Query psy2786
Match_columns 198
No_of_seqs 137 out of 965
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 16:50:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2786.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2786hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00075 RNase_H: RNase H; In 99.3 9.1E-13 2E-17 97.7 1.7 67 2-74 49-130 (132)
2 PRK08719 ribonuclease H; Revie 99.2 1.6E-11 3.4E-16 93.7 4.0 68 2-76 59-146 (147)
3 PRK00203 rnhA ribonuclease H; 99.1 3E-11 6.4E-16 92.3 3.0 70 3-76 53-141 (150)
4 PRK06548 ribonuclease H; Provi 99.1 5.9E-11 1.3E-15 91.6 2.5 71 3-76 52-141 (161)
5 cd06222 RnaseH RNase H (RNase 98.9 4E-09 8.7E-14 75.7 5.7 70 3-74 51-129 (130)
6 COG0328 RnhA Ribonuclease HI [ 98.8 1.1E-08 2.3E-13 78.2 5.6 72 3-76 53-144 (154)
7 KOG3752|consensus 98.2 2.5E-06 5.4E-11 73.0 5.1 74 2-77 265-365 (371)
8 PRK13907 rnhA ribonuclease H; 97.1 0.00055 1.2E-08 50.4 3.3 66 3-74 51-124 (128)
9 PF13966 zf-RVT: zinc-binding 97.0 0.00051 1.1E-08 47.3 2.3 40 141-180 38-83 (86)
10 PRK07708 hypothetical protein; 96.2 0.0062 1.3E-07 49.4 4.1 72 3-79 128-210 (219)
11 PF13456 RVT_3: Reverse transc 96.1 0.0054 1.2E-07 41.3 2.9 66 3-74 11-84 (87)
12 PRK07238 bifunctional RNase H/ 95.3 0.022 4.9E-07 49.5 4.3 66 3-74 55-129 (372)
13 PF04863 EGF_alliinase: Alliin 42.6 5.1 0.00011 25.1 -0.9 25 141-166 18-42 (56)
14 COG0296 GlgB 1,4-alpha-glucan 41.4 28 0.00061 32.8 3.2 28 42-69 222-249 (628)
15 PF15216 TSLP: Thymic stromal 37.5 10 0.00023 27.6 -0.1 77 19-106 39-122 (124)
16 PF05741 zf-nanos: Nanos RNA b 37.3 10 0.00022 23.8 -0.2 19 160-178 34-54 (55)
17 PF07754 DUF1610: Domain of un 28.1 43 0.00093 17.3 1.3 17 162-178 1-21 (24)
18 PF06839 zf-GRF: GRF zinc fing 26.5 42 0.00092 19.8 1.3 14 168-181 19-33 (45)
19 PRK12380 hydrogenase nickel in 26.0 25 0.00054 25.3 0.2 22 159-180 70-93 (113)
20 TIGR00100 hypA hydrogenase nic 23.7 30 0.00066 25.0 0.3 21 159-179 70-92 (115)
21 COG4744 Uncharacterized conser 22.7 51 0.0011 23.9 1.3 14 49-66 106-119 (121)
22 KOG3600|consensus 22.1 13 0.00028 37.6 -2.3 55 133-187 1925-1992(2238)
23 PRK03681 hypA hydrogenase nick 21.7 39 0.00085 24.3 0.6 22 159-180 70-94 (114)
24 PF08274 PhnA_Zn_Ribbon: PhnA 20.4 29 0.00063 19.0 -0.3 18 160-177 3-23 (30)
No 1
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.29 E-value=9.1e-13 Score=97.67 Aligned_cols=67 Identities=30% Similarity=0.433 Sum_probs=46.2
Q ss_pred hhhhhhhcCCCCCCeEEEEecchhhhccCCCC-------CC---c----hhHHHHHHHhCCeEEEEEecCCCCC-CcchH
Q psy2786 2 SYAVKIASCPANPTYSLLFPDNIDADIYPPNK-------PK---P----LCLRVHLLCYGKQLAFLWCPSHTGI-QGNEA 66 (198)
Q Consensus 2 ~~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~~-------~~---~----~~~~~~l~~~~~~i~l~WvPgH~gI-~GNE~ 66 (198)
..||+.+ . ...+.|||||+++ +..++. +. . ..+...+ ..+..|.|.|||||+|+ .|||.
T Consensus 49 ~~AL~~~--~--~~~v~I~tDS~~v-~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~ 122 (132)
T PF00075_consen 49 IEALKAL--E--HRKVTIYTDSQYV-LNALNKWLHGNGWKKTSNGRPIKNEIWELL-SRGIKVRFRWVPGHSGVPQGNER 122 (132)
T ss_dssp HHHHHTH--S--TSEEEEEES-HHH-HHHHHTHHHHTTSBSCTSSSBHTHHHHHHH-HHSSEEEEEESSSSSSSHHHHHH
T ss_pred HHHHHHh--h--cccccccccHHHH-HHHHHHhccccccccccccccchhheeecc-ccceEEeeeeccCcCCCchhHHH
Confidence 3567733 1 2788899999999 442221 11 1 1222333 55899999999999999 69999
Q ss_pred HHHHHhCC
Q psy2786 67 VDRAARNP 74 (198)
Q Consensus 67 AD~aAk~a 74 (198)
||++||.+
T Consensus 123 aD~lAk~a 130 (132)
T PF00075_consen 123 ADRLAKEA 130 (132)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 99999865
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.19 E-value=1.6e-11 Score=93.68 Aligned_cols=68 Identities=26% Similarity=0.275 Sum_probs=46.5
Q ss_pred hhhhhhhcCCCCCCeEEEEecchhhhccCCC----------------CCCc-hhH-HH--HHHHhCCeEEEEEecCCCCC
Q psy2786 2 SYAVKIASCPANPTYSLLFPDNIDADIYPPN----------------KPKP-LCL-RV--HLLCYGKQLAFLWCPSHTGI 61 (198)
Q Consensus 2 ~~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~----------------~~~~-~~~-~~--~l~~~~~~i~l~WvPgH~gI 61 (198)
..||+.+... ..|+|||+-+ +..++ .|.. ..+ +. .+. ....|+|.|||||+|+
T Consensus 59 ~~aL~~~~~~-----~~i~tDS~yv-i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~-~~~~i~~~~VkgH~g~ 131 (147)
T PRK08719 59 IEALEYARDG-----DVIYSDSDYC-VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELR-ARKYVEVEKVTAHSGI 131 (147)
T ss_pred HHHHHHcCCC-----CEEEechHHH-HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHh-CCCcEEEEEecCCCCC
Confidence 3577777643 2689999999 65541 1111 111 11 122 3567999999999999
Q ss_pred CcchHHHHHHhCCCC
Q psy2786 62 QGNEAVDRAARNPSA 76 (198)
Q Consensus 62 ~GNE~AD~aAk~a~~ 76 (198)
+|||.||++|+.|+.
T Consensus 132 ~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 132 EGNEAADMLAQAAAE 146 (147)
T ss_pred hhHHHHHHHHHHHhh
Confidence 999999999998753
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.12 E-value=3e-11 Score=92.34 Aligned_cols=70 Identities=21% Similarity=0.206 Sum_probs=47.7
Q ss_pred hhhhhhcCCCCCCeEEEEecchhhhccCCCC----------------CCch-hH-HHHH-HHhCCeEEEEEecCCCCCCc
Q psy2786 3 YAVKIASCPANPTYSLLFPDNIDADIYPPNK----------------PKPL-CL-RVHL-LCYGKQLAFLWCPSHTGIQG 63 (198)
Q Consensus 3 ~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~~----------------~~~~-~~-~~~l-~~~~~~i~l~WvPgH~gI~G 63 (198)
.||+.+.. ...+.|||||+.+ +..++. |... .+ +.+. ......|.|.|||||+|++|
T Consensus 53 ~AL~~~~~---~~~v~I~tDS~yv-i~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~~ 128 (150)
T PRK00203 53 EALEALKE---PCEVTLYTDSQYV-RQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHPE 128 (150)
T ss_pred HHHHHcCC---CCeEEEEECHHHH-HHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCHH
Confidence 56776653 2468899999999 554331 2111 11 1111 12347899999999999999
Q ss_pred chHHHHHHhCCCC
Q psy2786 64 NEAVDRAARNPSA 76 (198)
Q Consensus 64 NE~AD~aAk~a~~ 76 (198)
||.||++|+.+..
T Consensus 129 N~~AD~lA~~a~~ 141 (150)
T PRK00203 129 NERCDELARAGAE 141 (150)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999987754
No 4
>PRK06548 ribonuclease H; Provisional
Probab=99.07 E-value=5.9e-11 Score=91.61 Aligned_cols=71 Identities=21% Similarity=0.202 Sum_probs=46.8
Q ss_pred hhhhhhcCCCCCCeEEEEecchhhhccCCC---------CCCch--------hH-HHHH-HHhCCeEEEEEecCCCCCCc
Q psy2786 3 YAVKIASCPANPTYSLLFPDNIDADIYPPN---------KPKPL--------CL-RVHL-LCYGKQLAFLWCPSHTGIQG 63 (198)
Q Consensus 3 ~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~---------~~~~~--------~~-~~~l-~~~~~~i~l~WvPgH~gI~G 63 (198)
.||+.+..+ ...+.|||||+-+ +..++ ....+ .+ +.+. ......|+|.|||||+|++|
T Consensus 52 ~aL~~~~~~--~~~v~I~TDS~yv-i~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg~~g 128 (161)
T PRK06548 52 ELLIATRHT--DRPILILSDSKYV-INSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTGHPL 128 (161)
T ss_pred HHHHhhhcC--CceEEEEeChHHH-HHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCCCHH
Confidence 466544422 2458899999999 65543 22111 11 1111 12235799999999999999
Q ss_pred chHHHHHHhCCCC
Q psy2786 64 NEAVDRAARNPSA 76 (198)
Q Consensus 64 NE~AD~aAk~a~~ 76 (198)
||.||++|++++.
T Consensus 129 Ne~aD~LA~~aa~ 141 (161)
T PRK06548 129 NEAADSLARQAAN 141 (161)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999987653
No 5
>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=98.87 E-value=4e-09 Score=75.73 Aligned_cols=70 Identities=26% Similarity=0.309 Sum_probs=50.7
Q ss_pred hhhhhhcCCCCCCeEEEEecchhhhccCCCCCC---chhHHH------HHHHhCCeEEEEEecCCCCCCcchHHHHHHhC
Q psy2786 3 YAVKIASCPANPTYSLLFPDNIDADIYPPNKPK---PLCLRV------HLLCYGKQLAFLWCPSHTGIQGNEAVDRAARN 73 (198)
Q Consensus 3 ~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~~~~---~~~~~~------~l~~~~~~i~l~WvPgH~gI~GNE~AD~aAk~ 73 (198)
.|++.+.. .....+.|++||+.+ +...+.+. +..... .+...+..+.|.|||+|+|+++|+.||.+|+.
T Consensus 51 ~al~~~~~-~~~~~i~i~~Ds~~~-~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 51 EALELALE-LGGKKVNIYTDSQYV-INALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred HHHHHHHh-CCCceEEEEECHHHH-HHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 46777663 345777899999999 66665543 122111 11235789999999999999999999999987
Q ss_pred C
Q psy2786 74 P 74 (198)
Q Consensus 74 a 74 (198)
+
T Consensus 129 ~ 129 (130)
T cd06222 129 A 129 (130)
T ss_pred h
Confidence 5
No 6
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.79 E-value=1.1e-08 Score=78.19 Aligned_cols=72 Identities=21% Similarity=0.191 Sum_probs=50.1
Q ss_pred hhhhhhcCCCCCCeEEEEecchhhhccCCC---------CCCchh--------H-HH--HHHHhCCeEEEEEecCCCCCC
Q psy2786 3 YAVKIASCPANPTYSLLFPDNIDADIYPPN---------KPKPLC--------L-RV--HLLCYGKQLAFLWCPSHTGIQ 62 (198)
Q Consensus 3 ~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~---------~~~~~~--------~-~~--~l~~~~~~i~l~WvPgH~gI~ 62 (198)
+||+.+.. .....+.|+|||+-+ +..++ .+.... + +. .+...-..|.+.|||||.|.+
T Consensus 53 ~AL~~l~~-~~~~~v~l~tDS~yv-~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~ 130 (154)
T COG0328 53 EALEALKE-LGACEVTLYTDSKYV-VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHP 130 (154)
T ss_pred HHHHHHHh-cCCceEEEEecHHHH-HHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCCh
Confidence 68888885 345778899999999 44432 222111 1 11 223333499999999999999
Q ss_pred cchHHHHHHhCCCC
Q psy2786 63 GNEAVDRAARNPSA 76 (198)
Q Consensus 63 GNE~AD~aAk~a~~ 76 (198)
+||+||++|+.+..
T Consensus 131 ~NeraD~LA~~~~~ 144 (154)
T COG0328 131 ENERADQLAREAAR 144 (154)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999976643
No 7
>KOG3752|consensus
Probab=98.17 E-value=2.5e-06 Score=73.03 Aligned_cols=74 Identities=23% Similarity=0.183 Sum_probs=51.6
Q ss_pred hhhhhhhcCCCCCCeEEEEecchhhhccCCC---------------CCCchh--------H--HH-HHHH-hCCeEEEEE
Q psy2786 2 SYAVKIASCPANPTYSLLFPDNIDADIYPPN---------------KPKPLC--------L--RV-HLLC-YGKQLAFLW 54 (198)
Q Consensus 2 ~~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~---------------~~~~~~--------~--~~-~l~~-~~~~i~l~W 54 (198)
..||+-|.+... ..++|.|||.=. |..++ .+...+ + .. +++. .+..|++.|
T Consensus 265 ~~ALkka~~~~~-~kv~I~TDS~~~-i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~ 342 (371)
T KOG3752|consen 265 IEALKKARSKNI-NKVVIRTDSEYF-INSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEY 342 (371)
T ss_pred HHHHHHHHhcCC-CcEEEEechHHH-HHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEE
Confidence 468888876544 477899999988 55432 111001 0 11 2222 468999999
Q ss_pred ecCCCCCCcchHHHHHHhCCCCC
Q psy2786 55 CPSHTGIQGNEAVDRAARNPSAS 77 (198)
Q Consensus 55 vPgH~gI~GNE~AD~aAk~a~~~ 77 (198)
||||.||.|||+||.+|+.++.+
T Consensus 343 V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 343 VGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred ecCcCCcchHHHHHHHHhhhhhh
Confidence 99999999999999999987654
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=97.07 E-value=0.00055 Score=50.44 Aligned_cols=66 Identities=18% Similarity=0.077 Sum_probs=43.5
Q ss_pred hhhhhhcCCCCCCeEEEEecchhhhccCCCCCC-----chhH-HH--HHHHhCCeEEEEEecCCCCCCcchHHHHHHhCC
Q psy2786 3 YAVKIASCPANPTYSLLFPDNIDADIYPPNKPK-----PLCL-RV--HLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP 74 (198)
Q Consensus 3 ~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~~~~-----~~~~-~~--~l~~~~~~i~l~WvPgH~gI~GNE~AD~aAk~a 74 (198)
.||+.|.... ...+.|++||+-. +..++... .... +. .+...-..+.|.|||.+ .|+.||.+|+.+
T Consensus 51 ~aL~~a~~~g-~~~v~i~sDS~~v-i~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a 124 (128)
T PRK13907 51 AALKYCTEHN-YNIVSFRTDSQLV-ERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKA 124 (128)
T ss_pred HHHHHHHhCC-CCEEEEEechHHH-HHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHH
Confidence 4677777544 3568889999999 66655421 1111 11 11233346778999994 899999999865
No 9
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.97 E-value=0.00051 Score=47.30 Aligned_cols=40 Identities=20% Similarity=0.392 Sum_probs=30.4
Q ss_pred eeecccccc---cccccCCCCCCCc-ccCC-CCCcceeee-ccccH
Q psy2786 141 MRIGHTRAT---HGHLFKRAPPSTC-RCGE-TLSVQHILT-CTLHG 180 (198)
Q Consensus 141 lrtGH~~~~---hl~~~~~~~~p~C-~Cg~-~~t~~Hil~-Cp~~~ 180 (198)
.+.-|.++. -+.+.+...++.| .|+. .||++|+|+ ||...
T Consensus 38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 38 WRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred eeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 444555554 4566777889999 9997 899999999 99654
No 10
>PRK07708 hypothetical protein; Validated
Probab=96.20 E-value=0.0062 Score=49.41 Aligned_cols=72 Identities=10% Similarity=-0.076 Sum_probs=45.9
Q ss_pred hhhhhhcCCCCC-CeEEEEecchhhhccCCCCC------CchhH----HHHHHHhCCeEEEEEecCCCCCCcchHHHHHH
Q psy2786 3 YAVKIASCPANP-TYSLLFPDNIDADIYPPNKP------KPLCL----RVHLLCYGKQLAFLWCPSHTGIQGNEAVDRAA 71 (198)
Q Consensus 3 ~a~~~~~~~~~~-~~~~i~sDn~aa~i~~~~~~------~~~~~----~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~aA 71 (198)
.||+.|...+-. ..+.|++||+-+ +..++.- .-... ...+......+.+.|||-. -|+.||++|
T Consensus 128 ~aL~~A~e~g~~~~~V~I~~DSqlV-i~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~----~N~~AD~LA 202 (219)
T PRK07708 128 YAMQELEELGVKHEPVTFRGDSQVV-LNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK----QNKEADQLA 202 (219)
T ss_pred HHHHHHHHcCCCcceEEEEeccHHH-HHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch----hhhHHHHHH
Confidence 577777765432 347889999999 5554432 11111 1123334456788899774 599999999
Q ss_pred hCCCCCCC
Q psy2786 72 RNPSASLP 79 (198)
Q Consensus 72 k~a~~~~~ 79 (198)
+.|....+
T Consensus 203 k~Al~~~~ 210 (219)
T PRK07708 203 TQALEGTV 210 (219)
T ss_pred HHHHhcCC
Confidence 98876543
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=96.12 E-value=0.0054 Score=41.29 Aligned_cols=66 Identities=17% Similarity=0.018 Sum_probs=41.5
Q ss_pred hhhhhhcCCCCCCeEEEEecchhhhccCCCCCCch--hH----HH--HHHHhCCeEEEEEecCCCCCCcchHHHHHHhCC
Q psy2786 3 YAVKIASCPANPTYSLLFPDNIDADIYPPNKPKPL--CL----RV--HLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNP 74 (198)
Q Consensus 3 ~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~~~~~~--~~----~~--~l~~~~~~i~l~WvPgH~gI~GNE~AD~aAk~a 74 (198)
.||++|..-+ -+.+.|+|||+.+ +..++..... .. +. .+...-..+.|.|||-- +|..||.+||.+
T Consensus 11 ~al~~a~~~g-~~~i~v~sDs~~v-v~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~----~N~~A~~LA~~a 84 (87)
T PF13456_consen 11 EALQLAWELG-IRKIIVESDSQLV-VDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPRE----QNKVADALAKFA 84 (87)
T ss_dssp HHHHHHHCCT--SCEEEEES-HHH-HHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GG----GSHHHHHHHHHH
T ss_pred HHHHHHHHCC-CCEEEEEecCccc-cccccccccccccccccchhhhhhhccccceEEEEEChH----HhHHHHHHHHHH
Confidence 5788888655 5677889999999 6665543211 11 11 22333578999999974 799999999854
No 12
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=95.31 E-value=0.022 Score=49.52 Aligned_cols=66 Identities=15% Similarity=0.099 Sum_probs=44.1
Q ss_pred hhhhhhcCCCCCCeEEEEecchhhhccCCCCCC---chhHHH------HHHHhCCeEEEEEecCCCCCCcchHHHHHHhC
Q psy2786 3 YAVKIASCPANPTYSLLFPDNIDADIYPPNKPK---PLCLRV------HLLCYGKQLAFLWCPSHTGIQGNEAVDRAARN 73 (198)
Q Consensus 3 ~a~~~~~~~~~~~~~~i~sDn~aa~i~~~~~~~---~~~~~~------~l~~~~~~i~l~WvPgH~gI~GNE~AD~aAk~ 73 (198)
.||+.+.... ...+.|++||+-+ +..++.-. ...... .+...-..+.+.|||. .+|+.||.+|+.
T Consensus 55 ~gL~~a~~~g-~~~v~i~~DS~lv-i~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~ 128 (372)
T PRK07238 55 AGLEAAAELG-ATEVEVRMDSKLV-VEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANE 128 (372)
T ss_pred HHHHHHHhCC-CCeEEEEeCcHHH-HHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHH
Confidence 5778777554 3578899999999 66555321 111111 1223336799999998 689999998875
Q ss_pred C
Q psy2786 74 P 74 (198)
Q Consensus 74 a 74 (198)
+
T Consensus 129 a 129 (372)
T PRK07238 129 A 129 (372)
T ss_pred H
Confidence 4
No 13
>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=42.60 E-value=5.1 Score=25.14 Aligned_cols=25 Identities=24% Similarity=0.360 Sum_probs=12.1
Q ss_pred eeecccccccccccCCCCCCCcccCC
Q psy2786 141 MRIGHTRATHGHLFKRAPPSTCRCGE 166 (198)
Q Consensus 141 lrtGH~~~~hl~~~~~~~~p~C~Cg~ 166 (198)
-=+|||+. |+--+-....|.|.|+.
T Consensus 18 ~CSGHGr~-flDg~~~dG~p~CECn~ 42 (56)
T PF04863_consen 18 SCSGHGRA-FLDGLIADGSPVCECNS 42 (56)
T ss_dssp --TTSEE---TTS-EETTEE--EE-T
T ss_pred CcCCCCee-eeccccccCCccccccC
Confidence 35789987 66555555679998874
No 14
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=41.43 E-value=28 Score=32.77 Aligned_cols=28 Identities=21% Similarity=0.243 Sum_probs=24.5
Q ss_pred HHHHhCCeEEEEEecCCCCCCcchHHHH
Q psy2786 42 HLLCYGKQLAFLWCPSHTGIQGNEAVDR 69 (198)
Q Consensus 42 ~l~~~~~~i~l~WvPgH~gI~GNE~AD~ 69 (198)
...+.|..|-|-|||+|-+..||-++--
T Consensus 222 ~aH~~GIgViLD~V~~HF~~d~~~L~~f 249 (628)
T COG0296 222 AAHQAGIGVILDWVPNHFPPDGNYLARF 249 (628)
T ss_pred HHHHcCCEEEEEecCCcCCCCcchhhhc
Confidence 3467899999999999999999998874
No 15
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=37.52 E-value=10 Score=27.60 Aligned_cols=77 Identities=12% Similarity=0.185 Sum_probs=39.9
Q ss_pred EEecchhhhccC----CCCCCchhH--HHHHH-HhCCeEEEEEecCCCCCCcchHHHHHHhCCCCCCCCCCCCChhhchH
Q psy2786 19 LFPDNIDADIYP----PNKPKPLCL--RVHLL-CYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKP 91 (198)
Q Consensus 19 i~sDn~aa~i~~----~~~~~~~~~--~~~l~-~~~~~i~l~WvPgH~gI~GNE~AD~aAk~a~~~~~~~~~~s~s~~k~ 91 (198)
+|.|+.++.++- ...|.+.+. ...+- .+-.-.--.||||+++++-|.. -..+|+ . +....+.
T Consensus 39 ~~C~~r~~CLtkIe~~Tfnp~~gC~SLa~e~Fa~rT~aaL~~~CPGyse~QiN~t-Q~m~k~----~-----v~~n~Cl- 107 (124)
T PF15216_consen 39 VYCEDRPDCLTKIERLTFNPTPGCPSLAKETFANRTRAALANYCPGYSETQINNT-QAMKKR----K-----VTTNKCL- 107 (124)
T ss_pred cccCCchhHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHHHHhCCCcchhhcchh-HHHHHH----H-----HHHHHHH-
Confidence 578888885544 345665442 22211 1112223469999999999832 122333 0 1111222
Q ss_pred HHHHHHHHHHHhccc
Q psy2786 92 FIHKLIKDLWQNSWS 106 (198)
Q Consensus 92 ~i~~~~~~~Wq~~W~ 106 (198)
..-+.+...|.+-|.
T Consensus 108 eq~s~ll~lWr~f~r 122 (124)
T PF15216_consen 108 EQVSQLLELWRRFSR 122 (124)
T ss_pred HHHHHHHHHHHHHHh
Confidence 233456677877765
No 16
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=37.26 E-value=10 Score=23.85 Aligned_cols=19 Identities=32% Similarity=0.690 Sum_probs=7.9
Q ss_pred CCc-ccCCCCCcceeee-ccc
Q psy2786 160 STC-RCGETLSVQHILT-CTL 178 (198)
Q Consensus 160 p~C-~Cg~~~t~~Hil~-Cp~ 178 (198)
-.| .||+..+-.|... ||+
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 9999988999999 995
No 17
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=28.12 E-value=43 Score=17.32 Aligned_cols=17 Identities=24% Similarity=0.786 Sum_probs=8.1
Q ss_pred c-ccCCCCCc-c-eeee-ccc
Q psy2786 162 C-RCGETLSV-Q-HILT-CTL 178 (198)
Q Consensus 162 C-~Cg~~~t~-~-Hil~-Cp~ 178 (198)
| .||..... + =+-| ||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPn 21 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPN 21 (24)
T ss_pred CccCCCcccCcccCceEeCCC
Confidence 5 67653322 2 2345 664
No 18
>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=26.49 E-value=42 Score=19.75 Aligned_cols=14 Identities=7% Similarity=-0.002 Sum_probs=9.6
Q ss_pred CCcceeee-ccccHH
Q psy2786 168 LSVQHILT-CTLHGH 181 (198)
Q Consensus 168 ~t~~Hil~-Cp~~~~ 181 (198)
++....++ ||.+..
T Consensus 19 ~N~GR~Fy~C~~~~~ 33 (45)
T PF06839_consen 19 PNPGRRFYKCPNYKD 33 (45)
T ss_pred CCCCCcceECCCCCC
Confidence 35567778 887764
No 19
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.04 E-value=25 Score=25.34 Aligned_cols=22 Identities=14% Similarity=0.472 Sum_probs=12.2
Q ss_pred CCCc-ccCCCCCcceeee-ccccH
Q psy2786 159 PSTC-RCGETLSVQHILT-CTLHG 180 (198)
Q Consensus 159 ~p~C-~Cg~~~t~~Hil~-Cp~~~ 180 (198)
.-.| .||....+....+ ||.=.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 70 QAWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred EEEcccCCCEEecCCcCccCcCCC
Confidence 4456 6776555544555 77533
No 20
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=23.65 E-value=30 Score=24.95 Aligned_cols=21 Identities=29% Similarity=0.545 Sum_probs=12.1
Q ss_pred CCCc-ccCCCCCcceeee-cccc
Q psy2786 159 PSTC-RCGETLSVQHILT-CTLH 179 (198)
Q Consensus 159 ~p~C-~Cg~~~t~~Hil~-Cp~~ 179 (198)
.-.| .||....+....+ ||.=
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~C 92 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKC 92 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCC
Confidence 4557 7776555544455 7753
No 21
>COG4744 Uncharacterized conserved protein [Function unknown]
Probab=22.74 E-value=51 Score=23.89 Aligned_cols=14 Identities=36% Similarity=0.686 Sum_probs=10.7
Q ss_pred eEEEEEecCCCCCCcchH
Q psy2786 49 QLAFLWCPSHTGIQGNEA 66 (198)
Q Consensus 49 ~i~l~WvPgH~gI~GNE~ 66 (198)
.=+++|||| +|||.
T Consensus 106 dgr~I~Vp~----~~~~~ 119 (121)
T COG4744 106 DGRVIYVPE----EGNEA 119 (121)
T ss_pred CCeEEEecC----CCCcC
Confidence 447899999 67774
No 22
>KOG3600|consensus
Probab=22.12 E-value=13 Score=37.59 Aligned_cols=55 Identities=31% Similarity=0.526 Sum_probs=37.6
Q ss_pred chhhhhhee-eecccccc-cccccCCC--------CCCCc-ccCC-CCCcceeee-ccccHHhhhhCC
Q psy2786 133 HEEVVICRM-RIGHTRAT-HGHLFKRA--------PPSTC-RCGE-TLSVQHILT-CTLHGHIRASLP 187 (198)
Q Consensus 133 ~~~~~l~ql-rtGH~~~~-hl~~~~~~--------~~p~C-~Cg~-~~t~~Hil~-Cp~~~~~R~~l~ 187 (198)
...+++-|| |+|||-|. ..++.++. -.+.| .||- ..+---||- |..-.+.-..+.
T Consensus 1925 pWRvViGRLGRiGHGElkdWs~LL~k~sLq~~Sk~LKDiCrmCgiSaadsPsILSACLvamEPqgSfv 1992 (2238)
T KOG3600|consen 1925 PWRVVIGRLGRIGHGELKDWSHLLNKTSLQRYSKSLKDICRMCGISAADSPSILSACLVAMEPQGSFV 1992 (2238)
T ss_pred CeeEEeeeccccccchhhHHHHHhchhhHHHHHHHHHHHHHhcCCccCCCHHHHHHHhheecCCCceE
Confidence 445677777 99999998 66666554 36789 9995 445556777 877665554443
No 23
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=21.71 E-value=39 Score=24.33 Aligned_cols=22 Identities=14% Similarity=0.463 Sum_probs=12.1
Q ss_pred CCCc-ccCCCCCc-ceeee-ccccH
Q psy2786 159 PSTC-RCGETLSV-QHILT-CTLHG 180 (198)
Q Consensus 159 ~p~C-~Cg~~~t~-~Hil~-Cp~~~ 180 (198)
.-.| .||....+ .+.++ ||.=.
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcC
Confidence 4557 77764333 45546 77533
No 24
>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=20.37 E-value=29 Score=18.95 Aligned_cols=18 Identities=28% Similarity=0.654 Sum_probs=6.4
Q ss_pred CCc-ccCCCC-Ccceeee-cc
Q psy2786 160 STC-RCGETL-SVQHILT-CT 177 (198)
Q Consensus 160 p~C-~Cg~~~-t~~Hil~-Cp 177 (198)
|.| .|+.+. =.+..++ ||
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 678 898743 3555566 76
Done!