Query psy12035
Match_columns 251
No_of_seqs 193 out of 746
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 16:57:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12035.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12035hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.1 1.2E-10 2.6E-15 93.9 6.7 84 27-113 40-143 (161)
2 PRK08719 ribonuclease H; Revie 99.1 2.3E-10 5E-15 91.2 7.4 79 27-111 48-146 (147)
3 PRK00203 rnhA ribonuclease H; 99.1 2.9E-10 6.4E-15 90.9 6.6 83 28-113 42-143 (150)
4 COG0328 RnhA Ribonuclease HI [ 99.1 1.7E-10 3.6E-15 91.8 4.9 104 9-113 20-146 (154)
5 PF00075 RNase_H: RNase H; In 99.0 5.2E-10 1.1E-14 86.7 5.6 81 26-110 37-131 (132)
6 KOG3752|consensus 98.2 2.3E-06 5.1E-11 76.4 6.0 103 6-110 229-363 (371)
7 cd06222 RnaseH RNase H (RNase 98.0 1.4E-05 3E-10 59.9 5.8 102 7-109 14-129 (130)
8 PF13966 zf-RVT: zinc-binding 96.6 0.0011 2.5E-08 47.6 1.8 31 183-213 50-83 (86)
9 PRK13907 rnhA ribonuclease H; 95.5 0.027 5.9E-07 43.2 5.0 79 28-111 40-126 (128)
10 PRK07708 hypothetical protein; 91.1 0.64 1.4E-05 39.4 6.1 85 27-115 116-211 (219)
11 PF13456 RVT_3: Reverse transc 89.5 0.81 1.8E-05 31.8 4.6 75 31-110 3-85 (87)
12 PRK07238 bifunctional RNase H/ 89.2 0.55 1.2E-05 42.9 4.5 81 28-113 44-133 (372)
13 PF00098 zf-CCHC: Zinc knuckle 52.0 10 0.00022 18.8 1.2 15 194-211 2-18 (18)
14 PF05741 zf-nanos: Nanos RNA b 48.3 8.4 0.00018 25.3 0.7 19 193-211 34-54 (55)
15 PF04863 EGF_alliinase: Alliin 47.8 4.2 9.1E-05 26.5 -0.7 23 175-198 19-41 (56)
16 PF13696 zf-CCHC_2: Zinc knuck 44.8 10 0.00022 22.0 0.6 17 192-211 8-26 (32)
17 PF15322 PMSI1: Protein missin 43.7 13 0.00028 32.5 1.4 16 168-183 213-228 (311)
18 KOG1994|consensus 33.5 12 0.00026 31.8 -0.4 32 168-213 229-263 (268)
19 PF15216 TSLP: Thymic stromal 32.1 54 0.0012 25.0 2.9 12 88-99 80-91 (124)
20 COG0296 GlgB 1,4-alpha-glucan 28.0 49 0.0011 32.6 2.7 26 78-103 223-248 (628)
21 PF00325 Crp: Bacterial regula 27.7 98 0.0021 17.8 2.9 25 224-248 8-32 (32)
22 KOG2463|consensus 25.7 51 0.0011 29.7 2.1 35 215-250 43-79 (376)
23 PF13821 DUF4187: Domain of un 24.6 23 0.00049 23.1 -0.2 20 194-213 29-51 (55)
24 KOG4602|consensus 24.0 39 0.00085 29.3 1.1 21 192-212 268-290 (318)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.12 E-value=1.2e-10 Score=93.88 Aligned_cols=84 Identities=20% Similarity=0.194 Sum_probs=61.6
Q ss_pred hhhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhhh----------------HHH----HHHhhCCCceE
Q psy12035 27 DTIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAK----------------QEY----YFASTNGSQIS 86 (251)
Q Consensus 27 ~~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~k----------------~~~----~~~~~~~~~i~ 86 (251)
.+-+++|+.|++.|++..+.....+ -|.+||.++.+.+.+++.+ +++ ..+. ....|+
T Consensus 40 ~TNnraEl~Aii~aL~~~~~~~~~v--~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~-~~~~v~ 116 (161)
T PRK06548 40 ATNNIAELTAVRELLIATRHTDRPI--LILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLM-ENRNIR 116 (161)
T ss_pred CCHHHHHHHHHHHHHHhhhcCCceE--EEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHH-hcCceE
Confidence 4459999999999998765443333 4889999988877654431 111 1112 235799
Q ss_pred EEeeccCCCCccchHHhHHHhhhhcCC
Q psy12035 87 FMWIPSHSNIALNDKADQLAKNSINSK 113 (251)
Q Consensus 87 ~~WvPgH~gI~GNE~AD~lAk~a~~~~ 113 (251)
|.|||||+|.+|||.||+||++|+...
T Consensus 117 ~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 117 MSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred EEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999987543
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.11 E-value=2.3e-10 Score=91.16 Aligned_cols=79 Identities=16% Similarity=0.107 Sum_probs=59.7
Q ss_pred hhhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhhh----------------HHH----HHHhhCCCceE
Q psy12035 27 DTIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAK----------------QEY----YFASTNGSQIS 86 (251)
Q Consensus 27 ~~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~k----------------~~~----~~~~~~~~~i~ 86 (251)
.+-+++|+.|++.||+...... -|.+|+.++.+.+.+++.+ .++ ..+. ....|+
T Consensus 48 ~Tnn~aEl~A~~~aL~~~~~~~-----~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~-~~~~i~ 121 (147)
T PRK08719 48 TDNAELELLALIEALEYARDGD-----VIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELR-ARKYVE 121 (147)
T ss_pred ccHHHHHHHHHHHHHHHcCCCC-----EEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHh-CCCcEE
Confidence 4669999999999999876542 4889998888766443321 111 1122 356799
Q ss_pred EEeeccCCCCccchHHhHHHhhhhc
Q psy12035 87 FMWIPSHSNIALNDKADQLAKNSIN 111 (251)
Q Consensus 87 ~~WvPgH~gI~GNE~AD~lAk~a~~ 111 (251)
|.|||||+|++|||.||++|++|+.
T Consensus 122 ~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 122 VEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred EEEecCCCCChhHHHHHHHHHHHhh
Confidence 9999999999999999999999864
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.07 E-value=2.9e-10 Score=90.87 Aligned_cols=83 Identities=19% Similarity=0.227 Sum_probs=59.4
Q ss_pred hhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhhh----------------HHH-HHH--hhCCCceEEE
Q psy12035 28 TIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAK----------------QEY-YFA--STNGSQISFM 88 (251)
Q Consensus 28 ~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~k----------------~~~-~~~--~~~~~~i~~~ 88 (251)
+-+++|+++++.||+..+... ..-|.+|+.++...+..+..+ +++ ..+ ......|.|.
T Consensus 42 TN~~aEL~Ai~~AL~~~~~~~---~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~ 118 (150)
T PRK00203 42 TNNRMELMAAIEALEALKEPC---EVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWH 118 (150)
T ss_pred cHHHHHHHHHHHHHHHcCCCC---eEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEE
Confidence 448999999999999776532 234889998776555442220 111 011 1234789999
Q ss_pred eeccCCCCccchHHhHHHhhhhcCC
Q psy12035 89 WIPSHSNIALNDKADQLAKNSINSK 113 (251)
Q Consensus 89 WvPgH~gI~GNE~AD~lAk~a~~~~ 113 (251)
|||||+|++|||.||++||+|+..+
T Consensus 119 wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 119 WVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred EecCCCCCHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999987654
No 4
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.06 E-value=1.7e-10 Score=91.84 Aligned_cols=104 Identities=19% Similarity=0.196 Sum_probs=72.5
Q ss_pred chhchhccccchhhh--hhhhhh-hHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhhh-----------H-
Q psy12035 9 DYGCSIFMNANKKYL--SHLDTI-HHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAK-----------Q- 73 (251)
Q Consensus 9 ~Yga~iw~~~~~~~~--~~l~~~-~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~k-----------~- 73 (251)
.||+.+++...+... ....++ +++|+++++.||+.... .-....-+.+||.++.+.+..++.+ +
T Consensus 20 G~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~-~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~p 98 (154)
T COG0328 20 GWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKE-LGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKP 98 (154)
T ss_pred eEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHh-cCCceEEEEecHHHHHHHHHHHHhhccccCccccccCc
Confidence 478888865543311 122333 99999999999987663 1112234889999998888766542 1
Q ss_pred --------HHHHHhhCCCceEEEeeccCCCCccchHHhHHHhhhhcCC
Q psy12035 74 --------EYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNSINSK 113 (251)
Q Consensus 74 --------~~~~~~~~~~~i~~~WvPgH~gI~GNE~AD~lAk~a~~~~ 113 (251)
++..+..+-..|.+.|||||.|.++||.||+||+.|+...
T Consensus 99 vkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 99 VKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred cccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 1122234445899999999999999999999999987664
No 5
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.01 E-value=5.2e-10 Score=86.73 Aligned_cols=81 Identities=23% Similarity=0.333 Sum_probs=58.7
Q ss_pred hhhhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhhh-------------HHHHHHhhCCCceEEEeecc
Q psy12035 26 LDTIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAK-------------QEYYFASTNGSQISFMWIPS 92 (251)
Q Consensus 26 l~~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~k-------------~~~~~~~~~~~~i~~~WvPg 92 (251)
..+.+++|+.++..|++.. .. ....|.+|+..+...+.++..+ .++.....++..|.|.||||
T Consensus 37 ~~s~~~aEl~Ai~~AL~~~-~~---~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~ 112 (132)
T PF00075_consen 37 GQSNNRAELQAIIEALKAL-EH---RKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPG 112 (132)
T ss_dssp SECHHHHHHHHHHHHHHTH-ST---SEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSS
T ss_pred ccchhhhheehHHHHHHHh-hc---ccccccccHHHHHHHHHHhccccccccccccccchhheeeccccceEEeeeeccC
Confidence 6777999999999999954 22 2234889998877654442211 11222225588999999999
Q ss_pred CCCC-ccchHHhHHHhhhh
Q psy12035 93 HSNI-ALNDKADQLAKNSI 110 (251)
Q Consensus 93 H~gI-~GNE~AD~lAk~a~ 110 (251)
|+|+ .|||.||++||+|+
T Consensus 113 H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 113 HSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp SSSSHHHHHHHHHHHHHHH
T ss_pred cCCCchhHHHHHHHHHHhc
Confidence 9999 69999999999986
No 6
>KOG3752|consensus
Probab=98.21 E-value=2.3e-06 Score=76.39 Aligned_cols=103 Identities=18% Similarity=0.134 Sum_probs=68.5
Q ss_pred cccchhchhccccchhh----hh-hhhhhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhhh--------
Q psy12035 6 PILDYGCSIFMNANKKY----LS-HLDTIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAK-------- 72 (251)
Q Consensus 6 s~~~Yga~iw~~~~~~~----~~-~l~~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~k-------- 72 (251)
|+..||. -|+++.... +. -..+-+|++|.||..|++.+...-+. -.-|.+|+..+......++..
T Consensus 229 ~~AGyGv-ywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~-kv~I~TDS~~~i~~l~~wv~~~k~~~~k~ 306 (371)
T KOG3752|consen 229 SRAGYGV-YWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNIN-KVVIRTDSEYFINSLTLWVQGWKKNGWKT 306 (371)
T ss_pred CcceeEE-eeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCC-cEEEEechHHHHHHHHHHHhhhccCcccc
Confidence 4556664 355554322 22 34455999999999999876443332 124788888877655444431
Q ss_pred -------------H----HHHHH-hh-CCCceEEEeeccCCCCccchHHhHHHhhhh
Q psy12035 73 -------------Q----EYYFA-ST-NGSQISFMWIPSHSNIALNDKADQLAKNSI 110 (251)
Q Consensus 73 -------------~----~~~~~-~~-~~~~i~~~WvPgH~gI~GNE~AD~lAk~a~ 110 (251)
+ ++..+ +. ++..|++.|||||.||.|||+||.+|++++
T Consensus 307 ~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs 363 (371)
T KOG3752|consen 307 SNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGS 363 (371)
T ss_pred ccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence 0 01122 22 568999999999999999999999999874
No 7
>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=98.00 E-value=1.4e-05 Score=59.85 Aligned_cols=102 Identities=18% Similarity=0.107 Sum_probs=61.3
Q ss_pred ccchhchhccccchhh---hh--hhhhhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhh-----hH---
Q psy12035 7 ILDYGCSIFMNANKKY---LS--HLDTIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIA-----KQ--- 73 (251)
Q Consensus 7 ~~~Yga~iw~~~~~~~---~~--~l~~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~-----k~--- 73 (251)
...||..++....... .. .-.+.+.+|+.++..|++..-.... ...-|..|+..+...+.+... ..
T Consensus 14 ~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~-~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~ 92 (130)
T cd06222 14 PAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGG-KKVNIYTDSQYVINALTGWYEGKPVKNVDLW 92 (130)
T ss_pred ceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCC-ceEEEEECHHHHHHHhhccccCCChhhHHHH
Confidence 3456666665432111 11 3456689999999999977421111 111256666655544432110 00
Q ss_pred -HHHHHhhCCCceEEEeeccCCCCccchHHhHHHhhh
Q psy12035 74 -EYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNS 109 (251)
Q Consensus 74 -~~~~~~~~~~~i~~~WvPgH~gI~GNE~AD~lAk~a 109 (251)
.+.........+++.|||+|+|+.+|+.||.+||+|
T Consensus 93 ~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 93 QRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred HHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence 011112367889999999999999999999999986
No 8
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.61 E-value=0.0011 Score=47.59 Aligned_cols=31 Identities=29% Similarity=0.556 Sum_probs=26.3
Q ss_pred cccccCCCCCCCc-cCCC-Ccccceec-cccCch
Q psy12035 183 HSYLFTKTPHPIC-TCGF-PLTVKHIF-ECNKYK 213 (251)
Q Consensus 183 ~l~~~~~~~~~~C-~Cg~-~et~~Hil-~Cp~~~ 213 (251)
.+++.+...++.| .||. .||++|+| +||...
T Consensus 50 ~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 50 NLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred hhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 4667777889999 9995 99999999 999764
No 9
>PRK13907 rnhA ribonuclease H; Provisional
Probab=95.53 E-value=0.027 Score=43.24 Aligned_cols=79 Identities=23% Similarity=0.161 Sum_probs=50.9
Q ss_pred hhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhhhhhH--------HHHHHhhCCCceEEEeeccCCCCccc
Q psy12035 28 TIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNIIAKQ--------EYYFASTNGSQISFMWIPSHSNIALN 99 (251)
Q Consensus 28 ~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~~~k~--------~~~~~~~~~~~i~~~WvPgH~gI~GN 99 (251)
+-+.+|+.+++.|++......... .-+.+|+..+...+.+...+. ++..+..+-..+.+.|||.+ +|
T Consensus 40 tn~~AE~~All~aL~~a~~~g~~~-v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N 114 (128)
T PRK13907 40 SNHEAEYHALLAALKYCTEHNYNI-VSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QN 114 (128)
T ss_pred CCcHHHHHHHHHHHHHHHhCCCCE-EEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hc
Confidence 458899999999998655432211 236688877765554321111 11122334456778999995 79
Q ss_pred hHHhHHHhhhhc
Q psy12035 100 DKADQLAKNSIN 111 (251)
Q Consensus 100 E~AD~lAk~a~~ 111 (251)
+.||.+|+.|..
T Consensus 115 ~~Ad~LA~~a~~ 126 (128)
T PRK13907 115 KVADELARKAIL 126 (128)
T ss_pred hhHHHHHHHHHh
Confidence 999999999864
No 10
>PRK07708 hypothetical protein; Validated
Probab=91.06 E-value=0.64 Score=39.45 Aligned_cols=85 Identities=12% Similarity=-0.004 Sum_probs=52.4
Q ss_pred hhhhHHHHHHHHhhhccCCccchhhh-ccccchHHHHHHHHhhhh-hhH----HHH-----HHhhCCCceEEEeeccCCC
Q psy12035 27 DTIHHMGIRLISRALKSSPVNSLYAE-SAILPLSVRRRLLFSNII-AKQ----EYY-----FASTNGSQISFMWIPSHSN 95 (251)
Q Consensus 27 ~~~~r~~l~~i~~a~rt~~~~~~~~~-~~i~p~~l~~~~~~~~~~-~k~----~~~-----~~~~~~~~i~~~WvPgH~g 95 (251)
.+-+.++..|++.|++.......... .-|..|+..+...+.... .+. .|. .+..-...+.+.|||..
T Consensus 116 ~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~-- 193 (219)
T PRK07708 116 YDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK-- 193 (219)
T ss_pred ccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch--
Confidence 45588899999999987654332111 135677777665543211 111 111 11233445788999885
Q ss_pred CccchHHhHHHhhhhcCCCC
Q psy12035 96 IALNDKADQLAKNSINSKLL 115 (251)
Q Consensus 96 I~GNE~AD~lAk~a~~~~~~ 115 (251)
-|+.||.||+.|.....+
T Consensus 194 --~N~~AD~LAk~Al~~~~~ 211 (219)
T PRK07708 194 --QNKEADQLATQALEGTVI 211 (219)
T ss_pred --hhhHHHHHHHHHHhcCCC
Confidence 499999999999876543
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=89.46 E-value=0.81 Score=31.80 Aligned_cols=75 Identities=17% Similarity=0.008 Sum_probs=40.9
Q ss_pred HHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhhh-hhh-------HHHHHHhhCCCceEEEeeccCCCCccchHH
Q psy12035 31 HMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSNI-IAK-------QEYYFASTNGSQISFMWIPSHSNIALNDKA 102 (251)
Q Consensus 31 r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~~-~~k-------~~~~~~~~~~~~i~~~WvPgH~gI~GNE~A 102 (251)
-+|+.++..|++....-.... .-+.+|+..+...+.+. ..+ +++..+..+-..+.+.|||. ++|..|
T Consensus 3 ~aE~~al~~al~~a~~~g~~~-i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r----~~N~~A 77 (87)
T PF13456_consen 3 EAEALALLEALQLAWELGIRK-IIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPR----EQNKVA 77 (87)
T ss_dssp HHHHHHHHHHHHHHHCCT-SC-EEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--G----GGSHHH
T ss_pred HHHHHHHHHHHHHHHHCCCCE-EEEEecCccccccccccccccccccccchhhhhhhccccceEEEEECh----HHhHHH
Confidence 357777777776544322211 12456666555444221 000 11122344567899999998 569999
Q ss_pred hHHHhhhh
Q psy12035 103 DQLAKNSI 110 (251)
Q Consensus 103 D~lAk~a~ 110 (251)
|.+||.|.
T Consensus 78 ~~LA~~a~ 85 (87)
T PF13456_consen 78 DALAKFAL 85 (87)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 99999875
No 12
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=89.20 E-value=0.55 Score=42.87 Aligned_cols=81 Identities=19% Similarity=0.171 Sum_probs=50.8
Q ss_pred hhhHHHHHHHHhhhccCCccchhhhccccchHHHHHHHHhh-hhhhH--------HHHHHhhCCCceEEEeeccCCCCcc
Q psy12035 28 TIHHMGIRLISRALKSSPVNSLYAESAILPLSVRRRLLFSN-IIAKQ--------EYYFASTNGSQISFMWIPSHSNIAL 98 (251)
Q Consensus 28 ~~~r~~l~~i~~a~rt~~~~~~~~~~~i~p~~l~~~~~~~~-~~~k~--------~~~~~~~~~~~i~~~WvPgH~gI~G 98 (251)
+-+.+|+.+++.|++......... .-+.+|+..+...+.. +..++ ++..+..+-..+++.|||. .+
T Consensus 44 tnn~AE~~All~gL~~a~~~g~~~-v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~ 118 (372)
T PRK07238 44 TNNVAEYRGLIAGLEAAAELGATE-VEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----AR 118 (372)
T ss_pred CchHHHHHHHHHHHHHHHhCCCCe-EEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hh
Confidence 337899999999998655421111 1356777766654432 11111 1112233446799999998 67
Q ss_pred chHHhHHHhhhhcCC
Q psy12035 99 NDKADQLAKNSINSK 113 (251)
Q Consensus 99 NE~AD~lAk~a~~~~ 113 (251)
|+.||.+|+.|....
T Consensus 119 N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 119 NAHADRLANEAMDAA 133 (372)
T ss_pred hhHHHHHHHHHHHhh
Confidence 999999999986444
No 13
>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=52.00 E-value=10 Score=18.80 Aligned_cols=15 Identities=47% Similarity=1.008 Sum_probs=11.2
Q ss_pred Cc-cCCCCcccceec-cccC
Q psy12035 194 IC-TCGFPLTVKHIF-ECNK 211 (251)
Q Consensus 194 ~C-~Cg~~et~~Hil-~Cp~ 211 (251)
.| .||+ ..|+. +||.
T Consensus 2 ~C~~C~~---~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGE---PGHIARDCPK 18 (18)
T ss_dssp BCTTTSC---SSSCGCTSSS
T ss_pred cCcCCCC---cCcccccCcc
Confidence 57 7884 46999 9984
No 14
>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=48.34 E-value=8.4 Score=25.26 Aligned_cols=19 Identities=32% Similarity=0.655 Sum_probs=8.1
Q ss_pred CCc-cCCCCcccceec-cccC
Q psy12035 193 PIC-TCGFPLTVKHIF-ECNK 211 (251)
Q Consensus 193 ~~C-~Cg~~et~~Hil-~Cp~ 211 (251)
-.| .||+..+-.|.. .||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 468 899999999999 9996
No 15
>PF04863 EGF_alliinase: Alliinase EGF-like domain; InterPro: IPR006947 Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system [].; GO: 0016846 carbon-sulfur lyase activity; PDB: 1LK9_B 2HOX_C 2HOR_A.
Probab=47.85 E-value=4.2 Score=26.54 Aligned_cols=23 Identities=26% Similarity=0.511 Sum_probs=12.3
Q ss_pred hcCccccccccccCCCCCCCccCC
Q psy12035 175 RIGHTRITHSYLFTKTPHPICTCG 198 (251)
Q Consensus 175 rtGH~~~~~l~~~~~~~~~~C~Cg 198 (251)
-+|||+. |+--+.....|.|+|.
T Consensus 19 CSGHGr~-flDg~~~dG~p~CECn 41 (56)
T PF04863_consen 19 CSGHGRA-FLDGLIADGSPVCECN 41 (56)
T ss_dssp -TTSEE---TTS-EETTEE--EE-
T ss_pred cCCCCee-eeccccccCCcccccc
Confidence 4899998 7665555567999886
No 16
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=44.79 E-value=10 Score=21.95 Aligned_cols=17 Identities=29% Similarity=0.765 Sum_probs=13.1
Q ss_pred CCCc-cCCCCcccceec-cccC
Q psy12035 192 HPIC-TCGFPLTVKHIF-ECNK 211 (251)
Q Consensus 192 ~~~C-~Cg~~et~~Hil-~Cp~ 211 (251)
+=.| .|+... |++ +||.
T Consensus 8 ~Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CCEeecCCCCC---ccHhHCCC
Confidence 4568 888543 999 9997
No 17
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=43.71 E-value=13 Score=32.52 Aligned_cols=16 Identities=31% Similarity=0.227 Sum_probs=13.7
Q ss_pred HHhHhhhhcCcccccc
Q psy12035 168 EILLTRLRIGHTRITH 183 (251)
Q Consensus 168 ~~~l~qlrtGH~~~~~ 183 (251)
...|.||||.|-.++|
T Consensus 213 vGALsqLrTehrPCtY 228 (311)
T PF15322_consen 213 VGALSQLRTEHRPCTY 228 (311)
T ss_pred cchhhhhhhccCCccc
Confidence 4569999999999984
No 18
>KOG1994|consensus
Probab=33.47 E-value=12 Score=31.80 Aligned_cols=32 Identities=22% Similarity=0.456 Sum_probs=23.2
Q ss_pred HHhHhhhhcCccccccccccCCCCCCCc-cCCC-Ccccceec-cccCch
Q psy12035 168 EILLTRLRIGHTRITHSYLFTKTPHPIC-TCGF-PLTVKHIF-ECNKYK 213 (251)
Q Consensus 168 ~~~l~qlrtGH~~~~~l~~~~~~~~~~C-~Cg~-~et~~Hil-~Cp~~~ 213 (251)
..++.-||.||- +| .||. ..|.+-++ +||--.
T Consensus 229 t~in~~LR~eh~--------------YC~fCG~~y~~~edl~ehCPGvn 263 (268)
T KOG1994|consen 229 TKINIFLRSEHY--------------YCFFCGIKYKDEEDLYEHCPGVN 263 (268)
T ss_pred HHHHHHHhccce--------------EEEEeccccCCHHHHHHhCCCCC
Confidence 445566666654 47 8995 89999999 999653
No 19
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=32.06 E-value=54 Score=24.97 Aligned_cols=12 Identities=25% Similarity=0.432 Sum_probs=10.5
Q ss_pred EeeccCCCCccc
Q psy12035 88 MWIPSHSNIALN 99 (251)
Q Consensus 88 ~WvPgH~gI~GN 99 (251)
.|+||+++++-|
T Consensus 80 ~~CPGyse~QiN 91 (124)
T PF15216_consen 80 NYCPGYSETQIN 91 (124)
T ss_pred HhCCCcchhhcc
Confidence 489999998888
No 20
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=27.99 E-value=49 Score=32.61 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=22.4
Q ss_pred HhhCCCceEEEeeccCCCCccchHHh
Q psy12035 78 ASTNGSQISFMWIPSHSNIALNDKAD 103 (251)
Q Consensus 78 ~~~~~~~i~~~WvPgH~gI~GNE~AD 103 (251)
+...|..|-+-|||+|.+..||-.+-
T Consensus 223 aH~~GIgViLD~V~~HF~~d~~~L~~ 248 (628)
T COG0296 223 AHQAGIGVILDWVPNHFPPDGNYLAR 248 (628)
T ss_pred HHHcCCEEEEEecCCcCCCCcchhhh
Confidence 36789999999999999999987653
No 21
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=27.66 E-value=98 Score=17.80 Aligned_cols=25 Identities=16% Similarity=0.135 Sum_probs=21.1
Q ss_pred HHhhcCCChHHHHHHHHHHHHhccc
Q psy12035 224 IEIALSDNENMAEKTIKYMKMINLY 248 (251)
Q Consensus 224 l~~~l~~~~~~~~~i~~fi~~t~~~ 248 (251)
+...+|-..+.+..+++-+++.|++
T Consensus 8 iA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 8 IADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 7788898889999999999998874
No 22
>KOG2463|consensus
Probab=25.74 E-value=51 Score=29.74 Aligned_cols=35 Identities=31% Similarity=0.515 Sum_probs=25.6
Q ss_pred HhhhCC-Ccc-HHhhcCCChHHHHHHHHHHHHhccccC
Q psy12035 215 FREKLS-LPS-IEIALSDNENMAEKTIKYMKMINLYSK 250 (251)
Q Consensus 215 ~R~~l~-~~~-l~~~l~~~~~~~~~i~~fi~~t~~~~~ 250 (251)
.|..|. +|+ +... .|.++.++++++|.+.||=|+-
T Consensus 43 sRk~le~~pf~i~~r-ePspe~v~kV~~fak~TGDyss 79 (376)
T KOG2463|consen 43 SRKRLEFLPFTIKLR-EPSPEYVRKVIKFAKLTGDYSS 79 (376)
T ss_pred hhcchhhcccEEEEe-cCCHHHHHHHHHHHHhcCCccc
Confidence 344443 566 5544 6778999999999999997763
No 23
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=24.56 E-value=23 Score=23.15 Aligned_cols=20 Identities=20% Similarity=0.370 Sum_probs=15.4
Q ss_pred Cc-cCCC-Ccccceec-cccCch
Q psy12035 194 IC-TCGF-PLTVKHIF-ECNKYK 213 (251)
Q Consensus 194 ~C-~Cg~-~et~~Hil-~Cp~~~ 213 (251)
.| +||. ..+.+=+. .||-..
T Consensus 29 YC~~Cg~~Y~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDLERNCPGPT 51 (55)
T ss_pred eeeeeCCccCCHHHHHhCCCCCC
Confidence 57 8995 78888888 998643
No 24
>KOG4602|consensus
Probab=24.01 E-value=39 Score=29.31 Aligned_cols=21 Identities=24% Similarity=0.471 Sum_probs=18.5
Q ss_pred CCCc-cCCCCcccceec-cccCc
Q psy12035 192 HPIC-TCGFPLTVKHIF-ECNKY 212 (251)
Q Consensus 192 ~~~C-~Cg~~et~~Hil-~Cp~~ 212 (251)
+-.| .||...+-.|.+ .||.-
T Consensus 268 ~YVCPiCGATgDnAHTiKyCPl~ 290 (318)
T KOG4602|consen 268 SYVCPICGATGDNAHTIKYCPLA 290 (318)
T ss_pred hhcCccccccCCcccceeccccc
Confidence 5679 999998999999 99975
Done!