Query psy5156
Match_columns 389
No_of_seqs 245 out of 1707
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 18:48:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5156.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5156hhsearch_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 3.2E-23 7E-28 182.5 13.7 142 16-214 2-146 (154)
2 PRK06548 ribonuclease H; Provi 99.9 6.3E-23 1.4E-27 183.0 11.2 139 15-214 3-143 (161)
3 PRK08719 ribonuclease H; Revie 99.9 3.6E-22 7.8E-27 176.1 13.7 136 15-212 2-146 (147)
4 PRK00203 rnhA ribonuclease H; 99.9 3.4E-22 7.4E-27 176.7 10.5 138 17-214 3-143 (150)
5 PF00075 RNase_H: RNase H; In 99.9 6.4E-21 1.4E-25 163.2 12.8 127 16-211 2-131 (132)
6 cd06222 RnaseH RNase H (RNase 99.7 9.2E-17 2E-21 133.1 14.0 125 19-211 1-130 (130)
7 KOG3752|consensus 99.7 2.5E-17 5.5E-22 161.4 11.2 148 15-213 210-365 (371)
8 PRK13907 rnhA ribonuclease H; 99.7 3.6E-16 7.8E-21 134.2 12.4 122 18-212 2-126 (128)
9 PRK07708 hypothetical protein; 99.5 8.1E-14 1.7E-18 130.6 12.9 82 15-96 71-162 (219)
10 PRK07238 bifunctional RNase H/ 99.4 1.4E-12 3E-17 131.4 14.9 79 17-95 2-86 (372)
11 PF13456 RVT_3: Reverse transc 98.9 6.2E-09 1.4E-13 82.0 8.0 86 54-212 1-86 (87)
12 PF13966 zf-RVT: zinc-binding 95.7 0.0052 1.1E-07 49.0 1.5 30 289-318 52-82 (86)
13 PF05380 Peptidase_A17: Pao re 87.9 2.7 5.8E-05 37.3 8.0 54 16-71 80-143 (159)
14 PF13456 RVT_3: Reverse transc 77.0 2.3 4.9E-05 32.7 2.7 51 105-155 3-54 (87)
15 KOG3752|consensus 76.7 1.5 3.3E-05 44.1 2.0 80 101-209 254-333 (371)
16 cd06222 RnaseH RNase H (RNase 64.2 8.2 0.00018 30.7 3.4 42 103-144 41-82 (130)
17 PF00075 RNase_H: RNase H; In 46.8 9.1 0.0002 31.9 0.9 37 102-141 39-75 (132)
18 COG0295 Cdd Cytidine deaminase 42.9 69 0.0015 27.9 5.8 54 29-83 26-81 (134)
19 PF00336 DNA_pol_viral_C: DNA 39.4 34 0.00073 32.1 3.4 61 16-87 93-153 (245)
20 PRK08298 cytidine deaminase; V 36.2 88 0.0019 27.3 5.4 58 21-83 19-78 (136)
21 PRK13907 rnhA ribonuclease H; 35.0 32 0.0007 28.8 2.5 40 105-144 43-82 (128)
22 PF05741 zf-nanos: Nanos RNA b 34.7 21 0.00045 26.3 1.1 21 297-317 34-54 (55)
23 PRK06848 hypothetical protein; 31.3 92 0.002 27.2 4.8 55 28-83 26-82 (139)
24 PF05830 NodZ: Nodulation prot 26.6 3.3E+02 0.0071 27.2 8.1 38 59-96 196-236 (321)
25 TIGR01354 cyt_deam_tetra cytid 26.4 1.7E+02 0.0038 24.8 5.6 54 29-83 21-76 (127)
26 COG0296 GlgB 1,4-alpha-glucan 24.5 71 0.0015 34.9 3.4 23 181-203 225-247 (628)
27 PF00098 zf-CCHC: Zinc knuckle 24.5 44 0.00095 18.7 1.0 17 298-317 2-18 (18)
28 PRK06548 ribonuclease H; Provi 23.8 39 0.00084 30.3 1.1 36 105-141 44-79 (161)
29 cd01285 nucleoside_deaminase N 22.5 2.8E+02 0.006 22.6 6.0 59 29-87 17-78 (109)
30 PRK05578 cytidine deaminase; V 22.4 2E+02 0.0043 24.8 5.2 54 30-84 25-80 (131)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.90 E-value=3.2e-23 Score=182.47 Aligned_cols=142 Identities=19% Similarity=0.178 Sum_probs=110.8
Q ss_pred CcEEEEEcCCcc--CCCeEEEEEEecCCEEE-EEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHhc
Q psy5156 16 DFLKIYTDGSKD--ETGVGCALIIPQLNVTK-RFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISN 92 (389)
Q Consensus 16 ~~~~IyTDGS~~--~~~~G~avv~~~~~~~~-~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l~~ 92 (389)
..+.||||||+. +|..|+|+|+..+...+ .......+||++||+.|++.||+.+.+.+...|.|+|||++|+++|+.
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 468999999998 56789998887443333 222223899999999999999999998888999999999999999995
Q ss_pred CCCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCC
Q psy5156 93 LYHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHP 172 (389)
Q Consensus 93 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~ 172 (389)
+...++--.+. .++ +.++.+.+|++++.++.+...
T Consensus 82 w~~~w~~~~w~-----------------------------~~~----~~pvkn~dl~~~~~~~~~~~~------------ 116 (154)
T COG0328 82 WIVKWKKNGWK-----------------------------TAD----KKPVKNKDLWEELDELLKRHE------------ 116 (154)
T ss_pred HHhhccccCcc-----------------------------ccc----cCccccHHHHHHHHHHHhhCC------------
Confidence 54443211100 011 456666788888888876543
Q ss_pred CcccccccCCCceEEEEEeecCCCCccchHHHHHHhhhcCCC
Q psy5156 173 CWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214 (389)
Q Consensus 173 ~~~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~~~~ 214 (389)
.|.+.|||||+|.++||.||+||+.|++.+
T Consensus 117 ------------~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 117 ------------LVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred ------------eEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 899999999999999999999999998765
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.89 E-value=6.3e-23 Score=183.04 Aligned_cols=139 Identities=19% Similarity=0.181 Sum_probs=99.7
Q ss_pred CCcEEEEEcCCcc--CCCeEEEEEEecCCEEEEEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHhc
Q psy5156 15 KDFLKIYTDGSKD--ETGVGCALIIPQLNVTKRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISN 92 (389)
Q Consensus 15 ~~~~~IyTDGS~~--~~~~G~avv~~~~~~~~~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l~~ 92 (389)
+..+.||||||+. ++..|+|+++.+.. ...+....+||++|||+|++.||+.+.. ....+.|+|||++|+++++.
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~--~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~ 79 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENT--WDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTK 79 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCc--EEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHH
Confidence 4569999999998 36689998886432 2223345789999999999999986543 44679999999999999997
Q ss_pred CCCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCC
Q psy5156 93 LYHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHP 172 (389)
Q Consensus 93 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~ 172 (389)
|...+-... + ..++-+ +..+.+|+++|.++++.
T Consensus 80 W~~~Wk~~g-------------W----------------k~s~G~----pV~N~dL~~~l~~l~~~-------------- 112 (161)
T PRK06548 80 WVYSWKMRK-------------W----------------RKADGK----PVLNQEIIQEIDSLMEN-------------- 112 (161)
T ss_pred HHHHHHHCC-------------C----------------cccCCC----ccccHHHHHHHHHHHhc--------------
Confidence 544321000 0 011112 22334566666665532
Q ss_pred CcccccccCCCceEEEEEeecCCCCccchHHHHHHhhhcCCC
Q psy5156 173 CWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214 (389)
Q Consensus 173 ~~~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~~~~ 214 (389)
..|+|.|||||+|++|||.||+||++|+...
T Consensus 113 -----------~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 113 -----------RNIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred -----------CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 2699999999999999999999999998654
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.88 E-value=3.6e-22 Score=176.11 Aligned_cols=136 Identities=21% Similarity=0.267 Sum_probs=93.9
Q ss_pred CCcEEEEEcCCccCC-----CeEEEEEEecC--CEE--EEEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHH
Q psy5156 15 KDFLKIYTDGSKDET-----GVGCALIIPQL--NVT--KRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLS 85 (389)
Q Consensus 15 ~~~~~IyTDGS~~~~-----~~G~avv~~~~--~~~--~~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~ 85 (389)
.+.++||||||+..+ .+|+|+++... ... ...++.+..||++||+.|++.||+.+.+. ..|+|||++
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 467899999999742 35888877543 322 33445567899999999999999998752 379999999
Q ss_pred HHHHHhcCCCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhc
Q psy5156 86 SFQAISNLYHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKF 165 (389)
Q Consensus 86 al~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 165 (389)
|+++++.+...+-...+. .+. +.+..+.++++.|.+++.
T Consensus 78 vi~~i~~~~~~W~~~~w~-----------------------------~s~----g~~v~n~dl~~~i~~l~~-------- 116 (147)
T PRK08719 78 CVRGFNEWLDTWKQKGWR-----------------------------KSD----KKPVANRDLWQQVDELRA-------- 116 (147)
T ss_pred HHHHHHHHHHHHHhCCcc-----------------------------cCC----CcccccHHHHHHHHHHhC--------
Confidence 999996543322100000 000 112222345555554442
Q ss_pred ccCCCCCCcccccccCCCceEEEEEeecCCCCccchHHHHHHhhhcC
Q psy5156 166 LWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATS 212 (389)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~~ 212 (389)
...|+|.|||||+|++|||.||+||++|++
T Consensus 117 -----------------~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 117 -----------------RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred -----------------CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 247999999999999999999999999875
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.87 E-value=3.4e-22 Score=176.75 Aligned_cols=138 Identities=20% Similarity=0.197 Sum_probs=97.9
Q ss_pred cEEEEEcCCcc--CCCeEEEEEEecCCEEE-EEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHhcC
Q psy5156 17 FLKIYTDGSKD--ETGVGCALIIPQLNVTK-RFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNL 93 (389)
Q Consensus 17 ~~~IyTDGS~~--~~~~G~avv~~~~~~~~-~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l~~~ 93 (389)
.+.||||||+. ++..|+|+|+..++... ..+..+..||++|||.|++.||+.+.+ ...+.|+|||++++++|..+
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 48999999998 35678888876443322 223345789999999999999998864 46899999999999999975
Q ss_pred CCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCCC
Q psy5156 94 YHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPC 173 (389)
Q Consensus 94 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 173 (389)
...+....+. .+. +.+..+.+++++|.+++.
T Consensus 81 ~~~Wk~~~~~-----------------------------~~~----g~~v~n~dl~~~i~~l~~---------------- 111 (150)
T PRK00203 81 IHGWKKNGWK-----------------------------TAD----KKPVKNVDLWQRLDAALK---------------- 111 (150)
T ss_pred HHHHHHcCCc-----------------------------ccC----CCccccHHHHHHHHHHhc----------------
Confidence 4321100000 001 112223345555555442
Q ss_pred cccccccCCCceEEEEEeecCCCCccchHHHHHHhhhcCCC
Q psy5156 174 WYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214 (389)
Q Consensus 174 ~~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~~~~ 214 (389)
...|.|.|||||+|++||+.||+|||+|+..+
T Consensus 112 ---------~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 112 ---------RHQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred ---------cCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 24899999999999999999999999998765
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=99.85 E-value=6.4e-21 Score=163.19 Aligned_cols=127 Identities=35% Similarity=0.440 Sum_probs=90.2
Q ss_pred CcEEEEEcCCcc--CCCeEEEEEEecCCEEEEEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHhcC
Q psy5156 16 DFLKIYTDGSKD--ETGVGCALIIPQLNVTKRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNL 93 (389)
Q Consensus 16 ~~~~IyTDGS~~--~~~~G~avv~~~~~~~~~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l~~~ 93 (389)
+.+.||||||+. ++..|+|+++..+ ......++ ..|++.|||.||..||+ +.. ...+.|+|||++++..+..+
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 478999999987 3446777766544 33334445 89999999999999999 443 48999999999999988873
Q ss_pred CCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCCC
Q psy5156 94 YHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPC 173 (389)
Q Consensus 94 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 173 (389)
...+++.. .....++..+|.+++.
T Consensus 77 ~~~~~~~~----------------------------------------~~~~~~i~~~i~~~~~---------------- 100 (132)
T PF00075_consen 77 LHGNGWKK----------------------------------------TSNGRPIKNEIWELLS---------------- 100 (132)
T ss_dssp HHHTTSBS----------------------------------------CTSSSBHTHHHHHHHH----------------
T ss_pred cccccccc----------------------------------------ccccccchhheeeccc----------------
Confidence 22111000 0000123344555552
Q ss_pred cccccccCCCceEEEEEeecCCCC-ccchHHHHHHhhhc
Q psy5156 174 WYFWKRSSSQISIKFLWCPSHVGI-SGNDQADTEAKKAT 211 (389)
Q Consensus 174 ~~~~~~~~~~~~i~~~wvp~H~g~-~gNe~aD~~Ak~a~ 211 (389)
.+..|.|.|||||.|+ .|||.||+|||+|+
T Consensus 101 --------~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 101 --------RGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp --------HSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred --------cceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 2569999999999999 59999999999986
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=99.73 E-value=9.2e-17 Score=133.06 Aligned_cols=125 Identities=30% Similarity=0.411 Sum_probs=94.2
Q ss_pred EEEEcCCccC--CCeEEEEEEecCCEE--EE-EecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHhcC
Q psy5156 19 KIYTDGSKDE--TGVGCALIIPQLNVT--KR-FTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNL 93 (389)
Q Consensus 19 ~IyTDGS~~~--~~~G~avv~~~~~~~--~~-~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l~~~ 93 (389)
.+|||||... +++|+|+++.+.... .. .......+++.+|+.|+..||+.+...+..++.|++||+.++..+.+.
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 4899999884 478999888754322 11 122257899999999999999999888889999999999999999987
Q ss_pred CCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCCC
Q psy5156 94 YHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPC 173 (389)
Q Consensus 94 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 173 (389)
....+. .+. ++...+++++.
T Consensus 81 ~~~~~~-------~~~-------------------------------------~~~~~i~~~~~---------------- 100 (130)
T cd06222 81 YEGKPV-------KNV-------------------------------------DLWQRLLALLK---------------- 100 (130)
T ss_pred ccCCCh-------hhH-------------------------------------HHHHHHHHHHh----------------
Confidence 653221 001 12223333332
Q ss_pred cccccccCCCceEEEEEeecCCCCccchHHHHHHhhhc
Q psy5156 174 WYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKAT 211 (389)
Q Consensus 174 ~~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~ 211 (389)
.+..++|.|||+|+|+.+|+.||.|||.|.
T Consensus 101 --------~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 101 --------RFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred --------CCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 345899999999999999999999999874
No 7
>KOG3752|consensus
Probab=99.72 E-value=2.5e-17 Score=161.35 Aligned_cols=148 Identities=23% Similarity=0.249 Sum_probs=107.7
Q ss_pred CCcEEEEEcCCccC-----CCeEEEEEEecCC-EEEEEecC-CCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHH
Q psy5156 15 KDFLKIYTDGSKDE-----TGVGCALIIPQLN-VTKRFTLN-KYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSF 87 (389)
Q Consensus 15 ~~~~~IyTDGS~~~-----~~~G~avv~~~~~-~~~~~~l~-~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al 87 (389)
.+..++|||||+.. ..+|+|||++++. ......+. +..|||.|||.|+..||+.|.+....+++|.|||++++
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 34589999999984 3489999998654 45666664 89999999999999999999988888999999999999
Q ss_pred HHHhcCCCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhh-hccCCCCChhHHHHHHHHHhhhhhhhcc
Q psy5156 88 QAISNLYHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQA-ISNLYHPNPLVKEIQETYSSAQISIKFL 166 (389)
Q Consensus 88 ~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~~~~~~~~ 166 (389)
+.|+.|...+.... + . + +.... |.-..++-+...++.++.+..
T Consensus 290 ~~l~~wv~~~k~~~-~---------k----------------~---~~~~~~i~~~v~n~~~~~e~~~l~q~~------- 333 (371)
T KOG3752|consen 290 NSLTLWVQGWKKNG-W---------K----------------T---SNGSDRICAYVKNQDFFNELDELEQEI------- 333 (371)
T ss_pred HHHHHHHhhhccCc-c---------c----------------c---ccCCCccceeeecchHHHHHHHHHhhh-------
Confidence 99997766543210 0 0 0 00000 000012223445555555431
Q ss_pred cCCCCCCcccccccCCCceEEEEEeecCCCCccchHHHHHHhhhcCC
Q psy5156 167 WCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATSE 213 (389)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~~~ 213 (389)
++.+|.+.|||||.||.|||.||.||++....
T Consensus 334 ---------------~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 334 ---------------SNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred ---------------ccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 35699999999999999999999999998543
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.68 E-value=3.6e-16 Score=134.20 Aligned_cols=122 Identities=25% Similarity=0.280 Sum_probs=92.4
Q ss_pred EEEEEcCCcc--CCCeEEEEEEecCCEE-EEEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHhcCC
Q psy5156 18 LKIYTDGSKD--ETGVGCALIIPQLNVT-KRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNLY 94 (389)
Q Consensus 18 ~~IyTDGS~~--~~~~G~avv~~~~~~~-~~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l~~~~ 94 (389)
+.||||||+. ++.+|+|+|+.+.... .........||+.||+.|++.||+.+...+..++.|++||+.+++.+++.+
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 6899999998 3678999998755322 222223567999999999999999999988889999999999999999866
Q ss_pred CCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCCCc
Q psy5156 95 HPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPCW 174 (389)
Q Consensus 95 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~ 174 (389)
..++ .+ .+++++++.++....
T Consensus 82 ~~~~--------~~-------------------------------------~~l~~~~~~l~~~f~-------------- 102 (128)
T PRK13907 82 AKNK--------MF-------------------------------------APLLEEALQYIKSFD-------------- 102 (128)
T ss_pred hcCh--------hH-------------------------------------HHHHHHHHHHHhcCC--------------
Confidence 4221 00 123445555554432
Q ss_pred ccccccCCCceEEEEEeecCCCCccchHHHHHHhhhcC
Q psy5156 175 YFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATS 212 (389)
Q Consensus 175 ~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~~ 212 (389)
.+.|.|||.+ +|+.||.||+.|..
T Consensus 103 ----------~~~~~~v~r~----~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 103 ----------LFFIKWIPSS----QNKVADELARKAIL 126 (128)
T ss_pred ----------ceEEEEcCch----hchhHHHHHHHHHh
Confidence 6778999984 99999999999864
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.53 E-value=8.1e-14 Score=130.62 Aligned_cols=82 Identities=17% Similarity=0.166 Sum_probs=65.1
Q ss_pred CCcEEEEEcCCcc--CCCeEEEEEEec--CCEEE----EEecCCCCchhHHhHHHHHHHHHHHHhcCCce--EEEEcCCH
Q psy5156 15 KDFLKIYTDGSKD--ETGVGCALIIPQ--LNVTK----RFTLNKYSSIFHAELFSILQSLKNAKLLNIKK--VLIISDSL 84 (389)
Q Consensus 15 ~~~~~IyTDGS~~--~~~~G~avv~~~--~~~~~----~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~--i~I~sDSq 84 (389)
++.+.+|+|||+. ++++|+|+++.. ++... ...++...||+.||+.|++.||+.+.+.+.++ |.|++||+
T Consensus 71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSq 150 (219)
T PRK07708 71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQ 150 (219)
T ss_pred CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccH
Confidence 4579999999986 467888888853 33222 12455678999999999999999999887654 89999999
Q ss_pred HHHHHHhcCCCC
Q psy5156 85 SSFQAISNLYHP 96 (389)
Q Consensus 85 ~al~~l~~~~~~ 96 (389)
.+++.+++.+..
T Consensus 151 lVi~qi~g~wk~ 162 (219)
T PRK07708 151 VVLNQLAGEWPC 162 (219)
T ss_pred HHHHHhCCCcee
Confidence 999999987654
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.44 E-value=1.4e-12 Score=131.44 Aligned_cols=79 Identities=18% Similarity=0.157 Sum_probs=63.8
Q ss_pred cEEEEEcCCccC--CCeEEEEEEecC--C-E-EEEEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHH
Q psy5156 17 FLKIYTDGSKDE--TGVGCALIIPQL--N-V-TKRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAI 90 (389)
Q Consensus 17 ~~~IyTDGS~~~--~~~G~avv~~~~--~-~-~~~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l 90 (389)
.+.||||||+.. +.+|+|+++.+. . . ..........||+.||+.|++.||+.+.+.+.+++.|++||+.+++.+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i 81 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM 81 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence 478999999984 568999888753 2 2 222223347899999999999999999998889999999999999999
Q ss_pred hcCCC
Q psy5156 91 SNLYH 95 (389)
Q Consensus 91 ~~~~~ 95 (389)
.+.+.
T Consensus 82 ~~~~~ 86 (372)
T PRK07238 82 SGRWK 86 (372)
T ss_pred CCCCc
Confidence 87654
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.89 E-value=6.2e-09 Score=82.03 Aligned_cols=86 Identities=28% Similarity=0.322 Sum_probs=62.6
Q ss_pred hhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHhcCCCCCccccccchhhHHHHHHHhhhHHHhhhhhhhhhcccc
Q psy5156 54 IFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSL 133 (389)
Q Consensus 54 ~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~ 133 (389)
+..||+.|+..||+.+.+.+.+++.|.|||+.+++.+++....... + .
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~---~-----~------------------------ 48 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSE---L-----R------------------------ 48 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SC---C-----H------------------------
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCcccccccccccccccc---c-----c------------------------
Confidence 4689999999999999999999999999999999999888544221 1 1
Q ss_pred hhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCCCcccccccCCCceEEEEEeecCCCCccchHHHHHHhhhcC
Q psy5156 134 SSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATS 212 (389)
Q Consensus 134 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~a~~ 212 (389)
.+...|+.+.+.. ..+.|.|||. .+|..||.|||.|.+
T Consensus 49 -------------~~~~~i~~~~~~~------------------------~~~~~~~i~r----~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 49 -------------PLIQDIRSLLDRF------------------------WNVSVSHIPR----EQNKVADALAKFALS 86 (87)
T ss_dssp -------------HHHHHHHHHHCCC------------------------SCEEEEE--G----GGSHHHHHHHHHHHH
T ss_pred -------------ccchhhhhhhccc------------------------cceEEEEECh----HHhHHHHHHHHHHhh
Confidence 1233455555433 4899999997 699999999998864
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.69 E-value=0.0052 Score=49.01 Aligned_cols=30 Identities=30% Similarity=0.566 Sum_probs=25.3
Q ss_pred cccccCCCCCCcCCCC-CcccchhhcccCCc
Q psy5156 289 YLFKREERPICDSCHE-PVTVEHIILHCNKL 318 (389)
Q Consensus 289 ~r~~~~~sp~C~~Cg~-~eT~~HiL~~Cp~~ 318 (389)
.+.+...++.|..|+. .||++|+|++||..
T Consensus 52 ~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a 82 (86)
T PF13966_consen 52 QRRGIQVDPICPLCGNEEETIEHLFFHCPFA 82 (86)
T ss_pred hccCCccCCccccCCCccccccceeccCcCc
Confidence 4456678899999995 79999999999964
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=87.94 E-value=2.7 Score=37.33 Aligned_cols=54 Identities=26% Similarity=0.333 Sum_probs=35.7
Q ss_pred CcEEEEEcCCccCCCeEEEEEEec---CCEEEE--E---ec--CCCCchhHHhHHHHHHHHHHHHh
Q psy5156 16 DFLKIYTDGSKDETGVGCALIIPQ---LNVTKR--F---TL--NKYSSIFHAELFSILQSLKNAKL 71 (389)
Q Consensus 16 ~~~~IyTDGS~~~~~~G~avv~~~---~~~~~~--~---~l--~~~~t~~~AEl~AI~~AL~~a~~ 71 (389)
..+++|+|+| ..+.|+.+|... +..... + +. -...|+-+-||.|+..|.+.+..
T Consensus 80 ~~L~~F~DAS--~~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDAS--ESAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeeccc--ccceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 3689999999 345666666542 222111 1 11 13459999999999999998864
No 14
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=77.05 E-value=2.3 Score=32.66 Aligned_cols=51 Identities=31% Similarity=0.341 Sum_probs=38.2
Q ss_pred hhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCC-CCChhHHHHHHH
Q psy5156 105 HAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLY-HPNPLVKEIQET 155 (389)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~-~~~~~~~~i~~~ 155 (389)
.+|+.+++.+++..-.++++++++.||+....+.+.+.. .+.++...++++
T Consensus 3 ~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i 54 (87)
T PF13456_consen 3 EAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDI 54 (87)
T ss_dssp HHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhh
Confidence 468999999999999999999999999999999998863 333544444444
No 15
>KOG3752|consensus
Probab=76.66 E-value=1.5 Score=44.12 Aligned_cols=80 Identities=24% Similarity=0.242 Sum_probs=56.3
Q ss_pred cccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCCCChhHHHHHHHHHhhhhhhhcccCCCCCCccccccc
Q psy5156 101 KEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPCWYFWKRS 180 (389)
Q Consensus 101 ~~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 180 (389)
+.-+.+||.+|..||+++--.+++||+|.|||....+.+..++ ...++.+ |+..
T Consensus 254 qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv----------~~~k~~~----------------~k~~ 307 (371)
T KOG3752|consen 254 QTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWV----------QGWKKNG----------------WKTS 307 (371)
T ss_pred ccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHH----------hhhccCc----------------cccc
Confidence 4556799999999999998899999999999988877765321 1112211 2222
Q ss_pred CCCceEEEEEeecCCCCccchHHHHHHhh
Q psy5156 181 SSQISIKFLWCPSHVGISGNDQADTEAKK 209 (389)
Q Consensus 181 ~~~~~i~~~wvp~H~g~~gNe~aD~~Ak~ 209 (389)
.....| -+--|...++||..|..++.
T Consensus 308 ~~~~~i---~~~v~n~~~~~e~~~l~q~~ 333 (371)
T KOG3752|consen 308 NGSDRI---CAYVKNQDFFNELDELEQEI 333 (371)
T ss_pred cCCCcc---ceeeecchHHHHHHHHHhhh
Confidence 222233 34468889999999998884
No 16
>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=64.24 E-value=8.2 Score=30.71 Aligned_cols=42 Identities=33% Similarity=0.379 Sum_probs=37.1
Q ss_pred cchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCC
Q psy5156 103 IPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYH 144 (389)
Q Consensus 103 i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ 144 (389)
...+|+.+++.+++.....+.+++.|.||+....+.+.+...
T Consensus 41 ~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~ 82 (130)
T cd06222 41 NNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYE 82 (130)
T ss_pred HHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcccc
Confidence 457899999999998888899999999999999999988764
No 17
>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=46.82 E-value=9.1 Score=31.86 Aligned_cols=37 Identities=32% Similarity=0.401 Sum_probs=27.8
Q ss_pred ccchhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhcc
Q psy5156 102 EIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISN 141 (389)
Q Consensus 102 ~i~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 141 (389)
....+|+.+|+.||+.. ..++++|+|||.+.++.+..
T Consensus 39 s~~~aEl~Ai~~AL~~~---~~~~v~I~tDS~~v~~~l~~ 75 (132)
T PF00075_consen 39 SNNRAELQAIIEALKAL---EHRKVTIYTDSQYVLNALNK 75 (132)
T ss_dssp CHHHHHHHHHHHHHHTH---STSEEEEEES-HHHHHHHHT
T ss_pred chhhhheehHHHHHHHh---hcccccccccHHHHHHHHHH
Confidence 34578999999999843 44899999999888776443
No 18
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=42.95 E-value=69 Score=27.93 Aligned_cols=54 Identities=19% Similarity=0.262 Sum_probs=38.6
Q ss_pred CCeEEEEEEecCCEEEEEecC--CCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCC
Q psy5156 29 TGVGCALIIPQLNVTKRFTLN--KYSSIFHAELFSILQSLKNAKLLNIKKVLIISDS 83 (389)
Q Consensus 29 ~~~G~avv~~~~~~~~~~~l~--~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDS 83 (389)
=.+|+++...++.+..+...+ ...--.-||-.||..|+.. -......+.+++|+
T Consensus 26 F~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 26 FKVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred CcEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 458999888877665554432 2334577999999999987 33345688899997
No 19
>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=39.45 E-value=34 Score=32.07 Aligned_cols=61 Identities=16% Similarity=0.200 Sum_probs=37.3
Q ss_pred CcEEEEEcCCccCCCeEEEEEEecCCEEEEEecCCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHH
Q psy5156 16 DFLKIYTDGSKDETGVGCALIIPQLNVTKRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSF 87 (389)
Q Consensus 16 ~~~~IyTDGS~~~~~~G~avv~~~~~~~~~~~l~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al 87 (389)
.--.||+|+.- .|+|+.+..+... +.....-.++.+||+|...|.-+. ..++ |.|||..|+
T Consensus 93 ~lc~VfaDATp----Tgwgi~i~~~~~~--~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vl 153 (245)
T PF00336_consen 93 GLCQVFADATP----TGWGISITGQRMR--GTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVL 153 (245)
T ss_pred CCCceeccCCC----CcceeeecCceee--eeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEE
Confidence 34568888773 3444444322222 222334568999999998877654 2344 889998765
No 20
>PRK08298 cytidine deaminase; Validated
Probab=36.18 E-value=88 Score=27.25 Aligned_cols=58 Identities=16% Similarity=0.166 Sum_probs=39.5
Q ss_pred EEcCCccCCCeEEEEEEecCCEEEEEecC--CCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCC
Q psy5156 21 YTDGSKDETGVGCALIIPQLNVTKRFTLN--KYSSIFHAELFSILQSLKNAKLLNIKKVLIISDS 83 (389)
Q Consensus 21 yTDGS~~~~~~G~avv~~~~~~~~~~~l~--~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDS 83 (389)
|...| ++|+|+...++++..+.... ...--.-||..||..|+..-. .....|.|.+|.
T Consensus 19 Y~PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G~-~~~~~i~v~~~~ 78 (136)
T PRK08298 19 YPNGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQK-RVTHSICVAREN 78 (136)
T ss_pred cCCCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCCC-ceEEEEEEEcCC
Confidence 55555 79999999888877666553 233467899999998875421 124566777775
No 21
>PRK13907 rnhA ribonuclease H; Provisional
Probab=34.96 E-value=32 Score=28.77 Aligned_cols=40 Identities=28% Similarity=0.254 Sum_probs=35.7
Q ss_pred hhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhccCCC
Q psy5156 105 HAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYH 144 (389)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~ 144 (389)
.+|+.+++.+|+-...++.+.++|.|||.--.+.+.+.+.
T Consensus 43 ~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~ 82 (128)
T PRK13907 43 EAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYA 82 (128)
T ss_pred HHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHh
Confidence 5789999999999999999999999999999999887654
No 22
>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=34.66 E-value=21 Score=26.32 Aligned_cols=21 Identities=29% Similarity=0.518 Sum_probs=10.0
Q ss_pred CCCcCCCCCcccchhhcccCC
Q psy5156 297 PICDSCHEPVTVEHIILHCNK 317 (389)
Q Consensus 297 p~C~~Cg~~eT~~HiL~~Cp~ 317 (389)
-.|+.||...+-.|...+||.
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 489999999899999999995
No 23
>PRK06848 hypothetical protein; Validated
Probab=31.30 E-value=92 Score=27.18 Aligned_cols=55 Identities=16% Similarity=0.147 Sum_probs=37.1
Q ss_pred CCCeEEEEEEecCCEEEEEecC--CCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCC
Q psy5156 28 ETGVGCALIIPQLNVTKRFTLN--KYSSIFHAELFSILQSLKNAKLLNIKKVLIISDS 83 (389)
Q Consensus 28 ~~~~G~avv~~~~~~~~~~~l~--~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDS 83 (389)
+..+|+++...++.+..+.... ......-||-.||..|+..-. .....+.+.+++
T Consensus 26 ~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~g~-~~i~~i~~v~~~ 82 (139)
T PRK06848 26 WHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISEGD-HEIDTIVAVRHP 82 (139)
T ss_pred CCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHcCC-CceEEEEEEecC
Confidence 3679999999888877666553 233456899999999886421 123456566554
No 24
>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=26.61 E-value=3.3e+02 Score=27.22 Aligned_cols=38 Identities=16% Similarity=0.294 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHhc---CCceEEEEcCCHHHHHHHhcCCCC
Q psy5156 59 LFSILQSLKNAKLL---NIKKVLIISDSLSSFQAISNLYHP 96 (389)
Q Consensus 59 l~AI~~AL~~a~~~---~~~~i~I~sDSq~al~~l~~~~~~ 96 (389)
+.-+..+++.++.. ...+|.+.|||+.++..++...+.
T Consensus 196 L~~V~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~~FPd 236 (321)
T PF05830_consen 196 LRQVCTAIDKAKALAPPKPVRIFLATDSAEVIDQFRKKFPD 236 (321)
T ss_dssp HHHHHHHHHHHHTS--SS-EEEEEEES-HHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhccCCCCeeEEEecCcHHHHHHHHHHCCC
Confidence 34445666665543 235677889999999999988774
No 25
>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=26.44 E-value=1.7e+02 Score=24.83 Aligned_cols=54 Identities=15% Similarity=0.185 Sum_probs=36.3
Q ss_pred CCeEEEEEEecCCEEEEEecC--CCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCC
Q psy5156 29 TGVGCALIIPQLNVTKRFTLN--KYSSIFHAELFSILQSLKNAKLLNIKKVLIISDS 83 (389)
Q Consensus 29 ~~~G~avv~~~~~~~~~~~l~--~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDS 83 (389)
..+|++++..++++..+.... ...-...||..||..|...-.. ....+.|..+.
T Consensus 21 ~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~~-~i~~i~vv~~~ 76 (127)
T TIGR01354 21 FKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGYR-KFVAIAVADSA 76 (127)
T ss_pred CeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCCC-CeEEEEEEeCC
Confidence 358888877777776655443 2233567999999998875322 45688888775
No 26
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=24.51 E-value=71 Score=34.88 Aligned_cols=23 Identities=30% Similarity=0.540 Sum_probs=20.2
Q ss_pred CCCceEEEEEeecCCCCccchHH
Q psy5156 181 SSQISIKFLWCPSHVGISGNDQA 203 (389)
Q Consensus 181 ~~~~~i~~~wvp~H~g~~gNe~a 203 (389)
+.|+-|-+-|||+|.+..||-.+
T Consensus 225 ~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 225 QAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HcCCEEEEEecCCcCCCCcchhh
Confidence 46899999999999999888654
No 27
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=24.51 E-value=44 Score=18.70 Aligned_cols=17 Identities=35% Similarity=0.675 Sum_probs=13.0
Q ss_pred CCcCCCCCcccchhhcccCC
Q psy5156 298 ICDSCHEPVTVEHIILHCNK 317 (389)
Q Consensus 298 ~C~~Cg~~eT~~HiL~~Cp~ 317 (389)
.|..|| ...|+..+||.
T Consensus 2 ~C~~C~---~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCG---EPGHIARDCPK 18 (18)
T ss_dssp BCTTTS---CSSSCGCTSSS
T ss_pred cCcCCC---CcCcccccCcc
Confidence 577787 56799889984
No 28
>PRK06548 ribonuclease H; Provisional
Probab=23.82 E-value=39 Score=30.31 Aligned_cols=36 Identities=25% Similarity=0.303 Sum_probs=26.2
Q ss_pred hhhHHHHHHHhhhHHHhhhhhhhhhcccchhhhhhcc
Q psy5156 105 HAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISN 141 (389)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 141 (389)
.+||.+|++||+.... ...+++|+|||.-+++++..
T Consensus 44 raEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~ 79 (161)
T PRK06548 44 IAELTAVRELLIATRH-TDRPILILSDSKYVINSLTK 79 (161)
T ss_pred HHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHH
Confidence 3689999998865432 23468999999888877653
No 29
>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=22.51 E-value=2.8e+02 Score=22.59 Aligned_cols=59 Identities=10% Similarity=0.071 Sum_probs=35.3
Q ss_pred CCeEEEEEEecCCEE-EEEec--CCCCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCHHHH
Q psy5156 29 TGVGCALIIPQLNVT-KRFTL--NKYSSIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSF 87 (389)
Q Consensus 29 ~~~G~avv~~~~~~~-~~~~l--~~~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq~al 87 (389)
..+|+.+|..++++. ..+.- ........||..||..+.+..........++|+.-+...
T Consensus 17 ~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~EPC~ 78 (109)
T cd01285 17 VPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCP 78 (109)
T ss_pred CcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCCChH
Confidence 456776665544442 22221 123457889999999988865433346677777655443
No 30
>PRK05578 cytidine deaminase; Validated
Probab=22.38 E-value=2e+02 Score=24.80 Aligned_cols=54 Identities=15% Similarity=0.214 Sum_probs=37.8
Q ss_pred CeEEEEEEecCCEEEEEecCC--CCchhHHhHHHHHHHHHHHHhcCCceEEEEcCCH
Q psy5156 30 GVGCALIIPQLNVTKRFTLNK--YSSIFHAELFSILQSLKNAKLLNIKKVLIISDSL 84 (389)
Q Consensus 30 ~~G~avv~~~~~~~~~~~l~~--~~t~~~AEl~AI~~AL~~a~~~~~~~i~I~sDSq 84 (389)
.+|+++...+|++..+..... ..-..-||..||..|+..-. .....++|.+|+.
T Consensus 25 ~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G~-~~i~~i~vv~~~~ 80 (131)
T PRK05578 25 PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGG-GRLVAIACVGETG 80 (131)
T ss_pred ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHcCC-CceEEEEEEecCC
Confidence 599999888888877666542 22356789999999875321 2456788888763
Done!