Query psy8376
Match_columns 328
No_of_seqs 235 out of 1633
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 17:03:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8376hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.9 6.2E-24 1.3E-28 177.3 14.2 127 56-189 3-143 (161)
2 PF00075 RNase_H: RNase H; In 99.9 1.8E-23 3.9E-28 170.2 9.2 117 57-186 2-131 (132)
3 COG0328 RnhA Ribonuclease HI [ 99.9 6.4E-23 1.4E-27 168.3 12.1 126 57-189 2-146 (154)
4 PRK08719 ribonuclease H; Revie 99.9 1.5E-22 3.2E-27 167.5 13.5 121 57-187 3-146 (147)
5 PRK00203 rnhA ribonuclease H; 99.9 2E-22 4.3E-27 168.0 12.8 124 58-189 3-143 (150)
6 cd06222 RnaseH RNase H (RNase 99.8 1.9E-18 4.1E-23 137.7 14.2 121 60-186 1-130 (130)
7 PRK13907 rnhA ribonuclease H; 99.8 2.6E-18 5.7E-23 139.3 13.7 121 58-188 1-127 (128)
8 KOG3752|consensus 99.7 2.9E-17 6.3E-22 150.4 12.4 125 57-187 211-364 (371)
9 PRK07708 hypothetical protein; 99.7 5.6E-16 1.2E-20 136.2 15.0 129 53-189 68-209 (219)
10 PRK07238 bifunctional RNase H/ 99.6 3.7E-14 8.1E-19 135.3 14.7 122 58-189 2-133 (372)
11 PF13456 RVT_3: Reverse transc 99.4 3.6E-12 7.8E-17 95.5 9.0 85 93-187 1-86 (87)
12 PF13966 zf-RVT: zinc-binding 96.6 0.00083 1.8E-08 50.2 1.3 33 262-294 51-83 (86)
13 PF05380 Peptidase_A17: Pao re 90.0 1.7 3.6E-05 36.3 7.7 66 57-124 80-158 (159)
14 PF00336 DNA_pol_viral_C: DNA 72.6 4 8.6E-05 35.3 3.2 60 57-132 93-154 (245)
15 KOG1994|consensus 68.6 3.1 6.7E-05 36.4 1.7 38 243-294 226-263 (268)
16 KOG1812|consensus 60.5 39 0.00085 32.5 7.8 90 90-188 46-138 (384)
17 COG0296 GlgB 1,4-alpha-glucan 56.2 15 0.00033 37.5 4.3 36 144-179 213-248 (628)
18 PF15322 PMSI1: Protein missin 48.7 9.2 0.0002 34.6 1.3 20 243-262 210-229 (311)
19 PF00098 zf-CCHC: Zinc knuckle 47.8 12 0.00026 19.1 1.1 17 272-292 2-18 (18)
20 PF13821 DUF4187: Domain of un 44.7 18 0.00039 24.4 1.9 39 242-294 13-51 (55)
21 PF05741 zf-nanos: Nanos RNA b 43.7 12 0.00027 25.3 1.0 20 272-292 35-54 (55)
22 PF13917 zf-CCHC_3: Zinc knuck 38.4 20 0.00044 22.8 1.3 19 270-292 4-22 (42)
23 COG3341 Predicted double-stran 36.0 32 0.00069 30.2 2.6 144 37-189 39-202 (225)
24 COG2093 DNA-directed RNA polym 34.9 24 0.00052 24.5 1.3 20 263-283 11-30 (64)
25 PF08274 PhnA_Zn_Ribbon: PhnA 32.9 15 0.00032 21.6 0.0 22 271-292 3-24 (30)
26 PRK03681 hypA hydrogenase nick 31.8 19 0.00042 28.2 0.5 22 271-292 71-92 (114)
27 PRK09710 lar restriction allev 31.0 28 0.00061 24.3 1.2 17 270-286 6-22 (64)
28 COG0295 Cdd Cytidine deaminase 30.8 2.8E+02 0.0061 22.5 7.0 77 71-163 27-107 (134)
29 COG1244 Predicted Fe-S oxidore 26.5 83 0.0018 29.5 3.7 32 39-70 79-115 (358)
30 PRK07758 hypothetical protein; 24.5 2.2E+02 0.0049 21.5 5.1 59 266-324 18-92 (95)
31 PF13696 zf-CCHC_2: Zinc knuck 24.4 37 0.0008 20.3 0.7 18 271-292 9-26 (32)
32 PF06117 DUF957: Enterobacteri 24.2 1.4E+02 0.003 20.8 3.5 38 99-136 4-47 (65)
33 PF14205 Cys_rich_KTR: Cystein 24.1 39 0.00084 22.8 0.8 21 272-292 6-33 (55)
34 PRK12380 hydrogenase nickel in 23.5 33 0.00072 26.8 0.5 22 271-293 71-92 (113)
35 PF15216 TSLP: Thymic stromal 22.8 1.4E+02 0.003 23.6 3.7 43 164-216 80-122 (124)
36 TIGR00100 hypA hydrogenase nic 22.8 35 0.00077 26.7 0.6 22 271-293 71-92 (115)
37 PF09237 GAGA: GAGA factor; I 21.1 63 0.0014 21.6 1.4 27 264-300 18-44 (54)
38 smart00642 Aamy Alpha-amylase 20.8 2E+02 0.0043 23.9 4.8 30 143-172 68-97 (166)
39 PRK03824 hypA hydrogenase nick 20.7 44 0.00095 27.0 0.7 6 272-277 72-77 (135)
40 PRK12568 glycogen branching en 20.2 1.2E+02 0.0026 31.9 3.9 33 143-175 317-349 (730)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.91 E-value=6.2e-24 Score=177.27 Aligned_cols=127 Identities=26% Similarity=0.309 Sum_probs=96.8
Q ss_pred CCcEEEEecCCCCC--CCceEEEEEcCeeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHHH
Q psy8376 56 KDKILCYTDGSKTN--TFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQA 133 (328)
Q Consensus 56 ~~~~~iytDgS~~~--~~~G~g~~~~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~~ 133 (328)
+..+.||||||+.. +..|+|+++.+.....+-...+|+++||+.|++.|| +.+... ...+.|+|||++|+++
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL----~~~~~~--~~~v~I~TDS~yvi~~ 76 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELL----IATRHT--DRPILILSDSKYVINS 76 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHH----HhhhcC--CceEEEEeChHHHHHH
Confidence 45689999999884 347899888433222223346899999999999999 544432 4579999999999999
Q ss_pred HHc---------cCCCH--HHH-HHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376 134 LKF---------NLNDS--ILI-SKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR 189 (328)
Q Consensus 134 l~~---------~~~~~--~~~-~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 189 (328)
++. |...+ ++. +++++.+..+.+. ..|+|.|||||+|.+|||.||.||++|+...
T Consensus 77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 994 32222 333 6677777777655 4799999999999999999999999998654
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=99.89 E-value=1.8e-23 Score=170.21 Aligned_cols=117 Identities=32% Similarity=0.428 Sum_probs=90.0
Q ss_pred CcEEEEecCCCCC--CCceEEEEE-cCeeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHHH
Q psy8376 57 DKILCYTDGSKTN--TFTGGAYLL-NETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQA 133 (328)
Q Consensus 57 ~~~~iytDgS~~~--~~~G~g~~~-~~~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~~ 133 (328)
+.+.||||||+.. +..|+|+++ .+......++ ..|++.||+.||..|| +.+ . ...+.|+|||++++..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL----~~~-~---~~~v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEAL----KAL-E---HRKVTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHH----HTH-S---TSEEEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHH----HHh-h---cccccccccHHHHHHH
Confidence 5789999999763 336788766 3433444555 8899999999999999 633 2 6899999999999998
Q ss_pred HHc-----cCCCH----HHHHHHHHHHHHHHhcCCeEEEEEecCCCCC-ccchHHhHHHHHHh
Q psy8376 134 LKF-----NLNDS----ILISKILLKIKEISSFGSQVSFLWIPSHVGI-RENEMVDRAARNAV 186 (328)
Q Consensus 134 l~~-----~~~~~----~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi-~gNe~AD~lAk~a~ 186 (328)
+.. ..... ++..+|.+. ...+..|.|.|||||+|+ .|||.||+|||+|+
T Consensus 73 l~~~~~~~~~~~~~~~~~i~~~i~~~----~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 73 LNKWLHGNGWKKTSNGRPIKNEIWEL----LSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHTHHHHTTSBSCTSSSBHTHHHHHH----HHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred HHHhccccccccccccccchhheeec----cccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 887 22211 355555553 356889999999999999 79999999999986
No 3
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.89 E-value=6.4e-23 Score=168.29 Aligned_cols=126 Identities=21% Similarity=0.206 Sum_probs=101.3
Q ss_pred CcEEEEecCCCCC--CCceEEEEEc--Cee--eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHH
Q psy8376 57 DKILCYTDGSKTN--TFTGGAYLLN--ETV--EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKS 129 (328)
Q Consensus 57 ~~~~iytDgS~~~--~~~G~g~~~~--~~~--~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ 129 (328)
..+.||||||+.. |..|+|+|+. +.. .+..+. .+||++||+.|++.|| +++.. + ...|.|+|||++
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL----~~l~~~~--~~~v~l~tDS~y 74 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEAL----EALKELG--ACEVTLYTDSKY 74 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHH----HHHHhcC--CceEEEEecHHH
Confidence 4688999999983 4489998883 222 233344 8999999999999999 66665 5 889999999999
Q ss_pred HHHHHHccCCC-----------HH-HHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376 130 SLQALKFNLND-----------SI-LISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR 189 (328)
Q Consensus 130 ai~~l~~~~~~-----------~~-~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 189 (328)
|+++|+.+... .| ...++++.+.++......|.+.|||||.|.++||.||+||+.|+...
T Consensus 75 v~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 75 VVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 99999944111 12 24678888888888888999999999999999999999999998765
No 4
>PRK08719 ribonuclease H; Reviewed
Probab=99.89 E-value=1.5e-22 Score=167.52 Aligned_cols=121 Identities=23% Similarity=0.294 Sum_probs=91.9
Q ss_pred CcEEEEecCCCCCCC-----ceEEEEE--c--Ce--eeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEe
Q psy8376 57 DKILCYTDGSKTNTF-----TGGAYLL--N--ET--VEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICS 125 (328)
Q Consensus 57 ~~~~iytDgS~~~~~-----~G~g~~~--~--~~--~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~s 125 (328)
..++||||||+..++ +|+|+++ . +. .....+....|+++||+.|++.|| +.+.. ...|+|
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL----~~~~~-----~~~i~t 73 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEAL----EYARD-----GDVIYS 73 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHH----HHcCC-----CCEEEe
Confidence 568999999997432 5999886 2 21 233446666899999999999999 65543 137999
Q ss_pred cCHHHHHHHH--------ccCCCH---HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhh
Q psy8376 126 DSKSSLQALK--------FNLNDS---IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVN 187 (328)
Q Consensus 126 Ds~~ai~~l~--------~~~~~~---~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~ 187 (328)
||++|+++++ +.+..+ ++ ..++++.+..+.+ ...|+|.|||||+|++|||.||+||++|+.
T Consensus 74 DS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 74 DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred chHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 9999999984 333222 22 3567777777765 467999999999999999999999999874
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.89 E-value=2e-22 Score=167.99 Aligned_cols=124 Identities=20% Similarity=0.211 Sum_probs=91.9
Q ss_pred cEEEEecCCCCC--CCceEEEEE--cCee-eeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376 58 KILCYTDGSKTN--TFTGGAYLL--NETV-EQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ 132 (328)
Q Consensus 58 ~~~iytDgS~~~--~~~G~g~~~--~~~~-~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~ 132 (328)
.+.||||||+.. +.+|+|+++ .+.. ...+.....|+++|||.|++.|| +.+.. ...+.|+|||+++++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL----~~~~~---~~~v~I~tDS~yvi~ 75 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEAL----EALKE---PCEVTLYTDSQYVRQ 75 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHH----HHcCC---CCeEEEEECHHHHHH
Confidence 488999999984 347888887 2322 12223347899999999999999 65543 467999999999999
Q ss_pred HHHcc---------CCCH--HH-HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376 133 ALKFN---------LNDS--IL-ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR 189 (328)
Q Consensus 133 ~l~~~---------~~~~--~~-~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 189 (328)
+|..+ ...+ ++ ..++++.+..+... ..|.|.|||||+|++||+.||+||++|+...
T Consensus 76 ~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~ 143 (150)
T PRK00203 76 GITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEA 143 (150)
T ss_pred HHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHh
Confidence 99863 1111 22 23444545455433 6899999999999999999999999998765
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=99.79 E-value=1.9e-18 Score=137.71 Aligned_cols=121 Identities=26% Similarity=0.295 Sum_probs=92.7
Q ss_pred EEEecCCCCCC--CceEEEEEcCe--e---eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHHHH
Q psy8376 60 LCYTDGSKTNT--FTGGAYLLNET--V---EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKSSL 131 (328)
Q Consensus 60 ~iytDgS~~~~--~~G~g~~~~~~--~---~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ai 131 (328)
++|||||...+ ++|+|+++.+. . .........+++.||+.|++.|| +.+.. + ..++.|++||+.++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al----~~~~~~~--~~~i~i~~Ds~~~~ 74 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEAL----ELALELG--GKKVNIYTDSQYVI 74 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHH----HHHHhCC--CceEEEEECHHHHH
Confidence 48999999865 58999888321 1 11222257899999999999999 54434 4 89999999999999
Q ss_pred HHHHccCC-CHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHh
Q psy8376 132 QALKFNLN-DSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAV 186 (328)
Q Consensus 132 ~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~ 186 (328)
..++++.. .......+...+..+...+..+.|.|||+|+|..+|+.||.|||.|.
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 75 NALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 99998765 22233334444445556788999999999999999999999999873
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.79 E-value=2.6e-18 Score=139.34 Aligned_cols=121 Identities=21% Similarity=0.221 Sum_probs=94.4
Q ss_pred cEEEEecCCCCC--CCceEEEEEcCeee---eccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHHHH
Q psy8376 58 KILCYTDGSKTN--TFTGGAYLLNETVE---QFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKSSL 131 (328)
Q Consensus 58 ~~~iytDgS~~~--~~~G~g~~~~~~~~---~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ai 131 (328)
.++||||||+.. +.+|+|+++++... ........|++.||+.|++.|| +.+.. + ..++.|+|||+.++
T Consensus 1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL----~~a~~~g--~~~v~i~sDS~~vi 74 (128)
T PRK13907 1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAAL----KYCTEHN--YNIVSFRTDSQLVE 74 (128)
T ss_pred CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHH----HHHHhCC--CCEEEEEechHHHH
Confidence 368999999884 45899999843221 1122346799999999999999 66555 4 67899999999999
Q ss_pred HHHHccCCCHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhC
Q psy8376 132 QALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNA 188 (328)
Q Consensus 132 ~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~ 188 (328)
+.+++.....+-...+++.+..+..++..+.|.|||. +.|+.||.||++|...
T Consensus 75 ~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 75 RAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ 127 (128)
T ss_pred HHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence 9999876544445666666667777888899999995 6999999999999753
No 8
>KOG3752|consensus
Probab=99.73 E-value=2.9e-17 Score=150.39 Aligned_cols=125 Identities=24% Similarity=0.253 Sum_probs=96.0
Q ss_pred CcEEEEecCCCCCC-----CceEEEEEcC---eeeeccCC-CCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEec
Q psy8376 57 DKILCYTDGSKTNT-----FTGGAYLLNE---TVEQFQLN-QIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSD 126 (328)
Q Consensus 57 ~~~~iytDgS~~~~-----~~G~g~~~~~---~~~~~~l~-~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sD 126 (328)
+..+||||||+..+ .+|+|+++++ ......+. ..+++|.||+.||..|| +.+.. + ..+++|.||
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~AL----kka~~~~--~~kv~I~TD 284 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEAL----KKARSKN--INKVVIRTD 284 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHH----HHHHhcC--CCcEEEEec
Confidence 45899999998842 3899999943 44566665 88999999999999999 55544 4 669999999
Q ss_pred CHHHHHHHHccCCC-----------HH----H--HHHHHHHHHHHHh--cCCeEEEEEecCCCCCccchHHhHHHHHHhh
Q psy8376 127 SKSSLQALKFNLND-----------SI----L--ISKILLKIKEISS--FGSQVSFLWIPSHVGIRENEMVDRAARNAVN 187 (328)
Q Consensus 127 s~~ai~~l~~~~~~-----------~~----~--~~~i~~~~~~l~~--~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~ 187 (328)
|++++++|+.|... ++ + .......+.+|.+ ++.+|++.|||||.|+.|||+||.||+++..
T Consensus 285 S~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~ 364 (371)
T KOG3752|consen 285 SEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST 364 (371)
T ss_pred hHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence 99999999865321 11 1 1233334444443 3689999999999999999999999998854
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.69 E-value=5.6e-16 Score=136.18 Aligned_cols=129 Identities=16% Similarity=0.161 Sum_probs=94.6
Q ss_pred hhCCCcEEEEecCCCC--CCCceEEEEEc--C--eee----eccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceE
Q psy8376 53 KDNKDKILCYTDGSKT--NTFTGGAYLLN--E--TVE----QFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDF 121 (328)
Q Consensus 53 ~~~~~~~~iytDgS~~--~~~~G~g~~~~--~--~~~----~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i 121 (328)
...++.+++|+|||.. ++++|+|+++. + ... ...++...|++.||+.|++.|| +.+.. +.....|
T Consensus 68 ~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL----~~A~e~g~~~~~V 143 (219)
T PRK07708 68 EEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAM----QELEELGVKHEPV 143 (219)
T ss_pred ccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHH----HHHHHcCCCcceE
Confidence 4457789999999986 45689998883 1 111 1245666899999999999999 55554 3112348
Q ss_pred EEEecCHHHHHHHHccCCC-HHHHHHHHHHHHHHHhc-CCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376 122 VICSDSKSSLQALKFNLND-SILISKILLKIKEISSF-GSQVSFLWIPSHVGIRENEMVDRAARNAVNAR 189 (328)
Q Consensus 122 ~I~sDs~~ai~~l~~~~~~-~~~~~~i~~~~~~l~~~-~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 189 (328)
.|++||+.+++++++.+.. ++....+++.+..+.++ ...+.|.||| +..|+.||.||++|++..
T Consensus 144 ~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 144 TFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGT 209 (219)
T ss_pred EEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcC
Confidence 9999999999999987643 34455555555544433 4568889998 778999999999999754
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.57 E-value=3.7e-14 Score=135.32 Aligned_cols=122 Identities=20% Similarity=0.215 Sum_probs=94.4
Q ss_pred cEEEEecCCCCCC--CceEEEEEcCe--e----eeccCCCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCH
Q psy8376 58 KILCYTDGSKTNT--FTGGAYLLNET--V----EQFQLNQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSK 128 (328)
Q Consensus 58 ~~~iytDgS~~~~--~~G~g~~~~~~--~----~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~ 128 (328)
.+.||||||+..+ .+|+|+++.+. . .........|++.||+.|++.|| +.+.. + ...+.|++||+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL----~~a~~~g--~~~v~i~~DS~ 75 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGL----EAAAELG--ATEVEVRMDSK 75 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHH----HHHHhCC--CCeEEEEeCcH
Confidence 3689999998853 48999988321 1 11222237889999999999999 55555 5 77999999999
Q ss_pred HHHHHHHccCC-CHHHHHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHhHHHHHHhhCC
Q psy8376 129 SSLQALKFNLN-DSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR 189 (328)
Q Consensus 129 ~ai~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 189 (328)
.+++.+++.+. +++-...+...+..+.+++..+.|.||| ..+|+.||.||+.|+...
T Consensus 76 lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~----r~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 76 LVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIP----RARNAHADRLANEAMDAA 133 (372)
T ss_pred HHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECC----chhhhHHHHHHHHHHHhh
Confidence 99999988654 3444555666677788888999999999 479999999999997544
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.36 E-value=3.6e-12 Score=95.54 Aligned_cols=85 Identities=20% Similarity=0.210 Sum_probs=66.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHHHHHHHHccCCCHHHHHHHHHHHHHHHhcCCeEEEEEecCCCC
Q psy8376 93 IYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVG 171 (328)
Q Consensus 93 ~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g 171 (328)
+..||+.|++.|| +.+.. + .++|.|+|||+.+++.+++..........+...+..+.+.+..+.|.|||
T Consensus 1 ~~~aE~~al~~al----~~a~~~g--~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~---- 70 (87)
T PF13456_consen 1 PLEAEALALLEAL----QLAWELG--IRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP---- 70 (87)
T ss_dssp HHHHHHHHHHHHH----HHHHCCT---SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------
T ss_pred CcHHHHHHHHHHH----HHHHHCC--CCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----
Confidence 4789999999999 76666 6 89999999999999999987544324455666666788889999999999
Q ss_pred CccchHHhHHHHHHhh
Q psy8376 172 IRENEMVDRAARNAVN 187 (328)
Q Consensus 172 i~gNe~AD~lAk~a~~ 187 (328)
+++|..||.|||.|.+
T Consensus 71 r~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 71 REQNKVADALAKFALS 86 (87)
T ss_dssp GGGSHHHHHHHHHHHH
T ss_pred hHHhHHHHHHHHHHhh
Confidence 8999999999999874
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.64 E-value=0.00083 Score=50.23 Aligned_cols=33 Identities=18% Similarity=0.392 Sum_probs=27.6
Q ss_pred cccccCCCCCccccccccccccchhhcccccch
Q psy8376 262 KHLLERKDPPACEFCGQTPVYLNHWLTECHALG 294 (328)
Q Consensus 262 ~~r~~~~~~p~C~~Cg~~~etv~Hil~~Cp~~~ 294 (328)
+++.+...++.|..|+.+.||++|+++.||...
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 345666778999999977999999999999754
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=90.00 E-value=1.7 Score=36.29 Aligned_cols=66 Identities=15% Similarity=0.150 Sum_probs=38.7
Q ss_pred CcEEEEecCCCCCCCceEEEEEc---Cee----e---eccC--CCCCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEE
Q psy8376 57 DKILCYTDGSKTNTFTGGAYLLN---ETV----E---QFQL--NQIASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVI 123 (328)
Q Consensus 57 ~~~~iytDgS~~~~~~G~g~~~~---~~~----~---~~~l--~~~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I 123 (328)
..+++|+|+|.. +.|+.++++ +.. . ..++ -...|+-+-||.|+..|.+++-..... +....++.+
T Consensus 80 ~~L~~F~DAS~~--aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~~~~l~~~~~~~~~ 157 (159)
T PF05380_consen 80 VELHVFCDASES--AYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTVKKELDIEISQVVF 157 (159)
T ss_pred eeeeEeeccccc--ceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHHHHHcCCCcceeEE
Confidence 368899999954 344444442 111 0 1112 124599999999999999777444333 323455554
Q ss_pred E
Q psy8376 124 C 124 (328)
Q Consensus 124 ~ 124 (328)
.
T Consensus 158 w 158 (159)
T PF05380_consen 158 W 158 (159)
T ss_pred e
Confidence 4
No 14
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=72.59 E-value=4 Score=35.32 Aligned_cols=60 Identities=22% Similarity=0.212 Sum_probs=37.3
Q ss_pred CcEEEEecCCCCCCCceEEEEEcC--eeeeccCCCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHH
Q psy8376 57 DKILCYTDGSKTNTFTGGAYLLNE--TVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQ 132 (328)
Q Consensus 57 ~~~~iytDgS~~~~~~G~g~~~~~--~~~~~~l~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~ 132 (328)
.--.||+|+.-. |+|+.+.. ....| ...-.+++||++|.-.|. -+. ..+ .|.|||..|+.
T Consensus 93 ~lc~VfaDATpT----gwgi~i~~~~~~~Tf--s~~l~IhtaELlaaClAr----~~~-----~~r-~l~tDnt~Vls 154 (245)
T PF00336_consen 93 GLCQVFADATPT----GWGISITGQRMRGTF--SKPLPIHTAELLAACLAR----LMS-----GAR-CLGTDNTVVLS 154 (245)
T ss_pred CCCceeccCCCC----cceeeecCceeeeee--cccccchHHHHHHHHHHH----hcc-----CCc-EEeecCcEEEe
Confidence 345799998544 44444422 22333 234578999999998877 332 223 49999987763
No 15
>KOG1994|consensus
Probab=68.65 E-value=3.1 Score=36.43 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=29.3
Q ss_pred hhhHHHHHHhhhccccccccccccCCCCCccccccccccccchhhcccccch
Q psy8376 243 RQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALG 294 (328)
Q Consensus 243 R~~~~~l~qlrtGH~~l~~~~r~~~~~~p~C~~Cg~~~etv~Hil~~Cp~~~ 294 (328)
-+.+.+...||.||.+ |-+||-...|.+-++-+||--.
T Consensus 226 e~lt~in~~LR~eh~Y--------------C~fCG~~y~~~edl~ehCPGvn 263 (268)
T KOG1994|consen 226 ERLTKINIFLRSEHYY--------------CFFCGIKYKDEEDLYEHCPGVN 263 (268)
T ss_pred HHHHHHHHHHhccceE--------------EEEeccccCCHHHHHHhCCCCC
Confidence 3445667888888843 6689977889999999999643
No 16
>KOG1812|consensus
Probab=60.46 E-value=39 Score=32.49 Aligned_cols=90 Identities=17% Similarity=0.155 Sum_probs=51.4
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHh-cCCcceEEEEecCHHHHHHHHccCCCHH--HHHHHHHHHHHHHhcCCeEEEEEe
Q psy8376 90 IASIYTAELMAIDLCLNSILMYIQN-NFCFKDFVICSDSKSSLQALKFNLNDSI--LISKILLKIKEISSFGSQVSFLWI 166 (328)
Q Consensus 90 ~~s~~~AEl~Ai~~al~~~~~~~~~-~~~~~~i~I~sDs~~ai~~l~~~~~~~~--~~~~i~~~~~~l~~~~~~v~~~Wv 166 (328)
..+...||++|+..+| ..+.. + ...+.+++|+....+.+........ .+..+......+..+.....-.-+
T Consensus 46 ~~~~~~ae~~al~~~l----~ea~~~~--~~~~~~~~d~~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~l~~~~~i~~ 119 (384)
T KOG1812|consen 46 SITPLEAELMALKRGL----TEALELG--LNHIVIYCDDELIYESVAGREKPEQHRKIVLLVELVQRIREQLTSSEPILV 119 (384)
T ss_pred ccchhhHHHHHHhhcc----HHHHhhc--cccceEecccHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcccceec
Confidence 3778999999999999 44444 5 8899999996555554443333221 233333433334433322222233
Q ss_pred cCCCCCccchHHhHHHHHHhhC
Q psy8376 167 PSHVGIRENEMVDRAARNAVNA 188 (328)
Q Consensus 167 p~H~gi~gNe~AD~lAk~a~~~ 188 (328)
|- .....-|=.||+++..+
T Consensus 120 ~~---~~d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 120 PK---NADIKFAYKLAREAIVS 138 (384)
T ss_pred cc---chhhHHHHHHHHHhhcc
Confidence 31 11223477888888875
No 17
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=56.15 E-value=15 Score=37.50 Aligned_cols=36 Identities=17% Similarity=0.260 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhcCCeEEEEEecCCCCCccchHHh
Q psy8376 144 ISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVD 179 (328)
Q Consensus 144 ~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD 179 (328)
-++....|..+.+.|+.|-+-|||+|.+..||-.+-
T Consensus 213 Pedfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~ 248 (628)
T COG0296 213 PEDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLAR 248 (628)
T ss_pred HHHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhh
Confidence 456677777899999999999999999999887653
No 18
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=48.66 E-value=9.2 Score=34.61 Aligned_cols=20 Identities=30% Similarity=0.253 Sum_probs=15.5
Q ss_pred hhhHHHHHHhhhcccccccc
Q psy8376 243 RQEEVVLCRLRIGHCLATHK 262 (328)
Q Consensus 243 R~~~~~l~qlrtGH~~l~~~ 262 (328)
|-..-.|.||||.|-+.+|.
T Consensus 210 rLRvGALsqLrTehrPCtY~ 229 (311)
T PF15322_consen 210 RLRVGALSQLRTEHRPCTYQ 229 (311)
T ss_pred ceecchhhhhhhccCCcccc
Confidence 44466799999999998754
No 19
>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=47.77 E-value=12 Score=19.09 Aligned_cols=17 Identities=29% Similarity=0.649 Sum_probs=13.6
Q ss_pred ccccccccccccchhhccccc
Q psy8376 272 ACEFCGQTPVYLNHWLTECHA 292 (328)
Q Consensus 272 ~C~~Cg~~~etv~Hil~~Cp~ 292 (328)
.|-.|| ...|+-.+||.
T Consensus 2 ~C~~C~----~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCG----EPGHIARDCPK 18 (18)
T ss_dssp BCTTTS----CSSSCGCTSSS
T ss_pred cCcCCC----CcCcccccCcc
Confidence 577788 67899999984
No 20
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=44.68 E-value=18 Score=24.44 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=28.9
Q ss_pred chhhHHHHHHhhhccccccccccccCCCCCccccccccccccchhhcccccch
Q psy8376 242 IRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPVYLNHWLTECHALG 294 (328)
Q Consensus 242 ~R~~~~~l~qlrtGH~~l~~~~r~~~~~~p~C~~Cg~~~etv~Hil~~Cp~~~ 294 (328)
..+...++..||.-|. .|-+||-.-.+.+-+.-.||-..
T Consensus 13 ~e~L~~l~~YLR~~~~--------------YC~~Cg~~Y~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 13 EERLDKLLSYLREEHN--------------YCFWCGTKYDDEEDLERNCPGPT 51 (55)
T ss_pred HHHHHHHHHHHHhhCc--------------eeeeeCCccCCHHHHHhCCCCCC
Confidence 3566777888887763 46689966778888888999654
No 21
>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=43.72 E-value=12 Score=25.26 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=9.9
Q ss_pred ccccccccccccchhhccccc
Q psy8376 272 ACEFCGQTPVYLNHWLTECHA 292 (328)
Q Consensus 272 ~C~~Cg~~~etv~Hil~~Cp~ 292 (328)
.|+.|| +..+-.|....||.
T Consensus 35 ~Cp~Cg-AtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 35 VCPICG-ATGDNAHTIKYCPK 54 (55)
T ss_dssp --TTT----GGG---GGG-TT
T ss_pred cCCCCc-CcCccccccccCcC
Confidence 699999 88899999999995
No 22
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=38.35 E-value=20 Score=22.79 Aligned_cols=19 Identities=37% Similarity=0.912 Sum_probs=15.8
Q ss_pred CCccccccccccccchhhccccc
Q psy8376 270 PPACEFCGQTPVYLNHWLTECHA 292 (328)
Q Consensus 270 ~p~C~~Cg~~~etv~Hil~~Cp~ 292 (328)
...|..|+ ...|+.++||.
T Consensus 4 ~~~CqkC~----~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCG----QKGHWTYECPN 22 (42)
T ss_pred CCcCcccC----CCCcchhhCCC
Confidence 45798899 56799999995
No 23
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=36.01 E-value=32 Score=30.16 Aligned_cols=144 Identities=15% Similarity=-0.009 Sum_probs=80.3
Q ss_pred CCCChHHHHHHHHHhh---hhC--CCcEEEEecCCCCC-CCceEEEEE-cCee---eecc---CCCCCchHHHHHHHHHH
Q psy8376 37 DEELPSEINNKYLEFK---KDN--KDKILCYTDGSKTN-TFTGGAYLL-NETV---EQFQ---LNQIASIYTAELMAIDL 103 (328)
Q Consensus 37 ~~~~~~~~~~~~~~~~---~~~--~~~~~iytDgS~~~-~~~G~g~~~-~~~~---~~~~---l~~~~s~~~AEl~Ai~~ 103 (328)
.....++|...+..=+ ..+ ...+.-+.+|+... .+.+-..+. +... ..+. --...++..+|.+|++.
T Consensus 39 sf~s~EeA~a~~~g~i~~~tp~~~~e~~i~~~~G~y~~~p~t~~~k~yr~k~~~~~~~lt~~~~~~~~~n~s~d~la~ly 118 (225)
T COG3341 39 SFKSYEEAEAYCEGNIESVTPYLDFEYIISWAKGDYDAKPGTQEFKEYRGKCTIEYSWLTESSEFSIKSNDSGDVLAKLY 118 (225)
T ss_pred ccccHHHHHHHhccCccccCcccchhccceeccCCccccCCCcceeEEeccccccceeeeeecccccccCchHHHHHHhc
Confidence 3445566666555311 111 34566777787653 122222222 2211 1111 11245778999999999
Q ss_pred HHHHHHHHHHhcCCcceEEEE----ecCHHHHHHHHccCCCH-HHHHHHHHHHHHHHhc--CCeEEEEEecCCCCCccch
Q psy8376 104 CLNSILMYIQNNFCFKDFVIC----SDSKSSLQALKFNLNDS-ILISKILLKIKEISSF--GSQVSFLWIPSHVGIRENE 176 (328)
Q Consensus 104 al~~~~~~~~~~~~~~~i~I~----sDs~~ai~~l~~~~~~~-~~~~~i~~~~~~l~~~--~~~v~~~Wvp~H~gi~gNe 176 (328)
+| +........+.++++ .||++.+.-+.+-.... .+..+. +.... +....+.|+--|.++.-+.
T Consensus 119 ~~----~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~~~-----e~~~~~~~v~h~~k~i~~~~~~~~~~ 189 (225)
T COG3341 119 GL----RYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETKVNLLKDR-----EFFSIGKGVFHDEKDINIHIWIFESK 189 (225)
T ss_pred cc----cccccccCccceeeccCCcchhHHHHHHHhhhhhhHHHHHHhH-----Hhhhccchhhhhhhhcccccccchhh
Confidence 99 665541114555557 79999888776554222 111111 11222 2455678889999888888
Q ss_pred HHhHHHHHHhhCC
Q psy8376 177 MVDRAARNAVNAR 189 (328)
Q Consensus 177 ~AD~lAk~a~~~~ 189 (328)
.++.++..+....
T Consensus 190 ~~~s~~~~~~k~~ 202 (225)
T COG3341 190 KGNSHVYNTSKKE 202 (225)
T ss_pred hhhhhhhchhhhh
Confidence 8888877665554
No 24
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=34.92 E-value=24 Score=24.48 Aligned_cols=20 Identities=25% Similarity=0.546 Sum_probs=13.8
Q ss_pred ccccCCCCCcccccccccccc
Q psy8376 263 HLLERKDPPACEFCGQTPVYL 283 (328)
Q Consensus 263 ~r~~~~~~p~C~~Cg~~~etv 283 (328)
+|+--.+...||.|| ..+..
T Consensus 11 k~l~~~d~e~CP~Cg-s~~~t 30 (64)
T COG2093 11 KRLTPEDTEICPVCG-STDLT 30 (64)
T ss_pred cccCCCCCccCCCCC-Ccccc
Confidence 455566677799999 65443
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=32.92 E-value=15 Score=21.61 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=8.5
Q ss_pred Cccccccccccccchhhccccc
Q psy8376 271 PACEFCGQTPVYLNHWLTECHA 292 (328)
Q Consensus 271 p~C~~Cg~~~etv~Hil~~Cp~ 292 (328)
|.|+.||-+..=.+.-++.||.
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 6788888443445666666663
No 26
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.75 E-value=19 Score=28.21 Aligned_cols=22 Identities=27% Similarity=0.486 Sum_probs=14.0
Q ss_pred Cccccccccccccchhhccccc
Q psy8376 271 PACEFCGQTPVYLNHWLTECHA 292 (328)
Q Consensus 271 p~C~~Cg~~~etv~Hil~~Cp~ 292 (328)
-.|..||.......+.++.||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~ 92 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQ 92 (114)
T ss_pred EEcccCCCeeecCCccCCcCcC
Confidence 3688888444444565567885
No 27
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=30.98 E-value=28 Score=24.28 Aligned_cols=17 Identities=29% Similarity=0.659 Sum_probs=12.7
Q ss_pred CCccccccccccccchh
Q psy8376 270 PPACEFCGQTPVYLNHW 286 (328)
Q Consensus 270 ~p~C~~Cg~~~etv~Hi 286 (328)
-.-||+||....+++|.
T Consensus 6 lKPCPFCG~~~~~v~~~ 22 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI 22 (64)
T ss_pred ccCCCCCCCceeEEEec
Confidence 35699999777777764
No 28
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=30.75 E-value=2.8e+02 Score=22.47 Aligned_cols=77 Identities=14% Similarity=0.033 Sum_probs=44.6
Q ss_pred CceEEEEEcCeeeeccC----CCCCchHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEecCHHHHHHHHccCCCHHHHHH
Q psy8376 71 FTGGAYLLNETVEQFQL----NQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISK 146 (328)
Q Consensus 71 ~~G~g~~~~~~~~~~~l----~~~~s~~~AEl~Ai~~al~~~~~~~~~~~~~~~i~I~sDs~~ai~~l~~~~~~~~~~~~ 146 (328)
.||+++...+....++. ....--.-||-.||..|+ .. .. .....+.+++|+ ..+..+-+..++
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ai----s~-G~-~~~~~v~v~~~~-------~~~~sPCG~CRQ 93 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAI----SE-GK-RKFDAVVVVADT-------GKPVSPCGACRQ 93 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHH----Hc-CC-CcEEEEEEEcCC-------CCCcCCcHHHHH
Confidence 47777666432222211 123344779999999999 44 11 227889999998 333344455555
Q ss_pred HHHHHHHHHhcCCeEEE
Q psy8376 147 ILLKIKEISSFGSQVSF 163 (328)
Q Consensus 147 i~~~~~~l~~~~~~v~~ 163 (328)
... ++......|.+
T Consensus 94 ~i~---Ef~~~d~~ii~ 107 (134)
T COG0295 94 VLA---EFCGDDTLIIL 107 (134)
T ss_pred HHH---HhcCCCceEEE
Confidence 544 66655444443
No 29
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=26.48 E-value=83 Score=29.52 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=24.1
Q ss_pred CChHHHHHHHHHhhhhCC----C-cEEEEecCCCCCC
Q psy8376 39 ELPSEINNKYLEFKKDNK----D-KILCYTDGSKTNT 70 (328)
Q Consensus 39 ~~~~~~~~~~~~~~~~~~----~-~~~iytDgS~~~~ 70 (328)
.+.+.+.+.|.+.++++. + .++|||.||..+.
T Consensus 79 vs~E~l~~qfd~~~~k~~~~~~~~~vkIFTSGSFLD~ 115 (358)
T COG1244 79 VSEENLINQFDEAYSKYEGKFDEFVVKIFTSGSFLDP 115 (358)
T ss_pred CCHHHHHHHHHHHHHHhcccCCCceEEEEcccccCCh
Confidence 456678888888885443 3 5999999999865
No 30
>PRK07758 hypothetical protein; Provisional
Probab=24.50 E-value=2.2e+02 Score=21.55 Aligned_cols=59 Identities=17% Similarity=0.223 Sum_probs=35.6
Q ss_pred cCCCCCccccccccccccchhh--cccccchHHHHHHhhcc--------------cCCChhhHHHHHHHHHHhcc
Q psy8376 266 ERKDPPACEFCGQTPVYLNHWL--TECHALGNLRRQHQRSI--------------LQDNVETIDRCMKFLYHTKL 324 (328)
Q Consensus 266 ~~~~~p~C~~Cg~~~etv~Hil--~~Cp~~~~~R~~l~~~~--------------~~~~~~~~~~~~~fl~~t~~ 324 (328)
+..+.|.||.|+....+..+++ +.=|.++..+..=+... .+++++.+++|.+-|.+-|+
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E~GL 92 (95)
T PRK07758 18 KSSDCPTCPTCEKERKPKEGFLSLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGL 92 (95)
T ss_pred ccCCCCCCcccccccCCCCCCCccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHHcCC
Confidence 3457899999997777777776 22232222222100000 24578888888888887765
No 31
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=24.39 E-value=37 Score=20.25 Aligned_cols=18 Identities=33% Similarity=1.056 Sum_probs=14.3
Q ss_pred Cccccccccccccchhhccccc
Q psy8376 271 PACEFCGQTPVYLNHWLTECHA 292 (328)
Q Consensus 271 p~C~~Cg~~~etv~Hil~~Cp~ 292 (328)
-.|..|+ ...|++-.||.
T Consensus 9 Y~C~~C~----~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCG----QKGHWIQDCPT 26 (32)
T ss_pred CEeecCC----CCCccHhHCCC
Confidence 3688898 34599999997
No 32
>PF06117 DUF957: Enterobacterial protein of unknown function (DUF957); InterPro: IPR009301 This family consists of several hypothetical proteins from Escherichia coli, Salmonella typhi, Shigella flexneri and Proteus vulgaris. The function of this family is unknown.
Probab=24.23 E-value=1.4e+02 Score=20.82 Aligned_cols=38 Identities=18% Similarity=0.360 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHhcCCcceEEEE------ecCHHHHHHHHc
Q psy8376 99 MAIDLCLNSILMYIQNNFCFKDFVIC------SDSKSSLQALKF 136 (328)
Q Consensus 99 ~Ai~~al~~~~~~~~~~~~~~~i~I~------sDs~~ai~~l~~ 136 (328)
.....||+.++.|+..+.....-.|| +||..++.++..
T Consensus 4 lt~~~~L~iLi~WLedNi~~es~iiFDNded~tdSa~llp~ie~ 47 (65)
T PF06117_consen 4 LTTEEALEILIAWLEDNIDCESDIIFDNDEDKTDSAALLPAIEQ 47 (65)
T ss_pred chHHHHHHHHHHHHHcccCCCCCeeecCCCcccchHHHHHHHHH
Confidence 45677888888898874223444444 677777776543
No 33
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=24.07 E-value=39 Score=22.77 Aligned_cols=21 Identities=24% Similarity=0.654 Sum_probs=11.4
Q ss_pred cccccccc-------ccccchhhccccc
Q psy8376 272 ACEFCGQT-------PVYLNHWLTECHA 292 (328)
Q Consensus 272 ~C~~Cg~~-------~etv~Hil~~Cp~ 292 (328)
.||.||.. +--...|.+.||+
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpK 33 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPK 33 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCC
Confidence 47777741 1134456667775
No 34
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.54 E-value=33 Score=26.82 Aligned_cols=22 Identities=18% Similarity=0.320 Sum_probs=13.8
Q ss_pred Cccccccccccccchhhcccccc
Q psy8376 271 PACEFCGQTPVYLNHWLTECHAL 293 (328)
Q Consensus 271 p~C~~Cg~~~etv~Hil~~Cp~~ 293 (328)
-.|..|| ....+....+.||.=
T Consensus 71 ~~C~~Cg-~~~~~~~~~~~CP~C 92 (113)
T PRK12380 71 AWCWDCS-QVVEIHQHDAQCPHC 92 (113)
T ss_pred EEcccCC-CEEecCCcCccCcCC
Confidence 3687788 555555555568853
No 35
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=22.84 E-value=1.4e+02 Score=23.60 Aligned_cols=43 Identities=9% Similarity=0.128 Sum_probs=24.5
Q ss_pred EEecCCCCCccchHHhHHHHHHhhCCCCCCcChhHHHHHHHHHHHHHHHHHHH
Q psy8376 164 LWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEIWR 216 (328)
Q Consensus 164 ~Wvp~H~gi~gNe~AD~lAk~a~~~~~~~~~~~~~~k~~~k~~~~~~W~~~W~ 216 (328)
.|+||++++.-| ---.+.|. .+ ........-+.++..|+.-|.
T Consensus 80 ~~CPGyse~QiN-~tQ~m~k~--------~v-~~n~Cleq~s~ll~lWr~f~r 122 (124)
T PF15216_consen 80 NYCPGYSETQIN-NTQAMKKR--------KV-TTNKCLEQVSQLLELWRRFSR 122 (124)
T ss_pred HhCCCcchhhcc-hhHHHHHH--------HH-HHHHHHHHHHHHHHHHHHHHh
Confidence 499999999888 22233332 01 112233344556778877664
No 36
>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=22.80 E-value=35 Score=26.74 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=14.1
Q ss_pred Cccccccccccccchhhcccccc
Q psy8376 271 PACEFCGQTPVYLNHWLTECHAL 293 (328)
Q Consensus 271 p~C~~Cg~~~etv~Hil~~Cp~~ 293 (328)
-.|..|| ..-++....+.||.=
T Consensus 71 ~~C~~Cg-~~~~~~~~~~~CP~C 92 (115)
T TIGR00100 71 CECEDCS-EEVSPEIDLYRCPKC 92 (115)
T ss_pred EEcccCC-CEEecCCcCccCcCC
Confidence 4688888 555555455678853
No 37
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=21.13 E-value=63 Score=21.56 Aligned_cols=27 Identities=30% Similarity=0.610 Sum_probs=15.8
Q ss_pred cccCCCCCccccccccccccchhhcccccchHHHHHH
Q psy8376 264 LLERKDPPACEFCGQTPVYLNHWLTECHALGNLRRQH 300 (328)
Q Consensus 264 r~~~~~~p~C~~Cg~~~etv~Hil~~Cp~~~~~R~~l 300 (328)
+..-..++.||.|+ . .|+.-.+.|+.|
T Consensus 18 ~~~S~~PatCP~C~-a---------~~~~srnLrRHl 44 (54)
T PF09237_consen 18 KSQSEQPATCPICG-A---------VIRQSRNLRRHL 44 (54)
T ss_dssp CCTTS--EE-TTT------------EESSHHHHHHHH
T ss_pred hhccCCCCCCCcch-h---------hccchhhHHHHH
Confidence 33445567999999 4 677778888774
No 38
>smart00642 Aamy Alpha-amylase domain.
Probab=20.81 E-value=2e+02 Score=23.94 Aligned_cols=30 Identities=10% Similarity=0.044 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEEecCCCCC
Q psy8376 143 LISKILLKIKEISSFGSQVSFLWIPSHVGI 172 (328)
Q Consensus 143 ~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi 172 (328)
...++.+.+..+.++|.+|.+-.|+.|++.
T Consensus 68 t~~d~~~lv~~~h~~Gi~vilD~V~NH~~~ 97 (166)
T smart00642 68 TMEDFKELVDAAHARGIKVILDVVINHTSD 97 (166)
T ss_pred CHHHHHHHHHHHHHCCCEEEEEECCCCCCC
Confidence 357788888899999999999999999987
No 39
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.73 E-value=44 Score=27.04 Aligned_cols=6 Identities=50% Similarity=1.470 Sum_probs=3.9
Q ss_pred cccccc
Q psy8376 272 ACEFCG 277 (328)
Q Consensus 272 ~C~~Cg 277 (328)
.|+.||
T Consensus 72 ~C~~CG 77 (135)
T PRK03824 72 KCRNCG 77 (135)
T ss_pred ECCCCC
Confidence 566677
No 40
>PRK12568 glycogen branching enzyme; Provisional
Probab=20.19 E-value=1.2e+02 Score=31.86 Aligned_cols=33 Identities=12% Similarity=0.135 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhcCCeEEEEEecCCCCCccc
Q psy8376 143 LISKILLKIKEISSFGSQVSFLWIPSHVGIREN 175 (328)
Q Consensus 143 ~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gN 175 (328)
..+++...+..+.+.|+.|-+-|||.|++..++
T Consensus 317 ~~~dfk~lV~~~H~~Gi~VIlD~V~nH~~~d~~ 349 (730)
T PRK12568 317 SPDGFAQFVDACHRAGIGVILDWVSAHFPDDAH 349 (730)
T ss_pred CHHHHHHHHHHHHHCCCEEEEEeccccCCcccc
Confidence 366788888899999999999999999987654
Done!