Query psy15450
Match_columns 659
No_of_seqs 428 out of 2451
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 21:24:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.9 9.5E-23 2.1E-27 192.9 10.9 134 245-387 3-146 (154)
2 PRK06548 ribonuclease H; Provi 99.9 2E-21 4.4E-26 186.7 12.5 128 246-387 6-143 (161)
3 PRK08719 ribonuclease H; Revie 99.8 9.6E-21 2.1E-25 180.1 11.3 129 246-385 5-146 (147)
4 PRK00203 rnhA ribonuclease H; 99.8 2.6E-20 5.7E-25 177.8 11.2 131 246-388 4-144 (150)
5 PF00075 RNase_H: RNase H; In 99.7 3.5E-18 7.5E-23 158.2 9.8 121 246-384 4-131 (132)
6 KOG3752|consensus 99.7 5.7E-17 1.2E-21 170.5 9.3 145 238-386 205-365 (371)
7 PRK13907 rnhA ribonuclease H; 99.6 2.5E-15 5.3E-20 139.4 9.5 125 245-385 1-126 (128)
8 cd06222 RnaseH RNase H (RNase 99.6 9.7E-15 2.1E-19 131.0 12.8 129 247-384 1-130 (130)
9 PRK07708 hypothetical protein; 99.4 1.1E-12 2.3E-17 132.8 8.7 133 245-388 73-210 (219)
10 PRK07238 bifunctional RNase H/ 99.3 5.9E-12 1.3E-16 137.5 12.1 129 246-387 3-133 (372)
11 cd01651 RT_G2_intron RT_G2_int 99.3 3E-12 6.5E-17 128.8 8.8 99 48-184 40-138 (226)
12 cd03487 RT_Bac_retron_II RT_Ba 99.2 1.6E-11 3.5E-16 123.9 7.2 70 42-122 26-96 (214)
13 cd01650 RT_nLTR_like RT_nLTR: 99.2 2E-11 4.4E-16 122.5 7.0 59 48-107 47-105 (220)
14 PF13456 RVT_3: Reverse transc 99.0 2.6E-09 5.7E-14 91.2 9.4 86 292-385 1-86 (87)
15 PF00078 RVT_1: Reverse transc 98.9 6.4E-11 1.4E-15 117.3 -4.6 111 46-195 35-146 (214)
16 cd01709 RT_like_1 RT_like_1: A 98.0 2.4E-05 5.2E-10 83.5 10.2 85 71-184 11-95 (346)
17 cd01646 RT_Bac_retron_I RT_Bac 97.9 2.9E-06 6.2E-11 81.7 0.4 65 89-184 1-65 (158)
18 KOG4768|consensus 97.6 5E-05 1.1E-09 84.9 5.2 114 28-184 316-429 (796)
19 cd01648 TERT TERT: Telomerase 96.4 0.00095 2.1E-08 61.3 0.3 12 89-100 1-12 (119)
20 PF13966 zf-RVT: zinc-binding 94.8 0.017 3.6E-07 49.9 2.0 42 456-497 40-82 (86)
21 COG3344 Retron-type reverse tr 94.7 0.067 1.5E-06 57.6 6.9 104 46-183 145-249 (328)
22 KOG1005|consensus 93.3 0.22 4.7E-06 58.8 7.6 27 81-107 516-542 (888)
23 cd00304 RT_like RT_like: Rever 63.6 3.7 8.1E-05 35.3 1.3 9 174-184 15-23 (98)
24 cd01699 RNA_dep_RNAP RNA_dep_R 30.8 1.2E+02 0.0026 31.3 6.4 73 42-123 63-141 (278)
25 PRK00304 hypothetical protein; 26.0 33 0.00072 29.1 1.0 51 3-54 17-69 (75)
26 PF08173 YbgT_YccB: Membrane b 20.7 82 0.0018 21.7 1.9 16 604-619 2-17 (28)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.88 E-value=9.5e-23 Score=192.92 Aligned_cols=134 Identities=25% Similarity=0.288 Sum_probs=109.3
Q ss_pred HHHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450 245 ILQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS 323 (659)
Q Consensus 245 ~l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ 323 (659)
.+.||+||+|.+ ||+.|+|+|+.-.... ...+.... .+||++||+.|++.||+.+...+...|.|+|||+|
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~-------~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~y 74 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGE-------KELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKY 74 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCce-------EEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHH
Confidence 467999999985 6766777666521111 11223333 89999999999999999999888899999999999
Q ss_pred HHHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450 324 CLEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT 387 (659)
Q Consensus 324 ai~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~ 387 (659)
|+++|+.| ++++++|+ .+.++|+.+.++..+...|.+.|||||+|.++||+||+||+.+++..
T Consensus 75 v~~~i~~w~~~w~~~~w~~~~~~pv-kn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 75 VVEGITRWIVKWKKNGWKTADKKPV-KNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHHhhccccCccccccCcc-ccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 99999964 34556677 68999999999987666999999999999999999999999998864
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.86 E-value=2e-21 Score=186.67 Aligned_cols=128 Identities=27% Similarity=0.386 Sum_probs=101.7
Q ss_pred HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450 246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC 324 (659)
Q Consensus 246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a 324 (659)
+.|||||++.+ ||+.|.|+++.... + .. .....+||++|||.|++.||+.+.. ....+.|+|||+|+
T Consensus 6 ~~IytDGa~~gnpg~~G~g~~~~~~~-~---------~~-g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yv 73 (161)
T PRK06548 6 IIAATDGSSLANPGPSGWAWYVDENT-W---------DS-GGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYV 73 (161)
T ss_pred EEEEEeeccCCCCCceEEEEEEeCCc-E---------Ec-cCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHH
Confidence 67999999885 55666665543211 0 11 1124689999999999999987643 33579999999999
Q ss_pred HHHHhc---------CCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450 325 LEKLKN---------TSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT 387 (659)
Q Consensus 325 i~~I~~---------~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~ 387 (659)
+++|+. |++++|+|+ .+++||+.+..+.++ ..|+|.|||||+|++|||.||+||++|+...
T Consensus 74 i~~i~~W~~~Wk~~gWk~s~G~pV-~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 74 INSLTKWVYSWKMRKWRKADGKPV-LNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHHHHHHHHHHHCCCcccCCCcc-ccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 999995 466788887 689999999998764 5899999999999999999999999998753
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.84 E-value=9.6e-21 Score=180.11 Aligned_cols=129 Identities=23% Similarity=0.342 Sum_probs=98.9
Q ss_pred HHhhhhhcccCCC----ccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcCh
Q psy15450 246 LQALKYASSIKEK----EAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDS 321 (659)
Q Consensus 246 l~iytDGS~~~~g----~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDS 321 (659)
+.||||||+.+++ .+|+|+++.... +.........+...+||++|||.|++.||+.+... ..|+|||
T Consensus 5 ~~iYtDGs~~~n~~~~~~~G~G~vv~~~~-----~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS 75 (147)
T PRK08719 5 YSIYIDGAAPNNQHGCVRGGIGLVVYDEA-----GEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDS 75 (147)
T ss_pred EEEEEecccCCCCCCCCCcEEEEEEEeCC-----CCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEech
Confidence 5699999997543 356666543221 11111223335556899999999999999998653 3899999
Q ss_pred HHHHHHHhc---------CCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhc
Q psy15450 322 KSCLEKLKN---------TSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385 (659)
Q Consensus 322 q~ai~~I~~---------~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~ 385 (659)
+|++++|+. |++++|.++ .+.++|+.+..+.. ...|.|.|||||+|++|||.||+||++|++
T Consensus 76 ~yvi~~i~~~~~~W~~~~w~~s~g~~v-~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 76 DYCVRGFNEWLDTWKQKGWRKSDKKPV-ANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHHHHHHhCCcccCCCccc-ccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 999999954 345666776 47899999998865 577999999999999999999999999875
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.83 E-value=2.6e-20 Score=177.83 Aligned_cols=131 Identities=21% Similarity=0.298 Sum_probs=101.1
Q ss_pred HHhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450 246 LQALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC 324 (659)
Q Consensus 246 l~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a 324 (659)
+.||||||+.++ +..|.|++....+.. . ..... ....||++|||.|++.||+.+.. ...+.|||||+|+
T Consensus 4 v~iytDGs~~~n~~~~g~g~v~~~~~~~------~-~~~~~-~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yv 73 (150)
T PRK00203 4 VEIYTDGACLGNPGPGGWGAILRYKGHE------K-ELSGG-EALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYV 73 (150)
T ss_pred EEEEEEecccCCCCceEEEEEEEECCee------E-EEecC-CCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHH
Confidence 578999999864 555666555432211 1 11111 24689999999999999998865 4689999999999
Q ss_pred HHHHhcC---------CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450 325 LEKLKNT---------SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTD 388 (659)
Q Consensus 325 i~~I~~~---------~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~ 388 (659)
++.|+.| .+++|+++ .+.++|+.+.++.. ...|.|.|||||+|++||+.||+||++|+....
T Consensus 74 i~~i~~w~~~Wk~~~~~~~~g~~v-~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 74 RQGITEWIHGWKKNGWKTADKKPV-KNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHHHHHHHHcCCcccCCCcc-ccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 9999963 44567776 47888888888764 478999999999999999999999999987643
No 5
>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=99.75 E-value=3.5e-18 Score=158.19 Aligned_cols=121 Identities=35% Similarity=0.425 Sum_probs=87.1
Q ss_pred HHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHH
Q psy15450 246 LQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSC 324 (659)
Q Consensus 246 l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~a 324 (659)
+.+|||||+.. ++..|+|++. ..+ + .....++ ..|+++|||.||..||+.+ . ...++|||||+++
T Consensus 4 ~~iytDgS~~~~~~~~~~g~v~-~~~------~---~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v 69 (132)
T PF00075_consen 4 IIIYTDGSCRPNPGKGGAGYVV-WGG------R---NFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYV 69 (132)
T ss_dssp EEEEEEEEECTTTTEEEEEEEE-ETT------E---EEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHH
T ss_pred EEEEEeCCccCCCCceEEEEEE-ECC------e---EEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHH
Confidence 56899999875 4444555533 222 1 2233344 7899999999999999944 3 3999999999999
Q ss_pred HHHHhcC-----CcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCc-cchhhhhhHHHHHh
Q psy15450 325 LEKLKNT-----SKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGI-AGNEAVDRLAKETA 384 (659)
Q Consensus 325 i~~I~~~-----~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi-~GNE~AD~LAk~aa 384 (659)
++.+..+ +.......++..+|++.+ .++..|.|.|||||+|+ .|||.||+|||.|+
T Consensus 70 ~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 70 LNALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHhccccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 9988883 222111112445565555 34789999999999999 69999999999987
No 6
>KOG3752|consensus
Probab=99.68 E-value=5.7e-17 Score=170.55 Aligned_cols=145 Identities=28% Similarity=0.229 Sum_probs=114.0
Q ss_pred ehhhhHHHHHhhhhhcccCCCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEE
Q psy15450 238 FTAEAFAILQALKYASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVII 317 (659)
Q Consensus 238 F~~e~~g~l~iytDGS~~~~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I 317 (659)
-+.|..+.+.+|||||+..+|..++. ++.++++++++..+......++.+|||+|||.|+..||+.+.+....+++|
T Consensus 205 ~d~e~~~~~vvytDGS~~~ng~~~~~---AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I 281 (371)
T KOG3752|consen 205 NDREEIEIQVVYTDGSSSGNGRKSSR---AGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVI 281 (371)
T ss_pred cccccccceEEEecCccccCCCCCCc---ceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEE
Confidence 34445556889999999998876543 233466777777766555555899999999999999999998877789999
Q ss_pred EcChHHHHHHHhcC---------CcCCCCC-----cccHHHHHHHHHHHHhc--CCeeeEEEeecCCCccchhhhhhHHH
Q psy15450 318 ITDSKSCLEKLKNT---------SKSNGNP-----SHLILDIFKALSHLQEW--NISVRFIWVRGHAGIAGNEAVDRLAK 381 (659)
Q Consensus 318 ~TDSq~ai~~I~~~---------~~~~g~~-----~~~~~~i~~~l~~l~~~--~~~V~~~WVPgH~gi~GNE~AD~LAk 381 (659)
.|||++++++|+.| ..+++.+ + .+.+....+.+|.+. +.+|.+.|||||.|+.|||.||.||+
T Consensus 282 ~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v-~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lAR 360 (371)
T KOG3752|consen 282 RTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYV-KNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALAR 360 (371)
T ss_pred EechHHHHHHHHHHHhhhccCccccccCCCccceee-ecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHh
Confidence 99999999999986 3344444 3 356666667776543 48999999999999999999999999
Q ss_pred HHhcc
Q psy15450 382 ETARG 386 (659)
Q Consensus 382 ~aa~~ 386 (659)
+++..
T Consensus 361 kgs~~ 365 (371)
T KOG3752|consen 361 KGSTL 365 (371)
T ss_pred hhhhh
Confidence 98654
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.60 E-value=2.5e-15 Score=139.43 Aligned_cols=125 Identities=17% Similarity=0.129 Sum_probs=98.0
Q ss_pred HHHhhhhhcccC-CCccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450 245 ILQALKYASSIK-EKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS 323 (659)
Q Consensus 245 ~l~iytDGS~~~-~g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ 323 (659)
|++||+|||+.. +|..|+|+|+........ .... .+..||+.||+.|++.||+.+...+..++.|+|||++
T Consensus 1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~-------~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~ 72 (128)
T PRK13907 1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQ-------LSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQL 72 (128)
T ss_pred CEEEEEeeCCCCCCCccEEEEEEEECCeeEE-------EEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHH
Confidence 467899999875 678888888764332111 1112 2457999999999999999999988889999999999
Q ss_pred HHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhc
Q psy15450 324 CLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385 (659)
Q Consensus 324 ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~ 385 (659)
+++.+++.+..+ ..+..+++.+..+..+...+.+.|||+ +.|+.||.||+.|..
T Consensus 73 vi~~~~~~~~~~----~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 73 VERAVEKEYAKN----KMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred HHHHHhHHHhcC----hhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 999999975433 246777777777766667788899996 589999999999875
No 8
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.60 E-value=9.7e-15 Score=130.99 Aligned_cols=129 Identities=29% Similarity=0.289 Sum_probs=97.9
Q ss_pred HhhhhhcccCC-CccceEEEEeccceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHHHH
Q psy15450 247 QALKYASSIKE-KEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCL 325 (659)
Q Consensus 247 ~iytDGS~~~~-g~~G~g~v~~~~~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ai 325 (659)
++|+|||.... +..|+|++....+...... ........+++.+|+.|+..||+.+...+..++.|+|||+.++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~------~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~ 74 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLS------GGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVI 74 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEe------ccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHH
Confidence 36899998754 6778887776533211111 1111157899999999999999999887889999999999999
Q ss_pred HHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHh
Q psy15450 326 EKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETA 384 (659)
Q Consensus 326 ~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa 384 (659)
+.++++..... .....++..+..+..+...+.|.|||+|+++.+|+.||.||+.++
T Consensus 75 ~~~~~~~~~~~---~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 75 NALTGWYEGKP---VKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HHhhccccCCC---hhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 99998743121 235555556665555678999999999999999999999999873
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.37 E-value=1.1e-12 Score=132.78 Aligned_cols=133 Identities=14% Similarity=0.072 Sum_probs=94.1
Q ss_pred HHHhhhhhccc-CCCccceEEEEecc-ceeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCC--eEEEEcC
Q psy15450 245 ILQALKYASSI-KEKEAGYCKVSIRE-SLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKEN--EVIIITD 320 (659)
Q Consensus 245 ~l~iytDGS~~-~~g~~G~g~v~~~~-~~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~--~i~I~TD 320 (659)
.+.+|+|||+. +++.+|+|+++... +.... .......++...||+.||+.|++.||+.+...+.. .|.|++|
T Consensus 73 ~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~----~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D 148 (219)
T PRK07708 73 EILVYFDGGFDKETKLAGLGIVIYYKQGNKRY----RIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD 148 (219)
T ss_pred cEEEEEeeccCCCCCCcEEEEEEEECCCCEEE----EEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence 58999999986 47788888887532 11100 00111245556899999999999999999988754 4899999
Q ss_pred hHHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhc-CCeeeEEEeecCCCccchhhhhhHHHHHhccCC
Q psy15450 321 SKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEW-NISVRFIWVRGHAGIAGNEAVDRLAKETARGTD 388 (659)
Q Consensus 321 Sq~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~-~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~~ 388 (659)
|+++++.+++.|..... ....+.+.+..+..+ ...+.+.||| ...|+.||+||+.|+....
T Consensus 149 SqlVi~qi~g~wk~~~~---~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 149 SQVVLNQLAGEWPCYDE---HLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV 210 (219)
T ss_pred cHHHHHHhCCCceeCCh---hHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence 99999999997655432 233444444443332 2347788987 5679999999999998643
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.33 E-value=5.9e-12 Score=137.48 Aligned_cols=129 Identities=21% Similarity=0.173 Sum_probs=97.8
Q ss_pred HHhhhhhcccC-CCccceEEEEeccc-eeeeCCCccccccccCCCCCcHHHHHHHHHHHHHHHchhcCCCeEEEEcChHH
Q psy15450 246 LQALKYASSIK-EKEAGYCKVSIRES-LWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKS 323 (659)
Q Consensus 246 l~iytDGS~~~-~g~~G~g~v~~~~~-~~~~~~~~~~~~~~~l~~~~T~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ 323 (659)
+.||+||++.+ +|.+|+|+++...+ .... ......++ ..||+.||+.|++.||+.+.+.+...+.|++||++
T Consensus 3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~-----~~~~~~~~-~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~l 76 (372)
T PRK07238 3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVL-----AERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKL 76 (372)
T ss_pred EEEEecCCCCCCCCceEEEEEEEeCCCCcEE-----EEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHH
Confidence 46899999875 57788888876532 1110 01122333 68999999999999999999988899999999999
Q ss_pred HHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCccchhhhhhHHHHHhccC
Q psy15450 324 CLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGT 387 (659)
Q Consensus 324 ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~GNE~AD~LAk~aa~~~ 387 (659)
+++.+++.+.... +....++..+..+..+...+.+.|||+ .+|+.||.||+.|+...
T Consensus 77 vi~~i~~~~~~~~---~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 77 VVEQMSGRWKVKH---PDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAA 133 (372)
T ss_pred HHHHhCCCCccCC---hHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhh
Confidence 9999998654221 234555666666666678899999995 78999999999998753
No 11
>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=99.33 E-value=3e-12 Score=128.76 Aligned_cols=99 Identities=19% Similarity=0.155 Sum_probs=80.1
Q ss_pred CCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcccc
Q psy15450 48 ILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHG 127 (659)
Q Consensus 48 ~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl~~ 127 (659)
.+++.|||||+++ |+.+++..+... ......+++.+|+++|||+|+|+.|++.|...|.++.++.|+.+ |...
T Consensus 40 ~~~~~~~g~~~~r-s~~~~i~~i~~~-----~~~~~~~~~~~Di~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~-~~~~ 112 (226)
T cd01651 40 RFSDCSYGFRPGR-SAHDALKAIRRN-----VKGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRK-WLKA 112 (226)
T ss_pred ccccCCCCCCCCC-CHHHHHHHHHHH-----hcCCCeEEEEccHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHH-HHhc
Confidence 3677999999999 999998766554 34566889999999999999999999999999999999999998 4332
Q ss_pred eEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccchh
Q psy15450 128 RRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYA 184 (659)
Q Consensus 128 r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~ 184 (659)
... ..+.......|||| |+++ ||.|+
T Consensus 113 ~~~----------------~~~~~~~~~~Glpq-------------G~~l--Sp~L~ 138 (226)
T cd01651 113 GVL----------------EDGKLVETEKGTPQ-------------GGVI--SPLLA 138 (226)
T ss_pred eEc----------------cCCeEeCCCCCcCC-------------CccH--HHHHH
Confidence 111 12234456899999 9999 99983
No 12
>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=99.22 E-value=1.6e-11 Score=123.88 Aligned_cols=70 Identities=11% Similarity=-0.024 Sum_probs=58.5
Q ss_pred ccccCCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCC-hhhHHHH
Q psy15450 42 GKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKID-LKSATFC 120 (659)
Q Consensus 42 ~le~~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~-~~li~~I 120 (659)
+|..+-.+++.|+|||+|| ||.+++.. .....+++.+||++|||+|+|+.|+.+|...|.+ +.+..|+
T Consensus 26 ~l~~~~~~~~~~~g~~~gr-s~~~~~~~----------~~~~~~v~~~Di~~fFdsI~~~~L~~~l~~~~~~~~~~~~~l 94 (214)
T cd03487 26 NLLSKLPVHDAAHGFVKGR-SIITNAKP----------HCGAKYVLKLDIKDFFPSITFERVRGVFRSLGYFSPDVATIL 94 (214)
T ss_pred HHhccCCCCcceeeecCCC-CHHHHHHH----------hcCCCEEEEeehhhhcccCCHHHHHHHHHHcCCCCHHHHHHH
Confidence 3334556889999999999 99887642 2345788999999999999999999999999999 8888888
Q ss_pred hh
Q psy15450 121 VF 122 (659)
Q Consensus 121 ~s 122 (659)
..
T Consensus 95 ~~ 96 (214)
T cd03487 95 AK 96 (214)
T ss_pred HH
Confidence 77
No 13
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=99.20 E-value=2e-11 Score=122.49 Aligned_cols=59 Identities=29% Similarity=0.483 Sum_probs=55.5
Q ss_pred CCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHH
Q psy15450 48 ILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVI 107 (659)
Q Consensus 48 ~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL 107 (659)
.+.+.|+||++|+ |+.+++..+.+.++...+++....++++|++||||+|+|+.|+..|
T Consensus 47 ~~~~~q~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~Di~~aFdsi~~~~l~~~l 105 (220)
T cd01650 47 NILPNQFGFRPGR-STTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLLKAL 105 (220)
T ss_pred cCCcccccccCCC-hHHHHHHHHHHHHHHHHHcCCceEEEEEEHHhhcCcCCHHHHHHHh
Confidence 3458999999999 9999999999999999988999999999999999999999999999
No 14
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.98 E-value=2.6e-09 Score=91.16 Aligned_cols=86 Identities=22% Similarity=0.281 Sum_probs=67.8
Q ss_pred HHHHHHHHHHHHHHHchhcCCCeEEEEcChHHHHHHHhcCCcCCCCCcccHHHHHHHHHHHHhcCCeeeEEEeecCCCcc
Q psy15450 292 IFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIA 371 (659)
Q Consensus 292 ~~~AEL~AI~~AL~~a~~~~~~~i~I~TDSq~ai~~I~~~~~~~g~~~~~~~~i~~~l~~l~~~~~~V~~~WVPgH~gi~ 371 (659)
+..||+.|+..||+.+...+..++.|+|||+.+++.|++...... ....+...+..+.+....+.|.||| .+
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~----~~~~~~~~i~~~~~~~~~~~~~~i~----r~ 72 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRS----ELRPLIQDIRSLLDRFWNVSVSHIP----RE 72 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---S----CCHHHHHHHHHHHCCCSCEEEEE------GG
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccc----cccccchhhhhhhccccceEEEEEC----hH
Confidence 468999999999999999999999999999999999998633332 3456666666666677889999999 88
Q ss_pred chhhhhhHHHHHhc
Q psy15450 372 GNEAVDRLAKETAR 385 (659)
Q Consensus 372 GNE~AD~LAk~aa~ 385 (659)
+|..||.|||.|..
T Consensus 73 ~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 73 QNKVADALAKFALS 86 (87)
T ss_dssp GSHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHhh
Confidence 99999999999863
No 15
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=98.89 E-value=6.4e-11 Score=117.33 Aligned_cols=111 Identities=21% Similarity=0.327 Sum_probs=82.1
Q ss_pred CCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcc
Q psy15450 46 NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVF 125 (659)
Q Consensus 46 ~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl 125 (659)
+..+++.|+||++++ ||.+ .+...+.+....++++|+++|||+|+|+.|...|..++.+..++.||.+ ++
T Consensus 35 ~~~~~~~~~~~~~~~-~~~~--------~~~~~~~~~~~~~~~~Di~~~f~sI~~~~l~~~l~~~~~~~~~~~~i~~-~~ 104 (214)
T PF00078_consen 35 EPIFSPSQFGFRPGR-SCHD--------IKKLNRFKGYLYFLKLDISKAFDSIPHHRLLRKLKRFGVPKKLIRLIQN-LL 104 (214)
T ss_dssp ---HHHTTSSCSHGC-CCHH--------HHHHHC-CGSSEEEEEECCCCGGGSBBHTTTGGGGEEEEECCSCHHHHH-HH
T ss_pred cccCCCCCCCCcccc-cccc--------cccccccccccccceeccccccccceeeecccccccccccccccccccc-cc
Confidence 466888999999999 8887 3444566777999999999999999999999999999999999999999 55
Q ss_pred cceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccchhhhhhh-hhhhcc
Q psy15450 126 HGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCF-LNEVKD 195 (659)
Q Consensus 126 ~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~~~~~~-ln~I~d 195 (659)
..+...+. .+ +.. .......|||| |+++ ||.++ .. +..+..
T Consensus 105 ~~~~~~~~------~~----~~~-~~~~~~~glpq-------------G~~~--S~~l~---~~~l~~l~~ 146 (214)
T PF00078_consen 105 SDRTAKVY------LD----GDL-SPYFQKRGLPQ-------------GSPL--SPLLF---NIYLDDLDR 146 (214)
T ss_dssp HHHHH-EE------CG----CSS-SEEEEESBS-T-------------TSTC--HHHHH---HHHHHHHHH
T ss_pred cccccccc------cc----ccc-ccccccccccc-------------cccc--cchhh---ccccccccc
Confidence 55544441 11 112 34456799999 9999 99983 33 555443
No 16
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=98.02 E-value=2.4e-05 Score=83.54 Aligned_cols=85 Identities=19% Similarity=0.282 Sum_probs=65.6
Q ss_pred HHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcccceEEEEEecccccCCCCCccccCC
Q psy15450 71 KIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGD 150 (659)
Q Consensus 71 ~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl~~r~~~v~~~~~~~~~g~~~~~~s~ 150 (659)
..+++.. .+....++=.||++=||+|+|+.|+..|..+|++.+++.+|+. |+..--... -+|.. +.
T Consensus 11 e~~i~~~--l~G~~~vvd~Dik~fFdsIpH~~Lm~vL~~~~~~~~wL~li~r-~L~APl~~~-------~dg~~----~~ 76 (346)
T cd01709 11 EILINTA--LYGEVTVVQSDFKWFGPSLPHSTILAVLKFFGVPEKWLDFFKK-FLEAPLRFV-------ADGPD----AP 76 (346)
T ss_pred HHHHHHh--hcCCEEEEEeehHhhCCCCCHHHHHHHHHHhCCCHHHHHHHHH-HHhCceeec-------CCCCc----cc
Confidence 3444443 3567899999999999999999999999999999999999999 887644432 11111 22
Q ss_pred CCccccccCCCCCCCCCCcccCCCCccccccchh
Q psy15450 151 CPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYA 184 (659)
Q Consensus 151 ~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~ 184 (659)
...-++|+|| |.++ ||.|.
T Consensus 77 ~r~r~rGtPq-------------Ggvi--SplLa 95 (346)
T cd01709 77 PRIRKRGTPM-------------SHAL--SDVFG 95 (346)
T ss_pred ccccCCccCC-------------Cchh--hHHHH
Confidence 3344699999 9999 99995
No 17
>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=97.90 E-value=2.9e-06 Score=81.65 Aligned_cols=65 Identities=11% Similarity=0.011 Sum_probs=49.2
Q ss_pred EecchhcCCCCHHHHHHHHHHcCCChhhHHHHhhhcccceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCC
Q psy15450 89 IDLLKAYDNCPHEWMVKVIQMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGN 168 (659)
Q Consensus 89 lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~~I~s~yl~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~ 168 (659)
+||+|+||+|+|+.|..+|...+.+...+.+++. +.... . ....+.......||||
T Consensus 1 lDi~~fF~sI~~~~l~~~l~~~~~~~~~~~~~~~-~~~~~---~------------~~~~~~~~~~~~Glpq-------- 56 (158)
T cd01646 1 LDISNFYDSIYTHSLPWALHGKIKAKQLLKLLRL-LGNLL---D------------LLLLSSQYGQTNGLPI-------- 56 (158)
T ss_pred CchhhccCcchHHHHHHHHHhhhhhHhhhhhHHH-HHHHH---H------------HHHHhccCCCCceEcc--------
Confidence 6999999999999999999999999999988743 22110 0 0112223445789999
Q ss_pred cccCCCCccccccchh
Q psy15450 169 ATQDDGDQYESAPEYA 184 (659)
Q Consensus 169 ~~~~~G~~L~~~P~l~ 184 (659)
|+++ ||.|.
T Consensus 57 -----G~~l--S~~L~ 65 (158)
T cd01646 57 -----GPLT--SRFLA 65 (158)
T ss_pred -----Ccch--HHHHH
Confidence 9999 99994
No 18
>KOG4768|consensus
Probab=97.65 E-value=5e-05 Score=84.88 Aligned_cols=114 Identities=17% Similarity=0.141 Sum_probs=79.3
Q ss_pred HHHHhhhcccccccccccCCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHH
Q psy15450 28 QREVNRSGESLNTAGKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVI 107 (659)
Q Consensus 28 ~~~~~~~~~~l~~~~le~~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL 107 (659)
-.|+.|.+-. .+-++..+-.-+|||||+ ||.++++.....+. ...+.+-.|+.|-||+|+|+.|+..|
T Consensus 316 vQe~mRm~Le-----iiy~~~fst~shgfRpgl-Sc~tAi~~~~n~f~------gcnw~ie~DLkkcfdtIphd~LI~eL 383 (796)
T KOG4768|consen 316 VQECMRMGLE-----IIYGGEFSTVSHGFRPGL-SCKTAILKTHNLFR------GCNWFIEVDLKKCFDTIPHDELIIEL 383 (796)
T ss_pred HHHHHHHHHH-----HHhcceeeeeecccCCCc-hhhHHHHHHHHHhh------ccceEEechHHHHhccccHHHHHHHH
Confidence 3466665422 223566777889999999 99999988776554 33566778999999999999999999
Q ss_pred HHcCCChhhHHHHhhhcccceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccchh
Q psy15450 108 QMYKIDLKSATFCVFCVFHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYA 184 (659)
Q Consensus 108 ~~~Gi~~~li~~I~s~yl~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l~ 184 (659)
++.=-+..+++++.. .+.+-+.-. + +....+ --|.|| |++. +|.|.
T Consensus 384 ~~rIkdk~fidL~~k-ll~AGy~te--------n----~ry~~~---~lGtpq-------------gsvv--spil~ 429 (796)
T KOG4768|consen 384 QKRIKDKGFIDLNYK-LLRAGYTTE--------N----ARYHVE---FLGTPQ-------------GSVV--SPILC 429 (796)
T ss_pred HHHHhhhhHHHHHHH-HHhcCcccc--------c----cceecc---cccccc-------------cccC--CchhH
Confidence 887555666666655 333222211 1 111122 379999 9999 99984
No 19
>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=96.39 E-value=0.00095 Score=61.30 Aligned_cols=12 Identities=42% Similarity=0.822 Sum_probs=11.1
Q ss_pred EecchhcCCCCH
Q psy15450 89 IDLLKAYDNCPH 100 (659)
Q Consensus 89 lD~~KAFDsV~h 100 (659)
.|+++|||+|+|
T Consensus 1 ~d~~~~~~~~~~ 12 (119)
T cd01648 1 TDIKKCYDSIPQ 12 (119)
T ss_pred CChHHhccchhh
Confidence 389999999999
No 20
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=94.79 E-value=0.017 Score=49.90 Aligned_cols=42 Identities=24% Similarity=0.445 Sum_probs=32.8
Q ss_pred cccCCcchhccccccCCCCCCCccCCC-cccCcccccccCcCc
Q psy15450 456 LRSNHAICQAYLHKINIAPTNLCQECL-EREDMAHIILCCPKY 497 (659)
Q Consensus 456 lrTGHg~~~~yL~r~~~~~s~~C~cc~-~~et~~Hil~~Cp~~ 497 (659)
+..+--..++-|.+.+...++.|..|+ +.||++|+|+.||.-
T Consensus 40 ~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a 82 (86)
T PF13966_consen 40 ALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFA 82 (86)
T ss_pred eccccchhhhhhhccCCccCCccccCCCccccccceeccCcCc
Confidence 333444556678888888889999776 599999999999974
No 21
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=94.70 E-value=0.067 Score=57.63 Aligned_cols=104 Identities=16% Similarity=0.151 Sum_probs=69.8
Q ss_pred CCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHHHHHcCCChhhHH-HHhhhc
Q psy15450 46 NNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKVIQMYKIDLKSAT-FCVFCV 124 (659)
Q Consensus 46 ~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~kL~~~Gi~~~li~-~I~s~y 124 (659)
....++.=+||++++ ++.+.+.............. ...++..|+.+=||+++|..++..+... +.+..+. ++...+
T Consensus 145 ~~~f~~~s~Gf~~~~-~~~~a~~~~~~~~~~~~~~~-~~~~~~~di~~~fd~~~h~~ll~~~~~~-i~~~~~~~~~~r~~ 221 (328)
T COG3344 145 ENIFSPLSYGFRPGP-SASNAIAYAFDLPQGKICSP-NGWVYDRDIKKCFDSINHKLLLYALDVT-ISDKLVLLLLGRIL 221 (328)
T ss_pred HhccccCCCCCCCCh-hHHHHHHHHHhhhccCCCCC-ceEEEeehHHHHhcccCHHHHHHHhHhh-hcchHHHHHHHHHH
Confidence 355677889999999 88888776654444322211 2477889999999999999999999985 5433333 443323
Q ss_pred ccceEEEEEecccccCCCCCccccCCCCccccccCCCCCCCCCCcccCCCCccccccch
Q psy15450 125 FHGRRLVIVMSDFNNSDGEDITMSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEY 183 (659)
Q Consensus 125 l~~r~~~v~~~~~~~~~g~~~~~~s~~~~i~~GVpQ~~~~~~~~~~~~~G~~L~~~P~l 183 (659)
....-... ........|+|| |.++ +|.+
T Consensus 222 ~~~~~~~~----------------~~~~~~~~~~~q-------------~~~v--s~~l 249 (328)
T COG3344 222 IAGYKTKF----------------NLKKSKEKGTPQ-------------GGLV--SPIL 249 (328)
T ss_pred Hcccceee----------------cccccccccCCC-------------CCcc--Cchh
Confidence 33322222 112223699999 9999 9998
No 22
>KOG1005|consensus
Probab=93.25 E-value=0.22 Score=58.77 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=25.0
Q ss_pred CcceeEEEEecchhcCCCCHHHHHHHH
Q psy15450 81 YKNLSVAWIDLLKAYDNCPHEWMVKVI 107 (659)
Q Consensus 81 ~~~~~~v~lD~~KAFDsV~h~~L~~kL 107 (659)
++.++.+-+|++||||+|+|+.|+..+
T Consensus 516 ~~~LYfvk~DV~~cfDtIpqd~l~~II 542 (888)
T KOG1005|consen 516 NQKLYFVKADVSKCFDTIPQDELISII 542 (888)
T ss_pred cCceEEEEEEhhhhhccCchHHHHHHH
Confidence 347999999999999999999999988
No 23
>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=63.61 E-value=3.7 Score=35.35 Aligned_cols=9 Identities=33% Similarity=0.667 Sum_probs=8.1
Q ss_pred CCccccccchh
Q psy15450 174 GDQYESAPEYA 184 (659)
Q Consensus 174 G~~L~~~P~l~ 184 (659)
|.++ ||.++
T Consensus 15 G~~~--Sp~l~ 23 (98)
T cd00304 15 GSPL--SPALA 23 (98)
T ss_pred CCch--HHHHH
Confidence 9999 99983
No 24
>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=30.84 E-value=1.2e+02 Score=31.34 Aligned_cols=73 Identities=7% Similarity=-0.178 Sum_probs=46.9
Q ss_pred ccccCCCCCCCCccccCCCCCHHHHHHHHHHHHHHHHhcCcceeEEEEecchhcCCCCHHHHHHH---HHHcCCCh---h
Q psy15450 42 GKNDNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMVKV---IQMYKIDL---K 115 (659)
Q Consensus 42 ~le~~~~l~~~Q~GFr~gr~st~~~l~~~~~~i~~~~~~~~~~~~v~lD~~KAFDsV~h~~L~~k---L~~~Gi~~---~ 115 (659)
.+..+...++.+.|+.|.. +-.+.| .+.....+ -.++-+|+++=..++++..+... +..+.-++ .
T Consensus 63 ~~~~~~~~~~~~vG~~p~~-~~~~~l------~~~~~~~~--~~~~~~D~s~FD~s~~~~~l~~~~~i~~~~~~~~~~~~ 133 (278)
T cd01699 63 KLMKNRGGLPIAVGINPYS-RDWTIL------ANKLRSFS--PVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELE 133 (278)
T ss_pred HHHhcCCCCCcccccCCCc-hHHHHH------HHHHHhcC--CeEEeeeccccCCCCCHHHHHHHHHHHHHHHcCCchhH
Confidence 3334566788999999988 434332 33333332 55668999999999999887743 44444444 3
Q ss_pred hHHHHhhh
Q psy15450 116 SATFCVFC 123 (659)
Q Consensus 116 li~~I~s~ 123 (659)
+.+++..+
T Consensus 134 ~~~l~~~~ 141 (278)
T cd01699 134 RRNLLRSL 141 (278)
T ss_pred HHHHHHHH
Confidence 66777773
No 25
>PRK00304 hypothetical protein; Provisional
Probab=26.04 E-value=33 Score=29.13 Aligned_cols=51 Identities=16% Similarity=0.313 Sum_probs=35.9
Q ss_pred ccceeeeccccCCCCcchhhhhhHHHHHHhhhccccc-cccccc-CCCCCCCCc
Q psy15450 3 IRKYVIRKNVDNENGTNVQEKVDIAQREVNRSGESLN-TAGKND-NNILPMEQR 54 (659)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~le~-~~~l~~~Q~ 54 (659)
|..||.|..-|+......++|+...++-|++ |+-++ -+.+.. -++++..||
T Consensus 17 Ieefv~ReGTDyg~E~sL~~kv~qv~~qL~~-G~~vIvfse~~es~~i~~k~~~ 69 (75)
T PRK00304 17 IEDFVTRDGTDNGDETPLETRVLRVRQALTK-GQAVILFDPESQQCQLMLKHDV 69 (75)
T ss_pred HHHHHhccCccCcccccHHHHHHHHHHHHHc-CCEEEEECCCcceeeeeeHhhc
Confidence 5679999999887777899999999999976 44444 333322 256666654
No 26
>PF08173 YbgT_YccB: Membrane bound YbgT-like protein; InterPro: IPR012994 This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in Escherichia coli. Members have a consensus motif (MWYFXW), which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to proteobacteria [].
Probab=20.74 E-value=82 Score=21.72 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=13.1
Q ss_pred hHHHHHHHHHhHHhhc
Q psy15450 604 FTAIWFLYLGVACCLA 619 (659)
Q Consensus 604 ~~~~~~~~~~~~~~~~ 619 (659)
+-|.|+|-+++||+++
T Consensus 2 WYfaWilG~~lA~~~~ 17 (28)
T PF08173_consen 2 WYFAWILGVLLACAFG 17 (28)
T ss_pred hhHHHHHHHHHHHHHH
Confidence 3478999999999876
Done!