Query psy9745
Match_columns 570
No_of_seqs 527 out of 2923
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 18:27:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9745.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9745hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.9 5.4E-22 1.2E-26 179.5 11.8 127 373-506 3-143 (161)
2 COG0328 RnhA Ribonuclease HI [ 99.9 1.1E-21 2.3E-26 174.1 12.0 127 374-506 2-146 (154)
3 PRK08719 ribonuclease H; Revie 99.9 1E-21 2.2E-26 176.6 11.3 122 373-504 2-146 (147)
4 PF00075 RNase_H: RNase H; In 99.8 4.1E-21 8.8E-26 171.1 7.7 121 374-503 2-131 (132)
5 PRK00203 rnhA ribonuclease H; 99.8 1.2E-20 2.5E-25 171.5 10.3 125 375-507 3-144 (150)
6 cd06222 RnaseH RNase H (RNase 99.7 9.5E-17 2.1E-21 140.7 12.8 122 377-503 1-130 (130)
7 PRK13907 rnhA ribonuclease H; 99.7 1.8E-16 4E-21 140.3 11.3 120 376-504 2-126 (128)
8 KOG3752|consensus 99.7 2.1E-16 4.5E-21 156.6 11.1 126 374-504 211-364 (371)
9 PRK07708 hypothetical protein; 99.5 5.8E-14 1.3E-18 134.3 13.6 129 371-508 69-211 (219)
10 PRK07238 bifunctional RNase H/ 99.4 2E-12 4.4E-17 135.6 13.1 120 375-504 2-131 (372)
11 PF14529 Exo_endo_phos_2: Endo 99.2 5.6E-12 1.2E-16 109.8 4.8 81 83-165 18-101 (119)
12 PF13456 RVT_3: Reverse transc 99.1 1.4E-10 3E-15 94.9 6.6 85 410-503 1-85 (87)
13 cd03487 RT_Bac_retron_II RT_Ba 98.9 3.3E-10 7.2E-15 109.4 2.3 119 131-255 56-198 (214)
14 cd01651 RT_G2_intron RT_G2_int 98.9 4.3E-10 9.2E-15 109.5 2.8 120 131-252 69-226 (226)
15 cd01648 TERT TERT: Telomerase 98.9 3.1E-10 6.7E-15 98.8 1.5 61 177-237 13-81 (119)
16 cd01650 RT_nLTR_like RT_nLTR: 98.9 8.7E-10 1.9E-14 106.9 4.5 70 131-227 81-159 (220)
17 PF00078 RVT_1: Reverse transc 98.6 1.6E-08 3.4E-13 97.3 3.3 119 131-252 63-214 (214)
18 cd01646 RT_Bac_retron_I RT_Bac 98.5 1E-08 2.2E-13 94.1 -1.0 51 176-226 46-99 (158)
19 cd00304 RT_like RT_like: Rever 98.4 1.7E-07 3.8E-12 78.4 2.4 68 184-251 12-97 (98)
20 cd01709 RT_like_1 RT_like_1: A 98.3 1.8E-06 3.9E-11 86.7 8.9 105 131-237 21-140 (346)
21 KOG4768|consensus 97.4 0.00016 3.5E-09 76.4 4.8 133 177-309 411-644 (796)
22 cd01645 RT_Rtv RT_Rtv: Reverse 97.3 0.00012 2.6E-09 70.6 2.7 69 182-252 127-213 (213)
23 cd03714 RT_DIRS1 RT_DIRS1: Rev 97.0 0.00046 1E-08 59.9 2.7 69 184-252 34-119 (119)
24 cd03715 RT_ZFREV_like RT_ZFREV 96.7 0.00098 2.1E-08 64.1 3.0 70 181-252 122-210 (210)
25 PRK13911 exodeoxyribonuclease 95.9 0.018 4E-07 56.8 6.8 64 12-109 86-151 (250)
26 KOG1005|consensus 95.9 0.0065 1.4E-07 67.2 3.7 58 176-235 627-690 (888)
27 TIGR00633 xth exodeoxyribonucl 95.6 0.028 6.1E-07 55.5 6.8 17 93-109 140-156 (255)
28 COG0708 XthA Exonuclease III [ 94.9 0.037 8E-07 54.3 4.9 15 28-42 100-114 (261)
29 cd01647 RT_LTR RT_LTR: Reverse 94.8 0.03 6.5E-07 51.3 4.0 68 182-252 94-177 (177)
30 TIGR00195 exoDNase_III exodeox 92.6 0.23 5E-06 49.1 6.0 16 94-109 138-153 (254)
31 PF14529 Exo_endo_phos_2: Endo 92.3 0.097 2.1E-06 44.8 2.4 63 29-93 1-66 (119)
32 cd01644 RT_pepA17 RT_pepA17: R 92.1 0.15 3.3E-06 49.0 3.8 59 179-239 99-162 (213)
33 PRK11756 exonuclease III; Prov 91.7 0.32 6.9E-06 48.5 5.7 26 14-41 90-115 (268)
34 PF03372 Exo_endo_phos: Endonu 89.7 0.47 1E-05 45.5 4.8 13 96-108 158-170 (249)
35 PF09004 DUF1891: Domain of un 83.2 0.28 6E-06 33.7 -0.6 41 258-300 1-41 (42)
36 PF05380 Peptidase_A17: Pao re 81.4 3.9 8.5E-05 37.3 6.1 64 374-441 80-158 (159)
37 PRK05421 hypothetical protein; 77.4 2.9 6.2E-05 41.6 4.2 24 84-107 172-195 (263)
38 COG3344 Retron-type reverse tr 70.0 0.82 1.8E-05 47.1 -1.8 91 133-223 182-280 (328)
39 PF00336 DNA_pol_viral_C: DNA 65.6 5.6 0.00012 37.1 2.8 89 377-487 96-184 (245)
40 PRK05421 hypothetical protein; 59.6 8.4 0.00018 38.3 3.2 51 14-65 136-192 (263)
41 smart00128 IPPc Inositol polyp 58.9 18 0.00039 36.9 5.5 41 12-54 125-168 (310)
42 COG3021 Uncharacterized protei 54.2 7.7 0.00017 39.0 1.8 21 85-105 213-233 (309)
43 KOG1812|consensus 53.5 25 0.00055 37.0 5.7 90 408-505 47-138 (384)
44 KOG1645|consensus 52.8 18 0.00038 37.6 4.1 65 9-112 201-265 (463)
45 cd01699 RNA_dep_RNAP RNA_dep_R 43.2 12 0.00026 37.3 1.3 50 177-226 153-211 (278)
46 PRK11756 exonuclease III; Prov 42.2 21 0.00045 35.4 2.9 16 93-108 142-157 (268)
47 PF07727 RVT_2: Reverse transc 38.4 17 0.00038 35.7 1.6 69 182-254 122-211 (246)
48 smart00476 DNaseIc deoxyribonu 36.0 28 0.00061 34.8 2.6 14 93-106 175-188 (276)
49 TIGR03395 sphingomy sphingomye 34.9 51 0.0011 33.1 4.3 21 14-36 122-142 (283)
50 PLN03144 Carbon catabolite rep 33.6 33 0.00071 38.3 2.8 15 93-107 454-468 (606)
51 COG0296 GlgB 1,4-alpha-glucan 33.4 54 0.0012 36.7 4.5 37 459-495 211-247 (628)
52 PRK15251 cytolethal distending 33.2 1.1E+02 0.0024 30.5 6.2 27 84-110 172-200 (271)
53 PF08388 GIIM: Group II intron 29.0 1.3E+02 0.0027 23.4 4.9 58 272-332 4-62 (80)
54 TIGR03395 sphingomy sphingomye 28.6 53 0.0011 33.0 3.2 13 95-107 178-190 (283)
55 PRK15251 cytolethal distending 26.1 69 0.0015 31.9 3.4 50 13-68 142-197 (271)
56 smart00156 PP2Ac Protein phosp 25.5 1.1E+02 0.0024 30.5 4.9 34 56-104 28-65 (271)
57 PF03372 Exo_endo_phos: Endonu 23.6 54 0.0012 30.8 2.2 43 26-68 119-169 (249)
58 KOG3873|consensus 23.0 96 0.0021 32.0 3.7 44 67-114 144-190 (422)
59 cd07420 MPP_RdgC Drosophila me 22.1 1.5E+02 0.0033 30.4 5.1 33 57-104 52-89 (321)
60 PRK04036 DNA polymerase II sma 21.4 2.6E+02 0.0057 30.7 7.1 48 13-65 205-253 (504)
61 KOG4355|consensus 21.2 2.1E+02 0.0045 29.9 5.7 42 95-137 47-98 (547)
62 COG3568 ElsH Metal-dependent h 21.1 48 0.001 32.7 1.2 62 95-164 165-231 (259)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.87 E-value=5.4e-22 Score=179.53 Aligned_cols=127 Identities=22% Similarity=0.296 Sum_probs=98.5
Q ss_pred CCCeEEEecCCCCC--CCceEEEEEeceeeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHHH
Q psy9745 373 KLDTLCFTDGSKTT--DHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQA 450 (570)
Q Consensus 373 ~~~~~iytDGS~~~--~~~G~g~~~~~~~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~~ 450 (570)
+..+.||||||+.. +..|+|+++............+|+++||++|++.||+.+.. ....|.|+|||++|+++
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~ 76 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINS 76 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHH
Confidence 34589999999864 56889988854322222234689999999999999986542 34579999999999999
Q ss_pred Hhc---------CCCCChh--H-HHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccCCC
Q psy9745 451 LQN---------VYHVSPL--V-CDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVP 506 (570)
Q Consensus 451 l~~---------~~~~~~~--~-~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~~~ 506 (570)
++. +...++. . +++++.+.++.+. ..|+|.|||||+|++|||.||+||++|+...
T Consensus 77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 983 3333333 2 6788888888776 5799999999999999999999999988543
No 2
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.87 E-value=1.1e-21 Score=174.07 Aligned_cols=127 Identities=22% Similarity=0.265 Sum_probs=104.4
Q ss_pred CCeEEEecCCCC--CCCceEEEEEec---e-eeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHH
Q psy9745 374 LDTLCFTDGSKT--TDHTGAAFIIRD---E-ICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSS 447 (570)
Q Consensus 374 ~~~~iytDGS~~--~~~~G~g~~~~~---~-~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~a 447 (570)
..+.||||||+. +|..|+|+|+.. + ..+.... .+|+++||++|++.||+.+.+. +...|.|+|||+++
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~-----~~~~v~l~tDS~yv 75 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKEL-----GACEVTLYTDSKYV 75 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhc-----CCceEEEEecHHHH
Confidence 357899999986 467999999842 1 2344444 8999999999999999999986 78999999999999
Q ss_pred HHHHhcC---CCCChh---------HHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccCCC
Q psy9745 448 LQALQNV---YHVSPL---------VCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVP 506 (570)
Q Consensus 448 l~~l~~~---~~~~~~---------~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~~~ 506 (570)
++.|..+ +...+. -.++++++.++.+....|.+.|||||+|.++||.||+||+.|+...
T Consensus 76 ~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 76 VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 9999832 111111 2678999999999888999999999999999999999999998765
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.86 E-value=1e-21 Score=176.59 Aligned_cols=122 Identities=23% Similarity=0.326 Sum_probs=95.9
Q ss_pred CCCeEEEecCCCCCC-----CceEEEEEece------eeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEE
Q psy9745 373 KLDTLCFTDGSKTTD-----HTGAAFIIRDE------ICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIIC 441 (570)
Q Consensus 373 ~~~~~iytDGS~~~~-----~~G~g~~~~~~------~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~ 441 (570)
...++||||||+..+ .+|+|+++... ..+..+.+..|+++||+.|++.||+.+.+. ..|+
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~---------~~i~ 72 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG---------DVIY 72 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC---------CEEE
Confidence 356899999998643 35999987321 234445567899999999999999998643 3799
Q ss_pred ecCHHHHHHH--------hcCCCCC-hh---HHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccC
Q psy9745 442 SDSKSSLQAL--------QNVYHVS-PL---VCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCND 504 (570)
Q Consensus 442 tDs~~al~~l--------~~~~~~~-~~---~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~ 504 (570)
|||+++++++ ++++..+ +. -.++++.+..+.+ ...|+|.|||||+|++|||.||+||++|++
T Consensus 73 tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 73 SDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred echHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9999999999 4555443 22 2567788777766 477999999999999999999999999875
No 4
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.84 E-value=4.1e-21 Score=171.10 Aligned_cols=121 Identities=27% Similarity=0.393 Sum_probs=91.3
Q ss_pred CCeEEEecCCCC--CCCceEEEEEec-eeeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHHH
Q psy9745 374 LDTLCFTDGSKT--TDHTGAAFIIRD-EICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQA 450 (570)
Q Consensus 374 ~~~~iytDGS~~--~~~~G~g~~~~~-~~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~~ 450 (570)
..+.||||||+. ++..|+|+++.. ...+..++ ..+++.||++|+..||+ +. . ...++|+|||++++..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~-~------~~~v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-AL-E------HRKVTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-TH-S------TSEEEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hh-h------cccccccccHHHHHHH
Confidence 468999999965 445688886642 23444455 89999999999999999 44 3 2789999999999998
Q ss_pred Hhc-----CCCCChhHHHHHHHHHHHHHhCCceEEEeecCCCCC-Cccchhchhhhhcc
Q psy9745 451 LQN-----VYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGI-RENDNVDHAARHCN 503 (570)
Q Consensus 451 l~~-----~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi-~gNe~AD~lAk~a~ 503 (570)
+.. .+........+++.+.++...+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus 73 l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 73 LNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHhccccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 877 443332211244455555567899999999999999 69999999999986
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.83 E-value=1.2e-20 Score=171.53 Aligned_cols=125 Identities=19% Similarity=0.255 Sum_probs=94.9
Q ss_pred CeEEEecCCCCC--CCceEEEEEece--ee-eeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHH
Q psy9745 375 DTLCFTDGSKTT--DHTGAAFIIRDE--IC-SMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQ 449 (570)
Q Consensus 375 ~~~iytDGS~~~--~~~G~g~~~~~~--~~-~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~ 449 (570)
.+.||||||+.. +..|+|+++... .. .....+..|+++||++|++.||+.+.+ ...+.|+|||+++++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-------~~~v~I~tDS~yvi~ 75 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-------PCEVTLYTDSQYVRQ 75 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-------CCeEEEEECHHHHHH
Confidence 478999999863 568888888421 11 112235788999999999999998753 357999999999999
Q ss_pred HHhc--------CCC-CChh---HHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccCCCC
Q psy9745 450 ALQN--------VYH-VSPL---VCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCNDVPI 507 (570)
Q Consensus 450 ~l~~--------~~~-~~~~---~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~~~~ 507 (570)
+|.. .+. ..+. -.++++.+.++... ..|.|.|||||+|++|||.||+|||+|+..+.
T Consensus 76 ~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 76 GITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 9985 222 2222 24567777776654 78999999999999999999999999987553
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=99.71 E-value=9.5e-17 Score=140.73 Aligned_cols=122 Identities=26% Similarity=0.363 Sum_probs=98.7
Q ss_pred EEEecCCCCCC--CceEEEEEecee-----eeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHH
Q psy9745 377 LCFTDGSKTTD--HTGAAFIIRDEI-----CSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQ 449 (570)
Q Consensus 377 ~iytDGS~~~~--~~G~g~~~~~~~-----~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~ 449 (570)
.+|||||...+ .+|+|+++.+.. .........+++.||+.|+..||+.+... +..++.|++||+.++.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-----~~~~i~i~~Ds~~~~~ 75 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-----GGKKVNIYTDSQYVIN 75 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-----CCceEEEEECHHHHHH
Confidence 37999998754 789999985421 11112257899999999999999999865 7899999999999999
Q ss_pred HHhcCCC-CChhHHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhcc
Q psy9745 450 ALQNVYH-VSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCN 503 (570)
Q Consensus 450 ~l~~~~~-~~~~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~ 503 (570)
.+++... .......++..+.++...+..+.|.|||+|+|+.+|+.||.|||+|.
T Consensus 76 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 76 ALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 9998765 22334556677777777789999999999999999999999999874
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.69 E-value=1.8e-16 Score=140.27 Aligned_cols=120 Identities=18% Similarity=0.166 Sum_probs=98.9
Q ss_pred eEEEecCCCCC--CCceEEEEEeceee--ee-ccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHHH
Q psy9745 376 TLCFTDGSKTT--DHTGAAFIIRDEIC--SM-KLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQA 450 (570)
Q Consensus 376 ~~iytDGS~~~--~~~G~g~~~~~~~~--~~-~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~~ 450 (570)
+.||||||+.. +.+|+|+++.+... .. ......+++.||+.|++.||+.+.+. +..++.|+|||+.+++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-----g~~~v~i~sDS~~vi~~ 76 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-----NYNIVSFRTDSQLVERA 76 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-----CCCEEEEEechHHHHHH
Confidence 57999999864 57999999954322 11 12246799999999999999999987 77889999999999999
Q ss_pred HhcCCCCChhHHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccC
Q psy9745 451 LQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCND 504 (570)
Q Consensus 451 l~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~ 504 (570)
+++.+........+++.+..+...+..+.+.|||. ++|+.||.||+.|..
T Consensus 77 ~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 77 VEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred HhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 99977655556778888888888888899999995 589999999999864
No 8
>KOG3752|consensus
Probab=99.67 E-value=2.1e-16 Score=156.63 Aligned_cols=126 Identities=22% Similarity=0.223 Sum_probs=99.4
Q ss_pred CCeEEEecCCCCC-----CCceEEEEEec---eeeeeccC-CccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecC
Q psy9745 374 LDTLCFTDGSKTT-----DHTGAAFIIRD---EICSMKLN-PICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDS 444 (570)
Q Consensus 374 ~~~~iytDGS~~~-----~~~G~g~~~~~---~~~~~~~~-~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs 444 (570)
+.+++|||||+.. ..+|+|+++++ ...+..+. +..++|+||+.|+..||+.|.+. ...+|+|.|||
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-----~~~kv~I~TDS 285 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-----NINKVVIRTDS 285 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-----CCCcEEEEech
Confidence 4488999999864 25999999953 45666765 88999999999999999999876 67799999999
Q ss_pred HHHHHHHhcC--------CC---CChh------HHHHHHHHHHHHHh--CCceEEEeecCCCCCCccchhchhhhhccC
Q psy9745 445 KSSLQALQNV--------YH---VSPL------VCDIISTIQDIRDL--GTRVSFLWIPSHLGIRENDNVDHAARHCND 504 (570)
Q Consensus 445 ~~al~~l~~~--------~~---~~~~------~~~~~~~~~~l~~~--~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~ 504 (570)
++++++|+.+ +. .+.+ -+..+..+.++.+. ..+|.+.||+||.|+.|||+||.|||+++.
T Consensus 286 ~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 286 EYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred HHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 9999999752 11 1111 13345555555544 489999999999999999999999999854
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.55 E-value=5.8e-14 Score=134.27 Aligned_cols=129 Identities=15% Similarity=0.168 Sum_probs=99.9
Q ss_pred cCCCCeEEEecCCCC--CCCceEEEEEece----e----eeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcc--eE
Q psy9745 371 QHKLDTLCFTDGSKT--TDHTGAAFIIRDE----I----CSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQ--NF 438 (570)
Q Consensus 371 ~~~~~~~iytDGS~~--~~~~G~g~~~~~~----~----~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~--~v 438 (570)
.-++.+.+|+|||.. ++++|+|+++... . ....++...|++.||+.|++.||+.+.+. +.+ .|
T Consensus 69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~~~V 143 (219)
T PRK07708 69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKHEPV 143 (219)
T ss_pred cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCcceE
Confidence 346679999999975 4679999998531 1 12245556899999999999999999886 544 48
Q ss_pred EEEecCHHHHHHHhcCCCC-ChhHHHHHHHHHHHHHhC-CceEEEeecCCCCCCccchhchhhhhccCCCCC
Q psy9745 439 IICSDSKSSLQALQNVYHV-SPLVCDIISTIQDIRDLG-TRVSFLWIPSHLGIRENDNVDHAARHCNDVPIT 508 (570)
Q Consensus 439 ~I~tDs~~al~~l~~~~~~-~~~~~~~~~~~~~l~~~~-~~v~~~WVp~H~gi~gNe~AD~lAk~a~~~~~~ 508 (570)
.|++||+.+++.+++.+.. ++....+++.+.++.+.. ..+.+.||| ...|+.||+||++|+.....
T Consensus 144 ~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~ 211 (219)
T PRK07708 144 TFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVI 211 (219)
T ss_pred EEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCC
Confidence 9999999999999997754 345566777777666554 357889998 67899999999999975543
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.40 E-value=2e-12 Score=135.56 Aligned_cols=120 Identities=18% Similarity=0.244 Sum_probs=98.6
Q ss_pred CeEEEecCCCCC--CCceEEEEEecee-------eeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCH
Q psy9745 375 DTLCFTDGSKTT--DHTGAAFIIRDEI-------CSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSK 445 (570)
Q Consensus 375 ~~~iytDGS~~~--~~~G~g~~~~~~~-------~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~ 445 (570)
.+.||||||... +.+|+|+++.+.. .+..+ ...|++.||+.|++.||+.+.+. +...|.|++||+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~~-----g~~~v~i~~DS~ 75 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAEL-----GATEVEVRMDSK 75 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHhC-----CCCeEEEEeCcH
Confidence 478999999864 4689999995421 12223 37889999999999999999987 778999999999
Q ss_pred HHHHHHhcCCC-CChhHHHHHHHHHHHHHhCCceEEEeecCCCCCCccchhchhhhhccC
Q psy9745 446 SSLQALQNVYH-VSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNVDHAARHCND 504 (570)
Q Consensus 446 ~al~~l~~~~~-~~~~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~AD~lAk~a~~ 504 (570)
.+++.+++.+. ++.....+++.+.++.+.+..+.+.|||. .+|+.||.||+.|..
T Consensus 76 lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~ 131 (372)
T PRK07238 76 LVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMD 131 (372)
T ss_pred HHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHH
Confidence 99999998765 34456667788888888889999999994 789999999999864
No 11
>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B.
Probab=99.25 E-value=5.6e-12 Score=109.77 Aligned_cols=81 Identities=31% Similarity=0.451 Sum_probs=55.3
Q ss_pred hhHHHHHHHhCCC-CeEEEcCCCCCCCCcCCCCCC-ChhHHHHHHHhhcCCeEEEcc-CCCcccccCCCCcchhhHHhhh
Q psy9745 83 KDEIYNIKRQLPR-PYIICSDMNAHNTIWGGSKID-SNGVQVEKFLLENDDVCLLNT-NEATHFNSSNGTFSAIDLTLAS 159 (570)
Q Consensus 83 ~~~l~~i~~~~~~-~~Ii~GDfN~~~~~wg~~~~~-~~g~~l~~~~~~~~~l~lln~-~~~~~F~~~~~~~s~ID~~l~s 159 (570)
.+.+++++...+. ++||+||||++|..|++...+ .+|+.|.+++++. ++.+++. +...+|.+.++ .+.||.++++
T Consensus 18 ~~~l~~~~~~~~~~~~Ii~GDFN~~~~~w~~~~~~~~~~~~l~~~~~~~-~l~~~~~~~~~~T~~~~~~-~s~iD~~~~s 95 (119)
T PF14529_consen 18 FDQLRQLLKNLPPAPIIIGGDFNAHHPNWDSSNTNSRRGEQLLDWLDSH-NLVDLNPPGRPPTFISNSH-GSRIDLILTS 95 (119)
T ss_dssp HHHHHHHHHCCTTSSEEEEEE-----GGGT-SCHHHHHHHHHHHHHHHC-TEEE---TT---SEEECCC-EE--EEEEEE
T ss_pred HHHHHHHHHhCCCCCEEEEeECCCCchhhhhccccchhHHHHHHHhhhc-eeeeeecCCCCCcccCCCC-CceEEEEEEC
Confidence 4566677777655 899999999999999998777 8999999999988 8888876 44567777655 5999999999
Q ss_pred cCCCCc
Q psy9745 160 RSITPD 165 (570)
Q Consensus 160 ~~i~~~ 165 (570)
..+...
T Consensus 96 ~~~~~~ 101 (119)
T PF14529_consen 96 DNLLSW 101 (119)
T ss_dssp CCGCCC
T ss_pred ChHHhc
Confidence 988876
No 12
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.11 E-value=1.4e-10 Score=94.91 Aligned_cols=85 Identities=22% Similarity=0.218 Sum_probs=70.9
Q ss_pred cchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHHHHhcCCCCChhHHHHHHHHHHHHHhCCceEEEeecCCCCC
Q psy9745 410 IFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSPLVCDIISTIQDIRDLGTRVSFLWIPSHLGI 489 (570)
Q Consensus 410 ~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~~l~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi 489 (570)
+..||+.|+..||+.+.+. +..+|.|.|||+.++..+++..........++..+..+.+....+.+.||| .
T Consensus 1 ~~~aE~~al~~al~~a~~~-----g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r 71 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWEL-----GIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----R 71 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCC-----T-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------G
T ss_pred CcHHHHHHHHHHHHHHHHC-----CCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----h
Confidence 3579999999999999987 889999999999999999988654445667888899999999999999999 9
Q ss_pred Cccchhchhhhhcc
Q psy9745 490 RENDNVDHAARHCN 503 (570)
Q Consensus 490 ~gNe~AD~lAk~a~ 503 (570)
++|..||.|||.|.
T Consensus 72 ~~N~~A~~LA~~a~ 85 (87)
T PF13456_consen 72 EQNKVADALAKFAL 85 (87)
T ss_dssp GGSHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHHh
Confidence 99999999999885
No 13
>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=98.93 E-value=3.3e-10 Score=109.44 Aligned_cols=119 Identities=18% Similarity=0.217 Sum_probs=82.0
Q ss_pred CeEEEccCCCcccccCCCCcchhhHHhhhcCCC-CceEEEEecccceeEeeecccCCCCCCchhhHHHHhcCcCcccC--
Q psy9745 131 DVCLLNTNEATHFNSSNGTFSAIDLTLASRSIT-PDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYIP-- 207 (570)
Q Consensus 131 ~l~lln~~~~~~F~~~~~~~s~ID~~l~s~~i~-~~l~~~V~~~~~~~~~~~~GvPQGs~LSP~Lf~i~~~~l~~~~~-- 207 (570)
..+++..|...+|++.+ +..+-..+...... ..+. .-+........|+|||+++||+||++|++++...+.
T Consensus 56 ~~~v~~~Di~~fFdsI~--~~~L~~~l~~~~~~~~~~~----~~l~~~~~~~~GlpQG~~lSp~Lanl~l~~~d~~l~~~ 129 (214)
T cd03487 56 AKYVLKLDIKDFFPSIT--FERVRGVFRSLGYFSPDVA----TILAKLCTYNGHLPQGAPTSPALSNLVFRKLDERLSKL 129 (214)
T ss_pred CCEEEEeehhhhcccCC--HHHHHHHHHHcCCCCHHHH----HHHHHHHhCCCCcCCCCcccHHHHHHHHHHHHHHHHHH
Confidence 45677778889999997 44455555544433 2111 111122234459999999999999999999877653
Q ss_pred ---CCcceeEeeccceeeecCCC---HHHHHHHhccccc---------------cccceeeeeeeeccC
Q psy9745 208 ---TVVSHGMFVDDLAIFMRGKD---MDHIEETLQNTIQ---------------FKENTRYLGLNLDSS 255 (570)
Q Consensus 208 ---~~~~~~~yADD~~i~~~~~~---~~~~~~~l~~~l~---------------~~~~~kyLGv~ld~~ 255 (570)
.++....||||+++++.... ..++...++..+. ....+.+||+.+...
T Consensus 130 ~~~~~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~i~~~~~~~~~~G~~i~~~ 198 (214)
T cd03487 130 AKSNGLTYTRYADDITFSSNKKLKEALDKLLEIIRSILSEEGFKINKSKTRISSKGSRQIVTGLVVNNG 198 (214)
T ss_pred HHHcCCeEEEEeccEEEEccccchhHHHHHHHHHHHHHHHCCceeCCCceEEccCCCCcEEEEEEEeCC
Confidence 46788999999999987765 4455555554432 446899999999764
No 14
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=98.92 E-value=4.3e-10 Score=109.49 Aligned_cols=120 Identities=18% Similarity=0.226 Sum_probs=79.7
Q ss_pred CeEEEccCCCcccccCCCCcchhhHHhhhcCCCCceE-------EEEecccceeEeeecccCCCCCCchhhHHHHhcCcC
Q psy9745 131 DVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPDLK-------WSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLP 203 (570)
Q Consensus 131 ~l~lln~~~~~~F~~~~~~~s~ID~~l~s~~i~~~l~-------~~V~~~~~~~~~~~~GvPQGs~LSP~Lf~i~~~~l~ 203 (570)
..+++.-|...+|++.++ ..+...+........+. ...............|+|||+++||+||++|++++.
T Consensus 69 ~~~~~~~Di~~~Fdsi~~--~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~GlpqG~~lSp~L~~~~l~~ld 146 (226)
T cd01651 69 YTWVIEGDIKGFFDNIDH--DLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQGGVISPLLANIYLHELD 146 (226)
T ss_pred CeEEEEccHHHhcCCCCH--HHHHHHHHHhcccHHHHHHHHHHHhceEccCCeEeCCCCCcCCCccHHHHHHHHHHHHHH
Confidence 456777788899999873 44444444333222210 011122345678899999999999999999999987
Q ss_pred cccC--------------CCcceeEeeccceeeecCCC-HHHHHHHhccccc---------------c-ccceeeeeeee
Q psy9745 204 QYIP--------------TVVSHGMFVDDLAIFMRGKD-MDHIEETLQNTIQ---------------F-KENTRYLGLNL 252 (570)
Q Consensus 204 ~~~~--------------~~~~~~~yADD~~i~~~~~~-~~~~~~~l~~~l~---------------~-~~~~kyLGv~l 252 (570)
..+. ..+....||||+++++.+++ .+.....+++.++ . .+.++|||+.|
T Consensus 147 ~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~~~~~~~~~fLG~~~ 226 (226)
T cd01651 147 KFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFKSEGFDFLGFTF 226 (226)
T ss_pred HHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHHHHHHcCCeechhhcceeecCCCCCeeCCeEC
Confidence 6543 45678999999999977665 3344444444332 2 57888888764
No 15
>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at
Probab=98.92 E-value=3.1e-10 Score=98.83 Aligned_cols=61 Identities=25% Similarity=0.199 Sum_probs=45.1
Q ss_pred eEeeecccCCCCCCchhhHHHHhcCcCcccC-------CCcceeEeeccceeeecCCC-HHHHHHHhcc
Q psy9745 177 MLLVLTDIRQGSSLSGDLCNIATSDLPQYIP-------TVVSHGMFVDDLAIFMRGKD-MDHIEETLQN 237 (570)
Q Consensus 177 ~~~~~~GvPQGs~LSP~Lf~i~~~~l~~~~~-------~~~~~~~yADD~~i~~~~~~-~~~~~~~l~~ 237 (570)
.+..+.|+|||+++||+||++|++.+.+.+. .......||||+.+++.++. .++....+.+
T Consensus 13 ~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~~~~~~~~~~~l~~ 81 (119)
T cd01648 13 YYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSLDKAIKFLNLLLR 81 (119)
T ss_pred hhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCCHHHHHHHHHHHHH
Confidence 4567899999999999999999998876532 34567899999999976543 2333344443
No 16
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=98.91 E-value=8.7e-10 Score=106.92 Aligned_cols=70 Identities=29% Similarity=0.431 Sum_probs=55.6
Q ss_pred CeEEEccCCCcccccCCCCcchhhHHhhhcCCCCceEEEEecccceeEeeecccCCCCCCchhhHHHHhcCcCcccC---
Q psy9745 131 DVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYIP--- 207 (570)
Q Consensus 131 ~l~lln~~~~~~F~~~~~~~s~ID~~l~s~~i~~~l~~~V~~~~~~~~~~~~GvPQGs~LSP~Lf~i~~~~l~~~~~--- 207 (570)
...++.-|...+|++.++. .+...+ |+|||++|||+||++|++++.+.+.
T Consensus 81 ~~~~l~~Di~~aFdsi~~~--~l~~~l-------------------------GipQG~~lSp~l~~l~~~~l~~~~~~~~ 133 (220)
T cd01650 81 SLVLVFLDFEKAFDSVDHE--FLLKAL-------------------------GVRQGDPLSPLLFNLALDDLLRLLNKEE 133 (220)
T ss_pred ceEEEEEEHHhhcCcCCHH--HHHHHh-------------------------CCccCCcccHHHHHHHHHHHHHHHHhhc
Confidence 4667777778999998733 333323 9999999999999999999987653
Q ss_pred ------CCcceeEeeccceeeecCCC
Q psy9745 208 ------TVVSHGMFVDDLAIFMRGKD 227 (570)
Q Consensus 208 ------~~~~~~~yADD~~i~~~~~~ 227 (570)
..+....||||+++++.+..
T Consensus 134 ~~~~~~~~~~~~~yaDD~~i~~~~~~ 159 (220)
T cd01650 134 EIKLGGPGITHLAYADDIVLFSEGKS 159 (220)
T ss_pred cccCCCCccceEEeccceeeeccCCH
Confidence 46788999999999977764
No 17
>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=98.64 E-value=1.6e-08 Score=97.29 Aligned_cols=119 Identities=22% Similarity=0.295 Sum_probs=76.5
Q ss_pred CeEEEccCCCcccccCCCCcchhhHHhhhcCCCCc----e---------EEEEecccceeEeeecccCCCCCCchhhHHH
Q psy9745 131 DVCLLNTNEATHFNSSNGTFSAIDLTLASRSITPD----L---------KWSVHDDLYLMLLVLTDIRQGSSLSGDLCNI 197 (570)
Q Consensus 131 ~l~lln~~~~~~F~~~~~~~s~ID~~l~s~~i~~~----l---------~~~V~~~~~~~~~~~~GvPQGs~LSP~Lf~i 197 (570)
..+++.-|...+|++.++. .+...+........ + ...+.+.. .......|+|||+++||+||++
T Consensus 63 ~~~~~~~Di~~~f~sI~~~--~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-~~~~~~~glpqG~~~S~~l~~~ 139 (214)
T PF00078_consen 63 YLYFLKLDISKAFDSIPHH--RLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGDL-SPYFQKRGLPQGSPLSPLLFNI 139 (214)
T ss_dssp SSEEEEEECCCCGGGSBBH--TTTGGGGEEEEECCSCHHHHHHHHHHHH-EECGCSS-SEEEEESBS-TTSTCHHHHHHH
T ss_pred ccccceeccccccccceee--eccccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhcc
Confidence 5667777778899998633 23333332111111 0 12222333 6788999999999999999999
Q ss_pred HhcCcCcccC----CCcceeEeeccceeeecCCC-HHHHHHHhccccc---------------cccceeeeeeee
Q psy9745 198 ATSDLPQYIP----TVVSHGMFVDDLAIFMRGKD-MDHIEETLQNTIQ---------------FKENTRYLGLNL 252 (570)
Q Consensus 198 ~~~~l~~~~~----~~~~~~~yADD~~i~~~~~~-~~~~~~~l~~~l~---------------~~~~~kyLGv~l 252 (570)
|++++...+. .++....||||+.+++..+. .....+.+.+.++ ..++++|||+.+
T Consensus 140 ~l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~~~~~~~~~~~lG~~i 214 (214)
T PF00078_consen 140 YLDDLDRELQQELNPDISYLRYADDILIISKSKEELQKILEKISQWLEELGLKLNPEKTKILHPSDSVKFLGYVI 214 (214)
T ss_dssp HHHHHHHHHHHHS-TTSEEEEETTEEEEEESSHHHHHHHHHHHHHHHHHTTSBCSSTTTSCS--ESSEEETTEEE
T ss_pred ccccccccccccccccccceEeccccEEEECCHHHHHHHHHHHHHHHHHCCCEEChHHEEEEeCCCCEEEEeEEC
Confidence 9999987643 46788999999999966532 2233333333222 378899999875
No 18
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=98.54 E-value=1e-08 Score=94.12 Aligned_cols=51 Identities=25% Similarity=0.224 Sum_probs=43.2
Q ss_pred eeEeeecccCCCCCCchhhHHHHhcCcCcccC---CCcceeEeeccceeeecCC
Q psy9745 176 LMLLVLTDIRQGSSLSGDLCNIATSDLPQYIP---TVVSHGMFVDDLAIFMRGK 226 (570)
Q Consensus 176 ~~~~~~~GvPQGs~LSP~Lf~i~~~~l~~~~~---~~~~~~~yADD~~i~~~~~ 226 (570)
.......|+|||+++||+|+++|++++...+. .++....||||+++++..+
T Consensus 46 ~~~~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~ 99 (158)
T cd01646 46 SQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSK 99 (158)
T ss_pred ccCCCCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCH
Confidence 34667789999999999999999999877654 5678899999999997554
No 19
>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=98.37 E-value=1.7e-07 Score=78.40 Aligned_cols=68 Identities=24% Similarity=0.349 Sum_probs=49.5
Q ss_pred cCCCCCCchhhHHHHhcCcCcccC---CCcceeEeeccceeeecCCCHHHHHHHhccccc---------------cccce
Q psy9745 184 IRQGSSLSGDLCNIATSDLPQYIP---TVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQ---------------FKENT 245 (570)
Q Consensus 184 vPQGs~LSP~Lf~i~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~---------------~~~~~ 245 (570)
+|||+++||.||+++++.+...+. .++....|+||+.+.+...........+.+.+. ....+
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 999999999999999999987653 567889999999999765522233333332221 44667
Q ss_pred eeeeee
Q psy9745 246 RYLGLN 251 (570)
Q Consensus 246 kyLGv~ 251 (570)
+|||+.
T Consensus 92 ~flG~~ 97 (98)
T cd00304 92 KFLGIL 97 (98)
T ss_pred eeecee
Confidence 888875
No 20
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=98.33 E-value=1.8e-06 Score=86.70 Aligned_cols=105 Identities=12% Similarity=-0.042 Sum_probs=66.6
Q ss_pred CeEEEccCCCcccccCCCCcchhhHHhhhcCCCC--------ceEEEEe--ccc--ceeEeeecccCCCCCCchhhHHHH
Q psy9745 131 DVCLLNTNEATHFNSSNGTFSAIDLTLASRSITP--------DLKWSVH--DDL--YLMLLVLTDIRQGSSLSGDLCNIA 198 (570)
Q Consensus 131 ~l~lln~~~~~~F~~~~~~~s~ID~~l~s~~i~~--------~l~~~V~--~~~--~~~~~~~~GvPQGs~LSP~Lf~i~ 198 (570)
...++..|...+|++.+|. .+-..+..+.+.. ++..-+. ++- .....-.+|+|||+++||+|-|+|
T Consensus 21 ~~~vvd~Dik~fFdsIpH~--~Lm~vL~~~~~~~~wL~li~r~L~APl~~~~dg~~~~~r~r~rGtPqGgviSplLaNiy 98 (346)
T cd01709 21 EVTVVQSDFKWFGPSLPHS--TILAVLKFFGVPEKWLDFFKKFLEAPLRFVADGPDAPPRIRKRGTPMSHALSDVFGELV 98 (346)
T ss_pred CEEEEEeehHhhCCCCCHH--HHHHHHHHhCCCHHHHHHHHHHHhCceeecCCCCcccccccCCccCCCchhhHHHHHHH
Confidence 5667777778888888744 3333333322222 1222222 222 234566689999999999999999
Q ss_pred hcCcCcccC---CCcceeEeeccceeeecCCCHHHHHHHhcc
Q psy9745 199 TSDLPQYIP---TVVSHGMFVDDLAIFMRGKDMDHIEETLQN 237 (570)
Q Consensus 199 ~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~l~~ 237 (570)
++.+...++ .++.+..||||++++++.+....+...+++
T Consensus 99 L~~lD~~v~~~~~g~~l~RYaDD~vi~~~~~~a~~aw~~i~~ 140 (346)
T cd01709 99 LFCLDFAVNQATDGGLLYRLHDDLWFWGQPETCAKAWKAIQE 140 (346)
T ss_pred HHHHHHHHHhcCCCceEEEEcCeEEEEcCHHHHHHHHHHHHH
Confidence 997766655 467889999999999543333333334443
No 21
>KOG4768|consensus
Probab=97.40 E-value=0.00016 Score=76.44 Aligned_cols=133 Identities=22% Similarity=0.265 Sum_probs=81.6
Q ss_pred eEeeecccCCCCCCchhhHHHHhcCcCcccC-------------------------------------------------
Q psy9745 177 MLLVLTDIRQGSSLSGDLCNIATSDLPQYIP------------------------------------------------- 207 (570)
Q Consensus 177 ~~~~~~GvPQGs~LSP~Lf~i~~~~l~~~~~------------------------------------------------- 207 (570)
.....-|+||||+.||+|.|+|+..|.+.++
T Consensus 411 y~~~~lGtpqgsvvspil~nifL~~LDk~Lenk~~nefn~~~~~~~rhs~yr~L~~~iakaKl~s~~sKtirlrd~~qrn 490 (796)
T KOG4768|consen 411 YHVEFLGTPQGSVVSPILCNIFLRELDKRLENKHRNEFNAGHLRSARHSKYRNLSDSIAKAKLTSGMSKTIRLRDGVQRN 490 (796)
T ss_pred eecccccccccccCCchhHHHHHHHHHHHHHHHHHhhhcccCcccccChhhhhHHHHHHHHHHhhhhhhhhhhhhccccc
Confidence 3455679999999999999999988755321
Q ss_pred --------CCcceeEeeccceeeecCC--CHHHHHHHhccccc---------------cccceeeeeeeeccC------c
Q psy9745 208 --------TVVSHGMFVDDLAIFMRGK--DMDHIEETLQNTIQ---------------FKENTRYLGLNLDSS------L 256 (570)
Q Consensus 208 --------~~~~~~~yADD~~i~~~~~--~~~~~~~~l~~~l~---------------~~~~~kyLGv~ld~~------l 256 (570)
.....+.||||+++.+.|. +..+..+.++..++ ..+...+||..+... .
T Consensus 491 ~~n~~~gfkr~~yVRyadd~ii~v~GS~nd~K~ilr~In~f~sslGls~n~~kt~it~S~eg~~flg~nis~tP~r~~~~ 570 (796)
T KOG4768|consen 491 ETNDTAGFKRLMYVRYADDIIIGVWGSVNDCKQILRDINNFLSSLGLSNNSSKTQITVSREGTHFLGYNISTTPGRPAAG 570 (796)
T ss_pred ccCCccccceeeEEEecCCEEEEEeccHHHHHHHHHHHHHHHHhhCcccCcccceEEeeccceeeeeceeccCCCCccce
Confidence 0123478999999988877 34455555554443 344588999887543 1
Q ss_pred cchhhHHh---------hhhhhHHHHHHHHh--hhcCC----------CCCCHHHHHHHHhhhcccccccccee
Q psy9745 257 TWKFHIEQ---------TKSKSLKALNVMKI--LSNRN----------WGLRRETLRRLYYSFALPILDYGSIL 309 (570)
Q Consensus 257 ~~~~hi~~---------~~~ka~~~~~~Lr~--l~~~~----------~gl~~~~~~~ly~a~V~p~l~Yg~~v 309 (570)
.+..|..- +.+-.++.+.+|+. +.... -...+++.+..|.++.++.+.|..-+
T Consensus 571 ~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnYYr~a 644 (796)
T KOG4768|consen 571 EGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYCSHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILNYYRLA 644 (796)
T ss_pred eccccceEEeccCCceeecchHHHHHHHHHhcceeecCCcCceeeeeecccCHHHHHHHHHHHhhchhhhhhHh
Confidence 12222110 11112333444431 11111 13567888899999999999987543
No 22
>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=97.33 E-value=0.00012 Score=70.63 Aligned_cols=69 Identities=19% Similarity=0.229 Sum_probs=50.4
Q ss_pred cccCCCCCCchhhHHHHhcCcCcccC---CCcceeEeeccceeeecCCCHHHHHHHhccccc---------------ccc
Q psy9745 182 TDIRQGSSLSGDLCNIATSDLPQYIP---TVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQ---------------FKE 243 (570)
Q Consensus 182 ~GvPQGs~LSP~Lf~i~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~---------------~~~ 243 (570)
.++|||...||.+|+.+++.++..+. ..+.+..|+||+.+. +.+.++..+.++..++ ...
T Consensus 127 ~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~--s~~~~~~~~~l~~v~~~l~~~gl~ln~~K~~~~~ 204 (213)
T cd01645 127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIA--SDLEGQLREIYEELRQTLLRWGLTIPPEKVQKEP 204 (213)
T ss_pred EEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEE--cCCHHHHHHHHHHHHHHHHHCCCEeCHHHEeCCC
Confidence 56999999999999999999877543 245678999999998 5554444444443332 446
Q ss_pred ceeeeeeee
Q psy9745 244 NTRYLGLNL 252 (570)
Q Consensus 244 ~~kyLGv~l 252 (570)
+++|||+.+
T Consensus 205 ~v~fLG~~i 213 (213)
T cd01645 205 PFQYLGYEL 213 (213)
T ss_pred CeEeccEeC
Confidence 788888764
No 23
>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.
Probab=96.98 E-value=0.00046 Score=59.91 Aligned_cols=69 Identities=22% Similarity=0.264 Sum_probs=48.3
Q ss_pred cCCCCCCchhhHHHHhcCcCcccC-CCcceeEeeccceeeecCC-CHHHHHHHhccc--------cc-------ccccee
Q psy9745 184 IRQGSSLSGDLCNIATSDLPQYIP-TVVSHGMFVDDLAIFMRGK-DMDHIEETLQNT--------IQ-------FKENTR 246 (570)
Q Consensus 184 vPQGs~LSP~Lf~i~~~~l~~~~~-~~~~~~~yADD~~i~~~~~-~~~~~~~~l~~~--------l~-------~~~~~k 246 (570)
+|||-..||.+|..+++.+...+. .+..+..|+||+.+.+... ..++....+++. ++ .+++++
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 899999999999999998887653 3456789999999985542 122333333321 11 456799
Q ss_pred eeeeee
Q psy9745 247 YLGLNL 252 (570)
Q Consensus 247 yLGv~l 252 (570)
|||+.+
T Consensus 114 fLG~~~ 119 (119)
T cd03714 114 FLGLEL 119 (119)
T ss_pred ECcEeC
Confidence 999864
No 24
>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=96.74 E-value=0.00098 Score=64.12 Aligned_cols=70 Identities=19% Similarity=0.199 Sum_probs=53.8
Q ss_pred ecccCCCCCCchhhHHHHhcCcCcccC---CCcceeEeeccceeeecCCCHHHHHHHhccccc----------------c
Q psy9745 181 LTDIRQGSSLSGDLCNIATSDLPQYIP---TVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQ----------------F 241 (570)
Q Consensus 181 ~~GvPQGs~LSP~Lf~i~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~----------------~ 241 (570)
..-+|||-..||.+|.-+++.++..+. .+..+..|.||+.+. +++.++..+.++..+. .
T Consensus 122 ~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DDili~--s~~~~e~~~~l~~v~~~l~~~gl~l~~~K~~~~ 199 (210)
T cd03715 122 FTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLA--ADSEEDCLKGTDALLTHLGELGYKVSPKKAQIC 199 (210)
T ss_pred EEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCcEEEe--cCCHHHHHHHHHHHHHHHHHCCCCcCHHHeeCC
Confidence 456899999999999999988876543 345678899999999 6666666655555443 6
Q ss_pred ccceeeeeeee
Q psy9745 242 KENTRYLGLNL 252 (570)
Q Consensus 242 ~~~~kyLGv~l 252 (570)
..+++|||+.+
T Consensus 200 ~~~v~fLG~~~ 210 (210)
T cd03715 200 RAEVKFLGVVW 210 (210)
T ss_pred CCceEEeeEEC
Confidence 78899999864
No 25
>PRK13911 exodeoxyribonuclease III; Provisional
Probab=95.92 E-value=0.018 Score=56.81 Aligned_cols=64 Identities=13% Similarity=0.224 Sum_probs=37.7
Q ss_pred cceEEEEEeecCccccceeeEEEEecCCCCCChhHHHHHhhhCCCCeeeeccCCCCCccccccccCCCCCChhHHHHHHH
Q psy9745 12 PLQVVAARVRSPVLSCPLTVCCLYISHDRKITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKR 91 (570)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~i~~iy~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~i~~ 91 (570)
+.|.-.|....+ .++|+|||+||+..-++ ..+. ...| .+.+...+.
T Consensus 86 d~eGR~I~~~~~----~~~l~nvY~Pn~~~~~~-r~~~----------------------------K~~~-~~~~~~~l~ 131 (250)
T PRK13911 86 DKEGRVITCEFE----SFYLVNVYTPNSQQALS-RLSY----------------------------RMSW-EVEFKKFLK 131 (250)
T ss_pred cccCCEEEEEEC----CEEEEEEEecCCCCCCc-chHH----------------------------HHHH-HHHHHHHHH
Confidence 345555555543 79999999998764311 1100 0012 334445555
Q ss_pred hC--CCCeEEEcCCCCCCCC
Q psy9745 92 QL--PRPYIICSDMNAHNTI 109 (570)
Q Consensus 92 ~~--~~~~Ii~GDfN~~~~~ 109 (570)
.. ..++|++||||..|..
T Consensus 132 ~l~~~~~~Ii~GD~Nva~~~ 151 (250)
T PRK13911 132 ALELKKPVIVCGDLNVAHNE 151 (250)
T ss_pred hcccCCCEEEEccccCCCCh
Confidence 42 3689999999998743
No 26
>KOG1005|consensus
Probab=95.89 E-value=0.0065 Score=67.22 Aligned_cols=58 Identities=26% Similarity=0.304 Sum_probs=44.0
Q ss_pred eeEeeecccCCCCCCchhhHHHHhcCcCccc----CCC--cceeEeeccceeeecCCCHHHHHHHh
Q psy9745 176 LMLLVLTDIRQGSSLSGDLCNIATSDLPQYI----PTV--VSHGMFVDDLAIFMRGKDMDHIEETL 235 (570)
Q Consensus 176 ~~~~~~~GvPQGs~LSP~Lf~i~~~~l~~~~----~~~--~~~~~yADD~~i~~~~~~~~~~~~~l 235 (570)
..+....|+||||+||-+|..+|++++.+.. .++ +.++.|+||+.+++. +.+++...+
T Consensus 627 k~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt--~~~~a~kfl 690 (888)
T KOG1005|consen 627 KSYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITT--ENDQAKKFL 690 (888)
T ss_pred eEEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEec--CHHHHHHHH
Confidence 3567889999999999999999999998752 122 367899999999944 444444443
No 27
>TIGR00633 xth exodeoxyribonuclease III (xth). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.60 E-value=0.028 Score=55.47 Aligned_cols=17 Identities=47% Similarity=0.772 Sum_probs=14.0
Q ss_pred CCCCeEEEcCCCCCCCC
Q psy9745 93 LPRPYIICSDMNAHNTI 109 (570)
Q Consensus 93 ~~~~~Ii~GDfN~~~~~ 109 (570)
...+.|++||||+.+..
T Consensus 140 ~~~~~Il~GDFN~~~~~ 156 (255)
T TIGR00633 140 AGKPVIICGDMNVAHTE 156 (255)
T ss_pred cCCcEEEEeecccCCCh
Confidence 35689999999998754
No 28
>COG0708 XthA Exonuclease III [DNA replication, recombination, and repair]
Probab=94.88 E-value=0.037 Score=54.26 Aligned_cols=15 Identities=27% Similarity=0.426 Sum_probs=13.4
Q ss_pred ceeeEEEEecCCCCC
Q psy9745 28 PLTVCCLYISHDRKI 42 (570)
Q Consensus 28 ~~~i~~iy~p~~~~~ 42 (570)
.+.|+|+|.||+...
T Consensus 100 ~~~v~~~Y~PnG~~~ 114 (261)
T COG0708 100 GFRVINLYFPNGSSI 114 (261)
T ss_pred CEEEEEEEcCCCCCC
Confidence 599999999998875
No 29
>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=94.85 E-value=0.03 Score=51.32 Aligned_cols=68 Identities=13% Similarity=0.156 Sum_probs=48.2
Q ss_pred cccCCCCCCchhhHHHHhcCcCcccCCCcceeEeeccceeeecCCCHHHHHHHhccccc----------------cccce
Q psy9745 182 TDIRQGSSLSGDLCNIATSDLPQYIPTVVSHGMFVDDLAIFMRGKDMDHIEETLQNTIQ----------------FKENT 245 (570)
Q Consensus 182 ~GvPQGs~LSP~Lf~i~~~~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~----------------~~~~~ 245 (570)
..+|||...||.+|.-.+..+...+. ...+..|+||+.+. +.+.++....++..++ ...++
T Consensus 94 ~~~p~G~~~s~~~~~~~~~~~l~~~~-~~~~~~y~DDi~i~--~~~~~~~~~~~~~~~~~l~~~~~~~~~~K~~~~~~~~ 170 (177)
T cd01647 94 TRMPFGLKNAPATFQRLMNKILGDLL-GDFVEVYLDDILVY--SKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEV 170 (177)
T ss_pred EEecCCCccHHHHHHHHHHhhhcccc-ccccEEEecCcccc--CCCHHHHHHHHHHHHHHHHHcCCEeCHHHceeccCce
Confidence 45999999999999999998877643 23567899999998 5555544443333221 45678
Q ss_pred eeeeeee
Q psy9745 246 RYLGLNL 252 (570)
Q Consensus 246 kyLGv~l 252 (570)
+|||..+
T Consensus 171 ~~lG~~i 177 (177)
T cd01647 171 EFLGHIV 177 (177)
T ss_pred EeeeEEC
Confidence 8888753
No 30
>TIGR00195 exoDNase_III exodeoxyribonuclease III. The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family
Probab=92.62 E-value=0.23 Score=49.06 Aligned_cols=16 Identities=44% Similarity=0.777 Sum_probs=12.8
Q ss_pred CCCeEEEcCCCCCCCC
Q psy9745 94 PRPYIICSDMNAHNTI 109 (570)
Q Consensus 94 ~~~~Ii~GDfN~~~~~ 109 (570)
..|+|++||||.....
T Consensus 138 ~~pvIi~GDfN~~~~~ 153 (254)
T TIGR00195 138 DKPVLICGDMNIAPTE 153 (254)
T ss_pred CCcEEEEeecccCCCh
Confidence 4689999999987643
No 31
>PF14529 Exo_endo_phos_2: Endonuclease-reverse transcriptase ; PDB: 2EI9_A 1WDU_B.
Probab=92.27 E-value=0.097 Score=44.80 Aligned_cols=63 Identities=24% Similarity=0.442 Sum_probs=39.7
Q ss_pred eeeEEEEecCCC--CCChhHHHHHhhhCCC-CeeeeccCCCCCccccccccCCCCCChhHHHHHHHhC
Q psy9745 29 LTVCCLYISHDR--KITKDEIYNIKRQLPR-PYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKRQL 93 (570)
Q Consensus 29 ~~i~~iy~p~~~--~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~i~~~~ 93 (570)
|+|+|||+||.. +.-.+.+.+++++.|. +.+++||||+|...|+...... -..+.+.+++...
T Consensus 1 i~i~~vY~pp~~~~~~~~~~l~~~~~~~~~~~~Ii~GDFN~~~~~w~~~~~~~--~~~~~l~~~~~~~ 66 (119)
T PF14529_consen 1 ITIISVYAPPSSEREEFFDQLRQLLKNLPPAPIIIGGDFNAHHPNWDSSNTNS--RRGEQLLDWLDSH 66 (119)
T ss_dssp EEEEEEE--TTS-CHHHHHHHHHHHHCCTTSSEEEEEE-----GGGT-SCHHH--HHHHHHHHHHHHC
T ss_pred CEEEEEECCCCccHHHHHHHHHHHHHhCCCCCEEEEeECCCCchhhhhccccc--hhHHHHHHHhhhc
Confidence 689999999988 4445678888889998 9999999999999998865543 1223444555543
No 32
>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=92.08 E-value=0.15 Score=48.97 Aligned_cols=59 Identities=17% Similarity=0.268 Sum_probs=43.6
Q ss_pred eeecccCCCCCCchhhHHHHhcCcCcccCC-----CcceeEeeccceeeecCCCHHHHHHHhcccc
Q psy9745 179 LVLTDIRQGSSLSGDLCNIATSDLPQYIPT-----VVSHGMFVDDLAIFMRGKDMDHIEETLQNTI 239 (570)
Q Consensus 179 ~~~~GvPQGs~LSP~Lf~i~~~~l~~~~~~-----~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l 239 (570)
..-.-+|+|-.-||.+|..+++.+.+.+.. .+....|.||+.+. +.+.++....+++.+
T Consensus 99 Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~--~~s~~e~~~~~~~v~ 162 (213)
T cd01644 99 YRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVS--TDTLNEAVNVAKRLI 162 (213)
T ss_pred EEEEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceec--CCCHHHHHHHHHHHH
Confidence 334459999999999999999999887653 23457999999998 556655555544443
No 33
>PRK11756 exonuclease III; Provisional
Probab=91.65 E-value=0.32 Score=48.50 Aligned_cols=26 Identities=23% Similarity=0.413 Sum_probs=19.4
Q ss_pred eEEEEEeecCccccceeeEEEEecCCCC
Q psy9745 14 QVVAARVRSPVLSCPLTVCCLYISHDRK 41 (570)
Q Consensus 14 ~~~~~~~~~~~~~~~~~i~~iy~p~~~~ 41 (570)
-++.+.+..+ +.++.++|+|.|++..
T Consensus 90 r~l~~~i~~~--~g~~~v~n~y~P~~~~ 115 (268)
T PRK11756 90 RIIMATIPTP--NGNLTVINGYFPQGES 115 (268)
T ss_pred CEEEEEEEcC--CCCEEEEEEEecCCCC
Confidence 3567777765 4579999999997654
No 34
>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling []. Proteins this domain is found in include: AP endonuclease proteins (4.2.99.18 from EC), DNase I proteins (3.1.21.1 from EC), Synaptojanin an inositol-1,4,5-trisphosphate phosphatase (3.1.3.56 from EC) and Sphingomyelinase (3.1.4.12 from EC).; PDB: 2J63_A 2JC4_A 3TEB_B 3MTC_A 3N9V_B 1ZWX_A 2F1N_A 1Y21_A 1NTF_A 2IMQ_X ....
Probab=89.69 E-value=0.47 Score=45.46 Aligned_cols=13 Identities=31% Similarity=0.616 Sum_probs=9.4
Q ss_pred CeEEEcCCCCCCC
Q psy9745 96 PYIICSDMNAHNT 108 (570)
Q Consensus 96 ~~Ii~GDfN~~~~ 108 (570)
++|++||||+...
T Consensus 158 ~~iv~GDfN~~~~ 170 (249)
T PF03372_consen 158 PVIVMGDFNSRPD 170 (249)
T ss_dssp EEEEEEE-SS-BS
T ss_pred eEEEEeecccCCc
Confidence 6999999998764
No 35
>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=83.23 E-value=0.28 Score=33.65 Aligned_cols=41 Identities=17% Similarity=0.241 Sum_probs=7.1
Q ss_pred chhhHHhhhhhhHHHHHHHHhhhcCCCCCCHHHHHHHHhhhcc
Q psy9745 258 WKFHIEQTKSKSLKALNVMKILSNRNWGLRRETLRRLYYSFAL 300 (570)
Q Consensus 258 ~~~hi~~~~~ka~~~~~~Lr~l~~~~~gl~~~~~~~ly~a~V~ 300 (570)
|+.|+..+.+||..++..||.+.+. .+++..+..+|.++|.
T Consensus 1 W~~n~~~~~KKa~qRlyFLRkl~k~--~~~~~~l~lfY~s~Ie 41 (42)
T PF09004_consen 1 WTSNTTSLYKKAQQRLYFLRKLRKF--NVDSKLLTLFYHSVIE 41 (42)
T ss_dssp ---------------------------SS-----SHTTTTT--
T ss_pred CCcchHHHHHHHHhHHHHHHHHHHc--cchhHHHHHHHHHHhc
Confidence 6788899999999999999988764 5788888888888764
No 36
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=81.44 E-value=3.9 Score=37.25 Aligned_cols=64 Identities=16% Similarity=0.219 Sum_probs=37.4
Q ss_pred CCeEEEecCCCCCCCceEEEEE--ec---ee--e-----eeccC--CccccchhhHHHHHHHHHHHHhhhcc-cCCcceE
Q psy9745 374 LDTLCFTDGSKTTDHTGAAFII--RD---EI--C-----SMKLN--PICSIFTAELIAIEKCLEKIKDVVTH-DLVTQNF 438 (570)
Q Consensus 374 ~~~~iytDGS~~~~~~G~g~~~--~~---~~--~-----~~~~~--~~~s~~~aEl~ai~~al~~~~~~~~~-~~~~~~v 438 (570)
..+++|+|+|.. |+|+++ .. .. . ..++. ...|+=+.||+|+..|.+.+.....+ .....++
T Consensus 80 ~~L~~F~DAS~~----aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~ 155 (159)
T PF05380_consen 80 VELHVFCDASES----AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQV 155 (159)
T ss_pred eeeeEeeccccc----ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCccee
Confidence 468899999944 444444 21 11 0 01111 24588999999999999988654322 1234445
Q ss_pred EEE
Q psy9745 439 IIC 441 (570)
Q Consensus 439 ~I~ 441 (570)
+++
T Consensus 156 ~~w 158 (159)
T PF05380_consen 156 VFW 158 (159)
T ss_pred EEe
Confidence 444
No 37
>PRK05421 hypothetical protein; Provisional
Probab=77.36 E-value=2.9 Score=41.61 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=17.7
Q ss_pred hHHHHHHHhCCCCeEEEcCCCCCC
Q psy9745 84 DEIYNIKRQLPRPYIICSDMNAHN 107 (570)
Q Consensus 84 ~~l~~i~~~~~~~~Ii~GDfN~~~ 107 (570)
..+...+.....|.|++||||...
T Consensus 172 ~~l~~~~~~~~~p~Il~GDFN~~~ 195 (263)
T PRK05421 172 EPIGDQIAHHSGPVILAGDFNTWS 195 (263)
T ss_pred HHHHHHHHhCCCCEEEEcccccCc
Confidence 344456666667899999999976
No 38
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=69.97 E-value=0.82 Score=47.12 Aligned_cols=91 Identities=19% Similarity=0.096 Sum_probs=54.3
Q ss_pred EEEccCCCcccccCCCCcchhhHHhhhc--CCC----CceEEEEecccceeEeeecccCCCCCCchhhHHHHhcCcCccc
Q psy9745 133 CLLNTNEATHFNSSNGTFSAIDLTLASR--SIT----PDLKWSVHDDLYLMLLVLTDIRQGSSLSGDLCNIATSDLPQYI 206 (570)
Q Consensus 133 ~lln~~~~~~F~~~~~~~s~ID~~l~s~--~i~----~~l~~~V~~~~~~~~~~~~GvPQGs~LSP~Lf~i~~~~l~~~~ 206 (570)
+.+..+...+|++.++.+..-....... .+. ..+...+............|+|||+++||+|-|++++.+...+
T Consensus 182 ~~~~~di~~~fd~~~h~~ll~~~~~~i~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~q~~~vs~~l~n~~l~~~~~~~ 261 (328)
T COG3344 182 WVYDRDIKKCFDSINHKLLLYALDVTISDKLVLLLLGRILIAGYKTKFNLKKSKEKGTPQGGLVSPILVNIKLSKLDNEL 261 (328)
T ss_pred EEEeehHHHHhcccCHHHHHHHhHhhhcchHHHHHHHHHHHcccceeecccccccccCCCCCccCchhhhhhhhhhhHHH
Confidence 6666777788888876533222211111 111 1111222222223345778999999999999999999887754
Q ss_pred CCCc--ceeEeeccceeee
Q psy9745 207 PTVV--SHGMFVDDLAIFM 223 (570)
Q Consensus 207 ~~~~--~~~~yADD~~i~~ 223 (570)
.... ....|+||..+-.
T Consensus 262 ~~~~~~~~~~y~~~~~i~~ 280 (328)
T COG3344 262 RNRYLNLLRRYIDDGNIDK 280 (328)
T ss_pred HHHHhhhhhhhcccccCCH
Confidence 3211 3567999888763
No 39
>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=65.62 E-value=5.6 Score=37.13 Aligned_cols=89 Identities=21% Similarity=0.222 Sum_probs=52.0
Q ss_pred EEEecCCCCCCCceEEEEEeceeeeeccCCccccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHHHHhcCCC
Q psy9745 377 LCFTDGSKTTDHTGAAFIIRDEICSMKLNPICSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYH 456 (570)
Q Consensus 377 ~iytDGS~~~~~~G~g~~~~~~~~~~~~~~~~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~~l~~~~~ 456 (570)
.||+|+.-. |.|+.+......+.....-.+..||+.|...|--+.. .++ |.|||..|+. +...
T Consensus 96 ~VfaDATpT----gwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~---------~r~-l~tDnt~Vls---rkyt 158 (245)
T PF00336_consen 96 QVFADATPT----GWGISITGQRMRGTFSKPLPIHTAELLAACLARLMSG---------ARC-LGTDNTVVLS---RKYT 158 (245)
T ss_pred ceeccCCCC----cceeeecCceeeeeecccccchHHHHHHHHHHHhccC---------CcE-EeecCcEEEe---cccc
Confidence 489998754 4555554333333334456789999999987765442 233 9999987653 2333
Q ss_pred CChhHHHHHHHHHHHHHhCCceEEEeecCCC
Q psy9745 457 VSPLVCDIISTIQDIRDLGTRVSFLWIPSHL 487 (570)
Q Consensus 457 ~~~~~~~~~~~~~~l~~~~~~v~~~WVp~H~ 487 (570)
.-+....... . .....+.|..||+--
T Consensus 159 s~PW~lac~A--~---wiLrgts~~yVPS~~ 184 (245)
T PF00336_consen 159 SFPWLLACAA--N---WILRGTSFYYVPSKY 184 (245)
T ss_pred cCcHHHHHHH--H---HhhcCceEEEecccc
Confidence 3333322111 1 112568899999543
No 40
>PRK05421 hypothetical protein; Provisional
Probab=59.56 E-value=8.4 Score=38.26 Aligned_cols=51 Identities=16% Similarity=0.129 Sum_probs=35.8
Q ss_pred eEEEEEeecCccccceeeEEEEecCCC------CCChhHHHHHhhhCCCCeeeeccCC
Q psy9745 14 QVVAARVRSPVLSCPLTVCCLYISHDR------KITKDEIYNIKRQLPRPYIICSDMN 65 (570)
Q Consensus 14 ~~~~~~~~~~~~~~~~~i~~iy~p~~~------~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (570)
-++.+.+.++. +.++.|+|+..++.. .-..+.|.+.+++...|.|++||||
T Consensus 136 ~~l~a~~~~~~-g~~l~v~ntHl~~~~~~~~~r~~q~~~l~~~~~~~~~p~Il~GDFN 192 (263)
T PRK05421 136 SALITEYPLPN-GRTLLVVNIHAINFSLGVDVYSKQLEPIGDQIAHHSGPVILAGDFN 192 (263)
T ss_pred eeEEEEEEeCC-CCEEEEEEECccccCcChHHHHHHHHHHHHHHHhCCCCEEEEcccc
Confidence 45666776642 346999999996431 1123457777788889999999997
No 41
>smart00128 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes.
Probab=58.89 E-value=18 Score=36.91 Aligned_cols=41 Identities=15% Similarity=0.131 Sum_probs=28.6
Q ss_pred cceEEEEEeecCccccceeeEEEEecCCCCC---ChhHHHHHhhhC
Q psy9745 12 PLQVVAARVRSPVLSCPLTVCCLYISHDRKI---TKDEIYNIKRQL 54 (570)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~i~~iy~p~~~~~---~~~~~~~~~~~~ 54 (570)
+-.+++|++.+. +..++++|.+++....- --+|...|++.+
T Consensus 125 nKG~v~i~~~~~--~~~~~fv~~HL~a~~~~~~~R~~~~~~I~~~~ 168 (310)
T smart00128 125 NKGAVAVRFKLS--DTSFCFVNSHLAAGASNVEQRNQDYKTILRAL 168 (310)
T ss_pred cCceEEEEEEEc--CcEEEEEeeccccccchhhhhHHHHHHHHHhc
Confidence 457788888877 56899999999975531 234566665554
No 42
>COG3021 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.17 E-value=7.7 Score=39.05 Aligned_cols=21 Identities=29% Similarity=0.370 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCCeEEEcCCCC
Q psy9745 85 EIYNIKRQLPRPYIICSDMNA 105 (570)
Q Consensus 85 ~l~~i~~~~~~~~Ii~GDfN~ 105 (570)
.+.+.+....+++|++||||+
T Consensus 213 ~l~~~i~~~~gpvIlaGDfNa 233 (309)
T COG3021 213 ELGDQIAGHSGPVILAGDFNA 233 (309)
T ss_pred HHHHHHHcCCCCeEEeecCCC
Confidence 455566667899999999996
No 43
>KOG1812|consensus
Probab=53.52 E-value=25 Score=36.97 Aligned_cols=90 Identities=16% Similarity=0.193 Sum_probs=56.2
Q ss_pred cccchhhHHHHHHHHHHHHhhhcccCCcceEEEEecCHHHHHHHhcCCCCCh--hHHHHHHHHHHHHHhCCceEEEeecC
Q psy9745 408 CSIFTAELIAIEKCLEKIKDVVTHDLVTQNFIICSDSKSSLQALQNVYHVSP--LVCDIISTIQDIRDLGTRVSFLWIPS 485 (570)
Q Consensus 408 ~s~~~aEl~ai~~al~~~~~~~~~~~~~~~v~I~tDs~~al~~l~~~~~~~~--~~~~~~~~~~~l~~~~~~v~~~WVp~ 485 (570)
.+...||++|+..+|..+.+. +...+.+++|+.-....+........ ....+++....++.+.....-.-+|-
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~-----~~~~~~~~~d~~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~l~~~~~i~~~~ 121 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALEL-----GLNHIVIYCDDELIYESVAGREKPEQHRKIVLLVELVQRIREQLTSSEPILVPK 121 (384)
T ss_pred cchhhHHHHHHhhccHHHHhh-----ccccceEecccHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcccceeccc
Confidence 677899999999999999988 89999999996666565544433332 34455666666655542222222221
Q ss_pred CCCCCccchhchhhhhccCC
Q psy9745 486 HLGIRENDNVDHAARHCNDV 505 (570)
Q Consensus 486 H~gi~gNe~AD~lAk~a~~~ 505 (570)
- ...+.|=.+|+++..+
T Consensus 122 ~---~d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 122 N---ADIKFAYKLAREAIVS 138 (384)
T ss_pred c---hhhHHHHHHHHHhhcc
Confidence 0 0112355677777764
No 44
>KOG1645|consensus
Probab=52.75 E-value=18 Score=37.57 Aligned_cols=65 Identities=15% Similarity=0.048 Sum_probs=44.9
Q ss_pred ecCcceEEEEEeecCccccceeeEEEEecCCCCCChhHHHHHhhhCCCCeeeeccCCCCCccccccccCCCCCChhHHHH
Q psy9745 9 INSPLQVVAARVRSPVLSCPLTVCCLYISHDRKITKDEIYNIKRQLPRPYIICSDMNAHNTIWGGSKIDSNGITKDEIYN 88 (570)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~i~~iy~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~ 88 (570)
+.++.+-.+..-.++ ..|.|+.+|-. ...+-+++||-+|+|.|.-..
T Consensus 201 fSp~~~GLl~~asl~---nkiki~dlet~---------------------~~vssy~a~~~~wSC~wDlde--------- 247 (463)
T KOG1645|consen 201 FSPFNEGLLGLASLG---NKIKIMDLETS---------------------CVVSSYIAYNQIWSCCWDLDE--------- 247 (463)
T ss_pred cCccccceeeeeccC---ceEEEEecccc---------------------eeeeheeccCCceeeeeccCC---------
Confidence 334455444444443 37999999876 345678999999999997433
Q ss_pred HHHhCCCCeEEEcCCCCCCCCcCC
Q psy9745 89 IKRQLPRPYIICSDMNAHNTIWGG 112 (570)
Q Consensus 89 i~~~~~~~~Ii~GDfN~~~~~wg~ 112 (570)
.++|++||-|+----+.-
T Consensus 248 ------~h~IYaGl~nG~VlvyD~ 265 (463)
T KOG1645|consen 248 ------RHVIYAGLQNGMVLVYDM 265 (463)
T ss_pred ------cceeEEeccCceEEEEEc
Confidence 369999999987544443
No 45
>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=43.18 E-value=12 Score=37.26 Aligned_cols=50 Identities=14% Similarity=0.004 Sum_probs=34.8
Q ss_pred eEeeecccCCCCCCc----hhhHHHHhcCcCccc-----CCCcceeEeeccceeeecCC
Q psy9745 177 MLLVLTDIRQGSSLS----GDLCNIATSDLPQYI-----PTVVSHGMFVDDLAIFMRGK 226 (570)
Q Consensus 177 ~~~~~~GvPQGs~LS----P~Lf~i~~~~l~~~~-----~~~~~~~~yADD~~i~~~~~ 226 (570)
.+....|.|+|++.. +++-.+++......+ ...+.++.|.||.++.+...
T Consensus 153 ~~~~~~G~pSG~~~T~~~Nsl~n~~~~~~a~~~~~~~~~~~~~~~~~~GDD~li~~~~~ 211 (278)
T cd01699 153 VYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKA 211 (278)
T ss_pred EEEEcCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEcCCeEEEechh
Confidence 567789999999884 444555555443322 35567899999999987644
No 46
>PRK11756 exonuclease III; Provisional
Probab=42.17 E-value=21 Score=35.37 Aligned_cols=16 Identities=38% Similarity=0.513 Sum_probs=13.0
Q ss_pred CCCCeEEEcCCCCCCC
Q psy9745 93 LPRPYIICSDMNAHNT 108 (570)
Q Consensus 93 ~~~~~Ii~GDfN~~~~ 108 (570)
...|+|++||||.-+.
T Consensus 142 ~~~pvIl~GDfN~~~~ 157 (268)
T PRK11756 142 PDNPLLIMGDMNISPT 157 (268)
T ss_pred cCCCEEEEeecccCCC
Confidence 3568999999998764
No 47
>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=38.43 E-value=17 Score=35.65 Aligned_cols=69 Identities=14% Similarity=0.314 Sum_probs=43.8
Q ss_pred cccCCCCCCchhhHHHHhcCcCcccC-----------------CCcceeEeeccceeeecCCC-HHHHHHHhccccc---
Q psy9745 182 TDIRQGSSLSGDLCNIATSDLPQYIP-----------------TVVSHGMFVDDLAIFMRGKD-MDHIEETLQNTIQ--- 240 (570)
Q Consensus 182 ~GvPQGs~LSP~Lf~i~~~~l~~~~~-----------------~~~~~~~yADD~~i~~~~~~-~~~~~~~l~~~l~--- 240 (570)
-|+.| ||.+|.-.++..+..+. ..+.+..|.||+.+.+.... .++....|++.++
T Consensus 122 YGLKQ----a~r~W~~~l~~~L~~~GF~~~~~D~clfi~~~~~~~~ii~vYVDDili~~~~~~~i~~~~~~l~~~F~iKd 197 (246)
T PF07727_consen 122 YGLKQ----APRLWYKTLDKFLKKLGFKQSKADPCLFIKKSGDGFIIILVYVDDILIAGPSEEEIEEFKKELKKKFEIKD 197 (246)
T ss_pred eeccc----ccchhhhhcccccchhhhhcccccccccccccccccccccccccccccccccccceecccccccccccccc
Confidence 45555 67788877776655431 23567889999999955543 3345555555554
Q ss_pred cccceeeeeeeecc
Q psy9745 241 FKENTRYLGLNLDS 254 (570)
Q Consensus 241 ~~~~~kyLGv~ld~ 254 (570)
....-.|||+.+..
T Consensus 198 lG~~~~fLGi~i~~ 211 (246)
T PF07727_consen 198 LGELKYFLGIEIER 211 (246)
T ss_pred ccccccccceEEEE
Confidence 23345679998875
No 48
>smart00476 DNaseIc deoxyribonuclease I. Deoxyribonuclease I catalyzes the endonucleolytic cleavage of double-stranded DNA. The enzyme is secreted outside the cell and also involved in apoptosis in the nucleus.
Probab=36.01 E-value=28 Score=34.84 Aligned_cols=14 Identities=29% Similarity=0.237 Sum_probs=12.1
Q ss_pred CCCCeEEEcCCCCC
Q psy9745 93 LPRPYIICSDMNAH 106 (570)
Q Consensus 93 ~~~~~Ii~GDfN~~ 106 (570)
...++|++||||+.
T Consensus 175 ~~~~villGDFNa~ 188 (276)
T smart00476 175 GTEDVIFMGDFNAG 188 (276)
T ss_pred ccCCEEEEccCCCC
Confidence 56889999999984
No 49
>TIGR03395 sphingomy sphingomyelin phosphodiesterase. Members of this family are bacterial proteins that act as sphingomyelin phosphodiesterase (EC 3.1.4.12), also called sphingomyelinase. Some members of this family have been shown to act as hemolysins.
Probab=34.90 E-value=51 Score=33.14 Aligned_cols=21 Identities=5% Similarity=0.014 Sum_probs=13.1
Q ss_pred eEEEEEeecCccccceeeEEEEe
Q psy9745 14 QVVAARVRSPVLSCPLTVCCLYI 36 (570)
Q Consensus 14 ~~~~~~~~~~~~~~~~~i~~iy~ 36 (570)
-++.++|..+ +.++.|+|.=+
T Consensus 122 g~l~a~i~~~--g~~~~v~~THL 142 (283)
T TIGR03395 122 GFAYVKINKN--GKKFHVIGTHL 142 (283)
T ss_pred ceEEEEEecC--CeEEEEEEeCC
Confidence 3555666655 55777777755
No 50
>PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional
Probab=33.58 E-value=33 Score=38.34 Aligned_cols=15 Identities=27% Similarity=0.649 Sum_probs=12.4
Q ss_pred CCCCeEEEcCCCCCC
Q psy9745 93 LPRPYIICSDMNAHN 107 (570)
Q Consensus 93 ~~~~~Ii~GDfN~~~ 107 (570)
..-|+|++||||+..
T Consensus 454 ~~~PvIlcGDFNS~P 468 (606)
T PLN03144 454 ADIPMLVCGDFNSVP 468 (606)
T ss_pred CCCceEEeccCCCCC
Confidence 456899999999864
No 51
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=33.39 E-value=54 Score=36.69 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=31.2
Q ss_pred hhHHHHHHHHHHHHHhCCceEEEeecCCCCCCccchh
Q psy9745 459 PLVCDIISTIQDIRDLGTRVSFLWIPSHLGIRENDNV 495 (570)
Q Consensus 459 ~~~~~~~~~~~~l~~~~~~v~~~WVp~H~gi~gNe~A 495 (570)
|-..+....+..+.+.|..|-+-|||+|-+..||-++
T Consensus 211 GtPedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 211 GTPEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 3346677788889999999999999999999888755
No 52
>PRK15251 cytolethal distending toxin subunit CdtB; Provisional
Probab=33.20 E-value=1.1e+02 Score=30.48 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=18.0
Q ss_pred hHHHHHHH-hCC-CCeEEEcCCCCCCCCc
Q psy9745 84 DEIYNIKR-QLP-RPYIICSDMNAHNTIW 110 (570)
Q Consensus 84 ~~l~~i~~-~~~-~~~Ii~GDfN~~~~~w 110 (570)
+.+..... ..+ .+.+|+||||.....-
T Consensus 172 ~~I~~~f~~~~~~~pw~I~GDFNr~P~sl 200 (271)
T PRK15251 172 RAVHNFFRPNMRHINWMIAGDFNRSPDRL 200 (271)
T ss_pred HHHHHHHhhccCCCCEEEeccCCCCCcch
Confidence 34444444 433 6899999999887654
No 53
>PF08388 GIIM: Group II intron, maturase-specific domain; InterPro: IPR013597 This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [].
Probab=28.99 E-value=1.3e+02 Score=23.42 Aligned_cols=58 Identities=21% Similarity=0.126 Sum_probs=41.5
Q ss_pred HHHHHHhhh-cCCCCCCHHHHHHHHhhhccccccccceeccCCChhhHHHHHHHHHHHHHHH
Q psy9745 272 ALNVMKILS-NRNWGLRRETLRRLYYSFALPILDYGSILYSSASEPNLKKLNVVHHTGVRLI 332 (570)
Q Consensus 272 ~~~~Lr~l~-~~~~gl~~~~~~~ly~a~V~p~l~Yg~~vW~~~~~~~~~~L~~~qr~~lR~i 332 (570)
....++.+. +...+.+...+..-++++++++..|...... ......|+......++..
T Consensus 4 ~~~kik~~~~~~~~~~~~~~~i~~LN~~lrGW~nYy~~~~~---~~~f~~ld~~v~~~l~~w 62 (80)
T PF08388_consen 4 FRRKIKEITRRRNRGKSLEELIKKLNPILRGWANYYRIGNS---SKTFSKLDHYVWRRLRRW 62 (80)
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhhcchhH---HHHHHHHHHHHHHHHHHH
Confidence 345567777 6667899999999999999999999887632 344566655444444443
No 54
>TIGR03395 sphingomy sphingomyelin phosphodiesterase. Members of this family are bacterial proteins that act as sphingomyelin phosphodiesterase (EC 3.1.4.12), also called sphingomyelinase. Some members of this family have been shown to act as hemolysins.
Probab=28.63 E-value=53 Score=33.00 Aligned_cols=13 Identities=23% Similarity=0.463 Sum_probs=10.8
Q ss_pred CCeEEEcCCCCCC
Q psy9745 95 RPYIICSDMNAHN 107 (570)
Q Consensus 95 ~~~Ii~GDfN~~~ 107 (570)
.++|++||||...
T Consensus 178 ~pvIl~GDfN~~~ 190 (283)
T TIGR03395 178 ETVLIGGDLNVNK 190 (283)
T ss_pred ceEEEEeeCCCCC
Confidence 4699999999764
No 55
>PRK15251 cytolethal distending toxin subunit CdtB; Provisional
Probab=26.07 E-value=69 Score=31.90 Aligned_cols=50 Identities=12% Similarity=0.181 Sum_probs=33.7
Q ss_pred ceEEEEEeecCccccceeeEEEEecCCCCCCh----hHHHHHhh-hCC-CCeeeeccCCCCC
Q psy9745 13 LQVVAARVRSPVLSCPLTVCCLYISHDRKITK----DEIYNIKR-QLP-RPYIICSDMNAHN 68 (570)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~i~~iy~p~~~~~~~----~~~~~~~~-~~~-~~~~~~~~~~~~~ 68 (570)
--++++++. +..+||+=......-+. .+|.+... +.| -|.+++||||...
T Consensus 142 Rpilgi~i~------~~~ffstH~~a~~~~da~aiV~~I~~~f~~~~~~~pw~I~GDFNr~P 197 (271)
T PRK15251 142 RPIIGIRIG------NDVFFSIHALANGGTDAGAIVRAVHNFFRPNMRHINWMIAGDFNRSP 197 (271)
T ss_pred cceEEEEec------CeEEEEeeecCCCCccHHHHHHHHHHHHhhccCCCCEEEeccCCCCC
Confidence 346666664 47888887775544444 45555555 667 3999999999776
No 56
>smart00156 PP2Ac Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
Probab=25.47 E-value=1.1e+02 Score=30.48 Aligned_cols=34 Identities=18% Similarity=0.450 Sum_probs=23.7
Q ss_pred CCeeeeccCCCCCccccccccCCCCCChhHHHHHHH----hCCCCeEEEcCCC
Q psy9745 56 RPYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKR----QLPRPYIICSDMN 104 (570)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~i~~----~~~~~~Ii~GDfN 104 (570)
.|+++.||.|++- +.+..++. .....++.+||+-
T Consensus 28 ~~i~vvGDiHG~~---------------~~l~~ll~~~~~~~~~~~vfLGD~V 65 (271)
T smart00156 28 APVTVCGDIHGQF---------------DDLLRLFDLNGPPPDTNYVFLGDYV 65 (271)
T ss_pred CCEEEEEeCcCCH---------------HHHHHHHHHcCCCCCceEEEeCCcc
Confidence 4888999997654 44555555 2445688999986
No 57
>PF03372 Exo_endo_phos: Endonuclease/Exonuclease/phosphatase family Subset of Pfam family Subset of Pfam family; InterPro: IPR005135 This domain is found in a large number of proteins including magnesium dependent endonucleases and phosphatases involved in intracellular signalling []. Proteins this domain is found in include: AP endonuclease proteins (4.2.99.18 from EC), DNase I proteins (3.1.21.1 from EC), Synaptojanin an inositol-1,4,5-trisphosphate phosphatase (3.1.3.56 from EC) and Sphingomyelinase (3.1.4.12 from EC).; PDB: 2J63_A 2JC4_A 3TEB_B 3MTC_A 3N9V_B 1ZWX_A 2F1N_A 1Y21_A 1NTF_A 2IMQ_X ....
Probab=23.58 E-value=54 Score=30.84 Aligned_cols=43 Identities=23% Similarity=0.381 Sum_probs=26.1
Q ss_pred ccceeeEEEEecCCCCCCh-------hHHHHHhhhCC-CCeeeeccCCCCC
Q psy9745 26 SCPLTVCCLYISHDRKITK-------DEIYNIKRQLP-RPYIICSDMNAHN 68 (570)
Q Consensus 26 ~~~~~i~~iy~p~~~~~~~-------~~~~~~~~~~~-~~~~~~~~~~~~~ 68 (570)
+.+|+|+|+|.|+....-. +.+..+....+ .|.|++||||+..
T Consensus 119 ~~~i~v~~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iv~GDfN~~~ 169 (249)
T PF03372_consen 119 GKPITVVNVHLPSSNDERQEQWRELLARIQKIYADNPNEPVIVMGDFNSRP 169 (249)
T ss_dssp TEEEEEEEEETTSHHHHHHHHHHHHHHHHHHHHHTSSCCEEEEEEE-SS-B
T ss_pred ceEEEeeeccccccchhhhhhhhhhhhhhhhcccccccceEEEEeecccCC
Confidence 5589999999986433322 22223333333 3799999999875
No 58
>KOG3873|consensus
Probab=22.95 E-value=96 Score=32.02 Aligned_cols=44 Identities=14% Similarity=0.154 Sum_probs=26.7
Q ss_pred CCccccccccCCCCCChhHHHHHHHh---CCCCeEEEcCCCCCCCCcCCCC
Q psy9745 67 HNTIWGGSKIDSNGITKDEIYNIKRQ---LPRPYIICSDMNAHNTIWGGSK 114 (570)
Q Consensus 67 ~~~~~~~~~~p~~~~~~~~l~~i~~~---~~~~~Ii~GDfN~~~~~wg~~~ 114 (570)
.|+.|.|-++.-.+ ++.+.++. ..+-.|++||||.+...-|...
T Consensus 144 q~D~YL~HR~~QAw----dlaqfi~~t~q~~~vVI~~GDLN~~P~dl~~~l 190 (422)
T KOG3873|consen 144 QNDEYLCHRVAQAW----DLAQFIRATRQNADVVILAGDLNMQPQDLGHKL 190 (422)
T ss_pred cCchhhhHHHHHHH----HHHHHHHHHhcCCcEEEEecCCCCCccccceee
Confidence 35555555554333 34444443 4456888999999976666543
No 59
>cd07420 MPP_RdgC Drosophila melanogaster RdgC and related proteins, metallophosphatase domain. RdgC (retinal degeneration C) is a vertebrate serine-threonine protein phosphatase that is required to prevent light-induced retinal degeneration. In addition to its catalytic domain, RdgC has two C-terminal EF hands. Homologs of RdgC include the human phosphatases protein phosphatase with EF hands 1 and -2 (PPEF-1 and -2). PPEF-1 transcripts are present at low levels in the retina, PPEF-2 transcripts and PPEF-2 protein are present at high levels in photoreceptors. The PPP (phosphoprotein phosphatase) family, to which RdgC belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all
Probab=22.10 E-value=1.5e+02 Score=30.37 Aligned_cols=33 Identities=24% Similarity=0.531 Sum_probs=23.5
Q ss_pred CeeeeccCCCCCccccccccCCCCCChhHHHHHHHhC-----CCCeEEEcCCC
Q psy9745 57 PYIICSDMNAHNTIWGGSKIDSNGITKDEIYNIKRQL-----PRPYIICSDMN 104 (570)
Q Consensus 57 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~~l~~i~~~~-----~~~~Ii~GDfN 104 (570)
|.++.||.|+.- .++..++... .+.++.+||+-
T Consensus 52 ~~~vvGDiHG~~---------------~dL~~il~~~g~~~~~~~~lFLGDyV 89 (321)
T cd07420 52 QVTICGDLHGKL---------------DDLFLIFYKNGLPSPENPYVFNGDFV 89 (321)
T ss_pred CeEEEEeCCCCH---------------HHHHHHHHHcCCCCccceEEEecccc
Confidence 789999997764 5566666542 24588899985
No 60
>PRK04036 DNA polymerase II small subunit; Validated
Probab=21.45 E-value=2.6e+02 Score=30.67 Aligned_cols=48 Identities=6% Similarity=-0.093 Sum_probs=28.0
Q ss_pred ceEEEEEeecCccccceeeEEEEecCCCCC-ChhHHHHHhhhCCCCeeeeccCC
Q psy9745 13 LQVVAARVRSPVLSCPLTVCCLYISHDRKI-TKDEIYNIKRQLPRPYIICSDMN 65 (570)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~i~~iy~p~~~~~-~~~~~~~~~~~~~~~~~~~~~~~ 65 (570)
=+++||+......+.-+.+-.|+.|.-+.- .... ..-+....+.||+|
T Consensus 205 g~vv~v~G~~~~~g~~f~v~~i~~p~~p~~~~~~~-----~~~~~~i~~ISDlH 253 (504)
T PRK04036 205 DEVIGVEGTLSGDGGLIFADEIIRPDVPRTKEPPT-----KDEKVYAVFISDVH 253 (504)
T ss_pred ceEEEEEEEEcCCCCEEEEEEEECCCCCccCCCCc-----CCCccEEEEEcccC
Confidence 467899888653222578888887744432 1100 01233467899997
No 61
>KOG4355|consensus
Probab=21.22 E-value=2.1e+02 Score=29.91 Aligned_cols=42 Identities=26% Similarity=0.287 Sum_probs=25.3
Q ss_pred CCeEEEcCCCCCCCCcCCCCCCChhHHHHHHHh----------hcCCeEEEcc
Q psy9745 95 RPYIICSDMNAHNTIWGGSKIDSNGVQVEKFLL----------ENDDVCLLNT 137 (570)
Q Consensus 95 ~~~Ii~GDfN~~~~~wg~~~~~~~g~~l~~~~~----------~~~~l~lln~ 137 (570)
+...|-|-=--.-..||++.+|..++-+.--+. +. ++||+|.
T Consensus 47 s~s~ipgtqki~iktwgcshnnsdseymagqlaaygy~lte~eea-dlwllns 98 (547)
T KOG4355|consen 47 SSSKIPGTQKIYIKTWGCSHNNSDSEYMAGQLAAYGYALTEPEEA-DLWLLNS 98 (547)
T ss_pred ccccCCCccEEEEEeecccCCCchhHHHhhhHHhhhhccCCcccc-cEEEecc
Confidence 334444433333457999999888775433222 23 8999987
No 62
>COG3568 ElsH Metal-dependent hydrolase [General function prediction only]
Probab=21.11 E-value=48 Score=32.74 Aligned_cols=62 Identities=13% Similarity=0.112 Sum_probs=31.2
Q ss_pred CCeEEEcCCCCCC--CCcCCCCCCChhHHHHHHHhhcCCeEEEcc-CC--CcccccCCCCcchhhHHhhhcCCCC
Q psy9745 95 RPYIICSDMNAHN--TIWGGSKIDSNGVQVEKFLLENDDVCLLNT-NE--ATHFNSSNGTFSAIDLTLASRSITP 164 (570)
Q Consensus 95 ~~~Ii~GDfN~~~--~~wg~~~~~~~g~~l~~~~~~~~~l~lln~-~~--~~~F~~~~~~~s~ID~~l~s~~i~~ 164 (570)
.|+|++||||..- ..| +-..+.. ....... .-...+ .. ..+|.+.... ..||..+.++.+..
T Consensus 165 ~p~vl~GDFN~~p~s~~y-r~~~~~~----~~~~~~~--~~~~~~a~~~~~~tfps~~p~-lriD~Ifvs~~~~i 231 (259)
T COG3568 165 NPTVLMGDFNNEPGSAEY-RLAARSP----LNAQAAL--TGAFAPAVGRTIRTFPSNTPL-LRLDRIFVSKELAI 231 (259)
T ss_pred CceEEEccCCCCCCCccc-eeccCCc----hhhcccc--ccccCcccCcccCCCCCCCcc-ccccEEEecCcccE
Confidence 3899999999764 455 2111111 1111101 011111 11 1257665433 58899988876654
Done!