Query 000457
Match_columns 1484
No_of_seqs 267 out of 1277
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 09:26:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000457.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000457hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2520 5'-3' exonuclease [Rep 100.0 1.2E-44 2.7E-49 430.1 21.4 247 854-1106 434-704 (815)
2 TIGR00600 rad2 DNA excision re 100.0 3E-44 6.5E-49 436.8 22.2 279 832-1121 719-1032(1034)
3 PRK03980 flap endonuclease-1; 100.0 7.2E-41 1.6E-45 364.8 23.3 212 876-1098 69-292 (292)
4 PTZ00217 flap endonuclease-1; 100.0 6.8E-41 1.5E-45 377.2 21.8 227 870-1101 116-349 (393)
5 TIGR03674 fen_arch flap struct 100.0 3.2E-38 6.9E-43 349.1 23.1 211 876-1098 116-338 (338)
6 cd00128 XPG Xeroderma pigmento 100.0 1.9E-33 4.2E-38 305.6 20.9 133 876-1008 114-247 (316)
7 KOG2519 5'-3' exonuclease [Rep 100.0 2.2E-31 4.8E-36 301.7 11.1 227 871-1100 113-344 (449)
8 KOG2518 5'-3' exonuclease [Rep 99.9 9.5E-28 2.1E-32 275.1 14.6 152 858-1010 94-251 (556)
9 smart00475 53EXOc 5'-3' exonuc 99.9 2E-23 4.2E-28 225.2 15.5 127 890-1019 84-218 (259)
10 PF00867 XPG_I: XPG I-region; 99.9 2.7E-23 5.9E-28 193.3 7.4 85 900-984 1-94 (94)
11 cd00008 53EXOc 5'-3' exonuclea 99.9 6.7E-22 1.4E-26 210.4 15.3 124 889-1018 84-214 (240)
12 PRK14976 5'-3' exonuclease; Pr 99.9 9.6E-22 2.1E-26 214.3 15.5 120 890-1009 90-216 (281)
13 COG0258 Exo 5'-3' exonuclease 99.8 1.1E-20 2.3E-25 206.7 12.1 133 878-1013 92-227 (310)
14 TIGR00593 pola DNA polymerase 99.8 7E-20 1.5E-24 224.3 15.3 126 890-1019 84-217 (887)
15 PRK09482 flap endonuclease-lik 99.8 9.1E-20 2E-24 197.5 14.1 117 890-1010 84-208 (256)
16 PRK05755 DNA polymerase I; Pro 99.8 2.4E-19 5.2E-24 219.1 15.3 126 890-1019 86-219 (880)
17 smart00484 XPGI Xeroderma pigm 99.7 8.6E-17 1.9E-21 146.5 7.9 69 901-969 2-73 (73)
18 PHA00439 exonuclease 99.4 9.6E-13 2.1E-17 145.4 11.3 103 889-1003 96-206 (286)
19 cd00080 HhH2_motif Helix-hairp 99.3 5.3E-12 1.1E-16 115.0 5.5 51 966-1016 2-54 (75)
20 PHA02567 rnh RnaseH; Provision 98.8 9.8E-09 2.1E-13 114.9 10.1 88 893-990 110-206 (304)
21 smart00279 HhH2 Helix-hairpin- 98.7 1.6E-08 3.5E-13 82.2 3.7 33 971-1004 1-36 (36)
22 PF01367 5_3_exonuc: 5'-3' exo 98.7 1.2E-09 2.6E-14 105.6 -3.7 41 969-1009 1-43 (101)
23 PF12813 XPG_I_2: XPG domain c 98.3 5.8E-06 1.2E-10 90.3 11.6 121 891-1019 5-146 (246)
24 PF02739 5_3_exonuc_N: 5'-3' e 98.2 3E-06 6.4E-11 87.9 7.3 77 890-967 86-169 (169)
25 TIGR00600 rad2 DNA excision re 96.0 0.014 3E-07 75.1 7.8 101 203-304 189-292 (1034)
26 PF14377 DUF4414: Domain of un 95.0 0.03 6.5E-07 55.0 4.6 58 202-264 43-102 (108)
27 COG5366 Protein involved in pr 93.3 0.041 8.9E-07 65.7 2.0 112 895-1007 134-248 (531)
28 PF12826 HHH_2: Helix-hairpin- 88.1 0.36 7.9E-06 43.6 2.5 23 987-1009 6-28 (64)
29 KOG2044 5'-3' exonuclease HKE1 86.3 2.5 5.4E-05 54.0 8.8 138 856-993 125-351 (931)
30 PF05918 API5: Apoptosis inhib 81.6 0.6 1.3E-05 57.6 1.0 36 885-920 188-223 (556)
31 PF04599 Pox_G5: Poxvirus G5 p 78.4 5.2 0.00011 48.4 7.2 87 895-992 148-247 (425)
32 PF14377 DUF4414: Domain of un 75.7 1.5 3.4E-05 43.3 1.7 65 204-272 1-69 (108)
33 COG5049 XRN1 5'-3' exonuclease 75.2 9.7 0.00021 48.6 8.4 91 903-993 176-327 (953)
34 PRK14605 ruvA Holliday junctio 74.6 3.8 8.3E-05 44.5 4.4 40 961-1006 55-95 (194)
35 PRK14602 ruvA Holliday junctio 73.4 4.4 9.5E-05 44.4 4.5 39 961-1005 56-95 (203)
36 PRK14606 ruvA Holliday junctio 73.1 3.5 7.7E-05 44.7 3.7 51 961-1021 55-106 (188)
37 TIGR00084 ruvA Holliday juncti 71.2 4.7 0.0001 43.7 4.1 39 961-1005 54-93 (191)
38 PF10391 DNA_pol_lambd_f: Fing 70.1 4 8.7E-05 36.5 2.7 24 987-1010 5-29 (52)
39 PRK13901 ruvA Holliday junctio 68.4 5.1 0.00011 44.1 3.7 46 964-1019 57-103 (196)
40 PRK14603 ruvA Holliday junctio 68.1 5.2 0.00011 43.7 3.7 36 964-1005 57-93 (197)
41 PRK14600 ruvA Holliday junctio 67.8 6.8 0.00015 42.6 4.4 51 961-1021 55-106 (186)
42 PRK00116 ruvA Holliday junctio 67.4 4.7 0.0001 43.4 3.1 20 988-1007 77-96 (192)
43 PHA03065 Hypothetical protein; 67.3 13 0.00028 45.2 6.9 88 894-992 149-249 (438)
44 PRK14601 ruvA Holliday junctio 66.3 5.8 0.00013 43.1 3.6 39 961-1005 55-94 (183)
45 PRK14604 ruvA Holliday junctio 66.3 5.8 0.00013 43.3 3.6 38 962-1005 56-94 (195)
46 PRK14603 ruvA Holliday junctio 66.3 2.6 5.6E-05 45.9 1.0 48 958-1006 80-129 (197)
47 COG0632 RuvA Holliday junction 65.9 14 0.00029 41.1 6.3 54 957-1020 51-105 (201)
48 PF00633 HHH: Helix-hairpin-he 65.1 4.6 0.0001 32.6 1.9 16 987-1002 14-29 (30)
49 PRK14604 ruvA Holliday junctio 62.9 2.7 5.8E-05 45.8 0.3 47 959-1006 82-130 (195)
50 PF05918 API5: Apoptosis inhib 62.8 2.4 5.3E-05 52.5 0.0 18 1110-1127 435-452 (556)
51 PRK14667 uvrC excinuclease ABC 60.2 6.7 0.00015 48.9 3.0 24 986-1009 516-539 (567)
52 PRK14669 uvrC excinuclease ABC 60.0 6.3 0.00014 49.6 2.8 25 986-1010 554-578 (624)
53 TIGR00194 uvrC excinuclease AB 59.6 6.4 0.00014 49.1 2.7 25 986-1010 543-567 (574)
54 PRK14670 uvrC excinuclease ABC 58.8 7.3 0.00016 48.6 3.0 25 985-1009 515-539 (574)
55 PRK14602 ruvA Holliday junctio 58.6 4.2 9.1E-05 44.5 0.9 41 965-1006 89-131 (203)
56 PRK14671 uvrC excinuclease ABC 56.5 8.1 0.00018 48.6 2.9 24 987-1010 572-595 (621)
57 KOG2045 5'-3' exonuclease XRN1 56.4 50 0.0011 43.8 9.5 128 873-1000 118-306 (1493)
58 PRK14601 ruvA Holliday junctio 53.2 9.3 0.0002 41.6 2.4 37 968-1005 92-129 (183)
59 PF14520 HHH_5: Helix-hairpin- 52.1 12 0.00026 33.2 2.5 22 987-1008 8-30 (60)
60 COG0632 RuvA Holliday junction 50.8 6.8 0.00015 43.3 0.9 80 925-1005 48-129 (201)
61 PRK13901 ruvA Holliday junctio 49.4 11 0.00025 41.5 2.4 38 968-1006 91-129 (196)
62 PRK14672 uvrC excinuclease ABC 49.1 13 0.00028 47.5 3.0 25 986-1010 610-634 (691)
63 PRK14606 ruvA Holliday junctio 47.9 13 0.00028 40.6 2.4 47 959-1006 82-130 (188)
64 PF02371 Transposase_20: Trans 47.5 14 0.00031 35.0 2.4 24 984-1007 2-25 (87)
65 smart00278 HhH1 Helix-hairpin- 47.0 14 0.0003 28.5 1.8 18 986-1003 3-20 (26)
66 PRK14600 ruvA Holliday junctio 45.3 17 0.00038 39.5 2.9 47 958-1006 81-129 (186)
67 TIGR01448 recD_rel helicase, p 42.1 26 0.00057 44.7 4.2 40 967-1013 73-112 (720)
68 PRK12766 50S ribosomal protein 41.3 21 0.00046 40.6 2.9 24 986-1009 5-29 (232)
69 PF03159 XRN_N: XRN 5'-3' exon 41.2 82 0.0018 35.7 7.4 38 903-940 172-222 (237)
70 PRK00558 uvrC excinuclease ABC 40.6 21 0.00046 44.8 3.1 23 987-1009 546-568 (598)
71 KOG3428 Small nuclear ribonucl 39.3 14 0.0003 37.9 1.0 10 1218-1227 96-105 (109)
72 PRK14668 uvrC excinuclease ABC 35.0 27 0.00059 43.8 2.8 26 985-1010 526-551 (577)
73 COG0258 Exo 5'-3' exonuclease 34.6 30 0.00064 39.6 2.8 36 890-925 96-132 (310)
74 KOG2520 5'-3' exonuclease [Rep 32.5 22 0.00047 46.3 1.4 250 261-596 5-254 (815)
75 KOG2894 Uncharacterized conser 32.0 41 0.00089 39.4 3.3 83 163-245 102-188 (331)
76 PRK14666 uvrC excinuclease ABC 31.7 31 0.00067 44.4 2.5 26 986-1011 639-664 (694)
77 COG0322 UvrC Nuclease subunit 30.5 37 0.00079 42.9 2.8 26 986-1011 532-557 (581)
78 PRK02515 psbU photosystem II c 29.6 37 0.00079 36.0 2.2 22 988-1009 65-88 (132)
79 TIGR00575 dnlj DNA ligase, NAD 29.5 40 0.00087 42.9 3.0 24 987-1010 501-524 (652)
80 TIGR00084 ruvA Holliday juncti 28.7 43 0.00094 36.6 2.7 45 959-1004 81-127 (191)
81 PRK14351 ligA NAD-dependent DN 28.7 43 0.00092 43.0 3.0 34 205-238 20-53 (689)
82 cd00956 Transaldolase_FSA Tran 28.6 2E+02 0.0044 31.9 7.7 41 970-1015 167-207 (211)
83 PRK14605 ruvA Holliday junctio 27.3 37 0.00081 37.1 1.9 36 969-1005 93-129 (194)
84 TIGR00596 rad1 DNA repair prot 25.5 34 0.00073 44.7 1.4 23 987-1009 760-782 (814)
85 TIGR00426 competence protein C 25.4 67 0.0015 29.2 2.9 15 989-1003 22-36 (69)
86 COG4277 Predicted DNA-binding 25.0 1.2E+02 0.0026 36.3 5.5 48 956-1003 276-349 (404)
87 TIGR01259 comE comEA protein. 24.5 54 0.0012 33.4 2.4 19 987-1005 71-89 (120)
88 PF11798 IMS_HHH: IMS family H 23.8 51 0.0011 26.9 1.6 14 987-1000 14-27 (32)
89 COG1948 MUS81 ERCC4-type nucle 21.7 67 0.0015 37.1 2.6 23 987-1009 185-207 (254)
90 PF02809 UIM: Ubiquitin intera 21.1 1E+02 0.0022 23.0 2.5 16 578-593 2-17 (18)
91 cd00141 NT_POLXc Nucleotidyltr 20.8 78 0.0017 36.7 3.0 24 987-1010 88-112 (307)
92 smart00483 POLXc DNA polymeras 20.8 76 0.0016 37.2 2.9 26 987-1014 92-117 (334)
93 KOG4364 Chromatin assembly fac 20.6 48 0.001 42.5 1.3 54 506-585 520-573 (811)
94 PRK10590 ATP-dependent RNA hel 20.3 1.2E+02 0.0026 36.4 4.4 9 1266-1274 444-452 (456)
95 PRK07956 ligA NAD-dependent DN 20.2 70 0.0015 41.0 2.6 24 987-1010 514-537 (665)
96 PF06465 DUF1087: Domain of Un 20.2 47 0.001 31.7 0.8 22 1259-1280 40-61 (66)
97 COG1834 N-Dimethylarginine dim 20.2 73 0.0016 37.1 2.5 109 890-1018 38-152 (267)
No 1
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-44 Score=430.06 Aligned_cols=247 Identities=40% Similarity=0.641 Sum_probs=205.1
Q ss_pred hcHHHHHHHHHHhhHHHHhhChhHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCC
Q 000457 854 ATEKILEEEMQILDHEYMYLGDEQKKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDD 933 (1484)
Q Consensus 854 ~s~~~LeEE~q~L~qE~v~lG~Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITED 933 (1484)
....+.+++.....+-+. +++...|.+..||.+|+.+||+||+.||||||+||+|||||||.|.+.++||+|||+|
T Consensus 434 ~~e~n~ee~~~~~~el~~----ek~~~~r~~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDD 509 (815)
T KOG2520|consen 434 WDEANSEEEEKLSDELLS----EKYIQSRGADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDD 509 (815)
T ss_pred hcccchhhhhhhhhHHHH----HHHHHhccCchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeeccc
Confidence 344444444444333332 5677789999999999999999999999999999999999999999999999999999
Q ss_pred CceecccCCEEEEEccCCCCeEEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHH
Q 000457 934 SDVFLFGARSVYKNIFDDRKYVETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKF 1013 (1484)
Q Consensus 934 SDLLLFG~~kVIRN~fk~~K~VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekf 1013 (1484)
||+|+||+++||||||..+++|+.|.+.+|.+.|||++..+|-+|.|+||||+.||+||||++|+++|..|+..++|.+|
T Consensus 510 SDV~LFGg~~VYrn~F~knk~ve~y~~~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f 589 (815)
T KOG2520|consen 510 SDVFLFGGTRVYRNFFNKNKYVEKYQLDDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKF 589 (815)
T ss_pred ccceeeccchhhHHHhhcCccceeeehHHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999988999999
Q ss_pred HHhhhCCCCCccCcccccCCCcccccccCCCCCCcccCCCCccccccccccccccCcc--cccHHHHHHHHHHhhh----
Q 000457 1014 REWIESPDPTILGKFDVQTGASSRKRRSSDGDKDVNYAKNSVGGVSEFDESISQFDED--KQSAEYSQNMKKIFMD---- 1087 (1484)
Q Consensus 1014 rEW~ekp~~~ll~eld~ns~~~fKKK~kav~~~eipw~fPdleVL~~Fl~pvVs~seD--~~s~~~ierLrk~f~~---- 1087 (1484)
.+||..-.+... +........+|+|.+.. .+-++-.||+..|+.+|++|.|+.+-+ .|+.++++.||++.+.
T Consensus 590 ~~w~~~~~~~~~-~~~s~~~~~lrkkl~n~-~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~pdl~~lRef~~~~fgW 667 (815)
T KOG2520|consen 590 KKWVQQTGPADK-EVGSTQQKMLRKKLKNP-KIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGKPDLDILREFMKRLFGW 667 (815)
T ss_pred HHHHHHhCcccc-ccccHHHHHHHHHhcCc-ccccCcCCCchhHHHHhhCCccCCCcccccCCCCCHHHHHHHHHHHcCC
Confidence 999984333211 11111223445555543 245777899999999999999998854 6999999999987642
Q ss_pred ------------------cccccccccccchhhhHhh
Q 000457 1088 ------------------KHTQLRLEAFYTFNERFAK 1106 (1484)
Q Consensus 1088 ------------------k~tQlRIdsFFt~~~~~a~ 1106 (1484)
..+|+++++||.|..+.+.
T Consensus 668 ~~~kT~~~l~p~~~~~~~~~~~~~~~~~~~~f~~~~~ 704 (815)
T KOG2520|consen 668 PDEKTDEELIPVIKRLEKKKTQLKQDRISQFFEDEKT 704 (815)
T ss_pred CccccchhhhhhHHHHHHHhhhhccccHHHHHHhhhh
Confidence 2289999999988766653
No 2
>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=3e-44 Score=436.78 Aligned_cols=279 Identities=34% Similarity=0.535 Sum_probs=217.1
Q ss_pred ccccccchhhHHHHHHhhhhhh--hcHHHHHHHHHHhhHHHHhhChhHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeC
Q 000457 832 LKDSKQNTGIFATKAIENVHAE--ATEKILEEEMQILDHEYMYLGDEQKKLERNAESVSSEMFAECQELLQMFGLPYIIA 909 (1484)
Q Consensus 832 ~~~~e~~~~~~~~~~~en~~~q--~s~~~LeEE~q~L~qE~v~lG~Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVA 909 (1484)
+...+..+..|+..+...-..+ .....+.+++..++ .+..++.|++..||++|+..|++||++||||||+|
T Consensus 719 ~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~-------~~~~~~~r~~~~vt~~m~~~~~~LL~~~GIP~i~A 791 (1034)
T TIGR00600 719 MIEEEKDADDFKNEWQDISLEELEALEANLLAEQNSLK-------AQKQQQKRIAAEVTGQMILESQELLRLFGIPYIVA 791 (1034)
T ss_pred hhhhhhhHHHHHHHHhhhccccchhhHHHHHHHHHHHH-------HHHHHhccccccCCHHHHHHHHHHHHHCCCCeeeC
Confidence 3345556667777766443321 11223333333322 23456789999999999999999999999999999
Q ss_pred cchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccCCCCeEEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCC
Q 000457 910 PMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFDDRKYVETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGI 989 (1484)
Q Consensus 910 PYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K~VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGV 989 (1484)
|||||||||+|++.|+||+|+|+|+|+|+||+++||||++..+++|++|...+|++.+||+++|||+||+||||||++||
T Consensus 792 P~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~~~~ve~~~~~~i~~~lglt~~qli~laiL~G~DY~~GI 871 (1034)
T TIGR00600 792 PMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGI 871 (1034)
T ss_pred CccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCCCCceEEeeHHHHHHHhCCCHHHHHHHHHeeCCCCCCCC
Confidence 99999999999999999999999999999999999999998888999999999999999999999999999999999999
Q ss_pred CCccHHHHHHHHHhcCC--chHHHHHHHhhhCCCCCccCcccccCCCcccccccCCCCCCcccCCCCccccccccccccc
Q 000457 990 SGIGIVNAIEVVNAFPE--EDGLSKFREWIESPDPTILGKFDVQTGASSRKRRSSDGDKDVNYAKNSVGGVSEFDESISQ 1067 (1484)
Q Consensus 990 PGIGPKTAlKLLrqFGS--lDgLekfrEW~ekp~~~ll~eld~ns~~~fKKK~kav~~~eipw~fPdleVL~~Fl~pvVs 1067 (1484)
||||||||++||+.|++ ++.|..|++||...+... .+..+...+.+++++. .+.+|-.||+..|+.+|++|.|.
T Consensus 872 ~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~~~~~--~~~~~~~~~~~~~~~~--~~~lp~~FP~~~V~~~yl~P~V~ 947 (1034)
T TIGR00600 872 PTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDK--KKRENPNDTKVKKKLR--LLQLTPGFPNPAVADAYLRPVVD 947 (1034)
T ss_pred CcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhhcc--ccccccchhhhhhccc--ccccCCCCCcHHHHHHhcCCCCC
Confidence 99999999999999994 789999999998754321 1222233333333222 23477789999999999999999
Q ss_pred cCc--ccccHHHHHHHHHHhhh----------------------cccccccccccchh-------hhHhhHhhHHHHhhh
Q 000457 1068 FDE--DKQSAEYSQNMKKIFMD----------------------KHTQLRLEAFYTFN-------ERFAKIRSKRIKKAV 1116 (1484)
Q Consensus 1068 ~se--D~~s~~~ierLrk~f~~----------------------k~tQlRIdsFFt~~-------~~~a~iRSKRLqkAV 1116 (1484)
.+. -.|..|+++.|+++++. +.+|+||++||+.. .+.+.-++||+..|+
T Consensus 948 ~~~~~f~W~~PD~e~L~~Fl~~~~gws~eRv~~~l~plikk~~~~~~Q~~ld~FF~~~~~~~~~~~~~~~~~~~r~~~~~ 1027 (1034)
T TIGR00600 948 DSKGSFLWGKPDLDKIREFCQRYFGWNREKTDEVLLPVLKKLNAQQTQLRIDSFFRLAQQEKYDAKDIKSQRLKRAVTCM 1027 (1034)
T ss_pred CCcCCCCCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHccCCccCHHHhhCccccccccchhhhhhhhhHHHHHH
Confidence 753 36888888888887653 23899999999852 223334677888887
Q ss_pred hcccC
Q 000457 1117 KGITG 1121 (1484)
Q Consensus 1117 k~irg 1121 (1484)
.+++.
T Consensus 1028 ~~~~~ 1032 (1034)
T TIGR00600 1028 LRKEK 1032 (1034)
T ss_pred Hhhcc
Confidence 77753
No 3
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=7.2e-41 Score=364.80 Aligned_cols=212 Identities=27% Similarity=0.454 Sum_probs=178.6
Q ss_pred hHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccCCCC--
Q 000457 876 EQKKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFDDRK-- 953 (1484)
Q Consensus 876 Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K-- 953 (1484)
++.++.++++.||++|+..++++|++|||||++||||||||||+|++.|++|+|+|+|+|+|+||+++||++++..++
T Consensus 69 ~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~ 148 (292)
T PRK03980 69 EARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRK 148 (292)
T ss_pred HHHHHHhccccCCHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeeccccccc
Confidence 568889999999999999999999999999999999999999999999999999999999999999999999875431
Q ss_pred ----------eEEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhCCCCC
Q 000457 954 ----------YVETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIESPDPT 1023 (1484)
Q Consensus 954 ----------~VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ekp~~~ 1023 (1484)
.+++|+.+.|++.+||+++||+|||+|+||||+|||||||||||++||++|++++ .+++.+...-+
T Consensus 149 ~p~~~~~~~~~~e~~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle---~i~~~~~~~~~- 224 (292)
T PRK03980 149 LPGKNVYVEVKPELIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLE---KVLEERGFEIE- 224 (292)
T ss_pred CccccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHH---HHHHhccCCCC-
Confidence 4568999999999999999999999999999999999999999999999999954 44443321100
Q ss_pred ccCcccccCCCcccccccCCCCCCcccCCCCccccccccccccccCcccccHHHHHHHHHHhhhccccccccccc
Q 000457 1024 ILGKFDVQTGASSRKRRSSDGDKDVNYAKNSVGGVSEFDESISQFDEDKQSAEYSQNMKKIFMDKHTQLRLEAFY 1098 (1484)
Q Consensus 1024 ll~eld~ns~~~fKKK~kav~~~eipw~fPdleVL~~Fl~pvVs~seD~~s~~~ierLrk~f~~k~tQlRIdsFF 1098 (1484)
........|+...... ..+++|..||++.|..|++...+|+++ ++...+++|++.+ .+.+|+||++||
T Consensus 225 ---~~~~~r~~f~~p~v~~--~~~~~~~~pd~~~l~~fl~~e~~f~~~-rv~~~~~~l~~~~-~~~~q~~l~~ff 292 (292)
T PRK03980 225 ---NYDEIREFFLNPPVTD--DYELKWKEPDKEGIIEFLVEEHDFSEE-RVKKALERLEKAV-KEKKQTTLDSWF 292 (292)
T ss_pred ---CHHHHHHHhcCCCCCC--CCCccCCCCCHHHHHHHHhccCCCCHH-HHHHHHHHHHHHh-ccCcccchhhcC
Confidence 0000011222222222 456899999999999999999999987 8999999999986 667899999998
No 4
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=6.8e-41 Score=377.18 Aligned_cols=227 Identities=26% Similarity=0.456 Sum_probs=186.9
Q ss_pred HHhhCh--hHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEE
Q 000457 870 YMYLGD--EQKKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKN 947 (1484)
Q Consensus 870 ~v~lG~--Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN 947 (1484)
....|+ ++.++.++++.||++|+..++++|++||||||+||||||||||+|++.|++|+|+|+|+|+|+||+++||++
T Consensus 116 a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~ 195 (393)
T PTZ00217 116 AIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRN 195 (393)
T ss_pred HHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcCHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEc
Confidence 334454 567889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccC---CCCeEEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhCCCCCc
Q 000457 948 IFD---DRKYVETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIESPDPTI 1024 (1484)
Q Consensus 948 ~fk---~~K~VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ekp~~~l 1024 (1484)
++. ....+++|+.+.|.+.+||+++||+|||+|+||||+|||||||+|||++||++|++ |+.+++++......+
T Consensus 196 l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi~GIG~ktA~~Li~~~gs---le~il~~~~~~k~~~ 272 (393)
T PTZ00217 196 LNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKYKS---IEEILEHLDKTKYPV 272 (393)
T ss_pred ccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCC---HHHHHHHHHhcCCCC
Confidence 874 23467899999999999999999999999999999999999999999999999998 555555554321111
Q ss_pred cCccc--ccCCCcccccccCCCCCCcccCCCCccccccccccccccCcccccHHHHHHHHHHhhhcccccccccccchh
Q 000457 1025 LGKFD--VQTGASSRKRRSSDGDKDVNYAKNSVGGVSEFDESISQFDEDKQSAEYSQNMKKIFMDKHTQLRLEAFYTFN 1101 (1484)
Q Consensus 1025 l~eld--~ns~~~fKKK~kav~~~eipw~fPdleVL~~Fl~pvVs~seD~~s~~~ierLrk~f~~k~tQlRIdsFFt~~ 1101 (1484)
...+. .....|+..........+++|..||.+.|..|+.....|+++ ++...+++|++.. .+.+|+||++||+..
T Consensus 273 p~~~~~~~~~~~f~~p~V~~~~~~~l~w~~pD~~~l~~fl~~e~~f~~~-rv~~~i~rl~~~~-~~~~Q~~l~~ff~~~ 349 (393)
T PTZ00217 273 PENFDYKEARELFLNPEVTPAEEIDLKWNEPDEEGLKKFLVKEKNFNEE-RVEKYIERLKKAK-TKKTQTRLDSFFTAT 349 (393)
T ss_pred CCCCChHHHHHHhcCCCcCCCCCCCCCCCCCCHHHHHHHHHhccCCCHH-HHHHHHHHHHHHh-ccCccCCHHHhcCCC
Confidence 01111 111223333322222346899999999999999999999987 8888999998886 677999999999864
No 5
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=3.2e-38 Score=349.13 Aligned_cols=211 Identities=29% Similarity=0.470 Sum_probs=176.8
Q ss_pred hHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccCCCC--
Q 000457 876 EQKKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFDDRK-- 953 (1484)
Q Consensus 876 Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K-- 953 (1484)
++.++.+++..+|++|+..++++|++|||||++||||||||||+|++.|+||+|+|+|+|+|+||+++|+++++..++
T Consensus 116 ~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~ 195 (338)
T TIGR03674 116 EARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRK 195 (338)
T ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccC
Confidence 577888999999999999999999999999999999999999999999999999999999999999999999875432
Q ss_pred ----------eEEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhCCCCC
Q 000457 954 ----------YVETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIESPDPT 1023 (1484)
Q Consensus 954 ----------~VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ekp~~~ 1023 (1484)
++++|+.+.+.+.+||+++||+|+|+|+||||+|||||||+|||++||++|++ |+.+.+++..+-.
T Consensus 196 ~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~gs---ie~il~~~~~~~~- 271 (338)
T TIGR03674 196 LPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGD---LEKVLKARGEDIE- 271 (338)
T ss_pred CCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCC---HHHHHHhhcCCCC-
Confidence 45679999999999999999999999999999999999999999999999999 5555555432200
Q ss_pred ccCcccccCCCcccccccCCCCCCcccCCCCccccccccccccccCcccccHHHHHHHHHHhhhccccccccccc
Q 000457 1024 ILGKFDVQTGASSRKRRSSDGDKDVNYAKNSVGGVSEFDESISQFDEDKQSAEYSQNMKKIFMDKHTQLRLEAFY 1098 (1484)
Q Consensus 1024 ll~eld~ns~~~fKKK~kav~~~eipw~fPdleVL~~Fl~pvVs~seD~~s~~~ierLrk~f~~k~tQlRIdsFF 1098 (1484)
...++. ..|... ......++.|..|+.+.|..|+.....++++ ++.+.+++|++.+ +.+|+||++||
T Consensus 272 ~~~~~~---~~f~~~--~v~~~~~~~~~~pd~e~l~~fl~~e~~~~~~-rv~~~~~~l~~~~--~~~q~~l~~ff 338 (338)
T TIGR03674 272 NYDEIR---EFFLNP--PVTDDYELKWRKPDKEGIIEFLCDEHDFSED-RVERALERLEAAY--KSKQKTLDRWF 338 (338)
T ss_pred CHHHHH---HHhCCC--CCCCCCCccCCCCCHHHHHHHHhhcCCCCHH-HHHHHHHHHHHhh--cccccchhhcC
Confidence 000110 011111 1111236789999999999999999999987 8999999999886 78999999998
No 6
>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=1.9e-33 Score=305.65 Aligned_cols=133 Identities=54% Similarity=0.916 Sum_probs=125.9
Q ss_pred hHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccCCC-Ce
Q 000457 876 EQKKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFDDR-KY 954 (1484)
Q Consensus 876 Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk~~-K~ 954 (1484)
++.++.+++..+|++|+..++++|++|||||++||||||||||+|++.|++|+|+|+|+|+|+||+++||++++..+ ..
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~ 193 (316)
T cd00128 114 EAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKP 193 (316)
T ss_pred HHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCCCc
Confidence 45677888999999999999999999999999999999999999999999999999999999999999999987655 47
Q ss_pred EEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCch
Q 000457 955 VETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEED 1008 (1484)
Q Consensus 955 VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlD 1008 (1484)
+++|+.+.+.+.+||+++||++||+|+||||+|||||||+|||++||++|++++
T Consensus 194 ~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv~giG~k~A~~li~~~~~~~ 247 (316)
T cd00128 194 VEEIDLEKILKELGLTREKLIDLAILLGCDYTEGIPGIGPVTALKLIKKYGDIE 247 (316)
T ss_pred eEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCChH
Confidence 889999999999999999999999999999999999999999999999999854
No 7
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.97 E-value=2.2e-31 Score=301.65 Aligned_cols=227 Identities=27% Similarity=0.382 Sum_probs=186.7
Q ss_pred HhhChhHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccC
Q 000457 871 MYLGDEQKKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFD 950 (1484)
Q Consensus 871 v~lG~Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk 950 (1484)
.....+..++.++.+.||.++..+|+.||.+|||||+.||+||+||||+|++.|.|++++|+|+|+|.||++.+++++..
T Consensus 113 ~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~ 192 (449)
T KOG2519|consen 113 AGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPGEAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIH 192 (449)
T ss_pred hhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCchHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhcc
Confidence 33444678999999999999999999999999999999999999999999999999999999999999999999988753
Q ss_pred ---CCCeEEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHH-HHHhhhCCCCCccC
Q 000457 951 ---DRKYVETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSK-FREWIESPDPTILG 1026 (1484)
Q Consensus 951 ---~~K~VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLek-frEW~ekp~~~ll~ 1026 (1484)
.+..|.+|++..|++.|+|++.+|||+|+|+|||||++|.|||+++|++||++|++++.+.+ ...|.+.+-|....
T Consensus 193 s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGCDYc~~I~Gig~~~al~lir~~~~i~~ile~~~~~~~~~ip~~w~ 272 (449)
T KOG2519|consen 193 SLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGCDYCPTIRGIGPKKALKLIRQHGDIENILEINSDLKEYPIPEDWS 272 (449)
T ss_pred chhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcCcccccccccChHHHHHHHHHhcCHHHHhhhccchhhcCCCCCcc
Confidence 35689999999999999999999999999999999999999999999999999999766666 44454433221110
Q ss_pred cccccCCCcccccccCCCC-CCcccCCCCccccccccccccccCcccccHHHHHHHHHHhhhcccccccccccch
Q 000457 1027 KFDVQTGASSRKRRSSDGD-KDVNYAKNSVGGVSEFDESISQFDEDKQSAEYSQNMKKIFMDKHTQLRLEAFYTF 1100 (1484)
Q Consensus 1027 eld~ns~~~fKKK~kav~~-~eipw~fPdleVL~~Fl~pvVs~seD~~s~~~ierLrk~f~~k~tQlRIdsFFt~ 1100 (1484)
.. .....++-........ ..++|.-|+.+.+..|+.-...|+++ ++...+.+|.+.+ ...+|.|+++||+.
T Consensus 273 ~~-~~r~~f~~p~~~~~~~~~~i~w~~pd~~~li~fl~~~~~f~~~-rv~~~~~kl~~~~-~~~~qgrl~~f~~~ 344 (449)
T KOG2519|consen 273 YK-LARKLFLEPEFPNPESILDLKWKTPDTEGLIQFLVGEKQFNEE-RVRKGIRKLKSSL-KLGTQGRLDSFFKR 344 (449)
T ss_pred HH-HHHHHhcCcccCCccceeecccCCCChHHHHHHHHhhhccCHH-HHhhhhHHHhhhh-ccccccchhhhhcc
Confidence 00 0112233333333223 57899999999999999999998876 7777777777776 77899999999974
No 8
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.95 E-value=9.5e-28 Score=275.08 Aligned_cols=152 Identities=24% Similarity=0.392 Sum_probs=129.1
Q ss_pred HHHHHHHHhhHHHHhhCh--hHHHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCc
Q 000457 858 ILEEEMQILDHEYMYLGD--EQKKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSD 935 (1484)
Q Consensus 858 ~LeEE~q~L~qE~v~lG~--Ea~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSD 935 (1484)
..+++.....+.....|+ ++..++++++.||++|+..++++|+..||+||+||||||||||||.+.|+||+|||+|||
T Consensus 94 ~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~~~~i~~IITEDSD 173 (556)
T KOG2518|consen 94 ERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLEREGIVDAIITEDSD 173 (556)
T ss_pred HHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHHHhcCcceEEEecccc
Confidence 333444444444455666 578899999999999999999999999999999999999999999999999999999999
Q ss_pred eecccCCEEEEEccCCCCeEEEEeHHHHHHHh----CCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHH
Q 000457 936 VFLFGARSVYKNIFDDRKYVETYFMQDIEKDL----GLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 936 LLLFG~~kVIRN~fk~~K~VEvydledIeeeL----GLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
+|+|||+.||++|...+.. ..++...+...+ +|+.++|+.+|||+||||++||||||.+||+++|+.|.+.+.+
T Consensus 174 Ll~fGc~~vifK~d~~G~~-le~~~~~l~~~~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~v 251 (556)
T KOG2518|consen 174 LLVFGCKKVIFKMDSFGNG-LEINRSKLPECKPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDRV 251 (556)
T ss_pred ccccCchhheeeccCCCCc-ccccHhhhhhccccccccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHHH
Confidence 9999999999998765544 344666665444 3679999999999999999999999999999999999986543
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.90 E-value=2e-23 Score=225.23 Aligned_cols=127 Identities=26% Similarity=0.379 Sum_probs=109.1
Q ss_pred HHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHHc----CceeEEEcCCCceecccCCEEE-EEccCCCCeEEEEeHHHH
Q 000457 890 EMFAECQELLQMFGLPYIIAP-MEAEAQCAYMELA----NLVDGVVTDDSDVFLFGARSVY-KNIFDDRKYVETYFMQDI 963 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaKk----GlVDAVITEDSDLLLFG~~kVI-RN~fk~~K~VEvydledI 963 (1484)
.+++.++++|++|||||+.+| |||||+||+|++. |+.++|+|.|+|++||+++.|. ++........++++.+.|
T Consensus 84 ~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~~v 163 (259)
T smart00475 84 EQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENV 163 (259)
T ss_pred HHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEEcHHHH
Confidence 567889999999999999998 7999999999874 7889999999999999988664 333322223468999999
Q ss_pred HHHhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhC
Q 000457 964 EKDLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIES 1019 (1484)
Q Consensus 964 eeeLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ek 1019 (1484)
.+.||++|+||++||+|+| |||+|||||||||||.+||++||+ |+.++++++.
T Consensus 164 ~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygs---le~i~~~~~~ 218 (259)
T smart00475 164 IEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGS---LENILENLDK 218 (259)
T ss_pred HHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCC---HHHHHHHHHH
Confidence 9999999999999999999 899999999999999999999998 5555665554
No 10
>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=99.88 E-value=2.7e-23 Score=193.25 Aligned_cols=85 Identities=52% Similarity=0.879 Sum_probs=75.0
Q ss_pred HHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEcc-CC--------CCeEEEEeHHHHHHHhCCC
Q 000457 900 QMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIF-DD--------RKYVETYFMQDIEKDLGLT 970 (1484)
Q Consensus 900 rlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~f-k~--------~K~VEvydledIeeeLGLT 970 (1484)
++|||||++||||||||||||+++|+||+|+|+|+|+|+||+++||++++ .. ...+++|+...|.+.++|+
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~l~ 80 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILKELGLT 80 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHHHHTTS
T ss_pred CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHHHcCCC
Confidence 57999999999999999999999999999999999999999999999997 22 2468999999999999999
Q ss_pred HHHHHHHHHHcCCC
Q 000457 971 REKLIRMALLLGSD 984 (1484)
Q Consensus 971 peQFIDLcILsGcD 984 (1484)
++||+++|+|+|||
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 11
>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=99.87 E-value=6.7e-22 Score=210.36 Aligned_cols=124 Identities=20% Similarity=0.278 Sum_probs=106.0
Q ss_pred HHHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHH----cCceeEEEcCCCceecccCCEEEEEccCCCCeEEEEeHHHH
Q 000457 889 SEMFAECQELLQMFGLPYIIAP-MEAEAQCAYMEL----ANLVDGVVTDDSDVFLFGARSVYKNIFDDRKYVETYFMQDI 963 (1484)
Q Consensus 889 ~emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaK----kGlVDAVITEDSDLLLFG~~kVIRN~fk~~K~VEvydledI 963 (1484)
..+++.++++|+.||||++.+| |||||+||+|++ .|...+|+|.|+|++||++++|...... ..++++.+.+
T Consensus 84 ~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~~~---~~~~i~~~~v 160 (240)
T cd00008 84 REQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSPM---KKKLVTEENV 160 (240)
T ss_pred HHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEeCC---CceEEeHHHH
Confidence 3678999999999999999998 799999999985 5888899999999999987766422111 2357899999
Q ss_pred HHHhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhh
Q 000457 964 EKDLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIE 1018 (1484)
Q Consensus 964 eeeLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~e 1018 (1484)
.+.+|++|+||++||+|+| |||+|||||||||||.+||++|+++ +.+++...
T Consensus 161 ~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsl---e~i~~~~~ 214 (240)
T cd00008 161 IEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSL---EGILENLD 214 (240)
T ss_pred HHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCH---HHHHHhHH
Confidence 9999999999999999999 8999999999999999999999995 44444443
No 12
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.87 E-value=9.6e-22 Score=214.29 Aligned_cols=120 Identities=18% Similarity=0.259 Sum_probs=103.8
Q ss_pred HHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHHc----CceeEEEcCCCceecccCCEEEEEccCCCCeEEEEeHHHHH
Q 000457 890 EMFAECQELLQMFGLPYIIAP-MEAEAQCAYMELA----NLVDGVVTDDSDVFLFGARSVYKNIFDDRKYVETYFMQDIE 964 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaKk----GlVDAVITEDSDLLLFG~~kVIRN~fk~~K~VEvydledIe 964 (1484)
.+++.++++|+++|||++.+| |||||+||+|++. |...+|+|.|+|++||++++|............+++.+.+.
T Consensus 90 ~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~v~ 169 (281)
T PRK14976 90 SQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILNTNNFF 169 (281)
T ss_pred HHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEecCCCCcEEEcHHHHH
Confidence 578899999999999999999 7999999999864 77778999999999999876532221222124679999999
Q ss_pred HHhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchH
Q 000457 965 KDLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 965 eeLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
++||++|.||++|++|+| |||+|||||||+|||.+||++||++++
T Consensus 170 ~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~ 216 (281)
T PRK14976 170 ELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIEN 216 (281)
T ss_pred HHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHH
Confidence 999999999999999999 899999999999999999999999544
No 13
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.83 E-value=1.1e-20 Score=206.73 Aligned_cols=133 Identities=25% Similarity=0.350 Sum_probs=103.8
Q ss_pred HHHHhccCCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccCCCCeEEE
Q 000457 878 KKLERNAESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFDDRKYVET 957 (1484)
Q Consensus 878 ~K~kRravsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K~VEv 957 (1484)
..+..+...|++.+....+.+|..+||| +.+|.|+.||||+ +.|.+++|+|+|+|+|||+++++.......+....+
T Consensus 92 ~~l~~q~~~i~~~~~~~~~~~l~~~G~e-add~i~t~A~~a~--~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~~~~~~ 168 (310)
T COG0258 92 DELAPQIPILTELLVALGIPLLELMGIE-ADDPIETLAQKAY--KKGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKF 168 (310)
T ss_pred HHHHHHHHHHHHHHHHhCcHhhhcCCCC-cchhHHHHHHHHH--hcCCeEEEEeCCcchhhhcCCCcEEEeccCCCCccc
Confidence 3445555556666666666677777777 6666777777776 789999999999999999999865433322222125
Q ss_pred EeHHHHHHHh-CCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchHHHHH
Q 000457 958 YFMQDIEKDL-GLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDGLSKF 1013 (1484)
Q Consensus 958 ydledIeeeL-GLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDgLekf 1013 (1484)
++...+.+.| |+++.||+||++|+| |||+|||||||+|||++||++||+++.|...
T Consensus 169 ~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~ 227 (310)
T COG0258 169 LDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYEN 227 (310)
T ss_pred CCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHh
Confidence 7889999999 999999999999999 9999999999999999999999985554443
No 14
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.82 E-value=7e-20 Score=224.25 Aligned_cols=126 Identities=21% Similarity=0.332 Sum_probs=107.8
Q ss_pred HHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHHc----CceeEEEcCCCceecccCCEEE-EEccCCCCeEEEEeHHHH
Q 000457 890 EMFAECQELLQMFGLPYIIAP-MEAEAQCAYMELA----NLVDGVVTDDSDVFLFGARSVY-KNIFDDRKYVETYFMQDI 963 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaKk----GlVDAVITEDSDLLLFG~~kVI-RN~fk~~K~VEvydledI 963 (1484)
.+++.|+++|++||||++.+| |||||+||+|++. |+.++|+|.|+|++||++++|. ++... +....+|+.+.|
T Consensus 84 ~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~~~-~~~~~~~~~~~v 162 (887)
T TIGR00593 84 EQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPKG-KTSFTEITPEYV 162 (887)
T ss_pred HHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEeccC-CCCceEEcHHHH
Confidence 467899999999999999999 7999999999874 8889999999999999998763 22221 113457999999
Q ss_pred HHHhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhC
Q 000457 964 EKDLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIES 1019 (1484)
Q Consensus 964 eeeLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ek 1019 (1484)
.++||++|+||+||++|+| |||+|||||||||||.+||++||+ |+.+++..+.
T Consensus 163 ~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygs---le~i~~~~~~ 217 (887)
T TIGR00593 163 VEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGS---LENIYENLDQ 217 (887)
T ss_pred HHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCC---HHHHHHHHHH
Confidence 9999999999999999999 699999999999999999999999 5555555544
No 15
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.82 E-value=9.1e-20 Score=197.53 Aligned_cols=117 Identities=21% Similarity=0.271 Sum_probs=102.1
Q ss_pred HHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHH----cCceeEEEcCCCceecccCCEEE-EEccCCCCeEEEEeHHHH
Q 000457 890 EMFAECQELLQMFGLPYIIAP-MEAEAQCAYMEL----ANLVDGVVTDDSDVFLFGARSVY-KNIFDDRKYVETYFMQDI 963 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaK----kGlVDAVITEDSDLLLFG~~kVI-RN~fk~~K~VEvydledI 963 (1484)
.+++.++++|.++|||++..| |||||+||+|++ .|.-..|+|.|+|++|+..+.|. ++.+. ..+++.+.+
T Consensus 84 ~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~~----~~~~~~~~v 159 (256)
T PRK09482 84 QGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYFQ----KRWLDAPFI 159 (256)
T ss_pred HHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEeccc----cccCCHHHH
Confidence 567889999999999999999 799999999986 36677899999999999887663 33321 246899999
Q ss_pred HHHhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchHH
Q 000457 964 EKDLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 964 eeeLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
.++||++|.||+||++|+| +|++|||||||||||.+||++||+++.+
T Consensus 160 ~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i 208 (256)
T PRK09482 160 EQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENI 208 (256)
T ss_pred HHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHH
Confidence 9999999999999999999 8999999999999999999999995543
No 16
>PRK05755 DNA polymerase I; Provisional
Probab=99.80 E-value=2.4e-19 Score=219.12 Aligned_cols=126 Identities=24% Similarity=0.345 Sum_probs=108.1
Q ss_pred HHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHH----cCceeEEEcCCCceecccCCEEE-EEccCCCCeEEEEeHHHH
Q 000457 890 EMFAECQELLQMFGLPYIIAP-MEAEAQCAYMEL----ANLVDGVVTDDSDVFLFGARSVY-KNIFDDRKYVETYFMQDI 963 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaK----kGlVDAVITEDSDLLLFG~~kVI-RN~fk~~K~VEvydledI 963 (1484)
.+++.++++|+.+|||++.+| |||||+||+|++ .|..++|+|.|+|++||++++|. ..... ......++.+.|
T Consensus 86 ~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~~~~~-~~~~~~~~~~~v 164 (880)
T PRK05755 86 EQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTMG-VSKNEELDPEEV 164 (880)
T ss_pred HHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEeeccC-CCCCeEEcHHHH
Confidence 578899999999999999999 799999999985 48899999999999999988652 22211 123457999999
Q ss_pred HHHhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhC
Q 000457 964 EKDLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIES 1019 (1484)
Q Consensus 964 eeeLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ek 1019 (1484)
.++||++|+||+|||+|+| |||+|||||||+|||.+||++||+ |+.+++++..
T Consensus 165 ~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gs---le~i~~~~~~ 219 (880)
T PRK05755 165 VEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGS---LEGLYENLDE 219 (880)
T ss_pred HHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCC---HHHHHHhHHH
Confidence 9999999999999999999 799999999999999999999999 5555555554
No 17
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.67 E-value=8.6e-17 Score=146.46 Aligned_cols=69 Identities=48% Similarity=0.893 Sum_probs=64.5
Q ss_pred HcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccCCCC---eEEEEeHHHHHHHhCC
Q 000457 901 MFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFDDRK---YVETYFMQDIEKDLGL 969 (1484)
Q Consensus 901 lfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K---~VEvydledIeeeLGL 969 (1484)
.+||||++||||||||||+|+++|++|+|+|+|+|+|+||+++||++++..++ .++.++...+++++||
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 68999999999999999999999999999999999999999999999987654 6889999999999885
No 18
>PHA00439 exonuclease
Probab=99.40 E-value=9.6e-13 Score=145.42 Aligned_cols=103 Identities=17% Similarity=0.127 Sum_probs=83.1
Q ss_pred HHHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHH----cCc-eeEEEcCCCceecccCCEEEEEccCCCCeEEEEeHHH
Q 000457 889 SEMFAECQELLQMFGLPYIIAP-MEAEAQCAYMEL----ANL-VDGVVTDDSDVFLFGARSVYKNIFDDRKYVETYFMQD 962 (1484)
Q Consensus 889 ~emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaK----kGl-VDAVITEDSDLLLFG~~kVIRN~fk~~K~VEvydled 962 (1484)
..+++.+++++.++||+++..| ||||+.||+|++ .|+ -.+|+|.|+|++|+....+++. ..+. +..++.+
T Consensus 96 ~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~~~--~~~~-~~~~~~~- 171 (286)
T PHA00439 96 VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFLWC--TTGN-ILTQTPE- 171 (286)
T ss_pred hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEEEc--cCCc-eEEcCcc-
Confidence 4578889999999999999999 899999999985 366 6689999999999975544432 1111 1112221
Q ss_pred HHHHhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHh
Q 000457 963 IEKDLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNA 1003 (1484)
Q Consensus 963 IeeeLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrq 1003 (1484)
.+++|++|.+|+| +|++||||||| |||.+||++
T Consensus 172 -------~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 172 -------TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred -------cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 2899999999999 89999999999 999999999
No 19
>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=99.26 E-value=5.3e-12 Score=115.00 Aligned_cols=51 Identities=33% Similarity=0.573 Sum_probs=45.4
Q ss_pred HhCCCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHh
Q 000457 966 DLGLTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREW 1016 (1484)
Q Consensus 966 eLGLTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW 1016 (1484)
.||++|+||++||+|+| |||+|||||||+|||.+||++|++++.+-...++
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~ 54 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDK 54 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence 48999999999999999 9999999999999999999999996655554444
No 20
>PHA02567 rnh RnaseH; Provisional
Probab=98.84 E-value=9.8e-09 Score=114.92 Aligned_cols=88 Identities=16% Similarity=0.103 Sum_probs=73.0
Q ss_pred HHHHHHHHHcCCCeeeCc-chHHHHHHHHHH----cCceeEEEcCCCceecccC-CEEE-EEccCCCCeEEEEeHHHHHH
Q 000457 893 AECQELLQMFGLPYIIAP-MEAEAQCAYMEL----ANLVDGVVTDDSDVFLFGA-RSVY-KNIFDDRKYVETYFMQDIEK 965 (1484)
Q Consensus 893 ~eIKeLLrlfGIPyIVAP-YEADAQCAyLaK----kGlVDAVITEDSDLLLFG~-~kVI-RN~fk~~K~VEvydledIee 965 (1484)
..+++++.+|||+++..| ||||+.+|+|++ .|.-..|+|.|+|++|+.. +.|. +.. +..+.+..
T Consensus 110 ~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~~~~---------~~~~~V~~ 180 (304)
T PHA02567 110 KIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQWSP---------MQKKWVKP 180 (304)
T ss_pred HHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeEEeec---------CCHHHHHH
Confidence 456788899999999999 799999999986 4777789999999999974 4442 211 23467888
Q ss_pred HhCCCHHHHHHHHHHcC--CCCCCCCC
Q 000457 966 DLGLTREKLIRMALLLG--SDYTEGIS 990 (1484)
Q Consensus 966 eLGLTpeQFIDLcILsG--cDYiPGVP 990 (1484)
++| .|.|+++|.+|+| +|++||||
T Consensus 181 k~G-~P~q~iD~kaL~GDsSDNIPGVp 206 (304)
T PHA02567 181 KYG-SPEKDLMTKIIKGDKKDGVASIK 206 (304)
T ss_pred HhC-CHHHHHHHHHhCCcccCCcCCCC
Confidence 999 4999999999999 89999998
No 21
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.67 E-value=1.6e-08 Score=82.23 Aligned_cols=33 Identities=42% Similarity=0.841 Sum_probs=29.9
Q ss_pred HHHHHHHHHHcCCCCC---CCCCCccHHHHHHHHHhc
Q 000457 971 REKLIRMALLLGSDYT---EGISGIGIVNAIEVVNAF 1004 (1484)
Q Consensus 971 peQFIDLcILsGcDYi---PGVPGIGPKTAlKLLrqF 1004 (1484)
|+||++||+|+| ||. |||||||+|||++||++|
T Consensus 1 p~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 579999999999 665 599999999999999987
No 22
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=98.66 E-value=1.2e-09 Score=105.59 Aligned_cols=41 Identities=24% Similarity=0.468 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHcC--CCCCCCCCCccHHHHHHHHHhcCCchH
Q 000457 969 LTREKLIRMALLLG--SDYTEGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 969 LTpeQFIDLcILsG--cDYiPGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
+.|+||+||.+|+| +|++|||||||+|||.+||++||++++
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~ 43 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLEN 43 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHC
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHH
Confidence 47899999999999 899999999999999999999999544
No 23
>PF12813 XPG_I_2: XPG domain containing
Probab=98.26 E-value=5.8e-06 Score=90.32 Aligned_cols=121 Identities=24% Similarity=0.328 Sum_probs=81.2
Q ss_pred HHHHHHHHHHHc---CCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccC----CEE-EEEccCCC-------C--
Q 000457 891 MFAECQELLQMF---GLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGA----RSV-YKNIFDDR-------K-- 953 (1484)
Q Consensus 891 mI~eIKeLLrlf---GIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~----~kV-IRN~fk~~-------K-- 953 (1484)
++..+.+.|+.+ |++++..|+|||..||.++++--+ .|+|.|||+|+|.. ..| +..+.... .
T Consensus 5 ~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i 83 (246)
T PF12813_consen 5 LVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYI 83 (246)
T ss_pred hHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCee
Confidence 456788889988 999999999999999999976333 99999999999987 333 22222211 2
Q ss_pred eEEEEeHHHHHHHhCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHh---c-CCchHHHHHHHhhhC
Q 000457 954 YVETYFMQDIEKDLGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNA---F-PEEDGLSKFREWIES 1019 (1484)
Q Consensus 954 ~VEvydledIeeeLGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrq---F-GSlDgLekfrEW~ek 1019 (1484)
....|....|.+.||+. .|..|+. ||...+. -..-..++..+. . .....+..|.+|...
T Consensus 84 ~~~~y~~~~i~~~l~l~--~Lp~lA~----d~~~~~~-~~~~~~i~~~~~~~~~~~~~~~~~~fl~~y~~ 146 (246)
T PF12813_consen 84 SAKVYSPDKICKRLGLP--LLPLLAY----DYKRDPH-ETFSQLIKRAKSSRKVNEQQRRYQEFLNWYLS 146 (246)
T ss_pred EEEEEcHHHHHHHcCCc--hhHHHHH----Hhccchh-hhHHHHHHhhccccccccchHHHHHHHHHHhc
Confidence 24569999999999999 6666665 5522211 122222222222 1 111468889999844
No 24
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=98.20 E-value=3e-06 Score=87.87 Aligned_cols=77 Identities=22% Similarity=0.355 Sum_probs=58.7
Q ss_pred HHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHH----cCceeEEEcCCCceecccCC--EEEEEccCCCCeEEEEeHHH
Q 000457 890 EMFAECQELLQMFGLPYIIAP-MEAEAQCAYMEL----ANLVDGVVTDDSDVFLFGAR--SVYKNIFDDRKYVETYFMQD 962 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaK----kGlVDAVITEDSDLLLFG~~--kVIRN~fk~~K~VEvydled 962 (1484)
.+++.++++|..+||+++..| |||||.+|+|++ .|.-..|+|.|+|++|+..+ .|+. +........+|+.+.
T Consensus 86 ~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~~-~~~~~~~~~~~~~~~ 164 (169)
T PF02739_consen 86 PQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVYL-LDPGKKKFKVYDPEE 164 (169)
T ss_dssp HHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEEE-EETTTTCS-EB-HHH
T ss_pred HHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEEE-eecCCCCCEEEcHHH
Confidence 467889999999999999999 899999999986 47778999999999999998 5542 222223457888888
Q ss_pred HHHHh
Q 000457 963 IEKDL 967 (1484)
Q Consensus 963 IeeeL 967 (1484)
|.++|
T Consensus 165 v~eky 169 (169)
T PF02739_consen 165 VEEKY 169 (169)
T ss_dssp HHHHT
T ss_pred HhhcC
Confidence 87764
No 25
>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=95.99 E-value=0.014 Score=75.12 Aligned_cols=101 Identities=16% Similarity=0.290 Sum_probs=83.1
Q ss_pred CCChhhHhcCCccchHHHHHHHHHHHHHHHHHHHHHhhcCccchhhHHHHHHHhHhhhhHhHHHHHHHhhcCCCccc-cc
Q 000457 203 NVDPAVLAALPPSMQLDLLVQMREQLMAENRQKYQKVKKAPEKFSELQIQAYLKTVAFRREIDEVQKAAAGRGVAGV-QT 281 (1484)
Q Consensus 203 ~iDp~vlasLPps~qldll~~~re~~~aenR~~~~k~~~~p~~fS~lQi~~yLkt~a~~r~I~~~qk~a~~~~~ggv-~~ 281 (1484)
+|+-+-..+|||.+|-.+|--||++.++-- .+|..+-.+.-.||..||+--||--.|..+|..|+.--++...|-. ..
T Consensus 189 D~~S~~F~sLP~~~qyeILs~lRlrSRlRm-eQLeemfpdSmDFSkFQIkrv~kRN~lTQrLmnv~gm~~~~~~~~~~~~ 267 (1034)
T TIGR00600 189 DIESEEFSSLPPEVKHEILTDMKLFTKRRR-TLFEAMPENSMDFSQYQLKGLLKKNDLNQHIENVTKEMNQQHSGNIQRQ 267 (1034)
T ss_pred CCCCHHHHhCCHHHHHHHHHHHHHHHHHHH-HHHhhcCCCchhhhHHHHHHHHHHhHHHHHHHHHhhcccccccccccch
Confidence 344457899999999999999998877665 9999999999999999999999999999999999988777544322 44
Q ss_pred ccccccccceEEee--cccccchhh
Q 000457 282 SRIASEANREFIFS--SSFTGDKQV 304 (1484)
Q Consensus 282 srias~~Nrefi~s--sSftGDK~~ 304 (1484)
.|||.+-+|||+-- +|=-|---+
T Consensus 268 ~riag~~~kEy~l~k~~s~E~gw~L 292 (1034)
T TIGR00600 268 YRDEGGFLKEVELRRVVSEDTSHYI 292 (1034)
T ss_pred hhccccccceeEEEeccccCCceeE
Confidence 89999999999976 444444333
No 26
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=95.01 E-value=0.03 Score=55.01 Aligned_cols=58 Identities=33% Similarity=0.608 Sum_probs=38.9
Q ss_pred CCCChhhHhcCCccchHHHHHHHHHHHHHHHHHHHHHhhcCccchhhHHHHHHHhHh--hhhHhH
Q 000457 202 GNVDPAVLAALPPSMQLDLLVQMREQLMAENRQKYQKVKKAPEKFSELQIQAYLKTV--AFRREI 264 (1484)
Q Consensus 202 ~~iDp~vlasLPps~qldll~~~re~~~aenR~~~~k~~~~p~~fS~lQi~~yLkt~--a~~r~I 264 (1484)
..|||++|++||+.||-++|.+-|..+....+..=.. .-..+.-.-+||-|. .||++|
T Consensus 43 ~~I~pefL~ALP~diR~EVl~qe~~~~~~~~~~~~~~-----~~~~~~d~asflatl~p~LR~ev 102 (108)
T PF14377_consen 43 SQIDPEFLAALPPDIREEVLAQERRERRRQERQQNAR-----QHPQEMDNASFLATLPPELRREV 102 (108)
T ss_pred cccCHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccc-----cCCCCCCHHHHHHhCCHHHHHHH
Confidence 3799999999999999999999887665443321111 234444555666664 466665
No 27
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=93.34 E-value=0.041 Score=65.70 Aligned_cols=112 Identities=20% Similarity=0.315 Sum_probs=83.7
Q ss_pred HHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccC-CEEEEEccCC--CCeEEEEeHHHHHHHhCCCH
Q 000457 895 CQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGA-RSVYKNIFDD--RKYVETYFMQDIEKDLGLTR 971 (1484)
Q Consensus 895 IKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~-~kVIRN~fk~--~K~VEvydledIeeeLGLTp 971 (1484)
+-.++..-||.|+++||-|..|||||...-+++++.. -+|+++|.| +++|..+... .-++.++..-...+-+-.+-
T Consensus 134 ~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~g-p~d~l~ld~vdr~il~m~fg~d~Ppl~~~~vp~~lem~l~s~ 212 (531)
T COG5366 134 ASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAFG-PSDILLLDGVDRIILDMSFGSDKPPLDVFHVPRFLEMFLLSS 212 (531)
T ss_pred ccccccccceEEEehhhHHHHHHHHHHHHHHHHhcCC-chHhHHHhhhhhheeecccCCCCCCCcccccchHHHhccccc
Confidence 4456788899999999999999999999989988887 889998876 5666555332 23566666655555555677
Q ss_pred HHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCc
Q 000457 972 EKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEE 1007 (1484)
Q Consensus 972 eQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSl 1007 (1484)
.-|..+-.|.|||+++.++.|----+.-+-+-+|+.
T Consensus 213 ~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd~ 248 (531)
T COG5366 213 RLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGDM 248 (531)
T ss_pred chhhhhcccccccccccccccccchhHHHHHHHhcc
Confidence 889999999999999999986543355555545543
No 28
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=88.15 E-value=0.36 Score=43.61 Aligned_cols=23 Identities=26% Similarity=0.378 Sum_probs=18.6
Q ss_pred CCCCCccHHHHHHHHHhcCCchH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
-||||||+++|..|+++|++++.
T Consensus 6 LGI~~VG~~~ak~L~~~f~sl~~ 28 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFGSLEA 28 (64)
T ss_dssp CTSTT--HHHHHHHHHCCSCHHH
T ss_pred CCCCCccHHHHHHHHHHcCCHHH
Confidence 49999999999999999999543
No 29
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=86.28 E-value=2.5 Score=53.96 Aligned_cols=138 Identities=16% Similarity=0.257 Sum_probs=81.0
Q ss_pred HHHHHHHHHHhhHHHHhhChhH----HHHHhccCCCCH--HHHHHHHHHHHHc------------CCCeee----CcchH
Q 000457 856 EKILEEEMQILDHEYMYLGDEQ----KKLERNAESVSS--EMFAECQELLQMF------------GLPYII----APMEA 913 (1484)
Q Consensus 856 ~~~LeEE~q~L~qE~v~lG~Ea----~K~kRravsVT~--emI~eIKeLLrlf------------GIPyIV----APYEA 913 (1484)
.++.++|++.+++++..-|.-. .+..=.+..||| ..+..+-..|+-. +|.+|. .|+|.
T Consensus 125 aae~~~e~e~~ree~~~~G~~lpp~~~~e~fDSNcITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEG 204 (931)
T KOG2044|consen 125 AAEKEAEIERLREEFEAEGKFLPPKVKKETFDSNCITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEG 204 (931)
T ss_pred HHHHHHHHHHHHHHHHhcCCcCCchhhccccccCccCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcc
Confidence 3455556677777776655522 111112344443 3334444444332 566665 48999
Q ss_pred HHHHHHHHHc---------CceeEEEcCCCceecccCC------EEEEEccCC---------------------------
Q 000457 914 EAQCAYMELA---------NLVDGVVTDDSDVFLFGAR------SVYKNIFDD--------------------------- 951 (1484)
Q Consensus 914 DAQCAyLaKk---------GlVDAVITEDSDLLLFG~~------kVIRN~fk~--------------------------- 951 (1484)
|.-|-...+. +-+.++++-|-||+++|-- .|||..+.-
T Consensus 205 EHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~~~~~ 284 (931)
T KOG2044|consen 205 EHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLGLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKPRLGE 284 (931)
T ss_pred hhHHHHHHHHccCCCCCCCCceeeeecCCccceeeeccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCcCCccc
Confidence 9977655442 4588999999999999941 456654320
Q ss_pred ----------CCeEEEEeHHHHH----HHhC-------CC----HHHHHHHHHHcCCCCCCCCCCcc
Q 000457 952 ----------RKYVETYFMQDIE----KDLG-------LT----REKLIRMALLLGSDYTEGISGIG 993 (1484)
Q Consensus 952 ----------~K~VEvydledIe----eeLG-------LT----peQFIDLcILsGcDYiPGVPGIG 993 (1484)
.+.+.+++..-+. .+|- ++ -+.||.||-++|-||+|.+|-+-
T Consensus 285 ~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLe 351 (931)
T KOG2044|consen 285 TNELADVPGVEKPFIFLNISVLREYLERELRMPNLPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLE 351 (931)
T ss_pred ccccccCcccccceEEEEHHHHHHHHHHHhcCCCCCccccHHhhhcceEEEEeeecCccCCCCCchh
Confidence 0234444443332 2322 22 25677899999999999999653
No 30
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=81.58 E-value=0.6 Score=57.55 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHHHHHHcCCCeeeCcchHHHHHHHH
Q 000457 885 ESVSSEMFAECQELLQMFGLPYIIAPMEAEAQCAYM 920 (1484)
Q Consensus 885 vsVT~emI~eIKeLLrlfGIPyIVAPYEADAQCAyL 920 (1484)
.+||.+-+..++.+|+.+.+=-..+|-+.-.++.-|
T Consensus 188 ~DVTaeEF~l~m~lL~~lk~~~~~~t~~g~qeLv~i 223 (556)
T PF05918_consen 188 QDVTAEEFELFMSLLKSLKIYGGKQTIEGRQELVDI 223 (556)
T ss_dssp TT--HHHHHHHHHHHHTSGG---GSSHHHHHHHHHH
T ss_pred HhccHHHHHHHHHHHHhCccccccCChHHHHHHHHH
Confidence 568888888888888877762123344444445444
No 31
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=78.42 E-value=5.2 Score=48.37 Aligned_cols=87 Identities=18% Similarity=0.234 Sum_probs=54.5
Q ss_pred HHHHHHHc--CCCeeeCc-chHHHHHHHHH-----HcCceeEEEcCCCceecccCCEEEEEccCCCCeEEEEeHHHHHHH
Q 000457 895 CQELLQMF--GLPYIIAP-MEAEAQCAYME-----LANLVDGVVTDDSDVFLFGARSVYKNIFDDRKYVETYFMQDIEKD 966 (1484)
Q Consensus 895 IKeLLrlf--GIPyIVAP-YEADAQCAyLa-----KkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K~VEvydledIeee 966 (1484)
+..+|..+ +|..+..- .-||-++.+=+ +.|-=-.++|.|.|+|+|.+-....++.. .+-+.
T Consensus 148 l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~-----------t~~~~ 216 (425)
T PF04599_consen 148 LESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIK-----------TMNQL 216 (425)
T ss_pred HHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHH-----------hHHhH
Confidence 55666666 67766655 57887666533 35888899999999999987432222110 01111
Q ss_pred hCC-----CHHHHHHHHHHcCCCCCCCCCCc
Q 000457 967 LGL-----TREKLIRMALLLGSDYTEGISGI 992 (1484)
Q Consensus 967 LGL-----TpeQFIDLcILsGcDYiPGVPGI 992 (1484)
|-+ +.---...++.=||||.||+-|+
T Consensus 217 Y~~~P~~~s~YL~kL~~L~NGCDfFpGLyG~ 247 (425)
T PF04599_consen 217 YKFIPCSKSRYLSKLTALVNGCDFFPGLYGI 247 (425)
T ss_pred eeecCCchHHHHHHHHHHHhcccccCCccee
Confidence 221 22233445666789999999995
No 32
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=75.72 E-value=1.5 Score=43.28 Aligned_cols=65 Identities=25% Similarity=0.450 Sum_probs=40.4
Q ss_pred CChhhHhcCCccchHHHHHHHHHHHHHHHHHHH--HHhhcCccchhhHHHHHHHhHhh--hhHhHHHHHHHhh
Q 000457 204 VDPAVLAALPPSMQLDLLVQMREQLMAENRQKY--QKVKKAPEKFSELQIQAYLKTVA--FRREIDEVQKAAA 272 (1484)
Q Consensus 204 iDp~vlasLPps~qldll~~~re~~~aenR~~~--~k~~~~p~~fS~lQi~~yLkt~a--~~r~I~~~qk~a~ 272 (1484)
|||++|++||..|+.++|.+-+..+.+..+..- +.....+...+ ..||...- +|++|-+..+...
T Consensus 1 iDp~fLaaLPeDiR~Evl~~~~~~~~~~~~~~~~~~~~~~~~~~I~----pefL~ALP~diR~EVl~qe~~~~ 69 (108)
T PF14377_consen 1 IDPEFLAALPEDIREEVLAQQQRERRAQASQRQSPQSSAPQPSQID----PEFLAALPPDIREEVLAQERRER 69 (108)
T ss_pred CCHHHHHHCCHHHHHHHHHHHHhhccchhcccCcccccCCCccccC----HHHHHhCCHHHHHHHHHHHHHHH
Confidence 899999999999999998876555444321111 11111222222 26887643 8888888765543
No 33
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=75.23 E-value=9.7 Score=48.63 Aligned_cols=91 Identities=15% Similarity=0.288 Sum_probs=60.6
Q ss_pred CCCeee----CcchHHHHHHHHHHc---------CceeEEEcCCCceecccC----C--EEEE-EccCCC----------
Q 000457 903 GLPYII----APMEAEAQCAYMELA---------NLVDGVVTDDSDVFLFGA----R--SVYK-NIFDDR---------- 952 (1484)
Q Consensus 903 GIPyIV----APYEADAQCAyLaKk---------GlVDAVITEDSDLLLFG~----~--kVIR-N~fk~~---------- 952 (1484)
+|.+|. .|+|.|.-+-.+.+. +-..+|++-|.||+++|- + .|+| .+|...
T Consensus 176 nl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~ 255 (953)
T COG5049 176 NLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTK 255 (953)
T ss_pred eEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCccccccccccc
Confidence 455555 489999987776553 568899999999999994 2 4566 333210
Q ss_pred ----------------CeEEEEeHHHHHH----Hh---CC----C----HHHHHHHHHHcCCCCCCCCCCcc
Q 000457 953 ----------------KYVETYFMQDIEK----DL---GL----T----REKLIRMALLLGSDYTEGISGIG 993 (1484)
Q Consensus 953 ----------------K~VEvydledIee----eL---GL----T----peQFIDLcILsGcDYiPGVPGIG 993 (1484)
..+-+++..-+.+ +| ++ + -+.||.+|-++|-||+|.+|++-
T Consensus 256 ~g~t~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ld 327 (953)
T COG5049 256 CGRTGHSDEECKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLD 327 (953)
T ss_pred ccccccchhhhcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccc
Confidence 1234455443332 22 22 2 26788899999999999999874
No 34
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.63 E-value=3.8 Score=44.48 Aligned_cols=40 Identities=28% Similarity=0.370 Sum_probs=29.8
Q ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCC
Q 000457 961 QDIEKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPE 1006 (1484)
Q Consensus 961 edIeeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGS 1006 (1484)
++-..-||+ +.+.--.|..| -+|+|||||+|+.+|..|+.
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~ILs~~~~ 95 (194)
T PRK14605 55 EDALSLFGFATTEELSLFETL------IDVSGIGPKLGLAMLSAMNA 95 (194)
T ss_pred cCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHHhCCH
Confidence 344456887 55666666666 47999999999999999974
No 35
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.44 E-value=4.4 Score=44.37 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=27.9
Q ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcC
Q 000457 961 QDIEKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 961 edIeeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFG 1005 (1484)
++-...||+ +...--.|..| -+|+|||||+|+.+|..++
T Consensus 56 Ed~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~~ 95 (203)
T PRK14602 56 EDALELFGFATWDERQTFIVL------ISISKVGAKTALAILSQFR 95 (203)
T ss_pred cCcceeeCCCCHHHHHHHHHH------hCCCCcCHHHHHHHHhhCC
Confidence 333456786 56666666666 4688999999999998875
No 36
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=73.15 E-value=3.5 Score=44.69 Aligned_cols=51 Identities=22% Similarity=0.203 Sum_probs=34.6
Q ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhCCC
Q 000457 961 QDIEKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIESPD 1021 (1484)
Q Consensus 961 edIeeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ekp~ 1021 (1484)
++....||+ +.+.--.|..| -+|.|||||+|+.+|..+. .+.|.+.+.+-+
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~AL~iLs~~~----~~el~~aI~~~D 106 (188)
T PRK14606 55 QDGITLYGFSNERKKELFLSL------TKVSRLGPKTALKIISNED----AETLVTMIASQD 106 (188)
T ss_pred cCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCCC----HHHHHHHHHhCC
Confidence 444456887 45566666666 3789999999999998875 555555555433
No 37
>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=71.18 E-value=4.7 Score=43.70 Aligned_cols=39 Identities=23% Similarity=0.309 Sum_probs=28.6
Q ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcC
Q 000457 961 QDIEKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 961 edIeeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFG 1005 (1484)
++-..-||+ +.+.--.|..| -+|+|||||+|+.+|..++
T Consensus 54 ed~~~LyGF~~~~Er~lF~~L------~~V~GIGpK~Al~iL~~~~ 93 (191)
T TIGR00084 54 EDAELLFGFNTLEERELFKEL------IKVNGVGPKLALAILSNMS 93 (191)
T ss_pred cCCceeeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHhcCC
Confidence 333456786 55666666666 4799999999999998875
No 38
>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=70.05 E-value=4 Score=36.46 Aligned_cols=24 Identities=25% Similarity=0.286 Sum_probs=16.5
Q ss_pred CCCCCccHHHHHHHHHh-cCCchHH
Q 000457 987 EGISGIGIVNAIEVVNA-FPEEDGL 1010 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrq-FGSlDgL 1010 (1484)
-+|.||||+||.+++.+ |.+++.|
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl 29 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDL 29 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHH
T ss_pred hhcccccHHHHHHHHHhCCCCHHHH
Confidence 47999999999999997 7775554
No 39
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.41 E-value=5.1 Score=44.07 Aligned_cols=46 Identities=26% Similarity=0.410 Sum_probs=28.6
Q ss_pred HHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhC
Q 000457 964 EKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIES 1019 (1484)
Q Consensus 964 eeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ek 1019 (1484)
..-||+ +.+.--.|..| -+|+|||||+|+.+|..+. .+.|.+....
T Consensus 57 ~~LYGF~t~~Er~lF~~L------isVsGIGPK~ALaILs~~~----~~el~~aI~~ 103 (196)
T PRK13901 57 LKLFGFLNSSEREVFEEL------IGVDGIGPRAALRVLSGIK----YNEFRDAIDR 103 (196)
T ss_pred ceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCCC----HHHHHHHHHh
Confidence 345676 45555555555 3678888888888887774 4444444443
No 40
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.14 E-value=5.2 Score=43.69 Aligned_cols=36 Identities=31% Similarity=0.497 Sum_probs=21.2
Q ss_pred HHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcC
Q 000457 964 EKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 964 eeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFG 1005 (1484)
...||+ +.+.--.|-.| -+|.|||||+|+.+|..+.
T Consensus 57 ~~LyGF~~~~Er~lF~~L------~~V~GIGpK~AL~iLs~~~ 93 (197)
T PRK14603 57 LSLYGFPDEDSLELFELL------LGVSGVGPKLALALLSALP 93 (197)
T ss_pred ceeeCcCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCCC
Confidence 345665 33333334443 3677777777777777664
No 41
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.75 E-value=6.8 Score=42.57 Aligned_cols=51 Identities=18% Similarity=0.320 Sum_probs=32.7
Q ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhCCC
Q 000457 961 QDIEKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIESPD 1021 (1484)
Q Consensus 961 edIeeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ekp~ 1021 (1484)
++...-||+ +.+.--.|-.| -+|.|||||+|+.+|..|. .+.|.+.+.+-+
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~L------isV~GIGpK~Al~iLs~~~----~~~l~~aI~~~D 106 (186)
T PRK14600 55 DNVTQLYGFLNREEQDCLRML------VKVSGVNYKTAMSILSKLT----PEQLFSAIVNED 106 (186)
T ss_pred cCCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHccCC----HHHHHHHHHcCC
Confidence 444456786 45555555555 4788999999999998875 455555554433
No 42
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=67.40 E-value=4.7 Score=43.44 Aligned_cols=20 Identities=25% Similarity=0.529 Sum_probs=18.2
Q ss_pred CCCCccHHHHHHHHHhcCCc
Q 000457 988 GISGIGIVNAIEVVNAFPEE 1007 (1484)
Q Consensus 988 GVPGIGPKTAlKLLrqFGSl 1007 (1484)
.|||||||+|..|+..|+..
T Consensus 77 ~i~GIGpk~A~~il~~fg~~ 96 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSPE 96 (192)
T ss_pred cCCCCCHHHHHHHHHhCCHH
Confidence 49999999999999999863
No 43
>PHA03065 Hypothetical protein; Provisional
Probab=67.34 E-value=13 Score=45.22 Aligned_cols=88 Identities=18% Similarity=0.230 Sum_probs=54.3
Q ss_pred HHHHHHHHc--CCCeeeCc-chHHHHHHHHH-----HcCceeEEEcCCCceecccCCEEEEEccCCCCeEEEEeHHHHHH
Q 000457 894 ECQELLQMF--GLPYIIAP-MEAEAQCAYME-----LANLVDGVVTDDSDVFLFGARSVYKNIFDDRKYVETYFMQDIEK 965 (1484)
Q Consensus 894 eIKeLLrlf--GIPyIVAP-YEADAQCAyLa-----KkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K~VEvydledIee 965 (1484)
.+-+.|..+ +|.++..- --||-.+..=+ +.|-=-.++|.|.|+|+|.+-.-+.++ ...+.+
T Consensus 149 ~l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki-----------I~t~~~ 217 (438)
T PHA03065 149 LLESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI-----------IKTANQ 217 (438)
T ss_pred HHHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH-----------HHhHHH
Confidence 345667777 78777655 47777655433 358888999999999999873221111 111122
Q ss_pred HhCCC-----HHHHHHHHHHcCCCCCCCCCCc
Q 000457 966 DLGLT-----REKLIRMALLLGSDYTEGISGI 992 (1484)
Q Consensus 966 eLGLT-----peQFIDLcILsGcDYiPGVPGI 992 (1484)
.|.+- ..--...++.=||||.||+-|+
T Consensus 218 ~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~ 249 (438)
T PHA03065 218 LYKFIPCAKTRYLSKLVALVNGCDFFPGLYGI 249 (438)
T ss_pred HheeCCChhHHHHHHHHHHHhcccccCccceE
Confidence 23322 2222344555689999999996
No 44
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.34 E-value=5.8 Score=43.08 Aligned_cols=39 Identities=23% Similarity=0.422 Sum_probs=26.6
Q ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcC
Q 000457 961 QDIEKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 961 edIeeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFG 1005 (1484)
++-..-||+ +.+.--.|..| -+|.|||||+|+.+|..+.
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~L------i~VsGIGpK~Al~ILs~~~ 94 (183)
T PRK14601 55 EDSNKLYGFLDKDEQKMFEML------LKVNGIGANTAMAVCSSLD 94 (183)
T ss_pred cCCceeeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCCC
Confidence 333445776 45555555555 4688899999998888775
No 45
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.32 E-value=5.8 Score=43.32 Aligned_cols=38 Identities=26% Similarity=0.350 Sum_probs=23.9
Q ss_pred HHHHHhCC-CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcC
Q 000457 962 DIEKDLGL-TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 962 dIeeeLGL-TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFG 1005 (1484)
+....||+ +...--.|..| -+|.|||||+|+.+|..+.
T Consensus 56 d~~~LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~~ 94 (195)
T PRK14604 56 DALTLYGFSTPAQRQLFELL------IGVSGVGPKAALNLLSSGT 94 (195)
T ss_pred CCceeeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCCC
Confidence 33345675 44444445554 3678888888888887764
No 46
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.31 E-value=2.6 Score=45.94 Aligned_cols=48 Identities=23% Similarity=0.115 Sum_probs=31.3
Q ss_pred EeHHHHHHHhC-CCHHHHHHHHHHcCC-CCCCCCCCccHHHHHHHHHhcCC
Q 000457 958 YFMQDIEKDLG-LTREKLIRMALLLGS-DYTEGISGIGIVNAIEVVNAFPE 1006 (1484)
Q Consensus 958 ydledIeeeLG-LTpeQFIDLcILsGc-DYiPGVPGIGPKTAlKLLrqFGS 1006 (1484)
+.++.-+.-+. +++++|+.. |..|. ..+..|||||+|||-+|+-..++
T Consensus 80 IGpK~AL~iLs~~~~~~l~~a-I~~~D~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 80 VGPKLALALLSALPPALLARA-LLEGDARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred cCHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 33443334444 678877653 33332 34589999999999999977553
No 47
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=65.92 E-value=14 Score=41.06 Aligned_cols=54 Identities=19% Similarity=0.230 Sum_probs=32.4
Q ss_pred EEeHHHHHHHhCCC-HHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHHhhhCC
Q 000457 957 TYFMQDIEKDLGLT-REKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFREWIESP 1020 (1484)
Q Consensus 957 vydledIeeeLGLT-peQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrEW~ekp 1020 (1484)
.+-.++....||+. .+.=..|..| -.|.|||||+|+.+|..+. ++.|.+.+..-
T Consensus 51 ~~vREd~~~LyGF~~~~ER~lF~~L------isVnGIGpK~ALaiLs~~~----~~~l~~aI~~~ 105 (201)
T COG0632 51 LVVREDAHLLYGFLTEEERELFRLL------ISVNGIGPKLALAILSNLD----PEELAQAIANE 105 (201)
T ss_pred EeehhhHHHHcCCCCHHHHHHHHHH------HccCCccHHHHHHHHcCCC----HHHHHHHHHhc
Confidence 34456666778874 3333334444 4577888888888887654 55555555443
No 48
>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=65.14 E-value=4.6 Score=32.60 Aligned_cols=16 Identities=25% Similarity=0.395 Sum_probs=12.4
Q ss_pred CCCCCccHHHHHHHHH
Q 000457 987 EGISGIGIVNAIEVVN 1002 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLr 1002 (1484)
..|||||++||..++.
T Consensus 14 ~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 14 MKLPGIGPKTANAILS 29 (30)
T ss_dssp HTSTT-SHHHHHHHHH
T ss_pred HhCCCcCHHHHHHHHh
Confidence 4689999999988763
No 49
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.94 E-value=2.7 Score=45.82 Aligned_cols=47 Identities=19% Similarity=0.084 Sum_probs=30.7
Q ss_pred eHHHHHHHhC-CCHHHHHHHHHHcC-CCCCCCCCCccHHHHHHHHHhcCC
Q 000457 959 FMQDIEKDLG-LTREKLIRMALLLG-SDYTEGISGIGIVNAIEVVNAFPE 1006 (1484)
Q Consensus 959 dledIeeeLG-LTpeQFIDLcILsG-cDYiPGVPGIGPKTAlKLLrqFGS 1006 (1484)
..+.-..-+. +++++|+.. |..| ...+..|||||+|||-+|+-+..+
T Consensus 82 GpK~Al~iLs~~~~~el~~a-I~~~D~~~L~kvpGIGkKtAerIilELk~ 130 (195)
T PRK14604 82 GPKAALNLLSSGTPDELQLA-IAGGDVARLARVPGIGKKTAERIVLELKG 130 (195)
T ss_pred CHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 3333333343 677777654 3333 345689999999999999977543
No 50
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=62.79 E-value=2.4 Score=52.51 Aligned_cols=18 Identities=11% Similarity=0.111 Sum_probs=5.1
Q ss_pred HHHHhhhhcccCCCcccc
Q 000457 1110 KRIKKAVKGITGSQSLLL 1127 (1484)
Q Consensus 1110 KRLqkAVk~irg~~~s~l 1127 (1484)
..|..-|+.+-...|+..
T Consensus 435 ~NI~~lik~L~~~pPsf~ 452 (556)
T PF05918_consen 435 NNILALIKDLFHNPPSFK 452 (556)
T ss_dssp HHHHHHHCC---------
T ss_pred hhHHHHHHHHhhCCcccc
Confidence 345556666666666653
No 51
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=60.19 E-value=6.7 Score=48.88 Aligned_cols=24 Identities=25% Similarity=0.281 Sum_probs=21.4
Q ss_pred CCCCCCccHHHHHHHHHhcCCchH
Q 000457 986 TEGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
+..|||||+|+...||++||+++.
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fgs~~~ 539 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFKTLYD 539 (567)
T ss_pred cccCCCCCHHHHHHHHHHhCCHHH
Confidence 479999999999999999999543
No 52
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=59.99 E-value=6.3 Score=49.64 Aligned_cols=25 Identities=16% Similarity=0.299 Sum_probs=21.8
Q ss_pred CCCCCCccHHHHHHHHHhcCCchHH
Q 000457 986 TEGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
+.+|||||+|++.+||++||+++.+
T Consensus 554 L~~IpGIG~kr~~~LL~~FgSi~~I 578 (624)
T PRK14669 554 LLEIPGVGAKTVQRLLKHFGSLERV 578 (624)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHH
Confidence 4699999999999999999996443
No 53
>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=59.57 E-value=6.4 Score=49.08 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=21.7
Q ss_pred CCCCCCccHHHHHHHHHhcCCchHH
Q 000457 986 TEGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
+..|||||+|+..+||+.||+++.|
T Consensus 543 Ld~I~GIG~kr~~~LL~~Fgs~~~i 567 (574)
T TIGR00194 543 LLKIPGVGEKRVQKLLKYFGSLKGI 567 (574)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHH
Confidence 4799999999999999999995444
No 54
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=58.81 E-value=7.3 Score=48.64 Aligned_cols=25 Identities=20% Similarity=0.264 Sum_probs=21.9
Q ss_pred CCCCCCCccHHHHHHHHHhcCCchH
Q 000457 985 YTEGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 985 YiPGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
-+..|||||+|+..+||+.||+++.
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~ 539 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKD 539 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHH
Confidence 4579999999999999999999543
No 55
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.61 E-value=4.2 Score=44.51 Aligned_cols=41 Identities=20% Similarity=0.173 Sum_probs=28.5
Q ss_pred HHhC-CCHHHHHHHHHHcCC-CCCCCCCCccHHHHHHHHHhcCC
Q 000457 965 KDLG-LTREKLIRMALLLGS-DYTEGISGIGIVNAIEVVNAFPE 1006 (1484)
Q Consensus 965 eeLG-LTpeQFIDLcILsGc-DYiPGVPGIGPKTAlKLLrqFGS 1006 (1484)
.-+. +++++|+. ++..|. ..+..|||||+|||-+|+-...+
T Consensus 89 ~iLs~~~~~~l~~-aI~~~D~~~L~~ipGIGkKtAerIilELkd 131 (203)
T PRK14602 89 AILSQFRPDDLRR-LVAEEDVAALTRVSGIGKKTAQHIFLELKY 131 (203)
T ss_pred HHHhhCCHHHHHH-HHHhCCHHHHhcCCCcCHHHHHHHHHHHHH
Confidence 3343 57776654 344443 45689999999999999977543
No 56
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=56.49 E-value=8.1 Score=48.59 Aligned_cols=24 Identities=25% Similarity=0.419 Sum_probs=21.4
Q ss_pred CCCCCccHHHHHHHHHhcCCchHH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
.||||||+|+|..|++.||+++.|
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i 595 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKV 595 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHH
Confidence 799999999999999999996544
No 57
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=56.42 E-value=50 Score=43.78 Aligned_cols=128 Identities=18% Similarity=0.307 Sum_probs=70.9
Q ss_pred hChhHHHHHhccCCCCH--HHHHHHHHHHHHc------------CCCeee----CcchHHHHHHHHHHc---------Cc
Q 000457 873 LGDEQKKLERNAESVSS--EMFAECQELLQMF------------GLPYII----APMEAEAQCAYMELA---------NL 925 (1484)
Q Consensus 873 lG~Ea~K~kRravsVT~--emI~eIKeLLrlf------------GIPyIV----APYEADAQCAyLaKk---------Gl 925 (1484)
-|...+...=.+..||| +.+..+.+-|+.| ++.+|- +|+|.|.-|--+.+. +-
T Consensus 118 nGe~~p~erFDSNcITPGTeFM~rl~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNT 197 (1493)
T KOG2045|consen 118 NGELRPHERFDSNCITPGTEFMVRLQEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNT 197 (1493)
T ss_pred ccccCcccccccCCCCCcHHHHHHHHHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCc
Confidence 35544442223455555 5566666666665 566654 689999866544331 44
Q ss_pred eeEEEcCCCceecccC----C--EEEEEc--cCC---CCeE-----EEEeHH-----------HHHH--HhCCCH----H
Q 000457 926 VDGVVTDDSDVFLFGA----R--SVYKNI--FDD---RKYV-----ETYFMQ-----------DIEK--DLGLTR----E 972 (1484)
Q Consensus 926 VDAVITEDSDLLLFG~----~--kVIRN~--fk~---~K~V-----Evydle-----------dIee--eLGLTp----e 972 (1484)
-.++++-|-|++++|- + .++|-= |.. .+.+ -...+. ++.. .|.++- +
T Consensus 198 RHClYGLDADLImLGL~tHepHF~lLREEVtFgrrn~~k~lehqkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlD 277 (1493)
T KOG2045|consen 198 RHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRRNKRKSLEHQKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILD 277 (1493)
T ss_pred ceeecccchhhheeeeccCCcceeeeeeeeecccccccchhhhhhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHH
Confidence 6789999999999983 2 234321 111 1111 111111 1111 123343 4
Q ss_pred HHHHHHHHcCCCCCCCCCCccH-HHHHHH
Q 000457 973 KLIRMALLLGSDYTEGISGIGI-VNAIEV 1000 (1484)
Q Consensus 973 QFIDLcILsGcDYiPGVPGIGP-KTAlKL 1000 (1484)
.||.+..|+|-||+|.+|++-+ +.|+-|
T Consensus 278 D~ILl~flVGNDFLPhLP~LHIn~gAlpl 306 (1493)
T KOG2045|consen 278 DWILLGFLVGNDFLPHLPCLHINSGALPL 306 (1493)
T ss_pred HHHHHHHhhccccccCCCccccCCChHHH
Confidence 5666777777999999999854 234444
No 58
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.16 E-value=9.3 Score=41.56 Aligned_cols=37 Identities=24% Similarity=0.427 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHcCC-CCCCCCCCccHHHHHHHHHhcC
Q 000457 968 GLTREKLIRMALLLGS-DYTEGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 968 GLTpeQFIDLcILsGc-DYiPGVPGIGPKTAlKLLrqFG 1005 (1484)
.+++++|+. |+..|. ..+..|||||+|||-+|+-..+
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 467777764 444553 4568999999999999997654
No 59
>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=52.07 E-value=12 Score=33.17 Aligned_cols=22 Identities=27% Similarity=0.309 Sum_probs=18.9
Q ss_pred CCCCCccHHHHHHHHHh-cCCch
Q 000457 987 EGISGIGIVNAIEVVNA-FPEED 1008 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrq-FGSlD 1008 (1484)
..|||||+++|..|+.. |.+.+
T Consensus 8 ~~I~Gig~~~a~~L~~~G~~t~~ 30 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLYEAGIKTLE 30 (60)
T ss_dssp HTSTTCHHHHHHHHHHTTCSSHH
T ss_pred ccCCCCCHHHHHHHHhcCCCcHH
Confidence 36999999999999999 88743
No 60
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=50.80 E-value=6.8 Score=43.31 Aligned_cols=80 Identities=21% Similarity=0.151 Sum_probs=46.0
Q ss_pred ceeEEEcCCCceecccCCEE-EEEccCCCCeEEEEeHHHHHHHh-CCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHH
Q 000457 925 LVDGVVTDDSDVFLFGARSV-YKNIFDDRKYVETYFMQDIEKDL-GLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVN 1002 (1484)
Q Consensus 925 lVDAVITEDSDLLLFG~~kV-IRN~fk~~K~VEvydledIeeeL-GLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLr 1002 (1484)
++..++.+|. ..+||-... =|.+|..=-.|.-+..+.-+.-+ .++++.|+..-..---.++..+||||.|||-.|+-
T Consensus 48 ~t~~~vREd~-~~LyGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 48 FTHLVVREDA-HLLYGFLTEEERELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred EEEEeehhhH-HHHcCCCCHHHHHHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHH
Confidence 3556777887 777775321 01111100012223333333333 35777777655544456678999999999999998
Q ss_pred hcC
Q 000457 1003 AFP 1005 (1484)
Q Consensus 1003 qFG 1005 (1484)
...
T Consensus 127 eLk 129 (201)
T COG0632 127 ELK 129 (201)
T ss_pred HHh
Confidence 754
No 61
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.44 E-value=11 Score=41.46 Aligned_cols=38 Identities=13% Similarity=0.167 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHcCC-CCCCCCCCccHHHHHHHHHhcCC
Q 000457 968 GLTREKLIRMALLLGS-DYTEGISGIGIVNAIEVVNAFPE 1006 (1484)
Q Consensus 968 GLTpeQFIDLcILsGc-DYiPGVPGIGPKTAlKLLrqFGS 1006 (1484)
.+++++|+.. |..|. ..+..|||||+|||-+||-...+
T Consensus 91 ~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAeRIIlELkd 129 (196)
T PRK13901 91 GIKYNEFRDA-IDREDIELISKVKGIGNKMAGKIFLKLRG 129 (196)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 3677777653 44453 45689999999999999977543
No 62
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=49.14 E-value=13 Score=47.51 Aligned_cols=25 Identities=24% Similarity=0.300 Sum_probs=21.9
Q ss_pred CCCCCCccHHHHHHHHHhcCCchHH
Q 000457 986 TEGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
+..|||||+|++..||+.||+++.|
T Consensus 610 L~~IpGiG~kr~~~LL~~FgS~~~i 634 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFGSFRSL 634 (691)
T ss_pred cccCCCCCHHHHHHHHHHhcCHHHH
Confidence 4799999999999999999996543
No 63
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.91 E-value=13 Score=40.56 Aligned_cols=47 Identities=17% Similarity=0.128 Sum_probs=31.5
Q ss_pred eHHHHHHHh-CCCHHHHHHHHHHcC-CCCCCCCCCccHHHHHHHHHhcCC
Q 000457 959 FMQDIEKDL-GLTREKLIRMALLLG-SDYTEGISGIGIVNAIEVVNAFPE 1006 (1484)
Q Consensus 959 dledIeeeL-GLTpeQFIDLcILsG-cDYiPGVPGIGPKTAlKLLrqFGS 1006 (1484)
.++.-+.-+ ++++++|+.. |..| ...+..+||||+|||-+|+-+.++
T Consensus 82 GpK~AL~iLs~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAerIilELkd 130 (188)
T PRK14606 82 GPKTALKIISNEDAETLVTM-IASQDVEGLSKLPGISKKTAERIVMELKD 130 (188)
T ss_pred cHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 333333444 4677777653 4444 345689999999999999977543
No 64
>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=47.54 E-value=14 Score=34.99 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=20.7
Q ss_pred CCCCCCCCccHHHHHHHHHhcCCc
Q 000457 984 DYTEGISGIGIVNAIEVVNAFPEE 1007 (1484)
Q Consensus 984 DYiPGVPGIGPKTAlKLLrqFGSl 1007 (1484)
.-+..|||||+.+|..||...+++
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~ 25 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDI 25 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCc
Confidence 345789999999999999998874
No 65
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=46.96 E-value=14 Score=28.46 Aligned_cols=18 Identities=28% Similarity=0.387 Sum_probs=15.5
Q ss_pred CCCCCCccHHHHHHHHHh
Q 000457 986 TEGISGIGIVNAIEVVNA 1003 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrq 1003 (1484)
+..|||||+++|..|+..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 457999999999999864
No 66
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.28 E-value=17 Score=39.53 Aligned_cols=47 Identities=17% Similarity=0.159 Sum_probs=31.3
Q ss_pred EeHHHHHHHhC-CCHHHHHHHHHHcC-CCCCCCCCCccHHHHHHHHHhcCC
Q 000457 958 YFMQDIEKDLG-LTREKLIRMALLLG-SDYTEGISGIGIVNAIEVVNAFPE 1006 (1484)
Q Consensus 958 ydledIeeeLG-LTpeQFIDLcILsG-cDYiPGVPGIGPKTAlKLLrqFGS 1006 (1484)
+.++.-..-+. +++++|+.. |..| ...+ .|||||+|||-+|+-+..+
T Consensus 81 IGpK~Al~iLs~~~~~~l~~a-I~~~D~~~L-~vpGIGkKtAerIilELk~ 129 (186)
T PRK14600 81 VNYKTAMSILSKLTPEQLFSA-IVNEDKAAL-KVNGIGEKLINRIITELQY 129 (186)
T ss_pred cCHHHHHHHHccCCHHHHHHH-HHcCCHhhe-ECCCCcHHHHHHHHHHHHH
Confidence 34443334443 678877654 4445 3457 9999999999999977543
No 67
>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=42.11 E-value=26 Score=44.73 Aligned_cols=40 Identities=20% Similarity=0.314 Sum_probs=29.0
Q ss_pred hCCCHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHH
Q 000457 967 LGLTREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKF 1013 (1484)
Q Consensus 967 LGLTpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekf 1013 (1484)
+--+.+.++.|.. + .-|||||+|+|.+|+..||. +.++.+
T Consensus 73 ~p~~~~~i~~yL~-s-----~~~~GIG~~~A~~iv~~fg~-~~~~~i 112 (720)
T TIGR01448 73 APTSKEGIVAYLS-S-----RSIKGVGKKLAQRIVKTFGE-AAFDVL 112 (720)
T ss_pred CCCCHHHHHHHHh-c-----CCCCCcCHHHHHHHHHHhCH-hHHHHH
Confidence 4456778887754 3 24999999999999999985 334333
No 68
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=41.30 E-value=21 Score=40.57 Aligned_cols=24 Identities=33% Similarity=0.453 Sum_probs=21.2
Q ss_pred CCCCCCccHHHHHHHHHh-cCCchH
Q 000457 986 TEGISGIGIVNAIEVVNA-FPEEDG 1009 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrq-FGSlDg 1009 (1484)
+..|||||+++|.+|++. |++++.
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~ 29 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVED 29 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHH
Confidence 468999999999999999 999753
No 69
>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=41.23 E-value=82 Score=35.73 Aligned_cols=38 Identities=24% Similarity=0.306 Sum_probs=25.5
Q ss_pred CCCeeeC----cchHHHHHHHHHH---------cCceeEEEcCCCceeccc
Q 000457 903 GLPYIIA----PMEAEAQCAYMEL---------ANLVDGVVTDDSDVFLFG 940 (1484)
Q Consensus 903 GIPyIVA----PYEADAQCAyLaK---------kGlVDAVITEDSDLLLFG 940 (1484)
++.++.+ |+|+|--|..+.+ .+...+|+|.|+|+++++
T Consensus 172 ~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 172 NLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp CSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred ceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 4566664 6899997765443 267899999999999887
No 70
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=40.61 E-value=21 Score=44.77 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=20.6
Q ss_pred CCCCCccHHHHHHHHHhcCCchH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
.+|||||++++..|++.||+++.
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~~ 568 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLKA 568 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHHH
Confidence 79999999999999999999443
No 71
>KOG3428 consensus Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification]
Probab=39.30 E-value=14 Score=37.95 Aligned_cols=10 Identities=60% Similarity=1.232 Sum_probs=4.3
Q ss_pred CCCccccccc
Q 000457 1218 RGKGQRVGRG 1227 (1484)
Q Consensus 1218 ~g~g~~~~~g 1227 (1484)
|||||++|||
T Consensus 96 rgrgrg~Grg 105 (109)
T KOG3428|consen 96 RGRGRGRGRG 105 (109)
T ss_pred cccccccccC
Confidence 4444443333
No 72
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=34.98 E-value=27 Score=43.81 Aligned_cols=26 Identities=15% Similarity=0.411 Sum_probs=22.3
Q ss_pred CCCCCCCccHHHHHHHHHhcCCchHH
Q 000457 985 YTEGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 985 YiPGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
-+..|||||++++.+|++.||++..+
T Consensus 526 ~L~~IpGIG~kr~~~LL~~FGS~~~I 551 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRFGSVEGV 551 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHH
Confidence 34799999999999999999995443
No 73
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=34.61 E-value=30 Score=39.65 Aligned_cols=36 Identities=19% Similarity=0.267 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHcCCCeeeCc-chHHHHHHHHHHcCc
Q 000457 890 EMFAECQELLQMFGLPYIIAP-MEAEAQCAYMELANL 925 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAP-YEADAQCAyLaKkGl 925 (1484)
.++..+.+++..+||+++..+ +||||.++++++.-.
T Consensus 96 ~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~ 132 (310)
T COG0258 96 PQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY 132 (310)
T ss_pred HHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHH
Confidence 467789999999999999999 899999999999865
No 74
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=32.54 E-value=22 Score=46.31 Aligned_cols=250 Identities=12% Similarity=0.016 Sum_probs=146.3
Q ss_pred hHhHHHHHHHhhcCCCcccccccccccccceEEeecccccchhhhhcccccCCccccccCCCCCCCCCCCCCCCccccCC
Q 000457 261 RREIDEVQKAAAGRGVAGVQTSRIASEANREFIFSSSFTGDKQVLTSSRVEGKKDEQQQIPSEHPVSDSANNGASIDKSN 340 (1484)
Q Consensus 261 ~r~I~~~qk~a~~~~~ggv~~srias~~Nrefi~ssSftGDK~~l~~~g~~~~~~~q~~~p~~~~v~ds~~~~~~i~~s~ 340 (1484)
++.|...|..+.+...+|++. ++.+|+.+++++.++| ..-...| .+.+..+.+ +.-. ++...+..+....
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~--~~~~~~~-~~~~~s~~~-~~l~---~~~~~~~p~~~~~ 74 (815)
T KOG2520|consen 5 LEPTATEQPLAEGGSKLGLID---GSYAKKAAEIDDQPAP--LLSKLEG-EKMGVSTIW-EFLK---PSSPDVTPLELRA 74 (815)
T ss_pred ccchheeeccccCccceeeee---hhhccceeeeccccch--hhhhhhc-cccccceec-cccC---ccccCCCCchhhH
Confidence 677888899999999999988 9999999999999999 2222222 333333332 1111 1122222232222
Q ss_pred CccCCCCCCccccCCcccccccCCcchhhhcccCceEEeeeecccchhhHhhhhhHHHHHHHHhhcCCCCCccccCcccc
Q 000457 341 FSSTDQSNSVTKLGPEESRKSFADDVETYLDERGRVRLSKVRAMGIRMTRDLQRNLEMMKEIEQERPNGNNITGAGSMLT 420 (1484)
Q Consensus 341 f~s~~~s~~~~~~~~~ep~~~f~~dvetY~DErGR~RvSrvraMGirMTrDiQrNLd~mKe~Eq~~~~~~~~~~~gs~~~ 420 (1484)
.++...- +..++++..-| +++.|.+.++|....-....+. +. .
T Consensus 75 --------a~~~~~k---~~~~~~~e~~d-------------------~~~~~~~~~~~~q~~~~~~~~~------~~-~ 117 (815)
T KOG2520|consen 75 --------AVIDFQK---RQNRSPDEKID-------------------KANGKLFEDRKLQAIRISISSG------SR-N 117 (815)
T ss_pred --------HHHHHHH---hcCCChhhhcc-------------------HHHHHHHHhhhhhhhhhhcccc------cc-c
Confidence 2222222 22334555444 8899999999988755554432 22 2
Q ss_pred cccCCCCCCCCchhhccccccCCCCCcccccccccccccCCCCccEEEEEccCCCCCCCChhHHHHHhhcCCccccCCCC
Q 000457 421 LNETGTSKAVPSEKRKFIGTSLDDTNESVSSIERNKQSTLKSGISLELSFKDNSENNCDDDDDIFAHLAAGKPVIFPNSP 500 (1484)
Q Consensus 421 ~~e~~~~~~fp~~~~~~~~~~~~~~~~~v~~~~~~e~s~~~~~~sieisF~~d~~~~~d~ddd~F~~Lv~g~p~~~~s~~ 500 (1484)
..++..+.+++..-..-...+. .-..++...++..+++.....+.+.|..++. -+..+.+|...+++.++..-+++
T Consensus 118 ~~~~~s~~d~~~d~~~~~~~~~--~~~~t~~~~~~d~ss~~~~~e~~~~~~~~gd--~~~~~~~~~~~~~e~~~t~t~~e 193 (815)
T KOG2520|consen 118 DSEAKSIKDSDIDSKQESKNDV--SKDTTDKSVMNDDSSLKPLDELNVVFEGVGD--SNMSDKFESDDKHEENVTTTSDE 193 (815)
T ss_pred hhhhcchhhccchhhhhccCCc--ccccCCchhhccchhcccccchhheeecccc--cccccccccccccccccCccccc
Confidence 3333455555443332222211 1334467778899999999999999999993 47778888888888887776665
Q ss_pred CCCCCCCCCCCcccccccccCCCCCCCCCcccCCCCCcCCCCCCCCCCccccccCCCCCCCCCCCCCCcccccccchHHH
Q 000457 501 RAHSSISVSDSDWEEGTTERKGSSLSDDANAGINPPLNLEEGGISDESEVEWEEGPSCAPKSSLSFPAESEKTVSNIEEE 580 (1484)
Q Consensus 501 ~~~~~~~~sd~~weeg~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~d~eveWEeg~~c~~~~~~s~~~~~~~~~~~~eEe 580 (1484)
.- ..++=..|--+ .-..|-|+..+ |.-.+ -...-.+...+.+.++
T Consensus 194 ~e---p~~~~~~~~~~-----------------------------i~~~v~~~~~~-~~~~s--kd~s~~k~~r~l~~~~ 238 (815)
T KOG2520|consen 194 RE---PSDSVEQEQKS-----------------------------IAVPVSGQPDS-IKNPS--KDESVIKITRKLVDLE 238 (815)
T ss_pred cC---cCccHHHHhhh-----------------------------ccccCCCCccc-ccCcc--cChHHHHHHHHHHHhh
Confidence 51 11111111111 22456677666 54111 2333344555677777
Q ss_pred HHHHHHHHHHHHhhcc
Q 000457 581 ANLQEAIRRSLLDVCI 596 (1484)
Q Consensus 581 a~~QEAirrSLed~~~ 596 (1484)
.+.++.+.++.+-++.
T Consensus 239 ~d~~~~~~~~~~~~~d 254 (815)
T KOG2520|consen 239 NDAPIEAKDKSETLCD 254 (815)
T ss_pred ccchhhhcccccccCC
Confidence 7777777666655554
No 75
>KOG2894 consensus Uncharacterized conserved protein XAP-5 [Function unknown]
Probab=32.03 E-value=41 Score=39.38 Aligned_cols=83 Identities=27% Similarity=0.406 Sum_probs=59.7
Q ss_pred hhhhccCCCccCCCCccccCCCCccCCCccccee-ecccCCCC--ChhhHhc-CCccchHHHHHHHHHHHHHHHHHHHHH
Q 000457 163 IAAEEDGSLSNNASASAASLPLEEEDGDEDEEMI-LPAMTGNV--DPAVLAA-LPPSMQLDLLVQMREQLMAENRQKYQK 238 (1484)
Q Consensus 163 laaee~~~~~~~~~~~~~~~p~ee~d~d~deemi-~P~~~~~i--Dp~vlas-LPps~qldll~~~re~~~aenR~~~~k 238 (1484)
+|.|.+.-..-+-..+.-|..+|++++.||++-+ .|.-.|+| ||.|=-| ||.+-+-.-....||++.+|-+.+-.+
T Consensus 102 ~~~eKe~K~~kkr~~s~LSFa~DdEededD~~~k~~~~Kk~klGKdP~VDTSFLPDrEREeeEnr~RE~L~~eW~~~qe~ 181 (331)
T KOG2894|consen 102 LAREKEEKKEKKRQISRLSFALDDEEDEDDAEEKSIPLKKGKLGKDPDVDTSFLPDREREEEENRLREELRQEWEAKQEK 181 (331)
T ss_pred HHHHHHHHHHHhhccccccccccccccccccchhhcchhhhhcCCCCCcccccCCchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 3445554444455556666678766666666666 77755544 7877655 899999999999999999999999999
Q ss_pred hhcCccc
Q 000457 239 VKKAPEK 245 (1484)
Q Consensus 239 ~~~~p~~ 245 (1484)
++..+-.
T Consensus 182 ~K~Eei~ 188 (331)
T KOG2894|consen 182 IKNEEIE 188 (331)
T ss_pred hcCCceE
Confidence 9876643
No 76
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=31.72 E-value=31 Score=44.38 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=22.2
Q ss_pred CCCCCCccHHHHHHHHHhcCCchHHH
Q 000457 986 TEGISGIGIVNAIEVVNAFPEEDGLS 1011 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrqFGSlDgLe 1011 (1484)
+..|||||++++..|++.||+++.|.
T Consensus 639 L~~IPGIGpkr~k~LL~~FGSle~I~ 664 (694)
T PRK14666 639 LQRVEGIGPATARLLWERFGSLQAMA 664 (694)
T ss_pred HhhCCCCCHHHHHHHHHHhCCHHHHH
Confidence 46899999999999999999965443
No 77
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=30.49 E-value=37 Score=42.93 Aligned_cols=26 Identities=23% Similarity=0.422 Sum_probs=22.2
Q ss_pred CCCCCCccHHHHHHHHHhcCCchHHH
Q 000457 986 TEGISGIGIVNAIEVVNAFPEEDGLS 1011 (1484)
Q Consensus 986 iPGVPGIGPKTAlKLLrqFGSlDgLe 1011 (1484)
+..|||||+++...||+.||++.++.
T Consensus 532 Ld~I~GiG~~r~~~LL~~Fgs~~~i~ 557 (581)
T COG0322 532 LDDIPGIGPKRRKALLKHFGSLKGIK 557 (581)
T ss_pred cccCCCcCHHHHHHHHHHhhCHHHHH
Confidence 46899999999999999999965443
No 78
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=29.61 E-value=37 Score=36.02 Aligned_cols=22 Identities=14% Similarity=0.176 Sum_probs=16.8
Q ss_pred CCCCccHHHHHHHHHh--cCCchH
Q 000457 988 GISGIGIVNAIEVVNA--FPEEDG 1009 (1484)
Q Consensus 988 GVPGIGPKTAlKLLrq--FGSlDg 1009 (1484)
.+|||||++|.+||+. |.+.+.
T Consensus 65 ~lpGigP~~A~~IV~nGpf~sveD 88 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDSVED 88 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCCHHH
Confidence 4799999999999974 555433
No 79
>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=29.45 E-value=40 Score=42.91 Aligned_cols=24 Identities=33% Similarity=0.422 Sum_probs=21.0
Q ss_pred CCCCCccHHHHHHHHHhcCCchHH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
-||||||+++|..|++.|++++.|
T Consensus 501 LgIpgVG~~~ak~L~~~f~sl~~l 524 (652)
T TIGR00575 501 LGIRHVGEVTAKNLAKHFGTLDKL 524 (652)
T ss_pred ccCCCcCHHHHHHHHHHhCCHHHH
Confidence 589999999999999999985544
No 80
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=28.72 E-value=43 Score=36.55 Aligned_cols=45 Identities=13% Similarity=0.037 Sum_probs=27.7
Q ss_pred eHHHHHHHhC-CCHHHHHHHHHHcC-CCCCCCCCCccHHHHHHHHHhc
Q 000457 959 FMQDIEKDLG-LTREKLIRMALLLG-SDYTEGISGIGIVNAIEVVNAF 1004 (1484)
Q Consensus 959 dledIeeeLG-LTpeQFIDLcILsG-cDYiPGVPGIGPKTAlKLLrqF 1004 (1484)
..+....-++ +++++|+..+. .+ -..+..|||||+|||-+|+-..
T Consensus 81 GpK~Al~iL~~~~~~el~~aI~-~~d~~~L~~ipGiGkKtAerIileL 127 (191)
T TIGR00084 81 GPKLALAILSNMSPEEFVYAIE-TEEVKALVKIPGVGKKTAERLLLEL 127 (191)
T ss_pred CHHHHHHHHhcCCHHHHHHHHH-hCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 3343334444 45666655443 22 2335789999999999999543
No 81
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=28.67 E-value=43 Score=43.04 Aligned_cols=34 Identities=18% Similarity=0.228 Sum_probs=27.4
Q ss_pred ChhhHhcCCccchHHHHHHHHHHHHHHHHHHHHH
Q 000457 205 DPAVLAALPPSMQLDLLVQMREQLMAENRQKYQK 238 (1484)
Q Consensus 205 Dp~vlasLPps~qldll~~~re~~~aenR~~~~k 238 (1484)
|.+-+.+++++.-..-|.++|+++..-|+.-|..
T Consensus 20 ~~~~~~~~~~~~~~~~i~~L~~~i~~~~~~YY~~ 53 (689)
T PRK14351 20 DFEPVEELSEDEAEEQAEQLREAIREHDHRYYVE 53 (689)
T ss_pred CCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4566788898888777999999998888888853
No 82
>cd00956 Transaldolase_FSA Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases. FSA catalyze an aldol cleavage of fructose 6-phosphate and do not utilize fructose, fructose 1-phosphate, fructose 1,6-phosphate, or dihydroxyacetone phosphate. The enzymes belong to the transaldolase family that serves in transfer reactions in the pentose phosphate cycle, and are more distantly related to fructose 1,6-bisphosphate aldolase.
Probab=28.56 E-value=2e+02 Score=31.85 Aligned_cols=41 Identities=22% Similarity=0.276 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHcCCCCCCCCCCccHHHHHHHHHhcCCchHHHHHHH
Q 000457 970 TREKLIRMALLLGSDYTEGISGIGIVNAIEVVNAFPEEDGLSKFRE 1015 (1484)
Q Consensus 970 TpeQFIDLcILsGcDYiPGVPGIGPKTAlKLLrqFGSlDgLekfrE 1015 (1484)
++.+++. ++++|||++. |++....+|+..--+.++++.|.+
T Consensus 167 ~~~ei~~-a~~~Gad~vT----v~~~vl~~l~~~~~t~~~v~~F~~ 207 (211)
T cd00956 167 NPQHVIE-AALAGADAIT----LPPDVLEQLLKHPLTDKGVEKFLE 207 (211)
T ss_pred CHHHHHH-HHHcCCCEEE----eCHHHHHHHhcCccHHHHHHHHHH
Confidence 5777777 7889999874 667777777766556678888864
No 83
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.26 E-value=37 Score=37.14 Aligned_cols=36 Identities=25% Similarity=0.408 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHcCC-CCCCCCCCccHHHHHHHHHhcC
Q 000457 969 LTREKLIRMALLLGS-DYTEGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 969 LTpeQFIDLcILsGc-DYiPGVPGIGPKTAlKLLrqFG 1005 (1484)
+++++|+.. +..+. ..+..|||||+|||-+|+-...
T Consensus 93 ~~~~~l~~a-I~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 93 MNAEALASA-IISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred CCHHHHHHH-HHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 556665543 33332 2347899999999999987754
No 84
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=25.45 E-value=34 Score=44.66 Aligned_cols=23 Identities=9% Similarity=0.007 Sum_probs=20.3
Q ss_pred CCCCCccHHHHHHHHHhcCCchH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
-.+||||++.|..|+.+|+++..
T Consensus 760 ~~lPgI~~~~a~~ll~~f~si~~ 782 (814)
T TIGR00596 760 LKLPGVTKKNYRNLRKKVKSIRE 782 (814)
T ss_pred HHCCCCCHHHHHHHHHHcCCHHH
Confidence 47999999999999999999543
No 85
>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=25.41 E-value=67 Score=29.20 Aligned_cols=15 Identities=27% Similarity=0.589 Sum_probs=13.5
Q ss_pred CCCccHHHHHHHHHh
Q 000457 989 ISGIGIVNAIEVVNA 1003 (1484)
Q Consensus 989 VPGIGPKTAlKLLrq 1003 (1484)
+||||+++|..||..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 789999999999987
No 86
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=25.04 E-value=1.2e+02 Score=36.33 Aligned_cols=48 Identities=19% Similarity=0.254 Sum_probs=33.4
Q ss_pred EEEeHHHHHHHhCCCHHHHHHH--------------HHHcCCCCCC------------CCCCccHHHHHHHHHh
Q 000457 956 ETYFMQDIEKDLGLTREKLIRM--------------ALLLGSDYTE------------GISGIGIVNAIEVVNA 1003 (1484)
Q Consensus 956 EvydledIeeeLGLTpeQFIDL--------------cILsGcDYiP------------GVPGIGPKTAlKLLrq 1003 (1484)
..|..++++..||+.++.++.- ++|--.|..| .|||||+|+|..+|-.
T Consensus 276 RLYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 276 RLYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHH
Confidence 3577888889999988776532 3333333322 3899999999988865
No 87
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=24.49 E-value=54 Score=33.38 Aligned_cols=19 Identities=21% Similarity=0.394 Sum_probs=16.3
Q ss_pred CCCCCccHHHHHHHHHhcC
Q 000457 987 EGISGIGIVNAIEVVNAFP 1005 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFG 1005 (1484)
..+||||+++|.+||..+.
T Consensus 71 ~~lpGIG~~~A~~Ii~~R~ 89 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYRE 89 (120)
T ss_pred hcCCCCCHHHHHHHHHHHH
Confidence 4689999999999998863
No 88
>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=23.76 E-value=51 Score=26.90 Aligned_cols=14 Identities=29% Similarity=0.339 Sum_probs=10.9
Q ss_pred CCCCCccHHHHHHH
Q 000457 987 EGISGIGIVNAIEV 1000 (1484)
Q Consensus 987 PGVPGIGPKTAlKL 1000 (1484)
.-|+|||.+|+.+|
T Consensus 14 ~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 14 RKFWGIGKKTAKKL 27 (32)
T ss_dssp GGSTTS-HHHHHHH
T ss_pred HhhCCccHHHHHHH
Confidence 46899999999875
No 89
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=21.72 E-value=67 Score=37.13 Aligned_cols=23 Identities=30% Similarity=0.420 Sum_probs=20.2
Q ss_pred CCCCCccHHHHHHHHHhcCCchH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDG 1009 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDg 1009 (1484)
.++||||++.|..|++.||+...
T Consensus 185 ~s~pgig~~~a~~ll~~fgS~~~ 207 (254)
T COG1948 185 ESIPGIGPKLAERLLKKFGSVED 207 (254)
T ss_pred HcCCCccHHHHHHHHHHhcCHHH
Confidence 57899999999999999999543
No 90
>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.
Probab=21.05 E-value=1e+02 Score=22.97 Aligned_cols=16 Identities=38% Similarity=0.590 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHh
Q 000457 578 EEEANLQEAIRRSLLD 593 (1484)
Q Consensus 578 eEea~~QEAirrSLed 593 (1484)
+||.+||-||+-|+++
T Consensus 2 ~Ed~~L~~Al~~S~~e 17 (18)
T PF02809_consen 2 DEDEDLQRALEMSLEE 17 (18)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHhhhcc
Confidence 6899999999999986
No 91
>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=20.84 E-value=78 Score=36.67 Aligned_cols=24 Identities=17% Similarity=0.249 Sum_probs=17.3
Q ss_pred CCCCCccHHHHHHHHHh-cCCchHH
Q 000457 987 EGISGIGIVNAIEVVNA-FPEEDGL 1010 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrq-FGSlDgL 1010 (1484)
-.|||||||+|.+|... +.+++.|
T Consensus 88 ~~i~GiGpk~a~~l~~lGi~sl~dL 112 (307)
T cd00141 88 LRVPGVGPKTARKLYELGIRTLEDL 112 (307)
T ss_pred HcCCCCCHHHHHHHHHcCCCCHHHH
Confidence 47999999999999832 4454433
No 92
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=20.76 E-value=76 Score=37.21 Aligned_cols=26 Identities=15% Similarity=0.176 Sum_probs=18.8
Q ss_pred CCCCCccHHHHHHHHHhcCCchHHHHHH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDGLSKFR 1014 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDgLekfr 1014 (1484)
-.|||||||||..|.+ .| +..|+.++
T Consensus 92 ~~i~GiGpk~a~~l~~-lG-i~tl~eL~ 117 (334)
T smart00483 92 TNVFGVGPKTAAKWYR-KG-IRTLEELK 117 (334)
T ss_pred HccCCcCHHHHHHHHH-hC-CCCHHHHH
Confidence 5799999999999988 43 33344443
No 93
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=20.64 E-value=48 Score=42.52 Aligned_cols=54 Identities=30% Similarity=0.399 Sum_probs=31.5
Q ss_pred CCCCCCcccccccccCCCCCCCCCcccCCCCCcCCCCCCCCCCccccccCCCCCCCCCCCCCCcccccccchHHHHHHHH
Q 000457 506 ISVSDSDWEEGTTERKGSSLSDDANAGINPPLNLEEGGISDESEVEWEEGPSCAPKSSLSFPAESEKTVSNIEEEANLQE 585 (1484)
Q Consensus 506 ~~~sd~~weeg~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~d~eveWEeg~~c~~~~~~s~~~~~~~~~~~~eEea~~QE 585 (1484)
.=+|||.||| |..|++++ -.++ |++=+-||+ |. -+.+.+-.|-|||-|+-.+|+
T Consensus 520 EVdSDeEWEE---EepGESlS------------~sEd----dedd~~eEd--~e-----dEdDgffVPhgyLSedEgv~d 573 (811)
T KOG4364|consen 520 EVDSDEEWEE---EEPGESLS------------DSED----DEDDSLEED--CE-----DEDDGFFVPHGYLSEDEGVQD 573 (811)
T ss_pred cccCcccccc---cCCCcccc------------cccc----ccccccccc--cc-----cccCCeecCCccccccccccc
Confidence 4589999999 33455554 2232 222222333 22 356778889999887766553
No 94
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=20.31 E-value=1.2e+02 Score=36.40 Aligned_cols=9 Identities=56% Similarity=0.977 Sum_probs=4.5
Q ss_pred hhhccCCCC
Q 000457 1266 RRSTRSRKP 1274 (1484)
Q Consensus 1266 ~~s~r~r~~ 1274 (1484)
++++++|+|
T Consensus 444 ~~~~~~~~~ 452 (456)
T PRK10590 444 QRRRRPRKP 452 (456)
T ss_pred CCCCCCCCC
Confidence 344555555
No 95
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=20.24 E-value=70 Score=40.97 Aligned_cols=24 Identities=25% Similarity=0.320 Sum_probs=20.8
Q ss_pred CCCCCccHHHHHHHHHhcCCchHH
Q 000457 987 EGISGIGIVNAIEVVNAFPEEDGL 1010 (1484)
Q Consensus 987 PGVPGIGPKTAlKLLrqFGSlDgL 1010 (1484)
-||||||+++|..|++.|++++.|
T Consensus 514 lgi~~IG~~~ak~L~~~f~sl~~l 537 (665)
T PRK07956 514 LGIRHVGEKAAKALARHFGSLEAL 537 (665)
T ss_pred hhccCcCHHHHHHHHHHcCCHHHH
Confidence 489999999999999999985544
No 96
>PF06465 DUF1087: Domain of Unknown Function (DUF1087); InterPro: IPR009463 This is a group of proteins of unknown function.
Probab=20.17 E-value=47 Score=31.73 Aligned_cols=22 Identities=32% Similarity=0.525 Sum_probs=18.0
Q ss_pred ccchHHHhhhccCCCCccccCC
Q 000457 1259 FEGQQEVRRSTRSRKPVDYNVD 1280 (1484)
Q Consensus 1259 ~~g~~~~~~s~r~r~~~~y~~d 1280 (1484)
.+-.+.|.+.+|+||.|+|+..
T Consensus 40 ~e~~~~LGKGKR~RKqV~y~~~ 61 (66)
T PF06465_consen 40 EEEEKALGKGKRSRKQVNYAEE 61 (66)
T ss_pred HHHHHHhccccccccccccccc
Confidence 3445678899999999999874
No 97
>COG1834 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]
Probab=20.17 E-value=73 Score=37.08 Aligned_cols=109 Identities=19% Similarity=0.327 Sum_probs=74.8
Q ss_pred HHHHHHHHHHHHcCCCeeeCcchHHHHHHHHHHcCceeEEEcCCCceecccCCEEEEEccCCCCeEEEEeHHHHHHHhCC
Q 000457 890 EMFAECQELLQMFGLPYIIAPMEAEAQCAYMELANLVDGVVTDDSDVFLFGARSVYKNIFDDRKYVETYFMQDIEKDLGL 969 (1484)
Q Consensus 890 emI~eIKeLLrlfGIPyIVAPYEADAQCAyLaKkGlVDAVITEDSDLLLFG~~kVIRN~fk~~K~VEvydledIeeeLGL 969 (1484)
++...+.+++...||.+..-| -..|+-|-|+|.|. .|++|-..|+-.|-..-..-+....+...+.+|+
T Consensus 38 aQh~~lve~l~~~gv~V~ll~----------~~~~~Pd~VFt~D~-~~v~~~~avl~r~~~p~R~gE~~~~~~~~~~lgi 106 (267)
T COG1834 38 AQHEALVEALEKNGVEVHLLP----------PIEGLPDQVFTRDP-GLVTGEGAVLARMGAPERRGEEEAIKETLESLGI 106 (267)
T ss_pred HHHHHHHHHHHHCCCEEEEcC----------cccCCCcceEeccc-eeEecccEEEeccCChhhccCHHHHHHHHHHcCC
Confidence 566778889999999888766 45689999999988 4455655566555322112244455666788999
Q ss_pred CHHHHHHHHHHcC-CCCC-CC----CCCccHHHHHHHHHhcCCchHHHHHHHhhh
Q 000457 970 TREKLIRMALLLG-SDYT-EG----ISGIGIVNAIEVVNAFPEEDGLSKFREWIE 1018 (1484)
Q Consensus 970 TpeQFIDLcILsG-cDYi-PG----VPGIGPKTAlKLLrqFGSlDgLekfrEW~e 1018 (1484)
+.--.+.-+...| +|++ .+ +-|.|..| +.++++.++.|+.
T Consensus 107 ~i~~~~~~~~~eG~GD~l~~~~~~v~iG~s~RT---------n~egi~~l~~~L~ 152 (267)
T COG1834 107 PIYPRVEAGVFEGAGDVLMDGGDTVYIGYSFRT---------NLEGIEQLQAWLE 152 (267)
T ss_pred cccccccCCCccccccEEEeCCcEEEEEecccc---------chHHHHHHHHHhc
Confidence 9777777788888 8887 32 22455333 3467888999998
Done!