Query psy12036
Match_columns 236
No_of_seqs 221 out of 664
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 16:58:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12036.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12036hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08719 ribonuclease H; Revie 98.3 9.7E-07 2.1E-11 69.8 4.3 34 62-96 113-146 (147)
2 PF00075 RNase_H: RNase H; In 98.3 5.6E-07 1.2E-11 68.9 2.8 31 65-95 100-131 (132)
3 PRK00203 rnhA ribonuclease H; 98.2 1.3E-06 2.9E-11 69.1 3.6 33 66-98 111-143 (150)
4 PRK06548 ribonuclease H; Provi 98.1 3.1E-06 6.7E-11 67.8 4.2 40 57-97 103-142 (161)
5 COG0328 RnhA Ribonuclease HI [ 97.9 8.6E-06 1.9E-10 64.5 3.8 41 57-97 105-145 (154)
6 cd06222 RnaseH RNase H (RNase 97.4 0.00021 4.7E-09 52.7 4.6 33 62-94 97-129 (130)
7 KOG3752|consensus 96.9 0.00089 1.9E-08 59.7 3.6 31 66-96 334-364 (371)
8 PF13966 zf-RVT: zinc-binding 96.8 0.00067 1.5E-08 48.4 1.6 31 168-198 50-83 (86)
9 PRK13907 rnhA ribonuclease H; 87.8 0.77 1.7E-05 34.8 3.8 31 62-96 96-126 (128)
10 PF13456 RVT_3: Reverse transc 79.3 3.5 7.5E-05 28.2 4.0 33 59-95 53-85 (87)
11 PRK07238 bifunctional RNase H/ 65.2 7.8 0.00017 34.9 3.8 33 62-98 101-133 (372)
12 PRK07708 hypothetical protein; 61.6 6.2 0.00013 33.2 2.2 28 68-99 183-210 (219)
13 PF04863 EGF_alliinase: Alliin 58.3 2.3 4.9E-05 27.6 -0.7 23 160-183 19-41 (56)
14 PF15322 PMSI1: Protein missin 46.0 12 0.00025 32.6 1.4 15 154-168 214-228 (311)
15 KOG1994|consensus 39.8 9.8 0.00021 32.1 0.0 32 153-198 229-263 (268)
16 PF13696 zf-CCHC_2: Zinc knuck 38.9 17 0.00038 20.9 1.0 17 177-196 8-26 (32)
17 PF05741 zf-nanos: Nanos RNA b 35.7 17 0.00036 23.7 0.6 19 178-196 34-54 (55)
18 PF00098 zf-CCHC: Zinc knuckle 34.4 29 0.00063 17.0 1.3 15 179-196 2-18 (18)
19 KOG2463|consensus 32.4 39 0.00084 30.3 2.5 36 199-235 42-79 (376)
20 PF13821 DUF4187: Domain of un 32.2 17 0.00037 23.6 0.2 20 179-198 29-51 (55)
21 PF15216 TSLP: Thymic stromal 21.3 1.5E+02 0.0033 22.4 3.6 12 73-84 80-91 (124)
22 PF13395 HNH_4: HNH endonuclea 20.2 37 0.00079 21.6 0.1 11 187-197 19-30 (54)
No 1
>PRK08719 ribonuclease H; Reviewed
Probab=98.27 E-value=9.7e-07 Score=69.77 Aligned_cols=34 Identities=24% Similarity=0.238 Sum_probs=29.1
Q ss_pred HHhhCCCceEEEEeccCCCCCcchHHHHHHhhhhc
Q psy12036 62 FASTNGSQISFMWIPSHSNIALNDKADQLAKNSIN 96 (236)
Q Consensus 62 ~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~ 96 (236)
.+.. ...|.|.|||||+|++|||.||++|++|++
T Consensus 113 ~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 113 ELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 3434 466999999999999999999999999864
No 2
>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=98.26 E-value=5.6e-07 Score=68.91 Aligned_cols=31 Identities=39% Similarity=0.831 Sum_probs=28.6
Q ss_pred hCCCceEEEEeccCCCC-CcchHHHHHHhhhh
Q psy12036 65 TNGSQISFMWIPSHSNI-ALNDKADQLAKNSI 95 (236)
Q Consensus 65 ~~~~~v~~~wip~H~gi-~gNE~Ad~~Ak~a~ 95 (236)
.++..|.|.|||||+|+ .|||.||++||+|+
T Consensus 100 ~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 100 SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 56889999999999999 69999999999885
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.19 E-value=1.3e-06 Score=69.12 Aligned_cols=33 Identities=24% Similarity=0.544 Sum_probs=29.1
Q ss_pred CCCceEEEEeccCCCCCcchHHHHHHhhhhccC
Q psy12036 66 NGSQISFMWIPSHSNIALNDKADQLAKNSINSK 98 (236)
Q Consensus 66 ~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~~ 98 (236)
....|.|.|||+|+|++|||.||++|++++..+
T Consensus 111 ~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 111 KRHQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 346899999999999999999999999987643
No 4
>PRK06548 ribonuclease H; Provisional
Probab=98.11 E-value=3.1e-06 Score=67.82 Aligned_cols=40 Identities=33% Similarity=0.494 Sum_probs=31.8
Q ss_pred HHHHHHHhhCCCceEEEEeccCCCCCcchHHHHHHhhhhcc
Q psy12036 57 KQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNSINS 97 (236)
Q Consensus 57 ~~~~~~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~ 97 (236)
.+++..+..+ ..|.|.|||||+|.+|||.||+||++++..
T Consensus 103 ~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 103 IQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred HHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 3444444444 479999999999999999999999998743
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=97.94 E-value=8.6e-06 Score=64.54 Aligned_cols=41 Identities=22% Similarity=0.342 Sum_probs=35.0
Q ss_pred HHHHHHHhhCCCceEEEEeccCCCCCcchHHHHHHhhhhcc
Q psy12036 57 KQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNSINS 97 (236)
Q Consensus 57 ~~~~~~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~ 97 (236)
.+++..+..+-..|.+.|||||.|.++||.||++|+.++..
T Consensus 105 ~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~ 145 (154)
T COG0328 105 WEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA 145 (154)
T ss_pred HHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence 55556666676789999999999999999999999998764
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=97.43 E-value=0.00021 Score=52.70 Aligned_cols=33 Identities=36% Similarity=0.607 Sum_probs=29.0
Q ss_pred HHhhCCCceEEEEeccCCCCCcchHHHHHHhhh
Q psy12036 62 FASTNGSQISFMWIPSHSNIALNDKADQLAKNS 94 (236)
Q Consensus 62 ~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a 94 (236)
........+.|.|||+|+|+.+|+.||.+|+.+
T Consensus 97 ~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 97 ALLKRFHKVRFEWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred HHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence 333577889999999999999999999999986
No 7
>KOG3752|consensus
Probab=96.89 E-value=0.00089 Score=59.70 Aligned_cols=31 Identities=26% Similarity=0.384 Sum_probs=28.2
Q ss_pred CCCceEEEEeccCCCCCcchHHHHHHhhhhc
Q psy12036 66 NGSQISFMWIPSHSNIALNDKADQLAKNSIN 96 (236)
Q Consensus 66 ~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~ 96 (236)
++..|.+.|||||.||.|||+||.+|++++.
T Consensus 334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 334 SNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred ccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 4689999999999999999999999998753
No 8
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.77 E-value=0.00067 Score=48.42 Aligned_cols=31 Identities=29% Similarity=0.548 Sum_probs=26.0
Q ss_pred cccccCCCCCCCc-ccC-CCCCcchhc-cccCch
Q psy12036 168 HSYLFTKTPHPIC-TCG-FPLTVKHIF-ECNKYK 198 (236)
Q Consensus 168 ~l~~~~~~~~p~C-~CG-~~eTv~HiL-~Cp~~~ 198 (236)
.+.+.+...++.| .|| +.||++|+| .||...
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 4566777888999 999 599999999 999764
No 9
>PRK13907 rnhA ribonuclease H; Provisional
Probab=87.78 E-value=0.77 Score=34.75 Aligned_cols=31 Identities=32% Similarity=0.383 Sum_probs=24.3
Q ss_pred HHhhCCCceEEEEeccCCCCCcchHHHHHHhhhhc
Q psy12036 62 FASTNGSQISFMWIPSHSNIALNDKADQLAKNSIN 96 (236)
Q Consensus 62 ~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~ 96 (236)
.+..+-..+.+.|||.+ .|+.||.+|+.|..
T Consensus 96 ~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 96 QYIKSFDLFFIKWIPSS----QNKVADELARKAIL 126 (128)
T ss_pred HHHhcCCceEEEEcCch----hchhHHHHHHHHHh
Confidence 34455567778999995 89999999998864
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=79.29 E-value=3.5 Score=28.21 Aligned_cols=33 Identities=27% Similarity=0.203 Sum_probs=24.1
Q ss_pred HHHHHhhCCCceEEEEeccCCCCCcchHHHHHHhhhh
Q psy12036 59 EYYFASTNGSQISFMWIPSHSNIALNDKADQLAKNSI 95 (236)
Q Consensus 59 ~~~~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~ 95 (236)
+...+...-..+.+.|||.- +|..||.+||.|.
T Consensus 53 ~i~~~~~~~~~~~~~~i~r~----~N~~A~~LA~~a~ 85 (87)
T PF13456_consen 53 DIRSLLDRFWNVSVSHIPRE----QNKVADALAKFAL 85 (87)
T ss_dssp HHHHHHCCCSCEEEEE--GG----GSHHHHHHHHHHH
T ss_pred hhhhhhccccceEEEEEChH----HhHHHHHHHHHHh
Confidence 33455566788999999975 7999999999875
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=65.24 E-value=7.8 Score=34.94 Aligned_cols=33 Identities=27% Similarity=0.577 Sum_probs=25.6
Q ss_pred HHhhCCCceEEEEeccCCCCCcchHHHHHHhhhhccC
Q psy12036 62 FASTNGSQISFMWIPSHSNIALNDKADQLAKNSINSK 98 (236)
Q Consensus 62 ~~~~~~~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~~ 98 (236)
.+..+-..+.+.|||. .+|+.||.+|+.|....
T Consensus 101 ~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 101 ELASQFGRVTYTWIPR----ARNAHADRLANEAMDAA 133 (372)
T ss_pred HHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhh
Confidence 3444556799999998 58999999999986443
No 12
>PRK07708 hypothetical protein; Validated
Probab=61.56 E-value=6.2 Score=33.20 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=21.9
Q ss_pred CceEEEEeccCCCCCcchHHHHHHhhhhccCc
Q psy12036 68 SQISFMWIPSHSNIALNDKADQLAKNSINSKL 99 (236)
Q Consensus 68 ~~v~~~wip~H~gi~gNE~Ad~~Ak~a~~~~~ 99 (236)
..+.+.|||.. .|+.||++|+.|.+...
T Consensus 183 l~~~~~~VpR~----~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 183 LTPVYEPISRK----QNKEADQLATQALEGTV 210 (219)
T ss_pred ceEEEEECCch----hhhHHHHHHHHHHhcCC
Confidence 34677888774 59999999999987543
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=58.33 E-value=2.3 Score=27.63 Aligned_cols=23 Identities=26% Similarity=0.511 Sum_probs=12.3
Q ss_pred hcCccccccccccCCCCCCCcccC
Q psy12036 160 RIGHTRITHSYLFTKTPHPICTCG 183 (236)
Q Consensus 160 rTGH~~~~~l~~~~~~~~p~C~CG 183 (236)
-+|||+. |+--+-....|.|.|.
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 5899998 7665555567999886
No 14
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=45.99 E-value=12 Score=32.62 Aligned_cols=15 Identities=33% Similarity=0.284 Sum_probs=13.1
Q ss_pred HHHHHHhcCcccccc
Q psy12036 154 ILLTRLRIGHTRITH 168 (236)
Q Consensus 154 ~~l~qlrTGH~~~~~ 168 (236)
..|.||||.|-.++|
T Consensus 214 GALsqLrTehrPCtY 228 (311)
T PF15322_consen 214 GALSQLRTEHRPCTY 228 (311)
T ss_pred chhhhhhhccCCccc
Confidence 469999999999984
No 15
>KOG1994|consensus
Probab=39.76 E-value=9.8 Score=32.10 Aligned_cols=32 Identities=22% Similarity=0.411 Sum_probs=23.6
Q ss_pred HHHHHHHhcCccccccccccCCCCCCCc-ccC-CCCCcchhc-cccCch
Q psy12036 153 EILLTRLRIGHTRITHSYLFTKTPHPIC-TCG-FPLTVKHIF-ECNKYK 198 (236)
Q Consensus 153 ~~~l~qlrTGH~~~~~l~~~~~~~~p~C-~CG-~~eTv~HiL-~Cp~~~ 198 (236)
..++.-||.||. +| .|| ..+|.+-++ +||-..
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 344566666653 57 899 589999999 999764
No 16
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=38.94 E-value=17 Score=20.88 Aligned_cols=17 Identities=29% Similarity=0.765 Sum_probs=13.2
Q ss_pred CCCc-ccCCCCCcchhc-cccC
Q psy12036 177 HPIC-TCGFPLTVKHIF-ECNK 196 (236)
Q Consensus 177 ~p~C-~CG~~eTv~HiL-~Cp~ 196 (236)
+=.| .|+... |++ .||.
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 4468 888654 999 9997
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=35.74 E-value=17 Score=23.73 Aligned_cols=19 Identities=32% Similarity=0.655 Sum_probs=7.9
Q ss_pred CCc-ccCCCCCcchhc-cccC
Q psy12036 178 PIC-TCGFPLTVKHIF-ECNK 196 (236)
Q Consensus 178 p~C-~CG~~eTv~HiL-~Cp~ 196 (236)
-.| .||...+-.|.. .||.
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 369 899888888999 9995
No 18
>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=34.44 E-value=29 Score=17.01 Aligned_cols=15 Identities=53% Similarity=1.216 Sum_probs=10.3
Q ss_pred Cc-ccCCCCCcchhc-cccC
Q psy12036 179 IC-TCGFPLTVKHIF-ECNK 196 (236)
Q Consensus 179 ~C-~CG~~eTv~HiL-~Cp~ 196 (236)
.| .||.. .|+. +||.
T Consensus 2 ~C~~C~~~---GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEP---GHIARDCPK 18 (18)
T ss_dssp BCTTTSCS---SSCGCTSSS
T ss_pred cCcCCCCc---CcccccCcc
Confidence 57 77753 5888 8874
No 19
>KOG2463|consensus
Probab=32.39 E-value=39 Score=30.26 Aligned_cols=36 Identities=31% Similarity=0.497 Sum_probs=27.5
Q ss_pred HHHhhcC-Ccc-hhhhcCCChHHHHHHHHHHHHhccccc
Q psy12036 199 KFREKLS-LPS-IEIALSDNENMAEKTIKYMKMINLYSK 235 (236)
Q Consensus 199 ~~R~~l~-~~~-l~~~l~~~~~~~~~~~~Fi~~t~~~~~ 235 (236)
..|..|. +|+ +... .|.++.++++++|.+.||=|+.
T Consensus 42 asRk~le~~pf~i~~r-ePspe~v~kV~~fak~TGDyss 79 (376)
T KOG2463|consen 42 ASRKRLEFLPFTIKLR-EPSPEYVRKVIKFAKLTGDYSS 79 (376)
T ss_pred HhhcchhhcccEEEEe-cCCHHHHHHHHHHHHhcCCccc
Confidence 3455554 566 6555 7788999999999999998764
No 20
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=32.25 E-value=17 Score=23.60 Aligned_cols=20 Identities=20% Similarity=0.351 Sum_probs=16.2
Q ss_pred Cc-ccC-CCCCcchhc-cccCch
Q psy12036 179 IC-TCG-FPLTVKHIF-ECNKYK 198 (236)
Q Consensus 179 ~C-~CG-~~eTv~HiL-~Cp~~~ 198 (236)
.| +|| .-.+.+-+. .||-..
T Consensus 29 YC~~Cg~~Y~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDLERNCPGPT 51 (55)
T ss_pred eeeeeCCccCCHHHHHhCCCCCC
Confidence 68 899 588888888 999754
No 21
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=21.34 E-value=1.5e+02 Score=22.44 Aligned_cols=12 Identities=25% Similarity=0.432 Sum_probs=10.4
Q ss_pred EEeccCCCCCcc
Q psy12036 73 MWIPSHSNIALN 84 (236)
Q Consensus 73 ~wip~H~gi~gN 84 (236)
.|+||+++++-|
T Consensus 80 ~~CPGyse~QiN 91 (124)
T PF15216_consen 80 NYCPGYSETQIN 91 (124)
T ss_pred HhCCCcchhhcc
Confidence 589999998887
No 22
>PF13395 HNH_4: HNH endonuclease
Probab=20.17 E-value=37 Score=21.63 Aligned_cols=11 Identities=18% Similarity=0.311 Sum_probs=7.8
Q ss_pred Ccchhc-cccCc
Q psy12036 187 TVKHIF-ECNKY 197 (236)
Q Consensus 187 Tv~HiL-~Cp~~ 197 (236)
+++||+ .-...
T Consensus 19 ~iDHiiP~s~~~ 30 (54)
T PF13395_consen 19 EIDHIIPRSRGG 30 (54)
T ss_pred eeEEEecccccC
Confidence 789999 65443
Done!