Query psy11456
Match_columns 574
No_of_seqs 254 out of 1820
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 18:54:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11456.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11456hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00075 RNase_H: RNase H; In 99.8 3.9E-20 8.4E-25 164.7 6.0 117 311-435 2-131 (132)
2 PRK08719 ribonuclease H; Revie 99.8 4.7E-19 1E-23 159.1 12.1 121 311-436 3-146 (147)
3 PRK06548 ribonuclease H; Provi 99.8 3.8E-18 8.3E-23 154.3 11.8 125 311-437 4-142 (161)
4 PRK00203 rnhA ribonuclease H; 99.7 1.8E-17 3.9E-22 150.5 11.0 122 312-437 3-142 (150)
5 COG0328 RnhA Ribonuclease HI [ 99.7 8.8E-17 1.9E-21 142.6 11.7 125 312-437 3-145 (154)
6 cd06222 RnaseH RNase H (RNase 99.7 8.7E-16 1.9E-20 134.6 13.9 122 314-435 1-130 (130)
7 KOG3752|consensus 99.5 3.7E-14 8.1E-19 140.6 11.7 127 311-437 211-365 (371)
8 PRK13907 rnhA ribonuclease H; 99.5 4.3E-13 9.3E-18 118.6 10.8 119 313-436 2-126 (128)
9 PRK07708 hypothetical protein; 99.3 3.4E-11 7.3E-16 115.2 12.5 128 308-439 69-210 (219)
10 PRK07238 bifunctional RNase H/ 99.1 9.8E-10 2.1E-14 115.3 12.9 121 312-437 2-132 (372)
11 PF13456 RVT_3: Reverse transc 98.8 1.5E-08 3.3E-13 82.7 6.5 85 347-435 1-85 (87)
12 cd01650 RT_nLTR_like RT_nLTR: 98.6 5.7E-08 1.2E-12 94.2 6.0 82 9-98 139-220 (220)
13 cd01651 RT_G2_intron RT_G2_int 97.7 5.4E-05 1.2E-09 73.4 5.3 62 10-98 165-226 (226)
14 PF00078 RVT_1: Reverse transc 97.7 3.5E-05 7.5E-10 73.9 3.7 61 10-98 154-214 (214)
15 cd01648 TERT TERT: Telomerase 97.7 9.7E-05 2.1E-09 64.2 6.1 68 10-99 51-119 (119)
16 cd00304 RT_like RT_like: Rever 97.5 0.0002 4.4E-09 59.6 6.4 60 10-98 39-98 (98)
17 cd03487 RT_Bac_retron_II RT_Ba 97.4 0.0006 1.3E-08 65.8 8.0 66 10-101 133-198 (214)
18 cd01646 RT_Bac_retron_I RT_Bac 97.3 0.00046 1E-08 63.2 5.8 67 10-101 81-147 (158)
19 cd03714 RT_DIRS1 RT_DIRS1: Rev 96.9 0.002 4.4E-08 55.8 6.3 47 11-64 60-106 (119)
20 cd01709 RT_like_1 RT_like_1: A 95.5 0.22 4.8E-06 50.6 12.8 94 10-116 111-212 (346)
21 cd01645 RT_Rtv RT_Rtv: Reverse 95.4 0.016 3.6E-07 55.7 4.0 45 11-63 157-201 (213)
22 PF13966 zf-RVT: zinc-binding 95.2 0.0097 2.1E-07 48.3 1.6 28 512-539 53-83 (86)
23 cd03715 RT_ZFREV_like RT_ZFREV 94.2 0.07 1.5E-06 51.2 5.1 58 11-98 153-210 (210)
24 KOG4768|consensus 87.7 3.3 7.1E-05 44.9 9.5 127 12-152 501-641 (796)
25 PF09004 DUF1891: Domain of un 86.6 0.096 2.1E-06 35.8 -1.6 41 104-146 1-41 (42)
26 cd01647 RT_LTR RT_LTR: Reverse 85.8 0.97 2.1E-05 41.1 4.1 45 11-63 120-164 (177)
27 PF05380 Peptidase_A17: Pao re 65.9 15 0.00033 33.3 5.9 52 311-364 80-143 (159)
28 PF00336 DNA_pol_viral_C: DNA 54.7 26 0.00056 32.8 5.1 60 312-380 94-153 (245)
29 cd01644 RT_pepA17 RT_pepA17: R 39.7 30 0.00065 33.2 3.4 39 12-56 135-173 (213)
30 PF05741 zf-nanos: Nanos RNA b 37.3 16 0.00034 26.8 0.8 19 519-537 34-54 (55)
31 cd07049 BMC_EutL_repeat1 ethan 33.0 91 0.002 26.0 4.6 32 15-46 53-99 (103)
32 PF12633 Adenyl_cycl_N: Adenyl 32.3 70 0.0015 30.4 4.4 37 20-56 116-154 (204)
33 PF13696 zf-CCHC_2: Zinc knuck 31.5 23 0.00049 22.8 0.7 18 517-537 7-26 (32)
34 COG0296 GlgB 1,4-alpha-glucan 31.1 55 0.0012 36.6 4.1 37 392-428 212-248 (628)
35 COG0295 Cdd Cytidine deaminase 21.6 3.7E+02 0.0081 23.7 6.7 77 325-412 27-107 (134)
36 cd01699 RNA_dep_RNAP RNA_dep_R 20.6 1.3E+02 0.0027 29.8 4.2 47 10-65 193-239 (278)
37 KOG1812|consensus 20.2 2E+02 0.0044 30.3 5.7 42 345-386 47-88 (384)
No 1
>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=99.80 E-value=3.9e-20 Score=164.74 Aligned_cols=117 Identities=31% Similarity=0.401 Sum_probs=88.8
Q ss_pred CceEEEecCCCCC--CCeeEEEEec-ceeeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhc--
Q psy11456 311 NHTICFTDGSKSP--DVTGCAFSIG-DMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALAN-- 385 (574)
Q Consensus 311 ~~~~i~tDGS~~~--~~~G~~~~~~-~~~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~-- 385 (574)
.++.||||||... +..|+|++.. .....+.++ ..|++.||+.||..||+.+ ...++.|+|||+.++..+..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~---~~~~v~I~tDS~~v~~~l~~~~ 77 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL---EHRKVTIYTDSQYVLNALNKWL 77 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH---STSEEEEEES-HHHHHHHHTHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh---hcccccccccHHHHHHHHHHhc
Confidence 4789999999664 3356776543 333445556 8999999999999999944 33999999999999998877
Q ss_pred ---CCCCc----HHHHHHHHHHHHhhhcCceEEEEEecCCCCC-CcchhhhhhhcCCC
Q psy11456 386 ---VRFSN----PLVTKVFSTWSYLKLCDKEVSFIWCPSHCGI-RGNEIVDVAAKNPS 435 (574)
Q Consensus 386 ---~~~~~----~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi-~gNe~AD~~Ak~a~ 435 (574)
..... ++..+|.+.+ ..+..|.|.|||||+|+ .|||.||+|||.|+
T Consensus 78 ~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 78 HGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 33222 3555555543 45889999999999999 69999999999774
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.80 E-value=4.7e-19 Score=159.14 Aligned_cols=121 Identities=24% Similarity=0.293 Sum_probs=93.1
Q ss_pred CceEEEecCCCCCCC-----eeEEEEecc----e--eeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHH
Q psy11456 311 NHTICFTDGSKSPDV-----TGCAFSIGD----M--VQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSA 379 (574)
Q Consensus 311 ~~~~i~tDGS~~~~~-----~G~~~~~~~----~--~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa 379 (574)
+.+.||||||...++ .|+|++... . .....+....|++.||+.|+..||+.+.+. ..|+|||+-+
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv 78 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC 78 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence 468999999997543 488876422 1 234446666899999999999999998753 3899999999
Q ss_pred HHHH--------hcCCCCc---HH-HHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCC
Q psy11456 380 LAAL--------ANVRFSN---PL-VTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSD 436 (574)
Q Consensus 380 ~~~l--------~~~~~~~---~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~ 436 (574)
++.+ .++...+ ++ -.++...+..+.. ...|+|.|||||+|++|||.||+||++|+.
T Consensus 79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9999 4555433 22 2456666666655 467999999999999999999999999875
No 3
>PRK06548 ribonuclease H; Provisional
Probab=99.76 E-value=3.8e-18 Score=154.33 Aligned_cols=125 Identities=25% Similarity=0.302 Sum_probs=93.9
Q ss_pred CceEEEecCCCCCC--CeeEEEEecceeeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhc---
Q psy11456 311 NHTICFTDGSKSPD--VTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALAN--- 385 (574)
Q Consensus 311 ~~~~i~tDGS~~~~--~~G~~~~~~~~~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~--- 385 (574)
..+.||||||...+ ..|+|++.........-....|...||+.|+..||+.+.. +...+.|+|||+-|++.+..
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~ 82 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVY 82 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHH
Confidence 45899999998864 4788877654322112224579999999999999986643 44579999999999999993
Q ss_pred ------CCCCc--HHH-HHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCCC
Q psy11456 386 ------VRFSN--PLV-TKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDL 437 (574)
Q Consensus 386 ------~~~~~--~~~-~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 437 (574)
.+..+ ++. +++...+..+... ..|+|.|||||+|.+|||.||+||++|+..
T Consensus 83 ~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 83 SWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred HHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 22222 333 5666666666554 479999999999999999999999998755
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.73 E-value=1.8e-17 Score=150.49 Aligned_cols=122 Identities=17% Similarity=0.213 Sum_probs=89.4
Q ss_pred ceEEEecCCCCCC--CeeEEEEec--cee--eeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhc
Q psy11456 312 HTICFTDGSKSPD--VTGCAFSIG--DMV--QSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALAN 385 (574)
Q Consensus 312 ~~~i~tDGS~~~~--~~G~~~~~~--~~~--~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~ 385 (574)
.+.||||||.... ..|+|++.. +.. ..... ...|+..||+.|+..||+.+.. ...+.|+|||+.+++.|..
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~-~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~ 79 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGE-ALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITE 79 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCC-CCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHH
Confidence 4789999998753 468887653 221 22223 4678999999999999998864 4679999999999999985
Q ss_pred --------CCCC---cHHH-HHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCCC
Q psy11456 386 --------VRFS---NPLV-TKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDL 437 (574)
Q Consensus 386 --------~~~~---~~~~-~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 437 (574)
.... .++. .++.+.+..+.. ...|.|.|||||+|++|||.||+|||+|+..
T Consensus 80 w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 80 WIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred HHHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 2211 1221 334444444433 3689999999999999999999999988766
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.70 E-value=8.8e-17 Score=142.59 Aligned_cols=125 Identities=21% Similarity=0.198 Sum_probs=99.5
Q ss_pred ceEEEecCCCCCC--CeeEEEEec--cee--eeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhc
Q psy11456 312 HTICFTDGSKSPD--VTGCAFSIG--DMV--QSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALAN 385 (574)
Q Consensus 312 ~~~i~tDGS~~~~--~~G~~~~~~--~~~--~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~ 385 (574)
.+.||||||...+ .-|+|+|.. +.. .+..+. .+|+..+|+.|+..||+++.+.+...+.|+|||+-+++.|..
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 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR 81 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence 5789999998864 357776653 222 344445 899999999999999999999899999999999999999982
Q ss_pred C---CCC--------cH-HHHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCCC
Q psy11456 386 V---RFS--------NP-LVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDL 437 (574)
Q Consensus 386 ~---~~~--------~~-~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 437 (574)
- ... .| ...+++..+..+...-..|.+.|||||.|.++||.||+||+.|+..
T Consensus 82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~ 145 (154)
T COG0328 82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA 145 (154)
T ss_pred HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence 1 111 12 2456677777777666699999999999999999999999998776
No 6
>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=99.67 E-value=8.7e-16 Score=134.62 Aligned_cols=122 Identities=27% Similarity=0.335 Sum_probs=94.7
Q ss_pred EEEecCCCCCC--CeeEEEEeccee-----eeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhcC
Q psy11456 314 ICFTDGSKSPD--VTGCAFSIGDMV-----QSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANV 386 (574)
Q Consensus 314 ~i~tDGS~~~~--~~G~~~~~~~~~-----~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~~ 386 (574)
.+|||||...+ +.|+|++..+.. .........+++.+|+.|+..||+.+...+..++.|++||+.++..+.+.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~ 80 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW 80 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence 38999999875 688888764421 11222257899999999999999999988999999999999999999987
Q ss_pred CCC-cHHHHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCC
Q psy11456 387 RFS-NPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPS 435 (574)
Q Consensus 387 ~~~-~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~ 435 (574)
... ..........+..+......+.|.|||+|+|+.+|+.||.+||.|.
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 652 2222333333333445678899999999999999999999999863
No 7
>KOG3752|consensus
Probab=99.54 E-value=3.7e-14 Score=140.61 Aligned_cols=127 Identities=27% Similarity=0.281 Sum_probs=99.5
Q ss_pred CceEEEecCCCCCC-----CeeEEEEecce---eeeeeCC-CCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHH
Q psy11456 311 NHTICFTDGSKSPD-----VTGCAFSIGDM---VQSTLLN-PINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALA 381 (574)
Q Consensus 311 ~~~~i~tDGS~~~~-----~~G~~~~~~~~---~~~~~l~-~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~ 381 (574)
+..++|||||...+ .+|+||+.+.. ..++.+. ...+.|.||+.||..||+-+.+....+++|.|||+-+++
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~ 290 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFIN 290 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHH
Confidence 45899999998873 47999998653 4556665 789999999999999999999988889999999999999
Q ss_pred HHhcCC-----------CCcH----H--HHHHHHHHHHhhh--cCceEEEEEecCCCCCCcchhhhhhhcCCCCC
Q psy11456 382 ALANVR-----------FSNP----L--VTKVFSTWSYLKL--CDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDL 437 (574)
Q Consensus 382 ~l~~~~-----------~~~~----~--~~~i~~~~~~l~~--~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 437 (574)
.|+.-- ..++ + .+..+..+..|.. .+.+|.+.|||||.||.|||+||.+|++++..
T Consensus 291 ~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 291 SLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred HHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 987521 0111 1 1223334444433 47899999999999999999999999988655
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.45 E-value=4.3e-13 Score=118.61 Aligned_cols=119 Identities=18% Similarity=0.128 Sum_probs=89.1
Q ss_pred eEEEecCCCCCC--CeeEEEEeccee----eeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhcC
Q psy11456 313 TICFTDGSKSPD--VTGCAFSIGDMV----QSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANV 386 (574)
Q Consensus 313 ~~i~tDGS~~~~--~~G~~~~~~~~~----~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~~ 386 (574)
+.||||||.... ..|+|+|..+.. ..+. ....+...||+.|++.||+.+......++.|++||+-+++.+.+.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~-~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLP-LGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEec-ccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence 579999998763 578898864421 2222 235789999999999999999998888999999999999999986
Q ss_pred CCCcHHHHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCC
Q psy11456 387 RFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSD 436 (574)
Q Consensus 387 ~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~ 436 (574)
.........+...+..+...-..+.|.|||. ++|+.||.+|+.|..
T Consensus 81 ~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred HhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 5433333333434444444445677899998 499999999998753
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.28 E-value=3.4e-11 Score=115.22 Aligned_cols=128 Identities=15% Similarity=0.132 Sum_probs=93.6
Q ss_pred cCCCceEEEecCCCC--CCCeeEEEEecc--e--e----eeeeCCCCccchHHHHHHHHHHHHHHHcCCCCc--EEEEec
Q psy11456 308 KYPNHTICFTDGSKS--PDVTGCAFSIGD--M--V----QSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQ--FLIVSD 375 (574)
Q Consensus 308 ~~~~~~~i~tDGS~~--~~~~G~~~~~~~--~--~----~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~--~~I~~D 375 (574)
..++.+.+|+|||.. +++.|+|+++.. . . ....++...+...||+.|++.||+.+...+.+. |.|++|
T Consensus 69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D 148 (219)
T PRK07708 69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD 148 (219)
T ss_pred cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence 456789999999975 356788877532 1 1 123566668999999999999999999887654 899999
Q ss_pred cHHHHHHHhcCCCCc-HHHHHHHHHHH-HhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCCCCC
Q psy11456 376 SRSALAALANVRFSN-PLVTKVFSTWS-YLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDLAP 439 (574)
Q Consensus 376 s~sa~~~l~~~~~~~-~~~~~i~~~~~-~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~~ 439 (574)
|+-+++.+.+..... +..+...+.+. .+..-...+.+.|||. ..|+.||+||+.|....+
T Consensus 149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR----~~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISR----KQNKEADQLATQALEGTV 210 (219)
T ss_pred cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCc----hhhhHHHHHHHHHHhcCC
Confidence 999999999976543 33333333333 2233345678888875 569999999999998744
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.07 E-value=9.8e-10 Score=115.29 Aligned_cols=121 Identities=17% Similarity=0.172 Sum_probs=90.8
Q ss_pred ceEEEecCCCCCC--CeeEEEEecce-------eeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHH
Q psy11456 312 HTICFTDGSKSPD--VTGCAFSIGDM-------VQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAA 382 (574)
Q Consensus 312 ~~~i~tDGS~~~~--~~G~~~~~~~~-------~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~ 382 (574)
.+.||||||...+ ..|+|+++.+. .....++ .+++..||+.|++.||+.+.+....++.|++||+-+++.
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 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQ 80 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHH
Confidence 3689999998864 47888775431 1223344 678899999999999999999888999999999999999
Q ss_pred HhcCCCCc-HHHHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhhhhhcCCCCC
Q psy11456 383 LANVRFSN-PLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAKNPSDL 437 (574)
Q Consensus 383 l~~~~~~~-~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 437 (574)
+.+..... +-.......+..+...-..+.+.|||. .+|+.||.||+.|...
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 98865432 323333333444444446799999997 7899999999987543
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.77 E-value=1.5e-08 Score=82.70 Aligned_cols=85 Identities=20% Similarity=0.144 Sum_probs=62.6
Q ss_pred chHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhcCCCCcHHHHHHHHHHHHhhhcCceEEEEEecCCCCCCcchh
Q psy11456 347 IFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEI 426 (574)
Q Consensus 347 v~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~ 426 (574)
+..||+.|+..||+++.+.+.+++.|.|||+.++..|.+..........+...+..+...-..+.+.||| -.+|..
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~ 76 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV 76 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence 3579999999999999999999999999999999999988543222233333333455556789999999 689999
Q ss_pred hhhhhcCCC
Q psy11456 427 VDVAAKNPS 435 (574)
Q Consensus 427 AD~~Ak~a~ 435 (574)
||.+||.|.
T Consensus 77 A~~LA~~a~ 85 (87)
T PF13456_consen 77 ADALAKFAL 85 (87)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 999999763
No 12
>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=98.60 E-value=5.7e-08 Score=94.17 Aligned_cols=82 Identities=24% Similarity=0.509 Sum_probs=70.5
Q ss_pred CCCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeec
Q psy11456 9 KPPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFV 88 (574)
Q Consensus 9 ~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~ 88 (574)
...+....||||+++++.+.. ..++..++.+..|+..+|+.+| ++||+++.++..... ...+..++..+..+
T Consensus 139 ~~~~~~~~yaDD~~i~~~~~~-----~~~~~~~~~~~~~~~~~gl~in--~~Kt~~~~~~~~~~~-~~~~~~~~~~~~~~ 210 (220)
T cd01650 139 GPGITHLAYADDIVLFSEGKS-----RKLQELLQRLQEWSKESGLKIN--PSKSKVMLIGNKKKR-LKDITLNGTPIEAV 210 (220)
T ss_pred CCccceEEeccceeeeccCCH-----HHHHHHHHHHHHHHHHcCCEEC--hhheEEEEecCCCcc-hhhhhhcCCcccCC
Confidence 356789999999999977766 4589999999999999999999 999999999887655 33367788899999
Q ss_pred cCceEEEEEE
Q psy11456 89 TNNKFLGLLW 98 (574)
Q Consensus 89 ~~~kyLGv~i 98 (574)
..+||||+.|
T Consensus 211 ~~~kyLG~~i 220 (220)
T cd01650 211 ETFKYLGVTI 220 (220)
T ss_pred CCCeeccccC
Confidence 9999999975
No 13
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=97.67 E-value=5.4e-05 Score=73.44 Aligned_cols=62 Identities=26% Similarity=0.366 Sum_probs=53.2
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeecc
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVT 89 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~ 89 (574)
.++....||||+++++.+.+. ++++++.+.+|+...|+.+| ++||+++.++ .+
T Consensus 165 ~~~~~~rY~DD~~i~~~~~~~------~~~~~~~i~~~~~~~gl~ln--~~Kt~i~~~~-------------------~~ 217 (226)
T cd01651 165 RRLRYVRYADDFVIGVRGPKE------AEEIKELIREFLEELGLELN--PEKTRITHFK-------------------SE 217 (226)
T ss_pred CceEEEEecCceEEecCCHHH------HHHHHHHHHHHHHHcCCeec--hhhcceeecC-------------------CC
Confidence 568899999999998776654 78889999999999999999 9999999995 45
Q ss_pred CceEEEEEE
Q psy11456 90 NNKFLGLLW 98 (574)
Q Consensus 90 ~~kyLGv~i 98 (574)
.+.|||..|
T Consensus 218 ~~~fLG~~~ 226 (226)
T cd01651 218 GFDFLGFTF 226 (226)
T ss_pred CCeeCCeEC
Confidence 678888764
No 14
>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=97.66 E-value=3.5e-05 Score=73.89 Aligned_cols=61 Identities=31% Similarity=0.567 Sum_probs=50.6
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeecc
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVT 89 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~ 89 (574)
+++...-||||+.+++..... +++.++.+.+|+.++|+.+| ++||++++ +.+
T Consensus 154 ~~~~~~rY~DD~~i~~~~~~~------~~~~~~~i~~~~~~~gl~ln--~~Kt~~~~--------------------~~~ 205 (214)
T PF00078_consen 154 PDISYLRYADDILIISKSKEE------LQKILEKISQWLEELGLKLN--PEKTKILH--------------------PSD 205 (214)
T ss_dssp TTSEEEEETTEEEEEESSHHH------HHHHHHHHHHHHHHTTSBCS--STTTSCS----------------------ES
T ss_pred ccccceEeccccEEEECCHHH------HHHHHHHHHHHHHHCCCEEC--hHHEEEEe--------------------CCC
Confidence 467899999998888765332 89999999999999999999 99998666 567
Q ss_pred CceEEEEEE
Q psy11456 90 NNKFLGLLW 98 (574)
Q Consensus 90 ~~kyLGv~i 98 (574)
.++|||+.|
T Consensus 206 ~~~~lG~~i 214 (214)
T PF00078_consen 206 SVKFLGYVI 214 (214)
T ss_dssp SEEETTEEE
T ss_pred CEEEEeEEC
Confidence 889999875
No 15
>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=97.65 E-value=9.7e-05 Score=64.17 Aligned_cols=68 Identities=18% Similarity=0.082 Sum_probs=52.2
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHH-HHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeec
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWA-ETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFV 88 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~-~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~ 88 (574)
......-||||+.+++.+.. ..++.++.+.+|. .+.||.+| ++||++..... .....
T Consensus 51 ~~~~~~rYaDD~li~~~~~~------~~~~~~~~l~~~l~~~~gl~iN--~~Kt~~~~~~~--------------~~~~~ 108 (119)
T cd01648 51 KDSLLLRLVDDFLLITTSLD------KAIKFLNLLLRGFINQYKTFVN--FDKTQINFSFA--------------QLDSS 108 (119)
T ss_pred CCceEEEEeCcEEEEeCCHH------HHHHHHHHHHHhhHHhhCeEEC--cccceeecccc--------------ccCCC
Confidence 34567899999988866533 3788889999997 99999999 99999876532 11344
Q ss_pred cCceEEEEEEc
Q psy11456 89 TNNKFLGLLWD 99 (574)
Q Consensus 89 ~~~kyLGv~id 99 (574)
+.+.|||+.|+
T Consensus 109 ~~~~flG~~i~ 119 (119)
T cd01648 109 DLIPWCGLLIN 119 (119)
T ss_pred CccCceeEeeC
Confidence 56999999875
No 16
>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=97.55 E-value=0.0002 Score=59.59 Aligned_cols=60 Identities=22% Similarity=0.314 Sum_probs=48.7
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeecc
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVT 89 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~ 89 (574)
.++....|+||+.+.+... .++..+..+.+|+.++|+.+| ++||+.. ....
T Consensus 39 ~~~~~~~Y~DD~~i~~~~~-------~~~~~~~~l~~~l~~~gl~ln--~~Kt~~~--------------------~~~~ 89 (98)
T cd00304 39 LDITLIRYVDDLVVIAKSE-------QQAVKKRELEEFLARLGLNLS--DEKTQFT--------------------EKEK 89 (98)
T ss_pred CCceEEEeeCcEEEEeCcH-------HHHHHHHHHHHHHHHcCcEEC--hheeEEe--------------------cCCC
Confidence 4678999999988886555 477888899999999999999 9999875 2356
Q ss_pred CceEEEEEE
Q psy11456 90 NNKFLGLLW 98 (574)
Q Consensus 90 ~~kyLGv~i 98 (574)
.++|||+.+
T Consensus 90 ~~~flG~~~ 98 (98)
T cd00304 90 KFKFLGILV 98 (98)
T ss_pred CeeeeceeC
Confidence 788888753
No 17
>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=97.36 E-value=0.0006 Score=65.78 Aligned_cols=66 Identities=15% Similarity=0.133 Sum_probs=53.6
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeecc
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVT 89 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~ 89 (574)
.++...-||||+++++..... ..++++++.+..|+.+.||.+| ++||+++..+ .
T Consensus 133 ~~~~~~RYaDD~~i~~~~~~~----~~~~~~~~~i~~~l~~~gL~ln--~~Kt~i~~~~--------------------~ 186 (214)
T cd03487 133 NGLTYTRYADDITFSSNKKLK----EALDKLLEIIRSILSEEGFKIN--KSKTRISSKG--------------------S 186 (214)
T ss_pred cCCeEEEEeccEEEEccccch----hHHHHHHHHHHHHHHHCCceeC--CCceEEccCC--------------------C
Confidence 357889999999988776552 4588889999999999999999 9999988762 3
Q ss_pred CceEEEEEEcCC
Q psy11456 90 NNKFLGLLWDAK 101 (574)
Q Consensus 90 ~~kyLGv~id~~ 101 (574)
.+.+||+.+.+.
T Consensus 187 ~~~~~G~~i~~~ 198 (214)
T cd03487 187 RQIVTGLVVNNG 198 (214)
T ss_pred CcEEEEEEEeCC
Confidence 467889988664
No 18
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=97.27 E-value=0.00046 Score=63.15 Aligned_cols=67 Identities=18% Similarity=0.321 Sum_probs=53.7
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeecc
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVT 89 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~ 89 (574)
.++...-||||+++++..+. .+++.++.+.+|..+.||.+| ++||+.+.++... .
T Consensus 81 ~~~~~~RY~DD~~i~~~~~~------~~~~~~~~i~~~l~~~gL~ln--~~Kt~~~~~~~~~-----------------~ 135 (158)
T cd01646 81 KGVDYVRYVDDIRIFADSKE------EAEEILEELKEFLAELGLSLN--LSKTEILPLPEGT-----------------A 135 (158)
T ss_pred CCceEEEecCcEEEEcCCHH------HHHHHHHHHHHHHHHCCCEEC--hhhceeeecCCCC-----------------c
Confidence 46789999999999875433 268899999999999999999 9999999884321 5
Q ss_pred CceEEEEEEcCC
Q psy11456 90 NNKFLGLLWDAK 101 (574)
Q Consensus 90 ~~kyLGv~id~~ 101 (574)
.+.+||..+...
T Consensus 136 ~~~flg~~~~~~ 147 (158)
T cd01646 136 SKDFLGYRFSPI 147 (158)
T ss_pred cccccceEeehh
Confidence 677888877654
No 19
>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=96.93 E-value=0.002 Score=55.82 Aligned_cols=47 Identities=21% Similarity=0.195 Sum_probs=31.6
Q ss_pred CceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEE
Q psy11456 11 PLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVC 64 (574)
Q Consensus 11 ~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~ 64 (574)
+..+..|+||+.+.+.+ .+..+..-+.+..+ -++++|+.+| ++||++
T Consensus 60 ~~~v~~Y~DDili~~~~---~~~~~~~~~~l~~~--~l~~~gl~ln--~~K~~~ 106 (119)
T cd03714 60 GVRIFSYLDDLLIIASS---IKTSEAVLRHLRAT--LLANLGFTLN--LEKSKL 106 (119)
T ss_pred CeEEEEEecCeEEEeCc---HHHHHHHHHHHHHH--HHHHcCCccC--hhhcEe
Confidence 45789999997776554 23333333333322 6889999999 999975
No 20
>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=95.54 E-value=0.22 Score=50.60 Aligned_cols=94 Identities=16% Similarity=0.113 Sum_probs=58.9
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeecc
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVT 89 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~ 89 (574)
.+....=||||+.++.+ . ++ ..+++..+.++++..||++| ++||.++.....++.... .-...-|.-
T Consensus 111 ~g~~l~RYaDD~vi~~~--~-~~----a~~aw~~i~~fl~~lGLelN--~eKT~iV~~~~~~r~~~~----~~~~~LP~g 177 (346)
T cd01709 111 DGGLLYRLHDDLWFWGQ--P-ET----CAKAWKAIQEFAKVMGLELN--KEKTGSVYLSDDTKTRDT----TIDATLPEG 177 (346)
T ss_pred CCceEEEEcCeEEEEcC--H-HH----HHHHHHHHHHHHHHcCceec--cccceEEEeccCCccCCC----cccccCCCC
Confidence 35678889999988832 2 22 44555688889999999999 999999988654321100 001122344
Q ss_pred CceEEEEEEcCC-ccch-------HHHHHHHHHhH
Q psy11456 90 NNKFLGLLWDAK-MNWS-------LHIQYIKSRAM 116 (574)
Q Consensus 90 ~~kyLGv~id~~-L~~~-------~hi~~~~~ka~ 116 (574)
.++|-=+.+|+. ..|. .||+++.+...
T Consensus 178 ~i~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~QL~ 212 (346)
T cd01709 178 PVRWGFLKLDPKTGRWEIDQSQVDAHIDELRKQLD 212 (346)
T ss_pred CceeeeEEecCCCCcEEeeHHHHHHHHHHHHHHhh
Confidence 566655667754 5554 56665554443
No 21
>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=95.37 E-value=0.016 Score=55.73 Aligned_cols=45 Identities=18% Similarity=0.206 Sum_probs=33.6
Q ss_pred CceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcE
Q psy11456 11 PLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSV 63 (574)
Q Consensus 11 ~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~ 63 (574)
++.+..|+||+.|. +++.++ ..+.++.+.....++|+.+| ++||+
T Consensus 157 ~~~~~~Y~DDili~--s~~~~~----~~~~l~~v~~~l~~~gl~ln--~~K~~ 201 (213)
T cd01645 157 DIVIYHYMDDILIA--SDLEGQ----LREIYEELRQTLLRWGLTIP--PEKVQ 201 (213)
T ss_pred CeEEEEEcCCEEEE--cCCHHH----HHHHHHHHHHHHHHCCCEeC--HHHEe
Confidence 45688999997665 444444 45556677777778899999 99996
No 22
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.22 E-value=0.0097 Score=48.32 Aligned_cols=28 Identities=25% Similarity=0.600 Sum_probs=23.0
Q ss_pred ccCCCCCCCcC-CC-Ccccccccc-cccccH
Q psy11456 512 LFTKSAPPICQ-CG-APLSVRHIL-SCHRHD 539 (574)
Q Consensus 512 ~~~~~~~p~C~-Cg-~~~t~~H~l-~Cp~~~ 539 (574)
+.+...++.|. |+ ++||++|+| +||...
T Consensus 53 ~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 53 RRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred ccCCccCCccccCCCccccccceeccCcCcc
Confidence 34446779999 99 699999999 999764
No 23
>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=94.22 E-value=0.07 Score=51.19 Aligned_cols=58 Identities=24% Similarity=0.375 Sum_probs=41.8
Q ss_pred CceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeeccC
Q psy11456 11 PLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVTN 90 (574)
Q Consensus 11 ~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~~ 90 (574)
+..+..|.||+.|. +++.++... .++.+..-..++|+.+| ++||+. .+++
T Consensus 153 ~~~~~~Y~DDili~--s~~~~e~~~----~l~~v~~~l~~~gl~l~--~~K~~~----------------------~~~~ 202 (210)
T cd03715 153 GTILLQYVDDLLLA--ADSEEDCLK----GTDALLTHLGELGYKVS--PKKAQI----------------------CRAE 202 (210)
T ss_pred CeEEEEECCcEEEe--cCCHHHHHH----HHHHHHHHHHHCCCCcC--HHHeeC----------------------CCCc
Confidence 56788999996665 556655444 55666666777889999 999963 2367
Q ss_pred ceEEEEEE
Q psy11456 91 NKFLGLLW 98 (574)
Q Consensus 91 ~kyLGv~i 98 (574)
++|||.++
T Consensus 203 v~fLG~~~ 210 (210)
T cd03715 203 VKFLGVVW 210 (210)
T ss_pred eEEeeEEC
Confidence 88888764
No 24
>KOG4768|consensus
Probab=87.67 E-value=3.3 Score=44.95 Aligned_cols=127 Identities=13% Similarity=0.131 Sum_probs=75.2
Q ss_pred ceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEEEeccCCCCCCCceEeCCeeeeecc--
Q psy11456 12 LKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCIDFHRLRVARSPILSYNGTPLHFVT-- 89 (574)
Q Consensus 12 ~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~~f~~~~~~~~~~~~l~~~~i~~~~-- 89 (574)
...+=||||..+.+.|+-. ...+.+..+..++.+.|++.| ++||++.+-...- ..-|..|...+
T Consensus 501 ~~yVRyadd~ii~v~GS~n-----d~K~ilr~In~f~sslGls~n--~~kt~it~S~eg~-------~flg~nis~tP~r 566 (796)
T KOG4768|consen 501 LMYVRYADDIIIGVWGSVN-----DCKQILRDINNFLSSLGLSNN--SSKTQITVSREGT-------HFLGYNISTTPGR 566 (796)
T ss_pred eeEEEecCCEEEEEeccHH-----HHHHHHHHHHHHHHhhCcccC--cccceEEeeccce-------eeeeceeccCCCC
Confidence 4457899999998887643 245566777888888999999 9999988764321 11111111111
Q ss_pred -----CceEEEEEEcC--CccchHHHHHHHHHhHHHhhhhhhhhc----ccC-CCCHHHHHHHHHHhhhhhhhhc
Q psy11456 90 -----NNKFLGLLWDA--KMNWSLHIQYIKSRAMNSLNALKMVSC----KKF-GVRRDVLLKFYKSFTLPILDYG 152 (574)
Q Consensus 90 -----~~kyLGv~id~--~L~~~~hi~~~~~ka~~~~~~L~~l~~----~~~-g~~~~~~~~ly~a~v~p~l~Yg 152 (574)
.-.--|+-+.+ .+....-|+.+..|.+..-........ -.| -..++++...|.++.+..+.|=
T Consensus 567 ~~~~~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnYY 641 (796)
T KOG4768|consen 567 PAAGEGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYCSHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILNYY 641 (796)
T ss_pred ccceeccccceEEeccCCceeecchHHHHHHHHHhcceeecCCcCceeeeeecccCHHHHHHHHHHHhhchhhhh
Confidence 11111222222 234567777777777765443332110 001 2467788888888888888774
No 25
>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=86.62 E-value=0.096 Score=35.80 Aligned_cols=41 Identities=24% Similarity=0.404 Sum_probs=7.3
Q ss_pred chHHHHHHHHHhHHHhhhhhhhhcccCCCCHHHHHHHHHHhhh
Q psy11456 104 WSLHIQYIKSRAMNSLNALKMVSCKKFGVRRDVLLKFYKSFTL 146 (574)
Q Consensus 104 ~~~hi~~~~~ka~~~~~~L~~l~~~~~g~~~~~~~~ly~a~v~ 146 (574)
|+.|+..+.+||.+.++.||++.. ..+++..+..+|+++|.
T Consensus 1 W~~n~~~~~KKa~qRlyFLRkl~k--~~~~~~~l~lfY~s~Ie 41 (42)
T PF09004_consen 1 WTSNTTSLYKKAQQRLYFLRKLRK--FNVDSKLLTLFYHSVIE 41 (42)
T ss_dssp ---------------------------SS-----SHTTTTT--
T ss_pred CCcchHHHHHHHHhHHHHHHHHHH--ccchhHHHHHHHHHHhc
Confidence 778999999999999999999874 46788888888887764
No 26
>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=85.84 E-value=0.97 Score=41.08 Aligned_cols=45 Identities=18% Similarity=0.353 Sum_probs=31.1
Q ss_pred CceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcE
Q psy11456 11 PLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSV 63 (574)
Q Consensus 11 ~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~ 63 (574)
+.....|+||+.+. +.+.++....++..++.+ .++|+.+| ++||+
T Consensus 120 ~~~~~~y~DDi~i~--~~~~~~~~~~~~~~~~~l----~~~~~~~~--~~K~~ 164 (177)
T cd01647 120 GDFVEVYLDDILVY--SKTEEEHLEHLREVLERL----REAGLKLN--PEKCE 164 (177)
T ss_pred ccccEEEecCcccc--CCCHHHHHHHHHHHHHHH----HHcCCEeC--HHHce
Confidence 34578899996554 555666655555555544 45779999 99996
No 27
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=65.88 E-value=15 Score=33.34 Aligned_cols=52 Identities=17% Similarity=0.144 Sum_probs=34.5
Q ss_pred CceEEEecCCCCCCCeeEEEEecc---e--e-----eeeeCC--CCccchHHHHHHHHHHHHHHHc
Q psy11456 311 NHTICFTDGSKSPDVTGCAFSIGD---M--V-----QSTLLN--PINSIFSAELIAIFLCLEAIID 364 (574)
Q Consensus 311 ~~~~i~tDGS~~~~~~G~~~~~~~---~--~-----~~~~l~--~~~sv~~aE~~ai~~al~~~~~ 364 (574)
..+++|+|+|. .+.|+.++... . . ...++. ...||=.-|++|+..|.+.+..
T Consensus 80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 46899999994 45566555321 1 1 111222 2459999999999999998864
No 28
>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=54.68 E-value=26 Score=32.84 Aligned_cols=60 Identities=20% Similarity=0.155 Sum_probs=36.7
Q ss_pred ceEEEecCCCCCCCeeEEEEecceeeeeeCCCCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHH
Q psy11456 312 HTICFTDGSKSPDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSAL 380 (574)
Q Consensus 312 ~~~i~tDGS~~~~~~G~~~~~~~~~~~~~l~~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~ 380 (574)
--.+|+|+..... |+..+.....+....---|.+||+.|...|.-+. ..++ |.|||.-++
T Consensus 94 lc~VfaDATpTgw----gi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vl 153 (245)
T PF00336_consen 94 LCQVFADATPTGW----GISITGQRMRGTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVL 153 (245)
T ss_pred CCceeccCCCCcc----eeeecCceeeeeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEE
Confidence 4478899877544 4433322222222223458899999997776655 3344 899997554
No 29
>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=39.73 E-value=30 Score=33.16 Aligned_cols=39 Identities=15% Similarity=0.307 Sum_probs=24.4
Q ss_pred ceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCccc
Q psy11456 12 LKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFS 56 (574)
Q Consensus 12 ~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n 56 (574)
+....|.||+ ++.+++.++....+++ +.+...+.|+.+.
T Consensus 135 i~~~~YvDDi--li~~~s~~e~~~~~~~----v~~~L~~~Gf~l~ 173 (213)
T cd01644 135 IKRNFYVDDI--LVSTDTLNEAVNVAKR----LIALLKKGGFNLR 173 (213)
T ss_pred HHHeeecccc--eecCCCHHHHHHHHHH----HHHHHHhCCccch
Confidence 4568999994 4556666655555544 4444446667665
No 30
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=37.33 E-value=16 Score=26.78 Aligned_cols=19 Identities=32% Similarity=0.782 Sum_probs=8.1
Q ss_pred CCcC-CCCcccccccc-cccc
Q psy11456 519 PICQ-CGAPLSVRHIL-SCHR 537 (574)
Q Consensus 519 p~C~-Cg~~~t~~H~l-~Cp~ 537 (574)
-.|+ ||+..+-.|.. .||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 3599 99999999999 9995
No 31
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=32.97 E-value=91 Score=26.04 Aligned_cols=32 Identities=16% Similarity=0.171 Sum_probs=27.3
Q ss_pred EEEecce---------------EEEEecCCHHHHHHHHHHHHHHHHH
Q psy11456 15 VLFIDDL---------------LIIGRGKDLDLLIQRFQHTLDEIHL 46 (574)
Q Consensus 15 ~~yADD~---------------~i~~~~~~~~~~~~~lq~~l~~l~~ 46 (574)
+.|+||+ .++..|.+..+..+.|+.+++.+++
T Consensus 53 v~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~ 99 (103)
T cd07049 53 VVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIEN 99 (103)
T ss_pred EEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhc
Confidence 4599999 7789999999999999998887764
No 32
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=32.25 E-value=70 Score=30.37 Aligned_cols=37 Identities=30% Similarity=0.224 Sum_probs=29.6
Q ss_pred ceEEEEecCC-H-HHHHHHHHHHHHHHHHHHHHhCCccc
Q psy11456 20 DLLIIGRGKD-L-DLLIQRFQHTLDEIHLWAETNGTLFS 56 (574)
Q Consensus 20 D~~i~~~~~~-~-~~~~~~lq~~l~~l~~W~~~~gl~~n 56 (574)
|+=|++...+ + .+....||+.++.|.+|+.+.|+.+|
T Consensus 116 DlDiWvCh~~~L~~~~~~~Lq~K~~~i~~WA~~~gvEv~ 154 (204)
T PF12633_consen 116 DLDIWVCHDSDLSPEERQLLQQKCDLIEQWAASFGVEVH 154 (204)
T ss_pred CCeEEEEcCCCCCHHHHHHHHHHHHHHHHHHHHcCCEEE
Confidence 5556554433 2 67888999999999999999999998
No 33
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=31.46 E-value=23 Score=22.81 Aligned_cols=18 Identities=28% Similarity=0.778 Sum_probs=13.7
Q ss_pred CCCCcC-CCCcccccccc-cccc
Q psy11456 517 APPICQ-CGAPLSVRHIL-SCHR 537 (574)
Q Consensus 517 ~~p~C~-Cg~~~t~~H~l-~Cp~ 537 (574)
++-.|. |+... |++ +||.
T Consensus 7 ~~Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCC---ccHhHCCC
Confidence 345688 88655 999 9997
No 34
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=31.10 E-value=55 Score=36.61 Aligned_cols=37 Identities=16% Similarity=0.170 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhhhcCceEEEEEecCCCCCCcchhhh
Q psy11456 392 LVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVD 428 (574)
Q Consensus 392 ~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD 428 (574)
.-......++...+.|..|-+-|||+|.+..||-.+-
T Consensus 212 tPedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~ 248 (628)
T COG0296 212 TPEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLAR 248 (628)
T ss_pred CHHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhh
Confidence 3466777778888899999999999999999987653
No 35
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=21.58 E-value=3.7e+02 Score=23.67 Aligned_cols=77 Identities=16% Similarity=0.110 Sum_probs=42.6
Q ss_pred CeeEEEEeccee--eeeeCC--CCccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhcCCCCcHHHHHHHHHH
Q psy11456 325 VTGCAFSIGDMV--QSTLLN--PINSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANVRFSNPLVTKVFSTW 400 (574)
Q Consensus 325 ~~G~~~~~~~~~--~~~~l~--~~~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~~~~~~~~~~~i~~~~ 400 (574)
.|||++...+.. ....+. .+.----||-.||..|+.. -......+.+++|+ ..+-.+-+.-++..
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~-------~~~~sPCG~CRQ~i--- 95 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT-------GKPVSPCGACRQVL--- 95 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC-------CCCcCCcHHHHHHH---
Confidence 489988765532 222222 1222234899999888776 44456678999998 33333445544433
Q ss_pred HHhhhcCceEEE
Q psy11456 401 SYLKLCDKEVSF 412 (574)
Q Consensus 401 ~~l~~~~~~v~~ 412 (574)
.++......|.+
T Consensus 96 ~Ef~~~d~~ii~ 107 (134)
T COG0295 96 AEFCGDDTLIIL 107 (134)
T ss_pred HHhcCCCceEEE
Confidence 345444444443
No 36
>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=20.61 E-value=1.3e+02 Score=29.79 Aligned_cols=47 Identities=17% Similarity=0.244 Sum_probs=34.0
Q ss_pred CCceEEEEecceEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCcccCCCCCcEEE
Q psy11456 10 PPLKRVLFIDDLLIIGRGKDLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCI 65 (574)
Q Consensus 10 ~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~W~~~~gl~~n~~~~Kt~~~ 65 (574)
..+....|.||..+.+.... .....+.+.++..+.|+.++ ++|....
T Consensus 193 ~~~~~~~~GDD~li~~~~~~-------~~~~~~~~~~~~~~~G~~~~--~~~~~~~ 239 (278)
T cd01699 193 KNVRLLNYGDDCLLSVEKAD-------DKFNLETLAEWLKEYGLTMT--DEDKVES 239 (278)
T ss_pred hceEEEEEcCCeEEEechhH-------hhhCHHHHHHHHHHcCCEeC--CcccCCC
Confidence 45678999999888765431 12233567788888999999 8887764
No 37
>KOG1812|consensus
Probab=20.20 E-value=2e+02 Score=30.26 Aligned_cols=42 Identities=21% Similarity=0.228 Sum_probs=34.7
Q ss_pred ccchHHHHHHHHHHHHHHHcCCCCcEEEEeccHHHHHHHhcC
Q psy11456 345 NSIFSAELIAIFLCLEAIIDSPSNQFLIVSDSRSALAALANV 386 (574)
Q Consensus 345 ~sv~~aE~~ai~~al~~~~~~~~~~~~I~~Ds~sa~~~l~~~ 386 (574)
.+...||++|+..+|..+.+.+...+.+++|+.--.+.+...
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~ 88 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGR 88 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhh
Confidence 678999999999999999999999999999965444544433
Done!