Query 001233
Match_columns 1118
No_of_seqs 276 out of 562
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 19:25:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001233.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001233hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2044 5'-3' exonuclease HKE1 100.0 8E-270 2E-274 2298.9 63.9 806 1-864 1-810 (931)
2 COG5049 XRN1 5'-3' exonuclease 100.0 6E-216 1E-220 1827.5 51.4 771 1-821 1-818 (953)
3 KOG2045 5'-3' exonuclease XRN1 100.0 3E-184 6E-189 1586.0 38.6 640 1-719 1-655 (1493)
4 PF03159 XRN_N: XRN 5'-3' exon 100.0 5.5E-85 1.2E-89 698.8 17.4 237 1-255 1-237 (237)
5 cd00128 XPG Xeroderma pigmento 98.5 1.2E-06 2.6E-11 98.6 13.7 230 1-356 1-233 (316)
6 PTZ00217 flap endonuclease-1; 98.1 4.8E-05 1.1E-09 88.8 15.1 232 1-357 1-246 (393)
7 KOG2044 5'-3' exonuclease HKE1 97.7 0.00076 1.6E-08 82.7 16.7 88 781-871 702-791 (931)
8 PRK03980 flap endonuclease-1; 97.2 0.0086 1.9E-07 67.8 16.4 24 334-357 177-200 (292)
9 TIGR03674 fen_arch flap struct 96.8 0.021 4.6E-07 65.8 14.6 66 50-119 23-96 (338)
10 cd00008 53EXOc 5'-3' exonuclea 95.3 2.4 5.3E-05 46.8 21.1 57 50-107 3-62 (240)
11 smart00475 53EXOc 5'-3' exonuc 94.9 1.3 2.8E-05 49.7 17.5 56 51-107 4-61 (259)
12 PF00752 XPG_N: XPG N-terminal 93.6 0.06 1.3E-06 51.1 3.3 94 1-120 1-97 (101)
13 PRK14976 5'-3' exonuclease; Pr 92.8 2.6 5.7E-05 47.8 15.3 57 50-107 5-67 (281)
14 PF00867 XPG_I: XPG I-region; 91.6 0.44 9.6E-06 45.2 6.1 90 191-346 5-94 (94)
15 smart00485 XPGN Xeroderma pigm 90.8 0.54 1.2E-05 44.7 5.9 93 1-121 1-96 (99)
16 PF00098 zf-CCHC: Zinc knuckle 89.6 0.2 4.4E-06 34.5 1.4 17 262-278 1-17 (18)
17 COG0258 Exo 5'-3' exonuclease 85.8 35 0.00075 39.2 17.3 62 50-115 13-82 (310)
18 PRK05755 DNA polymerase I; Pro 85.5 22 0.00047 46.6 17.2 55 50-105 4-61 (880)
19 KOG2519 5'-3' exonuclease [Rep 84.4 14 0.0003 44.6 13.4 34 334-369 217-250 (449)
20 KOG2518 5'-3' exonuclease [Rep 83.5 4.5 9.8E-05 49.3 9.1 91 1-122 1-97 (556)
21 KOG0921 Dosage compensation co 77.9 23 0.0005 46.1 12.7 13 848-860 1119-1131(1282)
22 PF13696 zf-CCHC_2: Zinc knuck 72.7 1.5 3.2E-05 34.8 0.5 18 262-279 9-26 (32)
23 TIGR00593 pola DNA polymerase 71.0 1.2E+02 0.0026 40.1 17.2 56 51-107 2-61 (887)
24 TIGR00600 rad2 DNA excision re 70.2 6.3 0.00014 51.9 5.7 40 190-242 785-824 (1034)
25 KOG1984 Vesicle coat complex C 60.3 3.7E+02 0.008 35.7 17.7 10 1058-1067 220-229 (1007)
26 TIGR00600 rad2 DNA excision re 58.9 32 0.00069 45.8 8.8 90 1-120 1-94 (1034)
27 smart00157 PRP Major prion pro 48.5 43 0.00093 36.4 6.3 33 972-1009 6-38 (217)
28 cd00080 HhH2_motif Helix-hairp 47.2 19 0.0004 33.2 3.0 22 334-355 8-31 (75)
29 smart00343 ZnF_C2HC zinc finge 34.3 19 0.00042 26.4 0.9 16 263-278 1-16 (26)
30 smart00279 HhH2 Helix-hairpin- 33.6 31 0.00067 27.9 2.0 20 334-354 2-21 (36)
31 PF15288 zf-CCHC_6: Zinc knuck 31.8 23 0.0005 29.6 1.0 15 262-276 2-16 (40)
32 PF02739 5_3_exonuc_N: 5'-3' e 30.2 1.7E+02 0.0036 31.1 7.3 56 51-107 4-63 (169)
33 KOG4661 Hsp27-ERE-TATA-binding 29.8 5.9E+02 0.013 32.3 12.3 54 1013-1069 861-915 (940)
34 PF12287 Caprin-1_C: Cytoplasm 28.3 3.5E+02 0.0075 31.8 9.7 16 972-987 225-240 (316)
35 PF13917 zf-CCHC_3: Zinc knuck 27.3 34 0.00073 28.8 1.2 19 261-279 4-22 (42)
36 KOG0119 Splicing factor 1/bran 26.2 38 0.00082 41.5 1.9 92 167-283 214-307 (554)
37 smart00484 XPGI Xeroderma pigm 24.3 40 0.00086 31.2 1.3 35 200-243 10-44 (73)
38 PF14392 zf-CCHC_4: Zinc knuck 23.4 32 0.0007 29.2 0.5 20 259-278 29-48 (49)
39 KOG1924 RhoA GTPase effector D 23.0 1.5E+02 0.0031 38.6 5.9 10 205-214 209-218 (1102)
40 KOG0921 Dosage compensation co 22.7 5E+02 0.011 34.9 10.5 24 617-640 836-859 (1282)
41 smart00157 PRP Major prion pro 21.7 1.4E+02 0.003 32.8 4.7 8 979-986 23-30 (217)
42 COG5082 AIR1 Arginine methyltr 21.0 42 0.00091 36.6 0.8 18 261-278 60-77 (190)
No 1
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=100.00 E-value=8e-270 Score=2298.92 Aligned_cols=806 Identities=58% Similarity=0.976 Sum_probs=721.5
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQC 80 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe~~~~p~te~Emf~~ 80 (1118)
||||+|||||++|||++|++|+|++|+++||+.||+|.|+|||||+||||||||||||||||+|||++|+|+||+|||.+
T Consensus 1 MGVPaffRWLs~kyp~~I~~viEe~p~~~~g~~ip~D~s~pNPNg~E~DNLYLDMNGIIHPC~HPEdkPaP~tedEm~~a 80 (931)
T KOG2044|consen 1 MGVPAFFRWLSRKYPKTISPVIEEEPVDVDGVKIPVDYSKPNPNGVEFDNLYLDMNGIIHPCTHPEDKPAPETEDEMFVA 80 (931)
T ss_pred CCchHHHHHHHHhcchhhhhhhhcCcccCCCcccccccCCCCCCcccccceeeecCcccccCCCCCCCCCCccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccCcc
Q 001233 81 MFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSNVI 160 (1118)
Q Consensus 81 If~yIDrL~~~VRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~~g~~lp~~~~~~~fDSN~I 160 (1118)
||+||||||.||||||||||||||||||||||||||||||||||+.++++|++++++|++.+|..||++.++++||||||
T Consensus 81 vFeyiDrlf~mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fDSNcI 160 (931)
T KOG2044|consen 81 VFEYIDRLFSMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFDSNCI 160 (931)
T ss_pred HHHHHHHHHHhccchheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhccccccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHH
Q 001233 161 TPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLA 240 (1118)
Q Consensus 161 TPGT~FM~~L~~~L~~yI~~kl~~Dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~ 240 (1118)
||||+||++|+.+|+|||+.|||+||+|+||+||||||+||||||||||+|||+||++|+|||||+|||||+||||||||
T Consensus 161 TPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImLg 240 (931)
T KOG2044|consen 161 TPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLG 240 (931)
T ss_pred CCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccceeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCceEEEeecccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHHhcC
Q 001233 241 LATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRI 320 (1118)
Q Consensus 241 LatHep~f~ILRE~V~~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~~~~~~~~~~~~~f~~l~I~vLREYL~~el~~ 320 (1118)
|||||+||+||||+|| |+++++|++|||+||.+++|.|+.+ .++.++..+.. ..+++|+||+||||||||+.||.+
T Consensus 241 LATHE~hF~IlRE~~~-P~~~~~C~~cgq~gh~~~dc~g~~~--~~~~~~~~~~~-~~ek~fifl~I~vLREYLe~El~~ 316 (931)
T KOG2044|consen 241 LATHEPHFSILREEFF-PNKPRRCFLCGQTGHEAKDCEGKPR--LGETNELADVP-GVEKPFIFLNISVLREYLERELRM 316 (931)
T ss_pred ccccCCceEEeeeeec-CCCcccchhhcccCCcHhhcCCcCC--cccccccccCc-ccccceEEEEHHHHHHHHHHHhcC
Confidence 9999999999999976 9999999999999999999999866 66667666655 789999999999999999999999
Q ss_pred CCCCCccchhhhhhHHHHhhhhcccCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHHHhhh
Q 001233 321 PNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAVGSY 400 (1118)
Q Consensus 321 ~~~pf~~dlERiIDDfVfLcffvGNDFLPhLPsL~IreGaID~Li~iYK~~L~~~ggYLT~~G~INl~rl~~fl~~L~~~ 400 (1118)
|++||.||+||+||||||||||||||||||||||+|||||||+|+++||++|++|+||||++|.|||.||+.||+.||..
T Consensus 317 p~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeIRegAId~L~~iyk~~~~~~kgYLT~~g~vNL~rve~~~~avg~~ 396 (931)
T KOG2044|consen 317 PNLPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEIREGAIDRLMEIYKKSFPKMKGYLTDSGKVNLDRVEMFMQAVGSV 396 (931)
T ss_pred CCCCccccHHhhhcceEEEEeeecCccCCCCCchhhhhcHHHHHHHHHHHHHHhhcceeccCCcccHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCccccccccCCCCCCCCCCCCCcccccccccCCCCCCCCCC
Q 001233 401 EDRIFQKRARLHQRHAERIKREKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPSPSPYQQSECVGRLDNGKGTSGRP 480 (1118)
Q Consensus 401 Ed~iF~~r~~~e~r~~e~~kr~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 480 (1118)
||+||++|. |++|+++|+|+..++.++.+ ++++ .+.++.....+ .++...
T Consensus 397 Ed~IFkkR~----r~~e~frrrk~~rk~~~~~~------------~~sg-~~~~~~~~~~~-------------~~~~p~ 446 (931)
T KOG2044|consen 397 EDDIFKKRQ----RREERFRRRKAARKRQDRNA------------QDSG-TNFSLAGSREL-------------EASEPA 446 (931)
T ss_pred cchHHHHhH----hHHHHHHHhhhhhhhhhhhc------------cccc-ccccccccccc-------------cccchh
Confidence 999999994 45566666555433332221 1122 11111111000 011223
Q ss_pred CcccccCCCcchhhHHHhhhccCCCCccccHHHHHHHHHHHHhhhcccCCCCCchhhhhccCCCchhHHHHHHhcCCCCh
Q 001233 481 HKVPRLSSGATIGAAIVEAENSFETDPQENKEEFKAKLKELLRDKSDAFNSDNPEEDKVKLGEPGWKERYYEEKFNAKTP 560 (1118)
Q Consensus 481 ~k~~~~s~~~~~~~~~~~~e~~~~~~~~~~~e~lk~~l~~~~~~k~d~~~~~~~~eD~VkL~e~g~K~rYY~~KF~v~~~ 560 (1118)
+++.+++..++.++++++ .+++++++.+++..++++++.+++++..+|+|||||+|||+|||++||++++.
T Consensus 447 ~~~~~~~~~~~~~~~~~~---------~~~~e~~~~~~~~~~~~k~~~~~~~~~~~D~VkL~e~G~keRYY~~KF~v~~~ 517 (931)
T KOG2044|consen 447 QKALKVSLEKNESAANVE---------RDNTEDLKTKLKHGQRRKSEDSESEEENTDKVKLYEPGWKERYYEEKFDVTPD 517 (931)
T ss_pred hhhhhhccccccchhhhc---------ccchhhccccccccccccCccccCCCCCCcceeecCCchhhhhhhhhcCCCCH
Confidence 344555555666666653 34566788888888888998888999999999999999999999999999876
Q ss_pred hHHHHHHHHHHHHHHhhHHHHhhhhccCcCcccccccCCCCcccccccccccccceecCCCCCChhhhhhhcCCCCCCCC
Q 001233 561 EEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHA 640 (1118)
Q Consensus 561 ~di~~~r~~vv~~YvEGL~WVL~YYyqGcpSW~WYYPYHYAPfaSDl~~l~~~~i~Fe~G~Pf~PfEQLMsVLPaaS~~~ 640 (1118)
+ ++||++||++|||||||||+|||||||||+||||||||||||||++|..++|+|++|+||+||||||+||||||+++
T Consensus 518 e--eq~R~~vv~~YveGLcWVl~YYyqGc~SW~WyYPYHYAPfAsDf~~l~~ldikFe~g~PFkP~eQLmgVlPAAS~~~ 595 (931)
T KOG2044|consen 518 E--EQIRKDVVLKYVEGLCWVLRYYYQGCASWNWYYPYHYAPFASDFKGLSDLDIKFELGKPFKPLEQLMGVLPAASSHA 595 (931)
T ss_pred H--HHHHHHHHHHHhcchhhhhhhhhccccccccccccccchhhhhhhcccccccccccCCCCCcHHHHhhhcchhhcCC
Confidence 6 78999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeeccCCChHHHHHHHHhhcCCCCHHHHhhccCCCceEEeecC
Q 001233 641 LPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLFVLLS 720 (1118)
Q Consensus 641 LP~~~r~LMtdp~SpIiDFYP~dF~IDlNGKk~~WqGVaLLPFIDe~rLl~a~~~~~~~LT~eE~~RN~~g~d~Lfv~~~ 720 (1118)
||+.|++||+||+||||||||+||+||||||||+||||||||||||+|||+|+++++++||+||++||+.|.|+|||+.+
T Consensus 596 LPe~~r~LMsdpdSpIiDFYPedF~iDmNGKk~aWQGIalLPFiDe~rLl~a~~~~y~~Lt~EE~~RN~rg~d~Lfi~~~ 675 (931)
T KOG2044|consen 596 LPEEWRKLMSDPDSPIIDFYPEDFEIDMNGKKYAWQGIALLPFIDERRLLSAVAKVYPTLTDEEKRRNSRGPDLLFISDK 675 (931)
T ss_pred CcHHHHhhhcCCCCcccccccccceeeccCceeeccccccccccchhhHHHHHHhhccccCHHHHhccccCCceEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcchhhhhhhhHhhhhhhhhhhhhhhccCCCCCCceeecCCCCCCCCCcccCCCCCCcCccCCceEEEEEeCCCCCCC-
Q 001233 721 HPLSASIYTLDEHCKQLKIKERVEVKERLNPDDGMNGYISPCAGDPHPPVFRSPVASMEDIMGNQVLCAIYKLPDAHKH- 799 (1118)
Q Consensus 721 ~~l~~~i~~l~~~~~~~~~~~~~~~~~~id~~~Gm~G~v~~~~~~~~~~~~~sP~~~l~dI~~n~~~~~~y~~P~~~~h- 799 (1118)
||++++|.+||..+++ ...++..+...++ .|++|.++++.......+++||+..+.++..+..++++|..|..+..
T Consensus 676 hp~~e~i~~lysk~k~-~~~~~v~~~~~~~--p~~~~~~~~~~~~~~~~i~~~p~~~~~~~~~~~~v~~~~~~~~~~ed~ 752 (931)
T KOG2044|consen 676 HPLFEFILQLYSKKKK-SNEKNVKLAHGVD--PGLNGAISKDPEGLESGISKSPPGGLSDYNTNTGVCLKYVDPEYPEDY 752 (931)
T ss_pred CchHHHHHHHHHhhcc-CcccccccccccC--cccceeeccCccccccccccCChhhcccCCccceeeecccCccccccc
Confidence 9999999999988766 3333334443443 58999999988665467888999999999999999999999987422
Q ss_pred --CCCCCCCCccCCCCCCcccCCCCCccccCCCCCCCCCCC-CCCCCCCCCCCccChHHHHHHHhhhc
Q 001233 800 --VTRPPAGVIFPKKIVQLEDLKPAPVLWHEDSGRRPHENG-RHNPHGTISGRQLGEAAHRLVANSLQ 864 (1118)
Q Consensus 800 --~s~ll~g~~~p~~~l~~~d~~~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~l~~a~~r~~~~~~~ 864 (1118)
.++.|+|++.|.++|+ |-||...++ ..+.++ +|+.. ..+..+.+++||.|.+.+.
T Consensus 753 ~~~a~~l~G~~~p~~~lk-------P~dwn~sR~-~~~~~~~~~~~~--~~~~~~~~~~~~~v~~~~~ 810 (931)
T KOG2044|consen 753 IFPAIRLDGAKEPEKVLK-------PDDWNDRRD-GRYQPQAGFNRN--APRGSLPQSGHRQVHHYVR 810 (931)
T ss_pred cchhhhcCCCCCCccccC-------cchhhhhhh-hhcCcccccccC--CCCCcCCcccccccCcCCC
Confidence 4788889999988888 346765433 224444 66665 4478999999999888887
No 2
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=100.00 E-value=5.8e-216 Score=1827.49 Aligned_cols=771 Identities=44% Similarity=0.775 Sum_probs=608.3
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQC 80 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe~~~~p~te~Emf~~ 80 (1118)
||||+|||||++|||+||+.+.|+ +|| +|||||||||||||+|+||+++++|.||+||+.+
T Consensus 1 MGVPsfFRwlS~r~p~ii~~I~e~----------------~~P---~~DNLYLDMNgIlH~CtHp~d~~~petEeEm~~a 61 (953)
T COG5049 1 MGVPSFFRWLSERYPKIIQLIEEK----------------QIP---EFDNLYLDMNGILHNCTHPNDGSPPETEEEMYKA 61 (953)
T ss_pred CCchHHHHHHHhhhhHhhhhhhcc----------------CCC---CcceeEEecccccccCCCCCCCCCCCCHHHHHHH
Confidence 999999999999999999987653 345 4699999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHHHHHHHHHHHHHHHHh----CCCCCC-CCCCCCC
Q 001233 81 MFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFERE----GRKLPP-KSDSQVF 155 (1118)
Q Consensus 81 If~yIDrL~~~VRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~~----g~~lp~-~~~~~~f 155 (1118)
||+|||+|+.++|||||||||||||||||||||||+||||+|+||..++.+++.-.+++..+ |..+.. ...++.|
T Consensus 62 Vf~Yidhil~~irPrKllymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~f 141 (953)
T COG5049 62 VFEYIDHILLKIRPRKLLYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKF 141 (953)
T ss_pred HHHHHHHHHHhcCcceEEEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccccCCccchhhhhhccc
Confidence 99999999999999999999999999999999999999999999877665554333333332 222222 1346789
Q ss_pred ccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChh
Q 001233 156 DSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDAD 235 (1118)
Q Consensus 156 DSN~ITPGT~FM~~L~~~L~~yI~~kl~~Dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDAD 235 (1118)
|||||||||+||++|++.|+|||+.||++||.|+|++|||||+.||||||||||+|||+||++|+|+|||+|||||+|||
T Consensus 142 DSNcITPGTpFMerLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDAD 221 (953)
T COG5049 142 DSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDAD 221 (953)
T ss_pred cccCCCCCChHHHHHHHHHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCceEEEeecccccCCC---CCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHH
Q 001233 236 LIMLALATHEVHFSILREVVFTPGQ---QDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLRE 312 (1118)
Q Consensus 236 LImL~LatHep~f~ILRE~V~~~~~---~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~~~~~~~~~~~~~f~~l~I~vLRE 312 (1118)
||||||+||+|||.||||+|||+.. .++|..||.+||....|. .....+|.||||++|||
T Consensus 222 LImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~~k-----------------~~~~q~F~~LhiSlLRE 284 (953)
T COG5049 222 LIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECK-----------------VLTHQPFYLLHISLLRE 284 (953)
T ss_pred ceeeecccCCCeeEEeechhccCcccccccccccccccccchhhhc-----------------ccccCceEEEEHHHHHH
Confidence 9999999999999999999999853 458999999999888873 23457899999999999
Q ss_pred HHHHHhcCCCCCCccchhhhhhHHHHhhhhcccCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHH
Q 001233 313 YLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEH 392 (1118)
Q Consensus 313 YL~~el~~~~~pf~~dlERiIDDfVfLcffvGNDFLPhLPsL~IreGaID~Li~iYK~~L~~~ggYLT~~G~INl~rl~~ 392 (1118)
||+.||..+++||.||+|||||||||||||||||||||||+|+|++|||++|++|||+.|+.||||||++|.|||.||+.
T Consensus 285 YLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldir~gai~~l~ei~k~~lp~~~gYit~~G~iNl~rle~ 364 (953)
T COG5049 285 YLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDIREGAIETLTEIWKKSLPHMKGYITCDGVINLARLEV 364 (953)
T ss_pred HHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccccccchHHHHHHHHHHHhhhcCceeecCceecHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcC--CCCCCCC---CCCC---ccc--cccccCCCCCCCCCCCCCc
Q 001233 393 FIQAVGSYEDRIFQKRARLHQRHAERIKREKAQARRG--DDVEPLA---QPDS---LVP--VSRFHGSRLASGPSPSPYQ 462 (1118)
Q Consensus 393 fl~~L~~~Ed~iF~~r~~~e~r~~e~~kr~k~~~~~~--~~~~~~~---~~~~---~~p--~~~~~~~~l~~~~~~~~~~ 462 (1118)
||..|+.+|+.||+++..+++|..+...+.+.++.+. ....+.+ +.+. +.+ +..+...+-...+.+. +
T Consensus 365 ~L~~L~~~E~~iFk~~~~qe~r~ne~~~~~~~~k~~~e~~~~~~~vv~eq~~~~gS~k~t~~d~~~~kk~~~l~~e~-~- 442 (953)
T COG5049 365 ILAILGSFEDDIFKKDHIQEERKNESLERFSLRKERKEGLKGMPRVVYEQKKLIGSIKPTLMDQLQEKKSPDLPDEE-F- 442 (953)
T ss_pred HHHHHhhhhcchhhhhhhHhhhhccchhhHHHHhhhhhhhcccchhhhhhhhhcccccchhhhhhhhhccccCCCcc-c-
Confidence 9999999999999999988877776666554443221 1111100 1000 000 0000000000000000 0
Q ss_pred ccccccccCCCCCCCCCCCc-c-cccC--CCcchhhHHHhh-----hccC-CCCccccHHHHH--HHH-HHHHhhh-ccc
Q 001233 463 QSECVGRLDNGKGTSGRPHK-V-PRLS--SGATIGAAIVEA-----ENSF-ETDPQENKEEFK--AKL-KELLRDK-SDA 528 (1118)
Q Consensus 463 ~~~~~~~~~~~~~~~~~~~k-~-~~~s--~~~~~~~~~~~~-----e~~~-~~~~~~~~e~lk--~~l-~~~~~~k-~d~ 528 (1118)
.+.+..-+..+...+. . .++. .+..++.++... +... .....+.+++.+ ... .++.++. ++.
T Consensus 443 ----id~~a~~k~~d~kn~el~~~~~~ndl~ls~ska~ks~~n~~le~~iasds~~ed~ee~ese~d~i~~i~dk~vn~~ 518 (953)
T COG5049 443 ----IDTLALPKDLDMKNHELFLKRFANDLGLSISKAIKSKGNYSLEMDIASDSPDEDEEEFESEVDSIRKIPDKYVNII 518 (953)
T ss_pred ----cchhhchhhhhhhhhHHHHHHHHhhhhhhHHhhhhccCCchhhhhhhccccccchhhhhhccchhhhhhhhhhccc
Confidence 0000000000000000 0 0000 000111110000 0000 000000111111 000 1111111 111
Q ss_pred --CCCCCchhhhhccCCCchhHHHHHHhcCCCChhHHHHHHHHHHHHHHhhHHHHhhhhccCcCcccccccCCCCccccc
Q 001233 529 --FNSDNPEEDKVKLGEPGWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASD 606 (1118)
Q Consensus 529 --~~~~~~~eD~VkL~e~g~K~rYY~~KF~v~~~~di~~~r~~vv~~YvEGL~WVL~YYyqGcpSW~WYYPYHYAPfaSD 606 (1118)
...++..+++|+|.++|||+|||.+||++++ ++.+++| ++|++|||||||||.|||+|||||+|||||||||+|+|
T Consensus 519 v~ee~e~~~~~Tv~l~~~g~~erYY~~K~~~t~-~~~E~ir-dm~k~YVeGL~WVL~YYY~GC~SW~WyYpyHyAP~aaD 596 (953)
T COG5049 519 VEEEEENETEKTVNLRFPGWKERYYTSKLHFTT-DSEEKIR-DMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAAD 596 (953)
T ss_pred cccchhcccccchhhcccchhhhhhhhhcCCCc-CCHHHHH-HHHHHHhhhhhhhhhhhhcCCCCcccccccccchhhhh
Confidence 1223455789999999999999999999965 4556775 89999999999999999999999999999999999999
Q ss_pred ccccccccceecCCCCCChhhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeeccCCCh
Q 001233 607 LKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDE 686 (1118)
Q Consensus 607 l~~l~~~~i~Fe~G~Pf~PfEQLMsVLPaaS~~~LP~~~r~LMtdp~SpIiDFYP~dF~IDlNGKk~~WqGVaLLPFIDe 686 (1118)
|.++...+|+|++|+||+||||||+||||+|+++||++||.||+|++||||||||++|.+|||||+++||||||||||||
T Consensus 597 ~~k~~~~dIkFe~g~PF~P~EQLm~VLPa~Sk~~vP~~fr~LM~d~~S~IiDFYPe~f~lD~NGK~~~Wq~VvLlpFiDe 676 (953)
T COG5049 597 LSKLSDNDIKFELGTPFRPFEQLMAVLPARSKNLVPEGFRPLMDDEKSPIIDFYPEEFKLDMNGKTASWQAVVLLPFIDE 676 (953)
T ss_pred hhhcccceeeecCCCCCCcHHHHHhhcchhhcCcCchhhhhhhcCCCCcccccchhhcccccCCceeeeeeeEEeeecch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCCCCHHHHhhccCCCceEEeecCCCcchhhhhhhhHhhhhhhhhhhhhhhccCCC---CCCceeecCCC
Q 001233 687 ARLLDEVKKIEHTLTEEEARRNSIMADMLFVLLSHPLSASIYTLDEHCKQLKIKERVEVKERLNPD---DGMNGYISPCA 763 (1118)
Q Consensus 687 ~rLl~a~~~~~~~LT~eE~~RN~~g~d~Lfv~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~id~~---~Gm~G~v~~~~ 763 (1118)
+|||+||+..+++||+||++||.+|.++||+++.++.. ...++.+++++.....+.++.+ .|+.|.|.+..
T Consensus 677 ~RLl~A~~~~~~~Ls~eE~~RN~~g~~llf~s~~~~~~------~~l~~~lysk~~~~~~~~m~~~~~~~GL~g~v~~~a 750 (953)
T COG5049 677 RRLLSAVAVKYPTLSEEERKRNLRGLDLLFSSNKKSDL------SELFKDLYSKCKQKEYITMCSKESPYGLFGTVKLGA 750 (953)
T ss_pred hHHHHHHHhhcccCCHHHHhccccCCceeEeccCCccH------HHHHHHHHHhhccCCceeeecccccccccccccccc
Confidence 99999999999999999999999999999999988742 2334445554433323334433 69999998863
Q ss_pred -CCCCCCcccCCCC--C------CcCccCCceEEEEEeCCCC-CCCCCCCCCCCccCCCCCCcccCCC
Q 001233 764 -GDPHPPVFRSPVA--S------MEDIMGNQVLCAIYKLPDA-HKHVTRPPAGVIFPKKIVQLEDLKP 821 (1118)
Q Consensus 764 -~~~~~~~~~sP~~--~------l~dI~~n~~~~~~y~~P~~-~~h~s~ll~g~~~p~~~l~~~d~~~ 821 (1118)
+..+...+.+|+. . .-.+..|+++.+.+++|.. ..|++++++||+.|-.+|++-+++.
T Consensus 751 e~~~pn~~~lcp~~~~s~~~l~~~~~~~~n~S~~lv~~~pks~~~~ksi~~rg~~~~~~vl~py~~es 818 (953)
T COG5049 751 EGLAPNLLSLCPISFLSYPGLMVFLEYSKNQSARLVIEDPKSTVTNKSIVLRGFIKPINVLWPYLRES 818 (953)
T ss_pred ccccccccccCccccccccchhhhcccccCCceEEEeeccccccchHHHHHHhcCCccccCCHHHHHH
Confidence 3344455566773 2 2236678999999999985 5889999999999999999877763
No 3
>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=100.00 E-value=3e-184 Score=1585.98 Aligned_cols=640 Identities=44% Similarity=0.779 Sum_probs=502.5
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCC--CCCCHHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRP--APTTFDEVF 78 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe~~~--~p~te~Emf 78 (1118)
||||.||||+++|||++.. +|| +.+|| ||||||||||||||+|+|++|.. .+.||||||
T Consensus 1 MGvPKFfR~iSERyP~lse-lie-------e~qIP-----------EFDNLYLDMNgIlHNCsH~nDddvt~rLtEeEif 61 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCLSE-LIE-------EHQIP-----------EFDNLYLDMNGILHNCSHPNDDDVTFRLTEEEIF 61 (1493)
T ss_pred CCchHHHHHhhhhchHHHH-Hhh-------hccCC-----------cccceeeecccccccCCCCCCCccCcCCCHHHHH
Confidence 9999999999999999864 454 46787 99999999999999999998753 478999999
Q ss_pred HHHHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccC
Q 001233 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSN 158 (1118)
Q Consensus 79 ~~If~yIDrL~~~VRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~~g~~lp~~~~~~~fDSN 158 (1118)
.+||+|||+||.+|||+||+|||||||||||||||||+||||+|++|+.+.++ ....|+..|. +.||||
T Consensus 62 ~~IfnYIdhLf~~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaK-------A~enGe~~p~----erFDSN 130 (1493)
T KOG2045|consen 62 QEIFNYIDHLFYLIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAK-------AAENGELRPH----ERFDSN 130 (1493)
T ss_pred HHHHHHHHHHHHhhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHH-------HHhccccCcc----cccccC
Confidence 99999999999999999999999999999999999999999999998765433 3356766653 689999
Q ss_pred cccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHH
Q 001233 159 VITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238 (1118)
Q Consensus 159 ~ITPGT~FM~~L~~~L~~yI~~kl~~Dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLIm 238 (1118)
||||||+||.+|++.|+|||+.|++||+.|++++|||||++||||||||||+|||.++++|+||||||||||||||||||
T Consensus 131 cITPGTeFM~rl~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLIm 210 (1493)
T KOG2045|consen 131 CITPGTEFMVRLQEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIM 210 (1493)
T ss_pred CCCCcHHHHHHHHHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhhe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCceEEEeecccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHHh
Q 001233 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEF 318 (1118)
Q Consensus 239 L~LatHep~f~ILRE~V~~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~~~~~~~~~~~~~f~~l~I~vLREYL~~el 318 (1118)
|||+||||||++|||+|.|..+. ++| ....+.|-+||+++|||||+.||
T Consensus 211 LGL~tHepHF~lLREEVtFgrrn--------------------~~k-----------~lehqkFyLLHLsLLREYlelEF 259 (1493)
T KOG2045|consen 211 LGLCTHEPHFVLLREEVTFGRRN--------------------KRK-----------SLEHQKFYLLHLSLLREYLELEF 259 (1493)
T ss_pred eeeccCCcceeeeeeeeeccccc--------------------ccc-----------hhhhhhhhhhHHHHHHHHHHHHH
Confidence 99999999999999999775211 111 12345799999999999999999
Q ss_pred cC--CCCCCccchhhhhhHHHHhhhhcccCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHH
Q 001233 319 RI--PNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQA 396 (1118)
Q Consensus 319 ~~--~~~pf~~dlERiIDDfVfLcffvGNDFLPhLPsL~IreGaID~Li~iYK~~L~~~ggYLT~~G~INl~rl~~fl~~ 396 (1118)
.- ...+|++|+||||||||+|.||||||||||||+|+|.+||+.+|+.+||+++|++||||+++|+|||.||+.||.+
T Consensus 260 ~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlpllystykkvlpt~~GyINE~G~lNl~Rle~~L~e 339 (1493)
T KOG2045|consen 260 DELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLLYSTYKKVLPTLGGYINENGKLNLRRLEIFLSE 339 (1493)
T ss_pred HHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHHHHHHHHHhccCCccccccceecHHHHHHHHHH
Confidence 84 3578999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCccccccccCCCCCCCCC----CCCCcccccccccCC
Q 001233 397 VGSYEDRIFQKRARLHQRHAERIKREKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPS----PSPYQQSECVGRLDN 472 (1118)
Q Consensus 397 L~~~Ed~iF~~r~~~e~r~~e~~kr~k~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~~~~----~~~~~~~~~~~~~~~ 472 (1118)
|..+|.++|+++.+..+.. + -||. +-++... +......+..+.++....... ..++.+.... + +
T Consensus 340 L~nfeke~Fke~led~k~~-n-skr~-----r~~~~~~--~~~~~~dika~t~sq~~d~l~~~~~~~p~i~~~a~--l-d 407 (1493)
T KOG2045|consen 340 LTNFEKEHFKEHLEDLKYM-N-SKRE-----RFDDPEQ--QELAEMDIKAITESQNLDSLLGEESKDPLINKSAL--L-D 407 (1493)
T ss_pred HHhhhHHHHHHHHHhhhhc-c-cccc-----ccccHHH--HhhhcccHHhhhhhhhhhhhccccccccccccccc--c-c
Confidence 9999999999987654311 1 1110 0000000 000000011111100000000 0000000000 0 0
Q ss_pred CCCCCCCCCcccccCCCcchh-hHHHhhhccCC-CCccccHHHHHHHHHHH-Hhhhccc-CCC--CCchhhhhccC-CCc
Q 001233 473 GKGTSGRPHKVPRLSSGATIG-AAIVEAENSFE-TDPQENKEEFKAKLKEL-LRDKSDA-FNS--DNPEEDKVKLG-EPG 545 (1118)
Q Consensus 473 ~~~~~~~~~k~~~~s~~~~~~-~~~~~~e~~~~-~~~~~~~e~lk~~l~~~-~~~k~d~-~~~--~~~~eD~VkL~-e~g 545 (1118)
.+ ...-+.+...+.... ..+...+..+. ...++.++|+...+.++ +..+++. +.. +...+.+|... ...
T Consensus 408 ~d----D~~Fl~~~~eDl~~~~~~s~s~~~~ld~~~~de~EdEf~~~~~t~~ls~~~~~~~~n~eea~~eKti~n~~F~r 483 (1493)
T KOG2045|consen 408 DD----DSAFLSDHEEDLSDLEPGSGSDELLLDNLDADELEDEFAVELATLALSGMNDADFANDEEACWEKTILNKEFQR 483 (1493)
T ss_pred cc----hHHHHHHhhhhccccccccCccchhhccccchhhhHHHHHHHHHHHHhccccccccchHHHhhhhhhHHHHHHH
Confidence 00 000000000000000 00000000000 00111122332222222 1111111 111 11222333322 346
Q ss_pred hhHHHHHHhcCCCChhHHHHHHHHHHHHHHhhHHHHhhhhccCcCcccccccCCCCcccccccccccccceecCCCCCCh
Q 001233 546 WKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKP 625 (1118)
Q Consensus 546 ~K~rYY~~KF~v~~~~di~~~r~~vv~~YvEGL~WVL~YYyqGcpSW~WYYPYHYAPfaSDl~~l~~~~i~Fe~G~Pf~P 625 (1118)
||..||++||+.++.+ ++..+++|..|||||+|||.|||+||+||+||||||||||+||+++..+++|.|++|+||+|
T Consensus 484 wK~~yYrdKlkf~~~d--ee~lrelae~YVeaLQWvL~YYYrGc~SWsWyYphHyaP~ISDl~kgldv~ieF~mgtPF~P 561 (1493)
T KOG2045|consen 484 WKRNYYRDKLKFDPND--EELLRELAEHYVEALQWVLDYYYRGCQSWSWYYPHHYAPFISDLKKGLDVEIEFHMGTPFLP 561 (1493)
T ss_pred HHHHHhhhhhcCCCcc--HHHHHHHHHHHHHHHHHHHHHHhcCCccccccccccccchhHhHhcccceeEEEecCCCCCc
Confidence 9999999999997655 45667899999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeeccCCChHHHHHHHHhhcCCCCHHHH
Q 001233 626 FNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEA 705 (1118)
Q Consensus 626 fEQLMsVLPaaS~~~LP~~~r~LMtdp~SpIiDFYP~dF~IDlNGKk~~WqGVaLLPFIDe~rLl~a~~~~~~~LT~eE~ 705 (1118)
|||||||||++|+.+||.+||+||.++.|||+||||.+|+.|+|||+.+|++|||||||||+|||+||.+++..||+||+
T Consensus 562 FqQLlAVLPaaSa~llPp~frdLM~~~~SPI~DFYPaefelD~NGKtadWEAVVLIpFIdEkRLleAm~pk~~~Ls~EEr 641 (1493)
T KOG2045|consen 562 FQQLLAVLPAASAKLLPPAFRDLMLLPTSPIADFYPAEFELDLNGKTADWEAVVLIPFIDEKRLLEAMLPKEAQLSLEER 641 (1493)
T ss_pred HHHHHHhchhhhhccCChhhhHhhcCCCCchhhcchhhheecccCCccceeEEEEEeecchHHHHHHHhhHhhhcCHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCceEEeec
Q 001233 706 RRNSIMADMLFVLL 719 (1118)
Q Consensus 706 ~RN~~g~d~Lfv~~ 719 (1118)
.||++|.+++|...
T Consensus 642 ~RNs~g~~~vys~~ 655 (1493)
T KOG2045|consen 642 ERNSHGPMYVYSYS 655 (1493)
T ss_pred hhcccCCceeeecc
Confidence 99999999999754
No 4
>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=100.00 E-value=5.5e-85 Score=698.85 Aligned_cols=237 Identities=60% Similarity=1.088 Sum_probs=194.2
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQC 80 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe~~~~p~te~Emf~~ 80 (1118)
||||+|||||++|||+++..+.+.. ...+|||||||||||||+|+|++..+.+.++++||.+
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~------------------~~~~~D~LYiDmN~IIH~~~~~~~~~~~~~~~~~~~~ 62 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENS------------------IPSEFDNLYIDMNGIIHNCIHPNDSSIPKTEEEIFQR 62 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTT------------------SEE-ESEEEEETHHHHHHHHS-SSS----SHHHHHHH
T ss_pred CCHHHHHHHHHHhCCcceeeccccC------------------CCCcCCEEEEEcchhhhHhcCCcccCCCccHHHHHHH
Confidence 9999999999999999998765431 1126999999999999999999988888999999999
Q ss_pred HHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCccCcc
Q 001233 81 MFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSNVI 160 (1118)
Q Consensus 81 If~yIDrL~~~VRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~l~~e~~~~g~~lp~~~~~~~fDSN~I 160 (1118)
||+|||+||.+|||||+||||||||||||||||||+|||+++++++....+.....++...+|..++.......||||||
T Consensus 63 i~~~id~l~~~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn~I 142 (237)
T PF03159_consen 63 IFNYIDRLVRIVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFDSNCI 142 (237)
T ss_dssp HHHHHHHHHHHH-ESSEEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS----GGGS
T ss_pred HHHHHHHhheeecCceEEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhcccccccccccccccccee
Confidence 99999999999999999999999999999999999999999999998888777778887777766665445678999999
Q ss_pred cCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHH
Q 001233 161 TPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLA 240 (1118)
Q Consensus 161 TPGT~FM~~L~~~L~~yI~~kl~~Dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~ 240 (1118)
||||+||.+|+++|++||..|+++|+.|++++|||||++||||||||||+|||+++++|+|+||++|||||+||||||||
T Consensus 143 TPGT~FM~~l~~~L~~~~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 143 TPGTEFMEKLSDALRYYIKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp STTSHHHHHHHHHHHHHHHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHHHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCceEEEeeccc
Q 001233 241 LATHEVHFSILREVV 255 (1118)
Q Consensus 241 LatHep~f~ILRE~V 255 (1118)
|+||+++|+||||+|
T Consensus 223 L~~~~~~~~ilre~~ 237 (237)
T PF03159_consen 223 LATHEPNIYILREEV 237 (237)
T ss_dssp HHTT-SSEEEEEESS
T ss_pred HccCCCeEEEEeccC
Confidence 999999999999975
No 5
>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=98.49 E-value=1.2e-06 Score=98.64 Aligned_cols=230 Identities=20% Similarity=0.316 Sum_probs=121.5
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCC--CCCCHHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRP--APTTFDEVF 78 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe~~~--~p~te~Emf 78 (1118)
|||++|..||...-+.+ . +++ .. | --|=||.+..||-+....... ........+
T Consensus 1 MGI~gL~~~l~~~~~~~--~-i~~----l~--------------g---k~laID~~~~l~r~~~a~~~~~~~~g~~~~~l 56 (316)
T cd00128 1 MGIKGLWPLLKPVARPV--H-LEE----LR--------------G---KKVAIDASIWLYQFLKACRQELGSGGETTSHL 56 (316)
T ss_pred CchhhHHHHHHhhCCCC--C-HHH----hC--------------C---cEEEecHHHHHHHHHHHhhhhccCCCCCcHHH
Confidence 99999999999876654 1 111 01 1 157899999999865432110 001112233
Q ss_pred HHHHHHHHHHHhhccccceEEEEecCCCchhhhHHHHhhhccchhHHHHHHHHHHH-HHHHHHHhCCCCCCCCCCCCCcc
Q 001233 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEER-LRQEFEREGRKLPPKSDSQVFDS 157 (1118)
Q Consensus 79 ~~If~yIDrL~~~VRPrKlLyiAIDGVAPRAKMNQQRsRRFrsakea~~~~~~~~~-l~~e~~~~g~~lp~~~~~~~fDS 157 (1118)
..++..+.+|+.. . -+ ..+++||.+|-.|......|+-+.....+......++ ..++..+... ..
T Consensus 57 ~~~~~rl~~L~~~-~-i~-pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~-----------~~ 122 (316)
T cd00128 57 QGFFYRTCRLLEL-G-IK-PVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLER-----------RA 122 (316)
T ss_pred HHHHHHHHHHHHC-C-CE-EEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHh-----------cc
Confidence 4444555555432 2 23 3467999999888877665554322111110000000 0001111000 11
Q ss_pred CcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHH
Q 001233 158 NVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLI 237 (1118)
Q Consensus 158 N~ITPGT~FM~~L~~~L~~yI~~kl~~Dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLI 237 (1118)
..|||.+ ... ++..+.. + ++.+|.+ |+|+|-=|--+-+. .....|++.|+|++
T Consensus 123 ~~~~~~~--~~~----~~~lL~~-~-------gi~~i~a----p~EAdaq~a~l~~~---------g~v~~i~S~DsD~l 175 (316)
T cd00128 123 VRVTPQM--IEE----AKELLRL-M-------GIPYIVA----PYEAEAQCAYLAKK---------GLVDAIITEDSDLL 175 (316)
T ss_pred CcCCHHH--HHH----HHHHHHH-c-------CCCEEEC----CcCHHHHHHHHHhC---------CCeeEEEecCCCee
Confidence 2244432 222 3333322 1 5677764 89999765544331 23578999999998
Q ss_pred HHHhhcCCceEEEeecccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHH
Q 001233 238 MLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYE 317 (1118)
Q Consensus 238 mL~LatHep~f~ILRE~V~~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~~~~~~~~~~~~~f~~l~I~vLREYL~~e 317 (1118)
+++ + ++ ++|-. +..+ ...+++++..-+.+.|
T Consensus 176 ~fg-~---~~--vi~~~-~~~~---------------------------------------~~~~~~~~~~~~~~~l--- 206 (316)
T cd00128 176 LFG-A---PR--VYRNL-FDSG---------------------------------------AKPVEEIDLEKILKEL--- 206 (316)
T ss_pred eec-C---ce--EEEec-ccCC---------------------------------------CCceEEEEHHHHHHHc---
Confidence 876 2 22 33321 0000 0135567766554443
Q ss_pred hcCCCCCCccchhhhhhHHHHhhhhcccCCCCCCCcccc
Q 001233 318 FRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEI 356 (1118)
Q Consensus 318 l~~~~~pf~~dlERiIDDfVfLcffvGNDFLPhLPsL~I 356 (1118)
. ++. +.||.+|.|+|+||+|.+|.+-+
T Consensus 207 -g-------l~~----~q~id~~~L~G~Dy~~gv~giG~ 233 (316)
T cd00128 207 -G-------LTR----EKLIDLAILLGCDYTEGIPGIGP 233 (316)
T ss_pred -C-------CCH----HHHHHHHHhcCCCCCCCCCCccH
Confidence 1 222 57889999999999999997654
No 6
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.08 E-value=4.8e-05 Score=88.75 Aligned_cols=232 Identities=21% Similarity=0.294 Sum_probs=124.7
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCC----CCCCCCCH--
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPE----DRPAPTTF-- 74 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe----~~~~p~te-- 74 (1118)
|||.++..+|....|.+++.+-= .+.-| =-|=||....||-....- +...-.+.
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l---~~l~g-----------------k~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G 60 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQEL---KNYFG-----------------RVIAIDASMALYQFLIAIRDDSQGGNLTNEAG 60 (393)
T ss_pred CChhhHHHHHhhhccccccccCH---HHhCC-----------------cEEEEeHHHHHHHHHHHcccccccccchhccC
Confidence 99999999999999988764310 00111 157889999988743211 00000010
Q ss_pred --HHHHHHHHHHHHHHHhh-ccccceEEEEecCCCchhhhHHHHhhh--ccchhHHHHHHHH---HHHHHHHHHHhCCCC
Q 001233 75 --DEVFQCMFDYIDRLFVM-VRPRKLLYMAIDGVAPRAKMNQQRSRR--FRASKDAADSAAE---EERLRQEFEREGRKL 146 (1118)
Q Consensus 75 --~Emf~~If~yIDrL~~~-VRPrKlLyiAIDGVAPRAKMNQQRsRR--Frsakea~~~~~~---~~~l~~e~~~~g~~l 146 (1118)
..-+.-+|..+-+|+.. ++| .+++||..|-.|...-..|| -..+.+..+...+ .+++++...
T Consensus 61 ~~t~~l~g~~~r~~~Ll~~gikP----v~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~------ 130 (393)
T PTZ00217 61 EVTSHISGLFNRTIRLLEAGIKP----VYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSK------ 130 (393)
T ss_pred CccHHHHHHHHHHHHHHHCCCCE----EEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHh------
Confidence 01234455556666664 778 47999999976665543333 2222221111000 011111100
Q ss_pred CCCCCCCCCccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCc
Q 001233 147 PPKSDSQVFDSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTR 226 (1118)
Q Consensus 147 p~~~~~~~fDSN~ITPGT~FM~~L~~~L~~yI~~kl~~Dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~ 226 (1118)
.+..|| .+-+..+.+.|+. -++.+|.+ |||+|-=|-...+ -+..
T Consensus 131 ---------r~~~vt--~~~~~~~~~lL~~------------~Gip~i~A----P~EAdaq~A~L~~---------~g~v 174 (393)
T PTZ00217 131 ---------RTVRVT--KEQNEDAKKLLRL------------MGIPVIEA----PCEAEAQCAELVK---------KGKV 174 (393)
T ss_pred ---------hcccCC--HHHHHHHHHHHHH------------cCCceEEC----CcCHHHHHHHHHH---------CCCe
Confidence 011233 1222333332221 14667765 8999995544432 2456
Q ss_pred EEEEecChhHHHHHhhcCCceEEEeecccccCCCCCcccccCCCCCcccccccccccccCCCCcCCCcccCCCCCeEEEe
Q 001233 227 HCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLH 306 (1118)
Q Consensus 227 HcIYGlDADLImL~LatHep~f~ILRE~V~~~~~~~~c~~cgQ~gH~~~~c~g~~k~k~~e~~~~~~~~~~~~~~f~~l~ 306 (1118)
.+|++-|.|+++++- + .++|-. +..+ ..+..+++++
T Consensus 175 ~~ViS~D~D~l~fg~----~--~vi~~l-~~~~-------------------------------------~~~~~~~~~~ 210 (393)
T PTZ00217 175 YAVATEDMDALTFGT----P--VLLRNL-NFSE-------------------------------------AKKRPIQEIN 210 (393)
T ss_pred EEEeCCCcCeeecCC----c--EEEEcc-cccc-------------------------------------cCCCCeEEEE
Confidence 789999999998862 1 244431 0000 0012466777
Q ss_pred hhHHHHHHHHHhcCCCCCCccchhhhhhHHHHhhhhcccCCCCCCCccccc
Q 001233 307 IWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIR 357 (1118)
Q Consensus 307 I~vLREYL~~el~~~~~pf~~dlERiIDDfVfLcffvGNDFLPhLPsL~Ir 357 (1118)
+..+.+.+ .++ -+.||-||.|+|.||+|.+|.+-..
T Consensus 211 ~~~v~~~~-----------gl~----~~q~id~~iL~G~Dy~pgi~GIG~k 246 (393)
T PTZ00217 211 LSTVLEEL-----------GLS----MDQFIDLCILCGCDYCDTIKGIGPK 246 (393)
T ss_pred HHHHHHHh-----------CCC----HHHHHHHHHHhCCCCCCCCCCccHH
Confidence 76654432 122 2578889999999999999987643
No 7
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=97.71 E-value=0.00076 Score=82.70 Aligned_cols=88 Identities=18% Similarity=0.088 Sum_probs=72.8
Q ss_pred ccCCceEEEEEeCCCCC-CCCCCCCCCCccCCCCCCcccCCCCCccccCCCCCCCCC-CCCCCCCCCCCCCccChHHHHH
Q 001233 781 IMGNQVLCAIYKLPDAH-KHVTRPPAGVIFPKKIVQLEDLKPAPVLWHEDSGRRPHE-NGRHNPHGTISGRQLGEAAHRL 858 (1118)
Q Consensus 781 I~~n~~~~~~y~~P~~~-~h~s~ll~g~~~p~~~l~~~d~~~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~l~~a~~r~ 858 (1118)
...-.+.++.|..|+.+ .||+..+.|.++|.++++..++....-+||++...+-.. +++.++.++++ +.|++++ |+
T Consensus 702 ~~~p~~~~~~~~~~~~~~~~i~~~p~~~~~~~~~~~~v~~~~~~~~~~ed~~~~a~~l~G~~~p~~~lk-P~dwn~s-R~ 779 (931)
T KOG2044|consen 702 GVDPGLNGAISKDPEGLESGISKSPPGGLSDYNTNTGVCLKYVDPEYPEDYIFPAIRLDGAKEPEKVLK-PDDWNDR-RD 779 (931)
T ss_pred ccCcccceeeccCccccccccccCChhhcccCCccceeeecccCccccccccchhhhcCCCCCCccccC-cchhhhh-hh
Confidence 33346788999999875 799999999999999999999999999999998755332 34778888888 9999999 99
Q ss_pred HHhhhcccccCCC
Q 001233 859 VANSLQHMKVDRN 871 (1118)
Q Consensus 859 ~~~~~~~~~~~~~ 871 (1118)
+.+.++ ++.++|
T Consensus 780 ~~~~~~-~~~~~~ 791 (931)
T KOG2044|consen 780 GRYQPQ-AGFNRN 791 (931)
T ss_pred hhcCcc-cccccC
Confidence 999998 665544
No 8
>PRK03980 flap endonuclease-1; Provisional
Probab=97.23 E-value=0.0086 Score=67.80 Aligned_cols=24 Identities=21% Similarity=0.521 Sum_probs=20.9
Q ss_pred hHHHHhhhhcccCCCCCCCccccc
Q 001233 334 DDFIFMCFFVGNDFLPHMPTLEIR 357 (1118)
Q Consensus 334 DDfVfLcffvGNDFLPhLPsL~Ir 357 (1118)
+.||-||.|+|.||+|.+|.+-+.
T Consensus 177 ~q~id~~iL~G~Dy~~GI~GIG~k 200 (292)
T PRK03980 177 EQLIDIAILVGTDYNPGIKGIGPK 200 (292)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHH
Confidence 567889999999999999987654
No 9
>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=96.78 E-value=0.021 Score=65.83 Aligned_cols=66 Identities=17% Similarity=0.186 Sum_probs=38.7
Q ss_pred eEEEeccccccccccCC---CCCCCCCH----HHHHHHHHHHHHHHHhh-ccccceEEEEecCCCchhhhHHHHhhhc
Q 001233 50 NLYLDMNGIIHPCFHPE---DRPAPTTF----DEVFQCMFDYIDRLFVM-VRPRKLLYMAIDGVAPRAKMNQQRSRRF 119 (1118)
Q Consensus 50 NLYLDMNGIIH~C~Hpe---~~~~p~te----~Emf~~If~yIDrL~~~-VRPrKlLyiAIDGVAPRAKMNQQRsRRF 119 (1118)
-|-||....||-+...- +...-++. ..-+..+|..+-+|+.. ++| .+++||.+|-.|...-..||-
T Consensus 23 ~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~P----v~VFDG~~p~~K~~~~~~R~~ 96 (338)
T TIGR03674 23 VVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKP----VYVFDGKPPELKAETLEERRE 96 (338)
T ss_pred EEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeE----EEEECCCChhhhHhhHHHHHH
Confidence 57799999999754421 11100000 01233344445555555 777 689999999877776666654
No 10
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=95.33 E-value=2.4 Score=46.81 Aligned_cols=57 Identities=9% Similarity=0.082 Sum_probs=37.4
Q ss_pred eEEEeccccccccccCCCCCCC---CCHHHHHHHHHHHHHHHHhhccccceEEEEecCCCc
Q 001233 50 NLYLDMNGIIHPCFHPEDRPAP---TTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (1118)
Q Consensus 50 NLYLDMNGIIH~C~Hpe~~~~p---~te~Emf~~If~yIDrL~~~VRPrKlLyiAIDGVAP 107 (1118)
-|.||.|.+|+-+.|....... -.......-++..|-+++...+|.++ .+|+||-.|
T Consensus 3 ~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~-~~~fD~~~~ 62 (240)
T cd00008 3 LLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYV-AVVFDAGGK 62 (240)
T ss_pred EEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeE-EEEEeCCCC
Confidence 3789999999998876421110 01122444555667777777889887 699999633
No 11
>smart00475 53EXOc 5'-3' exonuclease.
Probab=94.88 E-value=1.3 Score=49.70 Aligned_cols=56 Identities=9% Similarity=0.115 Sum_probs=35.1
Q ss_pred EEEeccccccccccCCCCC--CCCCHHHHHHHHHHHHHHHHhhccccceEEEEecCCCc
Q 001233 51 LYLDMNGIIHPCFHPEDRP--APTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (1118)
Q Consensus 51 LYLDMNGIIH~C~Hpe~~~--~p~te~Emf~~If~yIDrL~~~VRPrKlLyiAIDGVAP 107 (1118)
|-||.|.+|+-++|.-... ..-.......-++..+-+|+...+|..+ .+|+||-.|
T Consensus 4 llIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~-~~~fD~~~~ 61 (259)
T smart00475 4 LLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYV-AVVFDAKGK 61 (259)
T ss_pred EEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeE-EEEEeCCCC
Confidence 7899999999988863110 0001112334455566667777789775 599997544
No 12
>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=93.59 E-value=0.06 Score=51.10 Aligned_cols=94 Identities=21% Similarity=0.344 Sum_probs=55.8
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCC--HHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTT--FDEVF 78 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe~~~~p~t--e~Emf 78 (1118)
|||++|..+|.... .+..+- ..+..| --|=||.+..||.|.+......... .+..+
T Consensus 1 MGI~gL~~~l~~~~--~v~~~~---~~~l~g-----------------~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~ 58 (101)
T PF00752_consen 1 MGIKGLWQLLKPAA--AVRKVS---LSELRG-----------------KRVAIDASCWLHQFLFSCREELGQGVGTDSHL 58 (101)
T ss_dssp ---TTHHHHCHHHE--GEEEEE---GGGGTT-----------------CEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHH
T ss_pred CCcccHHHHHHhhc--cCCccC---HHHhCC-----------------CEEEEEcHHHHHHHHHHhHHHhccccchHHHH
Confidence 99999999999986 222110 001112 2577999999998755433221111 13556
Q ss_pred HHHHHHHHHHHh-hccccceEEEEecCCCchhhhHHHHhhhcc
Q 001233 79 QCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120 (1118)
Q Consensus 79 ~~If~yIDrL~~-~VRPrKlLyiAIDGVAPRAKMNQQRsRRFr 120 (1118)
..+|..+..|.. -|.| ++.+||.+|-+|......||-+
T Consensus 59 ~~~~~r~~~L~~~gI~P----ifVFDG~~~~~K~~~~~~R~~~ 97 (101)
T PF00752_consen 59 RGLFSRLCRLLEHGIKP----IFVFDGKPPPLKRETIQKRRKR 97 (101)
T ss_dssp HHHHHHHHHHHHTTEEE----EEEE--STTGGCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCEE----EEEECCCCchhhHHHHHHHHHH
Confidence 677777776654 4666 6899999999999888777654
No 13
>PRK14976 5'-3' exonuclease; Provisional
Probab=92.84 E-value=2.6 Score=47.84 Aligned_cols=57 Identities=16% Similarity=0.251 Sum_probs=37.1
Q ss_pred eEEEeccccccccccCCC--CCCCC----CHHHHHHHHHHHHHHHHhhccccceEEEEecCCCc
Q 001233 50 NLYLDMNGIIHPCFHPED--RPAPT----TFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (1118)
Q Consensus 50 NLYLDMNGIIH~C~Hpe~--~~~p~----te~Emf~~If~yIDrL~~~VRPrKlLyiAIDGVAP 107 (1118)
-|.||.|++|+-|++... .+.-+ .....+.-+++.|-+|+...+|..+ -+|+||-.|
T Consensus 5 ~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~-~v~fD~~~~ 67 (281)
T PRK14976 5 ALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYI-LIAFDAGRK 67 (281)
T ss_pred EEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEE-EEEEECCCC
Confidence 468999999999888731 11111 1123444556667777777789876 589998543
No 14
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=91.56 E-value=0.44 Score=45.19 Aligned_cols=90 Identities=20% Similarity=0.371 Sum_probs=55.0
Q ss_pred cEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEeecccccCCCCCcccccCCC
Q 001233 191 IKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQP 270 (1118)
Q Consensus 191 lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~LatHep~f~ILRE~V~~~~~~~~c~~cgQ~ 270 (1118)
+.+|+ .|||+|.=+--.-|. +.-+.|++-|+|+++.|-- .|||... .. ....|
T Consensus 5 v~~i~----AP~EAeAq~A~L~~~---------g~vd~V~t~DsD~l~fG~~------~vi~~~~-~~-~~~~~------ 57 (94)
T PF00867_consen 5 VPYIV----APYEAEAQCAYLERN---------GLVDAVITEDSDLLLFGAP------KVIRKLS-DK-SSGKC------ 57 (94)
T ss_dssp -EEEE-----SS-HHHHHHHHHHT---------TSSSEEE-SSSHHHHTT-S------EEEESST--C-SCCST------
T ss_pred CeEEE----cCchHHHHHHHHHHh---------cceeEEEecCCCEEeeCCC------EEEEecc-cc-ccCCc------
Confidence 45555 389999988866653 4578999999999999755 4777531 00 00011
Q ss_pred CCcccccccccccccCCCCcCCCcccCCCCCeEEEehhHHHHHHHHHhcCCCCCCccchhhhhhHHHHhhhhcccC
Q 001233 271 GHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGND 346 (1118)
Q Consensus 271 gH~~~~c~g~~k~k~~e~~~~~~~~~~~~~~f~~l~I~vLREYL~~el~~~~~pf~~dlERiIDDfVfLcffvGND 346 (1118)
.......+.+++...+.+.|.. + -+.||.+|+|+|.|
T Consensus 58 ------------------------~~~~~~~~~~~~~~~i~~~l~l-----------~----~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 58 ------------------------SSKSEKEVEVIDLDDILKELGL-----------T----REQFIDLCILCGCD 94 (94)
T ss_dssp ------------------------S-CCESEEEEEEHHHHHHHHTT-----------S----HHHHHHHHHHHHET
T ss_pred ------------------------ccccccceEEEEHHHHHHHcCC-----------C----HHHHHHHheecCCC
Confidence 0001235778888777666431 1 24799999999998
No 15
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=90.76 E-value=0.54 Score=44.65 Aligned_cols=93 Identities=22% Similarity=0.298 Sum_probs=55.7
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCC--CCCCCHHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDR--PAPTTFDEVF 78 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C~Hpe~~--~~p~te~Emf 78 (1118)
|||++|..||... +..+ ...+..|. -|=||.+..||.|...... -......+.+
T Consensus 1 MGI~gL~~~l~~~----~~~~---~i~~l~g~-----------------~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l 56 (99)
T smart00485 1 MGIKGLWPLLKPV----VREV---PLEALRGK-----------------TLAIDASIWLYQFLTACREKLGTPLPNSKHL 56 (99)
T ss_pred CCHhHHHHHHHHh----cccC---CHHHhCCc-----------------eEeccHHHHHHHHHHHHhhhhcCCCCchHHH
Confidence 9999999999876 1111 00011222 4557888888876432211 0111112245
Q ss_pred HHHHHHHHHHHh-hccccceEEEEecCCCchhhhHHHHhhhccc
Q 001233 79 QCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFRA 121 (1118)
Q Consensus 79 ~~If~yIDrL~~-~VRPrKlLyiAIDGVAPRAKMNQQRsRRFrs 121 (1118)
..+|..|.+|+. -|.| ++.+||.+|-+|...+..||-+.
T Consensus 57 ~~~~~rl~~L~~~~I~P----ifVFDG~~~~~K~~t~~~R~~~r 96 (99)
T smart00485 57 MGLFYRTCRLLEFGIKP----IFVFDGKPPPLKSETLAKRRERR 96 (99)
T ss_pred HHHHHHHHHHHHCCCeE----EEEECCCCchhhHHHHHHHHHHH
Confidence 556666666554 2444 57899999999999988887643
No 16
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=89.57 E-value=0.2 Score=34.46 Aligned_cols=17 Identities=59% Similarity=1.491 Sum_probs=15.1
Q ss_pred CcccccCCCCCcccccc
Q 001233 262 DKCFLCGQPGHLAANCE 278 (1118)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~ 278 (1118)
+.|+.||+.||++.+|.
T Consensus 1 ~~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCP 17 (18)
T ss_dssp SBCTTTSCSSSCGCTSS
T ss_pred CcCcCCCCcCcccccCc
Confidence 36999999999999994
No 17
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=85.83 E-value=35 Score=39.15 Aligned_cols=62 Identities=19% Similarity=0.370 Sum_probs=44.0
Q ss_pred eEEEeccccccccccCCCC------CCCCCHHHHHHHHHHHHHHHHhhccccceEEEEecCCCc--hhhhHHHH
Q 001233 50 NLYLDMNGIIHPCFHPEDR------PAPTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP--RAKMNQQR 115 (1118)
Q Consensus 50 NLYLDMNGIIH~C~Hpe~~------~~p~te~Emf~~If~yIDrL~~~VRPrKlLyiAIDGVAP--RAKMNQQR 115 (1118)
-|-||-+++++-+.|.-.. ..++. ...-+...|.++++.++|.+ ..+++||-.| |.++...|
T Consensus 13 l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~---~~~~~~~~l~~~~~~~~~~~-~~~vFD~~~~tfR~~~~~~y 82 (310)
T COG0258 13 LLLIDGSSLLYRALHALPQPLGNPLGDPTG---AVSGFLGMLYRLIRLLEPTH-PVVVFDGKPPTFRHELLEEY 82 (310)
T ss_pred EEEEechHHHHHHHHhcchhcCCCCCCCcc---HHHHHHHHHHHHHHhcCCCc-EEEEEcCCCCcchHHHHHHH
Confidence 6889999999998887522 12333 34455667899999999966 4589999777 55555544
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=85.46 E-value=22 Score=46.55 Aligned_cols=55 Identities=13% Similarity=0.154 Sum_probs=34.1
Q ss_pred eEEEeccccccccccCCCCC---CCCCHHHHHHHHHHHHHHHHhhccccceEEEEecCC
Q 001233 50 NLYLDMNGIIHPCFHPEDRP---APTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGV 105 (1118)
Q Consensus 50 NLYLDMNGIIH~C~Hpe~~~---~p~te~Emf~~If~yIDrL~~~VRPrKlLyiAIDGV 105 (1118)
-|.||.|.+|+-+.|.-... ..-.....+.-++..|-+|+...+|..+ .+|+||-
T Consensus 4 ~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~-~v~fD~~ 61 (880)
T PRK05755 4 LLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHV-AVAFDAK 61 (880)
T ss_pred EEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEE-EEEEECC
Confidence 36899999999988864110 0011122333444556666677889775 5999974
No 19
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=84.39 E-value=14 Score=44.61 Aligned_cols=34 Identities=24% Similarity=0.461 Sum_probs=22.5
Q ss_pred hHHHHhhhhcccCCCCCCCccccccchHHHHHHHHH
Q 001233 334 DDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYK 369 (1118)
Q Consensus 334 DDfVfLcffvGNDFLPhLPsL~IreGaID~Li~iYK 369 (1118)
.-||-||+|+|+||.|.+-+ |....-=.|+..|+
T Consensus 217 ~~fidL~lLlGCDYc~~I~G--ig~~~al~lir~~~ 250 (449)
T KOG2519|consen 217 ESFIDLCLLLGCDYCPTIRG--IGPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHHhcCcccccccc--cChHHHHHHHHHhc
Confidence 45788999999999999644 33333333444443
No 20
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=83.52 E-value=4.5 Score=49.31 Aligned_cols=91 Identities=22% Similarity=0.360 Sum_probs=51.6
Q ss_pred CcchhHHHHHHhhCCcccccc-cccCccccCCccccCCCCCCCCCCCccCeEEEeccccccc----cccCCCCCCCCCHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADV-IEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHP----CFHPEDRPAPTTFD 75 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~v-ie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~----C~Hpe~~~~p~te~ 75 (1118)
|||.+|+-.|... ++.+ +. .++.+-|=+|.-+-+|- |.+.-....|+ +
T Consensus 1 MGI~GLlp~~k~~----~~~~hi~---------------------~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT--~ 53 (556)
T KOG2518|consen 1 MGIQGLLPLLKPA----LKPIHIS---------------------EYKGKTVAVDGYCWLHRGALACAEKLAKGKPT--D 53 (556)
T ss_pred CCcchhHHHHHHH----hhhhhHH---------------------HhcCceEEEehhhHHhhhHHhHHHHHhcCCCh--H
Confidence 9999999988762 2211 11 12456777888888886 44322222222 2
Q ss_pred HHHHHHHHHHHHHHh-hccccceEEEEecCCCchhhhHHHHhhhccch
Q 001233 76 EVFQCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAS 122 (1118)
Q Consensus 76 Emf~~If~yIDrL~~-~VRPrKlLyiAIDGVAPRAKMNQQRsRRFrsa 122 (1118)
.-+.=...++..|.. -|+| +|.+||=.=-+|--+-|.||-+..
T Consensus 54 ryi~y~ik~v~lL~~~gikP----ilVFDG~~LP~K~~te~~Rr~~R~ 97 (556)
T KOG2518|consen 54 RYIQFFIKRVKLLLSYGIKP----ILVFDGDPLPSKKETERKRRERRK 97 (556)
T ss_pred HHHHHHHHHHHHHHhcCCeE----EEEecCCCcccccccchHHHHHHH
Confidence 222222233333332 2455 789999887788777766665443
No 21
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=77.93 E-value=23 Score=46.05 Aligned_cols=13 Identities=31% Similarity=0.279 Sum_probs=9.3
Q ss_pred CCccChHHHHHHH
Q 001233 848 GRQLGEAAHRLVA 860 (1118)
Q Consensus 848 ~~~l~~a~~r~~~ 860 (1118)
-.+|++.--||++
T Consensus 1119 IsqLdpvnarlln 1131 (1282)
T KOG0921|consen 1119 ISQLDPVNARLLN 1131 (1282)
T ss_pred hhccCchhHHHHH
Confidence 3578888888874
No 22
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=72.66 E-value=1.5 Score=34.76 Aligned_cols=18 Identities=39% Similarity=0.887 Sum_probs=16.0
Q ss_pred CcccccCCCCCccccccc
Q 001233 262 DKCFLCGQPGHLAANCEG 279 (1118)
Q Consensus 262 ~~c~~cgQ~gH~~~~c~g 279 (1118)
-.|.+|+|.||+..+|--
T Consensus 9 Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CEeecCCCCCccHhHCCC
Confidence 479999999999999954
No 23
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.97 E-value=1.2e+02 Score=40.12 Aligned_cols=56 Identities=14% Similarity=0.202 Sum_probs=33.2
Q ss_pred EEEeccccccccccCCCCCCCCCH----HHHHHHHHHHHHHHHhhccccceEEEEecCCCc
Q 001233 51 LYLDMNGIIHPCFHPEDRPAPTTF----DEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (1118)
Q Consensus 51 LYLDMNGIIH~C~Hpe~~~~p~te----~Emf~~If~yIDrL~~~VRPrKlLyiAIDGVAP 107 (1118)
|.||-|++|+-++|.-....-+|. ...+.-++..+-+|+...+|..+ .+|+||-.|
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i-~v~FD~~~~ 61 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYV-AVAFDSGTP 61 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEE-EEEEcCCCC
Confidence 579999999998886421000011 11223334445555666789875 599998654
No 24
>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=70.19 E-value=6.3 Score=51.94 Aligned_cols=40 Identities=20% Similarity=0.199 Sum_probs=30.5
Q ss_pred ccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhh
Q 001233 190 KIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALA 242 (1118)
Q Consensus 190 ~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~La 242 (1118)
+|-+|.+ |||+|-=+-...+. .....|++-|+|+++.|=.
T Consensus 785 GIP~i~A----P~EAEAqcA~L~~~---------G~vd~V~TeDsD~llFGa~ 824 (1034)
T TIGR00600 785 GIPYIVA----PMEAEAQCAILDLL---------DQTSGTITDDSDIWLFGAR 824 (1034)
T ss_pred CCCeeeC----CccHHHHHHHHHhC---------CCeEEEEccccceeccCCc
Confidence 3566654 89999988877543 5678999999999977643
No 25
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.29 E-value=3.7e+02 Score=35.65 Aligned_cols=10 Identities=20% Similarity=0.398 Sum_probs=6.4
Q ss_pred cccccCCCCC
Q 001233 1058 NHQQRGNQGQ 1067 (1118)
Q Consensus 1058 ~~~~~~~~~~ 1067 (1118)
+.+++|.+|+
T Consensus 220 ~~~~~g~~~~ 229 (1007)
T KOG1984|consen 220 GAPAPGGPGS 229 (1007)
T ss_pred CCCCCCCCCC
Confidence 4566676666
No 26
>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=58.94 E-value=32 Score=45.77 Aligned_cols=90 Identities=24% Similarity=0.385 Sum_probs=48.3
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEecccccccc---ccCCCCCCCCCHHHH
Q 001233 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPC---FHPEDRPAPTTFDEV 77 (1118)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~vie~~~~~~dG~~iP~d~s~pNpNg~efDNLYLDMNGIIH~C---~Hpe~~~~p~te~Em 77 (1118)
|||.+|+.||...--.+ . ++ ...|. -|=||.-..||-+ ++.......++ ..
T Consensus 1 MGI~GLw~ll~~~~r~v-~--le----~l~Gk-----------------~vAIDasiWL~q~l~~vr~~~g~~l~n-~h- 54 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPV-S--PE----TLEGK-----------------RLAVDISIWLNQALKGVRDREGNAIKN-SH- 54 (1034)
T ss_pred CChhHHHHHHHHhcccc-c--HH----HhCCe-----------------EEEechHHHHHHHHHHHHhccCCccCC-HH-
Confidence 99999999995321011 0 11 12333 4556666777753 22222111222 22
Q ss_pred HHHHHHHHHHHHh-hccccceEEEEecCCCchhhhHHHHhhhcc
Q 001233 78 FQCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120 (1118)
Q Consensus 78 f~~If~yIDrL~~-~VRPrKlLyiAIDGVAPRAKMNQQRsRRFr 120 (1118)
+.-+|..|.+|+. -|+| ++.+||.+|-.|...-..||-|
T Consensus 55 l~g~f~Ri~~Ll~~gI~P----VfVFDG~~p~lK~~t~~~R~~r 94 (1034)
T TIGR00600 55 LLTLFHRLCKLLFFRIRP----IFVFDGGAPLLKRQTLAKRRQR 94 (1034)
T ss_pred HHHHHHHHHHHHHCCCeE----EEEECCCCchHhHHHHHHHHHH
Confidence 2334444555443 4555 6789999999888765555444
No 27
>smart00157 PRP Major prion protein. The prion protein is a major component of scrapie-associated fibrils in Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler syndrome and bovine spongiform encephalopathy.
Probab=48.53 E-value=43 Score=36.42 Aligned_cols=33 Identities=52% Similarity=0.948 Sum_probs=23.9
Q ss_pred CCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 001233 972 PSGIHQNGGPRYPPRPMGSTSSGANLYPPQGGYSGYQS 1009 (1118)
Q Consensus 972 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1009 (1118)
|-|+ .-++.|||.. -|+|-++|++|||..++|-
T Consensus 6 pggw-ntg~srypgq----gspGgnRYP~qgg~g~~~~ 38 (217)
T smart00157 6 PGGW-NTGGSRYPGQ----GSPGGNRYPPQGGGWGQPH 38 (217)
T ss_pred CCCC-CCCCCCCCCC----CCCCCCCCCCCCCCCCCCC
Confidence 3353 4466689865 4889999999999877664
No 28
>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=47.16 E-value=19 Score=33.21 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=18.9
Q ss_pred hHHHHhhhhcc--cCCCCCCCccc
Q 001233 334 DDFIFMCFFVG--NDFLPHMPTLE 355 (1118)
Q Consensus 334 DDfVfLcffvG--NDFLPhLPsL~ 355 (1118)
+.|+-+|.|+| -|++|.+|.+-
T Consensus 8 ~q~~d~~~L~GD~~D~i~gv~giG 31 (75)
T cd00080 8 EQFIDLAILVGDKSDNIPGVPGIG 31 (75)
T ss_pred HHHHHHHHHcCCccccCCCCCccc
Confidence 46778999999 99999999844
No 29
>smart00343 ZnF_C2HC zinc finger.
Probab=34.33 E-value=19 Score=26.45 Aligned_cols=16 Identities=50% Similarity=1.379 Sum_probs=14.2
Q ss_pred cccccCCCCCcccccc
Q 001233 263 KCFLCGQPGHLAANCE 278 (1118)
Q Consensus 263 ~c~~cgQ~gH~~~~c~ 278 (1118)
+|..|++.||.+.+|.
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4889999999999994
No 30
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=33.59 E-value=31 Score=27.87 Aligned_cols=20 Identities=25% Similarity=0.624 Sum_probs=16.2
Q ss_pred hHHHHhhhhcccCCCCCCCcc
Q 001233 334 DDFIFMCFFVGNDFLPHMPTL 354 (1118)
Q Consensus 334 DDfVfLcffvGNDFLPhLPsL 354 (1118)
+-|+-+|.|+| |+.+.+|++
T Consensus 2 ~q~~~~~~L~G-D~~dni~Gv 21 (36)
T smart00279 2 EQLIDYAILVG-DYSDNIPGV 21 (36)
T ss_pred HHHHHHHHHhC-cCCCCCCCC
Confidence 35788999999 999966654
No 31
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=31.76 E-value=23 Score=29.58 Aligned_cols=15 Identities=47% Similarity=0.862 Sum_probs=12.8
Q ss_pred CcccccCCCCCcccc
Q 001233 262 DKCFLCGQPGHLAAN 276 (1118)
Q Consensus 262 ~~c~~cgQ~gH~~~~ 276 (1118)
.+|..||+.||...+
T Consensus 2 ~kC~~CG~~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTN 16 (40)
T ss_pred ccccccccccccccC
Confidence 589999999998754
No 32
>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=30.16 E-value=1.7e+02 Score=31.09 Aligned_cols=56 Identities=14% Similarity=0.257 Sum_probs=38.4
Q ss_pred EEEeccccccccccCCCCCCCCC----HHHHHHHHHHHHHHHHhhccccceEEEEecCCCc
Q 001233 51 LYLDMNGIIHPCFHPEDRPAPTT----FDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (1118)
Q Consensus 51 LYLDMNGIIH~C~Hpe~~~~p~t----e~Emf~~If~yIDrL~~~VRPrKlLyiAIDGVAP 107 (1118)
|.||.|+++|-|.|.--...-.+ .-..+...+..|.+|+...+|.. +.+|+|+-.+
T Consensus 4 lLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~-~vv~fD~~~~ 63 (169)
T PF02739_consen 4 LLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDY-VVVAFDSKGP 63 (169)
T ss_dssp EEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEE-EEEEEEBSSC
T ss_pred EEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCce-EEEEecCCCc
Confidence 78999999999998754211001 11244455667777888888987 4599999887
No 33
>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]
Probab=29.81 E-value=5.9e+02 Score=32.30 Aligned_cols=54 Identities=22% Similarity=0.274 Sum_probs=29.2
Q ss_pred CcccccCCCCCCCCCCCCCCccccCCCcchhhhhhccCCCccccC-cccccCCCCCCC
Q 001233 1013 GSFNQWGGANQSMPRGYGQGQHHQRRDGGYQQYHDQQRNYSHLQG-NHQQRGNQGQHQ 1069 (1118)
Q Consensus 1013 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 1069 (1118)
++|..|.|-..||-- -+++.|-..+.|-.-.|..- +--+++| +.+..|-||+.+
T Consensus 861 r~h~rWqGGers~sG-~sGpGHm~nrgg~sgrg~fa--pgg~srGh~~p~gG~qGg~g 915 (940)
T KOG4661|consen 861 RSHSRWQGGERSHSG-SSGPGHMTNRGGKSGRGRFA--PGGFSRGHNEPSGGYQGGSG 915 (940)
T ss_pred cccccccCCcccccC-CCCCccccccccccCCcccc--CCccccCCcCCCCccccCCC
Confidence 488889888877753 34444555555444444432 2333444 334455555533
No 34
>PF12287 Caprin-1_C: Cytoplasmic activation/proliferation-associated protein-1 C term; InterPro: IPR022070 This family of proteins is found in eukaryotes. Proteins in this family are typically between 343 and 708 amino acids in length. This family is the C-terminal region of caprin-1. Caprin-1 is a protein involved in regulating cellular proliferation. In mutated phenotypes, the G1 phase of the cell cycle is greatly lengthened, impairing normal proliferation. The C-terminal region of caprin-1 contains RGG motifs which are characteristic of RNA binding domains. It is possible that caprin-1 functions through an RNA binding mechanism.
Probab=28.30 E-value=3.5e+02 Score=31.82 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=8.0
Q ss_pred CCCccCCCCCCCCCCC
Q 001233 972 PSGIHQNGGPRYPPRP 987 (1118)
Q Consensus 972 ~~~~~~~~~~~~~~~~ 987 (1118)
..+|-+.+-|-|.+|-
T Consensus 225 ~~~FpR~~Qpf~nsRg 240 (316)
T PF12287_consen 225 TNVFPRPTQPFYNSRG 240 (316)
T ss_pred CCcCCCCCCCCcccCc
Confidence 3445555555555544
No 35
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=27.32 E-value=34 Score=28.85 Aligned_cols=19 Identities=37% Similarity=0.893 Sum_probs=16.7
Q ss_pred CCcccccCCCCCccccccc
Q 001233 261 QDKCFLCGQPGHLAANCEG 279 (1118)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~g 279 (1118)
...|..|++.||.+.+|..
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4579999999999999974
No 36
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=26.19 E-value=38 Score=41.47 Aligned_cols=92 Identities=20% Similarity=0.249 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCCh--hhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcC
Q 001233 167 MAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEG--EHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATH 244 (1118)
Q Consensus 167 M~~L~~~L~~yI~~kl~~Dp~W~~lkVIlSds~VPGEG--EHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~LatH 244 (1118)
|++|..++. -|+-||+++-.-+|| |+|=+.-++..+..+... |+|+-.+.+.--
T Consensus 214 ~eki~~Ai~--------------vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r----------~~d~~~c~~cg~ 269 (554)
T KOG0119|consen 214 QEKIKKAIA--------------VIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLR----------DDDNRACRNCGS 269 (554)
T ss_pred HHHHHHHHH--------------HHHHHHHhhccCccccccccHHHHHHHHHhCCCCC----------ccccccccccCC
Q ss_pred CceEEEeecccccCCCCCcccccCCCCCccccccccccc
Q 001233 245 EVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKR 283 (1118)
Q Consensus 245 ep~f~ILRE~V~~~~~~~~c~~cgQ~gH~~~~c~g~~k~ 283 (1118)
--|=..+=-.- +++-...|++|+..||++.+|.-..++
T Consensus 270 ~~H~q~~cp~r-~~~~~n~c~~cg~~gH~~~dc~~~~q~ 307 (554)
T KOG0119|consen 270 TGHKQYDCPGR-IPNTTNVCKICGPLGHISIDCKVNDQQ 307 (554)
T ss_pred CccccccCCcc-cccccccccccCCcccccccCCCcccc
No 37
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=24.34 E-value=40 Score=31.24 Aligned_cols=35 Identities=17% Similarity=0.257 Sum_probs=28.2
Q ss_pred CCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhc
Q 001233 200 VPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALAT 243 (1118)
Q Consensus 200 VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~Lat 243 (1118)
-|||+|.-+--.-++ ..-+.|+|.|+|+++.|--.
T Consensus 10 AP~eAeAq~A~L~~~---------g~vdav~s~D~D~llfG~~~ 44 (73)
T smart00484 10 APYEAEAQCAYLAKS---------GLVDAIITEDSDLLLFGAPR 44 (73)
T ss_pred cCCcHHHHHHHHHhC---------CCeeEEEcCccceEecCCcE
Confidence 399999988777662 46789999999999987553
No 38
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=23.40 E-value=32 Score=29.20 Aligned_cols=20 Identities=35% Similarity=0.815 Sum_probs=17.0
Q ss_pred CCCCcccccCCCCCcccccc
Q 001233 259 GQQDKCFLCGQPGHLAANCE 278 (1118)
Q Consensus 259 ~~~~~c~~cgQ~gH~~~~c~ 278 (1118)
..+..|+.||..||...+|.
T Consensus 29 ~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 29 RLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred CcChhhcCCCCcCcCHhHcC
Confidence 34578999999999999993
No 39
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=22.97 E-value=1.5e+02 Score=38.64 Aligned_cols=10 Identities=10% Similarity=0.291 Sum_probs=4.6
Q ss_pred hhhHHHHHHH
Q 001233 205 EHKIMSYVRL 214 (1118)
Q Consensus 205 EHKImdfIR~ 214 (1118)
+|+|+..+|.
T Consensus 209 ~~eiIrClka 218 (1102)
T KOG1924|consen 209 LQEIIRCLKA 218 (1102)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 40
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=22.67 E-value=5e+02 Score=34.86 Aligned_cols=24 Identities=13% Similarity=0.404 Sum_probs=12.8
Q ss_pred ecCCCCCChhhhhhhcCCCCCCCC
Q 001233 617 FELGHPFKPFNQLLGVFPSASSHA 640 (1118)
Q Consensus 617 Fe~G~Pf~PfEQLMsVLPaaS~~~ 640 (1118)
++...+.+|+--+++-||-.-.-.
T Consensus 836 ld~n~elt~lg~~la~l~iep~~~ 859 (1282)
T KOG0921|consen 836 LDANDELTPLGRMLARLPIEPRIG 859 (1282)
T ss_pred hhccCcccchhhhhhhccCccccc
Confidence 444556666666666555444333
No 41
>smart00157 PRP Major prion protein. The prion protein is a major component of scrapie-associated fibrils in Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler syndrome and bovine spongiform encephalopathy.
Probab=21.68 E-value=1.4e+02 Score=32.76 Aligned_cols=8 Identities=75% Similarity=1.726 Sum_probs=4.6
Q ss_pred CCCCCCCC
Q 001233 979 GGPRYPPR 986 (1118)
Q Consensus 979 ~~~~~~~~ 986 (1118)
+++|||+.
T Consensus 23 GgnRYP~q 30 (217)
T smart00157 23 GGNRYPPQ 30 (217)
T ss_pred CCCCCCCC
Confidence 55566554
No 42
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.96 E-value=42 Score=36.56 Aligned_cols=18 Identities=50% Similarity=1.152 Sum_probs=16.2
Q ss_pred CCcccccCCCCCcccccc
Q 001233 261 QDKCFLCGQPGHLAANCE 278 (1118)
Q Consensus 261 ~~~c~~cgQ~gH~~~~c~ 278 (1118)
...|+.|||.||...+|.
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 368999999999999995
Done!