Query psy7142
Match_columns 1309
No_of_seqs 145 out of 152
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 19:17:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7142.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7142hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00128 XPG Xeroderma pigmento 97.7 7.7E-05 1.7E-09 86.3 7.9 96 1029-1141 149-246 (316)
2 smart00475 53EXOc 5'-3' exonuc 97.6 0.00056 1.2E-08 77.6 12.3 106 1030-1147 107-215 (259)
3 COG0258 Exo 5'-3' exonuclease 97.4 0.0013 2.7E-08 76.3 13.3 229 888-1169 11-249 (310)
4 cd00008 53EXOc 5'-3' exonuclea 97.4 0.002 4.3E-08 72.3 13.7 105 1029-1148 107-213 (240)
5 PRK14976 5'-3' exonuclease; Pr 97.3 0.0052 1.1E-07 70.6 15.5 107 1030-1148 113-221 (281)
6 PTZ00217 flap endonuclease-1; 97.2 0.0016 3.5E-08 77.9 10.6 108 1029-1149 159-266 (393)
7 PRK09482 flap endonuclease-lik 97.0 0.0049 1.1E-07 69.9 11.5 200 889-1148 4-212 (256)
8 TIGR03674 fen_arch flap struct 96.9 0.0047 1E-07 72.7 11.0 104 1030-1147 152-265 (338)
9 KOG2519|consensus 96.9 0.0014 3E-08 78.2 6.1 178 930-1146 74-257 (449)
10 PRK05755 DNA polymerase I; Pro 96.6 0.029 6.2E-07 73.9 16.0 108 1030-1149 109-218 (880)
11 KOG2518|consensus 96.5 0.011 2.3E-07 71.8 9.9 120 1028-1166 148-274 (556)
12 PRK03980 flap endonuclease-1; 96.4 0.0088 1.9E-07 69.2 8.5 97 1042-1148 113-219 (292)
13 TIGR00593 pola DNA polymerase 95.4 0.12 2.6E-06 68.0 13.3 109 1029-1150 106-217 (887)
14 PF03638 TCR: Tesmin/TSO1-like 94.5 0.021 4.6E-07 47.8 1.8 39 1261-1302 2-41 (42)
15 PHA00439 exonuclease 92.6 0.91 2E-05 52.6 11.4 86 1029-1137 119-206 (286)
16 PF05991 NYN_YacP: YacP-like N 92.1 0.41 8.8E-06 51.2 7.3 53 891-944 1-56 (166)
17 TIGR00600 rad2 DNA excision re 88.1 0.77 1.7E-05 61.1 6.3 95 1029-1140 793-888 (1034)
18 cd00080 HhH2_motif Helix-hairp 78.1 1.5 3.3E-05 41.0 2.3 40 1108-1147 10-51 (75)
19 KOG1171|consensus 77.8 0.77 1.7E-05 55.3 0.2 45 1252-1299 207-252 (406)
20 PF05033 Pre-SET: Pre-SET moti 68.8 3.6 7.8E-05 40.1 2.4 38 1262-1300 46-103 (103)
21 PF11403 Yeast_MT: Yeast metal 65.9 3.4 7.3E-05 33.2 1.3 18 1263-1280 22-39 (40)
22 KOG1079|consensus 60.0 4 8.8E-05 51.6 1.2 40 1262-1302 539-588 (739)
23 PF02739 5_3_exonuc_N: 5'-3' e 59.4 1.3E+02 0.0027 32.7 12.1 60 1029-1099 108-168 (169)
24 KOG3813|consensus 51.8 7.1 0.00015 48.0 1.4 43 1260-1303 305-352 (640)
25 smart00279 HhH2 Helix-hairpin- 48.0 7.8 0.00017 31.7 0.6 29 1109-1138 5-36 (36)
26 smart00570 AWS associated with 36.6 15 0.00032 32.6 0.6 40 1261-1303 2-47 (51)
27 PF04599 Pox_G5: Poxvirus G5 p 34.4 22 0.00047 43.6 1.7 149 887-1065 25-203 (425)
28 KOG4442|consensus 32.7 22 0.00049 45.5 1.6 29 1270-1300 83-112 (729)
29 PF03159 XRN_N: XRN 5'-3' exon 31.1 82 0.0018 36.0 5.6 39 1028-1066 183-225 (237)
30 PF00752 XPG_N: XPG N-terminal 28.4 62 0.0013 31.4 3.5 64 888-955 26-95 (101)
31 PF00867 XPG_I: XPG I-region; 26.7 24 0.00052 34.2 0.3 73 1029-1118 12-94 (94)
32 COG3688 Predicted RNA-binding 26.3 3.3E+02 0.0072 29.8 8.5 56 888-945 3-62 (173)
33 PF12813 XPG_I_2: XPG domain c 23.7 76 0.0016 36.4 3.6 69 1028-1111 27-105 (246)
34 smart00484 XPGI Xeroderma pigm 21.2 2E+02 0.0044 27.1 5.3 57 1029-1101 12-72 (73)
No 1
>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=97.69 E-value=7.7e-05 Score=86.35 Aligned_cols=96 Identities=21% Similarity=0.213 Sum_probs=72.0
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccC-C-CceeeeehhHHHHhhcccccc
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNY-G-KKQRFFAAHEIAVNLGTEKSV 1106 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~-g-~~~r~i~i~~i~~~lG~~~~~ 1106 (1309)
-|||-.+. .-+..|. ...|.|+|+|++++.. ..++..+.. + ...+.|+...+.+.+|-. -.
T Consensus 149 ~EAdaq~a----~l~~~g~-v~~i~S~DsD~l~fg~-----------~~vi~~~~~~~~~~~~~~~~~~~~~~lgl~-~~ 211 (316)
T cd00128 149 YEAEAQCA----YLAKKGL-VDAIITEDSDLLLFGA-----------PRVYRNLFDSGAKPVEEIDLEKILKELGLT-RE 211 (316)
T ss_pred cCHHHHHH----HHHhCCC-eeEEEecCCCeeeecC-----------ceEEEecccCCCCceEEEEHHHHHHHcCCC-HH
Confidence 48887642 2334453 5578899999998752 234443332 2 367889999999999753 34
Q ss_pred cccccccccCCcccccccccchhhHhhhhhccchH
Q psy7142 1107 ALRGFHAFSGCDTVSTFAFHGKQTAWKTWNSCDYV 1141 (1309)
Q Consensus 1107 al~~~HAftGcDtts~f~g~gK~~~~K~l~~~~~~ 1141 (1309)
-++-|=+++|||.+..+.|+|-++|+++++++..+
T Consensus 212 q~id~~~L~G~Dy~~gv~giG~k~A~~li~~~~~~ 246 (316)
T cd00128 212 KLIDLAILLGCDYTEGIPGIGPVTALKLIKKYGDI 246 (316)
T ss_pred HHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCh
Confidence 57888899999999999999999999999988775
No 2
>smart00475 53EXOc 5'-3' exonuclease.
Probab=97.57 E-value=0.00056 Score=77.59 Aligned_cols=106 Identities=19% Similarity=0.254 Sum_probs=76.5
Q ss_pred ccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCC-CceeeeehhHHHHhhcccccccc
Q psy7142 1030 EADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYG-KKQRFFAAHEIAVNLGTEKSVAL 1108 (1309)
Q Consensus 1030 EADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g-~~~r~i~i~~i~~~lG~~~~~al 1108 (1309)
|||-.|-.=|..+..+| ..++|.|.|.|.+-+.-- . ..+|.. ..+ ...+.++...+.+.+|- .-..+
T Consensus 107 EADD~iatla~~~~~~g-~~~~IvS~DkDl~ql~~~---~------v~~~~~-~~~~~~~~~~~~~~v~~~~Gv-~p~q~ 174 (259)
T smart00475 107 EADDVIATLAKKAEAEG-YEVRIVSGDKDLLQLVSD---K------VSVLDP-TKGIKEFELYTPENVIEKYGL-TPEQI 174 (259)
T ss_pred CHHHHHHHHHHHHHhCC-CeEEEEeCCCcHhhcCCC---C------EEEEec-cCCCCccEEEcHHHHHHHhCc-CHHHH
Confidence 89887655455555555 477888999998766411 0 123432 232 23467999999999985 23457
Q ss_pred cccccccC--CcccccccccchhhHhhhhhccchHHHHHHH
Q psy7142 1109 RGFHAFSG--CDTVSTFAFHGKQTAWKTWNSCDYVTSAFVA 1147 (1309)
Q Consensus 1109 ~~~HAftG--cDtts~f~g~gK~~~~K~l~~~~~~q~~f~~ 1147 (1309)
+-+.|+.| ||..+...|+|.++|.++++++..+-..+..
T Consensus 175 ~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~ 215 (259)
T smart00475 175 IDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILEN 215 (259)
T ss_pred HHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHH
Confidence 78899999 8999999999999999999998877555544
No 3
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=97.44 E-value=0.0013 Score=76.34 Aligned_cols=229 Identities=20% Similarity=0.249 Sum_probs=138.1
Q ss_pred cceEEeccceee----cccCC--CCccchhhhhHHHHHHHHHhhhcccCCCeeEEEEeccCCCCchhhhhhccCCCCcee
Q psy7142 888 CDVVVCDGAALI----HATPP--RNSRTFEGYCSQEFQRTIMGMIESCSADRIDVVWDLYFPDSLKNSLREVRGKSQRLQ 961 (1309)
Q Consensus 888 ~~~~IiDG~alv----h~l~~--~~~~tF~~ya~~~f~~yv~~~~~~~~~~ridVVFD~Y~~~SlK~~eR~kRGs~~~~~ 961 (1309)
..++.|||+.++ |++++ .+..-+..=+-..|..++.+.+.......+-||||. .++..|.++-++|=..-..
T Consensus 11 ~~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~-~~~tfR~~~~~~yK~~R~~- 88 (310)
T COG0258 11 GKLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDG-KPPTFRHELLEEYKANREK- 88 (310)
T ss_pred CcEEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcC-CCCcchHHHHHHHHhCCCc-
Confidence 478899996554 45543 211211111566777777777776666889999999 8888887776654221100
Q ss_pred ecCCCCCCcchhhhhcccCchhhhHHHHHHHHHhhccceEEEEecCceeeeccCCccccccCCCCcccccchHHHHHHHH
Q psy7142 962 VTPNSPVPRNWSEFLKNNHNKEELFSLLGKYLIENVKNVRVVTNIGTKYASSESNTSFLEGLDCSAFEEADGRIILHIRD 1041 (1309)
Q Consensus 962 V~~~t~iP~nW~~FLsn~~NK~eLi~fL~~~~~e~~~~k~vVt~~G~~v~~~~~~~~~~~~l~~c~hEEADTrIilHa~~ 1041 (1309)
..|.+... =+..+.+.+.+ .|..++. ..--|||--|=--|..
T Consensus 89 -----~~p~~l~~----------q~~~i~~~~~~----------~~~~~l~-------------~~G~eadd~i~t~A~~ 130 (310)
T COG0258 89 -----EMPDELAP----------QIPILTELLVA----------LGIPLLE-------------LMGIEADDPIETLAQK 130 (310)
T ss_pred -----cCHHHHHH----------HHHHHHHHHHH----------hCcHhhh-------------cCCCCcchhHHHHHHH
Confidence 12322111 12223333332 1211211 1122477766655666
Q ss_pred HHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCCcee-eeehhHHHHhh-cccccccccccccccC--C
Q psy7142 1042 AVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGKKQR-FFAAHEIAVNL-GTEKSVALRGFHAFSG--C 1117 (1309)
Q Consensus 1042 a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~~~r-~i~i~~i~~~l-G~~~~~al~~~HAftG--c 1117 (1309)
|...|+ .+.|.|.|.|.+.+.-- .+.+..+..+... ++++..+.+.+ |.... -|+-+=|++| |
T Consensus 131 a~~~g~-~~~I~S~DkD~lql~~~-----------~~~~~~~~~~~~~~~~~~~~~~e~~~g~~p~-qliD~~~L~Gd~s 197 (310)
T COG0258 131 AYKKGD-VVLIISGDKDLLQLVSP-----------NVLVINGKKGEPEKFLDLEEVEEKFKGLTPE-QLIDLKALVGDSS 197 (310)
T ss_pred HHhcCC-eEEEEeCCcchhhhcCC-----------CcEEEeccCCCCcccCCHHHHHHHHcCCCHH-HHHHHHHHhCCcc
Confidence 665555 67777999998887622 3444444433322 68899999998 65544 8899999999 9
Q ss_pred cccccccccchhhHhhhhhccchHHHHHHHhcCCCCchhHHHHHHHHHHhhh
Q psy7142 1118 DTVSTFAFHGKQTAWKTWNSCDYVTSAFVAISKPLPELGDELLQDLEQFVVY 1169 (1309)
Q Consensus 1118 Dtts~f~g~gK~~~~K~l~~~~~~q~~f~~l~~~~~~l~ee~f~~lErFvc~ 1169 (1309)
|.++.-.|+|.++|+++++.+..+-..+..+...+....+......|.+.+.
T Consensus 198 DnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~~~~~~l~~~~~~afl~ 249 (310)
T COG0258 198 DNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKLLEDKEKAFLS 249 (310)
T ss_pred cCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcchhhHHHHHHHHHHhcC
Confidence 9999999999999999999988665545443221222233345555555543
No 4
>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=97.40 E-value=0.002 Score=72.32 Aligned_cols=105 Identities=20% Similarity=0.263 Sum_probs=77.1
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCCceeeeehhHHHHhhcccccccc
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGKKQRFFAAHEIAVNLGTEKSVAL 1108 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~~~r~i~i~~i~~~lG~~~~~al 1108 (1309)
-|||=.|-.=|..+..+| ..++|.|.|.|.+-+. . ..+++.... +.+.|+...+.+.+|.. -.-+
T Consensus 107 ~EADD~ia~la~~~~~~g-~~~~I~S~DkD~~ql~-------~----~~v~~~~~~--~~~~i~~~~v~~~~g~~-p~q~ 171 (240)
T cd00008 107 YEADDVIGTLAKKAEAEG-YKVVIVSGDKDLLQLV-------S----DNVKVVSPM--KKKLVTEENVIEKYGVT-PAQI 171 (240)
T ss_pred cCHHHHHHHHHHHHHHcC-CeEEEEeCCCChhhhC-------C----CCEEEEeCC--CceEEeHHHHHHHhCcC-HHHH
Confidence 489987654444445555 5788889999988764 1 234333222 34578999898888853 3457
Q ss_pred cccccccC--CcccccccccchhhHhhhhhccchHHHHHHHh
Q psy7142 1109 RGFHAFSG--CDTVSTFAFHGKQTAWKTWNSCDYVTSAFVAI 1148 (1309)
Q Consensus 1109 ~~~HAftG--cDtts~f~g~gK~~~~K~l~~~~~~q~~f~~l 1148 (1309)
+-|.|+.| ||..+..-|+|.++|.++++++..+...+..+
T Consensus 172 ~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~ 213 (240)
T cd00008 172 IDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENL 213 (240)
T ss_pred HHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhH
Confidence 78899999 99999999999999999999988876666554
No 5
>PRK14976 5'-3' exonuclease; Provisional
Probab=97.27 E-value=0.0052 Score=70.65 Aligned_cols=107 Identities=20% Similarity=0.252 Sum_probs=77.9
Q ss_pred ccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCCceeeeehhHHHHhhccccccccc
Q psy7142 1030 EADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGKKQRFFAAHEIAVNLGTEKSVALR 1109 (1309)
Q Consensus 1030 EADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~~~r~i~i~~i~~~lG~~~~~al~ 1109 (1309)
|||=-|-.=+..+..+| ..|+|.|.|.|.+.|.-- . ..+|.. ..+..++.|+...+.+.+|-. -.-++
T Consensus 113 EADDviatla~~~~~~g-~~v~IvS~DkDl~ql~~~---~------v~~~~~-~~~~~~~~~~~~~v~~~~gv~-p~q~~ 180 (281)
T PRK14976 113 EADDLIGSLAKKLSKQN-ITVLIYSSDKDLLQLVNE---N------TDVLLK-KKGTSHFILNTNNFFELYGIE-PKQII 180 (281)
T ss_pred CHHHHHHHHHHHHHHCC-CeEEEEeCCCCcCccCCC---C------eEEEEe-cCCCCcEEEcHHHHHHHhCcC-HHHHH
Confidence 89876544444455555 467899999999887510 0 223332 334336789999999999852 23477
Q ss_pred ccccccC--CcccccccccchhhHhhhhhccchHHHHHHHh
Q psy7142 1110 GFHAFSG--CDTVSTFAFHGKQTAWKTWNSCDYVTSAFVAI 1148 (1309)
Q Consensus 1110 ~~HAftG--cDtts~f~g~gK~~~~K~l~~~~~~q~~f~~l 1148 (1309)
-+.|+.| ||..+...|+|.++|.++++++..+...+..+
T Consensus 181 d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~ 221 (281)
T PRK14976 181 DYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENI 221 (281)
T ss_pred HHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhH
Confidence 8899999 99999999999999999999988876655543
No 6
>PTZ00217 flap endonuclease-1; Provisional
Probab=97.18 E-value=0.0016 Score=77.89 Aligned_cols=108 Identities=19% Similarity=0.207 Sum_probs=74.7
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCCceeeeehhHHHHhhcccccccc
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGKKQRFFAAHEIAVNLGTEKSVAL 1108 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~~~r~i~i~~i~~~lG~~~~~al 1108 (1309)
.|||-.+ +.-+..|. ...|.|+|+|++++..- .+- -++...-+.+....+|+...+.+.+|-. -.-+
T Consensus 159 ~EAdaq~----A~L~~~g~-v~~ViS~D~D~l~fg~~---~vi----~~l~~~~~~~~~~~~~~~~~v~~~~gl~-~~q~ 225 (393)
T PTZ00217 159 CEAEAQC----AELVKKGK-VYAVATEDMDALTFGTP---VLL----RNLNFSEAKKRPIQEINLSTVLEELGLS-MDQF 225 (393)
T ss_pred cCHHHHH----HHHHHCCC-eEEEeCCCcCeeecCCc---EEE----EcccccccCCCCeEEEEHHHHHHHhCCC-HHHH
Confidence 3888753 22334555 45678999999987622 100 0111111123346789999999998753 2456
Q ss_pred cccccccCCcccccccccchhhHhhhhhccchHHHHHHHhc
Q psy7142 1109 RGFHAFSGCDTVSTFAFHGKQTAWKTWNSCDYVTSAFVAIS 1149 (1309)
Q Consensus 1109 ~~~HAftGcDtts~f~g~gK~~~~K~l~~~~~~q~~f~~l~ 1149 (1309)
+-|=+++|||.+..+.|+|-++|+++++++..+...+..+.
T Consensus 226 id~~iL~G~Dy~pgi~GIG~ktA~~Li~~~gsle~il~~~~ 266 (393)
T PTZ00217 226 IDLCILCGCDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLD 266 (393)
T ss_pred HHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHH
Confidence 77889999999999999999999999999988766655543
No 7
>PRK09482 flap endonuclease-like protein; Provisional
Probab=96.99 E-value=0.0049 Score=69.91 Aligned_cols=200 Identities=17% Similarity=0.239 Sum_probs=121.7
Q ss_pred ceEEeccceeecccCCCC--ccchhhhhHHHHHHHHHhhhcccCCCeeEEEEeccCCCCchhhhhhccCCCCceeec---
Q psy7142 889 DVVVCDGAALIHATPPRN--SRTFEGYCSQEFQRTIMGMIESCSADRIDVVWDLYFPDSLKNSLREVRGKSQRLQVT--- 963 (1309)
Q Consensus 889 ~~~IiDG~alvh~l~~~~--~~tF~~ya~~~f~~yv~~~~~~~~~~ridVVFD~Y~~~SlK~~eR~kRGs~~~~~V~--- 963 (1309)
.+++|||++++++---.. +..+ .-|-.-|...+.+.+...+...+-|+||.-.+.+ +.|+++.
T Consensus 4 ~llLiDg~~l~~R~~~a~~~~~g~-t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~-----------~fR~~l~p~Y 71 (256)
T PRK09482 4 HLLIIDALNLIRRIHAVQPSPNDI-NACVETCQHALDKLIRHSQPTHAVAVFDGDARSS-----------GWRHQLLPDY 71 (256)
T ss_pred eEEEEeCcHHHHHHHhCCCCCCCc-chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCc-----------ccHHHHhHHH
Confidence 489999999998641101 1222 4455677888888887667788999999743211 1222222
Q ss_pred --CCCCCCcchhhhhcccCchhhhHHHHHHHHHhhccceEEEEecCceeeeccCCccccccCCCCcccccchHHHHHHHH
Q psy7142 964 --PNSPVPRNWSEFLKNNHNKEELFSLLGKYLIENVKNVRVVTNIGTKYASSESNTSFLEGLDCSAFEEADGRIILHIRD 1041 (1309)
Q Consensus 964 --~~t~iP~nW~~FLsn~~NK~eLi~fL~~~~~e~~~~k~vVt~~G~~v~~~~~~~~~~~~l~~c~hEEADTrIilHa~~ 1041 (1309)
...+.|..+..-+ ..+ +.+.+. .|-.+... .-=|||=-|--=|..
T Consensus 72 Ka~R~~~Pe~l~~Q~----------~~i-~~~l~~---------~gi~~~~~-------------~g~EADDvIatla~~ 118 (256)
T PRK09482 72 KAGRKPMPEALQQGL----------PAI-RAAFEE---------LGIDSWHA-------------DGNEADDLIATLAVK 118 (256)
T ss_pred hcCCCCCcHHHHHHH----------HHH-HHHHHh---------CCCCEecc-------------CCcCHHHHHHHHHHH
Confidence 1123454433311 111 122211 13222111 123788766554555
Q ss_pred HHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCCceeeeehhHHHHhhcccccccccccccccC--Ccc
Q psy7142 1042 AVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGKKQRFFAAHEIAVNLGTEKSVALRGFHAFSG--CDT 1119 (1309)
Q Consensus 1042 a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~~~r~i~i~~i~~~lG~~~~~al~~~HAftG--cDt 1119 (1309)
+..+|+ .|+|.|.|.|.+-|. . ..+++-... +.++++...+.+.+|-. -.-++-|.|+.| +|.
T Consensus 119 ~~~~~~-~v~I~S~DKDl~Qlv-------~----~~v~~~~~~--~~~~~~~~~v~~~~Gv~-P~q~~D~~aL~GD~sDn 183 (256)
T PRK09482 119 VAQAGH-QATIVSTDKGYCQLL-------S----PTIQIRDYF--QKRWLDAPFIEQEFGVE-PQQLPDYWGLAGISSSK 183 (256)
T ss_pred HHHCCC-eEEEEECCCCccccC-------C----CCeEEEecc--ccccCCHHHHHHHhCCC-HHHHHHHHHHhCCCccC
Confidence 555664 688889999976553 1 233322111 23568999999999853 244567789999 889
Q ss_pred cccccccchhhHhhhhhccchHHHHHHHh
Q psy7142 1120 VSTFAFHGKQTAWKTWNSCDYVTSAFVAI 1148 (1309)
Q Consensus 1120 ts~f~g~gK~~~~K~l~~~~~~q~~f~~l 1148 (1309)
.+.-.|+|.++|.++++++..+-..+..+
T Consensus 184 IpGVpGIG~KtA~~LL~~~gsle~i~~~~ 212 (256)
T PRK09482 184 IPGVAGIGPKSAAELLNQFRSLENIYESL 212 (256)
T ss_pred CCCCCCcChHHHHHHHHHhCCHHHHHHhH
Confidence 99999999999999999988876666554
No 8
>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=96.92 E-value=0.0047 Score=72.69 Aligned_cols=104 Identities=18% Similarity=0.169 Sum_probs=71.6
Q ss_pred ccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCC----------ceeeeehhHHHHh
Q psy7142 1030 EADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGK----------KQRFFAAHEIAVN 1099 (1309)
Q Consensus 1030 EADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~----------~~r~i~i~~i~~~ 1099 (1309)
|||.. ++..+..|. ...|.|+|.|++.+..-.. + -+++. .|.++ ....|+..++.+.
T Consensus 152 EAeaq----~a~L~~~g~-vd~v~S~D~D~l~fg~~~v--i-----~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~v~~~ 218 (338)
T TIGR03674 152 EGEAQ----AAYMAKKGD-VDYVGSQDYDSLLFGAPRL--V-----RNLTI-SGKRKLPGKNIYVEVKPELIELEEVLSE 218 (338)
T ss_pred cHHHH----HHHHHHCCC-eeEEecCCcCeeeecCCEE--E-----Eeccc-ccccCCCcccccccccceeeeHHHHHHH
Confidence 88864 333445563 4477899999999863211 0 01111 12110 3456899999998
Q ss_pred hcccccccccccccccCCcccccccccchhhHhhhhhccchHHHHHHH
Q psy7142 1100 LGTEKSVALRGFHAFSGCDTVSTFAFHGKQTAWKTWNSCDYVTSAFVA 1147 (1309)
Q Consensus 1100 lG~~~~~al~~~HAftGcDtts~f~g~gK~~~~K~l~~~~~~q~~f~~ 1147 (1309)
+|-. -..++-+=+++|||......|+|.++|++++++|..+...+..
T Consensus 219 lgl~-~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~gsie~il~~ 265 (338)
T TIGR03674 219 LGIT-REQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKA 265 (338)
T ss_pred hCCC-HHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHh
Confidence 8742 3456777889999999999999999999999998887665554
No 9
>KOG2519|consensus
Probab=96.87 E-value=0.0014 Score=78.24 Aligned_cols=178 Identities=20% Similarity=0.174 Sum_probs=112.8
Q ss_pred CCCeeEEEEeccCCCCchhhhhhccCC---CCc--eeecCCCCCCcchhhhhcccCchhhhHHHHHHHHHhhccceEEEE
Q psy7142 930 SADRIDVVWDLYFPDSLKNSLREVRGK---SQR--LQVTPNSPVPRNWSEFLKNNHNKEELFSLLGKYLIENVKNVRVVT 1004 (1309)
Q Consensus 930 ~~~ridVVFD~Y~~~SlK~~eR~kRGs---~~~--~~V~~~t~iP~nW~~FLsn~~NK~eLi~fL~~~~~e~~~~k~vVt 1004 (1309)
++. .-+|||+-.+ -||+.|+.||+. ++. .+.+..+..+.+|.+|.+...-=+.=+..=++.+.+. -++.+++
T Consensus 74 gi~-Pv~VfDG~pP-~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~l-mGIp~i~ 150 (449)
T KOG2519|consen 74 GIK-PVYVFDGKPP-DLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSL-MGIPVLD 150 (449)
T ss_pred CCc-EEEEECCCCC-CcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHH-cCCeeec
Confidence 444 5599999988 999999999974 333 2333455667888888776422111111222333321 1233333
Q ss_pred ecCceeeeccCCccccccCCCCcccccchHHHHHHHHHHhcCC-eeEEEEecCCCeeeehhhhhhhhhccCccceEEEcc
Q psy7142 1005 NIGTKYASSESNTSFLEGLDCSAFEEADGRIILHIRDAVLQGA-KKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLN 1083 (1309)
Q Consensus 1005 ~~G~~v~~~~~~~~~~~~l~~c~hEEADTrIilHa~~a~~~g~-~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g 1083 (1309)
. ..|| ||.+|+.... ..-.+.++|.|.+-+..- .+. .++-...|
T Consensus 151 a----------------------p~EA------EAqCA~Lnk~g~V~~~at~DsD~l~fg~~---~~l----r~l~~s~~ 195 (449)
T KOG2519|consen 151 A----------------------PGEA------EAQCAALNKAGKVYAVATEDSDALTFGAP---VKL----RHLIHSLA 195 (449)
T ss_pred C----------------------CchH------HHHHHHHhhcCceeeeeccccchhhccCH---HHH----HHhccchh
Confidence 2 1122 5666665444 566788999996554422 111 12223367
Q ss_pred CCCceeeeehhHHHHhhcccccccccccccccCCcccccccccchhhHhhhhhccchHHHHHH
Q psy7142 1084 YGKKQRFFAAHEIAVNLGTEKSVALRGFHAFSGCDTVSTFAFHGKQTAWKTWNSCDYVTSAFV 1146 (1309)
Q Consensus 1084 ~g~~~r~i~i~~i~~~lG~~~~~al~~~HAftGcDtts~f~g~gK~~~~K~l~~~~~~q~~f~ 1146 (1309)
.|.-+.-|+...|.+.||-.. ..+..+=.++|||.-+...|+|+.+|+++++++.+.+..+.
T Consensus 196 ~~~pv~e~~~~~il~~l~l~~-~~fidL~lLlGCDYc~~I~Gig~~~al~lir~~~~i~~ile 257 (449)
T KOG2519|consen 196 SGLPVSEYDMSRILEGLGLSR-ESFIDLCLLLGCDYCPTIRGIGPKKALKLIRQHGDIENILE 257 (449)
T ss_pred cCCCeEEeeHHHHHHHhcccH-HHHHHHHHHhcCcccccccccChHHHHHHHHHhcCHHHHhh
Confidence 777777789999999886532 23445556899999999999999999999999988766554
No 10
>PRK05755 DNA polymerase I; Provisional
Probab=96.62 E-value=0.029 Score=73.85 Aligned_cols=108 Identities=21% Similarity=0.243 Sum_probs=79.6
Q ss_pred ccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCCceeeeehhHHHHhhccccccccc
Q psy7142 1030 EADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGKKQRFFAAHEIAVNLGTEKSVALR 1109 (1309)
Q Consensus 1030 EADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~~~r~i~i~~i~~~lG~~~~~al~ 1109 (1309)
|||-.|-.=|..+...| ..|+|.|.|.|.+-|.-- . ..+|...+ +...+.++...+.+.+|-. -.-++
T Consensus 109 EADD~ia~la~~~~~~~-~~~~i~S~DkD~~ql~~~---~------v~~~~~~~-~~~~~~~~~~~v~~~~g~~-p~q~~ 176 (880)
T PRK05755 109 EADDVIGTLAKQAEAAG-YEVLIVTGDKDLLQLVDD---N------VTLLDTMG-VSKNEELDPEEVVEKYGVT-PEQII 176 (880)
T ss_pred cHHHHHHHHHHHHHhCC-CcEEEEcCCCChhhhCCC---C------EEEeeccC-CCCCeEEcHHHHHHHHCcC-HHHHH
Confidence 89987654455555555 478899999998877511 1 23343332 2345679999999999842 34578
Q ss_pred ccccccC--CcccccccccchhhHhhhhhccchHHHHHHHhc
Q psy7142 1110 GFHAFSG--CDTVSTFAFHGKQTAWKTWNSCDYVTSAFVAIS 1149 (1309)
Q Consensus 1110 ~~HAftG--cDtts~f~g~gK~~~~K~l~~~~~~q~~f~~l~ 1149 (1309)
-+.|+.| ||..+..-|+|.++|.++++++..+...+..+.
T Consensus 177 d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~ 218 (880)
T PRK05755 177 DYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLD 218 (880)
T ss_pred HHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHH
Confidence 8999999 799999999999999999999998877666544
No 11
>KOG2518|consensus
Probab=96.49 E-value=0.011 Score=71.77 Aligned_cols=120 Identities=19% Similarity=0.259 Sum_probs=74.6
Q ss_pred ccccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEE---ccCCCceeeeehhHHHHhhccc-
Q psy7142 1028 FEEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVS---LNYGKKQRFFAAHEIAVNLGTE- 1103 (1309)
Q Consensus 1028 hEEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~---~g~g~~~r~i~i~~i~~~lG~~- 1103 (1309)
.=|||..|..= ..+|.-..|| |+|.|++|.+.- .+.++ +|.|-- |+..++....|-.
T Consensus 148 PyEADAQlayL----~~~~~i~~II-TEDSDLl~fGc~-----------~vifK~d~~G~~le---~~~~~l~~~~~l~~ 208 (556)
T KOG2518|consen 148 PYEADAQLAYL----EREGIVDAII-TEDSDLLVFGCK-----------KVIFKMDSFGNGLE---INRSKLPECKPLGD 208 (556)
T ss_pred CccccchhHHH----HhcCcceEEE-eccccccccCch-----------hheeeccCCCCccc---ccHhhhhhcccccc
Confidence 34788886432 2556655555 899999998633 33333 444433 3666665554433
Q ss_pred cc--ccccccccccCCcccccccccchhhHhhhhhccchHHHHHHHhc-CCCCchhHHHHHHHHHH
Q psy7142 1104 KS--VALRGFHAFSGCDTVSTFAFHGKQTAWKTWNSCDYVTSAFVAIS-KPLPELGDELLQDLEQF 1166 (1309)
Q Consensus 1104 ~~--~al~~~HAftGcDtts~f~g~gK~~~~K~l~~~~~~q~~f~~l~-~~~~~l~ee~f~~lErF 1166 (1309)
.. .-+..+=.|||||.+++.-|.|=.+|.|++..+...-.....+. ..--.+.++-+...|+.
T Consensus 209 ~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~vi~~~~~~~~l~Vpd~y~~~F~~A 274 (556)
T KOG2518|consen 209 KFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDRVIISHLLKKKLTVPDDYIENFERA 274 (556)
T ss_pred ccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHHHHHHHHhccCCcCCHHHHHHHHHH
Confidence 11 12455667999999999999999999999999888655443221 11123455555555544
No 12
>PRK03980 flap endonuclease-1; Provisional
Probab=96.43 E-value=0.0088 Score=69.15 Aligned_cols=97 Identities=18% Similarity=0.135 Sum_probs=68.4
Q ss_pred HHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCC----------CceeeeehhHHHHhhccccccccccc
Q psy7142 1042 AVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYG----------KKQRFFAAHEIAVNLGTEKSVALRGF 1111 (1309)
Q Consensus 1042 a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g----------~~~r~i~i~~i~~~lG~~~~~al~~~ 1111 (1309)
-+..|. ...|.|+|.|+|.+..-. +- -++++ .|.+ .....|+.+++.+.+|-. -.-++-|
T Consensus 113 L~~~g~-vd~V~S~D~D~l~fg~~~---vi----r~l~~-~~~~~~p~~~~~~~~~~e~~~~~~vl~~lgl~-~~q~id~ 182 (292)
T PRK03980 113 MAKKGD-AWAVGSQDYDSLLFGAPR---LV----RNLTI-SGKRKLPGKNVYVEVKPELIELEEVLKELGIT-REQLIDI 182 (292)
T ss_pred HHHCCC-eEEEecCCcCeeeecCCE---EE----Eeecc-cccccCccccccccccceeeeHHHHHHHhCCC-HHHHHHH
Confidence 335564 446789999999987321 10 11222 2221 135578999999998753 3456777
Q ss_pred ccccCCcccccccccchhhHhhhhhccchHHHHHHHh
Q psy7142 1112 HAFSGCDTVSTFAFHGKQTAWKTWNSCDYVTSAFVAI 1148 (1309)
Q Consensus 1112 HAftGcDtts~f~g~gK~~~~K~l~~~~~~q~~f~~l 1148 (1309)
=+++|||......|+|-++|+++++++..+...+..+
T Consensus 183 ~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~ 219 (292)
T PRK03980 183 AILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEER 219 (292)
T ss_pred HHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhc
Confidence 8899999999999999999999999998876665543
No 13
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.42 E-value=0.12 Score=67.99 Aligned_cols=109 Identities=18% Similarity=0.172 Sum_probs=79.0
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEE-ccCCCceeeeehhHHHHhhccccccc
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVS-LNYGKKQRFFAAHEIAVNLGTEKSVA 1107 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~-~g~g~~~r~i~i~~i~~~lG~~~~~a 1107 (1309)
-|||=.|--=|..+..+|+ .|+|.|.|.|.+-|.- .++++- ..++...+.++...+.+.+|-. -.-
T Consensus 106 ~EADDiIatla~~~~~~g~-~v~IvS~DkDllQLv~-----------~~v~~~~~~~~~~~~~~~~~~v~~~~Gv~-p~q 172 (887)
T TIGR00593 106 YEADDVIATLAKQAEKEGY-EVRIISGDKDLLQLVS-----------DNVKVLIPKGKTSFTEITPEYVVEKYGVT-PDQ 172 (887)
T ss_pred ccHHHHHHHHHHHHHhCCC-cEEEEECCCChhhcCC-----------CCEEEEeccCCCCceEEcHHHHHHHhCCC-HHH
Confidence 3898876554555556665 5888899999877641 123322 2222245678999999999853 334
Q ss_pred ccccccccC--CcccccccccchhhHhhhhhccchHHHHHHHhcC
Q psy7142 1108 LRGFHAFSG--CDTVSTFAFHGKQTAWKTWNSCDYVTSAFVAISK 1150 (1309)
Q Consensus 1108 l~~~HAftG--cDtts~f~g~gK~~~~K~l~~~~~~q~~f~~l~~ 1150 (1309)
++-+-|+.| ||..+..-|+|.++|.|+++++..+...+..+.+
T Consensus 173 ~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~ 217 (887)
T TIGR00593 173 LVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQ 217 (887)
T ss_pred HHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHH
Confidence 677899999 5999999999999999999999998777766543
No 14
>PF03638 TCR: Tesmin/TSO1-like CXC domain, cysteine-rich domain; InterPro: IPR005172 This entry includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin Q9Y4I5 from SWISSPROT [] and TSO1 Q9LE32 from SWISSPROT []. This group of proteins is called a CXC domain in [].
Probab=94.50 E-value=0.021 Score=47.81 Aligned_cols=39 Identities=28% Similarity=0.750 Sum_probs=33.7
Q ss_pred cccccccCC-CCCCCCcccccccCCcccccccCCCCCCCCCCC
Q psy7142 1261 DLVKCKCKT-GCSSTSNCSCKRSNVDCVPVLCSNCNGCSNMSQ 1302 (1309)
Q Consensus 1261 eLi~C~Ck~-gC~~~~~C~C~k~gl~Ct~~~C~~c~~C~N~~~ 1302 (1309)
+...|+|++ +|.- .-|.|..+|..|++ .|.| .+|.|.++
T Consensus 2 ~~~gC~Ckks~Clk-~YC~Cf~~g~~C~~-~C~C-~~C~N~~~ 41 (42)
T PF03638_consen 2 KKKGCNCKKSKCLK-LYCECFQAGRFCTP-NCKC-QNCKNTEE 41 (42)
T ss_pred CCCCCcccCcChhh-hhCHHHHCcCcCCC-Cccc-CCCCCcCC
Confidence 457899965 9996 59999999999999 9998 79999875
No 15
>PHA00439 exonuclease
Probab=92.60 E-value=0.91 Score=52.63 Aligned_cols=86 Identities=21% Similarity=0.220 Sum_probs=52.8
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccCCCceeeeehhHHHHhhcccccccc
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNYGKKQRFFAAHEIAVNLGTEKSVAL 1108 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~g~~~r~i~i~~i~~~lG~~~~~al 1108 (1309)
-|||=.|-.=|..+..+|+..|+|.|.|-|.+=|. . ...+|.. .+. . +. ++++...-+
T Consensus 119 ~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv-------~---~~~~~~~--~~~-~--~~-------~~~~~p~~~ 176 (286)
T PHA00439 119 LEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIP-------N---CDFLWCT--TGN-I--LT-------QTPETADRW 176 (286)
T ss_pred ccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcC-------c---ceEEEcc--CCc-e--EE-------cCcccHHHH
Confidence 48888775555556667777899999999976552 1 0112221 111 1 10 111211223
Q ss_pred cccccccC--CcccccccccchhhHhhhhhc
Q psy7142 1109 RGFHAFSG--CDTVSTFAFHGKQTAWKTWNS 1137 (1309)
Q Consensus 1109 ~~~HAftG--cDtts~f~g~gK~~~~K~l~~ 1137 (1309)
+-+-|+.| .|..+-..|+| ++|.+++++
T Consensus 177 ~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 177 HLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred HhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 34557777 67777889999 999999987
No 16
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=92.12 E-value=0.41 Score=51.21 Aligned_cols=53 Identities=25% Similarity=0.261 Sum_probs=36.0
Q ss_pred EEeccceeecccCCCC---ccchhhhhHHHHHHHHHhhhcccCCCeeEEEEeccCCC
Q psy7142 891 VVCDGAALIHATPPRN---SRTFEGYCSQEFQRTIMGMIESCSADRIDVVWDLYFPD 944 (1309)
Q Consensus 891 ~IiDG~alvh~l~~~~---~~tF~~ya~~~f~~yv~~~~~~~~~~ridVVFD~Y~~~ 944 (1309)
+||||.=++|+.|.-. ...--+-|+..++..+..+.. ....++.||||.|...
T Consensus 1 LlIDGYNli~~~~~l~~~~~~~~l~~aR~~Li~~L~~y~~-~~~~~v~VVFDa~~~~ 56 (166)
T PF05991_consen 1 LLIDGYNLIHAWPELRSLAERGDLEAARERLIEMLSEYAQ-FSGYEVIVVFDAYKVP 56 (166)
T ss_pred CeEcchhhhCCCHHHHhhcCcCCHHHHHHHHHHHHHHHhc-ccCCEEEEEEeCCcCC
Confidence 4899999999954211 111224566677777766554 5668999999999764
No 17
>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=88.06 E-value=0.77 Score=61.13 Aligned_cols=95 Identities=18% Similarity=0.172 Sum_probs=67.5
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEE-ccCCCceeeeehhHHHHhhccccccc
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVS-LNYGKKQRFFAAHEIAVNLGTEKSVA 1107 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~-~g~g~~~r~i~i~~i~~~lG~~~~~a 1107 (1309)
-|||..+ +.-...|. .-.|.|+|.|+|+.+.- .++.. ++.++...+|...++...||-. -..
T Consensus 793 ~EAEAqc----A~L~~~G~-vd~V~TeDsD~llFGa~-----------~v~rn~~~~~~~ve~~~~~~i~~~lglt-~~q 855 (1034)
T TIGR00600 793 MEAEAQC----AILDLLDQ-TSGTITDDSDIWLFGAR-----------HVYKNFFNQNKFVEYYQYVDIHNQLGLD-RNK 855 (1034)
T ss_pred ccHHHHH----HHHHhCCC-eEEEEccccceeccCCc-----------eeeecccCCCCceEEeeHHHHHHHhCCC-HHH
Confidence 5777643 22234455 56677999999977532 22211 2344456678888888888753 256
Q ss_pred ccccccccCCcccccccccchhhHhhhhhccch
Q psy7142 1108 LRGFHAFSGCDTVSTFAFHGKQTAWKTWNSCDY 1140 (1309)
Q Consensus 1108 l~~~HAftGcDtts~f~g~gK~~~~K~l~~~~~ 1140 (1309)
|..|=.+.|||.+....|+|-++|+++++.+..
T Consensus 856 li~laiL~G~DY~~GI~GIGpktAl~li~~~~~ 888 (1034)
T TIGR00600 856 LINLAYLLGSDYTEGIPTVGPVSAMEILNEFPG 888 (1034)
T ss_pred HHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCC
Confidence 777888999999999999999999999998773
No 18
>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=78.11 E-value=1.5 Score=40.97 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=34.2
Q ss_pred ccccccccC--CcccccccccchhhHhhhhhccchHHHHHHH
Q psy7142 1108 LRGFHAFSG--CDTVSTFAFHGKQTAWKTWNSCDYVTSAFVA 1147 (1309)
Q Consensus 1108 l~~~HAftG--cDtts~f~g~gK~~~~K~l~~~~~~q~~f~~ 1147 (1309)
+.-+-|++| ||.++...|+|.++|.+++.++..+...+..
T Consensus 10 ~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~ 51 (75)
T cd00080 10 FIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLEN 51 (75)
T ss_pred HHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHH
Confidence 344568999 9999999999999999999998887766655
No 19
>KOG1171|consensus
Probab=77.79 E-value=0.77 Score=55.25 Aligned_cols=45 Identities=31% Similarity=0.742 Sum_probs=39.3
Q ss_pred CcchhhhhccccccccCC-CCCCCCcccccccCCcccccccCCCCCCCC
Q psy7142 1252 LPTIWKGCRDLVKCKCKT-GCSSTSNCSCKRSNVDCVPVLCSNCNGCSN 1299 (1309)
Q Consensus 1252 ~p~aP~~lleLi~C~Ck~-gC~~~~~C~C~k~gl~Ct~~~C~~c~~C~N 1299 (1309)
.-.+|.+-+.-=.|+||+ ||-- +-|-|..+|+.|+. .|+| +.|.|
T Consensus 207 ~~~~~~sa~hkkGC~CkkSgClK-kYCECyQa~vlCS~-nCkC-~~CkN 252 (406)
T KOG1171|consen 207 ASKTPASARHKKGCNCKKSGCLK-KYCECYQAGVLCSS-NCKC-QGCKN 252 (406)
T ss_pred hhccchhhhhcCCCCCccccchH-HHHHHHhcCCCccc-cccC-cCCcc
Confidence 355677778889999988 9994 69999999999999 9998 79999
No 20
>PF05033 Pre-SET: Pre-SET motif; InterPro: IPR007728 This region is found in a number of histone lysine methyltransferases (HMTase), N-terminal to the SET domain; it is generally described as the pre-SET domain. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils and stabilising the SET domain. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site [] when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity []. ; GO: 0008270 zinc ion binding, 0018024 histone-lysine N-methyltransferase activity, 0034968 histone lysine methylation, 0005634 nucleus; PDB: 3K5K_A 2O8J_D 3RJW_B 1ML9_A 1PEG_B 1MVH_A 1MVX_A 3BO5_A 2RFI_B 3MO5_B ....
Probab=68.76 E-value=3.6 Score=40.14 Aligned_cols=38 Identities=37% Similarity=0.868 Sum_probs=23.0
Q ss_pred ccccccCCCCCCCCcccccccCC--------------------cccccccCCCCCCCCC
Q psy7142 1262 LVKCKCKTGCSSTSNCSCKRSNV--------------------DCVPVLCSNCNGCSNM 1300 (1309)
Q Consensus 1262 Li~C~Ck~gC~~~~~C~C~k~gl--------------------~Ct~~~C~~c~~C~N~ 1300 (1309)
+..|.|..+|.....|.|.+..- .|++ .|+|..+|.|+
T Consensus 46 ~~~C~C~~~C~~~~~C~C~~~~~~~~~Y~~~g~l~~~~~~~i~EC~~-~C~C~~~C~NR 103 (103)
T PF05033_consen 46 LQGCDCSGDCSNPSNCECLQRNGGIFAYDSNGRLRIPDKPPIFECND-NCGCSPSCRNR 103 (103)
T ss_dssp TS----SSSSTCTTTSHHHCCTSSS-SB-TTSSBSSSSTSEEE---T-TSSS-TTSTT-
T ss_pred CccCccCCCCCCCCCCcCccccCccccccCCCcCccCCCCeEEeCCC-CCCCCCCCCCC
Confidence 35999999995457999987663 4999 99998889985
No 21
>PF11403 Yeast_MT: Yeast metallothionein; InterPro: IPR022710 Metallothioneins are characterised by an abundance of cysteine residues and a lack of generic secondary structure motifs. This protein functions in primary metal storage, transport and detoxification []. For the first 40 residues in the protein the polypeptide wraps around the metal by forming two large parallel loops separated by a deep cleft containing the metal cluster []. ; PDB: 1AQS_A 1AQR_A 1RJU_V 1FMY_A 1AOO_A 1AQQ_A.
Probab=65.91 E-value=3.4 Score=33.24 Aligned_cols=18 Identities=44% Similarity=1.261 Sum_probs=11.7
Q ss_pred cccccCCCCCCCCccccc
Q psy7142 1263 VKCKCKTGCSSTSNCSCK 1280 (1309)
Q Consensus 1263 i~C~Ck~gC~~~~~C~C~ 1280 (1309)
-.|+|.+||.|..+|-|.
T Consensus 22 kscscptgcnsddkcpcg 39 (40)
T PF11403_consen 22 KSCSCPTGCNSDDKCPCG 39 (40)
T ss_dssp TS-SS-TTTTSSTT--TT
T ss_pred hcCCCCCCCCCCCcCCCC
Confidence 469999999998888874
No 22
>KOG1079|consensus
Probab=60.01 E-value=4 Score=51.58 Aligned_cols=40 Identities=30% Similarity=0.914 Sum_probs=34.0
Q ss_pred ccccccCCCCCCCCcccccccCCcccccccCCCC----------CCCCCCC
Q psy7142 1262 LVKCKCKTGCSSTSNCSCKRSNVDCVPVLCSNCN----------GCSNMSQ 1302 (1309)
Q Consensus 1262 Li~C~Ck~gC~~~~~C~C~k~gl~Ct~~~C~~c~----------~C~N~~~ 1302 (1309)
.-.|.|+.-|.+ +.|-|..++-.|.|-+|.+|+ +|-|...
T Consensus 539 F~GC~Ck~QC~t-kqCpC~~A~rECdPd~Cl~cg~~~~~d~~~~~C~N~~l 588 (739)
T KOG1079|consen 539 FPGCRCKAQCNT-KQCPCYLAVRECDPDVCLMCGNVDHFDSSKISCKNTNL 588 (739)
T ss_pred CCCCCccccccc-CcCchhhhccccCchHHhccCcccccccCccccccchh
Confidence 468999999997 489999999999977999986 6877654
No 23
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=59.41 E-value=1.3e+02 Score=32.65 Aligned_cols=60 Identities=22% Similarity=0.291 Sum_probs=36.7
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceE-EEccCCCceeeeehhHHHHh
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELF-VSLNYGKKQRFFAAHEIAVN 1099 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~-~~~g~g~~~r~i~i~~i~~~ 1099 (1309)
=|||=.|-.=|..+..+|. .|+|.|.|.|.+=|. . ....++ ...| +...+.++...+.+.
T Consensus 108 ~EADDvIatla~~~~~~~~-~v~IvS~DkD~~QLv-------~--~~~~V~~~~~~-~~~~~~~~~~~v~ek 168 (169)
T PF02739_consen 108 YEADDVIATLAKKASEEGF-EVIIVSGDKDLLQLV-------D--ENVNVYLLDPG-KKKFKVYDPEEVEEK 168 (169)
T ss_dssp B-HHHHHHHHHHHHHHTTC-EEEEE-SSGGGGGGT-------C--S-TSEEEEETT-TTCS-EB-HHHHHHH
T ss_pred CcHHHHHHHHHhhhccCCC-EEEEEcCCCCHHHhc-------C--CCceEEEeecC-CCCCEEEcHHHHhhc
Confidence 4899887777777777776 589999999965443 2 112455 4444 555677888777654
No 24
>KOG3813|consensus
Probab=51.77 E-value=7.1 Score=48.02 Aligned_cols=43 Identities=26% Similarity=0.790 Sum_probs=35.2
Q ss_pred ccccccccCCCCCCCCcccccccCCcccc----cccCCC-CCCCCCCCC
Q psy7142 1260 RDLVKCKCKTGCSSTSNCSCKRSNVDCVP----VLCSNC-NGCSNMSQL 1303 (1309)
Q Consensus 1260 leLi~C~Ck~gC~~~~~C~C~k~gl~Ct~----~~C~~c-~~C~N~~~~ 1303 (1309)
++--.|.|..-|.- --|.|-.+|++|-. .-|+|| +.|.|+...
T Consensus 305 ReeCGCsCr~~CdP-ETCaCSqaGIkCQvDr~~fPCgC~rEgCgNp~GR 352 (640)
T KOG3813|consen 305 REECGCSCRGVCDP-ETCACSQAGIKCQVDRGEFPCGCFREGCGNPEGR 352 (640)
T ss_pred HHhhCCcccceeCh-hhcchhccCceEeecCcccccccchhhcCCCccc
Confidence 34478999999996 59999999999964 259999 699998754
No 25
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=48.02 E-value=7.8 Score=31.68 Aligned_cols=29 Identities=21% Similarity=0.173 Sum_probs=23.9
Q ss_pred cccccccCCcccc---cccccchhhHhhhhhcc
Q psy7142 1109 RGFHAFSGCDTVS---TFAFHGKQTAWKTWNSC 1138 (1309)
Q Consensus 1109 ~~~HAftGcDtts---~f~g~gK~~~~K~l~~~ 1138 (1309)
.-+-+++| |++. ...|+|.++|+++++++
T Consensus 5 ~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 5 IDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred HHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 34557889 9888 88999999999998753
No 26
>smart00570 AWS associated with SET domains. subdomain of PRESET
Probab=36.61 E-value=15 Score=32.56 Aligned_cols=40 Identities=30% Similarity=0.713 Sum_probs=33.0
Q ss_pred cccccccC------CCCCCCCcccccccCCcccccccCCCCCCCCCCCC
Q psy7142 1261 DLVKCKCK------TGCSSTSNCSCKRSNVDCVPVLCSNCNGCSNMSQL 1303 (1309)
Q Consensus 1261 eLi~C~Ck------~gC~~~~~C~C~k~gl~Ct~~~C~~c~~C~N~~~~ 1303 (1309)
+...|.|+ .+|+ ..|-.|-.-+.|.. .|.|-..|.|..-+
T Consensus 2 e~~~C~C~~~~~~~~~Cg--sdClNR~l~~EC~~-~C~~G~~C~NqrFq 47 (51)
T smart00570 2 DIMTCECKPTDDDEGACG--SDCLNRMLLIECSS-DCPCGSYCSNQRFQ 47 (51)
T ss_pred CCceeeCccCCCCCCCcc--hHHHHHHHhhhcCC-CCCCCcCccCcccc
Confidence 46789998 5899 48999999999976 88886789997543
No 27
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=34.43 E-value=22 Score=43.55 Aligned_cols=149 Identities=15% Similarity=0.210 Sum_probs=83.3
Q ss_pred CcceEEeccceeecccCCCCccchhhhhHHHHHHHHHhhhcccCCCeeEEEEeccCCCCchhhhhhccCCCCc----ee-
Q psy7142 887 RCDVVVCDGAALIHATPPRNSRTFEGYCSQEFQRTIMGMIESCSADRIDVVWDLYFPDSLKNSLREVRGKSQR----LQ- 961 (1309)
Q Consensus 887 ~~~~~IiDG~alvh~l~~~~~~tF~~ya~~~f~~yv~~~~~~~~~~ridVVFD~Y~~~SlK~~eR~kRGs~~~----~~- 961 (1309)
++.+ -+|+|.+.=.+.-.... -.++- ..|..||+.... ...++-|..|+= .=.||...|+||-++.+ ++
T Consensus 25 ~~~i-fVD~msif~tiAysv~s-~~eL~-~~~~~~i~~w~~--~~~~VtlFvDRG-~I~iK~~lReKRr~a~k~~~~RK~ 98 (425)
T PF04599_consen 25 NNEI-FVDTMSIFMTIAYSVNS-LDELR-NSFEEYIQQWIK--NNGKVTLFVDRG-SINIKEPLREKRRKALKNTIKRKR 98 (425)
T ss_pred CccE-EEEcchhhhhhhhhhCC-HHHHH-HHHHHHHHHHHh--cCCeEEEEEecC-ccchhhHHHHHHHHHHHHHHHHHH
Confidence 4444 45999876555432211 12222 245555554322 667776666764 23589999999954322 11
Q ss_pred --------------ec----C------CCCC-CcchhhhhcccCchhhhHHHHHHHHHhhccceEEEEecCceeeeccCC
Q psy7142 962 --------------VT----P------NSPV-PRNWSEFLKNNHNKEELFSLLGKYLIENVKNVRVVTNIGTKYASSESN 1016 (1309)
Q Consensus 962 --------------V~----~------~t~i-P~nW~~FLsn~~NK~eLi~fL~~~~~e~~~~k~vVt~~G~~v~~~~~~ 1016 (1309)
+. + .-+| -..+.-||++.+|...++.-+-..+. .++.||
T Consensus 99 ~~i~~l~~~~~~ld~~d~~yeEikt~~~lki~K~~F~~fla~~~n~k~~l~~~L~~~~---~~V~Iv------------- 162 (425)
T PF04599_consen 99 EEIENLEDCIKNLDVDDEFYEEIKTDLELKIQKLSFQLFLANSNNLKTILESSLSRLK---EDVEIV------------- 162 (425)
T ss_pred HHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHHhcc---CCceEE-------------
Confidence 10 0 0112 13456677777776665443222221 233344
Q ss_pred ccccccCCCCcccccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhh
Q psy7142 1017 TSFLEGLDCSAFEEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAIS 1065 (1309)
Q Consensus 1017 ~~~~~~l~~c~hEEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~ 1065 (1309)
.|.+-+|-..|-.-|+.-+....+==++.+.|-|.+.+...
T Consensus 163 --------yCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~ 203 (425)
T PF04599_consen 163 --------YCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSC 203 (425)
T ss_pred --------EECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeec
Confidence 45667788888888887665555566777899998877644
No 28
>KOG4442|consensus
Probab=32.66 E-value=22 Score=45.54 Aligned_cols=29 Identities=24% Similarity=0.791 Sum_probs=23.0
Q ss_pred CCCCCCcccccccCCcccccccCCC-CCCCCC
Q psy7142 1270 GCSSTSNCSCKRSNVDCVPVLCSNC-NGCSNM 1300 (1309)
Q Consensus 1270 gC~~~~~C~C~k~gl~Ct~~~C~~c-~~C~N~ 1300 (1309)
+|+ ..|-|+-.++.|++..|..| ..|.|-
T Consensus 83 ~cg--~~CiNr~t~iECs~~~C~~cg~~C~NQ 112 (729)
T KOG4442|consen 83 ACG--EDCINRMTSIECSDRECPRCGVYCKNQ 112 (729)
T ss_pred ccC--ccccchhhhcccCCccCCCccccccch
Confidence 455 36669999999999999944 589984
No 29
>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=31.14 E-value=82 Score=36.03 Aligned_cols=39 Identities=18% Similarity=0.218 Sum_probs=28.4
Q ss_pred ccccchHHHHHHHHHHh----cCCeeEEEEecCCCeeeehhhh
Q psy7142 1028 FEEADGRIILHIRDAVL----QGAKKVLVRTVDTDVAVLAISF 1066 (1309)
Q Consensus 1028 hEEADTrIilHa~~a~~----~g~~~vvI~t~DTDVlVi~l~~ 1066 (1309)
..|..-.|+-+.+.... ....+.+|.|.|.|++.|+|+.
T Consensus 183 pGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L~~ 225 (237)
T PF03159_consen 183 PGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSLAT 225 (237)
T ss_dssp SS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHHHT
T ss_pred CCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHHcc
Confidence 46888999988888665 5678999999999999998873
No 30
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=28.40 E-value=62 Score=31.42 Aligned_cols=64 Identities=19% Similarity=0.176 Sum_probs=35.7
Q ss_pred cceEEeccceeeccc--CCC----CccchhhhhHHHHHHHHHhhhcccCCCeeEEEEeccCCCCchhhhhhccC
Q psy7142 888 CDVVVCDGAALIHAT--PPR----NSRTFEGYCSQEFQRTIMGMIESCSADRIDVVWDLYFPDSLKNSLREVRG 955 (1309)
Q Consensus 888 ~~~~IiDG~alvh~l--~~~----~~~tF~~ya~~~f~~yv~~~~~~~~~~ridVVFD~Y~~~SlK~~eR~kRG 955 (1309)
...+.|||...+|.. ... ....-..|....|. .+...+. .+. ..-+|||+-.+ ..|..|..+|.
T Consensus 26 g~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~-r~~~L~~-~gI-~PifVFDG~~~-~~K~~~~~~R~ 95 (101)
T PF00752_consen 26 GKRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFS-RLCRLLE-HGI-KPIFVFDGKPP-PLKRETIQKRR 95 (101)
T ss_dssp TCEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHH-HHHHHHH-TTE-EEEEEE--STT-GGCHHHHHHHH
T ss_pred CCEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHH-HHHHHHH-CCC-EEEEEECCCCc-hhhHHHHHHHH
Confidence 477899999888874 111 11111234443333 3333333 344 44599999865 99999998874
No 31
>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=26.67 E-value=24 Score=34.25 Aligned_cols=73 Identities=22% Similarity=0.321 Sum_probs=43.9
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEcc---CC-------CceeeeehhHHHH
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLN---YG-------KKQRFFAAHEIAV 1098 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g---~g-------~~~r~i~i~~i~~ 1098 (1309)
-|||..+. .-.+.|.-- .|.|+|+|+++...- .++..+- .| ...+.|+...+.+
T Consensus 12 ~EAeAq~A----~L~~~g~vd-~V~t~DsD~l~fG~~-----------~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 75 (94)
T PF00867_consen 12 YEAEAQCA----YLERNGLVD-AVITEDSDLLLFGAP-----------KVIRKLSDKSSGKCSSKSEKEVEVIDLDDILK 75 (94)
T ss_dssp S-HHHHHH----HHHHTTSSS-EEE-SSSHHHHTT-S-----------EEEESST-CSCCSTS-CCESEEEEEEHHHHHH
T ss_pred chHHHHHH----HHHHhccee-EEEecCCCEEeeCCC-----------EEEEeccccccCCcccccccceEEEEHHHHHH
Confidence 67887642 222455533 455999999888522 2333332 12 3478999999999
Q ss_pred hhcccccccccccccccCCc
Q psy7142 1099 NLGTEKSVALRGFHAFSGCD 1118 (1309)
Q Consensus 1099 ~lG~~~~~al~~~HAftGcD 1118 (1309)
.+|- ....+..+=.++|||
T Consensus 76 ~l~l-~~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 76 ELGL-TREQFIDLCILCGCD 94 (94)
T ss_dssp HHTT-SHHHHHHHHHHHHET
T ss_pred HcCC-CHHHHHHHheecCCC
Confidence 9873 333466667778887
No 32
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=26.30 E-value=3.3e+02 Score=29.76 Aligned_cols=56 Identities=18% Similarity=0.248 Sum_probs=36.7
Q ss_pred cceEEeccceeecccCCCCccchhh----hhHHHHHHHHHhhhcccCCCeeEEEEeccCCCC
Q psy7142 888 CDVVVCDGAALIHATPPRNSRTFEG----YCSQEFQRTIMGMIESCSADRIDVVWDLYFPDS 945 (1309)
Q Consensus 888 ~~~~IiDG~alvh~l~~~~~~tF~~----ya~~~f~~yv~~~~~~~~~~ridVVFD~Y~~~S 945 (1309)
..+.++||-=++-+ ||....++.. -|+..++.-+- .++++...+|-||||-+-.++
T Consensus 3 ~~iLLVDGYNmIga-Wp~Lk~lkd~~~LE~AR~~LIe~l~-~Y~s~~g~~iivVFDA~~v~g 62 (173)
T COG3688 3 MRILLVDGYNMIGA-WPELKQLKDRNGLEAARDKLIEALA-EYQSFTGYKIIVVFDAHYVPG 62 (173)
T ss_pred ceEEEeccchhccc-cHHHHHHHhhccHHHHHHHHHHHHH-HhhcccCceEEEEEEcccccc
Confidence 46788999866544 3334455554 56666665443 445678889999999886544
No 33
>PF12813 XPG_I_2: XPG domain containing
Probab=23.74 E-value=76 Score=36.37 Aligned_cols=69 Identities=20% Similarity=0.162 Sum_probs=45.7
Q ss_pred ccccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehh----hhhhhhhccCccceEEEc------cCCCceeeeehhHHH
Q psy7142 1028 FEEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAI----SFYFELKNYGLEELFVSL------NYGKKQRFFAAHEIA 1097 (1309)
Q Consensus 1028 hEEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l----~~~~~l~~~~~~~l~~~~------g~g~~~r~i~i~~i~ 1097 (1309)
..|||.-+..+|.+ -| ..|-|.|+|.+|.-+ ++.+. ..+.+.. +.+-..+.+....|+
T Consensus 27 ~~EAD~~~A~~A~~---~~---~~VLt~DSDf~I~dlg~~~~yipl------~~l~~~~~~~~~~~~~i~~~~y~~~~i~ 94 (246)
T PF12813_consen 27 PGEADRECAALARK---WG---CPVLTNDSDFLIHDLGQKGGYIPL------DSLEWDSVPKTGSGSYISAKVYSPDKIC 94 (246)
T ss_pred CccchHHHHHHHHH---cC---CeEEccCCCEEEeccCCCceEEEe------eeeEeecccccCCCCeeEEEEEcHHHHH
Confidence 46899988766644 23 378899999999987 22222 2233333 223346668999999
Q ss_pred Hhhccccccccccc
Q psy7142 1098 VNLGTEKSVALRGF 1111 (1309)
Q Consensus 1098 ~~lG~~~~~al~~~ 1111 (1309)
+.||.. .||.|
T Consensus 95 ~~l~l~---~Lp~l 105 (246)
T PF12813_consen 95 KRLGLP---LLPLL 105 (246)
T ss_pred HHcCCc---hhHHH
Confidence 999887 66555
No 34
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=21.18 E-value=2e+02 Score=27.10 Aligned_cols=57 Identities=19% Similarity=0.258 Sum_probs=34.4
Q ss_pred cccchHHHHHHHHHHhcCCeeEEEEecCCCeeeehhhhhhhhhccCccceEEEccC----CCceeeeehhHHHHhhc
Q psy7142 1029 EEADGRIILHIRDAVLQGAKKVLVRTVDTDVAVLAISFYFELKNYGLEELFVSLNY----GKKQRFFAAHEIAVNLG 1101 (1309)
Q Consensus 1029 EEADTrIilHa~~a~~~g~~~vvI~t~DTDVlVi~l~~~~~l~~~~~~~l~~~~g~----g~~~r~i~i~~i~~~lG 1101 (1309)
.||+.... .-.++|. .=.|.|+|+|+++.+.- .++..+-. +..++.|+..++.+.||
T Consensus 12 ~eAeAq~A----~L~~~g~-vdav~s~D~D~llfG~~-----------~vi~~~~~~~~~~~~~~~i~~~~vl~~L~ 72 (73)
T smart00484 12 YEAEAQCA----YLAKSGL-VDAIITEDSDLLLFGAP-----------RLYRNLFFSGKKKLEFRIIDLESVLKELG 72 (73)
T ss_pred CcHHHHHH----HHHhCCC-eeEEEcCccceEecCCc-----------EEEEecccCCCcccCeEEEEHHHHHHHcC
Confidence 47776532 2223443 22678999999988632 23322222 23588999988888875
Done!