261 (538)
..|..|++.+.. . .-+++...|-|..++|...-+|||+..++..
T Consensus 53 ---------------~~~~~~iq~w~~----~-------------~gkVtlFvDRG~I~IK~~lReKRr~a~~~~~kRK~ 100 (438)
T PHA03065 53 ---------------STFEEYVQQWVK----K-------------AGKVTLFVDRGSIPIKQSLREKRRKASKNTIKRKR 100 (438)
T ss_pred ---------------HHHHHHHHHHHh----c-------------CCcEEEEEecCccchhhHHHHHHHHHHHHHHHHHH
Confidence 224445444431 1 1123444498899999888888887653332
Q ss_pred ---hhhhhhh--hcccHHhHHHHHHHHHhhCCcEEeCCCchhhhh-hhhhhccccCCCCcchHhHH-HHHHHHHHc--CC
Q psy14291 262 ---GKQTRLA--STITEQMSREAQELLQLFGVPFIVAPGEAEAQC-ASLELGTDKKRRPYVSRKML-EAQELLQLF--GV 332 (538)
Q Consensus 262 ---~k~~R~A--~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqc-a~l~~~~~k~rr~~lt~q~~-~ik~lL~~~--GI 332 (538)
++..... -++...+.++.+.-+++. .+. .|..+ -+.. .++. .+.+.|..+ +|
T Consensus 101 ~ei~~l~~~i~~ld~~d~~yEEikt~~~lr------------I~Kl~F~~f---La~~----~nlk~~l~~~L~~~~~~v 161 (438)
T PHA03065 101 EEIEKLEDDIKNLDVDDEMYEEIKTDLELK------------IDKLSFQLF---LANS----NNLKRLLESALARLGENV 161 (438)
T ss_pred HHHHHHHHHHhcCCcchHHHHHHHHHHHHH------------HHHHHHHHH---Hcch----hhHHHHHHHHHHhccCCc
Confidence 2221111 123333444443332221 000 00000 0001 1222 345667777 88
Q ss_pred CcccCcc-hHHHHHHHHHhh-----cCCCceEecCCceEeecCe----EEEEecCCCCCcEEEEchhHHHHHhCCCHH--
Q psy14291 333 PFIVAPG-EAEAQCASLELG-----NHTQGVITDDSDIWLFGAR----TVYKNFFDKKSHVLRYTAPDIRYYFELTRE-- 400 (538)
Q Consensus 333 p~i~APg-EADaqiA~La~~-----g~vd~IiS~DsDllLfG~~----~Vi~~~~~~~~~~~~~~~~~i~~~~gl~~~-- 400 (538)
.++.-.| -||=++..=++. |.--.++|.|.|.++|.+. +++++ . -+.|.+-|.
T Consensus 162 ~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~KiI~t------------~---~~~Y~~~P~~~ 226 (438)
T PHA03065 162 EIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKIIKT------------A---NQLYKFIPCAK 226 (438)
T ss_pred eEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHHHHh------------H---HHHheeCCChh
Confidence 8888888 899877665554 4444599999999998542 22211 1 122222221
Q ss_pred --HH-HHHHHHcCCCCCCCCCCCC
Q psy14291 401 --KL-IQLALLVGSDYTPGLQGVG 421 (538)
Q Consensus 401 --q~-idl~~L~GsDyipGVpGIG 421 (538)
-+ ...+..-||||.||+-|+-
T Consensus 227 t~YL~kL~~L~NGCDfFpGLyG~~ 250 (438)
T PHA03065 227 TRYLSKLVALVNGCDFFPGLYGIS 250 (438)
T ss_pred HHHHHHHHHHHhcccccCccceEE
Confidence 11 2224455799999999964
No 30
>PRK03980 flap endonuclease-1; Provisional
Probab=96.88 E-value=0.0012 Score=68.66 Aligned_cols=48 Identities=33% Similarity=0.592 Sum_probs=43.1
Q ss_pred HHHhhhhhhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhh
Q psy14291 259 LERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLEL 306 (538)
Q Consensus 259 ee~~k~~R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~ 306 (538)
++..++.+++.+++++|...++++|+.+|+|++++|+||||||+++..
T Consensus 68 ~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~ 115 (292)
T PRK03980 68 EEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAK 115 (292)
T ss_pred HHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHH
Confidence 345667788889999999999999999999999999999999999873
No 31
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=96.73 E-value=0.0055 Score=61.90 Aligned_cols=32 Identities=25% Similarity=0.447 Sum_probs=19.7
Q ss_pred CcchHHHHHHHHHhh---------cCCCceEecCCceEeec
Q psy14291 337 APGEAEAQCASLELG---------NHTQGVITDDSDIWLFG 368 (538)
Q Consensus 337 APgEADaqiA~La~~---------g~vd~IiS~DsDllLfG 368 (538)
.|||+|--|-.+-+. .....|++.|+|+++++
T Consensus 182 vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 182 VPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp SSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred CCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 478999966655443 12234999999999663
No 32
>smart00475 53EXOc 5'-3' exonuclease.
Probab=96.53 E-value=0.008 Score=61.44 Aligned_cols=83 Identities=24% Similarity=0.327 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhhcccHHhHHHHH
Q psy14291 201 REMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTITEQMSREAQ 280 (538)
Q Consensus 201 ~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~~it~~m~~e~~ 280 (538)
.+|++.+.+++... +| ..+++|||++.+.-. .++-...+. .+. ..-..+..++ ..++
T Consensus 34 ~g~~~~l~~l~~~~-----~p----------~~~~~~fD~~~~~~R-~~l~p~YKa---~R~---~~pe~L~~q~-~~~~ 90 (259)
T smart00475 34 YGFLRMLLKLIKEE-----KP----------TYVAVVFDAKGKTFR-HELYPEYKA---NRP---KTPDELLEQI-PLIK 90 (259)
T ss_pred HHHHHHHHHHHHHc-----CC----------CeEEEEEeCCCCccc-cchhHHHHh---CCC---CCCHHHHHHH-HHHH
Confidence 56888877777642 23 224899998655442 232221111 110 1112233343 7889
Q ss_pred HHHHhhCCcEEeCCC-chhhhhhhhhh
Q psy14291 281 ELLQLFGVPFIVAPG-EAEAQCASLEL 306 (538)
Q Consensus 281 kLL~~~g~P~iv~d~-Eaeaqca~l~~ 306 (538)
++|+.+|+|++..++ ||.++|+.+..
T Consensus 91 ~~l~~~gi~~i~~~g~EADD~iatla~ 117 (259)
T smart00475 91 ELLDALGIPVLEVEGYEADDVIATLAK 117 (259)
T ss_pred HHHHHCCCCEEeeCCcCHHHHHHHHHH
Confidence 999999999999888 99999976653
No 33
>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=95.61 E-value=0.015 Score=60.59 Aligned_cols=47 Identities=57% Similarity=0.769 Sum_probs=40.5
Q ss_pred HHhhhhhhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhh
Q psy14291 260 ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLEL 306 (538)
Q Consensus 260 e~~k~~R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~ 306 (538)
+..++.+.+.+++.++...++++|+.+|+|++++|+||++||+++..
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~ 160 (316)
T cd00128 114 EAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYLAK 160 (316)
T ss_pred HHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHHHh
Confidence 34455566778899999999999999999999999999999998763
No 34
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=92.61 E-value=0.071 Score=43.05 Aligned_cols=20 Identities=35% Similarity=0.519 Sum_probs=17.6
Q ss_pred CCCCCCHHHHHHHHHHcCCC
Q psy14291 416 GLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygsl 435 (538)
||||||+++|..|+++||++
T Consensus 7 GI~~VG~~~ak~L~~~f~sl 26 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSL 26 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCH
T ss_pred CCCCccHHHHHHHHHHcCCH
Confidence 99999999999999999998
No 35
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=92.57 E-value=0.065 Score=44.72 Aligned_cols=22 Identities=68% Similarity=1.059 Sum_probs=20.0
Q ss_pred hhCCcEEeCCCchhhhhhhhhh
Q psy14291 285 LFGVPFIVAPGEAEAQCASLEL 306 (538)
Q Consensus 285 ~~g~P~iv~d~Eaeaqca~l~~ 306 (538)
.+|+||+++|+||+|||++++.
T Consensus 2 ~~gi~~i~AP~eAeAq~A~L~~ 23 (73)
T smart00484 2 LMGIPYIVAPYEAEAQCAYLAK 23 (73)
T ss_pred cCCCeEEEcCCcHHHHHHHHHh
Confidence 5799999999999999999874
No 36
>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=91.61 E-value=0.11 Score=44.97 Aligned_cols=22 Identities=77% Similarity=1.173 Sum_probs=17.2
Q ss_pred HhhCCcEEeCCCchhhhhhhhh
Q psy14291 284 QLFGVPFIVAPGEAEAQCASLE 305 (538)
Q Consensus 284 ~~~g~P~iv~d~Eaeaqca~l~ 305 (538)
+.+|+|++++|+||+|||+++.
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~ 22 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLE 22 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHH
T ss_pred CCCCCeEEEcCchHHHHHHHHH
Confidence 4689999999999999999987
No 37
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.72 E-value=0.54 Score=56.00 Aligned_cols=82 Identities=22% Similarity=0.287 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhhcccHHhHHHHH
Q psy14291 201 REMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTITEQMSREAQ 280 (538)
Q Consensus 201 ~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~~it~~m~~e~~ 280 (538)
.+|+..+.+++... +| .-+++|||++.+..+. ++-...+. .+.. .-..+. ..+..++
T Consensus 34 ~Gf~~~l~~ll~~~-----~p----------~~i~v~FD~~~~tfR~-~~~~~YKa---~R~~---~Pe~l~-~Q~~~i~ 90 (887)
T TIGR00593 34 YGFTKMLLKLLKEE-----KP----------TYVAVAFDSGTPTFRH-EAYAEYKA---NRAP---TPEELI-EQIPLIK 90 (887)
T ss_pred HHHHHHHHHHHHhc-----CC----------CEEEEEEcCCCCcchH-HHHHHHHh---CCCC---ChHHHH-HHHHHHH
Confidence 56777766666532 34 1248999997655543 22111110 0000 001111 2356889
Q ss_pred HHHHhhCCcEEeCCC-chhhhhhhhh
Q psy14291 281 ELLQLFGVPFIVAPG-EAEAQCASLE 305 (538)
Q Consensus 281 kLL~~~g~P~iv~d~-Eaeaqca~l~ 305 (538)
++|+.+|+|++..++ ||.++|+.+.
T Consensus 91 ~~l~~~gi~~i~~~g~EADDiIatla 116 (887)
T TIGR00593 91 ELLDALGIPILEVEGYEADDVIATLA 116 (887)
T ss_pred HHHHHCCCcEEeeCCccHHHHHHHHH
Confidence 999999999999988 9999886554
No 38
>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=89.55 E-value=0.27 Score=52.22 Aligned_cols=47 Identities=34% Similarity=0.589 Sum_probs=41.9
Q ss_pred HHhhhhhhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhh
Q psy14291 260 ERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLEL 306 (538)
Q Consensus 260 e~~k~~R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~ 306 (538)
+..++.+++..++.+|...++++|+.+|+|++++|+||+|||+++..
T Consensus 116 ~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~ 162 (338)
T TIGR03674 116 EARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAK 162 (338)
T ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHH
Confidence 45566777788999999999999999999999999999999999873
No 39
>PTZ00217 flap endonuclease-1; Provisional
Probab=89.29 E-value=0.28 Score=53.14 Aligned_cols=48 Identities=44% Similarity=0.643 Sum_probs=43.2
Q ss_pred HHHhhhhhhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhh
Q psy14291 259 LERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLEL 306 (538)
Q Consensus 259 ee~~k~~R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~ 306 (538)
+++.++.+++.++|.+|...++++|+.+|+|++++|+||+||||++..
T Consensus 123 ~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAdaq~A~L~~ 170 (393)
T PTZ00217 123 EEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVK 170 (393)
T ss_pred HHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcCHHHHHHHHHH
Confidence 355667788899999999999999999999999999999999999873
No 40
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=87.54 E-value=6 Score=45.84 Aligned_cols=93 Identities=23% Similarity=0.366 Sum_probs=56.9
Q ss_pred cCcchHHHHHHHHHhhcCCC---------ceEecCCceEeecC------eEEEE-ecCCC-C------------------
Q psy14291 336 VAPGEAEAQCASLELGNHTQ---------GVITDDSDIWLFGA------RTVYK-NFFDK-K------------------ 380 (538)
Q Consensus 336 ~APgEADaqiA~La~~g~vd---------~IiS~DsDllLfG~------~~Vi~-~~~~~-~------------------ 380 (538)
..|||.|--|-.+-+.-.++ .|..-|.|++++|- -.++| +.+.+ +
T Consensus 185 ~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e 264 (953)
T COG5049 185 LVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDE 264 (953)
T ss_pred cCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCcccccccccccccccccchh
Confidence 45899999877776654333 48899999997751 34666 22211 0
Q ss_pred -------CcEEEEchhHHHHHh-------C----CC----HHHHHHHHHHcCCCCCCCCCCCCH-HHHHHH
Q psy14291 381 -------SHVLRYTAPDIRYYF-------E----LT----REKLIQLALLVGSDYTPGLQGVGP-VTALEI 428 (538)
Q Consensus 381 -------~~~~~~~~~~i~~~~-------g----l~----~~q~idl~~L~GsDyipGVpGIG~-KtA~kL 428 (538)
..+.+....-+.+.+ + ++ -+.++.+|-++|.|++|.+|++-. ..|..+
T Consensus 265 ~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldir~gai~~ 335 (953)
T COG5049 265 ECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDIREGAIET 335 (953)
T ss_pred hhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccccccchHHH
Confidence 123444444443321 1 11 266778899999999999998753 234443
No 41
>KOG2520|consensus
Probab=86.58 E-value=0.34 Score=56.62 Aligned_cols=54 Identities=56% Similarity=0.762 Sum_probs=47.2
Q ss_pred HHHHHHHHHhhhhhhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhh
Q psy14291 253 DRDQLLLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLEL 306 (538)
Q Consensus 253 Rr~qLqee~~k~~R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~ 306 (538)
.-+.+..+..++.|.+.+++..|+.+|++||+.||+|||++|+||||||++++.
T Consensus 445 ~~~el~~ek~~~~r~~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~ 498 (815)
T KOG2520|consen 445 LSDELLSEKYIQSRGADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQ 498 (815)
T ss_pred hhhHHHHHHHHHhccCchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHH
Confidence 334455566777888999999999999999999999999999999999999874
No 42
>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=85.75 E-value=0.6 Score=32.47 Aligned_cols=15 Identities=53% Similarity=0.798 Sum_probs=11.7
Q ss_pred CCCCCCHHHHHHHHH
Q psy14291 416 GLQGVGPVTALEILA 430 (538)
Q Consensus 416 GVpGIG~KtA~kLL~ 430 (538)
.|||||++||..++.
T Consensus 15 ~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 15 KLPGIGPKTANAILS 29 (30)
T ss_dssp TSTT-SHHHHHHHHH
T ss_pred hCCCcCHHHHHHHHh
Confidence 689999999987653
No 43
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=85.35 E-value=0.36 Score=52.85 Aligned_cols=113 Identities=21% Similarity=0.275 Sum_probs=83.8
Q ss_pred HHHHHHHHcCCCcccCcchHHHHHHHHHhhcCCCceEecCCceEeecC-eEEEEecCCCC--CcEEEEchhHHHHHhCCC
Q psy14291 322 EAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIWLFGA-RTVYKNFFDKK--SHVLRYTAPDIRYYFELT 398 (538)
Q Consensus 322 ~ik~lL~~~GIp~i~APgEADaqiA~La~~g~vd~IiS~DsDllLfG~-~~Vi~~~~~~~--~~~~~~~~~~i~~~~gl~ 398 (538)
.+-.++..-|+.++.+|+-|-.|||||.....++++. +-+|++++++ .+++-.+..+. -.+.++......+.+-.+
T Consensus 133 ~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~-gp~d~l~ld~vdr~il~m~fg~d~Ppl~~~~vp~~lem~l~s 211 (531)
T COG5366 133 VASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAF-GPSDILLLDGVDRIILDMSFGSDKPPLDVFHVPRFLEMFLLS 211 (531)
T ss_pred cccccccccceEEEehhhHHHHHHHHHHHHHHHHhcC-CchHhHHHhhhhhheeecccCCCCCCCcccccchHHHhcccc
Confidence 3456677889999999999999999999998888654 7889998854 55555543222 245666666667777677
Q ss_pred HHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCC
Q psy14291 399 REKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 399 ~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl 435 (538)
-.-|..+..+.|||+++.++.|---.+..+-+.+|+.
T Consensus 212 ~~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd~ 248 (531)
T COG5366 212 SRLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGDM 248 (531)
T ss_pred cchhhhhcccccccccccccccccchhHHHHHHHhcc
Confidence 8888888999999999999986543355555556654
No 44
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.36 E-value=1.8 Score=42.56 Aligned_cols=37 Identities=24% Similarity=0.498 Sum_probs=27.3
Q ss_pred HHHhCCC-HHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCC
Q psy14291 392 RYYFELT-REKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 392 ~~~~gl~-~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygs 434 (538)
..-||+. .+.--.|..|. +|+|||||+|+.+|..|+.
T Consensus 58 ~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~ILs~~~~ 95 (194)
T PRK14605 58 LSLFGFATTEELSLFETLI------DVSGIGPKLGLAMLSAMNA 95 (194)
T ss_pred ceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHHhCCH
Confidence 3457864 44444555554 8999999999999999875
No 45
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.03 E-value=1.9 Score=42.69 Aligned_cols=44 Identities=27% Similarity=0.448 Sum_probs=30.9
Q ss_pred HHHhCC-CHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHH
Q psy14291 392 RYYFEL-TREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESM 447 (538)
Q Consensus 392 ~~~~gl-~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L 447 (538)
..-||+ +.+.--.|..|. +|.|||||+|+.+|..++. +++.+.+
T Consensus 59 ~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~~~------~~l~~aI 103 (203)
T PRK14602 59 LELFGFATWDERQTFIVLI------SISKVGAKTALAILSQFRP------DDLRRLV 103 (203)
T ss_pred ceeeCCCCHHHHHHHHHHh------CCCCcCHHHHHHHHhhCCH------HHHHHHH
Confidence 345776 455555555554 7999999999999998764 5555554
No 46
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=81.14 E-value=1.9 Score=42.25 Aligned_cols=45 Identities=33% Similarity=0.499 Sum_probs=30.1
Q ss_pred HHHhCC-CHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHH
Q psy14291 392 RYYFEL-TREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMR 448 (538)
Q Consensus 392 ~~~~gl-~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~ 448 (538)
..-||+ +.+.--.|..|. +|+|||||+|..+|..++. +++.+.+.
T Consensus 57 ~~LyGF~~~~Er~lF~~L~------~V~GIGpK~Al~iL~~~~~------~el~~aI~ 102 (191)
T TIGR00084 57 ELLFGFNTLEERELFKELI------KVNGVGPKLALAILSNMSP------EEFVYAIE 102 (191)
T ss_pred ceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHhcCCH------HHHHHHHH
Confidence 345776 344444455554 8999999999999887653 45555543
No 47
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.47 E-value=1.9 Score=42.24 Aligned_cols=19 Identities=53% Similarity=0.873 Sum_probs=18.0
Q ss_pred CCCCCCHHHHHHHHHHcCC
Q psy14291 416 GLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygs 434 (538)
.|||||||+|.+++..||.
T Consensus 77 ~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSP 95 (192)
T ss_pred cCCCCCHHHHHHHHHhCCH
Confidence 5999999999999999997
No 48
>KOG2519|consensus
Probab=78.61 E-value=0.99 Score=49.49 Aligned_cols=61 Identities=36% Similarity=0.457 Sum_probs=49.3
Q ss_pred HHHHhhhhhhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhhccccCCCCcchHhH
Q psy14291 258 LLERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLELGTDKKRRPYVSRKM 320 (538)
Q Consensus 258 qee~~k~~R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~~~~k~rr~~lt~q~ 320 (538)
..+.+++.++...+|++|..+|++||.++|+|++.+|+|||||||++... ++.+..+++++
T Consensus 116 ~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EAEAqCA~Lnk~--g~V~~~at~Ds 176 (449)
T KOG2519|consen 116 KENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEAEAQCAALNKA--GKVYAVATEDS 176 (449)
T ss_pred HHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchHHHHHHHHhhc--Cceeeeecccc
Confidence 34567778888999999999999999999999999999999999988744 33333444444
No 49
>KOG2045|consensus
Probab=78.06 E-value=34 Score=41.21 Aligned_cols=30 Identities=37% Similarity=0.570 Sum_probs=21.4
Q ss_pred HHHHHHHHHcCCCCCCCCCCCCH-HHHHHHH
Q psy14291 400 EKLIQLALLVGSDYTPGLQGVGP-VTALEIL 429 (538)
Q Consensus 400 ~q~idl~~L~GsDyipGVpGIG~-KtA~kLL 429 (538)
+.||.++.|+|.|++|.+|++-. +.|+-||
T Consensus 277 DD~ILl~flVGNDFLPhLP~LHIn~gAlpll 307 (1493)
T KOG2045|consen 277 DDWILLGFLVGNDFLPHLPCLHINSGALPLL 307 (1493)
T ss_pred HHHHHHHHhhccccccCCCccccCCChHHHH
Confidence 44556666677999999999864 3566554
No 50
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.02 E-value=1.4 Score=43.16 Aligned_cols=19 Identities=21% Similarity=0.475 Sum_probs=11.9
Q ss_pred CCCCCCHHHHHHHHHHcCC
Q psy14291 416 GLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygs 434 (538)
+|.|||||+|+.+|..++.
T Consensus 77 ~VsGIGpK~Al~ILs~~~~ 95 (183)
T PRK14601 77 KVNGIGANTAMAVCSSLDV 95 (183)
T ss_pred ccCCccHHHHHHHHcCCCH
Confidence 5666666666666665543
No 51
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=76.18 E-value=3.1 Score=40.83 Aligned_cols=46 Identities=22% Similarity=0.292 Sum_probs=30.8
Q ss_pred HHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHH
Q psy14291 390 DIRYYFELT-REKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESM 447 (538)
Q Consensus 390 ~i~~~~gl~-~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L 447 (538)
+-..-||+. .+.--.|..|. +|.|||||+|+.+|..+.- +++.+.+
T Consensus 56 d~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~AL~iLs~~~~------~el~~aI 102 (188)
T PRK14606 56 DGITLYGFSNERKKELFLSLT------KVSRLGPKTALKIISNEDA------ETLVTMI 102 (188)
T ss_pred CCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCCCH------HHHHHHH
Confidence 334467864 44445555554 7899999999999987753 4555554
No 52
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=76.14 E-value=1.6 Score=50.21 Aligned_cols=26 Identities=23% Similarity=0.373 Sum_probs=23.5
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
.+|||||+|++.+||++|||+ ++|.+
T Consensus 555 ~~IpGIG~kr~~~LL~~FgSi-----~~I~~ 580 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFGSL-----ERVRA 580 (624)
T ss_pred hcCCCCCHHHHHHHHHHcCCH-----HHHHh
Confidence 599999999999999999999 77765
No 53
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=76.06 E-value=2.1 Score=28.41 Aligned_cols=18 Identities=39% Similarity=0.556 Sum_probs=15.2
Q ss_pred CCCCCCCCHHHHHHHHHH
Q psy14291 414 TPGLQGVGPVTALEILAK 431 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~ 431 (538)
+..|||||+++|..++..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 357999999999998863
No 54
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.73 E-value=3.1 Score=40.65 Aligned_cols=37 Identities=30% Similarity=0.504 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy14291 396 ELTREKLIQLALLVG-SDYTPGLQGVGPVTALEILAKFS 433 (538)
Q Consensus 396 gl~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~~yg 433 (538)
++++++|.. ++..| ...+..+||||+|||.+++-+..
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 356777764 33334 33357999999999998875533
No 55
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.38 E-value=1.7 Score=42.91 Aligned_cols=18 Identities=39% Similarity=0.866 Sum_probs=10.9
Q ss_pred CCCCCCHHHHHHHHHHcC
Q psy14291 416 GLQGVGPVTALEILAKFS 433 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~yg 433 (538)
+|.|||||+|+.+|..++
T Consensus 76 sVsGIGPK~ALaILs~~~ 93 (196)
T PRK13901 76 GVDGIGPRAALRVLSGIK 93 (196)
T ss_pred CcCCcCHHHHHHHHcCCC
Confidence 556666666666665543
No 56
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.35 E-value=3.2 Score=40.94 Aligned_cols=44 Identities=27% Similarity=0.588 Sum_probs=28.4
Q ss_pred HHHhCCC-HHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHH
Q psy14291 392 RYYFELT-REKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESM 447 (538)
Q Consensus 392 ~~~~gl~-~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L 447 (538)
..-||+. .+.--.|-.|. +|.|||||+|+.+|..++. +++.+.+
T Consensus 57 ~~LyGF~~~~Er~lF~~L~------~V~GIGpK~AL~iLs~~~~------~~l~~aI 101 (197)
T PRK14603 57 LSLYGFPDEDSLELFELLL------GVSGVGPKLALALLSALPP------ALLARAL 101 (197)
T ss_pred ceeeCcCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCH------HHHHHHH
Confidence 3457764 33333344443 7899999999999988754 4555554
No 57
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=75.26 E-value=1.9 Score=49.06 Aligned_cols=27 Identities=19% Similarity=0.294 Sum_probs=23.7
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 414 TPGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
+.+|||||+|+..+||+.|||+ ++|.+
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fgs~-----~~ik~ 542 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFKTL-----YDFLK 542 (567)
T ss_pred cccCCCCCHHHHHHHHHHhCCH-----HHHHh
Confidence 3589999999999999999999 67664
No 58
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.12 E-value=3.4 Score=40.51 Aligned_cols=49 Identities=27% Similarity=0.437 Sum_probs=31.9
Q ss_pred hhHHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHH
Q psy14291 388 APDIRYYFELT-REKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESMR 448 (538)
Q Consensus 388 ~~~i~~~~gl~-~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~ 448 (538)
.++-..-||+. .+.--.|-.|. +|.|||||+|+.+|..++- +++...+.
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li------sV~GIGpK~Al~iLs~~~~------~~l~~aI~ 103 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRMLV------KVSGVNYKTAMSILSKLTP------EQLFSAIV 103 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHccCCH------HHHHHHHH
Confidence 34444567864 44444444443 8899999999999988754 55555543
No 59
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.74 E-value=3.6 Score=40.69 Aligned_cols=36 Identities=17% Similarity=0.253 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy14291 397 LTREKLIQLALLVG-SDYTPGLQGVGPVTALEILAKFS 433 (538)
Q Consensus 397 l~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~~yg 433 (538)
+++++|.. ++..| ...+..+||||+|||.+++-+..
T Consensus 92 ~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 92 IKYNEFRD-AIDREDIELISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred CCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 56777664 33333 33357999999999999876544
No 60
>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=73.55 E-value=2.2 Score=48.62 Aligned_cols=21 Identities=24% Similarity=0.368 Sum_probs=20.1
Q ss_pred CCCCCCCHHHHHHHHHHcCCC
Q psy14291 415 PGLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl 435 (538)
.+|||||+|+..+||+.|||+
T Consensus 544 d~I~GIG~kr~~~LL~~Fgs~ 564 (574)
T TIGR00194 544 LKIPGVGEKRVQKLLKYFGSL 564 (574)
T ss_pred hcCCCCCHHHHHHHHHHcCCH
Confidence 589999999999999999998
No 61
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.51 E-value=3.8 Score=40.44 Aligned_cols=44 Identities=25% Similarity=0.487 Sum_probs=28.9
Q ss_pred HHHhCCC-HHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHH
Q psy14291 392 RYYFELT-REKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPSDSPNQNYIVESM 447 (538)
Q Consensus 392 ~~~~gl~-~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L 447 (538)
..-||+. .+.--.|..|. +|.|||||+|+.+|..+.. +++.+.+
T Consensus 58 ~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~~~------~el~~aI 102 (195)
T PRK14604 58 LTLYGFSTPAQRQLFELLI------GVSGVGPKAALNLLSSGTP------DELQLAI 102 (195)
T ss_pred ceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCH------HHHHHHH
Confidence 3457763 44444444443 7899999999999987643 4555554
No 62
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.36 E-value=2.1 Score=41.89 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy14291 396 ELTREKLIQLALLVG-SDYTPGLQGVGPVTALEILAKFS 433 (538)
Q Consensus 396 gl~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~~yg 433 (538)
++++++|.. ++..| ...+..+||||+|||.+++-+..
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 92 NEDAETLVT-MIASQDVEGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 357777774 33334 33457999999999999876543
No 63
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=73.35 E-value=2.2 Score=48.51 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=24.5
Q ss_pred CCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 413 YTPGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 413 yipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
-+.+|||||+|+..+||+.|||+ ++|.+
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~-----~~I~~ 542 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTY-----KDILL 542 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCH-----HHHHh
Confidence 45699999999999999999999 77664
No 64
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.11 E-value=2.4 Score=41.82 Aligned_cols=36 Identities=25% Similarity=0.278 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy14291 397 LTREKLIQLALLVG-SDYTPGLQGVGPVTALEILAKFS 433 (538)
Q Consensus 397 l~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~~yg 433 (538)
+++++|+. ++..| ..-+..+||||+|||.+++-+..
T Consensus 93 ~~~~el~~-aI~~~D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 93 GTPDELQL-AIAGGDVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 56777774 23333 33357999999999999876543
No 65
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.74 E-value=2.4 Score=41.97 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy14291 397 LTREKLIQLALLVG-SDYTPGLQGVGPVTALEILAKFS 433 (538)
Q Consensus 397 l~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~~yg 433 (538)
+++++|+. ++..| .+-+..+||||+|||.+++-+..
T Consensus 94 ~~~~~l~~-aI~~~D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 94 FRPDDLRR-LVAEEDVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred CCHHHHHH-HHHhCCHHHHhcCCCcCHHHHHHHHHHHH
Confidence 56777764 33334 33367999999999998875543
No 66
>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=70.93 E-value=2.7 Score=33.18 Aligned_cols=20 Identities=20% Similarity=0.456 Sum_probs=17.9
Q ss_pred CCCCCCHHHHHHHHHH-cCCC
Q psy14291 416 GLQGVGPVTALEILAK-FSPS 435 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~-ygsl 435 (538)
.|||||+++|..|... |+++
T Consensus 9 ~I~Gig~~~a~~L~~~G~~t~ 29 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIKTL 29 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCSSH
T ss_pred cCCCCCHHHHHHHHhcCCCcH
Confidence 6899999999999988 7776
No 67
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=70.36 E-value=3 Score=47.98 Aligned_cols=26 Identities=23% Similarity=0.483 Sum_probs=22.8
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
.||||||+|+|..|++.|||+ ++|.+
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~-----~~i~~ 597 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSV-----EKVAK 597 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCH-----HHHHh
Confidence 499999999999999999998 66643
No 68
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.14 E-value=3.6 Score=40.33 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHHHc
Q psy14291 397 LTREKLIQLALLVG-SDYTPGLQGVGPVTALEILAKF 432 (538)
Q Consensus 397 l~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~~y 432 (538)
+++++|.. ++-.| ..-+ .+||||+|||.+++-+.
T Consensus 93 ~~~~~l~~-aI~~~D~~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 93 LTPEQLFS-AIVNEDKAAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred CCHHHHHH-HHHcCCHhhe-ECCCCcHHHHHHHHHHH
Confidence 67888775 34444 3447 89999999999887553
No 69
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.67 E-value=2.8 Score=41.33 Aligned_cols=35 Identities=26% Similarity=0.274 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHcCCCC--CCCCCCCCHHHHHHHHHHcC
Q psy14291 397 LTREKLIQLALLVGSDY--TPGLQGVGPVTALEILAKFS 433 (538)
Q Consensus 397 l~~~q~idl~~L~GsDy--ipGVpGIG~KtA~kLL~~yg 433 (538)
+++++|.. ++...|. +..+||||+|||.+++-+..
T Consensus 92 ~~~~~l~~--aI~~~D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 92 LPPALLAR--ALLEGDARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred CCHHHHHH--HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 67777774 3333443 57999999999998876543
No 70
>KOG2518|consensus
Probab=68.16 E-value=9.9 Score=42.71 Aligned_cols=48 Identities=33% Similarity=0.327 Sum_probs=42.5
Q ss_pred HHHhhhhhhhhcccHHhHHHHHHHHHhhCCcEEeCCCchhhhhhhhhh
Q psy14291 259 LERGKQTRLASTITEQMSREAQELLQLFGVPFIVAPGEAEAQCASLEL 306 (538)
Q Consensus 259 ee~~k~~R~A~~it~~m~~e~~kLL~~~g~P~iv~d~Eaeaqca~l~~ 306 (538)
.++..+-+.+..||.+|....-+.++..++.|+|+|.||.||=+|+..
T Consensus 113 ~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~ 160 (556)
T KOG2518|consen 113 SNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLER 160 (556)
T ss_pred HHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHHHh
Confidence 455667788999999999999999999999999999999999888873
No 71
>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=67.82 E-value=3.7 Score=32.15 Aligned_cols=20 Identities=45% Similarity=0.596 Sum_probs=13.6
Q ss_pred CCCCCCHHHHHHHHHH-cCCC
Q psy14291 416 GLQGVGPVTALEILAK-FSPS 435 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~-ygsl 435 (538)
+|.|||++||.++..+ |.|+
T Consensus 6 ~I~GVG~~tA~~w~~~G~rtl 26 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAKGIRTL 26 (52)
T ss_dssp TSTT--HHHHHHHHHTT--SH
T ss_pred hcccccHHHHHHHHHhCCCCH
Confidence 7899999999999974 5555
No 72
>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=67.06 E-value=5 Score=34.05 Aligned_cols=23 Identities=30% Similarity=0.605 Sum_probs=20.6
Q ss_pred CCCCCCCCCHHHHHHHHHHcCCC
Q psy14291 413 YTPGLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 413 yipGVpGIG~KtA~kLL~~ygsl 435 (538)
-+..|||||+.+|..|+.+.|++
T Consensus 3 ~l~sipGig~~~a~~llaeigd~ 25 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDI 25 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCc
Confidence 35689999999999999999887
No 73
>KOG2044|consensus
Probab=67.02 E-value=43 Score=39.64 Aligned_cols=99 Identities=20% Similarity=0.336 Sum_probs=59.1
Q ss_pred CCCccc----CcchHHHHHHHHHhhcC---------CCceEecCCceEeec-C-----eEEEEecCCC------------
Q psy14291 331 GVPFIV----APGEAEAQCASLELGNH---------TQGVITDDSDIWLFG-A-----RTVYKNFFDK------------ 379 (538)
Q Consensus 331 GIp~i~----APgEADaqiA~La~~g~---------vd~IiS~DsDllLfG-~-----~~Vi~~~~~~------------ 379 (538)
||.+|- .|||.|--|-..-+.-. .+.+..-|-|++++| + -.|+|..+..
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 566654 48899997766655422 234888999999775 2 2466643210
Q ss_pred -------------------------CCcEEEEchhHHHH----HhC-------CC----HHHHHHHHHHcCCCCCCCCCC
Q psy14291 380 -------------------------KSHVLRYTAPDIRY----YFE-------LT----REKLIQLALLVGSDYTPGLQG 419 (538)
Q Consensus 380 -------------------------~~~~~~~~~~~i~~----~~g-------l~----~~q~idl~~L~GsDyipGVpG 419 (538)
.+.+.+++..-+.+ .+- ++ -+.++.+|-++|.|++|.+|-
T Consensus 270 gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPs 349 (931)
T KOG2044|consen 270 GHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMPNLPFTFDLERAIDDWVFLCFFVGNDFLPHLPS 349 (931)
T ss_pred CCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCCCCCccccHHhhhcceEEEEeeecCccCCCCCc
Confidence 01234444433333 221 12 256677899999999999997
Q ss_pred CCH-HHHHHHH
Q psy14291 420 VGP-VTALEIL 429 (538)
Q Consensus 420 IG~-KtA~kLL 429 (538)
+-+ ..|.++|
T Consensus 350 LeIRegAId~L 360 (931)
T KOG2044|consen 350 LEIREGAIDRL 360 (931)
T ss_pred hhhhhcHHHHH
Confidence 643 2444443
No 74
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=66.45 E-value=13 Score=36.94 Aligned_cols=42 Identities=26% Similarity=0.481 Sum_probs=27.8
Q ss_pred EchhHHHHHhCCCH-HHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcC
Q psy14291 386 YTAPDIRYYFELTR-EKLIQLALLVGSDYTPGLQGVGPVTALEILAKFS 433 (538)
Q Consensus 386 ~~~~~i~~~~gl~~-~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~yg 433 (538)
+-+++...-||+.. +.=..|..|. +|.|||||+|+.+|..+.
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~Li------sVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLLI------SVNGIGPKLALAILSNLD 94 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHHH------ccCCccHHHHHHHHcCCC
Confidence 44566677889853 2222333333 688999999999987654
No 75
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=65.03 E-value=4.3 Score=47.07 Aligned_cols=27 Identities=30% Similarity=0.333 Sum_probs=23.5
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 414 TPGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
...|||||+|++.+||+.|||+ ++|.+
T Consensus 610 L~~IpGiG~kr~~~LL~~FgS~-----~~i~~ 636 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFGSF-----RSLQS 636 (691)
T ss_pred cccCCCCCHHHHHHHHHHhcCH-----HHHHh
Confidence 3589999999999999999999 66654
No 76
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=62.42 E-value=4.9 Score=46.06 Aligned_cols=26 Identities=27% Similarity=0.494 Sum_probs=23.1
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
.+|||||++++.+|++.|||+ ++|.+
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~-----~~i~~ 571 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSL-----KAIKE 571 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCH-----HHHHh
Confidence 589999999999999999998 66664
No 77
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=61.26 E-value=5 Score=45.78 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=24.5
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCchhHHHHH
Q psy14291 414 TPGLQGVGPVTALEILAKFSPSDSPNQNYIVES 446 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~ 446 (538)
+..|||||++++.+||+.|||+ ++|.++
T Consensus 527 L~~IpGIG~kr~~~LL~~FGS~-----~~I~~A 554 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRFGSV-----EGVREA 554 (577)
T ss_pred HhcCCCCCHHHHHHHHHHcCCH-----HHHHhC
Confidence 4689999999999999999999 777653
No 78
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=60.06 E-value=6 Score=40.13 Aligned_cols=22 Identities=27% Similarity=0.471 Sum_probs=20.3
Q ss_pred CCCCCCCCHHHHHHHHHH-cCCC
Q psy14291 414 TPGLQGVGPVTALEILAK-FSPS 435 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~-ygsl 435 (538)
+..|||||+++|.+|++. |+|+
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sv 27 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESV 27 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCH
Confidence 458899999999999999 9998
No 79
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=58.34 E-value=10 Score=37.70 Aligned_cols=36 Identities=25% Similarity=0.261 Sum_probs=23.5
Q ss_pred CCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHc
Q psy14291 397 LTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKF 432 (538)
Q Consensus 397 l~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~y 432 (538)
++++.|...-..---.++..+||||.|||.+++-+.
T Consensus 93 ~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 93 LDPEELAQAIANEDVKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHH
Confidence 466666643222113345799999999999887553
No 80
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=56.88 E-value=7.3 Score=45.32 Aligned_cols=26 Identities=23% Similarity=0.486 Sum_probs=23.6
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
..|||||++++.+|++.|||+ ++|.+
T Consensus 640 ~~IPGIGpkr~k~LL~~FGSl-----e~I~~ 665 (694)
T PRK14666 640 QRVEGIGPATARLLWERFGSL-----QAMAA 665 (694)
T ss_pred hhCCCCCHHHHHHHHHHhCCH-----HHHHh
Confidence 489999999999999999999 77776
No 81
>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=55.27 E-value=7.9 Score=34.06 Aligned_cols=28 Identities=14% Similarity=0.319 Sum_probs=24.3
Q ss_pred cchHHHHHHHHHhhcCCCceEecCCceE
Q psy14291 338 PGEAEAQCASLELGNHTQGVITDDSDIW 365 (538)
Q Consensus 338 PgEADaqiA~La~~g~vd~IiS~DsDll 365 (538)
+...|+.+..+|..+.+|.|+|+|+|++
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll 112 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLL 112 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHh
Confidence 4577888888889999999999999986
No 82
>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=54.36 E-value=8.9 Score=26.89 Aligned_cols=17 Identities=29% Similarity=0.452 Sum_probs=11.9
Q ss_pred CCCCCCCHHHHHHHHHHc
Q psy14291 415 PGLQGVGPVTALEILAKF 432 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~y 432 (538)
.-++|||.+|+.+| +++
T Consensus 14 ~~~~GIG~kt~~kL-~~~ 30 (32)
T PF11798_consen 14 RKFWGIGKKTAKKL-NKL 30 (32)
T ss_dssp GGSTTS-HHHHHHH-HCT
T ss_pred HhhCCccHHHHHHH-HHc
Confidence 46899999999764 443
No 83
>PF04796 RepA_C: Plasmid encoded RepA protein; InterPro: IPR006881 This is a family of plasmid encoded proteins involved in plasmid replication. The role of RepA in the replication process is not clearly understood [].
Probab=48.04 E-value=6.5 Score=37.76 Aligned_cols=38 Identities=21% Similarity=0.278 Sum_probs=29.4
Q ss_pred chHHHhhhcCcccccccc---cCeEEEeehhhHHHhhhhhh
Q psy14291 114 GLWKLLEASGKPVPVETL---ENKVLAVGILYFTQGRASAL 151 (538)
Q Consensus 114 GLw~~l~~~~~~~~~~~l---~G~~laiD~s~wl~~~~~~~ 151 (538)
+....|.....|+..+.+ +|.-+|+|+|+||-.+.+.+
T Consensus 111 ~Ff~~l~~hpVPld~ralraL~~Sp~AlDiY~WL~yR~~~l 151 (161)
T PF04796_consen 111 EFFQELIDHPVPLDLRALRALKGSPLALDIYAWLTYRLHRL 151 (161)
T ss_pred HHHHHHHHCCCCCCHHHHHHHccChHHHHHHHHHHHHHHhc
Confidence 566778777778876654 58999999999998776544
No 84
>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=47.47 E-value=15 Score=36.08 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=20.8
Q ss_pred CHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHH
Q psy14291 398 TREKLIQLALLVG-SDYTPGLQGVGPVTALEILA 430 (538)
Q Consensus 398 ~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~ 430 (538)
+++++...+ ..| ..-+..|||||+|||.+++-
T Consensus 93 ~~~el~~aI-~~~d~~~L~~ipGiGkKtAerIil 125 (191)
T TIGR00084 93 SPEEFVYAI-ETEEVKALVKIPGVGKKTAERLLL 125 (191)
T ss_pred CHHHHHHHH-HhCCHHHHHhCCCCCHHHHHHHHH
Confidence 566665422 222 22346899999999988873
No 85
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=47.23 E-value=13 Score=42.53 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=23.1
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVES 446 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~ 446 (538)
.+|||||+++..+||+.|||+ .+|.++
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~-----~~i~~A 559 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSL-----KGIKSA 559 (581)
T ss_pred ccCCCcCHHHHHHHHHHhhCH-----HHHHhc
Confidence 488999999999999999999 666543
No 86
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.58 E-value=13 Score=36.49 Aligned_cols=35 Identities=26% Similarity=0.499 Sum_probs=22.5
Q ss_pred CCHHHHHHHHHHcC-CCCCCCCCCCCHHHHHHHHHHc
Q psy14291 397 LTREKLIQLALLVG-SDYTPGLQGVGPVTALEILAKF 432 (538)
Q Consensus 397 l~~~q~idl~~L~G-sDyipGVpGIG~KtA~kLL~~y 432 (538)
+++++|+. ++..+ -.-+..|||||+|||.+++-+.
T Consensus 93 ~~~~~l~~-aI~~~D~~~L~~vpGIGkKtAerIilEL 128 (194)
T PRK14605 93 MNAEALAS-AIISGNAELLSTIPGIGKKTASRIVLEL 128 (194)
T ss_pred CCHHHHHH-HHHhCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 45676653 22233 2224689999999999887553
No 87
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=45.49 E-value=15 Score=37.79 Aligned_cols=26 Identities=27% Similarity=0.569 Sum_probs=22.5
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCchhHHHHH
Q psy14291 416 GLQGVGPVTALEILAKFSPSDSPNQNYIVES 446 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~ 446 (538)
++||||++.|..++..|||. +++..+
T Consensus 186 s~pgig~~~a~~ll~~fgS~-----~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSV-----EDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhcCH-----HHHhhc
Confidence 78999999999999999999 665543
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=44.96 E-value=32 Score=40.42 Aligned_cols=32 Identities=25% Similarity=0.453 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCCC
Q psy14291 398 TREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 398 ~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygsl 435 (538)
+.+.++.|.. |+ -+||||+|+|.+++..||.-
T Consensus 76 ~~~~i~~yL~---s~---~~~GIG~~~A~~iv~~fg~~ 107 (720)
T TIGR01448 76 SKEGIVAYLS---SR---SIKGVGKKLAQRIVKTFGEA 107 (720)
T ss_pred CHHHHHHHHh---cC---CCCCcCHHHHHHHHHHhCHh
Confidence 4567776654 22 48899999999999999964
No 89
>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=44.63 E-value=16 Score=42.43 Aligned_cols=20 Identities=35% Similarity=0.556 Sum_probs=19.0
Q ss_pred CCCCCCHHHHHHHHHHcCCC
Q psy14291 416 GLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygsl 435 (538)
||||||+++|..|++.|+++
T Consensus 502 gIpgVG~~~ak~L~~~f~sl 521 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTL 521 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCH
Confidence 89999999999999999988
No 90
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=44.25 E-value=16 Score=42.59 Aligned_cols=20 Identities=35% Similarity=0.609 Sum_probs=19.3
Q ss_pred CCCCCCHHHHHHHHHHcCCC
Q psy14291 416 GLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygsl 435 (538)
||||||+++|..|++.|+++
T Consensus 532 gIpgIG~~~ak~L~~~F~si 551 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTF 551 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCH
Confidence 89999999999999999998
No 91
>PRK09482 flap endonuclease-like protein; Provisional
Probab=43.48 E-value=1.7e+02 Score=30.21 Aligned_cols=29 Identities=24% Similarity=0.274 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhCCcEEeCCC-chhhhhhhh
Q psy14291 276 SREAQELLQLFGVPFIVAPG-EAEAQCASL 304 (538)
Q Consensus 276 ~~e~~kLL~~~g~P~iv~d~-Eaeaqca~l 304 (538)
+..+++++..+|+|++..++ ||.+.++.+
T Consensus 86 ~~~i~~~l~~~gi~~~~~~g~EADDvIatl 115 (256)
T PRK09482 86 LPAIRAAFEELGIDSWHADGNEADDLIATL 115 (256)
T ss_pred HHHHHHHHHhCCCCEeccCCcCHHHHHHHH
Confidence 46789999999999999988 888776544
No 92
>PF08258 WWamide: WWamide peptide; InterPro: IPR013271 This family contain neuropeptides, isolated from ganglia of Achatina fulica (Giant African snail). Each peptide has a Trp residue at both the N- and C-termini. Purified WWamide-1, -2 and -3 showed an inhibitory effect on the phasic contractions of the anterior byssus retractor muscle (ABRM) [].
Probab=43.10 E-value=11 Score=18.31 Aligned_cols=7 Identities=43% Similarity=1.574 Sum_probs=6.0
Q ss_pred Ccccccc
Q psy14291 11 WTNMSQW 17 (538)
Q Consensus 11 ~~~~~~~ 17 (538)
|.+|+-|
T Consensus 1 Wk~MavW 7 (7)
T PF08258_consen 1 WKQMAVW 7 (7)
T ss_pred CcccccC
Confidence 8889887
No 93
>PRK00076 recR recombination protein RecR; Reviewed
Probab=41.85 E-value=24 Score=35.00 Aligned_cols=39 Identities=18% Similarity=0.289 Sum_probs=22.6
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNW 453 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~ 453 (538)
.-+||||+|+|.++.-..-..+....+.+.+.|.+.+..
T Consensus 14 ~~LPGIG~KsA~Rla~~ll~~~~~~~~~la~~i~~~~~~ 52 (196)
T PRK00076 14 RKLPGIGPKSAQRLAFHLLQRDREDVLRLAQALEEAKEK 52 (196)
T ss_pred HHCCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc
Confidence 368999999999986543322111124444555555443
No 94
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.46 E-value=25 Score=34.86 Aligned_cols=39 Identities=18% Similarity=0.267 Sum_probs=22.2
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNW 453 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~ 453 (538)
.-+||||+|+|.++.-..-..+-...+.+.+.|.+.+..
T Consensus 14 ~~LPGIG~KsA~RlA~~ll~~~~~~~~~la~ai~~~~~~ 52 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKEN 52 (195)
T ss_pred HHCCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc
Confidence 368999999999985443222111124444555555443
No 95
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=40.18 E-value=24 Score=35.07 Aligned_cols=39 Identities=21% Similarity=0.300 Sum_probs=22.2
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNW 453 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~ 453 (538)
.-+||||+|+|.++.-..-..+-...+.+.+++.+.+..
T Consensus 15 ~kLPGvG~KsA~R~AfhLL~~~~~~~~~la~al~~a~~~ 53 (198)
T COG0353 15 KKLPGVGPKSAQRLAFHLLQRDREDVERLAKALLEAKEN 53 (198)
T ss_pred hhCCCCChhHHHHHHHHHHccCHHHHHHHHHHHHHHHhc
Confidence 478999999999885433222111124444555554443
No 96
>PRK13844 recombination protein RecR; Provisional
Probab=39.90 E-value=26 Score=34.96 Aligned_cols=40 Identities=10% Similarity=0.061 Sum_probs=22.8
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCchhHHHHHHHHHHHHH
Q psy14291 415 PGLQGVGPVTALEILAKFSPSDSPNQNYIVESMRRFKNWL 454 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~~L~~~k~~~ 454 (538)
.-+||||+|+|.++.-..-..+....+.+.+.|.+.+...
T Consensus 18 ~~LPGIG~KsA~Rla~~lL~~~~~~~~~la~~i~~~~~~i 57 (200)
T PRK13844 18 RKLPTIGKKSSQRLALYLLDKSPETAIAIANSLLDATANI 57 (200)
T ss_pred HHCCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhC
Confidence 3689999999999865432221111244555555554433
No 97
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=39.06 E-value=14 Score=44.08 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=23.4
Q ss_pred CCCCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 413 YTPGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 413 yipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
|+-++||||++.|..|+.+||++ +++..
T Consensus 758 ~L~~lPgI~~~~a~~ll~~f~si-----~~l~~ 785 (814)
T TIGR00596 758 FLLKLPGVTKKNYRNLRKKVKSI-----RELAK 785 (814)
T ss_pred HHHHCCCCCHHHHHHHHHHcCCH-----HHHHh
Confidence 33479999999999999999998 66554
No 98
>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=37.87 E-value=26 Score=27.46 Aligned_cols=19 Identities=26% Similarity=0.392 Sum_probs=15.4
Q ss_pred CCCCCCCCHHHHHHHHHHc
Q psy14291 414 TPGLQGVGPVTALEILAKF 432 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~y 432 (538)
+-.|||||+++|.+++...
T Consensus 40 L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 40 LAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHTSTTSSHHHHHHHHHHH
T ss_pred HhcCCCCCHHHHHHHHHHH
Confidence 3478999999999988653
No 99
>PRK13766 Hef nuclease; Provisional
Probab=36.02 E-value=26 Score=40.95 Aligned_cols=27 Identities=30% Similarity=0.521 Sum_probs=23.2
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCCCCchhHHHH
Q psy14291 414 TPGLQGVGPVTALEILAKFSPSDSPNQNYIVE 445 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~ygsl~~~~~e~Il~ 445 (538)
+.++||||+++|.+|++.||++ +++++
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~-----~~i~~ 743 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSV-----EAVMT 743 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCH-----HHHHh
Confidence 3589999999999999999998 66654
No 100
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=33.43 E-value=66 Score=34.28 Aligned_cols=53 Identities=17% Similarity=0.239 Sum_probs=37.5
Q ss_pred EEEEchhHHHHHhCCCHHHHHHH--------------HHHcCCCCCC------------CCCCCCHHHHHHHHH--HcCC
Q psy14291 383 VLRYTAPDIRYYFELTREKLIQL--------------ALLVGSDYTP------------GLQGVGPVTALEILA--KFSP 434 (538)
Q Consensus 383 ~~~~~~~~i~~~~gl~~~q~idl--------------~~L~GsDyip------------GVpGIG~KtA~kLL~--~ygs 434 (538)
-..|.++.+...||+.++.+.+- ++|--.|..| -|||||.|+|..++. .+-.
T Consensus 275 hRLYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~Rr~~r 354 (404)
T COG4277 275 HRLYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMTRRRTR 354 (404)
T ss_pred HHHHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHHhhhcc
Confidence 35688888889999988877642 3444344444 589999999999885 3444
Q ss_pred C
Q psy14291 435 S 435 (538)
Q Consensus 435 l 435 (538)
+
T Consensus 355 l 355 (404)
T COG4277 355 L 355 (404)
T ss_pred c
Confidence 4
No 101
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=33.19 E-value=37 Score=32.12 Aligned_cols=15 Identities=40% Similarity=0.753 Sum_probs=13.4
Q ss_pred CCCCCCHHHHHHHHH
Q psy14291 416 GLQGVGPVTALEILA 430 (538)
Q Consensus 416 GVpGIG~KtA~kLL~ 430 (538)
.+||||+++|.+++.
T Consensus 101 ~lpgIG~~kA~aIi~ 115 (149)
T COG1555 101 ALPGIGPKKAQAIID 115 (149)
T ss_pred HCCCCCHHHHHHHHH
Confidence 679999999999985
No 102
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=32.99 E-value=28 Score=40.52 Aligned_cols=20 Identities=25% Similarity=0.426 Sum_probs=18.0
Q ss_pred CCCCCCHHHHHHHHHHcCCC
Q psy14291 416 GLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygsl 435 (538)
||||||+++|..|++.|+++
T Consensus 515 gi~~IG~~~ak~L~~~f~sl 534 (665)
T PRK07956 515 GIRHVGEKAAKALARHFGSL 534 (665)
T ss_pred hccCcCHHHHHHHHHHcCCH
Confidence 88999999999999999887
No 103
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=32.89 E-value=74 Score=30.11 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecCCCCCcEEEEchhHHHHH
Q psy14291 340 EAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYY 394 (538)
Q Consensus 340 EADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~~~~~~~~~~i~~~ 394 (538)
+=|.-.=-+|-.+.++.++|+|+|++.... . ++.+++.+++.+.+.
T Consensus 91 p~Dn~~L~~A~~~kA~~lvTgD~dLL~lr~------~---n~~~~Iltp~eF~~~ 136 (142)
T COG1569 91 PKDNKLLALAYESKADYLVTGDQDLLVLRD------E---NKRVEILTPQEFLEE 136 (142)
T ss_pred chHHHHHHHHHhccCCEEEEcchhhheecc------c---CCcEEEcCHHHHHHH
Confidence 345555566778899999999999986522 1 114677776666553
No 104
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=32.06 E-value=38 Score=29.83 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=13.8
Q ss_pred CCCCCCCHHHHHHHHH
Q psy14291 415 PGLQGVGPVTALEILA 430 (538)
Q Consensus 415 pGVpGIG~KtA~kLL~ 430 (538)
..|||||+++|..|..
T Consensus 15 ~~iP~IG~a~a~DL~~ 30 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRL 30 (93)
T ss_pred hcCCCccHHHHHHHHH
Confidence 3789999999999874
No 105
>PRK14168 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=30.54 E-value=4.2e+02 Score=28.04 Aligned_cols=91 Identities=11% Similarity=0.061 Sum_probs=50.3
Q ss_pred HHHHHHHHcCCCcccC--c-----chHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecCCCCCcEEEEchhHHHHH
Q psy14291 322 EAQELLQLFGVPFIVA--P-----GEAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYY 394 (538)
Q Consensus 322 ~ik~lL~~~GIp~i~A--P-----gEADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~~~~~~~~~~i~~~ 394 (538)
..++.++.+||.+... | .|-.+.|..|+.-..+|||+- ..++. ..++...+.+.
T Consensus 53 ~k~k~~~~~Gi~~~~~~l~~~~t~~el~~~I~~lN~D~~V~GIiv-------------qlPlP------~~i~~~~i~~~ 113 (297)
T PRK14168 53 LKIKTAHRLGFHEIQDNQSVDITEEELLALIDKYNNDDSIHGILV-------------QLPLP------KHINEKKVLNA 113 (297)
T ss_pred HHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCCCCCEEEE-------------eCCCC------CCCCHHHHHhc
Confidence 4577889999998662 1 145556666666666777652 22221 11233333332
Q ss_pred h-------CCCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCC
Q psy14291 395 F-------ELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 395 ~-------gl~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygs 434 (538)
. |+++..+-.++ .| |.-+++--|-+.-.++||+.|+-
T Consensus 114 I~p~KDVDGl~~~n~g~l~--~~-~~~~~~~PcTp~avi~lL~~~~i 157 (297)
T PRK14168 114 IDPDKDVDGFHPVNVGRLM--IG-GDEVKFLPCTPAGIQEMLVRSGV 157 (297)
T ss_pred cCccccccccChhhHHHHh--cC-CCCCCCcCCCHHHHHHHHHHhCC
Confidence 1 55555444332 33 32245555777888888888764
No 106
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=30.48 E-value=45 Score=32.60 Aligned_cols=21 Identities=24% Similarity=0.366 Sum_probs=16.4
Q ss_pred CCCCCCCCHHHHHHHHHHcCC
Q psy14291 414 TPGLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~ygs 434 (538)
+..|||||+|+|.+++.++..
T Consensus 110 L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 110 LTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHhCCCCCHHHHHHHHHHHHH
Confidence 357999999999888766543
No 107
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=29.45 E-value=40 Score=31.52 Aligned_cols=15 Identities=27% Similarity=0.355 Sum_probs=13.1
Q ss_pred CCCCCCHHHHHHHHH
Q psy14291 416 GLQGVGPVTALEILA 430 (538)
Q Consensus 416 GVpGIG~KtA~kLL~ 430 (538)
.+|||||+.|.++++
T Consensus 65 ~lpGigP~~A~~IV~ 79 (132)
T PRK02515 65 QFPGMYPTLAGKIVK 79 (132)
T ss_pred HCCCCCHHHHHHHHH
Confidence 468999999999995
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=28.37 E-value=36 Score=30.85 Aligned_cols=18 Identities=33% Similarity=0.564 Sum_probs=16.1
Q ss_pred CCCCCCHHHHHHHHHHcC
Q psy14291 416 GLQGVGPVTALEILAKFS 433 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~yg 433 (538)
.+||||+++|.++|..+.
T Consensus 72 ~lpGIG~~~A~~Ii~~R~ 89 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYRE 89 (120)
T ss_pred cCCCCCHHHHHHHHHHHH
Confidence 789999999999998763
No 109
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=28.32 E-value=59 Score=28.71 Aligned_cols=35 Identities=17% Similarity=0.098 Sum_probs=27.1
Q ss_pred hHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEe
Q psy14291 340 EAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKN 375 (538)
Q Consensus 340 EADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~ 375 (538)
-+|+.++..+.... ..++|.|+|+--|+...++.+
T Consensus 105 ~~D~~i~a~A~~~~-~~lvT~D~~f~~~~~~~i~~P 139 (142)
T TIGR00028 105 VTDAHLAALAREHG-AELVTFDRGFARFAGIRWRDP 139 (142)
T ss_pred chHHHHHHHHHHcC-CEEEecCCCccccCCCeeeCC
Confidence 58999999988876 589999999656666666543
No 110
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=26.85 E-value=59 Score=26.14 Aligned_cols=19 Identities=32% Similarity=0.543 Sum_probs=16.4
Q ss_pred CCCCCHHHHHHHHHH---cCCC
Q psy14291 417 LQGVGPVTALEILAK---FSPS 435 (538)
Q Consensus 417 VpGIG~KtA~kLL~~---ygsl 435 (538)
+||||+++|.++|.. +|..
T Consensus 22 ipgig~~~a~~Il~~R~~~g~~ 43 (69)
T TIGR00426 22 MNGVGLKKAEAIVSYREEYGPF 43 (69)
T ss_pred CCCCCHHHHHHHHHHHHHcCCc
Confidence 789999999999987 6655
No 111
>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=25.95 E-value=4.4e+02 Score=25.19 Aligned_cols=22 Identities=41% Similarity=0.723 Sum_probs=16.8
Q ss_pred HHHHHHHHHhhCCcEEeCCC-ch
Q psy14291 276 SREAQELLQLFGVPFIVAPG-EA 297 (538)
Q Consensus 276 ~~e~~kLL~~~g~P~iv~d~-Ea 297 (538)
+..+++++..+|++++..+| ||
T Consensus 88 ~~~i~~~l~~~gi~~~~~~g~EA 110 (169)
T PF02739_consen 88 LPYIKELLEALGIPVLEVPGYEA 110 (169)
T ss_dssp HHHHHHHHHHTTSEEEEETTB-H
T ss_pred HHHHHHHHHHCCCCEecCCCCcH
Confidence 45678899999999888777 54
No 112
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=25.87 E-value=43 Score=32.78 Aligned_cols=19 Identities=32% Similarity=0.357 Sum_probs=15.2
Q ss_pred CCCCCCHHHHHHHHHHcCC
Q psy14291 416 GLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygs 434 (538)
.+||||+|||--+|..+|.
T Consensus 119 ~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 119 ALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred cCCCCCHHHHHHHHHHHHH
Confidence 7899999999777665554
No 113
>PF13052 DUF3913: Protein of unknown function (DUF3913)
Probab=25.55 E-value=36 Score=26.39 Aligned_cols=26 Identities=31% Similarity=0.503 Sum_probs=19.0
Q ss_pred HcC-CCCCCCCCCCCHHHHHHHHHHcCCC
Q psy14291 408 LVG-SDYTPGLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 408 L~G-sDyipGVpGIG~KtA~kLL~~ygsl 435 (538)
|+| -||.|.||.||.|. ++|+...+.
T Consensus 14 llgiwdnvptiprigekv--eilktirtv 40 (57)
T PF13052_consen 14 LLGIWDNVPTIPRIGEKV--EILKTIRTV 40 (57)
T ss_pred hhhhhccCCCccccchhh--hHHhhhhee
Confidence 557 79999999999875 455554443
No 114
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=25.29 E-value=53 Score=26.55 Aligned_cols=14 Identities=36% Similarity=0.517 Sum_probs=12.1
Q ss_pred CCCCCCCHHHHHHH
Q psy14291 415 PGLQGVGPVTALEI 428 (538)
Q Consensus 415 pGVpGIG~KtA~kL 428 (538)
.++||||.++|.++
T Consensus 50 ~~l~gIG~~ia~kI 63 (68)
T PF14716_consen 50 KKLPGIGKSIAKKI 63 (68)
T ss_dssp CTSTTTTHHHHHHH
T ss_pred hhCCCCCHHHHHHH
Confidence 68999999999765
No 115
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=24.93 E-value=86 Score=29.15 Aligned_cols=44 Identities=23% Similarity=0.357 Sum_probs=35.2
Q ss_pred chHhHHHHHHHHHHcCCCcccCcchHHHHHHHHHhhcCCCceEe
Q psy14291 316 VSRKMLEAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVIT 359 (538)
Q Consensus 316 lt~q~~~ik~lL~~~GIp~i~APgEADaqiA~La~~g~vd~IiS 359 (538)
+-+.+..+++-|+.+|++.+.-.|++.+.+..|++.-.++.|++
T Consensus 51 l~~sL~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~~~~V~~ 94 (165)
T PF00875_consen 51 LLESLADLQESLRKLGIPLLVLRGDPEEVLPELAKEYGATAVYF 94 (165)
T ss_dssp HHHHHHHHHHHHHHTTS-EEEEESSHHHHHHHHHHHHTESEEEE
T ss_pred HHHHHHHHHHHHHhcCcceEEEecchHHHHHHHHHhcCcCeeEe
Confidence 44567789999999999999999999999999988766665554
No 116
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=24.89 E-value=47 Score=35.30 Aligned_cols=18 Identities=33% Similarity=0.355 Sum_probs=15.2
Q ss_pred CCCCCCHHHHHHHHHHcCC
Q psy14291 416 GLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygs 434 (538)
.|||||||||..|.+ .|-
T Consensus 93 ~i~GiGpk~a~~l~~-lGi 110 (334)
T smart00483 93 NVFGVGPKTAAKWYR-KGI 110 (334)
T ss_pred ccCCcCHHHHHHHHH-hCC
Confidence 789999999999987 553
No 117
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=24.31 E-value=53 Score=32.86 Aligned_cols=26 Identities=23% Similarity=0.216 Sum_probs=18.9
Q ss_pred HHHHHHHHHhcCCChHhhhhhhHHHHH
Q psy14291 506 DGLRRFAANKFGWSQNRVDQTLIPIMK 532 (538)
Q Consensus 506 ~~L~~fl~~~~ew~~~kvd~~l~Pll~ 532 (538)
..|.++|.. +++.....|-.+--.++
T Consensus 178 ~~l~~~~~~-~~~~~~~Ldl~~w~~~~ 203 (208)
T PRK01229 178 EILREIAEE-LGISLGELDLYIWYKET 203 (208)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHHHHHh
Confidence 457778886 99988888877665543
No 118
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=24.01 E-value=52 Score=34.49 Aligned_cols=17 Identities=35% Similarity=0.655 Sum_probs=14.7
Q ss_pred CCCCCCHHHHHHHHHHcC
Q psy14291 416 GLQGVGPVTALEILAKFS 433 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~yg 433 (538)
+|+|||||||.+|. +.|
T Consensus 89 ~i~GiGpk~a~~l~-~lG 105 (307)
T cd00141 89 RVPGVGPKTARKLY-ELG 105 (307)
T ss_pred cCCCCCHHHHHHHH-HcC
Confidence 78999999999998 544
No 119
>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=23.59 E-value=90 Score=31.50 Aligned_cols=82 Identities=20% Similarity=0.254 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccccccceEEEecCCccccchhhHHHHHHHHHHHHhhhhhhhhcccHHhHHHHH
Q psy14291 201 REMLAEQQKILDSLVKKKAKSDDVIDVDLTETSTSGFFDYGCDVIKSSTLEKDRDQLLLERGKQTRLASTITEQMSREAQ 280 (538)
Q Consensus 201 ~~~~~r~~~ll~~l~~~~ikp~~~~~~~~~~~~~v~VFDG~~p~~K~~tLekRr~qLqee~~k~~R~A~~it~~m~~e~~ 280 (538)
.+|+..+.+++... +| ..+++||||+.+.-+.....+....+.+ .-.--......++
T Consensus 35 ~g~~~~l~~~~~~~-----~p----------~~~~~~fD~~~~~~R~~l~p~YK~~R~~--------~p~~l~~q~~~~~ 91 (240)
T cd00008 35 YGFLNMLLKLIKEY-----KP----------TYVAVVFDAGGKTFRHELYPEYKANRKK--------MPEELREQIPLIK 91 (240)
T ss_pred HHHHHHHHHHHHhc-----CC----------CeEEEEEeCCCCcccccccHHHHcCCCC--------CCHHHHHHHHHHH
Confidence 56777766666543 12 2349999998666654444332221110 0000123467889
Q ss_pred HHHHhhCCcEEeCCC-chhhhhhhhh
Q psy14291 281 ELLQLFGVPFIVAPG-EAEAQCASLE 305 (538)
Q Consensus 281 kLL~~~g~P~iv~d~-Eaeaqca~l~ 305 (538)
++|+.+|+|++..++ ||.++|+.+.
T Consensus 92 ~~l~~~gi~~i~~~~~EADD~ia~la 117 (240)
T cd00008 92 ELLEALGIPVLEIEGYEADDVIGTLA 117 (240)
T ss_pred HHHHHCCCCEEecCCcCHHHHHHHHH
Confidence 999999999999987 9998987665
No 120
>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=22.26 E-value=70 Score=29.82 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=36.6
Q ss_pred HHHHHHHHHHcCCCcccCcchHHHHHHHHHhhcCCCceEecCCceE
Q psy14291 320 MLEAQELLQLFGVPFIVAPGEAEAQCASLELGNHTQGVITDDSDIW 365 (538)
Q Consensus 320 ~~~ik~lL~~~GIp~i~APgEADaqiA~La~~g~vd~IiS~DsDll 365 (538)
+..+-..|+.+|+.++..+...|+.+..+|+... -.|+|-|++++
T Consensus 9 L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~-RillTrd~~l~ 53 (147)
T PF01927_consen 9 LGRLARWLRLLGYDTLYSRDIDDDEILELAREEG-RILLTRDRDLL 53 (147)
T ss_pred HHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCC-eEEEECCHHHH
Confidence 3467789999999999999878888888876531 24999999988
No 121
>PRK14187 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.10 E-value=6.8e+02 Score=26.47 Aligned_cols=91 Identities=14% Similarity=0.141 Sum_probs=49.3
Q ss_pred HHHHHHHHcCCCcccC--cc-----hHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecCCCCCcEEEEchhHHHHH
Q psy14291 322 EAQELLQLFGVPFIVA--PG-----EAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYY 394 (538)
Q Consensus 322 ~ik~lL~~~GIp~i~A--Pg-----EADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~~~~~~~~~~i~~~ 394 (538)
..++.++.+||.+-.. |. |..+.+..|+..-.+|||+ |..++- ..++...+.+.
T Consensus 52 ~k~k~a~~~Gi~~~~~~l~~~~~e~~l~~~I~~lN~d~~V~GIl-------------vqlPLP------~~i~~~~i~~~ 112 (294)
T PRK14187 52 NKQRKAEMLGLRSETILLPSTISESSLIEKINELNNDDSVHGIL-------------VQLPVP------NHIDKNLIINT 112 (294)
T ss_pred HHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCCCCCEEE-------------EeCCCC------CCCCHHHHHhc
Confidence 4567889999988553 32 3334555555556667765 222221 11233333332
Q ss_pred h-------CCCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCC
Q psy14291 395 F-------ELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 395 ~-------gl~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygs 434 (538)
. |+++..+-.++ .| |.-+++--|-+...++||+.|+-
T Consensus 113 I~p~KDVDGl~~~n~g~l~--~g-~~~~~~~PcTp~avi~lL~~~~i 156 (294)
T PRK14187 113 IDPEKDVDGFHNENVGRLF--TG-QKKNCLIPCTPKGCLYLIKTITR 156 (294)
T ss_pred cCcccCcccCChhhHHHHh--CC-CCCCCccCcCHHHHHHHHHHhCC
Confidence 2 56665554332 23 33345555777777888888863
No 122
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=21.79 E-value=3.3e+02 Score=27.47 Aligned_cols=29 Identities=17% Similarity=0.131 Sum_probs=22.3
Q ss_pred CcccccccccCeEEEeehhhHHHhhhhhh
Q psy14291 123 GKPVPVETLENKVLAVGILYFTQGRASAL 151 (538)
Q Consensus 123 ~~~~~~~~l~G~~laiD~s~wl~~~~~~~ 151 (538)
.+...+..++|+.|.||+|--|-...+.+
T Consensus 56 rk~~~~~~~rg~~l~iDGyNvLItleSl~ 84 (211)
T COG2454 56 RKRMKINSLRGQDLVIDGYNVLITLESLL 84 (211)
T ss_pred HhhccCCCcccceEEEechhhhhhHHHHh
Confidence 47899999999999999996655444433
No 123
>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=21.40 E-value=1.6e+02 Score=27.55 Aligned_cols=45 Identities=22% Similarity=0.284 Sum_probs=35.5
Q ss_pred cchHhH-HHHHHHHHHcCCC-----cccCcc--hHHHHHHHHHhhcCCCceEe
Q psy14291 315 YVSRKM-LEAQELLQLFGVP-----FIVAPG--EAEAQCASLELGNHTQGVIT 359 (538)
Q Consensus 315 ~lt~q~-~~ik~lL~~~GIp-----~i~APg--EADaqiA~La~~g~vd~IiS 359 (538)
+++..| .-+.+.|+..|+. .+..|| |-=-.+..|++.+..|+|++
T Consensus 13 ~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~ 65 (138)
T TIGR00114 13 DITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIA 65 (138)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 456555 4788889998875 778999 88888888998888888765
No 124
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=21.31 E-value=63 Score=31.75 Aligned_cols=22 Identities=27% Similarity=0.451 Sum_probs=18.8
Q ss_pred CCCCCCCCHHHHHHHHHHcCCC
Q psy14291 414 TPGLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 414 ipGVpGIG~KtA~kLL~~ygsl 435 (538)
+.|-||+|..|++++|+++|--
T Consensus 5 ITGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 5 ITGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred EeCCCCCchHHHHHHHHHhCCc
Confidence 3689999999999999977654
No 125
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=21.27 E-value=7.4e+02 Score=26.01 Aligned_cols=90 Identities=11% Similarity=0.167 Sum_probs=50.2
Q ss_pred HHHHHHHHcCCCcccC--cc-----hHHHHHHHHHhhcCCCceEecCCceEeecCeEEEEecCCCCCcEEEEchhHHHHH
Q psy14291 322 EAQELLQLFGVPFIVA--PG-----EAEAQCASLELGNHTQGVITDDSDIWLFGARTVYKNFFDKKSHVLRYTAPDIRYY 394 (538)
Q Consensus 322 ~ik~lL~~~GIp~i~A--Pg-----EADaqiA~La~~g~vd~IiS~DsDllLfG~~~Vi~~~~~~~~~~~~~~~~~i~~~ 394 (538)
..++.++.+||.+-.. |. |..+.|..|+.--.++||+- ..++- ..++...+.+.
T Consensus 51 ~k~k~~~~~Gi~~~~~~l~~~~~~~el~~~I~~lN~D~~V~GIiv-------------q~PlP------~~i~~~~i~~~ 111 (282)
T PRK14180 51 SKEKACAQVGIDSQVITLPEHTTESELLELIDQLNNDSSVHAILV-------------QLPLP------AHINKNNVIYS 111 (282)
T ss_pred HHHHHHHHcCCEEEEEECCCCCCHHHHHHHHHHHhCCCCCCeEEE-------------cCCCC------CCCCHHHHHhh
Confidence 4567889999998654 21 44556666666666677652 22221 11223333322
Q ss_pred h-------CCCHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHHHHcCC
Q psy14291 395 F-------ELTREKLIQLALLVGSDYTPGLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 395 ~-------gl~~~q~idl~~L~GsDyipGVpGIG~KtA~kLL~~ygs 434 (538)
. |+++..+-.++ .|.+ +++.-|-+....+||+.|+-
T Consensus 112 I~p~KDVDGl~~~n~g~l~--~g~~--~~~~PcTp~aii~lL~~y~i 154 (282)
T PRK14180 112 IKPEKDVDGFHPTNVGRLQ--LRDK--KCLESCTPKGIMTMLREYGI 154 (282)
T ss_pred cCccccccccChhhHHHHh--cCCC--CCcCCCCHHHHHHHHHHhCC
Confidence 1 56665554332 3422 45556778888888888864
No 126
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=21.11 E-value=52 Score=38.28 Aligned_cols=20 Identities=30% Similarity=0.484 Sum_probs=19.4
Q ss_pred CCCCCCHHHHHHHHHHcCCC
Q psy14291 416 GLQGVGPVTALEILAKFSPS 435 (538)
Q Consensus 416 GVpGIG~KtA~kLL~~ygsl 435 (538)
||+.||.++|..|.+.|+++
T Consensus 515 GIr~VG~~~Ak~La~~f~sl 534 (667)
T COG0272 515 GIRHVGETTAKSLARHFGTL 534 (667)
T ss_pred CCchhhHHHHHHHHHHhhhH
Confidence 99999999999999999998
No 127
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=20.86 E-value=1e+02 Score=29.50 Aligned_cols=35 Identities=11% Similarity=0.260 Sum_probs=26.9
Q ss_pred HHHHHHHHHcCCCCC---------CCCCCCCHHHHHHHHHHcCC
Q psy14291 400 EKLIQLALLVGSDYT---------PGLQGVGPVTALEILAKFSP 434 (538)
Q Consensus 400 ~q~idl~~L~GsDyi---------pGVpGIG~KtA~kLL~~ygs 434 (538)
++|..+.-++|+|-- ..|.|||..+|..+++..|-
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lgi 52 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGI 52 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcCc
Confidence 467777777785532 26889999999999998874
Done!