Query psy17815
Match_columns 599
No_of_seqs 278 out of 2185
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 23:44:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17815.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17815hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00075 RNase_H: RNase H; In 99.8 3.4E-20 7.4E-25 165.1 9.0 117 336-460 2-131 (132)
2 PRK06548 ribonuclease H; Provi 99.8 6.6E-19 1.4E-23 158.6 13.2 127 335-463 3-143 (161)
3 PRK08719 ribonuclease H; Revie 99.8 8.3E-19 1.8E-23 157.0 13.4 121 336-461 3-146 (147)
4 PRK00203 rnhA ribonuclease H; 99.8 1.7E-18 3.7E-23 156.9 12.0 124 337-463 3-143 (150)
5 COG0328 RnhA Ribonuclease HI [ 99.8 3.7E-18 8E-23 150.6 10.6 126 337-463 3-146 (154)
6 cd06222 RnaseH RNase H (RNase 99.7 8.1E-16 1.7E-20 135.2 14.0 122 339-460 1-130 (130)
7 cd01650 RT_nLTR_like RT_nLTR: 99.6 3.6E-16 7.8E-21 152.0 7.3 106 10-124 106-220 (220)
8 KOG3752|consensus 99.6 6.4E-15 1.4E-19 145.4 10.8 130 333-462 208-365 (371)
9 cd01648 TERT TERT: Telomerase 99.6 3.6E-15 7.9E-20 129.4 7.9 99 4-125 13-119 (119)
10 PRK13907 rnhA ribonuclease H; 99.5 2.4E-13 5.1E-18 120.1 12.8 119 338-461 2-126 (128)
11 cd01651 RT_G2_intron RT_G2_int 99.5 7.9E-14 1.7E-18 136.1 7.8 94 3-124 119-226 (226)
12 cd03487 RT_Bac_retron_II RT_Ba 99.4 2.1E-13 4.6E-18 131.6 7.0 95 6-127 99-198 (214)
13 cd01646 RT_Bac_retron_I RT_Bac 99.4 7.8E-13 1.7E-17 121.2 7.7 98 4-127 47-147 (158)
14 PF00078 RVT_1: Reverse transc 99.4 7.6E-13 1.7E-17 127.7 5.8 93 3-124 118-214 (214)
15 cd00304 RT_like RT_like: Rever 99.3 1.7E-11 3.7E-16 102.7 8.0 84 11-124 12-98 (98)
16 PRK07708 hypothetical protein; 99.2 1.1E-10 2.3E-15 111.5 14.1 127 333-463 69-209 (219)
17 PRK07238 bifunctional RNase H/ 99.1 7.5E-10 1.6E-14 116.2 13.9 122 337-463 2-133 (372)
18 cd01709 RT_like_1 RT_like_1: A 99.1 1.7E-09 3.7E-14 107.6 13.9 122 5-141 78-211 (346)
19 PF13456 RVT_3: Reverse transc 98.9 5.3E-09 1.2E-13 85.3 8.1 86 372-461 1-86 (87)
20 cd03714 RT_DIRS1 RT_DIRS1: Rev 98.7 5.6E-08 1.2E-12 84.5 7.6 71 11-89 34-106 (119)
21 cd01645 RT_Rtv RT_Rtv: Reverse 98.5 8.9E-08 1.9E-12 92.3 5.7 72 9-88 127-201 (213)
22 KOG4768|consensus 98.3 3.2E-06 7E-11 88.4 10.3 156 8-178 415-641 (796)
23 cd03715 RT_ZFREV_like RT_ZFREV 98.1 2.9E-06 6.2E-11 81.7 5.7 72 9-88 123-197 (210)
24 KOG1005|consensus 97.6 0.00015 3.3E-09 79.4 7.6 109 4-126 628-742 (888)
25 cd01647 RT_LTR RT_LTR: Reverse 97.3 0.00038 8.3E-09 64.3 5.2 72 9-89 94-165 (177)
26 cd01644 RT_pepA17 RT_pepA17: R 96.1 0.0056 1.2E-07 58.7 3.7 66 10-81 103-173 (213)
27 PF13966 zf-RVT: zinc-binding 95.3 0.0078 1.7E-07 48.7 1.3 30 534-563 51-83 (86)
28 cd01699 RNA_dep_RNAP RNA_dep_R 90.6 0.61 1.3E-05 46.7 6.6 78 4-90 153-239 (278)
29 PF00336 DNA_pol_viral_C: DNA 86.2 1.4 3E-05 40.8 5.0 91 335-444 92-184 (245)
30 PF09004 DUF1891: Domain of un 78.6 0.39 8.5E-06 32.6 -1.0 41 130-172 1-41 (42)
31 PF05380 Peptidase_A17: Pao re 74.7 9.2 0.0002 34.7 6.5 52 336-389 80-143 (159)
32 COG3344 Retron-type reverse tr 61.2 5.2 0.00011 41.2 2.1 44 7-50 235-280 (328)
33 PF05741 zf-nanos: Nanos RNA b 55.1 6.3 0.00014 28.6 1.0 19 543-561 34-54 (55)
34 PF13696 zf-CCHC_2: Zinc knuck 43.2 12 0.00026 23.8 0.8 16 543-561 9-26 (32)
35 COG0296 GlgB 1,4-alpha-glucan 42.0 32 0.0007 38.4 4.4 36 418-453 213-248 (628)
36 PF00680 RdRP_1: RNA dependent 36.7 47 0.001 36.3 4.7 78 4-89 299-388 (491)
37 cd07049 BMC_EutL_repeat1 ethan 28.0 1.3E+02 0.0028 25.1 4.6 32 40-71 53-99 (103)
38 COG3716 ManZ Phosphotransferas 27.4 39 0.00084 33.1 1.8 23 12-34 134-156 (269)
39 PF12633 Adenyl_cycl_N: Adenyl 26.2 1E+02 0.0022 29.2 4.3 26 56-81 129-154 (204)
40 CHL00002 matK maturase K 26.1 1.7E+02 0.0038 31.9 6.7 53 35-94 271-324 (504)
41 cd01285 nucleoside_deaminase N 23.5 2.7E+02 0.0058 23.2 6.1 34 369-402 42-75 (109)
42 KOG4602|consensus 23.4 32 0.0007 33.1 0.5 22 541-562 267-290 (318)
43 PF10865 DUF2703: Domain of un 21.8 1.1E+02 0.0024 26.3 3.4 64 57-127 20-83 (120)
No 1
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.82 E-value=3.4e-20 Score=165.06 Aligned_cols=117 Identities=31% Similarity=0.417 Sum_probs=89.2
Q ss_pred CceEEEecCCCCC--CCeeEEEE-eCCcceeeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhc--
Q psy17815 336 NSFICFTDGSKTI--QNTSCAVY-AGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-- 410 (599)
Q Consensus 336 ~~~~i~tDgS~~~--~~~G~~~~-~~~~~~~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~-- 410 (599)
..++||||||... +..|+|++ ..+...++.++ ..+++.||++||..||+.+ . ..+++|+|||++++..+..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~ 77 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWL 77 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhc
Confidence 4689999999653 33466655 44444445566 8999999999999999954 3 4999999999999997776
Q ss_pred ---CCCC---h-HHHHHHHHHHHHhhhCCceEEEEEeCCCCCC-CcchhHHHHHHHhc
Q psy17815 411 ---KNTS---I-PLIAHILNTWHTLKSCGKKVAFLWCPSHTGI-SGNEIVDRATRQLD 460 (599)
Q Consensus 411 ---~~~~---~-~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi-~gNe~AD~~Ak~a~ 460 (599)
.... . ++..+|.+. + .++..|.|.|||||+|+ .|||.||+|||+|+
T Consensus 78 ~~~~~~~~~~~~~i~~~i~~~---~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 78 HGNGWKKTSNGRPIKNEIWEL---L-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHTTSBSCTSSSBHTHHHHHH---H-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cccccccccccccchhheeec---c-ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 3221 1 355555533 3 55899999999999999 69999999999986
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.80 E-value=6.6e-19 Score=158.64 Aligned_cols=127 Identities=26% Similarity=0.289 Sum_probs=92.5
Q ss_pred CCceEEEecCCCCC--CCeeEEEEeCCcceeeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhc--
Q psy17815 335 NNSFICFTDGSKTI--QNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN-- 410 (599)
Q Consensus 335 ~~~~~i~tDgS~~~--~~~G~~~~~~~~~~~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~-- 410 (599)
+..+.||||||... +..|+|++..+......-....++..||++|+..||+.+.. ...++.|+|||+++++.+..
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 34589999999876 34788877332211111123579999999999999987653 34579999999999999993
Q ss_pred -------CCCC--hHHH-HHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHHHHHHHhccCC
Q psy17815 411 -------KNTS--IPLI-AHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 463 (599)
Q Consensus 411 -------~~~~--~~~~-~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~ 463 (599)
.... .++. +++.+.+..+.++ ..|.|.|||||+|.+|||.||+||++|+...
T Consensus 82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 2221 2333 4555555555544 4799999999999999999999999988654
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.79 E-value=8.3e-19 Score=157.00 Aligned_cols=121 Identities=21% Similarity=0.260 Sum_probs=90.2
Q ss_pred CceEEEecCCCCCCC-----eeEEEE--eC--Cc--ceeeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHH
Q psy17815 336 NSFICFTDGSKTIQN-----TSCAVY--AG--GS--AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSA 404 (599)
Q Consensus 336 ~~~~i~tDgS~~~~~-----~G~~~~--~~--~~--~~~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a 404 (599)
..++||||||...+. .|+|++ .. .. .....+....++++||+.|+..||+.+... ..|+|||+++
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 468999999986532 488876 22 22 233345556899999999999999999653 4899999999
Q ss_pred HHHh--------hcCCCC---hHH-HHHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHHHHHHHhcc
Q psy17815 405 LTSI--------ANKNTS---IPL-IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG 461 (599)
Q Consensus 405 ~~~l--------~~~~~~---~~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~ 461 (599)
++.+ .++... .++ -.+++..+..+.. ...|.|.|||||+|++|||.||+||++|+.
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 333321 122 2455555566655 467999999999999999999999999875
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.78 E-value=1.7e-18 Score=156.86 Aligned_cols=124 Identities=18% Similarity=0.186 Sum_probs=89.2
Q ss_pred ceEEEecCCCCC--CCeeEEEE--eCCcce-eeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhcC
Q psy17815 337 SFICFTDGSKTI--QNTSCAVY--AGGSAK-SYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK 411 (599)
Q Consensus 337 ~~~i~tDgS~~~--~~~G~~~~--~~~~~~-~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~~ 411 (599)
.+.||||||... +..|+|++ .++... ........++.+||++|+..||+.+.. ...+.|+|||+++++.|...
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 488999999874 34677766 333222 112234678999999999999998865 46799999999999999851
Q ss_pred --------C-C--ChHHH-HHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHHHHHHHhccCC
Q psy17815 412 --------N-T--SIPLI-AHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 463 (599)
Q Consensus 412 --------~-~--~~~~~-~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~ 463 (599)
. . ..++. .++++.+..+.. ...|.|.|||||+|++|||.||+||++|....
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 1 1 11221 223333333333 37899999999999999999999999998765
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.76 E-value=3.7e-18 Score=150.56 Aligned_cols=126 Identities=21% Similarity=0.183 Sum_probs=99.0
Q ss_pred ceEEEecCCCCC--CCeeEEEE-e-CCcc--eeeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhc
Q psy17815 337 SFICFTDGSKTI--QNTSCAVY-A-GGSA--KSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIAN 410 (599)
Q Consensus 337 ~~~i~tDgS~~~--~~~G~~~~-~-~~~~--~~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~ 410 (599)
.+.||||||... |-.|+|++ . +... .+.... .+|+..+|++|+..||+++.+.+...+.|+|||+++++.|..
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 579999999876 34677766 2 3222 333444 799999999999999999998778999999999999999983
Q ss_pred CCC----C-------hH-HHHHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHHHHHHHhccCC
Q psy17815 411 KNT----S-------IP-LIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 463 (599)
Q Consensus 411 ~~~----~-------~~-~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~ 463 (599)
.-. . .| --.+++..+.++..+...|.+.|||||.|.++||.||+||+.|+...
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 211 0 11 13456666677777767999999999999999999999999998765
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=99.67 E-value=8.1e-16 Score=135.19 Aligned_cols=122 Identities=25% Similarity=0.279 Sum_probs=93.7
Q ss_pred EEEecCCCCCC--CeeEEEE--eCCc-ce--eeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhcC
Q psy17815 339 ICFTDGSKTIQ--NTSCAVY--AGGS-AK--SYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK 411 (599)
Q Consensus 339 ~i~tDgS~~~~--~~G~~~~--~~~~-~~--~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~~ 411 (599)
.+|||||...+ +.|+|++ ..+. .. ........+++.||+.|+..||+++...+..++.|++||+.++..+.+.
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 6788877 2221 11 1122257899999999999999999988899999999999999999987
Q ss_pred CC-ChHHHHHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHHHHHHHhc
Q psy17815 412 NT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLD 460 (599)
Q Consensus 412 ~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~ 460 (599)
.. ...........+..+..+...+.|.|||+|+|+.+|+.||.+||.|.
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 54 22223333333344446778999999999999999999999999873
No 7
>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=99.63 E-value=3.6e-16 Score=152.02 Aligned_cols=106 Identities=30% Similarity=0.585 Sum_probs=92.5
Q ss_pred CCCCCCChHHHHHHHHHhchhhhcC---------CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcc
Q psy17815 10 GIPQGSSLSPLLFIIFLNDLLKIIK---------LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIF 80 (599)
Q Consensus 10 GvpQGs~LSP~Lf~l~~~~l~~~~~---------~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~ 80 (599)
|+|||++|||+||++|++++...+. ..+....||||+++++.+.. ..++..++.+.+|+.++|+++
T Consensus 106 GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~~~-----~~~~~~~~~~~~~~~~~gl~i 180 (220)
T cd01650 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKS-----RKLQELLQRLQEWSKESGLKI 180 (220)
T ss_pred CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEEeccceeeeccCCH-----HHHHHHHHHHHHHHHHcCCEE
Confidence 9999999999999999999988763 56789999999999985443 488899999999999999999
Q ss_pred cCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEE
Q psy17815 81 SADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIW 124 (599)
Q Consensus 81 n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~l 124 (599)
| ++||+++.++...... ..+..++..+..+..+||||+.|
T Consensus 181 n--~~Kt~~~~~~~~~~~~--~~~~~~~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 181 N--PSKSKVMLIGNKKKRL--KDITLNGTPIEAVETFKYLGVTI 220 (220)
T ss_pred C--hhheEEEEecCCCcch--hhhhhcCCcccCCCCCeeccccC
Confidence 9 9999999998766553 23677888899999999999975
No 8
>KOG3752|consensus
Probab=99.58 E-value=6.4e-15 Score=145.41 Aligned_cols=130 Identities=24% Similarity=0.226 Sum_probs=99.4
Q ss_pred cCCCceEEEecCCCCCC-----CeeEEEEeCC---cceeeecC-CcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHH
Q psy17815 333 KFNNSFICFTDGSKTIQ-----NTSCAVYAGG---SAKSYILN-NINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMS 403 (599)
Q Consensus 333 ~~~~~~~i~tDgS~~~~-----~~G~~~~~~~---~~~~~~l~-~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~ 403 (599)
.+.+..++|||||...+ .+|+|||.++ ...++.+. ...+.+.||+.||..||+-+.+.+..+++|.|||+.
T Consensus 208 e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~ 287 (371)
T KOG3752|consen 208 EEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEY 287 (371)
T ss_pred ccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHH
Confidence 34455899999998763 4899999432 24556665 679999999999999999999977889999999999
Q ss_pred HHHHhhcCCC-----------ChH------HHHHHHHHHHHhhh--CCceEEEEEeCCCCCCCcchhHHHHHHHhccC
Q psy17815 404 ALTSIANKNT-----------SIP------LIAHILNTWHTLKS--CGKKVAFLWCPSHTGISGNEIVDRATRQLDGA 462 (599)
Q Consensus 404 a~~~l~~~~~-----------~~~------~~~~i~~~~~~l~~--~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 462 (599)
+++.|...-. .++ .-+..+..+..|.+ ++..|.+.||+||.|+.|||+||.+|++++..
T Consensus 288 ~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 288 FINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred HHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 9999875311 111 12233333344433 46999999999999999999999999998644
No 9
>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=99.58 E-value=3.6e-15 Score=129.38 Aligned_cols=99 Identities=24% Similarity=0.262 Sum_probs=79.9
Q ss_pred cccccCCCCCCCChHHHHHHHHHhchhhhcC-------CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHH-hh
Q psy17815 4 SFPLENGIPQGSSLSPLLFIIFLNDLLKIIK-------LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWS-DT 75 (599)
Q Consensus 4 ~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~-------~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~-~~ 75 (599)
.+...+|+|||++|||+||++|++.+.+.+. .......||||+++++. ....++++++.+..+. .+
T Consensus 13 ~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~------~~~~~~~~~~~l~~~l~~~ 86 (119)
T cd01648 13 YYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITT------SLDKAIKFLNLLLRGFINQ 86 (119)
T ss_pred hhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeC------CHHHHHHHHHHHHHhhHHh
Confidence 4667899999999999999999999887643 34667999999999883 3457788999999997 99
Q ss_pred cCCcccCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEEc
Q psy17815 76 NGLIFSADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIWD 125 (599)
Q Consensus 76 ~gl~~n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~ld 125 (599)
.||.+| ++||++..... .....+.+.|||+.++
T Consensus 87 ~gl~iN--~~Kt~~~~~~~---------------~~~~~~~~~flG~~i~ 119 (119)
T cd01648 87 YKTFVN--FDKTQINFSFA---------------QLDSSDLIPWCGLLIN 119 (119)
T ss_pred hCeEEC--cccceeecccc---------------ccCCCCccCceeEeeC
Confidence 999999 99999876432 0123456899999875
No 10
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.50 E-value=2.4e-13 Score=120.06 Aligned_cols=119 Identities=18% Similarity=0.117 Sum_probs=89.5
Q ss_pred eEEEecCCCCC--CCeeEEEEe--C-Cc-ceeeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhcC
Q psy17815 338 FICFTDGSKTI--QNTSCAVYA--G-GS-AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANK 411 (599)
Q Consensus 338 ~~i~tDgS~~~--~~~G~~~~~--~-~~-~~~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~~ 411 (599)
+.||||||... +..|+|++. . +. ...+. ....++..||+.|++.||+.+...+..++.|+|||+.++..+.+.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence 57999999875 457888772 2 21 12222 235789999999999999999998778999999999999999885
Q ss_pred CCChHHHHHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHHHHHHHhcc
Q psy17815 412 NTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDG 461 (599)
Q Consensus 412 ~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~ 461 (599)
.....-...+...+..+..+-..+.|.|||. ++|+.||.+|+.|..
T Consensus 81 ~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred HhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 4333233444444445555667888899998 499999999999864
No 11
>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=99.47 E-value=7.9e-14 Score=136.05 Aligned_cols=94 Identities=31% Similarity=0.528 Sum_probs=79.7
Q ss_pred CcccccCCCCCCCChHHHHHHHHHhchhhhcC--------------CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHH
Q psy17815 3 RSFPLENGIPQGSSLSPLLFIIFLNDLLKIIK--------------LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNA 68 (599)
Q Consensus 3 ~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~--------------~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~ 68 (599)
..+...+|||||+++||+||++|++++...+. ..+....||||+++++.+ ...++.+++.
T Consensus 119 ~~~~~~~GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~------~~~~~~~~~~ 192 (226)
T cd01651 119 KLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRG------PKEAEEIKEL 192 (226)
T ss_pred eEeCCCCCcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCC------HHHHHHHHHH
Confidence 35678899999999999999999999977643 557889999999999843 3348889999
Q ss_pred HHHHHhhcCCcccCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEE
Q psy17815 69 IKTWSDTNGLIFSADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIW 124 (599)
Q Consensus 69 l~~w~~~~gl~~n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~l 124 (599)
+..|++..|+.+| ++||+++.++ .+.+.|||+.|
T Consensus 193 i~~~~~~~gl~ln--~~Kt~i~~~~--------------------~~~~~fLG~~~ 226 (226)
T cd01651 193 IREFLEELGLELN--PEKTRITHFK--------------------SEGFDFLGFTF 226 (226)
T ss_pred HHHHHHHcCCeec--hhhcceeecC--------------------CCCCeeCCeEC
Confidence 9999999999999 9999999985 34578899864
No 12
>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=99.42 E-value=2.1e-13 Score=131.59 Aligned_cols=95 Identities=19% Similarity=0.245 Sum_probs=78.8
Q ss_pred cccCCCCCCCChHHHHHHHHHhchhhhcC-----CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcc
Q psy17815 6 PLENGIPQGSSLSPLLFIIFLNDLLKIIK-----LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIF 80 (599)
Q Consensus 6 ~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~-----~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~ 80 (599)
....|||||+++||+||++|++++...+. .++....||||+++++.+... ..+++++..+..|+.+.||.+
T Consensus 99 ~~~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaDD~~i~~~~~~~----~~~~~~~~~i~~~l~~~gL~l 174 (214)
T cd03487 99 TYNGHLPQGAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYADDITFSSNKKLK----EALDKLLEIIRSILSEEGFKI 174 (214)
T ss_pred hCCCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEeccEEEEccccch----hHHHHHHHHHHHHHHHCCcee
Confidence 34569999999999999999999877653 568899999999998844331 478889999999999999999
Q ss_pred cCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEEccC
Q psy17815 81 SADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIWDSK 127 (599)
Q Consensus 81 n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~ld~~ 127 (599)
| ++||+++..+ ..+.+||+.+.+.
T Consensus 175 n--~~Kt~i~~~~---------------------~~~~~~G~~i~~~ 198 (214)
T cd03487 175 N--KSKTRISSKG---------------------SRQIVTGLVVNNG 198 (214)
T ss_pred C--CCceEEccCC---------------------CCcEEEEEEEeCC
Confidence 9 9999988853 3366899999764
No 13
>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=99.38 E-value=7.8e-13 Score=121.24 Aligned_cols=98 Identities=22% Similarity=0.345 Sum_probs=81.6
Q ss_pred cccccCCCCCCCChHHHHHHHHHhchhhhcC---CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcc
Q psy17815 4 SFPLENGIPQGSSLSPLLFIIFLNDLLKIIK---LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIF 80 (599)
Q Consensus 4 ~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~ 80 (599)
.....+|||||+++||+|+++|+.++-..+. ..+....||||+++++. ....++++++.+..|+.+.||.+
T Consensus 47 ~~~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~------~~~~~~~~~~~i~~~l~~~gL~l 120 (158)
T cd01646 47 QYGQTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFAD------SKEEAEEILEELKEFLAELGLSL 120 (158)
T ss_pred cCCCCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcC------CHHHHHHHHHHHHHHHHHCCCEE
Confidence 3456789999999999999999999877654 67889999999999983 34567889999999999999999
Q ss_pred cCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEEccC
Q psy17815 81 SADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIWDSK 127 (599)
Q Consensus 81 n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~ld~~ 127 (599)
| ++||+.+.+.... .++.+||..+...
T Consensus 121 n--~~Kt~~~~~~~~~------------------~~~~flg~~~~~~ 147 (158)
T cd01646 121 N--LSKTEILPLPEGT------------------ASKDFLGYRFSPI 147 (158)
T ss_pred C--hhhceeeecCCCC------------------ccccccceEeehh
Confidence 9 9999999875321 4567888888653
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=99.35 E-value=7.6e-13 Score=127.73 Aligned_cols=93 Identities=37% Similarity=0.643 Sum_probs=78.7
Q ss_pred CcccccCCCCCCCChHHHHHHHHHhchhhhcC----CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCC
Q psy17815 3 RSFPLENGIPQGSSLSPLLFIIFLNDLLKIIK----LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGL 78 (599)
Q Consensus 3 ~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~----~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl 78 (599)
......+|+|||+++||+||++|++++...+. +++.+..||||+.+++. ....+++.++.+.+|+.+.||
T Consensus 118 ~~~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~------~~~~~~~~~~~i~~~~~~~gl 191 (214)
T PF00078_consen 118 SPYFQKRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLRYADDILIISK------SKEELQKILEKISQWLEELGL 191 (214)
T ss_dssp SEEEEESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETTEEEEEES------SHHHHHHHHHHHHHHHHHTTS
T ss_pred ccccccccccccccccchhhccccccccccccccccccccceEeccccEEEEC------CHHHHHHHHHHHHHHHHHCCC
Confidence 34677899999999999999999999988754 46889999999999994 455689999999999999999
Q ss_pred cccCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEE
Q psy17815 79 IFSADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIW 124 (599)
Q Consensus 79 ~~n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~l 124 (599)
.+| ++||+.++ ..+.++|||+.+
T Consensus 192 ~ln--~~Kt~~~~---------------------~~~~~~~lG~~i 214 (214)
T PF00078_consen 192 KLN--PEKTKILH---------------------PSDSVKFLGYVI 214 (214)
T ss_dssp BCS--STTTSCS-----------------------ESSEEETTEEE
T ss_pred EEC--hHHEEEEe---------------------CCCCEEEEeEEC
Confidence 999 99999665 457799999875
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=99.25 E-value=1.7e-11 Score=102.74 Aligned_cols=84 Identities=29% Similarity=0.489 Sum_probs=71.1
Q ss_pred CCCCCChHHHHHHHHHhchhhhcC---CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcccCCCCCe
Q psy17815 11 IPQGSSLSPLLFIIFLNDLLKIIK---LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIFSADPQKS 87 (599)
Q Consensus 11 vpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~n~~~~Kt 87 (599)
+|||+++||+||+++++.+...+. .++....||||+++++... .++..+..+..++.+.|+.+| ++||
T Consensus 12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~-------~~~~~~~~l~~~l~~~gl~ln--~~Kt 82 (98)
T cd00304 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE-------QQAVKKRELEEFLARLGLNLS--DEKT 82 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH-------HHHHHHHHHHHHHHHcCcEEC--hhee
Confidence 999999999999999999988753 5778999999999988432 677888899999999999999 9999
Q ss_pred eEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEE
Q psy17815 88 VCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIW 124 (599)
Q Consensus 88 ~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~l 124 (599)
+... ....++|||+.+
T Consensus 83 ~~~~---------------------~~~~~~flG~~~ 98 (98)
T cd00304 83 QFTE---------------------KEKKFKFLGILV 98 (98)
T ss_pred EEec---------------------CCCCeeeeceeC
Confidence 9751 245688999753
No 16
>PRK07708 hypothetical protein; Validated
Probab=99.25 E-value=1.1e-10 Score=111.47 Aligned_cols=127 Identities=14% Similarity=0.099 Sum_probs=91.4
Q ss_pred cCCCceEEEecCCCCC--CCeeEEEE--eC-C-cce----eeecCCcccchhHHHHHHHHHHHHhhcCCCCc--EEEEec
Q psy17815 333 KFNNSFICFTDGSKTI--QNTSCAVY--AG-G-SAK----SYILNNINSIFTAELLALVFCLDSVKNRPDVN--TLIVCD 400 (599)
Q Consensus 333 ~~~~~~~i~tDgS~~~--~~~G~~~~--~~-~-~~~----~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~--~~i~sD 400 (599)
..++.+.+|+|||... +..|+|++ .. + ... ...++...++..||..|++.||+.+.+.+.++ |.|++|
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 4556799999999753 56788866 22 2 211 12455568999999999999999999865544 899999
Q ss_pred cHHHHHHhhcCCCC-hHHHHHHHHHHHHh-hhCCceEEEEEeCCCCCCCcchhHHHHHHHhccCC
Q psy17815 401 SMSALTSIANKNTS-IPLIAHILNTWHTL-KSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 463 (599)
Q Consensus 401 s~~a~~~l~~~~~~-~~~~~~i~~~~~~l-~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~ 463 (599)
|+.++..+.+.... ++..+...+.+..+ .+-...+.+.|||- ..|+.||+||+.|....
T Consensus 149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR----~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISR----KQNKEADQLATQALEGT 209 (219)
T ss_pred cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCc----hhhhHHHHHHHHHHhcC
Confidence 99999999986432 33333444433333 33345688899975 56999999999999765
No 17
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.11 E-value=7.5e-10 Score=116.21 Aligned_cols=122 Identities=16% Similarity=0.189 Sum_probs=91.7
Q ss_pred ceEEEecCCCCCC--CeeEEEE--eC--Cc---ceeeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHH
Q psy17815 337 SFICFTDGSKTIQ--NTSCAVY--AG--GS---AKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTS 407 (599)
Q Consensus 337 ~~~i~tDgS~~~~--~~G~~~~--~~--~~---~~~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~ 407 (599)
.+.||||||...+ ..|+|++ +. +. .....++ ..++..||+.|++.||+.+.+.+..++.|++||+.+++.
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 3689999998763 5788876 32 21 1223344 677889999999999999999878899999999999999
Q ss_pred hhcCCC-ChHHHHHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHHHHHHHhccCC
Q psy17815 408 IANKNT-SIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVDRATRQLDGAE 463 (599)
Q Consensus 408 l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~ 463 (599)
+.+... .++-.......+..+..+-..+.+.|||. .+|+.||.||+.|....
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAA 133 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhh
Confidence 987543 22333333444455555667899999997 68999999999987554
No 18
>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=99.08 E-value=1.7e-09 Score=107.64 Aligned_cols=122 Identities=16% Similarity=0.140 Sum_probs=83.7
Q ss_pred ccccCCCCCCCChHHHHHHHHHhchhhhcC---CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCccc
Q psy17815 5 FPLENGIPQGSSLSPLLFIIFLNDLLKIIK---LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIFS 81 (599)
Q Consensus 5 ~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~n 81 (599)
..-.+|+|||+++||+|-++|++.+-..+. .++.+.-||||++++++ .+....+...+.++++..||++|
T Consensus 78 r~r~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~-------~~~a~~aw~~i~~fl~~lGLelN 150 (346)
T cd01709 78 RIRKRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ-------PETCAKAWKAIQEFAKVMGLELN 150 (346)
T ss_pred cccCCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC-------HHHHHHHHHHHHHHHHHcCceec
Confidence 344579999999999999999996655554 57889999999999852 23455566788899999999999
Q ss_pred CCCCCeeEEEeccCCCC-CCCceeeeCCeEeeecccceeeeeEEccC-CCh-------HHHHHHHHHHH
Q psy17815 82 ADPQKSVCVDFTRLRSR-SVPLTLYYSDKELKFVDKTKFLGLIWDSK-LSW-------GPHVEYVKSRA 141 (599)
Q Consensus 82 ~~~~Kt~~~~~~~~~~~-~~~~~~~~~~~~I~~~~~~kyLGv~ld~~-l~~-------~~hi~~~~~ka 141 (599)
++||.++......+. .....-.+ |.-.++|-=+.||+. .+| ..||++..++.
T Consensus 151 --~eKT~iV~~~~~~r~~~~~~~~~L------P~g~i~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~QL 211 (346)
T cd01709 151 --KEKTGSVYLSDDTKTRDTTIDATL------PEGPVRWGFLKLDPKTGRWEIDQSQVDAHIDELRKQL 211 (346)
T ss_pred --cccceEEEeccCCccCCCcccccC------CCCCceeeeEEecCCCCcEEeeHHHHHHHHHHHHHHh
Confidence 999999988754331 11011111 334466655556654 444 45555554444
No 19
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.90 E-value=5.3e-09 Score=85.31 Aligned_cols=86 Identities=17% Similarity=0.131 Sum_probs=65.5
Q ss_pred chhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhcCCCChHHHHHHHHHHHHhhhCCceEEEEEeCCCCCCCcchh
Q psy17815 372 IFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEI 451 (599)
Q Consensus 372 v~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~ 451 (599)
+..||+.|+..||+++...+..++.|.|||+.++..|.+..........+...+..+.+.-..+.+.||| -++|..
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 4579999999999999999999999999999999999887433213334444445565667899999999 689999
Q ss_pred HHHHHHHhcc
Q psy17815 452 VDRATRQLDG 461 (599)
Q Consensus 452 AD~~Ak~a~~ 461 (599)
||.+||.|.+
T Consensus 77 A~~LA~~a~~ 86 (87)
T PF13456_consen 77 ADALAKFALS 86 (87)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHhh
Confidence 9999999864
No 20
>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=98.68 E-value=5.6e-08 Score=84.50 Aligned_cols=71 Identities=28% Similarity=0.483 Sum_probs=55.9
Q ss_pred CCCCCChHHHHHHHHHhchhhhcC-CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHH-HHhhcCCcccCCCCCee
Q psy17815 11 IPQGSSLSPLLFIIFLNDLLKIIK-LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKT-WSDTNGLIFSADPQKSV 88 (599)
Q Consensus 11 vpQGs~LSP~Lf~l~~~~l~~~~~-~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~-w~~~~gl~~n~~~~Kt~ 88 (599)
+|||-..||.+|.-+|+.+...+. ....+..|+||+.|.+.+ .+..++.+..+.. .++++|+.+| ++||+
T Consensus 34 mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~------~~~~~~~~~~l~~~~l~~~gl~ln--~~K~~ 105 (119)
T cd03714 34 LPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASS------IKTSEAVLRHLRATLLANLGFTLN--LEKSK 105 (119)
T ss_pred cCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCc------HHHHHHHHHHHHHHHHHHcCCccC--hhhcE
Confidence 799999999999999999998654 456789999999998854 2233334444433 6889999999 99999
Q ss_pred E
Q psy17815 89 C 89 (599)
Q Consensus 89 ~ 89 (599)
.
T Consensus 106 ~ 106 (119)
T cd03714 106 L 106 (119)
T ss_pred e
Confidence 6
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=98.55 E-value=8.9e-08 Score=92.27 Aligned_cols=72 Identities=24% Similarity=0.382 Sum_probs=61.1
Q ss_pred CCCCCCCChHHHHHHHHHhchhhhcC---CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcccCCCC
Q psy17815 9 NGIPQGSSLSPLLFIIFLNDLLKIIK---LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIFSADPQ 85 (599)
Q Consensus 9 ~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~n~~~~ 85 (599)
+++|||...||.+|+.+|+.++..+. ....+..|+||++|.+ .+.+...+.++.+...+.+.|+.+| ++
T Consensus 127 ~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s------~~~~~~~~~l~~v~~~l~~~gl~ln--~~ 198 (213)
T cd01645 127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIAS------DLEGQLREIYEELRQTLLRWGLTIP--PE 198 (213)
T ss_pred EEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEc------CCHHHHHHHHHHHHHHHHHCCCEeC--HH
Confidence 57999999999999999999988654 3456889999999987 3445667778888888899999999 99
Q ss_pred Cee
Q psy17815 86 KSV 88 (599)
Q Consensus 86 Kt~ 88 (599)
||+
T Consensus 199 K~~ 201 (213)
T cd01645 199 KVQ 201 (213)
T ss_pred HEe
Confidence 987
No 22
>KOG4768|consensus
Probab=98.30 E-value=3.2e-06 Score=88.44 Aligned_cols=156 Identities=17% Similarity=0.209 Sum_probs=99.6
Q ss_pred cCCCCCCCChHHHHHHHHHhchhhhcC-----------------------------------------------------
Q psy17815 8 ENGIPQGSSLSPLLFIIFLNDLLKIIK----------------------------------------------------- 34 (599)
Q Consensus 8 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~----------------------------------------------------- 34 (599)
.-|+||||+.||+|.++|+..|-+-++
T Consensus 415 ~lGtpqgsvvspil~nifL~~LDk~Lenk~~nefn~~~~~~~rhs~yr~L~~~iakaKl~s~~sKtirlrd~~qrn~~n~ 494 (796)
T KOG4768|consen 415 FLGTPQGSVVSPILCNIFLRELDKRLENKHRNEFNAGHLRSARHSKYRNLSDSIAKAKLTSGMSKTIRLRDGVQRNETND 494 (796)
T ss_pred cccccccccCCchhHHHHHHHHHHHHHHHHHhhhcccCcccccChhhhhHHHHHHHHHHhhhhhhhhhhhhcccccccCC
Confidence 359999999999999999987754331
Q ss_pred ----CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcccCCCCCeeEEEeccCCCCCCCceeeeCCeE
Q psy17815 35 ----LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIFSADPQKSVCVDFTRLRSRSVPLTLYYSDKE 110 (599)
Q Consensus 35 ----~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~ 110 (599)
.....+.||||+.+.+.|. .....+.+..+..++.+.|+++| ++||++.+-... ..+-|..
T Consensus 495 ~~gfkr~~yVRyadd~ii~v~GS-----~nd~K~ilr~In~f~sslGls~n--~~kt~it~S~eg--------~~flg~n 559 (796)
T KOG4768|consen 495 TAGFKRLMYVRYADDIIIGVWGS-----VNDCKQILRDINNFLSSLGLSNN--SSKTQITVSREG--------THFLGYN 559 (796)
T ss_pred ccccceeeEEEecCCEEEEEecc-----HHHHHHHHHHHHHHHHhhCcccC--cccceEEeeccc--------eeeeece
Confidence 0133588999999988755 34566778888899999999999 999998764322 1222222
Q ss_pred eeec-------ccceeeeeEEccC--CChHHHHHHHHHHHHHhhhhhhhhc-----cCCCCCCHHHHHHHHHHhcccccc
Q psy17815 111 LKFV-------DKTKFLGLIWDSK--LSWGPHVEYVKSRALNAMNVLKIVS-----NKNYGLHRQTLLKLYQSYVSPIID 176 (599)
Q Consensus 111 I~~~-------~~~kyLGv~ld~~--l~~~~hi~~~~~ka~~~~~~L~~l~-----~~~~g~~~~~~~~l~~~~v~p~l~ 176 (599)
|... ..-+.-|+-+.+. .....-|+.+..|.+..-.-..... ...-.....+....|+++.+..+.
T Consensus 560 is~tP~r~~~~~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~ln 639 (796)
T KOG4768|consen 560 ISTTPGRPAAGEGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYCSHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILN 639 (796)
T ss_pred eccCCCCccceeccccceEEeccCCceeecchHHHHHHHHHhcceeecCCcCceeeeeecccCHHHHHHHHHHHhhchhh
Confidence 2211 1111112222221 2234556667777766533322111 011246788889999999999999
Q ss_pred cc
Q psy17815 177 YG 178 (599)
Q Consensus 177 Yg 178 (599)
|-
T Consensus 640 YY 641 (796)
T KOG4768|consen 640 YY 641 (796)
T ss_pred hh
Confidence 85
No 23
>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=98.15 E-value=2.9e-06 Score=81.67 Aligned_cols=72 Identities=26% Similarity=0.262 Sum_probs=60.4
Q ss_pred CCCCCCCChHHHHHHHHHhchhhhcC---CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcccCCCC
Q psy17815 9 NGIPQGSSLSPLLFIIFLNDLLKIIK---LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIFSADPQ 85 (599)
Q Consensus 9 ~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~n~~~~ 85 (599)
+-+|||-..||.+|.-+|+.++..+. .+..+..|.||+.|++ .+.+...+.++.+...++++|+.+| ++
T Consensus 123 ~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DDili~s------~~~~e~~~~l~~v~~~l~~~gl~l~--~~ 194 (210)
T cd03715 123 TRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAA------DSEEDCLKGTDALLTHLGELGYKVS--PK 194 (210)
T ss_pred EEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCcEEEec------CCHHHHHHHHHHHHHHHHHCCCCcC--HH
Confidence 45899999999999999999988653 4567789999999987 3445566677888888899999999 99
Q ss_pred Cee
Q psy17815 86 KSV 88 (599)
Q Consensus 86 Kt~ 88 (599)
||+
T Consensus 195 K~~ 197 (210)
T cd03715 195 KAQ 197 (210)
T ss_pred Hee
Confidence 998
No 24
>KOG1005|consensus
Probab=97.58 E-value=0.00015 Score=79.36 Aligned_cols=109 Identities=22% Similarity=0.284 Sum_probs=76.5
Q ss_pred cccccCCCCCCCChHHHHHHHHHhchhhhc-C----CC-cEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcC
Q psy17815 4 SFPLENGIPQGSSLSPLLFIIFLNDLLKII-K----LP-LRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNG 77 (599)
Q Consensus 4 ~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~-~----~~-~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~g 77 (599)
.+....|+||||+||-+|.-+|++++.+.. . ++ +.++-|+||+.++++ ...++...+..+..=..+.+
T Consensus 628 ~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt------~~~~a~kfl~~l~~Gf~~yn 701 (888)
T KOG1005|consen 628 SYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITT------ENDQAKKFLKLLSRGFNKYN 701 (888)
T ss_pred EEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEec------CHHHHHHHHHHHhccccccc
Confidence 355678999999999999999999998863 2 22 478999999999994 44567777788877778888
Q ss_pred CcccCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEEcc
Q psy17815 78 LIFSADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIWDS 126 (599)
Q Consensus 78 l~~n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~ld~ 126 (599)
...| ..||. -|......... ..+.+..+ ..-+.|-|+.+++
T Consensus 702 ~~tn--~~K~~--nF~~se~~~~~--~~f~~~~~--~~~f~w~g~~i~s 742 (888)
T KOG1005|consen 702 FFTN--EPKTV--NFEVSEECGAS--IVFVWMHK--HLLFQWCGLLIRS 742 (888)
T ss_pred eecc--Ccccc--cccchhccCcc--eeeeccCc--cccccccceeeec
Confidence 8888 88987 55544433221 11111111 1446677777765
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=97.26 E-value=0.00038 Score=64.30 Aligned_cols=72 Identities=21% Similarity=0.311 Sum_probs=55.3
Q ss_pred CCCCCCCChHHHHHHHHHhchhhhcCCCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCcccCCCCCee
Q psy17815 9 NGIPQGSSLSPLLFIIFLNDLLKIIKLPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIFSADPQKSV 88 (599)
Q Consensus 9 ~GvpQGs~LSP~Lf~l~~~~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~n~~~~Kt~ 88 (599)
+.+|||...||.+|.-++..++..+. ...+..|+||+.+.+. ........++.+..-.++.|+.+| ++||+
T Consensus 94 ~~~p~G~~~s~~~~~~~~~~~l~~~~-~~~~~~y~DDi~i~~~------~~~~~~~~~~~~~~~l~~~~~~~~--~~K~~ 164 (177)
T cd01647 94 TRMPFGLKNAPATFQRLMNKILGDLL-GDFVEVYLDDILVYSK------TEEEHLEHLREVLERLREAGLKLN--PEKCE 164 (177)
T ss_pred EEecCCCccHHHHHHHHHHhhhcccc-ccccEEEecCccccCC------CHHHHHHHHHHHHHHHHHcCCEeC--HHHce
Confidence 46999999999999999999887653 2346789999999873 233444555666666678899999 99987
Q ss_pred E
Q psy17815 89 C 89 (599)
Q Consensus 89 ~ 89 (599)
.
T Consensus 165 ~ 165 (177)
T cd01647 165 F 165 (177)
T ss_pred e
Confidence 3
No 26
>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=96.05 E-value=0.0056 Score=58.73 Aligned_cols=66 Identities=15% Similarity=0.245 Sum_probs=52.3
Q ss_pred CCCCCCChHHHHHHHHHhchhhhcCC-----CcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHhhcCCccc
Q psy17815 10 GIPQGSSLSPLLFIIFLNDLLKIIKL-----PLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSDTNGLIFS 81 (599)
Q Consensus 10 GvpQGs~LSP~Lf~l~~~~l~~~~~~-----~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gl~~n 81 (599)
-+|+|-.-||.+|..+|+.+...+.. .+....|+||+.+.+ .+.+.++..+..+.+.+++.|+.+.
T Consensus 103 ~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~------~s~~e~~~~~~~v~~~L~~~Gf~l~ 173 (213)
T cd01644 103 VVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVST------DTLNEAVNVAKRLIALLKKGGFNLR 173 (213)
T ss_pred EEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecC------CCHHHHHHHHHHHHHHHHhCCccch
Confidence 48999999999999999999987653 245679999999977 4455666667777777778887765
No 27
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.30 E-value=0.0078 Score=48.71 Aligned_cols=30 Identities=30% Similarity=0.396 Sum_probs=24.2
Q ss_pred ccccCCCCCCCcc-CC-cccchhHhh-hccCcc
Q psy17815 534 SYLFTRSDPPSCQ-CG-LPLTIRHLL-ECRSYI 563 (599)
Q Consensus 534 ~~~~~~~~~~~C~-Cg-~~~t~~H~l-~Cp~~~ 563 (599)
+++.+...++.|. |+ ++||++|+| +||...
T Consensus 51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred hhccCCccCCccccCCCccccccceeccCcCcc
Confidence 3445556789999 99 589999999 999754
No 28
>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=90.60 E-value=0.61 Score=46.71 Aligned_cols=78 Identities=18% Similarity=0.342 Sum_probs=53.9
Q ss_pred cccccCCCCCCCChH----HHHHHHHHhchhhhc-----CCCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHHHHh
Q psy17815 4 SFPLENGIPQGSSLS----PLLFIIFLNDLLKII-----KLPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKTWSD 74 (599)
Q Consensus 4 ~~~~~~GvpQGs~LS----P~Lf~l~~~~l~~~~-----~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~ 74 (599)
.+....|+|+|+++. +++=++++......+ ...+....|.||.++.+... ......+.+..+.+
T Consensus 153 ~~~~~~G~pSG~~~T~~~Nsl~n~~~~~~a~~~~~~~~~~~~~~~~~~GDD~li~~~~~-------~~~~~~~~~~~~~~ 225 (278)
T cd01699 153 VYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKA-------DDKFNLETLAEWLK 225 (278)
T ss_pred EEEEcCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEcCCeEEEechh-------HhhhCHHHHHHHHH
Confidence 356678999999885 555555555554432 35678899999999988321 11223456778888
Q ss_pred hcCCcccCCCCCeeEE
Q psy17815 75 TNGLIFSADPQKSVCV 90 (599)
Q Consensus 75 ~~gl~~n~~~~Kt~~~ 90 (599)
+.|+.++ ++|....
T Consensus 226 ~~G~~~~--~~~~~~~ 239 (278)
T cd01699 226 EYGLTMT--DEDKVES 239 (278)
T ss_pred HcCCEeC--CcccCCC
Confidence 8999999 8887754
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=86.17 E-value=1.4 Score=40.76 Aligned_cols=91 Identities=20% Similarity=0.170 Sum_probs=52.5
Q ss_pred CCceEEEecCCCCCCCeeEEEEeCCcceeeecCCcccchhHHHHHHHHHHHHhhcCCCCcEEEEeccHHHHHHhhcCCCC
Q psy17815 335 NNSFICFTDGSKTIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTS 414 (599)
Q Consensus 335 ~~~~~i~tDgS~~~~~~G~~~~~~~~~~~~~l~~~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~~a~~~l~~~~~~ 414 (599)
+.--.||+|+.- +|.|+..++....+....---|..||++|.-.|.-+. ..++ |.|||..++..=-...+-
T Consensus 92 ~~lc~VfaDATp----Tgwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vlsrkyts~PW 162 (245)
T PF00336_consen 92 PGLCQVFADATP----TGWGISITGQRMRGTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVLSRKYTSFPW 162 (245)
T ss_pred CCCCceeccCCC----CcceeeecCceeeeeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEEecccccCcH
Confidence 334689999876 3444443333222222234568899999998887766 3444 999998766432211110
Q ss_pred --hHHHHHHHHHHHHhhhCCceEEEEEeCCCC
Q psy17815 415 --IPLIAHILNTWHTLKSCGKKVAFLWCPSHT 444 (599)
Q Consensus 415 --~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~ 444 (599)
.-...+|. ..+.|..||+--
T Consensus 163 ~lac~A~wiL----------rgts~~yVPS~~ 184 (245)
T PF00336_consen 163 LLACAANWIL----------RGTSFYYVPSKY 184 (245)
T ss_pred HHHHHHHHhh----------cCceEEEecccc
Confidence 01223333 457888899753
No 30
>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=78.58 E-value=0.39 Score=32.59 Aligned_cols=41 Identities=15% Similarity=0.394 Sum_probs=7.2
Q ss_pred hHHHHHHHHHHHHHhhhhhhhhccCCCCCCHHHHHHHHHHhcc
Q psy17815 130 WGPHVEYVKSRALNAMNVLKIVSNKNYGLHRQTLLKLYQSYVS 172 (599)
Q Consensus 130 ~~~hi~~~~~ka~~~~~~L~~l~~~~~g~~~~~~~~l~~~~v~ 172 (599)
|+.|+....+|++.++..|+.+.. ..+++..+..+|+++|.
T Consensus 1 W~~n~~~~~KKa~qRlyFLRkl~k--~~~~~~~l~lfY~s~Ie 41 (42)
T PF09004_consen 1 WTSNTTSLYKKAQQRLYFLRKLRK--FNVDSKLLTLFYHSVIE 41 (42)
T ss_dssp ---------------------------SS-----SHTTTTT--
T ss_pred CCcchHHHHHHHHhHHHHHHHHHH--ccchhHHHHHHHHHHhc
Confidence 678899999999999999998864 46778888888887764
No 31
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=74.73 E-value=9.2 Score=34.72 Aligned_cols=52 Identities=23% Similarity=0.282 Sum_probs=34.3
Q ss_pred CceEEEecCCCCCCCeeEEEE--e-C-Cc-c-----eeeecC--CcccchhHHHHHHHHHHHHhhc
Q psy17815 336 NSFICFTDGSKTIQNTSCAVY--A-G-GS-A-----KSYILN--NINSIFTAELLALVFCLDSVKN 389 (599)
Q Consensus 336 ~~~~i~tDgS~~~~~~G~~~~--~-~-~~-~-----~~~~l~--~~~sv~~aEl~ai~~al~~~~~ 389 (599)
..+++|+|+|. .+.|+.+| . . +. . .+.+.. ...|+=+-|++|+..|.+++..
T Consensus 80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 46899999995 34565555 1 1 11 1 111222 2459999999999999999864
No 32
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=61.16 E-value=5.2 Score=41.18 Aligned_cols=44 Identities=34% Similarity=0.344 Sum_probs=35.1
Q ss_pred ccCCCCCCCChHHHHHHHHHhchhhhcCCC--cEEEEEecCeEEEE
Q psy17815 7 LENGIPQGSSLSPLLFIIFLNDLLKIIKLP--LRSMLFIDDLLIIS 50 (599)
Q Consensus 7 ~~~GvpQGs~LSP~Lf~l~~~~l~~~~~~~--~~~~~yADD~~i~~ 50 (599)
-..|+|||+++||+|-++.++.+...+..- .....|+||..+-.
T Consensus 235 ~~~~~~q~~~vs~~l~n~~l~~~~~~~~~~~~~~~~~y~~~~~i~~ 280 (328)
T COG3344 235 KEKGTPQGGLVSPILVNIKLSKLDNELRNRYLNLLRRYIDDGNIDK 280 (328)
T ss_pred ccccCCCCCccCchhhhhhhhhhhHHHHHHHhhhhhhhcccccCCH
Confidence 567999999999999999998887765411 13568999999866
No 33
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=55.13 E-value=6.3 Score=28.60 Aligned_cols=19 Identities=26% Similarity=0.560 Sum_probs=8.3
Q ss_pred CCcc-CCcccchhHhh-hccC
Q psy17815 543 PSCQ-CGLPLTIRHLL-ECRS 561 (599)
Q Consensus 543 ~~C~-Cg~~~t~~H~l-~Cp~ 561 (599)
-.|+ ||+..+-.|.. .||+
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 4799 99999999999 9996
No 34
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=43.24 E-value=12 Score=23.83 Aligned_cols=16 Identities=31% Similarity=0.895 Sum_probs=12.9
Q ss_pred CCcc-CCcccchhHhh-hccC
Q psy17815 543 PSCQ-CGLPLTIRHLL-ECRS 561 (599)
Q Consensus 543 ~~C~-Cg~~~t~~H~l-~Cp~ 561 (599)
-.|. |+... |++ +||.
T Consensus 9 Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CEeecCCCCC---ccHhHCCC
Confidence 4588 88655 999 9998
No 35
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=42.04 E-value=32 Score=38.38 Aligned_cols=36 Identities=19% Similarity=0.286 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhhhCCceEEEEEeCCCCCCCcchhHH
Q psy17815 418 IAHILNTWHTLKSCGKKVAFLWCPSHTGISGNEIVD 453 (599)
Q Consensus 418 ~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD 453 (599)
..+.+..+...++.|..|-+-|||+|.+..||-.+-
T Consensus 213 Pedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~ 248 (628)
T COG0296 213 PEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLAR 248 (628)
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhh
Confidence 567777788999999999999999999998887664
No 36
>PF00680 RdRP_1: RNA dependent RNA polymerase; InterPro: IPR001205 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This entry represents RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses viruses. It is part of the genome polyprotein that contains other polypeptides such as coat proteins VP1 to VP4, core proteins P2A to P2C and P3A, genome-linked protein VPG and picornain 3C (3.4.22.28 from EC). Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [, ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SFU_C 3NAH_A 3UR0_C 3UPF_C 3SFG_A 3NAI_C 3QID_B 3UQS_A 3OLB_M 3OLA_M ....
Probab=36.69 E-value=47 Score=36.32 Aligned_cols=78 Identities=19% Similarity=0.234 Sum_probs=49.9
Q ss_pred cccccCCCCCCCChHHHHHHHHHhch----hhhcC-----C---CcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHHH
Q psy17815 4 SFPLENGIPQGSSLSPLLFIIFLNDL----LKIIK-----L---PLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIKT 71 (599)
Q Consensus 4 ~~~~~~GvpQGs~LSP~Lf~l~~~~l----~~~~~-----~---~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~ 71 (599)
.+.+..|+|=|+++--++=.++..=+ ...+. . .+.++.|=||.++.+...- ... ..+.+.+
T Consensus 299 ~y~~~~G~PSG~~~Tsi~NSi~N~i~~~~a~~~~~~~~~~~~~~~~~~i~YGDD~l~sv~~~~------~~~-n~~~i~~ 371 (491)
T PF00680_consen 299 VYRVNGGNPSGSPLTSIINSIVNNIYIRYAWRKLYPDPPREFFENVKLIVYGDDNLISVPPEI------DPW-NGETISE 371 (491)
T ss_dssp EEEEESSS-TTSTTHHHHHHHHHHHHHHHHHHHHSTSCHGGGHHHSEEEEETTEEEEEESSHH------HHH-HHHHHHH
T ss_pred eeeeccccccccccchhccccccceeechhhhhccccccccccceeeeeeeccccchhhhccc------ccc-hhHHHHH
Confidence 45678999999999755544443322 22111 2 3778999999999773211 111 4667777
Q ss_pred HHhhcCCcccCCCCCeeE
Q psy17815 72 WSDTNGLIFSADPQKSVC 89 (599)
Q Consensus 72 w~~~~gl~~n~~~~Kt~~ 89 (599)
.+++.|+.+.. ++|+..
T Consensus 372 ~~~~~G~~~T~-~dK~~~ 388 (491)
T PF00680_consen 372 FLAELGLTYTD-ADKTGE 388 (491)
T ss_dssp HHHTTTEEEEE-SSTSSS
T ss_pred HHHhccccccc-ccccCC
Confidence 88889999981 388774
No 37
>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=27.95 E-value=1.3e+02 Score=25.08 Aligned_cols=32 Identities=9% Similarity=0.287 Sum_probs=26.3
Q ss_pred EEEecCe---------------EEEEecCChHHHHHHHHHHHHHHHH
Q psy17815 40 MLFIDDL---------------LIISRGKDLSAILGRFQTTLNAIKT 71 (599)
Q Consensus 40 ~~yADD~---------------~i~~~~~~~~~~~~~lq~~l~~l~~ 71 (599)
+.|+||+ .++..|.+..+....++.+++.+..
T Consensus 53 v~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~ 99 (103)
T cd07049 53 VVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIEN 99 (103)
T ss_pred EEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhc
Confidence 4599999 8889998988888888888887654
No 38
>COG3716 ManZ Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]
Probab=27.39 E-value=39 Score=33.08 Aligned_cols=23 Identities=43% Similarity=0.676 Sum_probs=18.4
Q ss_pred CCCCChHHHHHHHHHhchhhhcC
Q psy17815 12 PQGSSLSPLLFIIFLNDLLKIIK 34 (599)
Q Consensus 12 pQGs~LSP~Lf~l~~~~l~~~~~ 34 (599)
-||++|+|+||.+..|-+.-.+.
T Consensus 134 ~~G~ilGpilf~~l~N~i~~~~r 156 (269)
T COG3716 134 LQGSILGPILFFLLFNILRLAIR 156 (269)
T ss_pred hcCCchHHHHHHHHHHHHHHHHH
Confidence 48999999999988887655443
No 39
>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=26.23 E-value=1e+02 Score=29.23 Aligned_cols=26 Identities=15% Similarity=0.268 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCccc
Q psy17815 56 SAILGRFQTTLNAIKTWSDTNGLIFS 81 (599)
Q Consensus 56 ~~~~~~lq~~l~~l~~w~~~~gl~~n 81 (599)
.+..+.+|+-.+.|++|+...|+.+|
T Consensus 129 ~~~~~~Lq~K~~~i~~WA~~~gvEv~ 154 (204)
T PF12633_consen 129 PEERQLLQQKCDLIEQWAASFGVEVH 154 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCEEE
Confidence 56778999999999999999999999
No 40
>CHL00002 matK maturase K
Probab=26.10 E-value=1.7e+02 Score=31.91 Aligned_cols=53 Identities=11% Similarity=0.153 Sum_probs=35.8
Q ss_pred CCcEEEEEecCeEEEEecCChHHHHHHHHHHHHHHH-HHHhhcCCcccCCCCCeeEEEecc
Q psy17815 35 LPLRSMLFIDDLLIISRGKDLSAILGRFQTTLNAIK-TWSDTNGLIFSADPQKSVCVDFTR 94 (599)
Q Consensus 35 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~-~w~~~~gl~~n~~~~Kt~~~~~~~ 94 (599)
+-+.-+-||||..|.+.|... . +.+.-..+. =|...-.+.++ ++|+.+-.+.+
T Consensus 271 p~ihYVRYaddfIIg~kGsk~--~---a~KwK~~l~~F~q~~f~l~~s--~eKi~I~~ls~ 324 (504)
T CHL00002 271 PFIHYVRYQGKSILASKGTPL--L---MNKWKYYLVNFWQCHFHLWSQ--PGRIHINQLSN 324 (504)
T ss_pred ceEEEEEECCcEEEEECCCHH--H---HHHHHHHHHHHHHHhceeeec--CCceeeccccC
Confidence 456779999999998877652 2 333333333 34455578899 99998777653
No 41
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=23.49 E-value=2.7e+02 Score=23.21 Aligned_cols=34 Identities=9% Similarity=-0.070 Sum_probs=24.8
Q ss_pred cccchhHHHHHHHHHHHHhhcCCCCcEEEEeccH
Q psy17815 369 INSIFTAELLALVFCLDSVKNRPDVNTLIVCDSM 402 (599)
Q Consensus 369 ~~sv~~aEl~ai~~al~~~~~~~~~~~~i~sDs~ 402 (599)
......||..||..+.+...........+++.-.
T Consensus 42 ~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~E 75 (109)
T cd01285 42 GDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLE 75 (109)
T ss_pred CCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCC
Confidence 4568899999999998886544456677776543
No 42
>KOG4602|consensus
Probab=23.43 E-value=32 Score=33.11 Aligned_cols=22 Identities=23% Similarity=0.419 Sum_probs=19.0
Q ss_pred CCCCcc-CCcccchhHhh-hccCc
Q psy17815 541 DPPSCQ-CGLPLTIRHLL-ECRSY 562 (599)
Q Consensus 541 ~~~~C~-Cg~~~t~~H~l-~Cp~~ 562 (599)
.+-.|+ ||+..+--|.+ .||..
T Consensus 267 R~YVCPiCGATgDnAHTiKyCPl~ 290 (318)
T KOG4602|consen 267 RSYVCPICGATGDNAHTIKYCPLA 290 (318)
T ss_pred hhhcCccccccCCcccceeccccc
Confidence 345799 99999999999 99974
No 43
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=21.79 E-value=1.1e+02 Score=26.26 Aligned_cols=64 Identities=8% Similarity=-0.006 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCcccCCCCCeeEEEeccCCCCCCCceeeeCCeEeeecccceeeeeEEccC
Q psy17815 57 AILGRFQTTLNAIKTWSDTNGLIFSADPQKSVCVDFTRLRSRSVPLTLYYSDKELKFVDKTKFLGLIWDSK 127 (599)
Q Consensus 57 ~~~~~lq~~l~~l~~w~~~~gl~~n~~~~Kt~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~kyLGv~ld~~ 127 (599)
.+-..+++.+..+..-....|+.+. .+|..+-.-.-.+....++.+.++|.+|.. |||..++..
T Consensus 20 ~Tg~~L~~av~~l~~~L~~~Giev~--l~~~~l~~~~~~~~~~~S~~I~inG~piE~-----~l~~~v~~s 83 (120)
T PF10865_consen 20 DTGETLREAVKELAPVLAPLGIEVR--LEEIELDEEEFARQPLESPTIRINGRPIED-----LLGAEVGES 83 (120)
T ss_pred hHHHHHHHHHHHHHHHHHhCCcEEE--EEEEECChHHHhhcccCCCeeeECCEehhH-----hhCCccccC
Confidence 5667888999999999999999999 888865443223233345788899998843 455555443
Done!