Query psy663
Match_columns 275
No_of_seqs 136 out of 281
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 23:05:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy663.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/663hhsearch_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 99.1 1.6E-10 3.6E-15 92.6 7.1 86 178-267 2-99 (132)
2 PRK06548 ribonuclease H; Provi 99.0 5E-09 1.1E-13 88.1 11.0 73 178-251 4-78 (161)
3 cd06222 RnaseH RNase H (RNase 98.9 1.3E-08 2.7E-13 78.9 10.8 75 181-255 1-82 (130)
4 PRK08719 ribonuclease H; Revie 98.9 9.4E-09 2E-13 85.3 10.2 69 178-250 3-82 (147)
5 PRK00203 rnhA ribonuclease H; 98.9 5.9E-09 1.3E-13 86.5 9.0 72 179-252 3-79 (150)
6 PRK13907 rnhA ribonuclease H; 98.9 1.4E-08 2.9E-13 81.8 9.7 74 180-254 2-81 (128)
7 COG0328 RnhA Ribonuclease HI [ 98.7 6.7E-08 1.5E-12 80.4 9.1 74 178-252 2-81 (154)
8 KOG3752|consensus 98.6 1.7E-07 3.7E-12 87.2 8.4 77 177-253 210-295 (371)
9 PRK07708 hypothetical protein; 98.3 9.5E-06 2.1E-10 71.6 11.9 92 176-267 70-174 (219)
10 PRK07238 bifunctional RNase H/ 98.2 1.7E-05 3.8E-10 75.0 11.9 91 179-270 2-102 (372)
11 PF13456 RVT_3: Reverse transc 97.6 0.00022 4.9E-09 52.3 6.2 41 215-255 2-42 (87)
12 PF05380 Peptidase_A17: Pao re 88.6 2 4.3E-05 35.7 7.1 52 178-231 80-143 (159)
13 PF00336 DNA_pol_viral_C: DNA 67.2 9.3 0.0002 33.5 4.3 60 179-247 94-153 (245)
14 COG0295 Cdd Cytidine deaminase 46.0 36 0.00078 27.8 4.2 51 192-243 27-81 (134)
15 PRK08298 cytidine deaminase; V 32.5 65 0.0014 26.3 3.8 56 183-243 19-78 (136)
16 cd01285 nucleoside_deaminase N 23.0 2.9E+02 0.0062 21.0 5.8 51 192-242 18-73 (109)
17 PRK05578 cytidine deaminase; V 22.6 1.5E+02 0.0033 23.8 4.3 58 183-243 18-79 (131)
18 TIGR01354 cyt_deam_tetra cytid 22.2 1.6E+02 0.0036 23.3 4.4 51 192-243 22-76 (127)
19 COG1697 DNA topoisomerase VI, 20.7 1.7E+02 0.0037 27.8 4.6 35 160-198 217-251 (356)
20 COG4047 Uncharacterized protei 20.1 87 0.0019 27.6 2.4 18 37-54 151-168 (243)
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=99.11 E-value=1.6e-10 Score=92.57 Aligned_cols=86 Identities=30% Similarity=0.344 Sum_probs=60.8
Q ss_pred CceEEEecCCCCC--CceeEEEEe-CcceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhC--
Q psy663 178 NHTICYTDGSKSP--DVTGCAFSI-GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN-- 252 (275)
Q Consensus 178 ~~~~IyTDGSk~~--~~~G~a~~~-~~~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n-- 252 (275)
+.+.||||||... +..|+|++. .+...+..++ ..|++.||+.||.+||+.+ ....++|+|||++++..|..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~---~~~~v~I~tDS~~v~~~l~~~~ 77 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL---EHRKVTIYTDSQYVLNALNKWL 77 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH---STSEEEEEES-HHHHHHHHTHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh---hcccccccccHHHHHHHHHHhc
Confidence 5789999999543 335666544 3333444566 8899999999999999944 33999999999999998877
Q ss_pred ---CC-CC--C-HHHHHHHHHH
Q psy663 253 ---VK-FS--N-PLVTKVFSTW 267 (275)
Q Consensus 253 ---~~-~~--~-~i~~~I~~~~ 267 (275)
.. .. . ++..+|.+.+
T Consensus 78 ~~~~~~~~~~~~~i~~~i~~~~ 99 (132)
T PF00075_consen 78 HGNGWKKTSNGRPIKNEIWELL 99 (132)
T ss_dssp HHTTSBSCTSSSBHTHHHHHHH
T ss_pred cccccccccccccchhheeecc
Confidence 22 11 2 4666666655
No 2
>PRK06548 ribonuclease H; Provisional
Probab=98.98 E-value=5e-09 Score=88.07 Aligned_cols=73 Identities=29% Similarity=0.267 Sum_probs=54.6
Q ss_pred CceEEEecCCCCCC--ceeEEEEeCcceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663 178 NHTICYTDGSKSPD--VTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA 251 (275)
Q Consensus 178 ~~~~IyTDGSk~~~--~~G~a~~~~~~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~ 251 (275)
..++||||||...+ ..|+|++..+......-....|...||+.|+..||+.+.. ....+.|+|||+.++.++.
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~ 78 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLT 78 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHH
Confidence 45899999998765 3788877643221111224578899999999999986542 3457999999999999999
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=98.93 E-value=1.3e-08 Score=78.89 Aligned_cols=75 Identities=29% Similarity=0.276 Sum_probs=59.8
Q ss_pred EEEecCCCCCC--ceeEEEEeCc--ceee---eecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCC
Q psy663 181 ICYTDGSKSPD--VTGCAFSIGD--MVRS---TLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV 253 (275)
Q Consensus 181 ~IyTDGSk~~~--~~G~a~~~~~--~~~~---~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~ 253 (275)
.+|||||...+ +.|+|++..+ .... .......|++.||+.|++.||+++......++.|++||+.++..+.+.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~ 80 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW 80 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence 48999998876 5788876532 1111 122257899999999999999999988889999999999999999987
Q ss_pred CC
Q psy663 254 KF 255 (275)
Q Consensus 254 ~~ 255 (275)
..
T Consensus 81 ~~ 82 (130)
T cd06222 81 YE 82 (130)
T ss_pred cc
Confidence 54
No 4
>PRK08719 ribonuclease H; Reviewed
Probab=98.92 E-value=9.4e-09 Score=85.26 Aligned_cols=69 Identities=22% Similarity=0.264 Sum_probs=53.5
Q ss_pred CceEEEecCCCCCCc-----eeEEEEe--Cc--c--eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHH
Q psy663 178 NHTICYTDGSKSPDV-----TGCAFSI--GD--M--VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSA 246 (275)
Q Consensus 178 ~~~~IyTDGSk~~~~-----~G~a~~~--~~--~--~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sa 246 (275)
..+.||||||...++ .|+|++. ++ . ..+..+....|...||+.|+..||+.+... .+|+|||+.+
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv 78 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC 78 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence 468999999997653 3788653 22 1 234445566899999999999999998653 3799999999
Q ss_pred HHHH
Q psy663 247 LAAL 250 (275)
Q Consensus 247 l~al 250 (275)
+.++
T Consensus 79 i~~i 82 (147)
T PRK08719 79 VRGF 82 (147)
T ss_pred HHHH
Confidence 9998
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.92 E-value=5.9e-09 Score=86.49 Aligned_cols=72 Identities=19% Similarity=0.190 Sum_probs=54.1
Q ss_pred ceEEEecCCCCCC--ceeEEEEe--Cccee-eeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhC
Q psy663 179 HTICYTDGSKSPD--VTGCAFSI--GDMVR-STLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALAN 252 (275)
Q Consensus 179 ~~~IyTDGSk~~~--~~G~a~~~--~~~~~-~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n 252 (275)
++.||||||...+ ..|+|++. ++... ........|...||+.|+..||+.+.. ...+.|+|||+.++.+|..
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~ 79 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITE 79 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHH
Confidence 4899999998754 27777664 23221 122234678899999999999998854 4679999999999999984
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.88 E-value=1.4e-08 Score=81.75 Aligned_cols=74 Identities=20% Similarity=0.133 Sum_probs=58.4
Q ss_pred eEEEecCCCCCC--ceeEEEEeCcc----eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCC
Q psy663 180 TICYTDGSKSPD--VTGCAFSIGDM----VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANV 253 (275)
Q Consensus 180 ~~IyTDGSk~~~--~~G~a~~~~~~----~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~ 253 (275)
++||||||-..+ ..|+|++..+. ..++. ....+...||+.|++.||+.+......++.|++||+.++..+.+.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence 579999997754 47888775332 12222 245688999999999999999988888999999999999999874
Q ss_pred C
Q psy663 254 K 254 (275)
Q Consensus 254 ~ 254 (275)
.
T Consensus 81 ~ 81 (128)
T PRK13907 81 Y 81 (128)
T ss_pred H
Confidence 3
No 7
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.73 E-value=6.7e-08 Score=80.39 Aligned_cols=74 Identities=23% Similarity=0.194 Sum_probs=59.6
Q ss_pred CceEEEecCCCCCC-c-eeEEEEe--Ccce--eeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHh
Q psy663 178 NHTICYTDGSKSPD-V-TGCAFSI--GDMV--RSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALA 251 (275)
Q Consensus 178 ~~~~IyTDGSk~~~-~-~G~a~~~--~~~~--~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~ 251 (275)
..++||||||...+ | -|+|+|. ++.. .+..+. .+|...||+.|+.+||+++.+.+...+.|+|||+.+++.|.
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~ 80 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT 80 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence 35799999998765 3 6777654 3322 333444 88999999999999999999988999999999999999998
Q ss_pred C
Q psy663 252 N 252 (275)
Q Consensus 252 n 252 (275)
.
T Consensus 81 ~ 81 (154)
T COG0328 81 R 81 (154)
T ss_pred H
Confidence 3
No 8
>KOG3752|consensus
Probab=98.59 E-value=1.7e-07 Score=87.18 Aligned_cols=77 Identities=26% Similarity=0.245 Sum_probs=65.3
Q ss_pred CCceEEEecCCCCCCc-----eeEEEEeCc---ceeeeecC-CccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHH
Q psy663 177 ANHTICYTDGSKSPDV-----TGCAFSIGD---MVRSTLLN-PINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSAL 247 (275)
Q Consensus 177 ~~~~~IyTDGSk~~~~-----~G~a~~~~~---~~~~~~l~-~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal 247 (275)
.+..++|||||-..+| +|+|++.++ ...+..+. .-.+.|.||+.||.+||+-+.+....+++|.|||.-.+
T Consensus 210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i 289 (371)
T KOG3752|consen 210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFI 289 (371)
T ss_pred ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHH
Confidence 3458999999988754 799998754 25556665 77899999999999999999998888999999999999
Q ss_pred HHHhCC
Q psy663 248 AALANV 253 (275)
Q Consensus 248 ~al~n~ 253 (275)
++|+.+
T Consensus 290 ~~l~~w 295 (371)
T KOG3752|consen 290 NSLTLW 295 (371)
T ss_pred HHHHHH
Confidence 999743
No 9
>PRK07708 hypothetical protein; Validated
Probab=98.31 E-value=9.5e-06 Score=71.61 Aligned_cols=92 Identities=16% Similarity=0.196 Sum_probs=64.4
Q ss_pred cCCceEEEecCCCC--CCceeEEEEe--Cccee------eeecCCccchhHHHHHHHHHHHHHHHcCCCC--eEEEEecc
Q psy663 176 YANHTICYTDGSKS--PDVTGCAFSI--GDMVR------STLLNPINSIFSAELIAIFLCLEAILENPSD--QFLIVSDS 243 (275)
Q Consensus 176 ~~~~~~IyTDGSk~--~~~~G~a~~~--~~~~~------~~~l~~~~sif~AEl~aI~~al~~~~~~~~~--~~~I~sDS 243 (275)
.++.+.+|+|||-. .++.|+|++. .+... ...++..++...||..|++.||+.+...+.+ .+.|++||
T Consensus 70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS 149 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS 149 (219)
T ss_pred CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence 45679999999964 3457777654 22111 1245556799999999999999999887654 48999999
Q ss_pred HHHHHHHhCCC-CCCHHHHHHHHHH
Q psy663 244 RSALAALANVK-FSNPLVTKVFSTW 267 (275)
Q Consensus 244 ~sal~al~n~~-~~~~i~~~I~~~~ 267 (275)
+-++..+.+.. ..++..+..++.+
T Consensus 150 qlVi~qi~g~wk~~~~~l~~y~~~i 174 (219)
T PRK07708 150 QVVLNQLAGEWPCYDEHLNHWLDRI 174 (219)
T ss_pred HHHHHHhCCCceeCChhHHHHHHHH
Confidence 99999998653 2333333444333
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.19 E-value=1.7e-05 Score=74.98 Aligned_cols=91 Identities=18% Similarity=0.174 Sum_probs=64.4
Q ss_pred ceEEEecCCCCCC--ceeEEEEe--Cc-c----eeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHH
Q psy663 179 HTICYTDGSKSPD--VTGCAFSI--GD-M----VRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSALAA 249 (275)
Q Consensus 179 ~~~IyTDGSk~~~--~~G~a~~~--~~-~----~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~a 249 (275)
.+.||||||...+ ..|+|++. .+ . .....++ .+|...||+.|++.||+.+.+....++.|++||+.++..
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~ 80 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ 80 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence 3689999998765 37888664 22 1 1122333 677889999999999999998888899999999999999
Q ss_pred HhCCC-CCCHHHHHHHHHHHHH
Q psy663 250 LANVK-FSNPLVTKVFSTWRYL 270 (275)
Q Consensus 250 l~n~~-~~~~i~~~I~~~~~~l 270 (275)
+.+.. ..++-....+..++.|
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l 102 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQAREL 102 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHH
Confidence 97643 2333233344444443
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.57 E-value=0.00022 Score=52.32 Aligned_cols=41 Identities=22% Similarity=0.260 Sum_probs=35.6
Q ss_pred hHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHHHHHhCCCC
Q psy663 215 FSAELIAIFLCLEAILENPSDQFLIVSDSRSALAALANVKF 255 (275)
Q Consensus 215 f~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal~al~n~~~ 255 (275)
..||+.|++.||+++.+.+..+++|.|||+.++..|.+...
T Consensus 2 ~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~ 42 (87)
T PF13456_consen 2 LEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSS 42 (87)
T ss_dssp HHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS-
T ss_pred cHHHHHHHHHHHHHHHHCCCCEEEEEecCcccccccccccc
Confidence 57999999999999999999999999999999999987743
No 12
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=88.57 E-value=2 Score=35.73 Aligned_cols=52 Identities=17% Similarity=0.149 Sum_probs=34.5
Q ss_pred CceEEEecCCCCCCceeEEEEeC---cceee-------eecC--CccchhHHHHHHHHHHHHHHHc
Q psy663 178 NHTICYTDGSKSPDVTGCAFSIG---DMVRS-------TLLN--PINSIFSAELIAIFLCLEAILE 231 (275)
Q Consensus 178 ~~~~IyTDGSk~~~~~G~a~~~~---~~~~~-------~~l~--~~~sif~AEl~aI~~al~~~~~ 231 (275)
..+++|+|+|+ .+.|+.++.. +.... .+.. ...||=.-||.|+..|.+++..
T Consensus 80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 46899999995 4556655531 11111 1221 3459999999999999999854
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=67.21 E-value=9.3 Score=33.49 Aligned_cols=60 Identities=17% Similarity=0.045 Sum_probs=35.0
Q ss_pred ceEEEecCCCCCCceeEEEEeCcceeeeecCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEeccHHHH
Q psy663 179 HTICYTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIVSDSRSAL 247 (275)
Q Consensus 179 ~~~IyTDGSk~~~~~G~a~~~~~~~~~~~l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS~sal 247 (275)
--+||+|+.-..+| .++-..-....|.. ---|.+||++|.-.|--+.. .+ .|.+||.-++
T Consensus 94 lc~VfaDATpTgwg--i~i~~~~~~~Tfs~--~l~IhtaELlaaClAr~~~~----~r-~l~tDnt~Vl 153 (245)
T PF00336_consen 94 LCQVFADATPTGWG--ISITGQRMRGTFSK--PLPIHTAELLAACLARLMSG----AR-CLGTDNTVVL 153 (245)
T ss_pred CCceeccCCCCcce--eeecCceeeeeecc--cccchHHHHHHHHHHHhccC----Cc-EEeecCcEEE
Confidence 44899999765433 22211222333332 23599999999977654442 23 3888886554
No 14
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=45.97 E-value=36 Score=27.77 Aligned_cols=51 Identities=27% Similarity=0.252 Sum_probs=31.2
Q ss_pred ceeEEEEeCcceeeeecCCccchhH----HHHHHHHHHHHHHHcCCCCeEEEEecc
Q psy663 192 VTGCAFSIGDMVRSTLLNPINSIFS----AELIAIFLCLEAILENPSDQFLIVSDS 243 (275)
Q Consensus 192 ~~G~a~~~~~~~~~~~l~~~~sif~----AEl~aI~~al~~~~~~~~~~~~I~sDS 243 (275)
.||+++...+....++-.=+...|. ||..||.+|+.. -...-..+++++|+
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 4888887644322222221111222 999999999866 33345688899988
No 15
>PRK08298 cytidine deaminase; Validated
Probab=32.50 E-value=65 Score=26.26 Aligned_cols=56 Identities=16% Similarity=0.092 Sum_probs=31.6
Q ss_pred EecCCCCCCceeEEEEeCcceeeeecCCccchh----HHHHHHHHHHHHHHHcCCCCeEEEEecc
Q psy663 183 YTDGSKSPDVTGCAFSIGDMVRSTLLNPINSIF----SAELIAIFLCLEAILENPSDQFLIVSDS 243 (275)
Q Consensus 183 yTDGSk~~~~~G~a~~~~~~~~~~~l~~~~sif----~AEl~aI~~al~~~~~~~~~~~~I~sDS 243 (275)
|...| +||+|+...+.....+..-+...| =||..||..|+..= ......+.|.+|.
T Consensus 19 Y~PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G-~~~~~~i~v~~~~ 78 (136)
T PRK08298 19 YPNGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQ-KRVTHSICVAREN 78 (136)
T ss_pred cCCCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCC-CceEEEEEEEcCC
Confidence 66666 899999865432222222122222 38999999887331 1123456667676
No 16
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=22.97 E-value=2.9e+02 Score=20.99 Aligned_cols=51 Identities=12% Similarity=-0.046 Sum_probs=29.8
Q ss_pred ceeEEEEeC-cceeeee----cCCccchhHHHHHHHHHHHHHHHcCCCCeEEEEec
Q psy663 192 VTGCAFSIG-DMVRSTL----LNPINSIFSAELIAIFLCLEAILENPSDQFLIVSD 242 (275)
Q Consensus 192 ~~G~a~~~~-~~~~~~~----l~~~~sif~AEl~aI~~al~~~~~~~~~~~~I~sD 242 (275)
.+|+.++.. +.....+ ..+.....-||..||..+.+..........++++.
T Consensus 18 ~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t 73 (109)
T cd01285 18 PFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTT 73 (109)
T ss_pred cEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEe
Confidence 478877765 3222221 12234577799999999887654333445555554
No 17
>PRK05578 cytidine deaminase; Validated
Probab=22.60 E-value=1.5e+02 Score=23.81 Aligned_cols=58 Identities=26% Similarity=0.108 Sum_probs=32.3
Q ss_pred EecCCCCCCceeEEEEeCcceeeeecCCccc----hhHHHHHHHHHHHHHHHcCCCCeEEEEecc
Q psy663 183 YTDGSKSPDVTGCAFSIGDMVRSTLLNPINS----IFSAELIAIFLCLEAILENPSDQFLIVSDS 243 (275)
Q Consensus 183 yTDGSk~~~~~G~a~~~~~~~~~~~l~~~~s----if~AEl~aI~~al~~~~~~~~~~~~I~sDS 243 (275)
|.-.|+. .||+|+...+.....+..-++. -.-||..||..|+..- ......++|.+|+
T Consensus 18 y~PyS~f--~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G-~~~i~~i~vv~~~ 79 (131)
T PRK05578 18 YAPYSKF--PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEG-GGRLVAIACVGET 79 (131)
T ss_pred CCCcCCC--ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHcC-CCceEEEEEEecC
Confidence 4445554 5999988644322222211122 2348999999987321 1134577787776
No 18
>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.
Probab=22.19 E-value=1.6e+02 Score=23.33 Aligned_cols=51 Identities=20% Similarity=0.003 Sum_probs=28.8
Q ss_pred ceeEEEEeCcceeeeecCC----ccchhHHHHHHHHHHHHHHHcCCCCeEEEEecc
Q psy663 192 VTGCAFSIGDMVRSTLLNP----INSIFSAELIAIFLCLEAILENPSDQFLIVSDS 243 (275)
Q Consensus 192 ~~G~a~~~~~~~~~~~l~~----~~sif~AEl~aI~~al~~~~~~~~~~~~I~sDS 243 (275)
.+|++++..+.....+..- ...-.-||..||..|...-. .....++|..|.
T Consensus 22 ~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~-~~i~~i~vv~~~ 76 (127)
T TIGR01354 22 KVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGY-RKFVAIAVADSA 76 (127)
T ss_pred eEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCC-CCeEEEEEEeCC
Confidence 3888887643221112211 22233599999998885422 234577777765
No 19
>COG1697 DNA topoisomerase VI, subunit A [DNA replication, recombination, and repair]
Probab=20.66 E-value=1.7e+02 Score=27.78 Aligned_cols=35 Identities=23% Similarity=0.334 Sum_probs=27.4
Q ss_pred ChHHHHHHHHHHHhhhcCCceEEEecCCCCCCceeEEEE
Q psy663 160 APVVFQQKFSEAINTKYANHTICYTDGSKSPDVTGCAFS 198 (275)
Q Consensus 160 ~~~~~~~~f~~~~~~~~~~~~~IyTDGSk~~~~~G~a~~ 198 (275)
.|+.+..+|...++....-.+.||||| |=.|+-++
T Consensus 217 qP~raTRrflkrL~eel~lpv~vftDg----DPyG~~Iy 251 (356)
T COG1697 217 QPDRATRRFLKRLNEELDLPVYVFTDG----DPYGWYIY 251 (356)
T ss_pred CccHHHHHHHHHHHHHhCCCEEEEecC----CCCEEEEE
Confidence 567888889988888777788999999 54566654
No 20
>COG4047 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.07 E-value=87 Score=27.61 Aligned_cols=18 Identities=28% Similarity=0.445 Sum_probs=14.4
Q ss_pred HHHHHHHHHhccCCCCch
Q psy663 37 VHHAGIRIATGALRSSPV 54 (275)
Q Consensus 37 Iq~~alR~ilGAfRTTpi 54 (275)
+-+-|+|.++|-||--|.
T Consensus 151 mfgYA~r~~~g~f~pyp~ 168 (243)
T COG4047 151 MFGYAARIVLGRFRPYPF 168 (243)
T ss_pred HhHHHHHHHhcCCCCCCc
Confidence 457789999999987664
Done!