Query psy8736
Match_columns 290
No_of_seqs 179 out of 444
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 17:53:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8736.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8736hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00075 RNase_H: RNase H; In 98.4 4E-07 8.7E-12 73.2 5.1 115 134-264 2-123 (132)
2 cd06222 RnaseH RNase H (RNase 98.0 2E-05 4.4E-10 61.1 7.4 69 137-210 1-76 (130)
3 PRK08719 ribonuclease H; Revie 98.0 2.3E-05 5.1E-10 65.1 6.9 117 134-264 3-137 (147)
4 PRK00203 rnhA ribonuclease H; 97.9 3.7E-05 8E-10 64.0 7.1 119 135-264 3-132 (150)
5 KOG3752|consensus 97.9 4.4E-05 9.5E-10 71.4 7.8 70 136-210 213-291 (371)
6 PRK06548 ribonuclease H; Provi 97.8 7.2E-05 1.6E-09 63.1 8.0 121 134-264 4-132 (161)
7 PRK13907 rnhA ribonuclease H; 97.8 8.6E-05 1.9E-09 59.8 7.0 70 136-210 2-76 (128)
8 COG0328 RnhA Ribonuclease HI [ 97.4 0.00058 1.3E-08 57.0 7.6 116 135-264 3-135 (154)
9 PRK07708 hypothetical protein; 96.9 0.0054 1.2E-07 54.4 9.0 73 133-210 71-155 (219)
10 PRK07238 bifunctional RNase H/ 96.7 0.0057 1.2E-07 58.2 7.9 68 136-209 3-79 (372)
11 PF13966 zf-RVT: zinc-binding 96.4 0.0013 2.9E-08 49.3 1.3 42 219-260 38-83 (86)
12 PF13456 RVT_3: Reverse transc 91.6 0.31 6.8E-06 35.4 4.2 35 171-210 2-36 (87)
13 PF05380 Peptidase_A17: Pao re 78.9 4.4 9.5E-05 33.8 5.1 52 135-188 81-144 (159)
14 PRK08298 cytidine deaminase; V 44.1 32 0.00069 28.1 3.7 41 139-183 19-63 (136)
15 COG0295 Cdd Cytidine deaminase 42.4 32 0.00069 28.1 3.4 51 148-204 27-81 (134)
16 PF00336 DNA_pol_viral_C: DNA 36.2 50 0.0011 29.1 3.8 87 136-239 95-191 (245)
17 PF09538 FYDLN_acid: Protein o 31.8 27 0.00059 27.4 1.4 20 230-250 19-39 (108)
18 PRK06848 hypothetical protein; 31.4 1.1E+02 0.0024 25.0 5.0 43 139-184 22-68 (139)
19 KOG1994|consensus 26.2 26 0.00057 31.1 0.4 33 213-259 229-262 (268)
20 PF05741 zf-nanos: Nanos RNA b 25.7 37 0.0008 23.4 1.0 21 238-258 34-54 (55)
21 PF13696 zf-CCHC_2: Zinc knuck 25.0 39 0.00084 20.6 0.9 18 238-258 9-26 (32)
22 PF05605 zf-Di19: Drought indu 24.2 44 0.00095 22.4 1.2 25 237-261 2-26 (54)
23 PRK05578 cytidine deaminase; V 21.9 1.3E+02 0.0028 24.3 3.7 36 148-183 25-64 (131)
24 COG4391 Uncharacterized protei 20.9 52 0.0011 23.1 1.0 20 228-247 38-58 (62)
No 1
>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=98.40 E-value=4e-07 Score=73.21 Aligned_cols=115 Identities=17% Similarity=0.175 Sum_probs=70.5
Q ss_pred CCeEEeecCCCC--CCceeEEEEec-CccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736 134 NYKQIFTDASKN--EHSVSSAFCCE-ETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS 210 (290)
Q Consensus 134 ~~~~iyTDgSk~--~~~~G~av~~~-~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~ 210 (290)
..+.||||||.. .+..|+|++.. +.+....++ ..+.+.||+.|+.+||+ .. . . .++.|++||..++..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~-~-----~-~~v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-AL-E-----H-RKVTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-TH-S-----T-SEEEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hh-h-----c-ccccccccHHHHHHH
Confidence 467899999953 33335554433 333445556 89999999999999999 54 3 2 689999999999874
Q ss_pred hhh-hhhhhhccCCcc--cccccccccCCCCCCCCCCcccchhehhhhccc-hhhccC
Q psy8736 211 REQ-VSLTRLRIGHTN--LTHVHLMKREPPPECDTCNCRLTVKHLLKYCNK-YHNIRS 264 (290)
Q Consensus 211 r~~-~~l~rlRtGH~~--l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~-~~~~R~ 264 (290)
-.. ......+.-+.. +-+ .++ ..+ ..+....+.||.-||.. ..|++.
T Consensus 73 l~~~~~~~~~~~~~~~~~i~~-~i~-----~~~-~~~~~v~~~~V~~H~~~~~~N~~a 123 (132)
T PF00075_consen 73 LNKWLHGNGWKKTSNGRPIKN-EIW-----ELL-SRGIKVRFRWVPGHSGVPQGNERA 123 (132)
T ss_dssp HHTHHHHTTSBSCTSSSBHTH-HHH-----HHH-HHSSEEEEEESSSSSSSHHHHHHH
T ss_pred HHHhccccccccccccccchh-hee-----ecc-ccceEEeeeeccCcCCCchhHHHH
Confidence 222 111122211111 111 111 112 23677999999999999 576653
No 2
>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=98.03 E-value=2e-05 Score=61.11 Aligned_cols=69 Identities=19% Similarity=0.238 Sum_probs=52.4
Q ss_pred EEeecCCCCCC--ceeEEEEecCcc--ce---eccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736 137 QIFTDASKNEH--SVSSAFCCEETK--FS---VKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ 209 (290)
Q Consensus 137 ~iyTDgSk~~~--~~G~av~~~~~~--~~---~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~ 209 (290)
.+|||||...+ +.|++++..+.. .. .......+++.+|+.|++.|++.+... ...++.|++||..++.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-----~~~~i~i~~Ds~~~~~ 75 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-----GGKKVNIYTDSQYVIN 75 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-----CCceEEEEECHHHHHH
Confidence 37999998654 577776655543 11 122257899999999999999999865 7789999999998766
Q ss_pred h
Q psy8736 210 S 210 (290)
Q Consensus 210 ~ 210 (290)
.
T Consensus 76 ~ 76 (130)
T cd06222 76 A 76 (130)
T ss_pred H
Confidence 5
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=97.96 E-value=2.3e-05 Score=65.12 Aligned_cols=117 Identities=14% Similarity=0.113 Sum_probs=69.5
Q ss_pred CCeEEeecCCCCCCc-----eeEEEEe--cCcc----ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEe
Q psy8736 134 NYKQIFTDASKNEHS-----VSSAFCC--EETK----FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYS 202 (290)
Q Consensus 134 ~~~~iyTDgSk~~~~-----~G~av~~--~~~~----~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~s 202 (290)
..+.||||||...++ .|+|++. ++.. ....+....+-..||+.|+..||+.+.+. ..|++
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~---------~~i~t 73 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG---------DVIYS 73 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC---------CEEEe
Confidence 457899999986443 3666654 3322 23345556789999999999999988642 27999
Q ss_pred cchhhhhhhhhhhhhhhccC-----Cccc--ccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736 203 DSLSALQSREQVSLTRLRIG-----HTNL--THVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS 264 (290)
Q Consensus 203 Ds~saL~~r~~~~l~rlRtG-----H~~l--~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~ 264 (290)
||+-++..-.. -+.+++.+ .... +.. |+..-+ ... .....++.||.-|+....|++.
T Consensus 74 DS~yvi~~i~~-~~~~W~~~~w~~s~g~~v~n~d-l~~~i~-~l~--~~~~i~~~~VkgH~g~~~Ne~a 137 (147)
T PRK08719 74 DSDYCVRGFNE-WLDTWKQKGWRKSDKKPVANRD-LWQQVD-ELR--ARKYVEVEKVTAHSGIEGNEAA 137 (147)
T ss_pred chHHHHHHHHH-HHHHHHhCCcccCCCcccccHH-HHHHHH-HHh--CCCcEEEEEecCCCCChhHHHH
Confidence 99987765321 11222221 1111 111 111000 011 1245889999999888777654
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.90 E-value=3.7e-05 Score=63.97 Aligned_cols=119 Identities=13% Similarity=0.061 Sum_probs=67.3
Q ss_pred CeEEeecCCCCCC--ceeEEEEec--Cccc-eeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhh
Q psy8736 135 YKQIFTDASKNEH--SVSSAFCCE--ETKF-SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ 209 (290)
Q Consensus 135 ~~~iyTDgSk~~~--~~G~av~~~--~~~~-~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~ 209 (290)
.+.||||||...+ ..|++++.. +... ........+...||+.|+..||+.+.+ ...+.|++||+.++.
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-------~~~v~I~tDS~yvi~ 75 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-------PCEVTLYTDSQYVRQ 75 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-------CCeEEEEECHHHHHH
Confidence 3689999998633 356665543 3221 122233566778999999999997753 246899999997776
Q ss_pred hhhhhhhhh-----hccCCc-ccccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736 210 SREQVSLTR-----LRIGHT-NLTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS 264 (290)
Q Consensus 210 ~r~~~~l~r-----lRtGH~-~l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~ 264 (290)
.-.. -+.+ +++..+ ...+.-|+..-+ -.. -.....+.||.-|+....|++.
T Consensus 76 ~i~~-w~~~Wk~~~~~~~~g~~v~n~dl~~~i~-~l~--~~~~v~~~wV~~H~~~~~N~~A 132 (150)
T PRK00203 76 GITE-WIHGWKKNGWKTADKKPVKNVDLWQRLD-AAL--KRHQIKWHWVKGHAGHPENERC 132 (150)
T ss_pred HHHH-HHHHHHHcCCcccCCCccccHHHHHHHH-HHh--ccCceEEEEecCCCCCHHHHHH
Confidence 5331 1111 121111 111110110000 000 1145899999999988877665
No 5
>KOG3752|consensus
Probab=97.88 E-value=4.4e-05 Score=71.43 Aligned_cols=70 Identities=24% Similarity=0.187 Sum_probs=58.4
Q ss_pred eEEeecCCCCCC-----ceeEEEEecCcc---ceeccC-CCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchh
Q psy8736 136 KQIFTDASKNEH-----SVSSAFCCEETK---FSVKLD-PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS 206 (290)
Q Consensus 136 ~~iyTDgSk~~~-----~~G~av~~~~~~---~~~~l~-~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~s 206 (290)
..+|||||...+ .+|.+||.++.. ....+. ...+-|.||+.|+.+||+.+++. +..++.|.+||.-
T Consensus 213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-----~~~kv~I~TDS~~ 287 (371)
T KOG3752|consen 213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-----NINKVVIRTDSEY 287 (371)
T ss_pred eEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-----CCCcEEEEechHH
Confidence 679999997653 489999988764 566665 77899999999999999999986 6779999999986
Q ss_pred hhhh
Q psy8736 207 ALQS 210 (290)
Q Consensus 207 aL~~ 210 (290)
.+..
T Consensus 288 ~i~~ 291 (371)
T KOG3752|consen 288 FINS 291 (371)
T ss_pred HHHH
Confidence 6554
No 6
>PRK06548 ribonuclease H; Provisional
Probab=97.84 E-value=7.2e-05 Score=63.11 Aligned_cols=121 Identities=14% Similarity=0.068 Sum_probs=69.5
Q ss_pred CCeEEeecCCCCCC--ceeEEEEecCccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhhh
Q psy8736 134 NYKQIFTDASKNEH--SVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSR 211 (290)
Q Consensus 134 ~~~~iyTDgSk~~~--~~G~av~~~~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~r 211 (290)
..+.|||||+...+ ..|.|+|..+......-....+--.||+.|+..||+.+.. ...++.|+|||.-++..-
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~i 77 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINSL 77 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHHH
Confidence 45789999997533 3677777654322222223456677999999999985542 334699999999887663
Q ss_pred hh-h---hhhhhccCCcc--cccccccccCCCCCCCCCCcccchhehhhhccchhhccC
Q psy8736 212 EQ-V---SLTRLRIGHTN--LTHVHLMKREPPPECDTCNCRLTVKHLLKYCNKYHNIRS 264 (290)
Q Consensus 212 ~~-~---~l~rlRtGH~~--l~h~~l~~~~~~p~C~~c~~~~tv~Hil~~Cp~~~~~R~ 264 (290)
.. . .-+.+|+.-+. .|.... ..-+ ..... ..+++.||--|+....|++.
T Consensus 78 ~~W~~~Wk~~gWk~s~G~pV~N~dL~-~~l~-~l~~~--~~v~~~wVkgHsg~~gNe~a 132 (161)
T PRK06548 78 TKWVYSWKMRKWRKADGKPVLNQEII-QEID-SLMEN--RNIRMSWVNAHTGHPLNEAA 132 (161)
T ss_pred HHHHHHHHHCCCcccCCCccccHHHH-HHHH-HHHhc--CceEEEEEecCCCCHHHHHH
Confidence 21 0 01122221111 111111 0000 01111 24788999999988888876
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=97.77 E-value=8.6e-05 Score=59.80 Aligned_cols=70 Identities=10% Similarity=0.083 Sum_probs=51.2
Q ss_pred eEEeecCCCCC--CceeEEEEecCccce--ec-cCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736 136 KQIFTDASKNE--HSVSSAFCCEETKFS--VK-LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS 210 (290)
Q Consensus 136 ~~iyTDgSk~~--~~~G~av~~~~~~~~--~~-l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~ 210 (290)
+.||||||... +..|+|++..+.... .. .....+-..||..|++.||+.+.+. +...+.|++||+-.+..
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-----g~~~v~i~sDS~~vi~~ 76 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-----NYNIVSFRTDSQLVERA 76 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-----CCCEEEEEechHHHHHH
Confidence 47999999653 346777776555421 11 1234677899999999999999986 55679999999977655
No 8
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=97.43 E-value=0.00058 Score=57.05 Aligned_cols=116 Identities=16% Similarity=0.040 Sum_probs=70.5
Q ss_pred CeEEeecCCCCC-Cc-eeEEEEe--cCccc--eeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhh
Q psy8736 135 YKQIFTDASKNE-HS-VSSAFCC--EETKF--SVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL 208 (290)
Q Consensus 135 ~~~iyTDgSk~~-~~-~G~av~~--~~~~~--~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL 208 (290)
.+.|||||+... +| -|.|+|. .+... ..... .++--.+|+.|+++||+.+.+. +...+.|++||+-+.
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~-----~~~~v~l~tDS~yv~ 76 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKEL-----GACEVTLYTDSKYVV 76 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhc-----CCceEEEEecHHHHH
Confidence 468999999753 23 3444443 33332 22333 6778889999999999999985 677899999999776
Q ss_pred hhhhhhhhhhhccCCcccccccccccCCCCCCC-----------CCCcccchhehhhhccchhhccC
Q psy8736 209 QSREQVSLTRLRIGHTNLTHVHLMKREPPPECD-----------TCNCRLTVKHLLKYCNKYHNIRS 264 (290)
Q Consensus 209 ~~r~~~~l~rlRtGH~~l~h~~l~~~~~~p~C~-----------~c~~~~tv~Hil~~Cp~~~~~R~ 264 (290)
..-. ++..+ +...++. ...-.|.|. .-.....++||.-|-....|+|.
T Consensus 77 ~~i~-----~w~~~--w~~~~w~-~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~Nera 135 (154)
T COG0328 77 EGIT-----RWIVK--WKKNGWK-TADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERA 135 (154)
T ss_pred HHHH-----HHHhh--ccccCcc-ccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHH
Confidence 6433 22111 1111111 011112211 11235688888888888888886
No 9
>PRK07708 hypothetical protein; Validated
Probab=96.94 E-value=0.0054 Score=54.36 Aligned_cols=73 Identities=12% Similarity=0.109 Sum_probs=51.2
Q ss_pred CCCeEEeecCCCC--CCceeEEEEec--Cccce------eccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCC--cEEE
Q psy8736 133 PNYKQIFTDASKN--EHSVSSAFCCE--ETKFS------VKLDPRISICNAELISIQYAISFIISTTPLQVPTP--KFVL 200 (290)
Q Consensus 133 ~~~~~iyTDgSk~--~~~~G~av~~~--~~~~~------~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~--~~~I 200 (290)
++...+|+|||-. .++.|+|++.. ..... ..++...+--.||..|++.||+.+.+. +.+ .+.|
T Consensus 71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~~~V~I 145 (219)
T PRK07708 71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKHEPVTF 145 (219)
T ss_pred CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCcceEEE
Confidence 5568999999964 34466665543 33222 245555788889999999999999986 333 3789
Q ss_pred Eecchhhhhh
Q psy8736 201 YSDSLSALQS 210 (290)
Q Consensus 201 ~sDs~saL~~ 210 (290)
++||+-.+..
T Consensus 146 ~~DSqlVi~q 155 (219)
T PRK07708 146 RGDSQVVLNQ 155 (219)
T ss_pred EeccHHHHHH
Confidence 9999866543
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=96.70 E-value=0.0057 Score=58.21 Aligned_cols=68 Identities=9% Similarity=0.009 Sum_probs=49.1
Q ss_pred eEEeecCCCCCC--ceeEEEEecCcc-------ceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchh
Q psy8736 136 KQIFTDASKNEH--SVSSAFCCEETK-------FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS 206 (290)
Q Consensus 136 ~~iyTDgSk~~~--~~G~av~~~~~~-------~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~s 206 (290)
+.||||||...+ ..|+|++..+.+ ....++ .++...||..|++.||+.+.+. +..++.|++||.-
T Consensus 3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~-----g~~~v~i~~DS~l 76 (372)
T PRK07238 3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAEL-----GATEVEVRMDSKL 76 (372)
T ss_pred EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhC-----CCCeEEEEeCcHH
Confidence 579999997543 356666654432 112333 4566789999999999999986 5668999999987
Q ss_pred hhh
Q psy8736 207 ALQ 209 (290)
Q Consensus 207 aL~ 209 (290)
.+.
T Consensus 77 vi~ 79 (372)
T PRK07238 77 VVE 79 (372)
T ss_pred HHH
Confidence 654
No 11
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.44 E-value=0.0013 Score=49.34 Aligned_cols=42 Identities=29% Similarity=0.389 Sum_probs=30.0
Q ss_pred hccCCccc-ccccc--cccCCCCCCCCCC-cccchhehhhhccchh
Q psy8736 219 LRIGHTNL-THVHL--MKREPPPECDTCN-CRLTVKHLLKYCNKYH 260 (290)
Q Consensus 219 lRtGH~~l-~h~~l--~~~~~~p~C~~c~-~~~tv~Hil~~Cp~~~ 260 (290)
+|.-|.+| +...| .+...++.|..|+ ..||++|++++||...
T Consensus 38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 38 WRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred eeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 34445555 22333 4456789999887 5999999999999754
No 12
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=91.61 E-value=0.31 Score=35.39 Aligned_cols=35 Identities=20% Similarity=0.220 Sum_probs=29.2
Q ss_pred hHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhh
Q psy8736 171 CNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS 210 (290)
Q Consensus 171 ftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~ 210 (290)
..||+.|++.|++.+++. +-.++.+.+||...+..
T Consensus 2 ~~aE~~al~~al~~a~~~-----g~~~i~v~sDs~~vv~~ 36 (87)
T PF13456_consen 2 LEAEALALLEALQLAWEL-----GIRKIIVESDSQLVVDA 36 (87)
T ss_dssp HHHHHHHHHHHHHHHHCC-----T-SCEEEEES-HHHHHH
T ss_pred cHHHHHHHHHHHHHHHHC-----CCCEEEEEecCcccccc
Confidence 469999999999999987 77899999999987664
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=78.89 E-value=4.4 Score=33.79 Aligned_cols=52 Identities=13% Similarity=0.207 Sum_probs=36.3
Q ss_pred CeEEeecCCCCCCceeEEEEecCc---c-------ceeccC--CCccchHHHHHHHHHHHHHHHhh
Q psy8736 135 YKQIFTDASKNEHSVSSAFCCEET---K-------FSVKLD--PRISICNAELISIQYAISFIIST 188 (290)
Q Consensus 135 ~~~iyTDgSk~~~~~G~av~~~~~---~-------~~~~l~--~~~siftAE~~aI~~Al~~~~~~ 188 (290)
..++|+|||+ .+.|+.+|.... . .+-+.. ...||-.-|+.|+..|.+++...
T Consensus 81 ~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~ 144 (159)
T PF05380_consen 81 ELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTV 144 (159)
T ss_pred eeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 4689999994 677777775441 1 122222 24599999999999999987654
No 14
>PRK08298 cytidine deaminase; Validated
Probab=44.07 E-value=32 Score=28.11 Aligned_cols=41 Identities=15% Similarity=0.128 Sum_probs=27.4
Q ss_pred eecCCCCCCceeEEEEecCccceeccCCCc----cchHHHHHHHHHHHH
Q psy8736 139 FTDASKNEHSVSSAFCCEETKFSVKLDPRI----SICNAELISIQYAIS 183 (290)
Q Consensus 139 yTDgSk~~~~~G~av~~~~~~~~~~l~~~~----siftAE~~aI~~Al~ 183 (290)
|...| .||+|+...|.+...+.--++ .-.=||..||..|+.
T Consensus 19 Y~PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~ 63 (136)
T PRK08298 19 YPNGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHK 63 (136)
T ss_pred cCCCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHH
Confidence 55556 899999998887444332222 233489999988763
No 15
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=42.44 E-value=32 Score=28.12 Aligned_cols=51 Identities=20% Similarity=0.083 Sum_probs=31.4
Q ss_pred ceeEEEEecCccceeccCCCccch----HHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecc
Q psy8736 148 SVSSAFCCEETKFSVKLDPRISIC----NAELISIQYAISFIISTTPLQVPTPKFVLYSDS 204 (290)
Q Consensus 148 ~~G~av~~~~~~~~~~l~~~~sif----tAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs 204 (290)
.||+++...+.+..++---+...| =||..||.+||.. -. ..-..+.++.|+
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~-----~~~~~v~v~~~~ 81 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GK-----RKFDAVVVVADT 81 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CC-----CcEEEEEEEcCC
Confidence 588888888876443332222233 3999999999877 21 134455666665
No 16
>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=36.21 E-value=50 Score=29.09 Aligned_cols=87 Identities=17% Similarity=0.199 Sum_probs=49.3
Q ss_pred eEEeecCCCCCCceeEEEEecCccceeccCCCccchHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEecchhhhhhhh---
Q psy8736 136 KQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSRE--- 212 (290)
Q Consensus 136 ~~iyTDgSk~~~~~G~av~~~~~~~~~~l~~~~siftAE~~aI~~Al~~~~~~~~~~~~~~~~~I~sDs~saL~~r~--- 212 (290)
-+||+|+.-...|+. .......+.....-.|.+||++|...|--+.- .+ .|.+||.-++.+|-
T Consensus 95 c~VfaDATpTgwgi~----i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~---------~r-~l~tDnt~Vlsrkyts~ 160 (245)
T PF00336_consen 95 CQVFADATPTGWGIS----ITGQRMRGTFSKPLPIHTAELLAACLARLMSG---------AR-CLGTDNTVVLSRKYTSF 160 (245)
T ss_pred CceeccCCCCcceee----ecCceeeeeecccccchHHHHHHHHHHHhccC---------Cc-EEeecCcEEEecccccC
Confidence 479999976544422 22222222222345689999998866654432 12 48899988887754
Q ss_pred ----hhhhhhhccCCcccccccc---cccCCCCC
Q psy8736 213 ----QVSLTRLRIGHTNLTHVHL---MKREPPPE 239 (290)
Q Consensus 213 ----~~~l~rlRtGH~~l~h~~l---~~~~~~p~ 239 (290)
...-+++.-|-+. .|. .+-.|.|.
T Consensus 161 PW~lac~A~wiLrgts~---~yVPS~~NPAD~Ps 191 (245)
T PF00336_consen 161 PWLLACAANWILRGTSF---YYVPSKYNPADDPS 191 (245)
T ss_pred cHHHHHHHHHhhcCceE---EEeccccCcCCCCC
Confidence 2344566655432 244 44455543
No 17
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=31.78 E-value=27 Score=27.37 Aligned_cols=20 Identities=15% Similarity=0.547 Sum_probs=15.9
Q ss_pred cc-cccCCCCCCCCCCcccchh
Q psy8736 230 HL-MKREPPPECDTCNCRLTVK 250 (290)
Q Consensus 230 ~l-~~~~~~p~C~~c~~~~tv~ 250 (290)
|. +++ ++-.|++||+.+.+.
T Consensus 19 FYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 19 FYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred hccCCC-CCccCCCCCCccCcc
Confidence 44 888 667799999988877
No 18
>PRK06848 hypothetical protein; Validated
Probab=31.43 E-value=1.1e+02 Score=24.95 Aligned_cols=43 Identities=23% Similarity=0.219 Sum_probs=28.6
Q ss_pred eecCCCCCCceeEEEEecCccceeccCCCc----cchHHHHHHHHHHHHH
Q psy8736 139 FTDASKNEHSVSSAFCCEETKFSVKLDPRI----SICNAELISIQYAISF 184 (290)
Q Consensus 139 yTDgSk~~~~~G~av~~~~~~~~~~l~~~~----siftAE~~aI~~Al~~ 184 (290)
|.. | +..||+|+...|.+...+.--+. .-.=||..||..|+..
T Consensus 22 y~p-s--~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~ 68 (139)
T PRK06848 22 YRN-D--WHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISE 68 (139)
T ss_pred cCC-C--CCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHc
Confidence 554 4 36799999998887444332222 2335999999988754
No 19
>KOG1994|consensus
Probab=26.19 E-value=26 Score=31.15 Aligned_cols=33 Identities=21% Similarity=0.237 Sum_probs=25.2
Q ss_pred hhhhhhhccCCcccccccccccCCCCCCCCCCcc-cchhehhhhccch
Q psy8736 213 QVSLTRLRIGHTNLTHVHLMKREPPPECDTCNCR-LTVKHLLKYCNKY 259 (290)
Q Consensus 213 ~~~l~rlRtGH~~l~h~~l~~~~~~p~C~~c~~~-~tv~Hil~~Cp~~ 259 (290)
+.+..-||.|| -.|-.||.. .|-+-++.|||-.
T Consensus 229 t~in~~LR~eh--------------~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 229 TKINIFLRSEH--------------YYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred HHHHHHHhccc--------------eEEEEeccccCCHHHHHHhCCCC
Confidence 45677889886 257789865 7888899999954
No 20
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.70 E-value=37 Score=23.36 Aligned_cols=21 Identities=33% Similarity=0.678 Sum_probs=10.2
Q ss_pred CCCCCCCcccchhehhhhccc
Q psy8736 238 PECDTCNCRLTVKHLLKYCNK 258 (290)
Q Consensus 238 p~C~~c~~~~tv~Hil~~Cp~ 258 (290)
-.|+.||+.....|-...||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 479999999999999999995
No 21
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=24.99 E-value=39 Score=20.58 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=14.8
Q ss_pred CCCCCCCcccchhehhhhccc
Q psy8736 238 PECDTCNCRLTVKHLLKYCNK 258 (290)
Q Consensus 238 p~C~~c~~~~tv~Hil~~Cp~ 258 (290)
-.|..|+... |.+-+||.
T Consensus 9 Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CEeecCCCCC---ccHhHCCC
Confidence 4688887665 99999997
No 22
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=24.24 E-value=44 Score=22.36 Aligned_cols=25 Identities=20% Similarity=0.485 Sum_probs=20.0
Q ss_pred CCCCCCCCcccchhehhhhccchhh
Q psy8736 237 PPECDTCNCRLTVKHLLKYCNKYHN 261 (290)
Q Consensus 237 ~p~C~~c~~~~tv~Hil~~Cp~~~~ 261 (290)
+-.|+.||...++.-+..||.....
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~ 26 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHR 26 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCc
Confidence 4579999988898888888877654
No 23
>PRK05578 cytidine deaminase; Validated
Probab=21.93 E-value=1.3e+02 Score=24.29 Aligned_cols=36 Identities=22% Similarity=0.135 Sum_probs=23.9
Q ss_pred ceeEEEEecCccceeccCCCc----cchHHHHHHHHHHHH
Q psy8736 148 SVSSAFCCEETKFSVKLDPRI----SICNAELISIQYAIS 183 (290)
Q Consensus 148 ~~G~av~~~~~~~~~~l~~~~----siftAE~~aI~~Al~ 183 (290)
.||+|+...+.+...+.--++ --.-||..||..|+.
T Consensus 25 ~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~ 64 (131)
T PRK05578 25 PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAIS 64 (131)
T ss_pred ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHH
Confidence 599999988877433322222 234589999998873
No 24
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.93 E-value=52 Score=23.12 Aligned_cols=20 Identities=35% Similarity=0.569 Sum_probs=16.1
Q ss_pred cccc-cccCCCCCCCCCCccc
Q psy8736 228 HVHL-MKREPPPECDTCNCRL 247 (290)
Q Consensus 228 h~~l-~~~~~~p~C~~c~~~~ 247 (290)
|.|| |+.+-.-.|++|++.-
T Consensus 38 rV~L~mg~~gev~CPYC~t~y 58 (62)
T COG4391 38 RVFLDMGDEGEVVCPYCSTRY 58 (62)
T ss_pred EEEEEcCCCCcEecCccccEE
Confidence 4588 9888888999998754
Done!