Query psy216
Match_columns 650
No_of_seqs 425 out of 2135
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 17:50:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/216hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.9 1.3E-22 2.9E-27 188.8 13.1 124 511-643 4-141 (161)
2 PRK08719 ribonuclease H; Revie 99.9 7.2E-22 1.6E-26 182.6 12.5 122 511-644 3-147 (147)
3 COG0328 RnhA Ribonuclease HI [ 99.9 7.6E-22 1.7E-26 180.0 12.3 127 512-645 3-146 (154)
4 PRK00203 rnhA ribonuclease H; 99.8 1.4E-20 3.1E-25 175.7 10.8 123 512-644 3-142 (150)
5 PF00075 RNase_H: RNase H; In 99.8 1.3E-20 2.7E-25 172.4 7.4 117 511-642 2-131 (132)
6 PF00075 RNase_H: RNase H; In 99.8 5.6E-20 1.2E-24 168.1 8.3 117 195-326 2-131 (132)
7 PRK08719 ribonuclease H; Revie 99.8 3.3E-18 7.2E-23 158.2 12.0 121 195-327 3-146 (147)
8 PRK06548 ribonuclease H; Provi 99.8 3.9E-18 8.5E-23 158.9 12.4 125 195-328 4-142 (161)
9 PRK00203 rnhA ribonuclease H; 99.7 8.7E-18 1.9E-22 156.9 11.1 124 196-329 3-143 (150)
10 COG0328 RnhA Ribonuclease HI [ 99.7 1.2E-16 2.7E-21 146.0 12.4 126 196-329 3-146 (154)
11 cd06222 RnaseH RNase H (RNase 99.7 2.4E-16 5.1E-21 141.7 13.6 121 514-641 1-129 (130)
12 KOG3752|consensus 99.7 1.1E-16 2.3E-21 163.1 12.1 125 511-644 211-365 (371)
13 PRK13907 rnhA ribonuclease H; 99.7 3.6E-16 7.8E-21 142.2 12.7 119 513-642 2-125 (128)
14 cd06222 RnaseH RNase H (RNase 99.6 8.1E-15 1.8E-19 131.6 13.4 122 198-326 1-130 (130)
15 KOG3752|consensus 99.5 1E-13 2.2E-18 141.5 11.7 128 194-328 210-365 (371)
16 PRK07708 hypothetical protein; 99.5 3.2E-13 7E-18 132.8 14.8 130 509-647 70-211 (219)
17 PRK07238 bifunctional RNase H/ 99.4 2E-12 4.4E-17 139.3 14.2 120 512-642 2-130 (372)
18 PRK13907 rnhA ribonuclease H; 99.4 3.7E-12 8.1E-17 115.8 13.0 120 197-327 2-126 (128)
19 PRK07708 hypothetical protein; 99.2 5.6E-10 1.2E-14 110.0 14.3 127 193-328 70-208 (219)
20 PF13456 RVT_3: Reverse transc 99.1 1.4E-10 3.1E-15 97.4 7.6 87 547-644 1-87 (87)
21 PRK07238 bifunctional RNase H/ 99.0 5.5E-09 1.2E-13 112.7 13.6 121 196-328 2-132 (372)
22 PF13456 RVT_3: Reverse transc 98.6 7.4E-08 1.6E-12 80.7 7.1 85 232-327 2-86 (87)
23 PF13966 zf-RVT: zinc-binding 95.6 0.0068 1.5E-07 50.7 1.9 32 401-432 51-83 (86)
24 PF05380 Peptidase_A17: Pao re 76.2 6.3 0.00014 36.9 6.0 52 511-564 80-143 (159)
25 PF09004 DUF1891: Domain of un 48.2 2.7 5.8E-05 29.8 -1.7 33 1-35 10-42 (42)
26 PF05380 Peptidase_A17: Pao re 46.3 42 0.0009 31.4 5.4 52 195-248 80-143 (159)
27 COG0296 GlgB 1,4-alpha-glucan 42.9 26 0.00057 40.2 4.0 36 283-318 212-247 (628)
28 PF00336 DNA_pol_viral_C: DNA 41.4 22 0.00048 34.3 2.6 90 513-626 95-184 (245)
29 COG0296 GlgB 1,4-alpha-glucan 36.1 39 0.00084 38.8 4.0 40 601-644 214-253 (628)
30 PF00336 DNA_pol_viral_C: DNA 27.6 1.1E+02 0.0025 29.6 4.9 64 192-271 90-153 (245)
31 PF00098 zf-CCHC: Zinc knuckle 22.8 63 0.0014 18.4 1.4 17 411-430 2-18 (18)
32 PF05741 zf-nanos: Nanos RNA b 22.2 44 0.00096 25.3 0.9 21 410-430 34-54 (55)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.89 E-value=1.3e-22 Score=188.76 Aligned_cols=124 Identities=23% Similarity=0.262 Sum_probs=97.8
Q ss_pred CcEEEEECCCCCCC--ceeEEEEEccceeeecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHHHH
Q psy216 511 NSLFCYTDGSKTAA--NSGCAYITETESQVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSSLL 588 (650)
Q Consensus 511 ~~~~IyTDgS~~~~--~~G~g~v~~~~~~~~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~al~ 588 (650)
..+.||||||+.++ .+|+|+++.......+....+||++|||+||+.||+.+... . ..|+|+|||++|++
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~~-~-------~~v~I~TDS~yvi~ 75 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRHT-D-------RPILILSDSKYVIN 75 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhcC-C-------ceEEEEeChHHHHH
Confidence 45899999999876 47889888754444444456899999999999999866431 1 45999999999999
Q ss_pred HhhC---------CC--CchhHH-HHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhhcc
Q psy216 589 ALKN---------IM--SPNHLV-NNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILKSS 643 (650)
Q Consensus 589 ~i~~---------~~--~~~~~~-~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~~~ 643 (650)
+|+. +. +++++. +++++.+..+..+ ..|+|.|||||+|++|||.||+||+.|+.
T Consensus 76 ~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~ 141 (161)
T PRK06548 76 SLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAAN 141 (161)
T ss_pred HHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 9983 32 445544 6677777777665 47999999999999999999999999874
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.87 E-value=7.2e-22 Score=182.57 Aligned_cols=122 Identities=21% Similarity=0.247 Sum_probs=94.0
Q ss_pred CcEEEEECCCCCCCc-----eeEEEEEccc------eeeecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEE
Q psy216 511 NSLFCYTDGSKTAAN-----SGCAYITETE------SQVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFI 579 (650)
Q Consensus 511 ~~~~IyTDgS~~~~~-----~G~g~v~~~~------~~~~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I 579 (650)
..++||||||+.+++ +|+|+++... ....++....||++|||.|++.||+.+.+. ..|
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~-----------~~i 71 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG-----------DVI 71 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC-----------CEE
Confidence 468999999997664 4899887421 122335556799999999999999998641 369
Q ss_pred EeccHHHHHHhh--------CCC--CchhHH--HHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhhccc
Q psy216 580 CTDSKSSLLALK--------NIM--SPNHLV--NNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILKSSY 644 (650)
Q Consensus 580 ~sDS~~al~~i~--------~~~--~~~~~~--~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~~~~ 644 (650)
+|||++++++|+ +.. +++..+ .++++.+.++.. ...|+|+|||||+|++|||.||+||+.|+++
T Consensus 72 ~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~~ 147 (147)
T PRK08719 72 YSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAEL 147 (147)
T ss_pred EechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhhC
Confidence 999999999994 322 222222 567777777766 4679999999999999999999999999863
No 3
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.87 E-value=7.6e-22 Score=180.04 Aligned_cols=127 Identities=16% Similarity=0.178 Sum_probs=100.4
Q ss_pred cEEEEECCCCCCC--ceeEEEEEcc-c--eeeecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHH
Q psy216 512 SLFCYTDGSKTAA--NSGCAYITET-E--SQVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSS 586 (650)
Q Consensus 512 ~~~IyTDgS~~~~--~~G~g~v~~~-~--~~~~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~a 586 (650)
.+.||||||+.++ ..|+|+|+.. . ....+....+||++||++|++.||+.+.+... ..|.|+|||+++
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~-------~~v~l~tDS~yv 75 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGA-------CEVTLYTDSKYV 75 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCC-------ceEEEEecHHHH
Confidence 5789999999776 4789998862 1 21223223789999999999999999997433 679999999999
Q ss_pred HHHhhCCC-----------CchhH-HHHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhhcccc
Q psy216 587 LLALKNIM-----------SPNHL-VNNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILKSSYK 645 (650)
Q Consensus 587 l~~i~~~~-----------~~~~~-~~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~~~~~ 645 (650)
++.|..+. .++++ -.++++.+.++..+...|.+.|||||+|.++||+||+||+.|.+-.
T Consensus 76 ~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 76 VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 99998441 11111 2577777888888888999999999999999999999999986543
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.83 E-value=1.4e-20 Score=175.72 Aligned_cols=123 Identities=15% Similarity=0.151 Sum_probs=92.0
Q ss_pred cEEEEECCCCCCC--ceeEEEEEccce---eeecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHH
Q psy216 512 SLFCYTDGSKTAA--NSGCAYITETES---QVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSS 586 (650)
Q Consensus 512 ~~~IyTDgS~~~~--~~G~g~v~~~~~---~~~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~a 586 (650)
.+.||||||+.++ ..|+|+|+.... ...+.....||++|||+|++.||+.+... ..|.|+|||+++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~~---------~~v~I~tDS~yv 73 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKEP---------CEVTLYTDSQYV 73 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCCC---------CeEEEEECHHHH
Confidence 4799999999765 478888875221 12333456799999999999999988541 459999999999
Q ss_pred HHHhhCC---------C--CchhHH-HHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhhccc
Q psy216 587 LLALKNI---------M--SPNHLV-NNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILKSSY 644 (650)
Q Consensus 587 l~~i~~~---------~--~~~~~~-~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~~~~ 644 (650)
++.|+.+ . .++++. .++++.+.++... ..|.|.|||||+|++|||.||+||+.|..-
T Consensus 74 i~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 74 RQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred HHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 9999852 1 233332 3444555555443 689999999999999999999999988653
No 5
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.82 E-value=1.3e-20 Score=172.42 Aligned_cols=117 Identities=30% Similarity=0.398 Sum_probs=87.7
Q ss_pred CcEEEEECCCCCCC--ceeEEEEEccce-eeecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHHH
Q psy216 511 NSLFCYTDGSKTAA--NSGCAYITETES-QVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSSL 587 (650)
Q Consensus 511 ~~~~IyTDgS~~~~--~~G~g~v~~~~~-~~~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~al 587 (650)
..+.||||||+.++ ..|+|+++.... ....++ ..|++.|||+||.+||+.+ . . ..++|+|||++++
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~-------~~v~I~tDS~~v~ 70 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--H-------RKVTIYTDSQYVL 70 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--T-------SEEEEEES-HHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--c-------ccccccccHHHHH
Confidence 46899999997644 467787665332 223334 7899999999999999944 3 1 5699999999999
Q ss_pred HHhhC-----CC---Cch-hHHHHHHHHHHHHhhcCCcEEEEEeCCCCCC-Cchhhhchhhhhhc
Q psy216 588 LALKN-----IM---SPN-HLVNNILVKINELKILNITVKFLWIPSHLGI-AGNVQVPFLEILKS 642 (650)
Q Consensus 588 ~~i~~-----~~---~~~-~~~~~i~~~i~~l~~~~~~v~~~WVPgH~gi-~gNe~AD~LA~~~~ 642 (650)
+.|.. .. +.. ++..+|++.+ .++..|.|+|||||+|+ .|||.||+||+.|.
T Consensus 71 ~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 71 NALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHhccccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 98877 22 112 4555555443 55889999999999999 69999999999885
No 6
>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=5.6e-20 Score=168.11 Aligned_cols=117 Identities=32% Similarity=0.465 Sum_probs=89.6
Q ss_pred CceEEEEcCCCCC--CceeEEEEecCCce-eeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHHHH
Q psy216 195 NSLFCYTDGSKTA--ANSGCAYITETESQ-VFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKSSL 271 (650)
Q Consensus 195 ~~~~iyTDGS~~~--~~~G~avv~~~~~~-~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~sal 271 (650)
..++||||||... +..|+|++...+.. ...++ ..|++.||++||..||+.+ . ...+.|+|||++++
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~--~--------~~~v~I~tDS~~v~ 70 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL--E--------HRKVTIYTDSQYVL 70 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH--S--------TSEEEEEES-HHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh--h--------cccccccccHHHHH
Confidence 4689999999663 44677765443334 55666 8999999999999999944 3 47899999999999
Q ss_pred HHHhC-----CCCCc----HHHHHHHHHHHHhhhcCceEEEEEecCCCCC-CCcchhcHHHhhhc
Q psy216 272 LALKN-----IMSPN----HLVNNILVKINELKILNITVKFLWIPSHLGI-AGNVQVDELAKNSQ 326 (650)
Q Consensus 272 ~~l~~-----~~~~s----~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi-~gNe~AD~lAk~a~ 326 (650)
..+.. ..... ++..+|...+ ..+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus 71 ~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 71 NALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHhccccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 98877 33211 3555555333 45899999999999999 69999999999986
No 7
>PRK08719 ribonuclease H; Reviewed
Probab=99.76 E-value=3.3e-18 Score=158.19 Aligned_cols=121 Identities=20% Similarity=0.254 Sum_probs=90.9
Q ss_pred CceEEEEcCCCCCCc-----eeEEEE-ecCC-c-e---eeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEE
Q psy216 195 NSLFCYTDGSKTAAN-----SGCAYI-TETE-S-Q---VFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFI 263 (650)
Q Consensus 195 ~~~~iyTDGS~~~~~-----~G~avv-~~~~-~-~---~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i 263 (650)
..+.||||||...++ .|+|++ .+.+ . . ...++...|++.||+.|+..||+.+... ..|
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~-----------~~i 71 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG-----------DVI 71 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC-----------CEE
Confidence 468999999997543 588854 3322 2 1 4445666899999999999999998642 379
Q ss_pred EeCcHHHHHHHh--------CCCCCc---HH-HHHHHHHHHHhhhcCceEEEEEecCCCCCCCcchhcHHHhhhcc
Q psy216 264 CTDSKSSLLALK--------NIMSPN---HL-VNNILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAKNSQN 327 (650)
Q Consensus 264 ~tDs~sal~~l~--------~~~~~s---~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~ 327 (650)
+|||+.+++++. +....+ ++ -.++++.+..+.. ...|+|.|||||+|++|||.||+||++|++
T Consensus 72 ~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 72 YSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred EechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 999999999993 433222 22 2456666666655 567999999999999999999999999875
No 8
>PRK06548 ribonuclease H; Provisional
Probab=99.76 E-value=3.9e-18 Score=158.86 Aligned_cols=125 Identities=25% Similarity=0.318 Sum_probs=93.0
Q ss_pred CceEEEEcCCCCCC--ceeEEEEecCCceeeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHHHHH
Q psy216 195 NSLFCYTDGSKTAA--NSGCAYITETESQVFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKSSLL 272 (650)
Q Consensus 195 ~~~~iyTDGS~~~~--~~G~avv~~~~~~~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~sal~ 272 (650)
..+.||||||...+ ..|+|++...+....+-....|...||++|+..||+.+... ...+.|+|||+.+++
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~~--------~~~v~I~TDS~yvi~ 75 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRHT--------DRPILILSDSKYVIN 75 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhcC--------CceEEEEeChHHHHH
Confidence 45899999998853 48888664433332222236799999999999999866532 457999999999999
Q ss_pred HHhC---------CCCC--cHHH-HHHHHHHHHhhhcCceEEEEEecCCCCCCCcchhcHHHhhhccC
Q psy216 273 ALKN---------IMSP--NHLV-NNILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAKNSQNA 328 (650)
Q Consensus 273 ~l~~---------~~~~--s~~~-~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~ 328 (650)
++.. .... .++. +++.+.+..+... ..|.|.|||||+|.+|||.||+||++|+..
T Consensus 76 ~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 76 SLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred HHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 9993 2222 2333 5566666666544 479999999999999999999999998863
No 9
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.74 E-value=8.7e-18 Score=156.94 Aligned_cols=124 Identities=19% Similarity=0.209 Sum_probs=90.0
Q ss_pred ceEEEEcCCCCC--CceeEEEE-ecCCce--eeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHHH
Q psy216 196 SLFCYTDGSKTA--ANSGCAYI-TETESQ--VFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKSS 270 (650)
Q Consensus 196 ~~~iyTDGS~~~--~~~G~avv-~~~~~~--~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~sa 270 (650)
.+.||||||... +..|+|+| ...+.. ..+.....|+..|||+|+..||+.+.. ...+.|+|||+.+
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~---------~~~v~I~tDS~yv 73 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE---------PCEVTLYTDSQYV 73 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC---------CCeEEEEECHHHH
Confidence 478999999974 34788854 333333 223334688999999999999998753 3569999999999
Q ss_pred HHHHhC--------CCC---CcHH-HHHHHHHHHHhhhcCceEEEEEecCCCCCCCcchhcHHHhhhccCC
Q psy216 271 LLALKN--------IMS---PNHL-VNNILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAKNSQNAP 329 (650)
Q Consensus 271 l~~l~~--------~~~---~s~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 329 (650)
++.|.. ... ..++ -.++++.+..+.. ...|.|.|||||+|++|||.||+|||+|...+
T Consensus 74 i~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 74 RQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred HHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 999985 111 1122 1233444444433 37899999999999999999999999998754
No 10
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.70 E-value=1.2e-16 Score=145.96 Aligned_cols=126 Identities=19% Similarity=0.208 Sum_probs=98.7
Q ss_pred ceEEEEcCCCCC--CceeEEEE-ecCCce---eeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHH
Q psy216 196 SLFCYTDGSKTA--ANSGCAYI-TETESQ---VFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKS 269 (650)
Q Consensus 196 ~~~iyTDGS~~~--~~~G~avv-~~~~~~---~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~s 269 (650)
.+.||||||... |..|+|+| ..+... +..+. .+|+..+|++|+..||+++... ....+.|+|||+.
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~-------~~~~v~l~tDS~y 74 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKEL-------GACEVTLYTDSKY 74 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhc-------CCceEEEEecHHH
Confidence 578999999985 34888844 433333 45555 8999999999999999999973 1678999999999
Q ss_pred HHHHHhCC---CC--------CcHH-HHHHHHHHHHhhhcCceEEEEEecCCCCCCCcchhcHHHhhhccCC
Q psy216 270 SLLALKNI---MS--------PNHL-VNNILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAKNSQNAP 329 (650)
Q Consensus 270 al~~l~~~---~~--------~s~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 329 (650)
+++.|..- .. ..++ -.+++..+.++......|.+.|||||.|.++||.||+||+.|+..+
T Consensus 75 v~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 75 VVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 99999831 00 1122 3566777777777777999999999999999999999999998754
No 11
>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=99.70 E-value=2.4e-16 Score=141.66 Aligned_cols=121 Identities=24% Similarity=0.289 Sum_probs=96.1
Q ss_pred EEEECCCCCCC--ceeEEEEEccce--eee---cCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHH
Q psy216 514 FCYTDGSKTAA--NSGCAYITETES--QVF---KLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSS 586 (650)
Q Consensus 514 ~IyTDgS~~~~--~~G~g~v~~~~~--~~~---~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~a 586 (650)
.+|||||...+ ++|+|+++.+.. ... ......+++.+|+.|+..||+.+..... .++.|++||+.+
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~-------~~i~i~~Ds~~~ 73 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGG-------KKVNIYTDSQYV 73 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCC-------ceEEEEECHHHH
Confidence 38999999776 689999887432 111 1224679999999999999999985333 779999999999
Q ss_pred HHHhhCCCC-chhHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhh
Q psy216 587 LLALKNIMS-PNHLVNNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILK 641 (650)
Q Consensus 587 l~~i~~~~~-~~~~~~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~ 641 (650)
+..+++... .......++..+..+...+..++|.|||+|+|+.+|+.||.||+.+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 74 INALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred HHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence 999998763 3334555556666666778899999999999999999999999976
No 12
>KOG3752|consensus
Probab=99.69 E-value=1.1e-16 Score=163.07 Aligned_cols=125 Identities=22% Similarity=0.208 Sum_probs=96.8
Q ss_pred CcEEEEECCCCCCCc-----eeEEEEEccc---eeeecCC-CCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEe
Q psy216 511 NSLFCYTDGSKTAAN-----SGCAYITETE---SQVFKLY-NENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICT 581 (650)
Q Consensus 511 ~~~~IyTDgS~~~~~-----~G~g~v~~~~---~~~~~~~-~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~s 581 (650)
+...||||||+..+| +|+|+++... .....+. ..+++|+|||.||..||+.+.+... .+++|.|
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~-------~kv~I~T 283 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNI-------NKVVIRT 283 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCC-------CcEEEEe
Confidence 348999999997763 8999999743 3334444 5789999999999999999987544 5799999
Q ss_pred ccHHHHHHhhCCC-----------Cc----------hhHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhh
Q psy216 582 DSKSSLLALKNIM-----------SP----------NHLVNNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEIL 640 (650)
Q Consensus 582 DS~~al~~i~~~~-----------~~----------~~~~~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~ 640 (650)
||.+++++|+.|. .+ ++.+..+.++.+++ ++..|.+.|||||.|+.|||.||.||+-
T Consensus 284 DS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~--~~~~vq~~~V~Gh~gi~gne~Ad~lARk 361 (371)
T KOG3752|consen 284 DSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEI--SNKKVQQEYVGGHSGILGNEMADALARK 361 (371)
T ss_pred chHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhh--ccCceEEEEecCcCCcchHHHHHHHHhh
Confidence 9999999997542 12 22333443333333 4689999999999999999999999998
Q ss_pred hccc
Q psy216 641 KSSY 644 (650)
Q Consensus 641 ~~~~ 644 (650)
++.+
T Consensus 362 gs~~ 365 (371)
T KOG3752|consen 362 GSTL 365 (371)
T ss_pred hhhh
Confidence 8654
No 13
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.68 E-value=3.6e-16 Score=142.23 Aligned_cols=119 Identities=18% Similarity=0.114 Sum_probs=95.7
Q ss_pred EEEEECCCCCCC--ceeEEEEEccceee---ecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHHH
Q psy216 513 LFCYTDGSKTAA--NSGCAYITETESQV---FKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSSL 587 (650)
Q Consensus 513 ~~IyTDgS~~~~--~~G~g~v~~~~~~~---~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~al 587 (650)
++||||||+..+ .+|+|+|+++.... .+.....||+.||++|++.||+.+..... .+|.|+|||++++
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~-------~~v~i~sDS~~vi 74 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNY-------NIVSFRTDSQLVE 74 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCC-------CEEEEEechHHHH
Confidence 689999999765 58999998743221 22234579999999999999999998654 5699999999999
Q ss_pred HHhhCCCCchhHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhhc
Q psy216 588 LALKNIMSPNHLVNNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILKS 642 (650)
Q Consensus 588 ~~i~~~~~~~~~~~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~~ 642 (650)
+.+++......-...+++.+..+..++..+.|.|||.+ .|+.||.||+.|.
T Consensus 75 ~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~ 125 (128)
T PRK13907 75 RAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKAI 125 (128)
T ss_pred HHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHHH
Confidence 99998664344456777777778888889999999996 5999999999874
No 14
>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=99.61 E-value=8.1e-15 Score=131.59 Aligned_cols=122 Identities=27% Similarity=0.306 Sum_probs=92.8
Q ss_pred EEEEcCCCCCC--ceeEEEE-ecCCce----eeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHHH
Q psy216 198 FCYTDGSKTAA--NSGCAYI-TETESQ----VFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKSS 270 (650)
Q Consensus 198 ~iyTDGS~~~~--~~G~avv-~~~~~~----~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~sa 270 (650)
.+|||||...+ ++|+|++ .+.+.. ........+++.+|+.|+..||+.+... ....+.|++||+.+
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-------~~~~i~i~~Ds~~~ 73 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-------GGKKVNIYTDSQYV 73 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-------CCceEEEEECHHHH
Confidence 38999999865 5888855 333322 2222257899999999999999999863 27899999999999
Q ss_pred HHHHhCCCC-CcHHHHHHHHHHHHhhhcCceEEEEEecCCCCCCCcchhcHHHhhhc
Q psy216 271 LLALKNIMS-PNHLVNNILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAKNSQ 326 (650)
Q Consensus 271 l~~l~~~~~-~s~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~ 326 (650)
+..+.+... .......+...+..+......+.|.|||+|+|+++|+.||.|||+|.
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 74 INALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 999998754 22223333334444445688999999999999999999999999873
No 15
>KOG3752|consensus
Probab=99.50 E-value=1e-13 Score=141.52 Aligned_cols=128 Identities=23% Similarity=0.264 Sum_probs=96.1
Q ss_pred CCceEEEEcCCCCCC-----ceeEEEEecCCce---eeecC-CCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEE
Q psy216 194 QNSLFCYTDGSKTAA-----NSGCAYITETESQ---VFKLY-NENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFIC 264 (650)
Q Consensus 194 ~~~~~iyTDGS~~~~-----~~G~avv~~~~~~---~~~l~-~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~ 264 (650)
-+..++|||||...+ .+|+||++..+-. ++.+. ..++.+.||+.|+..||+-+.+.. ..+++|.
T Consensus 210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~-------~~kv~I~ 282 (371)
T KOG3752|consen 210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKN-------INKVVIR 282 (371)
T ss_pred ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcC-------CCcEEEE
Confidence 345899999999863 3999987654433 66654 789999999999999999998731 5599999
Q ss_pred eCcHHHHHHHhCCC-----------CCcH-----H-HHHHHHHHHHhhh--cCceEEEEEecCCCCCCCcchhcHHHhhh
Q psy216 265 TDSKSSLLALKNIM-----------SPNH-----L-VNNILVKINELKI--LNITVKFLWIPSHLGIAGNVQVDELAKNS 325 (650)
Q Consensus 265 tDs~sal~~l~~~~-----------~~s~-----~-~~~i~~~~~~l~~--~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a 325 (650)
|||+-.++.|+.-- ..++ + -+.....++.|.. ++.+|.+.|||||.||.|||.||.||+++
T Consensus 283 TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 283 TDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred echHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 99999999987511 1112 1 1222333333332 47999999999999999999999999998
Q ss_pred ccC
Q psy216 326 QNA 328 (650)
Q Consensus 326 ~~~ 328 (650)
+.+
T Consensus 363 s~~ 365 (371)
T KOG3752|consen 363 STL 365 (371)
T ss_pred hhh
Confidence 653
No 16
>PRK07708 hypothetical protein; Validated
Probab=99.50 E-value=3.2e-13 Score=132.81 Aligned_cols=130 Identities=14% Similarity=0.108 Sum_probs=96.0
Q ss_pred CCCcEEEEECCCCCC--CceeEEEEEcc--ceee------ecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEE
Q psy216 509 NQNSLFCYTDGSKTA--ANSGCAYITET--ESQV------FKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIF 578 (650)
Q Consensus 509 ~~~~~~IyTDgS~~~--~~~G~g~v~~~--~~~~------~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~ 578 (650)
..+.+++|+|||..+ +++|+|+|+.. .... ..+....||+.||+.|++.||+.+...+... ..|.
T Consensus 70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~-----~~V~ 144 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKH-----EPVT 144 (219)
T ss_pred CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCc-----ceEE
Confidence 355799999999864 46888888863 2111 2344467999999999999999998865421 3489
Q ss_pred EEeccHHHHHHhhCCC-CchhHHHHHHHHHHHHhhc-CCcEEEEEeCCCCCCCchhhhchhhhhhcccccc
Q psy216 579 ICTDSKSSLLALKNIM-SPNHLVNNILVKINELKIL-NITVKFLWIPSHLGIAGNVQVPFLEILKSSYKYI 647 (650)
Q Consensus 579 I~sDS~~al~~i~~~~-~~~~~~~~i~~~i~~l~~~-~~~v~~~WVPgH~gi~gNe~AD~LA~~~~~~~~~ 647 (650)
|++||+.+++.+++.. ..++..+..+..+..+..+ ...+.|.|||... |+.||+||+.|.+...+
T Consensus 145 I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~----N~~AD~LAk~Al~~~~~ 211 (219)
T PRK07708 145 FRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQ----NKEADQLATQALEGTVI 211 (219)
T ss_pred EEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchh----hhHHHHHHHHHHhcCCC
Confidence 9999999999999865 3344455555555555443 3457889998765 99999999999876544
No 17
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.41 E-value=2e-12 Score=139.27 Aligned_cols=120 Identities=14% Similarity=0.121 Sum_probs=95.5
Q ss_pred cEEEEECCCCCCC--ceeEEEEEccc--e----eeecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEecc
Q psy216 512 SLFCYTDGSKTAA--NSGCAYITETE--S----QVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDS 583 (650)
Q Consensus 512 ~~~IyTDgS~~~~--~~G~g~v~~~~--~----~~~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS 583 (650)
.+.||||||+.++ ..|+|+++.+. . ...+.....||+.||+.|++.||+.+.+... ++|.|++||
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~-------~~v~i~~DS 74 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGA-------TEVEVRMDS 74 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCC-------CeEEEEeCc
Confidence 3689999999876 57999998742 2 1123333679999999999999999988654 679999999
Q ss_pred HHHHHHhhCCC-CchhHHHHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhhc
Q psy216 584 KSSLLALKNIM-SPNHLVNNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILKS 642 (650)
Q Consensus 584 ~~al~~i~~~~-~~~~~~~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~~ 642 (650)
+.+++.+++.. ..+.-+..++..+..+..++..++|.|||. .+|+.||.||+.|.
T Consensus 75 ~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~ 130 (372)
T PRK07238 75 KLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAM 130 (372)
T ss_pred HHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHH
Confidence 99999998765 334445566666777888889999999998 45999999999884
No 18
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.40 E-value=3.7e-12 Score=115.77 Aligned_cols=120 Identities=21% Similarity=0.180 Sum_probs=89.1
Q ss_pred eEEEEcCCCCC--CceeEEEE-ecCCce-e-eecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHHHH
Q psy216 197 LFCYTDGSKTA--ANSGCAYI-TETESQ-V-FKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKSSL 271 (650)
Q Consensus 197 ~~iyTDGS~~~--~~~G~avv-~~~~~~-~-~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~sal 271 (650)
+.||||||... +..|+|+| .+.... . .......|...||+.|+..||+.+... ...++.|++||+.++
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-------g~~~v~i~sDS~~vi 74 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-------NYNIVSFRTDSQLVE 74 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-------CCCEEEEEechHHHH
Confidence 57999999975 45899965 333333 2 222345789999999999999999873 156899999999999
Q ss_pred HHHhCCCCCcHHHHHHHHHHHHhhhcCceEEEEEecCCCCCCCcchhcHHHhhhcc
Q psy216 272 LALKNIMSPNHLVNNILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAKNSQN 327 (650)
Q Consensus 272 ~~l~~~~~~s~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~ 327 (650)
..+.+..........+...+..+......+.|.|||. ++|+.||.||+.|..
T Consensus 75 ~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 75 RAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred HHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 9998854333334444545555555667788899998 599999999999863
No 19
>PRK07708 hypothetical protein; Validated
Probab=99.15 E-value=5.6e-10 Score=109.97 Aligned_cols=127 Identities=17% Similarity=0.183 Sum_probs=90.2
Q ss_pred CCCceEEEEcCCCC--CCceeEEEE-e-cCC-ce-----eeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEE
Q psy216 193 NQNSLFCYTDGSKT--AANSGCAYI-T-ETE-SQ-----VFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVF 262 (650)
Q Consensus 193 ~~~~~~iyTDGS~~--~~~~G~avv-~-~~~-~~-----~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~ 262 (650)
.++.+.+|+|||.. .+++|+|+| . ..+ .. ...++..+|+..||..|+..||+.+... +.....|.
T Consensus 70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~~~V~ 144 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKHEPVT 144 (219)
T ss_pred CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCcceEE
Confidence 45679999999985 355888854 3 222 22 2356667899999999999999999873 01123489
Q ss_pred EEeCcHHHHHHHhCCCC-CcHHHHHHHHHHHHh-hhcCceEEEEEecCCCCCCCcchhcHHHhhhccC
Q psy216 263 ICTDSKSSLLALKNIMS-PNHLVNNILVKINEL-KILNITVKFLWIPSHLGIAGNVQVDELAKNSQNA 328 (650)
Q Consensus 263 i~tDs~sal~~l~~~~~-~s~~~~~i~~~~~~l-~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~ 328 (650)
|++||+-++..+.+... ..+..+.....+..+ ......+.|.||| -..|+.||+||+.|...
T Consensus 145 I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 145 FRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEG 208 (219)
T ss_pred EEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence 99999999999998643 233333444443333 3335568889997 46799999999999984
No 20
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.13 E-value=1.4e-10 Score=97.45 Aligned_cols=87 Identities=20% Similarity=0.157 Sum_probs=70.3
Q ss_pred chHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHHHHHhhCCCCchhHHHHHHHHHHHHhhcCCcEEEEEeCCCC
Q psy216 547 VFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSSLLALKNIMSPNHLVNNILVKINELKILNITVKFLWIPSHL 626 (650)
Q Consensus 547 ~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~al~~i~~~~~~~~~~~~i~~~i~~l~~~~~~v~~~WVPgH~ 626 (650)
+..||+.|+..||+.+.+.+. ++|.|+|||+.+++.|++.......+..+...+..+.+.+..+.|.|||.-.
T Consensus 1 ~~~aE~~al~~al~~a~~~g~-------~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~ 73 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGI-------RKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQ 73 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT--------SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGG
T ss_pred CcHHHHHHHHHHHHHHHHCCC-------CEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHH
Confidence 468999999999999998765 7799999999999999988644446677788888888999999999998654
Q ss_pred CCCchhhhchhhhhhccc
Q psy216 627 GIAGNVQVPFLEILKSSY 644 (650)
Q Consensus 627 gi~gNe~AD~LA~~~~~~ 644 (650)
|..||.||+.|.+|
T Consensus 74 ----N~~A~~LA~~a~~~ 87 (87)
T PF13456_consen 74 ----NKVADALAKFALSC 87 (87)
T ss_dssp ----SHHHHHHHHHHHH-
T ss_pred ----hHHHHHHHHHHhhC
Confidence 99999999999886
No 21
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.97 E-value=5.5e-09 Score=112.69 Aligned_cols=121 Identities=17% Similarity=0.184 Sum_probs=90.9
Q ss_pred ceEEEEcCCCCCC--ceeEEEE-ecC-Cc-e----eeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeC
Q psy216 196 SLFCYTDGSKTAA--NSGCAYI-TET-ES-Q----VFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTD 266 (650)
Q Consensus 196 ~~~iyTDGS~~~~--~~G~avv-~~~-~~-~----~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tD 266 (650)
.+.||||||...+ ..|+|++ .+. +. . ...++ .+|+..||+.|+..||+.+... ..+++.|++|
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~~-------g~~~v~i~~D 73 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAEL-------GATEVEVRMD 73 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHhC-------CCCeEEEEeC
Confidence 3689999999864 4888854 332 22 1 33344 6788899999999999999873 1678999999
Q ss_pred cHHHHHHHhCCCC-CcHHHHHHHHHHHHhhhcCceEEEEEecCCCCCCCcchhcHHHhhhccC
Q psy216 267 SKSSLLALKNIMS-PNHLVNNILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAKNSQNA 328 (650)
Q Consensus 267 s~sal~~l~~~~~-~s~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~ 328 (650)
|+.++..+.+... ...-...+...+..+...-..+.|.|||. .+|+.||.||+.|...
T Consensus 74 S~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 74 SKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred cHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 9999999987543 22333444445555656667899999996 7899999999999764
No 22
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.64 E-value=7.4e-08 Score=80.75 Aligned_cols=85 Identities=21% Similarity=0.160 Sum_probs=64.7
Q ss_pred hhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHHHHHHHhCCCCCcHHHHHHHHHHHHhhhcCceEEEEEecCCCC
Q psy216 232 FSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKSSLLALKNIMSPNHLVNNILVKINELKILNITVKFLWIPSHLG 311 (650)
Q Consensus 232 ~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~sal~~l~~~~~~s~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g 311 (650)
..||+.|+..||+.+... ..+++.|.|||+.++..|.+..........+...+..+.+....+.|.|||
T Consensus 2 ~~aE~~al~~al~~a~~~-------g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~---- 70 (87)
T PF13456_consen 2 LEAEALALLEALQLAWEL-------GIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP---- 70 (87)
T ss_dssp HHHHHHHHHHHHHHHHCC-------T-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------
T ss_pred cHHHHHHHHHHHHHHHHC-------CCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----
Confidence 579999999999999873 278999999999999999887543223444555555666678899999999
Q ss_pred CCCcchhcHHHhhhcc
Q psy216 312 IAGNVQVDELAKNSQN 327 (650)
Q Consensus 312 i~gNe~AD~lAk~a~~ 327 (650)
-++|..||.|||.|.+
T Consensus 71 r~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 71 REQNKVADALAKFALS 86 (87)
T ss_dssp GGGSHHHHHHHHHHHH
T ss_pred hHHhHHHHHHHHHHhh
Confidence 7899999999999864
No 23
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.58 E-value=0.0068 Score=50.74 Aligned_cols=32 Identities=22% Similarity=0.459 Sum_probs=26.3
Q ss_pred hhccCCCCCCCCCCCCc-ccccceeccccccch
Q psy216 401 NFLLKREDPPLCEWCNV-QLSIQHILLECRKFR 432 (650)
Q Consensus 401 ~~~~~~~~~~~C~~C~~-~~t~~H~l~~Cp~~~ 432 (650)
+.+.+...++.|+.|+. +||++|+|++||...
T Consensus 51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred hhccCCccCCccccCCCccccccceeccCcCcc
Confidence 34556677899999995 999999999999754
No 24
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=76.18 E-value=6.3 Score=36.94 Aligned_cols=52 Identities=17% Similarity=0.185 Sum_probs=34.0
Q ss_pred CcEEEEECCCCCCCceeEEEEEcc---ceee-------ecC--CCCCcchHHHHHHHHHHHHHHHh
Q psy216 511 NSLFCYTDGSKTAANSGCAYITET---ESQV-------FKL--YNENSVFSSELLAIFMLLSHIYS 564 (650)
Q Consensus 511 ~~~~IyTDgS~~~~~~G~g~v~~~---~~~~-------~~~--~~~~s~~~AEl~AI~~AL~~~~~ 564 (650)
..+++|+|+| ..+.|+.++.+. .... .+. ....|+=+-||+|+..|.+.+..
T Consensus 80 ~~L~~F~DAS--~~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDAS--ESAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeeccc--ccceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 3579999999 344555554432 1111 111 12459999999999999999865
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=48.25 E-value=2.7 Score=29.84 Aligned_cols=33 Identities=12% Similarity=0.291 Sum_probs=7.9
Q ss_pred CchHHHHHHHhhhccCCCCCCHHHHHHHHHHHhhh
Q psy216 1 IKSLKAINILKVLNNKTWGLSRACLLRLFYAFVRP 35 (650)
Q Consensus 1 ~Ka~~~~~~L~~l~~~~~G~~~~~~~~ly~a~v~p 35 (650)
+||++++-.||.|.+ ..++...+..+|+++|.+
T Consensus 10 KKa~qRlyFLRkl~k--~~~~~~~l~lfY~s~IeS 42 (42)
T PF09004_consen 10 KKAQQRLYFLRKLRK--FNVDSKLLTLFYHSVIES 42 (42)
T ss_dssp ------------------SS-----SHTTTTT---
T ss_pred HHHHhHHHHHHHHHH--ccchhHHHHHHHHHHhcC
Confidence 689999999999964 578889999999988754
No 26
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=46.31 E-value=42 Score=31.38 Aligned_cols=52 Identities=17% Similarity=0.186 Sum_probs=33.7
Q ss_pred CceEEEEcCCCCCCceeEEEE-e---cCCce------eeecC--CCccchhHHHHHHHHHHHHHHh
Q psy216 195 NSLFCYTDGSKTAANSGCAYI-T---ETESQ------VFKLY--NENSVFSSELLAIFMLLSHICN 248 (650)
Q Consensus 195 ~~~~iyTDGS~~~~~~G~avv-~---~~~~~------~~~l~--~~~sv~~AEl~ai~~al~~~~~ 248 (650)
..+++|+|+|. ...|+.++ . +++.. ..+.. ...|+=.-||.|+..|.+++..
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 33444432 1 12211 11222 2459999999999999999876
No 27
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=42.90 E-value=26 Score=40.17 Aligned_cols=36 Identities=19% Similarity=0.355 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHhhhcCceEEEEEecCCCCCCCcchh
Q psy216 283 LVNNILVKINELKILNITVKFLWIPSHLGIAGNVQV 318 (650)
Q Consensus 283 ~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~A 318 (650)
....+...++.+.+.|..|-+.|||+|.+..||-.+
T Consensus 212 tPedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 212 TPEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred CHHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 467788888999999999999999999999988655
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=41.39 E-value=22 Score=34.29 Aligned_cols=90 Identities=16% Similarity=0.080 Sum_probs=49.7
Q ss_pred EEEEECCCCCCCceeEEEEEccceeeecCCCCCcchHHHHHHHHHHHHHHHhccCCcccccCCeEEEEeccHHHHHHhhC
Q psy216 513 LFCYTDGSKTAANSGCAYITETESQVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIFRDSIFICTDSKSSLLALKN 592 (650)
Q Consensus 513 ~~IyTDgS~~~~~~G~g~v~~~~~~~~~~~~~~s~~~AEl~AI~~AL~~~~~~~~~~~~~~~~~i~I~sDS~~al~~i~~ 592 (650)
..||+|+.-.+.+..+| ......-....-.++.|||+|...|--+.. .++ |.|||..|+..=
T Consensus 95 c~VfaDATpTgwgi~i~----~~~~~~Tfs~~l~IhtaELlaaClAr~~~~-----------~r~-l~tDnt~Vlsrk-- 156 (245)
T PF00336_consen 95 CQVFADATPTGWGISIT----GQRMRGTFSKPLPIHTAELLAACLARLMSG-----------ARC-LGTDNTVVLSRK-- 156 (245)
T ss_pred CceeccCCCCcceeeec----CceeeeeecccccchHHHHHHHHHHHhccC-----------CcE-EeecCcEEEecc--
Confidence 47999987665543222 111111112234689999999988766553 123 899998776421
Q ss_pred CCCchhHHHHHHHHHHHHhhcCCcEEEEEeCCCC
Q psy216 593 IMSPNHLVNNILVKINELKILNITVKFLWIPSHL 626 (650)
Q Consensus 593 ~~~~~~~~~~i~~~i~~l~~~~~~v~~~WVPgH~ 626 (650)
..+-...+-..-+ -+. ..++|.+||+--
T Consensus 157 yts~PW~lac~A~---wiL---rgts~~yVPS~~ 184 (245)
T PF00336_consen 157 YTSFPWLLACAAN---WIL---RGTSFYYVPSKY 184 (245)
T ss_pred cccCcHHHHHHHH---Hhh---cCceEEEecccc
Confidence 1122333322221 121 257899999865
No 29
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=36.10 E-value=39 Score=38.83 Aligned_cols=40 Identities=20% Similarity=0.450 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhcCCcEEEEEeCCCCCCCchhhhchhhhhhccc
Q psy216 601 NNILVKINELKILNITVKFLWIPSHLGIAGNVQVPFLEILKSSY 644 (650)
Q Consensus 601 ~~i~~~i~~l~~~~~~v~~~WVPgH~gi~gNe~AD~LA~~~~~~ 644 (650)
......|..+.+.|+.|-+-|||+|-+..||- |+.++...
T Consensus 214 edfk~fVD~aH~~GIgViLD~V~~HF~~d~~~----L~~fdg~~ 253 (628)
T COG0296 214 EDFKALVDAAHQAGIGVILDWVPNHFPPDGNY----LARFDGTF 253 (628)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCcCCCCcch----hhhcCCcc
Confidence 45666778888999999999999999987764 45555443
No 30
>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=27.61 E-value=1.1e+02 Score=29.63 Aligned_cols=64 Identities=14% Similarity=0.088 Sum_probs=39.4
Q ss_pred cCCCceEEEEcCCCCCCceeEEEEecCCceeeecCCCccchhHHHHHHHHHHHHHHhcCCCCccccCCeEEEEeCcHHHH
Q psy216 192 ENQNSLFCYTDGSKTAANSGCAYITETESQVFKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIFRDSVFICTDSKSSL 271 (650)
Q Consensus 192 ~~~~~~~iyTDGS~~~~~~G~avv~~~~~~~~~l~~~~sv~~AEl~ai~~al~~~~~~~~~~~~~~~~~~~i~tDs~sal 271 (650)
..+.--.||+|..-...++.++ ++...+-...---+..+||.|...|.-+.. .++ |.|||.-++
T Consensus 90 qr~~lc~VfaDATpTgwgi~i~----~~~~~~Tfs~~l~IhtaELlaaClAr~~~~-----------~r~-l~tDnt~Vl 153 (245)
T PF00336_consen 90 QRPGLCQVFADATPTGWGISIT----GQRMRGTFSKPLPIHTAELLAACLARLMSG-----------ARC-LGTDNTVVL 153 (245)
T ss_pred CCCCCCceeccCCCCcceeeec----CceeeeeecccccchHHHHHHHHHHHhccC-----------CcE-EeecCcEEE
Confidence 3455668999998766543322 111122222345689999999988876553 233 899997654
No 31
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=22.79 E-value=63 Score=18.40 Aligned_cols=17 Identities=35% Similarity=0.616 Sum_probs=12.8
Q ss_pred CCCCCCcccccceecccccc
Q psy216 411 LCEWCNVQLSIQHILLECRK 430 (650)
Q Consensus 411 ~C~~C~~~~t~~H~l~~Cp~ 430 (650)
.|-.||+ ..|+..+||+
T Consensus 2 ~C~~C~~---~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGE---PGHIARDCPK 18 (18)
T ss_dssp BCTTTSC---SSSCGCTSSS
T ss_pred cCcCCCC---cCcccccCcc
Confidence 5777774 4799999984
No 32
>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=22.19 E-value=44 Score=25.30 Aligned_cols=21 Identities=24% Similarity=0.480 Sum_probs=9.9
Q ss_pred CCCCCCCcccccceecccccc
Q psy216 410 PLCEWCNVQLSIQHILLECRK 430 (650)
Q Consensus 410 ~~C~~C~~~~t~~H~l~~Cp~ 430 (650)
-.|+.||...+-.|....||+
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 479999998888999999995
Done!