Query psy3058
Match_columns 244
No_of_seqs 177 out of 1525
Neff 8.5
Searched_HMMs 46136
Date Sat Aug 17 00:36:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3058.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3058hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.8 5.8E-19 1.2E-23 139.4 10.3 93 9-104 39-143 (161)
2 PF00075 RNase_H: RNase H; In 99.8 1.4E-19 3E-24 138.8 6.6 90 4-102 33-132 (132)
3 PRK08719 ribonuclease H; Revie 99.8 1.2E-18 2.6E-23 136.3 10.2 91 6-102 44-146 (147)
4 COG0328 RnhA Ribonuclease HI [ 99.8 1.2E-18 2.5E-23 135.6 8.2 95 9-104 40-146 (154)
5 PRK00203 rnhA ribonuclease H; 99.8 3.9E-18 8.6E-23 134.1 9.6 95 8-106 39-145 (150)
6 cd06222 RnaseH RNase H (RNase 99.6 7.5E-15 1.6E-19 109.9 10.9 93 8-101 37-130 (130)
7 PRK13907 rnhA ribonuclease H; 99.5 5.1E-13 1.1E-17 102.1 9.8 91 8-103 37-127 (128)
8 KOG3752|consensus 99.5 3.1E-13 6.7E-18 117.4 9.5 99 4-103 247-365 (371)
9 PF13456 RVT_3: Reverse transc 99.4 1.1E-12 2.3E-17 92.9 8.8 86 12-102 1-86 (87)
10 PRK07708 hypothetical protein; 99.3 2.7E-11 5.8E-16 100.7 10.7 98 5-106 111-211 (219)
11 PRK07238 bifunctional RNase H/ 99.1 3.6E-10 7.8E-15 101.5 10.8 92 9-105 42-134 (372)
12 PF13966 zf-RVT: zinc-binding 97.0 0.00034 7.3E-09 49.5 1.8 32 173-204 51-83 (86)
13 COG3341 Predicted double-stran 68.0 8.4 0.00018 31.9 4.0 90 11-104 107-202 (225)
14 KOG1812|consensus 64.6 23 0.00049 32.2 6.5 90 10-103 47-138 (384)
15 COG0296 GlgB 1,4-alpha-glucan 63.1 11 0.00023 36.5 4.3 36 60-95 214-249 (628)
16 PF05741 zf-nanos: Nanos RNA b 59.8 4.8 0.0001 25.8 0.9 20 183-202 35-54 (55)
17 PF09538 FYDLN_acid: Protein o 41.1 20 0.00044 26.3 1.9 20 174-194 20-39 (108)
18 KOG1994|consensus 40.6 10 0.00023 31.5 0.3 32 158-203 230-262 (268)
19 PF00098 zf-CCHC: Zinc knuckle 40.3 26 0.00056 16.9 1.6 17 183-202 2-18 (18)
20 PF14169 YdjO: Cold-inducible 39.9 21 0.00045 23.2 1.6 22 175-196 33-56 (59)
21 PF15322 PMSI1: Protein missin 37.4 20 0.00044 30.8 1.5 23 150-172 206-228 (311)
22 PF13917 zf-CCHC_3: Zinc knuck 35.0 22 0.00047 21.5 1.0 19 181-202 4-22 (42)
23 PF10298 WhiA_N: WhiA N-termin 33.3 28 0.00061 24.1 1.5 38 13-50 4-41 (86)
24 COG2093 DNA-directed RNA polym 33.0 32 0.00069 22.6 1.6 18 176-193 13-30 (64)
25 PF09345 DUF1987: Domain of un 32.6 71 0.0015 23.0 3.6 26 57-82 60-85 (99)
26 TIGR00100 hypA hydrogenase nic 31.7 23 0.0005 26.2 0.9 25 182-206 71-95 (115)
27 PRK12380 hydrogenase nickel in 30.7 24 0.00052 26.1 0.9 25 182-206 71-95 (113)
28 PRK03824 hypA hydrogenase nick 30.5 25 0.00054 26.9 1.0 11 183-193 72-82 (135)
29 KOG0419|consensus 30.5 2.4E+02 0.0052 21.6 6.1 52 37-98 80-131 (152)
30 cd00350 rubredoxin_like Rubred 28.8 30 0.00065 19.4 0.9 10 180-189 16-25 (33)
31 PF08274 PhnA_Zn_Ribbon: PhnA 27.9 25 0.00054 19.5 0.4 21 182-202 3-24 (30)
32 PF14205 Cys_rich_KTR: Cystein 27.2 29 0.00064 22.1 0.7 22 183-204 6-35 (55)
33 TIGR03847 conserved hypothetic 27.2 40 0.00088 26.9 1.6 21 179-202 154-175 (177)
34 PF13395 HNH_4: HNH endonuclea 27.1 27 0.00059 21.9 0.6 14 184-197 1-24 (54)
35 PF13519 VWA_2: von Willebrand 26.5 1.3E+02 0.0027 22.6 4.4 53 17-83 83-136 (172)
36 COG4566 TtrR Response regulato 25.3 3.6E+02 0.0078 22.1 6.7 93 19-122 15-120 (202)
37 PF04863 EGF_alliinase: Alliin 25.0 14 0.00031 23.6 -1.0 24 164-189 19-42 (56)
38 PRK12568 glycogen branching en 24.4 1.1E+02 0.0023 30.4 4.2 32 59-90 318-349 (730)
39 PRK03681 hypA hydrogenase nick 23.9 39 0.00085 25.0 1.0 24 182-205 71-95 (114)
40 PF05830 NodZ: Nodulation prot 23.8 1.6E+02 0.0034 26.0 4.7 34 21-54 200-235 (321)
41 PRK09710 lar restriction allev 23.6 35 0.00076 22.6 0.6 23 182-204 7-34 (64)
42 TIGR01206 lysW lysine biosynth 23.6 52 0.0011 21.0 1.3 21 183-203 4-28 (54)
43 PF09107 SelB-wing_3: Elongati 23.2 1.2E+02 0.0026 18.8 3.0 26 216-241 15-40 (50)
44 PF03119 DNA_ligase_ZBD: NAD-d 23.1 33 0.00071 18.6 0.3 20 183-202 1-22 (28)
45 PF00325 Crp: Bacterial regula 22.8 1.2E+02 0.0026 17.0 2.6 27 215-241 6-32 (32)
46 PRK00398 rpoP DNA-directed RNA 22.4 50 0.0011 19.9 1.1 7 183-189 5-11 (46)
47 KOG3243|consensus 22.4 1E+02 0.0022 23.6 2.8 24 64-87 41-64 (158)
48 COG1326 Uncharacterized archae 21.9 42 0.00092 27.3 0.9 26 182-207 7-40 (201)
49 PF07282 OrfB_Zn_ribbon: Putat 21.9 52 0.0011 21.5 1.2 23 180-202 27-51 (69)
50 PRK00420 hypothetical protein; 21.1 64 0.0014 23.9 1.6 28 163-190 21-49 (112)
51 PF13821 DUF4187: Domain of un 20.6 31 0.00066 22.1 -0.2 22 183-204 29-51 (55)
52 PRK06393 rpoE DNA-directed RNA 20.1 71 0.0015 21.2 1.5 12 180-191 16-27 (64)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.79 E-value=5.8e-19 Score=139.40 Aligned_cols=93 Identities=25% Similarity=0.340 Sum_probs=76.3
Q ss_pred CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcc--------c---cccHHH-HHHHHHHHHHHhcCCeE
Q psy3058 9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQL--------F---CKNILI-HDIQVACHKLILKGNNV 76 (244)
Q Consensus 9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~--------~---~~~~~~-~~i~~~~~~l~~~~~~v 76 (244)
.+|++.|||.|++.||+.+.. ....|.|+|||++|+++++.+ + +++++. +++++.+..+... ..|
T Consensus 39 ~~TNnraEl~Aii~aL~~~~~--~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v 115 (161)
T PRK06548 39 IATNNIAELTAVRELLIATRH--TDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNI 115 (161)
T ss_pred CCCHHHHHHHHHHHHHHhhhc--CCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-Cce
Confidence 579999999999999986643 234699999999999999952 1 245665 6777888777654 479
Q ss_pred EEEeecCCCCCccchhhchHHHHHhhhc
Q psy3058 77 KIIWIPSHCGIAGNEEVDKAAQSFINAQ 104 (244)
Q Consensus 77 ~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 104 (244)
+|.|||||+|++|||.||+||++++...
T Consensus 116 ~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 116 RMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred EEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999988653
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=99.79 E-value=1.4e-19 Score=138.77 Aligned_cols=90 Identities=27% Similarity=0.455 Sum_probs=71.0
Q ss_pred ecCCCCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhc-----ccccc----HHHHHHHHHHHHHHhcCC
Q psy3058 4 YRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQ-----LFCKN----ILIHDIQVACHKLILKGN 74 (244)
Q Consensus 4 ~~l~~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~-----~~~~~----~~~~~i~~~~~~l~~~~~ 74 (244)
+.++ ..|++.||+.||..||+ +.. ...++|+|||+++++.+.. ..... ++...|.+.+ ..+.
T Consensus 33 ~~~~-~~s~~~aEl~Ai~~AL~-~~~---~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~ 103 (132)
T PF00075_consen 33 FRLG-GQSNNRAELQAIIEALK-ALE---HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGI 103 (132)
T ss_dssp EEEE-SECHHHHHHHHHHHHHH-THS---TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSS
T ss_pred eccc-ccchhhhheehHHHHHH-Hhh---cccccccccHHHHHHHHHHhccccccccccccccchhheeecc----ccce
Confidence 3455 88999999999999999 543 2789999999999998888 32222 3444444433 5689
Q ss_pred eEEEEeecCCCCC-ccchhhchHHHHHhh
Q psy3058 75 NVKIIWIPSHCGI-AGNEEVDKAAQSFIN 102 (244)
Q Consensus 75 ~v~~~Wvp~H~gi-~gNe~AD~lAk~a~~ 102 (244)
.|.|+|||||+|+ .||+.||+|||+|+.
T Consensus 104 ~v~~~~V~~H~~~~~~N~~aD~lAk~a~~ 132 (132)
T PF00075_consen 104 KVRFRWVPGHSGVPQGNERADRLAKEAAQ 132 (132)
T ss_dssp EEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred EEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence 9999999999999 699999999999873
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.78 E-value=1.2e-18 Score=136.28 Aligned_cols=91 Identities=22% Similarity=0.284 Sum_probs=73.9
Q ss_pred CCCCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhc--------ccc---ccHH-HHHHHHHHHHHHhcC
Q psy3058 6 LNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQ--------LFC---KNIL-IHDIQVACHKLILKG 73 (244)
Q Consensus 6 l~~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~--------~~~---~~~~-~~~i~~~~~~l~~~~ 73 (244)
+....|++.||+.|+..||+.+.+. .+|+|||++|+++++. .+. +.++ ..++++.+..+.. .
T Consensus 44 ~~~~~Tnn~aEl~A~~~aL~~~~~~-----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~ 117 (147)
T PRK08719 44 VNRYTDNAELELLALIEALEYARDG-----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-R 117 (147)
T ss_pred CCCCccHHHHHHHHHHHHHHHcCCC-----CEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-C
Confidence 5556899999999999999998542 3899999999999953 332 2233 2577777777755 5
Q ss_pred CeEEEEeecCCCCCccchhhchHHHHHhh
Q psy3058 74 NNVKIIWIPSHCGIAGNEEVDKAAQSFIN 102 (244)
Q Consensus 74 ~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~ 102 (244)
..|+|.|||||+|++|||.||+||++|+.
T Consensus 118 ~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 118 KYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred CcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 67999999999999999999999999875
No 4
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.77 E-value=1.2e-18 Score=135.57 Aligned_cols=95 Identities=22% Similarity=0.269 Sum_probs=80.8
Q ss_pred CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccc---c--------ccHH-HHHHHHHHHHHHhcCCeE
Q psy3058 9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLF---C--------KNIL-IHDIQVACHKLILKGNNV 76 (244)
Q Consensus 9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~---~--------~~~~-~~~i~~~~~~l~~~~~~v 76 (244)
.+||+.||++|++.||+.+.+. ....|.|+|||++|+++|+.+. . +.|+ -+++++.+.++..+...|
T Consensus 40 ~tTNNraEl~A~i~AL~~l~~~-~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v 118 (154)
T COG0328 40 RTTNNRAELRALIEALEALKEL-GACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELV 118 (154)
T ss_pred cccChHHHHHHHHHHHHHHHhc-CCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeE
Confidence 6899999999999999999863 3578999999999999999431 1 1233 257788888888877799
Q ss_pred EEEeecCCCCCccchhhchHHHHHhhhc
Q psy3058 77 KIIWIPSHCGIAGNEEVDKAAQSFINAQ 104 (244)
Q Consensus 77 ~~~Wvp~H~gi~gNe~AD~lAk~a~~~~ 104 (244)
.+.|||||+|.++||.||+||+.+++..
T Consensus 119 ~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 119 FWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred EEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999998765
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.76 E-value=3.9e-18 Score=134.09 Aligned_cols=95 Identities=20% Similarity=0.306 Sum_probs=75.4
Q ss_pred CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcc--------c---cccHHH-HHHHHHHHHHHhcCCe
Q psy3058 8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQL--------F---CKNILI-HDIQVACHKLILKGNN 75 (244)
Q Consensus 8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~--------~---~~~~~~-~~i~~~~~~l~~~~~~ 75 (244)
...|++.|||.|+..||+.+.+ ...|.|+|||++|++.|..+ + .++++. .++++.+.++.. ...
T Consensus 39 ~~~TN~~aEL~Ai~~AL~~~~~---~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~ 114 (150)
T PRK00203 39 ALTTNNRMELMAAIEALEALKE---PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQ 114 (150)
T ss_pred CCCcHHHHHHHHHHHHHHHcCC---CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCc
Confidence 4678999999999999998854 35799999999999999963 1 123332 345566666543 478
Q ss_pred EEEEeecCCCCCccchhhchHHHHHhhhcCC
Q psy3058 76 VKIIWIPSHCGIAGNEEVDKAAQSFINAQNY 106 (244)
Q Consensus 76 v~~~Wvp~H~gi~gNe~AD~lAk~a~~~~~~ 106 (244)
|.|.|||||+|++||+.||+|||+|......
T Consensus 115 v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~~ 145 (150)
T PRK00203 115 IKWHWVKGHAGHPENERCDELARAGAEEATL 145 (150)
T ss_pred eEEEEecCCCCCHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999876543
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=99.61 E-value=7.5e-15 Score=109.89 Aligned_cols=93 Identities=25% Similarity=0.363 Sum_probs=77.0
Q ss_pred CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcCCeEEEEeecCCCC
Q psy3058 8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKGNNVKIIWIPSHCG 86 (244)
Q Consensus 8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~g 86 (244)
...+++.||+.|+..||+.+... ....+.|++||+.+++.+.+... .......+...+..+...+..+.|.|||+|+|
T Consensus 37 ~~~s~~~aEl~al~~al~~~~~~-~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~ 115 (130)
T cd06222 37 GNTTNNRAELLALIEALELALEL-GGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSG 115 (130)
T ss_pred CCCcHHHHHHHHHHHHHHHHHhC-CCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCC
Confidence 57899999999999999999754 35789999999999999998754 22344455555555556788999999999999
Q ss_pred CccchhhchHHHHHh
Q psy3058 87 IAGNEEVDKAAQSFI 101 (244)
Q Consensus 87 i~gNe~AD~lAk~a~ 101 (244)
+++|+.||.|||++.
T Consensus 116 ~~~n~~ad~la~~~~ 130 (130)
T cd06222 116 IEGNERADALAKEAA 130 (130)
T ss_pred CcchHHHHHHHHhhC
Confidence 999999999999873
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.46 E-value=5.1e-13 Score=102.12 Aligned_cols=91 Identities=22% Similarity=0.228 Sum_probs=76.4
Q ss_pred CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCC
Q psy3058 8 SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGI 87 (244)
Q Consensus 8 ~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi 87 (244)
...|++.||+.|++.||+.+...+. ..|.|+|||+.+++.+++.+...+....+++.+..+..++..+.|.|||.
T Consensus 37 ~~~tn~~AE~~All~aL~~a~~~g~-~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r---- 111 (128)
T PRK13907 37 GTMSNHEAEYHALLAALKYCTEHNY-NIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPS---- 111 (128)
T ss_pred cccCCcHHHHHHHHHHHHHHHhCCC-CEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCc----
Confidence 3579999999999999999987643 57999999999999999976544455677777777777788888999995
Q ss_pred ccchhhchHHHHHhhh
Q psy3058 88 AGNEEVDKAAQSFINA 103 (244)
Q Consensus 88 ~gNe~AD~lAk~a~~~ 103 (244)
++|+.||.||+.|...
T Consensus 112 ~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 112 SQNKVADELARKAILQ 127 (128)
T ss_pred hhchhHHHHHHHHHhc
Confidence 6999999999998753
No 8
>KOG3752|consensus
Probab=99.45 E-value=3.1e-13 Score=117.44 Aligned_cols=99 Identities=23% Similarity=0.221 Sum_probs=77.2
Q ss_pred ecCC-CCCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-----------ccH-----H-HHHHHHH
Q psy3058 4 YRLN-SLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-----------KNI-----L-IHDIQVA 65 (244)
Q Consensus 4 ~~l~-~~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-----------~~~-----~-~~~i~~~ 65 (244)
++|. ..+|+|.|||.||..||+.+.+... .+++|.|||+.++++|+.+.. .++ + -......
T Consensus 247 ~pv~~g~qtNnrAEl~Av~~ALkka~~~~~-~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e 325 (371)
T KOG3752|consen 247 GPLAGGRQTNNRAELIAAIEALKKARSKNI-NKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNE 325 (371)
T ss_pred ccCCCCcccccHHHHHHHHHHHHHHHhcCC-CcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHH
Confidence 4555 7889999999999999999987543 489999999999999997531 122 1 1233444
Q ss_pred HHHHHh--cCCeEEEEeecCCCCCccchhhchHHHHHhhh
Q psy3058 66 CHKLIL--KGNNVKIIWIPSHCGIAGNEEVDKAAQSFINA 103 (244)
Q Consensus 66 ~~~l~~--~~~~v~~~Wvp~H~gi~gNe~AD~lAk~a~~~ 103 (244)
+.+|.+ ++..|.+.|||||.|+.|||.||.||++++..
T Consensus 326 ~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 326 LDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred HHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 444443 36899999999999999999999999998644
No 9
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.42 E-value=1.1e-12 Score=92.94 Aligned_cols=86 Identities=20% Similarity=0.197 Sum_probs=68.8
Q ss_pred hHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCCccch
Q psy3058 12 SFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNE 91 (244)
Q Consensus 12 ~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe 91 (244)
+..||+.|+..||+.+.+.+. ++|+|.|||+.+++.|++..........+...+..+...+..+.|.||| .++|.
T Consensus 1 ~~~aE~~al~~al~~a~~~g~-~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~ 75 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGI-RKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNK 75 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT--SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSH
T ss_pred CcHHHHHHHHHHHHHHHHCCC-CEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhH
Confidence 468999999999999988654 6899999999999999998543335566777777777888999999999 89999
Q ss_pred hhchHHHHHhh
Q psy3058 92 EVDKAAQSFIN 102 (244)
Q Consensus 92 ~AD~lAk~a~~ 102 (244)
.||.|||.|..
T Consensus 76 ~A~~LA~~a~~ 86 (87)
T PF13456_consen 76 VADALAKFALS 86 (87)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHhh
Confidence 99999999863
No 10
>PRK07708 hypothetical protein; Validated
Probab=99.29 E-value=2.7e-11 Score=100.66 Aligned_cols=98 Identities=11% Similarity=0.053 Sum_probs=76.4
Q ss_pred cCCCCCChHHHHHHHHHHHHHHhhcCCCC-CcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcC-CeEEEEee
Q psy3058 5 RLNSLSSSFTAEAFAMEMCLDNLINRPIP-DNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKG-NNVKIIWI 81 (244)
Q Consensus 5 ~l~~~~t~~~AEl~Ai~~al~~~~~~~~~-~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~-~~v~~~Wv 81 (244)
.|+...|++.||+.|++.||+.+.+.+.. ..|.|++||+.+++.+++.++ .++....+.+.+..+..+. ..+.|.||
T Consensus 111 ~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~V 190 (219)
T PRK07708 111 YIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPI 190 (219)
T ss_pred cccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEEC
Confidence 45556899999999999999999886543 248999999999999999874 3445555556665554443 35788999
Q ss_pred cCCCCCccchhhchHHHHHhhhcCC
Q psy3058 82 PSHCGIAGNEEVDKAAQSFINAQNY 106 (244)
Q Consensus 82 p~H~gi~gNe~AD~lAk~a~~~~~~ 106 (244)
| ...|+.||+||++|.+....
T Consensus 191 p----R~~N~~AD~LAk~Al~~~~~ 211 (219)
T PRK07708 191 S----RKQNKEADQLATQALEGTVI 211 (219)
T ss_pred C----chhhhHHHHHHHHHHhcCCC
Confidence 8 67899999999999986443
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.13 E-value=3.6e-10 Score=101.48 Aligned_cols=92 Identities=20% Similarity=0.233 Sum_probs=77.2
Q ss_pred CCChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhcccc-ccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCC
Q psy3058 9 LSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFC-KNILIHDIQVACHKLILKGNNVKIIWIPSHCGI 87 (244)
Q Consensus 9 ~~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~-~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi 87 (244)
..|++.||+.|++.||+.+.+.+. +.|.|++||+.+++.+++.+. .++-...+...+..+..++..++|.|||.
T Consensus 42 ~~tnn~AE~~All~gL~~a~~~g~-~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r---- 116 (372)
T PRK07238 42 RATNNVAEYRGLIAGLEAAAELGA-TEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR---- 116 (372)
T ss_pred CCCchHHHHHHHHHHHHHHHhCCC-CeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----
Confidence 678999999999999999987643 589999999999999998764 44445566667777778888999999994
Q ss_pred ccchhhchHHHHHhhhcC
Q psy3058 88 AGNEEVDKAAQSFINAQN 105 (244)
Q Consensus 88 ~gNe~AD~lAk~a~~~~~ 105 (244)
.+|+.||.||+.|.....
T Consensus 117 ~~N~~AD~LA~~a~~~~~ 134 (372)
T PRK07238 117 ARNAHADRLANEAMDAAA 134 (372)
T ss_pred hhhhHHHHHHHHHHHhhc
Confidence 799999999999976643
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=97.03 E-value=0.00034 Score=49.47 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=26.5
Q ss_pred ccccCCCCCCCCCCCCC-ccccccccccccCcH
Q psy3058 173 GFLMERTDPPQCEVCNV-TITVKHILCHCTKYT 204 (244)
Q Consensus 173 ~~~~~~~~~p~C~~Cg~-~et~~H~l~~Cp~~~ 204 (244)
+.+.+...++.|..|+. .||++|++++||...
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 34456677899999997 899999999999754
No 13
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=68.05 E-value=8.4 Score=31.87 Aligned_cols=90 Identities=10% Similarity=-0.025 Sum_probs=59.8
Q ss_pred ChHHHHHHHHHHHHHHhhcCCCCCcEEEE----eccHHHHHHHhccccccHHHHHHHHHHHHHHhcC--CeEEEEeecCC
Q psy3058 11 SSFTAEAFAMEMCLDNLINRPIPDNILIF----TDSKSLISSMQQLFCKNILIHDIQVACHKLILKG--NNVKIIWIPSH 84 (244)
Q Consensus 11 t~~~AEl~Ai~~al~~~~~~~~~~~i~i~----tDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~--~~v~~~Wvp~H 84 (244)
++..+|.+|++.+|+.+....+.+.++++ .||++...-+..-.-.. --.....+....| ....+.|+--|
T Consensus 107 ~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k----~~~~~~~e~~~~~~~v~h~~k~i~~~ 182 (225)
T COG3341 107 SNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETK----VNLLKDREFFSIGKGVFHDEKDINIH 182 (225)
T ss_pred cCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHhhhhhhH----HHHHHhHHhhhccchhhhhhhhcccc
Confidence 56789999999999999876555565668 79999988886532111 0011111112223 45577899999
Q ss_pred CCCccchhhchHHHHHhhhc
Q psy3058 85 CGIAGNEEVDKAAQSFINAQ 104 (244)
Q Consensus 85 ~gi~gNe~AD~lAk~a~~~~ 104 (244)
.++..+..++..+.......
T Consensus 183 ~~~~~~~~~~s~~~~~~k~~ 202 (225)
T COG3341 183 IWIFESKKGNSHVYNTSKKE 202 (225)
T ss_pred cccchhhhhhhhhhchhhhh
Confidence 99988888888776655443
No 14
>KOG1812|consensus
Probab=64.63 E-value=23 Score=32.19 Aligned_cols=90 Identities=17% Similarity=0.143 Sum_probs=56.7
Q ss_pred CChHHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccccH--HHHHHHHHHHHHHhcCCeEEEEeecCCCCC
Q psy3058 10 SSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNI--LIHDIQVACHKLILKGNNVKIIWIPSHCGI 87 (244)
Q Consensus 10 ~t~~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~~~--~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi 87 (244)
.+...||++|+..+|..+.+.+. ..+++++|+......+.+...+.. .+..+......++.+.....-+-||- .
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~-~~~~~~~d~~~~~~~v~~~~~~~~~~~~~~l~~~v~~~r~~l~~~~~i~~~~---~ 122 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGL-NHIVIYCDDELIYESVAGREKPEQHRKIVLLVELVQRIREQLTSSEPILVPK---N 122 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhcc-ccceEecccHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhcccceeccc---c
Confidence 67889999999999999987643 578999997777776655543332 34455555555554443333333331 1
Q ss_pred ccchhhchHHHHHhhh
Q psy3058 88 AGNEEVDKAAQSFINA 103 (244)
Q Consensus 88 ~gNe~AD~lAk~a~~~ 103 (244)
.....|=++|+++...
T Consensus 123 ~d~~~~~~lA~e~i~s 138 (384)
T KOG1812|consen 123 ADIKFAYKLAREAIVS 138 (384)
T ss_pred hhhHHHHHHHHHhhcc
Confidence 1123467778777764
No 15
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=63.12 E-value=11 Score=36.47 Aligned_cols=36 Identities=22% Similarity=0.312 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHhcCCeEEEEeecCCCCCccchhhch
Q psy3058 60 HDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDK 95 (244)
Q Consensus 60 ~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~ 95 (244)
..+...+..+-+.|..|-+-|||+|-+..||-.+--
T Consensus 214 edfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~f 249 (628)
T COG0296 214 EDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLARF 249 (628)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhhc
Confidence 355555666667899999999999999988876643
No 16
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=59.83 E-value=4.8 Score=25.84 Aligned_cols=20 Identities=30% Similarity=0.634 Sum_probs=9.9
Q ss_pred CCCCCCCccccccccccccC
Q psy3058 183 QCEVCNVTITVKHILCHCTK 202 (244)
Q Consensus 183 ~C~~Cg~~et~~H~l~~Cp~ 202 (244)
.|+.||+.-+-.|..-.||.
T Consensus 35 ~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 35 VCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp --TTT---GGG---GGG-TT
T ss_pred cCCCCcCcCccccccccCcC
Confidence 69999998888999999995
No 17
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=41.07 E-value=20 Score=26.34 Aligned_cols=20 Identities=20% Similarity=0.622 Sum_probs=14.6
Q ss_pred cccCCCCCCCCCCCCCccccc
Q psy3058 174 FLMERTDPPQCEVCNVTITVK 194 (244)
Q Consensus 174 ~~~~~~~~p~C~~Cg~~et~~ 194 (244)
|=+|+ ++-.|+.||....++
T Consensus 20 YDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 20 YDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCC-CCccCCCCCCccCcc
Confidence 45677 566799999876555
No 18
>KOG1994|consensus
Probab=40.55 E-value=10 Score=31.54 Aligned_cols=32 Identities=25% Similarity=0.375 Sum_probs=23.4
Q ss_pred hhhhhhhccccccccccccCCCCCCCCCCCCC-ccccccccccccCc
Q psy3058 158 IILSRLRIGHTRLTHGFLMERTDPPQCEVCNV-TITVKHILCHCTKY 203 (244)
Q Consensus 158 ~~L~qlrtGH~~~~~~~~~~~~~~p~C~~Cg~-~et~~H~l~~Cp~~ 203 (244)
.++.-||.||.+ |-+||. -.|.+-++-+||..
T Consensus 230 ~in~~LR~eh~Y--------------C~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 230 KINIFLRSEHYY--------------CFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred HHHHHHhccceE--------------EEEeccccCCHHHHHHhCCCC
Confidence 445566777754 557998 47999999999964
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=40.33 E-value=26 Score=16.86 Aligned_cols=17 Identities=35% Similarity=0.702 Sum_probs=11.9
Q ss_pred CCCCCCCccccccccccccC
Q psy3058 183 QCEVCNVTITVKHILCHCTK 202 (244)
Q Consensus 183 ~C~~Cg~~et~~H~l~~Cp~ 202 (244)
.|..||. ..|+.-+||.
T Consensus 2 ~C~~C~~---~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGE---PGHIARDCPK 18 (18)
T ss_dssp BCTTTSC---SSSCGCTSSS
T ss_pred cCcCCCC---cCcccccCcc
Confidence 4667775 4688888873
No 20
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=39.87 E-value=21 Score=23.24 Aligned_cols=22 Identities=14% Similarity=0.445 Sum_probs=16.1
Q ss_pred ccCCCCCCCCCCCCCc--cccccc
Q psy3058 175 LMERTDPPQCEVCNVT--ITVKHI 196 (244)
Q Consensus 175 ~~~~~~~p~C~~Cg~~--et~~H~ 196 (244)
-|...+.|.|+.|+.+ +...++
T Consensus 33 nFs~~~~p~CPlC~s~M~~~~r~L 56 (59)
T PF14169_consen 33 NFSFEEEPVCPLCKSPMVSGTRML 56 (59)
T ss_pred ccccCCCccCCCcCCccccceeec
Confidence 3667888999999973 455544
No 21
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=37.35 E-value=20 Score=30.80 Aligned_cols=23 Identities=30% Similarity=0.205 Sum_probs=16.1
Q ss_pred CCCCchhhhhhhhhhcccccccc
Q psy3058 150 NRNSRKEEIILSRLRIGHTRLTH 172 (244)
Q Consensus 150 ~l~~R~~~~~L~qlrtGH~~~~~ 172 (244)
+|+.|-..-.|.||||.|-..+|
T Consensus 206 GlsGrLRvGALsqLrTehrPCtY 228 (311)
T PF15322_consen 206 GLSGRLRVGALSQLRTEHRPCTY 228 (311)
T ss_pred ccccceecchhhhhhhccCCccc
Confidence 34434445669999999998884
No 22
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=35.01 E-value=22 Score=21.45 Aligned_cols=19 Identities=21% Similarity=0.581 Sum_probs=15.4
Q ss_pred CCCCCCCCCccccccccccccC
Q psy3058 181 PPQCEVCNVTITVKHILCHCTK 202 (244)
Q Consensus 181 ~p~C~~Cg~~et~~H~l~~Cp~ 202 (244)
...|..|+. ..|+.++||.
T Consensus 4 ~~~CqkC~~---~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQ---KGHWTYECPN 22 (42)
T ss_pred CCcCcccCC---CCcchhhCCC
Confidence 457988985 4699999996
No 23
>PF10298 WhiA_N: WhiA N-terminal LAGLIDADG-like domain; InterPro: IPR018478 This entry represents the N-terminal domain of sporulation factor WhiA []. This domain is related to the LAGLIDADG homing endonuclease domain while the C-terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain [].; PDB: 3HYI_A 3HYJ_D.
Probab=33.29 E-value=28 Score=24.14 Aligned_cols=38 Identities=16% Similarity=-0.024 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCcEEEEeccHHHHHHHh
Q psy3058 13 FTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQ 50 (244)
Q Consensus 13 ~~AEl~Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~ 50 (244)
-.||+.|++.---.+.-....-.+.|-|||.++.+.+-
T Consensus 4 ~~AELaAlir~~G~l~~~~~~~~l~~~ten~~vARri~ 41 (86)
T PF10298_consen 4 RIAELAALIRFSGSLSISNGRISLEISTENAAVARRIY 41 (86)
T ss_dssp HHHHHHHHHHHHEEECTTTTEEEE--EES-HHHHHHHH
T ss_pred HHHHHHHHHHhCCEEEEECCEEEEEEEeCCHHHHHHHH
Confidence 46999999776655433222236677888888766654
No 24
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=32.97 E-value=32 Score=22.62 Aligned_cols=18 Identities=28% Similarity=0.497 Sum_probs=12.1
Q ss_pred cCCCCCCCCCCCCCcccc
Q psy3058 176 MERTDPPQCEVCNVTITV 193 (244)
Q Consensus 176 ~~~~~~p~C~~Cg~~et~ 193 (244)
+-..+...|+.||.++..
T Consensus 13 l~~~d~e~CP~Cgs~~~t 30 (64)
T COG2093 13 LTPEDTEICPVCGSTDLT 30 (64)
T ss_pred cCCCCCccCCCCCCcccc
Confidence 445556679999986433
No 25
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=32.57 E-value=71 Score=23.05 Aligned_cols=26 Identities=23% Similarity=0.273 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHhcCCeEEEEeec
Q psy3058 57 ILIHDIQVACHKLILKGNNVKIIWIP 82 (244)
Q Consensus 57 ~~~~~i~~~~~~l~~~~~~v~~~Wvp 82 (244)
..+-.|++.+..+...|..|.+.|.-
T Consensus 60 k~l~~i~~~Le~~~~~g~~V~v~Wyy 85 (99)
T PF09345_consen 60 KALMDIFDLLEDAAQKGGKVTVNWYY 85 (99)
T ss_pred HHHHHHHHHHHHHHhcCCcEEEEEEE
Confidence 44567777777778889999999976
No 26
>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=31.73 E-value=23 Score=26.23 Aligned_cols=25 Identities=28% Similarity=0.538 Sum_probs=17.4
Q ss_pred CCCCCCCCccccccccccccCcHHH
Q psy3058 182 PQCEVCNVTITVKHILCHCTKYTQI 206 (244)
Q Consensus 182 p~C~~Cg~~et~~H~l~~Cp~~~~~ 206 (244)
-.|..||...++....+.||.....
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 71 CECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred EEcccCCCEEecCCcCccCcCCcCC
Confidence 4698899866665556789976543
No 27
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.68 E-value=24 Score=26.08 Aligned_cols=25 Identities=12% Similarity=0.320 Sum_probs=16.7
Q ss_pred CCCCCCCCccccccccccccCcHHH
Q psy3058 182 PQCEVCNVTITVKHILCHCTKYTQI 206 (244)
Q Consensus 182 p~C~~Cg~~et~~H~l~~Cp~~~~~ 206 (244)
-.|..||....+....+.||.....
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCCCC
Confidence 3688888765555555669976543
No 28
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.51 E-value=25 Score=26.89 Aligned_cols=11 Identities=18% Similarity=0.676 Sum_probs=6.8
Q ss_pred CCCCCCCcccc
Q psy3058 183 QCEVCNVTITV 193 (244)
Q Consensus 183 ~C~~Cg~~et~ 193 (244)
.|..||...++
T Consensus 72 ~C~~CG~~~~~ 82 (135)
T PRK03824 72 KCRNCGNEWSL 82 (135)
T ss_pred ECCCCCCEEec
Confidence 57778864433
No 29
>KOG0419|consensus
Probab=30.46 E-value=2.4e+02 Score=21.58 Aligned_cols=52 Identities=13% Similarity=0.197 Sum_probs=38.4
Q ss_pred EEEeccHHHHHHHhccccccHHHHHHHHHHHHHHhcCCeEEEEeecCCCCCccchhhchHHH
Q psy3058 37 LIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQ 98 (244)
Q Consensus 37 ~i~tDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gNe~AD~lAk 98 (244)
-|+.|-+..|+.|++.+++.+-+..|+..++.|...... ..+.|-.|-+|=+
T Consensus 80 Nvya~G~iClDiLqNrWsp~Ydva~ILtsiQslL~dPn~----------~sPaN~eAA~Lf~ 131 (152)
T KOG0419|consen 80 NVYADGSICLDILQNRWSPTYDVASILTSIQSLLNDPNP----------NSPANSEAARLFS 131 (152)
T ss_pred CcCCCCcchHHHHhcCCCCchhHHHHHHHHHHHhcCCCC----------CCcccHHHHHHHh
Confidence 367899999999999999988888898888888654321 2456666555443
No 30
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=28.82 E-value=30 Score=19.40 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=5.2
Q ss_pred CCCCCCCCCC
Q psy3058 180 DPPQCEVCNV 189 (244)
Q Consensus 180 ~~p~C~~Cg~ 189 (244)
++..|+.||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 3445555554
No 31
>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=27.87 E-value=25 Score=19.55 Aligned_cols=21 Identities=24% Similarity=0.602 Sum_probs=9.2
Q ss_pred CCCCCCCCcc-ccccccccccC
Q psy3058 182 PQCEVCNVTI-TVKHILCHCTK 202 (244)
Q Consensus 182 p~C~~Cg~~e-t~~H~l~~Cp~ 202 (244)
|.|+.|+.+. =.+..++.||.
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 6799999743 35556677874
No 32
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=27.24 E-value=29 Score=22.13 Aligned_cols=22 Identities=23% Similarity=0.513 Sum_probs=15.0
Q ss_pred CCCCCCC--c-----c-ccccccccccCcH
Q psy3058 183 QCEVCNV--T-----I-TVKHILCHCTKYT 204 (244)
Q Consensus 183 ~C~~Cg~--~-----e-t~~H~l~~Cp~~~ 204 (244)
.|+.||. + + -...+.+.||+..
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK 35 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCK 35 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCC
Confidence 4889994 1 2 4566778999754
No 33
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=27.20 E-value=40 Score=26.94 Aligned_cols=21 Identities=33% Similarity=0.861 Sum_probs=16.0
Q ss_pred CCCCCCCCCCCccc-cccccccccC
Q psy3058 179 TDPPQCEVCNVTIT-VKHILCHCTK 202 (244)
Q Consensus 179 ~~~p~C~~Cg~~et-~~H~l~~Cp~ 202 (244)
..-|.|+.||.+.+ --|+ ||+
T Consensus 154 AGRP~CPlCg~PldP~GH~---Cpr 175 (177)
T TIGR03847 154 AGRPPCPLCGRPIDPDGHI---CPR 175 (177)
T ss_pred CCCCCCCCCCCCCCCCCcc---CCC
Confidence 35799999999755 4576 886
No 34
>PF13395 HNH_4: HNH endonuclease
Probab=27.14 E-value=27 Score=21.94 Aligned_cols=14 Identities=29% Similarity=0.852 Sum_probs=9.7
Q ss_pred CCCCCCc----------ccccccc
Q psy3058 184 CEVCNVT----------ITVKHIL 197 (244)
Q Consensus 184 C~~Cg~~----------et~~H~l 197 (244)
|.+||.. -+++|++
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHii 24 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHII 24 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEe
Confidence 7889862 2668884
No 35
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=26.54 E-value=1.3e+02 Score=22.63 Aligned_cols=53 Identities=21% Similarity=0.132 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhcCC-CCCcEEEEeccHHHHHHHhccccccHHHHHHHHHHHHHHhcCCeEEEEeecC
Q psy3058 17 AFAMEMCLDNLINRP-IPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPS 83 (244)
Q Consensus 17 l~Ai~~al~~~~~~~-~~~~i~i~tDs~~al~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~Wvp~ 83 (244)
..|+..|.+.+.... ..+.|+++||.... + ... +.+..+...+..|.+..+..
T Consensus 83 ~~al~~a~~~~~~~~~~~~~iv~iTDG~~~---------~-~~~----~~~~~~~~~~i~i~~v~~~~ 136 (172)
T PF13519_consen 83 YDALQEAAKMLASSDNRRRAIVLITDGEDN---------S-SDI----EAAKALKQQGITIYTVGIGS 136 (172)
T ss_dssp HHHHHHHHHHHHC-SSEEEEEEEEES-TTH---------C-HHH----HHHHHHHCTTEEEEEEEES-
T ss_pred HHHHHHHHHHHHhCCCCceEEEEecCCCCC---------c-chh----HHHHHHHHcCCeEEEEEECC
Confidence 356777777776543 45689999996322 1 111 24445566777777776663
No 36
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=25.29 E-value=3.6e+02 Score=22.13 Aligned_cols=93 Identities=13% Similarity=0.173 Sum_probs=54.4
Q ss_pred HHHHHHHHhhcCCCCCcEEEEeccHHHHHHHhccccc---------cHHHHHHHHHHHHHHhcCCeEEEEeecCCCCCcc
Q psy3058 19 AMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCK---------NILIHDIQVACHKLILKGNNVKIIWIPSHCGIAG 89 (244)
Q Consensus 19 Ai~~al~~~~~~~~~~~i~i~tDs~~al~~l~~~~~~---------~~~~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~g 89 (244)
++..||.+++.. .+-.+.-|++.+.-+.......++ .-.-.++ ...|...|...-+..+-||.+|+
T Consensus 15 ~vr~al~~Ll~s-~G~~v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlel---q~~L~~~~~~~PVIfiTGhgDIp- 89 (202)
T COG4566 15 SVRDALAFLLES-AGFQVKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLEL---QDRLAERGIRLPVIFLTGHGDIP- 89 (202)
T ss_pred HHHHHHHHHHHh-CCceeeeecCHHHHHhhccCCCCCeEEEecCCCCCchHHH---HHHHHhcCCCCCEEEEeCCCChH-
Confidence 567788887764 345788999999988883222211 1111233 33445667777777899998886
Q ss_pred chhhchHHHHHhhhcCCC----cccHHHHHHHHHHHH
Q psy3058 90 NEEVDKAAQSFINAQNYS----LITHVDLKAFLKNEF 122 (244)
Q Consensus 90 Ne~AD~lAk~a~~~~~~~----~~~~a~ik~~ik~~~ 122 (244)
+|-+|.+.+... |++.+++...++..+
T Consensus 90 ------maV~AmK~GAvDFLeKP~~~q~Lldav~~Al 120 (202)
T COG4566 90 ------MAVQAMKAGAVDFLEKPFSEQDLLDAVERAL 120 (202)
T ss_pred ------HHHHHHHcchhhHHhCCCchHHHHHHHHHHH
Confidence 344444444332 445555555554433
No 37
>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=25.05 E-value=14 Score=23.59 Aligned_cols=24 Identities=33% Similarity=0.461 Sum_probs=11.0
Q ss_pred hccccccccccccCCCCCCCCCCCCC
Q psy3058 164 RIGHTRLTHGFLMERTDPPQCEVCNV 189 (244)
Q Consensus 164 rtGH~~~~~~~~~~~~~~p~C~~Cg~ 189 (244)
=+|||+. |+--+.....|.|. |+.
T Consensus 19 CSGHGr~-flDg~~~dG~p~CE-Cn~ 42 (56)
T PF04863_consen 19 CSGHGRA-FLDGLIADGSPVCE-CNS 42 (56)
T ss_dssp -TTSEE---TTS-EETTEE--E-E-T
T ss_pred cCCCCee-eeccccccCCcccc-ccC
Confidence 3799987 44333345568888 874
No 38
>PRK12568 glycogen branching enzyme; Provisional
Probab=24.39 E-value=1.1e+02 Score=30.44 Aligned_cols=32 Identities=13% Similarity=0.139 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhcCCeEEEEeecCCCCCccc
Q psy3058 59 IHDIQVACHKLILKGNNVKIIWIPSHCGIAGN 90 (244)
Q Consensus 59 ~~~i~~~~~~l~~~~~~v~~~Wvp~H~gi~gN 90 (244)
..++...+.++...|..|.+-|||.|++-.++
T Consensus 318 ~~dfk~lV~~~H~~Gi~VIlD~V~nH~~~d~~ 349 (730)
T PRK12568 318 PDGFAQFVDACHRAGIGVILDWVSAHFPDDAH 349 (730)
T ss_pred HHHHHHHHHHHHHCCCEEEEEeccccCCcccc
Confidence 46777788888889999999999999986544
No 39
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.93 E-value=39 Score=24.97 Aligned_cols=24 Identities=21% Similarity=0.499 Sum_probs=15.4
Q ss_pred CCCCCCCCccc-cccccccccCcHH
Q psy3058 182 PQCEVCNVTIT-VKHILCHCTKYTQ 205 (244)
Q Consensus 182 p~C~~Cg~~et-~~H~l~~Cp~~~~ 205 (244)
-.|..||.... ..+.++.||....
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCC
Confidence 36888987433 3455577997653
No 40
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=23.82 E-value=1.6e+02 Score=25.99 Aligned_cols=34 Identities=24% Similarity=0.302 Sum_probs=22.1
Q ss_pred HHHHHHhhcCCC--CCcEEEEeccHHHHHHHhcccc
Q psy3058 21 EMCLDNLINRPI--PDNILIFTDSKSLISSMQQLFC 54 (244)
Q Consensus 21 ~~al~~~~~~~~--~~~i~i~tDs~~al~~l~~~~~ 54 (244)
..+++.++.... +.+|.+.|||+.|++.+.+..+
T Consensus 200 ~~ai~~ak~~~~~k~~~IFLATDSaeVid~fr~~FP 235 (321)
T PF05830_consen 200 CTAIDKAKALAPPKPVRIFLATDSAEVIDQFRKKFP 235 (321)
T ss_dssp HHHHHHHHTS--SS-EEEEEEES-HHHHHHHHHHST
T ss_pred HHHHHHHHhccCCCCeeEEEecCcHHHHHHHHHHCC
Confidence 455555544322 3579999999999999987655
No 41
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=23.60 E-value=35 Score=22.57 Aligned_cols=23 Identities=26% Similarity=0.612 Sum_probs=14.4
Q ss_pred CCCCCCCC-ccccc----cccccccCcH
Q psy3058 182 PQCEVCNV-TITVK----HILCHCTKYT 204 (244)
Q Consensus 182 p~C~~Cg~-~et~~----H~l~~Cp~~~ 204 (244)
.-||+||. ..+++ ++.+.|..-.
T Consensus 7 KPCPFCG~~~~~v~~~~g~~~v~C~~Cg 34 (64)
T PRK09710 7 KPCPFCGCPSVTVKAISGYYRAKCNGCE 34 (64)
T ss_pred cCCCCCCCceeEEEecCceEEEEcCCCC
Confidence 45999997 34444 4456777543
No 42
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=23.56 E-value=52 Score=20.95 Aligned_cols=21 Identities=19% Similarity=0.396 Sum_probs=14.3
Q ss_pred CCCCCCC----ccccccccccccCc
Q psy3058 183 QCEVCNV----TITVKHILCHCTKY 203 (244)
Q Consensus 183 ~C~~Cg~----~et~~H~l~~Cp~~ 203 (244)
.|+.||. +.+...-++.||..
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~C 28 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDEC 28 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCC
Confidence 6888996 23455667888843
No 43
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=23.18 E-value=1.2e+02 Score=18.84 Aligned_cols=26 Identities=19% Similarity=0.401 Sum_probs=21.5
Q ss_pred cHHHHhCCChHhHHHHHHHHHHcCcC
Q psy3058 216 QIKDILGDNPRTIDLLFRFLKDSNLL 241 (244)
Q Consensus 216 ~~~~~l~~~~~~~~~~~~F~~~t~~~ 241 (244)
++++++|.+.+-+..+++|+.+.|+.
T Consensus 15 ~~rd~lg~sRK~ai~lLE~lD~~g~T 40 (50)
T PF09107_consen 15 EFRDLLGLSRKYAIPLLEYLDREGIT 40 (50)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHCccHHHHHHHHHHHhccCCE
Confidence 56888999888899999999998863
No 44
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=23.10 E-value=33 Score=18.59 Aligned_cols=20 Identities=20% Similarity=0.522 Sum_probs=8.2
Q ss_pred CCCCCCCc--cccccccccccC
Q psy3058 183 QCEVCNVT--ITVKHILCHCTK 202 (244)
Q Consensus 183 ~C~~Cg~~--et~~H~l~~Cp~ 202 (244)
.|+.||.. ...+-+.+.|+.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE--
T ss_pred CcCCCCCEeEcCCCCEeEECCC
Confidence 48889962 344445566663
No 45
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=22.83 E-value=1.2e+02 Score=17.03 Aligned_cols=27 Identities=26% Similarity=0.420 Sum_probs=21.9
Q ss_pred ccHHHHhCCChHhHHHHHHHHHHcCcC
Q psy3058 215 LQIKDILGDNPRTIDLLFRFLKDSNLL 241 (244)
Q Consensus 215 ~~~~~~l~~~~~~~~~~~~F~~~t~~~ 241 (244)
.++.+.+|-.++.+..+++-+++.|++
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 367788998889999999999998864
No 46
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.40 E-value=50 Score=19.89 Aligned_cols=7 Identities=29% Similarity=0.994 Sum_probs=4.1
Q ss_pred CCCCCCC
Q psy3058 183 QCEVCNV 189 (244)
Q Consensus 183 ~C~~Cg~ 189 (244)
.|+.||.
T Consensus 5 ~C~~CG~ 11 (46)
T PRK00398 5 KCARCGR 11 (46)
T ss_pred ECCCCCC
Confidence 3666665
No 47
>KOG3243|consensus
Probab=22.35 E-value=1e+02 Score=23.60 Aligned_cols=24 Identities=21% Similarity=0.558 Sum_probs=14.8
Q ss_pred HHHHHHHhcCCeEEEEeecCCCCC
Q psy3058 64 VACHKLILKGNNVKIIWIPSHCGI 87 (244)
Q Consensus 64 ~~~~~l~~~~~~v~~~Wvp~H~gi 87 (244)
+.+.++.-+-.+|.+.||||-=-+
T Consensus 41 Etm~~~~V~eenI~ie~VPGS~El 64 (158)
T KOG3243|consen 41 ETMKKYSVREENIEIEWVPGSFEL 64 (158)
T ss_pred HHHHHhCcchhceeEEEcCCceec
Confidence 334333334457999999986443
No 48
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=21.95 E-value=42 Score=27.33 Aligned_cols=26 Identities=15% Similarity=0.433 Sum_probs=15.8
Q ss_pred CCCCCCCCccc--------cccccccccCcHHHH
Q psy3058 182 PQCEVCNVTIT--------VKHILCHCTKYTQIR 207 (244)
Q Consensus 182 p~C~~Cg~~et--------~~H~l~~Cp~~~~~R 207 (244)
-.|+.||..+. -.|+++.|+......
T Consensus 7 ~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 7 IECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 45888883222 456777787655444
No 49
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=21.85 E-value=52 Score=21.52 Aligned_cols=23 Identities=13% Similarity=0.349 Sum_probs=15.2
Q ss_pred CCCCCCCCCCc--cccccccccccC
Q psy3058 180 DPPQCEVCNVT--ITVKHILCHCTK 202 (244)
Q Consensus 180 ~~p~C~~Cg~~--et~~H~l~~Cp~ 202 (244)
.+-.|+.||.. .+...-.+.||.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~ 51 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPN 51 (69)
T ss_pred CccCccCcccccccccccceEEcCC
Confidence 35678889973 335555688885
No 50
>PRK00420 hypothetical protein; Validated
Probab=21.06 E-value=64 Score=23.92 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=16.5
Q ss_pred hhccccccccccccC-CCCCCCCCCCCCc
Q psy3058 163 LRIGHTRLTHGFLME-RTDPPQCEVCNVT 190 (244)
Q Consensus 163 lrtGH~~~~~~~~~~-~~~~p~C~~Cg~~ 190 (244)
++.+|++.-..-+|+ +...-.|+.||..
T Consensus 21 ml~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 21 MLSKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred HccCCCCCCCCcceecCCCceECCCCCCe
Confidence 345666544223344 5556678888874
No 51
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=20.59 E-value=31 Score=22.07 Aligned_cols=22 Identities=18% Similarity=0.306 Sum_probs=15.8
Q ss_pred CCCCCCCc-cccccccccccCcH
Q psy3058 183 QCEVCNVT-ITVKHILCHCTKYT 204 (244)
Q Consensus 183 ~C~~Cg~~-et~~H~l~~Cp~~~ 204 (244)
.|-|||.. .|.+-+.-.||...
T Consensus 29 YC~~Cg~~Y~d~~dL~~~CPG~t 51 (55)
T PF13821_consen 29 YCFWCGTKYDDEEDLERNCPGPT 51 (55)
T ss_pred eeeeeCCccCCHHHHHhCCCCCC
Confidence 36689985 57767778899643
No 52
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=20.05 E-value=71 Score=21.16 Aligned_cols=12 Identities=17% Similarity=0.185 Sum_probs=9.1
Q ss_pred CCCCCCCCCCcc
Q psy3058 180 DPPQCEVCNVTI 191 (244)
Q Consensus 180 ~~p~C~~Cg~~e 191 (244)
+...|+.||...
T Consensus 16 ~~~~Cp~Cgs~~ 27 (64)
T PRK06393 16 PEKTCPVHGDEK 27 (64)
T ss_pred CCCcCCCCCCCc
Confidence 566899999753
Done!