Query psy5607
Match_columns 769
No_of_seqs 588 out of 4177
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 21:52:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5607.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5607hhsearch_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: 100.0 1.3E-34 2.9E-39 294.3 19.2 211 164-423 1-220 (220)
2 cd01651 RT_G2_intron RT_G2_int 100.0 6.2E-31 1.3E-35 268.4 19.4 211 167-423 2-226 (226)
3 PF00078 RVT_1: Reverse transc 100.0 3.5E-29 7.7E-34 253.0 5.0 210 170-423 1-214 (214)
4 cd03487 RT_Bac_retron_II RT_Ba 100.0 2.3E-27 5E-32 238.8 17.4 189 181-426 4-198 (214)
5 KOG4768|consensus 99.8 1.6E-17 3.4E-22 176.9 19.3 206 161-392 287-549 (796)
6 cd01709 RT_like_1 RT_like_1: A 99.7 4.1E-16 8.9E-21 160.5 22.8 181 232-426 6-189 (346)
7 cd01646 RT_Bac_retron_I RT_Bac 99.7 1.7E-17 3.7E-22 158.6 8.4 144 253-426 1-147 (158)
8 cd01648 TERT TERT: Telomerase 99.7 1.6E-16 3.5E-21 143.7 8.4 99 304-424 13-119 (119)
9 PRK06548 ribonuclease H; Provi 99.4 2.1E-13 4.6E-18 128.1 6.4 72 642-714 61-142 (161)
10 cd00304 RT_like RT_like: Rever 99.3 1.3E-11 2.9E-16 107.8 9.7 84 311-423 12-98 (98)
11 PRK08719 ribonuclease H; Revie 99.3 4E-12 8.7E-17 118.7 6.6 68 645-713 69-146 (147)
12 PRK00203 rnhA ribonuclease H; 99.3 3.4E-12 7.3E-17 120.6 5.2 72 642-714 61-142 (150)
13 COG0328 RnhA Ribonuclease HI [ 99.2 1.3E-11 2.7E-16 113.7 5.8 73 642-714 63-145 (154)
14 PF00075 RNase_H: RNase H; In 99.2 1.3E-11 2.8E-16 114.4 3.3 68 641-712 56-131 (132)
15 KOG1005|consensus 99.0 2.8E-08 6E-13 111.8 19.3 234 161-425 434-742 (888)
16 cd06222 RnaseH RNase H (RNase 98.6 8.4E-08 1.8E-12 87.4 7.6 71 641-712 60-130 (130)
17 COG3344 Retron-type reverse tr 98.6 3.2E-07 7E-12 98.8 11.9 174 164-351 105-281 (328)
18 cd01645 RT_Rtv RT_Rtv: Reverse 98.5 1.9E-07 4.1E-12 93.9 6.3 73 308-388 126-201 (213)
19 KOG3752|consensus 98.5 2E-07 4.4E-12 96.5 5.8 71 642-712 276-363 (371)
20 cd03714 RT_DIRS1 RT_DIRS1: Rev 98.3 2E-06 4.4E-11 77.9 8.9 72 310-389 33-106 (119)
21 cd01699 RNA_dep_RNAP RNA_dep_R 98.1 0.00011 2.3E-09 77.4 17.6 188 180-389 36-238 (278)
22 cd03715 RT_ZFREV_like RT_ZFREV 98.0 5.9E-06 1.3E-10 83.0 5.3 123 246-423 85-210 (210)
23 cd01647 RT_LTR RT_LTR: Reverse 97.9 3.9E-05 8.4E-10 74.3 9.0 110 246-389 56-165 (177)
24 cd01650 RT_nLTR_like RT_nLTR: 97.8 6.3E-06 1.4E-10 83.5 1.8 98 22-120 1-125 (220)
25 PRK13907 rnhA ribonuclease H; 97.8 2.5E-05 5.4E-10 71.8 5.3 65 642-712 61-125 (128)
26 PF13456 RVT_3: Reverse transc 97.3 0.0004 8.7E-09 58.6 5.6 65 642-712 21-85 (87)
27 PF00078 RVT_1: Reverse transc 97.0 9.7E-05 2.1E-09 74.1 -2.0 87 28-119 1-143 (214)
28 PRK07708 hypothetical protein; 96.9 0.0019 4.2E-08 64.5 6.3 66 644-714 142-208 (219)
29 cd01651 RT_G2_intron RT_G2_int 96.6 0.00056 1.2E-08 69.4 -0.0 84 25-119 2-144 (226)
30 PRK07238 bifunctional RNase H/ 96.5 0.0036 7.8E-08 68.8 5.8 66 642-712 65-130 (372)
31 cd01644 RT_pepA17 RT_pepA17: R 96.1 0.0056 1.2E-07 61.3 4.2 111 244-381 55-173 (213)
32 PHA00028 rep RNA replicase, be 89.8 7.1 0.00015 43.2 14.0 178 165-389 191-371 (561)
33 PF05919 Mitovir_RNA_pol: Mito 89.4 5 0.00011 44.4 12.5 176 181-390 96-278 (498)
34 PF00680 RdRP_1: RNA dependent 89.1 5.2 0.00011 45.7 13.5 186 181-389 182-388 (491)
35 cd03487 RT_Bac_retron_II RT_Ba 88.5 0.18 3.9E-06 50.7 0.8 25 38-62 4-28 (214)
36 PF03431 RNA_replicase_B: RNA 81.9 14 0.00031 40.3 11.1 176 165-388 183-363 (542)
37 PF09004 DUF1891: Domain of un 75.6 0.66 1.4E-05 32.8 -0.6 42 429-472 1-42 (42)
38 PF00998 RdRP_3: Viral RNA dep 57.0 1.9E+02 0.0042 32.8 13.5 184 178-386 144-337 (486)
39 CHL00002 matK maturase K 35.8 77 0.0017 36.0 6.3 52 335-393 271-323 (504)
40 PF00978 RdRP_2: RNA dependent 29.6 1.8E+02 0.0038 32.8 7.9 104 247-352 210-318 (440)
41 COG0296 GlgB 1,4-alpha-glucan 28.8 63 0.0014 37.7 4.2 34 671-704 214-247 (628)
42 TIGR00081 purC phosphoribosyla 27.4 83 0.0018 32.0 4.3 133 246-388 24-181 (237)
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=100.00 E-value=1.3e-34 Score=294.25 Aligned_cols=211 Identities=34% Similarity=0.529 Sum_probs=192.8
Q ss_pred ccEEEEeecCCCCCCCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhc
Q psy5607 164 ESLILPLLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLA 243 (769)
Q Consensus 164 ~a~i~~i~K~~kd~~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~ 243 (769)
.+++++|||++ ++.++++||||+++++.+|++++++..||..+++. .+++.|+||++|+++.+++..+.+.++...+
T Consensus 1 ~~~~~~ipK~~-~~~~~~~~RpI~~~~~~~k~~~~~i~~~l~~~~~~--~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (220)
T cd01650 1 KARIILIPKKG-KPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEE--NILPNQFGFRPGRSTTDAILLLREVIEKAKE 77 (220)
T ss_pred CCEEEEeeCCC-CCCCccCcCCchhhhHHHHHHHHHHHHHHHHHHhh--cCCcccccccCCChHHHHHHHHHHHHHHHHH
Confidence 47899999998 45599999999999999999999999999999985 6779999999999999999999999999998
Q ss_pred ccccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHH
Q psy5607 244 KKECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFI 323 (769)
Q Consensus 244 ~~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~ 323 (769)
++...+++++|+++|||+|+|+.|++.| |+|||+++||+||+
T Consensus 78 ~~~~~~~l~~Di~~aFdsi~~~~l~~~l--------------------------------------GipQG~~lSp~l~~ 119 (220)
T cd01650 78 KKKSLVLVFLDFEKAFDSVDHEFLLKAL--------------------------------------GVRQGDPLSPLLFN 119 (220)
T ss_pred cCCceEEEEEEHHhhcCcCCHHHHHHHh--------------------------------------CCccCCcccHHHHH
Confidence 8999999999999999999999999998 99999999999999
Q ss_pred HHHHHHHhhhc---------CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEeec
Q psy5607 324 IFMNDILDIIK---------VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILFSR 394 (769)
Q Consensus 324 l~~~~l~~~l~---------~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~~~ 394 (769)
++++++.+.+. ....+..||||+++++.+.. ..++..++.+..|+..+|+++| ++||++++++.
T Consensus 120 l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~~~-----~~~~~~~~~~~~~~~~~gl~in--~~Kt~~~~~~~ 192 (220)
T cd01650 120 LALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKS-----RKLQELLQRLQEWSKESGLKIN--PSKSKVMLIGN 192 (220)
T ss_pred HHHHHHHHHHHhhccccCCCCccceEEeccceeeeccCCH-----HHHHHHHHHHHHHHHHcCCEEC--hhheEEEEecC
Confidence 99999998874 57889999999999988631 4889999999999999999999 99999999987
Q ss_pred CCCCCCCCeecCCCCcccccceeEeeeEe
Q psy5607 395 ARNPTFPPLFYNGSELKFESNIKFLGLYW 423 (769)
Q Consensus 395 ~~~~~~~~i~i~~~~i~~~~~~kyLGv~i 423 (769)
..... ..+..++..+..+.++||||+++
T Consensus 193 ~~~~~-~~~~~~~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 193 KKKRL-KDITLNGTPIEAVETFKYLGVTI 220 (220)
T ss_pred CCcch-hhhhhcCCcccCCCCCeeccccC
Confidence 76554 33777888889999999999975
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=99.97 E-value=6.2e-31 Score=268.44 Aligned_cols=211 Identities=22% Similarity=0.285 Sum_probs=184.8
Q ss_pred EEEeecCCCCCCCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcccc
Q psy5607 167 ILPLLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAKKE 246 (769)
Q Consensus 167 i~~i~K~~kd~~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~~~ 246 (769)
-+.|||++ ++||||+++++..|+++++|..+|...++. .+++.|+||++|+|+.+++..+.+. ..+.
T Consensus 2 ~~~i~K~~------g~~RpI~~~~~~~ki~~~~i~~~L~~~~~~--~~~~~~~g~~~~rs~~~~i~~i~~~-----~~~~ 68 (226)
T cd01651 2 RVYIPKPN------GKKRPLGIPTVRDRIVQEALKLVLEPIYEP--RFSDCSYGFRPGRSAHDALKAIRRN-----VKGG 68 (226)
T ss_pred eeeecCCC------CCCCccCCCchHHHHHHHHHHHHHHHHHhh--ccccCCCCCCCCCCHHHHHHHHHHH-----hcCC
Confidence 36899988 599999999999999999999999999984 6899999999999999999877666 3456
Q ss_pred cEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHHH
Q psy5607 247 CTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFM 326 (769)
Q Consensus 247 ~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~~ 326 (769)
..+++.+|+++|||+|+|+.|.+.|...+.++.++.++.+++.... ...+..+...+|+|||+++||+||++++
T Consensus 69 ~~~~~~~Di~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~------~~~~~~~~~~~GlpqG~~lSp~L~~~~l 142 (226)
T cd01651 69 YTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGV------LEDGKLVETEKGTPQGGVISPLLANIYL 142 (226)
T ss_pred CeEEEEccHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHHHhceE------ccCCeEeCCCCCcCCCccHHHHHHHHHH
Confidence 7889999999999999999999999999999999999999865332 2234567789999999999999999999
Q ss_pred HHHHhhhc--------------CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEe
Q psy5607 327 NDILDIIK--------------VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILF 392 (769)
Q Consensus 327 ~~l~~~l~--------------~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~ 392 (769)
+++...+. ..+.+..||||+++++.+ .+.++.+++.+.+|++..||.+| ++||+++.+
T Consensus 143 ~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~------~~~~~~~~~~i~~~~~~~gl~ln--~~Kt~i~~~ 214 (226)
T cd01651 143 HELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRG------PKEAEEIKELIREFLEELGLELN--PEKTRITHF 214 (226)
T ss_pred HHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCC------HHHHHHHHHHHHHHHHHcCCeec--hhhcceeec
Confidence 99988764 457899999999999886 45588999999999999999999 999999987
Q ss_pred ecCCCCCCCCeecCCCCcccccceeEeeeEe
Q psy5607 393 SRARNPTFPPLFYNGSELKFESNIKFLGLYW 423 (769)
Q Consensus 393 ~~~~~~~~~~i~i~~~~i~~~~~~kyLGv~i 423 (769)
+ .+.+.|||+.|
T Consensus 215 ~-------------------~~~~~fLG~~~ 226 (226)
T cd01651 215 K-------------------SEGFDFLGFTF 226 (226)
T ss_pred C-------------------CCCCeeCCeEC
Confidence 4 34588999864
No 3
>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=99.95 E-value=3.5e-29 Score=253.03 Aligned_cols=210 Identities=32% Similarity=0.502 Sum_probs=174.2
Q ss_pred eecCCCCCCCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcccccEE
Q psy5607 170 LLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAKKECTV 249 (769)
Q Consensus 170 i~K~~kd~~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~~~~~~ 249 (769)
|||++ +++||||+++++..|++++++..+|.+.++ ..+++.|+||++++++.+ +......+...+
T Consensus 1 ipK~~-----~~~~RpI~~~~~~~r~~~~~~~~~l~~~~~--~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~ 65 (214)
T PF00078_consen 1 IPKKN-----VGKYRPISIPSVDDRIVQRVLNKRLQPILE--PIFSPSQFGFRPGRSCHD--------IKKLNRFKGYLY 65 (214)
T ss_dssp EESSS-----SSSEEEE----EBTHHHHHHBHH-----------HHHTTSSCSHGCCCHH--------HHHHHC-CGSSE
T ss_pred CCCcC-----CCCeeEcCCCCcHHHHHHHHHHhhcccccc--ccCCCCCCCCcccccccc--------cccccccccccc
Confidence 68876 689999999999999999999999999986 488999999999999998 333345667799
Q ss_pred EEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHHHHHH
Q psy5607 250 ALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDI 329 (769)
Q Consensus 250 ~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~~~~l 329 (769)
++++|+++|||+|+|+.+...+..++.+..++.|+.+++.++...+.+++.. .......|+|||+++||+||++|++++
T Consensus 66 ~~~~Di~~~f~sI~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-~~~~~~~glpqG~~~S~~l~~~~l~~l 144 (214)
T PF00078_consen 66 FLKLDISKAFDSIPHHRLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGDL-SPYFQKRGLPQGSPLSPLLFNIYLDDL 144 (214)
T ss_dssp EEEEECCCCGGGSBBHTTTGGGGEEEEECCSCHHHHHHHHHHHH-EECGCSS-SEEEEESBS-TTSTCHHHHHHHHHHHH
T ss_pred cceeccccccccceeeeccccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhccccccc
Confidence 9999999999999999999999999999999999999999999999888775 888899999999999999999999999
Q ss_pred Hhhhc----CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEeecCCCCCCCCeec
Q psy5607 330 LDIIK----VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILFSRARNPTFPPLFY 405 (769)
Q Consensus 330 ~~~l~----~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~~~~~~~~~~~i~i 405 (769)
.+.+. ..+.+..||||+.+++.+ .+.+++.++.+.+|++.+||++| ++||+.++
T Consensus 145 ~~~~~~~~~~~~~~~rY~DD~~i~~~~------~~~~~~~~~~i~~~~~~~gl~ln--~~Kt~~~~-------------- 202 (214)
T PF00078_consen 145 DRELQQELNPDISYLRYADDILIISKS------KEELQKILEKISQWLEELGLKLN--PEKTKILH-------------- 202 (214)
T ss_dssp HHHHHHHS-TTSEEEEETTEEEEEESS------HHHHHHHHHHHHHHHHHTTSBCS--STTTSCS---------------
T ss_pred cccccccccccccceEeccccEEEECC------HHHHHHHHHHHHHHHHHCCCEEC--hHHEEEEe--------------
Confidence 98865 367899999999999986 57799999999999999999999 99998754
Q ss_pred CCCCcccccceeEeeeEe
Q psy5607 406 NGSELKFESNIKFLGLYW 423 (769)
Q Consensus 406 ~~~~i~~~~~~kyLGv~i 423 (769)
+.+.++|||+.|
T Consensus 203 ------~~~~~~~lG~~i 214 (214)
T PF00078_consen 203 ------PSDSVKFLGYVI 214 (214)
T ss_dssp -------ESSEEETTEEE
T ss_pred ------CCCCEEEEeEEC
Confidence 456799999875
No 4
>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=99.95 E-value=2.3e-27 Score=238.75 Aligned_cols=189 Identities=16% Similarity=0.103 Sum_probs=161.7
Q ss_pred CCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcccccEEEEEecccCCCC
Q psy5607 181 SNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAKKECTVALLLDGQKAFD 260 (769)
Q Consensus 181 ~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~~~~~~~v~lD~~kAFD 260 (769)
+.+|||+..++..|+++++|+.+|... ..+++.|+||++|||+.+++.. .....+++.+|+++|||
T Consensus 4 g~~R~I~~p~~~~r~iq~~l~~~l~~~----~~~~~~~~g~~~grs~~~~~~~----------~~~~~~v~~~Di~~fFd 69 (214)
T cd03487 4 GGFRTIYAPKPELKAIQRKILSNLLSK----LPVHDAAHGFVKGRSIITNAKP----------HCGAKYVLKLDIKDFFP 69 (214)
T ss_pred CCeeeEeCCCHHHHHHHHHHHHHHhcc----CCCCcceeeecCCCCHHHHHHH----------hcCCCEEEEeehhhhcc
Confidence 679999999999999999999999743 3688999999999999998752 22357899999999999
Q ss_pred CCChHHHHHHHhcCCCC-chhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHHHHHHHhhhc-----
Q psy5607 261 MTWRFKIIETLKGFNIN-GYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILDIIK----- 334 (769)
Q Consensus 261 ~V~~~~L~~~L~~~g~~-~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~~~~l~~~l~----- 334 (769)
+|+|+.|.+.|...|.+ +.+..++..++... .|+|||+|+||+||++|++++...+.
T Consensus 70 sI~~~~L~~~l~~~~~~~~~~~~~l~~~~~~~-----------------~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~ 132 (214)
T cd03487 70 SITFERVRGVFRSLGYFSPDVATILAKLCTYN-----------------GHLPQGAPTSPALSNLVFRKLDERLSKLAKS 132 (214)
T ss_pred cCCHHHHHHHHHHcCCCCHHHHHHHHHHHhCC-----------------CCcCCCCcccHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998 88888888876422 29999999999999999999988764
Q ss_pred CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEeecCCCCCCCCeecCCCCccccc
Q psy5607 335 VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILFSRARNPTFPPLFYNGSELKFES 414 (769)
Q Consensus 335 ~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~~~~~~~~~~~i~i~~~~i~~~~ 414 (769)
..+.+..||||+++++.+... ..++.+++.+..|+...||.+| ++||+++.. ..
T Consensus 133 ~~~~~~RYaDD~~i~~~~~~~----~~~~~~~~~i~~~l~~~gL~ln--~~Kt~i~~~--------------------~~ 186 (214)
T cd03487 133 NGLTYTRYADDITFSSNKKLK----EALDKLLEIIRSILSEEGFKIN--KSKTRISSK--------------------GS 186 (214)
T ss_pred cCCeEEEEeccEEEEccccch----hHHHHHHHHHHHHHHHCCceeC--CCceEEccC--------------------CC
Confidence 468899999999998876321 3688899999999999999999 999999764 23
Q ss_pred ceeEeeeEecCc
Q psy5607 415 NIKFLGLYWDAK 426 (769)
Q Consensus 415 ~~kyLGv~id~~ 426 (769)
.+.+||+.+..+
T Consensus 187 ~~~~~G~~i~~~ 198 (214)
T cd03487 187 RQIVTGLVVNNG 198 (214)
T ss_pred CcEEEEEEEeCC
Confidence 468999999764
No 5
>KOG4768|consensus
Probab=99.77 E-value=1.6e-17 Score=176.93 Aligned_cols=206 Identities=19% Similarity=0.190 Sum_probs=173.3
Q ss_pred cccccEEEEeecCCCCCCCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHH
Q psy5607 161 SWGESLILPLLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQ 240 (769)
Q Consensus 161 ~~k~a~i~~i~K~~kd~~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~ 240 (769)
.|.-++.++|||.. +..||.++-+.-.|+++-++-.-|.-..+ +.++...+|||||+||.+|+..+...+..
T Consensus 287 kf~p~rrv~i~k~s------GG~RplsvgnpRDklvQe~mRm~Leiiy~--~~fst~shgfRpglSc~tAi~~~~n~f~g 358 (796)
T KOG4768|consen 287 KFEPARRVPIPKFS------GGERPLSVGNPRDKLVQECMRMGLEIIYG--GEFSTVSHGFRPGLSCKTAILKTHNLFRG 358 (796)
T ss_pred eccccceeecCccC------CCcCcccCCChhHHHHHHHHHHHHHHHhc--ceeeeeecccCCCchhhHHHHHHHHHhhc
Confidence 46778999999987 78999999999999999888777776665 68999999999999999999999888754
Q ss_pred hhcccccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHH
Q psy5607 241 GLAKKECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPV 320 (769)
Q Consensus 241 ~~~~~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPl 320 (769)
+.+.+..|+.+.||+|+|+.|+..|++.--+..+++++...++...+.. ++ ....-.-|.|||++.||+
T Consensus 359 ------cnw~ie~DLkkcfdtIphd~LI~eL~~rIkdk~fidL~~kll~AGy~te--n~---ry~~~~lGtpqgsvvspi 427 (796)
T KOG4768|consen 359 ------CNWFIEVDLKKCFDTIPHDELIIELQKRIKDKGFIDLNYKLLRAGYTTE--NA---RYHVEFLGTPQGSVVSPI 427 (796)
T ss_pred ------cceEEechHHHHhccccHHHHHHHHHHHHhhhhHHHHHHHHHhcCcccc--cc---ceecccccccccccCCch
Confidence 5788999999999999999999999998778888888888887555432 11 122234599999999999
Q ss_pred HHHHHHHHHHhhhc---------------------------------------------------------CCceeeeee
Q psy5607 321 LFIIFMNDILDIIK---------------------------------------------------------VPLRRLLFI 343 (769)
Q Consensus 321 Lf~l~~~~l~~~l~---------------------------------------------------------~~~~~~~yA 343 (769)
|.|+|+..|.+.++ ....++.||
T Consensus 428 l~nifL~~LDk~Lenk~~nefn~~~~~~~rhs~yr~L~~~iakaKl~s~~sKtirlrd~~qrn~~n~~~gfkr~~yVRya 507 (796)
T KOG4768|consen 428 LCNIFLRELDKRLENKHRNEFNAGHLRSARHSKYRNLSDSIAKAKLTSGMSKTIRLRDGVQRNETNDTAGFKRLMYVRYA 507 (796)
T ss_pred hHHHHHHHHHHHHHHHHHhhhcccCcccccChhhhhHHHHHHHHHHhhhhhhhhhhhhcccccccCCccccceeeEEEec
Confidence 99999998877652 234568999
Q ss_pred ccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEe
Q psy5607 344 DDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILF 392 (769)
Q Consensus 344 DD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~ 392 (769)
||..+.+.+ ...+....+..+..|+...|+..| ++||++.+-
T Consensus 508 dd~ii~v~G-----S~nd~K~ilr~In~f~sslGls~n--~~kt~it~S 549 (796)
T KOG4768|consen 508 DDIIIGVWG-----SVNDCKQILRDINNFLSSLGLSNN--SSKTQITVS 549 (796)
T ss_pred CCEEEEEec-----cHHHHHHHHHHHHHHHHhhCcccC--cccceEEee
Confidence 999999888 477888899999999999999999 999998764
No 6
>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=99.73 E-value=4.1e-16 Score=160.49 Aligned_cols=181 Identities=17% Similarity=0.068 Sum_probs=135.7
Q ss_pred HHHHHHHHHhhcccccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCC
Q psy5607 232 VFLEKEAAQGLAKKECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGI 311 (769)
Q Consensus 232 ~~l~~~i~~~~~~~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~Gv 311 (769)
+.+...+.-........+++-.|+++.||+|+|+.|+.+|+.+|++.+++.+|+.||+..-... -+|.........+|+
T Consensus 6 ~~l~te~~i~~~l~G~~~vvd~Dik~fFdsIpH~~Lm~vL~~~~~~~~wL~li~r~L~APl~~~-~dg~~~~~r~r~rGt 84 (346)
T cd01709 6 RLLATEILINTALYGEVTVVQSDFKWFGPSLPHSTILAVLKFFGVPEKWLDFFKKFLEAPLRFV-ADGPDAPPRIRKRGT 84 (346)
T ss_pred HHHHHHHHHHHhhcCCEEEEEeehHhhCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhCceeec-CCCCcccccccCCcc
Confidence 3333333333344678999999999999999999999999999999999999999997554332 123223445667899
Q ss_pred CCCCCchHHHHHHHHHHHHhhhc---CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceE
Q psy5607 312 VQGSSLSPVLFIIFMNDILDIIK---VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSA 388 (769)
Q Consensus 312 pQGs~LSPlLf~l~~~~l~~~l~---~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~ 388 (769)
|||.++||+|-|+|+..+...+. .......||||+.++++ .+....+...+.++++..||++| ++||.
T Consensus 85 PqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~-------~~~a~~aw~~i~~fl~~lGLelN--~eKT~ 155 (346)
T cd01709 85 PMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ-------PETCAKAWKAIQEFAKVMGLELN--KEKTG 155 (346)
T ss_pred CCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC-------HHHHHHHHHHHHHHHHHcCceec--cccce
Confidence 99999999999999998888876 47889999999999944 35566677789999999999999 99999
Q ss_pred EEEeecCCCCCCCCeecCCCCcccccceeEeeeEecCc
Q psy5607 389 CILFSRARNPTFPPLFYNGSELKFESNIKFLGLYWDAK 426 (769)
Q Consensus 389 ~i~~~~~~~~~~~~i~i~~~~i~~~~~~kyLGv~id~~ 426 (769)
++.+.......... -...+ |...++|-=+.+|+.
T Consensus 156 iV~~~~~~r~~~~~---~~~~L-P~g~i~wgfL~Ld~~ 189 (346)
T cd01709 156 SVYLSDDTKTRDTT---IDATL-PEGPVRWGFLKLDPK 189 (346)
T ss_pred EEEeccCCccCCCc---ccccC-CCCCceeeeEEecCC
Confidence 99876543211010 00111 345577766677754
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=99.71 E-value=1.7e-17 Score=158.61 Aligned_cols=144 Identities=19% Similarity=0.251 Sum_probs=118.5
Q ss_pred ecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHHHHHHHhh
Q psy5607 253 LDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILDI 332 (769)
Q Consensus 253 lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~~~~l~~~ 332 (769)
+|++++||+|+|+.|...+.+.+.+...+.+++.+... ..+..........+|+|||+++||+|+++++.++...
T Consensus 1 lDi~~fF~sI~~~~l~~~l~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~GlpqG~~lS~~L~~~~l~~~d~~ 75 (158)
T cd01646 1 LDISNFYDSIYTHSLPWALHGKIKAKQLLKLLRLLGNL-----LDLLLLSSQYGQTNGLPIGPLTSRFLANIYLNDVDHE 75 (158)
T ss_pred CchhhccCcchHHHHHHHHHhhhhhHhhhhhHHHHHHH-----HHHHHHhccCCCCceEccCcchHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999998877443321 1122233456678899999999999999999999988
Q ss_pred hc---CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEeecCCCCCCCCeecCCCC
Q psy5607 333 IK---VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILFSRARNPTFPPLFYNGSE 409 (769)
Q Consensus 333 l~---~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~~~~~~~~~~~i~i~~~~ 409 (769)
+. ..+.+..||||+++++.+ ...++++++.+.+|+++.||.+| ++||+.+.++...
T Consensus 76 i~~~~~~~~~~RY~DD~~i~~~~------~~~~~~~~~~i~~~l~~~gL~ln--~~Kt~~~~~~~~~------------- 134 (158)
T cd01646 76 LKSKLKGVDYVRYVDDIRIFADS------KEEAEEILEELKEFLAELGLSLN--LSKTEILPLPEGT------------- 134 (158)
T ss_pred HHhccCCceEEEecCcEEEEcCC------HHHHHHHHHHHHHHHHHCCCEEC--hhhceeeecCCCC-------------
Confidence 75 578999999999999875 56678899999999999999999 9999998874321
Q ss_pred cccccceeEeeeEecCc
Q psy5607 410 LKFESNIKFLGLYWDAK 426 (769)
Q Consensus 410 i~~~~~~kyLGv~id~~ 426 (769)
..+.+||..+...
T Consensus 135 ----~~~~flg~~~~~~ 147 (158)
T cd01646 135 ----ASKDFLGYRFSPI 147 (158)
T ss_pred ----ccccccceEeehh
Confidence 3478899888653
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=99.66 E-value=1.6e-16 Score=143.69 Aligned_cols=99 Identities=27% Similarity=0.278 Sum_probs=80.9
Q ss_pred eeeccCCCCCCCCchHHHHHHHHHHHHhhhc-------CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHH-HH
Q psy5607 304 SFPLQNGIVQGSSLSPVLFIIFMNDILDIIK-------VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWS-NQ 375 (769)
Q Consensus 304 ~~~~~~GvpQGs~LSPlLf~l~~~~l~~~l~-------~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~-~~ 375 (769)
.+...+|+|||+++||+||+++++.+.+.+. ....+..||||+.+++.+ .+.++++++.+..+. .+
T Consensus 13 ~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~------~~~~~~~~~~l~~~l~~~ 86 (119)
T cd01648 13 YYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTS------LDKAIKFLNLLLRGFINQ 86 (119)
T ss_pred hhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCC------HHHHHHHHHHHHHhhHHh
Confidence 4567889999999999999999999988754 356789999999998875 567888999999997 99
Q ss_pred hCcccccCCCceEEEEeecCCCCCCCCeecCCCCcccccceeEeeeEec
Q psy5607 376 NGLIFSADPKKSACILFSRARNPTFPPLFYNGSELKFESNIKFLGLYWD 424 (769)
Q Consensus 376 ~GL~in~~~~Kt~~i~~~~~~~~~~~~i~i~~~~i~~~~~~kyLGv~id 424 (769)
.||.+| ++||++..... .....+.+.|||+.++
T Consensus 87 ~gl~iN--~~Kt~~~~~~~--------------~~~~~~~~~flG~~i~ 119 (119)
T cd01648 87 YKTFVN--FDKTQINFSFA--------------QLDSSDLIPWCGLLIN 119 (119)
T ss_pred hCeEEC--cccceeecccc--------------ccCCCCccCceeEeeC
Confidence 999999 99999875422 0123456899999875
No 9
>PRK06548 ribonuclease H; Provisional
Probab=99.42 E-value=2.1e-13 Score=128.05 Aligned_cols=72 Identities=21% Similarity=0.318 Sum_probs=63.2
Q ss_pred CCeEEEEcCcHHHHHHHH---------ccCcCCCcchH-HHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCc
Q psy5607 642 HSKFLLVSDSMSAIQAIA---------NICSSYKNSLT-SKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNP 711 (769)
Q Consensus 642 ~~~~~i~tDs~~~~~~i~---------~~~~~~~~~~~-~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a 711 (769)
..++.|+|||+|++++|+ +|+.++|+++. +++++.+.++...+ .|+|.|||||+|++|||.||+||++|
T Consensus 61 ~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~a 139 (161)
T PRK06548 61 DRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQA 139 (161)
T ss_pred CceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHH
Confidence 457999999999999998 46677888876 68999988887654 79999999999999999999999999
Q ss_pred CCC
Q psy5607 712 CTS 714 (769)
Q Consensus 712 ~~~ 714 (769)
+..
T Consensus 140 a~~ 142 (161)
T PRK06548 140 ANN 142 (161)
T ss_pred HHH
Confidence 855
No 10
>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=99.29 E-value=1.3e-11 Score=107.84 Aligned_cols=84 Identities=27% Similarity=0.438 Sum_probs=72.4
Q ss_pred CCCCCCchHHHHHHHHHHHHhhhc---CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCce
Q psy5607 311 IVQGSSLSPVLFIIFMNDILDIIK---VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKS 387 (769)
Q Consensus 311 vpQGs~LSPlLf~l~~~~l~~~l~---~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt 387 (769)
+|||+++||.||+++++.+...+. .......|+||+.+.+.+ . .++..+..+..++.++|+.+| ++||
T Consensus 12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~------~-~~~~~~~~l~~~l~~~gl~ln--~~Kt 82 (98)
T cd00304 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKS------E-QQAVKKRELEEFLARLGLNLS--DEKT 82 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCc------H-HHHHHHHHHHHHHHHcCcEEC--hhee
Confidence 999999999999999999998864 578899999999999875 2 677889999999999999999 9999
Q ss_pred EEEEeecCCCCCCCCeecCCCCcccccceeEeeeEe
Q psy5607 388 ACILFSRARNPTFPPLFYNGSELKFESNIKFLGLYW 423 (769)
Q Consensus 388 ~~i~~~~~~~~~~~~i~i~~~~i~~~~~~kyLGv~i 423 (769)
+... ....++|||+.+
T Consensus 83 ~~~~--------------------~~~~~~flG~~~ 98 (98)
T cd00304 83 QFTE--------------------KEKKFKFLGILV 98 (98)
T ss_pred EEec--------------------CCCCeeeeceeC
Confidence 8852 244589999863
No 11
>PRK08719 ribonuclease H; Reviewed
Probab=99.29 E-value=4e-12 Score=118.68 Aligned_cols=68 Identities=26% Similarity=0.338 Sum_probs=55.5
Q ss_pred EEEEcCcHHHHHHHH--------ccCc-CCCcch-HHHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCcCC
Q psy5607 645 FLLVSDSMSAIQAIA--------NICS-SYKNSL-TSKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNPCT 713 (769)
Q Consensus 645 ~~i~tDs~~~~~~i~--------~~~~-~~~~~~-~~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a~~ 713 (769)
.+|+|||+|++++|+ +++. +.|.++ ..++++.+.++.. ...|+|.|||||+|++|||.||+||++|+.
T Consensus 69 ~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 69 DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 489999999999994 3333 334444 3588888888876 467999999999999999999999999974
No 12
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.27 E-value=3.4e-12 Score=120.62 Aligned_cols=72 Identities=18% Similarity=0.248 Sum_probs=59.8
Q ss_pred CCeEEEEcCcHHHHHHHHc---------cCcCCCcchH-HHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCc
Q psy5607 642 HSKFLLVSDSMSAIQAIAN---------ICSSYKNSLT-SKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNP 711 (769)
Q Consensus 642 ~~~~~i~tDs~~~~~~i~~---------~~~~~~~~~~-~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a 711 (769)
...+.|+|||+|++++|.. +...+|+++. .++++.+.++... ..|.|.|||||+|++|||.||+|||+|
T Consensus 61 ~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a 139 (150)
T PRK00203 61 PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAG 139 (150)
T ss_pred CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHH
Confidence 4679999999999999985 3445667775 4677777777544 689999999999999999999999999
Q ss_pred CCC
Q psy5607 712 CTS 714 (769)
Q Consensus 712 ~~~ 714 (769)
+..
T Consensus 140 ~~~ 142 (150)
T PRK00203 140 AEE 142 (150)
T ss_pred HHH
Confidence 865
No 13
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.22 E-value=1.3e-11 Score=113.72 Aligned_cols=73 Identities=19% Similarity=0.295 Sum_probs=61.4
Q ss_pred CCeEEEEcCcHHHHHHHHcc---------CcCCCcch-HHHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCc
Q psy5607 642 HSKFLLVSDSMSAIQAIANI---------CSSYKNSL-TSKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNP 711 (769)
Q Consensus 642 ~~~~~i~tDs~~~~~~i~~~---------~~~~~~~~-~~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a 711 (769)
...|.|+|||+|++++|..| ....++++ ..++|+.+.++......|.+.|||||+|.++||+||+||++|
T Consensus 63 ~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~ 142 (154)
T COG0328 63 ACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREA 142 (154)
T ss_pred CceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHH
Confidence 67899999999999999843 33333444 358899999998887799999999999999999999999999
Q ss_pred CCC
Q psy5607 712 CTS 714 (769)
Q Consensus 712 ~~~ 714 (769)
+..
T Consensus 143 ~~~ 145 (154)
T COG0328 143 ARA 145 (154)
T ss_pred HHh
Confidence 854
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=99.17 E-value=1.3e-11 Score=114.43 Aligned_cols=68 Identities=28% Similarity=0.485 Sum_probs=53.1
Q ss_pred cCCeEEEEcCcHHHHHHHHc-----cCcC-C-CcchHHHHHHHHHHHhcCCceEEEEEecCCCCC-ccchhhhhhhhCcC
Q psy5607 641 PHSKFLLVSDSMSAIQAIAN-----ICSS-Y-KNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCGI-SGNEAVDMAAKNPC 712 (769)
Q Consensus 641 ~~~~~~i~tDs~~~~~~i~~-----~~~~-~-~~~~~~~i~~~~~~~~~~~~~v~~~wvp~H~gi-~gNe~aD~~Ak~a~ 712 (769)
.+.+++|+|||+++++.+.. .+.. + +.++..++++.+ ..+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus 56 ~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 56 EHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp STSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred hcccccccccHHHHHHHHHHhccccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 36889999999999998887 3322 1 224666666654 45778999999999999 69999999999986
No 15
>KOG1005|consensus
Probab=98.97 E-value=2.8e-08 Score=111.79 Aligned_cols=234 Identities=21% Similarity=0.221 Sum_probs=143.2
Q ss_pred cccccEEEEeecCCCCCCCCCCCcccccCC---------chhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCC--hhh
Q psy5607 161 SWGESLILPLLKPGKDRLVPSNYRPISLLN---------CSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRS--TID 229 (769)
Q Consensus 161 ~~k~a~i~~i~K~~kd~~~~~~yRPIsll~---------~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs--~~d 229 (769)
.++.+++..|||++ ++|+|...+ ..-+..+-+-..|+...++- ++ +..| ..|-| ..|
T Consensus 434 t~~~S~iR~iPK~n-------g~R~iin~~k~r~~~~~~~~~~~~~~~q~~~~~siL~~--~~--e~~g-vlg~si~~~d 501 (888)
T KOG1005|consen 434 TLNPSKIRFIPKKN-------GFRLIINMSKLRGARKRRNTKKKEETMQLKRLNSILSY--LR--ERSG-VLGNSILIHD 501 (888)
T ss_pred cCCchheEecccCC-------CceEEEehhhhcccchhhhhHHHHHHHHHHHHHHHHHH--HH--hcCC-CCccceechH
Confidence 46678889999986 355554443 22233344444454444432 11 1111 11211 123
Q ss_pred HHHHHHHHHHHhhcccccEEEEEecccCCCCCCChHHHHHHHhcC---------------C--------------C----
Q psy5607 230 NLVFLEKEAAQGLAKKECTVALLLDGQKAFDMTWRFKIIETLKGF---------------N--------------I---- 276 (769)
Q Consensus 230 ~i~~l~~~i~~~~~~~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~---------------g--------------~---- 276 (769)
.+.......... -.++..+.+..|+++|||+|+++.++..++.. + +
T Consensus 502 ~~~~~~~~~k~r-~~~~~LYfvk~DV~~cfDtIpqd~l~~II~~~l~~~r~~~~~~~~~~~vr~~f~s~~~~~~d~~~n~ 580 (888)
T KOG1005|consen 502 DIYRKLDFLKKR-SRNQKLYFVKADVSKCFDTIPQDELISIIRDRLFVQRKDAYTVAGKGRVRGNFVSLIFCSADVEPNA 580 (888)
T ss_pred HHHHHHHHHHHH-hhcCceEEEEEEhhhhhccCchHHHHHHHHHHHHHHHHHHHHhhcccccccceeeeeeeccccchhH
Confidence 333222222221 23447999999999999999999999988321 0 1
Q ss_pred -------------------------CchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHHHHHHHh
Q psy5607 277 -------------------------NGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILD 331 (769)
Q Consensus 277 -------------------------~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~~~~l~~ 331 (769)
...+..+|.+++.+-.+ +++| ..+....|+|||++||.+|..+|++++.+
T Consensus 581 ~~~~~~~me~~~~lvie~~~~~~~Sss~l~~vi~~~l~~~~v--ki~~---k~yvq~~GIpQGs~LSslLc~lyy~dle~ 655 (888)
T KOG1005|consen 581 HVVNALKMETSDVLVIENVSREMLSSSDLFSVIRNMLSTNYV--KIGG---KSYVQKKGIPQGSILSSLLCHLYYGDLED 655 (888)
T ss_pred HHHHHhccCCCCeEEEEecceeecchhhHHHHHHHHHhhheE--EECC---eEEEEecCccCCCchhHHHHHHHHHhHHH
Confidence 12233444444443333 2333 34556779999999999999999999998
Q ss_pred hhc----CC--ceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEeecCCCCCCCCeec
Q psy5607 332 IIK----VP--LRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILFSRARNPTFPPLFY 405 (769)
Q Consensus 332 ~l~----~~--~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~~~~~~~~~~~i~i 405 (769)
..- .+ +..+.|+||..+++.. .+++...+..+..-...++...| .+|+. -|......... ...
T Consensus 656 ~y~~~~~~~g~~vLlR~vDDFLfITt~------~~~a~kfl~~l~~Gf~~yn~~tn--~~K~~--nF~~se~~~~~-~~f 724 (888)
T KOG1005|consen 656 KYFSFEKEDGSIVLLRYVDDFLFITTE------NDQAKKFLKLLSRGFNKYNFFTN--EPKTV--NFEVSEECGAS-IVF 724 (888)
T ss_pred HHhhcccCCCcEEEEEeecceEEEecC------HHHHHHHHHHHhccccccceecc--Ccccc--cccchhccCcc-eee
Confidence 742 23 3778899999999885 67888899999888899999999 99977 44443333211 222
Q ss_pred CCCCcccccceeEeeeEecC
Q psy5607 406 NGSELKFESNIKFLGLYWDA 425 (769)
Q Consensus 406 ~~~~i~~~~~~kyLGv~id~ 425 (769)
.+... ...+.|-|..+++
T Consensus 725 ~~~~~--~~~f~w~g~~i~s 742 (888)
T KOG1005|consen 725 VWMHK--HLLFQWCGLLIRS 742 (888)
T ss_pred eccCc--cccccccceeeec
Confidence 11111 1346777777765
No 16
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=98.62 E-value=8.4e-08 Score=87.45 Aligned_cols=71 Identities=25% Similarity=0.375 Sum_probs=56.6
Q ss_pred cCCeEEEEcCcHHHHHHHHccCcCCCcchHHHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCcC
Q psy5607 641 PHSKFLLVSDSMSAIQAIANICSSYKNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNPC 712 (769)
Q Consensus 641 ~~~~~~i~tDs~~~~~~i~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a~ 712 (769)
+..++.|++||++++..+.++.... ......++..+.++......++|.|||+|+|+.+|+.||.+||+|.
T Consensus 60 ~~~~i~i~~Ds~~~~~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 60 GGKKVNIYTDSQYVINALTGWYEGK-PVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred CCceEEEEECHHHHHHHhhccccCC-ChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 3788999999999999999875421 2234445555555556778899999999999999999999999874
No 17
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=98.58 E-value=3.2e-07 Score=98.80 Aligned_cols=174 Identities=16% Similarity=0.115 Sum_probs=131.7
Q ss_pred ccEEEEeecCCCCCCCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhc
Q psy5607 164 ESLILPLLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLA 243 (769)
Q Consensus 164 ~a~i~~i~K~~kd~~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~ 243 (769)
..+-+.|||+++ +..||+++..+..++++.....-+.+..+ ..+++..+||++++++.+++..+.........
T Consensus 105 p~~~~~ipk~~~-----~~~r~l~i~tv~d~~vq~~~~~~l~~~~~--~~f~~~s~Gf~~~~~~~~a~~~~~~~~~~~~~ 177 (328)
T COG3344 105 PVRRVFIPKKSK-----GGKRHLGIPTVADRIVQSAFPIILEPIIE--NIFSPLSYGFRPGPSASNAIAYAFDLPQGKIC 177 (328)
T ss_pred cccceeeecCCC-----CCceecCCchHHHHHHHHHHHHHHHHHHH--hccccCCCCCCCChhHHHHHHHHHhhhccCCC
Confidence 334478999874 56999999999999999999999999666 48899999999999999999988776655443
Q ss_pred ccccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHH-HHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHH
Q psy5607 244 KKECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYL-CNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLF 322 (769)
Q Consensus 244 ~~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i-~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf 322 (769)
.. ...++..|+.+.||+++|..++..+...--+.....++ +-+..+..... ...-....|+|||+++||+|-
T Consensus 178 ~~-~~~~~~~di~~~fd~~~h~~ll~~~~~~i~~~~~~~~~~r~~~~~~~~~~------~~~~~~~~~~~q~~~vs~~l~ 250 (328)
T COG3344 178 SP-NGWVYDRDIKKCFDSINHKLLLYALDVTISDKLVLLLLGRILIAGYKTKF------NLKKSKEKGTPQGGLVSPILV 250 (328)
T ss_pred CC-ceEEEeehHHHHhcccCHHHHHHHhHhhhcchHHHHHHHHHHHcccceee------cccccccccCCCCCccCchhh
Confidence 33 56999999999999999999999999874444444344 33333322221 122235679999999999999
Q ss_pred HHHHHHHHhhhcCCc--eeeeeeccceEEEe
Q psy5607 323 IIFMNDILDIIKVPL--RRLLFIDDFLVIAR 351 (769)
Q Consensus 323 ~l~~~~l~~~l~~~~--~~~~yADD~~l~~~ 351 (769)
++.++.+...+.... ....|+||..+-..
T Consensus 251 n~~l~~~~~~~~~~~~~~~~~y~~~~~i~~~ 281 (328)
T COG3344 251 NIKLSKLDNELRNRYLNLLRRYIDDGNIDKL 281 (328)
T ss_pred hhhhhhhhHHHHHHHhhhhhhhcccccCCHH
Confidence 999887777654211 36689999887654
No 18
>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=98.48 E-value=1.9e-07 Score=93.91 Aligned_cols=73 Identities=18% Similarity=0.272 Sum_probs=62.8
Q ss_pred cCCCCCCCCchHHHHHHHHHHHHhhhc---CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCC
Q psy5607 308 QNGIVQGSSLSPVLFIIFMNDILDIIK---VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADP 384 (769)
Q Consensus 308 ~~GvpQGs~LSPlLf~l~~~~l~~~l~---~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~ 384 (769)
.+++|||...||.+|+.+|+.++..+. .......|+||+.+++.+ .+...+.++.+...+.+.|+.+| +
T Consensus 126 ~~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~------~~~~~~~l~~v~~~l~~~gl~ln--~ 197 (213)
T cd01645 126 WKVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDL------EGQLREIYEELRQTLLRWGLTIP--P 197 (213)
T ss_pred EEEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCC------HHHHHHHHHHHHHHHHHCCCEeC--H
Confidence 357999999999999999999988764 245678999999998774 57778888899999999999999 9
Q ss_pred CceE
Q psy5607 385 KKSA 388 (769)
Q Consensus 385 ~Kt~ 388 (769)
+||+
T Consensus 198 ~K~~ 201 (213)
T cd01645 198 EKVQ 201 (213)
T ss_pred HHEe
Confidence 9987
No 19
>KOG3752|consensus
Probab=98.45 E-value=2e-07 Score=96.51 Aligned_cols=71 Identities=23% Similarity=0.317 Sum_probs=54.6
Q ss_pred CCeEEEEcCcHHHHHHHHcc---------CcCCCcc-----h-HHHHHHHHHHHhcC--CceEEEEEecCCCCCccchhh
Q psy5607 642 HSKFLLVSDSMSAIQAIANI---------CSSYKNS-----L-TSKIYSAWMDLKSG--GKEVTLMWCPSHCGISGNEAV 704 (769)
Q Consensus 642 ~~~~~i~tDs~~~~~~i~~~---------~~~~~~~-----~-~~~i~~~~~~~~~~--~~~v~~~wvp~H~gi~gNe~a 704 (769)
..+++|.|||++++++|+.| ....+++ + .......+.+|.+. +..|.+.|||||.||.|||+|
T Consensus 276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~A 355 (371)
T KOG3752|consen 276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMA 355 (371)
T ss_pred CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHH
Confidence 55999999999999999854 2223344 2 23445555555443 578999999999999999999
Q ss_pred hhhhhCcC
Q psy5607 705 DMAAKNPC 712 (769)
Q Consensus 705 D~~Ak~a~ 712 (769)
|.+|++++
T Consensus 356 d~lARkgs 363 (371)
T KOG3752|consen 356 DALARKGS 363 (371)
T ss_pred HHHHhhhh
Confidence 99999986
No 20
>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.
Probab=98.34 E-value=2e-06 Score=77.87 Aligned_cols=72 Identities=22% Similarity=0.368 Sum_probs=57.5
Q ss_pred CCCCCCCchHHHHHHHHHHHHhhhc-CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHH-HHHHhCcccccCCCce
Q psy5607 310 GIVQGSSLSPVLFIIFMNDILDIIK-VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILK-WSNQNGLIFSADPKKS 387 (769)
Q Consensus 310 GvpQGs~LSPlLf~l~~~~l~~~l~-~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~-w~~~~GL~in~~~~Kt 387 (769)
-+|||-..||.+|..+|+.+...+. .......|+||+.+++.+ .+..+..+..+.. .++++|+.+| ++||
T Consensus 33 ~mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~------~~~~~~~~~~l~~~~l~~~gl~ln--~~K~ 104 (119)
T cd03714 33 ALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASS------IKTSEAVLRHLRATLLANLGFTLN--LEKS 104 (119)
T ss_pred ecCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCc------HHHHHHHHHHHHHHHHHHcCCccC--hhhc
Confidence 4899999999999999999998764 456788999999998875 2333444444444 6899999999 9999
Q ss_pred EE
Q psy5607 388 AC 389 (769)
Q Consensus 388 ~~ 389 (769)
++
T Consensus 105 ~~ 106 (119)
T cd03714 105 KL 106 (119)
T ss_pred Ee
Confidence 86
No 21
>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=98.12 E-value=0.00011 Score=77.39 Aligned_cols=188 Identities=14% Similarity=0.085 Sum_probs=132.3
Q ss_pred CCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcccccEEEEEecccCCC
Q psy5607 180 PSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAKKECTVALLLDGQKAF 259 (769)
Q Consensus 180 ~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~~~~~~~v~lD~~kAF 259 (769)
.+.-|.|...+....++++.....+...+.......+.+.|+.|..+..+.+. +.+ ..+. -.++.+|+++..
T Consensus 36 ~~k~R~i~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~vG~~p~~~~~~~l~---~~~----~~~~-~~~~~~D~s~FD 107 (278)
T cd01699 36 AGKTRLIQPRPLDYNIALRMYLGPFEAKLMKNRGGLPIAVGINPYSRDWTILA---NKL----RSFS-PVAIALDYSRFD 107 (278)
T ss_pred CCCCcEEecCChHHHHHHHHHHHHHHHHHHhcCCCCCcccccCCCchHHHHHH---HHH----HhcC-CeEEeeeccccC
Confidence 46789999999999999999999999988876678899999999985544332 222 1222 678899999999
Q ss_pred CCCChHHHHHH---HhcCCCCc---hhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHH----HHHHHHHHH
Q psy5607 260 DMTWRFKIIET---LKGFNING---YMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPV----LFIIFMNDI 329 (769)
Q Consensus 260 D~V~~~~L~~~---L~~~g~~~---~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPl----Lf~l~~~~l 329 (769)
.++++..+... +....-++ .+..++..++.. .+...+ ...+....|+|+|++...+ +=++++...
T Consensus 108 ~s~~~~~l~~~~~i~~~~~~~~~~~~~~~l~~~~~~~---~~~~~~--~~~~~~~~G~pSG~~~T~~~Nsl~n~~~~~~a 182 (278)
T cd01699 108 SSLSPQLLEAEHSIYNALYDDDDELERRNLLRSLTNN---SLHIGF--NEVYKVRGGRPSGDPLTSIGNSIINCILVRYA 182 (278)
T ss_pred CCCCHHHHHHHHHHHHHHHcCCchhHHHHHHHHHhcC---hhhhhC--ceEEEEcCCCCCCCCchhHHHHHHHHHHHHHH
Confidence 99999887653 33443333 366777777655 111111 1456778899999998644 344444433
Q ss_pred Hhhh-----cCCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEE
Q psy5607 330 LDII-----KVPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSAC 389 (769)
Q Consensus 330 ~~~l-----~~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~ 389 (769)
...+ ...+....|.||..+.+... ......+.+..+++..|++++ .+|...
T Consensus 183 ~~~~~~~~~~~~~~~~~~GDD~li~~~~~-------~~~~~~~~~~~~~~~~G~~~~--~~~~~~ 238 (278)
T cd01699 183 FRKLGGKSFFKNVRLLNYGDDCLLSVEKA-------DDKFNLETLAEWLKEYGLTMT--DEDKVE 238 (278)
T ss_pred HHHHHHHHHhhceEEEEEcCCeEEEechh-------HhhhCHHHHHHHHHHcCCEeC--CcccCC
Confidence 3332 35678899999999988731 222345667888888999999 877654
No 22
>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=98.02 E-value=5.9e-06 Score=82.97 Aligned_cols=123 Identities=24% Similarity=0.249 Sum_probs=91.3
Q ss_pred ccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHH
Q psy5607 246 ECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIF 325 (769)
Q Consensus 246 ~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~ 325 (769)
...+...+|+++||..+..+ +.. ...+.+...+. .....-+|||-..||.+|.-+
T Consensus 85 ~~~~~s~lDl~~af~~i~l~------------~~~---------~~~taf~~~~~----~y~~~~lp~Gl~~sp~~f~~~ 139 (210)
T cd03715 85 KHQWYTVLDLANAFFSLPLA------------PDS---------QPLFAFEWEGQ----QYTFTRLPQGFKNSPTLFHEA 139 (210)
T ss_pred CCeEEEEeeccCeEEEEEcc------------ccc---------EEeEEEEECCe----eEEEEEEeccccCcHHHHHHH
Confidence 45678889999999888632 111 01122333331 123457999999999999999
Q ss_pred HHHHHhhhc---CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEEEeecCCCCCCCC
Q psy5607 326 MNDILDIIK---VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACILFSRARNPTFPP 402 (769)
Q Consensus 326 ~~~l~~~l~---~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i~~~~~~~~~~~~ 402 (769)
|+.++..+. .+.....|.||+.+++.. .+...+.++.+...+.++|+.+| ++||+..
T Consensus 140 ~~~~l~~~~~~~~~~~~~~Y~DDili~s~~------~~e~~~~l~~v~~~l~~~gl~l~--~~K~~~~------------ 199 (210)
T cd03715 140 LARDLAPFPLEHEGTILLQYVDDLLLAADS------EEDCLKGTDALLTHLGELGYKVS--PKKAQIC------------ 199 (210)
T ss_pred HHHHHHHHHhhCCCeEEEEECCcEEEecCC------HHHHHHHHHHHHHHHHHCCCCcC--HHHeeCC------------
Confidence 998888764 356778899999999874 56677888889999999999999 9998852
Q ss_pred eecCCCCcccccceeEeeeEe
Q psy5607 403 LFYNGSELKFESNIKFLGLYW 423 (769)
Q Consensus 403 i~i~~~~i~~~~~~kyLGv~i 423 (769)
.++++|||..+
T Consensus 200 ----------~~~v~fLG~~~ 210 (210)
T cd03715 200 ----------RAEVKFLGVVW 210 (210)
T ss_pred ----------CCceEEeeEEC
Confidence 34688999864
No 23
>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=97.93 E-value=3.9e-05 Score=74.29 Aligned_cols=110 Identities=18% Similarity=0.198 Sum_probs=77.3
Q ss_pred ccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHH
Q psy5607 246 ECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIF 325 (769)
Q Consensus 246 ~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~ 325 (769)
.......+|+.+||..+....-...+.. +...+.. + ....+|||...||.+|.-+
T Consensus 56 ~~~~~~~~D~~~~~~~i~l~~~~~~~~~---------------------~~~~~~~---~-~~~~~p~G~~~s~~~~~~~ 110 (177)
T cd01647 56 GAKVFSKLDLRSGYHQIPLAEESRPKTA---------------------FRTPFGL---Y-EYTRMPFGLKNAPATFQRL 110 (177)
T ss_pred cCcEEEecccccCcceeeeccCChhhce---------------------eecCCCc---c-EEEEecCCCccHHHHHHHH
Confidence 4457888999999999875322111111 1111111 1 1246999999999999999
Q ss_pred HHHHHhhhcCCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEE
Q psy5607 326 MNDILDIIKVPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSAC 389 (769)
Q Consensus 326 ~~~l~~~l~~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~ 389 (769)
+..+...+. ......|+||+.+.+.. .+.....++.+..-....|+.+| ++||+.
T Consensus 111 ~~~~l~~~~-~~~~~~y~DDi~i~~~~------~~~~~~~~~~~~~~l~~~~~~~~--~~K~~~ 165 (177)
T cd01647 111 MNKILGDLL-GDFVEVYLDDILVYSKT------EEEHLEHLREVLERLREAGLKLN--PEKCEF 165 (177)
T ss_pred HHhhhcccc-ccccEEEecCccccCCC------HHHHHHHHHHHHHHHHHcCCEeC--HHHcee
Confidence 988887653 34577899999998774 45555666777777788999999 999874
No 24
>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=97.84 E-value=6.3e-06 Score=83.47 Aligned_cols=98 Identities=22% Similarity=0.274 Sum_probs=64.8
Q ss_pred eEEEEEecCCCCCCCCCCcccccccccchhhhhhhccCcccccc---------CCc------hh---HHHHHHHHhhc-C
Q psy5607 22 VARADTFHKSGSRNLPSNFRPVCNYSIIPKTFEKLVYDKLSPLA---------SIS------GS---LLYWFHSFLTN-R 82 (769)
Q Consensus 22 ~~~~~~i~k~g~~~~~~~yrpi~l~~~~~K~~e~ii~~~l~~~~---------g~~------~~---l~~~~~sfl~~-R 82 (769)
.+++++|||+|++..+++||||++++...|++++++..+|.+.+ |+. .. +..++...... .
T Consensus 1 ~~~~~~ipK~~~~~~~~~~RpI~~~~~~~k~~~~~i~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (220)
T cd01650 1 KARIILIPKKGKPSDPKNYRPISLLSVLYKLLEKILANRLRPVLEENILPNQFGFRPGRSTTDAILLLREVIEKAKEKKK 80 (220)
T ss_pred CCEEEEeeCCCCCCCccCcCCchhhhHHHHHHHHHHHHHHHHHHhhcCCcccccccCCChHHHHHHHHHHHHHHHHHcCC
Confidence 37899999999988999999999999999999999999987642 111 11 22333333221 1
Q ss_pred -eEEEEEcCccccceeecc-------CCCCCCCCCCCCCCCCCccc
Q psy5607 83 -TQIVKVRKSKSTPIKVTS-------GCGQGGHMKNLAPPTDSNES 120 (769)
Q Consensus 83 -~~~v~v~~~~S~~~~v~~-------Gvpqg~~l~p~lf~~~~~~~ 120 (769)
...+.++-.. ..-.+.. |+|||+.++|++|..+.+..
T Consensus 81 ~~~~l~~Di~~-aFdsi~~~~l~~~lGipQG~~lSp~l~~l~~~~l 125 (220)
T cd01650 81 SLVLVFLDFEK-AFDSVDHEFLLKALGVRQGDPLSPLLFNLALDDL 125 (220)
T ss_pred ceEEEEEEHHh-hcCcCCHHHHHHHhCCccCCcccHHHHHHHHHHH
Confidence 2223322111 1111222 99999999999997765543
No 25
>PRK13907 rnhA ribonuclease H; Provisional
Probab=97.82 E-value=2.5e-05 Score=71.75 Aligned_cols=65 Identities=17% Similarity=0.193 Sum_probs=51.3
Q ss_pred CCeEEEEcCcHHHHHHHHccCcCCCcchHHHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCcC
Q psy5607 642 HSKFLLVSDSMSAIQAIANICSSYKNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNPC 712 (769)
Q Consensus 642 ~~~~~i~tDs~~~~~~i~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a~ 712 (769)
..++.|+|||+++++.+++.... ..-...+++.+..+..+-..+.+.|||. ++|+.||.+|+.|.
T Consensus 61 ~~~v~i~sDS~~vi~~~~~~~~~--~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~ 125 (128)
T PRK13907 61 YNIVSFRTDSQLVERAVEKEYAK--NKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAI 125 (128)
T ss_pred CCEEEEEechHHHHHHHhHHHhc--ChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHH
Confidence 45799999999999999985543 2334566666666666666788899998 49999999999986
No 26
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.32 E-value=0.0004 Score=58.65 Aligned_cols=65 Identities=25% Similarity=0.148 Sum_probs=47.7
Q ss_pred CCeEEEEcCcHHHHHHHHccCcCCCcchHHHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCcC
Q psy5607 642 HSKFLLVSDSMSAIQAIANICSSYKNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNPC 712 (769)
Q Consensus 642 ~~~~~i~tDs~~~~~~i~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a~ 712 (769)
-++++|.|||+.+++.|++..... .....+.+.+..+...-..+.|.||| =++|..||.+||.|.
T Consensus 21 ~~~i~v~sDs~~vv~~i~~~~~~~--~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~A~~LA~~a~ 85 (87)
T PF13456_consen 21 IRKIIVESDSQLVVDAINGRSSSR--SELRPLIQDIRSLLDRFWNVSVSHIP----REQNKVADALAKFAL 85 (87)
T ss_dssp -SCEEEEES-HHHHHHHTTSS-----SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHHHHHHHHHHH
T ss_pred CCEEEEEecCcccccccccccccc--ccccccchhhhhhhccccceEEEEEC----hHHhHHHHHHHHHHh
Confidence 568999999999999998874442 23445566666777777889999999 678999999999875
No 27
>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=96.98 E-value=9.7e-05 Score=74.11 Aligned_cols=87 Identities=18% Similarity=0.319 Sum_probs=65.0
Q ss_pred ecCCCCCCCCCCcccccccccchhhhhhhccCccccc-------------------------------------------
Q psy5607 28 FHKSGSRNLPSNFRPVCNYSIIPKTFEKLVYDKLSPL------------------------------------------- 64 (769)
Q Consensus 28 i~k~g~~~~~~~yrpi~l~~~~~K~~e~ii~~~l~~~------------------------------------------- 64 (769)
|||+| +++||||++.+...|++++++..+|.+.
T Consensus 1 ipK~~----~~~~RpI~~~~~~~r~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Di~~~f~ 76 (214)
T PF00078_consen 1 IPKKN----VGKYRPISIPSVDDRIVQRVLNKRLQPILEPIFSPSQFGFRPGRSCHDIKKLNRFKGYLYFLKLDISKAFD 76 (214)
T ss_dssp EESSS----SSSEEEE----EBTHHHHHHBHH---------HHHTTSSCSHGCCCHHHHHHHC-CGSSEEEEEECCCCGG
T ss_pred CCCcC----CCCeeEcCCCCcHHHHHHHHHHhhccccccccCCCCCCCCcccccccccccccccccccccceeccccccc
Confidence 67887 7889999999999999999998865531
Q ss_pred -------------cCCchhHHHHHHHHhhcCeEEEEEcCccccceeeccCCCCCCCCCCCCCCCCCcc
Q psy5607 65 -------------ASISGSLLYWFHSFLTNRTQIVKVRKSKSTPIKVTSGCGQGGHMKNLAPPTDSNE 119 (769)
Q Consensus 65 -------------~g~~~~l~~~~~sfl~~R~~~v~v~~~~S~~~~v~~Gvpqg~~l~p~lf~~~~~~ 119 (769)
++.++.+..|+..++.++...+.+++.. .......|+|||..++|++|..+...
T Consensus 77 sI~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~-~~~~~~~glpqG~~~S~~l~~~~l~~ 143 (214)
T PF00078_consen 77 SIPHHRLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGDL-SPYFQKRGLPQGSPLSPLLFNIYLDD 143 (214)
T ss_dssp GSBBHTTTGGGGEEEEECCSCHHHHHHHHHHHH-EECGCSS-SEEEEESBS-TTSTCHHHHHHHHHHH
T ss_pred cceeeeccccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhcccccc
Confidence 3567778999999999999888887775 77888999999999999999766544
No 28
>PRK07708 hypothetical protein; Validated
Probab=96.87 E-value=0.0019 Score=64.53 Aligned_cols=66 Identities=11% Similarity=0.005 Sum_probs=46.9
Q ss_pred eEEEEcCcHHHHHHHHccCcCCCcchHHHHHHHHHHHhc-CCceEEEEEecCCCCCccchhhhhhhhCcCCC
Q psy5607 644 KFLLVSDSMSAIQAIANICSSYKNSLTSKIYSAWMDLKS-GGKEVTLMWCPSHCGISGNEAVDMAAKNPCTS 714 (769)
Q Consensus 644 ~~~i~tDs~~~~~~i~~~~~~~~~~~~~~i~~~~~~~~~-~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a~~~ 714 (769)
.|.|++||+.+++.+.+.+... ++..+...+.+.++.. -...+.+.|||- ..|+.||+||+.|+..
T Consensus 142 ~V~I~~DSqlVi~qi~g~wk~~-~~~l~~y~~~i~~l~~~~~l~~~~~~VpR----~~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 142 PVTFRGDSQVVLNQLAGEWPCY-DEHLNHWLDRIEQKLKQLKLTPVYEPISR----KQNKEADQLATQALEG 208 (219)
T ss_pred eEEEEeccHHHHHHhCCCceeC-ChhHHHHHHHHHHHHhhCCceEEEEECCc----hhhhHHHHHHHHHHhc
Confidence 4899999999999998765442 2233344444443332 333578899985 5699999999999975
No 29
>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=96.56 E-value=0.00056 Score=69.37 Aligned_cols=84 Identities=15% Similarity=0.173 Sum_probs=61.7
Q ss_pred EEEecCCCCCCCCCCcccccccccchhhhhhhccCccccc----------------------------------------
Q psy5607 25 ADTFHKSGSRNLPSNFRPVCNYSIIPKTFEKLVYDKLSPL---------------------------------------- 64 (769)
Q Consensus 25 ~~~i~k~g~~~~~~~yrpi~l~~~~~K~~e~ii~~~l~~~---------------------------------------- 64 (769)
-+.|+|+|. .||||+++++..|++++++..+|.+.
T Consensus 2 ~~~i~K~~g-----~~RpI~~~~~~~ki~~~~i~~~L~~~~~~~~~~~~~g~~~~rs~~~~i~~i~~~~~~~~~~~~~~D 76 (226)
T cd01651 2 RVYIPKPNG-----KKRPLGIPTVRDRIVQEALKLVLEPIYEPRFSDCSYGFRPGRSAHDALKAIRRNVKGGYTWVIEGD 76 (226)
T ss_pred eeeecCCCC-----CCCccCCCchHHHHHHHHHHHHHHHHHhhccccCCCCCCCCCCHHHHHHHHHHHhcCCCeEEEEcc
Confidence 367888775 79999999999999999998877532
Q ss_pred -------------------cCCchhHHHHHHHHhhcCeEEEEEcCccccceeeccCCCCCCCCCCCCCCCCCcc
Q psy5607 65 -------------------ASISGSLLYWFHSFLTNRTQIVKVRKSKSTPIKVTSGCGQGGHMKNLAPPTDSNE 119 (769)
Q Consensus 65 -------------------~g~~~~l~~~~~sfl~~R~~~v~v~~~~S~~~~v~~Gvpqg~~l~p~lf~~~~~~ 119 (769)
.+.++.+..|+.+|+.... ...+.......|+|||+.++|+||......
T Consensus 77 i~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~------~~~~~~~~~~~GlpqG~~lSp~L~~~~l~~ 144 (226)
T cd01651 77 IKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGV------LEDGKLVETEKGTPQGGVISPLLANIYLHE 144 (226)
T ss_pred HHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHHHhceE------ccCCeEeCCCCCcCCCccHHHHHHHHHHHH
Confidence 2455666666666643321 122345577899999999999999876655
No 30
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=96.50 E-value=0.0036 Score=68.76 Aligned_cols=66 Identities=17% Similarity=0.193 Sum_probs=50.2
Q ss_pred CCeEEEEcCcHHHHHHHHccCcCCCcchHHHHHHHHHHHhcCCceEEEEEecCCCCCccchhhhhhhhCcC
Q psy5607 642 HSKFLLVSDSMSAIQAIANICSSYKNSLTSKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAVDMAAKNPC 712 (769)
Q Consensus 642 ~~~~~i~tDs~~~~~~i~~~~~~~~~~~~~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~aD~~Ak~a~ 712 (769)
.+++.|++||+++++.+.+.+......+ ..+.+.+.++..+-..+.+.|||. ++|+.||.||+.|.
T Consensus 65 ~~~v~i~~DS~lvi~~i~~~~~~~~~~l-~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~ 130 (372)
T PRK07238 65 ATEVEVRMDSKLVVEQMSGRWKVKHPDM-KPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAM 130 (372)
T ss_pred CCeEEEEeCcHHHHHHhCCCCccCChHH-HHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHH
Confidence 5689999999999999987554322333 334444566666667899999997 68999999999885
No 31
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=96.11 E-value=0.0056 Score=61.28 Aligned_cols=111 Identities=12% Similarity=0.062 Sum_probs=78.5
Q ss_pred ccccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCcc--ce-eeeccCCCCCCCCchHH
Q psy5607 244 KKECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSF--SN-SFPLQNGIVQGSSLSPV 320 (769)
Q Consensus 244 ~~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~--s~-~~~~~~GvpQGs~LSPl 320 (769)
-+...+++.+|+++||-.|.-+ +.- ...+.+.+.+.. .. ....-.-+|+|..-||.
T Consensus 55 ~R~~~~~~~~Di~~af~qI~i~------------~~d---------~~~~~F~w~~~~~~~~~~~Y~~~~~pFG~~~AP~ 113 (213)
T cd01644 55 FRQGKIAVSADIEKMFHQVKVR------------PED---------RDVLRFLWRKDGDEPKPIEYRMTVVPFGAASAPF 113 (213)
T ss_pred eecCceeEehhHHHhhhheecC------------ccc---------CceEEEEEeCCCCCCcceEEEEEEEccCCccchH
Confidence 3556788999999999887422 111 112333333221 11 23344569999999999
Q ss_pred HHHHHHHHHHhhhcC-----CceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccc
Q psy5607 321 LFIIFMNDILDIIKV-----PLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFS 381 (769)
Q Consensus 321 Lf~l~~~~l~~~l~~-----~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in 381 (769)
+|..+|+.+...+.. .+....|.||+.+.+.+ .+++...++.+.+.+.+.|+.+.
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s------~~e~~~~~~~v~~~L~~~Gf~l~ 173 (213)
T cd01644 114 LANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDT------LNEAVNVAKRLIALLKKGGFNLR 173 (213)
T ss_pred HHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCC------HHHHHHHHHHHHHHHHhCCccch
Confidence 999999999987653 23567999999998774 56777788888888888998775
No 32
>PHA00028 rep RNA replicase, beta subunit
Probab=89.83 E-value=7.1 Score=43.18 Aligned_cols=178 Identities=16% Similarity=0.060 Sum_probs=104.9
Q ss_pred cEEEEeecCCCCCCCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcc
Q psy5607 165 SLILPLLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAK 244 (769)
Q Consensus 165 a~i~~i~K~~kd~~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~ 244 (769)
.+++..||.+| -=|-|+..+-+.-.+++-+..-|+..+..-++==+.|. ..+.+ +..-
T Consensus 191 n~~~tVPKN~K------tDR~ia~EP~~NM~lQkgVG~~IRrrLr~~gIDLNdQs--------------~NQ~L--A~~g 248 (561)
T PHA00028 191 NRVFTVPKNNK------TDRAIAKEPDLNMFLQKGVGGFIRRRLRLAGIDLNDQS--------------RNQEL--ARLG 248 (561)
T ss_pred CceeeecCCcc------cchheecCCChhHHHHHhhHHHHHHHHHHcCCCcccch--------------hHHHH--HHhc
Confidence 45667788873 34888889988888888777766666654222112221 12222 2233
Q ss_pred cccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeee---ccCCCCCCCCchHHH
Q psy5607 245 KECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFP---LQNGIVQGSSLSPVL 321 (769)
Q Consensus 245 ~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~---~~~GvpQGs~LSPlL 321 (769)
.....+..+|++.|=|+|+...+..- +|+.+...+..+=+... .++|..-.+-. +.+|-- =-|=.++
T Consensus 249 S~d~sLATIDLSsASDSISl~LV~ll-----lPp~~~~~L~dlRS~~g---~ldG~~i~~ek~SSMGNGfT--FELeSLI 318 (561)
T PHA00028 249 SVDGSLATIDLSSASDSISLKLVWLL-----LPPHWYSVLTDLRSSYG---MLDGRLIEWEKFSSMGNGFT--FELESLI 318 (561)
T ss_pred cccCceeeEeccccccHHHHHHHHHH-----cCHHHHHHHHHhcCccc---eeCCEEeehhhhccccCcee--eeHHHHH
Confidence 34567899999999999987644433 58887777766544333 23554332211 222311 0122344
Q ss_pred HHHHHHHHHhhhcCCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEE
Q psy5607 322 FIIFMNDILDIIKVPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSAC 389 (769)
Q Consensus 322 f~l~~~~l~~~l~~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~ 389 (769)
|.-....+.........+..|-||+.+=.. +...+-+.....|+..| .+||-.
T Consensus 319 f~Aiars~~~~~~~~~ti~VYGDDIIvps~-------------~a~~li~vlsyvgF~pN--~kKTF~ 371 (561)
T PHA00028 319 FAAIARSFCLLFGGPGTISVYGDDIIVPTE-------------VAPPLINVLSYVGFMPN--LKKTFW 371 (561)
T ss_pred HHHHHHHHHHhcCCCCeeEEecCceEeehh-------------hhHHHHHHHHHhceecC--Cccccc
Confidence 433333332223356778899999988543 33344455567899999 999864
No 33
>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=89.38 E-value=5 Score=44.39 Aligned_cols=176 Identities=16% Similarity=0.115 Sum_probs=113.6
Q ss_pred CCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcccccEEEEEecccCCCC
Q psy5607 181 SNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAKKECTVALLLDGQKAFD 260 (769)
Q Consensus 181 ~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~~~~~~~v~lD~~kAFD 260 (769)
+.-|+|+..+...-.+-+=|.+.+-..+.. ++. -+|-|+..-+....... ..+ .+..+|++.|=|
T Consensus 96 gK~Ri~Am~D~~tQ~~L~PlH~~lf~~Lr~---ip~--------DgTF~Q~~~~~~~~~~~-~~~---~~~S~DLsaATD 160 (498)
T PF05919_consen 96 GKVRIFAMVDYWTQCVLKPLHDWLFSILRR---IPQ--------DGTFDQEPPFDRLVDSM-KEK---YFYSFDLSAATD 160 (498)
T ss_pred CceEEEEEEeHHHHHhhHHHHHHHHHHHhc---CCC--------CCCcCCCCchhhHhhcc-cCC---ceEEEeeccccc
Confidence 567999999988888888888877777763 332 22222222222221111 111 188999999999
Q ss_pred CCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHHHHHHHhhh-------
Q psy5607 261 MTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILDII------- 333 (769)
Q Consensus 261 ~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~~~~l~~~l------- 333 (769)
+.+-....+.|... ++..+-.-.++.+-+|.+ +. .......-..|-|.|.--|=-+|.+.=+-+....
T Consensus 161 R~Pi~lQ~~il~~l-~~~~~a~~W~~llv~r~~-~~---~~~~~v~y~vGQPmGa~SSW~~~altHH~iV~~aA~~~~~~ 235 (498)
T PF05919_consen 161 RFPIVLQERILSYL-FGDSFASSWRSLLVGRPY-LK---PNGDEVRYSVGQPMGAYSSWAMFALTHHLIVQYAAERVGGG 235 (498)
T ss_pred cccHHHHHHHHHHH-hCchHHHHHHHHHcCCcc-cc---CCCCeEEEecCCcchhccccHHHHhhHHHHHHHHHHHhhcc
Confidence 99998888888876 444666566788877777 22 2234567788999998777667777544443322
Q ss_pred cCCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEEE
Q psy5607 334 KVPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSACI 390 (769)
Q Consensus 334 ~~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~i 390 (769)
.....+..--||++|.-. . ....-..-+...|.++| ..||.+-
T Consensus 236 ~~f~~Y~iLGDDivi~~~--------~----vA~~Y~~~m~~Lgv~is--~~Ks~vS 278 (498)
T PF05919_consen 236 SRFTDYIILGDDIVIAND--------K----VAKQYLSIMTDLGVEIS--LSKSHVS 278 (498)
T ss_pred CCCCceEEEcCcEEEcCH--------H----HHHHHHHHHHHcCceec--cCccccc
Confidence 134456667799988633 2 22333444566899999 9998764
No 34
>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=89.11 E-value=5.2 Score=45.72 Aligned_cols=186 Identities=16% Similarity=0.133 Sum_probs=114.6
Q ss_pred CCCcccccCCchhHHHHHHHHhhhhHHHHhc-CCCCCCcccccCCCChhhHHHHHHHHHHHhhcccccEEEEEecccCCC
Q psy5607 181 SNYRPISLLNCSGKILEKMVNKRLFWVLENR-GLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAKKECTVALLLDGQKAF 259 (769)
Q Consensus 181 ~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~-~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~~~~~~~v~lD~~kAF 259 (769)
..-|-|...+...-|+.+.....+...+..+ ....+.+-|--+...-.+ .+...+.. ...++.+|++ .|
T Consensus 182 ~KtR~~~~~p~~~~i~~r~~~~~~~~~~~~~~~~~~~~aVGinp~~~~w~-------~l~~~l~~--~~~~~~~DyS-~F 251 (491)
T PF00680_consen 182 GKTRLFWASPLDYNIAFRMYFGPFIAAFMANPRIELPSAVGINPYSRDWT-------RLANRLRS--GDNVFCGDYS-NF 251 (491)
T ss_dssp TEEEEEEEE-HHHHHHHHHHHHHHHHHHHHTTBTTTTB-TTHHHTHHHHH-------HHHHHHTT--SSEEEEEEES-ST
T ss_pred CCccceEecChHHHHHHHHHHHHHHHHHHHhcccceeeeeccccccCchH-------HHHHHhhc--cceeEeeehh-hc
Confidence 4579999999999999999999999999876 555556666444221111 11122222 5578999998 57
Q ss_pred CCCChHHHHHHH----hcCC----CCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCchHHHHHHHHHHHHh
Q psy5607 260 DMTWRFKIIETL----KGFN----INGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLSPVLFIIFMNDILD 331 (769)
Q Consensus 260 D~V~~~~L~~~L----~~~g----~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LSPlLf~l~~~~l~~ 331 (769)
|+--+..++... ..+. -......++...+..+.. ..+| ..+.+.+|+|-|+++.-++=.++..-+..
T Consensus 252 D~s~~~~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~--~~~g---~~y~~~~G~PSG~~~Tsi~NSi~N~i~~~ 326 (491)
T PF00680_consen 252 DSSLSPQLIDAAFDILNRFYDDSEEFSRLRRNLIQSICNPIH--LCGG---KVYRVNGGNPSGSPLTSIINSIVNNIYIR 326 (491)
T ss_dssp HHHS-HHHHHHHHHHHHHTTHHHSSHHHHHHHHHHHHHEEEE--EETT---EEEEEESSS-TTSTTHHHHHHHHHHHHHH
T ss_pred CCcccHHHHHHHHHHhhhhhcccccchHHHHHHHHhcCCeee--eccc---ceeeeccccccccccchhccccccceeec
Confidence 866665555444 3333 123334455555544432 2344 56789999999999986655554333222
Q ss_pred h----hc-----C---CceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceEE
Q psy5607 332 I----IK-----V---PLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSAC 389 (769)
Q Consensus 332 ~----l~-----~---~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~~ 389 (769)
. +. . .+..+.|-||.++.+... .. .. ..+.+.+.+++.|+++.. ++|+..
T Consensus 327 ~a~~~~~~~~~~~~~~~~~~i~YGDD~l~sv~~~-----~~-~~-n~~~i~~~~~~~G~~~T~-~dK~~~ 388 (491)
T PF00680_consen 327 YAWRKLYPDPPREFFENVKLIVYGDDNLISVPPE-----ID-PW-NGETISEFLAELGLTYTD-ADKTGE 388 (491)
T ss_dssp HHHHHHSTSCHGGGHHHSEEEEETTEEEEEESSH-----HH-HH-HHHHHHHHHHTTTEEEEE-SSTSSS
T ss_pred hhhhhccccccccccceeeeeeeccccchhhhcc-----cc-cc-hhHHHHHHHHhccccccc-ccccCC
Confidence 2 11 1 367899999999988741 11 11 567777888889999981 377654
No 35
>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=88.46 E-value=0.18 Score=50.68 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=22.4
Q ss_pred CCcccccccccchhhhhhhccCccc
Q psy5607 38 SNFRPVCNYSIIPKTFEKLVYDKLS 62 (769)
Q Consensus 38 ~~yrpi~l~~~~~K~~e~ii~~~l~ 62 (769)
+.+|||+..+..-|++++++..+|.
T Consensus 4 g~~R~I~~p~~~~r~iq~~l~~~l~ 28 (214)
T cd03487 4 GGFRTIYAPKPELKAIQRKILSNLL 28 (214)
T ss_pred CCeeeEeCCCHHHHHHHHHHHHHHh
Confidence 3499999999999999999998885
No 36
>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=81.92 E-value=14 Score=40.33 Aligned_cols=176 Identities=15% Similarity=0.092 Sum_probs=90.2
Q ss_pred cEEEEeecCCCCCCCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcc
Q psy5607 165 SLILPLLKPGKDRLVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAK 244 (769)
Q Consensus 165 a~i~~i~K~~kd~~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~ 244 (769)
++++..||.. +-=|-|+..+.+--.+++-+..-|+..+..-++==..| .+.+.+.. .-
T Consensus 183 n~~~tVPKn~------k~dR~ia~EP~~NM~lQk~vg~~Ir~rLr~~gIdLndQ--------------t~NQ~lA~--~g 240 (542)
T PF03431_consen 183 NKAFTVPKNS------KTDRCIAKEPDWNMFLQKGVGGFIRRRLRLWGIDLNDQ--------------TINQRLAR--EG 240 (542)
T ss_dssp EEEEEEEEES------SEEEEEEE--HHHHHHHHHHHHHHHHHHGGGT--TT-T--------------HHHHHHHH--HH
T ss_pred CceeeecCcC------ccccceecCCcHHHHHHHhhHHHHHHHHHHcCCCcccc--------------chhHHHHH--hh
Confidence 5667789987 34588999999988888887777777665321111112 11122211 11
Q ss_pred cccEEEEEecccCCCCCCChHHHHHHHhcCCCCchhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCc----hHH
Q psy5607 245 KECTVALLLDGQKAFDMTWRFKIIETLKGFNINGYMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSL----SPV 320 (769)
Q Consensus 245 ~~~~~~v~lD~~kAFD~V~~~~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~L----SPl 320 (769)
.....+..+|++.|=|+|+......- +|+.+...+..+-+... .++|.. +..+.=--+|.-. -.+
T Consensus 241 S~d~~laTIDLSsASDsis~~Lv~~l-----lPp~~~~~l~~lRs~~~---~l~g~~---~~~ek~ssMGNGfTFELeSl 309 (542)
T PF03431_consen 241 SRDGSLATIDLSSASDSISLWLVELL-----LPPHWYRYLTDLRSPYG---SLDGKV---IRWEKISSMGNGFTFELESL 309 (542)
T ss_dssp HHHSSEEEEEBTTCCCT-BHHHHHHH-----S-HHHHHHHHHHS-SEE---E-TS-E---EE-SBS--TTSTTHHHHHHH
T ss_pred hhcccceeEeccccccHhHHHHHHHh-----CCHHHHHHHHHhccccc---eECCEE---EehhhhhccCCceeEeHHHH
Confidence 23346788999999999997654444 46777777666544333 356653 3333333344432 122
Q ss_pred HHHHHHHHHHhhh-cCCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCceE
Q psy5607 321 LFIIFMNDILDII-KVPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKKSA 388 (769)
Q Consensus 321 Lf~l~~~~l~~~l-~~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~Kt~ 388 (769)
+|.-....+-..+ .....+..|-||+.+=.. +...+.+.....|+..| .+||-
T Consensus 310 if~ai~rs~~~~~~~~~~~v~iYGDDIIvp~~-------------~~~~l~~~l~y~gF~~N--~~KTF 363 (542)
T PF03431_consen 310 IFWAIARSVCELLFGDTGTVRIYGDDIIVPSE-------------CAPDLIEVLSYVGFKPN--LKKTF 363 (542)
T ss_dssp HHHHHHHHHHHHCT--GGG-EEETTEEEEEGG-------------GHHHHHHHHHHCT--B---CCC-B
T ss_pred HHHHHHHHHHHHHcCCCCeeEEecCcEEechh-------------hhHHHHHHHHHhCcccC--ccccc
Confidence 2222111111111 145677889999988543 23334445567899999 99974
No 37
>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=75.62 E-value=0.66 Score=32.84 Aligned_cols=42 Identities=24% Similarity=0.392 Sum_probs=7.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHhhhcccCCCCHHHHHHHHhhcccc
Q psy5607 429 WALHINHTKSRAMVALNVLKMVCNKKYGVRRETLLTFYKSYIMP 472 (769)
Q Consensus 429 ~~~hi~~~~~ka~~~l~~lr~l~~~~~gl~~~~~~~l~~a~v~p 472 (769)
|+.|+..+.+++..++..||.+.+ ..+++..+..+|+++|.+
T Consensus 1 W~~n~~~~~KKa~qRlyFLRkl~k--~~~~~~~l~lfY~s~IeS 42 (42)
T PF09004_consen 1 WTSNTTSLYKKAQQRLYFLRKLRK--FNVDSKLLTLFYHSVIES 42 (42)
T ss_dssp ---------------------------SS-----SHTTTTT---
T ss_pred CCcchHHHHHHHHhHHHHHHHHHH--ccchhHHHHHHHHHHhcC
Confidence 677889999999999999998854 457788888888887643
No 38
>PF00998 RdRP_3: Viral RNA dependent RNA polymerase; InterPro: IPR002166 The RNA dependent RNA polymerase is also known as non-structural protein NS5B. NS5B is a 65 kDa protein that resembles other viral RNA polymerases. Hepatitis C virus (HCV) replication is thought to occur in membrane bound replication complexes. These complexes transcribe the positive strand and the resulting minus strand is used as a template for the synthesis of genomic RNA. There are two viral proteins involved in the reaction, NS3 and NS5B [, , ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0006351 transcription, DNA-dependent, 0019079 viral genome replication; PDB: 2XYM_A 3I5K_D 4AEX_A 4E7A_A 2XXD_A 4E78_A 4AEP_A 4E76_A 1S4F_D 1S48_A ....
Probab=56.99 E-value=1.9e+02 Score=32.76 Aligned_cols=184 Identities=13% Similarity=0.016 Sum_probs=110.1
Q ss_pred CCCCCCcccccCCchhHHHHHHHHhhhhHHHHhcCCCCCCcccccCCCChhhHHHHHHHHHHHhhcccccEEEEEecccC
Q psy5607 178 LVPSNYRPISLLNCSGKILEKMVNKRLFWVLENRGLINPFQSGGRFRRSTIDNLVFLEKEAAQGLAKKECTVALLLDGQK 257 (769)
Q Consensus 178 ~~~~~yRPIsll~~~~Ki~ekii~~rL~~~~~~~~~l~~~Q~Gfr~~rs~~d~i~~l~~~i~~~~~~~~~~~~v~lD~~k 257 (769)
-.|.+=|-|.-+..-.|.+|+.+..-|-..... +..-+|| + .....+.+...|+..+.-+.+.+|.+
T Consensus 144 i~pr~pR~~v~~g~~lr~~E~~~~~~l~~~~~g----p~~~kgy----~----~~q~~~~l~~~W~~f~~Pvai~~D~~- 210 (486)
T PF00998_consen 144 IQPRPPRYNVEPGRYLRPCEKRAYYALDKAWGG----PTVIKGY----T----PEQRGEILLKKWDSFKDPVAIGFDAS- 210 (486)
T ss_dssp TBSB--EEEEEE-HHHHHHHHHHHHHHHHHHHG----GGBGGGS----G----HHHHHHHHHHHHHTSSSEEEEEEEBT-
T ss_pred CCCCCCcEEEecCccchhhHHHHHHhhhhhccC----ceeeccC----C----HHHHHHHHHHHhhccCCceEEEecch-
Confidence 346777889999999999999998887665543 1222333 2 34556777788888889999999976
Q ss_pred CCC-CCChHHHH--HHHhcCCC-Cc-hhHHHHHHHhcCCeEEEEeCCccceeeeccCCCCCCCCch-----HHHHHHHHH
Q psy5607 258 AFD-MTWRFKII--ETLKGFNI-NG-YMLRYLCNFLYNRSFKVKCNGSFSNSFPLQNGIVQGSSLS-----PVLFIIFMN 327 (769)
Q Consensus 258 AFD-~V~~~~L~--~~L~~~g~-~~-~~~~~i~~~l~~~~~~v~~~~~~s~~~~~~~GvpQGs~LS-----PlLf~l~~~ 327 (769)
.|| +|+-+.|- +.+-..-+ ++ .++..+..-|.+...-+.-.|.. ..-.+|.+-...+. .++..+-+.
T Consensus 211 rFD~~Vs~~~l~~E~~iY~~~~~~~~~~~~~L~~~l~~~G~~~~~~G~~---~y~~~gcR~SGd~~TS~GN~l~~~~~~~ 287 (486)
T PF00998_consen 211 RFDQHVSEEDLRFEHSIYQCCFLDPEELIKLLTERLYNGGPMFNSDGQV---RYGYRGCRMSGDMNTSLGNCLTCYLKAY 287 (486)
T ss_dssp THHHH--HHHHHHHHHHHTTSBEGHHHHHHHHHHHTTTEEEEEETTSE----EEEEESS--TTSTTHHHHHHHHHHHHHH
T ss_pred hhccCCchhhhhhhheehhcccCCchhhhccchhceeeeEEEEecCCCe---eeccCCcccCCCCCcccccHHHHHHHHH
Confidence 787 45555442 22223223 33 57777776555555444444431 11223444443443 233333344
Q ss_pred HHHhhhcCCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCcccccCCCc
Q psy5607 328 DILDIIKVPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIFSADPKK 386 (769)
Q Consensus 328 ~l~~~l~~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~in~~~~K 386 (769)
.+.+.+..+...+---||.++++.+ ..+++..+.+..|....|.... .+|
T Consensus 288 a~~~~~g~~~~l~~~GDD~vvi~E~-------~~~~~~~~~l~~~~~~~Gf~~~--~e~ 337 (486)
T PF00998_consen 288 AACRAAGKDCSLLNCGDDCVVICES-------AGVDEDEAALTEAFTRYGFPMK--VEK 337 (486)
T ss_dssp HHHHHHTEEEEEEEETTEEEEEEEH-------CHHHHHHHHHHHHHHHTT-BSS--SCE
T ss_pred HHHhhcCCCccEeecCCceEEEecc-------cchHHHHHHHHHHHHhcCCCCC--CCC
Confidence 4444445677788889999999985 4455566688888999996666 555
No 39
>CHL00002 matK maturase K
Probab=35.81 E-value=77 Score=36.00 Aligned_cols=52 Identities=10% Similarity=0.106 Sum_probs=38.1
Q ss_pred CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHH-HHHhCcccccCCCceEEEEee
Q psy5607 335 VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKW-SNQNGLIFSADPKKSACILFS 393 (769)
Q Consensus 335 ~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w-~~~~GL~in~~~~Kt~~i~~~ 393 (769)
+.++++.||||..+...|. ...+++....+..| .....+.++ ++|+.+-+++
T Consensus 271 p~ihYVRYaddfIIg~kGs-----k~~a~KwK~~l~~F~q~~f~l~~s--~eKi~I~~ls 323 (504)
T CHL00002 271 PFIHYVRYQGKSILASKGT-----PLLMNKWKYYLVNFWQCHFHLWSQ--PGRIHINQLS 323 (504)
T ss_pred ceEEEEEECCcEEEEECCC-----HHHHHHHHHHHHHHHHHhceeeec--CCceeecccc
Confidence 4568899999999998874 44555666666554 456678899 9998876654
No 40
>PF00978 RdRP_2: RNA dependent RNA polymerase; InterPro: IPR001788 This entry represents RNA dependent RNA polymerases found in several types of viruses [], especially those with a tripartite genome (RNA1, RNA2 and RNA3) and an encapsidated subgenomic RNA (RNA4) from which the coat protein is expressed, such as Cucumber mosaic virus (strain NT9) (CMV). This entry contains the following proteins: Viral RNA-directed RNA polymerase 2A (protein 2A) []. Putative RNA dependent RNA polymerase from Tobacco mosaic virus []. Non structural polyprotein from Togavirus []. ; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=29.58 E-value=1.8e+02 Score=32.77 Aligned_cols=104 Identities=13% Similarity=0.018 Sum_probs=53.2
Q ss_pred cEEEEEecccCCCCCCChHHH----HHHHhcCCCCchhHHHHHHHhcCCeEEEEeCC-ccceeeeccCCCCCCCCchHHH
Q psy5607 247 CTVALLLDGQKAFDMTWRFKI----IETLKGFNINGYMLRYLCNFLYNRSFKVKCNG-SFSNSFPLQNGIVQGSSLSPVL 321 (769)
Q Consensus 247 ~~~~v~lD~~kAFD~V~~~~L----~~~L~~~g~~~~~~~~i~~~l~~~~~~v~~~~-~~s~~~~~~~GvpQGs~LSPlL 321 (769)
....+-.|++ |||+=-.... ...++.+|+|+.++.+...+-......-.-.| ..+-...-..|=+ +.-|+-.+
T Consensus 210 ~~~~~E~D~s-kFDkSQd~~~~~~E~~i~~~lG~p~~li~~w~~~~~~~~~~~~~~G~~~~i~~qR~SGe~-~T~l~NT~ 287 (440)
T PF00978_consen 210 SYYCTEIDFS-KFDKSQDEFHLAFEREIYKRLGVPEELIDLWFDSHEYSRIKDSKLGISFAIMYQRRSGEA-NTFLGNTI 287 (440)
T ss_pred CceeeeehHH-HHhhhhHHHHHHHHHHHHHHCCCCHHHHHHHHhheEEEEEEccCCceeeEeeeeeccCCc-hhhHHHHH
Confidence 4678899998 7886544333 45778899999999876554433322211111 1001111122321 22334444
Q ss_pred HHHHHHHHHhhhcCCceeeeeeccceEEEec
Q psy5607 322 FIIFMNDILDIIKVPLRRLLFIDDFLVIARG 352 (769)
Q Consensus 322 f~l~~~~l~~~l~~~~~~~~yADD~~l~~~~ 352 (769)
.|+++....-.+........--||..+....
T Consensus 288 ~nma~~~~~y~~~~~~~~~f~GDDsli~~~~ 318 (440)
T PF00978_consen 288 VNMAVLASRYDLDKVEAICFSGDDSLIFSPK 318 (440)
T ss_pred HHHHHHHHeeccCCceEEEEeCCchhccCCc
Confidence 4444433333333233344455777777664
No 41
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=28.77 E-value=63 Score=37.69 Aligned_cols=34 Identities=24% Similarity=0.315 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcCCceEEEEEecCCCCCccchhh
Q psy5607 671 SKIYSAWMDLKSGGKEVTLMWCPSHCGISGNEAV 704 (769)
Q Consensus 671 ~~i~~~~~~~~~~~~~v~~~wvp~H~gi~gNe~a 704 (769)
.++...++++.+.|..|-+-|||||.+..||=.+
T Consensus 214 edfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 214 EDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 5677777789999999999999999999888765
No 42
>TIGR00081 purC phosphoribosylaminoimidazole-succinocarboxamide synthase. Check length. Longer versions may be multifunctional enzymes.
Probab=27.40 E-value=83 Score=31.97 Aligned_cols=133 Identities=20% Similarity=0.197 Sum_probs=78.2
Q ss_pred ccEEEEEecccCCCCCCChH--------------HHHHHHhcCCCCchhHHHHHHHhcCCeEEEE----------eCCcc
Q psy5607 246 ECTVALLLDGQKAFDMTWRF--------------KIIETLKGFNINGYMLRYLCNFLYNRSFKVK----------CNGSF 301 (769)
Q Consensus 246 ~~~~~v~lD~~kAFD~V~~~--------------~L~~~L~~~g~~~~~~~~i~~~l~~~~~~v~----------~~~~~ 301 (769)
..+.+++-|=-.|||.+-++ ++++.|...|+|.+++. ..+.+.+.|+ +.+..
T Consensus 24 ~~li~~f~D~~tafdg~~~~~i~gKG~~~~~is~~~F~~L~~~GI~tH~i~----~~~~~~~lv~k~~~iPlEvIvR~~a 99 (237)
T TIGR00081 24 DLLRFVFRDDISAFDGEKKDQIPGKGRLNTKISAFIFEKLEEAGIPTHYID----LIEDREMLVKKLDIIPLEVIVRNIA 99 (237)
T ss_pred CEEEEEEeCCccccCcccCCCCCCHHHHHHHHHHHHHHHHHhCCCCcceec----ccCCCEEEEEEcceecEEEEEeccc
Confidence 34558999999999988665 56788888999988885 5556665543 44555
Q ss_pred ceeeeccCCCCCCCCchHHHHHHHHHHHHhhhc-CCceeeeeeccceEEEeccCHHHHHHHHHHHHHHHHHHHHHhCccc
Q psy5607 302 SNSFPLQNGIVQGSSLSPVLFIIFMNDILDIIK-VPLRRLLFIDDFLVIARGKVIELLRIKIQKALNDILKWSNQNGLIF 380 (769)
Q Consensus 302 s~~~~~~~GvpQGs~LSPlLf~l~~~~l~~~l~-~~~~~~~yADD~~l~~~~~~~~~~~~~lq~~l~~l~~w~~~~GL~i 380 (769)
+..+.-.-|+|.|-.+.|-|.-++.-+ .... +.++ .-++.-.-+ ++....++..+...+.-+.+..++...|+.+
T Consensus 100 ~GS~~rr~~~~eG~~~~~pl~E~~~k~--d~~~Dp~i~-~~~~~~~~~-~~~~e~~~i~~~a~~v~~~l~~~~~~~gl~L 175 (237)
T TIGR00081 100 AGSLLKRLGIPEGLELEQPLVEFIFKP--DEVGDPMLN-ESYAEALGL-ATEEELERIKELALKVNEVLKKYFDEKGIIL 175 (237)
T ss_pred cccceeccCCCCCCcCCCCccceEEcc--cccCCCCCC-HhHHHHhcc-CCHHHHHHHHHHHHHHHHHHHHHHHHCCCEE
Confidence 555544457888887766544333222 1110 0000 001100111 1111223344555666777788899999999
Q ss_pred ccCCCceE
Q psy5607 381 SADPKKSA 388 (769)
Q Consensus 381 n~~~~Kt~ 388 (769)
- .-|-+
T Consensus 176 v--D~K~E 181 (237)
T TIGR00081 176 V--DFKLE 181 (237)
T ss_pred E--EEeEE
Confidence 8 77755
Done!