Query psy8412
Match_columns 271
No_of_seqs 204 out of 1453
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 18:07:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8412.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8412hhsearch_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 8.1E-24 1.7E-28 172.7 13.9 128 11-140 3-144 (161)
2 COG0328 RnhA Ribonuclease HI [ 99.9 8.4E-24 1.8E-28 170.0 12.9 127 12-139 2-146 (154)
3 PF00075 RNase_H: RNase H; In 99.9 8.9E-24 1.9E-28 167.2 11.2 122 12-137 2-132 (132)
4 PRK08719 ribonuclease H; Revie 99.9 3.4E-23 7.5E-28 167.3 14.5 122 11-137 2-146 (147)
5 PRK00203 rnhA ribonuclease H; 99.9 1.1E-22 2.5E-27 165.2 13.3 124 13-139 3-143 (150)
6 cd06222 RnaseH RNase H (RNase 99.8 4.4E-19 9.6E-24 136.9 14.5 122 15-136 1-130 (130)
7 KOG3752|consensus 99.8 4.6E-19 1E-23 158.6 11.8 136 3-138 202-365 (371)
8 PRK13907 rnhA ribonuclease H; 99.8 2.3E-18 5E-23 136.0 12.4 121 14-138 2-127 (128)
9 PRK07708 hypothetical protein; 99.7 1.3E-15 2.8E-20 130.7 15.1 126 11-140 71-210 (219)
10 PRK07238 bifunctional RNase H/ 99.6 1.9E-14 4E-19 133.4 15.0 124 13-140 2-134 (372)
11 PF13456 RVT_3: Reverse transc 99.4 1.1E-12 2.4E-17 95.7 10.6 86 48-137 1-86 (87)
12 PF13966 zf-RVT: zinc-binding 95.5 0.008 1.7E-07 43.8 1.7 32 200-231 37-73 (86)
13 PF05380 Peptidase_A17: Pao re 89.2 1.1 2.3E-05 36.5 5.8 51 13-65 81-143 (159)
14 PF00336 DNA_pol_viral_C: DNA 83.1 1.6 3.6E-05 36.9 3.8 89 13-118 94-182 (245)
15 COG3341 Predicted double-stran 59.2 26 0.00057 30.0 5.5 127 12-142 64-205 (225)
16 PF08274 PhnA_Zn_Ribbon: PhnA 58.9 3.8 8.3E-05 23.7 0.3 20 220-239 3-23 (30)
17 KOG1812|consensus 50.7 50 0.0011 30.9 6.6 43 45-87 46-88 (384)
18 PF13696 zf-CCHC_2: Zinc knuck 50.4 6 0.00013 23.2 0.3 22 219-244 8-30 (32)
19 PF15322 PMSI1: Protein missin 48.3 6.6 0.00014 34.8 0.3 22 189-210 206-228 (311)
20 PF00220 Hormone_4: Neurohypop 47.4 6.8 0.00015 16.2 0.1 7 234-240 2-8 (9)
21 PF00098 zf-CCHC: Zinc knuckle 42.7 9.9 0.00021 19.1 0.3 15 221-239 2-17 (18)
22 COG0296 GlgB 1,4-alpha-glucan 42.0 44 0.00095 33.4 4.9 34 95-128 214-247 (628)
23 COG5082 AIR1 Arginine methyltr 41.8 13 0.00028 31.2 1.0 19 217-239 58-77 (190)
24 cd01285 nucleoside_deaminase N 38.2 1.5E+02 0.0032 22.0 6.4 52 26-77 18-74 (109)
25 PRK10860 tRNA-specific adenosi 34.7 1.3E+02 0.0029 24.7 6.0 50 26-75 34-87 (172)
26 COG2093 DNA-directed RNA polym 33.8 26 0.00057 23.8 1.4 19 213-231 12-31 (64)
27 cd01284 Riboflavin_deaminase-r 30.8 1.8E+02 0.004 22.1 5.9 46 26-75 20-66 (115)
28 PF15288 zf-CCHC_6: Zinc knuck 29.7 33 0.00072 21.2 1.2 13 253-265 18-30 (40)
29 COG0295 Cdd Cytidine deaminase 29.5 1.7E+02 0.0038 23.1 5.6 51 26-77 27-81 (134)
30 PF06839 zf-GRF: GRF zinc fing 28.9 38 0.00082 21.1 1.4 15 245-259 19-33 (45)
31 TIGR03847 conserved hypothetic 28.3 34 0.00073 28.3 1.4 16 216-231 153-169 (177)
32 cd01286 deoxycytidylate_deamin 26.9 2.4E+02 0.0053 21.9 6.1 27 47-75 67-93 (131)
33 TIGR00686 phnA alkylphosphonat 26.7 37 0.0008 25.8 1.3 13 219-231 2-15 (109)
34 COG0590 CumB Cytosine/adenosin 26.0 1.9E+02 0.0041 23.2 5.4 50 26-75 29-83 (152)
35 PF13917 zf-CCHC_3: Zinc knuck 25.0 34 0.00075 21.3 0.7 18 219-256 4-22 (42)
36 PF14205 Cys_rich_KTR: Cystein 24.0 36 0.00078 22.5 0.7 12 228-239 21-32 (55)
37 PRK10933 trehalose-6-phosphate 23.8 1.8E+02 0.0039 28.7 5.8 72 51-122 30-108 (551)
38 PRK08298 cytidine deaminase; V 23.2 2.3E+02 0.0049 22.4 5.2 56 17-77 19-78 (136)
39 smart00642 Aamy Alpha-amylase 22.7 3E+02 0.0065 22.3 6.1 71 52-122 17-97 (166)
40 PF05741 zf-nanos: Nanos RNA b 22.7 29 0.00062 23.1 0.0 20 220-240 34-54 (55)
41 PF14169 YdjO: Cold-inducible 21.9 54 0.0012 22.1 1.2 13 214-226 34-47 (59)
42 COG0333 RpmF Ribosomal protein 21.8 51 0.0011 22.1 1.1 26 218-260 26-52 (57)
43 PF13395 HNH_4: HNH endonuclea 20.9 57 0.0012 21.2 1.2 6 222-227 1-7 (54)
44 PRK10220 hypothetical protein; 20.4 58 0.0013 24.8 1.2 13 219-231 3-16 (111)
45 TIGR01354 cyt_deam_tetra cytid 20.0 2.5E+02 0.0053 21.7 4.8 51 26-77 22-76 (127)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.91 E-value=8.1e-24 Score=172.67 Aligned_cols=128 Identities=27% Similarity=0.267 Sum_probs=94.1
Q ss_pred CCcEEEEEcCCCCCC--CeeEEEEECCeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc-
Q psy8412 11 ANHTICFTDGSKTPD--STSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI- 87 (271)
Q Consensus 11 ~~~~~iytDGS~~~~--~~G~a~~~~~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~- 87 (271)
+..+.||||||+.++ ..|+|++..+...........|++.|||.||+.||+.+.. +...|.|+|||++|++.++.+
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~ 81 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWV 81 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHH
Confidence 356999999998864 4788877543222222234689999999999999986643 446799999999999999942
Q ss_pred --------ccCCccH---HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412 88 --------RFTNPLI---SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP 140 (271)
Q Consensus 88 --------~~~~~~~---~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~ 140 (271)
...++.+ ++++.++..+... ..|+|.|||||+|++|||.||+||++|+....
T Consensus 82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~ 144 (161)
T PRK06548 82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFS 144 (161)
T ss_pred HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence 2233322 3444444444443 47999999999999999999999999997653
No 2
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.91 E-value=8.4e-24 Score=169.96 Aligned_cols=127 Identities=24% Similarity=0.225 Sum_probs=98.9
Q ss_pred CcEEEEEcCCCCCC--CeeEEEEE--CCeE--EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHh
Q psy8412 12 NHTICFTDGSKTPD--STSCAFSI--GDVV--HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALF 85 (271)
Q Consensus 12 ~~~~iytDGS~~~~--~~G~a~~~--~~~~--~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~ 85 (271)
..+.||||||+..+ ..|+|+|. ++.. .+.... .+||+.||+.|++.||+.+...+...|.|+|||++|++.|+
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~ 80 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT 80 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence 46899999999864 36777664 2222 233333 89999999999999999999888999999999999999999
Q ss_pred cccc---CCcc---------HHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412 86 NIRF---TNPL---------ISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID 139 (271)
Q Consensus 86 ~~~~---~~~~---------~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~ 139 (271)
.+.. ..++ ..+++..+..+..+...|.+.|||||+|.++||+||+||+.|++..
T Consensus 81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 5422 1111 1234444445666777999999999999999999999999998875
No 3
>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=99.91 E-value=8.9e-24 Score=167.16 Aligned_cols=122 Identities=31% Similarity=0.345 Sum_probs=89.0
Q ss_pred CcEEEEEcCCCCCC--CeeEEEE-ECCeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhc--
Q psy8412 12 NHTICFTDGSKTPD--STSCAFS-IGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFN-- 86 (271)
Q Consensus 12 ~~~~iytDGS~~~~--~~G~a~~-~~~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~-- 86 (271)
+.+.||||||+.++ ..|+|++ ..+......++ ..|++.|||.||..||+ +.. ...++|+|||+++++.+..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~ 77 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWL 77 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhc
Confidence 57899999997643 2455554 44444444455 88999999999999999 543 4999999999999998877
Q ss_pred ---cccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCC-ccchHHHHHHHHhhc
Q psy8412 87 ---IRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGI-RGNEIVDEAARNAAS 137 (271)
Q Consensus 87 ---~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi-~gNe~AD~lAk~a~~ 137 (271)
..........+...+.++...+..|.|+|||||+|+ .||+.||+|||+|+.
T Consensus 78 ~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~ 132 (132)
T PF00075_consen 78 HGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ 132 (132)
T ss_dssp HHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred cccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence 332221111233333333356899999999999999 699999999999973
No 4
>PRK08719 ribonuclease H; Reviewed
Probab=99.90 E-value=3.4e-23 Score=167.29 Aligned_cols=122 Identities=22% Similarity=0.232 Sum_probs=89.5
Q ss_pred CCcEEEEEcCCCCCCC-----eeEEEEE--CC--eE--EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHH
Q psy8412 11 ANHTICFTDGSKTPDS-----TSCAFSI--GD--VV--HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKS 79 (271)
Q Consensus 11 ~~~~~iytDGS~~~~~-----~G~a~~~--~~--~~--~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~ 79 (271)
.+.++||||||+..++ .|+|++. .+ .. ....+....|++.|||.|++.||+.+.+. ..|+|||++
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y 77 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY 77 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence 4678999999997543 4788653 22 22 33445566899999999999999998652 479999999
Q ss_pred HHHHHhc--------cccCC-ccH---HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhc
Q psy8412 80 SLTALFN--------IRFTN-PLI---SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAAS 137 (271)
Q Consensus 80 al~~l~~--------~~~~~-~~~---~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~ 137 (271)
|++.++. .+..+ +.+ .+++..+..+.. ...|+|.|||||+|++|||.||+||++|++
T Consensus 78 vi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 78 CVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9999943 33322 221 233333333444 577999999999999999999999999975
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.89 E-value=1.1e-22 Score=165.16 Aligned_cols=124 Identities=19% Similarity=0.194 Sum_probs=90.9
Q ss_pred cEEEEEcCCCCCC--CeeEEEEE--CCeEE-EEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc
Q psy8412 13 HTICFTDGSKTPD--STSCAFSI--GDVVH-STLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI 87 (271)
Q Consensus 13 ~~~iytDGS~~~~--~~G~a~~~--~~~~~-~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~ 87 (271)
.+.||||||+..+ ..|+|++. .+... ........|++.|||.|++.||+.+.. ...+.|+|||+++++.|+.+
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w 80 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW 80 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence 4899999998753 46777653 33322 222235788999999999999998865 46899999999999999863
Q ss_pred cc---------CCccH---HHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCC
Q psy8412 88 RF---------TNPLI---SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASID 139 (271)
Q Consensus 88 ~~---------~~~~~---~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~ 139 (271)
.. ..+.. .+++..+.++. ....|.|.|||||+|++||+.||+|||+|+...
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 21 11111 22333333343 347899999999999999999999999998764
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=99.82 E-value=4.4e-19 Score=136.90 Aligned_cols=122 Identities=29% Similarity=0.338 Sum_probs=94.6
Q ss_pred EEEEcCCCCCC--CeeEEEEECC--eE---EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc
Q psy8412 15 ICFTDGSKTPD--STSCAFSIGD--VV---HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI 87 (271)
Q Consensus 15 ~iytDGS~~~~--~~G~a~~~~~--~~---~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~ 87 (271)
++|||||...+ ++|+|++..+ .. .........+++.+|+.|+..||+++...+..++.|++||+.+++.+++.
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 48999998865 5788876432 11 11122257899999999999999999988899999999999999999987
Q ss_pred ccCC-ccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhh
Q psy8412 88 RFTN-PLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAA 136 (271)
Q Consensus 88 ~~~~-~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~ 136 (271)
.... .........+..+...+..+.|.|||+|++.++|+.||.|||.|.
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 6522 222333334444446788999999999999999999999999874
No 7
>KOG3752|consensus
Probab=99.80 E-value=4.6e-19 Score=158.64 Aligned_cols=136 Identities=21% Similarity=0.208 Sum_probs=104.1
Q ss_pred hhhHhhccCCcEEEEEcCCCCCC-----CeeEEEEECCe---EEEEecC-CCCchHHHHHHHHHHHHHHHHcCCCceEEE
Q psy8412 3 CETINNKYANHTICFTDGSKTPD-----STSCAFSIGDV---VHSTLLN-PVNSIFSAELMAIFLCLEAILESPDHHFLI 73 (271)
Q Consensus 3 ~~~~~~~~~~~~~iytDGS~~~~-----~~G~a~~~~~~---~~~~~l~-~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I 73 (271)
+.+++..+.+..++|||||+..+ .+|+||+.++. ..+..+. +..|+|.|||.||..||+-|.+.+..+|+|
T Consensus 202 k~~~d~e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I 281 (371)
T KOG3752|consen 202 KLENDREEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVI 281 (371)
T ss_pred hcccccccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEE
Confidence 34445555566999999998874 37999997643 3456664 899999999999999999999988889999
Q ss_pred EeCCHHHHHHHhccccC-----------Ccc------HHHHHHHHHHHHh--CCCceEEEEecCCCCCccchHHHHHHHH
Q psy8412 74 VSDSKSSLTALFNIRFT-----------NPL------ISKVYSTWSFLKL--NNKNVSFMWCPSHCGIRGNEIVDEAARN 134 (271)
Q Consensus 74 ~tDS~~al~~l~~~~~~-----------~~~------~~~~~~~~~~l~~--~~~~v~~~WVpgH~gi~gNe~AD~lAk~ 134 (271)
.|||+++++.|+.|... ++. .+..+..+..|.+ .+..|.+.|||||.|+.||++||.||++
T Consensus 282 ~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARk 361 (371)
T KOG3752|consen 282 RTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARK 361 (371)
T ss_pred EechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhh
Confidence 99999999999866321 110 1122222233433 4789999999999999999999999999
Q ss_pred hhcC
Q psy8412 135 AASI 138 (271)
Q Consensus 135 a~~~ 138 (271)
++..
T Consensus 362 gs~~ 365 (371)
T KOG3752|consen 362 GSTL 365 (371)
T ss_pred hhhh
Confidence 8654
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.78 E-value=2.3e-18 Score=136.02 Aligned_cols=121 Identities=19% Similarity=0.126 Sum_probs=93.9
Q ss_pred EEEEEcCCCCCC--CeeEEEEECC--eEEEE-ecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhccc
Q psy8412 14 TICFTDGSKTPD--STSCAFSIGD--VVHST-LLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIR 88 (271)
Q Consensus 14 ~~iytDGS~~~~--~~G~a~~~~~--~~~~~-~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~~ 88 (271)
+.||||||+..+ ..|+|++..+ ..... ......|++.||+.|++.||+.+...+..++.|+|||+.+++.+++.+
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~ 81 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY 81 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence 689999998764 5788877532 21111 223567999999999999999999988889999999999999999876
Q ss_pred cCCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcC
Q psy8412 89 FTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASI 138 (271)
Q Consensus 89 ~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~ 138 (271)
...+....++..+..+......+.|.|||+ +.|+.||.||+.|...
T Consensus 82 ~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 82 AKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ 127 (128)
T ss_pred hcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence 543333445555555667778889999996 5999999999999753
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.68 E-value=1.3e-15 Score=130.67 Aligned_cols=126 Identities=13% Similarity=0.067 Sum_probs=93.8
Q ss_pred CCcEEEEEcCCCCC--CCeeEEEEE--C-C-eEE----EEecCCCCchHHHHHHHHHHHHHHHHcCCCce--EEEEeCCH
Q psy8412 11 ANHTICFTDGSKTP--DSTSCAFSI--G-D-VVH----STLLNPVNSIFSAELMAIFLCLEAILESPDHH--FLIVSDSK 78 (271)
Q Consensus 11 ~~~~~iytDGS~~~--~~~G~a~~~--~-~-~~~----~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~--v~I~tDS~ 78 (271)
++.+++|+|||... +++|+|++. . + ... ...++...|++.||+.|++.||+.+...+.+. |.|++||+
T Consensus 71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSq 150 (219)
T PRK07708 71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQ 150 (219)
T ss_pred CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccH
Confidence 34799999999864 457777653 2 2 221 22455668999999999999999999887654 89999999
Q ss_pred HHHHHHhccccC-CccHHHHHHHHHHHH-hCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412 79 SSLTALFNIRFT-NPLISKVYSTWSFLK-LNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP 140 (271)
Q Consensus 79 ~al~~l~~~~~~-~~~~~~~~~~~~~l~-~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~ 140 (271)
.+++.+++.+.. .+....+...+..+. +....+.+.||| ++.|+.||+||+.|.+..+
T Consensus 151 lVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 151 VVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV 210 (219)
T ss_pred HHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence 999999987653 333444444444333 344568889998 5789999999999998654
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.60 E-value=1.9e-14 Score=133.38 Aligned_cols=124 Identities=17% Similarity=0.127 Sum_probs=96.1
Q ss_pred cEEEEEcCCCCCC--CeeEEEEEC--C-e--E-EEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHH
Q psy8412 13 HTICFTDGSKTPD--STSCAFSIG--D-V--V-HSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTAL 84 (271)
Q Consensus 13 ~~~iytDGS~~~~--~~G~a~~~~--~-~--~-~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l 84 (271)
.+.||||||+..+ .+|+|++.. + . . .........|++.||+.|++.||+.+.+.+.+.|.|++||+.+++.+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i 81 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM 81 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence 4789999998865 478887642 1 1 1 22222347889999999999999999999899999999999999999
Q ss_pred hcccc-CCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchHHHHHHHHhhcCCC
Q psy8412 85 FNIRF-TNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIVDEAARNAASIDP 140 (271)
Q Consensus 85 ~~~~~-~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~ 140 (271)
++.+. .++....+...+..+.+....++|.|||. ++|+.||.||+.|.....
T Consensus 82 ~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~~ 134 (372)
T PRK07238 82 SGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAAA 134 (372)
T ss_pred CCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhhc
Confidence 98764 23333444445555677888999999995 699999999999987653
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.44 E-value=1.1e-12 Score=95.73 Aligned_cols=86 Identities=22% Similarity=0.162 Sum_probs=69.0
Q ss_pred hHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhccccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCCccchH
Q psy8412 48 IFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEI 127 (271)
Q Consensus 48 ~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~ 127 (271)
+..||+.|+..||+++...+.++|.|+|||+.+++.|++..........+...+..+......+.|.||| .++|..
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 4689999999999999999999999999999999999988544334456666666677789999999999 789999
Q ss_pred HHHHHHHhhc
Q psy8412 128 VDEAARNAAS 137 (271)
Q Consensus 128 AD~lAk~a~~ 137 (271)
||.|||.|.+
T Consensus 77 A~~LA~~a~~ 86 (87)
T PF13456_consen 77 ADALAKFALS 86 (87)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHhh
Confidence 9999999874
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.47 E-value=0.008 Score=43.76 Aligned_cols=32 Identities=22% Similarity=0.358 Sum_probs=22.0
Q ss_pred eeeeccccc--cc-ccccCCCCCCCcc-cC-Ccccce
Q psy8412 200 RLRIGHTRI--TH-NHLFTKTDPPFCQ-CG-AALSVI 231 (271)
Q Consensus 200 qlrtGH~~~--~h-~~r~~~~~sp~C~-Cg-~~et~~ 231 (271)
--+.-|..+ +. +.+.+...++.|. |+ +.||++
T Consensus 37 ~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~ 73 (86)
T PF13966_consen 37 LWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIE 73 (86)
T ss_pred eeeeccccchhhhhhhccCCccCCccccCCCcccccc
Confidence 344555565 23 3466677889999 99 489998
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=89.15 E-value=1.1 Score=36.46 Aligned_cols=51 Identities=18% Similarity=0.172 Sum_probs=33.2
Q ss_pred cEEEEEcCCCCCCCeeEEEEEC---C-e-E-----EEEec-C-CCCchHHHHHHHHHHHHHHHHc
Q psy8412 13 HTICFTDGSKTPDSTSCAFSIG---D-V-V-----HSTLL-N-PVNSIFSAELMAIFLCLEAILE 65 (271)
Q Consensus 13 ~~~iytDGS~~~~~~G~a~~~~---~-~-~-----~~~~l-~-~~~s~~~AEl~Ai~~AL~~a~~ 65 (271)
.+.+|+|+|.. +.|+.+|.+ + . . ...++ | ...|+-+-||.|+..|.+++..
T Consensus 81 ~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 81 ELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 58899999954 455555432 1 1 1 11112 1 3459999999999999998853
No 14
>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=83.14 E-value=1.6 Score=36.87 Aligned_cols=89 Identities=21% Similarity=0.259 Sum_probs=52.3
Q ss_pred cEEEEEcCCCCCCCeeEEEEECCeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhccccCCc
Q psy8412 13 HTICFTDGSKTPDSTSCAFSIGDVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNIRFTNP 92 (271)
Q Consensus 13 ~~~iytDGS~~~~~~G~a~~~~~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~~~~~~ 92 (271)
--.||+|+.-. |+|+...+....+.....-.+..|||.|...|.-+. ..++ |.|||..|+ .+....-|
T Consensus 94 lc~VfaDATpT----gwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vl---srkyts~P 161 (245)
T PF00336_consen 94 LCQVFADATPT----GWGISITGQRMRGTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVL---SRKYTSFP 161 (245)
T ss_pred CCceeccCCCC----cceeeecCceeeeeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEE---ecccccCc
Confidence 46788888753 444444433333333334568999999998887665 3344 999998654 33334445
Q ss_pred cHHHHHHHHHHHHhCCCceEEEEecC
Q psy8412 93 LISKVYSTWSFLKLNNKNVSFMWCPS 118 (271)
Q Consensus 93 ~~~~~~~~~~~l~~~~~~v~~~WVpg 118 (271)
|.......+ + -..+.|..||+
T Consensus 162 W~lac~A~w--i---Lrgts~~yVPS 182 (245)
T PF00336_consen 162 WLLACAANW--I---LRGTSFYYVPS 182 (245)
T ss_pred HHHHHHHHH--h---hcCceEEEecc
Confidence 533322221 2 23467888996
No 15
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=59.21 E-value=26 Score=29.99 Aligned_cols=127 Identities=11% Similarity=-0.068 Sum_probs=76.8
Q ss_pred CcEEEEEcCCCCCC--CeeEEEEECC------eEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEE-E----eCCH
Q psy8412 12 NHTICFTDGSKTPD--STSCAFSIGD------VVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLI-V----SDSK 78 (271)
Q Consensus 12 ~~~~iytDGS~~~~--~~G~a~~~~~------~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I-~----tDS~ 78 (271)
+.+.-+.+|+.... ..++-++.+. ......--...++..+|.+|++.+|+.+...+.++..| + .||+
T Consensus 64 e~~i~~~~G~y~~~p~t~~~k~yr~k~~~~~~~lt~~~~~~~~~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~ 143 (225)
T COG3341 64 EYIISWAKGDYDAKPGTQEFKEYRGKCTIEYSWLTESSEFSIKSNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSW 143 (225)
T ss_pred hccceeccCCccccCCCcceeEEeccccccceeeeeecccccccCchHHHHHHhccccccccccCccceeeccCCcchhH
Confidence 34666777775542 2333333332 11111112456788899999999999998776555555 7 7999
Q ss_pred HHHHHHhccccCCccHHHHHHHHHHHHhC--CCceEEEEecCCCCCccchHHHHHHHHhhcCCCCC
Q psy8412 79 SSLTALFNIRFTNPLISKVYSTWSFLKLN--NKNVSFMWCPSHCGIRGNEIVDEAARNAASIDPYK 142 (271)
Q Consensus 79 ~al~~l~~~~~~~~~~~~~~~~~~~l~~~--~~~v~~~WVpgH~gi~gNe~AD~lAk~a~~~~~~~ 142 (271)
+.++-+.+-....-. .......-.. +....+.|+.-|..+.-+..++.++.........+
T Consensus 144 a~~k~~k~~~~~k~~----~~~~~e~~~~~~~v~h~~k~i~~~~~~~~~~~~~s~~~~~~k~~~~~ 205 (225)
T COG3341 144 AYFKYVKDKCETKVN----LLKDREFFSIGKGVFHDEKDINIHIWIFESKKGNSHVYNTSKKELSP 205 (225)
T ss_pred HHHHHHhhhhhhHHH----HHHhHHhhhccchhhhhhhhcccccccchhhhhhhhhhchhhhhccc
Confidence 988888754311100 0001111122 24556788999999999999998887777666443
No 16
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=58.85 E-value=3.8 Score=23.67 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=6.2
Q ss_pred CCcc-cCCcccceeeeeeecc
Q psy8412 220 PFCQ-CGAALSVILNYIVDNF 239 (271)
Q Consensus 220 p~C~-Cg~~et~~~h~~~~c~ 239 (271)
|.|+ |+...+-...-++.||
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp 23 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCP 23 (30)
T ss_dssp ---TTT-----EE-SSSEEET
T ss_pred CCCCCCCCcceeccCCEEeCC
Confidence 7899 9976555434444444
No 17
>KOG1812|consensus
Probab=50.71 E-value=50 Score=30.93 Aligned_cols=43 Identities=26% Similarity=0.206 Sum_probs=35.9
Q ss_pred CCchHHHHHHHHHHHHHHHHcCCCceEEEEeCCHHHHHHHhcc
Q psy8412 45 VNSIFSAELMAIFLCLEAILESPDHHFLIVSDSKSSLTALFNI 87 (271)
Q Consensus 45 ~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS~~al~~l~~~ 87 (271)
..+...||++|+..+|..+.+.+...+.+++|+......+...
T Consensus 46 ~~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~ 88 (384)
T KOG1812|consen 46 SITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGR 88 (384)
T ss_pred ccchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhh
Confidence 3678899999999999999999999999999976655644433
No 18
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=50.38 E-value=6 Score=23.21 Aligned_cols=22 Identities=27% Similarity=0.378 Sum_probs=15.2
Q ss_pred CCCcc-cCCcccceeeeeeecchhccc
Q psy8412 219 PPFCQ-CGAALSVILNYIVDNFILVHK 244 (271)
Q Consensus 219 sp~C~-Cg~~et~~~h~~~~c~~~~~~ 244 (271)
+=.|. |+..- |+|-|||...-|
T Consensus 8 ~Y~C~~C~~~G----H~i~dCP~~~Pk 30 (32)
T PF13696_consen 8 GYVCHRCGQKG----HWIQDCPTNKPK 30 (32)
T ss_pred CCEeecCCCCC----ccHhHCCCCCCC
Confidence 34788 88764 888888875443
No 19
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=48.34 E-value=6.6 Score=34.77 Aligned_cols=22 Identities=23% Similarity=0.058 Sum_probs=15.5
Q ss_pred CCCchh-hheeeeeeeccccccc
Q psy8412 189 QNKRLQ-EVILTRLRIGHTRITH 210 (271)
Q Consensus 189 ~l~R~~-~~~L~qlrtGH~~~~h 210 (271)
.|+.+. ...|.||||.|-+.+|
T Consensus 206 GlsGrLRvGALsqLrTehrPCtY 228 (311)
T PF15322_consen 206 GLSGRLRVGALSQLRTEHRPCTY 228 (311)
T ss_pred ccccceecchhhhhhhccCCccc
Confidence 454444 3378999999999874
No 20
>PF00220 Hormone_4: Neurohypophysial hormones, N-terminal Domain; InterPro: IPR022423 Oxytocin (or ocytocin) and vasopressin [] are small (nine amino acid residues), structurally and functionally related neurohypophysial peptide hormones. Oxytocin causes contraction of the smooth muscle of the uterus and of the mammary gland while vasopressin has a direct antidiuretic action on the kidney and also causes vasoconstriction of the peripheral vessels. Like the majority of active peptides, both hormones are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Peptides belonging to this family are also found in birds, fish, reptiles and amphibians (mesotocin, isotocin, valitocin, glumitocin, aspargtocin, vasotocin, seritocin, asvatocin, phasvatocin), in worms (annetocin), octopi (cephalotocin), locust (locupressin or neuropeptide F1/F2) and in molluscs (conopressins G and S) []. The pattern developed to detect this category of peptides spans their entire sequence and includes four invariant amino acid residues. .; GO: 0005185 neurohypophyseal hormone activity, 0005576 extracellular region
Probab=47.45 E-value=6.8 Score=16.23 Aligned_cols=7 Identities=43% Similarity=0.496 Sum_probs=4.4
Q ss_pred eeeecch
Q psy8412 234 YIVDNFI 240 (271)
Q Consensus 234 ~~~~c~~ 240 (271)
+|-+||+
T Consensus 2 ~i~nCP~ 8 (9)
T PF00220_consen 2 YIRNCPI 8 (9)
T ss_pred ccccCCC
Confidence 4567775
No 21
>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=42.72 E-value=9.9 Score=19.10 Aligned_cols=15 Identities=27% Similarity=0.366 Sum_probs=8.7
Q ss_pred Ccc-cCCcccceeeeeeecc
Q psy8412 221 FCQ-CGAALSVILNYIVDNF 239 (271)
Q Consensus 221 ~C~-Cg~~et~~~h~~~~c~ 239 (271)
.|. ||..- |+..+||
T Consensus 2 ~C~~C~~~G----H~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPG----HIARDCP 17 (18)
T ss_dssp BCTTTSCSS----SCGCTSS
T ss_pred cCcCCCCcC----cccccCc
Confidence 467 77653 5555554
No 22
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=41.97 E-value=44 Score=33.41 Aligned_cols=34 Identities=18% Similarity=0.246 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhCCCceEEEEecCCCCCccchHH
Q psy8412 95 SKVYSTWSFLKLNNKNVSFMWCPSHCGIRGNEIV 128 (271)
Q Consensus 95 ~~~~~~~~~l~~~~~~v~~~WVpgH~gi~gNe~A 128 (271)
......+....+.+..|-+-|||+|-+..||-.+
T Consensus 214 edfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~ 247 (628)
T COG0296 214 EDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLA 247 (628)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhh
Confidence 3444445558899999999999999999988766
No 23
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=41.84 E-value=13 Score=31.23 Aligned_cols=19 Identities=26% Similarity=0.482 Sum_probs=14.7
Q ss_pred CCCCCcc-cCCcccceeeeeeecc
Q psy8412 217 TDPPFCQ-CGAALSVILNYIVDNF 239 (271)
Q Consensus 217 ~~sp~C~-Cg~~et~~~h~~~~c~ 239 (271)
.+.+.|. ||..- |..-|||
T Consensus 58 ~~~~~C~nCg~~G----H~~~DCP 77 (190)
T COG5082 58 EENPVCFNCGQNG----HLRRDCP 77 (190)
T ss_pred ccccccchhcccC----cccccCC
Confidence 4678899 98764 7778888
No 24
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=38.25 E-value=1.5e+02 Score=22.04 Aligned_cols=52 Identities=12% Similarity=-0.084 Sum_probs=32.6
Q ss_pred CeeEEEEEC-CeEEEEecC----CCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCC
Q psy8412 26 STSCAFSIG-DVVHSTLLN----PVNSIFSAELMAIFLCLEAILESPDHHFLIVSDS 77 (271)
Q Consensus 26 ~~G~a~~~~-~~~~~~~l~----~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS 77 (271)
.+|+.++.. +........ .......||..||..+.+..........++|+--
T Consensus 18 ~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~ 74 (109)
T cd01285 18 PFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTL 74 (109)
T ss_pred cEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeC
Confidence 478777765 433222222 2345778999999998887543335677777753
No 25
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=34.71 E-value=1.3e+02 Score=24.73 Aligned_cols=50 Identities=10% Similarity=-0.067 Sum_probs=28.8
Q ss_pred CeeEEEEECCeEEEEec----CCCCchHHHHHHHHHHHHHHHHcCCCceEEEEe
Q psy8412 26 STSCAFSIGDVVHSTLL----NPVNSIFSAELMAIFLCLEAILESPDHHFLIVS 75 (271)
Q Consensus 26 ~~G~a~~~~~~~~~~~l----~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~t 75 (271)
.+|+.+|..+......- ........||+.||..|.+..........++|+
T Consensus 34 pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~~~~~l~g~tlY~ 87 (172)
T PRK10860 34 PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYV 87 (172)
T ss_pred CEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhcCCCCcCCcEEEe
Confidence 57887776554322221 112224579999999987755433344556665
No 26
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=33.81 E-value=26 Score=23.83 Aligned_cols=19 Identities=26% Similarity=0.513 Sum_probs=13.0
Q ss_pred ccCCCCCCCcc-cCCcccce
Q psy8412 213 LFTKTDPPFCQ-CGAALSVI 231 (271)
Q Consensus 213 r~~~~~sp~C~-Cg~~et~~ 231 (271)
|+-..|...|+ ||.++..+
T Consensus 12 ~l~~~d~e~CP~Cgs~~~te 31 (64)
T COG2093 12 RLTPEDTEICPVCGSTDLTE 31 (64)
T ss_pred ccCCCCCccCCCCCCcccch
Confidence 45556677799 99765443
No 27
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=30.85 E-value=1.8e+02 Score=22.10 Aligned_cols=46 Identities=11% Similarity=-0.044 Sum_probs=28.4
Q ss_pred CeeEEEEEC-CeEEEEecCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEe
Q psy8412 26 STSCAFSIG-DVVHSTLLNPVNSIFSAELMAIFLCLEAILESPDHHFLIVS 75 (271)
Q Consensus 26 ~~G~a~~~~-~~~~~~~l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~t 75 (271)
.+|+.++.. +.......+.......||..||..|.+. .....++|+
T Consensus 20 pvGaviv~~~g~iv~~g~n~~~~~~HAE~~ai~~a~~~----~l~g~tly~ 66 (115)
T cd01284 20 PVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEK----LARGATLYV 66 (115)
T ss_pred CEEEEEEeCCCeEEEEecCCCCCcccHHHHHHHHHhhc----CCCCeEEEE
Confidence 478877765 4333333332335678999999998774 234556665
No 28
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=29.66 E-value=33 Score=21.19 Aligned_cols=13 Identities=31% Similarity=0.493 Sum_probs=8.3
Q ss_pred ecccccccccCcC
Q psy8412 253 ACRMWNTSSLNVP 265 (271)
Q Consensus 253 ~c~~~~~~~~~~~ 265 (271)
.||+|......+|
T Consensus 18 ~CP~~~~~~a~~p 30 (40)
T PF15288_consen 18 RCPMYCWSGALAP 30 (40)
T ss_pred cCCCCCCCCCCCC
Confidence 6888876544443
No 29
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=29.49 E-value=1.7e+02 Score=23.11 Aligned_cols=51 Identities=18% Similarity=0.210 Sum_probs=34.2
Q ss_pred CeeEEEEECC--eEEEEecC--CCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCC
Q psy8412 26 STSCAFSIGD--VVHSTLLN--PVNSIFSAELMAIFLCLEAILESPDHHFLIVSDS 77 (271)
Q Consensus 26 ~~G~a~~~~~--~~~~~~l~--~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS 77 (271)
.+|+++...+ ......+. ...-...||-.||..|+.. -......|.+++|+
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 5888877544 22233232 2334566999999999887 34457889999997
No 30
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=28.89 E-value=38 Score=21.15 Aligned_cols=15 Identities=20% Similarity=0.463 Sum_probs=12.1
Q ss_pred ccceEEEEecccccc
Q psy8412 245 HDIGVLFLACRMWNT 259 (271)
Q Consensus 245 ~~~~h~~~~c~~~~~ 259 (271)
..-+..|+.||.+..
T Consensus 19 ~N~GR~Fy~C~~~~~ 33 (45)
T PF06839_consen 19 PNPGRRFYKCPNYKD 33 (45)
T ss_pred CCCCCcceECCCCCC
Confidence 466789999998876
No 31
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=28.26 E-value=34 Score=28.30 Aligned_cols=16 Identities=25% Similarity=0.625 Sum_probs=12.9
Q ss_pred CCCCCCcc-cCCcccce
Q psy8412 216 KTDPPFCQ-CGAALSVI 231 (271)
Q Consensus 216 ~~~sp~C~-Cg~~et~~ 231 (271)
....|.|+ ||.+.+++
T Consensus 153 aAGRP~CPlCg~PldP~ 169 (177)
T TIGR03847 153 AAGRPPCPLCGRPIDPD 169 (177)
T ss_pred hCCCCCCCCCCCCCCCC
Confidence 44679999 99887776
No 32
>cd01286 deoxycytidylate_deaminase Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.
Probab=26.88 E-value=2.4e+02 Score=21.85 Aligned_cols=27 Identities=15% Similarity=-0.026 Sum_probs=17.9
Q ss_pred chHHHHHHHHHHHHHHHHcCCCceEEEEe
Q psy8412 47 SIFSAELMAIFLCLEAILESPDHHFLIVS 75 (271)
Q Consensus 47 s~~~AEl~Ai~~AL~~a~~~~~~~v~I~t 75 (271)
....||..||..|.+. .......++|+
T Consensus 67 ~~~HAE~~Ai~~a~~~--~~~~~~~tLyv 93 (131)
T cd01286 67 RTVHAEQNAILQAARH--GVSLEGATLYV 93 (131)
T ss_pred CCCCHHHHHHHHHhHc--CCCcCCeEEEE
Confidence 3567999999988664 22345566665
No 33
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=26.68 E-value=37 Score=25.78 Aligned_cols=13 Identities=23% Similarity=0.616 Sum_probs=8.9
Q ss_pred CCCcc-cCCcccce
Q psy8412 219 PPFCQ-CGAALSVI 231 (271)
Q Consensus 219 sp~C~-Cg~~et~~ 231 (271)
.|.|+ |+...|-+
T Consensus 2 lp~CP~C~seytY~ 15 (109)
T TIGR00686 2 LPPCPKCNSEYTYH 15 (109)
T ss_pred CCcCCcCCCcceEe
Confidence 47888 88765554
No 34
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=26.00 E-value=1.9e+02 Score=23.23 Aligned_cols=50 Identities=10% Similarity=-0.016 Sum_probs=29.4
Q ss_pred CeeEEEEE-CCeEEEEe----cCCCCchHHHHHHHHHHHHHHHHcCCCceEEEEe
Q psy8412 26 STSCAFSI-GDVVHSTL----LNPVNSIFSAELMAIFLCLEAILESPDHHFLIVS 75 (271)
Q Consensus 26 ~~G~a~~~-~~~~~~~~----l~~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~t 75 (271)
.+|+.+|. .+...... .....-.-.||+.||..|.+..........++|+
T Consensus 29 PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyv 83 (152)
T COG0590 29 PVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYV 83 (152)
T ss_pred CEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEE
Confidence 46777776 33222211 1122223479999999999988654455555555
No 35
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=25.01 E-value=34 Score=21.34 Aligned_cols=18 Identities=28% Similarity=0.462 Sum_probs=13.6
Q ss_pred CCCcc-cCCcccceeeeeeecchhcccccceEEEEeccc
Q psy8412 219 PPFCQ-CGAALSVILNYIVDNFILVHKHDIGVLFLACRM 256 (271)
Q Consensus 219 sp~C~-Cg~~et~~~h~~~~c~~~~~~~~~~h~~~~c~~ 256 (271)
+..|. |+... |.-++||.
T Consensus 4 ~~~CqkC~~~G--------------------H~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKG--------------------HWTYECPN 22 (42)
T ss_pred CCcCcccCCCC--------------------cchhhCCC
Confidence 56799 98664 88888884
No 36
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=23.95 E-value=36 Score=22.51 Aligned_cols=12 Identities=17% Similarity=0.038 Sum_probs=5.8
Q ss_pred ccceeeeeeecc
Q psy8412 228 LSVILNYIVDNF 239 (271)
Q Consensus 228 et~~~h~~~~c~ 239 (271)
.|+--+|.+.||
T Consensus 21 DT~LkNfPlyCp 32 (55)
T PF14205_consen 21 DTVLKNFPLYCP 32 (55)
T ss_pred CceeccccccCC
Confidence 344335555555
No 37
>PRK10933 trehalose-6-phosphate hydrolase; Provisional
Probab=23.75 E-value=1.8e+02 Score=28.65 Aligned_cols=72 Identities=10% Similarity=0.020 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHcCCCceEEEEe-------CCHHHHHHHhccccCCccHHHHHHHHHHHHhCCCceEEEEecCCCCC
Q psy8412 51 AELMAIFLCLEAILESPDHHFLIVS-------DSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCGI 122 (271)
Q Consensus 51 AEl~Ai~~AL~~a~~~~~~~v~I~t-------DS~~al~~l~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~gi 122 (271)
+.+.||...|+++...+...|++-- |+-+.+.-.......-+........+..+++++.+|.+-.|+.|++.
T Consensus 30 Gdl~gi~~~ldyl~~lGv~~i~l~P~~~~~~~~~gY~~~d~~~id~~~Gt~~d~~~lv~~~h~~gi~vilD~V~NH~s~ 108 (551)
T PRK10933 30 GDLRGVTQRLDYLQKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTYGTLDDFDELVAQAKSRGIRIILDMVFNHTST 108 (551)
T ss_pred cCHHHHHHhhHHHHhCCCCEEEECCCCCCCCCCCCCCcccCCCcCcccCCHHHHHHHHHHHHHCCCEEEEEECCCCccC
Confidence 4699999999999999887777632 21111111000000112223444445558889999999999999876
No 38
>PRK08298 cytidine deaminase; Validated
Probab=23.19 E-value=2.3e+02 Score=22.44 Aligned_cols=56 Identities=14% Similarity=0.198 Sum_probs=34.8
Q ss_pred EEcCCCCCCCeeEEEEECC--eEEEEecC--CCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCC
Q psy8412 17 FTDGSKTPDSTSCAFSIGD--VVHSTLLN--PVNSIFSAELMAIFLCLEAILESPDHHFLIVSDS 77 (271)
Q Consensus 17 ytDGS~~~~~~G~a~~~~~--~~~~~~l~--~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS 77 (271)
|...| .+|+++...+ ......+. ....-..||..||..|+..-. .....|.|.+|.
T Consensus 19 Y~PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G~-~~~~~i~v~~~~ 78 (136)
T PRK08298 19 YPNGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQK-RVTHSICVAREN 78 (136)
T ss_pred cCCCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCCC-ceEEEEEEEcCC
Confidence 54555 7999988644 33344432 233456799999998875432 235667777775
No 39
>smart00642 Aamy Alpha-amylase domain.
Probab=22.66 E-value=3e+02 Score=22.26 Aligned_cols=71 Identities=8% Similarity=-0.046 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHcCCCceEEEEe----------CCHHHHHHHhccccCCccHHHHHHHHHHHHhCCCceEEEEecCCCC
Q psy8412 52 ELMAIFLCLEAILESPDHHFLIVS----------DSKSSLTALFNIRFTNPLISKVYSTWSFLKLNNKNVSFMWCPSHCG 121 (271)
Q Consensus 52 El~Ai~~AL~~a~~~~~~~v~I~t----------DS~~al~~l~~~~~~~~~~~~~~~~~~~l~~~~~~v~~~WVpgH~g 121 (271)
-+.+|..-|.++.+.+...|.+-- +.-+.+.-.......-+........+..+++++..|-+-.|+.|++
T Consensus 17 ~~~gi~~~l~yl~~lG~~~I~l~Pi~~~~~~~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~Gi~vilD~V~NH~~ 96 (166)
T smart00642 17 DLQGIIEKLDYLKDLGVTAIWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVILDVVINHTS 96 (166)
T ss_pred CHHHHHHHHHHHHHCCCCEEEECcceeCCCCCCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHCCCEEEEEECCCCCC
Confidence 366777777777777766665531 1111111111111111222344444555788999999999999988
Q ss_pred C
Q psy8412 122 I 122 (271)
Q Consensus 122 i 122 (271)
.
T Consensus 97 ~ 97 (166)
T smart00642 97 D 97 (166)
T ss_pred C
Confidence 7
No 40
>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=22.65 E-value=29 Score=23.07 Aligned_cols=20 Identities=25% Similarity=0.228 Sum_probs=6.5
Q ss_pred CCcc-cCCcccceeeeeeecch
Q psy8412 220 PFCQ-CGAALSVILNYIVDNFI 240 (271)
Q Consensus 220 p~C~-Cg~~et~~~h~~~~c~~ 240 (271)
-.|+ ||+.-+.. |.+..||.
T Consensus 34 y~Cp~CgAtGd~A-HT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNA-HTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG----GGG-TT
T ss_pred CcCCCCcCcCccc-cccccCcC
Confidence 4799 99865554 66666663
No 41
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=21.92 E-value=54 Score=22.11 Aligned_cols=13 Identities=31% Similarity=0.968 Sum_probs=10.4
Q ss_pred cCCCCCCCcc-cCC
Q psy8412 214 FTKTDPPFCQ-CGA 226 (271)
Q Consensus 214 ~~~~~sp~C~-Cg~ 226 (271)
|...+.|.|+ |+.
T Consensus 34 Fs~~~~p~CPlC~s 47 (59)
T PF14169_consen 34 FSFEEEPVCPLCKS 47 (59)
T ss_pred cccCCCccCCCcCC
Confidence 4556789999 995
No 42
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.85 E-value=51 Score=22.06 Aligned_cols=26 Identities=19% Similarity=0.433 Sum_probs=19.4
Q ss_pred CCCCcc-cCCcccceeeeeeecchhcccccceEEEEeccccccc
Q psy8412 218 DPPFCQ-CGAALSVILNYIVDNFILVHKHDIGVLFLACRMWNTS 260 (271)
Q Consensus 218 ~sp~C~-Cg~~et~~~h~~~~c~~~~~~~~~~h~~~~c~~~~~~ 260 (271)
.-..|+ ||+-.-.- ||-+.|..|...
T Consensus 26 ~~~~c~~cG~~~l~H-----------------rvc~~cg~Y~g~ 52 (57)
T COG0333 26 TLSVCPNCGEYKLPH-----------------RVCLKCGYYKGR 52 (57)
T ss_pred cceeccCCCCcccCc-----------------eEcCCCCCccCe
Confidence 347899 99866565 788888888764
No 43
>PF13395 HNH_4: HNH endonuclease
Probab=20.86 E-value=57 Score=21.17 Aligned_cols=6 Identities=50% Similarity=1.625 Sum_probs=3.8
Q ss_pred cc-cCCc
Q psy8412 222 CQ-CGAA 227 (271)
Q Consensus 222 C~-Cg~~ 227 (271)
|. ||..
T Consensus 1 C~Y~g~~ 7 (54)
T PF13395_consen 1 CPYCGKP 7 (54)
T ss_pred CCCCCCC
Confidence 67 7753
No 44
>PRK10220 hypothetical protein; Provisional
Probab=20.37 E-value=58 Score=24.79 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=8.7
Q ss_pred CCCcc-cCCcccce
Q psy8412 219 PPFCQ-CGAALSVI 231 (271)
Q Consensus 219 sp~C~-Cg~~et~~ 231 (271)
.|.|+ |+...|-+
T Consensus 3 lP~CP~C~seytY~ 16 (111)
T PRK10220 3 LPHCPKCNSEYTYE 16 (111)
T ss_pred CCcCCCCCCcceEc
Confidence 47888 88655544
No 45
>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.
Probab=20.02 E-value=2.5e+02 Score=21.71 Aligned_cols=51 Identities=14% Similarity=0.042 Sum_probs=32.3
Q ss_pred CeeEEEEECC--eEEEEecC--CCCchHHHHHHHHHHHHHHHHcCCCceEEEEeCC
Q psy8412 26 STSCAFSIGD--VVHSTLLN--PVNSIFSAELMAIFLCLEAILESPDHHFLIVSDS 77 (271)
Q Consensus 26 ~~G~a~~~~~--~~~~~~l~--~~~s~~~AEl~Ai~~AL~~a~~~~~~~v~I~tDS 77 (271)
.+|++++..+ ........ .......||..||..|...-. .....+.|..+.
T Consensus 22 ~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~-~~i~~i~vv~~~ 76 (127)
T TIGR01354 22 KVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGY-RKFVAIAVADSA 76 (127)
T ss_pred eEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCC-CCeEEEEEEeCC
Confidence 4788877543 33333222 223345699999999887633 257888888876
Done!