Query psy16896
Match_columns 423
No_of_seqs 254 out of 1595
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 16:27:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16896.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16896hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.9 1.9E-24 4.1E-29 192.7 14.1 143 56-225 2-147 (154)
2 PRK08719 ribonuclease H; Revie 99.9 2.4E-24 5.2E-29 192.5 13.6 136 55-222 2-146 (147)
3 PRK06548 ribonuclease H; Provi 99.9 7.4E-24 1.6E-28 191.5 13.8 141 55-226 3-145 (161)
4 PRK00203 rnhA ribonuclease H; 99.9 2.5E-23 5.5E-28 186.4 13.7 140 57-226 3-145 (150)
5 PF00075 RNase_H: RNase H; In 99.9 7.1E-22 1.5E-26 171.4 11.3 128 56-222 2-132 (132)
6 KOG3752|consensus 99.8 9E-19 2E-23 173.7 13.6 149 55-224 210-366 (371)
7 cd06222 RnaseH RNase H (RNase 99.8 1.5E-17 3.2E-22 139.7 14.8 125 59-221 1-130 (130)
8 PRK13907 rnhA ribonuclease H; 99.7 1.6E-16 3.4E-21 138.2 14.2 122 58-222 2-126 (128)
9 PRK07708 hypothetical protein; 99.6 4.3E-15 9.3E-20 141.1 15.5 142 41-225 59-210 (219)
10 PRK07238 bifunctional RNase H/ 99.5 4.3E-13 9.2E-18 137.0 15.5 126 57-225 2-134 (372)
11 PF13456 RVT_3: Reverse transc 99.1 8.8E-10 1.9E-14 88.1 9.9 86 94-222 1-86 (87)
12 PF13966 zf-RVT: zinc-binding 95.2 0.011 2.5E-07 47.7 1.9 30 368-397 52-82 (86)
13 PF05380 Peptidase_A17: Pao re 85.1 3.3 7.2E-05 37.3 7.1 54 56-111 80-143 (159)
14 COG3341 Predicted double-stran 82.0 2.6 5.6E-05 40.1 5.1 173 8-226 11-204 (225)
15 PF00336 DNA_pol_viral_C: DNA 65.2 6.9 0.00015 37.0 3.4 61 56-127 93-153 (245)
16 COG0296 GlgB 1,4-alpha-glucan 33.1 47 0.001 36.7 3.9 32 182-213 216-247 (628)
17 cd01285 nucleoside_deaminase N 32.3 1.6E+02 0.0035 24.4 6.4 55 70-124 16-75 (109)
18 COG0590 CumB Cytosine/adenosin 31.3 1.1E+02 0.0024 27.3 5.5 55 70-124 27-86 (152)
19 KOG1812|consensus 30.7 57 0.0012 33.9 3.9 61 71-131 19-86 (384)
20 PRK10860 tRNA-specific adenosi 30.1 1.5E+02 0.0032 27.2 6.2 53 71-123 33-89 (172)
21 PF05741 zf-nanos: Nanos RNA b 24.8 38 0.00082 25.3 1.0 21 376-396 34-54 (55)
22 cd01284 Riboflavin_deaminase-r 23.2 2.7E+02 0.0058 23.7 6.1 48 71-122 19-67 (115)
23 COG0336 TrmD tRNA-(guanine-N1) 22.8 20 0.00043 34.6 -1.0 37 386-423 168-206 (240)
24 COG0295 Cdd Cytidine deaminase 22.0 2E+02 0.0043 25.5 5.1 53 70-123 27-81 (134)
25 PF05830 NodZ: Nodulation prot 21.0 2.1E+02 0.0046 28.9 5.7 64 71-134 168-234 (321)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.92 E-value=1.9e-24 Score=192.71 Aligned_cols=143 Identities=21% Similarity=0.278 Sum_probs=114.9
Q ss_pred CcEEEEEcCCcCC--CCceEEEEEecCCeEEEEecC-CCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHhC
Q psy16896 56 DHLKIYTDGSKDE--TGVGCALTIPQLNETKRFALN-KHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAISN 132 (423)
Q Consensus 56 ~~i~IyTDGS~~~--~~~G~g~vi~~~~~~~~~~l~-~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~~ 132 (423)
..+.|||||||.. +..|+|+|+..+...+.++.+ ..+||++||+.|++.||+++.+.+...|.|+|||++|+++|+.
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~ 81 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR 81 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence 4589999999983 349999998865544433322 3899999999999999999998888999999999999999984
Q ss_pred CCCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCCcCCHH
Q psy16896 133 LHHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGISGNER 212 (423)
Q Consensus 133 ~~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi~GNe~ 212 (423)
+. ..|..++|+++ =+.++++.+|++++.+++ .....|.+.|||||+|.++||+
T Consensus 82 w~-----~~w~~~~w~~~---------------------~~~pvkn~dl~~~~~~~~-~~~~~v~~~WVkgH~g~~~Ner 134 (154)
T COG0328 82 WI-----VKWKKNGWKTA---------------------DKKPVKNKDLWEELDELL-KRHELVFWEWVKGHAGHPENER 134 (154)
T ss_pred HH-----hhccccCcccc---------------------ccCccccHHHHHHHHHHH-hhCCeEEEEEeeCCCCChHHHH
Confidence 32 24454444321 256789999999988776 3345899999999999999999
Q ss_pred HHHHHHHHhhhhh
Q psy16896 213 ADVEAKKATKMEY 225 (423)
Q Consensus 213 AD~lAk~A~~~~~ 225 (423)
||+||+.|++...
T Consensus 135 aD~LA~~~~~~~~ 147 (154)
T COG0328 135 ADQLAREAARAAK 147 (154)
T ss_pred HHHHHHHHHHhhh
Confidence 9999999998774
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.92 E-value=2.4e-24 Score=192.48 Aligned_cols=136 Identities=21% Similarity=0.280 Sum_probs=107.2
Q ss_pred CCcEEEEEcCCcCCCC-----ceEEEEEecCCe----EEEEecCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHH
Q psy16896 55 EDHLKIYTDGSKDETG-----VGCALTIPQLNE----TKRFALNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLS 125 (423)
Q Consensus 55 ~~~i~IyTDGS~~~~~-----~G~g~vi~~~~~----~~~~~l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~s 125 (423)
...++||||||+.+++ +|+|++++..+. ..+..+....|+++|||.|++.||+.+.+. ..|+|||++
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y 77 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY 77 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence 3578999999997543 599998876532 234445566899999999999999998752 489999999
Q ss_pred HHHHHhCCCCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCC
Q psy16896 126 SFQAISNLHHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHV 205 (423)
Q Consensus 126 ai~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~ 205 (423)
|+++|+.+ +..|.+++|++++ ..++.+.+|+++|..++. ...|.|.|||||+
T Consensus 78 vi~~i~~~-----~~~W~~~~w~~s~---------------------g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~ 129 (147)
T PRK08719 78 CVRGFNEW-----LDTWKQKGWRKSD---------------------KKPVANRDLWQQVDELRA--RKYVEVEKVTAHS 129 (147)
T ss_pred HHHHHHHH-----HHHHHhCCcccCC---------------------CcccccHHHHHHHHHHhC--CCcEEEEEecCCC
Confidence 99999875 3577777775432 235567788888766653 4679999999999
Q ss_pred CCcCCHHHHHHHHHHhh
Q psy16896 206 GISGNERADVEAKKATK 222 (423)
Q Consensus 206 gi~GNe~AD~lAk~A~~ 222 (423)
|++|||.||.||++|++
T Consensus 130 g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 130 GIEGNEAADMLAQAAAE 146 (147)
T ss_pred CChhHHHHHHHHHHHhh
Confidence 99999999999999875
No 3
>PRK06548 ribonuclease H; Provisional
Probab=99.91 E-value=7.4e-24 Score=191.52 Aligned_cols=141 Identities=21% Similarity=0.221 Sum_probs=110.2
Q ss_pred CCcEEEEEcCCcCC--CCceEEEEEecCCeEEEEecCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHhC
Q psy16896 55 EDHLKIYTDGSKDE--TGVGCALTIPQLNETKRFALNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAISN 132 (423)
Q Consensus 55 ~~~i~IyTDGS~~~--~~~G~g~vi~~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~~ 132 (423)
+..++||||||+.. +.+|+|+++.... ... .....+|+++|||.||+.||+.+.. +...|.|+|||++|+++|+.
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~-~~~-g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~ 79 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENT-WDS-GGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTK 79 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCc-EEc-cCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHH
Confidence 35699999999984 3488998876432 111 1124689999999999999986653 44679999999999999997
Q ss_pred CCCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCCcCCHH
Q psy16896 133 LHHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGISGNER 212 (423)
Q Consensus 133 ~~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi~GNe~ 212 (423)
+. ..|..++|+++. +.++.|.+|+++|..++.. ..|.|.|||||+|++|||.
T Consensus 80 W~-----~~Wk~~gWk~s~---------------------G~pV~N~dL~~~l~~l~~~--~~v~~~wVkgHsg~~gNe~ 131 (161)
T PRK06548 80 WV-----YSWKMRKWRKAD---------------------GKPVLNQEIIQEIDSLMEN--RNIRMSWVNAHTGHPLNEA 131 (161)
T ss_pred HH-----HHHHHCCCcccC---------------------CCccccHHHHHHHHHHHhc--CceEEEEEecCCCCHHHHH
Confidence 63 467777775432 3467788999998877743 4799999999999999999
Q ss_pred HHHHHHHHhhhhhh
Q psy16896 213 ADVEAKKATKMEYR 226 (423)
Q Consensus 213 AD~lAk~A~~~~~~ 226 (423)
||+||++|+.....
T Consensus 132 aD~LA~~aa~~~~~ 145 (161)
T PRK06548 132 ADSLARQAANNFST 145 (161)
T ss_pred HHHHHHHHHHHhcc
Confidence 99999999977643
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.90 E-value=2.5e-23 Score=186.40 Aligned_cols=140 Identities=19% Similarity=0.244 Sum_probs=108.1
Q ss_pred cEEEEEcCCcCC--CCceEEEEEecCCeEEEEe-cCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHhCC
Q psy16896 57 HLKIYTDGSKDE--TGVGCALTIPQLNETKRFA-LNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAISNL 133 (423)
Q Consensus 57 ~i~IyTDGS~~~--~~~G~g~vi~~~~~~~~~~-l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~~~ 133 (423)
.+.||||||+.. +.+|+|+|+...+....+. .....|++.|||.|++.||+.+.+ ...|.|+|||++++++|..+
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w 80 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW 80 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence 489999999984 3488999887655443332 234678999999999999998865 46799999999999999864
Q ss_pred CCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCCcCCHHH
Q psy16896 134 HHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGISGNERA 213 (423)
Q Consensus 134 ~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi~GNe~A 213 (423)
. ..|-.++|.++ -+.++.+.+|+++|.+++. ...|.|.|||||+|++||+.|
T Consensus 81 ~-----~~Wk~~~~~~~---------------------~g~~v~n~dl~~~i~~l~~--~~~v~~~wV~~H~~~~~N~~A 132 (150)
T PRK00203 81 I-----HGWKKNGWKTA---------------------DKKPVKNVDLWQRLDAALK--RHQIKWHWVKGHAGHPENERC 132 (150)
T ss_pred H-----HHHHHcCCccc---------------------CCCccccHHHHHHHHHHhc--cCceEEEEecCCCCCHHHHHH
Confidence 2 24554444321 2345667788888877763 378999999999999999999
Q ss_pred HHHHHHHhhhhhh
Q psy16896 214 DVEAKKATKMEYR 226 (423)
Q Consensus 214 D~lAk~A~~~~~~ 226 (423)
|+|||+|+.....
T Consensus 133 D~lA~~a~~~~~~ 145 (150)
T PRK00203 133 DELARAGAEEATL 145 (150)
T ss_pred HHHHHHHHHHhhh
Confidence 9999999987743
No 5
>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=99.87 E-value=7.1e-22 Score=171.38 Aligned_cols=128 Identities=31% Similarity=0.450 Sum_probs=92.9
Q ss_pred CcEEEEEcCCcCC--CCceEEEEEecCCeEEEEecCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHhCC
Q psy16896 56 DHLKIYTDGSKDE--TGVGCALTIPQLNETKRFALNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAISNL 133 (423)
Q Consensus 56 ~~i~IyTDGS~~~--~~~G~g~vi~~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~~~ 133 (423)
..+.||||||+.. +..|+|++++.+ ......++ ..+++.|||.||..||+ +.. ...|+|+|||++++..|..+
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~ 76 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKW 76 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHh
Confidence 4689999999873 336888865444 45555666 88999999999999999 443 49999999999999988763
Q ss_pred CCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCC-cCCHH
Q psy16896 134 HHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGI-SGNER 212 (423)
Q Consensus 134 ~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi-~GNe~ 212 (423)
... +.|.. .....+++.+|.+++ ..+..|.|.|||||+|+ .||+.
T Consensus 77 ~~~--------~~~~~-------------------------~~~~~~i~~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~ 122 (132)
T PF00075_consen 77 LHG--------NGWKK-------------------------TSNGRPIKNEIWELL-SRGIKVRFRWVPGHSGVPQGNER 122 (132)
T ss_dssp HHH--------TTSBS-------------------------CTSSSBHTHHHHHHH-HHSSEEEEEESSSSSSSHHHHHH
T ss_pred ccc--------ccccc-------------------------ccccccchhheeecc-ccceEEeeeeccCcCCCchhHHH
Confidence 210 01100 000012344556666 45899999999999999 69999
Q ss_pred HHHHHHHHhh
Q psy16896 213 ADVEAKKATK 222 (423)
Q Consensus 213 AD~lAk~A~~ 222 (423)
||+|||+|+.
T Consensus 123 aD~lAk~a~~ 132 (132)
T PF00075_consen 123 ADRLAKEAAQ 132 (132)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHhcC
Confidence 9999999973
No 6
>KOG3752|consensus
Probab=99.79 E-value=9e-19 Score=173.66 Aligned_cols=149 Identities=20% Similarity=0.244 Sum_probs=113.7
Q ss_pred CCcEEEEEcCCcCCC-----CceEEEEEecCC-eEEEEecC-CCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHH
Q psy16896 55 EDHLKIYTDGSKDET-----GVGCALTIPQLN-ETKRFALN-KHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSF 127 (423)
Q Consensus 55 ~~~i~IyTDGS~~~~-----~~G~g~vi~~~~-~~~~~~l~-~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai 127 (423)
.+.++||||||+..+ .+|+||++..+. ...+..+. +.+++|.|||.||..||+.|.+.+..+|+|.|||++++
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 344999999999742 399999876654 35667765 79999999999999999999998888999999999999
Q ss_pred HHHhCCCCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhc-CCCceEEEEccCCCC
Q psy16896 128 QAISNLHHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSN-SQANIKFLWCPSHVG 206 (423)
Q Consensus 128 ~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~-~~~~V~~~WVpgH~g 206 (423)
++|+.+-+ .|-..+|+++. .-..|.-.+++.+++.++.++.+. .+.+|.+.||+||.|
T Consensus 290 ~~l~~wv~-----~~k~~~~k~~~----------------~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~g 348 (371)
T KOG3752|consen 290 NSLTLWVQ-----GWKKNGWKTSN----------------GSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSG 348 (371)
T ss_pred HHHHHHHh-----hhccCcccccc----------------CCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCC
Confidence 99984421 12222232211 111123346677788887777755 579999999999999
Q ss_pred CcCCHHHHHHHHHHhhhh
Q psy16896 207 ISGNERADVEAKKATKME 224 (423)
Q Consensus 207 i~GNe~AD~lAk~A~~~~ 224 (423)
|.|||+||.||++++...
T Consensus 349 i~gne~Ad~lARkgs~~~ 366 (371)
T KOG3752|consen 349 ILGNEMADALARKGSTLA 366 (371)
T ss_pred cchHHHHHHHHhhhhhhh
Confidence 999999999999987654
No 7
>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=99.76 E-value=1.5e-17 Score=139.73 Aligned_cols=125 Identities=30% Similarity=0.446 Sum_probs=97.2
Q ss_pred EEEEcCCcCCC--CceEEEEEecCCeEEEEe---cCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHhCC
Q psy16896 59 KIYTDGSKDET--GVGCALTIPQLNETKRFA---LNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAISNL 133 (423)
Q Consensus 59 ~IyTDGS~~~~--~~G~g~vi~~~~~~~~~~---l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~~~ 133 (423)
++|||||...+ ++|+|+++.+.+....+. .....+++.||+.|++.||+.+...+..++.|++||+.+++.+++.
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 48999999854 699999988765433322 2257899999999999999999988899999999999999999987
Q ss_pred CCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCCcCCHHH
Q psy16896 134 HHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGISGNERA 213 (423)
Q Consensus 134 ~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi~GNe~A 213 (423)
....+ ... .+++..+.+.+ .....+.|.|||+|+|+.+|+.|
T Consensus 81 ~~~~~--~~~-----------------------------------~~~~~~i~~~~-~~~~~~~i~~v~~h~~~~~n~~a 122 (130)
T cd06222 81 YEGKP--VKN-----------------------------------VDLWQRLLALL-KRFHKVRFEWVPGHSGIEGNERA 122 (130)
T ss_pred ccCCC--hhh-----------------------------------HHHHHHHHHHH-hCCCeEEEEEcCCCCCCcchHHH
Confidence 53111 111 11334444444 45788999999999999999999
Q ss_pred HHHHHHHh
Q psy16896 214 DVEAKKAT 221 (423)
Q Consensus 214 D~lAk~A~ 221 (423)
|.|||+|.
T Consensus 123 d~la~~~~ 130 (130)
T cd06222 123 DALAKEAA 130 (130)
T ss_pred HHHHHhhC
Confidence 99999873
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.71 E-value=1.6e-16 Score=138.23 Aligned_cols=122 Identities=24% Similarity=0.261 Sum_probs=94.7
Q ss_pred EEEEEcCCcCC--CCceEEEEEecCCeEEEEec-CCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHhCCC
Q psy16896 58 LKIYTDGSKDE--TGVGCALTIPQLNETKRFAL-NKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAISNLH 134 (423)
Q Consensus 58 i~IyTDGS~~~--~~~G~g~vi~~~~~~~~~~l-~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~~~~ 134 (423)
+.||||||+.. +.+|+|+|+.+.+.....+. ....+++.||+.|++.||+.+.+.+...|.|+|||+++++.+++..
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~ 81 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY 81 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence 57999999984 45999999876654333322 3467999999999999999999988889999999999999998754
Q ss_pred CCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCCcCCHHHH
Q psy16896 135 HPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGISGNERAD 214 (423)
Q Consensus 135 ~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi~GNe~AD 214 (423)
.... ...+++.++..++ +....+.|.|||++ +|+.||
T Consensus 82 ~~~~--------------------------------------~~~~l~~~~~~l~-~~f~~~~~~~v~r~----~N~~Ad 118 (128)
T PRK13907 82 AKNK--------------------------------------MFAPLLEEALQYI-KSFDLFFIKWIPSS----QNKVAD 118 (128)
T ss_pred hcCh--------------------------------------hHHHHHHHHHHHH-hcCCceEEEEcCch----hchhHH
Confidence 2111 1124566766666 44567788999995 999999
Q ss_pred HHHHHHhh
Q psy16896 215 VEAKKATK 222 (423)
Q Consensus 215 ~lAk~A~~ 222 (423)
.||+.|..
T Consensus 119 ~LA~~a~~ 126 (128)
T PRK13907 119 ELARKAIL 126 (128)
T ss_pred HHHHHHHh
Confidence 99999875
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.64 E-value=4.3e-15 Score=141.06 Aligned_cols=142 Identities=15% Similarity=0.153 Sum_probs=101.8
Q ss_pred HHHHHHHHHHHhhcCCcEEEEEcCCcC--CCCceEEEEEecCCe--EEE----EecCCCccchhhhHHHHHHHHHHHHhh
Q psy16896 41 IIQDRFQEILHEKYEDHLKIYTDGSKD--ETGVGCALTIPQLNE--TKR----FALNKHSSVFHAELFSILQSLNHVKEL 112 (423)
Q Consensus 41 ~~~~~~~~~~~~~~~~~i~IyTDGS~~--~~~~G~g~vi~~~~~--~~~----~~l~~~~sv~~AEl~AI~~AL~~a~~~ 112 (423)
+.++..+++- ..++.+++|+|||+. ++++|+|+|++..+. ... ..++...+++.||+.|++.||+.|.+.
T Consensus 59 ~~~~~~~~~~--~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~ 136 (219)
T PRK07708 59 ELKKLSKEVE--EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL 136 (219)
T ss_pred HHhhhhhhhc--cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc
Confidence 3445554432 236679999999986 356999999876432 221 235556899999999999999999998
Q ss_pred CCCc--EEEEcCCHHHHHHHhCCCCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHh
Q psy16896 113 NTRK--ILIISDSLSSFQAISNLHHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYS 190 (423)
Q Consensus 113 ~~~~--v~I~sDS~sai~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~ 190 (423)
+.+. |.|++||+.+++.+++.+.... ..+ ..+..++.+++.
T Consensus 137 g~~~~~V~I~~DSqlVi~qi~g~wk~~~--~~l-----------------------------------~~y~~~i~~l~~ 179 (219)
T PRK07708 137 GVKHEPVTFRGDSQVVLNQLAGEWPCYD--EHL-----------------------------------NHWLDRIEQKLK 179 (219)
T ss_pred CCCcceEEEEeccHHHHHHhCCCceeCC--hhH-----------------------------------HHHHHHHHHHHh
Confidence 7654 8999999999999987653221 011 113344455554
Q ss_pred cCCCceEEEEccCCCCCcCCHHHHHHHHHHhhhhh
Q psy16896 191 NSQANIKFLWCPSHVGISGNERADVEAKKATKMEY 225 (423)
Q Consensus 191 ~~~~~V~~~WVpgH~gi~GNe~AD~lAk~A~~~~~ 225 (423)
+....+.+.|||.. .|+.||+||+.|.....
T Consensus 180 ~~~l~~~~~~VpR~----~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 180 QLKLTPVYEPISRK----QNKEADQLATQALEGTV 210 (219)
T ss_pred hCCceEEEEECCch----hhhHHHHHHHHHHhcCC
Confidence 44556888999874 89999999999998654
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.49 E-value=4.3e-13 Score=137.05 Aligned_cols=126 Identities=17% Similarity=0.246 Sum_probs=94.8
Q ss_pred cEEEEEcCCcCCC--CceEEEEEecCC-e-E-EE--EecCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHH
Q psy16896 57 HLKIYTDGSKDET--GVGCALTIPQLN-E-T-KR--FALNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQA 129 (423)
Q Consensus 57 ~i~IyTDGS~~~~--~~G~g~vi~~~~-~-~-~~--~~l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~ 129 (423)
.+.||||||+..+ .+|+|+++.+.+ . . .. ..++ ..|++.||+.|++.||+.+.+.+.+.|.|++||+.+++.
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 3789999999853 589999998753 2 1 22 2233 778999999999999999999888999999999999999
Q ss_pred HhCCCCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCCcC
Q psy16896 130 ISNLHHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGISG 209 (423)
Q Consensus 130 l~~~~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi~G 209 (423)
+++...... ..+ ..++.++..++ +....+.|.|||+ .+
T Consensus 81 i~~~~~~~~--~~l-----------------------------------~~~~~~i~~l~-~~f~~~~i~~v~r----~~ 118 (372)
T PRK07238 81 MSGRWKVKH--PDM-----------------------------------KPLAAQARELA-SQFGRVTYTWIPR----AR 118 (372)
T ss_pred hCCCCccCC--hHH-----------------------------------HHHHHHHHHHH-hcCCceEEEECCc----hh
Confidence 987542110 001 11344555554 4457899999998 59
Q ss_pred CHHHHHHHHHHhhhhh
Q psy16896 210 NERADVEAKKATKMEY 225 (423)
Q Consensus 210 Ne~AD~lAk~A~~~~~ 225 (423)
|+.||.||+.|.....
T Consensus 119 N~~AD~LA~~a~~~~~ 134 (372)
T PRK07238 119 NAHADRLANEAMDAAA 134 (372)
T ss_pred hhHHHHHHHHHHHhhc
Confidence 9999999999976554
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.08 E-value=8.8e-10 Score=88.11 Aligned_cols=86 Identities=29% Similarity=0.342 Sum_probs=65.0
Q ss_pred chhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHhCCCCCChhhHHHHhhhhccccccccccCCCCCCcchhhhhhc
Q psy16896 94 VFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAISNLHHPNPLVKKIHEEYSNSQANIKFLWCPSHVDSLSSFQAIS 173 (423)
Q Consensus 94 v~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~W~~~~~~~~~~~~~i~ 173 (423)
+..||+.|+..||+.+.+.+..+|.|.|||+.+++.|++....... +
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~---~------------------------------ 47 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSE---L------------------------------ 47 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SC---C------------------------------
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCcccccccccccccccc---c------------------------------
Confidence 4679999999999999999999999999999999999887422110 1
Q ss_pred cCCCCcHHHHHHHHHHhcCCCceEEEEccCCCCCcCCHHHHHHHHHHhh
Q psy16896 174 NLHHPNPLVKKIQEEYSNSQANIKFLWCPSHVGISGNERADVEAKKATK 222 (423)
Q Consensus 174 ~~~~~~~l~~~i~~~l~~~~~~V~~~WVpgH~gi~GNe~AD~lAk~A~~ 222 (423)
..++.+|..++ +....+.|.|||. ++|..||.|||.|.+
T Consensus 48 -----~~~~~~i~~~~-~~~~~~~~~~i~r----~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 48 -----RPLIQDIRSLL-DRFWNVSVSHIPR----EQNKVADALAKFALS 86 (87)
T ss_dssp -----HHHHHHHHHHH-CCCSCEEEEE--G----GGSHHHHHHHHHHHH
T ss_pred -----cccchhhhhhh-ccccceEEEEECh----HHhHHHHHHHHHHhh
Confidence 12455666666 4578899999998 699999999999864
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.16 E-value=0.011 Score=47.67 Aligned_cols=30 Identities=30% Similarity=0.557 Sum_probs=24.6
Q ss_pred cccCCCCCCCCCCCCC-ccccceecccccCc
Q psy16896 368 HLFKREERPECDTCHE-PVTVEHLLLHCNKL 397 (423)
Q Consensus 368 ~~~~~~~~p~C~~Cg~-~etv~Hil~~Cp~~ 397 (423)
++.+...++.|..|+. .||++|+|++||..
T Consensus 52 ~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a 82 (86)
T PF13966_consen 52 QRRGIQVDPICPLCGNEEETIEHLFFHCPFA 82 (86)
T ss_pred hccCCccCCccccCCCccccccceeccCcCc
Confidence 3455567899999985 89999999999964
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=85.12 E-value=3.3 Score=37.27 Aligned_cols=54 Identities=17% Similarity=0.292 Sum_probs=33.4
Q ss_pred CcEEEEEcCCcCCCCceEEEEEec--CCeEE---EE---ecC--CCccchhhhHHHHHHHHHHHHh
Q psy16896 56 DHLKIYTDGSKDETGVGCALTIPQ--LNETK---RF---ALN--KHSSVFHAELFSILQSLNHVKE 111 (423)
Q Consensus 56 ~~i~IyTDGS~~~~~~G~g~vi~~--~~~~~---~~---~l~--~~~sv~~AEl~AI~~AL~~a~~ 111 (423)
..+++|+|+|.. +.|+.+++.. ++... .+ ++. ...|+-+-||.|+..|.+.+..
T Consensus 80 ~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 468899999953 3333333333 11111 11 121 3459999999999999998854
No 14
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=81.95 E-value=2.6 Score=40.05 Aligned_cols=173 Identities=15% Similarity=0.110 Sum_probs=106.4
Q ss_pred ccccCCCCCCCCCCCCcccccccccccCCCChHHHHHHHHHHHHh------hc--CCcEEEEEcCCcCC-CCceEEEEEe
Q psy16896 8 LNTVKPKNQRRLLKEPDCDLTLTVYKKHDICARIIQDRFQEILHE------KY--EDHLKIYTDGSKDE-TGVGCALTIP 78 (423)
Q Consensus 8 ~E~I~P~~~~PW~~~~~~~~~l~~~~~~~t~~~~~~~~~~~~~~~------~~--~~~i~IyTDGS~~~-~~~G~g~vi~ 78 (423)
-+-..|+.+..| .+|.-++..|..+.+.+....+.++.++.. +. ...+.-+.+|+... .+.+-.. .+
T Consensus 11 k~GR~tGIyktW---~Ec~~qVkGy~ga~YKsf~s~EeA~a~~~g~i~~~tp~~~~e~~i~~~~G~y~~~p~t~~~k-~y 86 (225)
T COG3341 11 KKGRKTGIYKTW---DECEKQVKGYPGAKYKSFKSYEEAEAYCEGNIESVTPYLDFEYIISWAKGDYDAKPGTQEFK-EY 86 (225)
T ss_pred ecccccceeccH---HHHHHHhcCCCcccccccccHHHHHHHhccCccccCcccchhccceeccCCccccCCCccee-EE
Confidence 456789999999 778888999999988888877777777752 11 33455566666553 2222222 23
Q ss_pred cCCeEE---EEec---CCCccchhhhHHHHHHHHHHHHhhCCCcEEE-E----cCCHHHHHHHhCCCCCChhhHHHHhhh
Q psy16896 79 QLNETK---RFAL---NKHSSVFHAELFSILQSLNHVKELNTRKILI-I----SDSLSSFQAISNLHHPNPLVKKIHEEY 147 (423)
Q Consensus 79 ~~~~~~---~~~l---~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I-~----sDS~sai~~l~~~~~~~~~~~~i~~~~ 147 (423)
.+.... ...- -...++..+|.+|++.+|+.+...+.++..| + .||++.+.-+.+-.... .
T Consensus 87 r~k~~~~~~~lt~~~~~~~~~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k-----~---- 157 (225)
T COG3341 87 RGKCTIEYSWLTESSEFSIKSNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETK-----V---- 157 (225)
T ss_pred eccccccceeeeeecccccccCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHhhhhhhH-----H----
Confidence 332111 1111 1345778899999999999988766655555 6 79998887776542110 0
Q ss_pred hccccccccccCCCCCCcchhhhhhccCCCCcHHHHHHHHHH-hcCCCceEEEEccCCCCCcCCHHHHHHHHHHhhhhhh
Q psy16896 148 SNSQANIKFLWCPSHVDSLSSFQAISNLHHPNPLVKKIQEEY-SNSQANIKFLWCPSHVGISGNERADVEAKKATKMEYR 226 (423)
Q Consensus 148 ~~~~~~~~~~W~~~~~~~~~~~~~i~~~~~~~~l~~~i~~~l-~~~~~~V~~~WVpgH~gi~GNe~AD~lAk~A~~~~~~ 226 (423)
+ ++.. .+.. .-.+....+.|+--|.++.-+..++.++..+......
T Consensus 158 --------------------------~------~~~~-~e~~~~~~~v~h~~k~i~~~~~~~~~~~~~s~~~~~~k~~~~ 204 (225)
T COG3341 158 --------------------------N------LLKD-REFFSIGKGVFHDEKDINIHIWIFESKKGNSHVYNTSKKELS 204 (225)
T ss_pred --------------------------H------HHHh-HHhhhccchhhhhhhhcccccccchhhhhhhhhhchhhhhcc
Confidence 0 0000 1111 1122455667888898888888888887766655543
No 15
>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=65.16 E-value=6.9 Score=36.98 Aligned_cols=61 Identities=15% Similarity=0.219 Sum_probs=38.1
Q ss_pred CcEEEEEcCCcCCCCceEEEEEecCCeEEEEecCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHH
Q psy16896 56 DHLKIYTDGSKDETGVGCALTIPQLNETKRFALNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSF 127 (423)
Q Consensus 56 ~~i~IyTDGS~~~~~~G~g~vi~~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai 127 (423)
.--.||+|+.- .|+|+.+-.......|. ..-.+.+|||+|...|.-+.. .++ |.|||..|+
T Consensus 93 ~lc~VfaDATp----Tgwgi~i~~~~~~~Tfs--~~l~IhtaELlaaClAr~~~~----~r~-l~tDnt~Vl 153 (245)
T PF00336_consen 93 GLCQVFADATP----TGWGISITGQRMRGTFS--KPLPIHTAELLAACLARLMSG----ARC-LGTDNTVVL 153 (245)
T ss_pred CCCceeccCCC----CcceeeecCceeeeeec--ccccchHHHHHHHHHHHhccC----CcE-EeecCcEEE
Confidence 34578888754 46666532222222332 345789999999998876653 234 899997554
No 16
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=33.14 E-value=47 Score=36.73 Aligned_cols=32 Identities=22% Similarity=0.386 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCCceEEEEccCCCCCcCCHHH
Q psy16896 182 VKKIQEEYSNSQANIKFLWCPSHVGISGNERA 213 (423)
Q Consensus 182 ~~~i~~~l~~~~~~V~~~WVpgH~gi~GNe~A 213 (423)
++++++.+.+.|..|-+-|||+|-+..||-.|
T Consensus 216 fk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 216 FKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 45667788899999999999999999998754
No 17
>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=32.31 E-value=1.6e+02 Score=24.36 Aligned_cols=55 Identities=13% Similarity=0.035 Sum_probs=32.8
Q ss_pred CceEEEEEecC-CeEEEEecC----CCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCH
Q psy16896 70 GVGCALTIPQL-NETKRFALN----KHSSVFHAELFSILQSLNHVKELNTRKILIISDSL 124 (423)
Q Consensus 70 ~~G~g~vi~~~-~~~~~~~l~----~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~ 124 (423)
...+|.++.+. +........ .......||..||..+.+..........++|+.-+
T Consensus 16 ~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~E 75 (109)
T cd01285 16 EVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLE 75 (109)
T ss_pred CCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCC
Confidence 34455555555 444333322 23467889999999988765433356677777644
No 18
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=31.30 E-value=1.1e+02 Score=27.33 Aligned_cols=55 Identities=13% Similarity=0.083 Sum_probs=32.8
Q ss_pred CceEEEEEec-CCeEEEEe----cCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCH
Q psy16896 70 GVGCALTIPQ-LNETKRFA----LNKHSSVFHAELFSILQSLNHVKELNTRKILIISDSL 124 (423)
Q Consensus 70 ~~G~g~vi~~-~~~~~~~~----l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~ 124 (423)
.+.+|.|+.+ .+...... ....--.-.||+.||..|.+.+........++|+=-.
T Consensus 27 e~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyvT~E 86 (152)
T COG0590 27 EVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYVTLE 86 (152)
T ss_pred CCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEEecC
Confidence 4667766666 33333222 1122234589999999999988654455566665443
No 19
>KOG1812|consensus
Probab=30.74 E-value=57 Score=33.87 Aligned_cols=61 Identities=18% Similarity=0.292 Sum_probs=43.4
Q ss_pred ceEEEEEecCCe---EEEEe--cC--CCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCCHHHHHHHh
Q psy16896 71 VGCALTIPQLNE---TKRFA--LN--KHSSVFHAELFSILQSLNHVKELNTRKILIISDSLSSFQAIS 131 (423)
Q Consensus 71 ~G~g~vi~~~~~---~~~~~--l~--~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS~sai~~l~ 131 (423)
+|.|+++.+.+. .+... .. ...+...||+.|+..+|..+.+.+...+.+++|+.-....+.
T Consensus 19 ~g~~vai~d~~d~~~~f~~k~~~~~~~~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~ 86 (384)
T KOG1812|consen 19 AGFGVAICDEHDDDLLFQMKASDHDSDSITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVA 86 (384)
T ss_pred ccCceeeeccccHHHHHHhhcCcccccccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHh
Confidence 677777766421 11111 11 236788999999999999999999999999999765555443
No 20
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=30.11 E-value=1.5e+02 Score=27.21 Aligned_cols=53 Identities=13% Similarity=0.098 Sum_probs=29.0
Q ss_pred ceEEEEEecCCeEEEEec----CCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCC
Q psy16896 71 VGCALTIPQLNETKRFAL----NKHSSVFHAELFSILQSLNHVKELNTRKILIISDS 123 (423)
Q Consensus 71 ~G~g~vi~~~~~~~~~~l----~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS 123 (423)
..+|.||..++...+..- +.......||..||..|.+.+........++|+--
T Consensus 33 ~pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~~~~~l~g~tlY~Tl 89 (172)
T PRK10860 33 VPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTL 89 (172)
T ss_pred CCEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhcCCCCcCCcEEEeeC
Confidence 344444445555443321 12223568999999998875543333456666543
No 21
>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=24.84 E-value=38 Score=25.31 Aligned_cols=21 Identities=24% Similarity=0.428 Sum_probs=10.0
Q ss_pred CCCCCCCCccccceecccccC
Q psy16896 376 PECDTCHEPVTVEHLLLHCNK 396 (423)
Q Consensus 376 p~C~~Cg~~etv~Hil~~Cp~ 396 (423)
-.|+.||+..+-.|....||.
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 479999999999999999996
No 22
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=23.15 E-value=2.7e+02 Score=23.66 Aligned_cols=48 Identities=13% Similarity=0.023 Sum_probs=27.5
Q ss_pred ceEEEEEecC-CeEEEEecCCCccchhhhHHHHHHHHHHHHhhCCCcEEEEcC
Q psy16896 71 VGCALTIPQL-NETKRFALNKHSSVFHAELFSILQSLNHVKELNTRKILIISD 122 (423)
Q Consensus 71 ~G~g~vi~~~-~~~~~~~l~~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sD 122 (423)
..+|.++.++ +...............||..||..|.+. .....++|+-
T Consensus 19 ~pvGaviv~~~g~iv~~g~n~~~~~~HAE~~ai~~a~~~----~l~g~tly~T 67 (115)
T cd01284 19 PPVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEK----LARGATLYVT 67 (115)
T ss_pred CCEEEEEEeCCCeEEEEecCCCCCcccHHHHHHHHHhhc----CCCCeEEEEe
Confidence 3445454444 4444433332336778999999998874 2344555543
No 23
>COG0336 TrmD tRNA-(guanine-N1)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=22.77 E-value=20 Score=34.59 Aligned_cols=37 Identities=24% Similarity=0.210 Sum_probs=25.8
Q ss_pred ccc-eecccccCcc-CCCCCCCCccHHhhhCCCCCCCCCC
Q psy16896 386 TVE-HLLLHCNKLR-FRPPSFLGNSLSNILSDNPDSISRW 423 (423)
Q Consensus 386 tv~-Hil~~Cp~~~-~R~~l~~~~~l~~~L~~~~~~~~~~ 423 (423)
+-+ -=|++||.|. ++ .+.....-..+|++|..+|.+|
T Consensus 168 SF~~~gLLe~P~YTRP~-~~~g~~VP~VLlSGnH~~I~~W 206 (240)
T COG0336 168 SFENNGLLEYPHYTRPR-EFEGMKVPEVLLSGNHAKIAQW 206 (240)
T ss_pred ccccCCccCCCCcCChh-hcCCCcCChhhhcCcHHHHHHH
Confidence 444 3678999998 66 3334444456788999999887
No 24
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=21.98 E-value=2e+02 Score=25.48 Aligned_cols=53 Identities=15% Similarity=0.189 Sum_probs=34.0
Q ss_pred CceEEEEEecCCeEEEEecC--CCccchhhhHHHHHHHHHHHHhhCCCcEEEEcCC
Q psy16896 70 GVGCALTIPQLNETKRFALN--KHSSVFHAELFSILQSLNHVKELNTRKILIISDS 123 (423)
Q Consensus 70 ~~G~g~vi~~~~~~~~~~l~--~~~sv~~AEl~AI~~AL~~a~~~~~~~v~I~sDS 123 (423)
.||+++..-++.......+. ...--..||-.||..|+.. -......|.|++|+
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 47777744333333333332 2344567999999999987 33346789999998
No 25
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=21.00 E-value=2.1e+02 Score=28.93 Aligned_cols=64 Identities=11% Similarity=0.087 Sum_probs=28.7
Q ss_pred ceEEEEEecCCeEEEEecCCCccchhhhHHHHHHHHHHHHhhC---CCcEEEEcCCHHHHHHHhCCC
Q psy16896 71 VGCALTIPQLNETKRFALNKHSSVFHAELFSILQSLNHVKELN---TRKILIISDSLSSFQAISNLH 134 (423)
Q Consensus 71 ~G~g~vi~~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~a~~~~---~~~v~I~sDS~sai~~l~~~~ 134 (423)
.-+||.|..++..-...-....+....=+.-|..++..++... ..+|-+.|||+.++..++...
T Consensus 168 ~~IGVHVRhGngeD~~~h~~~~~D~e~~L~~V~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~~F 234 (321)
T PF05830_consen 168 SVIGVHVRHGNGEDIMDHAPYWADEERALRQVCTAIDKAKALAPPKPVRIFLATDSAEVIDQFRKKF 234 (321)
T ss_dssp EEEEEEE---------------HHHHHHHHHHHHHHHHHHTS--SS-EEEEEEES-HHHHHHHHHHS
T ss_pred ceEEEEEeccCCcchhccCccccCchHHHHHHHHHHHHHHhccCCCCeeEEEecCcHHHHHHHHHHC
Confidence 4568887766543222111122221112334445666555432 356888899999999987654
Done!