Query psy4044
Match_columns 460
No_of_seqs 321 out of 1886
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 23:55:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4044.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4044hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03715 RT_ZFREV_like RT_ZFREV 100.0 1.6E-39 3.4E-44 303.4 18.2 192 39-231 3-210 (210)
2 cd01645 RT_Rtv RT_Rtv: Reverse 100.0 1.1E-35 2.3E-40 277.7 18.4 166 60-231 32-213 (213)
3 cd01647 RT_LTR RT_LTR: Reverse 100.0 1.9E-31 4.1E-36 240.5 12.4 167 62-231 7-177 (177)
4 cd01644 RT_pepA17 RT_pepA17: R 100.0 2.7E-30 5.8E-35 239.9 11.2 164 65-233 2-189 (213)
5 cd03714 RT_DIRS1 RT_DIRS1: Rev 100.0 7.2E-30 1.6E-34 216.5 11.3 118 114-231 1-119 (119)
6 PF00078 RVT_1: Reverse transc 99.8 1.5E-17 3.3E-22 154.8 15.1 160 72-231 1-214 (214)
7 cd00304 RT_like RT_like: Rever 99.6 6.8E-15 1.5E-19 119.9 8.8 95 114-231 1-98 (98)
8 cd01648 TERT TERT: Telomerase 99.2 4.3E-11 9.4E-16 101.1 8.3 104 114-232 1-119 (119)
9 cd03487 RT_Bac_retron_II RT_Ba 99.2 1.1E-10 2.4E-15 109.2 10.1 144 106-251 54-213 (214)
10 cd06222 RnaseH RNase H (RNase 99.1 2.8E-10 6.1E-15 95.9 9.2 116 279-396 1-128 (130)
11 cd01650 RT_nLTR_like RT_nLTR: 99.1 1.3E-10 2.8E-15 108.9 7.1 101 107-220 80-189 (220)
12 PRK13907 rnhA ribonuclease H; 99.0 1.9E-09 4.1E-14 92.3 9.1 116 278-396 2-123 (128)
13 cd01651 RT_G2_intron RT_G2_int 98.9 6.2E-09 1.4E-13 97.8 9.5 127 105-231 66-226 (226)
14 PF00075 RNase_H: RNase H; In 98.9 4.5E-09 9.8E-14 90.2 7.4 112 276-395 2-128 (132)
15 PRK07708 hypothetical protein; 98.8 1.5E-08 3.2E-13 94.3 9.8 120 277-396 73-204 (219)
16 COG0328 RnhA Ribonuclease HI [ 98.8 1.8E-08 3.8E-13 87.6 8.8 119 276-396 2-141 (154)
17 PRK00203 rnhA ribonuclease H; 98.7 9.5E-08 2.1E-12 84.1 9.5 115 277-396 3-138 (150)
18 cd01646 RT_Bac_retron_I RT_Bac 98.7 1E-07 2.2E-12 84.7 9.0 92 143-234 50-147 (158)
19 PRK06548 ribonuclease H; Provi 98.6 3.7E-07 8.1E-12 80.7 10.3 114 276-396 4-138 (161)
20 PRK07238 bifunctional RNase H/ 98.6 2.2E-07 4.7E-12 94.4 9.5 118 277-396 2-128 (372)
21 PF13456 RVT_3: Reverse transc 98.4 1.8E-07 3.9E-12 73.8 3.5 82 312-396 2-83 (87)
22 PRK08719 ribonuclease H; Revie 98.3 3.2E-06 6.9E-11 74.0 9.0 113 276-396 3-143 (147)
23 PF00336 DNA_pol_viral_C: DNA 98.2 5.8E-06 1.3E-10 73.5 7.9 100 278-397 95-194 (245)
24 KOG3752|consensus 97.7 0.00012 2.6E-09 71.7 8.7 117 278-397 213-362 (371)
25 cd01709 RT_like_1 RT_like_1: A 97.0 0.0065 1.4E-07 59.8 11.3 73 144-217 81-155 (346)
26 PF05380 Peptidase_A17: Pao re 96.7 0.0028 6.1E-08 56.2 5.2 50 276-326 80-141 (159)
27 PF07727 RVT_2: Reverse transc 95.8 0.0035 7.6E-08 59.8 1.0 125 108-243 76-221 (246)
28 KOG1005|consensus 94.7 0.11 2.3E-06 56.4 8.1 74 143-216 631-709 (888)
29 KOG4768|consensus 94.2 0.23 4.9E-06 52.0 8.9 137 98-234 349-563 (796)
30 cd01699 RNA_dep_RNAP RNA_dep_R 83.9 3.3 7.1E-05 39.9 7.0 63 173-236 194-259 (278)
31 PHA00028 rep RNA replicase, be 75.8 5.3 0.00012 41.4 5.5 35 175-216 335-369 (561)
32 PF05869 Dam: DNA N-6-adenine- 69.8 4.4 9.5E-05 36.7 3.1 40 397-436 9-48 (181)
33 PF03431 RNA_replicase_B: RNA 64.2 8.7 0.00019 39.4 4.1 128 109-247 244-396 (542)
34 PF05919 Mitovir_RNA_pol: Mito 63.3 98 0.0021 32.4 11.5 145 66-219 85-278 (498)
35 PF00680 RdRP_1: RNA dependent 50.6 1.3E+02 0.0028 31.6 10.6 61 174-235 344-409 (491)
36 TIGR01712 phage_N6A_met phage 40.8 21 0.00045 31.8 2.2 41 397-437 9-49 (166)
37 PF12237 PCIF1_WW: Phosphoryla 34.4 35 0.00075 30.7 2.7 43 400-443 44-86 (176)
38 PF12386 Peptidase_C71: Pseudo 23.2 1.8E+02 0.004 24.3 4.7 65 314-387 21-85 (142)
39 PF08902 DUF1848: Domain of un 21.4 7.4E+02 0.016 23.9 9.2 83 122-205 40-144 (266)
40 PF01910 DUF77: Domain of unkn 21.2 3.9E+02 0.0084 21.1 6.3 64 143-209 2-65 (92)
41 PRK10270 putative aminodeoxych 21.0 1.5E+02 0.0033 29.6 4.8 72 135-208 267-338 (340)
No 1
>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=100.00 E-value=1.6e-39 Score=303.39 Aligned_cols=192 Identities=18% Similarity=0.301 Sum_probs=169.6
Q ss_pred CCCCCCCchHHHHHHHHhhh-h-------hcCCcccccceEeecCCC-Ceeeeeecc----ccCCCCccCCCccchhhhc
Q psy4044 39 DHPPNQDSFFEVARHTAILL-L-------LCSGRRVHDLTLLLSSRD-GFQDLGDRA----FLSLKKFHLINHFRVPDFL 105 (460)
Q Consensus 39 ~~~p~~~~~~~~~~~~~~~~-~-------~~~~~~~sp~~~V~Kk~g-~~R~~~D~r----~~~~~~~plp~i~~ll~~l 105 (460)
..+|++.+.-+....++..+ + ++++.+.||+++|+||+| ++|+|+||| .+..+.+++|++++++..+
T Consensus 3 ~~~~~~~~~~~~~~~~~~v~~ll~~G~I~~~~s~~~sp~~~V~Kk~g~~~R~~vD~r~lN~~~~~~~~~~p~~~~~l~~l 82 (210)
T cd03715 3 NQKQYPLPREAREGITPHIQELLEAGILVPCQSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLL 82 (210)
T ss_pred CcCCCCCCHHHHHHHHHHHHHHHHCCCeECCCCCCCCceEEEEeCCCCcceEEEEhhhhhhcccccCcCCCcHHHHHHHh
Confidence 34666666544444444333 2 446788999999999999 999999999 4556789999999999999
Q ss_pred c-CCceEEEEeccccccccccCCCCcceeEEEEcCeeEEEcccCccCCCchHHHHHHHHHHHHHHHh--cCCEEEEEecC
Q psy4044 106 Q-RGDFLVKIDLSQAYFHVPIRPSHQRFLSVVYRDTLYCMTCLPFGLASAPQVFAKLTNWIANYLRN--LGMRVIVYLDD 182 (460)
Q Consensus 106 ~-~~~~~s~lDl~~ay~qi~l~~~~~~~taF~~~~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~--~g~~v~~YvDD 182 (460)
. ++++|+++|+++|||||+|+|+++++|||++++|+|+|++||||+++||++||+.|+.++..+.. .+..+.+|+||
T Consensus 83 ~~~~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~y~~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DD 162 (210)
T cd03715 83 PPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDD 162 (210)
T ss_pred ccCCeEEEEeeccCeEEEEEcccccEEeEEEEECCeeEEEEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCc
Confidence 6 89999999999999999999999999999999999999999999999999999999999977643 35678999999
Q ss_pred eEEecCCHHHHHHHHHHHHHHHHHcCCcccccccccccccccccccEEE
Q psy4044 183 LLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLWPVQTCQYLGIMW 231 (460)
Q Consensus 183 ili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~~~~~v~~LG~~i 231 (460)
|+|++++.++|.++++.|+.+|+++|+.+|++||+++ ..+++|||++|
T Consensus 163 ili~s~~~~e~~~~l~~v~~~l~~~gl~l~~~K~~~~-~~~v~fLG~~~ 210 (210)
T cd03715 163 LLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQIC-RAEVKFLGVVW 210 (210)
T ss_pred EEEecCCHHHHHHHHHHHHHHHHHCCCCcCHHHeeCC-CCceEEeeEEC
Confidence 9999999999999999999999999999999999866 67999999985
No 2
>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=100.00 E-value=1.1e-35 Score=277.73 Aligned_cols=166 Identities=18% Similarity=0.260 Sum_probs=146.4
Q ss_pred hcCCcccccceEeecCCCCeeeeeeccccCC----CCc---cCCCccchhhhccCCceEEEEeccccccccccCCCCcce
Q psy4044 60 LCSGRRVHDLTLLLSSRDGFQDLGDRAFLSL----KKF---HLINHFRVPDFLQRGDFLVKIDLSQAYFHVPIRPSHQRF 132 (460)
Q Consensus 60 ~~~~~~~sp~~~V~Kk~g~~R~~~D~r~~~~----~~~---plp~i~~ll~~l~~~~~~s~lDl~~ay~qi~l~~~~~~~ 132 (460)
++...+.||+++|+||+|++|+|+|||.+|+ +.+ ++|.+ ..+.++.+|+++|+++|||||+++|+++.+
T Consensus 32 ~~~s~~~sp~~~v~K~~g~~R~~~D~r~lN~~~~~~~~~~~~~p~~----~~l~~~~~~s~lDl~~af~~i~l~~~~~~~ 107 (213)
T cd01645 32 PSTSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHP----AALPKGWPLIVLDLKDCFFSIPLHPDDRER 107 (213)
T ss_pred cCCCCCcCcEEEEEcCCCCeEEEechHHHhhhcccccccCCCCCCh----HHcCCCceEEEEEccCcEEEeeeccCCcce
Confidence 4556789999999999999999999995443 322 23433 457889999999999999999999999999
Q ss_pred eEEEEc-------CeeEEEcccCccCCCchHHHHHHHHHHHHHHHhc--CCEEEEEecCeEEecCCHHHHHHHHHHHHHH
Q psy4044 133 LSVVYR-------DTLYCMTCLPFGLASAPQVFAKLTNWIANYLRNL--GMRVIVYLDDLLLGNQDSVLLRSQARAAVAT 203 (460)
Q Consensus 133 taF~~~-------~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~~--g~~v~~YvDDili~s~~~~~~~~~l~~v~~~ 203 (460)
|||.|+ +|.|+|++||||+++||++||++|+.++..+... +..+.+|+|||+|++++.++|.++++.++++
T Consensus 108 taf~~~~~~~~~~~~~~~~~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~~~~~~~l~~v~~~ 187 (213)
T cd01645 108 FAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQT 187 (213)
T ss_pred eEEEeccccCCCCCceEEEEEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCHHHHHHHHHHHHHH
Confidence 999995 7999999999999999999999999999877643 3468899999999999999999999999999
Q ss_pred HHHcCCcccccccccccccccccccEEE
Q psy4044 204 LQSLRWSVNLERSVLWPVQTCQYLGIMW 231 (460)
Q Consensus 204 l~~~gl~l~~~K~~~~~~~~v~~LG~~i 231 (460)
|+++|+.+|++||++ ..+++||||.|
T Consensus 188 l~~~gl~ln~~K~~~--~~~v~fLG~~i 213 (213)
T cd01645 188 LLRWGLTIPPEKVQK--EPPFQYLGYEL 213 (213)
T ss_pred HHHCCCEeCHHHEeC--CCCeEeccEeC
Confidence 999999999999976 36899999985
No 3
>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=99.97 E-value=1.9e-31 Score=240.46 Aligned_cols=167 Identities=23% Similarity=0.286 Sum_probs=155.4
Q ss_pred CCcccccceEeecCCCCeeeeeecc----ccCCCCccCCCccchhhhccCCceEEEEeccccccccccCCCCcceeEEEE
Q psy4044 62 SGRRVHDLTLLLSSRDGFQDLGDRA----FLSLKKFHLINHFRVPDFLQRGDFLVKIDLSQAYFHVPIRPSHQRFLSVVY 137 (460)
Q Consensus 62 ~~~~~sp~~~V~Kk~g~~R~~~D~r----~~~~~~~plp~i~~ll~~l~~~~~~s~lDl~~ay~qi~l~~~~~~~taF~~ 137 (460)
...+.+|+++|+|++|++|+|+|+| .+.++.+++|.+++++..+.++.+++++|+++||+|++++++++.+++|.+
T Consensus 7 ~~~~~~p~~~v~k~~~k~R~~~D~r~ln~~~~~~~~~~p~i~~~~~~~~~~~~~~~~D~~~~~~~i~l~~~~~~~~~~~~ 86 (177)
T cd01647 7 SSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRT 86 (177)
T ss_pred CCCCCCceEEEECCCCCEEEEEcCHHHhcccCCCCCCCCCHHHHHHHhhcCcEEEecccccCcceeeeccCChhhceeec
Confidence 3344589999999999999999999 445689999999999999999999999999999999999999999999999
Q ss_pred cCeeEEEcccCccCCCchHHHHHHHHHHHHHHHhcCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccccccc
Q psy4044 138 RDTLYCMTCLPFGLASAPQVFAKLTNWIANYLRNLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSV 217 (460)
Q Consensus 138 ~~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~ 217 (460)
+++.|++++||||+++||..|++.|+.++..+. +..+..|+||+++.+++.++|..+++.+++.++++|+.+|++||+
T Consensus 87 ~~~~~~~~~~p~G~~~s~~~~~~~~~~~l~~~~--~~~~~~y~DDi~i~~~~~~~~~~~~~~~~~~l~~~~~~~~~~K~~ 164 (177)
T cd01647 87 PFGLYEYTRMPFGLKNAPATFQRLMNKILGDLL--GDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCE 164 (177)
T ss_pred CCCccEEEEecCCCccHHHHHHHHHHhhhcccc--ccccEEEecCccccCCCHHHHHHHHHHHHHHHHHcCCEeCHHHce
Confidence 999999999999999999999999999997664 457899999999999999999999999999999999999999998
Q ss_pred cccccccccccEEE
Q psy4044 218 LWPVQTCQYLGIMW 231 (460)
Q Consensus 218 ~~~~~~v~~LG~~i 231 (460)
+. .++++||||++
T Consensus 165 ~~-~~~~~~lG~~i 177 (177)
T cd01647 165 FG-VPEVEFLGHIV 177 (177)
T ss_pred ec-cCceEeeeEEC
Confidence 76 67999999975
No 4
>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=99.96 E-value=2.7e-30 Score=239.90 Aligned_cols=164 Identities=20% Similarity=0.225 Sum_probs=145.9
Q ss_pred ccccceEeecC---CCCeeeeeecc----------ccCCCCccCCCccchhhhccCCceEEEEeccccccccccCCCCcc
Q psy4044 65 RVHDLTLLLSS---RDGFQDLGDRA----------FLSLKKFHLINHFRVPDFLQRGDFLVKIDLSQAYFHVPIRPSHQR 131 (460)
Q Consensus 65 ~~sp~~~V~Kk---~g~~R~~~D~r----------~~~~~~~plp~i~~ll~~l~~~~~~s~lDl~~ay~qi~l~~~~~~ 131 (460)
++-|.++|.|+ .|++|+|+||| .+.++++++|.+.+++.+++++++++++|+++|||||+|+|+|+.
T Consensus 2 ~y~ph~~V~~~~~~~~k~R~V~D~s~~~~g~sLN~~l~~gp~~~~~l~~iL~~~R~~~~~~~~Di~~af~qI~i~~~d~~ 81 (213)
T cd01644 2 WYLPHHAVIKPSKTTTKLRVVFDASARYNGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRD 81 (213)
T ss_pred cccCCceecCCCCCCCccEEEEecccccCCchhhHHhccCCccccchhhhheeeecCceeEehhHHHhhhheecCcccCc
Confidence 46688899877 68999999998 235688999999999999999999999999999999999999999
Q ss_pred eeEEEEcC-------eeEEEcccCccCCCchHHHHHHHHHHHHHHHhc----CCEEEEEecCeEEecCCHHHHHHHHHHH
Q psy4044 132 FLSVVYRD-------TLYCMTCLPFGLASAPQVFAKLTNWIANYLRNL----GMRVIVYLDDLLLGNQDSVLLRSQARAA 200 (460)
Q Consensus 132 ~taF~~~~-------g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~~----g~~v~~YvDDili~s~~~~~~~~~l~~v 200 (460)
+++|.|++ +.|+|++||||+++||++||++|+.++..+... ...+..|||||++.+++.+||...+++|
T Consensus 82 ~~~F~w~~~~~~~~~~~Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s~~e~~~~~~~v 161 (213)
T cd01644 82 VLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKRL 161 (213)
T ss_pred eEEEEEeCCCCCCcceEEEEEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCCHHHHHHHHHHH
Confidence 99999875 899999999999999999999999999877632 1245799999999999999999999999
Q ss_pred HHHHHHcCCcccccccccccccccccccEEEcC
Q psy4044 201 VATLQSLRWSVNLERSVLWPVQTCQYLGIMWNP 233 (460)
Q Consensus 201 ~~~l~~~gl~l~~~K~~~~~~~~v~~LG~~i~~ 233 (460)
+++|+++||.+ |+|. +.+.++||.+...
T Consensus 162 ~~~L~~~Gf~l----~kw~-sn~~~~l~~~~~~ 189 (213)
T cd01644 162 IALLKKGGFNL----RKWA-SNSQEVLDDLPEE 189 (213)
T ss_pred HHHHHhCCccc----hhcc-cCchhhhhccccc
Confidence 99999999977 4444 6688899888764
No 5
>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=99.96 E-value=7.2e-30 Score=216.48 Aligned_cols=118 Identities=38% Similarity=0.644 Sum_probs=106.4
Q ss_pred EeccccccccccCCCCcceeEEEEcCeeEEEcccCccCCCchHHHHHHHHHHHHHHHhcCCEEEEEecCeEEecCCHHHH
Q psy4044 114 IDLSQAYFHVPIRPSHQRFLSVVYRDTLYCMTCLPFGLASAPQVFAKLTNWIANYLRNLGMRVIVYLDDLLLGNQDSVLL 193 (460)
Q Consensus 114 lDl~~ay~qi~l~~~~~~~taF~~~~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~~g~~v~~YvDDili~s~~~~~~ 193 (460)
+|+++|||||+|+|+++++|||++++|.|+|++||||+++||++||++|+.++..++..+..+.+|+|||+|++++.+.+
T Consensus 1 lD~~~ay~~i~l~~~~~~~~af~~~~~~~~~~~mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~~~~~ 80 (119)
T cd03714 1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASSIKTS 80 (119)
T ss_pred CchhhceEEEecCCCCcceeeEEECCCcEEEEecCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCcHHHH
Confidence 69999999999999999999999999999999999999999999999999999988877778999999999999985555
Q ss_pred HHHHHHHHH-HHHHcCCcccccccccccccccccccEEE
Q psy4044 194 RSQARAAVA-TLQSLRWSVNLERSVLWPVQTCQYLGIMW 231 (460)
Q Consensus 194 ~~~l~~v~~-~l~~~gl~l~~~K~~~~~~~~v~~LG~~i 231 (460)
.++++.+.+ +++++|+.+|++||+++++++++|||++|
T Consensus 81 ~~~~~~l~~~~l~~~gl~ln~~K~~~~~~~~v~fLG~~~ 119 (119)
T cd03714 81 EAVLRHLRATLLANLGFTLNLEKSKLGPTQRITFLGLEL 119 (119)
T ss_pred HHHHHHHHHHHHHHcCCccChhhcEecCCCcEEECcEeC
Confidence 555444444 69999999999999866788999999985
No 6
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=99.75 E-value=1.5e-17 Score=154.78 Aligned_cols=160 Identities=16% Similarity=0.262 Sum_probs=133.8
Q ss_pred eecCC-CCeeee----eeccc----cC------------CCCccCCCccch-----hhhccCCceEEEEecccccccccc
Q psy4044 72 LLSSR-DGFQDL----GDRAF----LS------------LKKFHLINHFRV-----PDFLQRGDFLVKIDLSQAYFHVPI 125 (460)
Q Consensus 72 V~Kk~-g~~R~~----~D~r~----~~------------~~~~plp~i~~l-----l~~l~~~~~~s~lDl~~ay~qi~l 125 (460)
|||++ |++|++ +++|. +. ...+..+....+ +....+..++.++|+++||++|+.
T Consensus 1 ipK~~~~~~RpI~~~~~~~r~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Di~~~f~sI~~ 80 (214)
T PF00078_consen 1 IPKKNVGKYRPISIPSVDDRIVQRVLNKRLQPILEPIFSPSQFGFRPGRSCHDIKKLNRFKGYLYFLKLDISKAFDSIPH 80 (214)
T ss_dssp EESSSSSSEEEE----EBTHHHHHHBHH---------HHHTTSSCSHGCCCHHHHHHHC-CGSSEEEEEECCCCGGGSBB
T ss_pred CCCcCCCCeeEcCCCCcHHHHHHHHHHhhccccccccCCCCCCCCcccccccccccccccccccccceecccccccccee
Confidence 68999 999998 78881 11 123333333222 456678899999999999999999
Q ss_pred CCCCcceeEEEEc------------------------CeeEEEcccCccCCCchHHHHHHHHHHHHHHHh---cCCEEEE
Q psy4044 126 RPSHQRFLSVVYR------------------------DTLYCMTCLPFGLASAPQVFAKLTNWIANYLRN---LGMRVIV 178 (460)
Q Consensus 126 ~~~~~~~taF~~~------------------------~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~---~g~~v~~ 178 (460)
++-.+....+.++ ...+....+|||...||.+|+.+|..+...+.. .+..+..
T Consensus 81 ~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~r 160 (214)
T PF00078_consen 81 HRLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGDLSPYFQKRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLR 160 (214)
T ss_dssp HTTTGGGGEEEEECCSCHHHHHHHHHHHH-EECGCSSSEEEEESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEE
T ss_pred eecccccccccccccccccccccccccccccccccccccccccccccccccccchhhccccccccccccccccccccceE
Confidence 9999999999887 457899999999999999999999999977776 4578999
Q ss_pred EecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccccccccc-cccccccccEEE
Q psy4044 179 YLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLW-PVQTCQYLGIMW 231 (460)
Q Consensus 179 YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~-~~~~v~~LG~~i 231 (460)
|+||+++.+++.+++...++.+.+.++++|+.+|++||+.. .+.+++|||+.|
T Consensus 161 Y~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~~~~~~~~~~~lG~~i 214 (214)
T PF00078_consen 161 YADDILIISKSKEELQKILEKISQWLEELGLKLNPEKTKILHPSDSVKFLGYVI 214 (214)
T ss_dssp ETTEEEEEESSHHHHHHHHHHHHHHHHHTTSBCSSTTTSCS--ESSEEETTEEE
T ss_pred eccccEEEECCHHHHHHHHHHHHHHHHHCCCEEChHHEEEEeCCCCEEEEeEEC
Confidence 99999999999999999999999999999999999999765 367999999986
No 7
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=99.58 E-value=6.8e-15 Score=119.90 Aligned_cols=95 Identities=20% Similarity=0.327 Sum_probs=86.0
Q ss_pred EeccccccccccCCCCcceeEEEEcCeeEEEcccCccCCCchHHHHHHHHHHHHHHHh--cCCEEEEEecCeEEecCCHH
Q psy4044 114 IDLSQAYFHVPIRPSHQRFLSVVYRDTLYCMTCLPFGLASAPQVFAKLTNWIANYLRN--LGMRVIVYLDDLLLGNQDSV 191 (460)
Q Consensus 114 lDl~~ay~qi~l~~~~~~~taF~~~~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~--~g~~v~~YvDDili~s~~~~ 191 (460)
+|++++|+||+ +|||...||.+|+.+|..+...+.. .+..+..|+||+++.+++.
T Consensus 1 ~d~~~~~~~~~----------------------lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~- 57 (98)
T cd00304 1 FDVKSFFTSIP----------------------LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE- 57 (98)
T ss_pred CCHHHcCCCCc----------------------cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH-
Confidence 59999999999 9999999999999999999987754 4568999999999999999
Q ss_pred HHHHHHHHHHHHHHHcCCccccccccc-ccccccccccEEE
Q psy4044 192 LLRSQARAAVATLQSLRWSVNLERSVL-WPVQTCQYLGIMW 231 (460)
Q Consensus 192 ~~~~~l~~v~~~l~~~gl~l~~~K~~~-~~~~~v~~LG~~i 231 (460)
++...+..+.+.++++|+.+|++||++ .+.++++|||+++
T Consensus 58 ~~~~~~~~l~~~l~~~gl~ln~~Kt~~~~~~~~~~flG~~~ 98 (98)
T cd00304 58 QQAVKKRELEEFLARLGLNLSDEKTQFTEKEKKFKFLGILV 98 (98)
T ss_pred HHHHHHHHHHHHHHHcCcEEChheeEEecCCCCeeeeceeC
Confidence 899999999999999999999999976 2477999999975
No 8
>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=99.21 E-value=4.3e-11 Score=101.14 Aligned_cols=104 Identities=14% Similarity=0.193 Sum_probs=86.5
Q ss_pred EeccccccccccCCCCcceeEEEEcCeeEEE-cccCccCCCchHHHHHHHHHHHHHHHhc------CCEEEEEecCeEEe
Q psy4044 114 IDLSQAYFHVPIRPSHQRFLSVVYRDTLYCM-TCLPFGLASAPQVFAKLTNWIANYLRNL------GMRVIVYLDDLLLG 186 (460)
Q Consensus 114 lDl~~ay~qi~l~~~~~~~taF~~~~g~y~~-~~lpfGl~~ap~~fq~~~~~il~~l~~~------g~~v~~YvDDili~ 186 (460)
.|+++||-+|+. .|.. +-+|+|...||.+|.-+++.+...+... +.....|+||+++.
T Consensus 1 ~d~~~~~~~~~~---------------~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~ 65 (119)
T cd01648 1 TDIKKCYDSIPQ---------------YYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLI 65 (119)
T ss_pred CChHHhccchhh---------------hhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEE
Confidence 388999999988 3333 3499999999999999998888665533 34678999999999
Q ss_pred cCCHHHHHHHHHHHHHHH-HHcCCcccccccccc-------cccccccccEEEc
Q psy4044 187 NQDSVLLRSQARAAVATL-QSLRWSVNLERSVLW-------PVQTCQYLGIMWN 232 (460)
Q Consensus 187 s~~~~~~~~~l~~v~~~l-~~~gl~l~~~K~~~~-------~~~~v~~LG~~i~ 232 (460)
+.+.++....+..+.+.+ ++.|+.+|++|++.. ..+.+.|||+.|+
T Consensus 66 ~~~~~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~~~~~~~~~~~~~~flG~~i~ 119 (119)
T cd01648 66 TTSLDKAIKFLNLLLRGFINQYKTFVNFDKTQINFSFAQLDSSDLIPWCGLLIN 119 (119)
T ss_pred eCCHHHHHHHHHHHHHhhHHhhCeEECcccceeeccccccCCCCccCceeEeeC
Confidence 999988888888888887 999999999999764 3667899999875
No 9
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=99.18 E-value=1.1e-10 Score=109.20 Aligned_cols=144 Identities=16% Similarity=0.228 Sum_probs=105.6
Q ss_pred cCCceEEEEeccccccccccCCCCcceeEEEEc-C-------e-eEEEcccCccCCCchHHHHHHHHHHHHHHH----hc
Q psy4044 106 QRGDFLVKIDLSQAYFHVPIRPSHQRFLSVVYR-D-------T-LYCMTCLPFGLASAPQVFAKLTNWIANYLR----NL 172 (460)
Q Consensus 106 ~~~~~~s~lDl~~ay~qi~l~~~~~~~taF~~~-~-------g-~y~~~~lpfGl~~ap~~fq~~~~~il~~l~----~~ 172 (460)
.+..++.++|++++|..|..+.--......... . . ...-..+|+|...||.++.-+|..+...+. ..
T Consensus 54 ~~~~~v~~~Di~~fFdsI~~~~L~~~l~~~~~~~~~~~~~l~~~~~~~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~ 133 (214)
T cd03487 54 CGAKYVLKLDIKDFFPSITFERVRGVFRSLGYFSPDVATILAKLCTYNGHLPQGAPTSPALSNLVFRKLDERLSKLAKSN 133 (214)
T ss_pred cCCCEEEEeehhhhcccCCHHHHHHHHHHcCCCCHHHHHHHHHHHhCCCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHc
Confidence 467899999999999998753311111000000 0 0 000128999999999999999987765543 34
Q ss_pred CCEEEEEecCeEEecCCHH--HHHHHHHHHHHHHHHcCCccccccccccc-ccccccccEEEcCCCCcccCCccchHHHH
Q psy4044 173 GMRVIVYLDDLLLGNQDSV--LLRSQARAAVATLQSLRWSVNLERSVLWP-VQTCQYLGIMWNPTLDSKSLPLEKQSTIQ 249 (460)
Q Consensus 173 g~~v~~YvDDili~s~~~~--~~~~~l~~v~~~l~~~gl~l~~~K~~~~~-~~~v~~LG~~i~~~g~~~~~p~~k~~~l~ 249 (460)
|.....|+||+++.+++.+ +....+..+-+.|.+.|+.+|++|++... .....|||+.++.+. ++++..+.++++
T Consensus 134 ~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~i~~~~~~~~~~G~~i~~~~--~~~~~~~~~~i~ 211 (214)
T cd03487 134 GLTYTRYADDITFSSNKKLKEALDKLLEIIRSILSEEGFKINKSKTRISSKGSRQIVTGLVVNNGK--PSLPRKEKRKIR 211 (214)
T ss_pred CCeEEEEeccEEEEccccchhHHHHHHHHHHHHHHHCCceeCCCceEEccCCCCcEEEEEEEeCCc--CCCCHHHHHHHH
Confidence 6778999999999999887 67777888888889999999999997653 257899999999885 557777777776
Q ss_pred HH
Q psy4044 250 RY 251 (460)
Q Consensus 250 ~f 251 (460)
.+
T Consensus 212 ~~ 213 (214)
T cd03487 212 AL 213 (214)
T ss_pred hh
Confidence 54
No 10
>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=99.12 E-value=2.8e-10 Score=95.87 Aligned_cols=116 Identities=26% Similarity=0.228 Sum_probs=88.5
Q ss_pred EEEEccccc------cceeEEeeeecceecCCcc--ccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHhh
Q psy4044 279 FVSTDASNS------GWGAIVDNHSLGGVWSDHQ--EMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHK 350 (460)
Q Consensus 279 ~l~tDAS~~------g~Gavl~q~~~s~~~~~~e--~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~~ 350 (460)
.++||||.. |+|+++.+......+.... ..+++++.|+.|++.|++... .....++.|+|||+.++..+++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~-~~~~~~i~i~~Ds~~~~~~~~~ 79 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELAL-ELGGKKVNIYTDSQYVINALTG 79 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHH-hCCCceEEEEECHHHHHHHhhc
Confidence 378999975 8888888653333333322 478999999999999999865 5667899999999999999987
Q ss_pred cCCCcchhhhHHHHHHHHHHHHcCCeEEEEEeCC----CCCCCCCccccC
Q psy4044 351 EGGTKSFKLLREVEALFDLAVRHNITLMARYIPG----KFNTWADSLSRQ 396 (460)
Q Consensus 351 ~~~~~~~~~~~~~r~i~~~~~~~~~~~~i~~vpg----~~N~~AD~LSR~ 396 (460)
...........+.+.+..++. ....+.+.|+|| ..|..||.|+|.
T Consensus 80 ~~~~~~~~~~~~~~~i~~~~~-~~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 80 WYEGKPVKNVDLWQRLLALLK-RFHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred cccCCChhhHHHHHHHHHHHh-CCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 543334455666666666653 345799999999 999999999874
No 11
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=99.11 E-value=1.3e-10 Score=108.89 Aligned_cols=101 Identities=17% Similarity=0.174 Sum_probs=84.7
Q ss_pred CCceEEEEeccccccccccCCCCcceeEEEEcCeeEEEcccCccCCCchHHHHHHHHHHHHHHHh--------cCCEEEE
Q psy4044 107 RGDFLVKIDLSQAYFHVPIRPSHQRFLSVVYRDTLYCMTCLPFGLASAPQVFAKLTNWIANYLRN--------LGMRVIV 178 (460)
Q Consensus 107 ~~~~~s~lDl~~ay~qi~l~~~~~~~taF~~~~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~--------~g~~v~~ 178 (460)
+..++.++|+++||..|+-+.-.... .+|+|...||.+|..+++.+...+.. .+..+..
T Consensus 80 ~~~~~l~~Di~~aFdsi~~~~l~~~l-------------GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 146 (220)
T cd01650 80 KSLVLVFLDFEKAFDSVDHEFLLKAL-------------GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLA 146 (220)
T ss_pred CceEEEEEEHHhhcCcCCHHHHHHHh-------------CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEE
Confidence 45789999999999988744322221 89999999999999999999887762 3557889
Q ss_pred EecCeEEecCCHH-HHHHHHHHHHHHHHHcCCccccccccccc
Q psy4044 179 YLDDLLLGNQDSV-LLRSQARAAVATLQSLRWSVNLERSVLWP 220 (460)
Q Consensus 179 YvDDili~s~~~~-~~~~~l~~v~~~l~~~gl~l~~~K~~~~~ 220 (460)
|+||+++++.+.+ .....++.+...+.+.|+.+|++||+...
T Consensus 147 yaDD~~i~~~~~~~~~~~~~~~~~~~~~~~gl~in~~Kt~~~~ 189 (220)
T cd01650 147 YADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKSKVML 189 (220)
T ss_pred eccceeeeccCCHHHHHHHHHHHHHHHHHcCCEEChhheEEEE
Confidence 9999999999988 88888888999999999999999997653
No 12
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.99 E-value=1.9e-09 Score=92.33 Aligned_cols=116 Identities=22% Similarity=0.198 Sum_probs=84.7
Q ss_pred eEEEEcccc------ccceeEEeeeecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHhhc
Q psy4044 278 VFVSTDASN------SGWGAIVDNHSLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHKE 351 (460)
Q Consensus 278 ~~l~tDAS~------~g~Gavl~q~~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~~~ 351 (460)
+.||||||- .|+|+++.........+......+.++.|+.|++.||+... -+...++.|+||++.++..+++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~-~~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCT-EHNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHH-hCCCCEEEEEechHHHHHHHhHH
Confidence 478999874 47888886432111122223346889999999999998743 33346899999999999999873
Q ss_pred CCCcchhhhHHHHHHHHHHHHcCCeEEEEEeCCCCCCCCCccccC
Q psy4044 352 GGTKSFKLLREVEALFDLAVRHNITLMARYIPGKFNTWADSLSRQ 396 (460)
Q Consensus 352 ~~~~~~~~~~~~r~i~~~~~~~~~~~~i~~vpg~~N~~AD~LSR~ 396 (460)
. .+...+..+.+.+..+...+. .+.+.|+|+..|..||.|+|.
T Consensus 81 ~-~~~~~~~~l~~~~~~l~~~f~-~~~~~~v~r~~N~~Ad~LA~~ 123 (128)
T PRK13907 81 Y-AKNKMFAPLLEEALQYIKSFD-LFFIKWIPSSQNKVADELARK 123 (128)
T ss_pred H-hcChhHHHHHHHHHHHHhcCC-ceEEEEcCchhchhHHHHHHH
Confidence 3 234456677777777777665 566799999999999999985
No 13
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=98.89 E-value=6.2e-09 Score=97.78 Aligned_cols=127 Identities=14% Similarity=0.222 Sum_probs=94.5
Q ss_pred ccCCceEEEEecccccccccc-------CCC--Cccee---------EEEEcCe-eEEEcccCccCCCchHHHHHHHHHH
Q psy4044 105 LQRGDFLVKIDLSQAYFHVPI-------RPS--HQRFL---------SVVYRDT-LYCMTCLPFGLASAPQVFAKLTNWI 165 (460)
Q Consensus 105 l~~~~~~s~lDl~~ay~qi~l-------~~~--~~~~t---------aF~~~~g-~y~~~~lpfGl~~ap~~fq~~~~~i 165 (460)
-.+..++.++|++++|..|.- ... +.... ....... ...-..+|+|...||.+|.-++..+
T Consensus 66 ~~~~~~~~~~Di~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~GlpqG~~lSp~L~~~~l~~l 145 (226)
T cd01651 66 KGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQGGVISPLLANIYLHEL 145 (226)
T ss_pred cCCCeEEEEccHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHHHhceEccCCeEeCCCCCcCCCccHHHHHHHHHHHHH
Confidence 345679999999999998852 110 00000 0001111 1234569999999999999999888
Q ss_pred HHHHHh-------------cCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCccccccccccc--ccccccccEE
Q psy4044 166 ANYLRN-------------LGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLWP--VQTCQYLGIM 230 (460)
Q Consensus 166 l~~l~~-------------~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~~--~~~v~~LG~~ 230 (460)
...+.. .+.....|+||+++..++.++....++.+.+.++..|+.+|++|++... ...+.|||+.
T Consensus 146 d~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~~~~~~~~~fLG~~ 225 (226)
T cd01651 146 DKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFKSEGFDFLGFT 225 (226)
T ss_pred HHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHHHHHHcCCeechhhcceeecCCCCCeeCCeE
Confidence 766654 3457889999999999999988888888889999999999999997765 4689999986
Q ss_pred E
Q psy4044 231 W 231 (460)
Q Consensus 231 i 231 (460)
+
T Consensus 226 ~ 226 (226)
T cd01651 226 F 226 (226)
T ss_pred C
Confidence 4
No 14
>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=98.88 E-value=4.5e-09 Score=90.22 Aligned_cols=112 Identities=26% Similarity=0.280 Sum_probs=75.2
Q ss_pred CeeEEEEcccc------ccceeEEeeeecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHh
Q psy4044 276 PQVFVSTDASN------SGWGAIVDNHSLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIH 349 (460)
Q Consensus 276 ~~~~l~tDAS~------~g~Gavl~q~~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~ 349 (460)
..+++|||||- .|+|.++... +.++..-...++++.|+.|+..||+.+. ..+++|+|||+.++..++
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~---~~~~~~~~~~s~~~aEl~Ai~~AL~~~~----~~~v~I~tDS~~v~~~l~ 74 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGG---RNFSFRLGGQSNNRAELQAIIEALKALE----HRKVTIYTDSQYVLNALN 74 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETT---EEEEEEEESECHHHHHHHHHHHHHHTHS----TSEEEEEES-HHHHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECC---eEEEecccccchhhhheehHHHHHHHhh----cccccccccHHHHHHHHH
Confidence 35799999993 3666655322 2222222278999999999999999652 289999999999998776
Q ss_pred h----cCCCcchhhhHHHHHHHHHHHHcCCeEEEEEeCCCCCC-----CCCcccc
Q psy4044 350 K----EGGTKSFKLLREVEALFDLAVRHNITLMARYIPGKFNT-----WADSLSR 395 (460)
Q Consensus 350 ~----~~~~~~~~~~~~~r~i~~~~~~~~~~~~i~~vpg~~N~-----~AD~LSR 395 (460)
+ .+.........+...++.++.. +..+.+.||||+.|. .||.|+|
T Consensus 75 ~~~~~~~~~~~~~~~~i~~~i~~~~~~-~~~v~~~~V~~H~~~~~~N~~aD~lAk 128 (132)
T PF00075_consen 75 KWLHGNGWKKTSNGRPIKNEIWELLSR-GIKVRFRWVPGHSGVPQGNERADRLAK 128 (132)
T ss_dssp THHHHTTSBSCTSSSBHTHHHHHHHHH-SSEEEEEESSSSSSSHHHHHHHHHHHH
T ss_pred Hhccccccccccccccchhheeecccc-ceEEeeeeccCcCCCchhHHHHHHHHH
Confidence 5 1111111111344566666643 678999999999775 5888776
No 15
>PRK07708 hypothetical protein; Validated
Probab=98.84 E-value=1.5e-08 Score=94.33 Aligned_cols=120 Identities=18% Similarity=0.127 Sum_probs=89.2
Q ss_pred eeEEEEcccc------ccceeEEeeeeccee--c---CCccccCChhHHHHHHHHHHHHhhCCcC-CCcEEEEEeCchhh
Q psy4044 277 QVFVSTDASN------SGWGAIVDNHSLGGV--W---SDHQEMWHINLKEMFAVRSALERKLPVL-QDKVVLIQSDNQTV 344 (460)
Q Consensus 277 ~~~l~tDAS~------~g~Gavl~q~~~s~~--~---~~~e~~ys~~~~EllAi~~al~~~~~~l-~g~~v~i~tD~~~l 344 (460)
.+++|+|+|. .|+|+++........ . ..-....+.++.|+.|++.||+.....= ...+|.|++|++-+
T Consensus 73 ~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlV 152 (219)
T PRK07708 73 EILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVV 152 (219)
T ss_pred cEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHH
Confidence 5899999974 578888864211111 1 1112235889999999999998754331 22359999999999
Q ss_pred HHHHhhcCCCcchhhhHHHHHHHHHHHHcCCeEEEEEeCCCCCCCCCccccC
Q psy4044 345 VSYIHKEGGTKSFKLLREVEALFDLAVRHNITLMARYIPGKFNTWADSLSRQ 396 (460)
Q Consensus 345 ~~~l~~~~~~~~~~~~~~~r~i~~~~~~~~~~~~i~~vpg~~N~~AD~LSR~ 396 (460)
+.++++.-..+++.+......+..++..+.+.+.+.|||++.|..||.|++.
T Consensus 153 i~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~ 204 (219)
T PRK07708 153 LNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQ 204 (219)
T ss_pred HHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHH
Confidence 9999975556666677777777778887777788999999999999999986
No 16
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.82 E-value=1.8e-08 Score=87.59 Aligned_cols=119 Identities=28% Similarity=0.265 Sum_probs=86.3
Q ss_pred CeeEEEEcccc------ccceeEEeeeecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHh
Q psy4044 276 PQVFVSTDASN------SGWGAIVDNHSLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIH 349 (460)
Q Consensus 276 ~~~~l~tDAS~------~g~Gavl~q~~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~ 349 (460)
..+.||||++. .|+|+||...-.....+..+...+.++.|+.|++.||+..+. +....+.|+|||+.++..++
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~-~~~~~v~l~tDS~yv~~~i~ 80 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKE-LGACEVTLYTDSKYVVEGIT 80 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHh-cCCceEEEEecHHHHHHHHH
Confidence 35789999884 588888884323334555666889999999999999999665 56688999999999987776
Q ss_pred hc----C------CCcc-hhhhHHHHHHHHHHHHcCCeEEEEEeCCCC----CCCCCccccC
Q psy4044 350 KE----G------GTKS-FKLLREVEALFDLAVRHNITLMARYIPGKF----NTWADSLSRQ 396 (460)
Q Consensus 350 ~~----~------~~~~-~~~~~~~r~i~~~~~~~~~~~~i~~vpg~~----N~~AD~LSR~ 396 (460)
.- . ..+. -....+.+.+.+++..+. .+.++||||+. |..||.|.|.
T Consensus 81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~-~v~~~WVkgH~g~~~NeraD~LA~~ 141 (154)
T COG0328 81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHE-LVFWEWVKGHAGHPENERADQLARE 141 (154)
T ss_pred HHHhhccccCccccccCccccHHHHHHHHHHHhhCC-eEEEEEeeCCCCChHHHHHHHHHHH
Confidence 21 0 1111 123456777777777653 68899999755 6678988875
No 17
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.69 E-value=9.5e-08 Score=84.14 Aligned_cols=115 Identities=27% Similarity=0.257 Sum_probs=75.9
Q ss_pred eeEEEEcccc------ccceeEEeeeecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHhh
Q psy4044 277 QVFVSTDASN------SGWGAIVDNHSLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHK 350 (460)
Q Consensus 277 ~~~l~tDAS~------~g~Gavl~q~~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~~ 350 (460)
.+.||||+|. .|+|+++...-....++......+.+..||.|++.||+... ....+.|+|||+.++..+++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~---~~~~v~I~tDS~yvi~~i~~ 79 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALK---EPCEVTLYTDSQYVRQGITE 79 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcC---CCCeEEEEECHHHHHHHHHH
Confidence 4789999995 47777765321111233334466889999999999998753 24679999999988776653
Q ss_pred ------cCCCc----ch-hhhHHHHHHHHHHHHcCCeEEEEEeCCCC----CCCCCccccC
Q psy4044 351 ------EGGTK----SF-KLLREVEALFDLAVRHNITLMARYIPGKF----NTWADSLSRQ 396 (460)
Q Consensus 351 ------~~~~~----~~-~~~~~~r~i~~~~~~~~~~~~i~~vpg~~----N~~AD~LSR~ 396 (460)
.++-+ .+ ....+...+..++.. ..+.+.||||+. |..||.|+|.
T Consensus 80 w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~--~~v~~~wV~~H~~~~~N~~AD~lA~~ 138 (150)
T PRK00203 80 WIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR--HQIKWHWVKGHAGHPENERCDELARA 138 (150)
T ss_pred HHHHHHHcCCcccCCCccccHHHHHHHHHHhcc--CceEEEEecCCCCCHHHHHHHHHHHH
Confidence 01111 11 123355566555543 468889999877 6788988874
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=98.66 E-value=1e-07 Score=84.70 Aligned_cols=92 Identities=20% Similarity=0.289 Sum_probs=80.2
Q ss_pred EEcccCccCCCchHHHHHHHHHHHHHHHh--cCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCccccccccccc
Q psy4044 143 CMTCLPFGLASAPQVFAKLTNWIANYLRN--LGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLWP 220 (460)
Q Consensus 143 ~~~~lpfGl~~ap~~fq~~~~~il~~l~~--~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~~ 220 (460)
....+|+|...||.+++.+|..+-..+.. .+.....|+||+++.+++.+.....++.+-+.+.+.|+.+|++|+....
T Consensus 50 ~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~~~ 129 (158)
T cd01646 50 QTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILP 129 (158)
T ss_pred CCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCHHHHHHHHHHHHHHHHHCCCEEChhhceeee
Confidence 44679999999999999999988777765 4668899999999999999988889999999999999999999997765
Q ss_pred ccc----cccccEEEcCC
Q psy4044 221 VQT----CQYLGIMWNPT 234 (460)
Q Consensus 221 ~~~----v~~LG~~i~~~ 234 (460)
..+ .+|||+.+...
T Consensus 130 ~~~~~~~~~flg~~~~~~ 147 (158)
T cd01646 130 LPEGTASKDFLGYRFSPI 147 (158)
T ss_pred cCCCCccccccceEeehh
Confidence 544 69999999753
No 19
>PRK06548 ribonuclease H; Provisional
Probab=98.59 E-value=3.7e-07 Score=80.69 Aligned_cols=114 Identities=26% Similarity=0.302 Sum_probs=79.4
Q ss_pred CeeEEEEcccc------ccceeEEeeeecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHh
Q psy4044 276 PQVFVSTDASN------SGWGAIVDNHSLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIH 349 (460)
Q Consensus 276 ~~~~l~tDAS~------~g~Gavl~q~~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~ 349 (460)
..++||||+|. .|+|+++... ...+..+..-+.++.|+.|++.||+.... ...++.|+|||+.++..++
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~---~~~~g~~~~~TNnraEl~Aii~aL~~~~~--~~~~v~I~TDS~yvi~~i~ 78 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDEN---TWDSGGWDIATNNIAELTAVRELLIATRH--TDRPILILSDSKYVINSLT 78 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCC---cEEccCCCCCCHHHHHHHHHHHHHHhhhc--CCceEEEEeChHHHHHHHH
Confidence 45899999874 3566665422 23344455668999999999999975432 2357999999999988887
Q ss_pred h------cC----CCcch-hhhHHHHHHHHHHHHcCCeEEEEEeCCCC----CCCCCccccC
Q psy4044 350 K------EG----GTKSF-KLLREVEALFDLAVRHNITLMARYIPGKF----NTWADSLSRQ 396 (460)
Q Consensus 350 ~------~~----~~~~~-~~~~~~r~i~~~~~~~~~~~~i~~vpg~~----N~~AD~LSR~ 396 (460)
+ .. ....+ ....+.+.+..+.... .+++.||+|+. |..||.|+|.
T Consensus 79 ~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~--~v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR--NIRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred HHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC--ceEEEEEecCCCCHHHHHHHHHHHH
Confidence 3 11 11122 2355667776776644 58889999977 7789999886
No 20
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.57 E-value=2.2e-07 Score=94.42 Aligned_cols=118 Identities=22% Similarity=0.242 Sum_probs=88.7
Q ss_pred eeEEEEcccc------ccceeEEeeeecc---eecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHH
Q psy4044 277 QVFVSTDASN------SGWGAIVDNHSLG---GVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSY 347 (460)
Q Consensus 277 ~~~l~tDAS~------~g~Gavl~q~~~s---~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~ 347 (460)
.++||||+|. .|+|+++...... ..+.......+.+..|+.|++.||+... -+..+++.|++|++.++..
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~-~~g~~~v~i~~DS~lvi~~ 80 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAA-ELGATEVEVRMDSKLVVEQ 80 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHH-hCCCCeEEEEeCcHHHHHH
Confidence 4789999984 3777777643211 1223333356888999999999999743 3345789999999999999
Q ss_pred HhhcCCCcchhhhHHHHHHHHHHHHcCCeEEEEEeCCCCCCCCCccccC
Q psy4044 348 IHKEGGTKSFKLLREVEALFDLAVRHNITLMARYIPGKFNTWADSLSRQ 396 (460)
Q Consensus 348 l~~~~~~~~~~~~~~~r~i~~~~~~~~~~~~i~~vpg~~N~~AD~LSR~ 396 (460)
+++....++..+..+...+..+...+. .+++.|||++.|..||.|++.
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~-~~~i~~v~r~~N~~AD~LA~~ 128 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFG-RVTYTWIPRARNAHADRLANE 128 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCC-ceEEEECCchhhhHHHHHHHH
Confidence 886444455666777777777777665 688999999999999999996
No 21
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.42 E-value=1.8e-07 Score=73.85 Aligned_cols=82 Identities=26% Similarity=0.278 Sum_probs=62.9
Q ss_pred hHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHhhcCCCcchhhhHHHHHHHHHHHHcCCeEEEEEeCCCCCCCCC
Q psy4044 312 NLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHKEGGTKSFKLLREVEALFDLAVRHNITLMARYIPGKFNTWAD 391 (460)
Q Consensus 312 ~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~~~~~~~~~~~~~~~r~i~~~~~~~~~~~~i~~vpg~~N~~AD 391 (460)
.+.|++|+..||+... -+.-.++++.||++.++..+++...... ....+...+..++..+. .+.++|+|++.|..||
T Consensus 2 ~~aE~~al~~al~~a~-~~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~-~~~~~~i~r~~N~~A~ 78 (87)
T PF13456_consen 2 LEAEALALLEALQLAW-ELGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFW-NVSVSHIPREQNKVAD 78 (87)
T ss_dssp HHHHHHHHHHHHHHHH-CCT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCS-CEEEEE--GGGSHHHH
T ss_pred cHHHHHHHHHHHHHHH-HCCCCEEEEEecCccccccccccccccc-cccccchhhhhhhcccc-ceEEEEEChHHhHHHH
Confidence 5789999999998853 3445789999999999999988554444 67788888888887654 7899999999999999
Q ss_pred ccccC
Q psy4044 392 SLSRQ 396 (460)
Q Consensus 392 ~LSR~ 396 (460)
.|+|.
T Consensus 79 ~LA~~ 83 (87)
T PF13456_consen 79 ALAKF 83 (87)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 99873
No 22
>PRK08719 ribonuclease H; Reviewed
Probab=98.31 E-value=3.2e-06 Score=73.99 Aligned_cols=113 Identities=17% Similarity=0.073 Sum_probs=72.0
Q ss_pred CeeEEEEcccc----c-----cceeEEeee----ecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCch
Q psy4044 276 PQVFVSTDASN----S-----GWGAIVDNH----SLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQ 342 (460)
Q Consensus 276 ~~~~l~tDAS~----~-----g~Gavl~q~----~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~ 342 (460)
.++++|||+|. . |+|+++... ....... .+...+.++.|+.|++.||+..... ..|+|||+
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~-~~~~~Tnn~aEl~A~~~aL~~~~~~-----~~i~tDS~ 76 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSIT-VNRYTDNAELELLALIEALEYARDG-----DVIYSDSD 76 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEec-CCCCccHHHHHHHHHHHHHHHcCCC-----CEEEechH
Confidence 46899999886 2 777776532 1111221 2223589999999999999985432 37999999
Q ss_pred hhHHHHhh------cCCCc----ch-hhhHHHHHHHHHHHHcCCeEEEEEeCCC----CCCCCCccccC
Q psy4044 343 TVVSYIHK------EGGTK----SF-KLLREVEALFDLAVRHNITLMARYIPGK----FNTWADSLSRQ 396 (460)
Q Consensus 343 ~l~~~l~~------~~~~~----~~-~~~~~~r~i~~~~~~~~~~~~i~~vpg~----~N~~AD~LSR~ 396 (460)
.++..+++ +++-+ .+ ....+...+..+.. .-.++++||||+ .|..||.|.|.
T Consensus 77 yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~g~~~Ne~aD~lA~~ 143 (147)
T PRK08719 77 YCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHSGIEGNEAADMLAQA 143 (147)
T ss_pred HHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCCCChhHHHHHHHHHH
Confidence 88777642 11111 11 12334555544544 235889999994 58889988874
No 23
>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=98.19 E-value=5.8e-06 Score=73.53 Aligned_cols=100 Identities=26% Similarity=0.345 Sum_probs=73.4
Q ss_pred eEEEEccccccceeEEeeeecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHhhcCCCcch
Q psy4044 278 VFVSTDASNSGWGAIVDNHSLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHKEGGTKSF 357 (460)
Q Consensus 278 ~~l~tDAS~~g~Gavl~q~~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~~~~~~~~~ 357 (460)
-.+++||+.+|+|.++......+.|+.. .+|+..||+|.++|-.. .|.++ +.|||..+++ + +-.
T Consensus 95 c~VfaDATpTgwgi~i~~~~~~~Tfs~~---l~IhtaELlaaClAr~~-----~~~r~-l~tDnt~Vls---r----kyt 158 (245)
T PF00336_consen 95 CQVFADATPTGWGISITGQRMRGTFSKP---LPIHTAELLAACLARLM-----SGARC-LGTDNTVVLS---R----KYT 158 (245)
T ss_pred CceeccCCCCcceeeecCceeeeeeccc---ccchHHHHHHHHHHHhc-----cCCcE-EeecCcEEEe---c----ccc
Confidence 4789999999999998877788888874 68999999999888544 34444 8899988752 2 112
Q ss_pred hhhHHHHHHHHHHHHcCCeEEEEEeCCCCCCCCCccccCC
Q psy4044 358 KLLREVEALFDLAVRHNITLMARYIPGKFNTWADSLSRQK 397 (460)
Q Consensus 358 ~~~~~~r~i~~~~~~~~~~~~i~~vpg~~N~~AD~LSR~~ 397 (460)
...-+......|+. . ...+.|||++.| +||..||..
T Consensus 159 s~PW~lac~A~wiL--r-gts~~yVPS~~N-PAD~PsR~~ 194 (245)
T PF00336_consen 159 SFPWLLACAANWIL--R-GTSFYYVPSKYN-PADDPSRGK 194 (245)
T ss_pred cCcHHHHHHHHHhh--c-CceEEEeccccC-cCCCCCCCc
Confidence 23334444444443 1 366799999999 999999984
No 24
>KOG3752|consensus
Probab=97.74 E-value=0.00012 Score=71.72 Aligned_cols=117 Identities=23% Similarity=0.249 Sum_probs=76.2
Q ss_pred eEEEEccccc---------cceeEEeee---ecceecCCccccCChhHHHHHHHHHHHHhhCCcCCCcEEEEEeCchhhH
Q psy4044 278 VFVSTDASNS---------GWGAIVDNH---SLGGVWSDHQEMWHINLKEMFAVRSALERKLPVLQDKVVLIQSDNQTVV 345 (460)
Q Consensus 278 ~~l~tDAS~~---------g~Gavl~q~---~~s~~~~~~e~~ys~~~~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~ 345 (460)
.+||||+|.. |+|+..... -.++.+. -..-+.+..|+.||..||++...- ...+++|.||+..++
T Consensus 213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~--~g~qtNnrAEl~Av~~ALkka~~~-~~~kv~I~TDS~~~i 289 (371)
T KOG3752|consen 213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLA--GGRQTNNRAELIAAIEALKKARSK-NINKVVIRTDSEYFI 289 (371)
T ss_pred eEEEecCccccCCCCCCcceeEEeeCCCCcccccccCC--CCcccccHHHHHHHHHHHHHHHhc-CCCcEEEEechHHHH
Confidence 7899999854 455444321 1222222 134578999999999999985332 234899999999998
Q ss_pred HHHhh---------cCCCcch-------hhhHHHHHHHHHHHH-cCCeEEEEEeCCCC----CCCCCccccCC
Q psy4044 346 SYIHK---------EGGTKSF-------KLLREVEALFDLAVR-HNITLMARYIPGKF----NTWADSLSRQK 397 (460)
Q Consensus 346 ~~l~~---------~~~~~~~-------~~~~~~r~i~~~~~~-~~~~~~i~~vpg~~----N~~AD~LSR~~ 397 (460)
.+++. ..+.... ........+.++.++ .+..+.+.||+|.. |..||.|+|..
T Consensus 290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 88863 0111111 122344455566665 35689999999976 67899999974
No 25
>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=97.04 E-value=0.0065 Score=59.77 Aligned_cols=73 Identities=14% Similarity=0.001 Sum_probs=59.6
Q ss_pred EcccCccCCCchHHHHHHHHHHHHHHHh--cCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccccccc
Q psy4044 144 MTCLPFGLASAPQVFAKLTNWIANYLRN--LGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSV 217 (460)
Q Consensus 144 ~~~lpfGl~~ap~~fq~~~~~il~~l~~--~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~ 217 (460)
-+-+|+|-..||-+-.-++..+-..+.. .|..+..|.||+++++. .+++....+.+-+.++..|+.+|++|..
T Consensus 81 ~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~-~~~a~~aw~~i~~fl~~lGLelN~eKT~ 155 (346)
T cd01709 81 KRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ-PETCAKAWKAIQEFAKVMGLELNKEKTG 155 (346)
T ss_pred CCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC-HHHHHHHHHHHHHHHHHcCceeccccce
Confidence 3679999999999888888833344433 37789999999999954 6778888889999999999999999973
No 26
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=96.67 E-value=0.0028 Score=56.24 Aligned_cols=50 Identities=24% Similarity=0.189 Sum_probs=37.3
Q ss_pred CeeEEEEccccccceeEEeeeec-----------ce-ecCCccccCChhHHHHHHHHHHHHhh
Q psy4044 276 PQVFVSTDASNSGWGAIVDNHSL-----------GG-VWSDHQEMWHINLKEMFAVRSALERK 326 (460)
Q Consensus 276 ~~~~l~tDAS~~g~Gavl~q~~~-----------s~-~~~~~e~~ys~~~~EllAi~~al~~~ 326 (460)
..+++|||||..|+|||++-+.. ++ +..+ ....+|.++||+|++.|++..
T Consensus 80 ~~L~~F~DAS~~aygavvYlr~~~~~~~~~~ll~aKsrv~P-~k~~tIPRlEL~a~~l~~~l~ 141 (159)
T PF05380_consen 80 VELHVFCDASESAYGAVVYLRSYSDGSVQVRLLFAKSRVAP-LKTVTIPRLELLAALLGVRLA 141 (159)
T ss_pred eeeeEeecccccceeeEeEeeeccCCceeeeeeeecccccC-CCCCcHHHHHHHHHHHHHHHH
Confidence 46999999999999999875431 11 1222 234599999999999998763
No 27
>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=95.77 E-value=0.0035 Score=59.80 Aligned_cols=125 Identities=18% Similarity=0.233 Sum_probs=80.2
Q ss_pred CceEEEEeccccccccccCCCC--cceeEEEEc---CeeEEEcccCccCCCchHHHHHHHHHHHHHHH------------
Q psy4044 108 GDFLVKIDLSQAYFHVPIRPSH--QRFLSVVYR---DTLYCMTCLPFGLASAPQVFAKLTNWIANYLR------------ 170 (460)
Q Consensus 108 ~~~~s~lDl~~ay~qi~l~~~~--~~~taF~~~---~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~------------ 170 (460)
.-.+-.+|++.||-+=++.++= +.-.+|..+ +..++..+--+||+.||..+...++..|..+.
T Consensus 76 ~~~~~q~Dv~tAfL~~~l~e~iym~~P~g~~~~~~~~~v~~L~kaLYGLKQa~r~W~~~l~~~L~~~GF~~~~~D~clfi 155 (246)
T PF07727_consen 76 GLELHQMDVKTAFLNGDLDEEIYMRQPPGFEDPGPPGKVCRLKKALYGLKQAPRLWYKTLDKFLKKLGFKQSKADPCLFI 155 (246)
T ss_pred ccccccccccceeeecccccchhhcccccccccccccccccccccceecccccchhhhhcccccchhhhhcccccccccc
Confidence 3467789999999999988752 122355544 34577777888999999999988887764443
Q ss_pred ----hcCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccccccccccccccccccEEEcCCCCcccCCcc
Q psy4044 171 ----NLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLWPVQTCQYLGIMWNPTLDSKSLPLE 243 (460)
Q Consensus 171 ----~~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~~~~~v~~LG~~i~~~g~~~~~p~~ 243 (460)
.....+.+||||+++.+.+.+.... +.+.|.+ .|.++. .+ .--.|||..|......+.+..+
T Consensus 156 ~~~~~~~~ii~vYVDDili~~~~~~~i~~----~~~~l~~-~F~iKd----lG--~~~~fLGi~i~~~~~~i~lsQ~ 221 (246)
T PF07727_consen 156 KKSGDGFIIILVYVDDILIAGPSEEEIEE----FKKELKK-KFEIKD----LG--ELKYFLGIEIERTKGGIFLSQK 221 (246)
T ss_pred cccccccccccccccccccccccccceec----ccccccc-cccccc----cc--ccccccceEEEECCCEEEEcHH
Confidence 0123577999999999998764322 3333321 233221 11 1346899999875554444443
No 28
>KOG1005|consensus
Probab=94.72 E-value=0.11 Score=56.36 Aligned_cols=74 Identities=11% Similarity=0.135 Sum_probs=60.4
Q ss_pred EEcccCccCCCchHHHHHHHHHHHHHH----HhcCC-EEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCccccccc
Q psy4044 143 CMTCLPFGLASAPQVFAKLTNWIANYL----RNLGM-RVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERS 216 (460)
Q Consensus 143 ~~~~lpfGl~~ap~~fq~~~~~il~~l----~~~g~-~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~ 216 (460)
+-.-+|+|-..|.-+..-.++.+.+.+ .+.|. .+..|+||.++.+.+.++....++....-..++|+..|.+|.
T Consensus 631 q~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt~~~~a~kfl~~l~~Gf~~yn~~tn~~K~ 709 (888)
T KOG1005|consen 631 QKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITTENDQAKKFLKLLSRGFNKYNFFTNEPKT 709 (888)
T ss_pred EecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEecCHHHHHHHHHHHhccccccceeccCccc
Confidence 456789999999888777777665333 33453 567899999999999999999999999999999999999993
No 29
>KOG4768|consensus
Probab=94.23 E-value=0.23 Score=52.04 Aligned_cols=137 Identities=15% Similarity=0.224 Sum_probs=99.1
Q ss_pred ccchhhhccCCceEEEEeccccccccccCCC---------Ccc---------eeEEEEcCe--eEEEcccCccCCCchHH
Q psy4044 98 HFRVPDFLQRGDFLVKIDLSQAYFHVPIRPS---------HQR---------FLSVVYRDT--LYCMTCLPFGLASAPQV 157 (460)
Q Consensus 98 i~~ll~~l~~~~~~s~lDl~~ay~qi~l~~~---------~~~---------~taF~~~~g--~y~~~~lpfGl~~ap~~ 157 (460)
+-++...++++.||...||++.|-.||-++- |.- ..+.+|..+ ++++.-.|+|-..||-+
T Consensus 349 i~~~~n~f~gcnw~ie~DLkkcfdtIphd~LI~eL~~rIkdk~fidL~~kll~AGy~ten~ry~~~~lGtpqgsvvspil 428 (796)
T KOG4768|consen 349 ILKTHNLFRGCNWFIEVDLKKCFDTIPHDELIIELQKRIKDKGFIDLNYKLLRAGYTTENARYHVEFLGTPQGSVVSPIL 428 (796)
T ss_pred HHHHHHHhhccceEEechHHHHhccccHHHHHHHHHHHHhhhhHHHHHHHHHhcCccccccceecccccccccccCCchh
Confidence 3455677889999999999999999984321 110 123455554 46788899999999998
Q ss_pred HHHHHHHHHHHHH-----------------------------------------------------hcCC---EEEEEec
Q psy4044 158 FAKLTNWIANYLR-----------------------------------------------------NLGM---RVIVYLD 181 (460)
Q Consensus 158 fq~~~~~il~~l~-----------------------------------------------------~~g~---~v~~YvD 181 (460)
..-+++.+-..++ ..|. .-+.|-|
T Consensus 429 ~nifL~~LDk~Lenk~~nefn~~~~~~~rhs~yr~L~~~iakaKl~s~~sKtirlrd~~qrn~~n~~~gfkr~~yVRyad 508 (796)
T KOG4768|consen 429 CNIFLRELDKRLENKHRNEFNAGHLRSARHSKYRNLSDSIAKAKLTSGMSKTIRLRDGVQRNETNDTAGFKRLMYVRYAD 508 (796)
T ss_pred HHHHHHHHHHHHHHHHHhhhcccCcccccChhhhhHHHHHHHHHHhhhhhhhhhhhhcccccccCCccccceeeEEEecC
Confidence 8777766543332 0111 1357999
Q ss_pred CeEEec-CCHHHHHHHHHHHHHHHHHcCCccccccccccc-ccccccccEEEcCC
Q psy4044 182 DLLLGN-QDSVLLRSQARAAVATLQSLRWSVNLERSVLWP-VQTCQYLGIMWNPT 234 (460)
Q Consensus 182 Dili~s-~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~~-~~~v~~LG~~i~~~ 234 (460)
|+++.- .+..++.+.++.+-..+...|+..|++|.+... ...+.|||+.|+..
T Consensus 509 d~ii~v~GS~nd~K~ilr~In~f~sslGls~n~~kt~it~S~eg~~flg~nis~t 563 (796)
T KOG4768|consen 509 DIIIGVWGSVNDCKQILRDINNFLSSLGLSNNSSKTQITVSREGTHFLGYNISTT 563 (796)
T ss_pred CEEEEEeccHHHHHHHHHHHHHHHHhhCcccCcccceEEeeccceeeeeceeccC
Confidence 998875 478888888999999999999999999985533 23478999998765
No 30
>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=83.86 E-value=3.3 Score=39.88 Aligned_cols=63 Identities=17% Similarity=0.187 Sum_probs=47.2
Q ss_pred CCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccccccccc---cccccccccEEEcCCCC
Q psy4044 173 GMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLW---PVQTCQYLGIMWNPTLD 236 (460)
Q Consensus 173 g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~---~~~~v~~LG~~i~~~g~ 236 (460)
...+.+|=||.++..++. ........+.+.+.++|+.++.+|.... ...++.|||+.+.....
T Consensus 194 ~~~~~~~GDD~li~~~~~-~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~Fl~r~f~~~~~ 259 (278)
T cd01699 194 NVRLLNYGDDCLLSVEKA-DDKFNLETLAEWLKEYGLTMTDEDKVESPFRPLEEVEFLKRRFVLDEG 259 (278)
T ss_pred ceEEEEEcCCeEEEechh-HhhhCHHHHHHHHHHcCCEeCCcccCCCCCCCHhhCcccCCccEECCC
Confidence 346889999999988765 2233456677888889999999988542 45689999988765443
No 31
>PHA00028 rep RNA replicase, beta subunit
Probab=75.75 E-value=5.3 Score=41.41 Aligned_cols=35 Identities=23% Similarity=0.419 Sum_probs=30.6
Q ss_pred EEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCccccccc
Q psy4044 175 RVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERS 216 (460)
Q Consensus 175 ~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~ 216 (460)
.|.+|=|||+|-++ ....+++.|.-.||..|.+|.
T Consensus 335 ti~VYGDDIIvps~-------~a~~li~vlsyvgF~pN~kKT 369 (561)
T PHA00028 335 TISVYGDDIIVPTE-------VAPPLINVLSYVGFMPNLKKT 369 (561)
T ss_pred eeEEecCceEeehh-------hhHHHHHHHHHhceecCCccc
Confidence 68999999999775 556678889999999999998
No 32
>PF05869 Dam: DNA N-6-adenine-methyltransferase (Dam); InterPro: IPR008593 This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences [].; GO: 0003677 DNA binding, 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0032775 DNA methylation on adenine
Probab=69.81 E-value=4.4 Score=36.66 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=35.6
Q ss_pred CCCCCcccChHHHHHHHHhcCCCccceecCcccccccccC
Q psy4044 397 KELPDWHLLPEVTQHIFAQWGVPEIDLFATANSAAFLVQG 436 (460)
Q Consensus 397 ~~~~~~~l~~~~~~~i~~~~~~~~id~fa~~~~~~~~~~~ 436 (460)
...++|.-.+++|+.+...||.-++|.+|++.|++|..|-
T Consensus 9 ~~~d~W~TP~~lf~~l~~~fg~f~LD~aa~~~Na~~~~y~ 48 (181)
T PF05869_consen 9 SDKDEWQTPPELFDALNREFGPFDLDPAASDENAKCPRYY 48 (181)
T ss_pred cCCCCCcCCHHHHHHHHHHhCCccccccCCCCChhhhhhc
Confidence 4667999999999999999999999999999999995443
No 33
>PF03431 RNA_replicase_B: RNA replicase, beta-chain ; InterPro: IPR005093 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This is a family of Leviviridae RNA replicases.; GO: 0003968 RNA-directed RNA polymerase activity, 0019079 viral genome replication; PDB: 3MMP_G 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A.
Probab=64.22 E-value=8.7 Score=39.39 Aligned_cols=128 Identities=16% Similarity=0.197 Sum_probs=57.1
Q ss_pred ceEEEEecccccccccc-------CCCC-------cceeEEEEcCeeEEEccc-CccCCCchHHHHHHHHHHH-HHH---
Q psy4044 109 DFLVKIDLSQAYFHVPI-------RPSH-------QRFLSVVYRDTLYCMTCL-PFGLASAPQVFAKLTNWIA-NYL--- 169 (460)
Q Consensus 109 ~~~s~lDl~~ay~qi~l-------~~~~-------~~~taF~~~~g~y~~~~l-pfGl~~ap~~fq~~~~~il-~~l--- 169 (460)
.-+.++||++|=-.|.+ .|+- +-..+. ..+..++|..+ .||- .--.-.+.++-..+ ..+
T Consensus 244 ~~laTIDLSsASDsis~~Lv~~llPp~~~~~l~~lRs~~~~-l~g~~~~~ek~ssMGN-GfTFELeSlif~ai~rs~~~~ 321 (542)
T PF03431_consen 244 GSLATIDLSSASDSISLWLVELLLPPHWYRYLTDLRSPYGS-LDGKVIRWEKISSMGN-GFTFELESLIFWAIARSVCEL 321 (542)
T ss_dssp SSEEEEEBTTCCCT-BHHHHHHHS-HHHHHHHHHHS-SEEE--TS-EEE-SBS--TTS-TTHHHHHHHHHHHHHHHHHHH
T ss_pred ccceeEeccccccHhHHHHHHHhCCHHHHHHHHHhccccce-ECCEEEehhhhhccCC-ceeEeHHHHHHHHHHHHHHHH
Confidence 36889999999887753 1111 111122 25567777655 3332 11112222222222 111
Q ss_pred -HhcCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccccccccccc-----cccccccEEEcCCCCcccCCcc
Q psy4044 170 -RNLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLWPV-----QTCQYLGIMWNPTLDSKSLPLE 243 (460)
Q Consensus 170 -~~~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~~~-----~~v~~LG~~i~~~g~~~~~p~~ 243 (460)
......|.+|=|||++-++ ....+++.|.-.||..|.+|.-+.+. -.--|.|+.|.+-- ++.|-.
T Consensus 322 ~~~~~~~v~iYGDDIIvp~~-------~~~~l~~~l~y~gF~~N~~KTF~~G~FRESCG~h~f~g~DVtPfY--ik~pi~ 392 (542)
T PF03431_consen 322 LFGDTGTVRIYGDDIIVPSE-------CAPDLIEVLSYVGFKPNLKKTFWTGPFRESCGAHYFDGVDVTPFY--IKRPID 392 (542)
T ss_dssp CT--GGG-EEETTEEEEEGG-------GHHHHHHHHHHCT--B-CCC-BSSSSEEEETTEEEETTEE---------S---
T ss_pred HcCCCCeeEEecCcEEechh-------hhHHHHHHHHHhCcccCcccccccccchhhhhhhhcCCccccceE--eccccc
Confidence 1111258899999999875 44567788999999999999832220 01125566655544 334555
Q ss_pred chHH
Q psy4044 244 KQST 247 (460)
Q Consensus 244 k~~~ 247 (460)
.+..
T Consensus 393 ~l~d 396 (542)
T PF03431_consen 393 NLPD 396 (542)
T ss_dssp SHHH
T ss_pred CHHH
Confidence 4444
No 34
>PF05919 Mitovir_RNA_pol: Mitovirus RNA-dependent RNA polymerase; InterPro: IPR008686 This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana [].
Probab=63.30 E-value=98 Score=32.39 Aligned_cols=145 Identities=20% Similarity=0.234 Sum_probs=85.2
Q ss_pred cccceEeecCCCCeee--eeecc---cc--------------CC-CCccC-CCccchhhhccCCceEEEEeccccccccc
Q psy4044 66 VHDLTLLLSSRDGFQD--LGDRA---FL--------------SL-KKFHL-INHFRVPDFLQRGDFLVKIDLSQAYFHVP 124 (460)
Q Consensus 66 ~sp~~~V~Kk~g~~R~--~~D~r---~~--------------~~-~~~pl-p~i~~ll~~l~~~~~~s~lDl~~ay~qi~ 124 (460)
..-+.++..+.||.|+ .+||- .+ .- ..|-. +.++-+..... .+.+..+||++|=-..|
T Consensus 85 ~gkLs~~~d~~gK~Ri~Am~D~~tQ~~L~PlH~~lf~~Lr~ip~DgTF~Q~~~~~~~~~~~~-~~~~~S~DLsaATDR~P 163 (498)
T PF05919_consen 85 LGKLSIKEDPEGKVRIFAMVDYWTQCVLKPLHDWLFSILRRIPQDGTFDQEPPFDRLVDSMK-EKYFYSFDLSAATDRFP 163 (498)
T ss_pred hcceEEeEcCCCceEEEEEEeHHHHHhhHHHHHHHHHHHhcCCCCCCcCCCCchhhHhhccc-CCceEEEeecccccccc
Confidence 3445677788899998 46765 11 11 12222 22222222222 22278899999998888
Q ss_pred cCCC---------------------CcceeEEEEcCeeEEEcc-cCccCCCchHHHHHHHHHHHHH--HHhcC-C---EE
Q psy4044 125 IRPS---------------------HQRFLSVVYRDTLYCMTC-LPFGLASAPQVFAKLTNWIANY--LRNLG-M---RV 176 (460)
Q Consensus 125 l~~~---------------------~~~~taF~~~~g~y~~~~-lpfGl~~ap~~fq~~~~~il~~--l~~~g-~---~v 176 (460)
|.=. ++++ +...++..+|.+ =|||.-+|=++|...-.-+.+. .+..+ . .-
T Consensus 164 i~lQ~~il~~l~~~~~a~~W~~llv~r~~--~~~~~~~v~y~vGQPmGa~SSW~~~altHH~iV~~aA~~~~~~~~f~~Y 241 (498)
T PF05919_consen 164 IVLQERILSYLFGDSFASSWRSLLVGRPY--LKPNGDEVRYSVGQPMGAYSSWAMFALTHHLIVQYAAERVGGGSRFTDY 241 (498)
T ss_pred HHHHHHHHHHHhCchHHHHHHHHHcCCcc--ccCCCCeEEEecCCcchhccccHHHHhhHHHHHHHHHHHhhccCCCCce
Confidence 6321 1112 123345556654 5999999999987666555522 22111 1 23
Q ss_pred EEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccccccccc
Q psy4044 177 IVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNLERSVLW 219 (460)
Q Consensus 177 ~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~~K~~~~ 219 (460)
.+-=|||+|..+. ..+.-...+.+.|..+|..|+...
T Consensus 242 ~iLGDDivi~~~~------vA~~Y~~~m~~Lgv~is~~Ks~vS 278 (498)
T PF05919_consen 242 IILGDDIVIANDK------VAKQYLSIMTDLGVEISLSKSHVS 278 (498)
T ss_pred EEEcCcEEEcCHH------HHHHHHHHHHHcCceeccCccccc
Confidence 3456888886542 334456778889999999998543
No 35
>PF00680 RdRP_1: RNA dependent RNA polymerase; InterPro: IPR001205 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This entry represents RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses viruses. It is part of the genome polyprotein that contains other polypeptides such as coat proteins VP1 to VP4, core proteins P2A to P2C and P3A, genome-linked protein VPG and picornain 3C (3.4.22.28 from EC). Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [, ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SFU_C 3NAH_A 3UR0_C 3UPF_C 3SFG_A 3NAI_C 3QID_B 3UQS_A 3OLB_M 3OLA_M ....
Probab=50.60 E-value=1.3e+02 Score=31.65 Aligned_cols=61 Identities=18% Similarity=0.255 Sum_probs=46.5
Q ss_pred CEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCCcccc-ccccc----ccccccccccEEEcCCC
Q psy4044 174 MRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRWSVNL-ERSVL----WPVQTCQYLGIMWNPTL 235 (460)
Q Consensus 174 ~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl~l~~-~K~~~----~~~~~v~~LG~~i~~~g 235 (460)
..+.+|=||.++..+..-... ....+.+.+++.|+.+.. +|..- .+-.++.||...+....
T Consensus 344 ~~~i~YGDD~l~sv~~~~~~~-n~~~i~~~~~~~G~~~T~~dK~~~~~~~~~~~~v~FLkR~f~~~~ 409 (491)
T PF00680_consen 344 VKLIVYGDDNLISVPPEIDPW-NGETISEFLAELGLTYTDADKTGEFPPFRPLEEVSFLKRTFVPDP 409 (491)
T ss_dssp SEEEEETTEEEEEESSHHHHH-HHHHHHHHHHTTTEEEEESSTSSSCSSBBCTTTHEETTEEEEEET
T ss_pred eeeeeeccccchhhhcccccc-hhHHHHHHHHhcccccccccccCCccccCccccccccccceeecc
Confidence 357899999999988665555 788899999999999986 77632 22457899998874443
No 36
>TIGR01712 phage_N6A_met phage N-6-adenine-methyltransferase. This is a model for a phage-borne DNA N-6-adenine-methyltransferase.
Probab=40.83 E-value=21 Score=31.77 Aligned_cols=41 Identities=17% Similarity=0.102 Sum_probs=35.1
Q ss_pred CCCCCcccChHHHHHHHHhcCCCccceecCcccccccccCC
Q psy4044 397 KELPDWHLLPEVTQHIFAQWGVPEIDLFATANSAAFLVQGG 437 (460)
Q Consensus 397 ~~~~~~~l~~~~~~~i~~~~~~~~id~fa~~~~~~~~~~~~ 437 (460)
.+.+.|.=.+.+|..+.+.+|.-++|.+|+..|++|..+-.
T Consensus 9 ~~~D~W~TP~~lf~~L~~~~g~F~LD~~A~~~Na~c~~~~T 49 (166)
T TIGR01712 9 AVRDLWSTPREVFAYLEGRYGKFDLDAAASEENAVCAKFYT 49 (166)
T ss_pred hhCCcCCChHHHHHHHHhhcCceEEecCCCCCccchhhhcC
Confidence 35678888888999999999988999999999999966554
No 37
>PF12237 PCIF1_WW: Phosphorylated CTD interacting factor 1 WW domain; InterPro: IPR022035 This domain is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. It is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity.
Probab=34.43 E-value=35 Score=30.67 Aligned_cols=43 Identities=23% Similarity=0.293 Sum_probs=35.0
Q ss_pred CCcccChHHHHHHHHhcCCCccceecCcccccccccCCccccCC
Q psy4044 400 PDWHLLPEVTQHIFAQWGVPEIDLFATANSAAFLVQGGPLKFPD 443 (460)
Q Consensus 400 ~~~~l~~~~~~~i~~~~~~~~id~fa~~~~~~~~~~~~~~~~~~ 443 (460)
..+.+.+++|+.+.+.+|. +.+.||++.|+.+.-|..-..++|
T Consensus 44 ~q~a~p~~vf~~L~~~f~v-~~EcFASPlN~~~~~ycSaFpDtD 86 (176)
T PF12237_consen 44 LQAALPPEVFDALHKRFGV-SFECFASPLNCYFRQYCSAFPDTD 86 (176)
T ss_pred ccccCCHHHHHHHHHHcCC-CEEEecChhhhhHHHhcCcCcCcc
Confidence 3467899999999999996 799999999999877766654444
No 38
>PF12386 Peptidase_C71: Pseudomurein endo-isopeptidase Pei; InterPro: IPR022119 This peptidase has the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. It catalyses the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteristics of metal-activated peptidases.
Probab=23.16 E-value=1.8e+02 Score=24.33 Aligned_cols=65 Identities=6% Similarity=0.117 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhhCCcCCCcEEEEEeCchhhHHHHhhcCCCcchhhhHHHHHHHHHHHHcCCeEEEEEeCCCCC
Q psy4044 314 KEMFAVRSALERKLPVLQDKVVLIQSDNQTVVSYIHKEGGTKSFKLLREVEALFDLAVRHNITLMARYIPGKFN 387 (460)
Q Consensus 314 ~EllAi~~al~~~~~~l~g~~v~i~tD~~~l~~~l~~~~~~~~~~~~~~~r~i~~~~~~~~~~~~i~~vpg~~N 387 (460)
-|+++++..-+.+..|...+ .+|+.++..+.+ + |+.... ...-...+++.++|+++|+||.-+-|
T Consensus 21 ~~~~~~i~kr~~Y~~Yyn~q----~~~~~ti~~~~~-~-GiNCtD---~~Qlf~~v~~~lGY~Vq~~HVk~rc~ 85 (142)
T PF12386_consen 21 DSLYNIISKRCKYKYYYNSQ----KPNHETINKMRT-S-GINCTD---ACQLFYRVIESLGYDVQFEHVKCRCN 85 (142)
T ss_pred HHHHHHHHhhcccceeccCC----CCcHHHHHHHHh-c-CCCchh---HHHHHHHHHHhcCceEEEEEEEEEec
Confidence 57788887777777776554 466677755554 2 343322 22333345566799999999987744
No 39
>PF08902 DUF1848: Domain of unknown function (DUF1848); InterPro: IPR014998 This group of proteins are functionally uncharacterised. The C terminus contains a cluster of cysteines that are similar to the iron-sulphur cluster found at the N terminus of IPR007197 from INTERPRO.
Probab=21.40 E-value=7.4e+02 Score=23.90 Aligned_cols=83 Identities=14% Similarity=0.173 Sum_probs=57.4
Q ss_pred ccccCCCCcceeEEEEcC-----------------eeEEEcccCccCCC---chHHHHHHHHHHHHHHHhcCC-EEEEEe
Q psy4044 122 HVPIRPSHQRFLSVVYRD-----------------TLYCMTCLPFGLAS---APQVFAKLTNWIANYLRNLGM-RVIVYL 180 (460)
Q Consensus 122 qi~l~~~~~~~taF~~~~-----------------g~y~~~~lpfGl~~---ap~~fq~~~~~il~~l~~~g~-~v~~Yv 180 (460)
.|.++|++..-..|-|++ -.|+|+..|+|-.. .|..-+ .++.....-...|. .|.-=.
T Consensus 40 rv~l~p~~Vd~iVFWTKnp~P~l~~L~~l~~~gy~~yfq~Tit~Y~~~lEp~vP~~~~-~i~~f~~Ls~~iG~~rViWRY 118 (266)
T PF08902_consen 40 RVSLSPEDVDCIVFWTKNPAPFLPYLDELDERGYPYYFQFTITGYGKDLEPNVPPKDE-RIETFRELSERIGPERVIWRY 118 (266)
T ss_pred EEEcChhcceEEEEecCCcHHHHhhHHHHHhCCCceEEEEEeCCCCccccCCCCCHHH-HHHHHHHHHHHHCCCcEEEec
Confidence 467888999999998876 24789999999743 444333 44433333333455 455567
Q ss_pred cCeEEecC-CHHHHHHHHHHHHHHHH
Q psy4044 181 DDLLLGNQ-DSVLLRSQARAAVATLQ 205 (460)
Q Consensus 181 DDili~s~-~~~~~~~~l~~v~~~l~ 205 (460)
|-|++..+ +.+.|.+..+.+.+.|.
T Consensus 119 DPIil~~~~~~~~h~~~F~~la~~L~ 144 (266)
T PF08902_consen 119 DPIILTDKYTVDYHLEAFERLAEALA 144 (266)
T ss_pred CCEeECCCCCHHHHHHHHHHHHHHHh
Confidence 88888776 67888888888888887
No 40
>PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B.
Probab=21.23 E-value=3.9e+02 Score=21.10 Aligned_cols=64 Identities=9% Similarity=0.057 Sum_probs=41.6
Q ss_pred EEcccCccCCCchHHHHHHHHHHHHHHHhcCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcCC
Q psy4044 143 CMTCLPFGLASAPQVFAKLTNWIANYLRNLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLRW 209 (460)
Q Consensus 143 ~~~~lpfGl~~ap~~fq~~~~~il~~l~~~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~gl 209 (460)
+++++|+|-. .+ -+...+..+...++..|....+-==--.|-++ .++....++++.+.+.+.|.
T Consensus 2 ei~v~P~g~~-~~-s~~~~V~~~i~~i~~sgl~y~v~pm~T~iEGe-~dev~~~i~~~~e~~~~~G~ 65 (92)
T PF01910_consen 2 EISVIPIGTG-GE-SVSAYVAEAIEVIKESGLKYEVGPMGTTIEGE-LDEVMALIKEAHEALFEAGA 65 (92)
T ss_dssp EEEEEEESSS-SS-HHHHHHHHHHHHHHTSSSEEEEETTEEEEEEE-HHHHHHHHHHHHHHHHCTTS
T ss_pred EEEEEeCCCC-CC-CHHHHHHHHHHHHHHcCCceEEcCCccEEEec-HHHHHHHHHHHHHHHHHcCC
Confidence 4678899953 22 23345566667777777654433223344455 88899999999888887764
No 41
>PRK10270 putative aminodeoxychorismate lyase; Provisional
Probab=21.02 E-value=1.5e+02 Score=29.62 Aligned_cols=72 Identities=13% Similarity=-0.004 Sum_probs=50.3
Q ss_pred EEEcCeeEEEcccCccCCCchHHHHHHHHHHHHHHHhcCCEEEEEecCeEEecCCHHHHHHHHHHHHHHHHHcC
Q psy4044 135 VVYRDTLYCMTCLPFGLASAPQVFAKLTNWIANYLRNLGMRVIVYLDDLLLGNQDSVLLRSQARAAVATLQSLR 208 (460)
Q Consensus 135 F~~~~g~y~~~~lpfGl~~ap~~fq~~~~~il~~l~~~g~~v~~YvDDili~s~~~~~~~~~l~~v~~~l~~~g 208 (460)
..+|+.+|.+.-||=|--++|+. ..++.++.+-...-.+.++=-|.--.+++|.+||..++++....+++.+
T Consensus 267 ~~sPYNTY~~~GLPPgPI~nPg~--~ai~Aal~P~~~dyLYFva~~~G~h~Fs~T~~EH~~~v~ky~~~~~~~~ 338 (340)
T PRK10270 267 TPTAYNTYTITGLPPGPIATPGE--ASLKAAAHPAKTPYLYFVADGKGGHTFNTNLASHNRSVQDYLKVLKEKN 338 (340)
T ss_pred CCCCcccCccCCCCCCcCcCCCH--HHHHHHhCCCCCCeEEEEEeCCCCEEeCCCHHHHHHHHHHHHHHHHhcc
Confidence 45788999999999999999985 5566666443211112222234456789999999999999877766544
Done!