Query psy4359
Match_columns 220
No_of_seqs 150 out of 389
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 23:30:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4359.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4359hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.4 2.1E-12 4.5E-17 104.7 7.4 89 14-119 3-94 (161)
2 PRK08719 ribonuclease H; Revie 99.3 7.5E-12 1.6E-16 100.1 6.9 84 15-118 3-98 (147)
3 PRK00203 rnhA ribonuclease H; 99.2 1.7E-11 3.8E-16 98.0 7.0 85 15-117 2-92 (150)
4 PF00075 RNase_H: RNase H; In 99.2 1.6E-11 3.5E-16 94.7 5.9 72 15-95 2-76 (132)
5 COG0328 RnhA Ribonuclease HI [ 99.2 1.1E-10 2.4E-15 93.7 8.1 75 15-95 2-82 (154)
6 PRK13907 rnhA ribonuclease H; 99.0 1.7E-09 3.8E-14 83.7 7.5 75 17-96 2-81 (128)
7 KOG3752|consensus 99.0 1.2E-09 2.7E-14 97.8 7.4 76 15-95 211-295 (371)
8 cd06222 RnaseH RNase H (RNase 98.9 3.9E-09 8.4E-14 78.5 7.0 75 18-97 1-82 (130)
9 PRK07708 hypothetical protein; 98.7 7.8E-08 1.7E-12 81.7 7.6 84 11-99 68-163 (219)
10 PRK07238 bifunctional RNase H/ 98.5 4.1E-07 9E-12 82.6 7.7 80 16-100 2-89 (372)
11 PF13456 RVT_3: Reverse transc 97.4 0.0002 4.2E-09 50.6 3.8 42 52-98 2-43 (87)
12 PF13966 zf-RVT: zinc-binding 96.8 0.00023 5E-09 51.5 -0.9 46 145-190 34-83 (86)
13 PF05380 Peptidase_A17: Pao re 93.5 0.22 4.7E-06 40.0 5.9 53 15-69 80-144 (159)
14 PF00336 DNA_pol_viral_C: DNA 84.4 0.74 1.6E-05 38.9 2.3 61 16-90 94-154 (245)
15 PRK06848 hypothetical protein; 65.6 8.1 0.00018 30.5 3.4 43 20-65 22-68 (139)
16 PF09538 FYDLN_acid: Protein o 65.0 3 6.5E-05 31.6 0.8 22 158-180 18-39 (108)
17 PRK08298 cytidine deaminase; V 64.6 7 0.00015 30.8 2.9 56 20-85 19-78 (136)
18 PRK05578 cytidine deaminase; V 54.9 14 0.0003 28.8 3.0 59 20-86 18-80 (131)
19 PRK12411 cytidine deaminase; P 53.7 14 0.00029 28.9 2.8 51 29-85 25-79 (132)
20 TIGR02300 FYDLN_acid conserved 50.7 8 0.00017 30.2 1.1 22 158-180 18-39 (129)
21 PF00035 dsrm: Double-stranded 50.0 68 0.0015 20.7 6.0 63 2-66 1-67 (67)
22 TIGR01354 cyt_deam_tetra cytid 49.9 19 0.00041 27.8 3.0 51 29-85 22-76 (127)
23 COG0295 Cdd Cytidine deaminase 47.6 23 0.00051 27.9 3.2 51 29-85 27-81 (134)
24 PF05605 zf-Di19: Drought indu 46.8 19 0.00041 23.3 2.3 26 167-192 2-27 (54)
25 cd01285 nucleoside_deaminase N 45.4 38 0.00083 25.0 4.1 55 27-86 16-75 (109)
26 PF00383 dCMP_cyt_deam_1: Cyti 36.7 76 0.0017 22.6 4.5 40 26-65 22-66 (102)
27 PF05741 zf-nanos: Nanos RNA b 33.9 9.9 0.00021 25.3 -0.7 20 169-188 35-54 (55)
28 COG2093 DNA-directed RNA polym 29.8 26 0.00057 24.0 0.8 17 161-177 12-28 (64)
29 PF15322 PMSI1: Protein missin 27.8 13 0.00029 32.8 -1.1 22 137-158 206-228 (311)
30 KOG1123|consensus 27.5 70 0.0015 31.1 3.5 30 61-92 530-559 (776)
31 PF09967 DUF2201: VWA-like dom 26.2 51 0.0011 25.2 2.1 25 2-26 69-95 (126)
32 PF07057 TraI: DNA helicase Tr 25.1 24 0.00052 27.5 0.0 15 11-25 4-18 (126)
33 PF14255 Cys_rich_CPXG: Cystei 24.5 24 0.00053 23.1 -0.0 8 169-176 2-9 (52)
34 PRK10860 tRNA-specific adenosi 23.9 1.1E+02 0.0023 25.0 3.6 39 28-66 33-75 (172)
35 cd01284 Riboflavin_deaminase-r 22.8 1.3E+02 0.0029 22.7 3.7 38 28-65 19-57 (115)
36 PF13696 zf-CCHC_2: Zinc knuck 22.8 25 0.00054 20.8 -0.2 17 169-188 10-26 (32)
37 PF13005 zf-IS66: zinc-finger 22.7 38 0.00082 21.0 0.6 12 166-177 1-12 (47)
38 PF04423 Rad50_zn_hook: Rad50 22.0 34 0.00074 22.1 0.3 13 169-181 22-34 (54)
39 PF11023 DUF2614: Protein of u 21.5 29 0.00063 26.5 -0.2 17 162-180 82-98 (114)
40 KOG2893|consensus 20.6 60 0.0013 28.3 1.5 26 162-187 5-30 (341)
41 KOG1930|consensus 20.5 35 0.00075 32.0 0.1 62 126-188 208-282 (483)
42 cd00729 rubredoxin_SM Rubredox 20.4 49 0.0011 19.5 0.7 13 164-176 15-27 (34)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.35 E-value=2.1e-12 Score=104.75 Aligned_cols=89 Identities=18% Similarity=0.185 Sum_probs=66.4
Q ss_pred CCceeeeecCCCCC--CcceeeeeCCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHh
Q psy4359 14 PQSTKIYTDASKND--SSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQS 91 (220)
Q Consensus 14 ~~~~~IyTDgSk~~--~~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~a 91 (220)
+..+.||||||... +..|+|++..+.....+.....|.+.||++|++.||+.+.. ...++.|+|||++|+++
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~ 76 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINS 76 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHH
Confidence 45689999999874 34778766333222334445679999999999999986543 24579999999999999
Q ss_pred hhhhhCCChHhHHHHHHhhh-hccchhhc
Q psy4359 92 LQDIFSPNLHTLRQIMSLWH-EDWNYLIG 119 (220)
Q Consensus 92 i~~~~~P~~~Di~~I~~~Wq-~~W~~~~~ 119 (220)
+..+ ...|+ +.|+.+.+
T Consensus 77 i~~W-----------~~~Wk~~gWk~s~G 94 (161)
T PRK06548 77 LTKW-----------VYSWKMRKWRKADG 94 (161)
T ss_pred HHHH-----------HHHHHHCCCcccCC
Confidence 9998 88895 48876544
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.28 E-value=7.5e-12 Score=100.11 Aligned_cols=84 Identities=15% Similarity=0.266 Sum_probs=63.7
Q ss_pred CceeeeecCCCCCCc-----ceeeee--CCCc----ceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEec
Q psy4359 15 QSTKIYTDASKNDSS-----VSAAFW--SPDF----SFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCT 83 (220)
Q Consensus 15 ~~~~IyTDgSk~~~~-----~G~ai~--~~~~----~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~s 83 (220)
..+.||||||+..++ .|+|++ .++. .....+.+..|.++||+.||..||+.+.+. ..|+|
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~---------~~i~t 73 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG---------DVIYS 73 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC---------CEEEe
Confidence 568999999997543 477754 3322 123446666899999999999999997643 37999
Q ss_pred cchHHHHhhhhhhCCChHhHHHHHHhhh-hccchhh
Q psy4359 84 DSLSALQSLQDIFSPNLHTLRQIMSLWH-EDWNYLI 118 (220)
Q Consensus 84 DS~sal~ai~~~~~P~~~Di~~I~~~Wq-~~W~~~~ 118 (220)
||++++++++.+ ...|+ +.|..+.
T Consensus 74 DS~yvi~~i~~~-----------~~~W~~~~w~~s~ 98 (147)
T PRK08719 74 DSDYCVRGFNEW-----------LDTWKQKGWRKSD 98 (147)
T ss_pred chHHHHHHHHHH-----------HHHHHhCCcccCC
Confidence 999999999988 88894 5887643
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.24 E-value=1.7e-11 Score=97.99 Aligned_cols=85 Identities=20% Similarity=0.184 Sum_probs=62.6
Q ss_pred CceeeeecCCCCCC--cceeeee--CCCcc-eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHH
Q psy4359 15 QSTKIYTDASKNDS--SVSAAFW--SPDFS-FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSAL 89 (220)
Q Consensus 15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~-~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal 89 (220)
+.+.||||||...+ ..|+|++ .++.. ...+..+..|...||+.||+.||+.+.. ...+.|+|||++++
T Consensus 2 ~~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-------~~~v~I~tDS~yvi 74 (150)
T PRK00203 2 KQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-------PCEVTLYTDSQYVR 74 (150)
T ss_pred ceEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-------CCeEEEEECHHHHH
Confidence 35899999998743 3666644 33322 2334445788899999999999998743 35799999999999
Q ss_pred HhhhhhhCCChHhHHHHHHhhhh-ccchh
Q psy4359 90 QSLQDIFSPNLHTLRQIMSLWHE-DWNYL 117 (220)
Q Consensus 90 ~ai~~~~~P~~~Di~~I~~~Wq~-~W~~~ 117 (220)
++|..+ ...|+. .|...
T Consensus 75 ~~i~~w-----------~~~Wk~~~~~~~ 92 (150)
T PRK00203 75 QGITEW-----------IHGWKKNGWKTA 92 (150)
T ss_pred HHHHHH-----------HHHHHHcCCccc
Confidence 999887 667854 68753
No 4
>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=99.23 E-value=1.6e-11 Score=94.70 Aligned_cols=72 Identities=28% Similarity=0.242 Sum_probs=54.3
Q ss_pred CceeeeecCCCC--CCcceee-eeCCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHh
Q psy4359 15 QSTKIYTDASKN--DSSVSAA-FWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQS 91 (220)
Q Consensus 15 ~~~~IyTDgSk~--~~~~G~a-i~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~a 91 (220)
+++.||||||.. .+..|+| ++..+......++ ..|++.||+.||.+||+.+ . ..+++|+|||++++.+
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~--~------~~~v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL--E------HRKVTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH--S------TSEEEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh--h------cccccccccHHHHHHH
Confidence 578999999965 3334555 3444434445566 8999999999999999944 4 3889999999999998
Q ss_pred hhhh
Q psy4359 92 LQDI 95 (220)
Q Consensus 92 i~~~ 95 (220)
+..+
T Consensus 73 l~~~ 76 (132)
T PF00075_consen 73 LNKW 76 (132)
T ss_dssp HHTH
T ss_pred HHHh
Confidence 8774
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.16 E-value=1.1e-10 Score=93.70 Aligned_cols=75 Identities=17% Similarity=0.058 Sum_probs=59.0
Q ss_pred CceeeeecCCCCCC--cceeeee--CCCcc--eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHH
Q psy4359 15 QSTKIYTDASKNDS--SVSAAFW--SPDFS--FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSA 88 (220)
Q Consensus 15 ~~~~IyTDgSk~~~--~~G~ai~--~~~~~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sa 88 (220)
..+.||||||+..+ -.|+|+| +++.. .+.+.. .+|.+.||+.|+++||+++.+. +...+.|+|||+++
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~-----~~~~v~l~tDS~yv 75 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKEL-----GACEVTLYTDSKYV 75 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhc-----CCceEEEEecHHHH
Confidence 46899999998743 3556644 34433 334444 8999999999999999999875 68899999999999
Q ss_pred HHhhhhh
Q psy4359 89 LQSLQDI 95 (220)
Q Consensus 89 l~ai~~~ 95 (220)
+++|..+
T Consensus 76 ~~~i~~w 82 (154)
T COG0328 76 VEGITRW 82 (154)
T ss_pred HHHHHHH
Confidence 9999844
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.98 E-value=1.7e-09 Score=83.74 Aligned_cols=75 Identities=16% Similarity=0.177 Sum_probs=57.5
Q ss_pred eeeeecCCCCC--Ccceeeee--CCCccee-eecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHh
Q psy4359 17 TKIYTDASKND--SSVSAAFW--SPDFSFK-VKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQS 91 (220)
Q Consensus 17 ~~IyTDgSk~~--~~~G~ai~--~~~~~~~-~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~a 91 (220)
++||||||... +..|+|++ +...... .+.....|...||+.|++.||+.+... ...++.|+|||+.++..
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-----g~~~v~i~sDS~~vi~~ 76 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-----NYNIVSFRTDSQLVERA 76 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-----CCCEEEEEechHHHHHH
Confidence 57999999864 45777755 2222212 222345788999999999999999986 56789999999999999
Q ss_pred hhhhh
Q psy4359 92 LQDIF 96 (220)
Q Consensus 92 i~~~~ 96 (220)
+++.+
T Consensus 77 ~~~~~ 81 (128)
T PRK13907 77 VEKEY 81 (128)
T ss_pred HhHHH
Confidence 99864
No 7
>KOG3752|consensus
Probab=98.97 E-value=1.2e-09 Score=97.81 Aligned_cols=76 Identities=20% Similarity=0.143 Sum_probs=63.2
Q ss_pred CceeeeecCCCCCC-----cceeeeeCCC---cceeeecc-hhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccc
Q psy4359 15 QSTKIYTDASKNDS-----SVSAAFWSPD---FSFKVKLN-PLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDS 85 (220)
Q Consensus 15 ~~~~IyTDgSk~~~-----~~G~ai~~~~---~~~~~~l~-~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS 85 (220)
+.+++|||||...+ .+|+||+.++ ......+. .-.+.|.||+.||.+||+-+.+. +..++.|.|||
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-----~~~kv~I~TDS 285 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-----NINKVVIRTDS 285 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-----CCCcEEEEech
Confidence 34899999999864 3899998543 24456665 77899999999999999999886 57799999999
Q ss_pred hHHHHhhhhh
Q psy4359 86 LSALQSLQDI 95 (220)
Q Consensus 86 ~sal~ai~~~ 95 (220)
+..+++|+.+
T Consensus 286 ~~~i~~l~~w 295 (371)
T KOG3752|consen 286 EYFINSLTLW 295 (371)
T ss_pred HHHHHHHHHH
Confidence 9999999877
No 8
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=98.91 E-value=3.9e-09 Score=78.48 Aligned_cols=75 Identities=24% Similarity=0.225 Sum_probs=58.5
Q ss_pred eeeecCCCCCC--cceeeee--CCCccee---eecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHH
Q psy4359 18 KIYTDASKNDS--SVSAAFW--SPDFSFK---VKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQ 90 (220)
Q Consensus 18 ~IyTDgSk~~~--~~G~ai~--~~~~~~~---~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~ 90 (220)
.+|||||...+ +.|+|++ .++.... .......|++.||+.|++.||+++... ...++.|++||+.++.
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-----~~~~i~i~~Ds~~~~~ 75 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-----GGKKVNIYTDSQYVIN 75 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-----CCceEEEEECHHHHHH
Confidence 48999998765 5777755 3332222 222257899999999999999999865 6899999999999999
Q ss_pred hhhhhhC
Q psy4359 91 SLQDIFS 97 (220)
Q Consensus 91 ai~~~~~ 97 (220)
.+.+...
T Consensus 76 ~~~~~~~ 82 (130)
T cd06222 76 ALTGWYE 82 (130)
T ss_pred Hhhcccc
Confidence 9998754
No 9
>PRK07708 hypothetical protein; Validated
Probab=98.65 E-value=7.8e-08 Score=81.74 Aligned_cols=84 Identities=14% Similarity=0.127 Sum_probs=62.3
Q ss_pred hhCCCceeeeecCCCC--CCcceeeee--CCCc--ce----eeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccC--c
Q psy4359 11 SKYPQSTKIYTDASKN--DSSVSAAFW--SPDF--SF----KVKLNPLLSICNAELMAILYAVYFILANCLSEARNS--S 78 (220)
Q Consensus 11 ~~~~~~~~IyTDgSk~--~~~~G~ai~--~~~~--~~----~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~--~ 78 (220)
+.-|+...+|+|||.. .++.|+|++ .+.. .. ...+....|.+.||+.|++.||+.+... +.+ .
T Consensus 68 ~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~~~ 142 (219)
T PRK07708 68 EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKHEP 142 (219)
T ss_pred ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCcce
Confidence 3466789999999974 345777743 3322 11 1356666899999999999999999886 333 4
Q ss_pred eEEeccchHHHHhhhhhhCCC
Q psy4359 79 FLLCTDSLSALQSLQDIFSPN 99 (220)
Q Consensus 79 ~~I~sDS~sal~ai~~~~~P~ 99 (220)
+.|++||+.+++.+.+.|...
T Consensus 143 V~I~~DSqlVi~qi~g~wk~~ 163 (219)
T PRK07708 143 VTFRGDSQVVLNQLAGEWPCY 163 (219)
T ss_pred EEEEeccHHHHHHhCCCceeC
Confidence 899999999999999876543
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.47 E-value=4.1e-07 Score=82.63 Aligned_cols=80 Identities=8% Similarity=-0.026 Sum_probs=60.2
Q ss_pred ceeeeecCCCCCC--cceeeee--CCCc--c--eeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchH
Q psy4359 16 STKIYTDASKNDS--SVSAAFW--SPDF--S--FKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLS 87 (220)
Q Consensus 16 ~~~IyTDgSk~~~--~~G~ai~--~~~~--~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~s 87 (220)
.+.||||||...+ ..|+|++ +++. . ...+....+|.+.||+.|++.||+++.+. ...++.|++||+.
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~-----g~~~v~i~~DS~l 76 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAEL-----GATEVEVRMDSKL 76 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhC-----CCCeEEEEeCcHH
Confidence 4689999998754 4677744 4322 1 12233336788999999999999999886 5778999999999
Q ss_pred HHHhhhhhhCCCh
Q psy4359 88 ALQSLQDIFSPNL 100 (220)
Q Consensus 88 al~ai~~~~~P~~ 100 (220)
+++.+.+.+...+
T Consensus 77 vi~~i~~~~~~~~ 89 (372)
T PRK07238 77 VVEQMSGRWKVKH 89 (372)
T ss_pred HHHHhCCCCccCC
Confidence 9999988765444
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.39 E-value=0.0002 Score=50.64 Aligned_cols=42 Identities=19% Similarity=0.175 Sum_probs=35.3
Q ss_pred hhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHHhhhhhhCC
Q psy4359 52 CNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQSLQDIFSP 98 (220)
Q Consensus 52 ~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~ai~~~~~P 98 (220)
..||+.|++.||+++.+. +..+++|.|||+.++..|++...+
T Consensus 2 ~~aE~~al~~al~~a~~~-----g~~~i~v~sDs~~vv~~i~~~~~~ 43 (87)
T PF13456_consen 2 LEAEALALLEALQLAWEL-----GIRKIIVESDSQLVVDAINGRSSS 43 (87)
T ss_dssp HHHHHHHHHHHHHHHHCC-----T-SCEEEEES-HHHHHHHTTSS--
T ss_pred cHHHHHHHHHHHHHHHHC-----CCCEEEEEecCccccccccccccc
Confidence 579999999999999887 689999999999999999988543
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.77 E-value=0.00023 Score=51.46 Aligned_cols=46 Identities=24% Similarity=0.364 Sum_probs=33.7
Q ss_pred EEeEEeeccccc-ce--eeecccCCCCccceec-ccccHHHHHHHHHhcc
Q psy4359 145 TLTRLRIGHTNL-TH--VHLMKKEQPPECEICS-CNLTVKHLLKYCLKYQ 190 (220)
Q Consensus 145 ~l~rlRtGH~~l-~h--~~~~~~~~~p~C~~Cg-~~eTv~HiL~~Cp~~~ 190 (220)
.+.--|.-|.++ +- +.+.+...++.|..|+ ++||++|++++||...
T Consensus 34 ~~f~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 34 KFFLWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred EEEeeeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 344445556663 32 4556778899999999 5899999999999754
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=93.48 E-value=0.22 Score=40.00 Aligned_cols=53 Identities=26% Similarity=0.279 Sum_probs=36.1
Q ss_pred CceeeeecCCCCCCcceeeee---CCCcc----e-----eeecchhhhhhhHHHHHHHHHHHHHHHh
Q psy4359 15 QSTKIYTDASKNDSSVSAAFW---SPDFS----F-----KVKLNPLLSICNAELMAILYAVYFILAN 69 (220)
Q Consensus 15 ~~~~IyTDgSk~~~~~G~ai~---~~~~~----~-----~~~l~~~~si~~AEl~AI~~AL~~~~~~ 69 (220)
..+++|+|+|+ .+.|+.+| ..+.. . ........||=.-|+.|++.|.+++...
T Consensus 80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~ 144 (159)
T PF05380_consen 80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTV 144 (159)
T ss_pred eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 46899999994 45555554 12211 1 1333335599999999999999998774
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=84.38 E-value=0.74 Score=38.88 Aligned_cols=61 Identities=23% Similarity=0.215 Sum_probs=38.7
Q ss_pred ceeeeecCCCCCCcceeeeeCCCcceeeecchhhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccchHHHH
Q psy4359 16 STKIYTDASKNDSSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSLSALQ 90 (220)
Q Consensus 16 ~~~IyTDgSk~~~~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~sal~ 90 (220)
--.||+|+.-..+++ ++-.......| ..---|.+||++|...|.-++... .|.|||.-++.
T Consensus 94 lc~VfaDATpTgwgi--~i~~~~~~~Tf--s~~l~IhtaELlaaClAr~~~~~r----------~l~tDnt~Vls 154 (245)
T PF00336_consen 94 LCQVFADATPTGWGI--SITGQRMRGTF--SKPLPIHTAELLAACLARLMSGAR----------CLGTDNTVVLS 154 (245)
T ss_pred CCceeccCCCCccee--eecCceeeeee--cccccchHHHHHHHHHHHhccCCc----------EEeecCcEEEe
Confidence 347899987664433 22222222222 223458999999999888776544 59999987763
No 15
>PRK06848 hypothetical protein; Validated
Probab=65.57 E-value=8.1 Score=30.51 Aligned_cols=43 Identities=21% Similarity=0.086 Sum_probs=29.7
Q ss_pred eecCCCCCCcceeeeeCCCcceeeecchhhhh----hhHHHHHHHHHHHH
Q psy4359 20 YTDASKNDSSVSAAFWSPDFSFKVKLNPLLSI----CNAELMAILYAVYF 65 (220)
Q Consensus 20 yTDgSk~~~~~G~ai~~~~~~~~~~l~~~~si----~~AEl~AI~~AL~~ 65 (220)
|.. | +..||+|+...+..+..|..-+... -.||..||..|+..
T Consensus 22 y~p-s--~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~ 68 (139)
T PRK06848 22 YRN-D--WHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISE 68 (139)
T ss_pred cCC-C--CCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHc
Confidence 554 4 4689999886665555554444433 48999999998855
No 16
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=64.97 E-value=3 Score=31.64 Aligned_cols=22 Identities=18% Similarity=0.425 Sum_probs=16.9
Q ss_pred eeeecccCCCCccceecccccHH
Q psy4359 158 HVHLMKKEQPPECEICSCNLTVK 180 (220)
Q Consensus 158 h~~~~~~~~~p~C~~Cg~~eTv~ 180 (220)
..|=+++ ++..|++||..+.+.
T Consensus 18 kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 18 KFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred hhccCCC-CCccCCCCCCccCcc
Confidence 3456788 777899999887666
No 17
>PRK08298 cytidine deaminase; Validated
Probab=64.58 E-value=7 Score=30.81 Aligned_cols=56 Identities=18% Similarity=0.086 Sum_probs=35.3
Q ss_pred eecCCCCCCcceeeeeCCCcceeeecchhh----hhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccc
Q psy4359 20 YTDASKNDSSVSAAFWSPDFSFKVKLNPLL----SICNAELMAILYAVYFILANCLSEARNSSFLLCTDS 85 (220)
Q Consensus 20 yTDgSk~~~~~G~ai~~~~~~~~~~l~~~~----si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS 85 (220)
|...| +||+|+...+..+..|..-+. .-..||..||..|+..-. +....+.|.+|.
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 55556 899998865555544443222 236899999998874421 135566677665
No 18
>PRK05578 cytidine deaminase; Validated
Probab=54.93 E-value=14 Score=28.85 Aligned_cols=59 Identities=24% Similarity=0.039 Sum_probs=36.4
Q ss_pred eecCCCCCCcceeeeeCCCcceeeecchhhh----hhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccch
Q psy4359 20 YTDASKNDSSVSAAFWSPDFSFKVKLNPLLS----ICNAELMAILYAVYFILANCLSEARNSSFLLCTDSL 86 (220)
Q Consensus 20 yTDgSk~~~~~G~ai~~~~~~~~~~l~~~~s----i~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~ 86 (220)
|.-.|+. .||+|+...+..+..|..-++. -..||..||..|+..-. .....+.|.+|+.
T Consensus 18 y~PyS~f--~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G~------~~i~~i~vv~~~~ 80 (131)
T PRK05578 18 YAPYSKF--PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGG------GRLVAIACVGETG 80 (131)
T ss_pred CCCcCCC--ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHcCC------CceEEEEEEecCC
Confidence 3334544 5999988655555444333322 35899999999974321 2456778887763
No 19
>PRK12411 cytidine deaminase; Provisional
Probab=53.69 E-value=14 Score=28.94 Aligned_cols=51 Identities=22% Similarity=0.027 Sum_probs=33.7
Q ss_pred cceeeeeCCCcceeeecchhhhhh----hHHHHHHHHHHHHHHHhhhhhhccCceEEeccc
Q psy4359 29 SVSAAFWSPDFSFKVKLNPLLSIC----NAELMAILYAVYFILANCLSEARNSSFLLCTDS 85 (220)
Q Consensus 29 ~~G~ai~~~~~~~~~~l~~~~si~----~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS 85 (220)
.||+|+...+..+..|..-++..| .||..||..|+..-. .....+.|.+|.
T Consensus 25 ~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~g~------~~i~~i~v~~~~ 79 (132)
T PRK12411 25 QVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGD------KEFVAIAIVADT 79 (132)
T ss_pred ceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHCCC------CceEEEEEEeCC
Confidence 589988866655555544444444 899999999864421 235677777765
No 20
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=50.70 E-value=8 Score=30.20 Aligned_cols=22 Identities=5% Similarity=0.098 Sum_probs=16.7
Q ss_pred eeeecccCCCCccceecccccHH
Q psy4359 158 HVHLMKKEQPPECEICSCNLTVK 180 (220)
Q Consensus 158 h~~~~~~~~~p~C~~Cg~~eTv~ 180 (220)
..|-+++ ++..|++||....+.
T Consensus 18 kFYDLnk-~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 18 KFYDLNR-RPAVSPYTGEQFPPE 39 (129)
T ss_pred cccccCC-CCccCCCcCCccCcc
Confidence 3455777 889999999876555
No 21
>PF00035 dsrm: Double-stranded RNA binding motif; InterPro: IPR001159 The DsRBD domain is found in a variety of RNA-binding proteins with different structures and exhibiting a diversity of functions []. It is involved in localisation of at least five different mRNAs in the early Drosophila embryo and by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.; GO: 0003725 double-stranded RNA binding, 0005622 intracellular; PDB: 1EKZ_A 1STU_A 1QU6_A 2L2M_A 3ADJ_A 1WHN_A 3LLH_B 2B7V_A 2L3J_A 1UHZ_A ....
Probab=50.03 E-value=68 Score=20.72 Aligned_cols=63 Identities=14% Similarity=0.039 Sum_probs=37.7
Q ss_pred cchhHHHHhhhCCCceeee---ecCCCCC-CcceeeeeCCCcceeeecchhhhhhhHHHHHHHHHHHHH
Q psy4359 2 IKSSFLEIVSKYPQSTKIY---TDASKND-SSVSAAFWSPDFSFKVKLNPLLSICNAELMAILYAVYFI 66 (220)
Q Consensus 2 ~~~~f~~i~~~~~~~~~Iy---TDgSk~~-~~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~ 66 (220)
+++.++++.+++.-....| .+|.... ...-+.+..++..+. -....|-=.||..|...||+.+
T Consensus 1 ~~~~L~e~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~i~~~~~~--~g~g~sKk~Ak~~AA~~al~~L 67 (67)
T PF00035_consen 1 PKSRLNEYCQKNKFPPPYYYIEEEGPSHHRPRFICTVYIDGKEYG--EGEGSSKKEAKQQAAKKALQKL 67 (67)
T ss_dssp HHHHHHHHHHHCTSSEEEEEEEEESSSSSSEEEEEEEEETTEEEE--EEEESSHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCCCEEEEEEeCCCCCCceEEEEEEECCEEEe--EeccCCHHHHHHHHHHHHHHhC
Confidence 4567888777666555555 3333332 233334444554333 3334588999999999999863
No 22
>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=49.86 E-value=19 Score=27.78 Aligned_cols=51 Identities=20% Similarity=0.023 Sum_probs=32.6
Q ss_pred cceeeeeCCCcceeeecchhhhh----hhHHHHHHHHHHHHHHHhhhhhhccCceEEeccc
Q psy4359 29 SVSAAFWSPDFSFKVKLNPLLSI----CNAELMAILYAVYFILANCLSEARNSSFLLCTDS 85 (220)
Q Consensus 29 ~~G~ai~~~~~~~~~~l~~~~si----~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS 85 (220)
.+|++++..+..+..+..-+... ..||..||..|...-. .....+.|..+.
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 48888885554444444444333 4799999999886522 146677787765
No 23
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=47.55 E-value=23 Score=27.88 Aligned_cols=51 Identities=22% Similarity=0.096 Sum_probs=33.6
Q ss_pred cceeeeeCCCcceeeecchhhhh----hhHHHHHHHHHHHHHHHhhhhhhccCceEEeccc
Q psy4359 29 SVSAAFWSPDFSFKVKLNPLLSI----CNAELMAILYAVYFILANCLSEARNSSFLLCTDS 85 (220)
Q Consensus 29 ~~G~ai~~~~~~~~~~l~~~~si----~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS 85 (220)
.||+++...+..+.+|..=+... -.||..||..|+.. -. .....+.|++|+
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~-----~~~~~v~v~~~~ 81 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GK-----RKFDAVVVVADT 81 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CC-----CcEEEEEEEcCC
Confidence 58888774443343332222222 57999999999887 22 257789999998
No 24
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=46.80 E-value=19 Score=23.29 Aligned_cols=26 Identities=15% Similarity=0.370 Sum_probs=20.6
Q ss_pred CCccceecccccHHHHHHHHHhcccC
Q psy4359 167 PPECEICSCNLTVKHLLKYCLKYQNI 192 (220)
Q Consensus 167 ~p~C~~Cg~~eTv~HiL~~Cp~~~~~ 192 (220)
+-.|++||...++.-++..|......
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~ 27 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRS 27 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcC
Confidence 45799999867988888888876543
No 25
>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=45.42 E-value=38 Score=25.01 Aligned_cols=55 Identities=18% Similarity=-0.022 Sum_probs=33.8
Q ss_pred CCcceeeeeCC-Ccceeeecch----hhhhhhHHHHHHHHHHHHHHHhhhhhhccCceEEeccch
Q psy4359 27 DSSVSAAFWSP-DFSFKVKLNP----LLSICNAELMAILYAVYFILANCLSEARNSSFLLCTDSL 86 (220)
Q Consensus 27 ~~~~G~ai~~~-~~~~~~~l~~----~~si~~AEl~AI~~AL~~~~~~~~~~~~~~~~~I~sDS~ 86 (220)
+..+|+.++++ +.....+... .....-||..||..|.+..... .....++++.-.
T Consensus 16 ~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~-----~~~~~~ly~t~E 75 (109)
T cd01285 16 EVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSY-----LLSGCTLYTTLE 75 (109)
T ss_pred CCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCC-----ccCCeEEEEeCC
Confidence 34588888866 3333333322 3467889999999988764332 345667776443
No 26
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=36.69 E-value=76 Score=22.60 Aligned_cols=40 Identities=20% Similarity=0.023 Sum_probs=25.8
Q ss_pred CCCcceeeeeC-CCcceeeecchhh----hhhhHHHHHHHHHHHH
Q psy4359 26 NDSSVSAAFWS-PDFSFKVKLNPLL----SICNAELMAILYAVYF 65 (220)
Q Consensus 26 ~~~~~G~ai~~-~~~~~~~~l~~~~----si~~AEl~AI~~AL~~ 65 (220)
.+..+|++++. .+.....+..... ..--||..||..|-+.
T Consensus 22 ~~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~ 66 (102)
T PF00383_consen 22 GNFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN 66 (102)
T ss_dssp TSSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT
T ss_pred CCCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh
Confidence 34569998887 4455555554443 3346899888888776
No 27
>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=33.93 E-value=9.9 Score=25.33 Aligned_cols=20 Identities=40% Similarity=0.831 Sum_probs=9.8
Q ss_pred ccceecccccHHHHHHHHHh
Q psy4359 169 ECEICSCNLTVKHLLKYCLK 188 (220)
Q Consensus 169 ~C~~Cg~~eTv~HiL~~Cp~ 188 (220)
.|+.||...+-.|....||+
T Consensus 35 ~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 35 VCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp --TTT---GGG---GGG-TT
T ss_pred cCCCCcCcCccccccccCcC
Confidence 79999988888899999996
No 28
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=29.83 E-value=26 Score=23.97 Aligned_cols=17 Identities=18% Similarity=0.473 Sum_probs=12.3
Q ss_pred ecccCCCCccceecccc
Q psy4359 161 LMKKEQPPECEICSCNL 177 (220)
Q Consensus 161 ~~~~~~~p~C~~Cg~~e 177 (220)
++--+|...|+.||.++
T Consensus 12 ~l~~~d~e~CP~Cgs~~ 28 (64)
T COG2093 12 RLTPEDTEICPVCGSTD 28 (64)
T ss_pred ccCCCCCccCCCCCCcc
Confidence 45556677799999764
No 29
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=27.84 E-value=13 Score=32.81 Aligned_cols=22 Identities=36% Similarity=0.400 Sum_probs=14.2
Q ss_pred ccccccce-EEeEEeecccccce
Q psy4359 137 TFSRRDQV-TLTRLRIGHTNLTH 158 (220)
Q Consensus 137 ~l~R~~~~-~l~rlRtGH~~l~h 158 (220)
.|+.+--| .|.||||.|-..+|
T Consensus 206 GlsGrLRvGALsqLrTehrPCtY 228 (311)
T PF15322_consen 206 GLSGRLRVGALSQLRTEHRPCTY 228 (311)
T ss_pred ccccceecchhhhhhhccCCccc
Confidence 34444333 78888888887765
No 30
>KOG1123|consensus
Probab=27.54 E-value=70 Score=31.11 Aligned_cols=30 Identities=23% Similarity=0.383 Sum_probs=22.2
Q ss_pred HHHHHHHHhhhhhhccCceEEeccchHHHHhh
Q psy4359 61 YAVYFILANCLSEARNSSFLLCTDSLSALQSL 92 (220)
Q Consensus 61 ~AL~~~~~~~~~~~~~~~~~I~sDS~sal~ai 92 (220)
.|.+++.+.. ++.+.++++||||..||+.-
T Consensus 530 raCqfLI~~H--E~RgDKiIVFsDnvfALk~Y 559 (776)
T KOG1123|consen 530 RACQFLIKFH--ERRGDKIIVFSDNVFALKEY 559 (776)
T ss_pred HHHHHHHHHH--HhcCCeEEEEeccHHHHHHH
Confidence 4556666542 34689999999999999953
No 31
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=26.18 E-value=51 Score=25.21 Aligned_cols=25 Identities=16% Similarity=0.264 Sum_probs=18.0
Q ss_pred cchhHHHHhhhCCCc--eeeeecCCCC
Q psy4359 2 IKSSFLEIVSKYPQS--TKIYTDASKN 26 (220)
Q Consensus 2 ~~~~f~~i~~~~~~~--~~IyTDgSk~ 26 (220)
|+.-|.-+.++.+.. +.+||||=..
T Consensus 69 f~pvf~~~~~~~~~~~~vi~fTDg~~~ 95 (126)
T PF09967_consen 69 FRPVFEYLEENRPRPSVVIYFTDGEGW 95 (126)
T ss_pred chHHHHHHHhcCCCCCEEEEEeCCCCC
Confidence 677888887755555 3459998874
No 32
>PF07057 TraI: DNA helicase TraI; InterPro: IPR009767 This entry represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI. TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer [].; GO: 0003677 DNA binding, 0003678 DNA helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0000746 conjugation; PDB: 3FLD_B.
Probab=25.10 E-value=24 Score=27.50 Aligned_cols=15 Identities=27% Similarity=0.490 Sum_probs=0.0
Q ss_pred hhCCCceeeeecCCC
Q psy4359 11 SKYPQSTKIYTDASK 25 (220)
Q Consensus 11 ~~~~~~~~IyTDgSk 25 (220)
+.-++|+.||||+-.
T Consensus 4 SRaKeHVQvYTDn~~ 18 (126)
T PF07057_consen 4 SRAKEHVQVYTDNLE 18 (126)
T ss_dssp ---------------
T ss_pred hhhhheeeeEeCCHH
Confidence 455788999999753
No 33
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.48 E-value=24 Score=23.12 Aligned_cols=8 Identities=25% Similarity=0.833 Sum_probs=6.6
Q ss_pred ccceeccc
Q psy4359 169 ECEICSCN 176 (220)
Q Consensus 169 ~C~~Cg~~ 176 (220)
.|++||+.
T Consensus 2 ~CPyCge~ 9 (52)
T PF14255_consen 2 QCPYCGEP 9 (52)
T ss_pred CCCCCCCe
Confidence 59999965
No 34
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=23.88 E-value=1.1e+02 Score=25.03 Aligned_cols=39 Identities=18% Similarity=0.098 Sum_probs=23.3
Q ss_pred CcceeeeeCCCcceeeecc----hhhhhhhHHHHHHHHHHHHH
Q psy4359 28 SSVSAAFWSPDFSFKVKLN----PLLSICNAELMAILYAVYFI 66 (220)
Q Consensus 28 ~~~G~ai~~~~~~~~~~l~----~~~si~~AEl~AI~~AL~~~ 66 (220)
..+|+.||..+.....+-. .....--||..||..|.+..
T Consensus 33 ~pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~ 75 (172)
T PRK10860 33 VPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVL 75 (172)
T ss_pred CCEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhc
Confidence 3588877765543332211 11234569999999987644
No 35
>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=22.81 E-value=1.3e+02 Score=22.66 Aligned_cols=38 Identities=13% Similarity=-0.123 Sum_probs=25.2
Q ss_pred CcceeeeeCC-CcceeeecchhhhhhhHHHHHHHHHHHH
Q psy4359 28 SSVSAAFWSP-DFSFKVKLNPLLSICNAELMAILYAVYF 65 (220)
Q Consensus 28 ~~~G~ai~~~-~~~~~~~l~~~~si~~AEl~AI~~AL~~ 65 (220)
..+|+.++.+ +.....+........-||..||.+|.+.
T Consensus 19 ~pvGaviv~~~g~iv~~g~n~~~~~~HAE~~ai~~a~~~ 57 (115)
T cd01284 19 PPVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEK 57 (115)
T ss_pred CCEEEEEEeCCCeEEEEecCCCCCcccHHHHHHHHHhhc
Confidence 3588888865 4333433333336678999999998764
No 36
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=22.80 E-value=25 Score=20.81 Aligned_cols=17 Identities=24% Similarity=0.581 Sum_probs=13.8
Q ss_pred ccceecccccHHHHHHHHHh
Q psy4359 169 ECEICSCNLTVKHLLKYCLK 188 (220)
Q Consensus 169 ~C~~Cg~~eTv~HiL~~Cp~ 188 (220)
.|-.|+... |.+-+||.
T Consensus 10 ~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 10 VCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred EeecCCCCC---ccHhHCCC
Confidence 577787654 99999998
No 37
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=22.74 E-value=38 Score=20.97 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=9.0
Q ss_pred CCCccceecccc
Q psy4359 166 QPPECEICSCNL 177 (220)
Q Consensus 166 ~~p~C~~Cg~~e 177 (220)
|+..|+.||..+
T Consensus 1 e~~~C~~Cg~~l 12 (47)
T PF13005_consen 1 EPRACPDCGGEL 12 (47)
T ss_pred CCCcCCCCCcee
Confidence 567899998653
No 38
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=21.98 E-value=34 Score=22.11 Aligned_cols=13 Identities=31% Similarity=0.741 Sum_probs=6.8
Q ss_pred ccceecccccHHH
Q psy4359 169 ECEICSCNLTVKH 181 (220)
Q Consensus 169 ~C~~Cg~~eTv~H 181 (220)
.||.||.+.+-+|
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999997766555
No 39
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=21.53 E-value=29 Score=26.54 Aligned_cols=17 Identities=24% Similarity=0.534 Sum_probs=13.0
Q ss_pred cccCCCCccceecccccHH
Q psy4359 162 MKKEQPPECEICSCNLTVK 180 (220)
Q Consensus 162 ~~~~~~p~C~~Cg~~eTv~ 180 (220)
++++| .|.+|++++|.+
T Consensus 82 LGr~D--~CM~C~~pLTLd 98 (114)
T PF11023_consen 82 LGRVD--ACMHCKEPLTLD 98 (114)
T ss_pred hchhh--ccCcCCCcCccC
Confidence 46664 999999988765
No 40
>KOG2893|consensus
Probab=20.60 E-value=60 Score=28.32 Aligned_cols=26 Identities=23% Similarity=0.326 Sum_probs=19.3
Q ss_pred cccCCCCccceecccccHHHHHHHHH
Q psy4359 162 MKKEQPPECEICSCNLTVKHLLKYCL 187 (220)
Q Consensus 162 ~~~~~~p~C~~Cg~~eTv~HiL~~Cp 187 (220)
-++++-|.|-||+.+.+=+-||++-.
T Consensus 5 kkk~~kpwcwycnrefddekiliqhq 30 (341)
T KOG2893|consen 5 KKKVDKPWCWYCNREFDDEKILIQHQ 30 (341)
T ss_pred ccccCCceeeecccccchhhhhhhhh
Confidence 46789999999997766666666533
No 41
>KOG1930|consensus
Probab=20.54 E-value=35 Score=32.00 Aligned_cols=62 Identities=27% Similarity=0.349 Sum_probs=42.9
Q ss_pred cccCCCCCCCCccccccceEEeE--------Eeeccccc-ceeeecccCCCCc-cc-eecc--cccHHHHHHHHHh
Q psy4359 126 KEENKPWHPPQTFSRRDQVTLTR--------LRIGHTNL-THVHLMKKEQPPE-CE-ICSC--NLTVKHLLKYCLK 188 (220)
Q Consensus 126 ~~~~~~w~~~~~l~R~~~~~l~r--------lRtGH~~l-~h~~~~~~~~~p~-C~-~Cg~--~eTv~HiL~~Cp~ 188 (220)
+.+.|.|..+ +++|.+.+.|-| +|--|++. .|+--|++..+|- -. .=|. .|-|+|+|+||-.
T Consensus 208 ~DTSKyWYKP-~isREQAIalLrdkePGtFvvRDS~SfrGayGLAlKVstPPPs~~~~~g~~~neLVRHFLIE~sp 282 (483)
T KOG1930|consen 208 KDTSKYWYKP-NISREQAIALLRDKEPGTFVVRDSHSFRGAYGLALKVSTPPPSVQPGDGSDSNELVRHFLIEPSP 282 (483)
T ss_pred ecccccccCC-CCCHHHHHHHhhcCCCCeEEEecCCcCCCccceEEEeccCCCcccCCCCCchhhhhhhheeccCC
Confidence 3467788776 899988776644 58888885 4666688876553 22 1232 3899999999863
No 42
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.44 E-value=49 Score=19.51 Aligned_cols=13 Identities=38% Similarity=1.009 Sum_probs=9.7
Q ss_pred cCCCCccceeccc
Q psy4359 164 KEQPPECEICSCN 176 (220)
Q Consensus 164 ~~~~p~C~~Cg~~ 176 (220)
...+..|+.||.+
T Consensus 15 ~~~p~~CP~Cg~~ 27 (34)
T cd00729 15 EEAPEKCPICGAP 27 (34)
T ss_pred CcCCCcCcCCCCc
Confidence 3466799999964
Done!