Query psy16039
Match_columns 586
No_of_seqs 345 out of 2696
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 19:17:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16039.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16039hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.8 1.8E-20 3.9E-25 170.7 14.4 126 412-538 3-146 (154)
2 PRK06548 ribonuclease H; Provi 99.8 2.5E-20 5.5E-25 172.9 14.9 127 411-539 4-144 (161)
3 PRK08719 ribonuclease H; Revie 99.8 5E-20 1.1E-24 169.5 14.1 121 411-536 3-146 (147)
4 PF00075 RNase_H: RNase H; In 99.8 1.9E-20 4.2E-25 169.5 11.1 121 411-535 2-131 (132)
5 PRK00203 rnhA ribonuclease H; 99.8 3E-19 6.6E-24 165.6 14.0 126 412-540 3-145 (150)
6 cd06222 RnaseH RNase H (RNase 99.7 2.6E-16 5.6E-21 139.4 14.0 122 414-535 1-130 (130)
7 PRK13907 rnhA ribonuclease H; 99.6 1.4E-15 3E-20 137.3 11.9 120 413-536 2-126 (128)
8 KOG3752|consensus 99.6 1.9E-15 4E-20 153.6 12.3 127 410-536 210-364 (371)
9 PRK07708 hypothetical protein; 99.5 8.9E-13 1.9E-17 129.0 15.5 128 408-539 69-210 (219)
10 PRK07238 bifunctional RNase H/ 99.3 1.1E-11 2.3E-16 132.3 14.0 122 412-538 2-133 (372)
11 cd01650 RT_nLTR_like RT_nLTR: 99.3 8.9E-13 1.9E-17 129.8 2.0 109 70-198 106-220 (220)
12 PF13456 RVT_3: Reverse transc 99.2 7.6E-11 1.7E-15 98.2 9.9 86 447-536 1-86 (87)
13 cd01648 TERT TERT: Telomerase 99.1 4.1E-11 8.8E-16 106.7 1.4 106 60-199 9-119 (119)
14 PF00078 RVT_1: Reverse transc 99.0 1.1E-11 2.3E-16 120.9 -3.3 116 38-198 98-214 (214)
15 cd01651 RT_G2_intron RT_G2_int 98.9 2.7E-10 6E-15 112.3 1.5 98 62-198 118-226 (226)
16 cd01646 RT_Bac_retron_I RT_Bac 98.8 2.6E-09 5.6E-14 100.0 2.0 102 63-201 46-147 (158)
17 cd03487 RT_Bac_retron_II RT_Ba 98.7 3.9E-09 8.5E-14 103.9 2.7 98 66-201 99-198 (214)
18 cd00304 RT_like RT_like: Rever 98.4 1.1E-07 2.5E-12 81.0 2.1 87 71-198 12-98 (98)
19 cd01709 RT_like_1 RT_like_1: A 98.3 2.4E-06 5.2E-11 87.9 8.7 125 65-214 78-210 (346)
20 cd01645 RT_Rtv RT_Rtv: Reverse 96.8 0.00032 7E-09 68.9 0.2 74 69-163 127-201 (213)
21 cd03714 RT_DIRS1 RT_DIRS1: Rev 96.8 0.00069 1.5E-08 60.1 1.9 70 71-164 34-106 (119)
22 cd03715 RT_ZFREV_like RT_ZFREV 95.4 0.0059 1.3E-07 59.8 1.2 86 70-198 124-210 (210)
23 KOG4768|consensus 94.9 0.054 1.2E-06 59.3 6.7 129 109-251 503-640 (796)
24 PF09004 DUF1891: Domain of un 91.7 0.036 7.8E-07 39.3 -0.7 42 204-247 1-42 (42)
25 cd01647 RT_LTR RT_LTR: Reverse 90.8 0.19 4.2E-06 46.4 3.0 72 69-164 94-165 (177)
26 KOG1005|consensus 90.8 0.19 4E-06 57.4 3.2 105 38-173 611-718 (888)
27 PF05380 Peptidase_A17: Pao re 81.5 4.4 9.6E-05 37.7 6.6 52 411-464 80-143 (159)
28 cd01644 RT_pepA17 RT_pepA17: R 58.3 3.6 7.9E-05 40.4 0.3 68 70-156 103-173 (213)
29 PF00336 DNA_pol_viral_C: DNA 55.4 16 0.00034 35.2 4.0 62 410-480 92-153 (245)
30 KOG1812|consensus 33.9 88 0.0019 33.7 6.1 90 445-537 47-138 (384)
31 COG3341 Predicted double-stran 33.1 45 0.00097 32.5 3.3 95 445-543 106-207 (225)
32 PF15364 PAXIP1_C: PAXIP1-asso 31.1 81 0.0018 28.8 4.4 57 493-551 21-89 (141)
33 cd01699 RNA_dep_RNAP RNA_dep_R 22.7 27 0.00058 35.2 -0.2 45 107-165 195-239 (278)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.85 E-value=1.8e-20 Score=170.73 Aligned_cols=126 Identities=20% Similarity=0.166 Sum_probs=102.3
Q ss_pred ceEEEEcCCCCC--CCceeEEecC--Cee--EEeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhc
Q psy16039 412 SVLCFTDGSKTV--NSTSCAYSIG--NQV--HAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISN 485 (586)
Q Consensus 412 ~~~iytDGS~~~--~~~G~av~~~--~~~--~~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~ 485 (586)
.+.||||||+.. |..|+|++.. +.. .+.... .+|+++||++|++.||+.+.+.+...|.|+|||++++++|..
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~ 81 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR 81 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence 578999999884 4477776553 222 233334 789999999999999999999889999999999999999972
Q ss_pred C---CCCC--------c-cHHHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHHHHHHHhhhccCC
Q psy16039 486 C---KNDH--------P-LVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNI 538 (586)
Q Consensus 486 ~---~~~~--------~-~~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~~~ 538 (586)
. +... | .-.++|+++.++..+...|.+.|||||+|.++||.||+||++|++..
T Consensus 82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 2 1111 2 24678899999988888999999999999999999999999999765
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.84 E-value=2.5e-20 Score=172.89 Aligned_cols=127 Identities=17% Similarity=0.231 Sum_probs=96.7
Q ss_pred CceEEEEcCCCCC--CCceeEEecCCeeEEeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhc---
Q psy16039 411 DSVLCFTDGSKTV--NSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISN--- 485 (586)
Q Consensus 411 ~~~~iytDGS~~~--~~~G~av~~~~~~~~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~--- 485 (586)
..+.||||||+.. +..|+|++..+......-....|+++||++|++.||+.+.. ....|.|+|||+++++++..
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~ 82 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVY 82 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHH
Confidence 3489999999884 45788877653321111123579999999999999986643 44679999999999999973
Q ss_pred -----CCCC-C--ccH-HHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHHHHHHHhhhccCCC
Q psy16039 486 -----CKND-H--PLV-SLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNIT 539 (586)
Q Consensus 486 -----~~~~-~--~~~-~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~~~~ 539 (586)
++.. + ++. +++++++.++... ..|+|.|||||+|.+|||.||+||++|+....
T Consensus 83 ~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~ 144 (161)
T PRK06548 83 SWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFS 144 (161)
T ss_pred HHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence 3322 2 343 7777888887654 58999999999999999999999999986544
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.83 E-value=5e-20 Score=169.47 Aligned_cols=121 Identities=18% Similarity=0.191 Sum_probs=92.6
Q ss_pred CceEEEEcCCCCCCC-----ceeEEec--CC-e-e--EEeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHH
Q psy16039 411 DSVLCFTDGSKTVNS-----TSCAYSI--GN-Q-V--HAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSA 479 (586)
Q Consensus 411 ~~~~iytDGS~~~~~-----~G~av~~--~~-~-~--~~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~a 479 (586)
..+.||||||+..++ .|+|++. ++ . . ....+....|+++||+.|+..||+.+.+. ..|+|||+++
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 457999999997433 4777654 22 1 2 23334555799999999999999999653 3799999999
Q ss_pred HHHH--------hcCCCCCc---c-HHHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHHHHHHHhhhcc
Q psy16039 480 LLAI--------SNCKNDHP---L-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPIT 536 (586)
Q Consensus 480 l~~i--------~~~~~~~~---~-~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~ 536 (586)
++++ ++++..+. + -.++++.+..+.. ...|+|+|||||+|++|||.||+||++|++
T Consensus 79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9998 45554431 1 2566677777754 677999999999999999999999999874
No 4
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.83 E-value=1.9e-20 Score=169.50 Aligned_cols=121 Identities=26% Similarity=0.378 Sum_probs=88.5
Q ss_pred CceEEEEcCCCC--CCCceeEEe-cCCeeEEeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhc--
Q psy16039 411 DSVLCFTDGSKT--VNSTSCAYS-IGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISN-- 485 (586)
Q Consensus 411 ~~~~iytDGS~~--~~~~G~av~-~~~~~~~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~-- 485 (586)
+.+.||||||.. ++..|+|++ ..+......++ ..++++||++|+..||+ +. ..++++|+|||++++..+..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~--~~~~v~I~tDS~~v~~~l~~~~ 77 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-AL--EHRKVTIYTDSQYVLNALNKWL 77 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-TH--STSEEEEEES-HHHHHHHHTHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hh--hcccccccccHHHHHHHHHHhc
Confidence 468999999966 333466653 33433445556 78999999999999999 44 34999999999999998876
Q ss_pred ---CCCCCccHHHHHHHHHHHHhCCCcEEEEEcCCCCCC-hhhHHHHHHHhhhc
Q psy16039 486 ---CKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGI-TGNELVDIAARNPI 535 (586)
Q Consensus 486 ---~~~~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi-~gNe~AD~lAk~a~ 535 (586)
.+........++..+.++...+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus 78 ~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 78 HGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 333222111222333443356899999999999999 69999999999987
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.81 E-value=3e-19 Score=165.62 Aligned_cols=126 Identities=21% Similarity=0.190 Sum_probs=94.0
Q ss_pred ceEEEEcCCCCC--CCceeEEec--CCeeE-EeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhc-
Q psy16039 412 SVLCFTDGSKTV--NSTSCAYSI--GNQVH-AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISN- 485 (586)
Q Consensus 412 ~~~iytDGS~~~--~~~G~av~~--~~~~~-~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~- 485 (586)
.+.||||||+.. +..|+|++. ++... ........|+++|||+|+..||+.+.+ ...+.|+|||+++++.|..
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 478999999874 346777654 33222 112234678999999999999998864 4689999999999999875
Q ss_pred -------CCCC---Ccc-HHHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHHHHHHHhhhccCCCC
Q psy16039 486 -------CKND---HPL-VSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITL 540 (586)
Q Consensus 486 -------~~~~---~~~-~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~~~~~ 540 (586)
++.. .++ -.++++.+.++. ....|.|.|||||+|++|||.||+|||+|+.....
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~ 145 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEEATL 145 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHhhh
Confidence 2221 122 245567777664 34789999999999999999999999999976553
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=99.70 E-value=2.6e-16 Score=139.39 Aligned_cols=122 Identities=20% Similarity=0.266 Sum_probs=98.1
Q ss_pred EEEEcCCCCCC--CceeEEecCCe--eE---EeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhcC
Q psy16039 414 LCFTDGSKTVN--STSCAYSIGNQ--VH---AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNC 486 (586)
Q Consensus 414 ~iytDGS~~~~--~~G~av~~~~~--~~---~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~~ 486 (586)
.+|||||...+ +.|+|++..+. .. ........+++.+|+.|+..||+.+...+..++.|++||+.++..+.+.
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 38999998854 68888766332 11 1112246799999999999999999988899999999999999999987
Q ss_pred CC-CCccHHHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHHHHHHHhhhc
Q psy16039 487 KN-DHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPI 535 (586)
Q Consensus 487 ~~-~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~ 535 (586)
.. .......+++.+.++......+.|.|||+|+|+.+|+.||.|||+|+
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 65 22335555577777667889999999999999999999999999874
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.64 E-value=1.4e-15 Score=137.31 Aligned_cols=120 Identities=17% Similarity=0.128 Sum_probs=97.2
Q ss_pred eEEEEcCCCCC--CCceeEEecCCeeE--Eee-cCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhcCC
Q psy16039 413 VLCFTDGSKTV--NSTSCAYSIGNQVH--AFK-LNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCK 487 (586)
Q Consensus 413 ~~iytDGS~~~--~~~G~av~~~~~~~--~~~-l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~~~ 487 (586)
+.||||||+.. +..|+|++..+... ... .....+++.||+.|++.||+.+.+.+..++.|+|||+.+++.+++.+
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 57999999874 45888877643211 111 12457899999999999999999988899999999999999999876
Q ss_pred CCCccHHHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHHHHHHHhhhcc
Q psy16039 488 NDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPIT 536 (586)
Q Consensus 488 ~~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~ 536 (586)
....-...+++.+..+......+.|.|||. +.|+.||.||+.|+.
T Consensus 82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 555456667788888878888889999995 689999999999974
No 8
>KOG3752|consensus
Probab=99.63 E-value=1.9e-15 Score=153.63 Aligned_cols=127 Identities=20% Similarity=0.175 Sum_probs=99.2
Q ss_pred CCceEEEEcCCCCCCC-----ceeEEecCCe---eEEeecC-CCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHH
Q psy16039 410 SDSVLCFTDGSKTVNS-----TSCAYSIGNQ---VHAFKLN-KVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSAL 480 (586)
Q Consensus 410 ~~~~~iytDGS~~~~~-----~G~av~~~~~---~~~~~l~-~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al 480 (586)
.+.+.+|||||+..+| +|+||+.++. -.++.+. ...++++|||.|+..||+.|.+....+++|.|||.+++
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 4458999999988643 8999999753 2455664 77899999999999999999998888999999999999
Q ss_pred HHHhcC---CCC--------Cc----c--HHHHHHHHHHHHhC--CCcEEEEEcCCCCCChhhHHHHHHHhhhcc
Q psy16039 481 LAISNC---KND--------HP----L--VSLVYTTWLEAKDC--GKNLNFVWCPSHCGITGNELVDIAARNPIT 536 (586)
Q Consensus 481 ~~i~~~---~~~--------~~----~--~~~i~~~~~~l~~~--~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~ 536 (586)
++++.. +.. ++ + -+..+..+.+|.+. ..+|.+.||+||.|+.|||.||.||+++..
T Consensus 290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 998642 111 11 1 12223455555433 699999999999999999999999999853
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.47 E-value=8.9e-13 Score=129.04 Aligned_cols=128 Identities=12% Similarity=0.021 Sum_probs=95.0
Q ss_pred cCCCceEEEEcCCCC--CCCceeEEec--CCe--eE----EeecCCCcchhHHHHHHHHHHHHHhhhCCCCe--EEEEeC
Q psy16039 408 KYSDSVLCFTDGSKT--VNSTSCAYSI--GNQ--VH----AFKLNKVNSVLSSELMAILLCVKNLIFLPSTN--FTLISD 475 (586)
Q Consensus 408 ~~~~~~~iytDGS~~--~~~~G~av~~--~~~--~~----~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~--i~I~sD 475 (586)
..++.+.+|+|||.. ++++|+|++. .+. .. ...++...+++.||+.|++.||+.|.+.+.+. |.|++|
T Consensus 69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D 148 (219)
T PRK07708 69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD 148 (219)
T ss_pred cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence 345679999999976 4567888654 221 11 12345557999999999999999999987654 899999
Q ss_pred cHHHHHHHhcCCCCC-ccHHHHHHHHHHHHhC-CCcEEEEEcCCCCCChhhHHHHHHHhhhccCCC
Q psy16039 476 SMSALLAISNCKNDH-PLVSLVYTTWLEAKDC-GKNLNFVWCPSHCGITGNELVDIAARNPITNIT 539 (586)
Q Consensus 476 S~~al~~i~~~~~~~-~~~~~i~~~~~~l~~~-~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~~~~ 539 (586)
|+.+++++.+.+... +-....++.+..+... ...+.+.||| +..|+.||+||++|+....
T Consensus 149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV 210 (219)
T ss_pred cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence 999999999877553 3444454555554333 3457889998 7889999999999997544
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.33 E-value=1.1e-11 Score=132.29 Aligned_cols=122 Identities=16% Similarity=0.142 Sum_probs=96.7
Q ss_pred ceEEEEcCCCCCC--CceeEEecCC---e-e-E--EeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHH
Q psy16039 412 SVLCFTDGSKTVN--STSCAYSIGN---Q-V-H--AFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLA 482 (586)
Q Consensus 412 ~~~iytDGS~~~~--~~G~av~~~~---~-~-~--~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~ 482 (586)
.+.||||||+..+ ..|+|++..+ . . . ...++ ..+++.||+.|++.||+.+.+.+.+++.|++||+.+++.
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 3689999998854 5788876532 1 1 1 22233 578899999999999999999888999999999999999
Q ss_pred HhcCCC-CCccHHHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHHHHHHHhhhccCC
Q psy16039 483 ISNCKN-DHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNI 538 (586)
Q Consensus 483 i~~~~~-~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~AD~lAk~a~~~~ 538 (586)
+.+.+. +++-...++..+..+.++...+.+.||| .++|+.||.||+.|+...
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIP----RARNAHADRLANEAMDAA 133 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECC----chhhhHHHHHHHHHHHhh
Confidence 988764 3344555557778887888999999999 478999999999997443
No 11
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=99.28 E-value=8.9e-13 Score=129.76 Aligned_cols=109 Identities=17% Similarity=0.156 Sum_probs=83.7
Q ss_pred CCCCCCcccCCCCccccceeeeeccCCCCCc------ccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHH
Q psy16039 70 TRPQPVATHCCLGLTGRLSASVRQTARTPLS------RADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDE 143 (586)
Q Consensus 70 GvPQGs~~~~~~~vLsPlLf~~~~~~~~~~~------~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~ 143 (586)
|+|||+ +|||+||++......... ...........||||+.++.... + ..++..++.
T Consensus 106 GipQG~-------~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~~--------~--~~~~~~~~~ 168 (220)
T cd01650 106 GVRQGD-------PLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGK--------S--RKLQELLQR 168 (220)
T ss_pred CCccCC-------cccHHHHHHHHHHHHHHHHhhccccCCCCccceEEeccceeeeccCC--------H--HHHHHHHHH
Confidence 999999 999999993221100000 01123456899999999975432 1 588999999
Q ss_pred HHHHHHhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEe
Q psy16039 144 VLKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVW 198 (586)
Q Consensus 144 l~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~l 198 (586)
+..|+.++|+++| ++||+++.++...... ..+.+++..+..++.+||||+.|
T Consensus 169 ~~~~~~~~gl~in--~~Kt~~~~~~~~~~~~-~~~~~~~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 169 LQEWSKESGLKIN--PSKSKVMLIGNKKKRL-KDITLNGTPIEAVETFKYLGVTI 220 (220)
T ss_pred HHHHHHHcCCEEC--hhheEEEEecCCCcch-hhhhhcCCcccCCCCCeeccccC
Confidence 9999999999999 9999999998876653 33778888999999999999875
No 12
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.21 E-value=7.6e-11 Score=98.21 Aligned_cols=86 Identities=19% Similarity=0.118 Sum_probs=71.6
Q ss_pred hhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhcCCCCCccHHHHHHHHHHHHhCCCcEEEEEcCCCCCChhhHH
Q psy16039 447 VLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNEL 526 (586)
Q Consensus 447 v~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~~~~~~~~~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~gNe~ 526 (586)
+..||+.|+..||+.+.+.+.+++.|+|||+.++..+++..........++..+..+.+....+.+.||| .++|..
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~ 76 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV 76 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence 4689999999999999999999999999999999999988554435666668899988899999999999 999999
Q ss_pred HHHHHhhhcc
Q psy16039 527 VDIAARNPIT 536 (586)
Q Consensus 527 AD~lAk~a~~ 536 (586)
||.|||.|.+
T Consensus 77 A~~LA~~a~~ 86 (87)
T PF13456_consen 77 ADALAKFALS 86 (87)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHhh
Confidence 9999999863
No 13
>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at
Probab=99.06 E-value=4.1e-11 Score=106.70 Aligned_cols=106 Identities=16% Similarity=-0.024 Sum_probs=73.2
Q ss_pred ccccccccCCCCCCCCcccCCCCccccceeeeecc--CCCCCcc--cCcCCceeEEeeccchhhhhcccccccchHHHHH
Q psy16039 60 SLLTRSPLGLTRPQPVATHCCLGLTGRLSASVRQT--ARTPLSR--ADVGRDSLRSAADRKDVIRFFFREEKREMGDKKI 135 (586)
Q Consensus 60 ~~S~~~~~~~GvPQGs~~~~~~~vLsPlLf~~~~~--~~~~~~~--~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~ 135 (586)
+++..+..+.|+|||+ +|||+||++... ....... ..........||||+.++... ..
T Consensus 9 ~~~~~~~~~~GlpQG~-------~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~-----------~~ 70 (119)
T cd01648 9 SIPQYYRQKVGIPQGS-------PLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTS-----------LD 70 (119)
T ss_pred chhhhhhhcCcccCCc-------chHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCC-----------HH
Confidence 4555677889999999 999999992210 0000000 011234578899999776432 25
Q ss_pred HHHHHHHHHHHHH-HhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEec
Q psy16039 136 LFRKTLDEVLKWS-QANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVWD 199 (586)
Q Consensus 136 ~lq~~l~~l~~W~-~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~ld 199 (586)
.+++.++.+..|. .+.||.+| ++||+....... ......+.|||+.||
T Consensus 71 ~~~~~~~~l~~~l~~~~gl~iN--~~Kt~~~~~~~~--------------~~~~~~~~flG~~i~ 119 (119)
T cd01648 71 KAIKFLNLLLRGFINQYKTFVN--FDKTQINFSFAQ--------------LDSSDLIPWCGLLIN 119 (119)
T ss_pred HHHHHHHHHHHhhHHhhCeEEC--cccceeeccccc--------------cCCCCccCceeEeeC
Confidence 6788999999997 99999999 999998865431 123356999999875
No 14
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase 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. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=99.04 E-value=1.1e-11 Score=120.87 Aligned_cols=116 Identities=22% Similarity=0.173 Sum_probs=85.7
Q ss_pred hhhcccccCceeEEEECCeeccccccccccCCCCCCCCcccCCCCccccceeeeeccCCCCCcccC-cCCceeEEeeccc
Q psy16039 38 STLSPYLSRHTDMLCRGTRIWRSLLTRSPLGLTRPQPVATHCCLGLTGRLSASVRQTARTPLSRAD-VGRDSLRSAADRK 116 (586)
Q Consensus 38 ~~i~syL~~R~~~V~~~~~~~~~~S~~~~~~~GvPQGs~~~~~~~vLsPlLf~~~~~~~~~~~~~~-~~~~~~~~yADD~ 116 (586)
.|+.+++.++...+.+++ .. .......|+|||+ ++||+||++............ ...+....||||+
T Consensus 98 ~~i~~~~~~~~~~~~~~~----~~-~~~~~~~glpqG~-------~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~DD~ 165 (214)
T PF00078_consen 98 RLIQNLLSDRTAKVYLDG----DL-SPYFQKRGLPQGS-------PLSPLLFNIYLDDLDRELQQELNPDISYLRYADDI 165 (214)
T ss_dssp HHHHHHHHHHHH-EECGC----SS-SEEEEESBS-TTS-------TCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETTEE
T ss_pred cccccccccccccccccc----cc-ccccccccccccc-------cccchhhccccccccccccccccccccceEecccc
Confidence 688999999999999877 54 6777899999999 999999993221000000000 1234589999999
Q ss_pred hhhhhcccccccchHHHHHHHHHHHHHHHHHHHhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEE
Q psy16039 117 DVIRFFFREEKREMGDKKILFRKTLDEVLKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGL 196 (586)
Q Consensus 117 ~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV 196 (586)
.++... ...+++.++.+.+|++++||.+| ++||+.++ ..++++|||+
T Consensus 166 ~i~~~~-----------~~~~~~~~~~i~~~~~~~gl~ln--~~Kt~~~~--------------------~~~~~~~lG~ 212 (214)
T PF00078_consen 166 LIISKS-----------KEELQKILEKISQWLEELGLKLN--PEKTKILH--------------------PSDSVKFLGY 212 (214)
T ss_dssp EEEESS-----------HHHHHHHHHHHHHHHHHTTSBCS--STTTSCS----------------------ESSEEETTE
T ss_pred EEEECC-----------HHHHHHHHHHHHHHHHHCCCEEC--hHHEEEEe--------------------CCCCEEEEeE
Confidence 987532 24589999999999999999999 99999776 5688999998
Q ss_pred Ee
Q psy16039 197 VW 198 (586)
Q Consensus 197 ~l 198 (586)
.|
T Consensus 213 ~i 214 (214)
T PF00078_consen 213 VI 214 (214)
T ss_dssp EE
T ss_pred EC
Confidence 75
No 15
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=98.92 E-value=2.7e-10 Score=112.34 Aligned_cols=98 Identities=15% Similarity=0.049 Sum_probs=71.1
Q ss_pred ccccccCCCCCCCCcccCCCCccccceeeeeccCC--CCCc---------ccCcCCceeEEeeccchhhhhcccccccch
Q psy16039 62 LTRSPLGLTRPQPVATHCCLGLTGRLSASVRQTAR--TPLS---------RADVGRDSLRSAADRKDVIRFFFREEKREM 130 (586)
Q Consensus 62 S~~~~~~~GvPQGs~~~~~~~vLsPlLf~~~~~~~--~~~~---------~~~~~~~~~~~yADD~~i~~~~~~~~g~~~ 130 (586)
+.......|+|||+ ++||+||++..... .... ...........||||+.++....
T Consensus 118 ~~~~~~~~GlpqG~-------~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~------- 183 (226)
T cd01651 118 GKLVETEKGTPQGG-------VISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGP------- 183 (226)
T ss_pred CeEeCCCCCcCCCc-------cHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCCH-------
Confidence 34567889999999 99999999322100 0000 00113456889999999975322
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEe
Q psy16039 131 GDKKILFRKTLDEVLKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVW 198 (586)
Q Consensus 131 ~~~~~~lq~~l~~l~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~l 198 (586)
..+++.++.+..|+++.||.+| ++||+++.|+ .+.+.|||..|
T Consensus 184 ----~~~~~~~~~i~~~~~~~gl~ln--~~Kt~i~~~~-------------------~~~~~fLG~~~ 226 (226)
T cd01651 184 ----KEAEEIKELIREFLEELGLELN--PEKTRITHFK-------------------SEGFDFLGFTF 226 (226)
T ss_pred ----HHHHHHHHHHHHHHHHcCCeec--hhhcceeecC-------------------CCCCeeCCeEC
Confidence 2388899999999999999999 9999999996 35677888754
No 16
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=98.76 E-value=2.6e-09 Score=100.00 Aligned_cols=102 Identities=15% Similarity=0.096 Sum_probs=72.2
Q ss_pred cccccCCCCCCCCcccCCCCccccceeeeeccCCCCCcccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHH
Q psy16039 63 TRSPLGLTRPQPVATHCCLGLTGRLSASVRQTARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLD 142 (586)
Q Consensus 63 ~~~~~~~GvPQGs~~~~~~~vLsPlLf~~~~~~~~~~~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~ 142 (586)
.......|+|||+ ++||+|+++....................||||+.++.... ..+++.++
T Consensus 46 ~~~~~~~GlpqG~-------~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~-----------~~~~~~~~ 107 (158)
T cd01646 46 SQYGQTNGLPIGP-------LTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSK-----------EEAEEILE 107 (158)
T ss_pred ccCCCCceEccCc-------chHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCH-----------HHHHHHHH
Confidence 4456778999999 99999999322100000000023456889999999875322 45688999
Q ss_pred HHHHHHHhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEecCC
Q psy16039 143 EVLKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVWDSK 201 (586)
Q Consensus 143 ~l~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~ld~~ 201 (586)
.+.+|..+.||.+| ++||+.+.++... ..+.+||..+...
T Consensus 108 ~i~~~l~~~gL~ln--~~Kt~~~~~~~~~-----------------~~~~flg~~~~~~ 147 (158)
T cd01646 108 ELKEFLAELGLSLN--LSKTEILPLPEGT-----------------ASKDFLGYRFSPI 147 (158)
T ss_pred HHHHHHHHCCCEEC--hhhceeeecCCCC-----------------ccccccceEeehh
Confidence 99999999999999 9999999986432 5567777777543
No 17
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=98.74 E-value=3.9e-09 Score=103.86 Aligned_cols=98 Identities=13% Similarity=-0.024 Sum_probs=68.6
Q ss_pred ccCCCCCCCCcccCCCCccccceeeeeccCCCCC--cccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHH
Q psy16039 66 PLGLTRPQPVATHCCLGLTGRLSASVRQTARTPL--SRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDE 143 (586)
Q Consensus 66 ~~~~GvPQGs~~~~~~~vLsPlLf~~~~~~~~~~--~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~ 143 (586)
....|+|||+ ++||+||++........ .......+....||||+.++.... .+ ..+++.++.
T Consensus 99 ~~~~GlpQG~-------~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaDD~~i~~~~~-------~~--~~~~~~~~~ 162 (214)
T cd03487 99 TYNGHLPQGA-------PTSPALSNLVFRKLDERLSKLAKSNGLTYTRYADDITFSSNKK-------LK--EALDKLLEI 162 (214)
T ss_pred hCCCCcCCCC-------cccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEeccEEEEcccc-------ch--hHHHHHHHH
Confidence 3455999999 99999999322110000 001112345789999998864321 11 478889999
Q ss_pred HHHHHHhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEecCC
Q psy16039 144 VLKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVWDSK 201 (586)
Q Consensus 144 l~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~ld~~ 201 (586)
+..|+.+.||.+| ++||+++..+ +...+||+.+.+.
T Consensus 163 i~~~l~~~gL~ln--~~Kt~i~~~~--------------------~~~~~~G~~i~~~ 198 (214)
T cd03487 163 IRSILSEEGFKIN--KSKTRISSKG--------------------SRQIVTGLVVNNG 198 (214)
T ss_pred HHHHHHHCCceeC--CCceEEccCC--------------------CCcEEEEEEEeCC
Confidence 9999999999999 9999988753 3456888888765
No 18
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=98.40 E-value=1.1e-07 Score=81.01 Aligned_cols=87 Identities=18% Similarity=0.059 Sum_probs=61.0
Q ss_pred CCCCCcccCCCCccccceeeeeccCCCCCcccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHHHHHh
Q psy16039 71 RPQPVATHCCLGLTGRLSASVRQTARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLKWSQA 150 (586)
Q Consensus 71 vPQGs~~~~~~~vLsPlLf~~~~~~~~~~~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W~~~ 150 (586)
+|||+ ++||.||+.....................|+||+.+... +. .++..++.+..|+.+
T Consensus 12 lPqG~-------~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~-------~~-----~~~~~~~~l~~~l~~ 72 (98)
T cd00304 12 LPQGS-------PLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAK-------SE-----QQAVKKRELEEFLAR 72 (98)
T ss_pred cCCCC-------chHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeC-------cH-----HHHHHHHHHHHHHHH
Confidence 99999 999999993220000000001123458899999987531 21 677889999999999
Q ss_pred cCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEe
Q psy16039 151 NGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVW 198 (586)
Q Consensus 151 ~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~l 198 (586)
+|+.+| ++||+.. .....++|||..+
T Consensus 73 ~gl~ln--~~Kt~~~--------------------~~~~~~~flG~~~ 98 (98)
T cd00304 73 LGLNLS--DEKTQFT--------------------EKEKKFKFLGILV 98 (98)
T ss_pred cCcEEC--hheeEEe--------------------cCCCCeeeeceeC
Confidence 999999 9999985 1246688888753
No 19
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=98.28 E-value=2.4e-06 Score=87.88 Aligned_cols=125 Identities=12% Similarity=0.028 Sum_probs=78.5
Q ss_pred cccCCCCCCCCcccCCCCccccceeeeeccCCCCCcccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHH
Q psy16039 65 SPLGLTRPQPVATHCCLGLTGRLSASVRQTARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEV 144 (586)
Q Consensus 65 ~~~~~GvPQGs~~~~~~~vLsPlLf~~~~~~~~~~~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l 144 (586)
..-.+|+|||+ ++||+|-|++.....-........+.+.-||||..+... ......++..+
T Consensus 78 r~r~rGtPqGg-------viSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~------------~~~a~~aw~~i 138 (346)
T cd01709 78 RIRKRGTPMSH-------ALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ------------PETCAKAWKAI 138 (346)
T ss_pred cccCCccCCCc-------hhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC------------HHHHHHHHHHH
Confidence 33457999999 999999993221000000001113458899999987621 14456677788
Q ss_pred HHHHHhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEecCC-CChh-------hhHHHHHHh
Q psy16039 145 LKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVWDSK-LNWS-------LHINYVKTR 214 (586)
Q Consensus 145 ~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~ld~~-L~f~-------~Hi~~~~~k 214 (586)
.++++..||++| ++||.++......+.... .-...-|...++|-=+.||+. .+|. +||+...+.
T Consensus 139 ~~fl~~lGLelN--~eKT~iV~~~~~~r~~~~----~~~~~LP~g~i~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~Q 210 (346)
T cd01709 139 QEFAKVMGLELN--KEKTGSVYLSDDTKTRDT----TIDATLPEGPVRWGFLKLDPKTGRWEIDQSQVDAHIDELRKQ 210 (346)
T ss_pred HHHHHHcCceec--cccceEEEeccCCccCCC----cccccCCCCCceeeeEEecCCCCcEEeeHHHHHHHHHHHHHH
Confidence 999999999999 999999988655431101 111123456677777778854 6665 455554443
No 20
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=96.81 E-value=0.00032 Score=68.91 Aligned_cols=74 Identities=15% Similarity=0.030 Sum_probs=50.2
Q ss_pred CCCCCCCcccCCCCccccceeeeecc-CCCCCcccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHHH
Q psy16039 69 LTRPQPVATHCCLGLTGRLSASVRQT-ARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLKW 147 (586)
Q Consensus 69 ~GvPQGs~~~~~~~vLsPlLf~~~~~-~~~~~~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W 147 (586)
...|||- ..||.+|...+. ...... .......+..|+||+.|.+. +. ....+.++.+...
T Consensus 127 ~~lP~Gl-------~~SP~~f~~~m~~~l~~~~-~~~~~~~~~~Y~DDili~s~-------~~----~~~~~~l~~v~~~ 187 (213)
T cd01645 127 KVLPQGM-------KNSPTICQSFVAQALEPFR-KQYPDIVIYHYMDDILIASD-------LE----GQLREIYEELRQT 187 (213)
T ss_pred EEeCCCC-------cChHHHHHHHHHHHHHHHH-HHCCCeEEEEEcCCEEEEcC-------CH----HHHHHHHHHHHHH
Confidence 4699999 999999992220 000000 01112346899999987542 22 4556778888888
Q ss_pred HHhcCCccCCCCCceE
Q psy16039 148 SQANGLIFSTDPQKSV 163 (586)
Q Consensus 148 ~~~~gL~~n~~~~Kt~ 163 (586)
++++|+.+| ++||+
T Consensus 188 l~~~gl~ln--~~K~~ 201 (213)
T cd01645 188 LLRWGLTIP--PEKVQ 201 (213)
T ss_pred HHHCCCEeC--HHHEe
Confidence 999999999 99997
No 21
>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.
Probab=96.76 E-value=0.00069 Score=60.06 Aligned_cols=70 Identities=14% Similarity=-0.011 Sum_probs=44.3
Q ss_pred CCCCCcccCCCCccccceeee--eccCCCCCcccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHH-H
Q psy16039 71 RPQPVATHCCLGLTGRLSASV--RQTARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLK-W 147 (586)
Q Consensus 71 vPQGs~~~~~~~vLsPlLf~~--~~~~~~~~~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~-W 147 (586)
.|||- ..||.+|.. +.... .. ......+..|+||+.+.+. + ++ ..++.+..+.. -
T Consensus 34 mp~Gl-------~~sp~~f~~~~~~i~~-~~---~~~~~~v~~Y~DDili~~~-------~-~~---~~~~~~~~l~~~~ 91 (119)
T cd03714 34 LPFGL-------SLAPRVFTKVVEALLA-PL---RLLGVRIFSYLDDLLIIAS-------S-IK---TSEAVLRHLRATL 91 (119)
T ss_pred cCCcc-------cchHHHHHHHHHHHHH-Hh---hcCCeEEEEEecCeEEEeC-------c-HH---HHHHHHHHHHHHH
Confidence 79999 999999982 21100 00 0112347899999987542 2 22 22333333333 6
Q ss_pred HHhcCCccCCCCCceEE
Q psy16039 148 SQANGLIFSTDPQKSVC 164 (586)
Q Consensus 148 ~~~~gL~~n~~~~Kt~~ 164 (586)
++++|+.+| ++||+.
T Consensus 92 l~~~gl~ln--~~K~~~ 106 (119)
T cd03714 92 LANLGFTLN--LEKSKL 106 (119)
T ss_pred HHHcCCccC--hhhcEe
Confidence 899999999 999996
No 22
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=95.43 E-value=0.0059 Score=59.78 Aligned_cols=86 Identities=21% Similarity=0.165 Sum_probs=57.7
Q ss_pred CCCCCCcccCCCCccccceeeeecc-CCCCCcccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHHHH
Q psy16039 70 TRPQPVATHCCLGLTGRLSASVRQT-ARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLKWS 148 (586)
Q Consensus 70 GvPQGs~~~~~~~vLsPlLf~~~~~-~~~~~~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W~ 148 (586)
-.|||- ..||.+|...+. ...+... ......+..|.||+.|.+. +. ....+.++.+..-.
T Consensus 124 ~lp~Gl-------~~sp~~f~~~~~~~l~~~~~-~~~~~~~~~Y~DDili~s~-------~~----~e~~~~l~~v~~~l 184 (210)
T cd03715 124 RLPQGF-------KNSPTLFHEALARDLAPFPL-EHEGTILLQYVDDLLLAAD-------SE----EDCLKGTDALLTHL 184 (210)
T ss_pred EEeccc-------cCcHHHHHHHHHHHHHHHHh-hCCCeEEEEECCcEEEecC-------CH----HHHHHHHHHHHHHH
Confidence 489999 999999992210 0000000 0012346789999988642 33 34556788888889
Q ss_pred HhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeeeecceeEEEEEe
Q psy16039 149 QANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGLVW 198 (586)
Q Consensus 149 ~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~~~~~kyLGV~l 198 (586)
+++|+.+| ++||+.- ..+++|||.++
T Consensus 185 ~~~gl~l~--~~K~~~~----------------------~~~v~fLG~~~ 210 (210)
T cd03715 185 GELGYKVS--PKKAQIC----------------------RAEVKFLGVVW 210 (210)
T ss_pred HHCCCCcC--HHHeeCC----------------------CCceEEeeEEC
Confidence 99999999 9999832 36788888764
No 23
>KOG4768|consensus
Probab=94.93 E-value=0.054 Score=59.31 Aligned_cols=129 Identities=9% Similarity=-0.005 Sum_probs=66.0
Q ss_pred eEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHHHHHhcCCccCCCCCceEEEEecCCCCCCCCceEeCCEEeee-
Q psy16039 109 LRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKF- 187 (586)
Q Consensus 109 ~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~~~~~l~i~~~~I~~- 187 (586)
.+.||||..+..-. + .....+.+..+...+.+.||+.| ++||+..+=...-.. ..+.+.-.+..+
T Consensus 503 yVRyadd~ii~v~G------S----~nd~K~ilr~In~f~sslGls~n--~~kt~it~S~eg~~f--lg~nis~tP~r~~ 568 (796)
T KOG4768|consen 503 YVRYADDIIIGVWG------S----VNDCKQILRDINNFLSSLGLSNN--SSKTQITVSREGTHF--LGYNISTTPGRPA 568 (796)
T ss_pred EEEecCCEEEEEec------c----HHHHHHHHHHHHHHHHhhCcccC--cccceEEeeccceee--eeceeccCCCCcc
Confidence 47899998774321 1 24455677788888999999999 999998764332110 111111010011
Q ss_pred -ecceeEEEEEecCC--CChhhhHHHHHHhhHHHHHHHHhhh-----ccCCCchHHHHHHHHHhccccceee
Q psy16039 188 -ANSTKFLGLVWDSK--LNWSLHINYVKTRAAKALNALKMVC-----NKNYGVRRALLLVFYKSFILPIFDY 251 (586)
Q Consensus 188 -~~~~kyLGV~ld~~--L~f~~Hi~~~~~ka~~~~~~Lr~l~-----~~~~gl~~~~~~~ly~a~V~P~l~Y 251 (586)
...-+--|+.+.+. +.-++-|..+..|.+..-....... ...-...+++....|.++.+.++.|
T Consensus 569 ~~~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnY 640 (796)
T KOG4768|consen 569 AGEGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYCSHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILNY 640 (796)
T ss_pred ceeccccceEEeccCCceeecchHHHHHHHHHhcceeecCCcCceeeeeecccCHHHHHHHHHHHhhchhhh
Confidence 11111112222211 2235556666655554433322111 0001245667777777777777766
No 24
>PF09004 DUF1891: Domain of unknown function (DUF1891); InterPro: IPR015095 This domain is found at the extreme N terminus of eukaryotic alkylated DNA repair protein homologs. ; GO: 0008168 methyltransferase activity, 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process; PDB: 2CQ2_A 3THT_C 3THP_A.
Probab=91.73 E-value=0.036 Score=39.28 Aligned_cols=42 Identities=26% Similarity=0.479 Sum_probs=7.9
Q ss_pred hhhhHHHHHHhhHHHHHHHHhhhccCCCchHHHHHHHHHhcccc
Q psy16039 204 WSLHINYVKTRAAKALNALKMVCNKNYGVRRALLLVFYKSFILP 247 (586)
Q Consensus 204 f~~Hi~~~~~ka~~~~~~Lr~l~~~~~gl~~~~~~~ly~a~V~P 247 (586)
|+.|+..+.+||.++++.||++.+ .+++...+..+|+++|.+
T Consensus 1 W~~n~~~~~KKa~qRlyFLRkl~k--~~~~~~~l~lfY~s~IeS 42 (42)
T PF09004_consen 1 WTSNTTSLYKKAQQRLYFLRKLRK--FNVDSKLLTLFYHSVIES 42 (42)
T ss_dssp ---------------------------SS-----SHTTTTT---
T ss_pred CCcchHHHHHHHHhHHHHHHHHHH--ccchhHHHHHHHHHHhcC
Confidence 788999999999999999999864 568899999999988753
No 25
>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.
Probab=90.80 E-value=0.19 Score=46.42 Aligned_cols=72 Identities=19% Similarity=0.129 Sum_probs=44.6
Q ss_pred CCCCCCCcccCCCCccccceeeeeccCCCCCcccCcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHHHH
Q psy16039 69 LTRPQPVATHCCLGLTGRLSASVRQTARTPLSRADVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLKWS 148 (586)
Q Consensus 69 ~GvPQGs~~~~~~~vLsPlLf~~~~~~~~~~~~~~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W~ 148 (586)
..+|||- ..||.+|...+... .. .........|.||+.+... +.++.. ..++.+..-.
T Consensus 94 ~~~p~G~-------~~s~~~~~~~~~~~--l~--~~~~~~~~~y~DDi~i~~~-------~~~~~~----~~~~~~~~~l 151 (177)
T cd01647 94 TRMPFGL-------KNAPATFQRLMNKI--LG--DLLGDFVEVYLDDILVYSK-------TEEEHL----EHLREVLERL 151 (177)
T ss_pred EEecCCC-------ccHHHHHHHHHHhh--hc--cccccccEEEecCccccCC-------CHHHHH----HHHHHHHHHH
Confidence 3589999 99999888222000 00 0011236789999887532 334444 4444555556
Q ss_pred HhcCCccCCCCCceEE
Q psy16039 149 QANGLIFSTDPQKSVC 164 (586)
Q Consensus 149 ~~~gL~~n~~~~Kt~~ 164 (586)
+++|+.+| ++||+.
T Consensus 152 ~~~~~~~~--~~K~~~ 165 (177)
T cd01647 152 REAGLKLN--PEKCEF 165 (177)
T ss_pred HHcCCEeC--HHHcee
Confidence 67999999 999973
No 26
>KOG1005|consensus
Probab=90.78 E-value=0.19 Score=57.36 Aligned_cols=105 Identities=15% Similarity=-0.006 Sum_probs=68.5
Q ss_pred hhhcccccCceeEEEECCeeccccccccccCCCCCCCCcccCCCCccccceee-eec-cCCCC-CcccCcCCceeEEeec
Q psy16039 38 STLSPYLSRHTDMLCRGTRIWRSLLTRSPLGLTRPQPVATHCCLGLTGRLSAS-VRQ-TARTP-LSRADVGRDSLRSAAD 114 (586)
Q Consensus 38 ~~i~syL~~R~~~V~~~~~~~~~~S~~~~~~~GvPQGs~~~~~~~vLsPlLf~-~~~-~~~~~-~~~~~~~~~~~~~yAD 114 (586)
.||..+|++. .|++||. .+....|+|||| +||-+|-. ++. ....- .-....++..++.|+|
T Consensus 611 ~vi~~~l~~~--~vki~~k-------~yvq~~GIpQGs-------~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vD 674 (888)
T KOG1005|consen 611 SVIRNMLSTN--YVKIGGK-------SYVQKKGIPQGS-------ILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVD 674 (888)
T ss_pred HHHHHHHhhh--eEEECCe-------EEEEecCccCCC-------chhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeec
Confidence 5888888766 5567882 244568999999 99988877 111 00000 0011223345788999
Q ss_pred cchhhhhcccccccchHHHHHHHHHHHHHHHHHHHhcCCccCCCCCceEEEEecCCCCC
Q psy16039 115 RKDVIRFFFREEKREMGDKKILFRKTLDEVLKWSQANGLIFSTDPQKSVCVLFSRARNP 173 (586)
Q Consensus 115 D~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W~~~~gL~~n~~~~Kt~~~~f~~~~~~ 173 (586)
|.-+++... +.+.+.++.+..=..+++-..| ..||. -|......
T Consensus 675 DFLfITt~~-----------~~a~kfl~~l~~Gf~~yn~~tn--~~K~~--nF~~se~~ 718 (888)
T KOG1005|consen 675 DFLFITTEN-----------DQAKKFLKLLSRGFNKYNFFTN--EPKTV--NFEVSEEC 718 (888)
T ss_pred ceEEEecCH-----------HHHHHHHHHHhccccccceecc--Ccccc--cccchhcc
Confidence 998876432 5566777777777888888888 88877 66555443
No 27
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=81.49 E-value=4.4 Score=37.73 Aligned_cols=52 Identities=19% Similarity=0.157 Sum_probs=35.4
Q ss_pred CceEEEEcCCCCCCCceeEEecCC---ee------E-Eeec-C-CCcchhHHHHHHHHHHHHHhhh
Q psy16039 411 DSVLCFTDGSKTVNSTSCAYSIGN---QV------H-AFKL-N-KVNSVLSSELMAILLCVKNLIF 464 (586)
Q Consensus 411 ~~~~iytDGS~~~~~~G~av~~~~---~~------~-~~~l-~-~~~tv~~AEl~AI~~AL~~a~~ 464 (586)
..+++|+|+| ..+.|+.+|... .. . ..+. | ...|+=+-||.|+..|.+++..
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 456777766532 11 0 1111 2 2358999999999999999864
No 28
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=58.29 E-value=3.6 Score=40.35 Aligned_cols=68 Identities=10% Similarity=0.006 Sum_probs=39.4
Q ss_pred CCCCCCcccCCCCccccceee--eeccCCCCCccc-CcCCceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHH
Q psy16039 70 TRPQPVATHCCLGLTGRLSAS--VRQTARTPLSRA-DVGRDSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLK 146 (586)
Q Consensus 70 GvPQGs~~~~~~~vLsPlLf~--~~~~~~~~~~~~-~~~~~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~ 146 (586)
-+|+|- .-||.+|. +..... +.... ....+....|.||+.+.+. +.+ ..+..++.+.+
T Consensus 103 ~~pFG~-------~~AP~~~~~~~~~~~~-~~~~~~~~~~i~~~~YvDDili~~~-------s~~----e~~~~~~~v~~ 163 (213)
T cd01644 103 VVPFGA-------ASAPFLANRALKQHAE-DHPHEAAAKIIKRNFYVDDILVSTD-------TLN----EAVNVAKRLIA 163 (213)
T ss_pred EEccCC-------ccchHHHHHHHHHHHh-hcchhhHHHHHHHeeecccceecCC-------CHH----HHHHHHHHHHH
Confidence 399999 99999999 222111 01000 0011235689999877432 333 44555566666
Q ss_pred HHHhcCCccC
Q psy16039 147 WSQANGLIFS 156 (586)
Q Consensus 147 W~~~~gL~~n 156 (586)
..+++|+.+.
T Consensus 164 ~L~~~Gf~l~ 173 (213)
T cd01644 164 LLKKGGFNLR 173 (213)
T ss_pred HHHhCCccch
Confidence 6677888776
No 29
>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=55.38 E-value=16 Score=35.21 Aligned_cols=62 Identities=23% Similarity=0.180 Sum_probs=38.4
Q ss_pred CCceEEEEcCCCCCCCceeEEecCCeeEEeecCCCcchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHH
Q psy16039 410 SDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSAL 480 (586)
Q Consensus 410 ~~~~~iytDGS~~~~~~G~av~~~~~~~~~~l~~~~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al 480 (586)
..--.+|+|+.-. |.|+..+.....+.....-.+..+|+.|...|--+. ..++ |.|||..++
T Consensus 92 ~~lc~VfaDATpT----gwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vl 153 (245)
T PF00336_consen 92 PGLCQVFADATPT----GWGISITGQRMRGTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVL 153 (245)
T ss_pred CCCCceeccCCCC----cceeeecCceeeeeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEE
Confidence 4456789998644 344334333222222223578999999998887666 3344 889996554
No 30
>KOG1812|consensus
Probab=33.93 E-value=88 Score=33.65 Aligned_cols=90 Identities=13% Similarity=0.114 Sum_probs=55.3
Q ss_pred cchhHHHHHHHHHHHHHhhhCCCCeEEEEeCcHHHHHHHhcCCCCCc--cHHHHHHHHHHHHhCCCcEEEEEcCCCCCCh
Q psy16039 445 NSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHP--LVSLVYTTWLEAKDCGKNLNFVWCPSHCGIT 522 (586)
Q Consensus 445 ~tv~~AEl~AI~~AL~~a~~~~~~~i~I~sDS~~al~~i~~~~~~~~--~~~~i~~~~~~l~~~~~~V~~~WVpgH~Gi~ 522 (586)
.+...||++|+..+|..+.+.+...+.+++|+.-....+.......- .+..++.....++.......-.-+|- ..
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~l~~~~~i~~~~---~~ 123 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHRKIVLLVELVQRIREQLTSSEPILVPK---NA 123 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcccceeccc---ch
Confidence 67899999999999999999999999999997655564443332221 23333344444333322222222210 11
Q ss_pred hhHHHHHHHhhhccC
Q psy16039 523 GNELVDIAARNPITN 537 (586)
Q Consensus 523 gNe~AD~lAk~a~~~ 537 (586)
-.+.|=.||+++..+
T Consensus 124 d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 124 DIKFAYKLAREAIVS 138 (384)
T ss_pred hhHHHHHHHHHhhcc
Confidence 224578888888865
No 31
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=33.09 E-value=45 Score=32.55 Aligned_cols=95 Identities=15% Similarity=0.007 Sum_probs=65.0
Q ss_pred cchhHHHHHHHHHHHHHhhhCCCCeEEE-E----eCcHHHHHHHhcCCCCCccHHHHHHHHHHHH--hCCCcEEEEEcCC
Q psy16039 445 NSVLSSELMAILLCVKNLIFLPSTNFTL-I----SDSMSALLAISNCKNDHPLVSLVYTTWLEAK--DCGKNLNFVWCPS 517 (586)
Q Consensus 445 ~tv~~AEl~AI~~AL~~a~~~~~~~i~I-~----sDS~~al~~i~~~~~~~~~~~~i~~~~~~l~--~~~~~V~~~WVpg 517 (586)
.++..+|.+|++.+|+.+...+.++..| + .||++..+-+.+-.... +... .+ .+.- -.+....+.|+.-
T Consensus 106 ~~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k--~~~~-~~-~e~~~~~~~v~h~~k~i~~ 181 (225)
T COG3341 106 KSNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETK--VNLL-KD-REFFSIGKGVFHDEKDINI 181 (225)
T ss_pred ccCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHhhhhhhH--HHHH-Hh-HHhhhccchhhhhhhhccc
Confidence 3567899999999999998765555544 7 79999998886544222 1110 01 1111 2235566789999
Q ss_pred CCCChhhHHHHHHHhhhccCCCCCCC
Q psy16039 518 HCGITGNELVDIAARNPITNITLKNC 543 (586)
Q Consensus 518 H~Gi~gNe~AD~lAk~a~~~~~~~~~ 543 (586)
|.++.-+..++.++.........+..
T Consensus 182 ~~~~~~~~~~~s~~~~~~k~~~~~~~ 207 (225)
T COG3341 182 HIWIFESKKGNSHVYNTSKKELSPKY 207 (225)
T ss_pred ccccchhhhhhhhhhchhhhhccccc
Confidence 99999999999999888776665433
No 32
>PF15364 PAXIP1_C: PAXIP1-associated-protein-1 C term PTIP binding protein
Probab=31.12 E-value=81 Score=28.79 Aligned_cols=57 Identities=21% Similarity=0.324 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHhCCCcEEEEE-cCCCCC-----------ChhhHHHHHHHhhhccCCCCCCCCCCCCCCC
Q psy16039 493 VSLVYTTWLEAKDCGKNLNFVW-CPSHCG-----------ITGNELVDIAARNPITNITLKNCTSFDFRPN 551 (586)
Q Consensus 493 ~~~i~~~~~~l~~~~~~V~~~W-VpgH~G-----------i~gNe~AD~lAk~a~~~~~~~~~~~~~~~~~ 551 (586)
...| ..++.+...+..+.|.| |||... ...++.|+..|.+...... ...+.|||-+.
T Consensus 21 p~eI-~~LYe~L~~~~~leL~w~~pgRR~Psp~~~~~~~~~~~~~~~~~~~~E~~e~k~-~~~~eFDFdde 89 (141)
T PF15364_consen 21 PEEI-VSLYELLAKGGTLELQWKCPGRRPPSPEPSPEEEQDEESDGADEEAEEEEEEKP-QEPTEFDFDDE 89 (141)
T ss_pred HHHH-HHHHHHHhcCCCcceeeecCCCCCCCCCCCCcccccccccccchhhhhhhhcCC-CCCCccCcccc
Confidence 5666 55555558899999999 666654 3456667778887774333 34478998766
No 33
>cd01699 RNA_dep_RNAP RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.
Probab=22.69 E-value=27 Score=35.25 Aligned_cols=45 Identities=16% Similarity=0.088 Sum_probs=31.5
Q ss_pred ceeEEeeccchhhhhcccccccchHHHHHHHHHHHHHHHHHHHhcCCccCCCCCceEEE
Q psy16039 107 DSLRSAADRKDVIRFFFREEKREMGDKKILFRKTLDEVLKWSQANGLIFSTDPQKSVCV 165 (586)
Q Consensus 107 ~~~~~yADD~~i~~~~~~~~g~~~~~~~~~lq~~l~~l~~W~~~~gL~~n~~~~Kt~~~ 165 (586)
+....|.||..+... . ......++.+..+..+.|++++ ++|....
T Consensus 195 ~~~~~~GDD~li~~~-~-----------~~~~~~~~~~~~~~~~~G~~~~--~~~~~~~ 239 (278)
T cd01699 195 VRLLNYGDDCLLSVE-K-----------ADDKFNLETLAEWLKEYGLTMT--DEDKVES 239 (278)
T ss_pred eEEEEEcCCeEEEec-h-----------hHhhhCHHHHHHHHHHcCCEeC--CcccCCC
Confidence 457899999877431 0 1122345678888889999999 8887764
Done!