Query psy5357
Match_columns 181
No_of_seqs 130 out of 468
Neff 6.1
Searched_HMMs 46136
Date Sat Aug 17 00:29:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5357hhsearch_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 1.5E-29 3.4E-34 200.7 6.3 84 2-91 57-140 (159)
2 PF00336 DNA_pol_viral_C: DNA 98.9 5.1E-10 1.1E-14 92.6 3.7 99 31-153 94-195 (245)
3 cd06222 RnaseH RNase H (RNase 98.4 5.8E-07 1.3E-11 64.3 5.9 109 34-150 2-127 (130)
4 PF00075 RNase_H: RNase H; In 98.3 6.7E-07 1.5E-11 66.9 3.7 68 74-144 37-116 (132)
5 PRK13907 rnhA ribonuclease H; 97.8 9.5E-05 2.1E-09 55.8 7.6 106 32-150 2-122 (128)
6 COG0328 RnhA Ribonuclease HI [ 97.8 0.0001 2.3E-09 58.8 7.6 101 31-143 3-128 (154)
7 PRK00203 rnhA ribonuclease H; 97.8 0.00011 2.4E-09 57.5 7.6 96 32-142 4-124 (150)
8 PRK08719 ribonuclease H; Revie 97.7 0.00033 7.1E-09 55.2 9.6 102 30-142 3-129 (147)
9 PRK06548 ribonuclease H; Provi 97.5 0.00089 1.9E-08 53.7 9.3 97 31-141 5-123 (161)
10 PF13456 RVT_3: Reverse transc 97.4 0.00032 6.9E-09 48.4 4.8 69 80-148 4-80 (87)
11 PRK07238 bifunctional RNase H/ 97.2 0.0023 4.9E-08 56.8 8.8 116 30-152 1-129 (372)
12 PRK07708 hypothetical protein; 97.1 0.005 1.1E-07 51.6 10.2 114 30-148 72-201 (219)
13 KOG3752|consensus 93.4 0.41 8.8E-06 43.2 7.9 65 32-107 213-293 (371)
No 1
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=99.96 E-value=1.5e-29 Score=200.70 Aligned_cols=84 Identities=40% Similarity=0.649 Sum_probs=77.3
Q ss_pred cccccCCCCeeeeeeecCCCCCCCCCCceeeEEEeccCcccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhh
Q psy5357 2 IDSMNFVSNIPVARYFDVPNNHDDQSVRYEPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLE 81 (181)
Q Consensus 2 ~~~l~~l~~i~ipR~~~~~~~~~~~~~~~~L~~F~DAS~~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlE 81 (181)
.++|.++++++|||++.. ....+++||+|||||+.|||||+|+|. ..+|..+++|++||+||+|+|..||||||
T Consensus 57 ~~~l~~~~~i~iPR~i~~-----~~~~~~~L~~F~DAS~~aygavvYlr~-~~~~~~~~~ll~aKsrv~P~k~~tIPRlE 130 (159)
T PF05380_consen 57 LKELESLSPIRIPRCIPI-----SDYRSVELHVFCDASESAYGAVVYLRS-YSDGSVQVRLLFAKSRVAPLKTVTIPRLE 130 (159)
T ss_pred HHHHhhcccccCCccccc-----ccccceeeeEeecccccceeeEeEeee-ccCCceeeeeeeecccccCCCCCcHHHHH
Confidence 568889999999997653 356789999999999999999999999 78888999999999999999999999999
Q ss_pred HhHHHHHhhc
Q psy5357 82 LLGALIAYRN 91 (181)
Q Consensus 82 L~a~~l~~~l 91 (181)
|+|+++|+++
T Consensus 131 L~a~~l~~~l 140 (159)
T PF05380_consen 131 LLAALLGVRL 140 (159)
T ss_pred HHHHHHHHHH
Confidence 9999999998
No 2
>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=98.95 E-value=5.1e-10 Score=92.62 Aligned_cols=99 Identities=22% Similarity=0.248 Sum_probs=70.2
Q ss_pred eeEEEeccCcccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc--cceeeeccHHHHHHHhc
Q psy5357 31 EPHAFSDACSYSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN--KCYLWIDNQCVIHWLTG 108 (181)
Q Consensus 31 ~L~~F~DAS~~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l--~~~~~tDS~i~l~~i~~ 108 (181)
.--||+||+..++|.++--+ .. +.-+ .+|+. |.-.||+|+.+|..+ .-.+-|||++|++.-..
T Consensus 94 lc~VfaDATpTgwgi~i~~~------~~--~~Tf----s~~l~---IhtaELlaaClAr~~~~~r~l~tDnt~Vlsrkyt 158 (245)
T PF00336_consen 94 LCQVFADATPTGWGISITGQ------RM--RGTF----SKPLP---IHTAELLAACLARLMSGARCLGTDNTVVLSRKYT 158 (245)
T ss_pred CCceeccCCCCcceeeecCc------ee--eeee----ccccc---chHHHHHHHHHHHhccCCcEEeecCcEEEecccc
Confidence 33589999999999884322 11 2222 33444 889999999998876 34489999999875332
Q ss_pred C-ccccceecchhchHHHHHhccCCcceEEeCCCCCCCcccCCCCC
Q psy5357 109 N-KVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNPADLACKGSS 153 (181)
Q Consensus 109 ~-~~~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~~NPAD~~SRG~~ 153 (181)
. --.-..++|.+- ...++-||||+.||||..|||..
T Consensus 159 s~PW~lac~A~wiL---------rgts~~yVPS~~NPAD~PsR~~~ 195 (245)
T PF00336_consen 159 SFPWLLACAANWIL---------RGTSFYYVPSKYNPADDPSRGKL 195 (245)
T ss_pred cCcHHHHHHHHHhh---------cCceEEEeccccCcCCCCCCCcc
Confidence 2 111233456555 67899999999999999999974
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=98.42 E-value=5.8e-07 Score=64.34 Aligned_cols=109 Identities=22% Similarity=0.227 Sum_probs=69.9
Q ss_pred EEeccCcc----cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeeeccHHH
Q psy5357 34 AFSDACSY----SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWIDNQCV 102 (181)
Q Consensus 34 ~F~DAS~~----aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~tDS~i~ 102 (181)
+|+|||-. .+|+.++++. .++. .. ..+.... ...+.-..|+.|++.|.+. .+.++|||..+
T Consensus 2 ~~~Dgs~~~~~~~~g~g~v~~~--~~~~--~~-~~~~~~~---~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~ 73 (130)
T cd06222 2 IYTDGSCRGNPGPAGAGVVLRD--PGGE--VL-LSGGLLG---GNTTNNRAELLALIEALELALELGGKKVNIYTDSQYV 73 (130)
T ss_pred EEecccCCCCCCceEEEEEEEe--CCCe--EE-EeccccC---CCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHH
Confidence 68999987 3455555553 2221 11 1111111 4567889999999999886 79999999999
Q ss_pred HHHHhcCcc-ccceecchhchHHHHHhccCCcceEEeCC-----CCCCCcccCC
Q psy5357 103 IHWLTGNKV-FTTFVNNRVKALKEIKASVFPIVYKYIPT-----DSNPADLACK 150 (181)
Q Consensus 103 l~~i~~~~~-~~~fV~nRv~~i~~I~~~~~~~~~~hV~t-----~~NPAD~~SR 150 (181)
+..+.+... ...-....+..++++.+......++|||+ ..+.||.++|
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~ 127 (130)
T cd06222 74 INALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAK 127 (130)
T ss_pred HHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHH
Confidence 999998732 22222333332223333446788899999 5558887655
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=98.29 E-value=6.7e-07 Score=66.93 Aligned_cols=68 Identities=21% Similarity=0.311 Sum_probs=47.8
Q ss_pred CCCcchhhHhHHHHHhhc----cceeeeccHHHHHHHhcC---cccc-c----eecchhchHHHHHhccCCcceEEeCCC
Q psy5357 74 KPTLPRLELLGALIAYRN----KCYLWIDNQCVIHWLTGN---KVFT-T----FVNNRVKALKEIKASVFPIVYKYIPTD 141 (181)
Q Consensus 74 ~~tIPrlEL~a~~l~~~l----~~~~~tDS~i~l~~i~~~---~~~~-~----fV~nRv~~i~~I~~~~~~~~~~hV~t~ 141 (181)
..|.-+.||.|+..|.+. .+.+||||+.++.++... +.++ . -+.+++. +.......+.++|||+.
T Consensus 37 ~~s~~~aEl~Ai~~AL~~~~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~---~~~~~~~~v~~~~V~~H 113 (132)
T PF00075_consen 37 GQSNNRAELQAIIEALKALEHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIW---ELLSRGIKVRFRWVPGH 113 (132)
T ss_dssp SECHHHHHHHHHHHHHHTHSTSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHH---HHHHHSSEEEEEESSSS
T ss_pred ccchhhhheehHHHHHHHhhcccccccccHHHHHHHHHHhccccccccccccccchhhee---eccccceEEeeeeccCc
Confidence 678889999999999885 589999999999988872 1121 1 1223333 33333456899999998
Q ss_pred CCC
Q psy5357 142 SNP 144 (181)
Q Consensus 142 ~NP 144 (181)
.|-
T Consensus 114 ~~~ 116 (132)
T PF00075_consen 114 SGV 116 (132)
T ss_dssp SSS
T ss_pred CCC
Confidence 765
No 5
>PRK13907 rnhA ribonuclease H; Provisional
Probab=97.82 E-value=9.5e-05 Score=55.82 Aligned_cols=106 Identities=17% Similarity=0.164 Sum_probs=64.1
Q ss_pred eEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeeeccH
Q psy5357 32 PHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWIDNQ 100 (181)
Q Consensus 32 L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~tDS~ 100 (181)
+++|+|||..+ .|+.+.++. .+|.. . . +. +....|=-..|+.|++.|.++ .+.++|||+
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~--~~~~~--~-~-~~----~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~ 71 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKG--VQPAV--Q-L-SL----PLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQ 71 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEE--CCeeE--E-E-Ee----cccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechH
Confidence 57899988652 233333442 33322 1 1 11 222346679999999998875 788999999
Q ss_pred HHHHHHhcCccccceecchhchHHHHHhc---cCCcceEEeCCCCCC-CcccCC
Q psy5357 101 CVIHWLTGNKVFTTFVNNRVKALKEIKAS---VFPIVYKYIPTDSNP-ADLACK 150 (181)
Q Consensus 101 i~l~~i~~~~~~~~fV~nRv~~i~~I~~~---~~~~~~~hV~t~~NP-AD~~SR 150 (181)
.+..++++......-...- +++++++ .....+.|||...|- ||.+.|
T Consensus 72 ~vi~~~~~~~~~~~~~~~l---~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~ 122 (128)
T PRK13907 72 LVERAVEKEYAKNKMFAPL---LEEALQYIKSFDLFFIKWIPSSQNKVADELAR 122 (128)
T ss_pred HHHHHHhHHHhcChhHHHH---HHHHHHHHhcCCceEEEEcCchhchhHHHHHH
Confidence 9999999762111101111 2244443 445666899998875 776544
No 6
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=97.79 E-value=0.0001 Score=58.79 Aligned_cols=101 Identities=17% Similarity=0.255 Sum_probs=64.4
Q ss_pred eeEEEeccCc------ccceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeee
Q psy5357 31 EPHAFSDACS------YSYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWI 97 (181)
Q Consensus 31 ~L~~F~DAS~------~aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~t 97 (181)
.+++|+|+|. .|||+|++ +.++.. .+ .-+....|=-|+||+|++.|.+. .+.+||
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~----~~~~~~--~~------s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~t 70 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLR----YGDGEK--EL------SGGEGRTTNNRAELRALIEALEALKELGACEVTLYT 70 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEE----cCCceE--EE------eeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEe
Confidence 5789999984 57888776 223322 11 11233567889999999998875 699999
Q ss_pred ccHHHHHHHh----cC--cccc----ceecch--hchHHHHHhccCCcceEEeCCCCC
Q psy5357 98 DNQCVIHWLT----GN--KVFT----TFVNNR--VKALKEIKASVFPIVYKYIPTDSN 143 (181)
Q Consensus 98 DS~i~l~~i~----~~--~~~~----~fV~nR--v~~i~~I~~~~~~~~~~hV~t~~N 143 (181)
||+.+..-|. +. ..|+ .+|.|+ .+.+.+..+....+.|++|++..+
T Consensus 71 DS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g 128 (154)
T COG0328 71 DSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAG 128 (154)
T ss_pred cHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCC
Confidence 9998886554 33 3333 345544 332223333334579999997654
No 7
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.78 E-value=0.00011 Score=57.45 Aligned_cols=96 Identities=17% Similarity=0.269 Sum_probs=59.5
Q ss_pred eEEEeccCcc------cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-----cceeeeccH
Q psy5357 32 PHAFSDACSY------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-----KCYLWIDNQ 100 (181)
Q Consensus 32 L~~F~DAS~~------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-----~~~~~tDS~ 100 (181)
+.+|+|+|.. +||+|++ . .++ ... + +. +....|-.|.||.|++.|.+. .+.++|||+
T Consensus 4 v~iytDGs~~~n~~~~g~g~v~~--~--~~~--~~~-~-~~----~~~~~TN~~aEL~Ai~~AL~~~~~~~~v~I~tDS~ 71 (150)
T PRK00203 4 VEIYTDGACLGNPGPGGWGAILR--Y--KGH--EKE-L-SG----GEALTTNNRMELMAAIEALEALKEPCEVTLYTDSQ 71 (150)
T ss_pred EEEEEEecccCCCCceEEEEEEE--E--CCe--eEE-E-ec----CCCCCcHHHHHHHHHHHHHHHcCCCCeEEEEECHH
Confidence 7899999973 4554443 1 222 111 1 11 123578899999999998875 688999998
Q ss_pred HHHHHHhcC------ccc----cceecch--hchHHHHHhcc--CCcceEEeCCCC
Q psy5357 101 CVIHWLTGN------KVF----TTFVNNR--VKALKEIKASV--FPIVYKYIPTDS 142 (181)
Q Consensus 101 i~l~~i~~~------~~~----~~fV~nR--v~~i~~I~~~~--~~~~~~hV~t~~ 142 (181)
.++.-|..- +.| ..-|.|+ ++ +|.++. ..+.|.|||+-.
T Consensus 72 yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~---~i~~l~~~~~v~~~wV~~H~ 124 (150)
T PRK00203 72 YVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQ---RLDAALKRHQIKWHWVKGHA 124 (150)
T ss_pred HHHHHHHHHHHHHHHcCCcccCCCccccHHHHH---HHHHHhccCceEEEEecCCC
Confidence 887644431 222 2345565 34 444433 457899998654
No 8
>PRK08719 ribonuclease H; Reviewed
Probab=97.73 E-value=0.00033 Score=55.16 Aligned_cols=102 Identities=17% Similarity=0.153 Sum_probs=62.5
Q ss_pred eeeEEEeccCcc---------cceeEEEEEEeecCCceeEEEEeccccccCCC-CCCcchhhHhHHHHHhhc---cceee
Q psy5357 30 YEPHAFSDACSY---------SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTN-KPTLPRLELLGALIAYRN---KCYLW 96 (181)
Q Consensus 30 ~~L~~F~DAS~~---------aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk-~~tIPrlEL~a~~l~~~l---~~~~~ 96 (181)
.++++|+|+|.. |+|+++|. ++|...... + .|+. ..|--|+||.|+..|.+. ...++
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~----~~~~~~~~~--~----~~~~~~~Tnn~aEl~A~~~aL~~~~~~~~i~ 72 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYD----EAGEIVDEQ--S----ITVNRYTDNAELELLALIEALEYARDGDVIY 72 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEe----CCCCeeEEE--E----ecCCCCccHHHHHHHHHHHHHHHcCCCCEEE
Confidence 478899999882 55655543 333221111 1 1222 258899999999999886 57899
Q ss_pred eccHHHHHHHh--------cC-c-cccceecchhchHHHHHhcc--CCcceEEeCCCC
Q psy5357 97 IDNQCVIHWLT--------GN-K-VFTTFVNNRVKALKEIKASV--FPIVYKYIPTDS 142 (181)
Q Consensus 97 tDS~i~l~~i~--------~~-~-~~~~fV~nRv~~i~~I~~~~--~~~~~~hV~t~~ 142 (181)
|||+.++.-|+ +. + +-...|.|+=- +++|.++. ..+.|.||++-.
T Consensus 73 tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl-~~~i~~l~~~~~i~~~~VkgH~ 129 (147)
T PRK08719 73 SDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDL-WQQVDELRARKYVEVEKVTAHS 129 (147)
T ss_pred echHHHHHHHHHHHHHHHhCCcccCCCcccccHHH-HHHHHHHhCCCcEEEEEecCCC
Confidence 99998886663 33 2 22344666422 22333332 357899999843
No 9
>PRK06548 ribonuclease H; Provisional
Probab=97.51 E-value=0.00089 Score=53.72 Aligned_cols=97 Identities=20% Similarity=0.091 Sum_probs=59.9
Q ss_pred eeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc------cceeeeccH
Q psy5357 31 EPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN------KCYLWIDNQ 100 (181)
Q Consensus 31 ~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l------~~~~~tDS~ 100 (181)
++++|+|||..+ -|..+|+. .++ . ...+....|=-|+||.|+..|... .+.+||||+
T Consensus 5 ~~~IytDGa~~gnpg~~G~g~~~~---~~~----~------~~g~~~~~TNnraEl~Aii~aL~~~~~~~~~v~I~TDS~ 71 (161)
T PRK06548 5 EIIAATDGSSLANPGPSGWAWYVD---ENT----W------DSGGWDIATNNIAELTAVRELLIATRHTDRPILILSDSK 71 (161)
T ss_pred EEEEEEeeccCCCCCceEEEEEEe---CCc----E------EccCCCCCCHHHHHHHHHHHHHHhhhcCCceEEEEeChH
Confidence 589999988762 22223332 111 1 112233467789999999888754 588999999
Q ss_pred HHHHHHhc--------C--ccccceecchhchHHHHHhcc--CCcceEEeCCC
Q psy5357 101 CVIHWLTG--------N--KVFTTFVNNRVKALKEIKASV--FPIVYKYIPTD 141 (181)
Q Consensus 101 i~l~~i~~--------~--~~~~~fV~nRv~~i~~I~~~~--~~~~~~hV~t~ 141 (181)
.++.-+.. . ++-...|.|+=- +++|.++. ..+.|.||++-
T Consensus 72 yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL-~~~l~~l~~~~~v~~~wVkgH 123 (161)
T PRK06548 72 YVINSLTKWVYSWKMRKWRKADGKPVLNQEI-IQEIDSLMENRNIRMSWVNAH 123 (161)
T ss_pred HHHHHHHHHHHHHHHCCCcccCCCccccHHH-HHHHHHHHhcCceEEEEEecC
Confidence 99976662 3 223456787733 22333322 35889999864
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.39 E-value=0.00032 Score=48.38 Aligned_cols=69 Identities=20% Similarity=0.248 Sum_probs=48.5
Q ss_pred hhHhHHHHHhhc-------cceeeeccHHHHHHHhcCccccceecchhchHHHHHhccCCcceEEeCCCCCC-Cccc
Q psy5357 80 LELLGALIAYRN-------KCYLWIDNQCVIHWLTGNKVFTTFVNNRVKALKEIKASVFPIVYKYIPTDSNP-ADLA 148 (181)
Q Consensus 80 lEL~a~~l~~~l-------~~~~~tDS~i~l~~i~~~~~~~~fV~nRv~~i~~I~~~~~~~~~~hV~t~~NP-AD~~ 148 (181)
.|+.|+..|.++ ++.+.|||..++..|++...........+..|+.+.+......++|||-+.|- ||.+
T Consensus 4 aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~L 80 (87)
T PF13456_consen 4 AEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNKVADAL 80 (87)
T ss_dssp HHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhHHHHHH
Confidence 689999888876 89999999999999998843333667777733344445567899999999885 5543
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.16 E-value=0.0023 Score=56.79 Aligned_cols=116 Identities=13% Similarity=0.120 Sum_probs=69.2
Q ss_pred eeeEEEeccCccc----ceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc-------cceeeec
Q psy5357 30 YEPHAFSDACSYS----YASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN-------KCYLWID 98 (181)
Q Consensus 30 ~~L~~F~DAS~~a----ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l-------~~~~~tD 98 (181)
+++++|+|||..+ -|+.+.++. .+|.. .+...+. ++...|-...|+.|++.|.++ .+.+++|
T Consensus 1 ~~~~i~~DGa~~~n~g~aG~G~vi~~--~~~~~--~~~~~~~---~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~D 73 (372)
T PRK07238 1 MKVVVEADGGSRGNPGPAGYGAVVWD--ADRGE--VLAERAE---AIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMD 73 (372)
T ss_pred CeEEEEecCCCCCCCCceEEEEEEEe--CCCCc--EEEEeec---ccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeC
Confidence 3689999999873 344444543 33311 1111111 222456678999999999886 7899999
Q ss_pred cHHHHHHHhcCcccc-ceecchhchHHHHHhccCCcceEEeCCCCCC-CcccCCCC
Q psy5357 99 NQCVIHWLTGNKVFT-TFVNNRVKALKEIKASVFPIVYKYIPTDSNP-ADLACKGS 152 (181)
Q Consensus 99 S~i~l~~i~~~~~~~-~fV~nRv~~i~~I~~~~~~~~~~hV~t~~NP-AD~~SRG~ 152 (181)
|..++..+.++.+.+ .-...-+..++++........+.||+.+.|- ||.+.+..
T Consensus 74 S~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a 129 (372)
T PRK07238 74 SKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEA 129 (372)
T ss_pred cHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHH
Confidence 999999998751111 0000001111144444567889999987664 77765543
No 12
>PRK07708 hypothetical protein; Validated
Probab=97.14 E-value=0.005 Score=51.61 Aligned_cols=114 Identities=18% Similarity=0.168 Sum_probs=66.4
Q ss_pred eeeEEEeccCcc----cceeEEEEEEeecCCceeEEEEeccccccCCCCCCcchhhHhHHHHHhhc---------cceee
Q psy5357 30 YEPHAFSDACSY----SYASVVYLRSVSHSGDIRTNIVFAKSRVAPTNKPTLPRLELLGALIAYRN---------KCYLW 96 (181)
Q Consensus 30 ~~L~~F~DAS~~----aygavvYlr~~~~~g~~~~~ll~aKsrvaPlk~~tIPrlEL~a~~l~~~l---------~~~~~ 96 (181)
-.+++|+|||.. .+|+.+.++. .+|.....+- ....+.+ ..|=...|+.|++.|.+. .+.++
T Consensus 72 ~~~~vY~DGs~~~n~g~aG~GvVI~~--~~g~~~~~~~-~~~~l~~--~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~ 146 (219)
T PRK07708 72 HEILVYFDGGFDKETKLAGLGIVIYY--KQGNKRYRIR-RNAYIEG--IYDNNEAEYAALYYAMQELEELGVKHEPVTFR 146 (219)
T ss_pred CcEEEEEeeccCCCCCCcEEEEEEEE--CCCCEEEEEE-eeccccc--cccCcHHHHHHHHHHHHHHHHcCCCcceEEEE
Confidence 368999999872 3444444443 2332222221 1122322 246678899999998875 27899
Q ss_pred eccHHHHHHHhcC-ccccceecchhchHHH-HHhccCCcceEEeCCCCCC-Cccc
Q psy5357 97 IDNQCVIHWLTGN-KVFTTFVNNRVKALKE-IKASVFPIVYKYIPTDSNP-ADLA 148 (181)
Q Consensus 97 tDS~i~l~~i~~~-~~~~~fV~nRv~~i~~-I~~~~~~~~~~hV~t~~NP-AD~~ 148 (181)
+||+.++.|+.+. +...+....-...+.+ +........+.|||-+.|= ||.+
T Consensus 147 ~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~L 201 (219)
T PRK07708 147 GDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQL 201 (219)
T ss_pred eccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHH
Confidence 9999999999987 3332222212221112 2223233677899998885 6654
No 13
>KOG3752|consensus
Probab=93.39 E-value=0.41 Score=43.25 Aligned_cols=65 Identities=25% Similarity=0.279 Sum_probs=46.6
Q ss_pred eEEEeccCccc-------ceeEEEEEEeecCCceeEEEEeccccccCCC--CCCcchhhHhHHHHHhhc-------ccee
Q psy5357 32 PHAFSDACSYS-------YASVVYLRSVSHSGDIRTNIVFAKSRVAPTN--KPTLPRLELLGALIAYRN-------KCYL 95 (181)
Q Consensus 32 L~~F~DAS~~a-------ygavvYlr~~~~~g~~~~~ll~aKsrvaPlk--~~tIPrlEL~a~~l~~~l-------~~~~ 95 (181)
+.+++|+|-.+ =|.+||..--++.+ +-.|+. ..|--|.||.|+..|..- ++++
T Consensus 213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N-----------~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I 281 (371)
T KOG3752|consen 213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELN-----------VSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVI 281 (371)
T ss_pred eEEEecCccccCCCCCCcceeEEeeCCCCccc-----------ccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEE
Confidence 67899998665 23456766322221 223443 378889999999998864 8999
Q ss_pred eeccHHHHHHHh
Q psy5357 96 WIDNQCVIHWLT 107 (181)
Q Consensus 96 ~tDS~i~l~~i~ 107 (181)
.|||.-++.||+
T Consensus 282 ~TDS~~~i~~l~ 293 (371)
T KOG3752|consen 282 RTDSEYFINSLT 293 (371)
T ss_pred EechHHHHHHHH
Confidence 999999998776
Done!