Query psy556
Match_columns 435
No_of_seqs 218 out of 2032
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 20:38:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy556.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/556hhsearch_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 99.2 3.6E-12 7.7E-17 108.2 3.6 61 242-302 36-131 (132)
2 PRK08719 ribonuclease H; Revie 99.2 1.1E-11 2.4E-16 106.8 5.9 61 243-303 47-146 (147)
3 cd01648 TERT TERT: Telomerase 99.2 7.9E-12 1.7E-16 104.1 4.8 89 13-101 10-119 (119)
4 PRK00203 rnhA ribonuclease H; 99.2 7.7E-12 1.7E-16 108.6 4.7 64 242-305 39-143 (150)
5 PRK06548 ribonuclease H; Provi 99.2 1.2E-11 2.5E-16 107.6 5.3 57 248-304 46-142 (161)
6 cd01650 RT_nLTR_like RT_nLTR: 99.1 1.2E-10 2.7E-15 107.6 4.7 79 22-100 106-220 (220)
7 COG0328 RnhA Ribonuclease HI [ 98.9 7.4E-10 1.6E-14 94.7 3.9 53 253-305 66-146 (154)
8 cd01651 RT_G2_intron RT_G2_int 98.9 2.8E-09 6.1E-14 98.8 5.9 87 14-100 118-226 (226)
9 PF00078 RVT_1: Reverse transc 98.9 1.6E-09 3.4E-14 99.3 3.7 95 5-100 109-214 (214)
10 cd03487 RT_Bac_retron_II RT_Ba 98.8 4.2E-09 9.2E-14 97.1 5.5 85 19-103 100-198 (214)
11 cd06222 RnaseH RNase H (RNase 98.7 3.9E-08 8.4E-13 81.6 5.8 60 243-302 38-130 (130)
12 cd00304 RT_like RT_like: Rever 98.6 4.2E-08 9.1E-13 78.5 4.7 78 23-100 12-98 (98)
13 cd01646 RT_Bac_retron_I RT_Bac 98.5 6.3E-08 1.4E-12 84.9 3.9 90 14-103 45-147 (158)
14 KOG3752|consensus 98.3 7.9E-07 1.7E-11 85.5 5.1 61 242-302 252-363 (371)
15 cd01645 RT_Rtv RT_Rtv: Reverse 97.8 1.2E-05 2.7E-10 74.0 2.4 78 21-100 127-213 (213)
16 cd01709 RT_like_1 RT_like_1: A 97.7 4.5E-05 9.7E-10 73.6 5.3 49 15-63 76-127 (346)
17 cd03714 RT_DIRS1 RT_DIRS1: Rev 97.7 3.1E-05 6.7E-10 64.4 3.3 78 23-100 34-119 (119)
18 PRK13907 rnhA ribonuclease H; 97.6 7E-05 1.5E-09 63.0 3.8 46 253-302 64-125 (128)
19 KOG1005|consensus 97.1 0.00059 1.3E-08 72.1 5.3 60 6-68 621-686 (888)
20 cd03715 RT_ZFREV_like RT_ZFREV 96.8 0.00085 1.8E-08 61.6 2.6 79 20-100 122-210 (210)
21 PF13456 RVT_3: Reverse transc 96.5 0.0021 4.6E-08 49.5 3.1 47 253-303 24-86 (87)
22 PRK07708 hypothetical protein; 96.5 0.0034 7.3E-08 57.8 4.7 48 253-304 143-208 (219)
23 PRK07238 bifunctional RNase H/ 96.5 0.0034 7.3E-08 62.9 5.0 48 253-304 68-132 (372)
24 PF13966 zf-RVT: zinc-binding 95.6 0.005 1.1E-07 47.8 1.0 31 377-407 51-83 (86)
25 KOG4768|consensus 95.1 0.019 4.1E-07 58.9 3.4 23 21-43 416-438 (796)
26 cd01647 RT_LTR RT_LTR: Reverse 92.7 0.087 1.9E-06 45.8 2.7 43 21-64 94-136 (177)
27 cd01644 RT_pepA17 RT_pepA17: R 92.4 0.11 2.4E-06 47.7 3.1 47 18-64 99-150 (213)
28 cd01699 RNA_dep_RNAP RNA_dep_R 57.9 17 0.00036 34.4 4.8 50 16-65 153-211 (278)
29 COG3344 Retron-type reverse tr 45.5 6.3 0.00014 38.7 -0.3 46 17-62 233-280 (328)
30 PF05741 zf-nanos: Nanos RNA b 41.5 14 0.00031 25.9 1.0 20 386-405 34-54 (55)
31 PF07727 RVT_2: Reverse transc 29.2 20 0.00043 33.7 0.2 42 21-66 122-180 (246)
32 COG3716 ManZ Phosphotransferas 26.1 50 0.0011 31.1 2.2 20 24-43 134-153 (269)
33 PF13917 zf-CCHC_3: Zinc knuck 25.6 43 0.00092 22.1 1.3 19 384-405 3-22 (42)
34 COG0296 GlgB 1,4-alpha-glucan 23.2 64 0.0014 34.6 2.7 33 262-294 215-247 (628)
35 PF15216 TSLP: Thymic stromal 22.5 1.1E+02 0.0023 25.1 3.2 12 280-291 80-91 (124)
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=99.25 E-value=3.6e-12 Score=108.15 Aligned_cols=61 Identities=26% Similarity=0.464 Sum_probs=48.4
Q ss_pred CCCChh--hhhcc-----------cccccCCHHHHHHhhc-----cCCCC----C------------ceEEEEEecccCC
Q psy556 242 DRCDMM--EYKDL-----------TPPWSDDMSEVIDLWR-----NLTSN----N------------IKLTFIWCPSHCG 287 (435)
Q Consensus 242 ~~~~v~--El~ai-----------~~i~sDs~sa~~~l~~-----~~~~~----~------------i~v~~~Wvp~H~g 287 (435)
+..+++ ||.|| +.|+|||++++..+.. ..... . +.|.|.|||||+|
T Consensus 36 ~~~s~~~aEl~Ai~~AL~~~~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~ 115 (132)
T PF00075_consen 36 GGQSNNRAELQAIIEALKALEHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSG 115 (132)
T ss_dssp ESECHHHHHHHHHHHHHHTHSTSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSS
T ss_pred cccchhhhheehHHHHHHHhhcccccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeeccCcCC
Confidence 355665 98888 5899999999998866 22111 1 3899999999999
Q ss_pred C-CcchHHhHHHhhcc
Q psy556 288 I-EGNEEVDRAANRDG 302 (435)
Q Consensus 288 i-~gNe~AD~~Ak~a~ 302 (435)
+ .|||.||++||+|+
T Consensus 116 ~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 116 VPQGNERADRLAKEAA 131 (132)
T ss_dssp SHHHHHHHHHHHHHHH
T ss_pred CchhHHHHHHHHHHhc
Confidence 9 69999999999986
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.23 E-value=1.1e-11 Score=106.76 Aligned_cols=61 Identities=25% Similarity=0.257 Sum_probs=50.4
Q ss_pred CCChh--hhhcc----------cccccCCHHHHHHh--------hccCCCCC------------c-------eEEEEEec
Q psy556 243 RCDMM--EYKDL----------TPPWSDDMSEVIDL--------WRNLTSNN------------I-------KLTFIWCP 283 (435)
Q Consensus 243 ~~~v~--El~ai----------~~i~sDs~sa~~~l--------~~~~~~~~------------i-------~v~~~Wvp 283 (435)
..|.. |+.|+ ..|+|||+++++.+ ++.+..++ | .|+|.|||
T Consensus 47 ~~Tnn~aEl~A~~~aL~~~~~~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~Vk 126 (147)
T PRK08719 47 YTDNAELELLALIEALEYARDGDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVT 126 (147)
T ss_pred CccHHHHHHHHHHHHHHHcCCCCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEec
Confidence 35555 99988 67999999999999 45544332 1 79999999
Q ss_pred ccCCCCcchHHhHHHhhccC
Q psy556 284 SHCGIEGNEEVDRAANRDGH 303 (435)
Q Consensus 284 ~H~gi~gNe~AD~~Ak~a~~ 303 (435)
||+|++|||.||++|++|++
T Consensus 127 gH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 127 AHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred CCCCChhHHHHHHHHHHHhh
Confidence 99999999999999999974
No 3
>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=99.23 E-value=7.9e-12 Score=104.14 Aligned_cols=89 Identities=22% Similarity=0.217 Sum_probs=62.3
Q ss_pred cccceeccCCCCCCCchhHHHHHHHHHhhhhhcC-------CCcceeeeccceeEEEecCCHhHhh----ccCC-CCCce
Q psy556 13 ISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN-------LPTRGLLFVDDLLLTIRGKILEQLG----SRNP-TLPLI 80 (435)
Q Consensus 13 ~s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~-------~~~~~~~yADD~~i~~~~~~~~~l~----k~~~-~~~~~ 80 (435)
.+..+...+|+|||++|||+||++|++.+.+.+. .......||||+.+++......+.. +..+ ....+
T Consensus 10 ~~~~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~~~~~~~~~~~l~~~l~~~~gl 89 (119)
T cd01648 10 IPQYYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSLDKAIKFLNLLLRGFINQYKT 89 (119)
T ss_pred hhhhhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCCHHHHHHHHHHHHHhhHHhhCe
Confidence 3345677889999999999999999999987742 3456899999999887765433211 2222 33455
Q ss_pred EeCCeeee---------ccCcceeeceeec
Q psy556 81 MLNGNQLK---------FDNTAKFLGLIWD 101 (435)
Q Consensus 81 ~l~~~~I~---------~~~~~kyLGv~ld 101 (435)
.+|..+.+ ..+.+.|||+.|+
T Consensus 90 ~iN~~Kt~~~~~~~~~~~~~~~~flG~~i~ 119 (119)
T cd01648 90 FVNFDKTQINFSFAQLDSSDLIPWCGLLIN 119 (119)
T ss_pred EECcccceeeccccccCCCCccCceeEeeC
Confidence 55543332 3567999999885
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.23 E-value=7.7e-12 Score=108.64 Aligned_cols=64 Identities=16% Similarity=0.215 Sum_probs=50.5
Q ss_pred CCCChh--hhhcc------------cccccCCHHHHHHhhc--------cC-CCCC------------------ceEEEE
Q psy556 242 DRCDMM--EYKDL------------TPPWSDDMSEVIDLWR--------NL-TSNN------------------IKLTFI 280 (435)
Q Consensus 242 ~~~~v~--El~ai------------~~i~sDs~sa~~~l~~--------~~-~~~~------------------i~v~~~ 280 (435)
...|.. ||.|+ +.|+|||+++++.|.. .. ..++ ..|.|.
T Consensus 39 ~~~TN~~aEL~Ai~~AL~~~~~~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~ 118 (150)
T PRK00203 39 ALTTNNRMELMAAIEALEALKEPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWH 118 (150)
T ss_pred CCCcHHHHHHHHHHHHHHHcCCCCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEE
Confidence 334443 99888 6799999999999964 22 1222 279999
Q ss_pred EecccCCCCcchHHhHHHhhccCCC
Q psy556 281 WCPSHCGIEGNEEVDRAANRDGHTQ 305 (435)
Q Consensus 281 Wvp~H~gi~gNe~AD~~Ak~a~~~~ 305 (435)
|||||+|++|||.||++||+|+..+
T Consensus 119 wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 119 WVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred EecCCCCCHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999998654
No 5
>PRK06548 ribonuclease H; Provisional
Probab=99.22 E-value=1.2e-11 Score=107.60 Aligned_cols=57 Identities=21% Similarity=0.275 Sum_probs=48.1
Q ss_pred hhhcc-------------cccccCCHHHHHHhh---------ccCCCCC-----------c-------eEEEEEecccCC
Q psy556 248 EYKDL-------------TPPWSDDMSEVIDLW---------RNLTSNN-----------I-------KLTFIWCPSHCG 287 (435)
Q Consensus 248 El~ai-------------~~i~sDs~sa~~~l~---------~~~~~~~-----------i-------~v~~~Wvp~H~g 287 (435)
||.|+ +.|+|||+++++.+. +....+| | .|+|.|||||+|
T Consensus 46 El~Aii~aL~~~~~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg 125 (161)
T PRK06548 46 ELTAVRELLIATRHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTG 125 (161)
T ss_pred HHHHHHHHHHhhhcCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCC
Confidence 98888 679999999999997 3333333 1 799999999999
Q ss_pred CCcchHHhHHHhhccCC
Q psy556 288 IEGNEEVDRAANRDGHT 304 (435)
Q Consensus 288 i~gNe~AD~~Ak~a~~~ 304 (435)
++|||.||++|++|+..
T Consensus 126 ~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 126 HPLNEAADSLARQAANN 142 (161)
T ss_pred CHHHHHHHHHHHHHHHH
Confidence 99999999999998754
No 6
>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=99.06 E-value=1.2e-10 Score=107.56 Aligned_cols=79 Identities=37% Similarity=0.558 Sum_probs=59.7
Q ss_pred CCCCCCchhHHHHHHHHHhhhhhcC---------CCcceeeeccceeEEEecCC-HhH--hh-----------ccCCC--
Q psy556 22 GLVQGSSLSTLLFAVFMNDIFHVIN---------LPTRGLLFVDDLLLTIRGKI-LEQ--LG-----------SRNPT-- 76 (435)
Q Consensus 22 GvpQGs~LSP~Lf~l~~~~l~~~~~---------~~~~~~~yADD~~i~~~~~~-~~~--l~-----------k~~~~-- 76 (435)
|+|||++|||+||++|++++.+.+. ..+....||||+++++.+.. ..+ +. +.+..
T Consensus 106 GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~~~~~~~~~~~~~~~~~~~~gl~in~~Kt 185 (220)
T cd01650 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKS 185 (220)
T ss_pred CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEEeccceeeeccCCHHHHHHHHHHHHHHHHHcCCEEChhhe
Confidence 9999999999999999999988753 56789999999999988886 221 11 11111
Q ss_pred -----------CCceEeCCeeeeccCcceeeceee
Q psy556 77 -----------LPLIMLNGNQLKFDNTAKFLGLIW 100 (435)
Q Consensus 77 -----------~~~~~l~~~~I~~~~~~kyLGv~l 100 (435)
...+.+++..+..+..+||||+.|
T Consensus 186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 186 KVMLIGNKKKRLKDITLNGTPIEAVETFKYLGVTI 220 (220)
T ss_pred EEEEecCCCcchhhhhhcCCcccCCCCCeeccccC
Confidence 111345667778889999999975
No 7
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.92 E-value=7.4e-10 Score=94.70 Aligned_cols=53 Identities=21% Similarity=0.287 Sum_probs=42.8
Q ss_pred cccccCCHHHHHHhhcc---CCCCC------------------------c-eEEEEEecccCCCCcchHHhHHHhhccCC
Q psy556 253 TPPWSDDMSEVIDLWRN---LTSNN------------------------I-KLTFIWCPSHCGIEGNEEVDRAANRDGHT 304 (435)
Q Consensus 253 ~~i~sDs~sa~~~l~~~---~~~~~------------------------i-~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 304 (435)
+.|+|||+.+++.|..- +...+ . .|.+.|||||.|.++||.||++|++|+..
T Consensus 66 v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~ 145 (154)
T COG0328 66 VTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA 145 (154)
T ss_pred EEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence 78999999999999611 11111 1 89999999999999999999999999865
Q ss_pred C
Q psy556 305 Q 305 (435)
Q Consensus 305 ~ 305 (435)
.
T Consensus 146 ~ 146 (154)
T COG0328 146 A 146 (154)
T ss_pred h
Confidence 4
No 8
>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=98.86 E-value=2.8e-09 Score=98.80 Aligned_cols=87 Identities=20% Similarity=0.351 Sum_probs=59.8
Q ss_pred ccceeccCCCCCCCchhHHHHHHHHHhhhhhcC--------------CCcceeeeccceeEEEecCCHhH-hh---ccCC
Q psy556 14 SNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN--------------LPTRGLLFVDDLLLTIRGKILEQ-LG---SRNP 75 (435)
Q Consensus 14 s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~--------------~~~~~~~yADD~~i~~~~~~~~~-l~---k~~~ 75 (435)
+..+....|||||+++||+||++|++++...+. .++....||||+++++.+....+ .. ..-+
T Consensus 118 ~~~~~~~~GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~ 197 (226)
T cd01651 118 GKLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFL 197 (226)
T ss_pred CeEeCCCCCcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHHHH
Confidence 456678899999999999999999999977643 55779999999999988877432 11 0000
Q ss_pred CCCceEeC--Ceeeec--cCcceeeceee
Q psy556 76 TLPLIMLN--GNQLKF--DNTAKFLGLIW 100 (435)
Q Consensus 76 ~~~~~~l~--~~~I~~--~~~~kyLGv~l 100 (435)
....+.++ ...+-. .+.+.|||+.|
T Consensus 198 ~~~gl~ln~~Kt~i~~~~~~~~~fLG~~~ 226 (226)
T cd01651 198 EELGLELNPEKTRITHFKSEGFDFLGFTF 226 (226)
T ss_pred HHcCCeechhhcceeecCCCCCeeCCeEC
Confidence 11122222 222222 57899999875
No 9
>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=98.85 E-value=1.6e-09 Score=99.29 Aligned_cols=95 Identities=27% Similarity=0.291 Sum_probs=63.7
Q ss_pred EEEEECCccccceeccCCCCCCCchhHHHHHHHHHhhhhhcC----CCcceeeeccceeEEEecCCHhHhh----ccCCC
Q psy556 5 IAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN----LPTRGLLFVDDLLLTIRGKILEQLG----SRNPT 76 (435)
Q Consensus 5 ~~v~~~g~~s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~----~~~~~~~yADD~~i~~~~~~~~~l~----k~~~~ 76 (435)
..+.+++.. .......|+|||+++||+||++|++++.+.+. +++.+..||||+.+++......+.. ..-+.
T Consensus 109 ~~~~~~~~~-~~~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~ 187 (214)
T PF00078_consen 109 AKVYLDGDL-SPYFQKRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLRYADDILIISKSKEELQKILEKISQWLE 187 (214)
T ss_dssp H-EECGCSS-SEEEEESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETTEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred ccccccccc-ccccccccccccccccchhhccccccccccccccccccccceEeccccEEEECCHHHHHHHHHHHHHHHH
Confidence 345666665 77889999999999999999999999988743 5788999999999998874432111 00000
Q ss_pred CCceEeCCeeee---ccCcceeeceee
Q psy556 77 LPLIMLNGNQLK---FDNTAKFLGLIW 100 (435)
Q Consensus 77 ~~~~~l~~~~I~---~~~~~kyLGv~l 100 (435)
...+.++..+.+ ..++++|||+.|
T Consensus 188 ~~gl~ln~~Kt~~~~~~~~~~~lG~~i 214 (214)
T PF00078_consen 188 ELGLKLNPEKTKILHPSDSVKFLGYVI 214 (214)
T ss_dssp HTTSBCSSTTTSCS--ESSEEETTEEE
T ss_pred HCCCEEChHHEEEEeCCCCEEEEeEEC
Confidence 112233322211 468899999975
No 10
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=98.82 E-value=4.2e-09 Score=97.12 Aligned_cols=85 Identities=14% Similarity=0.138 Sum_probs=59.9
Q ss_pred ccCCCCCCCchhHHHHHHHHHhhhhhcC-----CCcceeeeccceeEEEecCCH---hHhh---ccCCCCCceEeCCee-
Q psy556 19 LENGLVQGSSLSTLLFAVFMNDIFHVIN-----LPTRGLLFVDDLLLTIRGKIL---EQLG---SRNPTLPLIMLNGNQ- 86 (435)
Q Consensus 19 i~~GvpQGs~LSP~Lf~l~~~~l~~~~~-----~~~~~~~yADD~~i~~~~~~~---~~l~---k~~~~~~~~~l~~~~- 86 (435)
...|||||+++||+||++|++++...+. .++....||||+++++..... +++. ..-+....+.++..+
T Consensus 100 ~~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt 179 (214)
T cd03487 100 YNGHLPQGAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYADDITFSSNKKLKEALDKLLEIIRSILSEEGFKINKSKT 179 (214)
T ss_pred CCCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEeccEEEEccccchhHHHHHHHHHHHHHHHCCceeCCCce
Confidence 4459999999999999999999887653 567899999999999888762 2211 111112344554432
Q ss_pred -e-eccCcceeeceeecCc
Q psy556 87 -L-KFDNTAKFLGLIWDRK 103 (435)
Q Consensus 87 -I-~~~~~~kyLGv~ld~~ 103 (435)
+ ...+.+.+||+.+.++
T Consensus 180 ~i~~~~~~~~~~G~~i~~~ 198 (214)
T cd03487 180 RISSKGSRQIVTGLVVNNG 198 (214)
T ss_pred EEccCCCCcEEEEEEEeCC
Confidence 2 2345799999999864
No 11
>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=98.66 E-value=3.9e-08 Score=81.56 Aligned_cols=60 Identities=28% Similarity=0.389 Sum_probs=50.3
Q ss_pred CCChh--hhhcc--------------cccccCCHHHHHHhhccCCCCC-----------------ceEEEEEecccCCCC
Q psy556 243 RCDMM--EYKDL--------------TPPWSDDMSEVIDLWRNLTSNN-----------------IKLTFIWCPSHCGIE 289 (435)
Q Consensus 243 ~~~v~--El~ai--------------~~i~sDs~sa~~~l~~~~~~~~-----------------i~v~~~Wvp~H~gi~ 289 (435)
..+++ |+.|+ +.|++||+.++..+.+...... ..++|.|||+|+|+.
T Consensus 38 ~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~ 117 (130)
T cd06222 38 NTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIE 117 (130)
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCc
Confidence 55665 98888 6899999999999987654211 289999999999999
Q ss_pred cchHHhHHHhhcc
Q psy556 290 GNEEVDRAANRDG 302 (435)
Q Consensus 290 gNe~AD~~Ak~a~ 302 (435)
+|+.||.+||+|.
T Consensus 118 ~n~~ad~la~~~~ 130 (130)
T cd06222 118 GNERADALAKEAA 130 (130)
T ss_pred chHHHHHHHHhhC
Confidence 9999999999874
No 12
>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=98.62 E-value=4.2e-08 Score=78.49 Aligned_cols=78 Identities=24% Similarity=0.285 Sum_probs=55.0
Q ss_pred CCCCCchhHHHHHHHHHhhhhhc---CCCcceeeeccceeEEEecCCHhHhh---ccCCCCCceEeCCeeee---ccCcc
Q psy556 23 LVQGSSLSTLLFAVFMNDIFHVI---NLPTRGLLFVDDLLLTIRGKILEQLG---SRNPTLPLIMLNGNQLK---FDNTA 93 (435)
Q Consensus 23 vpQGs~LSP~Lf~l~~~~l~~~~---~~~~~~~~yADD~~i~~~~~~~~~l~---k~~~~~~~~~l~~~~I~---~~~~~ 93 (435)
+|||+++||.||+++++.+...+ ..++....|+||+.+++......... ...+....+.++..+.+ ....+
T Consensus 12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~~~~~~~~~l~~~l~~~gl~ln~~Kt~~~~~~~~~ 91 (98)
T cd00304 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQQAVKKRELEEFLARLGLNLSDEKTQFTEKEKKF 91 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcHHHHHHHHHHHHHHHHcCcEEChheeEEecCCCCe
Confidence 99999999999999999998875 35778999999999998776111111 11111234455544433 56789
Q ss_pred eeeceee
Q psy556 94 KFLGLIW 100 (435)
Q Consensus 94 kyLGv~l 100 (435)
+|||+.+
T Consensus 92 ~flG~~~ 98 (98)
T cd00304 92 KFLGILV 98 (98)
T ss_pred eeeceeC
Confidence 9999864
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=98.53 E-value=6.3e-08 Score=84.86 Aligned_cols=90 Identities=23% Similarity=0.269 Sum_probs=60.1
Q ss_pred ccceeccCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhH-hh---ccCCCCCceEeCCee
Q psy556 14 SNFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQ-LG---SRNPTLPLIMLNGNQ 86 (435)
Q Consensus 14 s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~-l~---k~~~~~~~~~l~~~~ 86 (435)
+.......|+|||+++||+|+++|+.++...+. .++....||||+++++......+ .. ..-+....+.++..+
T Consensus 45 ~~~~~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i~~~l~~~gL~ln~~K 124 (158)
T cd01646 45 SSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSK 124 (158)
T ss_pred hccCCCCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCHHHHHHHHHHHHHHHHHCCCEEChhh
Confidence 345567789999999999999999999987753 57889999999999986554331 11 000111233333221
Q ss_pred ---eecc---CcceeeceeecCc
Q psy556 87 ---LKFD---NTAKFLGLIWDRK 103 (435)
Q Consensus 87 ---I~~~---~~~kyLGv~ld~~ 103 (435)
.... ..+.+||..+...
T Consensus 125 t~~~~~~~~~~~~~flg~~~~~~ 147 (158)
T cd01646 125 TEILPLPEGTASKDFLGYRFSPI 147 (158)
T ss_pred ceeeecCCCCccccccceEeehh
Confidence 1222 2489999999754
No 14
>KOG3752|consensus
Probab=98.29 E-value=7.9e-07 Score=85.45 Aligned_cols=61 Identities=21% Similarity=0.143 Sum_probs=48.3
Q ss_pred CCCChh--hhhcc--------------cccccCCHHHHHHhhcc--------CCC---CC--------------------
Q psy556 242 DRCDMM--EYKDL--------------TPPWSDDMSEVIDLWRN--------LTS---NN-------------------- 274 (435)
Q Consensus 242 ~~~~v~--El~ai--------------~~i~sDs~sa~~~l~~~--------~~~---~~-------------------- 274 (435)
..+|.+ ||.|+ +.|.|||+..++.|+.- ... +.
T Consensus 252 g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q 331 (371)
T KOG3752|consen 252 GRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQ 331 (371)
T ss_pred CcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHh
Confidence 445555 99888 78999999999998421 111 11
Q ss_pred ----ceEEEEEecccCCCCcchHHhHHHhhcc
Q psy556 275 ----IKLTFIWCPSHCGIEGNEEVDRAANRDG 302 (435)
Q Consensus 275 ----i~v~~~Wvp~H~gi~gNe~AD~~Ak~a~ 302 (435)
..|.+.|||||.||.|||+||.+|++++
T Consensus 332 ~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs 363 (371)
T KOG3752|consen 332 EISNKKVQQEYVGGHSGILGNEMADALARKGS 363 (371)
T ss_pred hhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence 1799999999999999999999999985
No 15
>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=97.77 E-value=1.2e-05 Score=73.97 Aligned_cols=78 Identities=15% Similarity=0.154 Sum_probs=57.3
Q ss_pred CCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh------ccCCCCCceEeCCeeeeccC
Q psy556 21 NGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG------SRNPTLPLIMLNGNQLKFDN 91 (435)
Q Consensus 21 ~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~------k~~~~~~~~~l~~~~I~~~~ 91 (435)
+.+|||...||.+|+.+|+.++..+. .++.+..|+||+.+.+... ++.. ...+....+.++..+.....
T Consensus 127 ~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~--~~~~~~l~~v~~~l~~~gl~ln~~K~~~~~ 204 (213)
T cd01645 127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE--GQLREIYEELRQTLLRWGLTIPPEKVQKEP 204 (213)
T ss_pred EEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCH--HHHHHHHHHHHHHHHHCCCEeCHHHEeCCC
Confidence 57999999999999999999987643 3456899999999875443 3222 22233456677766666678
Q ss_pred cceeeceee
Q psy556 92 TAKFLGLIW 100 (435)
Q Consensus 92 ~~kyLGv~l 100 (435)
+++|||+.+
T Consensus 205 ~v~fLG~~i 213 (213)
T cd01645 205 PFQYLGYEL 213 (213)
T ss_pred CeEeccEeC
Confidence 899999864
No 16
>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=97.71 E-value=4.5e-05 Score=73.61 Aligned_cols=49 Identities=14% Similarity=-0.013 Sum_probs=40.6
Q ss_pred cceeccCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEe
Q psy556 15 NFKGLENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIR 63 (435)
Q Consensus 15 ~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~ 63 (435)
....-.+|+|||+++||+|=|+|+..+...++ +++.+.-||||+.++.+
T Consensus 76 ~~r~r~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~ 127 (346)
T cd01709 76 PPRIRKRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ 127 (346)
T ss_pred cccccCCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC
Confidence 44556679999999999999999997765554 57889999999999944
No 17
>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=97.68 E-value=3.1e-05 Score=64.35 Aligned_cols=78 Identities=23% Similarity=0.221 Sum_probs=55.5
Q ss_pred CCCCCchhHHHHHHHHHhhhhhcC-CCcceeeeccceeEEEecCCHhHhh----cc-CCCCCceEeCCeeee--ccCcce
Q psy556 23 LVQGSSLSTLLFAVFMNDIFHVIN-LPTRGLLFVDDLLLTIRGKILEQLG----SR-NPTLPLIMLNGNQLK--FDNTAK 94 (435)
Q Consensus 23 vpQGs~LSP~Lf~l~~~~l~~~~~-~~~~~~~yADD~~i~~~~~~~~~l~----k~-~~~~~~~~l~~~~I~--~~~~~k 94 (435)
+|||...||.+|.-+|+.++..+. .+..+..|+||+.+.+......+.. +. -+....+.++..+.. +.++++
T Consensus 34 mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~~~~~~~~~~~l~~~~l~~~gl~ln~~K~~~~~~~~v~ 113 (119)
T cd03714 34 LPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASSIKTSEAVLRHLRATLLANLGFTLNLEKSKLGPTQRIT 113 (119)
T ss_pred cCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCcHHHHHHHHHHHHHHHHHHcCCccChhhcEecCCCcEE
Confidence 899999999999999999988653 4567899999999987752211111 11 123445666655555 578899
Q ss_pred eeceee
Q psy556 95 FLGLIW 100 (435)
Q Consensus 95 yLGv~l 100 (435)
|||..|
T Consensus 114 fLG~~~ 119 (119)
T cd03714 114 FLGLEL 119 (119)
T ss_pred ECcEeC
Confidence 999865
No 18
>PRK13907 rnhA ribonuclease H; Provisional
Probab=97.56 E-value=7e-05 Score=63.02 Aligned_cols=46 Identities=17% Similarity=0.174 Sum_probs=37.0
Q ss_pred cccccCCHHHHHHhhccCCCCC--------c--------eEEEEEecccCCCCcchHHhHHHhhcc
Q psy556 253 TPPWSDDMSEVIDLWRNLTSNN--------I--------KLTFIWCPSHCGIEGNEEVDRAANRDG 302 (435)
Q Consensus 253 ~~i~sDs~sa~~~l~~~~~~~~--------i--------~v~~~Wvp~H~gi~gNe~AD~~Ak~a~ 302 (435)
+.|++||+..+..+.+...... + .+.+.|||.+ .|+.||.+|+.|.
T Consensus 64 v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~ 125 (128)
T PRK13907 64 VSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKAI 125 (128)
T ss_pred EEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHHH
Confidence 6799999999999987443221 1 6778999994 7999999999986
No 19
>KOG1005|consensus
Probab=97.12 E-value=0.00059 Score=72.07 Aligned_cols=60 Identities=27% Similarity=0.271 Sum_probs=47.5
Q ss_pred EEEECCccccceeccCCCCCCCchhHHHHHHHHHhhhhhc-C---CC--cceeeeccceeEEEecCCHh
Q psy556 6 AVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVI-N---LP--TRGLLFVDDLLLTIRGKILE 68 (435)
Q Consensus 6 ~v~~~g~~s~~~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~-~---~~--~~~~~yADD~~i~~~~~~~~ 68 (435)
-|+++| ..+....|+||||+||-+|-.+|+++|.+.. . .+ +.++-|+||..++++..+..
T Consensus 621 ~vki~~---k~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt~~~~a 686 (888)
T KOG1005|consen 621 YVKIGG---KSYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITTENDQA 686 (888)
T ss_pred eEEECC---eEEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEecCHHHH
Confidence 366666 3355677999999999999999999999872 2 22 36899999999998777655
No 20
>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=96.76 E-value=0.00085 Score=61.57 Aligned_cols=79 Identities=25% Similarity=0.218 Sum_probs=54.2
Q ss_pred cCCCCCCCchhHHHHHHHHHhhhhhcC---CCcceeeeccceeEEEecCCHhHhh------ccCCCCCceEeCCeeeec-
Q psy556 20 ENGLVQGSSLSTLLFAVFMNDIFHVIN---LPTRGLLFVDDLLLTIRGKILEQLG------SRNPTLPLIMLNGNQLKF- 89 (435)
Q Consensus 20 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~l~------k~~~~~~~~~l~~~~I~~- 89 (435)
..-+|||...||.+|+-++..++..+. .+..+..|.||+.+++. +.++.. ...+....+.++..+...
T Consensus 122 ~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DDili~s~--~~~e~~~~l~~v~~~l~~~gl~l~~~K~~~~ 199 (210)
T cd03715 122 FTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAAD--SEEDCLKGTDALLTHLGELGYKVSPKKAQIC 199 (210)
T ss_pred EEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCcEEEecC--CHHHHHHHHHHHHHHHHHCCCCcCHHHeeCC
Confidence 457899999999999999999988753 45678899999999854 444322 111223334444333332
Q ss_pred cCcceeeceee
Q psy556 90 DNTAKFLGLIW 100 (435)
Q Consensus 90 ~~~~kyLGv~l 100 (435)
.++++|||..+
T Consensus 200 ~~~v~fLG~~~ 210 (210)
T cd03715 200 RAEVKFLGVVW 210 (210)
T ss_pred CCceEEeeEEC
Confidence 57899999874
No 21
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=96.54 E-value=0.0021 Score=49.55 Aligned_cols=47 Identities=21% Similarity=0.073 Sum_probs=35.3
Q ss_pred cccccCCHHHHHHhhccCCC-CC-------c--------eEEEEEecccCCCCcchHHhHHHhhccC
Q psy556 253 TPPWSDDMSEVIDLWRNLTS-NN-------I--------KLTFIWCPSHCGIEGNEEVDRAANRDGH 303 (435)
Q Consensus 253 ~~i~sDs~sa~~~l~~~~~~-~~-------i--------~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~ 303 (435)
+.+.|||+.+++.+++.... +. | .+.+.|||- .+|..||.+||.|.+
T Consensus 24 i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r----~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 24 IIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPR----EQNKVADALAKFALS 86 (87)
T ss_dssp EEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--G----GGSHHHHHHHHHHHH
T ss_pred EEEEecCccccccccccccccccccccchhhhhhhccccceEEEEECh----HHhHHHHHHHHHHhh
Confidence 78999999999999877433 23 1 799999997 679999999998853
No 22
>PRK07708 hypothetical protein; Validated
Probab=96.51 E-value=0.0034 Score=57.78 Aligned_cols=48 Identities=13% Similarity=0.046 Sum_probs=37.5
Q ss_pred cccccCCHHHHHHhhccCCCCC------------------ceEEEEEecccCCCCcchHHhHHHhhccCC
Q psy556 253 TPPWSDDMSEVIDLWRNLTSNN------------------IKLTFIWCPSHCGIEGNEEVDRAANRDGHT 304 (435)
Q Consensus 253 ~~i~sDs~sa~~~l~~~~~~~~------------------i~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 304 (435)
+.|++||+.++..+.+-..... +++.+.|||-. -|+.||++|+.|...
T Consensus 143 V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~----~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 143 VTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK----QNKEADQLATQALEG 208 (219)
T ss_pred EEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch----hhhHHHHHHHHHHhc
Confidence 4689999999999987543222 25778899874 499999999999864
No 23
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=96.49 E-value=0.0034 Score=62.93 Aligned_cols=48 Identities=21% Similarity=0.292 Sum_probs=38.8
Q ss_pred cccccCCHHHHHHhhccCCCCC---------c--------eEEEEEecccCCCCcchHHhHHHhhccCC
Q psy556 253 TPPWSDDMSEVIDLWRNLTSNN---------I--------KLTFIWCPSHCGIEGNEEVDRAANRDGHT 304 (435)
Q Consensus 253 ~~i~sDs~sa~~~l~~~~~~~~---------i--------~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 304 (435)
+.|++||+.+++.+.+...... | .+++.|||. .+|+.||.+|+.|...
T Consensus 68 v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 68 VEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred EEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 6799999999999976543221 1 799999998 6799999999998644
No 24
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.58 E-value=0.005 Score=47.84 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=25.7
Q ss_pred cccccCCCCCCCCCCCc-ccchhHH-hhccCcH
Q psy556 377 SYLFERTTPPLCSCGEN-LLTVKHL-LDCVHHA 407 (435)
Q Consensus 377 ~~~~~~~~~~~C~~c~~-~et~~H~-~~Cp~~~ 407 (435)
+.+.+...++.|..|+. .||++|+ ++||...
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 45666678899998886 7999999 9999764
No 25
>KOG4768|consensus
Probab=95.06 E-value=0.019 Score=58.94 Aligned_cols=23 Identities=30% Similarity=0.517 Sum_probs=20.9
Q ss_pred CCCCCCCchhHHHHHHHHHhhhh
Q psy556 21 NGLVQGSSLSTLLFAVFMNDIFH 43 (435)
Q Consensus 21 ~GvpQGs~LSP~Lf~l~~~~l~~ 43 (435)
=|+||||+.||+|-|+|+..|.+
T Consensus 416 lGtpqgsvvspil~nifL~~LDk 438 (796)
T KOG4768|consen 416 LGTPQGSVVSPILCNIFLRELDK 438 (796)
T ss_pred ccccccccCCchhHHHHHHHHHH
Confidence 39999999999999999988864
No 26
>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=92.68 E-value=0.087 Score=45.84 Aligned_cols=43 Identities=19% Similarity=0.225 Sum_probs=35.1
Q ss_pred CCCCCCCchhHHHHHHHHHhhhhhcCCCcceeeeccceeEEEec
Q psy556 21 NGLVQGSSLSTLLFAVFMNDIFHVINLPTRGLLFVDDLLLTIRG 64 (435)
Q Consensus 21 ~GvpQGs~LSP~Lf~l~~~~l~~~~~~~~~~~~yADD~~i~~~~ 64 (435)
..+|||...||.+|.-.+..++..+. +..+..|+||+.+....
T Consensus 94 ~~~p~G~~~s~~~~~~~~~~~l~~~~-~~~~~~y~DDi~i~~~~ 136 (177)
T cd01647 94 TRMPFGLKNAPATFQRLMNKILGDLL-GDFVEVYLDDILVYSKT 136 (177)
T ss_pred EEecCCCccHHHHHHHHHHhhhcccc-ccccEEEecCccccCCC
Confidence 46999999999999999998887642 33578899999998554
No 27
>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=92.39 E-value=0.11 Score=47.67 Aligned_cols=47 Identities=13% Similarity=0.069 Sum_probs=37.6
Q ss_pred eccCCCCCCCchhHHHHHHHHHhhhhhcCC-----CcceeeeccceeEEEec
Q psy556 18 GLENGLVQGSSLSTLLFAVFMNDIFHVINL-----PTRGLLFVDDLLLTIRG 64 (435)
Q Consensus 18 ~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~~-----~~~~~~yADD~~i~~~~ 64 (435)
.--.-+|+|-.-||.+|+.+++.+++.+.. .+....|+||+.+.+..
T Consensus 99 Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s 150 (213)
T cd01644 99 YRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDT 150 (213)
T ss_pred EEEEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCC
Confidence 344569999999999999999999987553 23467999999997444
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=57.91 E-value=17 Score=34.45 Aligned_cols=50 Identities=20% Similarity=0.323 Sum_probs=34.4
Q ss_pred ceeccCCCCCCCchh----HHHHHHHHHhhhhhc-----CCCcceeeeccceeEEEecC
Q psy556 16 FKGLENGLVQGSSLS----TLLFAVFMNDIFHVI-----NLPTRGLLFVDDLLLTIRGK 65 (435)
Q Consensus 16 ~~~i~~GvpQGs~LS----P~Lf~l~~~~l~~~~-----~~~~~~~~yADD~~i~~~~~ 65 (435)
.+....|+|+|++.. +++=++++......+ ...+.++.|.||..+.+...
T Consensus 153 ~~~~~~G~pSG~~~T~~~Nsl~n~~~~~~a~~~~~~~~~~~~~~~~~~GDD~li~~~~~ 211 (278)
T cd01699 153 VYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKA 211 (278)
T ss_pred EEEEcCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEcCCeEEEechh
Confidence 566788999999885 444444444333321 35678899999999988754
No 29
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=45.47 E-value=6.3 Score=38.66 Aligned_cols=46 Identities=20% Similarity=0.195 Sum_probs=34.2
Q ss_pred eeccCCCCCCCchhHHHHHHHHHhhhhhcCC-C-cceeeeccceeEEE
Q psy556 17 KGLENGLVQGSSLSTLLFAVFMNDIFHVINL-P-TRGLLFVDDLLLTI 62 (435)
Q Consensus 17 ~~i~~GvpQGs~LSP~Lf~l~~~~l~~~~~~-~-~~~~~yADD~~i~~ 62 (435)
..-..|+|||+++||+|-++.++.+...+.. . ....-|+||-.+-.
T Consensus 233 ~~~~~~~~q~~~vs~~l~n~~l~~~~~~~~~~~~~~~~~y~~~~~i~~ 280 (328)
T COG3344 233 KSKEKGTPQGGLVSPILVNIKLSKLDNELRNRYLNLLRRYIDDGNIDK 280 (328)
T ss_pred ccccccCCCCCccCchhhhhhhhhhhHHHHHHHhhhhhhhcccccCCH
Confidence 3467799999999999999998877665321 0 13678899887754
No 30
>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=41.55 E-value=14 Score=25.90 Aligned_cols=20 Identities=15% Similarity=0.139 Sum_probs=9.2
Q ss_pred CCCCCCCcccchhHH-hhccC
Q psy556 386 PLCSCGENLLTVKHL-LDCVH 405 (435)
Q Consensus 386 ~~C~~c~~~et~~H~-~~Cp~ 405 (435)
-.|+.||+..+..|. ..||.
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 469999999999999 99995
No 31
>PF07727 RVT_2: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR013103 A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This entry includes reverse transcriptases not recognised by IPR000477 from INTERPRO [].
Probab=29.23 E-value=20 Score=33.67 Aligned_cols=42 Identities=21% Similarity=0.264 Sum_probs=31.3
Q ss_pred CCCCCCCchhHHHHHHHHHhhhhhcC-----------------CCcceeeeccceeEEEecCC
Q psy556 21 NGLVQGSSLSTLLFAVFMNDIFHVIN-----------------LPTRGLLFVDDLLLTIRGKI 66 (435)
Q Consensus 21 ~GvpQGs~LSP~Lf~l~~~~l~~~~~-----------------~~~~~~~yADD~~i~~~~~~ 66 (435)
.|++| ||.+|.-.++..+..+. ..+-+..|.||+.+.+....
T Consensus 122 YGLKQ----a~r~W~~~l~~~L~~~GF~~~~~D~clfi~~~~~~~~ii~vYVDDili~~~~~~ 180 (246)
T PF07727_consen 122 YGLKQ----APRLWYKTLDKFLKKLGFKQSKADPCLFIKKSGDGFIIILVYVDDILIAGPSEE 180 (246)
T ss_pred eeccc----ccchhhhhcccccchhhhhccccccccccccccccccccccccccccccccccc
Confidence 37788 89999988887776532 13558899999999866554
No 32
>COG3716 ManZ Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IID [Carbohydrate transport and metabolism]
Probab=26.08 E-value=50 Score=31.10 Aligned_cols=20 Identities=35% Similarity=0.511 Sum_probs=16.3
Q ss_pred CCCCchhHHHHHHHHHhhhh
Q psy556 24 VQGSSLSTLLFAVFMNDIFH 43 (435)
Q Consensus 24 pQGs~LSP~Lf~l~~~~l~~ 43 (435)
-||++|+|+||.+..+-+.-
T Consensus 134 ~~G~ilGpilf~~l~N~i~~ 153 (269)
T COG3716 134 LQGSILGPILFFLLFNILRL 153 (269)
T ss_pred hcCCchHHHHHHHHHHHHHH
Confidence 48999999999977776643
No 33
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=25.63 E-value=43 Score=22.10 Aligned_cols=19 Identities=16% Similarity=0.321 Sum_probs=15.0
Q ss_pred CCCCCCCCCcccchhHH-hhccC
Q psy556 384 TPPLCSCGENLLTVKHL-LDCVH 405 (435)
Q Consensus 384 ~~~~C~~c~~~et~~H~-~~Cp~ 405 (435)
....|.-|+.. .|+ ++||.
T Consensus 3 ~~~~CqkC~~~---GH~tyeC~~ 22 (42)
T PF13917_consen 3 ARVRCQKCGQK---GHWTYECPN 22 (42)
T ss_pred CCCcCcccCCC---CcchhhCCC
Confidence 45779888754 699 99996
No 34
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=23.21 E-value=64 Score=34.56 Aligned_cols=33 Identities=21% Similarity=0.342 Sum_probs=24.9
Q ss_pred HHHHhhccCCCCCceEEEEEecccCCCCcchHH
Q psy556 262 EVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEV 294 (435)
Q Consensus 262 a~~~l~~~~~~~~i~v~~~Wvp~H~gi~gNe~A 294 (435)
.++.+-+.-.+-||.|-+.|||+|.+..||-.+
T Consensus 215 dfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 215 DFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 344444444555689999999999999998776
No 35
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=22.54 E-value=1.1e+02 Score=25.10 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=10.8
Q ss_pred EEecccCCCCcc
Q psy556 280 IWCPSHCGIEGN 291 (435)
Q Consensus 280 ~Wvp~H~gi~gN 291 (435)
.|+||++|+.-|
T Consensus 80 ~~CPGyse~QiN 91 (124)
T PF15216_consen 80 NYCPGYSETQIN 91 (124)
T ss_pred HhCCCcchhhcc
Confidence 699999999887
Done!