Query psy4967
Match_columns 354
No_of_seqs 254 out of 1435
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 22:26:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4967.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4967hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.9 3.5E-22 7.7E-27 170.0 14.2 121 140-271 3-142 (161)
2 COG0328 RnhA Ribonuclease HI [ 99.9 3E-22 6.5E-27 167.6 13.0 122 141-271 2-145 (154)
3 PRK08719 ribonuclease H; Revie 99.9 5.4E-22 1.2E-26 167.4 14.1 121 141-270 3-146 (147)
4 PF00075 RNase_H: RNase H; In 99.9 4.6E-22 1E-26 164.9 11.9 118 141-270 2-132 (132)
5 PRK00203 rnhA ribonuclease H; 99.9 7.5E-22 1.6E-26 167.7 12.6 118 142-271 3-142 (150)
6 cd06222 RnaseH RNase H (RNase 99.8 2E-17 4.3E-22 134.0 13.7 118 144-269 1-130 (130)
7 KOG3752|consensus 99.7 1.1E-17 2.3E-22 156.2 11.5 125 141-271 211-365 (371)
8 PRK13907 rnhA ribonuclease H; 99.7 3.5E-16 7.5E-21 129.3 12.9 116 143-271 2-127 (128)
9 PRK07708 hypothetical protein; 99.6 3.5E-15 7.5E-20 133.8 14.6 128 135-271 66-208 (219)
10 PRK07238 bifunctional RNase H/ 99.5 7.4E-13 1.6E-17 128.9 14.0 117 142-271 2-132 (372)
11 PF13456 RVT_3: Reverse transc 99.2 2.3E-10 4.9E-15 87.2 10.0 82 177-270 1-86 (87)
12 PF05380 Peptidase_A17: Pao re 90.1 1.3 2.8E-05 37.7 7.1 65 142-208 81-158 (159)
13 PF00336 DNA_pol_viral_C: DNA 73.9 3.9 8.5E-05 36.0 3.5 86 142-251 94-182 (245)
14 COG0296 GlgB 1,4-alpha-glucan 35.3 48 0.001 34.7 4.2 34 228-261 213-247 (628)
15 COG4566 TtrR Response regulato 32.6 3.5E+02 0.0076 23.9 8.6 67 184-257 15-90 (202)
16 COG3341 Predicted double-stran 31.3 38 0.00083 30.3 2.3 96 175-276 106-207 (225)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.88 E-value=3.5e-22 Score=170.03 Aligned_cols=121 Identities=27% Similarity=0.281 Sum_probs=90.4
Q ss_pred CCcEEEEeCCCCCCC--CceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967 140 PDSTVVYTDASKNDV--AVSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ 216 (354)
Q Consensus 140 ~~~~~iytDGS~~~~--~~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~ 216 (354)
+..++||||||+..+ ..|+|++ .+....+... ...||+.|||.|++.||+.+ . .....|.|+|||++|++
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~-~~~TNnraEl~Aii~aL~~~-----~-~~~~~v~I~TDS~yvi~ 75 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGW-DIATNNIAELTAVRELLIAT-----R-HTDRPILILSDSKYVIN 75 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCC-CCCCHHHHHHHHHHHHHHhh-----h-cCCceEEEEeChHHHHH
Confidence 456899999999853 4788877 3322223222 35799999999999999866 2 23457999999999999
Q ss_pred Hhcc---------cCCCC-------hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967 217 TLQN---------IFSLN-------PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271 (354)
Q Consensus 217 ~i~~---------~~~~~-------~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~ 271 (354)
++.. +...+ +++++|..++. ...|+|.|||||+|++|||.||+||++|+..
T Consensus 76 ~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~----~~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 76 SLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLME----NRNIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred HHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHh----cCceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 9994 22222 24444444443 3579999999999999999999999999977
No 2
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.88 E-value=3e-22 Score=167.62 Aligned_cols=122 Identities=21% Similarity=0.238 Sum_probs=95.7
Q ss_pred CcEEEEeCCCCCC--CCceEEEE--eCC-e-eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHH
Q psy4967 141 DSTVVYTDASKND--VAVSSAFC--SQD-T-KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSA 214 (354)
Q Consensus 141 ~~~~iytDGS~~~--~~~G~a~~--~~~-~-~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~a 214 (354)
..+.||||||+.. |-.|+|+| .+. . ..+..+. .+||+.||+.|++.||+.+ ...+...|.|+|||++|
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l-----~~~~~~~v~l~tDS~yv 75 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEAL-----KELGACEVTLYTDSKYV 75 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHH-----HhcCCceEEEEecHHHH
Confidence 3589999999985 34777776 332 2 3455555 7899999999999999999 44688999999999999
Q ss_pred HHHhcccCC----CC------------hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967 215 LQTLQNIFS----LN------------PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271 (354)
Q Consensus 215 l~~i~~~~~----~~------------~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~ 271 (354)
+++|..+.. .. .+++++.++.. ....|.+.|||||.|.++||.||+||+.|++.
T Consensus 76 ~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~---~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~ 145 (154)
T COG0328 76 VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLK---RHELVFWEWVKGHAGHPENERADQLAREAARA 145 (154)
T ss_pred HHHHHHHHhhccccCccccccCccccHHHHHHHHHHHh---hCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence 999985411 11 23555555544 35699999999999999999999999999987
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.88 E-value=5.4e-22 Score=167.41 Aligned_cols=121 Identities=21% Similarity=0.259 Sum_probs=87.6
Q ss_pred CcEEEEeCCCCCCCC-----ceEEEE--eC--Ce--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEe
Q psy4967 141 DSTVVYTDASKNDVA-----VSSAFC--SQ--DT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICS 209 (354)
Q Consensus 141 ~~~~iytDGS~~~~~-----~G~a~~--~~--~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~s 209 (354)
+.++||||||+..++ .|+|++ .. .. ..+..+....|++.||+.|++.||+.+. .. ..|+|
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~-----~~----~~i~t 73 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYAR-----DG----DVIYS 73 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcC-----CC----CEEEe
Confidence 468999999997542 477776 32 22 3445566667999999999999999983 21 37999
Q ss_pred CCHHHHHHhc--------ccCC-CCh--h-HHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhc
Q psy4967 210 DSLSALQTLQ--------NIFS-LNP--I-AGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT 270 (354)
Q Consensus 210 DS~~al~~i~--------~~~~-~~~--~-~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~ 270 (354)
||++|++++. +.+. ..+ + -.++.+.+..+.....|+|.|||||+|++|||.||+||++|++
T Consensus 74 DS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 74 DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred chHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9999999984 3222 211 1 1233333333334677999999999999999999999999975
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=99.88 E-value=4.6e-22 Score=164.86 Aligned_cols=118 Identities=37% Similarity=0.508 Sum_probs=91.3
Q ss_pred CcEEEEeCCCCCC--CCceEEEE-eCCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHHH
Q psy4967 141 DSTVVYTDASKND--VAVSSAFC-SQDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQT 217 (354)
Q Consensus 141 ~~~~iytDGS~~~--~~~G~a~~-~~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~~ 217 (354)
+.+.||||||+.. +..|+|++ ..+...+..++ ..+++.||+.||..||+.+ ....+.|+|||++++..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~--------~~~~v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL--------EHRKVTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH--------STSEEEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh--------hcccccccccHHHHHHH
Confidence 4689999999773 33466655 44445555566 7899999999999999943 23899999999999997
Q ss_pred hcc-----cCC-C--C-hhHHHHHHHHHhhcCCCceEEEEeCCCCCC-ccchHHhHHHHHhhc
Q psy4967 218 LQN-----IFS-L--N-PIAGEIRDLILTNKSKLNVRFIWVPSHVGI-AGNEEADRLAKEALT 270 (354)
Q Consensus 218 i~~-----~~~-~--~-~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi-~gNe~AD~lAk~a~~ 270 (354)
+.. ... . . ++..++.+++. .+..|.|+|||||+|+ .|||.||+|||+|+.
T Consensus 73 l~~~~~~~~~~~~~~~~~i~~~i~~~~~---~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~ 132 (132)
T PF00075_consen 73 LNKWLHGNGWKKTSNGRPIKNEIWELLS---RGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ 132 (132)
T ss_dssp HHTHHHHTTSBSCTSSSBHTHHHHHHHH---HSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred HHHhccccccccccccccchhheeeccc---cceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence 777 222 1 2 46677777774 4899999999999999 699999999999973
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.87 E-value=7.5e-22 Score=167.70 Aligned_cols=118 Identities=18% Similarity=0.222 Sum_probs=89.3
Q ss_pred cEEEEeCCCCCC--CCceEEEE--eCCe--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHH
Q psy4967 142 STVVYTDASKND--VAVSSAFC--SQDT--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSAL 215 (354)
Q Consensus 142 ~~~iytDGS~~~--~~~G~a~~--~~~~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al 215 (354)
.++||||||+.. +..|+|+| .++. ...... ...|++.|||.|++.||+.+ . ....+.|+|||++++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~-----~--~~~~v~I~tDS~yvi 74 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEAL-----K--EPCEVTLYTDSQYVR 74 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHc-----C--CCCeEEEEECHHHHH
Confidence 489999999984 34777776 3322 223333 45789999999999999988 2 246799999999999
Q ss_pred HHhccc---------CCCC-------hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967 216 QTLQNI---------FSLN-------PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271 (354)
Q Consensus 216 ~~i~~~---------~~~~-------~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~ 271 (354)
++|..+ .... ++++++.+++ ....|.|.|||||+|++||+.||+|||+|+..
T Consensus 75 ~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~----~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 75 QGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL----KRHQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred HHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHh----ccCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 999863 1111 2344444443 34789999999999999999999999999987
No 6
>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=99.75 E-value=2e-17 Score=134.05 Aligned_cols=118 Identities=31% Similarity=0.407 Sum_probs=91.3
Q ss_pred EEEeCCCCCCC--CceEEEE--eC-C-ee-eeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967 144 VVYTDASKNDV--AVSSAFC--SQ-D-TK-FSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ 216 (354)
Q Consensus 144 ~iytDGS~~~~--~~G~a~~--~~-~-~~-~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~ 216 (354)
.+|||||...+ ++|+|++ +. + .. .........+++.+|+.|++.||+.+. .....++.|++||+.++.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~-----~~~~~~i~i~~Ds~~~~~ 75 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELAL-----ELGGKKVNIYTDSQYVIN 75 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHH-----hCCCceEEEEECHHHHHH
Confidence 48999999865 6888877 32 2 11 122222567999999999999999994 457899999999999999
Q ss_pred HhcccCC-CC----hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhh
Q psy4967 217 TLQNIFS-LN----PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEAL 269 (354)
Q Consensus 217 ~i~~~~~-~~----~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~ 269 (354)
.+.+... .. .++..+.+++ .....+.|.|||+|+|+.+|+.||.|||.|.
T Consensus 76 ~~~~~~~~~~~~~~~~~~~i~~~~---~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 76 ALTGWYEGKPVKNVDLWQRLLALL---KRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HhhccccCCChhhHHHHHHHHHHH---hCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 9998764 11 2344444444 2588999999999999999999999999874
No 7
>KOG3752|consensus
Probab=99.74 E-value=1.1e-17 Score=156.24 Aligned_cols=125 Identities=28% Similarity=0.244 Sum_probs=97.4
Q ss_pred CcEEEEeCCCCCCC-----CceEEEE--eCC-eeeeecCC-CCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCC
Q psy4967 141 DSTVVYTDASKNDV-----AVSSAFC--SQD-TKFSSRLH-PLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDS 211 (354)
Q Consensus 141 ~~~~iytDGS~~~~-----~~G~a~~--~~~-~~~~~~l~-~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS 211 (354)
+..++|||||+..+ .+|+|++ ++. ...++++. ...++|.||+.|+..||+.+. .....+|+|.|||
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~-----~~~~~kv~I~TDS 285 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKAR-----SKNINKVVIRTDS 285 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHH-----hcCCCcEEEEech
Confidence 35899999999863 4999998 332 35677775 788999999999999999994 4466799999999
Q ss_pred HHHHHHhcccCCC-----------Ch----------hHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhc
Q psy4967 212 LSALQTLQNIFSL-----------NP----------IAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALT 270 (354)
Q Consensus 212 ~~al~~i~~~~~~-----------~~----------~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~ 270 (354)
+++++.|+.|... ++ .+.++.++.+.. ...+|.+.||+||.|+.|||.||.||+++..
T Consensus 286 ~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~-~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 286 EYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI-SNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred HHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhh-ccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 9999999866321 11 223333443321 4689999999999999999999999999865
Q ss_pred C
Q psy4967 271 S 271 (354)
Q Consensus 271 ~ 271 (354)
.
T Consensus 365 ~ 365 (371)
T KOG3752|consen 365 L 365 (371)
T ss_pred h
Confidence 4
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.69 E-value=3.5e-16 Score=129.31 Aligned_cols=116 Identities=24% Similarity=0.301 Sum_probs=88.3
Q ss_pred EEEEeCCCCCC--CCceEEEE--eC-C-eeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHH
Q psy4967 143 TVVYTDASKND--VAVSSAFC--SQ-D-TKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQ 216 (354)
Q Consensus 143 ~~iytDGS~~~--~~~G~a~~--~~-~-~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~ 216 (354)
+.||||||+.. +..|+|+| +. + ...++.. ...|++.||+.|++.||+.+. ..+..++.|++||+.+++
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~-~~~tn~~AE~~All~aL~~a~-----~~g~~~v~i~sDS~~vi~ 75 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCT-----EHNYNIVSFRTDSQLVER 75 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecc-cccCCcHHHHHHHHHHHHHHH-----hCCCCEEEEEechHHHHH
Confidence 68999999985 45888887 32 2 2233333 457999999999999999994 446678999999999999
Q ss_pred HhcccCCCC----hhHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967 217 TLQNIFSLN----PIAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271 (354)
Q Consensus 217 ~i~~~~~~~----~~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~ 271 (354)
.+++..... ++++++..++. ....+.|.|||+ +.|+.||.||+.|+..
T Consensus 76 ~~~~~~~~~~~~~~l~~~~~~l~~---~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 76 AVEKEYAKNKMFAPLLEEALQYIK---SFDLFFIKWIPS----SQNKVADELARKAILQ 127 (128)
T ss_pred HHhHHHhcChhHHHHHHHHHHHHh---cCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence 999865432 34555555543 467788899995 6999999999999753
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.64 E-value=3.5e-15 Score=133.76 Aligned_cols=128 Identities=19% Similarity=0.228 Sum_probs=93.2
Q ss_pred HHhcCCCcEEEEeCCCCC--CCCceEEEE--e--CCee----eeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCce
Q psy4967 135 LLQKTPDSTVVYTDASKN--DVAVSSAFC--S--QDTK----FSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAY 204 (354)
Q Consensus 135 ~~~~~~~~~~iytDGS~~--~~~~G~a~~--~--~~~~----~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~ 204 (354)
.+...|+.+++|+|||.. ++++|+|+| . ++.. ....+....|++.||+.|++.||+.+... ......
T Consensus 66 ~~~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~---g~~~~~ 142 (219)
T PRK07708 66 EVEEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL---GVKHEP 142 (219)
T ss_pred hhccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc---CCCcce
Confidence 345677889999999986 456888876 2 2222 12345556799999999999999999541 222335
Q ss_pred EEEEeCCHHHHHHhcccCC-CChhH----HHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967 205 LVICSDSLSALQTLQNIFS-LNPIA----GEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271 (354)
Q Consensus 205 i~I~sDS~~al~~i~~~~~-~~~~~----~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~ 271 (354)
|.|++||+.+++.+.+.+. .++.. ..+.++++. ....+.+.||| ...|+.||+||+.|+..
T Consensus 143 V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~--~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 143 VTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQ--LKLTPVYEPIS----RKQNKEADQLATQALEG 208 (219)
T ss_pred EEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhh--CCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence 9999999999999998764 44433 334444433 34457889998 67899999999999987
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.46 E-value=7.4e-13 Score=128.86 Aligned_cols=117 Identities=20% Similarity=0.295 Sum_probs=88.3
Q ss_pred cEEEEeCCCCCCC--CceEEEE--e--CC-e--eeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCH
Q psy4967 142 STVVYTDASKNDV--AVSSAFC--S--QD-T--KFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSL 212 (354)
Q Consensus 142 ~~~iytDGS~~~~--~~G~a~~--~--~~-~--~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~ 212 (354)
.+.||||||+..+ ..|+|++ + ++ . ..+..++ .+|++.||+.|++.||+.+. ..+...|.|++||+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~-----~~g~~~v~i~~DS~ 75 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAA-----ELGATEVEVRMDSK 75 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHH-----hCCCCeEEEEeCcH
Confidence 3689999999854 5788876 3 22 1 2233344 67899999999999999994 44677999999999
Q ss_pred HHHHHhcccCC-CCh----hHHHHHHHHHhhcCCCceEEEEeCCCCCCccchHHhHHHHHhhcC
Q psy4967 213 SALQTLQNIFS-LNP----IAGEIRDLILTNKSKLNVRFIWVPSHVGIAGNEEADRLAKEALTS 271 (354)
Q Consensus 213 ~al~~i~~~~~-~~~----~~~~i~~~~~~~~~~~~V~~~WVpgH~gi~gNe~AD~lAk~a~~~ 271 (354)
.+++.+.+... ++. ++.++..+.+ ....|.|.|||+ .+|+.||.||+.|+..
T Consensus 76 lvi~~i~~~~~~~~~~l~~~~~~i~~l~~---~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 76 LVVEQMSGRWKVKHPDMKPLAAQARELAS---QFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred HHHHHhCCCCccCChHHHHHHHHHHHHHh---cCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 99999988654 333 2333444333 568899999994 7999999999999754
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.17 E-value=2.3e-10 Score=87.24 Aligned_cols=82 Identities=28% Similarity=0.304 Sum_probs=63.2
Q ss_pred hHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHHHhcccCC-CCh---hHHHHHHHHHhhcCCCceEEEEeCCC
Q psy4967 177 ICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFS-LNP---IAGEIRDLILTNKSKLNVRFIWVPSH 252 (354)
Q Consensus 177 ~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~~i~~~~~-~~~---~~~~i~~~~~~~~~~~~V~~~WVpgH 252 (354)
+..||+.|+..||+.+ ...+..+|.|+|||+.++..|++... .+. ++.+|+.++ .....+.|.|||
T Consensus 1 ~~~aE~~al~~al~~a-----~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~---~~~~~~~~~~i~-- 70 (87)
T PF13456_consen 1 PLEAEALALLEALQLA-----WELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLL---DRFWNVSVSHIP-- 70 (87)
T ss_dssp HHHHHHHHHHHHHHHH-----HCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHH---CCCSCEEEEE----
T ss_pred CcHHHHHHHHHHHHHH-----HHCCCCEEEEEecCccccccccccccccccccccchhhhhhh---ccccceEEEEEC--
Confidence 4689999999999999 56688999999999999999998753 333 344444444 358999999999
Q ss_pred CCCccchHHhHHHHHhhc
Q psy4967 253 VGIAGNEEADRLAKEALT 270 (354)
Q Consensus 253 ~gi~gNe~AD~lAk~a~~ 270 (354)
.++|..||.|||.|.+
T Consensus 71 --r~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 71 --REQNKVADALAKFALS 86 (87)
T ss_dssp --GGGSHHHHHHHHHHHH
T ss_pred --hHHhHHHHHHHHHHhh
Confidence 8999999999999864
No 12
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=90.05 E-value=1.3 Score=37.75 Aligned_cols=65 Identities=22% Similarity=0.259 Sum_probs=38.6
Q ss_pred cEEEEeCCCCCCCCceEEEE--e---CCee-----eeecC-C-CCCchHHHHHHHHHHHHHHHHHhc-cccCCCceEEEE
Q psy4967 142 STVVYTDASKNDVAVSSAFC--S---QDTK-----FSSRL-H-PLLSICNAELTAILFAIHFSISAH-LNNVNRAYLVIC 208 (354)
Q Consensus 142 ~~~iytDGS~~~~~~G~a~~--~---~~~~-----~~~~l-~-~~~t~~~AEl~Ai~~aL~~~~~~~-~~~~~~~~i~I~ 208 (354)
.+++|+|+|. .+.|+.+| . +... ...++ + ...|+-+-||.|+..|.+++.... ........+.++
T Consensus 81 ~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~w 158 (159)
T PF05380_consen 81 ELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVFW 158 (159)
T ss_pred eeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEEe
Confidence 6899999994 35565554 1 2211 11112 1 234999999999999999885431 122344555544
No 13
>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=73.94 E-value=3.9 Score=36.04 Aligned_cols=86 Identities=24% Similarity=0.248 Sum_probs=48.5
Q ss_pred cEEEEeCCCCCCCCceEEEEe--CCeeeeecCCCCCchHHHHHHHHHHHHHHHHHhccccCCCceEEEEeCCHHHHHHhc
Q psy4967 142 STVVYTDASKNDVAVSSAFCS--QDTKFSSRLHPLLSICNAELTAILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQ 219 (354)
Q Consensus 142 ~~~iytDGS~~~~~~G~a~~~--~~~~~~~~l~~~~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~~i~ 219 (354)
--.||+|+.-. |.|+.. +.....+. ..-.+..||+.|...|.-+. ..++ |.|||..|+.
T Consensus 94 lc~VfaDATpT----gwgi~i~~~~~~~Tfs--~~l~IhtaELlaaClAr~~~---------~~r~-l~tDnt~Vls--- 154 (245)
T PF00336_consen 94 LCQVFADATPT----GWGISITGQRMRGTFS--KPLPIHTAELLAACLARLMS---------GARC-LGTDNTVVLS--- 154 (245)
T ss_pred CCceeccCCCC----cceeeecCceeeeeec--ccccchHHHHHHHHHHHhcc---------CCcE-EeecCcEEEe---
Confidence 34889998754 333332 22233333 34578999999997776554 2333 8999986653
Q ss_pred ccCCCCh-hHHHHHHHHHhhcCCCceEEEEeCC
Q psy4967 220 NIFSLNP-IAGEIRDLILTNKSKLNVRFIWVPS 251 (354)
Q Consensus 220 ~~~~~~~-~~~~i~~~~~~~~~~~~V~~~WVpg 251 (354)
.....-+ .....-+.+ -..+.|..||+
T Consensus 155 rkyts~PW~lac~A~wi-----Lrgts~~yVPS 182 (245)
T PF00336_consen 155 RKYTSFPWLLACAANWI-----LRGTSFYYVPS 182 (245)
T ss_pred cccccCcHHHHHHHHHh-----hcCceEEEecc
Confidence 2222222 222222222 24577888995
No 14
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=35.31 E-value=48 Score=34.66 Aligned_cols=34 Identities=26% Similarity=0.485 Sum_probs=26.2
Q ss_pred HHHHHHHHHh-hcCCCceEEEEeCCCCCCccchHH
Q psy4967 228 AGEIRDLILT-NKSKLNVRFIWVPSHVGIAGNEEA 261 (354)
Q Consensus 228 ~~~i~~~~~~-~~~~~~V~~~WVpgH~gi~gNe~A 261 (354)
-.++++++.. .+.+..|-+-|||+|.+..||-.+
T Consensus 213 Pedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 213 PEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 3455666654 358999999999999999888644
No 15
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=32.63 E-value=3.5e+02 Score=23.91 Aligned_cols=67 Identities=12% Similarity=0.048 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHhccccCCCceEEEEeCCHHHHHHhcccCCC--------Ch-hHHHHHHHHHhhcCCCceEEEEeCCCCC
Q psy4967 184 AILFAIHFSISAHLNNVNRAYLVICSDSLSALQTLQNIFSL--------NP-IAGEIRDLILTNKSKLNVRFIWVPSHVG 254 (354)
Q Consensus 184 Ai~~aL~~~~~~~~~~~~~~~i~I~sDS~~al~~i~~~~~~--------~~-~~~~i~~~~~~~~~~~~V~~~WVpgH~g 254 (354)
++..||.+++ ...+-.+..|++.+..+......... .+ -..++++.+.. .+...-+..+-||-+
T Consensus 15 ~vr~al~~Ll-----~s~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~~L~~--~~~~~PVIfiTGhgD 87 (202)
T COG4566 15 SVRDALAFLL-----ESAGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQDRLAE--RGIRLPVIFLTGHGD 87 (202)
T ss_pred HHHHHHHHHH-----HhCCceeeeecCHHHHHhhccCCCCCeEEEecCCCCCchHHHHHHHHh--cCCCCCEEEEeCCCC
Confidence 5667777774 34567788888888887774222211 11 23466666666 678888888999998
Q ss_pred Ccc
Q psy4967 255 IAG 257 (354)
Q Consensus 255 i~g 257 (354)
|+-
T Consensus 88 Ipm 90 (202)
T COG4566 88 IPM 90 (202)
T ss_pred hHH
Confidence 873
No 16
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=31.32 E-value=38 Score=30.28 Aligned_cols=96 Identities=11% Similarity=0.090 Sum_probs=60.6
Q ss_pred CchHHHHHHHHHHHHHHHHHhccccCCCceEEEE----eCCHHHHHHhcccCC-CChhHHHHHHHHHhhcCCCceEEEEe
Q psy4967 175 LSICNAELTAILFAIHFSISAHLNNVNRAYLVIC----SDSLSALQTLQNIFS-LNPIAGEIRDLILTNKSKLNVRFIWV 249 (354)
Q Consensus 175 ~t~~~AEl~Ai~~aL~~~~~~~~~~~~~~~i~I~----sDS~~al~~i~~~~~-~~~~~~~i~~~~~~~~~~~~V~~~WV 249 (354)
.++..+|.+|++.+|+.++ ...+.+.++++ .||++.+.-+.+-.. ...+.. -.+... ...+....+.|+
T Consensus 106 ~~n~s~d~la~ly~~~~~~----~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~-~~e~~~-~~~~v~h~~k~i 179 (225)
T COG3341 106 KSNDSGDVLAKLYGLRYEV----PLDNRKSVINYLTPGNDSWAYFKYVKDKCETKVNLLK-DREFFS-IGKGVFHDEKDI 179 (225)
T ss_pred ccCchHHHHHHhccccccc----cccCccceeeccCCcchhHHHHHHHhhhhhhHHHHHH-hHHhhh-ccchhhhhhhhc
Confidence 4677899999999999884 22244455557 788888776655431 111111 011100 012355677899
Q ss_pred CCCCCCccchHHhHHHHHhhcC-CCCCC
Q psy4967 250 PSHVGIAGNEEADRLAKEALTS-THPTI 276 (354)
Q Consensus 250 pgH~gi~gNe~AD~lAk~a~~~-~~p~~ 276 (354)
.-|.++..+..++.++...... ..|..
T Consensus 180 ~~~~~~~~~~~~~s~~~~~~k~~~~~~~ 207 (225)
T COG3341 180 NIHIWIFESKKGNSHVYNTSKKELSPKY 207 (225)
T ss_pred ccccccchhhhhhhhhhchhhhhccccc
Confidence 9999999999999988877766 34443
Done!