Query psy11442
Match_columns 1362
No_of_seqs 801 out of 1642
Neff 6.5
Searched_HMMs 29240
Date Fri Aug 16 18:36:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11442.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/11442hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1rw3_A POL polyprotein; RNA an 98.2 1E-07 3.5E-12 115.7 -2.4 220 73-365 221-445 (455)
2 3oym_A PFV integrase, P42IN; p 97.4 0.00013 4.5E-09 86.1 6.7 200 509-735 14-277 (395)
3 3hst_B Protein RV2228C/MT2287; 97.0 0.0018 6.3E-08 65.0 9.3 78 298-382 44-125 (141)
4 3u3g_D Ribonuclease H, RNAse H 96.8 0.0039 1.3E-07 62.3 9.6 77 298-381 43-128 (140)
5 2ehg_A Ribonuclease HI; RNAse 96.6 0.0049 1.7E-07 62.8 9.0 81 298-385 46-129 (149)
6 3s8i_A Protein DDI1 homolog 1; 96.5 0.0011 3.7E-08 68.1 2.9 40 17-56 34-76 (148)
7 2kq2_A Ribonuclease H-related 96.0 0.01 3.5E-07 60.7 7.1 71 298-377 48-119 (147)
8 2qkb_A Ribonuclease H1, HS-RNA 95.3 0.023 7.8E-07 58.3 6.8 73 298-377 48-133 (154)
9 2x78_A Integrase; viral protei 95.2 0.019 6.3E-07 60.8 5.8 116 605-734 6-164 (200)
10 2i1a_A DNA damage-inducible pr 94.9 0.0087 3E-07 61.0 2.1 43 13-57 34-79 (148)
11 1zbf_A Ribonuclease H-related 94.8 0.046 1.6E-06 55.6 7.0 42 298-347 49-90 (142)
12 3p1g_A Xenotropic murine leuke 94.6 0.083 2.8E-06 55.0 8.6 67 298-378 61-134 (165)
13 3f9k_A Integrase; protein-prot 93.6 0.11 3.7E-06 55.6 7.4 102 608-723 55-190 (210)
14 2e4l_A Ribonuclease HI, RNAse 93.5 0.12 4.1E-06 53.3 7.1 70 298-376 44-126 (158)
15 1jl1_A Ribonuclease HI; RNAse 92.9 0.12 4.1E-06 53.1 6.0 70 298-376 42-124 (155)
16 1cxq_A Avian sarcoma virus int 92.7 0.14 4.7E-06 52.3 6.2 106 606-719 5-152 (162)
17 3h08_A RNH (ribonuclease H); R 92.5 0.15 5E-06 51.7 6.0 39 298-345 42-80 (146)
18 3qio_A GAG-POL polyprotein; RN 92.3 0.25 8.5E-06 50.5 7.5 69 298-377 47-129 (150)
19 2zd1_A Reverse transcriptase/r 92.3 0.2 7E-06 62.0 8.2 67 298-376 474-541 (557)
20 4htu_A Ribonuclease H, RNAse H 92.0 0.064 2.2E-06 53.9 2.6 76 298-383 43-134 (134)
21 1ril_A Ribonuclease H; hydrola 90.7 0.27 9.1E-06 51.1 5.8 70 298-376 46-129 (166)
22 1k6y_A Integrase; HIV-1, domai 89.0 0.4 1.4E-05 51.1 5.7 102 608-722 54-188 (212)
23 2lsn_A Reverse transcriptase; 88.1 1.7 5.7E-05 45.2 9.5 73 301-377 53-139 (165)
24 1mu2_A HIV-2 RT; HIV-2 reverse 86.7 1.3 4.5E-05 54.7 9.1 68 298-377 471-539 (555)
25 1c6v_A Protein (SIV integrase) 85.7 1.2 3.9E-05 44.8 6.6 88 625-721 40-138 (164)
26 1fmb_A EIAV protease; hydrolas 85.2 0.44 1.5E-05 45.7 2.9 51 17-70 18-69 (104)
27 3hph_A Integrase, IN; protein- 80.5 1.7 5.7E-05 46.4 5.6 86 625-723 91-191 (219)
28 1c0m_A Protein (integrase); HI 76.6 3.2 0.00011 45.1 6.4 90 625-719 45-151 (238)
29 3kks_A Integrase, IN; beta-str 75.8 2.4 8.3E-05 41.8 4.8 95 615-723 20-132 (152)
30 3l3u_A POL polyprotein; DNA in 64.5 10 0.00035 37.9 6.6 88 625-721 40-138 (163)
31 3av9_A Integrase, IN; protein- 46.4 11 0.00038 38.8 3.3 85 625-722 60-159 (183)
32 2zd1_A Reverse transcriptase/r 45.9 2E+02 0.0069 35.1 15.0 174 116-343 227-405 (557)
33 2hs1_A HIV-1 protease; ultra-h 40.8 11 0.00036 35.8 1.8 46 17-69 18-63 (99)
34 1ex4_A Integrase; SH3-like dom 40.2 24 0.00081 38.0 4.8 85 625-722 40-139 (239)
35 2zd1_B P51 RT; P51/P66, hetero 35.7 98 0.0034 36.6 9.6 111 206-345 293-405 (428)
36 3ec0_A Protease; HIV-2, inhibi 33.3 17 0.00056 34.5 1.8 35 17-57 18-53 (99)
37 3slz_A GAG-Pro-POL polyprotein 31.8 7.1 0.00024 39.0 -1.0 38 17-59 32-69 (132)
38 2hah_A Protease, retropepsin; 25.2 35 0.0012 33.2 2.6 40 17-57 23-62 (116)
39 3ka2_A [L-Ala51;Gly51']HIV-1 p 21.8 35 0.0012 36.5 2.0 35 17-56 18-52 (203)
No 1
>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse transcriptase, transferase, replication; 3.00A {Moloney murine leukemia virus} SCOP: e.8.1.2
Probab=98.19 E-value=1e-07 Score=115.66 Aligned_cols=220 Identities=9% Similarity=-0.008 Sum_probs=130.2
Q ss_pred HHHHHHHHHhcCCceeEEeechHHHhccCCCCCcccCCcCCCCCCceEEeeeeecCCceEEEEEecccccCCCCCccccC
Q psy11442 73 SNKVIFSENKGCFELRKWASNSQQLLNTVPHEHCEVPLRQNEESTFKILSVFIGNQQLTLSLIMLLRSILSAPSDQFFIS 152 (1362)
Q Consensus 73 ~~~~~~~~~~~~f~lrk~~sN~~~~~~~i~~~~~~~~~~~~~~~~~K~LG~~w~~~~D~l~~~~~~~~~~~~~~~~~~~~ 152 (1362)
..+|.+.|.+.||.|. .+.+. -.....+.||+.|+.... .+...++-.. ..
T Consensus 221 l~~v~~~l~~~gl~l~--------------~~K~~-----f~~~~~~fLG~~i~~~gi----~~~~~kv~~i------~~ 271 (455)
T 1rw3_A 221 TRALLQTLGNLGYRAS--------------AKKAQ-----ICQKQVKYLGYLLKEGQR----WLTEARKETV------MG 271 (455)
T ss_dssp HHHHHHHHHHHTCCBC--------------GGGCC-----CSBSSCEETTEEESSSEE----CCCTTCCCCC------CC
T ss_pred HHHHHHHHHHcCCccC--------------ccchh-----hhccceeEeeeeccCCee----EEChhHhhhh------cc
Confidence 4677888888888774 12221 123567999999986542 2221111110 01
Q ss_pred CCCCCCcccccchhhHHHHHHHHHhhccccccchhhccccccceecccccc-----ccccccCCCChhhHHHHHHHHHhh
Q psy11442 153 PSKVAPTKQLLSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTTFFSDSN-----IVLAWLRTAPHLLQTYVANRVVEI 227 (1362)
Q Consensus 153 ~~~~~tkR~~lS~p~~el~~a~~~a~~~Dpl~G~l~p~~~~~k~~~q~~~~-----~~l~Wd~~l~~~~~~~w~~~~~~l 227 (1362)
-..+.|++++.|+ +. .+ |++..++-....+++-++. ....|++.. ...|..+.+.+
T Consensus 272 ~~~p~t~k~l~~f----------lG----~~-~y~r~fi~~~~~~~~pL~~llkk~~~~~W~~~~----~~af~~lK~~l 332 (455)
T 1rw3_A 272 QPTPKTPRQLREF----------LG----TA-GFCRLWIPGFAEMAAPLYPLTKTGTLFNWGPDQ----QKAYQEIKQAL 332 (455)
T ss_dssp CCTTTHHHHHHHT----------TT----TT-CCCSSCCCCCGGGCCTTCC--------CCCCCC----SSSCCHHHHHT
T ss_pred CCCCCCHHHhhhh----------cc----cc-hHHHHHHhhhhhhcccHHHHhcCCCCcCchHHH----HHHHHHHHHHh
Confidence 1234578888877 32 23 3334444334444444443 257787664 44566677777
Q ss_pred ccccccccceeeeeecceeeecccccccceEEEEEeccccccccccCCCceeeeeeeeeeccccccCcccccchhhHHHH
Q psy11442 228 NNDITFLLRKILVIVLRVIYFPSNLFLIRYGGMVLSFSPLLIGQSYPSGFKFCNRGLIKAKSKVAPTKQLLSIPRLELCA 307 (1362)
Q Consensus 228 ~~~~~~~ipR~~~~~~~~~~F~~DAS~~ayga~~Ylr~~~~~g~~~~~~~~~~~~~li~aKsrv~P~k~~~tIPRlEL~a 307 (1362)
.....+..|.. ....++|| |||..|||||.+-. .+|.. . .-..+||+...+.+. ++++.+||+|
T Consensus 333 ~~~pvL~~p~~---~~~~~l~~-DAS~~~~gavL~q~---------~~~~~-~-~i~y~Sk~l~~~e~~-ys~~ekEllA 396 (455)
T 1rw3_A 333 LTAPALGLPDL---TKPFELFV-DEKQGYAKGVLTQK---------LGPWR-R-PVAYLSKKLDPVAAG-WPPCLRMVAA 396 (455)
T ss_dssp CSSCCSCCSSS---CCTTSCEE-EEEECSSSBEECCB---------CTTTT-C-CCCCCCBCSCSSCSS-SCCSSHHHHH
T ss_pred hcCcccccCCC---CCcEEEEE-eccCCcceeEEEEe---------cCCcE-E-EEEEEcccCCccccc-cchHHHHHHH
Confidence 76544455542 11128899 99999999987655 23433 2 334455655555455 9999999999
Q ss_pred HHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhC
Q psy11442 308 ALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLA 365 (1362)
Q Consensus 308 ~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~ 365 (1362)
++.|++.... .| .-..+++|||+. +++|+.+...+| +..+|+.+....+
T Consensus 397 i~~a~~~~~~---yl---~g~~~~v~tDh~-~~~~l~~~~~~~--~~~~Rl~rW~~~L 445 (455)
T 1rw3_A 397 IAVLTKDAGK---LT---MGQPLVIKAPHA-VEALVKQPPDRW--LSNARMTHYQALL 445 (455)
T ss_dssp HHHHHHHHHG---GG---CSSCEEEECSSC-TTTTSSSTTTTT--CCCCCCSCCCCCC
T ss_pred HHHHHHHHHH---Hc---CCCcEEEEecCh-HHHHhCCCcccc--ccchHHHHHHHHh
Confidence 9998865543 33 346799999998 999999876544 3445555444433
No 2
>3oym_A PFV integrase, P42IN; protein-DNA complex; HET: DNA; 2.02A {Human spumaretrovirus} PDB: 3oyn_A* 3s3o_A* 4be2_A* 3l2q_A 3l2s_A 3l2r_A* 3l2u_A* 3l2v_A* 3l2w_A* 3l2t_A* 3os1_A* 3os2_A* 3os0_A* 3oya_A* 3oy9_A* 3oyc_A* 3oyd_A* 3oye_A* 3oyb_A* 3oyg_A* ...
Probab=97.41 E-value=0.00013 Score=86.15 Aligned_cols=200 Identities=13% Similarity=0.061 Sum_probs=119.3
Q ss_pred HHHhhcCCCCCCccccCCCcceecCCccEEecccccCCCCCCCCCCCeeecCCc--eEEEEEEEeccccCCc--------
Q psy11442 509 VLTSLKNDSPLKDASLRKLTPFIDDAGLIRVGGRLHNADLPYHRKHPLLLPKLY--ARIFAECTGRFLCDRK-------- 578 (1362)
Q Consensus 509 e~~~l~~~~~~~~s~l~~L~PflD~~GllRvgGRL~~s~L~~e~KhPIlLP~~h--~LIi~~~H~~~h~~~~-------- 578 (1362)
+++++..++.+. ...+-..|.-++|++.+.+. +...++|... ..|+..+|+..|.+.+
T Consensus 14 ~~~~l~~~~~~~--~~~~~~~y~~~~g~ly~~~~----------~g~~~~~~~~~~~~il~~~H~~gH~g~~~~~~~l~~ 81 (395)
T 3oym_A 14 ELDQLLQGHYIK--GYPKQYTYFLEDGKVKVSRP----------EGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIAN 81 (395)
T ss_dssp HHHHHHTTCCCT--TSCTTSCEEEETTEEEEEET----------TEEEECCCHHHHHHHHHHHHHTTTCCHHHHHHHHHT
T ss_pred HHHHHHhccCCC--CCCccCcEEEECCEEEEEcC----------CCcEEECCHHHHHHHHHHHHhcCCCCHHHHHHHHhC
Confidence 445555555432 12233446667899888652 1224555555 6777888874344321
Q ss_pred c-ccccc---------cccccc-cccc-CccCCCCCCCCcccccccee-cccccccccc---------------------
Q psy11442 579 T-ENINT---------NSGVEM-AMRV-STSMNLLPSHQSTVSRDVSG-RYSIAMPFQH--------------------- 624 (1362)
Q Consensus 579 ~-~~~~~---------H~G~~~-~~p~-~p~m~~LP~~Rv~~~~PF~~-GvDy~GP~~~--------------------- 624 (1362)
. .|..+ .|..++ .++. ......++. ..+..||+. ++|+.||+..
T Consensus 82 ~~~~~~~~~~v~~~~~~C~~C~~~k~~~~~~~~~~~~--~~~~~p~~~~~~D~~~~~~~~~g~~y~l~~vD~~sr~~~~~ 159 (395)
T 3oym_A 82 LYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRP--DRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLY 159 (395)
T ss_dssp TBCCTTHHHHHHHHHTTCHHHHHHSCCCSEECCCCCC--CCCSSTTSEEEEEEECCCSCBTTBCEEEEEEETTTCCEEEE
T ss_pred CeECCCHHHHHHHhCccChhhcccCCCCCCCCCCcCC--CCCCCCceEEEEEEecccCCCCCccEEEEEEecCCceEEEE
Confidence 1 11111 111111 2221 111111222 457899999 9999999732
Q ss_pred -cCCCchhhHHHHhhhhhhcccc---ee-cCCccccccchhhhhhHhhhHhhh-hhc---------cccccc--hhhhHH
Q psy11442 625 -NPSNLGNSYLGAERRFYSLERK---LH-ANPSLLFSGVAWSKFKCKACRVLI-SII---------HALHGL--AYIKSA 687 (1362)
Q Consensus 625 -v~~lst~sfl~al~rf~~rrG~---fv-a~~~~~~~~~~~~~~~~~~~~~l~-~~i---------~W~GGl--r~Vksv 687 (1362)
+.+.++...+.+| .++.+.|. ++ ++..++.+.. ++++ +. .+| +|.+|. |..+.+
T Consensus 160 ~~~~~~~~~~~~~l-~~~~~~g~p~~i~sDnG~~f~s~~----~~~~----~~~~gi~~~~s~~~~p~~nG~~Er~n~~l 230 (395)
T 3oym_A 160 PTKAPSTSATVKSL-NVLTSIAIPKVIHSDQGAAFTSST----FAEW----AKERGIHLEFSTPYHPQSSGKVERKHSDI 230 (395)
T ss_dssp EESSSCHHHHHHHH-HHHTTTCCCSEEEECSCHHHHSHH----HHHH----HHHTTCEEEECCTTCGGGGHHHHHHHHHH
T ss_pred EecCCcHHHHHHHh-hHhhccCCceEEEeCCCCceecHH----HHHH----HHHcCCceeecCCcCCcccChhhhHHHHH
Confidence 5678888999999 88889998 55 5554444332 2322 33 444 567788 999999
Q ss_pred HHHHHHHhccCCCchhhHHhHHHHHHHhhcccCCccc-cCc--ceeccccc
Q psy11442 688 KHHLRRVIGAQLLTFEEFTTLLCKIEAILRFDERLAY-ADD--VVLTGARC 735 (1362)
Q Consensus 688 K~~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Plt~-s~d--h~l~g~~~ 735 (1362)
|..|++.+...... ....|..++..+|.+ |-+. ..- .++.|...
T Consensus 231 k~~l~~~~~~~~~~---w~~~l~~~~~~~N~~-~~~~~g~tP~~l~~g~~~ 277 (395)
T 3oym_A 231 KRLLTKLLVGRPTK---WYDLLPVVQLALNNT-YSPVLKYTPHQLLFGIDS 277 (395)
T ss_dssp HHHHHHHHTTSCCC---CGGGHHHHHHHHHTC-CBTTTTBCHHHHHHSSCC
T ss_pred HHHHHHHhhcCccC---HHHHHHHHHHHHhCC-CCcccCCCHHHHHcCCCC
Confidence 99999988765543 556777888999999 7654 111 66667653
No 3
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}
Probab=97.01 E-value=0.0018 Score=65.02 Aligned_cols=78 Identities=15% Similarity=0.098 Sum_probs=55.7
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhC---CCCceEeec
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLA---DGCKWYHVP 374 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~---~~~~w~hvp 374 (1362)
.|--+.|+.|++.|.+++.. ..+.++.++|||+.++.+|++.-+.-..-....+.+|+++. ....|.|||
T Consensus 44 ~tn~~aEl~A~~~aL~~a~~-------~~~~~v~i~tDS~~vv~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~v~~~~V~ 116 (141)
T 3hst_B 44 ATNNVAEYRGLIAGLDDAVK-------LGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQFRRINYEWVP 116 (141)
T ss_dssp ECHHHHHHHHHHHHHHHHHH-------HTCSEEEEEESCHHHHHHHTTSSCCCSHHHHHHHHHHHHHHTTSSEEEEEECC
T ss_pred CchHHHHHHHHHHHHHHHHH-------CCCceEEEEeChHHHHHHHhCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEcC
Confidence 67789999999999887633 24678999999999999999742111222334455555554 468999999
Q ss_pred CCCCC-CCC
Q psy11442 375 TSENP-CDC 382 (1362)
Q Consensus 375 t~~NP-AD~ 382 (1362)
...|= ||-
T Consensus 117 ~~~N~~AD~ 125 (141)
T 3hst_B 117 RARNTYADR 125 (141)
T ss_dssp GGGCHHHHH
T ss_pred CcccHHHHH
Confidence 88873 553
No 4
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}
Probab=96.80 E-value=0.0039 Score=62.28 Aligned_cols=77 Identities=14% Similarity=0.165 Sum_probs=53.0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcc----cEEEeechHHHHHHHhcCCCccchhHH---HHHHHH-HhhCCCCc
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVK----NVTFFSDSNIVLAWLRTAPHLLQTYVA---NRVVEI-NKLADGCK 369 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~----~~~~~tDS~i~L~wi~~~~~~~~~fv~---NRv~~I-~~~~~~~~ 369 (1362)
.|--+.|+.|++.|.+++.. ..+. ++.++|||+.++.|+++.-+.-..-.. .++.++ .+......
T Consensus 43 ~tn~~aEl~A~~~aL~~a~~-------~~~~~~~~~v~i~tDS~~vi~~i~~~~~~~~~~l~~~~~~i~~l~~~~~~~v~ 115 (140)
T 3u3g_D 43 TTNNVAEYEALIRALEDLQM-------FGDKLVDMEVEVRMDSELIVRQMQGVYKVKEPTLKEKFAKIAHIKMERVPNLV 115 (140)
T ss_dssp ECHHHHHHHHHHHHHHHHGG-------GGGGGTTCEEEEEESCHHHHHHHTTSSCCCCGGGHHHHHHHHHHHHHHCTTCE
T ss_pred CchHHHHHHHHHHHHHHHHH-------cCCCCCCceEEEEeChHHHHHHhCCCcccCCHHHHHHHHHHHHHhhcCCCcEE
Confidence 57889999999999876532 3455 899999999999999974221111122 334443 34445899
Q ss_pred eEeecCCCCC-CC
Q psy11442 370 WYHVPTSENP-CD 381 (1362)
Q Consensus 370 w~hvpt~~NP-AD 381 (1362)
|.|||...|= ||
T Consensus 116 ~~~V~~~~N~~AD 128 (140)
T 3u3g_D 116 FVHIPREKNARAD 128 (140)
T ss_dssp EEECCGGGGHHHH
T ss_pred EEEcCchhhHHHH
Confidence 9999987773 44
No 5
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A
Probab=96.62 E-value=0.0049 Score=62.81 Aligned_cols=81 Identities=17% Similarity=0.144 Sum_probs=54.8
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHHHHHhhCC--CCceEeecC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVVEINKLAD--GCKWYHVPT 375 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~~I~~~~~--~~~w~hvpt 375 (1362)
.|--+.|+.|++.|.+++.. ..+.++.++|||+.+..||.+.-+.-..-...-+++|+++.. ...|.|||.
T Consensus 46 ~tnn~aEl~A~~~aL~~a~~-------~g~~~v~i~tDS~~vi~~i~~~w~~~~~~~~~l~~~i~~l~~~~~v~~~~V~~ 118 (149)
T 2ehg_A 46 STNNVAEYSGLICLMETMLR-------LGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAIELKKKLNATLIWVPR 118 (149)
T ss_dssp CCHHHHHHHHHHHHHHHHHH-------HTCCSCEEEESCHHHHHHHTTSSCCCCTTHHHHHHHHHHHHHHHTCEEEECCG
T ss_pred ccHHHHHHHHHHHHHHHHHH-------cCCCEEEEEeChHHHHHHHhCccccCCHHHHHHHHHHHHHHhcCCEEEEEcCC
Confidence 67889999999999876642 245789999999999999987521111112222333333222 599999999
Q ss_pred CCC-CCCCCCC
Q psy11442 376 SEN-PCDCASR 385 (1362)
Q Consensus 376 ~~N-PAD~~SR 385 (1362)
+.| .||-+.+
T Consensus 119 ~~N~~AD~LA~ 129 (149)
T 2ehg_A 119 EENKEADRLSR 129 (149)
T ss_dssp GGCHHHHHHHH
T ss_pred cccHHHHHHHH
Confidence 988 3775543
No 6
>3s8i_A Protein DDI1 homolog 1; protease, structural genomics, structural genomics consortiu retropepsin-like domain, protein turnover, hydrolase; 1.70A {Homo sapiens}
Probab=96.48 E-value=0.0011 Score=68.13 Aligned_cols=40 Identities=23% Similarity=0.562 Sum_probs=31.2
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCccee---eeceeeeecCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRY---KCGISISGIGD 56 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 56 (1362)
+|+|||+|+|+|.++|+.+||+||||.+. +....+.|.|+
T Consensus 34 ~~v~~LVDTGAs~s~Is~~~A~rlGL~~~~~~~~~~~a~g~G~ 76 (148)
T 3s8i_A 34 HPLKAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGVAKGVGT 76 (148)
T ss_dssp EEEEEEECTTCSSCEEEHHHHHHTTCGGGEEGGGCEECCC---
T ss_pred EEEEEEEeCCCCcEeeCHHHHHHcCCccccCcceeEEEEcCCc
Confidence 49999999999999999999999999753 23455667654
No 7
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A
Probab=95.99 E-value=0.01 Score=60.68 Aligned_cols=71 Identities=15% Similarity=0.102 Sum_probs=48.9
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCcc-chhHHHHHHHHHhhCCCCceEeecCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLL-QTYVANRVVEINKLADGCKWYHVPTS 376 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~-~~fv~NRv~~I~~~~~~~~w~hvpt~ 376 (1362)
.|--|.||+|++.|.+++.. . .. ++.++|||+.+..|+.+.-+.- +..+.|+ ..++++.....|.|||+.
T Consensus 48 ~tNn~aEl~A~~~AL~~a~~----~---~~-~v~I~tDS~~i~~w~~~~w~~~~~~~~~~~-~l~~~l~~~v~~~wV~gH 118 (147)
T 2kq2_A 48 MRNVAGEIAAALYAVKKASQ----L---GV-KIRILHDYAGIAFWATGEWKAKNEFTQAYA-KLMNQYRGIYSFEKVKAH 118 (147)
T ss_dssp TCTTHHHHHHHHHHHHHHHH----H---TC-CCCBSSCCSTHHHHTTSSSSCCHHHHHHHH-CGGGGGSTTCCBCCCCCC
T ss_pred ccHHHHHHHHHHHHHHHHHH----C---CC-eEEEEECcHHHHHHHhCCCccCCcchHHHH-HHHHHhcCCeeEEEecCc
Confidence 68889999999999886422 2 23 7899999999999998642211 1123332 335555557899999975
Q ss_pred C
Q psy11442 377 E 377 (1362)
Q Consensus 377 ~ 377 (1362)
.
T Consensus 119 ~ 119 (147)
T 2kq2_A 119 S 119 (147)
T ss_dssp C
T ss_pred C
Confidence 4
No 8
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*
Probab=95.33 E-value=0.023 Score=58.34 Aligned_cols=73 Identities=19% Similarity=0.317 Sum_probs=49.3
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCC-----Cccc----hhHHHH--HHHHHhhCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAP-----HLLQ----TYVANR--VVEINKLAD 366 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~-----~~~~----~fv~NR--v~~I~~~~~ 366 (1362)
.|--+.||+|++.|.+++.. ....++.++|||+.++.-|.+-. +.|+ .-|.|+ +.+|.++..
T Consensus 48 ~tn~~aEl~A~~~aL~~~~~-------~~~~~v~i~tDS~~vi~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~~ 120 (154)
T 2qkb_A 48 QTNQRAEIHAACKAIEQAKT-------QNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQ 120 (154)
T ss_dssp CCHHHHHHHHHHHHHHHHHH-------TTCCEEEEEESCHHHHHHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHHT
T ss_pred CchHHHHHHHHHHHHHHHHh-------CCCceEEEEECcHHHHhhhhhhHHHHHhccccccCCCccccHHHHHHHHHHHc
Confidence 68899999999999987642 34678999999998886554310 1122 123333 455555443
Q ss_pred --CCceEeecCCC
Q psy11442 367 --GCKWYHVPTSE 377 (1362)
Q Consensus 367 --~~~w~hvpt~~ 377 (1362)
...|.|||+..
T Consensus 121 ~~~v~~~~V~~H~ 133 (154)
T 2qkb_A 121 GMDIQWMHVPGHS 133 (154)
T ss_dssp TCEEEEEECCTTS
T ss_pred CCceEEEEccCCC
Confidence 48899999864
No 9
>2x78_A Integrase; viral protein, DNA-directed DNA polyme nucleotidyltransferase, DNA integration, aspartyl protease, recombination, transferase; 2.00A {Human spumaretrovirus} PDB: 2x6n_A 2x6s_A 2x74_A 3dlr_A
Probab=95.19 E-value=0.019 Score=60.84 Aligned_cols=116 Identities=10% Similarity=-0.011 Sum_probs=73.8
Q ss_pred Ccccccccee-cccccccccc----------------------cCCCchhhHHHHhhhhhhcccc---ee-cCCcccccc
Q psy11442 605 QSTVSRDVSG-RYSIAMPFQH----------------------NPSNLGNSYLGAERRFYSLERK---LH-ANPSLLFSG 657 (1362)
Q Consensus 605 Rv~~~~PF~~-GvDy~GP~~~----------------------v~~lst~sfl~al~rf~~rrG~---fv-a~~~~~~~~ 657 (1362)
+..++.||+. ++|+.||+.. +.+.+++..+.+|..++. .|. ++ ++..++.+.
T Consensus 6 ~~~~~~p~~~~~~D~~~~~~~~~g~~y~~~~iD~~Sr~~~~~~~~~~~~~~~~~~l~~~~~-~g~p~~i~sDnG~~f~s~ 84 (200)
T 2x78_A 6 PDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTS-IAIPRVIHSDQGAAFTSS 84 (200)
T ss_dssp ----CCTTSEEEEEEECCCSCBTTBCEEEEEEETTTCCEEEEEESSSCHHHHHHHHHHHTT-TCCCSEEEECSCHHHHSH
T ss_pred CCCCCCcccEEEEEEeCCCccCCCCeEEEEEEeCCCCcEEEEECCCCCHHHHHHHHHHHHH-hCCCcEEEecCCcceehH
Confidence 4456899999 9999998743 567788889999987764 476 44 555444332
Q ss_pred chhhhhhHhhhHhhh-hh---------ccccccc--hhhhHHHHHHHHHhccCCCchhhHHhHHHHHHHhhcccCCcccc
Q psy11442 658 VAWSKFKCKACRVLI-SI---------IHALHGL--AYIKSAKHHLRRVIGAQLLTFEEFTTLLCKIEAILRFDERLAYA 725 (1362)
Q Consensus 658 ~~~~~~~~~~~~~l~-~~---------i~W~GGl--r~VksvK~~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Plt~s 725 (1362)
. +..+ +. .+ .+|..|. |..+.+|..+++.+.....+ ....|.+++..+|.+ |-..
T Consensus 85 ~----~~~~----~~~~gi~~~~~~p~~p~~ng~~Er~~~~l~~~~~~~~~~~~~~---w~~~l~~~~~~~N~~-~~~~- 151 (200)
T 2x78_A 85 T----FAEW----AKERGIHLEFSTPYHPQSGSKVERKNSDIKRLLTKLLVGRPTK---WYDLLPVVQLALNNT-YSPV- 151 (200)
T ss_dssp H----HHHH----HHHHTCEEEECC-------CHHHHHHHHHHHHHHHHHHTCTTT---TTTTHHHHHHHHHTS-CBTT-
T ss_pred H----HHHH----HHHcCceEeECCCCCCCccCHhHhhHHHHHHHHHHHHhcCccc---HHHHHHHHHHHHcCC-CCcc-
Confidence 2 2222 22 33 4567777 99999999999988665433 455678888899999 7543
Q ss_pred Cc----ceecccc
Q psy11442 726 DD----VVLTGAR 734 (1362)
Q Consensus 726 ~d----h~l~g~~ 734 (1362)
.+ .++.|..
T Consensus 152 ~~~tP~e~~~g~~ 164 (200)
T 2x78_A 152 LKYTPHQLLFGID 164 (200)
T ss_dssp TTBCHHHHHHCCC
T ss_pred cCCChHHHHhCCC
Confidence 12 5556664
No 10
>2i1a_A DNA damage-inducible protein DDI1; acid protease fold, dimer, retroviral protease domain, protein turnover; HET: DNA; 2.30A {Saccharomyces cerevisiae}
Probab=94.90 E-value=0.0087 Score=60.99 Aligned_cols=43 Identities=21% Similarity=0.446 Sum_probs=29.0
Q ss_pred CCCeEEEEEeecCCCcchhhHHHHHHHhCcceeee-ce--eeeecCCC
Q psy11442 13 SGQLSSIRVIVDPGSQVSCITNDCVQRLGLKRYKC-GI--SISGIGDN 57 (1362)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~ 57 (1362)
+|+ |+++|||+|++.++|+.+||++|||..... .+ ...|+|+.
T Consensus 34 nG~--~~~~LvDTGAs~s~is~~~a~~lgl~~~~~~~~~~~a~g~g~~ 79 (148)
T 2i1a_A 34 NNY--PVKAFVDTGAQTTIMSTRLAKKTGLSRMIDKRFIGEARGVGTG 79 (148)
T ss_dssp TTE--EEEEEECTTCSSCEEEHHHHHHHTGGGGCBCCCC---------
T ss_pred CCE--EEEEEEECCCCccccCHHHHHHcCCCccCCcceEEEEecCCCc
Confidence 454 999999999999999999999999975422 22 34577764
No 11
>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*
Probab=94.76 E-value=0.046 Score=55.61 Aligned_cols=42 Identities=14% Similarity=0.169 Sum_probs=35.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAP 347 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~ 347 (1362)
.|--|.|++|++.|.+++.. +. + ++.++|||+.|+.|+++.-
T Consensus 49 ~TNN~aEl~A~i~aL~~~~~----~~---~-~v~i~tDS~~vi~w~~~~~ 90 (142)
T 1zbf_A 49 GTNNMGEFLAIVHGLRYLKE----RN---S-RKPIYSNSQTAIKWVKDKK 90 (142)
T ss_dssp ECHHHHHHHHHHHHHHHHHH----TT---C-CCCEEESCHHHHHHHHHTC
T ss_pred cCcHHHHHHHHHHHHHHHHh----CC---C-eEEEEEehHHHHHHHHcCC
Confidence 67889999999999987642 23 3 7899999999999999764
No 12
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A
Probab=94.57 E-value=0.083 Score=55.03 Aligned_cols=67 Identities=21% Similarity=0.301 Sum_probs=46.8
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHH--HHhcCCCccchhHHHH--HHHHHh-h--CCCCce
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLA--WLRTAPHLLQTYVANR--VVEINK-L--ADGCKW 370 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~--wi~~~~~~~~~fv~NR--v~~I~~-~--~~~~~w 370 (1362)
.|.-|.||+|++.|.+++ ....+.++|||+.|+. |+.+.. ..|.|+ ++++.+ + .....|
T Consensus 61 ~Tnn~aEl~Ai~~AL~~~----------~~~~v~I~tDS~~vi~~iw~~~~g----~~v~n~dl~~~l~~~l~~~~~v~~ 126 (165)
T 3p1g_A 61 TSAQRAELIALTQALKMA----------EGKKLNVYTDSRYAFATAHVHSEG----REIKNKNEILALLKALFLPKRLSI 126 (165)
T ss_dssp CCHHHHHHHHHHHHHHHT----------BTSEEEEEECCHHHHHHHHSCCCS----CCCSSHHHHHHHHHHTTSBSEEEE
T ss_pred CcHHHHHHHHHHHHHHHc----------cCceEEEEEchHHHHhhhhcccCC----CcccCHHHHHHHHHHHhcCCceEE
Confidence 688999999999998865 1468999999997775 654332 234454 334422 2 235899
Q ss_pred EeecCCCC
Q psy11442 371 YHVPTSEN 378 (1362)
Q Consensus 371 ~hvpt~~N 378 (1362)
.||++..+
T Consensus 127 ~wVkgH~g 134 (165)
T 3p1g_A 127 IHCPGHQK 134 (165)
T ss_dssp EECCSSCC
T ss_pred EEecCCCC
Confidence 99998873
No 13
>3f9k_A Integrase; protein-protein complex, AIDS, DNA integration, endonuclease magnesium, metal-binding, multifunctional enzyme; 3.20A {Human immunodeficiency virus type 2} PDB: 1e0e_A
Probab=93.63 E-value=0.11 Score=55.65 Aligned_cols=102 Identities=16% Similarity=0.097 Sum_probs=73.9
Q ss_pred cccccee-cccccccccc------------------cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhH
Q psy11442 608 VSRDVSG-RYSIAMPFQH------------------NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKC 665 (1362)
Q Consensus 608 ~~~PF~~-GvDy~GP~~~------------------v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~ 665 (1362)
...||.. ++|+.+ +.. +.+.+++.++.++.+++++.|. ++ ++..++.+.. +++
T Consensus 55 ~~~p~~~w~~D~~~-~~~~y~l~~vD~~sr~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~i~sDnG~~F~s~~----~~~ 129 (210)
T 3f9k_A 55 VNAELGTWQMDCTH-LEGKIIIVAVHVASGFIEAEVIPQESGRQTALFLLKLASRWPITHLHTDNGANFTSQE----VKM 129 (210)
T ss_dssp TTSCTTEEEEEEEE-ETTEEEEEEEETTTTEEEEEEESSCCHHHHHHHHHHHHTTSCCSEEEECCCTTTSSHH----HHH
T ss_pred CCCCCCeEeEeecc-cCCeEEEEEEEcCCCcEEEEEeCCcchHHHHHHHHHHHHHcCCCEEEeCCCchhhHHH----HHH
Confidence 3568888 888733 221 6778999999999999999998 55 5555554432 222
Q ss_pred hhhHhhh-hh---------ccccccc--hhhhHHHHHHHHHhccCCCchhhHHhHHHHHHHhhcccCCcc
Q psy11442 666 KACRVLI-SI---------IHALHGL--AYIKSAKHHLRRVIGAQLLTFEEFTTLLCKIEAILRFDERLA 723 (1362)
Q Consensus 666 ~~~~~l~-~~---------i~W~GGl--r~VksvK~~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Plt 723 (1362)
+ +. .+ -+|..|. |..+.+|..|++... +.+++.+.|..++...|.+ |..
T Consensus 130 ~----~~~~gi~~~~s~~~~p~~nG~~Er~n~~lk~~l~~~~~----~~~~~~~~l~~~~~~~N~~-~~~ 190 (210)
T 3f9k_A 130 V----AWWIGIEQSFGVPYNPQSQGVVEAMNHHLKNQISRIRE----QANTIETIVLMAVHCMNFK-RRG 190 (210)
T ss_dssp H----HHHHTCEEEESSCCCTTCTTHHHHHHHHHHHHHHHTGG----GCSSHHHHHHHHHHHHHHS-CCB
T ss_pred H----HHHCCCceeeCCCcCCCcccHHHHHHHHHHHHHHHHhc----chhhHHHHHHHHHHHHhcc-CCC
Confidence 2 22 34 4567777 999999999988663 3468899999999999998 653
No 14
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A
Probab=93.45 E-value=0.12 Score=53.29 Aligned_cols=70 Identities=21% Similarity=0.165 Sum_probs=45.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhc--------CCCc-cchhHHHH--HHHHHhhCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRT--------APHL-LQTYVANR--VVEINKLAD 366 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~--------~~~~-~~~fv~NR--v~~I~~~~~ 366 (1362)
.|--+.||.|++.|.+++ . ...++.++|||+.|+.-|.+ .-+. -..-|.|+ +.+|.++..
T Consensus 44 ~tn~~aEl~A~~~AL~~~-------~--~~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~ 114 (158)
T 2e4l_A 44 TTNNRMELLAPIVALEAL-------K--EPCKIILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQ 114 (158)
T ss_dssp ECHHHHHHHHHHHHHHTC-------S--SCCEEEEEECCHHHHHHHHTHHHHHHHTTTBCTTSSBCTTHHHHHHHHHHHT
T ss_pred CccHHHHHHHHHHHHHHh-------c--cCCeEEEEeCHHHHHHHHHHHHHHHHHccccccCCCcccCHHHHHHHHHHHc
Confidence 577899999999988753 2 12789999999988874433 1100 01134443 344555443
Q ss_pred --CCceEeecCC
Q psy11442 367 --GCKWYHVPTS 376 (1362)
Q Consensus 367 --~~~w~hvpt~ 376 (1362)
...|.|||+.
T Consensus 115 ~~~v~~~wV~gH 126 (158)
T 2e4l_A 115 LHQIDWRWVKGH 126 (158)
T ss_dssp TSEEEEEECCTT
T ss_pred cCcEEEEEccCC
Confidence 5789999975
No 15
>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...
Probab=92.86 E-value=0.12 Score=53.08 Aligned_cols=70 Identities=20% Similarity=0.148 Sum_probs=47.0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCC-----Ccc----chhHHHH--HHHHHhhCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAP-----HLL----QTYVANR--VVEINKLAD 366 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~-----~~~----~~fv~NR--v~~I~~~~~ 366 (1362)
.|--+.||.|++.|.+++. ...++.++|||+.++.-|.+-- +.| +..|.|+ +.+|.++..
T Consensus 42 ~tn~~aEl~A~~~aL~~~~---------~~~~v~I~tDS~~vi~~i~~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~~ 112 (155)
T 1jl1_A 42 TTNNRMELMAAIVALEALK---------EHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALG 112 (155)
T ss_dssp ECHHHHHHHHHHHHHHTCC---------SCCEEEEEECCHHHHHHHHTTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHTT
T ss_pred CcHHHHHHHHHHHHHHHhC---------cCCcEEEEeCHHHHHHHHHHHHHHHhhcccccccCCccCCHHHHHHHHHHHc
Confidence 5778999999998886432 2368999999999986665410 012 1234443 455666554
Q ss_pred --CCceEeecCC
Q psy11442 367 --GCKWYHVPTS 376 (1362)
Q Consensus 367 --~~~w~hvpt~ 376 (1362)
...|.|||+.
T Consensus 113 ~~~v~~~wV~gH 124 (155)
T 1jl1_A 113 QHQIKWEWVKGH 124 (155)
T ss_dssp TCEEEEEECCSS
T ss_pred cCceEEEEcCCC
Confidence 4789999965
No 16
>1cxq_A Avian sarcoma virus integrase; mixed beta-sheet surrounded by alpha-helices, transferase; HET: EPE; 1.02A {Avian sarcoma virus} SCOP: c.55.3.2 PDB: 1cxu_A* 1czb_A* 1cz9_A* 1asu_A* 1asw_A* 1asv_A 1a5v_A* 1a5w_A* 1a5x_A* 1vsf_A* 1vse_A* 3o4n_A* 1vsm_A 3o4q_A* 1vsd_A* 1vsh_A* 1vsi_A* 1vsj_A* 1vsk_A 1vsl_A
Probab=92.66 E-value=0.14 Score=52.31 Aligned_cols=106 Identities=10% Similarity=-0.061 Sum_probs=73.3
Q ss_pred cccccccee-cccccccccc---------------------cCCCchhhHHHHhhhhhhcccc---ee-cCCccccccch
Q psy11442 606 STVSRDVSG-RYSIAMPFQH---------------------NPSNLGNSYLGAERRFYSLERK---LH-ANPSLLFSGVA 659 (1362)
Q Consensus 606 v~~~~PF~~-GvDy~GP~~~---------------------v~~lst~sfl~al~rf~~rrG~---fv-a~~~~~~~~~~ 659 (1362)
....+|++. ++|+.++-.. +.+.+++..+.+|.+.+.++|. ++ ++..++.+..
T Consensus 5 ~~~~~p~~~~~~D~~~~~~~~g~~yl~~~iD~~Sr~i~~~~~~~~~~~~v~~~l~~~~~~~g~p~~i~sDnG~~f~s~~- 83 (162)
T 1cxq_A 5 GRGLGPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVAAQHHWATAIAVLGRPKAIKTDNGSCFTSKS- 83 (162)
T ss_dssp CCTTSCCCEEEEEEEECGGGTTSCEEEEEEETTTCCEEEEEESSCCHHHHHHHHHHHHHHHCCCSEEECCSCHHHHSHH-
T ss_pred CCCCCCCCEEEeeeeecccCCCCEEEEEEEEcCCCeEEEEECCCccHHHHHHHHHHHHHHHCCCeEEEeCCchhhhhHH-
Confidence 345678888 8887765321 5578899999999999999997 44 5554443322
Q ss_pred hhhhhHhhhHhhh-hhc---------cccccc--hhhhHHHHHHHHHhccC----CCchhhHHhHHHHHHHhhccc
Q psy11442 660 WSKFKCKACRVLI-SII---------HALHGL--AYIKSAKHHLRRVIGAQ----LLTFEEFTTLLCKIEAILRFD 719 (1362)
Q Consensus 660 ~~~~~~~~~~~l~-~~i---------~W~GGl--r~VksvK~~L~k~ig~~----~lt~eel~t~l~eiea~lNsr 719 (1362)
++.+ +. .+| +|..|. |..+.+|..+.+.+... .|........|..++-.+|..
T Consensus 84 ---~~~~----~~~~gi~~~~~~p~~p~~ng~~Er~~~tlk~~~~~~~~~~~~~~~l~~~~w~~~l~~~~~~~N~~ 152 (162)
T 1cxq_A 84 ---TREW----LARWGIAHTTGIPGNSQGQAMVERANRLLKDKIRVLAEGDGFMKRIPTSKQGELLAKAMYALNHF 152 (162)
T ss_dssp ---HHHH----HHHHTCEEECCCCC----CHHHHHHHHHHHHHHHHHHHHTTCSSSCCHHHHHHHHHHHHHHHHC-
T ss_pred ---HHHH----HHHCCCeEeeCCCCCCccCCEEehHHHHHHHHHHHHcCcccccccCCcchHHHHhhheeeeeecc
Confidence 2222 33 344 567777 99999999999988655 456678888999999999976
No 17
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}
Probab=92.49 E-value=0.15 Score=51.67 Aligned_cols=39 Identities=23% Similarity=0.258 Sum_probs=30.9
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhc
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRT 345 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~ 345 (1362)
.|--|.||.|++.|.+.+. ...++.++|||+.|+.-|.+
T Consensus 42 ~Tnn~aEl~A~~~AL~~~~---------~~~~v~I~tDS~~vi~~i~~ 80 (146)
T 3h08_A 42 TTNNRMELMAAIKGLEALK---------EPARVQLYSDSAYLVNAMNE 80 (146)
T ss_dssp ECHHHHHHHHHHHHHHTCS---------SCCEEEEEESCHHHHHHHHS
T ss_pred CcHHHHHHHHHHHHHHhcC---------ccCcEEEEeChHHHHHHHHH
Confidence 6788999999998887542 24789999999988875543
No 18
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Probab=92.29 E-value=0.25 Score=50.54 Aligned_cols=69 Identities=22% Similarity=0.121 Sum_probs=43.6
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcC-----CCccch----hHHHH--HHHHHhh--
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTA-----PHLLQT----YVANR--VVEINKL-- 364 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~-----~~~~~~----fv~NR--v~~I~~~-- 364 (1362)
.|--|.||+|++.|.+.. ..++.++|||+.++.-|.+- .+.|++ -|.|+ +++|.+.
T Consensus 47 ~Tnn~aEl~A~i~AL~~~-----------~~~v~i~tDS~~v~~~i~~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~ 115 (150)
T 3qio_A 47 TTNQKTELQAIYLALQDS-----------GLEVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLI 115 (150)
T ss_dssp CCHHHHHHHHHHHHHHHS-----------CSEEEEEESCHHHHHHHHHHHHHHCC------------CHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHhC-----------CCcEEEEeCcHHHHHHHHHHHHHHhhcCcCcCcCcccccHHHHHHHHHHHh
Confidence 788999999999988751 26899999999888655431 111222 34443 3333332
Q ss_pred -CCCCceEeecCCC
Q psy11442 365 -ADGCKWYHVPTSE 377 (1362)
Q Consensus 365 -~~~~~w~hvpt~~ 377 (1362)
.....|.|||+..
T Consensus 116 ~~~~v~~~wV~gH~ 129 (150)
T 3qio_A 116 KKEKVYLAWVPAHK 129 (150)
T ss_dssp TCSEEEEEECCTTS
T ss_pred hcCceEEEEccCcC
Confidence 2358899999985
No 19
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...
Probab=92.29 E-value=0.2 Score=61.97 Aligned_cols=67 Identities=19% Similarity=0.230 Sum_probs=49.5
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccchhHHHHHH-HHHhhCCCCceEeecCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQTYVANRVV-EINKLADGCKWYHVPTS 376 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~fv~NRv~-~I~~~~~~~~w~hvpt~ 376 (1362)
.|--+.||.|++.|.+++ ..++.++|||+.|+..|.+...+-..-+.+++- ++.+. ....|.|||+.
T Consensus 474 ~TNn~aEl~Ai~~aL~~~-----------~~~v~I~tDS~~vi~~i~~~~~~~~~~l~~~~~~~l~~~-~~v~~~wV~~H 541 (557)
T 2zd1_A 474 TTNQKTELQAIYLALQDS-----------GLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKK-EKVYLAWVPAH 541 (557)
T ss_dssp CCHHHHHHHHHHHHHHHS-----------CSEEEEEECCHHHHHHHTTCCSEESSHHHHHHHHHHHHC-SEEEEEECCSS
T ss_pred CCHHHHHHHHHHHHHHhC-----------CCcEEEEeChHHHHHHHhcCCccCCHHHHHHHHHHHhcC-CCEEEEEcCCC
Confidence 788899999999999865 357999999999999998765442223334433 44443 46899999995
No 20
>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A
Probab=92.03 E-value=0.064 Score=53.89 Aligned_cols=76 Identities=17% Similarity=0.135 Sum_probs=49.3
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCCccch----hHHHH-----HHHH----Hhh
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPHLLQT----YVANR-----VVEI----NKL 364 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~~~~~----fv~NR-----v~~I----~~~ 364 (1362)
.|--|+||+|++.|.+++.. .. . ++.++|||+.|+.||.+. .|++ =|.|+ +.+. +.+
T Consensus 43 tTNN~aEl~A~i~aL~~l~~----~~-~---~v~i~tDSqyVi~wi~~~--~~kt~~~~~vkN~dLw~~ld~~~~~l~~~ 112 (134)
T 4htu_A 43 GTNNMGEFLAIVHGLRYLKE----RN-S---RKPIYSNSQTAIKWVKDK--KAKSTLVRNEETALIWKLVDEAEEWLNTH 112 (134)
T ss_dssp ECHHHHHHHHHHHHHHHHHH----TT-C---CCCEEESCHHHHHHHHHT--CCCCCCCCSSTTHHHHHHHHHHHHHHHHC
T ss_pred CchHHHHHHHHHHHHHHHHh----CC-C---CEEEEcchHHHHHHHHcC--CcccCCCCCccCHHHHHHHHHHHHHHHhC
Confidence 68889999999999877542 22 2 268999999999999964 3433 23443 2222 222
Q ss_pred C---CCCceEeecCCCCCCCCC
Q psy11442 365 A---DGCKWYHVPTSENPCDCA 383 (1362)
Q Consensus 365 ~---~~~~w~hvpt~~NPAD~~ 383 (1362)
. +...|.--.=.+.|||..
T Consensus 113 ~~~~~~~kw~~~~wge~~ad~g 134 (134)
T 4htu_A 113 TYETPILKWQTDKWGEIKADYG 134 (134)
T ss_dssp CCCCCEEECCHHHHCSCTTCCC
T ss_pred CCCCceEEEEecccccccCCCC
Confidence 2 224555555567888863
No 21
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Probab=90.73 E-value=0.27 Score=51.12 Aligned_cols=70 Identities=17% Similarity=0.115 Sum_probs=45.1
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcC------CCccc----hhHHHH--HHHHHhhC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTA------PHLLQ----TYVANR--VVEINKLA 365 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~------~~~~~----~fv~NR--v~~I~~~~ 365 (1362)
.|--+.||+|++.|.+++ . ...++.++|||+.++.-|.+. .+.|+ ..|.|+ +.+|.++.
T Consensus 46 ~Tnn~aEl~Ai~~AL~~~-------~--~~~~v~I~tDS~~vi~~i~~~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~ 116 (166)
T 1ril_A 46 TTNNRMELKAAIEGLKAL-------K--EPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAM 116 (166)
T ss_dssp ECHHHHHHHHHHHHHHSC-------C--SCCEEEEECCCHHHHHHHHSSHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHh-------c--cCCeEEEEeChHHHHHHHhhhHHHHHHhcccccccCCccCcHHHHHHHHHHH
Confidence 678899999999988643 1 235899999999998744430 01122 234442 44555444
Q ss_pred C--CCceEeecCC
Q psy11442 366 D--GCKWYHVPTS 376 (1362)
Q Consensus 366 ~--~~~w~hvpt~ 376 (1362)
. .+.|.|||+.
T Consensus 117 ~~~~v~~~wV~gH 129 (166)
T 1ril_A 117 APHRVRFHFVKGH 129 (166)
T ss_dssp TTSEEECCCCCGG
T ss_pred hcCeEEEEEeeCC
Confidence 4 4789999854
No 22
>1k6y_A Integrase; HIV-1, domain organization, transferase; 2.40A {Human immunodeficiency virus 1} SCOP: a.4.10.1 c.55.3.2 PDB: 1wjb_A 1wjd_A 1wjf_A 1wja_A 1wjc_A 1wje_A
Probab=89.03 E-value=0.4 Score=51.07 Aligned_cols=102 Identities=17% Similarity=-0.007 Sum_probs=66.1
Q ss_pred cccccee-ccccccccc---c--------------cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhHh
Q psy11442 608 VSRDVSG-RYSIAMPFQ---H--------------NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKCK 666 (1362)
Q Consensus 608 ~~~PF~~-GvDy~GP~~---~--------------v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~~ 666 (1362)
...|+.. ++|+.|+=. . +.+.++...+.++.+.+.+.|. ++ ++..++.+.. ++.+
T Consensus 54 ~~~p~~~w~~D~~~~~~~~~l~~vD~~Sr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~sDnG~~f~s~~----~~~~ 129 (212)
T 1k6y_A 54 VDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTT----VKAA 129 (212)
T ss_dssp --CCTTEEEEEEEEETTEEEEEEEETTTTEEEEEEESSCCHHHHHHHHHHHHHHSCCCEEECCCSTTTTSHH----HHHH
T ss_pred CCCCCCeeeEEEecCCCeEEEEEEEccCCcEEEEEecCcchHHHHHHHHHHHHhcCCeEEEcCCCcccccHH----HHHH
Confidence 3578888 888876610 0 6677888888899888888786 44 5555554432 2222
Q ss_pred hhHhhh-hhc---------cccccc--hhhhHHHHHHHHHhccCCCchhhHHhHHHHHHHhhcccCCc
Q psy11442 667 ACRVLI-SII---------HALHGL--AYIKSAKHHLRRVIGAQLLTFEEFTTLLCKIEAILRFDERL 722 (1362)
Q Consensus 667 ~~~~l~-~~i---------~W~GGl--r~VksvK~~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Pl 722 (1362)
+. .+| +|..|. |..+.+|..|++.. .+.+++...|.+++...|.| |-
T Consensus 130 ----~~~~gi~~~~s~p~~p~~nG~~Er~~~~lk~~l~~~~----~~~~~~~~~l~~~~~~~N~~-~~ 188 (212)
T 1k6y_A 130 ----CDWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVR----DQAEHLKTAVQMAVFIHNKK-RK 188 (212)
T ss_dssp ----HHHHTCEECCC---------HHHHHHHHHHHHHHTTG----GGCSSHHHHHHHHHHHHHHS-CC
T ss_pred ----HHHCCCeeeECCCCCCcchhHHHHHHHHHHHHHHHHh----cchhhHHHHHHHHHHHhccc-cc
Confidence 33 344 567777 99999999885543 34577888999999999999 74
No 23
>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}
Probab=88.10 E-value=1.7 Score=45.16 Aligned_cols=73 Identities=12% Similarity=-0.023 Sum_probs=42.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHH----HHhcC-CCccc----hhHHHH--HHHHHhh---CC
Q psy11442 301 PRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLA----WLRTA-PHLLQ----TYVANR--VVEINKL---AD 366 (1362)
Q Consensus 301 PRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~----wi~~~-~~~~~----~fv~NR--v~~I~~~---~~ 366 (1362)
-|.|++|.+.|+..+. ...+. . -.++.++|||+-|+. |+.+= .+.|+ .-|.|+ .++|.++ ..
T Consensus 53 n~te~~Aei~Al~~al--~~al~-~-~~~v~I~TDS~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~ 128 (165)
T 2lsn_A 53 NHTAQMAEIAAVEFAC--KKALK-I-PGPVLVITDSFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKP 128 (165)
T ss_dssp SCCHHHHHHHHHHHHH--HHHHH-S-SSCEEEEESCHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHH--HHHhc-C-CCeEEEEeChHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCC
Confidence 3778888887775442 33444 2 246999999998864 33210 01122 235554 2334332 34
Q ss_pred CCceEeecCCC
Q psy11442 367 GCKWYHVPTSE 377 (1362)
Q Consensus 367 ~~~w~hvpt~~ 377 (1362)
.+.|.||++..
T Consensus 129 ~v~~~~VkgH~ 139 (165)
T 2lsn_A 129 DITIQHEKGHQ 139 (165)
T ss_dssp TCEEEECCSSS
T ss_pred CEEEEEEeCCC
Confidence 68999999864
No 24
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B
Probab=86.72 E-value=1.3 Score=54.69 Aligned_cols=68 Identities=19% Similarity=0.154 Sum_probs=47.2
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhcCCC-ccchhHHHHHHHHHhhCCCCceEeecCC
Q psy11442 298 LSIPRLELCAALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRTAPH-LLQTYVANRVVEINKLADGCKWYHVPTS 376 (1362)
Q Consensus 298 ~tIPRlEL~a~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~~~~-~~~~fv~NRv~~I~~~~~~~~w~hvpt~ 376 (1362)
.|--+.|+.|++.|.+. ...++.++|||+.|+.+|.+-.. ..+.....-+..+.+ .....|.|||+.
T Consensus 471 ~TNn~aEl~A~i~aL~~-----------~~~~v~I~tDS~~v~~~i~~~~~~~~~~l~~~~~~~~~~-~~~v~~~wV~~H 538 (555)
T 1mu2_A 471 TTNQQAELEAFAMALTD-----------SGPKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMIK-KEAIYVAWVPAH 538 (555)
T ss_dssp CCHHHHHHHHHHHHHHT-----------SCSEEEEEESCHHHHHHHHTCCSEESCHHHHHHHHHHHH-CSEEEEEECCSS
T ss_pred CCHHHHHHHHHHHHHHc-----------CCCeEEEEEehHHHHHHHhcccccccHHHHHHHHHHhcc-CCcEEEEEEECC
Confidence 67889999999999875 34689999999999999986321 122233222223333 345789999985
Q ss_pred C
Q psy11442 377 E 377 (1362)
Q Consensus 377 ~ 377 (1362)
.
T Consensus 539 ~ 539 (555)
T 1mu2_A 539 K 539 (555)
T ss_dssp S
T ss_pred C
Confidence 3
No 25
>1c6v_A Protein (SIV integrase); DNA integration, DNA binding protein; 3.00A {Simian immunodeficiency virus} SCOP: c.55.3.2
Probab=85.69 E-value=1.2 Score=44.77 Aligned_cols=88 Identities=16% Similarity=0.047 Sum_probs=55.3
Q ss_pred cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhHhh-----hHhhh-hhccccccc--hhhhHHHHHHHH
Q psy11442 625 NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKCKA-----CRVLI-SIIHALHGL--AYIKSAKHHLRR 693 (1362)
Q Consensus 625 v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~~~-----~~~l~-~~i~W~GGl--r~VksvK~~L~k 693 (1362)
+.+.++..++.++...+.+.|. ++ +|..++.+.. ++.+. .-... .+.+|..|. |..+.+|..+.+
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~i~sDnG~~f~s~~----~~~~~~~~gi~~~~~~p~~p~~ng~vEr~~~~lk~~l~~ 115 (164)
T 1c6v_A 40 IPQETGRQTALFLLKLAGRWPITHLHTDNGANFASQE----VKMVAWWAGIEHTFGVPYNPQSQGVVEAMNHHLKNQIDR 115 (164)
T ss_dssp CSSCSHHHHHHHHHHHHTTSCCCEEECCCCSSTTSSH----HHHHHHHHTCEEECC-----------CCTTTHHHHHHHT
T ss_pred cCCCchHHHHHHHHHHHHhcCCCEEEeCCchhhhhHH----HHHHHHHcCCeEeECCCCCCcccceehHHHHHHHHHHHH
Confidence 6788888999999998888886 44 6555554432 22220 00011 344666677 999999997765
Q ss_pred HhccCCCchhhHHhHHHHHHHhhcccCC
Q psy11442 694 VIGAQLLTFEEFTTLLCKIEAILRFDER 721 (1362)
Q Consensus 694 ~ig~~~lt~eel~t~l~eiea~lNsr~P 721 (1362)
...+.+++...+.++....|.+ |
T Consensus 116 ----~~~~~~~~~~~l~~~~~~~N~~-~ 138 (164)
T 1c6v_A 116 ----IREQANSVETIVLMAVHCMNHK-R 138 (164)
T ss_dssp ----TTTSSSCHHHHHHHHHHHHHSC-C
T ss_pred ----HhccHHHHHHHHHHHHHHHhcC-c
Confidence 3345678999999999999999 6
No 26
>1fmb_A EIAV protease; hydrolase (acid proteinase), RNA-directed DNA polymerase, AS protease, endonuclease, polyprotein; HET: HYB; 1.80A {Equine infectious anemia virus} SCOP: b.50.1.1 PDB: 2fmb_A*
Probab=85.15 E-value=0.44 Score=45.74 Aligned_cols=51 Identities=27% Similarity=0.514 Sum_probs=40.3
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeee-ceeeeecCCCCcccCCCccchhh
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKC-GISISGIGDNGVPDNKGAVSCTL 70 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 70 (1362)
+++.||||.|+..++|...-...++|..++| ..+|.|+||. ..|+ .-+|.+
T Consensus 18 q~~e~LLDTGAD~TVl~~~~w~~i~lp~~~w~p~~i~GiGG~--i~v~-~~~i~i 69 (104)
T 1fmb_A 18 TPLNVLLDTGADTSVLTTAHYNRLKYRGRKYQGTGIGGVGGN--VETF-STPVTI 69 (104)
T ss_dssp EEEEEEECTTCSSCEEEHHHHHHCSSCCCCEECCCEEETTEE--ECCE-EEEEEE
T ss_pred EEEEEEeccCCCcEEEccccCcccCCCCccCCccEEEeCCCe--EEee-EeeeEE
Confidence 4899999999999999999999999998843 4689999985 3444 444433
No 27
>3hph_A Integrase, IN; protein-protein complex, tetramer, DNA integration, endonucl magnesium, metal-binding, multifunctional enzyme; 2.64A {Maedi visna virus} PDB: 3hpg_A
Probab=80.54 E-value=1.7 Score=46.43 Aligned_cols=86 Identities=16% Similarity=0.209 Sum_probs=63.5
Q ss_pred cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhHhhhHhhh-hhc---------cccccc--hhhhHHHH
Q psy11442 625 NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKCKACRVLI-SII---------HALHGL--AYIKSAKH 689 (1362)
Q Consensus 625 v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~~~~~~l~-~~i---------~W~GGl--r~VksvK~ 689 (1362)
+.+.++..+..++.+++++.|. ++ ++..++.+.. +.++ +. .+| +|.+|. |..+.+|.
T Consensus 91 ~~~~~~~~~~~~l~~~~~~~gp~~i~sDnG~~F~s~~----~~~~----~~~~gi~~~~s~p~~p~~nG~~Er~~~~lk~ 162 (219)
T 3hph_A 91 VKGETGQEFRVQTMKWYAMFAPKSLQSDNGPAFVAES----TQLL----MKYLGIEHTTGIPWNPQSQALVERTHQTLKN 162 (219)
T ss_dssp ESCCCHHHHHHHHHHHHHHHCCCEEEECCCHHHHSHH----HHHH----HHHHTCEEEESCCCCHHHHHHHHHHHHHHHH
T ss_pred eCCCCHHHHHHHHHHHHHHhCCcEEEeCCCchhhhHH----HHHH----HHHcCCeEeECCCCCCcccChhhhHHHHHHH
Confidence 6788899999999999999997 44 5554433322 2222 33 444 456677 99999999
Q ss_pred HHHHHhccCCCchhhHHhHHHHHHHhhcccCCcc
Q psy11442 690 HLRRVIGAQLLTFEEFTTLLCKIEAILRFDERLA 723 (1362)
Q Consensus 690 ~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Plt 723 (1362)
.|.+.... .+++.+.|.+++...|.+ |..
T Consensus 163 ~l~~~~~~----~~~~~~~l~~~~~~~N~~-~~~ 191 (219)
T 3hph_A 163 TLEKLIPM----FNAFESALAGTLITLNIK-RKG 191 (219)
T ss_dssp HHHHHGGG----CSSHHHHHHHHHHHHHTT-CCC
T ss_pred HHHHHhcc----cccHHHHHHHHHHHHhCC-CCC
Confidence 99987664 358999999999999999 664
No 28
>1c0m_A Protein (integrase); HIV, X-RAY crystallography, protein structure, transferase; 2.53A {Rous sarcoma virus} SCOP: b.34.7.1 c.55.3.2 PDB: 1c1a_A
Probab=76.57 E-value=3.2 Score=45.11 Aligned_cols=90 Identities=12% Similarity=-0.040 Sum_probs=60.3
Q ss_pred cCCCchhhHHHHhhhhhhcccc---ee-cCCccccccchhhhhhHh-----hhHhhh-hhccccccc--hhhhHHHHHHH
Q psy11442 625 NPSNLGNSYLGAERRFYSLERK---LH-ANPSLLFSGVAWSKFKCK-----ACRVLI-SIIHALHGL--AYIKSAKHHLR 692 (1362)
Q Consensus 625 v~~lst~sfl~al~rf~~rrG~---fv-a~~~~~~~~~~~~~~~~~-----~~~~l~-~~i~W~GGl--r~VksvK~~L~ 692 (1362)
+.+.+++..+.+|.+.+.++|. +. +|..++.+.. +..+ +...+. .+-+|..|. |..+.+|..+.
T Consensus 45 ~~~~~~~~v~~~l~~~~~~~g~p~~i~sDnG~~f~s~~----~~~~~~~~gI~~~~~~p~~p~~ng~vEr~~~tlk~~~~ 120 (238)
T 1c0m_A 45 HGRVTSVAVQHHWATAIAVLGRPKAIKTDNGSCFTSKS----TREWLARWGIAHTTGIPGNSQGQAMVERANRLLKDRIR 120 (238)
T ss_dssp ESSCCHHHHHHHHHHHHHHHCCCSEEEECSCHHHHSHH----HHHHHHHHTCEEEECCSSSSTTSHHHHHHHHHHHHHHH
T ss_pred ccCCCHHHHHHHHHHHHHHhCCCcEEEECCCCccccHH----HHHHHHHCCCEEEecCCCCcccccHHHHHHHHHHHHHH
Confidence 5588999999999999999997 44 5554443322 2222 000011 334567777 99999999998
Q ss_pred HHh-ccCC----CchhhHHhHHHHHHHhhccc
Q psy11442 693 RVI-GAQL----LTFEEFTTLLCKIEAILRFD 719 (1362)
Q Consensus 693 k~i-g~~~----lt~eel~t~l~eiea~lNsr 719 (1362)
+.+ +... -+.+++. .|.+.....|.+
T Consensus 121 ~~~~~~~~~~~~~~~~~~~-~l~~~i~~yN~~ 151 (238)
T 1c0m_A 121 VLAEGDGFMKRIPTSKQGE-LLAKAMYALNHK 151 (238)
T ss_dssp HHHHHTTCSSSCCGGGHHH-HHHHHHHHHHSS
T ss_pred HhcccccccccCCcHHHHH-HHHHHHHHHcCC
Confidence 876 3332 4778875 777777788987
No 29
>3kks_A Integrase, IN; beta-strands flanked by alpha-helices, DNA binding protein; 2.20A {Bovine immunodeficiency virus} PDB: 3kkr_A
Probab=75.83 E-value=2.4 Score=41.83 Aligned_cols=95 Identities=12% Similarity=-0.015 Sum_probs=65.5
Q ss_pred cccccccccc---cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhHhhhHhhh-hh---------cccc
Q psy11442 615 RYSIAMPFQH---NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKCKACRVLI-SI---------IHAL 678 (1362)
Q Consensus 615 GvDy~GP~~~---v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~~~~~~l~-~~---------i~W~ 678 (1362)
-+|.+--+.+ ..+.+++..+.+|.+++.+.|. +. ++..++.+.. +... +. .+ .+|.
T Consensus 20 ~iD~~sr~~~~~~~~~~~~~~~~~~l~~~~~~~gp~~i~sDnG~~f~s~~----~~~~----~~~~gi~~~~~~p~~p~~ 91 (152)
T 3kks_A 20 AVETNSGLVEAQVIPEETALQVALCILQLIQRYTVLHLHSDNGPCFTAHR----IENL----CKYLGITKTTGIPYNPQS 91 (152)
T ss_dssp EEETTTCCEEEEEESSSCHHHHHHHHHHHHHHSCCSEEEECSCHHHHSHH----HHHH----HHHTTCEEEESSCSCHHH
T ss_pred EEEcCCCcEEEEEeCCcCHHHHHHHHHHHHHHhCCcEEecCCchHhhHHH----HHHH----HHHcCCeecccCCcCCCc
Confidence 4454443333 6688999999999999999997 44 5544443322 2222 23 34 3556
Q ss_pred ccc--hhhhHHHHHHHHHhccCCCchhhHHhHHHHHHHhhcccCCcc
Q psy11442 679 HGL--AYIKSAKHHLRRVIGAQLLTFEEFTTLLCKIEAILRFDERLA 723 (1362)
Q Consensus 679 GGl--r~VksvK~~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Plt 723 (1362)
.|. |..+.+|..+.+... +.+++...|.++....| | |-.
T Consensus 92 ng~~Er~~~~lk~~~~~~~~----~~~~~~~~l~~~~~~~N-~-~~~ 132 (152)
T 3kks_A 92 QGVVERAHRDLKDRLAAYQG----DCETVEAALSLALVSLN-K-KRG 132 (152)
T ss_dssp HHHHHHHHHHHHHHHHHHGG----GCSSHHHHHHHHHHHHH-H-SCC
T ss_pred cchhHHHHHHHHHHHHHHhC----CHHHHHHHHHHHHHHHc-C-ccc
Confidence 776 999999999988773 44688889999999999 8 644
No 30
>3l3u_A POL polyprotein; DNA integration, AIDS, integrase, endonuclease, polynucleotidyl transferase, DNA binding, viral protein; 1.40A {Human immunodeficiency virus 1} PDB: 3ao1_A 3l3v_A* 3ovn_A* 3ao2_A* 3ao3_A* 3ao4_A* 3ao5_A* 2itg_A 1biz_A 1biu_A 1b9d_A 4dmn_A* 2b4j_A 1itg_A 1b92_A 1bl3_A 1bi4_A 1bis_A 1b9f_A 1bi4_B ...
Probab=64.52 E-value=10 Score=37.95 Aligned_cols=88 Identities=17% Similarity=0.033 Sum_probs=60.1
Q ss_pred cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhHh-----hhHhhh-hhccccccc--hhhhHHHHHHHH
Q psy11442 625 NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKCK-----ACRVLI-SIIHALHGL--AYIKSAKHHLRR 693 (1362)
Q Consensus 625 v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~~-----~~~~l~-~~i~W~GGl--r~VksvK~~L~k 693 (1362)
+.+.+++....++.+.+.+.|. +. ++..++.+.. ++++ +...+. .+.+|..|. |..+.+|..+.+
T Consensus 40 ~~~~~~~~~~~~l~~~~~~~~~~~i~sD~G~~f~s~~----~~~~~~~~gi~~~~~~p~~p~~ng~~Er~~~~lk~~~~~ 115 (163)
T 3l3u_A 40 IPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTT----VKAACDWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQ 115 (163)
T ss_dssp ESSCCHHHHHHHHHHHHHHSCCCEEEECCCGGGGSHH----HHHHHHHHTCEEEETCCCCCCSTTCCSCHHHHHHHHHHH
T ss_pred eCCCcHHHHHHHHHHHHHHcCCcEEeecChHhhhhHH----HHHHHHHCCceeeeCCCCCcccccHHHHHHHHHHHHHHH
Confidence 6677889999999998888887 44 5555544332 2222 000012 334667777 999999998888
Q ss_pred HhccCCCchhhHHhHHHHHHHhhcccCC
Q psy11442 694 VIGAQLLTFEEFTTLLCKIEAILRFDER 721 (1362)
Q Consensus 694 ~ig~~~lt~eel~t~l~eiea~lNsr~P 721 (1362)
... +.+++...+..+....|.| |
T Consensus 116 ~~~----~~~~~~~~l~~~~~~~N~~-~ 138 (163)
T 3l3u_A 116 VRD----QAEHLKTAVQMAVFIHNHK-R 138 (163)
T ss_dssp HGG----GCSSHHHHHHHHHHHHHHC-E
T ss_pred hhh----hHHHHHHHHHHHHHHHccC-C
Confidence 653 3456888888888899999 6
No 31
>3av9_A Integrase, IN; protein-protein interactions, HIV, recombination-inhibitor C; 1.70A {Human immunodeficiency virus type 1} PDB: 3ava_A 3avb_A 3avc_A 3avg_A 3avh_A 3avi_A 3avj_A 3avk_A 3avl_A 3avm_A 3avn_A 3nf6_A* 3nf7_A* 3nf8_A* 3nf9_A* 3nfa_A* 3avf_A
Probab=46.42 E-value=11 Score=38.84 Aligned_cols=85 Identities=18% Similarity=0.034 Sum_probs=56.9
Q ss_pred cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhHhhhHhhh-hh---------ccccccc--hhhhHHHH
Q psy11442 625 NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKCKACRVLI-SI---------IHALHGL--AYIKSAKH 689 (1362)
Q Consensus 625 v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~~~~~~l~-~~---------i~W~GGl--r~VksvK~ 689 (1362)
+.+-++...+.++.+.+.+.|. +. +|..++.+.. +..+ +. .+ .+|..|. |..+.+|.
T Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~i~sDnG~ef~s~~----~~~~----~~~~gI~~~~s~p~~P~~nG~vEr~~~tlk~ 131 (183)
T 3av9_A 60 IPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTT----VKAA----CWWAGIKQEDGIPYNPQSQGVIESMNKELKK 131 (183)
T ss_dssp ESSCCHHHHHHHHHHHHHHSCCCEEECSSHHHHHCHH----HHHH----HHHHTCEEECCCCSSHHHHHHHHHHHHHHHH
T ss_pred eCCccchHHHHHHHHHHHHcCCcEEEecCchhcchHH----HHHH----HHHCCCEEeecCCCCCcchhHHHHHHHHHHH
Confidence 5677888888888888877776 33 4444433322 2222 22 33 4566677 99999999
Q ss_pred HHHHHhccCCCchhhHHhHHHHHHHhhcccCCc
Q psy11442 690 HLRRVIGAQLLTFEEFTTLLCKIEAILRFDERL 722 (1362)
Q Consensus 690 ~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Pl 722 (1362)
.+.+.. .+.+++...+.++....|.+ |.
T Consensus 132 ~l~~~~----~~~~~~~~~l~~~~~~yN~~-~~ 159 (183)
T 3av9_A 132 IIGQVR----DQAEHLKTAVQMAVFIHNHK-RK 159 (183)
T ss_dssp HHHHHG----GGCSSHHHHHHHHHHHHHHC-BC
T ss_pred HHHHHh----cCHHHHHHHHHHHHHHHhcC-CC
Confidence 887743 34567888888888889988 54
No 32
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...
Probab=45.85 E-value=2e+02 Score=35.07 Aligned_cols=174 Identities=7% Similarity=-0.021 Sum_probs=86.6
Q ss_pred CCceEEeeeeecCCceEEEEEecccccCCCCCccccCCCCCCCcccccchhhHHHHHHHHHhhccccccchhhccccccc
Q psy11442 116 STFKILSVFIGNQQLTLSLIMLLRSILSAPSDQFFISPSKVAPTKQLLSIPRLELCAALLLSRLYNSLHNYLTKLNVKNV 195 (1362)
Q Consensus 116 ~~~K~LG~~w~~~~D~l~~~~~~~~~~~~~~~~~~~~~~~~~tkR~~lS~p~~el~~a~~~a~~~Dpl~G~l~p~~~~~k 195 (1362)
...+.||+.++...- ++. | ..++.....|++++-++ +|.+--.|-|=|--+ +.|+.-
T Consensus 227 ~~~~fLG~~i~~~gi----~~~-------~---~k~~~~~~~t~k~lr~f-----lG~~~~yrrfi~~~~-~~pl~~--- 283 (557)
T 2zd1_A 227 PPFLWMGYELHPDKW----TVQ-------P---IVLPEKDSWTVNDIQKL-----VGKLNWASQIYPGIK-VRQLSK--- 283 (557)
T ss_dssp SSEEETTEEECSSCE----EES-------C---CCCCCCSCEEHHHHHHH-----HHHHHHHTTTSTTCC-CHHHHG---
T ss_pred CceEEeeEEEccCcE----EEc-------c---eecccccCCCHHHHHHH-----hhHHHhhhhhccchh-HHHHHH---
Confidence 357899999977642 332 1 11223334488888887 333222222222101 122210
Q ss_pred eecccccc--ccccccCCCChhhHHHHHHHHHhhccccccccceeeeeecceeeeccccccc-ceEEEEEeccccccccc
Q psy11442 196 TTFFSDSN--IVLAWLRTAPHLLQTYVANRVVEINNDITFLLRKILVIVLRVIYFPSNLFLI-RYGGMVLSFSPLLIGQS 272 (1362)
Q Consensus 196 ~~~q~~~~--~~l~Wd~~l~~~~~~~w~~~~~~l~~~~~~~ipR~~~~~~~~~~F~~DAS~~-ayga~~Ylr~~~~~g~~ 272 (1362)
++...-. ....|+ ++....+.++.+.+.+...+..|. +.....+.| |||.. ++|+|++=.
T Consensus 284 -ll~~~~~~~~~~~Wt----~~~~~af~~lK~~L~~~p~L~~pd---~~~~~~l~~-das~~g~~g~vl~q~-------- 346 (557)
T 2zd1_A 284 -LLRGTKALTEVIPLT----EEAELELAENREILKEPVHGVYYD---PSKDLIAEI-QKQGQGQWTYQIYQE-------- 346 (557)
T ss_dssp -GGTTCCCTTCEECCC----HHHHHHHHHHHHHTSSCCCBCCCC---TTSCCEEEE-EEEETTEEEEEEEEE--------
T ss_pred -HhcccCCCCCceecC----HHHHHHHHHHHHHHhCccceeecC---CCCCEEEEE-ecCCCCcEEEEEecC--------
Confidence 1111111 235555 456778888888777633333332 222228889 99997 468886543
Q ss_pred cCCCceeeeeeeeeeccccccCcccccchhhHHHH-HHHHHHHHHHHHHHhccCCcccEEE-eechHHHHHHH
Q psy11442 273 YPSGFKFCNRGLIKAKSKVAPTKQLLSIPRLELCA-ALLLSRLYNSLHNYLTKLNVKNVTF-FSDSNIVLAWL 343 (1362)
Q Consensus 273 ~~~~~~~~~~~li~aKsrv~P~k~~~tIPRlEL~a-~~l~~~l~~~~~~~l~~~~i~~~~~-~tDS~i~L~wi 343 (1362)
++..+. +. +.+..+. +++..+|++| ++.+.+- ..-+|-. ....+.+ .||++...+|.
T Consensus 347 --~~~~~~-~~------~~~~~~~-y~~~e~e~la~vv~~l~~---~~~~l~g-~~p~~~vp~~~~~~~~~~~ 405 (557)
T 2zd1_A 347 --PFKNLK-TG------KYARMRG-AHTNDVKQLTEAVQKITT---ESIVIWG-KTPKFKLPIQKETWETWWT 405 (557)
T ss_dssp --TTEEEE-EE------EEECCSC-SEECHHHHHHHHHHHHHH---HHHHHHS-SCCEEEESBCHHHHHHHHH
T ss_pred --CCceee-ee------ecccccc-cCCChHHHHHHHHHHhhh---hheEEeC-CCCCEECCCcHHHHHHHhh
Confidence 222211 11 1222334 8889999998 5444333 2333321 1113444 78988555443
No 33
>2hs1_A HIV-1 protease; ultra-high resolution active site surface binding site, HYDR; HET: 017; 0.84A {Human immunodeficiency virus 1} PDB: 3nu4_A* 3tl9_A* 3tkw_A* 3tkg_A* 3ndu_A* 3ndt_A* 3k4v_A* 3a2o_A* 1fgc_C* 2a1e_A* 2aod_A* 2aoi_A* 2aoj_A* 2hb3_A* 2ien_A* 1sdt_A* 2z4o_A* 2zye_A* 2nmw_A* 3b7v_A* ...
Probab=40.80 E-value=11 Score=35.84 Aligned_cols=46 Identities=17% Similarity=0.137 Sum_probs=32.6
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCCCcccCCCccchh
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGVPDNKGAVSCT 69 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 (1362)
+++.||||.|...++|.. ..|+.+-...+|.|+||. ..|+..-+|.
T Consensus 18 q~~eaLLDTGAD~TVl~~-----~~~p~~wkpk~igGiGG~--i~v~qy~qi~ 63 (99)
T 2hs1_A 18 QLKEALLDTGADDTIIEE-----MSLPGRWKPKMIGGIGGF--IKVRQYDQII 63 (99)
T ss_dssp EEEEEEECTTCSSEEESC-----CSSCCCCEEEEEEETTEE--EEEEEEEEEE
T ss_pred EEEEEEeccCCCcEEEec-----ccCCCCCCCcEEEeCCCc--EeeeEeccEE
Confidence 689999999999999984 355544334699999974 4444444443
No 34
>1ex4_A Integrase; SH3-like domain, nonspecific DNA binding beta sheet, CIS-Pro viral protein; HET: CPS; 2.80A {Human immunodeficiency virus 1} SCOP: b.34.7.1 c.55.3.2 PDB: 1qmc_A 1ihv_A 1ihw_A
Probab=40.22 E-value=24 Score=38.04 Aligned_cols=85 Identities=15% Similarity=0.015 Sum_probs=52.8
Q ss_pred cCCCchhhHHHHhhhhhhcccc--ee-cCCccccccchhhhhhHhhhHhhh-hh---------ccccccc--hhhhHHHH
Q psy11442 625 NPSNLGNSYLGAERRFYSLERK--LH-ANPSLLFSGVAWSKFKCKACRVLI-SI---------IHALHGL--AYIKSAKH 689 (1362)
Q Consensus 625 v~~lst~sfl~al~rf~~rrG~--fv-a~~~~~~~~~~~~~~~~~~~~~l~-~~---------i~W~GGl--r~VksvK~ 689 (1362)
+.+-++..+..++...+.+.|. +. +|..++.+.. +..+ +. .+ .+|..|. |..+.+|.
T Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~~i~sDnG~eF~s~~----~~~~----~~~~gI~~~~s~p~~P~~NG~vEr~n~tlk~ 111 (239)
T 1ex4_A 40 IPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGAT----VRAA----CDWAGIKQEDGIPYNPQSQGVVESMNKELKK 111 (239)
T ss_dssp CSSSSTTHHHHHHHHHHHHSCCCEEEECCCHHHHCHH----HHHH----HTTTTCEECCCCC---CSSHHHHHHHHHHHH
T ss_pred eCCCCHHHHHHHHHHHHHhcCCcEEEecCcHHHHHHH----HHHH----HHHCCCeEEECCCCCcccchHHHHHHHHHHH
Confidence 5566777777777777776665 44 5554433322 2222 22 33 4567777 99999999
Q ss_pred HHHHHhccCCCchhhHHhHHHHHHHhhcccCCc
Q psy11442 690 HLRRVIGAQLLTFEEFTTLLCKIEAILRFDERL 722 (1362)
Q Consensus 690 ~L~k~ig~~~lt~eel~t~l~eiea~lNsr~Pl 722 (1362)
.+.+.. .+.+++...+.+..-..|.| |-
T Consensus 112 ~l~~~~----~~~~~~~~~l~~~~~~~n~~-~~ 139 (239)
T 1ex4_A 112 IIGQVR----DQAEHLKTAVQMAVFIHNKK-RK 139 (239)
T ss_dssp HHHHHG----GGCSSSHHHHHHHHHHHHHC-CS
T ss_pred HHHHHh----hhHHHHHHHHHHHHHHHhCC-cc
Confidence 886654 34466777777777788988 64
No 35
>2zd1_B P51 RT; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} SCOP: e.8.1.2 PDB: 2ykm_B* 2ykn_B* 2ze2_B* 3bgr_B* 3ig1_B* 3irx_B* 3is9_B* 3qo9_B* 3v4i_B* 3v6d_B* 3v81_B* 3klf_B* 3kk1_B* 3kjv_B* 3kk2_B* 3kk3_B* 2be2_B* 1n5y_B* 1bqm_B* 1n6q_B* ...
Probab=35.67 E-value=98 Score=36.61 Aligned_cols=111 Identities=7% Similarity=-0.121 Sum_probs=63.7
Q ss_pred ccccCCCChhhHHHHHHHHHhhccccccccceeeeeecceeeeccccccc-ceEEEEEeccccccccccCCCceeeeeee
Q psy11442 206 LAWLRTAPHLLQTYVANRVVEINNDITFLLRKILVIVLRVIYFPSNLFLI-RYGGMVLSFSPLLIGQSYPSGFKFCNRGL 284 (1362)
Q Consensus 206 l~Wd~~l~~~~~~~w~~~~~~l~~~~~~~ipR~~~~~~~~~~F~~DAS~~-ayga~~Ylr~~~~~g~~~~~~~~~~~~~l 284 (1362)
..|+ ++....+.++.+.+.+...+..| .+.....+.| |||.. ++|+|++-. +|..
T Consensus 293 ~~Wt----~~~~~af~~lK~~L~~~p~l~~p---d~~~~~~l~~-das~~g~~g~vl~q~----------~~~~------ 348 (428)
T 2zd1_B 293 IPLT----EEAELELAENREILKEPVHGVYY---DPSKDLIAEI-QKQGQGQWTYQIYQE----------PFKN------ 348 (428)
T ss_dssp ECCC----HHHHHHHHHHHHHTTSCCTTCCC---CTTSCCEEEE-EEEETTEEEEEEESS----------TTCE------
T ss_pred ecCC----HHHHHHHHHHHHHHhcchhcccc---CCCCCEEEEE-ecCCCCcEEEEEecC----------CCce------
Confidence 5564 55677788877777663222222 2222228888 99995 668876544 2332
Q ss_pred eeeccccccCcccccchhhHHHH-HHHHHHHHHHHHHHhccCCcccEEEeechHHHHHHHhc
Q psy11442 285 IKAKSKVAPTKQLLSIPRLELCA-ALLLSRLYNSLHNYLTKLNVKNVTFFSDSNIVLAWLRT 345 (1362)
Q Consensus 285 i~aKsrv~P~k~~~tIPRlEL~a-~~l~~~l~~~~~~~l~~~~i~~~~~~tDS~i~L~wi~~ 345 (1362)
..++ +.++.+. .++.-+|++| ++.+.+ ...-+|-.-....++.+||.+..-+|...
T Consensus 349 ~~s~-~~~~~~~-y~~~~~e~la~vv~al~---~~r~yl~G~~~~~~i~~td~~~~~~~~~~ 405 (428)
T 2zd1_B 349 LKTG-KYARMRG-AHTNDVKQLTEAVQKIT---TESIVIWGKTPKFKLPIQKETWETWWTEY 405 (428)
T ss_dssp EEEE-EEECCSS-CTTCHHHHHHHHHHHHH---HHHHHHHSSCCEEEESSCHHHHHHHHHHH
T ss_pred eeec-ccchhhh-cccchHHHHHHHHHHhh---ccceEEECCCCcEECCccHHHHHHHHHhc
Confidence 2232 2334454 8888899998 554443 33333311123456789999976666543
No 36
>3ec0_A Protease; HIV-2, inhibitor, hydrolase; HET: GRL; 1.18A {Human immunodeficiency virus type 2} SCOP: b.50.1.1 PDB: 1hii_A* 1hsi_A 1hsh_A* 1idb_A* 1jld_A* 2mip_A 1ida_A* 3ebz_A* 3ecg_A* 3s45_A* 4upj_A* 1ivq_A* 1ivp_A 2hpf_A 3upj_A* 2hpe_A* 5upj_A* 6upj_A* 1sip_A 1tcw_A* ...
Probab=33.27 E-value=17 Score=34.53 Aligned_cols=35 Identities=23% Similarity=0.418 Sum_probs=25.8
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeee-ceeeeecCCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKC-GISISGIGDN 57 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 57 (1362)
+++.||||.|...++|.. ..|. .+| .-+|.|+||.
T Consensus 18 q~~e~LLDTGAD~TVl~~-----~~~P-g~w~pk~igGiGG~ 53 (99)
T 3ec0_A 18 QPVEVLLDTGADDSIVAG-----IELG-NNYSPKIVGGIGGF 53 (99)
T ss_dssp EEEEEEECTTCSSCEESS-----CCCC-SCCEEEEEEETTEE
T ss_pred EEEEEEEecCCCceEEcC-----cccC-CCCCceEEEecCCc
Confidence 589999999999999952 3333 223 3489999973
No 37
>3slz_A GAG-Pro-POL polyprotein; beta sheet and dimer, protease, peptide inhibitor, TL-3 PEPS virus, hydrolase-hydrolase inhibitor complex; HET: 3TL; 1.40A {Dg-75 murine leukemia virus} PDB: 3nr6_A* 3sm1_A* 3sm2_A* 4exh_A*
Probab=31.77 E-value=7.1 Score=38.96 Aligned_cols=38 Identities=21% Similarity=0.260 Sum_probs=29.3
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCCCc
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDNGV 59 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 (1362)
+++++|||.|...++|...-+. +++ ....|.|+||...
T Consensus 32 ~~~~~LlDTGAd~tVl~~~~~p---~~~--~p~~I~GiGG~i~ 69 (132)
T 3slz_A 32 QPVTFLVDTGAQHSVLTQNPGP---LSD--KSAWVQGATGGKR 69 (132)
T ss_dssp EEEEEEECTTCSSCEECSCCCS---EEE--EEEEEECSSCEEE
T ss_pred EEEEEEEeCCCCeEEEccccCC---CCC--CceEEEccCCEEE
Confidence 6999999999999999864332 333 3478999999754
No 38
>2hah_A Protease, retropepsin; retroviral, aspartyl, hydrolase-hydrolase complex; HET: 3TL; 1.70A {Feline immunodeficiency virus} PDB: 3ogp_A* 3ogq_A* 2fiv_A* 6fiv_A* 3fiv_A* 5fiv_A* 4fiv_A* 1fiv_A* 1b11_A*
Probab=25.25 E-value=35 Score=33.23 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=26.4
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGDN 57 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (1362)
+++.||||.|.-+++|...--.++-.+++ -++.|.|+||.
T Consensus 23 q~~eaLLDTGAD~TVi~~~~~~~~p~~wk-pk~~igGiGG~ 62 (116)
T 2hah_A 23 YPIKFLLDTGADITVLNRRDFQVKNSIEN-GRQMIGGIGGF 62 (116)
T ss_dssp EEEEEEECTTCSSCEEEGGGCCCTTCEEE-EEEEEEETTEE
T ss_pred EEEEEEecCCCCcEEEcccccccCCCCCC-CceEEecCCCc
Confidence 58999999999999998532211122222 22338999974
No 39
>3ka2_A [L-Ala51;Gly51']HIV-1 protease; beta-barrel, hydrolase-hydrolase inhibitor complex; HET: YCM 2NC; 1.40A {Synthetic} PDB: 3fsm_A* 3gi0_A* 2o40_A* 3hzc_A* 3hlo_A* 3iaw_A* 3nxe_A* 3nxn_A* 4epj_A 4ep2_A 4ep3_A 4eq0_A 4eqj_A 1hvc_A* 1g6l_A 2whh_A* 1lv1_A* 3dox_A 3kt5_A 3kt2_A ...
Probab=21.80 E-value=35 Score=36.46 Aligned_cols=35 Identities=23% Similarity=0.266 Sum_probs=28.9
Q ss_pred EEEEEeecCCCcchhhHHHHHHHhCcceeeeceeeeecCC
Q psy11442 17 SSIRVIVDPGSQVSCITNDCVQRLGLKRYKCGISISGIGD 56 (1362)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (1362)
+++.+|||.|..-++|+ .+.|..+--..+|.|+||
T Consensus 18 q~~e~LLDTGAD~TVl~-----~~~lpg~w~pk~igGIGG 52 (203)
T 3ka2_A 18 QLKEALLDTGADDTVIE-----ELNLPGXWKPKLIGGIAG 52 (203)
T ss_dssp EEEEEEECTTCSSCEEC-----SCCCSSCEEEEEEEETTE
T ss_pred EEEEEEEecCCCceEEe-----cccCCCCCCceEEEEccC
Confidence 48999999999999998 477776433568999997
Done!