Query psy2213
Match_columns 194
No_of_seqs 134 out of 1549
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 19:06:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2213hhsearch_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 99.5 6.3E-15 1.4E-19 108.5 3.3 65 6-74 57-131 (132)
2 PRK06548 ribonuclease H; Provi 99.5 2.2E-14 4.8E-19 109.7 6.3 70 6-76 61-142 (161)
3 PRK08719 ribonuclease H; Revie 99.5 4.2E-14 9.2E-19 106.9 6.5 66 9-75 69-146 (147)
4 PRK00203 rnhA ribonuclease H; 99.4 4.3E-13 9.3E-18 101.7 6.0 71 6-77 61-143 (150)
5 COG0328 RnhA Ribonuclease HI [ 99.3 3.8E-12 8.1E-17 96.3 6.0 73 4-76 61-145 (154)
6 cd06222 RnaseH RNase H (RNase 99.2 7.6E-11 1.6E-15 84.3 8.2 71 4-74 59-130 (130)
7 KOG3752|consensus 98.7 2.1E-08 4.6E-13 84.8 5.0 71 6-76 276-365 (371)
8 PRK13907 rnhA ribonuclease H; 98.5 3.6E-07 7.9E-12 67.1 5.9 66 6-75 61-126 (128)
9 PF13456 RVT_3: Reverse transc 98.2 2.9E-06 6.4E-11 57.3 4.7 67 4-74 19-85 (87)
10 PRK07238 bifunctional RNase H/ 97.9 4.5E-05 9.8E-10 65.8 7.2 68 5-76 64-132 (372)
11 PRK07708 hypothetical protein; 97.7 9E-05 2E-09 59.6 6.6 67 7-77 141-209 (219)
12 PF13966 zf-RVT: zinc-binding 96.7 0.0011 2.3E-08 45.4 1.9 30 150-179 51-83 (86)
13 COG0296 GlgB 1,4-alpha-glucan 71.2 5.9 0.00013 36.8 4.2 37 32-68 213-249 (628)
14 KOG1994|consensus 42.6 5.6 0.00012 32.1 -0.9 23 157-179 238-263 (268)
15 PF09345 DUF1987: Domain of un 40.8 38 0.00082 23.7 3.1 26 31-56 61-86 (99)
16 PF13821 DUF4187: Domain of un 37.3 8 0.00017 24.1 -0.7 21 159-179 28-51 (55)
17 PF05741 zf-nanos: Nanos RNA b 37.2 12 0.00026 23.3 0.1 19 159-177 34-54 (55)
18 PF06839 zf-GRF: GRF zinc fing 36.0 21 0.00046 20.9 1.1 22 159-180 1-33 (45)
19 PF13696 zf-CCHC_2: Zinc knuck 35.6 19 0.00042 19.8 0.8 18 157-177 7-26 (32)
20 PRK03681 hypA hydrogenase nick 28.7 24 0.00052 25.2 0.6 24 156-179 68-94 (114)
21 PF15216 TSLP: Thymic stromal 26.9 21 0.00044 25.9 -0.1 12 52-63 80-91 (124)
22 PRK12380 hydrogenase nickel in 25.3 27 0.00059 24.9 0.3 24 156-179 68-93 (113)
23 PRK12568 glycogen branching en 24.7 97 0.0021 29.6 3.9 34 31-64 317-350 (730)
24 TIGR00100 hypA hydrogenase nic 23.3 32 0.0007 24.6 0.4 24 156-179 68-93 (115)
25 PF08274 PhnA_Zn_Ribbon: PhnA 23.0 25 0.00054 19.0 -0.2 19 159-177 3-24 (30)
26 PF04863 EGF_alliinase: Alliin 21.1 21 0.00045 22.2 -0.8 25 140-165 18-42 (56)
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=99.52 E-value=6.3e-15 Score=108.53 Aligned_cols=65 Identities=37% Similarity=0.596 Sum_probs=50.9
Q ss_pred CCeEEEEeCcHHHHHHHhC-----CCCCC----hHHHHHHHHHHHHHhcCCcEEEEeecCCCCC-hhhHHHhHHhcCCC
Q psy2213 6 KEKFVIISDSKSTLLALSN-----PSNTN----PIVSLIHSCWSDLLCCGKQLAFLWCPSHTGI-QGNEAVDRAARNPS 74 (194)
Q Consensus 6 ~~~~~i~sDs~~al~~l~~-----~~~~~----~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi-~gNe~AD~~Ak~a~ 74 (194)
...++|+|||++++..|.. .+... ++..+|++. + ..+..|.|.|||||+|+ .|||.||+|||.|+
T Consensus 57 ~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~---~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 57 HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWEL---L-SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHH---H-HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cccccccccHHHHHHHHHHhccccccccccccccchhheeec---c-ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 3789999999999998887 44322 355555533 3 55889999999999999 69999999999875
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.52 E-value=2.2e-14 Score=109.74 Aligned_cols=70 Identities=27% Similarity=0.425 Sum_probs=56.7
Q ss_pred CCeEEEEeCcHHHHHHHh---------CCCCCC--hHH-HHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213 6 KEKFVIISDSKSTLLALS---------NPSNTN--PIV-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP 73 (194)
Q Consensus 6 ~~~~~i~sDs~~al~~l~---------~~~~~~--~~~-~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a 73 (194)
...+.|+|||++++++|. ++...+ ++. +++++.+..+.. ...|+|.|||||+|++|||.||+||++|
T Consensus 61 ~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~-~~~v~~~wVkgHsg~~gNe~aD~LA~~a 139 (161)
T PRK06548 61 DRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLME-NRNIRMSWVNAHTGHPLNEAADSLARQA 139 (161)
T ss_pred CceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHh-cCceEEEEEecCCCCHHHHHHHHHHHHH
Confidence 357999999999999999 333332 444 677777777754 4589999999999999999999999998
Q ss_pred CCC
Q psy2213 74 SAS 76 (194)
Q Consensus 74 ~~~ 76 (194)
+..
T Consensus 140 a~~ 142 (161)
T PRK06548 140 ANN 142 (161)
T ss_pred HHH
Confidence 865
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.50 E-value=4.2e-14 Score=106.92 Aligned_cols=66 Identities=26% Similarity=0.286 Sum_probs=53.7
Q ss_pred EEEEeCcHHHHHHH--------hCCCCCC---hH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCC
Q psy2213 9 FVIISDSKSTLLAL--------SNPSNTN---PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA 75 (194)
Q Consensus 9 ~~i~sDs~~al~~l--------~~~~~~~---~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~ 75 (194)
..|+|||++++++| ++++..+ ++ -.++++.+..+.. ...|+|.|||||+|++|||.||+||+.|++
T Consensus 69 ~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 69 DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 47999999999999 4555443 22 1567777777755 678999999999999999999999999875
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.40 E-value=4.3e-13 Score=101.72 Aligned_cols=71 Identities=20% Similarity=0.278 Sum_probs=54.1
Q ss_pred CCeEEEEeCcHHHHHHHhC--------CCCC---ChHH-HHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCC
Q psy2213 6 KEKFVIISDSKSTLLALSN--------PSNT---NPIV-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNP 73 (194)
Q Consensus 6 ~~~~~i~sDs~~al~~l~~--------~~~~---~~~~-~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a 73 (194)
...+.|+|||++++++|.+ ++.. .++. .++++.+..+. ....|.|.|||||+|++|||.||+||++|
T Consensus 61 ~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a 139 (150)
T PRK00203 61 PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAG 139 (150)
T ss_pred CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHH
Confidence 3579999999999999985 2222 2332 34555555653 34789999999999999999999999998
Q ss_pred CCCC
Q psy2213 74 SASL 77 (194)
Q Consensus 74 ~~~~ 77 (194)
+...
T Consensus 140 ~~~~ 143 (150)
T PRK00203 140 AEEA 143 (150)
T ss_pred HHHh
Confidence 7753
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.31 E-value=3.8e-12 Score=96.25 Aligned_cols=73 Identities=21% Similarity=0.290 Sum_probs=58.0
Q ss_pred CCCCeEEEEeCcHHHHHHHhCC---CCC--------ChH-HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhc
Q psy2213 4 LPKEKFVIISDSKSTLLALSNP---SNT--------NPI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 71 (194)
Q Consensus 4 ~~~~~~~i~sDs~~al~~l~~~---~~~--------~~~-~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak 71 (194)
.....+.|+|||+++++.|..+ +.. .|+ ..++++.+.++......|.+.|||||+|.++||.||+||+
T Consensus 61 ~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~ 140 (154)
T COG0328 61 LGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140 (154)
T ss_pred cCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHH
Confidence 3567899999999999999822 111 122 3467777788866566999999999999999999999999
Q ss_pred CCCCC
Q psy2213 72 NPSAS 76 (194)
Q Consensus 72 ~a~~~ 76 (194)
.++..
T Consensus 141 ~~~~~ 145 (154)
T COG0328 141 EAARA 145 (154)
T ss_pred HHHHh
Confidence 98775
No 6
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.21 E-value=7.6e-11 Score=84.29 Aligned_cols=71 Identities=28% Similarity=0.339 Sum_probs=55.5
Q ss_pred CCCCeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCC
Q psy2213 4 LPKEKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS 74 (194)
Q Consensus 4 ~~~~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~ 74 (194)
.+..++.|++||+.++..+.+.... ......+...+..+...+..+.|.|||+|+|+.+|+.||.+|+.+.
T Consensus 59 ~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 59 LGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred CCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 5678999999999999999987642 2223333334444445688999999999999999999999999863
No 7
>KOG3752|consensus
Probab=98.68 E-value=2.1e-08 Score=84.80 Aligned_cols=71 Identities=27% Similarity=0.259 Sum_probs=52.2
Q ss_pred CCeEEEEeCcHHHHHHHhCCC--------CC---Ch-----H-HHHHHHHHHHHHh--cCCcEEEEeecCCCCChhhHHH
Q psy2213 6 KEKFVIISDSKSTLLALSNPS--------NT---NP-----I-VSLIHSCWSDLLC--CGKQLAFLWCPSHTGIQGNEAV 66 (194)
Q Consensus 6 ~~~~~i~sDs~~al~~l~~~~--------~~---~~-----~-~~~i~~~~~~l~~--~~~~i~~~Wvp~H~gi~gNe~A 66 (194)
..+++|.|||...++.|+.+. .. ++ + .......+.+|.. ++.+|++.|||||.||.|||+|
T Consensus 276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~A 355 (371)
T KOG3752|consen 276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMA 355 (371)
T ss_pred CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHH
Confidence 448999999999999998322 11 22 1 1233334445532 3689999999999999999999
Q ss_pred hHHhcCCCCC
Q psy2213 67 DRAARNPSAS 76 (194)
Q Consensus 67 D~~Ak~a~~~ 76 (194)
|.+|++++..
T Consensus 356 d~lARkgs~~ 365 (371)
T KOG3752|consen 356 DALARKGSTL 365 (371)
T ss_pred HHHHhhhhhh
Confidence 9999998654
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.47 E-value=3.6e-07 Score=67.10 Aligned_cols=66 Identities=17% Similarity=0.134 Sum_probs=50.4
Q ss_pred CCeEEEEeCcHHHHHHHhCCCCCChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCC
Q psy2213 6 KEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA 75 (194)
Q Consensus 6 ~~~~~i~sDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~ 75 (194)
..++.|++||+.+++.+++.+....-...+++.+..+...-..+.|.|||.+ +|+.||.+|+.|..
T Consensus 61 ~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 61 YNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKAIL 126 (128)
T ss_pred CCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHHHh
Confidence 4579999999999999998664433344555555556555667788999995 99999999998753
No 9
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.18 E-value=2.9e-06 Score=57.32 Aligned_cols=67 Identities=19% Similarity=0.136 Sum_probs=46.6
Q ss_pred CCCCeEEEEeCcHHHHHHHhCCCCCChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCC
Q psy2213 4 LPKEKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS 74 (194)
Q Consensus 4 ~~~~~~~i~sDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~ 74 (194)
+..+++.|.|||+.++..|++..........+...+..+......+.|.|||.- +|..||.+||.|.
T Consensus 19 ~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~----~N~~A~~LA~~a~ 85 (87)
T PF13456_consen 19 LGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPRE----QNKVADALAKFAL 85 (87)
T ss_dssp CT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GG----GSHHHHHHHHHHH
T ss_pred CCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChH----HhHHHHHHHHHHh
Confidence 456799999999999999998754422333444445566566788999999975 8999999998764
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.86 E-value=4.5e-05 Score=65.85 Aligned_cols=68 Identities=18% Similarity=0.223 Sum_probs=51.9
Q ss_pred CCCeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhHHhcCCCCC
Q psy2213 5 PKEKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS 76 (194)
Q Consensus 5 ~~~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~~ 76 (194)
..+++.|++||+.+++.+.+.+.. ++-...+.+.+..+...-..+.|.|||. .+|+.||.+|+.|...
T Consensus 64 g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 64 GATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred CCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 456899999999999999976643 3333344445556656667899999998 5899999999987654
No 11
>PRK07708 hypothetical protein; Validated
Probab=97.74 E-value=9e-05 Score=59.61 Aligned_cols=67 Identities=13% Similarity=0.019 Sum_probs=48.9
Q ss_pred CeEEEEeCcHHHHHHHhCCCCC-ChHHHHHHHHHHHHHh-cCCcEEEEeecCCCCChhhHHHhHHhcCCCCCC
Q psy2213 7 EKFVIISDSKSTLLALSNPSNT-NPIVSLIHSCWSDLLC-CGKQLAFLWCPSHTGIQGNEAVDRAARNPSASL 77 (194)
Q Consensus 7 ~~~~i~sDs~~al~~l~~~~~~-~~~~~~i~~~~~~l~~-~~~~i~~~Wvp~H~gi~gNe~AD~~Ak~a~~~~ 77 (194)
..+.|++||+.+++.+.+.+.. ++....+.+.+..+.. -...+.|.|||.. .|+.||+||+.|....
T Consensus 141 ~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~----~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 141 EPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK----QNKEADQLATQALEGT 209 (219)
T ss_pred ceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch----hhhHHHHHHHHHHhcC
Confidence 4589999999999999987644 4444444444444422 2445788999875 6999999999998863
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.67 E-value=0.0011 Score=45.36 Aligned_cols=30 Identities=17% Similarity=0.362 Sum_probs=25.3
Q ss_pred ccccCCCCCCCc-ccCC-CCccceeee-cccch
Q psy2213 150 GHLFKRAPPSTC-GCGE-ILSVQHILT-CALHG 179 (194)
Q Consensus 150 ~~~~~~~~~p~C-~Cg~-~et~~H~l~-Cp~~~ 179 (194)
+.+.+...++.| .|+. .||++|+|+ ||...
T Consensus 51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred hhccCCccCCccccCCCccccccceeccCcCcc
Confidence 445667888999 9998 899999999 99764
No 13
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=71.17 E-value=5.9 Score=36.84 Aligned_cols=37 Identities=16% Similarity=0.155 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHhcCCcEEEEeecCCCCChhhHHHhH
Q psy2213 32 VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDR 68 (194)
Q Consensus 32 ~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe~AD~ 68 (194)
-..++..++.....|.-|-+-|||+|.+..||-++--
T Consensus 213 Pedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~f 249 (628)
T COG0296 213 PEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLARF 249 (628)
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhhc
Confidence 3678888889999999999999999999999987653
No 14
>KOG1994|consensus
Probab=42.57 E-value=5.6 Score=32.12 Aligned_cols=23 Identities=17% Similarity=0.330 Sum_probs=18.6
Q ss_pred CCCCc-ccCC-CCccceeee-cccch
Q psy2213 157 PPSTC-GCGE-ILSVQHILT-CALHG 179 (194)
Q Consensus 157 ~~p~C-~Cg~-~et~~H~l~-Cp~~~ 179 (194)
+.-+| +||. ..|.+-++- ||-..
T Consensus 238 eh~YC~fCG~~y~~~edl~ehCPGvn 263 (268)
T KOG1994|consen 238 EHYYCFFCGIKYKDEEDLYEHCPGVN 263 (268)
T ss_pred cceEEEEeccccCCHHHHHHhCCCCC
Confidence 33468 9998 899999999 99754
No 15
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=40.78 E-value=38 Score=23.69 Aligned_cols=26 Identities=15% Similarity=0.165 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHhcCCcEEEEeecC
Q psy2213 31 IVSLIHSCWSDLLCCGKQLAFLWCPS 56 (194)
Q Consensus 31 ~~~~i~~~~~~l~~~~~~i~~~Wvp~ 56 (194)
.+..|.+.+..+...|..|++.|.--
T Consensus 61 ~l~~i~~~Le~~~~~g~~V~v~Wyyd 86 (99)
T PF09345_consen 61 ALMDIFDLLEDAAQKGGKVTVNWYYD 86 (99)
T ss_pred HHHHHHHHHHHHHhcCCcEEEEEEEC
Confidence 34566666677778899999999754
No 16
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=37.30 E-value=8 Score=24.08 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=16.5
Q ss_pred CCc-ccCC-CCccceeee-cccch
Q psy2213 159 STC-GCGE-ILSVQHILT-CALHG 179 (194)
Q Consensus 159 p~C-~Cg~-~et~~H~l~-Cp~~~ 179 (194)
-.| +||. ..+.+-+.. ||-..
T Consensus 28 ~YC~~Cg~~Y~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLERNCPGPT 51 (55)
T ss_pred ceeeeeCCccCCHHHHHhCCCCCC
Confidence 468 9998 688888888 99654
No 17
>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=37.19 E-value=12 Score=23.34 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=7.9
Q ss_pred CCc-ccCCCCccceeee-ccc
Q psy2213 159 STC-GCGEILSVQHILT-CAL 177 (194)
Q Consensus 159 p~C-~Cg~~et~~H~l~-Cp~ 177 (194)
-.| .||+..+-.|... ||+
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 478 9999888889999 996
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=35.96 E-value=21 Score=20.89 Aligned_cols=22 Identities=23% Similarity=0.419 Sum_probs=15.1
Q ss_pred CCcccCC----------CCccceeee-cccchh
Q psy2213 159 STCGCGE----------ILSVQHILT-CALHGH 180 (194)
Q Consensus 159 p~C~Cg~----------~et~~H~l~-Cp~~~~ 180 (194)
|.|.||. .++....++ ||.+..
T Consensus 1 p~C~Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~ 33 (45)
T PF06839_consen 1 PKCPCGEPAVRRTSKKTGPNPGRRFYKCPNYKD 33 (45)
T ss_pred CCCCCCCEeEEEEEeCCCCCCCCcceECCCCCC
Confidence 5677774 145667888 988775
No 19
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=35.57 E-value=19 Score=19.82 Aligned_cols=18 Identities=33% Similarity=0.840 Sum_probs=13.8
Q ss_pred CCCCc-ccCCCCccceeee-ccc
Q psy2213 157 PPSTC-GCGEILSVQHILT-CAL 177 (194)
Q Consensus 157 ~~p~C-~Cg~~et~~H~l~-Cp~ 177 (194)
++-.| .|+... |++- ||.
T Consensus 7 ~~Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCC---ccHhHCCC
Confidence 45567 787755 9999 998
No 20
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.74 E-value=24 Score=25.24 Aligned_cols=24 Identities=13% Similarity=0.343 Sum_probs=12.8
Q ss_pred CCCCCc-ccCCC-Cccceeee-cccch
Q psy2213 156 APPSTC-GCGEI-LSVQHILT-CALHG 179 (194)
Q Consensus 156 ~~~p~C-~Cg~~-et~~H~l~-Cp~~~ 179 (194)
...-.| .||.. ....+.++ ||.=.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcC
Confidence 344567 67763 33345445 77543
No 21
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=26.94 E-value=21 Score=25.89 Aligned_cols=12 Identities=33% Similarity=0.570 Sum_probs=10.8
Q ss_pred EeecCCCCChhh
Q psy2213 52 LWCPSHTGIQGN 63 (194)
Q Consensus 52 ~Wvp~H~gi~gN 63 (194)
.|+||+++++-|
T Consensus 80 ~~CPGyse~QiN 91 (124)
T PF15216_consen 80 NYCPGYSETQIN 91 (124)
T ss_pred HhCCCcchhhcc
Confidence 489999999988
No 22
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.28 E-value=27 Score=24.94 Aligned_cols=24 Identities=13% Similarity=0.493 Sum_probs=12.6
Q ss_pred CCCCCc-ccCCCCccceeee-cccch
Q psy2213 156 APPSTC-GCGEILSVQHILT-CALHG 179 (194)
Q Consensus 156 ~~~p~C-~Cg~~et~~H~l~-Cp~~~ 179 (194)
...-.| .||..-.+....+ ||.=.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCC
Confidence 344556 6666444444445 66543
No 23
>PRK12568 glycogen branching enzyme; Provisional
Probab=24.71 E-value=97 Score=29.64 Aligned_cols=34 Identities=9% Similarity=0.032 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHhcCCcEEEEeecCCCCChhhH
Q psy2213 31 IVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNE 64 (194)
Q Consensus 31 ~~~~i~~~~~~l~~~~~~i~~~Wvp~H~gi~gNe 64 (194)
...+++..+..+...|..|-+-|||.|++-.++.
T Consensus 317 ~~~dfk~lV~~~H~~Gi~VIlD~V~nH~~~d~~~ 350 (730)
T PRK12568 317 SPDGFAQFVDACHRAGIGVILDWVSAHFPDDAHG 350 (730)
T ss_pred CHHHHHHHHHHHHHCCCEEEEEeccccCCccccc
Confidence 3568888899999999999999999999876543
No 24
>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=23.27 E-value=32 Score=24.62 Aligned_cols=24 Identities=25% Similarity=0.410 Sum_probs=13.2
Q ss_pred CCCCCc-ccCCCCccceeee-cccch
Q psy2213 156 APPSTC-GCGEILSVQHILT-CALHG 179 (194)
Q Consensus 156 ~~~p~C-~Cg~~et~~H~l~-Cp~~~ 179 (194)
...-.| .||..-.+....+ ||.=.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCH 93 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCc
Confidence 344567 7776444444445 77544
No 25
>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=23.04 E-value=25 Score=19.02 Aligned_cols=19 Identities=26% Similarity=0.468 Sum_probs=6.4
Q ss_pred CCc-ccCCC-Cccceeee-ccc
Q psy2213 159 STC-GCGEI-LSVQHILT-CAL 177 (194)
Q Consensus 159 p~C-~Cg~~-et~~H~l~-Cp~ 177 (194)
|.| .|+.. .=.+..++ ||-
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~ 24 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPE 24 (30)
T ss_dssp ---TTT-----EE-SSSEEETT
T ss_pred CCCCCCCCcceeccCCEEeCCc
Confidence 678 88873 33445555 663
No 26
>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=21.08 E-value=21 Score=22.24 Aligned_cols=25 Identities=24% Similarity=0.316 Sum_probs=11.1
Q ss_pred hcccccccccccccCCCCCCCcccCC
Q psy2213 140 MRIGHTRATHGHLFKRAPPSTCGCGE 165 (194)
Q Consensus 140 lrtGH~~~~h~~~~~~~~~p~C~Cg~ 165 (194)
--+|||+.. +--+.....|.|.|+.
T Consensus 18 ~CSGHGr~f-lDg~~~dG~p~CECn~ 42 (56)
T PF04863_consen 18 SCSGHGRAF-LDGLIADGSPVCECNS 42 (56)
T ss_dssp --TTSEE---TTS-EETTEE--EE-T
T ss_pred CcCCCCeee-eccccccCCccccccC
Confidence 458999862 2222245669999986
Done!