Query psy3199
Match_columns 1144
No_of_seqs 296 out of 935
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 18:49:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3199hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06222 RnaseH RNase H (RNase 99.1 1.1E-10 2.4E-15 103.4 8.2 116 870-987 1-128 (130)
2 PF05869 Dam: DNA N-6-adenine- 99.1 6.1E-11 1.3E-15 122.3 6.2 118 989-1116 10-135 (181)
3 TIGR01712 phage_N6A_met phage 99.1 1.8E-10 3.9E-15 117.7 7.4 133 989-1133 10-148 (166)
4 PRK13907 rnhA ribonuclease H; 98.8 8.6E-09 1.9E-13 98.3 8.6 116 869-987 2-123 (128)
5 PF00075 RNase_H: RNase H; In 98.8 6.4E-09 1.4E-13 97.5 5.4 112 867-986 2-128 (132)
6 PF00336 DNA_pol_viral_C: DNA 98.6 2.2E-07 4.8E-12 98.0 10.4 182 781-989 14-195 (245)
7 PRK07708 hypothetical protein; 98.5 2.4E-07 5.2E-12 98.3 9.0 123 866-988 71-205 (219)
8 PRK00203 rnhA ribonuclease H; 98.5 3.8E-07 8.3E-12 90.3 7.7 115 868-987 3-138 (150)
9 COG0328 RnhA Ribonuclease HI [ 98.4 3.5E-07 7.5E-12 93.1 6.8 119 868-988 3-142 (154)
10 PRK07238 bifunctional RNase H/ 98.4 4.9E-07 1.1E-11 100.8 8.6 118 868-987 2-128 (372)
11 PRK06548 ribonuclease H; Provi 98.3 1.4E-06 3E-11 89.1 8.6 114 867-987 4-138 (161)
12 PF13456 RVT_3: Reverse transc 98.2 9.2E-07 2E-11 77.1 3.2 82 903-987 2-83 (87)
13 PRK08719 ribonuclease H; Revie 98.1 8.5E-06 1.9E-10 81.7 7.3 115 866-987 2-143 (147)
14 PF05380 Peptidase_A17: Pao re 97.3 0.00088 1.9E-08 67.6 9.0 115 796-917 2-141 (159)
15 PF12237 PCIF1_WW: Phosphoryla 96.9 0.0012 2.6E-08 69.2 5.4 133 950-1101 16-161 (176)
16 KOG3752|consensus 96.8 0.0044 9.6E-08 70.9 8.7 117 869-988 213-362 (371)
17 cd03715 RT_ZFREV_like RT_ZFREV 95.3 0.0042 9.2E-08 64.4 -0.5 80 687-767 125-208 (210)
18 cd01645 RT_Rtv RT_Rtv: Reverse 94.6 0.0088 1.9E-07 62.7 -0.2 77 688-766 130-210 (213)
19 PF06817 RVT_thumb: Reverse tr 93.5 0.06 1.3E-06 49.4 2.9 56 793-851 13-68 (70)
20 cd01647 RT_LTR RT_LTR: Reverse 91.4 0.053 1.1E-06 51.8 -0.2 78 687-765 96-173 (177)
21 cd03714 RT_DIRS1 RT_DIRS1: Rev 89.9 0.08 1.7E-06 50.5 -0.4 41 688-729 35-77 (119)
22 cd01644 RT_pepA17 RT_pepA17: R 89.6 0.11 2.5E-06 55.3 0.4 63 681-744 98-166 (213)
23 cd00304 RT_like RT_like: Rever 39.0 7.9 0.00017 35.0 -0.7 41 688-729 13-57 (98)
24 PF00078 RVT_1: Reverse transc 33.9 7.7 0.00017 38.8 -1.7 79 687-766 126-211 (214)
No 1
>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=99.15 E-value=1.1e-10 Score=103.38 Aligned_cols=116 Identities=21% Similarity=0.166 Sum_probs=89.2
Q ss_pred EEEecCCCC------ceEEEEeeccccccccccc--cccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHHh
Q psy3199 870 FVTSDASDS------GWGARVDNRMIKGSWTECQ--KKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQK 941 (1144)
Q Consensus 870 iLyTDASdS------GIGAVL~Qe~aSgtWSeaE--rnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLnK 941 (1144)
.++||||.. |+|+++.+......|.... ...+++..|+.|++.||+... .+..+.+.|+|||+.++..+++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~-~~~~~~i~i~~Ds~~~~~~~~~ 79 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELAL-ELGGKKVNIYTDSQYVINALTG 79 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHH-hCCCceEEEEECHHHHHHHhhc
Confidence 379999986 9999998755444443332 477999999999999999866 5677899999999999999987
Q ss_pred cCCCCChhhhhHHHHHHHHHHhcceeEEEEEecC----CcccCCCcCCCC
Q psy3199 942 QGGTKSINLLRGVEEIFRIATVHNITVQAQYIPG----MYNNIADSLSRS 987 (1144)
Q Consensus 942 qgSkrSp~LnrLARrI~~wLee~nIdftaeHIPG----keNvVADALSR~ 987 (1144)
........+..+.+.+..+. .....+++.|||| ..|..||.|+|.
T Consensus 80 ~~~~~~~~~~~~~~~i~~~~-~~~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 80 WYEGKPVKNVDLWQRLLALL-KRFHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred cccCCChhhHHHHHHHHHHH-hCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 64323445556666666655 2344688999999 999999999875
No 2
>PF05869 Dam: DNA N-6-adenine-methyltransferase (Dam); InterPro: IPR008593 This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences [].; GO: 0003677 DNA binding, 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0032775 DNA methylation on adenine
Probab=99.12 E-value=6.1e-11 Score=122.32 Aligned_cols=118 Identities=19% Similarity=0.315 Sum_probs=99.1
Q ss_pred CCCccccchHHHHHHHhhcCCCcccccccccccCccceeecccCCCCccccccccccccCc---cccccCCCCC-hHHHH
Q psy3199 989 VLPDWHLLPHLTSWIFQNWGRPVIDLFASAGSAVVPRYVSRSARDTQASFIDAFSMDWTFP---LAWVFPPPPL-MPRVL 1064 (1144)
Q Consensus 989 D~~EW~LSpeVFqqIqelWGppEIDLFASriNAKLpRF~Sw~~PDpGA~avDAFs~dWs~~---~~YAFPPfSL-IpRVL 1064 (1144)
+.++|...+.+|..+++.||++++|.+|+..|++|++|++. ..|+++++|... ..|+||||+. +...+
T Consensus 10 ~~d~W~TP~~lf~~l~~~fg~f~LD~aa~~~Na~~~~y~T~--------~~DgL~~~W~~~~~g~vf~NPPYs~~i~~wv 81 (181)
T PF05869_consen 10 DKDEWQTPPELFDALNREFGPFDLDPAASDENAKCPRYYTE--------EDDGLAQDWSAELMGRVFCNPPYSRGIGPWV 81 (181)
T ss_pred CCCCCcCCHHHHHHHHHHhCCccccccCCCCChhhhhhcCc--------cccHhhhhhhhcccceEEecCchhhhHHHHH
Confidence 46899999999999999999999999999999999999995 359999999965 8899999999 99999
Q ss_pred HHHHhcC---cc-EEEEeecCCCCcCcHHHHHHhhhCCccccCCCcccccCCCCCC
Q psy3199 1065 NHLNSAQ---GL-FIVIAPTWDKVFWYPDLQRRAICAPLSLKNLSSCLVDLSTGRP 1116 (1144)
Q Consensus 1065 qKLrq~r---a~-gILVvP~WpSq~WyP~L~~ra~e~P~~lksls~~LL~t~Tg~p 1116 (1144)
+|+.++. .. ++||.|.+.+..||..+...+-+. .+|++ +..++...||..
T Consensus 82 ~Ka~~e~~~g~~~VvLL~~~~~st~W~~~~~~~a~~I-~fi~G-Rl~F~~p~~g~~ 135 (181)
T PF05869_consen 82 EKAIEEYERGNQTVVLLPPADTSTWWFEDALENADEI-RFIRG-RLKFINPVTGKE 135 (181)
T ss_pred HHHHHHHHhCCcEEEEEeccCCCccHHHHHHhcCCEE-EEecC-ceeeccCCCCcc
Confidence 9986432 34 568889999999999887775553 34544 777888777766
No 3
>TIGR01712 phage_N6A_met phage N-6-adenine-methyltransferase. This is a model for a phage-borne DNA N-6-adenine-methyltransferase.
Probab=99.08 E-value=1.8e-10 Score=117.73 Aligned_cols=133 Identities=14% Similarity=0.181 Sum_probs=108.7
Q ss_pred CCCccccchHHHHHHHhhcCCCcccccccccccCccceeecccCCCCccccccccccccCc-cccccCCCCChHHHHHHH
Q psy3199 989 VLPDWHLLPHLTSWIFQNWGRPVIDLFASAGSAVVPRYVSRSARDTQASFIDAFSMDWTFP-LAWVFPPPPLMPRVLNHL 1067 (1144)
Q Consensus 989 D~~EW~LSpeVFqqIqelWGppEIDLFASriNAKLpRF~Sw~~PDpGA~avDAFs~dWs~~-~~YAFPPfSLIpRVLqKL 1067 (1144)
+.+.|...+.+|..++..+|++++|.+|+..|++|++|++. ..|++.++|.+. ..|+||||+.+.+-++|+
T Consensus 10 ~~D~W~TP~~lf~~L~~~~g~F~LD~~A~~~Na~c~~~~T~--------edd~L~~~W~~~~~vf~NPPYS~~~~~v~ka 81 (166)
T TIGR01712 10 VRDLWSTPREVFAYLEGRYGKFDLDAAASEENAVCAKFYTQ--------EDNALKRWWGKNKAVWLNPPYSRPDIFVNKT 81 (166)
T ss_pred hCCcCCChHHHHHHHHhhcCceEEecCCCCCccchhhhcCc--------ccchhhhccccCceEEecCCCCcHHHHHHHH
Confidence 46899999999999999999999999999999999999995 349999999975 899999999887777664
Q ss_pred ----HhcCccEEEEeecCCCCcCcHHHHHHhhhCCccccCCCcccccCCCCCCCCccc-cccceeeeecCC
Q psy3199 1068 ----NSAQGLFIVIAPTWDKVFWYPDLQRRAICAPLSLKNLSSCLVDLSTGRPPPDVV-SLRLQAWLVRGG 1133 (1144)
Q Consensus 1068 ----rq~ra~gILVvP~WpSq~WyP~L~~ra~e~P~~lksls~~LL~t~Tg~phP~v~-~L~L~aW~isG~ 1133 (1144)
++.+..+|+++|.-+|..||+..+ ++-..|++.+..++...||++-.... ..-|.+|..-..
T Consensus 82 ae~~~~~g~~~VmLlpa~tst~W~~~~a----~ei~fi~~GRi~F~~p~tg~~~~~~~~gs~l~i~~p~~~ 148 (166)
T TIGR01712 82 AWFTEARQAAEVILIEADLSTVWWPEDI----DGNEYIRSGRIAFISPETGKEKDGNNKGSVIFIMREFKE 148 (166)
T ss_pred HHHHHhhCCeEEEEEecCCcchhHHhcC----CeeEEeeCCceeeEcCCCCcccCCCCCCEEEEEEeccCC
Confidence 344578999999999999997543 44456777799999999999653333 356777765543
No 4
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.85 E-value=8.6e-09 Score=98.25 Aligned_cols=116 Identities=19% Similarity=0.166 Sum_probs=86.1
Q ss_pred EEEEecCCC------CceEEEEeeccccccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHHhc
Q psy3199 869 VFVTSDASD------SGWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQKQ 942 (1144)
Q Consensus 869 fiLyTDASd------SGIGAVL~Qe~aSgtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLnKq 942 (1144)
++||||||. .|+|+|+.........+......+-+..|+.|++.||+.... +.-+++.|+||++.++..+++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~-~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTE-HNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHh-CCCCEEEEEechHHHHHHHhHH
Confidence 579999885 399999975432212222223457789999999999997532 2335799999999999999985
Q ss_pred CCCCChhhhhHHHHHHHHHHhcceeEEEEEecCCcccCCCcCCCC
Q psy3199 943 GGTKSINLLRGVEEIFRIATVHNITVQAQYIPGMYNNIADSLSRS 987 (1144)
Q Consensus 943 gSkrSp~LnrLARrI~~wLee~nIdftaeHIPGkeNvVADALSR~ 987 (1144)
.. +...+..+++.+..++.++. .+.+.|||+..|..||.|+|.
T Consensus 81 ~~-~~~~~~~l~~~~~~l~~~f~-~~~~~~v~r~~N~~Ad~LA~~ 123 (128)
T PRK13907 81 YA-KNKMFAPLLEEALQYIKSFD-LFFIKWIPSSQNKVADELARK 123 (128)
T ss_pred Hh-cChhHHHHHHHHHHHHhcCC-ceEEEEcCchhchhHHHHHHH
Confidence 43 34556677888877777666 356799999999999999875
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=98.79 E-value=6.4e-09 Score=97.52 Aligned_cols=112 Identities=23% Similarity=0.226 Sum_probs=77.1
Q ss_pred ccEEEEecCCC------CceEEEEeeccccccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHH
Q psy3199 867 TQVFVTSDASD------SGWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQ 940 (1144)
Q Consensus 867 ~dfiLyTDASd------SGIGAVL~Qe~aSgtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLn 940 (1144)
..+.||||||- .|+|+++... ..+...-...+++..||.||..||+.+ ..+.++|+||++.++..++
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~---~~~~~~~~~~s~~~aEl~Ai~~AL~~~----~~~~v~I~tDS~~v~~~l~ 74 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGG---RNFSFRLGGQSNNRAELQAIIEALKAL----EHRKVTIYTDSQYVLNALN 74 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETT---EEEEEEEESECHHHHHHHHHHHHHHTH----STSEEEEEES-HHHHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECC---eEEEecccccchhhhheehHHHHHHHh----hcccccccccHHHHHHHHH
Confidence 35789999993 3888866433 123222227789999999999999965 2289999999999999887
Q ss_pred hc---CCCCChhhh-hHHHHHHHHHHhcceeEEEEEecCCccc-----CCCcCCC
Q psy3199 941 KQ---GGTKSINLL-RGVEEIFRIATVHNITVQAQYIPGMYNN-----IADSLSR 986 (1144)
Q Consensus 941 Kq---gSkrSp~Ln-rLARrI~~wLee~nIdftaeHIPGkeNv-----VADALSR 986 (1144)
+. .+.+..... .+..+|+.++ ..+..+.++||||..|. .||.|.|
T Consensus 75 ~~~~~~~~~~~~~~~~i~~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk 128 (132)
T PF00075_consen 75 KWLHGNGWKKTSNGRPIKNEIWELL-SRGIKVRFRWVPGHSGVPQGNERADRLAK 128 (132)
T ss_dssp THHHHTTSBSCTSSSBHTHHHHHHH-HHSSEEEEEESSSSSSSHHHHHHHHHHHH
T ss_pred Hhccccccccccccccchhheeecc-ccceEEeeeeccCcCCCchhHHHHHHHHH
Confidence 61 011111222 3566777777 44677899999999654 6887765
No 6
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=98.59 E-value=2.2e-07 Score=97.96 Aligned_cols=182 Identities=20% Similarity=0.268 Sum_probs=119.1
Q ss_pred ChHHHHHHHhhCCCCCHHHHHHHhcccchhhhcCChhHHHHHHHHHHHHhcccCCCccccCCHHHHHHHHHHHHHhCCCC
Q psy3199 781 DPKSLAEAMRAQSSSSWKKAEVIMGFLSFASFVIPLGKLMFRHIQRLSLRLKKDPLKLCKIPPMALSQMRWWIAALGTPS 860 (1144)
Q Consensus 781 DpKkLLEa~rs~~~~SvKELQSFLGlLNhVS~VIP~GR~YyRrLyr~lskLrK~p~a~~rLSeEAreDLeWWKe~LsS~~ 860 (1144)
.++..++.+.-..+...|=.|++.|+|||++.+..-|-..+..+|..... .+.+..+..-+.=|-.. .+.-..
T Consensus 14 kik~~~rKlpvnrpiDwKvcQRivGlLgF~aPFTqcgy~aL~PlY~~iq~-----k~aF~FS~~Yk~~L~kq--y~~l~p 86 (245)
T PF00336_consen 14 KIKQCFRKLPVNRPIDWKVCQRIVGLLGFAAPFTQCGYPALMPLYAAIQS-----KQAFTFSPTYKAFLCKQ--YMNLYP 86 (245)
T ss_pred HHHHHHhcCCCCCCcchHHHHhhhhhhhcccccccCCchhhhhHHHHHhh-----hheeecCHHHHHHHHHh--hccccc
Confidence 44555566677788899999999999998888766555556666654311 23355555544433221 111111
Q ss_pred ccccCCccEEEEecCCCCceEEEEeeccccccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHH
Q psy3199 861 PIFRRRTQVFVTSDASDSGWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQ 940 (1144)
Q Consensus 861 pI~pP~~dfiLyTDASdSGIGAVL~Qe~aSgtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLn 940 (1144)
....+..--.|++||..+|||..+......++|+. -.+|+..||+|..+|-.+ .|.++ +.|||+.++ .
T Consensus 87 varqr~~lc~VfaDATpTgwgi~i~~~~~~~Tfs~---~l~IhtaELlaaClAr~~-----~~~r~-l~tDnt~Vl---s 154 (245)
T PF00336_consen 87 VARQRPGLCQVFADATPTGWGISITGQRMRGTFSK---PLPIHTAELLAACLARLM-----SGARC-LGTDNTVVL---S 154 (245)
T ss_pred cccCCCCCCceeccCCCCcceeeecCceeeeeecc---cccchHHHHHHHHHHHhc-----cCCcE-EeecCcEEE---e
Confidence 11223345679999999999999988888888875 568999999999876553 44455 899998654 2
Q ss_pred hcCCCCChhhhhHHHHHHHHHHhcceeEEEEEecCCcccCCCcCCCCCC
Q psy3199 941 KQGGTKSINLLRGVEEIFRIATVHNITVQAQYIPGMYNNIADSLSRSQV 989 (1144)
Q Consensus 941 KqgSkrSp~LnrLARrI~~wLee~nIdftaeHIPGkeNvVADALSR~~D 989 (1144)
++..+-.-.+.-.++||.+ + ..+.|||++-| -||..||..-
T Consensus 155 rkyts~PW~lac~A~wiLr-----g--ts~~yVPS~~N-PAD~PsR~~~ 195 (245)
T PF00336_consen 155 RKYTSFPWLLACAANWILR-----G--TSFYYVPSKYN-PADDPSRGKL 195 (245)
T ss_pred cccccCcHHHHHHHHHhhc-----C--ceEEEeccccC-cCCCCCCCcc
Confidence 3222211122234455432 3 46799999999 5999999863
No 7
>PRK07708 hypothetical protein; Validated
Probab=98.53 E-value=2.4e-07 Score=98.34 Aligned_cols=123 Identities=15% Similarity=0.098 Sum_probs=92.4
Q ss_pred CccEEEEecCCC------CceEEEEeeccccccc--c---ccccccccchhhHHHHHHHHHHhhc-ccCCcEEEEEeCCh
Q psy3199 866 RTQVFVTSDASD------SGWGARVDNRMIKGSW--T---ECQKKWHINVKELFAVQMSLEKNLA-YVQNKVVLIQSDNL 933 (1144)
Q Consensus 866 ~~dfiLyTDASd------SGIGAVL~Qe~aSgtW--S---eaErnySIneRELLAVVlALe~fr~-yL~Gk~flVrTDNK 933 (1144)
+..+++|+|||. .|+|+|+........+ . .-....+.|..|+.|++.||+.... ......|.|++|++
T Consensus 71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSq 150 (219)
T PRK07708 71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQ 150 (219)
T ss_pred CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccH
Confidence 346899999986 3899998643221111 1 1112347788999999999997643 22333599999999
Q ss_pred hHHHHHHhcCCCCChhhhhHHHHHHHHHHhcceeEEEEEecCCcccCCCcCCCCC
Q psy3199 934 TVVCYIQKQGGTKSINLLRGVEEIFRIATVHNITVQAQYIPGMYNNIADSLSRSQ 988 (1144)
Q Consensus 934 TAVSyLnKqgSkrSp~LnrLARrI~~wLee~nIdftaeHIPGkeNvVADALSR~~ 988 (1144)
-++..+++....+++.++.....+...+.++.+.++++|||+++|..||.|++.-
T Consensus 151 lVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~A 205 (219)
T PRK07708 151 VVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQA 205 (219)
T ss_pred HHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHH
Confidence 9999999876666777777777777777778777889999999999999998863
No 8
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.46 E-value=3.8e-07 Score=90.32 Aligned_cols=115 Identities=20% Similarity=0.153 Sum_probs=75.9
Q ss_pred cEEEEecCCC------CceEEEEeeccccccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHHh
Q psy3199 868 QVFVTSDASD------SGWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQK 941 (1144)
Q Consensus 868 dfiLyTDASd------SGIGAVL~Qe~aSgtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLnK 941 (1144)
.+.||||+|. .|+|+|+........+...+...+.+..||.|++.||+.+. ....+.|+||++.++..+++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~---~~~~v~I~tDS~yvi~~i~~ 79 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALK---EPCEVTLYTDSQYVRQGITE 79 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcC---CCCeEEEEECHHHHHHHHHH
Confidence 4789999996 38888876432212222233455678899999999999653 24679999999988877764
Q ss_pred c----------CCCCCh-hhhhHHHHHHHHHHhcceeEEEEEecCCc----ccCCCcCCCC
Q psy3199 942 Q----------GGTKSI-NLLRGVEEIFRIATVHNITVQAQYIPGMY----NNIADSLSRS 987 (1144)
Q Consensus 942 q----------gSkrSp-~LnrLARrI~~wLee~nIdftaeHIPGke----NvVADALSR~ 987 (1144)
. .+...+ ....++..+..++.. ..+.+.||||.. |..||.|+|.
T Consensus 80 w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~--~~v~~~wV~~H~~~~~N~~AD~lA~~ 138 (150)
T PRK00203 80 WIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR--HQIKWHWVKGHAGHPENERCDELARA 138 (150)
T ss_pred HHHHHHHcCCcccCCCccccHHHHHHHHHHhcc--CceEEEEecCCCCCHHHHHHHHHHHH
Confidence 1 000011 112356666665544 356789999655 8889988874
No 9
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.44 E-value=3.5e-07 Score=93.08 Aligned_cols=119 Identities=23% Similarity=0.144 Sum_probs=84.4
Q ss_pred cEEEEecCCC------CceEEEEeeccccccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHHh
Q psy3199 868 QVFVTSDASD------SGWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQK 941 (1144)
Q Consensus 868 dfiLyTDASd------SGIGAVL~Qe~aSgtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLnK 941 (1144)
.++||||+|. .|||+||.........+..+...+.|+.|+.|++.||+.... +.-+.|.|+||++-++..++.
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~-~~~~~v~l~tDS~yv~~~i~~ 81 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKE-LGACEVTLYTDSKYVVEGITR 81 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHh-cCCceEEEEecHHHHHHHHHH
Confidence 5789999996 399999983333333555555778899999999999998654 455789999999999887772
Q ss_pred c----CCC------CChh-hhhHHHHHHHHHHhcceeEEEEEec----CCcccCCCcCCCCC
Q psy3199 942 Q----GGT------KSIN-LLRGVEEIFRIATVHNITVQAQYIP----GMYNNIADSLSRSQ 988 (1144)
Q Consensus 942 q----gSk------rSp~-LnrLARrI~~wLee~nIdftaeHIP----GkeNvVADALSR~~ 988 (1144)
. ... +.+. ...+++++..++..+. .+.++||+ ...|..||.|.|..
T Consensus 82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~-~v~~~WVkgH~g~~~NeraD~LA~~~ 142 (154)
T COG0328 82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHE-LVFWEWVKGHAGHPENERADQLAREA 142 (154)
T ss_pred HHhhccccCccccccCccccHHHHHHHHHHHhhCC-eEEEEEeeCCCCChHHHHHHHHHHHH
Confidence 2 000 0111 1235677776666664 47889999 56777889888753
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.43 E-value=4.9e-07 Score=100.76 Aligned_cols=118 Identities=22% Similarity=0.199 Sum_probs=89.3
Q ss_pred cEEEEecCCCC------ceEEEEeecccc---ccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHH
Q psy3199 868 QVFVTSDASDS------GWGARVDNRMIK---GSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCY 938 (1144)
Q Consensus 868 dfiLyTDASdS------GIGAVL~Qe~aS---gtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSy 938 (1144)
.++||||||.. |+|+++...... ..+.......+.|..|+.|++.||+.... +..+++.|++|++.++..
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~-~g~~~v~i~~DS~lvi~~ 80 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAE-LGATEVEVRMDSKLVVEQ 80 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHh-CCCCeEEEEeCcHHHHHH
Confidence 47899999963 999998764321 11222223567789999999999997543 345689999999999999
Q ss_pred HHhcCCCCChhhhhHHHHHHHHHHhcceeEEEEEecCCcccCCCcCCCC
Q psy3199 939 IQKQGGTKSINLLRGVEEIFRIATVHNITVQAQYIPGMYNNIADSLSRS 987 (1144)
Q Consensus 939 LnKqgSkrSp~LnrLARrI~~wLee~nIdftaeHIPGkeNvVADALSR~ 987 (1144)
+++....++..+..+...+..+...+. .+++.|||+++|..||.|.+.
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~-~~~i~~v~r~~N~~AD~LA~~ 128 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFG-RVTYTWIPRARNAHADRLANE 128 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCC-ceEEEECCchhhhHHHHHHHH
Confidence 987655556677777777777766665 478899999999999999995
No 11
>PRK06548 ribonuclease H; Provisional
Probab=98.34 E-value=1.4e-06 Score=89.06 Aligned_cols=114 Identities=25% Similarity=0.272 Sum_probs=79.1
Q ss_pred ccEEEEecCCCC------ceEEEEeeccccccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHH
Q psy3199 867 TQVFVTSDASDS------GWGARVDNRMIKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQ 940 (1144)
Q Consensus 867 ~dfiLyTDASdS------GIGAVL~Qe~aSgtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLn 940 (1144)
..+.||||+|.. |||+++... ......+...+-|..||.|++.||+.... .+..++|+||++.++..++
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~---~~~~g~~~~~TNnraEl~Aii~aL~~~~~--~~~~v~I~TDS~yvi~~i~ 78 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDEN---TWDSGGWDIATNNIAELTAVRELLIATRH--TDRPILILSDSKYVINSLT 78 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCC---cEEccCCCCCCHHHHHHHHHHHHHHhhhc--CCceEEEEeChHHHHHHHH
Confidence 348899998863 788887632 12223334557788999999999975432 2357999999999999888
Q ss_pred h--------c--CCCCChhh-hhHHHHHHHHHHhcceeEEEEEecCCc----ccCCCcCCCC
Q psy3199 941 K--------Q--GGTKSINL-LRGVEEIFRIATVHNITVQAQYIPGMY----NNIADSLSRS 987 (1144)
Q Consensus 941 K--------q--gSkrSp~L-nrLARrI~~wLee~nIdftaeHIPGke----NvVADALSR~ 987 (1144)
+ + .++..+.. ..++.+|..++.... +++.||+|.. |..||.|.|.
T Consensus 79 ~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~--v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRN--IRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred HHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCc--eEEEEEecCCCCHHHHHHHHHHHH
Confidence 3 1 11112223 347777777766654 6789999966 8889988886
No 12
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.20 E-value=9.2e-07 Score=77.08 Aligned_cols=82 Identities=22% Similarity=0.258 Sum_probs=61.4
Q ss_pred chhhHHHHHHHHHHhhcccCCcEEEEEeCChhHHHHHHhcCCCCChhhhhHHHHHHHHHHhcceeEEEEEecCCcccCCC
Q psy3199 903 NVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVVCYIQKQGGTKSINLLRGVEEIFRIATVHNITVQAQYIPGMYNNIAD 982 (1144)
Q Consensus 903 neRELLAVVlALe~fr~yL~Gk~flVrTDNKTAVSyLnKqgSkrSp~LnrLARrI~~wLee~nIdftaeHIPGkeNvVAD 982 (1144)
+..|++|+..||+.... +.-++|.|.||++.++..+++....++ .+..+...|..++..+. .+.+.|||++.|..||
T Consensus 2 ~~aE~~al~~al~~a~~-~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~-~~~~~~i~r~~N~~A~ 78 (87)
T PF13456_consen 2 LEAEALALLEALQLAWE-LGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFW-NVSVSHIPREQNKVAD 78 (87)
T ss_dssp HHHHHHHHHHHHHHHHC-CT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCS-CEEEEE--GGGSHHHH
T ss_pred cHHHHHHHHHHHHHHHH-CCCCEEEEEecCccccccccccccccc-cccccchhhhhhhcccc-ceEEEEEChHHhHHHH
Confidence 35799999999997533 344689999999999999998755544 66778888887777655 5789999999999999
Q ss_pred cCCCC
Q psy3199 983 SLSRS 987 (1144)
Q Consensus 983 ALSR~ 987 (1144)
.|+|.
T Consensus 79 ~LA~~ 83 (87)
T PF13456_consen 79 ALAKF 83 (87)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 99874
No 13
>PRK08719 ribonuclease H; Reviewed
Probab=98.07 E-value=8.5e-06 Score=81.68 Aligned_cols=115 Identities=18% Similarity=0.065 Sum_probs=73.4
Q ss_pred CccEEEEecCCC----C-----ceEEEEeeccccc--cccc-cccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCCh
Q psy3199 866 RTQVFVTSDASD----S-----GWGARVDNRMIKG--SWTE-CQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNL 933 (1144)
Q Consensus 866 ~~dfiLyTDASd----S-----GIGAVL~Qe~aSg--tWSe-aErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNK 933 (1144)
+..+.||||+|. . |||+++....... .++. -+...+.+..||.|+..||+..... ..|+||++
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~-----~~i~tDS~ 76 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG-----DVIYSDSD 76 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC-----CEEEechH
Confidence 356889999887 2 8899875432111 1111 1223478899999999999975431 37999999
Q ss_pred hHHHHHHh-------cCCCC---Chh-hhhHHHHHHHHHHhcceeEEEEEecC----CcccCCCcCCCC
Q psy3199 934 TVVCYIQK-------QGGTK---SIN-LLRGVEEIFRIATVHNITVQAQYIPG----MYNNIADSLSRS 987 (1144)
Q Consensus 934 TAVSyLnK-------qgSkr---Sp~-LnrLARrI~~wLee~nIdftaeHIPG----keNvVADALSR~ 987 (1144)
.++..+++ ++-++ .+. ...++..|..+.... .++++|||| ..|..||.|.|.
T Consensus 77 yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~--~i~~~~VkgH~g~~~Ne~aD~lA~~ 143 (147)
T PRK08719 77 YCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARK--YVEVEKVTAHSGIEGNEAADMLAQA 143 (147)
T ss_pred HHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCC--cEEEEEecCCCCChhHHHHHHHHHH
Confidence 88888752 11111 111 123555555444433 478899999 679999988764
No 14
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=97.34 E-value=0.00088 Score=67.64 Aligned_cols=115 Identities=23% Similarity=0.276 Sum_probs=67.5
Q ss_pred CHHHHHHHhcc----cchhhhcCChhHHHHHHHHHHHHhcccCCCccccCCHHHHHHHHHHHHHhCC--C----Cccc-c
Q psy3199 796 SWKKAEVIMGF----LSFASFVIPLGKLMFRHIQRLSLRLKKDPLKLCKIPPMALSQMRWWIAALGT--P----SPIF-R 864 (1144)
Q Consensus 796 SvKELQSFLGl----LNhVS~VIP~GR~YyRrLyr~lskLrK~p~a~~rLSeEAreDLeWWKe~LsS--~----~pI~-p 864 (1144)
|++++-|++-. +..++.++=.+|.++|.+.+.. .+|+. .++++....+..|.+.+.. . +.+. .
T Consensus 2 TKR~ils~ia~~yDPlGl~~p~~i~~K~llq~lw~~~----l~WD~--~lp~el~~~w~~~~~~l~~~~~i~iPR~i~~~ 75 (159)
T PF05380_consen 2 TKRQILSFIASIYDPLGLLAPIIIRAKLLLQKLWQSK----LDWDD--PLPDELRKEWKKWLKELESLSPIRIPRCIPIS 75 (159)
T ss_pred ChHHHHHHHHHHcCcchhhHHHHHHHHHHHHhhhccc----cchhh--hhhHHHHHHHHHHHHHHhhcccccCCcccccc
Confidence 55555554322 2333333334444555444321 23442 3567778888888888753 1 1111 1
Q ss_pred --CCccEEEEecCCCCceEEEEeeccc-ccc-----------ccccccccccchhhHHHHHHHHHHh
Q psy3199 865 --RRTQVFVTSDASDSGWGARVDNRMI-KGS-----------WTECQKKWHINVKELFAVQMSLEKN 917 (1144)
Q Consensus 865 --P~~dfiLyTDASdSGIGAVL~Qe~a-Sgt-----------WSeaErnySIneRELLAVVlALe~f 917 (1144)
....+++|+|||..|+|||+.-+.. ++. -.+ -+..+|-.+||+|+++|++..
T Consensus 76 ~~~~~~L~~F~DAS~~aygavvYlr~~~~~~~~~~ll~aKsrv~P-~k~~tIPRlEL~a~~l~~~l~ 141 (159)
T PF05380_consen 76 DYRSVELHVFCDASESAYGAVVYLRSYSDGSVQVRLLFAKSRVAP-LKTVTIPRLELLAALLGVRLA 141 (159)
T ss_pred cccceeeeEeecccccceeeEeEeeeccCCceeeeeeeecccccC-CCCCcHHHHHHHHHHHHHHHH
Confidence 1357999999999999999753321 111 111 234599999999999999865
No 15
>PF12237 PCIF1_WW: Phosphorylated CTD interacting factor 1 WW domain; InterPro: IPR022035 This domain is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. It is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity.
Probab=96.92 E-value=0.0012 Score=69.16 Aligned_cols=133 Identities=21% Similarity=0.216 Sum_probs=92.5
Q ss_pred hhhHHHHHHHHHHhcceeEEEEEecCCcccCCCcCCCCCCCCccccchHHHHHHHhhcCCCcccccccccccCccceeec
Q psy3199 950 LLRGVEEIFRIATVHNITVQAQYIPGMYNNIADSLSRSQVLPDWHLLPHLTSWIFQNWGRPVIDLFASAGSAVVPRYVSR 1029 (1144)
Q Consensus 950 LnrLARrI~~wLee~nIdftaeHIPGkeNvVADALSR~~D~~EW~LSpeVFqqIqelWGppEIDLFASriNAKLpRF~Sw 1029 (1144)
......+++.++.+|+--+ |.+. +......+.+.+.+|.-+.+.|| .+.+.||+.+|+.+++|+|.
T Consensus 16 ~~~F~~~v~~lL~RY~tl~------G~~~-------~~~~g~q~a~p~~vf~~L~~~f~-v~~EcFASPlN~~~~~ycSa 81 (176)
T PF12237_consen 16 DQRFLSRVFCLLLRYQTLF------GGQY-------QEGGGLQAALPPEVFDALHKRFG-VSFECFASPLNCYFRQYCSA 81 (176)
T ss_pred HHHHHHHHHHHHHHHHHHc------CCCc-------CCCCcccccCCHHHHHHHHHHcC-CCEEEecChhhhhHHHhcCc
Confidence 3345566777777776311 3221 11234578899999999999999 67999999999999999998
Q ss_pred ccCCCCcc---ccccccccccCccccccCCCC--ChHHHHHHHH----hc----CccEEEEeecCCCCcCcHHHHHHhhh
Q psy3199 1030 SARDTQAS---FIDAFSMDWTFPLAWVFPPPP--LMPRVLNHLN----SA----QGLFIVIAPTWDKVFWYPDLQRRAIC 1096 (1144)
Q Consensus 1030 ~~PDpGA~---avDAFs~dWs~~~~YAFPPfS--LIpRVLqKLr----q~----ra~gILVvP~WpSq~WyP~L~~ra~e 1096 (1144)
+||..+. .=++|...+..+..=++|||. +|.|++.++. .. ....|+|+|.|+...- ..++.+
T Consensus 82 -FpDtD~~FGS~GsFf~f~p~~Gsfe~NPPF~~elm~~~~~h~~~~L~~~~~~~~LsFvvvvP~w~~~~~----~~~l~~ 156 (176)
T PF12237_consen 82 -FPDTDAYFGSLGSFFDFEPVSGSFEANPPFDEELMERMVNHIERLLRAENSSEPLSFVVVVPEWRDPPA----WERLES 156 (176)
T ss_pred -CcCccccccCCcchhcccCCCCceeeCCCCCHHHHHHHHHHHHHHHHhccccCceEEEEEecCCCCcHH----HHHHhc
Confidence 7877543 235677777777666999998 6666655532 11 2378999999988633 344455
Q ss_pred CCccc
Q psy3199 1097 APLSL 1101 (1144)
Q Consensus 1097 ~P~~l 1101 (1144)
-++..
T Consensus 157 S~~~r 161 (176)
T PF12237_consen 157 SPYKR 161 (176)
T ss_pred CCcCc
Confidence 55554
No 16
>KOG3752|consensus
Probab=96.76 E-value=0.0044 Score=70.92 Aligned_cols=117 Identities=22% Similarity=0.248 Sum_probs=78.0
Q ss_pred EEEEecCCC---------CceEEEEeecc---ccccccccccccccchhhHHHHHHHHHHhhcccCCcEEEEEeCChhHH
Q psy3199 869 VFVTSDASD---------SGWGARVDNRM---IKGSWTECQKKWHINVKELFAVQMSLEKNLAYVQNKVVLIQSDNLTVV 936 (1144)
Q Consensus 869 fiLyTDASd---------SGIGAVL~Qe~---aSgtWSeaErnySIneRELLAVVlALe~fr~yL~Gk~flVrTDNKTAV 936 (1144)
..||||+|. .|||++.+... .++... ....+-|..||.||..||+.-... ...+++|+||+..++
T Consensus 213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~--~g~qtNnrAEl~Av~~ALkka~~~-~~~kv~I~TDS~~~i 289 (371)
T KOG3752|consen 213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLA--GGRQTNNRAELIAAIEALKKARSK-NINKVVIRTDSEYFI 289 (371)
T ss_pred eEEEecCccccCCCCCCcceeEEeeCCCCcccccccCC--CCcccccHHHHHHHHHHHHHHHhc-CCCcEEEEechHHHH
Confidence 779999985 37888877432 233332 134577899999999999985332 233899999999988
Q ss_pred HHHHhcC---------CCCChh-------hhhHHHHHHHHHHh-cceeEEEEEecCCc----ccCCCcCCCCC
Q psy3199 937 CYIQKQG---------GTKSIN-------LLRGVEEIFRIATV-HNITVQAQYIPGMY----NNIADSLSRSQ 988 (1144)
Q Consensus 937 SyLnKqg---------SkrSp~-------LnrLARrI~~wLee-~nIdftaeHIPGke----NvVADALSR~~ 988 (1144)
.+|+..- ++.+.. .......+-.+..+ .+..+.+.||+|.. |..||.|+|..
T Consensus 290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 8776321 111111 11233445555555 46788999999965 66799999975
No 17
>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=95.26 E-value=0.0042 Score=64.43 Aligned_cols=80 Identities=13% Similarity=0.036 Sum_probs=66.5
Q ss_pred CccccccchhhHhhhhHHHHHHHHh----cCCCccccchhhhhccccccccccccchhhhhccchhHHHHhhhhccCccc
Q psy3199 687 GAFGILCHGLILQRLALADTINMVV----SKHPSVKSDLISALSSKESMFKKTSDNLLQYVCGKRAEAIASRRKLLEPAI 762 (1144)
Q Consensus 687 ~~fg~~~~~~ifqrl~l~d~~~e~~----~~~~~V~~Dli~~~s~~e~~~~~~~~n~L~~lc~~~~~~va~k~~ll~pTV 762 (1144)
=.||++|+|.+||+ .+..++.... +.+..+|.|||.+.++.+..|..+..-++..+-........+|+++...+|
T Consensus 125 lp~Gl~~sp~~f~~-~~~~~l~~~~~~~~~~~~~~Y~DDili~s~~~~e~~~~l~~v~~~l~~~gl~l~~~K~~~~~~~v 203 (210)
T cd03715 125 LPQGFKNSPTLFHE-ALARDLAPFPLEHEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRAEV 203 (210)
T ss_pred EeccccCcHHHHHH-HHHHHHHHHHhhCCCeEEEEECCcEEEecCCHHHHHHHHHHHHHHHHHCCCCcCHHHeeCCCCce
Confidence 35899999999999 8999999874 346678999999999999889888888888887777777788888877777
Q ss_pred ccCcc
Q psy3199 763 RVPPR 767 (1144)
Q Consensus 763 RLP~r 767 (1144)
...+-
T Consensus 204 ~fLG~ 208 (210)
T cd03715 204 KFLGV 208 (210)
T ss_pred EEeeE
Confidence 66654
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=94.61 E-value=0.0088 Score=62.66 Aligned_cols=77 Identities=16% Similarity=0.048 Sum_probs=64.5
Q ss_pred ccccccchhhHhhhhHHHHHHHHhcCC----CccccchhhhhccccccccccccchhhhhccchhHHHHhhhhccCcccc
Q psy3199 688 AFGILCHGLILQRLALADTINMVVSKH----PSVKSDLISALSSKESMFKKTSDNLLQYVCGKRAEAIASRRKLLEPAIR 763 (1144)
Q Consensus 688 ~fg~~~~~~ifqrl~l~d~~~e~~~~~----~~V~~Dli~~~s~~e~~~~~~~~n~L~~lc~~~~~~va~k~~ll~pTVR 763 (1144)
.||+.|+|.+||+ .+..++..+.++. ..+|.|||.+.++.+..+..+....+..+++.......+|+++ ..+|.
T Consensus 130 P~Gl~~SP~~f~~-~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~~~~~~~l~~v~~~l~~~gl~ln~~K~~~-~~~v~ 207 (213)
T cd01645 130 PQGMKNSPTICQS-FVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQK-EPPFQ 207 (213)
T ss_pred CCCCcChHHHHHH-HHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCHHHHHHHHHHHHHHHHHCCCEeCHHHEeC-CCCeE
Confidence 4899999999999 8999999988764 5789999999999998899888888888888888877888876 45555
Q ss_pred cCc
Q psy3199 764 VPP 766 (1144)
Q Consensus 764 LP~ 766 (1144)
.++
T Consensus 208 fLG 210 (213)
T cd01645 208 YLG 210 (213)
T ss_pred ecc
Confidence 444
No 19
>PF06817 RVT_thumb: Reverse transcriptase thumb domain; InterPro: IPR010661 This domain is known as the thumb domain. It is composed of a four helix bundle []. Reverse transcriptase converts the viral RNA genome into double-stranded viral DNA. Reverse transcriptase often occurs in a polyprotein; with integrase, ribonuclease H and/or protease, which is cleaved before the enzyme takes action. The impact of antiretroviral treatment on the first 400 amino acids of HIV reverse transcriptase is good. Little is known, however, of the antiretroviral drug impact on the C-terminal domains of Pol, which includes the thumb, connection and RNase H []. Evidence suggests that these might be well conserved domains.; GO: 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 2JLE_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B 1FK9_B 3DM2_B 1JLQ_B 3LAM_A ....
Probab=93.52 E-value=0.06 Score=49.40 Aligned_cols=56 Identities=18% Similarity=0.141 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHhcccchhhhcCChhHHHHHHHHHHHHhcccCCCccccCCHHHHHHHHH
Q psy3199 793 SSSSWKKAEVIMGFLSFASFVIPLGKLMFRHIQRLSLRLKKDPLKLCKIPPMALSQMRW 851 (1144)
Q Consensus 793 ~~~SvKELQSFLGlLNhVS~VIP~GR~YyRrLyr~lskLrK~p~a~~rLSeEAreDLeW 851 (1144)
...|+.|+|+++|.+||++.++|-.+ ++.|++.+..- +.....+.|++++..+|+.
T Consensus 13 ~~~TlndiQKLvG~lnW~sqi~~gi~--~k~L~kllrG~-~~l~~~~~lT~eA~~eL~e 68 (70)
T PF06817_consen 13 ESWTLNDIQKLVGKLNWASQIYPGIK--LKQLCKLLRGD-KALTSPVELTEEAELELEE 68 (70)
T ss_dssp SSEBHHHHHHHHHHHHHHTCTSTTS---THHHHHCTTSS-SSTTSBESTTHHHHHHHHH
T ss_pred CchhHHHHHHHHhheeeeeeeecCcc--hhHHHHHhcCC-CCccceecCCHHHHHHHHh
Confidence 35699999999999999998876533 44555433222 3557789999999999864
No 20
>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=91.43 E-value=0.053 Score=51.84 Aligned_cols=78 Identities=14% Similarity=0.121 Sum_probs=58.0
Q ss_pred CccccccchhhHhhhhHHHHHHHHhcCCCccccchhhhhccccccccccccchhhhhccchhHHHHhhhhccCcccccC
Q psy3199 687 GAFGILCHGLILQRLALADTINMVVSKHPSVKSDLISALSSKESMFKKTSDNLLQYVCGKRAEAIASRRKLLEPAIRVP 765 (1144)
Q Consensus 687 ~~fg~~~~~~ifqrl~l~d~~~e~~~~~~~V~~Dli~~~s~~e~~~~~~~~n~L~~lc~~~~~~va~k~~ll~pTVRLP 765 (1144)
=.||+.+++.+||+ .+..++.+.....-.+|.|++.+.+.....+.......+..+-........+|+.+...++...
T Consensus 96 ~p~G~~~s~~~~~~-~~~~~l~~~~~~~~~~y~DDi~i~~~~~~~~~~~~~~~~~~l~~~~~~~~~~K~~~~~~~~~~l 173 (177)
T cd01647 96 MPFGLKNAPATFQR-LMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGVPEVEFL 173 (177)
T ss_pred ecCCCccHHHHHHH-HHHhhhccccccccEEEecCccccCCCHHHHHHHHHHHHHHHHHcCCEeCHHHceeccCceEee
Confidence 35999999999999 9999999988999999999999988887777766555555543444444556666655444433
No 21
>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=89.93 E-value=0.08 Score=50.46 Aligned_cols=41 Identities=10% Similarity=0.078 Sum_probs=33.7
Q ss_pred ccccccchhhHhhhhHHHHHHHHh--cCCCccccchhhhhcccc
Q psy3199 688 AFGILCHGLILQRLALADTINMVV--SKHPSVKSDLISALSSKE 729 (1144)
Q Consensus 688 ~fg~~~~~~ifqrl~l~d~~~e~~--~~~~~V~~Dli~~~s~~e 729 (1144)
.||++|+|.+||+ .+..+++++. +....+|.||+.+.+..+
T Consensus 35 p~Gl~~sp~~f~~-~~~~i~~~~~~~~~~v~~Y~DDili~~~~~ 77 (119)
T cd03714 35 PFGLSLAPRVFTK-VVEALLAPLRLLGVRIFSYLDDLLIIASSI 77 (119)
T ss_pred CCcccchHHHHHH-HHHHHHHHhhcCCeEEEEEecCeEEEeCcH
Confidence 5999999999999 7888888753 445678999999977653
No 22
>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=89.60 E-value=0.11 Score=55.27 Aligned_cols=63 Identities=13% Similarity=0.056 Sum_probs=49.4
Q ss_pred hhhcCCCccccccchhhHhhhhHHHHHHHHhcC------CCccccchhhhhccccccccccccchhhhhc
Q psy3199 681 LLACNDGAFGILCHGLILQRLALADTINMVVSK------HPSVKSDLISALSSKESMFKKTSDNLLQYVC 744 (1144)
Q Consensus 681 ~~~~~~~~fg~~~~~~ifqrl~l~d~~~e~~~~------~~~V~~Dli~~~s~~e~~~~~~~~n~L~~lc 744 (1144)
....+-=.||++|+|.+||+ .+.++++++... ...+|.|+|.+.++.+..+......++..+.
T Consensus 98 ~Y~~~~~pFG~~~AP~~~~~-~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s~~e~~~~~~~v~~~L~ 166 (213)
T cd01644 98 EYRMTVVPFGAASAPFLANR-ALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKRLIALLK 166 (213)
T ss_pred EEEEEEEccCCccchHHHHH-HHHHHHhhcchhhHHHHHHHeeecccceecCCCHHHHHHHHHHHHHHHH
Confidence 44455557999999999999 999999987753 3579999999998888777776666555544
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=38.98 E-value=7.9 Score=35.00 Aligned_cols=41 Identities=7% Similarity=-0.044 Sum_probs=32.5
Q ss_pred ccccccchhhHhhhhHHHHHHHH----hcCCCccccchhhhhcccc
Q psy3199 688 AFGILCHGLILQRLALADTINMV----VSKHPSVKSDLISALSSKE 729 (1144)
Q Consensus 688 ~fg~~~~~~ifqrl~l~d~~~e~----~~~~~~V~~Dli~~~s~~e 729 (1144)
.+|..+.|.+|+. .+.+..+++ .+..-..|.||+.+.+..+
T Consensus 13 PqG~~~Sp~l~~~-~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~ 57 (98)
T cd00304 13 PQGSPLSPALANL-YMEKLEAPILKQLLDITLIRYVDDLVVIAKSE 57 (98)
T ss_pred CCCCchHHHHHHH-HHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH
Confidence 5899999999998 788877775 3456678899998877665
No 24
>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=33.88 E-value=7.7 Score=38.83 Aligned_cols=79 Identities=14% Similarity=0.088 Sum_probs=56.4
Q ss_pred CccccccchhhHhhhhHHHHHHHHhcC-----CCccccchhhhhccccccccccccchhhhhccchhHHHHhhhhcc--C
Q psy3199 687 GAFGILCHGLILQRLALADTINMVVSK-----HPSVKSDLISALSSKESMFKKTSDNLLQYVCGKRAEAIASRRKLL--E 759 (1144)
Q Consensus 687 ~~fg~~~~~~ifqrl~l~d~~~e~~~~-----~~~V~~Dli~~~s~~e~~~~~~~~n~L~~lc~~~~~~va~k~~ll--~ 759 (1144)
-.+|...+|.||+. -|.+..+++... ....|.||+.+++..+...........+++-........+|++++ .
T Consensus 126 lpqG~~~S~~l~~~-~l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~~~~~~ 204 (214)
T PF00078_consen 126 LPQGSPLSPLLFNI-YLDDLDRELQQELNPDISYLRYADDILIISKSKEELQKILEKISQWLEELGLKLNPEKTKILHPS 204 (214)
T ss_dssp S-TTSTCHHHHHHH-HHHHHHHHHHHHS-TTSEEEEETTEEEEEESSHHHHHHHHHHHHHHHHHTTSBCSSTTTSCS--E
T ss_pred ccccccccchhhcc-ccccccccccccccccccceEeccccEEEECCHHHHHHHHHHHHHHHHHCCCEEChHHEEEEeCC
Confidence 35799999999998 888888888773 467899999998888766666666666655555555556666665 4
Q ss_pred cccccCc
Q psy3199 760 PAIRVPP 766 (1144)
Q Consensus 760 pTVRLP~ 766 (1144)
.++++.+
T Consensus 205 ~~~~~lG 211 (214)
T PF00078_consen 205 DSVKFLG 211 (214)
T ss_dssp SSEEETT
T ss_pred CCEEEEe
Confidence 4455443
Done!