Query psy3306
Match_columns 535
No_of_seqs 345 out of 2273
Neff 9.3
Searched_HMMs 46136
Date Fri Aug 16 21:37:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3306.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3306hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01650 RT_nLTR_like RT_nLTR: 99.7 1.7E-17 3.7E-22 157.1 6.9 106 44-157 106-220 (220)
2 cd01651 RT_G2_intron RT_G2_int 99.7 6.1E-17 1.3E-21 154.0 7.1 122 2-157 91-226 (226)
3 cd01648 TERT TERT: Telomerase 99.7 1.7E-16 3.7E-21 134.0 7.4 99 38-158 13-119 (119)
4 PF00078 RVT_1: Reverse transc 99.7 2.7E-17 5.9E-22 154.9 1.9 126 2-157 85-214 (214)
5 cd01709 RT_like_1 RT_like_1: A 99.6 3.3E-15 7.2E-20 143.9 13.5 116 2-128 43-163 (346)
6 cd03487 RT_Bac_retron_II RT_Ba 99.6 1.4E-15 3.1E-20 142.8 9.5 115 2-160 78-198 (214)
7 cd01646 RT_Bac_retron_I RT_Bac 99.6 2.1E-15 4.5E-20 134.6 4.4 128 2-160 17-147 (158)
8 cd00304 RT_like RT_like: Rever 99.4 1.5E-12 3.2E-17 106.4 7.7 71 45-122 12-85 (98)
9 cd03714 RT_DIRS1 RT_DIRS1: Rev 98.8 1.2E-08 2.6E-13 86.3 7.5 73 43-121 32-106 (119)
10 KOG4768|consensus 98.7 7.2E-08 1.6E-12 97.9 10.5 184 10-213 389-643 (796)
11 cd01645 RT_Rtv RT_Rtv: Reverse 98.7 1.5E-08 3.3E-13 95.0 4.5 73 42-120 126-201 (213)
12 COG0328 RnhA Ribonuclease HI [ 98.7 8.1E-08 1.8E-12 82.9 7.8 69 367-436 2-74 (154)
13 PF00075 RNase_H: RNase H; In 98.4 3.8E-07 8.3E-12 78.6 5.3 65 367-436 2-68 (132)
14 PRK13907 rnhA ribonuclease H; 98.4 1.3E-06 2.7E-11 74.9 7.8 68 369-436 2-72 (128)
15 PRK08719 ribonuclease H; Revie 98.3 1.1E-06 2.4E-11 76.7 6.6 66 367-436 3-77 (147)
16 cd03715 RT_ZFREV_like RT_ZFREV 98.3 5E-07 1.1E-11 84.6 4.7 74 42-121 122-198 (210)
17 KOG1005|consensus 98.3 1.6E-06 3.5E-11 91.9 8.2 104 10-127 606-715 (888)
18 PRK00203 rnhA ribonuclease H; 98.3 1.9E-06 4.2E-11 75.9 6.7 67 368-436 3-72 (150)
19 PRK06548 ribonuclease H; Provi 98.3 3.1E-06 6.6E-11 74.6 7.8 67 367-436 4-72 (161)
20 KOG3752|consensus 98.1 6.6E-06 1.4E-10 80.1 7.6 71 366-436 210-287 (371)
21 PRK07708 hypothetical protein; 98.1 1E-05 2.3E-10 75.3 8.2 72 365-436 70-151 (219)
22 cd06222 RnaseH RNase H (RNase 97.9 3.5E-05 7.5E-10 65.2 7.5 67 370-436 1-72 (130)
23 PRK07238 bifunctional RNase H/ 97.6 0.00015 3.3E-09 74.2 8.3 68 368-436 2-76 (372)
24 cd01647 RT_LTR RT_LTR: Reverse 97.6 6.1E-05 1.3E-09 67.9 4.5 72 43-121 94-165 (177)
25 cd01644 RT_pepA17 RT_pepA17: R 95.8 0.0072 1.6E-07 56.4 3.1 70 39-114 98-172 (213)
26 PF13966 zf-RVT: zinc-binding 95.3 0.0084 1.8E-07 47.1 1.5 31 467-497 52-83 (86)
27 cd01699 RNA_dep_RNAP RNA_dep_R 93.2 0.22 4.7E-06 48.7 6.6 98 12-122 133-239 (278)
28 PF13456 RVT_3: Reverse transc 92.1 0.14 3.1E-06 39.8 3.0 32 405-436 1-32 (87)
29 PF09004 DUF1891: Domain of un 85.5 0.14 3.1E-06 33.7 -1.1 41 163-205 1-41 (42)
30 CHL00002 matK maturase K 78.4 24 0.00052 37.4 11.3 168 70-254 272-455 (504)
31 COG3344 Retron-type reverse tr 68.1 1.7 3.8E-05 43.5 0.1 46 40-85 234-281 (328)
32 PF05380 Peptidase_A17: Pao re 65.1 27 0.00059 30.8 7.1 64 367-432 80-159 (159)
33 PF00680 RdRP_1: RNA dependent 55.1 21 0.00046 37.9 5.6 96 13-121 280-388 (491)
34 PF00336 DNA_pol_viral_C: DNA 42.8 83 0.0018 28.7 6.2 58 368-436 94-151 (245)
35 PF00098 zf-CCHC: Zinc knuckle 42.2 17 0.00037 19.1 1.2 17 476-495 2-18 (18)
36 PF13696 zf-CCHC_2: Zinc knuck 41.4 15 0.00032 22.7 1.0 20 473-495 7-26 (32)
37 PF07727 RVT_2: Reverse transc 36.4 8.9 0.00019 36.7 -0.8 43 43-89 122-181 (246)
38 PF12633 Adenyl_cycl_N: Adenyl 32.4 71 0.0015 29.4 4.3 27 89-115 128-154 (204)
39 PF08388 GIIM: Group II intron 31.3 1.6E+02 0.0035 22.0 5.7 57 181-240 8-66 (80)
40 COG2093 DNA-directed RNA polym 30.0 39 0.00085 24.3 1.8 22 466-487 10-31 (64)
41 PF13917 zf-CCHC_3: Zinc knuck 28.8 74 0.0016 21.1 2.8 23 473-499 3-26 (42)
42 cd07049 BMC_EutL_repeat1 ethan 28.6 1.2E+02 0.0027 24.5 4.5 32 74-105 53-99 (103)
43 PF15322 PMSI1: Protein missin 25.7 43 0.00093 31.9 1.8 32 447-478 210-248 (311)
44 cd02974 AhpF_NTD_N Alkyl hydro 25.4 1.1E+02 0.0025 24.2 3.9 74 62-160 12-85 (94)
45 cd01414 SAICAR_synt_Sc non-met 23.6 27 0.00059 34.0 0.1 75 43-122 124-198 (279)
46 TIGR00081 purC phosphoribosyla 21.7 69 0.0015 30.3 2.3 111 2-121 61-182 (237)
47 PF05741 zf-nanos: Nanos RNA b 20.9 56 0.0012 23.1 1.2 21 475-495 34-54 (55)
48 PF06565 DUF1126: Repeat of un 20.7 60 0.0013 20.2 1.2 26 20-52 5-30 (33)
49 PF00325 Crp: Bacterial regula 20.1 1.1E+02 0.0023 19.0 2.1 27 506-532 6-32 (32)
No 1
>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=99.70 E-value=1.7e-17 Score=157.09 Aligned_cols=106 Identities=29% Similarity=0.623 Sum_probs=93.6
Q ss_pred CCCCCCchhHHHHHHHhhchhhhcC---------CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccc
Q psy3306 44 GIPQGGVASSTLFAIAINTITSYIH---------PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYF 114 (535)
Q Consensus 44 GvpQGs~LSP~Lf~l~~~~l~~~~~---------~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~l 114 (535)
|+|||++|||+||++|++++.+.+. ..+.+..||||+++++.+.. ..++..++.+.+|+..+|+++
T Consensus 106 GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~~~-----~~~~~~~~~~~~~~~~~gl~i 180 (220)
T cd01650 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKS-----RKLQELLQRLQEWSKESGLKI 180 (220)
T ss_pred CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEEeccceeeeccCCH-----HHHHHHHHHHHHHHHHcCCEE
Confidence 9999999999999999999998764 56789999999999988876 238999999999999999999
Q ss_pred cCCceeEEEecccCcCCCCCceeeecCeeeeeeccccceeeEe
Q psy3306 115 SPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVVDQFRFLGLTF 157 (535)
Q Consensus 115 n~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~i 157 (535)
|++||+++.++...... ..+..++..+..++.+||||++|
T Consensus 181 n~~Kt~~~~~~~~~~~~---~~~~~~~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 181 NPSKSKVMLIGNKKKRL---KDITLNGTPIEAVETFKYLGVTI 220 (220)
T ss_pred ChhheEEEEecCCCcch---hhhhhcCCcccCCCCCeeccccC
Confidence 99999999998876554 33677888899999999999875
No 2
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=99.67 E-value=6.1e-17 Score=153.99 Aligned_cols=122 Identities=25% Similarity=0.427 Sum_probs=101.7
Q ss_pred hhhhhCCCCChHHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC-------------
Q psy3306 2 RQLHKWNLRGHLPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH------------- 68 (535)
Q Consensus 2 ~~L~~~g~~~~~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~------------- 68 (535)
+.|+..|.++.++.++.+|+... +..+ + .......|||||+++||+||++|++++...+.
T Consensus 91 ~~l~~~~~~~~~~~~i~~~~~~~---~~~~---~-~~~~~~~GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~ 163 (226)
T cd01651 91 KILKRRIGDKRVLRLIRKWLKAG---VLED---G-KLVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPK 163 (226)
T ss_pred HHHHHhcccHHHHHHHHHHHhce---EccC---C-eEeCCCCCcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccc
Confidence 46788899999999999996432 2222 2 56678999999999999999999999987643
Q ss_pred -CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEEEecccCcCCCCCceeeecCeeeeee
Q psy3306 69 -PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVV 147 (535)
Q Consensus 69 -~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~ 147 (535)
.++...+||||+++++.++.. ++++++.+.+|+...||.+|++||+++.++ .
T Consensus 164 ~~~~~~~rY~DD~~i~~~~~~~------~~~~~~~i~~~~~~~gl~ln~~Kt~i~~~~---------------------~ 216 (226)
T cd01651 164 FRRLRYVRYADDFVIGVRGPKE------AEEIKELIREFLEELGLELNPEKTRITHFK---------------------S 216 (226)
T ss_pred cCceEEEEecCceEEecCCHHH------HHHHHHHHHHHHHHcCCeechhhcceeecC---------------------C
Confidence 557899999999999888765 788999999999999999999999998775 2
Q ss_pred ccccceeeEe
Q psy3306 148 DQFRFLGLTF 157 (535)
Q Consensus 148 ~~~kyLGv~i 157 (535)
+.+.|||+.|
T Consensus 217 ~~~~fLG~~~ 226 (226)
T cd01651 217 EGFDFLGFTF 226 (226)
T ss_pred CCCeeCCeEC
Confidence 4678999864
No 3
>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at
Probab=99.66 E-value=1.7e-16 Score=133.98 Aligned_cols=99 Identities=22% Similarity=0.242 Sum_probs=79.8
Q ss_pred ccccccCCCCCCchhHHHHHHHhhchhhhcC-------CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHH-hh
Q psy3306 38 DFSNVCGIPQGGVASSTLFAIAINTITSYIH-------PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFS-DQ 109 (535)
Q Consensus 38 ~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~-------~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~-~~ 109 (535)
.+...+|+|||++|||+||+++++.+.+.+. .......||||+++++.++.. +++.++.+.++. .+
T Consensus 13 ~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~~~~------~~~~~~~l~~~l~~~ 86 (119)
T cd01648 13 YYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSLDK------AIKFLNLLLRGFINQ 86 (119)
T ss_pred hhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCCHHH------HHHHHHHHHHhhHHh
Confidence 4667899999999999999999999887643 346689999999999877543 788999999997 99
Q ss_pred cCccccCCceeEEEecccCcCCCCCceeeecCeeeeeeccccceeeEec
Q psy3306 110 TGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVVDQFRFLGLTFD 158 (535)
Q Consensus 110 ~gl~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~i~ 158 (535)
.||.+|++||++...... ....+.+.|||+.|+
T Consensus 87 ~gl~iN~~Kt~~~~~~~~----------------~~~~~~~~flG~~i~ 119 (119)
T cd01648 87 YKTFVNFDKTQINFSFAQ----------------LDSSDLIPWCGLLIN 119 (119)
T ss_pred hCeEECcccceeeccccc----------------cCCCCccCceeEeeC
Confidence 999999999998643220 012356899999875
No 4
>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=99.65 E-value=2.7e-17 Score=154.86 Aligned_cols=126 Identities=25% Similarity=0.537 Sum_probs=107.6
Q ss_pred hhhhhCCCCChHHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC----CCceeEEee
Q psy3306 2 RQLHKWNLRGHLPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH----PSLSSSLFV 77 (535)
Q Consensus 2 ~~L~~~g~~~~~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~----~~~~~~~yA 77 (535)
+.|...+.++.++.||.++++++...+.+++. . .......|+|||+++||+||++|++++.+.+. +++.+..||
T Consensus 85 ~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~-~-~~~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~ 162 (214)
T PF00078_consen 85 RKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGD-L-SPYFQKRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLRYA 162 (214)
T ss_dssp GGGGEEEEECCSCHHHHHHHHHHHH-EECGCS-S-SEEEEESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEEET
T ss_pred cccccccccccccccccccccccccccccccc-c-ccccccccccccccccchhhccccccccccccccccccccceEec
Confidence 45667788999999999999999999999776 3 56788999999999999999999999998754 468899999
Q ss_pred cceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEEEecccCcCCCCCceeeecCeeeeeeccccceeeEe
Q psy3306 78 DDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVVDQFRFLGLTF 157 (535)
Q Consensus 78 DD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~i 157 (535)
||+++++.++.. +++.++.+.+|+.++||.+|++||+.++ ..+.++|||+.|
T Consensus 163 DD~~i~~~~~~~------~~~~~~~i~~~~~~~gl~ln~~Kt~~~~----------------------~~~~~~~lG~~i 214 (214)
T PF00078_consen 163 DDILIISKSKEE------LQKILEKISQWLEELGLKLNPEKTKILH----------------------PSDSVKFLGYVI 214 (214)
T ss_dssp TEEEEEESSHHH------HHHHHHHHHHHHHHTTSBCSSTTTSCS------------------------ESSEEETTEEE
T ss_pred cccEEEECCHHH------HHHHHHHHHHHHHHCCCEEChHHEEEEe----------------------CCCCEEEEeEEC
Confidence 999999988544 8999999999999999999999999764 357789999875
No 5
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=99.63 E-value=3.3e-15 Score=143.94 Aligned_cols=116 Identities=15% Similarity=0.198 Sum_probs=94.0
Q ss_pred hhhhhCCCCChHHHHHHHhcCCceEEEEE--CCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC---CCceeEEe
Q psy3306 2 RQLHKWNLRGHLPNFLFKYMDERSFKIRL--NNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH---PSLSSSLF 76 (535)
Q Consensus 2 ~~L~~~g~~~~~~~~I~~~l~~r~~~v~~--~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~y 76 (535)
..|+.+|++.+++.+|+.|| .+-|+. +|... ....-.+|+|||+++||+|-|+|++.+-..++ +++.+..|
T Consensus 43 ~vL~~~~~~~~wL~li~r~L---~APl~~~~dg~~~-~~r~r~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RY 118 (346)
T cd01709 43 AVLKFFGVPEKWLDFFKKFL---EAPLRFVADGPDA-PPRIRKRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRL 118 (346)
T ss_pred HHHHHhCCCHHHHHHHHHHH---hCceeecCCCCcc-cccccCCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEE
Confidence 46778899999999999999 445655 44223 45667899999999999999999997776665 57889999
Q ss_pred ecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEEEecccC
Q psy3306 77 VDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKY 128 (535)
Q Consensus 77 ADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~~~~~~~ 128 (535)
|||++++... . +..++.+.+.++++..||++|++||.++++....
T Consensus 119 aDD~vi~~~~-~------~a~~aw~~i~~fl~~lGLelN~eKT~iV~~~~~~ 163 (346)
T cd01709 119 HDDLWFWGQP-E------TCAKAWKAIQEFAKVMGLELNKEKTGSVYLSDDT 163 (346)
T ss_pred cCeEEEEcCH-H------HHHHHHHHHHHHHHHcCceeccccceEEEeccCC
Confidence 9999999432 1 2566777889999999999999999999887653
No 6
>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=99.62 E-value=1.4e-15 Score=142.83 Aligned_cols=115 Identities=15% Similarity=0.222 Sum_probs=94.1
Q ss_pred hhhhhCCCC-ChHHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC-----CCceeEE
Q psy3306 2 RQLHKWNLR-GHLPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH-----PSLSSSL 75 (535)
Q Consensus 2 ~~L~~~g~~-~~~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~-----~~~~~~~ 75 (535)
+.|++.|.+ +.+..+|..+++. ..|||||+|+||+||++|++++...+. .++.+..
T Consensus 78 ~~l~~~~~~~~~~~~~l~~~~~~------------------~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~R 139 (214)
T cd03487 78 GVFRSLGYFSPDVATILAKLCTY------------------NGHLPQGAPTSPALSNLVFRKLDERLSKLAKSNGLTYTR 139 (214)
T ss_pred HHHHHcCCCCHHHHHHHHHHHhC------------------CCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEE
Confidence 467788888 7788888877632 239999999999999999999887653 4688999
Q ss_pred eecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEEEecccCcCCCCCceeeecCeeeeeeccccceee
Q psy3306 76 FVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVVDQFRFLGL 155 (535)
Q Consensus 76 yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv 155 (535)
||||+++++.+... ..++++++.+..|+.+.||.+|++||+++..+ +.+.+||+
T Consensus 140 YaDD~~i~~~~~~~----~~~~~~~~~i~~~l~~~gL~ln~~Kt~i~~~~----------------------~~~~~~G~ 193 (214)
T cd03487 140 YADDITFSSNKKLK----EALDKLLEIIRSILSEEGFKINKSKTRISSKG----------------------SRQIVTGL 193 (214)
T ss_pred EeccEEEEccccch----hHHHHHHHHHHHHHHHCCceeCCCceEEccCC----------------------CCcEEEEE
Confidence 99999999888762 23789999999999999999999999987532 34588999
Q ss_pred Eeccc
Q psy3306 156 TFDKK 160 (535)
Q Consensus 156 ~i~~~ 160 (535)
.+.+.
T Consensus 194 ~i~~~ 198 (214)
T cd03487 194 VVNNG 198 (214)
T ss_pred EEeCC
Confidence 99764
No 7
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=99.56 E-value=2.1e-15 Score=134.61 Aligned_cols=128 Identities=22% Similarity=0.279 Sum_probs=98.5
Q ss_pred hhhhhCCCCChHHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC---CCceeEEeec
Q psy3306 2 RQLHKWNLRGHLPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH---PSLSSSLFVD 78 (535)
Q Consensus 2 ~~L~~~g~~~~~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yAD 78 (535)
+.|.+.+.++..+.++..+... ..+.... .......|+|||+++||+|+++++.++...+. .++....|||
T Consensus 17 ~~l~~~~~~~~~~~~~~~~~~~-----~~~~~~~-~~~~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~D 90 (158)
T cd01646 17 WALHGKIKAKQLLKLLRLLGNL-----LDLLLLS-SQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVD 90 (158)
T ss_pred HHHHhhhhhHhhhhhHHHHHHH-----HHHHHHh-ccCCCCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecC
Confidence 4566677777777776433321 1122223 45667889999999999999999999887664 5788999999
Q ss_pred ceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEEEecccCcCCCCCceeeecCeeeeeeccccceeeEec
Q psy3306 79 DFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVVDQFRFLGLTFD 158 (535)
Q Consensus 79 D~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~i~ 158 (535)
|+++++..+.. ++++++.+.+|+.+.||.+|++||+++.++... ..+.+||..+.
T Consensus 91 D~~i~~~~~~~------~~~~~~~i~~~l~~~gL~ln~~Kt~~~~~~~~~-------------------~~~~flg~~~~ 145 (158)
T cd01646 91 DIRIFADSKEE------AEEILEELKEFLAELGLSLNLSKTEILPLPEGT-------------------ASKDFLGYRFS 145 (158)
T ss_pred cEEEEcCCHHH------HHHHHHHHHHHHHHCCCEEChhhceeeecCCCC-------------------ccccccceEee
Confidence 99999976544 788999999999999999999999998764421 45688888886
Q ss_pred cc
Q psy3306 159 KK 160 (535)
Q Consensus 159 ~~ 160 (535)
..
T Consensus 146 ~~ 147 (158)
T cd01646 146 PI 147 (158)
T ss_pred hh
Confidence 53
No 8
>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=99.37 E-value=1.5e-12 Score=106.36 Aligned_cols=71 Identities=24% Similarity=0.393 Sum_probs=64.2
Q ss_pred CCCCCchhHHHHHHHhhchhhhcC---CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeE
Q psy3306 45 IPQGGVASSTLFAIAINTITSYIH---PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQC 121 (535)
Q Consensus 45 vpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~ 121 (535)
+|||+++||+||+++++.+...+. .++....||||+++.+.+. . ++..+..+.+++.+.|+.+|++||+.
T Consensus 12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~-~------~~~~~~~l~~~l~~~gl~ln~~Kt~~ 84 (98)
T cd00304 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE-Q------QAVKKRELEEFLARLGLNLSDEKTQF 84 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH-H------HHHHHHHHHHHHHHcCcEEChheeEE
Confidence 999999999999999999998763 5788999999999998876 2 78888999999999999999999997
Q ss_pred E
Q psy3306 122 V 122 (535)
Q Consensus 122 ~ 122 (535)
.
T Consensus 85 ~ 85 (98)
T cd00304 85 T 85 (98)
T ss_pred e
Confidence 5
No 9
>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.
Probab=98.81 E-value=1.2e-08 Score=86.35 Aligned_cols=73 Identities=12% Similarity=0.247 Sum_probs=57.7
Q ss_pred cCCCCCCchhHHHHHHHhhchhhhcC-CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHH-HHhhcCccccCCcee
Q psy3306 43 CGIPQGGVASSTLFAIAINTITSYIH-PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNH-FSDQTGLYFSPQKTQ 120 (535)
Q Consensus 43 ~GvpQGs~LSP~Lf~l~~~~l~~~~~-~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~-w~~~~gl~ln~~Kt~ 120 (535)
.-+|||-..||.+|.-+|+.+...+. .++.+..|+||+.|.+.+.. . .+..+..+.+ .++++|+.+|++||+
T Consensus 32 ~~mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~~~---~---~~~~~~~l~~~~l~~~gl~ln~~K~~ 105 (119)
T cd03714 32 KALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASSIK---T---SEAVLRHLRATLLANLGFTLNLEKSK 105 (119)
T ss_pred EecCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCcHH---H---HHHHHHHHHHHHHHHcCCccChhhcE
Confidence 34899999999999999999988654 45678999999999888622 2 3344444444 689999999999999
Q ss_pred E
Q psy3306 121 C 121 (535)
Q Consensus 121 ~ 121 (535)
+
T Consensus 106 ~ 106 (119)
T cd03714 106 L 106 (119)
T ss_pred e
Confidence 5
No 10
>KOG4768|consensus
Probab=98.71 E-value=7.2e-08 Score=97.93 Aligned_cols=184 Identities=16% Similarity=0.183 Sum_probs=113.6
Q ss_pred CChHHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC---------------------
Q psy3306 10 RGHLPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH--------------------- 68 (535)
Q Consensus 10 ~~~~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~--------------------- 68 (535)
+.-+++++...+.. -.+..++ ....-.-|+||||+.||+|.|+|++.|.+-++
T Consensus 389 dk~fidL~~kll~A--Gy~ten~----ry~~~~lGtpqgsvvspil~nifL~~LDk~Lenk~~nefn~~~~~~~rhs~yr 462 (796)
T KOG4768|consen 389 DKGFIDLNYKLLRA--GYTTENA----RYHVEFLGTPQGSVVSPILCNIFLRELDKRLENKHRNEFNAGHLRSARHSKYR 462 (796)
T ss_pred hhhHHHHHHHHHhc--Ccccccc----ceecccccccccccCCchhHHHHHHHHHHHHHHHHHhhhcccCcccccChhhh
Confidence 44455555555543 2222232 12234579999999999999999988776432
Q ss_pred ------------------------------------CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCc
Q psy3306 69 ------------------------------------PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGL 112 (535)
Q Consensus 69 ------------------------------------~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl 112 (535)
.....+.||||+++.+.+.-. ...+.+..+..++.+.|+
T Consensus 463 ~L~~~iakaKl~s~~sKtirlrd~~qrn~~n~~~gfkr~~yVRyadd~ii~v~GS~n-----d~K~ilr~In~f~sslGl 537 (796)
T KOG4768|consen 463 NLSDSIAKAKLTSGMSKTIRLRDGVQRNETNDTAGFKRLMYVRYADDIIIGVWGSVN-----DCKQILRDINNFLSSLGL 537 (796)
T ss_pred hHHHHHHHHHHhhhhhhhhhhhhcccccccCCccccceeeEEEecCCEEEEEeccHH-----HHHHHHHHHHHHHHhhCc
Confidence 013468999999999888653 267788888999999999
Q ss_pred cccCCceeEEEecccCcCCCCCceeeecCeeeeeeccc-------cceeeEeccc--cchhhHHHHHHHHHHHHHHHhhh
Q psy3306 113 YFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVVDQF-------RFLGLTFDKK--MNWKIHLRNLKQSCVARSRILKI 183 (535)
Q Consensus 113 ~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~~~~-------kyLGv~i~~~--l~~~~hi~~~~~ka~~~~~~l~~ 183 (535)
+.|++||++.+-... ..+.|..|...+-- .--|+.+.+. ...+.-+..+..|.+..-.....
T Consensus 538 s~n~~kt~it~S~eg---------~~flg~nis~tP~r~~~~~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~s~~ 608 (796)
T KOG4768|consen 538 SNNSSKTQITVSREG---------THFLGYNISTTPGRPAAGEGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYCSHG 608 (796)
T ss_pred ccCcccceEEeeccc---------eeeeeceeccCCCCccceeccccceEEeccCCceeecchHHHHHHHHHhcceeecC
Confidence 999999998753322 22233333222111 1111222211 22455666666666655433221
Q ss_pred hc-----cCCCCCCHHHHHHHHHHhhccccccccc
Q psy3306 184 LS-----KKSWASDRKMLIRMYKSLIRSKLDYGCP 213 (535)
Q Consensus 184 l~-----~~~~gl~~~~~~~l~~~~v~p~l~Yg~~ 213 (535)
.. ...-....++.+..|.++.++.+.|..-
T Consensus 609 r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnYYr~ 643 (796)
T KOG4768|consen 609 RPWPRHVGRLTNEEDRTIINWYAAIGRGILNYYRL 643 (796)
T ss_pred CcCceeeeeecccCHHHHHHHHHHHhhchhhhhhH
Confidence 11 0011367889999999999999999843
No 11
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=98.68 E-value=1.5e-08 Score=94.96 Aligned_cols=73 Identities=22% Similarity=0.274 Sum_probs=62.0
Q ss_pred ccCCCCCCchhHHHHHHHhhchhhhcC---CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCc
Q psy3306 42 VCGIPQGGVASSTLFAIAINTITSYIH---PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQK 118 (535)
Q Consensus 42 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~K 118 (535)
.+++|||...||.+|+.+|+.++..+. +++.+..|+||++|.+.+... +.+.++.+.+.++++|+.+|++|
T Consensus 126 ~~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~~~------~~~~l~~v~~~l~~~gl~ln~~K 199 (213)
T cd01645 126 WKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQ------LREIYEELRQTLLRWGLTIPPEK 199 (213)
T ss_pred EEEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCHHH------HHHHHHHHHHHHHHCCCEeCHHH
Confidence 367999999999999999999987654 345688999999998766533 67788888889999999999999
Q ss_pred ee
Q psy3306 119 TQ 120 (535)
Q Consensus 119 t~ 120 (535)
|+
T Consensus 200 ~~ 201 (213)
T cd01645 200 VQ 201 (213)
T ss_pred Ee
Confidence 97
No 12
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.66 E-value=8.1e-08 Score=82.91 Aligned_cols=69 Identities=30% Similarity=0.288 Sum_probs=56.4
Q ss_pred CceEEEecCCCC--CCCeeEEEEEcCCCeee--eecCCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 367 DHVKIFTDGSKN--DLGVGCALTIPERNISK--RFALNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 367 ~~~~i~tDgS~~--~~~~g~a~~~~~~~~~~--~~~l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
..+.||||||+. +|..|+|+|+..+.... +.... .+|+..||+.|++.||+++.+.+...+.|+|||+-
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~y 74 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKY 74 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHH
Confidence 357899999984 46688888887543333 33333 79999999999999999999988999999999998
No 13
>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=98.40 E-value=3.8e-07 Score=78.61 Aligned_cols=65 Identities=29% Similarity=0.286 Sum_probs=50.2
Q ss_pred CceEEEecCCCC--CCCeeEEEEEcCCCeeeeecCCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 367 DHVKIFTDGSKN--DLGVGCALTIPERNISKRFALNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 367 ~~~~i~tDgS~~--~~~~g~a~~~~~~~~~~~~~l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
+++.||||||.. ++..|+|++++.+ ......++ ..|++.||+.|+..||+.+ ...++.|+|||++
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~~~---~~~~v~I~tDS~~ 68 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALKAL---EHRKVTIYTDSQY 68 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHHTH---STSEEEEEES-HH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHHHh---hcccccccccHHH
Confidence 478999999964 3446778866544 34455556 8899999999999999955 3489999999998
No 14
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.37 E-value=1.3e-06 Score=74.94 Aligned_cols=68 Identities=25% Similarity=0.256 Sum_probs=54.5
Q ss_pred eEEEecCCCCC--CCeeEEEEEcCCCeeeeecC-CCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 369 VKIFTDGSKND--LGVGCALTIPERNISKRFAL-NKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 369 ~~i~tDgS~~~--~~~g~a~~~~~~~~~~~~~l-~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
+.||||||... +..|+|+++.+......... ....++..||+.|++.||+.+...+..++.|++||+.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~ 72 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQL 72 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHH
Confidence 57999999854 56899999866543322222 2357999999999999999999988889999999998
No 15
>PRK08719 ribonuclease H; Reviewed
Probab=98.33 E-value=1.1e-06 Score=76.71 Aligned_cols=66 Identities=24% Similarity=0.341 Sum_probs=49.1
Q ss_pred CceEEEecCCCCCC-----CeeEEEEEcCC--Cee--eeecCCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 367 DHVKIFTDGSKNDL-----GVGCALTIPER--NIS--KRFALNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 367 ~~~~i~tDgS~~~~-----~~g~a~~~~~~--~~~--~~~~l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
..+.||||||+..+ ..|+|+++... ... ....+....|+++||+.|++.||+.+... ..|+|||+.
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y 77 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY 77 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence 46799999999543 25888876553 222 33345556899999999999999998653 379999976
No 16
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=98.33 E-value=5e-07 Score=84.62 Aligned_cols=74 Identities=24% Similarity=0.262 Sum_probs=62.5
Q ss_pred ccCCCCCCchhHHHHHHHhhchhhhcC---CCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCc
Q psy3306 42 VCGIPQGGVASSTLFAIAINTITSYIH---PSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQK 118 (535)
Q Consensus 42 ~~GvpQGs~LSP~Lf~l~~~~l~~~~~---~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~K 118 (535)
..-+|||-..||.+|.-+|+.++..+. .+..+..|.||+.|...+... ..+.++.+...++++|+.+|++|
T Consensus 122 ~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DDili~s~~~~e------~~~~l~~v~~~l~~~gl~l~~~K 195 (210)
T cd03715 122 FTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAADSEED------CLKGTDALLTHLGELGYKVSPKK 195 (210)
T ss_pred EEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCcEEEecCCHHH------HHHHHHHHHHHHHHCCCCcCHHH
Confidence 457999999999999999999887763 356778999999998765433 67788888888999999999999
Q ss_pred eeE
Q psy3306 119 TQC 121 (535)
Q Consensus 119 t~~ 121 (535)
|+.
T Consensus 196 ~~~ 198 (210)
T cd03715 196 AQI 198 (210)
T ss_pred eeC
Confidence 985
No 17
>KOG1005|consensus
Probab=98.31 E-value=1.6e-06 Score=91.88 Aligned_cols=104 Identities=18% Similarity=0.295 Sum_probs=85.1
Q ss_pred CChHHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC----C--CceeEEeecceEEE
Q psy3306 10 RGHLPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH----P--SLSSSLFVDDFAIF 83 (535)
Q Consensus 10 ~~~~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~----~--~~~~~~yADD~~i~ 83 (535)
...+..||..++++ ..|+++| ..+....|+||||+||-+|..+|++++.+..- . .+.++.|+||..++
T Consensus 606 ss~l~~vi~~~l~~--~~vki~~----k~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfI 679 (888)
T KOG1005|consen 606 SSDLFSVIRNMLST--NYVKIGG----KSYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFI 679 (888)
T ss_pred hhhHHHHHHHHHhh--heEEECC----eEEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEE
Confidence 45678899999976 6677787 44567899999999999999999999998632 2 24789999999999
Q ss_pred EecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEEEeccc
Q psy3306 84 TRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRK 127 (535)
Q Consensus 84 ~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~~~~~~ 127 (535)
+...+. +...+..+..-..+++...|..||. -|...
T Consensus 680 Tt~~~~------a~kfl~~l~~Gf~~yn~~tn~~K~~--nF~~s 715 (888)
T KOG1005|consen 680 TTENDQ------AKKFLKLLSRGFNKYNFFTNEPKTV--NFEVS 715 (888)
T ss_pred ecCHHH------HHHHHHHHhccccccceeccCcccc--cccch
Confidence 888765 7888888888888899999999977 45443
No 18
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.26 E-value=1.9e-06 Score=75.87 Aligned_cols=67 Identities=24% Similarity=0.251 Sum_probs=50.2
Q ss_pred ceEEEecCCCCC--CCeeEEEEEcCCCeeeeec-CCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 368 HVKIFTDGSKND--LGVGCALTIPERNISKRFA-LNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 368 ~~~i~tDgS~~~--~~~g~a~~~~~~~~~~~~~-l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
.+.||||||... +..|+|+++...+....+. .....|++.||+.|+..||+.+.. ...+.|+|||+.
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~y 72 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQY 72 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHH
Confidence 478999999863 4578888776544332222 234678999999999999998854 467999999986
No 19
>PRK06548 ribonuclease H; Provisional
Probab=98.26 E-value=3.1e-06 Score=74.59 Aligned_cols=67 Identities=27% Similarity=0.182 Sum_probs=49.4
Q ss_pred CceEEEecCCCCC--CCeeEEEEEcCCCeeeeecCCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 367 DHVKIFTDGSKND--LGVGCALTIPERNISKRFALNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 367 ~~~~i~tDgS~~~--~~~g~a~~~~~~~~~~~~~l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
..+.||||||+.. +..|.|+++...... . ......|++.||+.|++.||+.+.. ...++.|+|||+-
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~-~-g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~y 72 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWD-S-GGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKY 72 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEE-c-cCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHH
Confidence 4589999999864 558888887543211 1 1123589999999999999986643 3457999999999
No 20
>KOG3752|consensus
Probab=98.13 E-value=6.6e-06 Score=80.06 Aligned_cols=71 Identities=24% Similarity=0.244 Sum_probs=60.0
Q ss_pred CCceEEEecCCCCCC-----CeeEEEEEcCCCe-eeeecCC-CCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 366 KDHVKIFTDGSKNDL-----GVGCALTIPERNI-SKRFALN-KNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 366 ~~~~~i~tDgS~~~~-----~~g~a~~~~~~~~-~~~~~l~-~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
.+...+|||||...+ .+|+|+++.++.. ..+..+. ...+++.||++|++.||+-+.+.+..++.|.|||.-
T Consensus 210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~ 287 (371)
T KOG3752|consen 210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEY 287 (371)
T ss_pred ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHH
Confidence 345899999998653 3999999877654 4666775 689999999999999999999988889999999987
No 21
>PRK07708 hypothetical protein; Validated
Probab=98.10 E-value=1e-05 Score=75.26 Aligned_cols=72 Identities=21% Similarity=0.197 Sum_probs=56.1
Q ss_pred cCCceEEEecCCCC--CCCeeEEEEEcCC--Ceee----eecCCCCCCchHHHHHHHHHHHHHHHHcCCCc--EEEecCC
Q psy3306 365 FKDHVKIFTDGSKN--DLGVGCALTIPER--NISK----RFALNKNASIFHAELLALLQSLITIKELGVNK--ALIITDS 434 (535)
Q Consensus 365 ~~~~~~i~tDgS~~--~~~~g~a~~~~~~--~~~~----~~~l~~~~s~~~aE~~ai~~al~~~~~~~~~~--~~I~tDs 434 (535)
.++.+.+|+|||.. ++.+|+|+++... +... ...++...+++.||..|++.||+.+.+.+... +.|++||
T Consensus 70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS 149 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS 149 (219)
T ss_pred CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence 45689999999974 5678999988643 2222 12455568999999999999999999887654 8999999
Q ss_pred CC
Q psy3306 435 LM 436 (535)
Q Consensus 435 ~s 436 (535)
+-
T Consensus 150 ql 151 (219)
T PRK07708 150 QV 151 (219)
T ss_pred HH
Confidence 98
No 22
>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=97.92 E-value=3.5e-05 Score=65.20 Aligned_cols=67 Identities=34% Similarity=0.373 Sum_probs=53.7
Q ss_pred EEEecCCCCCC--CeeEEEEEcCCCeeeeec---CCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 370 KIFTDGSKNDL--GVGCALTIPERNISKRFA---LNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 370 ~i~tDgS~~~~--~~g~a~~~~~~~~~~~~~---l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
.+|||||...+ ..|+|+++.+......+. .....+++.||+.|+..|++.+......++.|++||+.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~ 72 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQY 72 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHH
Confidence 37999998654 688898887654332222 12478999999999999999999888999999999997
No 23
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.64 E-value=0.00015 Score=74.15 Aligned_cols=68 Identities=22% Similarity=0.215 Sum_probs=54.2
Q ss_pred ceEEEecCCCCC--CCeeEEEEEcCCC--ee-ee--ecCCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 368 HVKIFTDGSKND--LGVGCALTIPERN--IS-KR--FALNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 368 ~~~i~tDgS~~~--~~~g~a~~~~~~~--~~-~~--~~l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
.+.||||||... +..|+|+++.+.+ .. .. ..++ ..++..||+.|++.||+.+.+.+...+.|++||+.
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~l 76 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKL 76 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHH
Confidence 368999999864 4689999887642 11 22 2233 67889999999999999999988889999999998
No 24
>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.
Probab=97.61 E-value=6.1e-05 Score=67.90 Aligned_cols=72 Identities=17% Similarity=0.301 Sum_probs=57.1
Q ss_pred cCCCCCCchhHHHHHHHhhchhhhcCCCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeE
Q psy3306 43 CGIPQGGVASSTLFAIAINTITSYIHPSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQC 121 (535)
Q Consensus 43 ~GvpQGs~LSP~Lf~l~~~~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~ 121 (535)
..+|||...||.+|.-++..++..+. +..+..|+||+.+...... + ....++.+..-.++.|+.+|++||+.
T Consensus 94 ~~~p~G~~~s~~~~~~~~~~~l~~~~-~~~~~~y~DDi~i~~~~~~--~----~~~~~~~~~~~l~~~~~~~~~~K~~~ 165 (177)
T cd01647 94 TRMPFGLKNAPATFQRLMNKILGDLL-GDFVEVYLDDILVYSKTEE--E----HLEHLREVLERLREAGLKLNPEKCEF 165 (177)
T ss_pred EEecCCCccHHHHHHHHHHhhhcccc-ccccEEEecCccccCCCHH--H----HHHHHHHHHHHHHHcCCEeCHHHcee
Confidence 56999999999999999999887653 2357789999999877532 2 45556666667778999999999985
No 25
>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=95.79 E-value=0.0072 Score=56.42 Aligned_cols=70 Identities=16% Similarity=0.201 Sum_probs=55.5
Q ss_pred cccccCCCCCCchhHHHHHHHhhchhhhcCC-----CceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCcc
Q psy3306 39 FSNVCGIPQGGVASSTLFAIAINTITSYIHP-----SLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLY 113 (535)
Q Consensus 39 ~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~~-----~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ 113 (535)
.....-+|+|-.-||.+|..+|+.+...+.. .+....|+||+.+.+.+... +...++.+.+.+++.|+.
T Consensus 98 ~Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s~~e------~~~~~~~v~~~L~~~Gf~ 171 (213)
T cd01644 98 EYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLNE------AVNVAKRLIALLKKGGFN 171 (213)
T ss_pred EEEEEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCCHHH------HHHHHHHHHHHHHhCCcc
Confidence 3445679999999999999999999987664 24567999999998766433 667777777778888887
Q ss_pred c
Q psy3306 114 F 114 (535)
Q Consensus 114 l 114 (535)
+
T Consensus 172 l 172 (213)
T cd01644 172 L 172 (213)
T ss_pred c
Confidence 7
No 26
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.30 E-value=0.0084 Score=47.15 Aligned_cols=31 Identities=29% Similarity=0.529 Sum_probs=25.0
Q ss_pred cccCCCCCCCCCCCCC-CcchhhhhhhccCcC
Q psy3306 467 HLFRREDRPMCQQCQV-PMTIEHILIACRNMR 497 (535)
Q Consensus 467 ~~~~~~~~~~C~~c~~-~~t~~H~l~~C~~~~ 497 (535)
.+.+...++.|..|+. .||++|++++||...
T Consensus 52 ~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 52 QRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred hccCCccCCccccCCCccccccceeccCcCcc
Confidence 4455567899998875 889999999999754
No 27
>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=93.20 E-value=0.22 Score=48.67 Aligned_cols=98 Identities=12% Similarity=0.175 Sum_probs=64.5
Q ss_pred hHHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchh----HHHHHHHhhchhhhc-----CCCceeEEeecceEE
Q psy3306 12 HLPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVAS----STLFAIAINTITSYI-----HPSLSSSLFVDDFAI 82 (535)
Q Consensus 12 ~~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LS----P~Lf~l~~~~l~~~~-----~~~~~~~~yADD~~i 82 (535)
.+..+++.++.. .+..++. ..+....|+|+|++.. +++=.+++......+ ...+....|.||.++
T Consensus 133 ~~~~l~~~~~~~---~~~~~~~---~~~~~~~G~pSG~~~T~~~Nsl~n~~~~~~a~~~~~~~~~~~~~~~~~~GDD~li 206 (278)
T cd01699 133 ERRNLLRSLTNN---SLHIGFN---EVYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLL 206 (278)
T ss_pred HHHHHHHHHhcC---hhhhhCc---eEEEEcCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEcCCeEE
Confidence 366777777755 1212211 2445678999999885 444555555444332 356788999999999
Q ss_pred EEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEE
Q psy3306 83 FTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCV 122 (535)
Q Consensus 83 ~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~ 122 (535)
.+.... .....+.+.++..+.|++++++|....
T Consensus 207 ~~~~~~-------~~~~~~~~~~~~~~~G~~~~~~~~~~~ 239 (278)
T cd01699 207 SVEKAD-------DKFNLETLAEWLKEYGLTMTDEDKVES 239 (278)
T ss_pred EechhH-------hhhCHHHHHHHHHHcCCEeCCcccCCC
Confidence 887651 123445677888889999999998754
No 28
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=92.06 E-value=0.14 Score=39.77 Aligned_cols=32 Identities=41% Similarity=0.533 Sum_probs=27.8
Q ss_pred chHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 405 IFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 405 ~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
+..||+.|+..||+.+.+.+..++.+.+||+.
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~ 32 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQL 32 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCcc
Confidence 35799999999999999999999999999987
No 29
>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=85.53 E-value=0.14 Score=33.67 Aligned_cols=41 Identities=29% Similarity=0.442 Sum_probs=7.1
Q ss_pred hhhHHHHHHHHHHHHHHHhhhhccCCCCCCHHHHHHHHHHhhc
Q psy3306 163 WKIHLRNLKQSCVARSRILKILSKKSWASDRKMLIRMYKSLIR 205 (535)
Q Consensus 163 ~~~hi~~~~~ka~~~~~~l~~l~~~~~gl~~~~~~~l~~~~v~ 205 (535)
|+.|+..+.+||..++..||.+.+. ++++..+..+|+++|-
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 6788899999999999999988854 6788888888887763
No 30
>CHL00002 matK maturase K
Probab=78.41 E-value=24 Score=37.36 Aligned_cols=168 Identities=14% Similarity=0.150 Sum_probs=89.4
Q ss_pred CceeEEeecceEEEEecCChHHHHHHHHHHHHHH-HHHHhhcCccccCCceeEEEecccCcCCCCCceeeecCeeeeee-
Q psy3306 70 SLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKL-NHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYDSRIEVV- 147 (535)
Q Consensus 70 ~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l-~~w~~~~gl~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g~~I~~~- 147 (535)
-+..+.||||..+...|.... +++....+ .=|.....+.+.|+|+.+.+++... +.+-|-.+...
T Consensus 272 ~ihYVRYaddfIIg~kGsk~~-----a~KwK~~l~~F~q~~f~l~~s~eKi~I~~ls~~s--------~~FLGY~~sv~~ 338 (504)
T CHL00002 272 FIHYVRYQGKSILASKGTPLL-----MNKWKYYLVNFWQCHFHLWSQPGRIHINQLSNHS--------FDFLGYLSSVRL 338 (504)
T ss_pred eEEEEEECCcEEEEECCCHHH-----HHHHHHHHHHHHHHhceeeecCCceeeccccCCc--------ceeeeEEeeeee
Confidence 356799999999998887642 44444444 3356667899999999987765432 22222221110
Q ss_pred -c---cccce--eeEec---cccchhhHHHHHHHHHHHH-HHHh--hhhccCCCC-CCHHHHHHHHHHhhcccccccccc
Q psy3306 148 -D---QFRFL--GLTFD---KKMNWKIHLRNLKQSCVAR-SRIL--KILSKKSWA-SDRKMLIRMYKSLIRSKLDYGCPA 214 (535)
Q Consensus 148 -~---~~kyL--Gv~i~---~~l~~~~hi~~~~~ka~~~-~~~l--~~l~~~~~g-l~~~~~~~l~~~~v~p~l~Yg~~~ 214 (535)
. ..+.| |+.++ .++....-+..+++++.+. ...+ ..+.+..|. ++......-|+++.+....|.+..
T Consensus 339 ~~~~vRsqml~n~f~~~~~~kk~~~~VPi~~lI~~L~k~kfcni~G~PisK~~w~~lsD~dII~rf~~i~Rgl~~YYSgs 418 (504)
T CHL00002 339 NPSVVRSQMLENSFLIDNAIKKFDTIVPIIPLIGSLAKAKFCNVLGHPISKPVWTDLSDSDIIDRFGRICRNLSHYYSGS 418 (504)
T ss_pred ccceeEechhhcceeeeccCCeEEeccCcHHHHHHHHHcCcccCCCCCcCCccccCCCHHHHHHHHHHHHhhhheecccc
Confidence 0 00111 22221 1111122222333333222 1111 134444553 788899999999999999998765
Q ss_pred cccccHHHHHHHHHH-HHHHHHHHhCCCCCCcHHHHHHHhC
Q psy3306 215 YNSASANTLQILNPV-QNLCLRLATGAFRSSPVVSLEAETG 254 (535)
Q Consensus 215 w~~~~~~~~~~L~~~-q~~~lr~i~g~~~t~~~~~l~~~~g 254 (535)
-. +..+.++.-+ +-.|++...+..+++ ...+....|
T Consensus 419 ~n---k~~L~rikYIlr~Sc~KTLA~KhKst-vr~v~kk~g 455 (504)
T CHL00002 419 SK---KKSLYRIKYILRLSCAKTLARKHKST-VRAFLKRLG 455 (504)
T ss_pred cc---ccchhhhHHHHHHHHHHHhHHhhcCc-HHHHHHHHh
Confidence 32 2333344433 344666666666654 333433344
No 31
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=68.07 E-value=1.7 Score=43.52 Aligned_cols=46 Identities=26% Similarity=0.357 Sum_probs=36.4
Q ss_pred ccccCCCCCCchhHHHHHHHhhchhhhcCCCc--eeEEeecceEEEEe
Q psy3306 40 SNVCGIPQGGVASSTLFAIAINTITSYIHPSL--SSSLFVDDFAIFTR 85 (535)
Q Consensus 40 ~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~~~~--~~~~yADD~~i~~~ 85 (535)
....|+|||+++||+|-++.++.+...+..-. ....|+||..+-..
T Consensus 234 ~~~~~~~q~~~vs~~l~n~~l~~~~~~~~~~~~~~~~~y~~~~~i~~~ 281 (328)
T COG3344 234 SKEKGTPQGGLVSPILVNIKLSKLDNELRNRYLNLLRRYIDDGNIDKL 281 (328)
T ss_pred cccccCCCCCccCchhhhhhhhhhhHHHHHHHhhhhhhhcccccCCHH
Confidence 46789999999999999999888877654211 36789999998755
No 32
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=65.09 E-value=27 Score=30.76 Aligned_cols=64 Identities=20% Similarity=0.317 Sum_probs=38.5
Q ss_pred CceEEEecCCCCCCCeeEEEEEcC--C-Ceeee-----ecC-C-CCCCchHHHHHHHHHHHHHHHHc------CCCcEEE
Q psy3306 367 DHVKIFTDGSKNDLGVGCALTIPE--R-NISKR-----FAL-N-KNASIFHAELLALLQSLITIKEL------GVNKALI 430 (535)
Q Consensus 367 ~~~~i~tDgS~~~~~~g~a~~~~~--~-~~~~~-----~~l-~-~~~s~~~aE~~ai~~al~~~~~~------~~~~~~I 430 (535)
..+.+|+|+|.. +.|+.++... + ..... -+. | ...|+-.-|+.|+..|.+++... ...++.+
T Consensus 80 ~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~ 157 (159)
T PF05380_consen 80 VELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVF 157 (159)
T ss_pred eeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEE
Confidence 468999999943 3444443322 1 11111 112 1 24599999999999999998642 3455555
Q ss_pred ec
Q psy3306 431 IT 432 (535)
Q Consensus 431 ~t 432 (535)
||
T Consensus 158 wt 159 (159)
T PF05380_consen 158 WT 159 (159)
T ss_pred eC
Confidence 54
No 33
>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=55.13 E-value=21 Score=37.94 Aligned_cols=96 Identities=18% Similarity=0.179 Sum_probs=61.7
Q ss_pred HHHHHHHhcCCceEEEEECCeecccccccccCCCCCCchhHHHHHHHhhchhhh----cC-----C---CceeEEeecce
Q psy3306 13 LPNFLFKYMDERSFKIRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSY----IH-----P---SLSSSLFVDDF 80 (535)
Q Consensus 13 ~~~~I~~~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~----~~-----~---~~~~~~yADD~ 80 (535)
...++...+..+ .+..+| ..+.+..|+|-|+++--++=+++..-+... +. . .+.++.|=||.
T Consensus 280 ~~~~l~~~~~~~--~~~~~g----~~y~~~~G~PSG~~~Tsi~NSi~N~i~~~~a~~~~~~~~~~~~~~~~~~i~YGDD~ 353 (491)
T PF00680_consen 280 LRRNLIQSICNP--IHLCGG----KVYRVNGGNPSGSPLTSIINSIVNNIYIRYAWRKLYPDPPREFFENVKLIVYGDDN 353 (491)
T ss_dssp HHHHHHHHHHEE--EEEETT----EEEEEESSS-TTSTTHHHHHHHHHHHHHHHHHHHHSTSCHGGGHHHSEEEEETTEE
T ss_pred HHHHHHHhcCCe--eeeccc----ceeeeccccccccccchhccccccceeechhhhhccccccccccceeeeeeecccc
Confidence 344555555443 234566 455899999999998766655544433221 11 1 26789999999
Q ss_pred EEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccC-CceeE
Q psy3306 81 AIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSP-QKTQC 121 (535)
Q Consensus 81 ~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~-~Kt~~ 121 (535)
++.+...-. .. ..+.+.+.+++.|+++.. +|+..
T Consensus 354 l~sv~~~~~------~~-n~~~i~~~~~~~G~~~T~~dK~~~ 388 (491)
T PF00680_consen 354 LISVPPEID------PW-NGETISEFLAELGLTYTDADKTGE 388 (491)
T ss_dssp EEEESSHHH------HH-HHHHHHHHHHTTTEEEEESSTSSS
T ss_pred chhhhcccc------cc-hhHHHHHHHHhcccccccccccCC
Confidence 998775432 11 466777788889999986 88875
No 34
>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=42.78 E-value=83 Score=28.71 Aligned_cols=58 Identities=22% Similarity=0.335 Sum_probs=34.0
Q ss_pred ceEEEecCCCCCCCeeEEEEEcCCCeeeeecCCCCCCchHHHHHHHHHHHHHHHHcCCCcEEEecCCCC
Q psy3306 368 HVKIFTDGSKNDLGVGCALTIPERNISKRFALNKNASIFHAELLALLQSLITIKELGVNKALIITDSLM 436 (535)
Q Consensus 368 ~~~i~tDgS~~~~~~g~a~~~~~~~~~~~~~l~~~~s~~~aE~~ai~~al~~~~~~~~~~~~I~tDs~s 436 (535)
--.||+|+.-+ |.|+.+...... +....-..+++||+.|...|--+.. .++ |.|||.-
T Consensus 94 lc~VfaDATpT----gwgi~i~~~~~~--~Tfs~~l~IhtaELlaaClAr~~~~----~r~-l~tDnt~ 151 (245)
T PF00336_consen 94 LCQVFADATPT----GWGISITGQRMR--GTFSKPLPIHTAELLAACLARLMSG----ARC-LGTDNTV 151 (245)
T ss_pred CCceeccCCCC----cceeeecCceee--eeecccccchHHHHHHHHHHHhccC----CcE-EeecCcE
Confidence 45789998643 333333222222 2223345799999999987766653 233 7777765
No 35
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=42.23 E-value=17 Score=19.13 Aligned_cols=17 Identities=35% Similarity=0.806 Sum_probs=12.6
Q ss_pred CCCCCCCCcchhhhhhhccC
Q psy3306 476 MCQQCQVPMTIEHILIACRN 495 (535)
Q Consensus 476 ~C~~c~~~~t~~H~l~~C~~ 495 (535)
.|..||.. .|+..+||.
T Consensus 2 ~C~~C~~~---GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEP---GHIARDCPK 18 (18)
T ss_dssp BCTTTSCS---SSCGCTSSS
T ss_pred cCcCCCCc---CcccccCcc
Confidence 57777764 788899984
No 36
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=41.43 E-value=15 Score=22.69 Aligned_cols=20 Identities=20% Similarity=0.531 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCcchhhhhhhccC
Q psy3306 473 DRPMCQQCQVPMTIEHILIACRN 495 (535)
Q Consensus 473 ~~~~C~~c~~~~t~~H~l~~C~~ 495 (535)
+.-.|.-|+... |++.+||.
T Consensus 7 ~~Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCC---ccHhHCCC
Confidence 345688888775 99999998
No 37
>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=36.40 E-value=8.9 Score=36.66 Aligned_cols=43 Identities=16% Similarity=0.281 Sum_probs=31.7
Q ss_pred cCCCCCCchhHHHHHHHhhchhhhcC-----------------CCceeEEeecceEEEEecCCh
Q psy3306 43 CGIPQGGVASSTLFAIAINTITSYIH-----------------PSLSSSLFVDDFAIFTRDKNK 89 (535)
Q Consensus 43 ~GvpQGs~LSP~Lf~l~~~~l~~~~~-----------------~~~~~~~yADD~~i~~~~~~~ 89 (535)
-|++| ||.+|.-.++..+..+. ..+.+..|.||+.|.+.....
T Consensus 122 YGLKQ----a~r~W~~~l~~~L~~~GF~~~~~D~clfi~~~~~~~~ii~vYVDDili~~~~~~~ 181 (246)
T PF07727_consen 122 YGLKQ----APRLWYKTLDKFLKKLGFKQSKADPCLFIKKSGDGFIIILVYVDDILIAGPSEEE 181 (246)
T ss_pred eeccc----ccchhhhhcccccchhhhhcccccccccccccccccccccccccccccccccccc
Confidence 47777 78888888777776543 236688999999998776653
No 38
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=32.41 E-value=71 Score=29.38 Aligned_cols=27 Identities=11% Similarity=0.150 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhhcCcccc
Q psy3306 89 KDLLISTMQESIDKLNHFSDQTGLYFS 115 (535)
Q Consensus 89 ~~~~~~~l~~~l~~l~~w~~~~gl~ln 115 (535)
..+..+.+++-.+.+++|+.+.|+++|
T Consensus 128 ~~~~~~~Lq~K~~~i~~WA~~~gvEv~ 154 (204)
T PF12633_consen 128 SPEERQLLQQKCDLIEQWAASFGVEVH 154 (204)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcCCEEE
Confidence 377788899999999999999999886
No 39
>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=31.26 E-value=1.6e+02 Score=22.05 Aligned_cols=57 Identities=16% Similarity=0.165 Sum_probs=37.4
Q ss_pred hhhhc-cCCCCCCHHHHHHHHHHhhcccccccccccccccHHHHHHHHHHHH-HHHHHHhCC
Q psy3306 181 LKILS-KKSWASDRKMLIRMYKSLIRSKLDYGCPAYNSASANTLQILNPVQN-LCLRLATGA 240 (535)
Q Consensus 181 l~~l~-~~~~gl~~~~~~~l~~~~v~p~l~Yg~~~w~~~~~~~~~~L~~~q~-~~lr~i~g~ 240 (535)
++.+. +...+.+...++.-++.+++++..|..... +......|+.... +..+.+...
T Consensus 8 ik~~~~~~~~~~~~~~~i~~LN~~lrGW~nYy~~~~---~~~~f~~ld~~v~~~l~~w~~rr 66 (80)
T PF08388_consen 8 IKEITRRRNRGKSLEELIKKLNPILRGWANYYRIGN---SSKTFSKLDHYVWRRLRRWLRRR 66 (80)
T ss_pred HHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhhcchh---HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34444 444578999999999999999999997763 3445666654443 333443333
No 40
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=30.05 E-value=39 Score=24.35 Aligned_cols=22 Identities=23% Similarity=0.419 Sum_probs=14.9
Q ss_pred hcccCCCCCCCCCCCCCCcchh
Q psy3306 466 SHLFRREDRPMCQQCQVPMTIE 487 (535)
Q Consensus 466 ~~~~~~~~~~~C~~c~~~~t~~ 487 (535)
.+++-..+...||.||.++..+
T Consensus 10 Ck~l~~~d~e~CP~Cgs~~~te 31 (64)
T COG2093 10 CKRLTPEDTEICPVCGSTDLTE 31 (64)
T ss_pred ccccCCCCCccCCCCCCcccch
Confidence 3445556667799999986433
No 41
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=28.76 E-value=74 Score=21.09 Aligned_cols=23 Identities=35% Similarity=0.642 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCcchhhhhhhccCcC-CC
Q psy3306 473 DRPMCQQCQVPMTIEHILIACRNMR-FR 499 (535)
Q Consensus 473 ~~~~C~~c~~~~t~~H~l~~C~~~~-~r 499 (535)
....|+-|+.. .|+-++||. . .|
T Consensus 3 ~~~~CqkC~~~---GH~tyeC~~-~~~r 26 (42)
T PF13917_consen 3 ARVRCQKCGQK---GHWTYECPN-KNER 26 (42)
T ss_pred CCCcCcccCCC---CcchhhCCC-CCCc
Confidence 34678888754 699999997 4 55
No 42
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=28.63 E-value=1.2e+02 Score=24.45 Aligned_cols=32 Identities=13% Similarity=0.201 Sum_probs=25.0
Q ss_pred EEeecce---------------EEEEecCChHHHHHHHHHHHHHHHH
Q psy3306 74 SLFVDDF---------------AIFTRDKNKDLLISTMQESIDKLNH 105 (535)
Q Consensus 74 ~~yADD~---------------~i~~~~~~~~~~~~~l~~~l~~l~~ 105 (535)
+.|+||+ +++..+++..+..+.++..++.+++
T Consensus 53 v~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~ 99 (103)
T cd07049 53 VVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIEN 99 (103)
T ss_pred EEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhc
Confidence 4599999 8888998888877777777776653
No 43
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=25.66 E-value=43 Score=31.94 Aligned_cols=32 Identities=31% Similarity=0.428 Sum_probs=21.6
Q ss_pred cchhHHHhhhccCCCchhh-hcccCCC------CCCCCC
Q psy3306 447 RLDEVCLMRMRLGHSKITH-SHLFRRE------DRPMCQ 478 (535)
Q Consensus 447 r~~~~~~~~lr~gh~~~~~-~~~~~~~------~~~~C~ 478 (535)
|-..-.|.|||+.|.+.|| ...+++. |.+.|+
T Consensus 210 rLRvGALsqLrTehrPCtY~~C~Cnr~~eECPLD~~lc~ 248 (311)
T PF15322_consen 210 RLRVGALSQLRTEHRPCTYQQCPCNREREECPLDSSLCP 248 (311)
T ss_pred ceecchhhhhhhccCCcccccCCcccccccCCCCCCCCC
Confidence 4445689999999999993 3334432 455666
No 44
>cd02974 AhpF_NTD_N Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD forming two contiguous TRX-fold subdomain similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The N-terminal TRX-fold subdomain of AhpF NTD is redox inactive, but is proposed to contain an important residue that aids in the catalytic function of the redox-active CXXC motif contained in the C-terminal TRX-
Probab=25.43 E-value=1.1e+02 Score=24.20 Aligned_cols=74 Identities=12% Similarity=0.141 Sum_probs=39.8
Q ss_pred chhhhcCCCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEEEecccCcCCCCCceeeecC
Q psy3306 62 TITSYIHPSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCVLFSRKYKQNNIAVNLTMYD 141 (535)
Q Consensus 62 ~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~~~~~~~~~~~~~~~~~~~g 141 (535)
++...+..++.+..|.||- +.+..+.+.++.+.+-+.+..+.... ... ..|.+.+.+
T Consensus 12 ~~f~~l~~pV~l~~f~~~~----------~~~~e~~~ll~e~a~lSdkI~~~~~~---------~~~----~~P~~~i~~ 68 (94)
T cd02974 12 AYLERLENPVELVASLDDS----------EKSAELLELLEEIASLSDKITLEEDN---------DDE----RKPSFSINR 68 (94)
T ss_pred HHHHhCCCCEEEEEEeCCC----------cchHHHHHHHHHHHHhCCceEEEEec---------CCC----CCCEEEEec
Confidence 3444566777788888872 33455777777776655432222211 111 125555533
Q ss_pred eeeeeeccccceeeEeccc
Q psy3306 142 SRIEVVDQFRFLGLTFDKK 160 (535)
Q Consensus 142 ~~I~~~~~~kyLGv~i~~~ 160 (535)
.. ....++|.|++....
T Consensus 69 ~~--~~~gIrF~GiP~GhE 85 (94)
T cd02974 69 PG--EDTGIRFAGIPMGHE 85 (94)
T ss_pred CC--CcccEEEEecCCchh
Confidence 22 124589999887654
No 45
>cd01414 SAICAR_synt_Sc non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase. Eukaryotic, bacterial, and archaeal group of SAICAR synthetases represented by the Saccharomyces cerevisiae (Sc) enzyme, mostly absent in metazoans. SAICAR synthetase catalyzes the seventh step of the de novo biosynthesis of purine nucleotides (also reported as eighth step). It converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP, and phosphate.
Probab=23.61 E-value=27 Score=33.96 Aligned_cols=75 Identities=11% Similarity=0.127 Sum_probs=48.2
Q ss_pred cCCCCCCchhHHHHHHHhhchhhhcCCCceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeEE
Q psy3306 43 CGIPQGGVASSTLFAIAINTITSYIHPSLSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQCV 122 (535)
Q Consensus 43 ~GvpQGs~LSP~Lf~l~~~~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~~ 122 (535)
.|++.|..|.+-+|..+.=.=. ...+.+. -|++.-++.....+++.+...++-+.+.+++.+.|+.+---|-++-
T Consensus 124 ~g~~eg~~L~~Pi~e~~tK~d~-~~D~~Is----~~~~~~~~~~~~~~~i~~~al~i~~~l~~~~~~~GiiLvD~K~EFG 198 (279)
T cd01414 124 EGLREAQKLPEPIFTPSTKAEE-GHDENIS----FEEAVEIIGAELADELRELALALYERAAEYAAKRGLILADTKFEFG 198 (279)
T ss_pred CCccccCcCCCCEEeccccccc-CCCCCCC----HHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEeeeEee
Confidence 3899999998877777643221 0111111 1222222333344666667777888899999999999999998853
No 46
>TIGR00081 purC phosphoribosylaminoimidazole-succinocarboxamide synthase. Check length. Longer versions may be multifunctional enzymes.
Probab=21.67 E-value=69 Score=30.35 Aligned_cols=111 Identities=14% Similarity=0.284 Sum_probs=68.7
Q ss_pred hhhhhCCCCChHHHHHHHhcCCceEE----------EEECCeecccccccccCCCCCCchhHHHHHHHhhchhhhcC-CC
Q psy3306 2 RQLHKWNLRGHLPNFLFKYMDERSFK----------IRLNNSTLSQDFSNVCGIPQGGVASSTLFAIAINTITSYIH-PS 70 (535)
Q Consensus 2 ~~L~~~g~~~~~~~~I~~~l~~r~~~----------v~~~~~~s~~~~~~~~GvpQGs~LSP~Lf~l~~~~l~~~~~-~~ 70 (535)
+.|.+.|+|.+++. .++++..- |.+.|..+ +.+--.-|+|.|-.+.|-|.-++.-+ +... +.
T Consensus 61 ~~L~~~GI~tH~i~----~~~~~~~lv~k~~~iPlEvIvR~~a~-GS~~rr~~~~eG~~~~~pl~E~~~k~--d~~~Dp~ 133 (237)
T TIGR00081 61 EKLEEAGIPTHYID----LIEDREMLVKKLDIIPLEVIVRNIAA-GSLLKRLGIPEGLELEQPLVEFIFKP--DEVGDPM 133 (237)
T ss_pred HHHHhCCCCcceec----ccCCCEEEEEEcceecEEEEEecccc-ccceeccCCCCCCcCCCCccceEEcc--cccCCCC
Confidence 46788899999986 55566544 45666666 66655678899988877665554433 1111 11
Q ss_pred ceeEEeecceEEEEecCChHHHHHHHHHHHHHHHHHHhhcCccccCCceeE
Q psy3306 71 LSSSLFVDDFAIFTRDKNKDLLISTMQESIDKLNHFSDQTGLYFSPQKTQC 121 (535)
Q Consensus 71 ~~~~~yADD~~i~~~~~~~~~~~~~l~~~l~~l~~w~~~~gl~ln~~Kt~~ 121 (535)
+. .-+|.-+.+ ++....++..+...++-+.+..++.+.|+.+-.-|-++
T Consensus 134 i~-~~~~~~~~~-~~~~e~~~i~~~a~~v~~~l~~~~~~~gl~LvD~K~EF 182 (237)
T TIGR00081 134 LN-ESYAEALGL-ATEEELERIKELALKVNEVLKKYFDEKGIILVDFKLEF 182 (237)
T ss_pred CC-HhHHHHhcc-CCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEeEEe
Confidence 10 011111111 22222355666677778888999999999999999874
No 47
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=20.86 E-value=56 Score=23.07 Aligned_cols=21 Identities=19% Similarity=0.439 Sum_probs=10.0
Q ss_pred CCCCCCCCCcchhhhhhhccC
Q psy3306 475 PMCQQCQVPMTIEHILIACRN 495 (535)
Q Consensus 475 ~~C~~c~~~~t~~H~l~~C~~ 495 (535)
-.|+.||+..+-.|-...||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 469999999999999999995
No 48
>PF06565 DUF1126: Repeat of unknown function (DUF1126); InterPro: IPR010554 This group contains several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.; PDB: 2Z14_A 2Z13_A.
Probab=20.73 E-value=60 Score=20.20 Aligned_cols=26 Identities=19% Similarity=0.332 Sum_probs=9.7
Q ss_pred hcCCceEEEEECCeecccccccccCCCCCCchh
Q psy3306 20 YMDERSFKIRLNNSTLSQDFSNVCGIPQGGVAS 52 (535)
Q Consensus 20 ~l~~r~~~v~~~~~~s~~~~~~~~GvpQGs~LS 52 (535)
||.+-+..|. ++..-++|.+||--|+
T Consensus 5 ~L~DdTi~I~-------E~~~~NSG~~~g~fl~ 30 (33)
T PF06565_consen 5 YLADDTISIF-------EPPVRNSGRPGGKFLK 30 (33)
T ss_dssp ETTTTEEEEE------------------SSEEE
T ss_pred EccCCCEEEE-------EeccCCCCCCCCeEee
Confidence 5666677765 5556678998887653
No 49
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=20.12 E-value=1.1e+02 Score=18.99 Aligned_cols=27 Identities=26% Similarity=0.433 Sum_probs=22.3
Q ss_pred cchHhhhcCChhhHHHHHHHHHhcccc
Q psy3306 506 TSISDILKNDEGTLKEVLQFLKRNNFL 532 (535)
Q Consensus 506 ~~~~~~l~~~~~~~~~~~~f~~~~~~~ 532 (535)
..+.++||-..+.++-+++.+++.|++
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 357788888899999999999999875
Done!