Query psy3428
Match_columns 682
No_of_seqs 650 out of 3836
Neff 8.8
Searched_HMMs 46136
Date Sat Aug 17 00:47:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3428.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3428hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.9 1.8E-22 3.9E-27 182.1 10.3 127 327-454 2-146 (154)
2 PRK06548 ribonuclease H; Provi 99.9 9.5E-22 2.1E-26 181.3 13.1 129 326-456 3-145 (161)
3 PRK08719 ribonuclease H; Revie 99.9 4.5E-21 9.7E-26 175.8 13.0 121 327-452 3-146 (147)
4 PRK00203 rnhA ribonuclease H; 99.8 4.1E-20 8.9E-25 171.6 11.4 125 328-455 3-144 (150)
5 PF00075 RNase_H: RNase H; In 99.8 1E-20 2.3E-25 172.5 7.2 117 327-451 2-131 (132)
6 cd06222 RnaseH RNase H (RNase 99.7 2.3E-16 4.9E-21 142.1 13.8 122 330-451 1-130 (130)
7 KOG3752|consensus 99.7 6.5E-17 1.4E-21 163.1 11.0 128 325-452 209-364 (371)
8 PRK13907 rnhA ribonuclease H; 99.7 1.6E-16 3.5E-21 143.8 10.6 120 329-452 2-126 (128)
9 PRK07708 hypothetical protein; 99.6 2.1E-14 4.5E-19 140.2 14.0 128 325-456 70-211 (219)
10 PRK07238 bifunctional RNase H/ 99.4 1.5E-12 3.2E-17 140.1 13.3 123 328-455 2-134 (372)
11 PF13456 RVT_3: Reverse transc 99.1 9.8E-11 2.1E-15 98.0 7.3 85 363-451 1-85 (87)
12 cd01650 RT_nLTR_like RT_nLTR: 98.9 2.8E-09 6E-14 106.1 6.1 98 8-114 112-220 (220)
13 cd01651 RT_G2_intron RT_G2_int 98.1 2.5E-06 5.3E-11 85.2 5.3 80 7-114 131-226 (226)
14 cd01648 TERT TERT: Telomerase 98.1 7.7E-06 1.7E-10 72.7 7.3 85 8-115 25-119 (119)
15 cd00304 RT_like RT_like: Rever 98.0 1.6E-05 3.6E-10 67.9 7.0 80 5-114 14-98 (98)
16 PF00078 RVT_1: Reverse transc 97.9 5.8E-06 1.3E-10 81.5 3.2 78 8-114 131-214 (214)
17 cd03487 RT_Bac_retron_II RT_Ba 97.9 2.8E-05 6E-10 77.0 7.5 85 6-117 107-198 (214)
18 cd01646 RT_Bac_retron_I RT_Bac 97.8 3.7E-05 8.1E-10 72.1 6.7 85 7-117 58-147 (158)
19 cd03714 RT_DIRS1 RT_DIRS1: Rev 96.7 0.0049 1.1E-07 54.7 7.0 68 4-80 35-106 (119)
20 cd01709 RT_like_1 RT_like_1: A 96.3 0.058 1.3E-06 55.9 12.9 109 8-130 89-210 (346)
21 cd01645 RT_Rtv RT_Rtv: Reverse 96.3 0.0051 1.1E-07 60.7 4.7 67 4-79 130-201 (213)
22 cd03715 RT_ZFREV_like RT_ZFREV 95.2 0.023 4.9E-07 56.0 4.6 81 3-114 125-210 (210)
23 PF09004 DUF1891: Domain of un 92.9 0.017 3.8E-07 40.0 -1.1 42 120-163 1-42 (42)
24 cd01647 RT_LTR RT_LTR: Reverse 88.5 0.67 1.4E-05 43.4 4.8 68 4-80 97-165 (177)
25 KOG1832|consensus 86.1 0.2 4.4E-06 56.9 -0.3 15 31-46 627-642 (1516)
26 KOG4768|consensus 83.3 4.9 0.00011 44.5 8.4 129 25-168 499-641 (796)
27 KOG1832|consensus 80.0 0.81 1.8E-05 52.3 1.2 6 394-399 1169-1174(1516)
28 PF05380 Peptidase_A17: Pao re 69.8 14 0.00031 34.3 6.7 52 326-379 79-142 (159)
29 PF00336 DNA_pol_viral_C: DNA 64.8 8.3 0.00018 36.7 3.8 61 327-396 93-153 (245)
30 KOG1189|consensus 48.2 4.7 0.0001 45.7 -0.8 37 6-46 12-48 (960)
31 KOG1812|consensus 44.6 52 0.0011 35.5 6.4 91 360-453 46-138 (384)
32 COG5137 Histone chaperone invo 40.0 8.8 0.00019 36.7 -0.2 15 574-588 157-171 (279)
33 PF03344 Daxx: Daxx Family; I 39.7 9.7 0.00021 44.2 0.0 8 412-419 246-253 (713)
34 KOG0943|consensus 39.2 9.4 0.0002 45.5 -0.2 13 30-43 746-758 (3015)
35 PF03115 Astro_capsid: Astrovi 38.5 10 0.00023 44.2 0.0 13 662-674 709-721 (787)
36 PF02724 CDC45: CDC45-like pro 38.1 12 0.00026 43.1 0.4 9 424-432 26-34 (622)
37 KOG1189|consensus 35.6 12 0.00025 42.7 -0.2 18 512-529 781-798 (960)
38 COG5414 TATA-binding protein-a 34.1 48 0.001 33.4 3.8 13 548-560 233-245 (392)
39 PRK06548 ribonuclease H; Provi 32.9 38 0.00083 31.6 2.8 26 499-524 113-138 (161)
40 COG5406 Nucleosome binding fac 32.6 20 0.00042 40.0 0.9 21 511-531 832-852 (1001)
41 COG5167 VID27 Protein involved 32.2 37 0.0008 37.2 2.8 30 535-564 316-349 (776)
42 COG0296 GlgB 1,4-alpha-glucan 31.1 54 0.0012 37.5 4.1 36 409-444 213-248 (628)
43 cd01644 RT_pepA17 RT_pepA17: R 29.6 39 0.00084 33.2 2.4 62 4-72 105-173 (213)
44 cd01699 RNA_dep_RNAP RNA_dep_R 28.8 75 0.0016 32.3 4.5 48 24-81 192-239 (278)
45 PF02724 CDC45: CDC45-like pro 28.7 21 0.00045 41.2 0.3 6 463-468 39-44 (622)
46 TIGR00927 2A1904 K+-dependent 28.2 18 0.00039 42.8 -0.2 11 7-17 20-30 (1096)
47 COG5406 Nucleosome binding fac 26.5 20 0.00043 40.0 -0.3 12 9-20 47-58 (1001)
48 KOG0262|consensus 25.9 22 0.00048 42.9 -0.1 23 185-207 825-847 (1640)
49 PTZ00415 transmission-blocking 23.7 22 0.00048 44.3 -0.6 11 437-447 30-40 (2849)
50 KOG0262|consensus 23.3 28 0.0006 42.1 0.1 35 193-227 818-855 (1640)
51 PRK08719 ribonuclease H; Revie 23.1 25 0.00055 32.2 -0.2 28 498-525 117-144 (147)
52 cd07049 BMC_EutL_repeat1 ethan 22.5 1.9E+02 0.004 24.8 4.7 32 30-62 53-99 (103)
53 COG0328 RnhA Ribonuclease HI [ 22.4 27 0.00059 32.2 -0.2 25 501-525 118-142 (154)
54 KOG1005|consensus 22.3 4.3E+02 0.0094 31.3 9.1 73 5-88 635-717 (888)
55 PRK10933 trehalose-6-phosphate 20.9 1.9E+02 0.0042 32.9 6.2 72 366-437 30-108 (551)
56 PF12633 Adenyl_cycl_N: Adenyl 20.9 1.3E+02 0.0029 29.2 4.1 28 45-72 127-154 (204)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.88 E-value=1.8e-22 Score=182.08 Aligned_cols=127 Identities=20% Similarity=0.206 Sum_probs=105.2
Q ss_pred CeEEEEeCCCCC--CCCceEEEEEc-c-e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhh
Q psy3428 327 SHTICYTDGSKT--PTTTGCAYSVG-N-V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALS 400 (682)
Q Consensus 327 ~~~~iytDgS~~--~~~~G~g~~~~-~-~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~ 400 (682)
..+.||||||+. +|..|+|+|+. . . ..+.... .+||++||+.|++.||+++.+.+...|.|+|||++|+++|.
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~ 80 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT 80 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence 368999999975 46799998875 1 1 2333344 89999999999999999999888999999999999999997
Q ss_pred cCCCC-----------cH-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCC
Q psy3428 401 NVRFI-----------NP-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGT 454 (682)
Q Consensus 401 ~~~~~-----------~~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~ 454 (682)
.+..+ .| ..++++..+.++..+...|.+.|||||+|.++||+||+||+.|+...
T Consensus 81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 43111 12 35688999999998888999999999999999999999999998765
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.87 E-value=9.5e-22 Score=181.33 Aligned_cols=129 Identities=23% Similarity=0.261 Sum_probs=99.8
Q ss_pred CCeEEEEeCCCCCC--CCceEEEEEcceeeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhh---
Q psy3428 326 TSHTICYTDGSKTP--TTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALS--- 400 (682)
Q Consensus 326 ~~~~~iytDgS~~~--~~~G~g~~~~~~~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~--- 400 (682)
+..+.||||||+.. +..|+|+++............+||++|||+|++.||+.+.. ....|.|+|||++|++++.
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~ 81 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWV 81 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHH
Confidence 45699999999764 56889988764322222234689999999999999986643 4457999999999999997
Q ss_pred ------cCCCC--cHH-HHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCCC
Q psy3428 401 ------NVRFI--NPL-ITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTP 456 (682)
Q Consensus 401 ------~~~~~--~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~ 456 (682)
+++.. .++ .+++++.+..+... ..|.|.|||||+|++|||.||+||++|+.....
T Consensus 82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~~ 145 (161)
T PRK06548 82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFST 145 (161)
T ss_pred HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhcc
Confidence 33332 233 47888888887766 579999999999999999999999999865543
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.85 E-value=4.5e-21 Score=175.84 Aligned_cols=121 Identities=22% Similarity=0.276 Sum_probs=94.2
Q ss_pred CeEEEEeCCCCCCCC-----ceEEEEEcc----e--eeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHH
Q psy3428 327 SHTICYTDGSKTPTT-----TGCAYSVGN----V--VRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSS 395 (682)
Q Consensus 327 ~~~~iytDgS~~~~~-----~G~g~~~~~----~--~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~ 395 (682)
..++||||||+..++ +|+|+++.. . .....+....||++||+.|++.||+.+.+. ..|+|||++|
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 468999999985432 589987642 1 234445566899999999999999998652 3799999999
Q ss_pred HHhhh--------cCCCCc---H-HHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCccc
Q psy3428 396 LAALS--------NVRFIN---P-LITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTT 452 (682)
Q Consensus 396 i~~l~--------~~~~~~---~-~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~ 452 (682)
++++. ++...+ + ..+++++.+..+.. ...|.|.|||||+|++|||.||+||++|++
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 99983 333222 2 23677888877766 477999999999999999999999999875
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.82 E-value=4.1e-20 Score=171.58 Aligned_cols=125 Identities=19% Similarity=0.224 Sum_probs=94.5
Q ss_pred eEEEEeCCCCCC--CCceEEEEEc--ceee-eecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428 328 HTICYTDGSKTP--TTTGCAYSVG--NVVR-STLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV 402 (682)
Q Consensus 328 ~~~iytDgS~~~--~~~G~g~~~~--~~~~-~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~ 402 (682)
.+.||||||+.. +..|+|+++. +... ........||+.|||.|++.||+.+.. ...+.|+|||++++++|..+
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 489999999864 4588888764 2221 112234679999999999999998864 46799999999999999752
Q ss_pred ---------CCC--cHH-HHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCC
Q psy3428 403 ---------RFI--NPL-ITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTT 455 (682)
Q Consensus 403 ---------~~~--~~~-~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~ 455 (682)
... .++ .+++++.+..+... ..|.|.|||||+|++||+.||+|||+|+....
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 111 122 24566666666544 78999999999999999999999999987653
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=99.82 E-value=1e-20 Score=172.54 Aligned_cols=117 Identities=34% Similarity=0.405 Sum_probs=88.4
Q ss_pred CeEEEEeCCCCCC--CCceEEEEEc-ceeeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhc--
Q psy3428 327 SHTICYTDGSKTP--TTTGCAYSVG-NVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSN-- 401 (682)
Q Consensus 327 ~~~~iytDgS~~~--~~~G~g~~~~-~~~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~-- 401 (682)
..+.||||||+.+ +..|+|+++. +......++ ..+++.||+.||..||+ +. ..+.+.|+|||++++..+..
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 4689999999653 3457776554 333444455 88999999999999999 44 33899999999999998866
Q ss_pred ---CCCCc----HHHHHHHHHHHHHHhcCCceEEEEecCCCCC-chhHHHHHHhcCcc
Q psy3428 402 ---VRFIN----PLITKVYSTWSYLKLCKKDITFMWCPSHCGI-KGNEIVDVAAKNPT 451 (682)
Q Consensus 402 ---~~~~~----~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~a~ 451 (682)
..... ++..+|++.+ ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus 78 ~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 78 HGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 33222 3444555433 55789999999999999 69999999999886
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=2.3e-16 Score=142.11 Aligned_cols=122 Identities=29% Similarity=0.322 Sum_probs=98.2
Q ss_pred EEEeCCCCCCC--CceEEEEEccee--ee---ecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcC
Q psy3428 330 ICYTDGSKTPT--TTGCAYSVGNVV--RS---TLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNV 402 (682)
Q Consensus 330 ~iytDgS~~~~--~~G~g~~~~~~~--~~---~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~ 402 (682)
.+|||||...+ ++|+|+++.+.. .. .......+++.+|+.|++.||+.+...+..++.|++||+.++..+.+.
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 48999998764 689998876421 11 112257899999999999999999988899999999999999999987
Q ss_pred CC-CcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcc
Q psy3428 403 RF-INPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPT 451 (682)
Q Consensus 403 ~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~ 451 (682)
.. .......++..+..+...+..+.|.|||+|+|+.+|+.||.|||.|+
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 65 23344555555666666788999999999999999999999999874
No 7
>KOG3752|consensus
Probab=99.70 E-value=6.5e-17 Score=163.13 Aligned_cols=128 Identities=25% Similarity=0.240 Sum_probs=100.6
Q ss_pred CCCeEEEEeCCCCCCC-----CceEEEEEcc---eeeeecCC-CCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHH
Q psy3428 325 YTSHTICYTDGSKTPT-----TTGCAYSVGN---VVRSTLLN-PVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSS 395 (682)
Q Consensus 325 ~~~~~~iytDgS~~~~-----~~G~g~~~~~---~~~~~~~~-~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~ 395 (682)
+.+..++|||||+..+ .+|+|++++. ...+..+. ..+|||.|||.|+..||+.+.+.+..+|+|.|||+++
T Consensus 209 ~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~ 288 (371)
T KOG3752|consen 209 EIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYF 288 (371)
T ss_pred cccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHH
Confidence 3456899999998763 3899999974 24455554 7899999999999999999998888899999999999
Q ss_pred HHhhhcCCCC-----------cH------HHHHHHHHHHHHHhc--CCceEEEEecCCCCCchhHHHHHHhcCccc
Q psy3428 396 LAALSNVRFI-----------NP------LITKVYSTWSYLKLC--KKDITFMWCPSHCGIKGNEIVDVAAKNPTT 452 (682)
Q Consensus 396 i~~l~~~~~~-----------~~------~~~~i~~~~~~l~~~--~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~ 452 (682)
+++|+.+... ++ ..+..+..+..|... +..|.+.|||||.|+.|||+||.||++++.
T Consensus 289 i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 289 INSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred HHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 9998643211 11 123444555555443 689999999999999999999999999854
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.68 E-value=1.6e-16 Score=143.76 Aligned_cols=120 Identities=18% Similarity=0.139 Sum_probs=98.8
Q ss_pred EEEEeCCCCCC--CCceEEEEEcceeee--e-cCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcCC
Q psy3428 329 TICYTDGSKTP--TTTGCAYSVGNVVRS--T-LLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVR 403 (682)
Q Consensus 329 ~~iytDgS~~~--~~~G~g~~~~~~~~~--~-~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~~ 403 (682)
+.||||||+.. +.+|+|+++.+.... . ......+|+.||+.|++.||+.+...+..+|.|++||+.+++.+.+..
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 67999999864 569999988643221 1 122457999999999999999999988889999999999999999876
Q ss_pred CCcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCccc
Q psy3428 404 FINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTT 452 (682)
Q Consensus 404 ~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~ 452 (682)
...+....+++.+..+...+..+.|.|||+ ++|+.||.||+.|+.
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 555556777888888888888899999995 689999999998864
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.58 E-value=2.1e-14 Score=140.16 Aligned_cols=128 Identities=13% Similarity=0.070 Sum_probs=99.1
Q ss_pred CCCeEEEEeCCCCC--CCCceEEEEEcc--e--ee----eecCCCCCchHHHHHHHHHHHHHHHHcCCCCc--EEEEcCC
Q psy3428 325 YTSHTICYTDGSKT--PTTTGCAYSVGN--V--VR----STLLNPVNSIFSAELIAIFLCLEAILDSPSGK--FLIVTDS 392 (682)
Q Consensus 325 ~~~~~~iytDgS~~--~~~~G~g~~~~~--~--~~----~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~--v~i~sDs 392 (682)
.++.+++|+|||.. ++++|+|+++.. . .. ...++..+||+.||+.|++.||+.+...+.+. |.|++||
T Consensus 70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS 149 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS 149 (219)
T ss_pred CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence 45679999999974 567999988752 1 11 12455568999999999999999999887654 8999999
Q ss_pred HHHHHhhhcCC-CCcHHHHHHHHHHHHHHhcC-CceEEEEecCCCCCchhHHHHHHhcCcccCCCC
Q psy3428 393 RSSLAALSNVR-FINPLITKVYSTWSYLKLCK-KDITFMWCPSHCGIKGNEIVDVAAKNPTTGTTP 456 (682)
Q Consensus 393 ~~~i~~l~~~~-~~~~~~~~i~~~~~~l~~~~-~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~ 456 (682)
+.+++.+.+.. ..++..+.+.+.+..+..+. ..+.|.||| +..|+.||+||++|+.....
T Consensus 150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~ 211 (219)
T PRK07708 150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVI 211 (219)
T ss_pred HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCC
Confidence 99999998765 34555666666666555443 357889998 78899999999999986544
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.41 E-value=1.5e-12 Score=140.06 Aligned_cols=123 Identities=17% Similarity=0.164 Sum_probs=100.4
Q ss_pred eEEEEeCCCCCC--CCceEEEEEccee-------eeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHh
Q psy3428 328 HTICYTDGSKTP--TTTGCAYSVGNVV-------RSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAA 398 (682)
Q Consensus 328 ~~~iytDgS~~~--~~~G~g~~~~~~~-------~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~ 398 (682)
.+.||||||+.. +.+|+|+++.+.. ....++ .+||+.||+.|++.||+.+.+.+.++|.|++||+.+++.
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 478999999765 4689998876321 122233 789999999999999999999888999999999999999
Q ss_pred hhcCCC-CcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHHHHhcCcccCCC
Q psy3428 399 LSNVRF-INPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVDVAAKNPTTGTT 455 (682)
Q Consensus 399 l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~ 455 (682)
+.+... +++-...++..+..+..++..+.|.||| ..+|+.||.||+.|+....
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~~ 134 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIP----RARNAHADRLANEAMDAAA 134 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECC----chhhhHHHHHHHHHHHhhc
Confidence 987653 4555667777778888888999999999 4789999999999976554
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.14 E-value=9.8e-11 Score=98.04 Aligned_cols=85 Identities=16% Similarity=0.143 Sum_probs=70.0
Q ss_pred hHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcCCCCcHHHHHHHHHHHHHHhcCCceEEEEecCCCCCchhHH
Q psy3428 363 IFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEI 442 (682)
Q Consensus 363 ~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~ 442 (682)
+..||+.|+..||+.+.+.+.++|.|.|||+.++..|.+..........+...+..+...+..+.|.||| ..+|..
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 4689999999999999999999999999999999999887544335567777778888889999999999 999999
Q ss_pred HHHHhcCcc
Q psy3428 443 VDVAAKNPT 451 (682)
Q Consensus 443 AD~lAk~a~ 451 (682)
||.|||.|.
T Consensus 77 A~~LA~~a~ 85 (87)
T PF13456_consen 77 ADALAKFAL 85 (87)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 999999875
No 12
>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=98.86 E-value=2.8e-09 Score=106.11 Aligned_cols=98 Identities=23% Similarity=0.387 Sum_probs=83.0
Q ss_pred hhHHHHHHHHhhccc-----------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCC
Q psy3428 8 HKVILMSLLFVGFAV-----------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPG 76 (682)
Q Consensus 8 ~~~~llfllyi~~~~-----------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~ 76 (682)
..|++||.+|.+++. ....+....||| |+++++.+.. ..++..++.+..|+..+|+++| ++
T Consensus 112 ~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaD-D~~i~~~~~~-----~~~~~~~~~~~~~~~~~gl~in--~~ 183 (220)
T cd01650 112 PLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYAD-DIVLFSEGKS-----RKLQELLQRLQEWSKESGLKIN--PS 183 (220)
T ss_pred cccHHHHHHHHHHHHHHHHhhccccCCCCccceEEecc-ceeeeccCCH-----HHHHHHHHHHHHHHHHcCCEEC--hh
Confidence 356799999988752 245788999999 9999988876 3489999999999999999999 99
Q ss_pred eeEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428 77 KSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW 114 (682)
Q Consensus 77 Kt~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l 114 (682)
||++++++..... ...+.+++..+..+..+||||+.|
T Consensus 184 Kt~~~~~~~~~~~-~~~~~~~~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 184 KSKVMLIGNKKKR-LKDITLNGTPIEAVETFKYLGVTI 220 (220)
T ss_pred heEEEEecCCCcc-hhhhhhcCCcccCCCCCeeccccC
Confidence 9999999987654 333788899999999999999975
No 13
>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=98.14 E-value=2.5e-06 Score=85.16 Aligned_cols=80 Identities=18% Similarity=0.157 Sum_probs=65.2
Q ss_pred hhhHHHHHHHHhhccc----------------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCc
Q psy3428 7 IHKVILMSLLFVGFAV----------------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTI 70 (682)
Q Consensus 7 ~~~~~llfllyi~~~~----------------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~ 70 (682)
-..|++||.+|+.++. ....+....||| |+++++.+... ++..++.+..|+...||.
T Consensus 131 ~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~D-D~~i~~~~~~~------~~~~~~~i~~~~~~~gl~ 203 (226)
T cd01651 131 GVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYAD-DFVIGVRGPKE------AEEIKELIREFLEELGLE 203 (226)
T ss_pred ccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecC-ceEEecCCHHH------HHHHHHHHHHHHHHcCCe
Confidence 3456789999987641 126788999999 99999877665 788899999999999999
Q ss_pred ccCCCCeeEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428 71 FSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW 114 (682)
Q Consensus 71 ~n~~~~Kt~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l 114 (682)
+| ++||++++|+ .+.+.|||..|
T Consensus 204 ln--~~Kt~i~~~~-------------------~~~~~fLG~~~ 226 (226)
T cd01651 204 LN--PEKTRITHFK-------------------SEGFDFLGFTF 226 (226)
T ss_pred ec--hhhcceeecC-------------------CCCCeeCCeEC
Confidence 99 9999999997 35677888764
No 14
>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=98.11 E-value=7.7e-06 Score=72.67 Aligned_cols=85 Identities=18% Similarity=0.020 Sum_probs=63.0
Q ss_pred hhHHHHHHHHhhccc---------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHH-hHhCCcccCCCCe
Q psy3428 8 HKVILMSLLFVGFAV---------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWS-DLNGTIFSTDPGK 77 (682)
Q Consensus 8 ~~~~llfllyi~~~~---------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~-~~~gl~~n~~~~K 77 (682)
--|++||.+|...+. .........||| |+.+++.+.. .++..++.+..|. .+.||.+| ++|
T Consensus 25 ~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaD-D~li~~~~~~------~~~~~~~~l~~~l~~~~gl~iN--~~K 95 (119)
T cd01648 25 PLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVD-DFLLITTSLD------KAIKFLNLLLRGFINQYKTFVN--FDK 95 (119)
T ss_pred chHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeC-cEEEEeCCHH------HHHHHHHHHHHhhHHhhCeEEC--ccc
Confidence 346688999976541 124566788999 9988876643 3688999999997 99999999 999
Q ss_pred eEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeC
Q psy3428 78 SVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWD 115 (682)
Q Consensus 78 t~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld 115 (682)
|++..... .......+.|||+.|+
T Consensus 96 t~~~~~~~--------------~~~~~~~~~flG~~i~ 119 (119)
T cd01648 96 TQINFSFA--------------QLDSSDLIPWCGLLIN 119 (119)
T ss_pred ceeecccc--------------ccCCCCccCceeEeeC
Confidence 99886542 0123356899999875
No 15
>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=98.00 E-value=1.6e-05 Score=67.86 Aligned_cols=80 Identities=19% Similarity=0.137 Sum_probs=63.5
Q ss_pred eehhhHHHHHHHHhhcccc-----CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeE
Q psy3428 5 VQIHKVILMSLLFVGFAVT-----GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSV 79 (682)
Q Consensus 5 ~~~~~~~llfllyi~~~~~-----~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~ 79 (682)
+|.-.|+++|.+|...+.. ..++....|+| |+.+.+... .++..+..+..|+.++|+.+| ++||+
T Consensus 14 qG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~D-D~~i~~~~~-------~~~~~~~~l~~~l~~~gl~ln--~~Kt~ 83 (98)
T cd00304 14 QGSPLSPALANLYMEKLEAPILKQLLDITLIRYVD-DLVVIAKSE-------QQAVKKRELEEFLARLGLNLS--DEKTQ 83 (98)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeC-cEEEEeCcH-------HHHHHHHHHHHHHHHcCcEEC--hheeE
Confidence 3455678899998877532 35788999999 999987766 368889999999999999999 99998
Q ss_pred EEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428 80 CIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW 114 (682)
Q Consensus 80 ~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l 114 (682)
.+ .....++|||+.+
T Consensus 84 ~~--------------------~~~~~~~flG~~~ 98 (98)
T cd00304 84 FT--------------------EKEKKFKFLGILV 98 (98)
T ss_pred Ee--------------------cCCCCeeeeceeC
Confidence 86 1346688888763
No 16
>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=97.92 E-value=5.8e-06 Score=81.49 Aligned_cols=78 Identities=26% Similarity=0.357 Sum_probs=63.7
Q ss_pred hhHHHHHHHHhhccc-----c-CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEE
Q psy3428 8 HKVILMSLLFVGFAV-----T-GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCI 81 (682)
Q Consensus 8 ~~~~llfllyi~~~~-----~-~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i 81 (682)
.-|+++|.+|...+. . ..++....||| |+.+++..... ++..++.+.+|+.++||.+| ++||+++
T Consensus 131 ~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~D-D~~i~~~~~~~------~~~~~~~i~~~~~~~gl~ln--~~Kt~~~ 201 (214)
T PF00078_consen 131 PLSPLLFNIYLDDLDRELQQELNPDISYLRYAD-DILIISKSKEE------LQKILEKISQWLEELGLKLN--PEKTKIL 201 (214)
T ss_dssp TCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETT-EEEEEESSHHH------HHHHHHHHHHHHHHTTSBCS--STTTSCS
T ss_pred cccchhhccccccccccccccccccccceEecc-ccEEEECCHHH------HHHHHHHHHHHHHHCCCEEC--hHHEEEE
Confidence 347899999988751 1 26788999999 99999877444 89999999999999999999 9999877
Q ss_pred EecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428 82 DFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW 114 (682)
Q Consensus 82 ~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l 114 (682)
+ ..+.++|||+.|
T Consensus 202 ~--------------------~~~~~~~lG~~i 214 (214)
T PF00078_consen 202 H--------------------PSDSVKFLGYVI 214 (214)
T ss_dssp ----------------------ESSEEETTEEE
T ss_pred e--------------------CCCCEEEEeEEC
Confidence 6 568899999875
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=97.90 E-value=2.8e-05 Score=76.96 Aligned_cols=85 Identities=15% Similarity=0.073 Sum_probs=66.6
Q ss_pred ehhhHHHHHHHHhhccc-------cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428 6 QIHKVILMSLLFVGFAV-------TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS 78 (682)
Q Consensus 6 ~~~~~~llfllyi~~~~-------~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt 78 (682)
|...|++||.+|..++. ...++....||| |++|++.+... ..++..+..+..|+.+.||.+| ++||
T Consensus 107 G~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaD-D~~i~~~~~~~----~~~~~~~~~i~~~l~~~gL~ln--~~Kt 179 (214)
T cd03487 107 GAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYAD-DITFSSNKKLK----EALDKLLEIIRSILSEEGFKIN--KSKT 179 (214)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEec-cEEEEccccch----hHHHHHHHHHHHHHHHCCceeC--CCce
Confidence 34456799999988642 234678899999 99998877653 3478899999999999999999 9999
Q ss_pred EEEEecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428 79 VCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK 117 (682)
Q Consensus 79 ~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~ 117 (682)
+++..+ ..+.+||+.+...
T Consensus 180 ~i~~~~--------------------~~~~~~G~~i~~~ 198 (214)
T cd03487 180 RISSKG--------------------SRQIVTGLVVNNG 198 (214)
T ss_pred EEccCC--------------------CCcEEEEEEEeCC
Confidence 998653 3456889888764
No 18
>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=97.83 E-value=3.7e-05 Score=72.11 Aligned_cols=85 Identities=16% Similarity=0.195 Sum_probs=67.0
Q ss_pred hhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEE
Q psy3428 7 IHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCI 81 (682)
Q Consensus 7 ~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i 81 (682)
-..|++|+.+|+.++. ....+....||| |+++++..... ++..++.+..|..+.||.+| ++||+.+
T Consensus 58 ~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~D-D~~i~~~~~~~------~~~~~~~i~~~l~~~gL~ln--~~Kt~~~ 128 (158)
T cd01646 58 PLTSRFLANIYLNDVDHELKSKLKGVDYVRYVD-DIRIFADSKEE------AEEILEELKEFLAELGLSLN--LSKTEIL 128 (158)
T ss_pred cchHHHHHHHHHHHHHHHHHhccCCceEEEecC-cEEEEcCCHHH------HHHHHHHHHHHHHHCCCEEC--hhhceee
Confidence 3457788888887752 146788999999 99999865433 68899999999999999999 9999999
Q ss_pred EecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC
Q psy3428 82 DFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK 117 (682)
Q Consensus 82 ~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~ 117 (682)
++.... ..+.+||..+...
T Consensus 129 ~~~~~~-----------------~~~~flg~~~~~~ 147 (158)
T cd01646 129 PLPEGT-----------------ASKDFLGYRFSPI 147 (158)
T ss_pred ecCCCC-----------------ccccccceEeehh
Confidence 886532 5577888877653
No 19
>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=96.70 E-value=0.0049 Score=54.65 Aligned_cols=68 Identities=19% Similarity=0.056 Sum_probs=45.3
Q ss_pred eeehhhHHHHHHHHhhcccc---CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHH-HHhHhCCcccCCCCeeE
Q psy3428 4 EVQIHKVILMSLLFVGFAVT---GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHK-WSDLNGTIFSTDPGKSV 79 (682)
Q Consensus 4 ~~~~~~~~llfllyi~~~~~---~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~-W~~~~gl~~n~~~~Kt~ 79 (682)
.+|.-.||.+|--++.-+.. .....+..|+| |+.|.+.+ .+. .+..+..+.. -++++|+.+| ++||+
T Consensus 35 p~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~D-Dili~~~~---~~~---~~~~~~~l~~~~l~~~gl~ln--~~K~~ 105 (119)
T cd03714 35 PFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLD-DLLIIASS---IKT---SEAVLRHLRATLLANLGFTLN--LEKSK 105 (119)
T ss_pred CCcccchHHHHHHHHHHHHHHhhcCCeEEEEEec-CeEEEeCc---HHH---HHHHHHHHHHHHHHHcCCccC--hhhcE
Confidence 35666677777666654321 34567889999 99987665 222 2334443333 6889999999 99998
Q ss_pred E
Q psy3428 80 C 80 (682)
Q Consensus 80 ~ 80 (682)
+
T Consensus 106 ~ 106 (119)
T cd03714 106 L 106 (119)
T ss_pred e
Confidence 6
No 20
>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=96.33 E-value=0.058 Score=55.89 Aligned_cols=109 Identities=16% Similarity=0.128 Sum_probs=72.0
Q ss_pred hhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEEE
Q psy3428 8 HKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCID 82 (682)
Q Consensus 8 ~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i~ 82 (682)
-.|+||=.+|.+++. ...+....-||| |+.+++. . .+ ...++..+.++++..||++| ++||.++.
T Consensus 89 viSplLaNiyL~~lD~~v~~~~~g~~l~RYaD-D~vi~~~--~-~~----a~~aw~~i~~fl~~lGLelN--~eKT~iV~ 158 (346)
T cd01709 89 ALSDVFGELVLFCLDFAVNQATDGGLLYRLHD-DLWFWGQ--P-ET----CAKAWKAIQEFAKVMGLELN--KEKTGSVY 158 (346)
T ss_pred hhhHHHHHHHHHHHHHHHHhcCCCceEEEEcC-eEEEEcC--H-HH----HHHHHHHHHHHHHHcCceec--cccceEEE
Confidence 356788888877652 225678899999 9999833 2 22 45666688899999999999 99999998
Q ss_pred ecCCCCCCCCceeeCCeeeccccceeEEeEEeCCC-CCch-------HHHHHHHHH
Q psy3428 83 FNRLRNSRSPALSYNGIQLKFVTSTKFLGLTWDAK-MNWS-------LHIQLLKNR 130 (682)
Q Consensus 83 f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~ld~~-L~~~-------~Hi~~~~~k 130 (682)
....++.... .-...=|...++|-=+.||+. .+|. .||+.....
T Consensus 159 ~~~~~r~~~~----~~~~~LP~g~i~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~Q 210 (346)
T cd01709 159 LSDDTKTRDT----TIDATLPEGPVRWGFLKLDPKTGRWEIDQSQVDAHIDELRKQ 210 (346)
T ss_pred eccCCccCCC----cccccCCCCCceeeeEEecCCCCcEEeeHHHHHHHHHHHHHH
Confidence 8754331111 011122455677777788864 6675 466555443
No 21
>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=96.26 E-value=0.0051 Score=60.70 Aligned_cols=67 Identities=16% Similarity=0.104 Sum_probs=50.7
Q ss_pred eeehhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCee
Q psy3428 4 EVQIHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKS 78 (682)
Q Consensus 4 ~~~~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt 78 (682)
-+|.-.|+.+|-.|+.... ...++....|+| |+.|.+. +.++ ....+..+...+.++|+.+| ++||
T Consensus 130 P~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~D-Dili~s~--~~~~----~~~~l~~v~~~l~~~gl~ln--~~K~ 200 (213)
T cd01645 130 PQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMD-DILIASD--LEGQ----LREIYEELRQTLLRWGLTIP--PEKV 200 (213)
T ss_pred CCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcC-CEEEEcC--CHHH----HHHHHHHHHHHHHHCCCEeC--HHHE
Confidence 3566778889988887542 123567889999 9987744 4333 67788888888999999999 9999
Q ss_pred E
Q psy3428 79 V 79 (682)
Q Consensus 79 ~ 79 (682)
+
T Consensus 201 ~ 201 (213)
T cd01645 201 Q 201 (213)
T ss_pred e
Confidence 6
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=95.22 E-value=0.023 Score=55.96 Aligned_cols=81 Identities=19% Similarity=0.146 Sum_probs=59.5
Q ss_pred eeeehhhHHHHHHHHhhccc-----cCCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCe
Q psy3428 3 TEVQIHKVILMSLLFVGFAV-----TGVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGK 77 (682)
Q Consensus 3 ~~~~~~~~~llfllyi~~~~-----~~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~K 77 (682)
..+|.--++.+|-.++.... ...++....|.| |+.|.. ++.++ ....++.+..-+.++|+.+| ++|
T Consensus 125 lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~D-Dili~s--~~~~e----~~~~l~~v~~~l~~~gl~l~--~~K 195 (210)
T cd03715 125 LPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVD-DLLLAA--DSEED----CLKGTDALLTHLGELGYKVS--PKK 195 (210)
T ss_pred EeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECC-cEEEec--CCHHH----HHHHHHHHHHHHHHCCCCcC--HHH
Confidence 34666677888877765431 124567889999 998874 45544 56788888888999999999 999
Q ss_pred eEEEEecCCCCCCCCceeeCCeeeccccceeEEeEEe
Q psy3428 78 SVCIDFNRLRNSRSPALSYNGIQLKFVTSTKFLGLTW 114 (682)
Q Consensus 78 t~~i~f~~~~~~~~~~~~i~g~~I~~~~~~k~LGv~l 114 (682)
|+.. +++++|||.++
T Consensus 196 ~~~~----------------------~~~v~fLG~~~ 210 (210)
T cd03715 196 AQIC----------------------RAEVKFLGVVW 210 (210)
T ss_pred eeCC----------------------CCceEEeeEEC
Confidence 9743 36788999764
No 23
>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=92.92 E-value=0.017 Score=40.04 Aligned_cols=42 Identities=26% Similarity=0.431 Sum_probs=7.9
Q ss_pred chHHHHHHHHHHHHHHHHHHhhhcccCCCChHHHHHHHHHhccc
Q psy3428 120 WSLHIQLLKNRALNSLNALKMVSCKKWGVRRSMLLRFYKSFTLP 163 (682)
Q Consensus 120 ~~~Hi~~~~~ka~~~~~~L~~l~~~~~g~~~~~~~~ly~a~v~p 163 (682)
|+.|+..+.+||...++.||++. +..+++..+..+|+++|.+
T Consensus 1 W~~n~~~~~KKa~qRlyFLRkl~--k~~~~~~~l~lfY~s~IeS 42 (42)
T PF09004_consen 1 WTSNTTSLYKKAQQRLYFLRKLR--KFNVDSKLLTLFYHSVIES 42 (42)
T ss_dssp ---------------------------SS-----SHTTTTT---
T ss_pred CCcchHHHHHHHHhHHHHHHHHH--HccchhHHHHHHHHHHhcC
Confidence 78899999999999999999995 5678999999999988753
No 24
>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=88.54 E-value=0.67 Score=43.36 Aligned_cols=68 Identities=13% Similarity=0.097 Sum_probs=44.1
Q ss_pred eeehhhHHHHHHHHhhcccc-CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEE
Q psy3428 4 EVQIHKVILMSLLFVGFAVT-GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVC 80 (682)
Q Consensus 4 ~~~~~~~~llfllyi~~~~~-~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~ 80 (682)
.+|.-.++.+|.-.+..+.. ........|.| |+.|... +.++. ...+..+..-..++|+.+| ++||+.
T Consensus 97 p~G~~~s~~~~~~~~~~~l~~~~~~~~~~y~D-Di~i~~~--~~~~~----~~~~~~~~~~l~~~~~~~~--~~K~~~ 165 (177)
T cd01647 97 PFGLKNAPATFQRLMNKILGDLLGDFVEVYLD-DILVYSK--TEEEH----LEHLREVLERLREAGLKLN--PEKCEF 165 (177)
T ss_pred cCCCccHHHHHHHHHHhhhccccccccEEEec-CccccCC--CHHHH----HHHHHHHHHHHHHcCCEeC--HHHcee
Confidence 35555666666666554422 12456778999 9988754 44443 4455555566667999999 999964
No 25
>KOG1832|consensus
Probab=86.10 E-value=0.2 Score=56.88 Aligned_cols=15 Identities=13% Similarity=0.036 Sum_probs=6.5
Q ss_pred EEEecCe-EEEEecCCH
Q psy3428 31 CDQDYDL-LIIGRSKDL 46 (682)
Q Consensus 31 ~yAD~D~-~i~~~~~~~ 46 (682)
.||= |+ +|++.-++.
T Consensus 627 ~~Al-~vL~i~t~iP~i 642 (1516)
T KOG1832|consen 627 QYAL-GVLHIVTSIPDI 642 (1516)
T ss_pred HHHH-hheeeeEecchH
Confidence 4555 44 333444444
No 26
>KOG4768|consensus
Probab=83.30 E-value=4.9 Score=44.53 Aligned_cols=129 Identities=11% Similarity=0.072 Sum_probs=72.8
Q ss_pred CCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEEEecCCCCCCCCceeeCCeeeccc
Q psy3428 25 VGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCIDFNRLRNSRSPALSYNGIQLKFV 104 (682)
Q Consensus 25 ~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i~f~~~~~~~~~~~~i~g~~I~~~ 104 (682)
.....+.||| |+.+.+.|.-.+ ....+..+..++.+.||+.| ++||++.+-.... .+-|..|...
T Consensus 499 kr~~yVRyad-d~ii~v~GS~nd-----~K~ilr~In~f~sslGls~n--~~kt~it~S~eg~-------~flg~nis~t 563 (796)
T KOG4768|consen 499 KRLMYVRYAD-DIIIGVWGSVND-----CKQILRDINNFLSSLGLSNN--SSKTQITVSREGT-------HFLGYNISTT 563 (796)
T ss_pred ceeeEEEecC-CEEEEEeccHHH-----HHHHHHHHHHHHHhhCcccC--cccceEEeeccce-------eeeeceeccC
Confidence 3455688999 999988885442 45667777788888999999 9999987654321 1111111111
Q ss_pred c-------ceeEEeEEeCC--CCCchHHHHHHHHHHHHHHHHHHhhh-----cccCCCChHHHHHHHHHhcccceeec
Q psy3428 105 T-------STKFLGLTWDA--KMNWSLHIQLLKNRALNSLNALKMVS-----CKKWGVRRSMLLRFYKSFTLPILDYG 168 (682)
Q Consensus 105 ~-------~~k~LGv~ld~--~L~~~~Hi~~~~~ka~~~~~~L~~l~-----~~~~g~~~~~~~~ly~a~v~p~l~Yg 168 (682)
+ .-+--|+-+.+ .+.-+.-|..++.|.+..-....+.. +..-...+.+..-.|.++.+.++.|=
T Consensus 564 P~r~~~~~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnYY 641 (796)
T KOG4768|consen 564 PGRPAAGEGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYCSHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILNYY 641 (796)
T ss_pred CCCccceeccccceEEeccCCceeecchHHHHHHHHHhcceeecCCcCceeeeeecccCHHHHHHHHHHHhhchhhhh
Confidence 1 11111111211 12344556666665554433333221 00112456677778888888888763
No 27
>KOG1832|consensus
Probab=80.00 E-value=0.81 Score=52.32 Aligned_cols=6 Identities=33% Similarity=0.124 Sum_probs=2.4
Q ss_pred HHHHhh
Q psy3428 394 SSLAAL 399 (682)
Q Consensus 394 ~~i~~l 399 (682)
++++.+
T Consensus 1169 saLW~~ 1174 (1516)
T KOG1832|consen 1169 SALWDA 1174 (1516)
T ss_pred HHHhcc
Confidence 344433
No 28
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=69.83 E-value=14 Score=34.31 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=32.6
Q ss_pred CCeEEEEeCCCCCCCCceEEEEEcc---ee----e---eecCC--CCCchHHHHHHHHHHHHHHHH
Q psy3428 326 TSHTICYTDGSKTPTTTGCAYSVGN---VV----R---STLLN--PVNSIFSAELIAIFLCLEAIL 379 (682)
Q Consensus 326 ~~~~~iytDgS~~~~~~G~g~~~~~---~~----~---~~~~~--~~~~~~~aEl~Ai~~al~~~~ 379 (682)
...+++|+|+|.. +.|+.++... .. . ..+.. ...|+-+-||.|+..|.+.+.
T Consensus 79 ~~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~ 142 (159)
T PF05380_consen 79 SVELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLAN 142 (159)
T ss_pred ceeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHH
Confidence 3478999999943 3443333321 11 0 01111 234999999999999999985
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=64.83 E-value=8.3 Score=36.70 Aligned_cols=61 Identities=21% Similarity=0.213 Sum_probs=39.1
Q ss_pred CeEEEEeCCCCCCCCceEEEEEcceeeeecCCCCCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHH
Q psy3428 327 SHTICYTDGSKTPTTTGCAYSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSL 396 (682)
Q Consensus 327 ~~~~iytDgS~~~~~~G~g~~~~~~~~~~~~~~~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i 396 (682)
.--.||+|+.- +|+|+.+......+.....-.+..||+.|.-.|.-+. ..++ |.|||..|+
T Consensus 93 ~lc~VfaDATp----Tgwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vl 153 (245)
T PF00336_consen 93 GLCQVFADATP----TGWGISITGQRMRGTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVL 153 (245)
T ss_pred CCCceeccCCC----CcceeeecCceeeeeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEE
Confidence 34568888753 4555555443333333345578999999997776554 3344 999998765
No 30
>KOG1189|consensus
Probab=48.17 E-value=4.7 Score=45.71 Aligned_cols=37 Identities=19% Similarity=0.082 Sum_probs=22.8
Q ss_pred ehhhHHHHHHHHhhccccCCCcEEEEEEecCeEEEEecCCH
Q psy3428 6 QIHKVILMSLLFVGFAVTGVGMTCNCDQDYDLLIIGRSKDL 46 (682)
Q Consensus 6 ~~~~~~llfllyi~~~~~~~~~~~~~yAD~D~~i~~~~~~~ 46 (682)
+.-++..||+..+++.- +-..+.|.| |.+++.++...
T Consensus 12 ~Y~KssAL~~WLlGYEf---pdTilv~~~-~~i~iltSkkK 48 (960)
T KOG1189|consen 12 PYQKSSALFTWLLGYEF---PDTILVLCK-DKIYILTSKKK 48 (960)
T ss_pred chhHHHHHHHHHhcccc---CceEEEEec-CcEEEEecchh
Confidence 44566777766666542 336677888 76666655554
No 31
>KOG1812|consensus
Probab=44.58 E-value=52 Score=35.51 Aligned_cols=91 Identities=12% Similarity=0.045 Sum_probs=55.3
Q ss_pred CCchHHHHHHHHHHHHHHHHcCCCCcEEEEcCCHHHHHhhhcCCCCcH--HHHHHHHHHHHHHhcCCceEEEEecCCCCC
Q psy3428 360 VNSIFSAELIAIFLCLEAILDSPSGKFLIVTDSRSSLAALSNVRFINP--LITKVYSTWSYLKLCKKDITFMWCPSHCGI 437 (682)
Q Consensus 360 ~~~~~~aEl~Ai~~al~~~~~~~~~~v~i~sDs~~~i~~l~~~~~~~~--~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi 437 (682)
..+...||++|+..+|..+...+...+.+++|+......+.......- .+..+.+....++.+.....-.-||- .
T Consensus 46 ~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~l~~~~~i~~~~---~ 122 (384)
T KOG1812|consen 46 SITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGREKPEQHRKIVLLVELVQRIREQLTSSEPILVPK---N 122 (384)
T ss_pred ccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcccceeccc---c
Confidence 368899999999999999999999999999996555543333322221 23444454444444433322222321 1
Q ss_pred chhHHHHHHhcCcccC
Q psy3428 438 KGNEIVDVAAKNPTTG 453 (682)
Q Consensus 438 ~gNe~AD~lAk~a~~~ 453 (682)
.-..-|=.||+++..+
T Consensus 123 ~d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 123 ADIKFAYKLAREAIVS 138 (384)
T ss_pred hhhHHHHHHHHHhhcc
Confidence 1123466777777765
No 32
>COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]
Probab=40.04 E-value=8.8 Score=36.66 Aligned_cols=15 Identities=20% Similarity=0.687 Sum_probs=7.9
Q ss_pred cccCCCCcccCChhh
Q psy3428 574 VWKTSDQDEIGSPRI 588 (682)
Q Consensus 574 ~~~~~~~~e~~~~~~ 588 (682)
+|.+....+...|..
T Consensus 157 vwDn~~d~d~apP~q 171 (279)
T COG5137 157 VWDNDEDNDEAPPAQ 171 (279)
T ss_pred EecCCcccccCCCCC
Confidence 566655555554433
No 33
>PF03344 Daxx: Daxx Family; InterPro: IPR005012 Daxx is a ubiquitously expressed protein that functions, in part, as a transcriptional co-repressor through its interaction with a growing number of nuclear, DNA-associated proteins. Human Daxx contains four structural domains commonly found in transcriptional regulatory proteins: two predicted paired amphipathic helices, an acid-rich domain and a Ser/Pro/Thr (SPT)-rich domain. The post-translational modification status of the SPT-domain of hDaxx regulates its association with transcription factors such as Pax3 and ETS-1, effectively bringing hDaxx to sites of active transcription. Through its presence at the site of active transcription, hDaxx could then be able to associate with acetylated histones present in the nucleosomes and Dek that is associated with chromatin. Through its association with the SPT-domain of hDaxx, histone deacetylases may also be brought to the site of active transcription. As a consequence, nucleosomes in the vicinity of the site of active transcription will have the histone tails deacetylated, allowing the deactylated tail to bind to DNA, thereby leading to an inactive chromatin structure and transcriptional repression []. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis as a component of nuclear promyelocytic leukemia protein (PML) oncogenic domains (PODS). Daxx associates with PODs through a direct interaction with PML, a critical component of PODs. The interaction is a dynamic, cell cycle regulated event and is dependent on the post-translational modification of PML by the small ubiquitin-related modifier SUMO-1. ; PDB: 2KZS_A 2KZU_A.
Probab=39.72 E-value=9.7 Score=44.24 Aligned_cols=8 Identities=25% Similarity=0.497 Sum_probs=0.0
Q ss_pred HHHHHHHH
Q psy3428 412 VYSTWSYL 419 (682)
Q Consensus 412 i~~~~~~l 419 (682)
||+.+..|
T Consensus 246 i~~klC~l 253 (713)
T PF03344_consen 246 IYEKLCEL 253 (713)
T ss_dssp --------
T ss_pred cccccccc
Confidence 33333333
No 34
>KOG0943|consensus
Probab=39.20 E-value=9.4 Score=45.47 Aligned_cols=13 Identities=31% Similarity=0.322 Sum_probs=6.8
Q ss_pred EEEEecCeEEEEec
Q psy3428 30 NCDQDYDLLIIGRS 43 (682)
Q Consensus 30 ~~yAD~D~~i~~~~ 43 (682)
++-.| |+-++-++
T Consensus 746 LlR~d-dLQVidt~ 758 (3015)
T KOG0943|consen 746 LLRID-DLQVIDTG 758 (3015)
T ss_pred hhhhh-heeeeccC
Confidence 44555 66665533
No 35
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=38.47 E-value=10 Score=44.25 Aligned_cols=13 Identities=8% Similarity=0.061 Sum_probs=0.0
Q ss_pred hhhhhhhhhhcCC
Q psy3428 662 SLHFYVLYVLSKG 674 (682)
Q Consensus 662 ~~~~~~~~~~~~~ 674 (682)
...-+++++|.||
T Consensus 709 ~R~~L~nTLVNqG 721 (787)
T PF03115_consen 709 NRVTLFNTLVNQG 721 (787)
T ss_dssp -------------
T ss_pred hHHHHHHHHHHcC
Confidence 3344455555555
No 36
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=38.14 E-value=12 Score=43.13 Aligned_cols=9 Identities=22% Similarity=0.641 Sum_probs=6.0
Q ss_pred CceEEEEec
Q psy3428 424 KDITFMWCP 432 (682)
Q Consensus 424 ~~v~~~WVp 432 (682)
..|.+..||
T Consensus 26 d~I~~~l~P 34 (622)
T PF02724_consen 26 DNIQYSLVP 34 (622)
T ss_pred cCCCeeEEE
Confidence 456677777
No 37
>KOG1189|consensus
Probab=35.64 E-value=12 Score=42.70 Aligned_cols=18 Identities=17% Similarity=0.078 Sum_probs=9.5
Q ss_pred ccCCccccccccCCccCC
Q psy3428 512 IKGNELVDVAAKNPTTGT 529 (682)
Q Consensus 512 i~~~r~~~~~~~~~r~g~ 529 (682)
+.|++-...++-|...|-
T Consensus 781 vtL~eVEiv~~ERV~f~l 798 (960)
T KOG1189|consen 781 VTLEEVEIVNLERVQFGL 798 (960)
T ss_pred Eeecceeeeeeeeeeecc
Confidence 345555555555555553
No 38
>COG5414 TATA-binding protein-associated factor [Transcription]
Probab=34.08 E-value=48 Score=33.37 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=8.7
Q ss_pred HHHHHHhhhhcCC
Q psy3428 548 MNSEWQSLWDNVP 560 (682)
Q Consensus 548 ~~~~w~~~w~~~~ 560 (682)
-+....+.|.++.
T Consensus 233 AR~~~vs~~En~~ 245 (392)
T COG5414 233 ARQERVSSWENFK 245 (392)
T ss_pred hhhhhhhhhhccc
Confidence 4566677787754
No 39
>PRK06548 ribonuclease H; Provisional
Probab=32.88 E-value=38 Score=31.59 Aligned_cols=26 Identities=31% Similarity=0.550 Sum_probs=22.3
Q ss_pred CcceeecCCCCCCccCCccccccccC
Q psy3428 499 KDITFMWCPSHCGIKGNELVDVAAKN 524 (682)
Q Consensus 499 ~~~~~~~~p~~~~i~~~r~~~~~~~~ 524 (682)
..+.|.|+|.|.|..+|+.+|..+.+
T Consensus 113 ~~v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 113 RNIRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred CceEEEEEecCCCCHHHHHHHHHHHH
Confidence 35789999999999999999987654
No 40
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=32.55 E-value=20 Score=40.04 Aligned_cols=21 Identities=19% Similarity=0.017 Sum_probs=12.3
Q ss_pred CccCCccccccccCCccCCCC
Q psy3428 511 GIKGNELVDVAAKNPTTGTTP 531 (682)
Q Consensus 511 ~i~~~r~~~~~~~~~r~g~~~ 531 (682)
-|.+++-.-+++-|...|--.
T Consensus 832 VitLeevEi~~lERVqfglKn 852 (1001)
T COG5406 832 VITLEEVEIVNLERVQFGLKN 852 (1001)
T ss_pred EEEecceeEEeeeeEEeeccc
Confidence 345666666666666666433
No 41
>COG5167 VID27 Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]
Probab=32.24 E-value=37 Score=37.20 Aligned_cols=30 Identities=23% Similarity=0.513 Sum_probs=16.8
Q ss_pred CCccccHHHHHHHHHHHH----HhhhhcCCCCCC
Q psy3428 535 CTPEDFKPFVTALMNSEW----QSLWDNVPNTNK 564 (682)
Q Consensus 535 ~~~~d~~~~i~~~~~~~w----~~~w~~~~n~~~ 564 (682)
-+..+...+...+|.+.| +..|.+.+...+
T Consensus 316 ~d~~~~~qF~~~~i~cLw~~lN~e~w~~~~~e~k 349 (776)
T COG5167 316 LDNLDFLQFLSKYIGCLWRNLNNEKWGNEEAERK 349 (776)
T ss_pred cchhHHHHHHHHHHHHHHHHhhhhhccCchhhhh
Confidence 344455566677788877 344555444433
No 42
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=31.13 E-value=54 Score=37.54 Aligned_cols=36 Identities=14% Similarity=0.210 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhcCCceEEEEecCCCCCchhHHHH
Q psy3428 409 ITKVYSTWSYLKLCKKDITFMWCPSHCGIKGNEIVD 444 (682)
Q Consensus 409 ~~~i~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD 444 (682)
-..+...++.....|..|-+-|||+|-+..||-.+-
T Consensus 213 Pedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~ 248 (628)
T COG0296 213 PEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLAR 248 (628)
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhh
Confidence 346666777888899999999999999999887653
No 43
>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=29.63 E-value=39 Score=33.17 Aligned_cols=62 Identities=10% Similarity=0.016 Sum_probs=40.8
Q ss_pred eeehhhHHHHHHHHhhccccCC-------CcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCccc
Q psy3428 4 EVQIHKVILMSLLFVGFAVTGV-------GMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFS 72 (682)
Q Consensus 4 ~~~~~~~~llfllyi~~~~~~~-------~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n 72 (682)
-||.-.+|-+|..+++.+.... .+....|.| |+.+. +.+.++ ++..+..+.+..+++|+.+.
T Consensus 105 pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvD-Dili~--~~s~~e----~~~~~~~v~~~L~~~Gf~l~ 173 (213)
T cd01644 105 PFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVD-DILVS--TDTLNE----AVNVAKRLIALLKKGGFNLR 173 (213)
T ss_pred ccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecc-cceec--CCCHHH----HHHHHHHHHHHHHhCCccch
Confidence 3666677777777776652221 234679999 99885 444544 56666666677778887765
No 44
>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=28.76 E-value=75 Score=32.26 Aligned_cols=48 Identities=15% Similarity=0.083 Sum_probs=35.6
Q ss_pred CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCCCCeeEEE
Q psy3428 24 GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTDPGKSVCI 81 (682)
Q Consensus 24 ~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~~~Kt~~i 81 (682)
...+....|.| |..+.+... . ....++.+..+..+.|++++ +.|....
T Consensus 192 ~~~~~~~~~GD-D~li~~~~~-~------~~~~~~~~~~~~~~~G~~~~--~~~~~~~ 239 (278)
T cd01699 192 FKNVRLLNYGD-DCLLSVEKA-D------DKFNLETLAEWLKEYGLTMT--DEDKVES 239 (278)
T ss_pred hhceEEEEEcC-CeEEEechh-H------hhhCHHHHHHHHHHcCCEeC--CcccCCC
Confidence 46778899999 999887554 1 23345567788888999999 7777654
No 45
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=28.72 E-value=21 Score=41.24 Aligned_cols=6 Identities=0% Similarity=0.163 Sum_probs=2.3
Q ss_pred ccchHH
Q psy3428 463 EDFKPF 468 (682)
Q Consensus 463 ~~~~~~ 468 (682)
.++++.
T Consensus 39 ~el~~~ 44 (622)
T PF02724_consen 39 SELERA 44 (622)
T ss_pred HHHHHH
Confidence 344333
No 46
>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger.
Probab=28.22 E-value=18 Score=42.76 Aligned_cols=11 Identities=36% Similarity=0.265 Sum_probs=6.9
Q ss_pred hhhHHHHHHHH
Q psy3428 7 IHKVILMSLLF 17 (682)
Q Consensus 7 ~~~~~llflly 17 (682)
.|.+-|||+|=
T Consensus 20 ~~~~~~~~~~~ 30 (1096)
T TIGR00927 20 LHWSRLLFLLG 30 (1096)
T ss_pred hhHHHHHHHHH
Confidence 46666777653
No 47
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=26.52 E-value=20 Score=39.98 Aligned_cols=12 Identities=17% Similarity=0.540 Sum_probs=5.8
Q ss_pred hHHHHHHHHhhc
Q psy3428 9 KVILMSLLFVGF 20 (682)
Q Consensus 9 ~~~llfllyi~~ 20 (682)
+...|++..+++
T Consensus 47 k~taLh~wLLgY 58 (1001)
T COG5406 47 KNTALHIWLLGY 58 (1001)
T ss_pred hhhHHHHHHHhc
Confidence 444555544444
No 48
>KOG0262|consensus
Probab=25.87 E-value=22 Score=42.85 Aligned_cols=23 Identities=22% Similarity=0.143 Sum_probs=16.0
Q ss_pred hHHHHHHHHHhcCCCCCcHHHHH
Q psy3428 185 TVHHAGIRIATGALRSSPVVSLY 207 (682)
Q Consensus 185 ~~q~~~~R~i~g~~rtt~~~~l~ 207 (682)
.+-+++++.++|....+|++.+.
T Consensus 825 ~vG~qa~~~~~~l~~da~~del~ 847 (1640)
T KOG0262|consen 825 NVGNQAAKEAFGLDVDAPPDELR 847 (1640)
T ss_pred cccHHHHHHHhCCCCCCCHHHHH
Confidence 35567778888887777777444
No 49
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=23.69 E-value=22 Score=44.33 Aligned_cols=11 Identities=45% Similarity=0.516 Sum_probs=4.9
Q ss_pred CchhHHHHHHh
Q psy3428 437 IKGNEIVDVAA 447 (682)
Q Consensus 437 i~gNe~AD~lA 447 (682)
+.||-..|..-
T Consensus 30 ~~~~~~~~~~~ 40 (2849)
T PTZ00415 30 IIGNGICDDED 40 (2849)
T ss_pred eecCCcccchh
Confidence 34444444433
No 50
>KOG0262|consensus
Probab=23.33 E-value=28 Score=42.10 Aligned_cols=35 Identities=20% Similarity=0.115 Sum_probs=20.4
Q ss_pred HHhcCCCCCcHHHHHHHcCC---CCHHHHHHHHHHHHH
Q psy3428 193 IATGALRSSPVVSLYVDSGI---PPLSLRRSKLMLNYV 227 (682)
Q Consensus 193 ~i~g~~rtt~~~~l~~~~gl---~pl~~~~~~~~~~~~ 227 (682)
.++.-.+++-..++....|+ .|.++.+.++...|.
T Consensus 818 ~il~e~~~vG~qa~~~~~~l~~da~~del~~~le~~y~ 855 (1640)
T KOG0262|consen 818 EILRESRNVGNQAAKEAFGLDVDAPPDELRSRLEAIYL 855 (1640)
T ss_pred HHHHhhhcccHHHHHHHhCCCCCCCHHHHHHHHHHHHh
Confidence 34444566777777777777 466655444444443
No 51
>PRK08719 ribonuclease H; Reviewed
Probab=23.14 E-value=25 Score=32.22 Aligned_cols=28 Identities=32% Similarity=0.497 Sum_probs=23.1
Q ss_pred CCcceeecCCCCCCccCCccccccccCC
Q psy3428 498 KKDITFMWCPSHCGIKGNELVDVAAKNP 525 (682)
Q Consensus 498 ~~~~~~~~~p~~~~i~~~r~~~~~~~~~ 525 (682)
...+.|.|+|+|.|+.+|+.+|..+..+
T Consensus 117 ~~~i~~~~VkgH~g~~~Ne~aD~lA~~a 144 (147)
T PRK08719 117 RKYVEVEKVTAHSGIEGNEAADMLAQAA 144 (147)
T ss_pred CCcEEEEEecCCCCChhHHHHHHHHHHH
Confidence 3558899999999999999999876543
No 52
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=22.46 E-value=1.9e+02 Score=24.77 Aligned_cols=32 Identities=9% Similarity=-0.005 Sum_probs=26.8
Q ss_pred EEEEecCe---------------EEEEecCCHHHHHHHHHHHHHHHHH
Q psy3428 30 NCDQDYDL---------------LIIGRSKDLDLLLQRFQHTLDEIHK 62 (682)
Q Consensus 30 ~~yAD~D~---------------~i~~~~~~~~~~~~~lq~~l~~~~~ 62 (682)
+.|+| |+ .++..|++..+....|+..++.+.+
T Consensus 53 v~~~~-~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~ 99 (103)
T cd07049 53 VVYAR-SFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIEN 99 (103)
T ss_pred EEEEe-ecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhc
Confidence 34999 99 7789999999998888888887654
No 53
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=22.35 E-value=27 Score=32.23 Aligned_cols=25 Identities=28% Similarity=0.529 Sum_probs=20.6
Q ss_pred ceeecCCCCCCccCCccccccccCC
Q psy3428 501 ITFMWCPSHCGIKGNELVDVAAKNP 525 (682)
Q Consensus 501 ~~~~~~p~~~~i~~~r~~~~~~~~~ 525 (682)
+.+-|+|+|.|..+|+++|..+..+
T Consensus 118 v~~~WVkgH~g~~~NeraD~LA~~~ 142 (154)
T COG0328 118 VFWEWVKGHAGHPENERADQLAREA 142 (154)
T ss_pred EEEEEeeCCCCChHHHHHHHHHHHH
Confidence 3456899999999999999887654
No 54
>KOG1005|consensus
Probab=22.32 E-value=4.3e+02 Score=31.26 Aligned_cols=73 Identities=16% Similarity=0.171 Sum_probs=49.1
Q ss_pred eehhhHH--HHHHHHhhccc------c--CCCcEEEEEEecCeEEEEecCCHHHHHHHHHHHHHHHHHHHhHhCCcccCC
Q psy3428 5 VQIHKVI--LMSLLFVGFAV------T--GVGMTCNCDQDYDLLIIGRSKDLDLLLQRFQHTLDEIHKWSDLNGTIFSTD 74 (682)
Q Consensus 5 ~~~~~~~--llfllyi~~~~------~--~~~~~~~~yAD~D~~i~~~~~~~~~~~~~lq~~l~~~~~W~~~~gl~~n~~ 74 (682)
+++++++ ||=-||.+|+. . ...+-.+-|+| |..++++..+. ....+..+..=..+++...|
T Consensus 635 IpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vD-DFLfITt~~~~------a~kfl~~l~~Gf~~yn~~tn-- 705 (888)
T KOG1005|consen 635 IPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVD-DFLFITTENDQ------AKKFLKLLSRGFNKYNFFTN-- 705 (888)
T ss_pred ccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeec-ceEEEecCHHH------HHHHHHHHhccccccceecc--
Confidence 4455544 66677777752 1 22346777999 99999776655 56677777777778887777
Q ss_pred CCeeEEEEecCCCC
Q psy3428 75 PGKSVCIDFNRLRN 88 (682)
Q Consensus 75 ~~Kt~~i~f~~~~~ 88 (682)
..||. -|.....
T Consensus 706 ~~K~~--nF~~se~ 717 (888)
T KOG1005|consen 706 EPKTV--NFEVSEE 717 (888)
T ss_pred Ccccc--cccchhc
Confidence 88876 5654433
No 55
>PRK10933 trehalose-6-phosphate hydrolase; Provisional
Probab=20.93 E-value=1.9e+02 Score=32.91 Aligned_cols=72 Identities=10% Similarity=0.019 Sum_probs=48.2
Q ss_pred HHHHHHHHHHHHHHcCCCCcEEEEc-------CCHHHHHhhhcCCCCcHHHHHHHHHHHHHHhcCCceEEEEecCCCCC
Q psy3428 366 AELIAIFLCLEAILDSPSGKFLIVT-------DSRSSLAALSNVRFINPLITKVYSTWSYLKLCKKDITFMWCPSHCGI 437 (682)
Q Consensus 366 aEl~Ai~~al~~~~~~~~~~v~i~s-------Ds~~~i~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WVpgH~gi 437 (682)
+.+.||...|..+.+.+.+.|.+.- |.-+.+.-.-.....=+....+...+..++..|..|.+-.|+-|++.
T Consensus 30 Gdl~gi~~~ldyl~~lGv~~i~l~P~~~~~~~~~gY~~~d~~~id~~~Gt~~d~~~lv~~~h~~gi~vilD~V~NH~s~ 108 (551)
T PRK10933 30 GDLRGVTQRLDYLQKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTYGTLDDFDELVAQAKSRGIRIILDMVFNHTST 108 (551)
T ss_pred cCHHHHHHhhHHHHhCCCCEEEECCCCCCCCCCCCCCcccCCCcCcccCCHHHHHHHHHHHHHCCCEEEEEECCCCccC
Confidence 3588999999999998888777631 22222111111111112346777788889999999999999999975
No 56
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=20.90 E-value=1.3e+02 Score=29.17 Aligned_cols=28 Identities=21% Similarity=0.143 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHhHhCCccc
Q psy3428 45 DLDLLLQRFQHTLDEIHKWSDLNGTIFS 72 (682)
Q Consensus 45 ~~~~~~~~lq~~l~~~~~W~~~~gl~~n 72 (682)
=..+....||...+.|.+|+...|+.+|
T Consensus 127 L~~~~~~~Lq~K~~~i~~WA~~~gvEv~ 154 (204)
T PF12633_consen 127 LSPEERQLLQQKCDLIEQWAASFGVEVH 154 (204)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHcCCEEE
Confidence 3455677899999999999999999998
Done!