Query psy17737
Match_columns 493
No_of_seqs 201 out of 671
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 21:40:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17737.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17737hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05380 Peptidase_A17: Pao re 100.0 8E-47 1.7E-51 346.7 10.4 158 50-209 1-159 (159)
2 PF09337 zf-H2C2: His(2)-Cys(2 98.7 6.9E-09 1.5E-13 71.8 2.3 38 447-487 1-39 (39)
3 cd06222 RnaseH RNase H (RNase 98.3 1.8E-06 3.8E-11 73.8 7.5 112 134-260 2-128 (130)
4 PF00075 RNase_H: RNase H; In 98.3 9.4E-07 2E-11 77.8 4.9 100 131-253 3-116 (132)
5 PF00336 DNA_pol_viral_C: DNA 98.3 1.6E-06 3.5E-11 80.3 6.5 102 132-263 95-196 (245)
6 PRK13907 rnhA ribonuclease H; 97.9 5.1E-05 1.1E-09 66.8 8.2 111 132-260 2-123 (128)
7 PRK07708 hypothetical protein; 97.8 6.5E-05 1.4E-09 72.5 8.8 121 131-261 73-205 (219)
8 COG0328 RnhA Ribonuclease HI [ 97.7 0.00027 5.9E-09 64.1 9.4 113 131-260 3-141 (154)
9 PRK00203 rnhA ribonuclease H; 97.5 0.00052 1.1E-08 62.3 9.1 110 131-259 3-137 (150)
10 PRK08719 ribonuclease H; Revie 97.4 0.00019 4.2E-09 65.0 5.1 108 130-257 3-140 (147)
11 PF13456 RVT_3: Reverse transc 97.3 0.00016 3.4E-09 58.5 2.9 76 179-260 4-83 (87)
12 PRK07238 bifunctional RNase H/ 97.2 0.0012 2.5E-08 69.1 8.0 117 131-261 2-129 (372)
13 PRK06548 ribonuclease H; Provi 97.0 0.0043 9.4E-08 57.0 9.5 110 130-260 4-138 (161)
14 KOG3752|consensus 92.6 0.71 1.5E-05 47.5 9.4 113 131-259 212-360 (371)
15 PF02022 Integrase_Zn: Integra 68.4 1.8 3.9E-05 30.2 0.2 35 445-488 3-38 (40)
16 PF13976 gag_pre-integrs: GAG- 39.4 26 0.00056 26.6 2.4 42 443-490 24-66 (67)
17 PF14948 RESP18: RESP18 domain 21.0 42 0.0009 28.6 0.7 34 65-98 13-46 (105)
No 1
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=100.00 E-value=8e-47 Score=346.74 Aligned_cols=158 Identities=38% Similarity=0.678 Sum_probs=148.3
Q ss_pred ccHhHHHHhHhcccccCCCCcceeecchhhhhhhhhccCCCCccCChhHHHHHHHHHHHHhcccceeceeEEeccCCCCc
Q psy17737 50 LTKRLLLSVYGSIYDVLGLFTPVVLPLKILIQSVWQRNLSWDEELSTEDKITFMKLIEDIKLIHTVHIPRLIGNLIPGTQ 129 (493)
Q Consensus 50 ~TkR~ilS~ias~yDPLGl~~p~~l~~K~llq~l~~~~~~WD~~i~~e~~~~w~~~~~~l~~~~~~~iPR~~~~~~~~~~ 129 (493)
+|||+++|.+|++|||||+++|+++++|+++|++|+.+++||++||+++.+.|.+|.+++..++++.|||++ .......
T Consensus 1 pTKR~ils~ia~~yDPlGl~~p~~i~~K~llq~lw~~~l~WD~~lp~el~~~w~~~~~~l~~~~~i~iPR~i-~~~~~~~ 79 (159)
T PF05380_consen 1 PTKRQILSFIASIYDPLGLLAPIIIRAKLLLQKLWQSKLDWDDPLPDELRKEWKKWLKELESLSPIRIPRCI-PISDYRS 79 (159)
T ss_pred CChHHHHHHHHHHcCcchhhHHHHHHHHHHHHhhhccccchhhhhhHHHHHHHHHHHHHHhhcccccCCccc-ccccccc
Confidence 599999999999999999999999999999999999999999999999999999999999998889999987 3222223
Q ss_pred eeEEeecccccccceeeEEEEEeeCCCcee-eeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEEe
Q psy17737 130 YELHGFSDASATSYSMVIYLKCITGNSVTS-NLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLW 208 (493)
Q Consensus 130 ~~L~vF~DAS~~a~gav~y~r~~~~~g~~~-~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~~ 208 (493)
.+||+|||||+.|||||+|+|. ..||... ++++||+||+|+|..|||||||+|+++|++++.++.+++++++.++++|
T Consensus 80 ~~L~~F~DAS~~aygavvYlr~-~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~w 158 (159)
T PF05380_consen 80 VELHVFCDASESAYGAVVYLRS-YSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVFW 158 (159)
T ss_pred eeeeEeecccccceeeEeEeee-ccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEEe
Confidence 8999999999999999999999 6777777 9999999999999899999999999999999999999999999999999
Q ss_pred c
Q psy17737 209 I 209 (493)
Q Consensus 209 t 209 (493)
|
T Consensus 159 t 159 (159)
T PF05380_consen 159 T 159 (159)
T ss_pred C
Confidence 7
No 2
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 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 an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=98.71 E-value=6.9e-09 Score=71.80 Aligned_cols=38 Identities=18% Similarity=0.229 Sum_probs=35.6
Q ss_pred HHhCCCCChhhhhHHHHHHhhhc-cccchHHHHHhcCCcccc
Q psy17737 447 HTSGYHTGDKESKKLSNVARGYY-LDGNHLERRVLLGSRLLS 487 (493)
Q Consensus 447 H~~~~H~G~~~t~~l~~lr~~yW-~~~r~~vr~vi~~C~~C~ 487 (493)
|+. +|.|.+.| ++.|+++|| |+|+..|+++|+.|..||
T Consensus 1 H~~-~H~Gi~kT--~~~i~~~y~W~gm~~~V~~~ir~C~~Cq 39 (39)
T PF09337_consen 1 HNQ-GHPGINKT--TAKISQRYHWPGMKKDVRRVIRSCPQCQ 39 (39)
T ss_pred CCc-cCCCHHHH--HHHHHHhheecCHHHHHHHHHhcCcccC
Confidence 454 59999999 999999999 999999999999999997
No 3
>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=98.32 E-value=1.8e-06 Score=73.84 Aligned_cols=112 Identities=21% Similarity=0.214 Sum_probs=75.7
Q ss_pred eecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEE
Q psy17737 134 GFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYL 207 (493)
Q Consensus 134 vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~ 207 (493)
+|+|||-. |||++ ++. .++.. ........ ...|.-..|+.|++.|++.+. ......+.+
T Consensus 2 ~~~Dgs~~~~~~~~g~g~v--~~~--~~~~~---~~~~~~~~--~~~s~~~aEl~al~~al~~~~------~~~~~~i~i 66 (130)
T cd06222 2 IYTDGSCRGNPGPAGAGVV--LRD--PGGEV---LLSGGLLG--GNTTNNRAELLALIEALELAL------ELGGKKVNI 66 (130)
T ss_pred EEecccCCCCCCceEEEEE--EEe--CCCeE---EEeccccC--CCCcHHHHHHHHHHHHHHHHH------hCCCceEEE
Confidence 79999987 55543 332 22221 21111111 577889999999999998876 346789999
Q ss_pred ecchhhhHHHHhcCCc-cChhhhHHHHHHHHhc---cccceEEecC----CCC-CCcccccc
Q psy17737 208 WIDSQIVIHWILGNKV-LPTFINNRVKEIKNRS---FKLDVHYVPT----DMN-PADIACRG 260 (493)
Q Consensus 208 ~tDS~i~l~~l~~~~~-~~~fv~nRv~~I~~~~---~~~~~~hv~~----~~N-pAD~~SRg 260 (493)
+|||..++..+.+... ...-....+..|++.. ..+.+.|||+ ..| .||.++|.
T Consensus 67 ~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 67 YTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred EECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 9999999999998722 2223344445555544 5688999999 666 69988764
No 4
>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=98.27 E-value=9.4e-07 Score=77.78 Aligned_cols=100 Identities=21% Similarity=0.251 Sum_probs=65.4
Q ss_pred eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737 131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK 204 (493)
Q Consensus 131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~ 204 (493)
.+.+|+|||- .|+|+|++ +|. . . -.++...|..+.||.|+..|++.+.. ..
T Consensus 3 ~~~iytDgS~~~~~~~~~~g~v~~------~~~-~--~-----~~~~~~~s~~~aEl~Ai~~AL~~~~~---------~~ 59 (132)
T PF00075_consen 3 AIIIYTDGSCRPNPGKGGAGYVVW------GGR-N--F-----SFRLGGQSNNRAELQAIIEALKALEH---------RK 59 (132)
T ss_dssp SEEEEEEEEECTTTTEEEEEEEEE------TTE-E--E-----EEEEESECHHHHHHHHHHHHHHTHST---------SE
T ss_pred cEEEEEeCCccCCCCceEEEEEEE------CCe-E--E-----EecccccchhhhheehHHHHHHHhhc---------cc
Confidence 5899999993 35554322 221 1 0 11122778999999999999994421 68
Q ss_pred EEEecchhhhHHHHhc-----CC--c-cChhhhHHHHHHHHhccccceEEecCCCCC
Q psy17737 205 YYLWIDSQIVIHWILG-----NK--V-LPTFINNRVKEIKNRSFKLDVHYVPTDMNP 253 (493)
Q Consensus 205 ~~~~tDS~i~l~~l~~-----~~--~-~~~fv~nRv~~I~~~~~~~~~~hv~~~~Np 253 (493)
+.++|||+.++.+|.. .. + ...-+.+++.+.......+.++||||..|-
T Consensus 60 v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~ 116 (132)
T PF00075_consen 60 VTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV 116 (132)
T ss_dssp EEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred ccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence 8999999999998887 31 1 111234455555444456899999999765
No 5
>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=98.27 E-value=1.6e-06 Score=80.26 Aligned_cols=102 Identities=25% Similarity=0.223 Sum_probs=64.3
Q ss_pred EEeecccccccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeEEEecch
Q psy17737 132 LHGFSDASATSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKYYLWIDS 211 (493)
Q Consensus 132 L~vF~DAS~~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~~~~tDS 211 (493)
=-||+||+..|||.++- .|.. +.-+++ ..-|--.||+|+.+|--... .-.+-|||
T Consensus 95 c~VfaDATpTgwgi~i~------~~~~-~~Tfs~-------~l~IhtaELlaaClAr~~~~-----------~r~l~tDn 149 (245)
T PF00336_consen 95 CQVFADATPTGWGISIT------GQRM-RGTFSK-------PLPIHTAELLAACLARLMSG-----------ARCLGTDN 149 (245)
T ss_pred CceeccCCCCcceeeec------Ccee-eeeecc-------cccchHHHHHHHHHHHhccC-----------CcEEeecC
Confidence 35899999999997631 1211 222222 34566789999866543322 22377999
Q ss_pred hhhHHHHhcCCccChhhhHHHHHHHHhccccceEEecCCCCCCccccccccc
Q psy17737 212 QIVIHWILGNKVLPTFINNRVKEIKNRSFKLDVHYVPTDMNPADIACRGEKL 263 (493)
Q Consensus 212 ~i~l~~l~~~~~~~~fv~nRv~~I~~~~~~~~~~hv~~~~NpAD~~SRg~~~ 263 (493)
+.|++ +++..|-=+---.-..++...++.||||+.||||..|||..+
T Consensus 150 t~Vls-----rkyts~PW~lac~A~wiLrgts~~yVPS~~NPAD~PsR~~~~ 196 (245)
T PF00336_consen 150 TVVLS-----RKYTSFPWLLACAANWILRGTSFYYVPSKYNPADDPSRGKLG 196 (245)
T ss_pred cEEEe-----cccccCcHHHHHHHHHhhcCceEEEeccccCcCCCCCCCccc
Confidence 99986 344443111111112235678999999999999999999754
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=97.89 E-value=5.1e-05 Score=66.85 Aligned_cols=111 Identities=16% Similarity=0.110 Sum_probs=73.1
Q ss_pred EEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccceeE
Q psy17737 132 LHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIKY 205 (493)
Q Consensus 132 L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~~ 205 (493)
+++|+|||-. |||+|+ + +.+|... . + .+....|=.+-|+.|++.|++++..+ .+..+
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi--~--~~~~~~~--~-~----~~~~~~tn~~AE~~All~aL~~a~~~------g~~~v 64 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFI--K--GVQPAVQ--L-S----LPLGTMSNHEAEYHALLAALKYCTEH------NYNIV 64 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEE--E--ECCeeEE--E-E----ecccccCCcHHHHHHHHHHHHHHHhC------CCCEE
Confidence 5789998864 556554 3 2233221 1 1 12234577899999999999988743 34579
Q ss_pred EEecchhhhHHHHhcC-CccChhhhHHHHHHHHh---ccccceEEecCCCCC-Ccccccc
Q psy17737 206 YLWIDSQIVIHWILGN-KVLPTFINNRVKEIKNR---SFKLDVHYVPTDMNP-ADIACRG 260 (493)
Q Consensus 206 ~~~tDS~i~l~~l~~~-~~~~~fv~nRv~~I~~~---~~~~~~~hv~~~~Np-AD~~SRg 260 (493)
.++|||+.++.++.+. ++- .-...-+.+++.+ ...+.+.|||...|- ||.+.|.
T Consensus 65 ~i~sDS~~vi~~~~~~~~~~-~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~ 123 (128)
T PRK13907 65 SFRTDSQLVERAVEKEYAKN-KMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARK 123 (128)
T ss_pred EEEechHHHHHHHhHHHhcC-hhHHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHH
Confidence 9999999999999986 211 1123334555444 345667999999995 9987664
No 7
>PRK07708 hypothetical protein; Validated
Probab=97.84 E-value=6.5e-05 Score=72.52 Aligned_cols=121 Identities=18% Similarity=0.148 Sum_probs=76.2
Q ss_pred eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737 131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK 204 (493)
Q Consensus 131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~ 204 (493)
.+++|+|||- .|+|+|++. .+|.....+.....+.+ ..|=..-|+.|++.|++++..+ ++.-..
T Consensus 73 ~~~vY~DGs~~~n~g~aG~GvVI~~----~~g~~~~~~~~~~~l~~--~~TNN~AEy~Ali~aL~~A~e~----g~~~~~ 142 (219)
T PRK07708 73 EILVYFDGGFDKETKLAGLGIVIYY----KQGNKRYRIRRNAYIEG--IYDNNEAEYAALYYAMQELEEL----GVKHEP 142 (219)
T ss_pred cEEEEEeeccCCCCCCcEEEEEEEE----CCCCEEEEEEeeccccc--cccCcHHHHHHHHHHHHHHHHc----CCCcce
Confidence 5789999976 456666554 22322211211122332 3577888999999999988743 333345
Q ss_pred EEEecchhhhHHHHhcC-CccChhhhHHHHHHHHhcc----ccceEEecCCCCC-Cccccccc
Q psy17737 205 YYLWIDSQIVIHWILGN-KVLPTFINNRVKEIKNRSF----KLDVHYVPTDMNP-ADIACRGE 261 (493)
Q Consensus 205 ~~~~tDS~i~l~~l~~~-~~~~~fv~nRv~~I~~~~~----~~~~~hv~~~~Np-AD~~SRg~ 261 (493)
|.+++||+.++.|+.+. +....-...-+.+|++... .+.+.|||-+.|- ||.+.+-.
T Consensus 143 V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~A 205 (219)
T PRK07708 143 VTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQA 205 (219)
T ss_pred EEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHH
Confidence 89999999999999988 3322222223344443332 3667899999995 99776543
No 8
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=97.67 E-value=0.00027 Score=64.11 Aligned_cols=113 Identities=22% Similarity=0.265 Sum_probs=74.7
Q ss_pred eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737 131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK 204 (493)
Q Consensus 131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~ 204 (493)
.+++|+|+|. -|||+|++ +.++... -..+...-|=.|+||.|++.|++.+.. .....
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~----~~~~~~~-------~s~~~~~tTNNraEl~A~i~AL~~l~~------~~~~~ 65 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLR----YGDGEKE-------LSGGEGRTTNNRAELRALIEALEALKE------LGACE 65 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEE----cCCceEE-------EeeeeecccChHHHHHHHHHHHHHHHh------cCCce
Confidence 5789999985 67888766 2233221 112223678899999999999998885 35678
Q ss_pred EEEecchhhhHH----HHhcC--CccC----hhhhHH--HHHHHHhc---cccceEEecCCCC-C----Ccccccc
Q psy17737 205 YYLWIDSQIVIH----WILGN--KVLP----TFINNR--VKEIKNRS---FKLDVHYVPTDMN-P----ADIACRG 260 (493)
Q Consensus 205 ~~~~tDS~i~l~----~l~~~--~~~~----~fv~nR--v~~I~~~~---~~~~~~hv~~~~N-p----AD~~SRg 260 (493)
+.+||||+.+.. |+.+. ..|+ ..|.|+ ..++.++. ..+.|.+|+|..+ | ||.+-|.
T Consensus 66 v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~ 141 (154)
T COG0328 66 VTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLARE 141 (154)
T ss_pred EEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHH
Confidence 999999987764 44333 3444 345443 44454444 4579999997665 2 6665554
No 9
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.51 E-value=0.00052 Score=62.31 Aligned_cols=110 Identities=19% Similarity=0.195 Sum_probs=67.5
Q ss_pred eEEeeccccc------ccceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737 131 ELHGFSDASA------TSYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK 204 (493)
Q Consensus 131 ~L~vF~DAS~------~a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~ 204 (493)
.+.+|+|+|. .|||+|+.. .++.. . +. . +....|-.|.||.|++.|++.+.. ...
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~----~~~~~-~-~~-~----~~~~~TN~~aEL~Ai~~AL~~~~~--------~~~ 63 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRY----KGHEK-E-LS-G----GEALTTNNRMELMAAIEALEALKE--------PCE 63 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEE----CCeeE-E-Ee-c----CCCCCcHHHHHHHHHHHHHHHcCC--------CCe
Confidence 4789999997 456655432 22211 1 11 1 123678899999999999885531 256
Q ss_pred EEEecchhhhHHHHhcC------Ccc----ChhhhHH--HHHHHHhcc--ccceEEecCCC----C-CCccccc
Q psy17737 205 YYLWIDSQIVIHWILGN------KVL----PTFINNR--VKEIKNRSF--KLDVHYVPTDM----N-PADIACR 259 (493)
Q Consensus 205 ~~~~tDS~i~l~~l~~~------~~~----~~fv~nR--v~~I~~~~~--~~~~~hv~~~~----N-pAD~~SR 259 (493)
+.++|||+.++.=|..- +.| ..-|+|+ +.+|.++.. .+.|.|||+-. | -||.+.|
T Consensus 64 v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~N~~AD~lA~ 137 (150)
T PRK00203 64 VTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELAR 137 (150)
T ss_pred EEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHHH
Confidence 89999998877544421 122 2345554 456655543 58899999665 3 2775544
No 10
>PRK08719 ribonuclease H; Reviewed
Probab=97.43 E-value=0.00019 Score=65.00 Aligned_cols=108 Identities=17% Similarity=0.160 Sum_probs=66.3
Q ss_pred eeEEeecccccc---------cceeeEEEEEeeCCCcee-eeeecccccCCCC-CCccchhhhhHHHHHhhhhHHHhhhh
Q psy17737 130 YELHGFSDASAT---------SYSMVIYLKCITGNSVTS-NLVFAKARIAPLS-RPTLPRLELLGALIAYRGLKFVGESL 198 (493)
Q Consensus 130 ~~L~vF~DAS~~---------a~gav~y~r~~~~~g~~~-~ll~aksrv~P~k-~~tIpRlEL~a~~~~~~l~~~~~~~l 198 (493)
..+.+|||+|.. |+|+++|. ++|... ... .|+. ..|-.|.||.|+..|++.+..
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~----~~~~~~~~~~------~~~~~~~Tnn~aEl~A~~~aL~~~~~----- 67 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYD----EAGEIVDEQS------ITVNRYTDNAELELLALIEALEYARD----- 67 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEe----CCCCeeEEEE------ecCCCCccHHHHHHHHHHHHHHHcCC-----
Confidence 468999998882 67766553 234322 111 1222 469999999999999987652
Q ss_pred cccceeEEEecchhhhHHHH--------hcC-C-ccChhhhHH--HHHHHHhc--cccceEEecC----CCC-CCccc
Q psy17737 199 KVKDIKYYLWIDSQIVIHWI--------LGN-K-VLPTFINNR--VKEIKNRS--FKLDVHYVPT----DMN-PADIA 257 (493)
Q Consensus 199 ~~~~~~~~~~tDS~i~l~~l--------~~~-~-~~~~fv~nR--v~~I~~~~--~~~~~~hv~~----~~N-pAD~~ 257 (493)
...++|||+-++.=| ++. + +-...|.|+ ..+|.++. ..++|.|||+ ..| -||.+
T Consensus 68 -----~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~l 140 (147)
T PRK08719 68 -----GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADML 140 (147)
T ss_pred -----CCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHH
Confidence 126999998887655 333 1 223445553 33444433 3588999999 344 26643
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.31 E-value=0.00016 Score=58.45 Aligned_cols=76 Identities=22% Similarity=0.154 Sum_probs=55.6
Q ss_pred hhhhHHHHHhhhhHHHhhhhcccceeEEEecchhhhHHHHhcCCccChhhhHHHHHHHHhcc---ccceEEecCCCCC-C
Q psy17737 179 LELLGALIAYRGLKFVGESLKVKDIKYYLWIDSQIVIHWILGNKVLPTFINNRVKEIKNRSF---KLDVHYVPTDMNP-A 254 (493)
Q Consensus 179 lEL~a~~~~~~l~~~~~~~l~~~~~~~~~~tDS~i~l~~l~~~~~~~~fv~nRv~~I~~~~~---~~~~~hv~~~~Np-A 254 (493)
.|+.|+..|++++.. ..+.++.+.|||..++..|++...........+.+|+.+.. .+.++|||-+.|- |
T Consensus 4 aE~~al~~al~~a~~------~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A 77 (87)
T PF13456_consen 4 AEALALLEALQLAWE------LGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVA 77 (87)
T ss_dssp HHHHHHHHHHHHHHC------CT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHH
T ss_pred HHHHHHHHHHHHHHH------CCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHH
Confidence 589999999988873 35679999999999999999883332366677777777664 5889999999995 9
Q ss_pred cccccc
Q psy17737 255 DIACRG 260 (493)
Q Consensus 255 D~~SRg 260 (493)
|.+.|-
T Consensus 78 ~~LA~~ 83 (87)
T PF13456_consen 78 DALAKF 83 (87)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 877653
No 12
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.15 E-value=0.0012 Score=69.06 Aligned_cols=117 Identities=16% Similarity=0.237 Sum_probs=75.3
Q ss_pred eEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhccccee
Q psy17737 131 ELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDIK 204 (493)
Q Consensus 131 ~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~~ 204 (493)
.++||+|||.. |+|+++.. .+|.. .+...+ .++...|-...|+.|++.|++++..+ .+..
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~----~~~~~--~~~~~~--~~~~~~tnn~AE~~All~gL~~a~~~------g~~~ 67 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWD----ADRGE--VLAERA--EAIGRATNNVAEYRGLIAGLEAAAEL------GATE 67 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEe----CCCCc--EEEEee--cccCCCCchHHHHHHHHHHHHHHHhC------CCCe
Confidence 57899999876 44544332 23211 111111 12225677889999999999988754 3457
Q ss_pred EEEecchhhhHHHHhcC-CccChhhh---HHHHHHHHhccccceEEecCCCCC-Cccccccc
Q psy17737 205 YYLWIDSQIVIHWILGN-KVLPTFIN---NRVKEIKNRSFKLDVHYVPTDMNP-ADIACRGE 261 (493)
Q Consensus 205 ~~~~tDS~i~l~~l~~~-~~~~~fv~---nRv~~I~~~~~~~~~~hv~~~~Np-AD~~SRg~ 261 (493)
+.+++||..++.-+.+. +.-..=.. ..+.++.+.+..+.+.|||...|- ||.+.+..
T Consensus 68 v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a 129 (372)
T PRK07238 68 VEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129 (372)
T ss_pred EEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHH
Confidence 99999999999998876 21111111 233444444567899999999995 99877754
No 13
>PRK06548 ribonuclease H; Provisional
Probab=97.02 E-value=0.0043 Score=57.02 Aligned_cols=110 Identities=20% Similarity=0.178 Sum_probs=67.1
Q ss_pred eeEEeecccccc------cceeeEEEEEeeCCCceeeeeecccccCCCCCCccchhhhhHHHHHhhhhHHHhhhhcccce
Q psy17737 130 YELHGFSDASAT------SYSMVIYLKCITGNSVTSNLVFAKARIAPLSRPTLPRLELLGALIAYRGLKFVGESLKVKDI 203 (493)
Q Consensus 130 ~~L~vF~DAS~~------a~gav~y~r~~~~~g~~~~ll~aksrv~P~k~~tIpRlEL~a~~~~~~l~~~~~~~l~~~~~ 203 (493)
.++++|||||.. |||+ |+. .++ . ...+....|=.|.||.|+..|++... ....
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~--~~~---~~~---~------~~g~~~~~TNnraEl~Aii~aL~~~~-------~~~~ 62 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAW--YVD---ENT---W------DSGGWDIATNNIAELTAVRELLIATR-------HTDR 62 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEE--EEe---CCc---E------EccCCCCCCHHHHHHHHHHHHHHhhh-------cCCc
Confidence 368999998865 3444 332 111 1 11222356889999999988765322 1223
Q ss_pred eEEEecchhhhHHHHhc--------C--CccChhhhHH--HHHHHHhc--cccceEEecCCC----CC-Ccccccc
Q psy17737 204 KYYLWIDSQIVIHWILG--------N--KVLPTFINNR--VKEIKNRS--FKLDVHYVPTDM----NP-ADIACRG 260 (493)
Q Consensus 204 ~~~~~tDS~i~l~~l~~--------~--~~~~~fv~nR--v~~I~~~~--~~~~~~hv~~~~----Np-AD~~SRg 260 (493)
.+.++|||+.++.-+.. . ++-..-|.|+ +.+|.++. ..++|.||+|-. |- ||.+-|-
T Consensus 63 ~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 63 PILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred eEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHHHHHHHHHHHH
Confidence 68999999999966663 2 2223557776 44554444 258899999855 32 6755443
No 14
>KOG3752|consensus
Probab=92.60 E-value=0.71 Score=47.51 Aligned_cols=113 Identities=22% Similarity=0.228 Sum_probs=68.6
Q ss_pred eEEeeccccccc-------ceeeEEEEEeeCCCceeeeeecccccCCCC--CCccchhhhhHHHHHhhhhHHHhhhhccc
Q psy17737 131 ELHGFSDASATS-------YSMVIYLKCITGNSVTSNLVFAKARIAPLS--RPTLPRLELLGALIAYRGLKFVGESLKVK 201 (493)
Q Consensus 131 ~L~vF~DAS~~a-------~gav~y~r~~~~~g~~~~ll~aksrv~P~k--~~tIpRlEL~a~~~~~~l~~~~~~~l~~~ 201 (493)
.+.|+||+|-.+ -|.++|.- +|..-. .-.|+. ..|-.|-||.|+..|++-+.. .+
T Consensus 212 ~~vvytDGS~~~ng~~~~~AGyGvywg----~~~e~N------~s~pv~~g~qtNnrAEl~Av~~ALkka~~------~~ 275 (371)
T KOG3752|consen 212 IQVVYTDGSSSGNGRKSSRAGYGVYWG----PGHELN------VSGPLAGGRQTNNRAELIAAIEALKKARS------KN 275 (371)
T ss_pred ceEEEecCccccCCCCCCcceeEEeeC----CCCccc------ccccCCCCcccccHHHHHHHHHHHHHHHh------cC
Confidence 378999998755 23335763 332111 123332 789999999999888776553 34
Q ss_pred ceeEEEecchhhhHHHHhcC------Ccc---------Chhhh-----HHHHHHHHh--ccccceEEecCCCC-----CC
Q psy17737 202 DIKYYLWIDSQIVIHWILGN------KVL---------PTFIN-----NRVKEIKNR--SFKLDVHYVPTDMN-----PA 254 (493)
Q Consensus 202 ~~~~~~~tDS~i~l~~l~~~------~~~---------~~fv~-----nRv~~I~~~--~~~~~~~hv~~~~N-----pA 254 (493)
+.++++.|||.-++.||..- +.| ..+|. +.+.+..+- -..++|.||+|... .|
T Consensus 276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~A 355 (371)
T KOG3752|consen 276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMA 355 (371)
T ss_pred CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHH
Confidence 56999999999888777633 111 11222 222332222 24589999998743 25
Q ss_pred ccccc
Q psy17737 255 DIACR 259 (493)
Q Consensus 255 D~~SR 259 (493)
|.+.|
T Consensus 356 d~lAR 360 (371)
T KOG3752|consen 356 DALAR 360 (371)
T ss_pred HHHHh
Confidence 65555
No 15
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=68.45 E-value=1.8 Score=30.16 Aligned_cols=35 Identities=11% Similarity=0.224 Sum_probs=24.2
Q ss_pred HHHHhCCCCChhhhhHHHHHHhhhc-cccchHHHHHhcCCccccc
Q psy17737 445 DIHTSGYHTGDKESKKLSNVARGYY-LDGNHLERRVLLGSRLLSG 488 (493)
Q Consensus 445 ~~H~~~~H~G~~~t~~l~~lr~~yW-~~~r~~vr~vi~~C~~C~r 488 (493)
+.|+. .|.+.+ .|+.+|= |+ ..+|.++..|..||.
T Consensus 3 e~H~k-~H~n~~------~L~~~f~ip~--~vAk~IV~~C~~Cq~ 38 (40)
T PF02022_consen 3 EEHEK-YHSNAK------ALRHKFGIPR--LVAKQIVNQCPKCQQ 38 (40)
T ss_dssp HHHHH-HHH-HH------HHHHHHT--H--HHHHHHHHHSCCHHS
T ss_pred hHHHH-HccCHH------HHHHHHccCH--HHHHHHHHHCHHHhh
Confidence 44554 555544 4577888 74 688999999999985
No 16
>PF13976 gag_pre-integrs: GAG-pre-integrase domain
Probab=39.42 E-value=26 Score=26.57 Aligned_cols=42 Identities=5% Similarity=-0.375 Sum_probs=28.1
Q ss_pred HHHHHHhCCCCChhhhhHHHHHHhhhc-cccchHHHHHhcCCccccccc
Q psy17737 443 VNDIHTSGYHTGDKESKKLSNVARGYY-LDGNHLERRVLLGSRLLSGWV 490 (493)
Q Consensus 443 i~~~H~~~~H~G~~~t~~l~~lr~~yW-~~~r~~vr~vi~~C~~C~r~~ 490 (493)
..-.|.+.||.+.+.+ -..+ ++.- ++... .-...|..|+..|
T Consensus 24 ~~lWH~RLGH~~~~~l--~~l~-~~~~~~~~~~---~~~~~C~~C~~gK 66 (67)
T PF13976_consen 24 TDLWHRRLGHPSFQVL--KKLS-KKGLLPGLKI---SKSSVCESCILGK 66 (67)
T ss_pred HHHHHHhcCCCCHHHH--HHHh-hccCcCCCCC---CCCccChhhhhcc
Confidence 4567999999999988 3333 3444 44432 2266899998765
No 17
>PF14948 RESP18: RESP18 domain
Probab=21.02 E-value=42 Score=28.55 Aligned_cols=34 Identities=18% Similarity=0.483 Sum_probs=28.8
Q ss_pred cCCCCcceeecchhhhhhhhhccCCCCccCChhH
Q psy17737 65 VLGLFTPVVLPLKILIQSVWQRNLSWDEELSTED 98 (493)
Q Consensus 65 PLGl~~p~~l~~K~llq~l~~~~~~WD~~i~~e~ 98 (493)
..|+-+|+.-+++.+||+|-..++.|-|.|..++
T Consensus 13 ~~~vs~pvlQrLQ~vLqqL~~qGl~WqDDiTQ~v 46 (105)
T PF14948_consen 13 LYQVSPPVLQRLQVVLQQLMPQGLFWQDDITQYV 46 (105)
T ss_pred ccccCHHHHHHHHHHHHHHHhcCCcccchHHHHH
Confidence 4488999999999999999999999988665444
Done!