Query psy7629
Match_columns 468
No_of_seqs 254 out of 1185
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 23:13:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7629.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7629hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 100.0 7.3E-30 1.6E-34 236.0 14.3 133 310-453 4-143 (161)
2 COG0328 RnhA Ribonuclease HI [ 100.0 1.4E-28 3.1E-33 224.8 14.1 134 311-453 3-146 (154)
3 PRK00203 rnhA ribonuclease H; 99.9 4.2E-27 9.1E-32 214.8 12.9 132 311-454 3-144 (150)
4 PRK08719 ribonuclease H; Revie 99.9 6E-27 1.3E-31 213.8 12.1 128 311-451 4-146 (147)
5 KOG3752|consensus 99.9 2.1E-22 4.6E-27 204.3 11.5 135 311-451 212-364 (371)
6 PF00075 RNase_H: RNase H; In 99.8 1.7E-20 3.7E-25 164.9 13.1 123 310-451 2-132 (132)
7 PRK13907 rnhA ribonuclease H; 99.8 2.8E-18 6.1E-23 151.9 13.7 120 312-452 2-127 (128)
8 PRK07708 hypothetical protein; 99.7 1.6E-15 3.5E-20 147.1 14.9 134 310-459 72-215 (219)
9 cd06222 RnaseH RNase H (RNase 99.7 1.8E-15 4E-20 127.9 13.3 119 313-450 1-130 (130)
10 PRK07238 bifunctional RNase H/ 99.6 7.9E-15 1.7E-19 152.1 12.9 123 311-452 2-132 (372)
11 PF13456 RVT_3: Reverse transc 98.9 1.5E-08 3.3E-13 82.2 10.0 84 348-451 1-86 (87)
12 PF00336 DNA_pol_viral_C: DNA 82.2 1.1 2.3E-05 43.6 2.7 61 311-384 94-154 (245)
13 PF05380 Peptidase_A17: Pao re 79.2 6.9 0.00015 36.1 7.0 51 311-365 81-143 (159)
14 PF10897 DUF2713: Protein of u 35.0 13 0.00028 36.1 0.0 52 84-135 172-238 (246)
15 KOG1812|consensus 26.3 92 0.002 33.2 4.7 40 346-387 47-86 (384)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.97 E-value=7.3e-30 Score=235.97 Aligned_cols=133 Identities=23% Similarity=0.233 Sum_probs=114.3
Q ss_pred CcEEEEEeccccCCCCceEEEEEEecCeE-EeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHhhc
Q psy7629 310 DWLHIYTDGSLINPEDGAGAGIFCELFSF-YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITN 388 (468)
Q Consensus 310 ~~i~IYTDGS~~~n~~~aG~GVv~~~~~~-~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I~~ 388 (468)
..++|||||||.+|++++|||+++.+... ....+ .+|||+|||+||++||+.+.. ...+|.|+|||+||+++|+.
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~-~~TNnraEl~Aii~aL~~~~~---~~~~v~I~TDS~yvi~~i~~ 79 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWD-IATNNIAELTAVRELLIATRH---TDRPILILSDSKYVINSLTK 79 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCC-CCCHHHHHHHHHHHHHHhhhc---CCceEEEEeChHHHHHHHHH
Confidence 36999999999999999999998765432 33333 459999999999999986642 34579999999999999999
Q ss_pred ccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhhcC
Q psy7629 389 CSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLKTS 453 (468)
Q Consensus 389 ~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~~~ 453 (468)
|..+ |++|||++++|+||+|++||++|+ ++.. ..|+|.|||||+ |.||+||++|+...
T Consensus 80 W~~~--Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-----~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 80 WVYS--WKMRKWRKADGKPVLNQEIIQEIDSLMEN-----RNIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHH--HHHCCCcccCCCccccHHHHHHHHHHHhc-----CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 9998 999999999999999999999998 5543 269999999999 99999999999754
No 2
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.96 E-value=1.4e-28 Score=224.77 Aligned_cols=134 Identities=21% Similarity=0.232 Sum_probs=119.2
Q ss_pred cEEEEEeccccCCCCceEEEEEEecCe----EEeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHh
Q psy7629 311 WLHIYTDGSLINPEDGAGAGIFCELFS----FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSI 386 (468)
Q Consensus 311 ~i~IYTDGS~~~n~~~aG~GVv~~~~~----~~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I 386 (468)
.+.|||||||.+|+|++|||+|+..+. ++...+ .+|||+||++|+++||+.+.+. +...|.|+|||+||+++|
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~--~~~~v~l~tDS~yv~~~i 79 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKEL--GACEVTLYTDSKYVVEGI 79 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhc--CCceEEEEecHHHHHHHH
Confidence 689999999999999999998875332 355555 6799999999999999999875 789999999999999999
Q ss_pred hcccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhhcC
Q psy7629 387 TNCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLKTS 453 (468)
Q Consensus 387 ~~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~~~ 453 (468)
+.|..+ |+++||+++.++||+|++||+++. ++.++ ..|.+.|||||+ |.||+||+.|++..
T Consensus 80 ~~w~~~--w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~----~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 80 TRWIVK--WKKNGWKTADKKPVKNKDLWEELDELLKRH----ELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHhh--ccccCccccccCccccHHHHHHHHHHHhhC----CeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 999888 999999999999999999999998 65543 479999999999 99999999998764
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.94 E-value=4.2e-27 Score=214.80 Aligned_cols=132 Identities=21% Similarity=0.208 Sum_probs=112.8
Q ss_pred cEEEEEeccccCCCCceEEEEEEecCe----EEeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHh
Q psy7629 311 WLHIYTDGSLINPEDGAGAGIFCELFS----FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSI 386 (468)
Q Consensus 311 ~i~IYTDGS~~~n~~~aG~GVv~~~~~----~~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I 386 (468)
.++|||||||.+|++.+|+|+++..+. +.+..+ .+||++|||+|++.||+.+.+ ...+.|+|||+|++++|
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~-~~TN~~aEL~Ai~~AL~~~~~----~~~v~I~tDS~yvi~~i 77 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEA-LTTNNRMELMAAIEALEALKE----PCEVTLYTDSQYVRQGI 77 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCC-CCcHHHHHHHHHHHHHHHcCC----CCeEEEEECHHHHHHHH
Confidence 589999999998888899998764332 233333 569999999999999998743 35799999999999999
Q ss_pred hcccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhhcCC
Q psy7629 387 TNCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLKTSP 454 (468)
Q Consensus 387 ~~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~~~p 454 (468)
+.|... |+++||+++.|++|+|+++++.|. ++.. ..|.|.|||||+ +.||+||++|+....
T Consensus 78 ~~w~~~--Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-----~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 78 TEWIHG--WKKNGWKTADKKPVKNVDLWQRLDAALKR-----HQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHH--HHHcCCcccCCCccccHHHHHHHHHHhcc-----CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 999988 999999999999999999999998 5433 479999999999 999999999997643
No 4
>PRK08719 ribonuclease H; Reviewed
Probab=99.94 E-value=6e-27 Score=213.79 Aligned_cols=128 Identities=19% Similarity=0.189 Sum_probs=108.9
Q ss_pred cEEEEEeccccCCCC---ceEEEEEEec--Ce----EEeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHH
Q psy7629 311 WLHIYTDGSLINPED---GAGAGIFCEL--FS----FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKA 381 (468)
Q Consensus 311 ~i~IYTDGS~~~n~~---~aG~GVv~~~--~~----~~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqy 381 (468)
.++|||||||.+|++ .+|+|+++.+ +. +...++..+||++|||.|++.||+.+.+. ..|+|||+|
T Consensus 4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~------~~i~tDS~y 77 (147)
T PRK08719 4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG------DVIYSDSDY 77 (147)
T ss_pred eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC------CEEEechHH
Confidence 689999999988876 4799987533 22 24445556799999999999999998542 379999999
Q ss_pred HHHHhhcccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhh
Q psy7629 382 AIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLK 451 (468)
Q Consensus 382 ai~~I~~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~ 451 (468)
|+++|+.|... |+++||+++.|++|+|+++|+.|+ ++. ...|+|.|||||+ |.||+||++|++
T Consensus 78 vi~~i~~~~~~--W~~~~w~~s~g~~v~n~dl~~~i~~l~~-----~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 78 CVRGFNEWLDT--WKQKGWRKSDKKPVANRDLWQQVDELRA-----RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHH--HHhCCcccCCCcccccHHHHHHHHHHhC-----CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 99999999998 999999999999999999999988 443 2469999999999 999999999975
No 5
>KOG3752|consensus
Probab=99.87 E-value=2.1e-22 Score=204.28 Aligned_cols=135 Identities=26% Similarity=0.269 Sum_probs=121.2
Q ss_pred cEEEEEeccccCCCCc---eEEEEEEecCe---EEeecC-ccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHH
Q psy7629 311 WLHIYTDGSLINPEDG---AGAGIFCELFS---FYKRLG-TFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAI 383 (468)
Q Consensus 311 ~i~IYTDGS~~~n~~~---aG~GVv~~~~~---~~~~L~-~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai 383 (468)
.++|||||||..||.. +|||||++++. .++++. ...|||+|||.||.+||+.|.+. ...+|+|.|||+|++
T Consensus 212 ~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~--~~~kv~I~TDS~~~i 289 (371)
T KOG3752|consen 212 IQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK--NINKVVIRTDSEYFI 289 (371)
T ss_pred ceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc--CCCcEEEEechHHHH
Confidence 5899999999988765 89999998766 477776 66799999999999999999876 566999999999999
Q ss_pred HHhhcccCCchhhhccCcccCCCC-----cchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhhh
Q psy7629 384 QSITNCSEDPSIKHNKRLRNEGQG-----KKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGLK 451 (468)
Q Consensus 384 ~~I~~~~~~~~Wk~ngW~ts~G~~-----V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa~ 451 (468)
++|+.|... |++++|+++.+.+ |.|++.+..++ +.+.+ ++..|++.||+||+ ++||.||++++.
T Consensus 290 ~~l~~wv~~--~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~--~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 290 NSLTLWVQG--WKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI--SNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred HHHHHHHhh--hccCccccccCCCccceeeecchHHHHHHHHHhhh--ccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 999999999 9999999999999 99999999998 76654 45789999999999 999999999954
No 6
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.84 E-value=1.7e-20 Score=164.91 Aligned_cols=123 Identities=26% Similarity=0.296 Sum_probs=93.1
Q ss_pred CcEEEEEeccccCCCCceEEEEEEecCe-EEeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHhhc
Q psy7629 310 DWLHIYTDGSLINPEDGAGAGIFCELFS-FYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITN 388 (468)
Q Consensus 310 ~~i~IYTDGS~~~n~~~aG~GVv~~~~~-~~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I~~ 388 (468)
+.++||||||+..+++.+|+|+++..+. +...++ ..|+++|||+||++||+.+ . ..+++|+|||+++++.|+.
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~----~~~v~I~tDS~~v~~~l~~ 75 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E----HRKVTIYTDSQYVLNALNK 75 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S----TSEEEEEES-HHHHHHHHT
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h----cccccccccHHHHHHHHHH
Confidence 3789999999987777788888765444 466666 6699999999999999954 2 2889999999999999998
Q ss_pred ccCCchhhhccCcccC-CCCcchHHHHHHHHhcCCCCCCCcceEEEEEcchh------HHHHHHHHHhhh
Q psy7629 389 CSEDPSIKHNKRLRNE-GQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHD------CLAEHLHRFGLK 451 (468)
Q Consensus 389 ~~~~~~Wk~ngW~ts~-G~~V~n~~li~~I~li~~l~~~g~~V~f~WVpgH~------E~AD~LAK~Aa~ 451 (468)
+.. .++|.... +.++.+ ++++.+ .++..|.|.|||||+ +.||+|||+|++
T Consensus 76 ~~~-----~~~~~~~~~~~~i~~-~i~~~~-------~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~ 132 (132)
T PF00075_consen 76 WLH-----GNGWKKTSNGRPIKN-EIWELL-------SRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ 132 (132)
T ss_dssp HHH-----HTTSBSCTSSSBHTH-HHHHHH-------HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred hcc-----ccccccccccccchh-heeecc-------ccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence 643 25675433 334544 444433 235689999999995 899999999974
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.78 E-value=2.8e-18 Score=151.85 Aligned_cols=120 Identities=18% Similarity=0.269 Sum_probs=96.4
Q ss_pred EEEEEeccccCCCCceEEEEEEecCeE----EeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHhh
Q psy7629 312 LHIYTDGSLINPEDGAGAGIFCELFSF----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSIT 387 (468)
Q Consensus 312 i~IYTDGS~~~n~~~aG~GVv~~~~~~----~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I~ 387 (468)
+.||||||+..+++.+|+|+++.+... .+..+ .+||+.||+.|++.||+.+.+. +..++.|+|||++++++++
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~-~~tn~~AE~~All~aL~~a~~~--g~~~v~i~sDS~~vi~~~~ 78 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLG-TMSNHEAEYHALLAALKYCTEH--NYNIVSFRTDSQLVERAVE 78 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEeccc-ccCCcHHHHHHHHHHHHHHHhC--CCCEEEEEechHHHHHHHh
Confidence 579999999888888999998865432 23333 4599999999999999999876 6678999999999999999
Q ss_pred cccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-HHHHHHHHHhhhc
Q psy7629 388 NCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-CLAEHLHRFGLKT 452 (468)
Q Consensus 388 ~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-E~AD~LAK~Aa~~ 452 (468)
+.... ...+.++++.+. ++..+ ..+.|.|||+++ +.||.||+.|+.+
T Consensus 79 ~~~~~--------------~~~~~~l~~~~~~l~~~f----~~~~~~~v~r~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 79 KEYAK--------------NKMFAPLLEEALQYIKSF----DLFFIKWIPSSQNKVADELARKAILQ 127 (128)
T ss_pred HHHhc--------------ChhHHHHHHHHHHHHhcC----CceEEEEcCchhchhHHHHHHHHHhc
Confidence 74211 124678888887 55443 468889999999 9999999999865
No 8
>PRK07708 hypothetical protein; Validated
Probab=99.66 E-value=1.6e-15 Score=147.11 Aligned_cols=134 Identities=16% Similarity=0.173 Sum_probs=97.9
Q ss_pred CcEEEEEeccccCCCCceEEEEEEec--CeE------EeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHH
Q psy7629 310 DWLHIYTDGSLINPEDGAGAGIFCEL--FSF------YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKA 381 (468)
Q Consensus 310 ~~i~IYTDGS~~~n~~~aG~GVv~~~--~~~------~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqy 381 (468)
+.+++|+|||+.++++++|+|+++.+ +.. ...++..+||+.||+.|++.||+.+.+.......|.|++||++
T Consensus 72 ~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSql 151 (219)
T PRK07708 72 HEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQV 151 (219)
T ss_pred CcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHH
Confidence 47999999999878888999987632 322 1245555799999999999999999876222335899999999
Q ss_pred HHHHhhcccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-HHHHHHHHHhhhcCCCCCCC
Q psy7629 382 AIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-CLAEHLHRFGLKTSPIGSRD 459 (468)
Q Consensus 382 ai~~I~~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-E~AD~LAK~Aa~~~pi~~r~ 459 (468)
+++.+++. |+.+ +- .-+.+...+. ++..+ ...+.|.|||+.+ +.||+||+.|+...|+.++-
T Consensus 152 Vi~qi~g~-----wk~~-----~~---~l~~y~~~i~~l~~~~---~l~~~~~~VpR~~N~~AD~LAk~Al~~~~~~~~~ 215 (219)
T PRK07708 152 VLNQLAGE-----WPCY-----DE---HLNHWLDRIEQKLKQL---KLTPVYEPISRKQNKEADQLATQALEGTVIESHK 215 (219)
T ss_pred HHHHhCCC-----ceeC-----Ch---hHHHHHHHHHHHHhhC---CceEEEEECCchhhhHHHHHHHHHHhcCCCCchh
Confidence 99999863 3222 11 1123444444 44443 3458899999999 99999999999998887653
No 9
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.65 E-value=1.8e-15 Score=127.86 Aligned_cols=119 Identities=27% Similarity=0.252 Sum_probs=90.7
Q ss_pred EEEEeccccCCCCceEEEEEEecCe--E---EeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHhh
Q psy7629 313 HIYTDGSLINPEDGAGAGIFCELFS--F---YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSIT 387 (468)
Q Consensus 313 ~IYTDGS~~~n~~~aG~GVv~~~~~--~---~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I~ 387 (468)
.+|||||...+.+.+|+|+++.+.. . ........+++.+|+.|++.||+.+... +..++.|+|||+++++.++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~--~~~~i~i~~Ds~~~~~~~~ 78 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL--GGKKVNIYTDSQYVINALT 78 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC--CCceEEEEECHHHHHHHhh
Confidence 3899999976666799998875433 2 1122245699999999999999999754 6899999999999999999
Q ss_pred cccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCCCcceEEEEEcchh-----HHHHHHHHHhh
Q psy7629 388 NCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRKAAVAHFRLLTGHD-----CLAEHLHRFGL 450 (468)
Q Consensus 388 ~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~g~~V~f~WVpgH~-----E~AD~LAK~Aa 450 (468)
++... .+.....++..+. .+ .++..+.|.|||+|+ +.||.||++|+
T Consensus 79 ~~~~~-------------~~~~~~~~~~~i~~~~----~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 79 GWYEG-------------KPVKNVDLWQRLLALL----KRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccccC-------------CChhhHHHHHHHHHHH----hCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 86531 1223456666666 33 335689999999986 99999999874
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.59 E-value=7.9e-15 Score=152.11 Aligned_cols=123 Identities=15% Similarity=0.096 Sum_probs=93.1
Q ss_pred cEEEEEeccccCCCCceEEEEEEecC--e-E----EeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHH
Q psy7629 311 WLHIYTDGSLINPEDGAGAGIFCELF--S-F----YKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAI 383 (468)
Q Consensus 311 ~i~IYTDGS~~~n~~~aG~GVv~~~~--~-~----~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai 383 (468)
.+.||||||+.+|++.+|+|+++.+. . . ...++ .+||+.||+.|++.||+.+.+. +...|.|++||++|+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~--g~~~v~i~~DS~lvi 78 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAEL--GATEVEVRMDSKLVV 78 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhC--CCCeEEEEeCcHHHH
Confidence 47899999999998889999887542 2 1 33444 5699999999999999999876 678999999999999
Q ss_pred HHhhcccCCchhhhccCcccCCCCcchHHHHHHHHhcCCCCCCCcceEEEEEcchh-HHHHHHHHHhhhc
Q psy7629 384 QSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHDIIPNLPRKAAVAHFRLLTGHD-CLAEHLHRFGLKT 452 (468)
Q Consensus 384 ~~I~~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~li~~l~~~g~~V~f~WVpgH~-E~AD~LAK~Aa~~ 452 (468)
+.|++. |+ ++|.++...+..+..+.++...|.|.|||++. +.||.||+.|+..
T Consensus 79 ~~i~~~-----~~-----------~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 79 EQMSGR-----WK-----------VKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDA 132 (372)
T ss_pred HHhCCC-----Cc-----------cCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHh
Confidence 999752 21 23344444332222233344579999999988 9999999999864
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.88 E-value=1.5e-08 Score=82.18 Aligned_cols=84 Identities=15% Similarity=0.236 Sum_probs=64.2
Q ss_pred chHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHhhcccCCchhhhccCcccCCCCcchHHHHHHHH-hcCCCCCC
Q psy7629 348 NFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTHD-IIPNLPRK 426 (468)
Q Consensus 348 n~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I~~~~~~~~Wk~ngW~ts~G~~V~n~~li~~I~-li~~l~~~ 426 (468)
+..||+.|++.||+.+.+. +..+|.|.|||+.+++.|++.... .. ....++..|. +++.
T Consensus 1 ~~~aE~~al~~al~~a~~~--g~~~i~v~sDs~~vv~~i~~~~~~-------------~~-~~~~~~~~i~~~~~~---- 60 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWEL--GIRKIIVESDSQLVVDAINGRSSS-------------RS-ELRPLIQDIRSLLDR---- 60 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCC--T-SCEEEEES-HHHHHHHTTSS----------------S-CCHHHHHHHHHHHCC----
T ss_pred CcHHHHHHHHHHHHHHHHC--CCCEEEEEecCccccccccccccc-------------cc-cccccchhhhhhhcc----
Confidence 4679999999999999877 789999999999999999875322 01 2356777777 5554
Q ss_pred CcceEEEEEcchh-HHHHHHHHHhhh
Q psy7629 427 AAVAHFRLLTGHD-CLAEHLHRFGLK 451 (468)
Q Consensus 427 g~~V~f~WVpgH~-E~AD~LAK~Aa~ 451 (468)
...+.|.|||+.. ..||.|||.|..
T Consensus 61 ~~~~~~~~i~r~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 61 FWNVSVSHIPREQNKVADALAKFALS 86 (87)
T ss_dssp CSCEEEEE--GGGSHHHHHHHHHHHH
T ss_pred ccceEEEEEChHHhHHHHHHHHHHhh
Confidence 3579999999999 999999999863
No 12
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=82.21 E-value=1.1 Score=43.58 Aligned_cols=61 Identities=16% Similarity=0.143 Sum_probs=42.1
Q ss_pred cEEEEEeccccCCCCceEEEEEEecCeEEeecCccccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHH
Q psy7629 311 WLHIYTDGSLINPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQ 384 (468)
Q Consensus 311 ~i~IYTDGS~~~n~~~aG~GVv~~~~~~~~~L~~~~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~ 384 (468)
--.||+|+.- .|+|+....+...+.....-.+.+|||+|...|.-+... + .|.|||-+|+.
T Consensus 94 lc~VfaDATp------Tgwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~~------r-~l~tDnt~Vls 154 (245)
T PF00336_consen 94 LCQVFADATP------TGWGISITGQRMRGTFSKPLPIHTAELLAACLARLMSGA------R-CLGTDNTVVLS 154 (245)
T ss_pred CCceeccCCC------CcceeeecCceeeeeecccccchHHHHHHHHHHHhccCC------c-EEeecCcEEEe
Confidence 3478999876 567776655554333333336899999999888766532 2 49999988776
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=79.23 E-value=6.9 Score=36.06 Aligned_cols=51 Identities=22% Similarity=0.138 Sum_probs=32.8
Q ss_pred cEEEEEeccccCCCCceEEEEEEec---CeE-------EeecC--ccccchHHHHHHHHHHHHHHHh
Q psy7629 311 WLHIYTDGSLINPEDGAGAGIFCEL---FSF-------YKRLG--TFTTNFDGEIAAIKIALLQILN 365 (468)
Q Consensus 311 ~i~IYTDGS~~~n~~~aG~GVv~~~---~~~-------~~~L~--~~~Tn~~AEL~AIl~ALe~a~~ 365 (468)
.+++|+|+|. .+ .|+.+|... +.. ..++. ...|+=+.||.|++.|.+++..
T Consensus 81 ~L~~F~DAS~--~a--ygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 81 ELHVFCDASE--SA--YGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeEeecccc--cc--eeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 6899999997 22 233344322 221 11221 2349999999999999999864
No 14
>PF10897 DUF2713: Protein of unknown function (DUF2713); InterPro: IPR020404 This entry contains proteins with no known function. In some organisms this represents the C-terminal domain of a fusion protein with YjbL.
Probab=35.00 E-value=13 Score=36.11 Aligned_cols=52 Identities=25% Similarity=0.339 Sum_probs=40.7
Q ss_pred hhhccccchhhhHhhh---------------cccccccchhhhhhhccccccccccccccCCCCCCc
Q psy7629 84 INSSKRSSFNTFVEKM---------------DYRKDGPKAYSFISSIKKGQTSVNKPFSHNGRSISD 135 (468)
Q Consensus 84 ~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 135 (468)
+-..+.-.||.++++| .||--|||+..|+.|.--.++--|++.--++..|+|
T Consensus 172 Lad~geldFn~iL~~Mk~~~~Egk~d~~~iTKM~~Aa~kLI~F~qSfDPdSte~I~I~~d~s~~iyd 238 (246)
T PF10897_consen 172 LADKGELDFNDILDKMKLQVNEGKLDPDIITKMRDAAPKLIKFVQSFDPDSTEPIKIGKDMSKLIYD 238 (246)
T ss_pred hhhcCCCcHHHHHHHHHHhhccCCcCcHHHHHHHHhhHHHHHHHHhcCCCCcCceeeecchHHHHHH
Confidence 3344556799999998 389999999999999999999888887665554443
No 15
>KOG1812|consensus
Probab=26.34 E-value=92 Score=33.15 Aligned_cols=40 Identities=25% Similarity=0.378 Sum_probs=33.0
Q ss_pred ccchHHHHHHHHHHHHHHHhhcCCCceEEEEecCHHHHHHhh
Q psy7629 346 TTNFDGEIAAIKIALLQILNRTNQFERAVILSDSKAAIQSIT 387 (468)
Q Consensus 346 ~Tn~~AEL~AIl~ALe~a~~~~~~~~~v~I~TDSqyai~~I~ 387 (468)
.+...||+.|+..+|..+.+. +...+.+++|+......+.
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~--~~~~~~~~~d~~~~~~~v~ 86 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALEL--GLNHIVIYCDDELIYESVA 86 (384)
T ss_pred cchhhHHHHHHhhccHHHHhh--ccccceEecccHHHHHHHh
Confidence 578899999999999999887 7889999999765555333
Done!