Query psy16114
Match_columns 202
No_of_seqs 132 out of 1356
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 21:14:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16114.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16114hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08719 ribonuclease H; Revie 99.1 6.1E-11 1.3E-15 90.4 5.2 60 7-67 74-145 (147)
2 PRK06548 ribonuclease H; Provi 99.1 1.5E-10 3.2E-15 89.3 5.6 60 7-67 69-140 (161)
3 PF00075 RNase_H: RNase H; In 99.1 5.7E-11 1.2E-15 88.0 1.8 56 7-66 65-130 (132)
4 PRK00203 rnhA ribonuclease H; 99.0 1.8E-10 3.8E-15 88.1 3.7 62 7-69 69-142 (150)
5 cd06222 RnaseH RNase H (RNase 98.7 2.7E-08 5.9E-13 71.5 6.6 60 7-66 69-129 (130)
6 COG0328 RnhA Ribonuclease HI [ 98.4 2.2E-07 4.8E-12 70.9 4.2 43 26-68 102-144 (154)
7 KOG3752|consensus 97.8 2.9E-05 6.2E-10 66.6 4.4 29 38-66 334-362 (371)
8 PF13966 zf-RVT: zinc-binding 96.8 0.00062 1.4E-08 46.9 1.6 30 142-171 51-83 (86)
9 PRK13907 rnhA ribonuclease H; 96.7 0.0038 8.1E-08 46.0 5.4 57 7-67 69-125 (128)
10 PF13456 RVT_3: Reverse transc 96.5 0.0034 7.5E-08 42.3 3.7 55 7-65 29-83 (87)
11 PRK07238 bifunctional RNase H/ 94.8 0.069 1.5E-06 46.5 5.8 56 7-66 73-129 (372)
12 PRK07708 hypothetical protein; 94.1 0.096 2.1E-06 42.5 4.8 58 7-68 148-207 (219)
13 PF05741 zf-nanos: Nanos RNA b 69.1 2.1 4.6E-05 26.9 0.6 19 151-169 34-54 (55)
14 COG0296 GlgB 1,4-alpha-glucan 68.3 6.8 0.00015 36.7 4.0 39 26-64 214-252 (628)
15 PF15322 PMSI1: Protein missin 63.3 4.1 8.9E-05 34.1 1.4 16 126-141 213-228 (311)
16 PF09345 DUF1987: Domain of un 54.2 18 0.00038 25.6 3.2 27 23-49 60-86 (99)
17 COG2875 CobM Precorrin-4 methy 39.0 48 0.001 27.4 3.8 31 19-51 82-113 (254)
18 PF13696 zf-CCHC_2: Zinc knuck 38.4 15 0.00032 20.4 0.6 15 152-169 10-26 (32)
19 KOG4602|consensus 37.3 17 0.00038 30.1 1.1 21 150-170 268-290 (318)
20 PF14169 YdjO: Cold-inducible 36.6 24 0.00052 22.5 1.4 19 145-163 34-55 (59)
21 TIGR01506 ribC_arch riboflavin 35.6 37 0.00081 25.9 2.6 32 31-64 18-51 (151)
22 PRK00061 ribH 6,7-dimethyl-8-r 35.6 36 0.00079 26.0 2.6 34 30-65 33-69 (154)
23 PF00885 DMRL_synthase: 6,7-di 35.0 45 0.00098 25.1 3.0 34 30-65 24-60 (144)
24 PRK12419 riboflavin synthase s 33.2 41 0.00088 25.9 2.5 33 31-65 32-67 (158)
25 PRK06455 riboflavin synthase; 31.5 48 0.001 25.4 2.6 32 31-64 20-53 (155)
26 KOG1402|consensus 31.1 69 0.0015 28.0 3.7 60 5-64 61-137 (427)
27 PLN02404 6,7-dimethyl-8-ribity 30.6 52 0.0011 24.8 2.7 33 31-65 29-64 (141)
28 PF00098 zf-CCHC: Zinc knuckle 30.3 36 0.00077 16.1 1.1 15 152-169 2-18 (18)
29 KOG3243|consensus 30.2 62 0.0013 24.2 2.9 32 23-54 34-65 (158)
30 PF15216 TSLP: Thymic stromal 28.6 17 0.00038 26.4 -0.2 12 45-56 80-91 (124)
31 COG2093 DNA-directed RNA polym 28.5 41 0.00088 21.7 1.5 15 145-159 13-28 (64)
32 TIGR00114 lumazine-synth 6,7-d 28.0 60 0.0013 24.3 2.6 33 31-65 22-57 (138)
33 KOG1994|consensus 27.6 31 0.00067 28.2 1.1 30 127-170 230-262 (268)
34 PF14090 HTH_39: Helix-turn-he 27.1 53 0.0011 21.3 1.9 39 7-50 14-52 (70)
35 PRK12568 glycogen branching en 26.9 84 0.0018 30.2 4.0 33 25-57 318-350 (730)
36 PF04863 EGF_alliinase: Alliin 26.5 11 0.00025 23.5 -1.2 25 132-157 18-42 (56)
37 PF10580 Neuromodulin_N: Gap j 25.5 56 0.0012 17.8 1.5 20 46-65 4-23 (32)
38 cd00729 rubredoxin_SM Rubredox 24.2 37 0.00081 18.8 0.7 10 149-158 17-27 (34)
39 PF13894 zf-C2H2_4: C2H2-type 23.0 46 0.001 15.7 0.9 14 1-14 5-18 (24)
40 PHA02446 hypothetical protein 22.9 37 0.0008 24.8 0.6 21 150-170 62-94 (166)
41 PF08274 PhnA_Zn_Ribbon: PhnA 22.6 30 0.00066 18.8 0.1 18 151-168 3-23 (30)
42 PF11658 DUF3260: Protein of u 22.3 1.3E+02 0.0029 27.5 4.1 33 24-56 381-414 (518)
43 PF02810 SEC-C: SEC-C motif; 22.2 55 0.0012 16.2 1.0 9 150-158 2-10 (21)
44 KOG2879|consensus 22.1 49 0.0011 27.9 1.2 21 148-168 237-259 (298)
45 PRK14706 glycogen branching en 21.1 1.2E+02 0.0027 28.6 3.8 31 25-55 216-246 (639)
46 PF13912 zf-C2H2_6: C2H2-type 20.9 42 0.00091 16.9 0.4 13 2-14 7-19 (27)
47 smart00642 Aamy Alpha-amylase 20.5 1.6E+02 0.0035 22.4 3.9 29 25-53 69-97 (166)
No 1
>PRK08719 ribonuclease H; Reviewed
Probab=99.14 E-value=6.1e-11 Score=90.37 Aligned_cols=60 Identities=22% Similarity=0.236 Sum_probs=48.3
Q ss_pred ChHHHHHHH--------Hcc---cCCCHHH-HHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcCCC
Q psy16114 7 GFISALSAL--------SNI---KFTNPLV-SKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPT 67 (202)
Q Consensus 7 ~s~sal~al--------~~~---~~~~~~~-~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a~ 67 (202)
||+-++++| +|. +.+.|+. .++++.+..|.. ...|+|.|||||+|++|||.||+||+.+.
T Consensus 74 DS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~ 145 (147)
T PRK08719 74 DSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAA 145 (147)
T ss_pred chHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHh
Confidence 899999998 444 3344543 468888888876 56799999999999999999999999654
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.09 E-value=1.5e-10 Score=89.30 Aligned_cols=60 Identities=23% Similarity=0.365 Sum_probs=51.6
Q ss_pred ChHHHHHHHH---------cc--cCCCHHH-HHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcCCC
Q psy16114 7 GFISALSALS---------NI--KFTNPLV-SKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPT 67 (202)
Q Consensus 7 ~s~sal~al~---------~~--~~~~~~~-~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a~ 67 (202)
||+-++++|. ++ .+|+|+. +++++.+..+... ..|+|.|||||+|++|||.||+||+.+.
T Consensus 69 DS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa 140 (161)
T PRK06548 69 DSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAA 140 (161)
T ss_pred ChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHH
Confidence 8999999999 33 6788877 6788888888765 5799999999999999999999999644
No 3
>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=99.05 E-value=5.7e-11 Score=88.00 Aligned_cols=56 Identities=30% Similarity=0.547 Sum_probs=43.0
Q ss_pred ChHHHHHHHHc-----c---cCCC-HHHHHHHHHHHHHHhCCCceEEEEecccCCC-ccchhhhhhhcCC
Q psy16114 7 GFISALSALSN-----I---KFTN-PLVSKAYSCWDLLTSNNKDVRFMWCPSHCGI-RGNEDVDQAARNP 66 (202)
Q Consensus 7 ~s~sal~al~~-----~---~~~~-~~~~~i~~~~~~l~~~~~~i~l~WvPgH~gI-~GNE~AD~~Ak~a 66 (202)
||++++++|.. . .+.. ++..+|++.+ ..+..|.|.|||||+|+ .|||.||+|||.+
T Consensus 65 DS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a 130 (132)
T PF00075_consen 65 DSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEA 130 (132)
T ss_dssp S-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHhccccccccccccccchhheeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHh
Confidence 89999998877 2 2222 4666665554 45899999999999999 6999999999853
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.03 E-value=1.8e-10 Score=88.06 Aligned_cols=62 Identities=16% Similarity=0.276 Sum_probs=47.9
Q ss_pred ChHHHHHHHHc---------c--cCCCHHH-HHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcCCCCC
Q psy16114 7 GFISALSALSN---------I--KFTNPLV-SKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPTDL 69 (202)
Q Consensus 7 ~s~sal~al~~---------~--~~~~~~~-~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a~~~ 69 (202)
||+.++++|.. . +.|.|+. .++++.+..+.. ...|.|.|||||+|++|||.||+|||.+...
T Consensus 69 DS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 69 DSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred CHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 88889998885 2 3566654 346666666653 4789999999999999999999999966543
No 5
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=98.75 E-value=2.7e-08 Score=71.46 Aligned_cols=60 Identities=27% Similarity=0.348 Sum_probs=49.0
Q ss_pred ChHHHHHHHHcccC-CCHHHHHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcCC
Q psy16114 7 GFISALSALSNIKF-TNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNP 66 (202)
Q Consensus 7 ~s~sal~al~~~~~-~~~~~~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a 66 (202)
||..++..+.+... ..+.....+..+..+......++|.|||+|+|+.+|+.||.+||.+
T Consensus 69 Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 69 DSQYVINALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred CHHHHHHHhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence 88999999998833 4445555666666666788999999999999999999999999864
No 6
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.44 E-value=2.2e-07 Score=70.89 Aligned_cols=43 Identities=28% Similarity=0.392 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcCCCC
Q psy16114 26 SKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPTD 68 (202)
Q Consensus 26 ~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a~~ 68 (202)
.+.++.+.++...-..|.+.|||||.|.++||.||+||+.++.
T Consensus 102 ~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~ 144 (154)
T COG0328 102 KDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAAR 144 (154)
T ss_pred HHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHH
Confidence 3578888888877779999999999999999999999996544
No 7
>KOG3752|consensus
Probab=97.77 E-value=2.9e-05 Score=66.57 Aligned_cols=29 Identities=41% Similarity=0.539 Sum_probs=26.9
Q ss_pred CCCceEEEEecccCCCccchhhhhhhcCC
Q psy16114 38 NNKDVRFMWCPSHCGIRGNEDVDQAARNP 66 (202)
Q Consensus 38 ~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a 66 (202)
++..|++.|||||.||.|||+||.+|+..
T Consensus 334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 334 SNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred ccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 47899999999999999999999999954
No 8
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.80 E-value=0.00062 Score=46.85 Aligned_cols=30 Identities=23% Similarity=0.472 Sum_probs=24.8
Q ss_pred ccccCCCCCCCcc-CCC-CCcccccc-cccccH
Q psy16114 142 GFIFTKTDPPNCP-CGE-HLSVRHIL-TCHRHA 171 (202)
Q Consensus 142 ~~~~~~~~~~~C~-Cg~-~et~~H~l-~Cp~~~ 171 (202)
+.+.+...++.|. |+. .||++|+| .||...
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 3456667889999 995 89999999 999764
No 9
>PRK13907 rnhA ribonuclease H; Provisional
Probab=96.73 E-value=0.0038 Score=45.96 Aligned_cols=57 Identities=16% Similarity=0.055 Sum_probs=41.2
Q ss_pred ChHHHHHHHHcccCCCHHHHHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcCCC
Q psy16114 7 GFISALSALSNIKFTNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPT 67 (202)
Q Consensus 7 ~s~sal~al~~~~~~~~~~~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a~ 67 (202)
||+-.+.+|.+.....+-....++.+..|..+-..+.|.|||.+ +|+.||.+|+.+.
T Consensus 69 DS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~----~N~~Ad~LA~~a~ 125 (128)
T PRK13907 69 DSQLVERAVEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS----QNKVADELARKAI 125 (128)
T ss_pred chHHHHHHHhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCch----hchhHHHHHHHHH
Confidence 78888888877522233445556666666666667888999995 9999999998653
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=96.51 E-value=0.0034 Score=42.32 Aligned_cols=55 Identities=13% Similarity=0.013 Sum_probs=40.2
Q ss_pred ChHHHHHHHHcccCCCHHHHHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcC
Q psy16114 7 GFISALSALSNIKFTNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARN 65 (202)
Q Consensus 7 ~s~sal~al~~~~~~~~~~~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~ 65 (202)
||+.++.+|.+.......+..+...+..+...-.++.|.|||- ++|..||.+||.
T Consensus 29 Ds~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r----~~N~~A~~LA~~ 83 (87)
T PF13456_consen 29 DSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPR----EQNKVADALAKF 83 (87)
T ss_dssp S-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--G----GGSHHHHHHHHH
T ss_pred cCccccccccccccccccccccchhhhhhhccccceEEEEECh----HHhHHHHHHHHH
Confidence 8999999999883332256667777777777888899999995 589999999984
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=94.76 E-value=0.069 Score=46.51 Aligned_cols=56 Identities=20% Similarity=0.232 Sum_probs=40.6
Q ss_pred ChHHHHHHHHcc-cCCCHHHHHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhcCC
Q psy16114 7 GFISALSALSNI-KFTNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNP 66 (202)
Q Consensus 7 ~s~sal~al~~~-~~~~~~~~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a 66 (202)
||.-.++.+.+. +..++-+...+..+..|...-..++|.|||. .+|+.||.+|+.+
T Consensus 73 DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a 129 (372)
T PRK07238 73 DSKLVVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEA 129 (372)
T ss_pred CcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHH
Confidence 677777777654 3344555555556666766667899999998 5899999999943
No 12
>PRK07708 hypothetical protein; Validated
Probab=94.10 E-value=0.096 Score=42.50 Aligned_cols=58 Identities=12% Similarity=0.045 Sum_probs=37.1
Q ss_pred ChHHHHHHHHcc-cCCCHHHHHHHHHHHH-HHhCCCceEEEEecccCCCccchhhhhhhcCCCC
Q psy16114 7 GFISALSALSNI-KFTNPLVSKAYSCWDL-LTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPTD 68 (202)
Q Consensus 7 ~s~sal~al~~~-~~~~~~~~~i~~~~~~-l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak~a~~ 68 (202)
||+-.+..+..- +..++.....++.+.. +..-...+.+.|||-. -|+.||.||+.+..
T Consensus 148 DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~----~N~~AD~LAk~Al~ 207 (219)
T PRK07708 148 DSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRK----QNKEADQLATQALE 207 (219)
T ss_pred ccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCch----hhhHHHHHHHHHHh
Confidence 666666666665 4444444444444443 3333455788999864 69999999997654
No 13
>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=69.09 E-value=2.1 Score=26.88 Aligned_cols=19 Identities=32% Similarity=0.777 Sum_probs=8.1
Q ss_pred CCcc-CCCCCcccccc-cccc
Q psy16114 151 PNCP-CGEHLSVRHIL-TCHR 169 (202)
Q Consensus 151 ~~C~-Cg~~et~~H~l-~Cp~ 169 (202)
-.|+ ||+..+-.|.. .||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 4799 99988999999 9996
No 14
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=68.33 E-value=6.8 Score=36.71 Aligned_cols=39 Identities=18% Similarity=0.155 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhCCCceEEEEecccCCCccchhhhhhhc
Q psy16114 26 SKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAAR 64 (202)
Q Consensus 26 ~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE~AD~~Ak 64 (202)
.+....++...+.|..|-|-|||+|-+..||-++-..-.
T Consensus 214 edfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~fdg~ 252 (628)
T COG0296 214 EDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLARFDGT 252 (628)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhhcCCc
Confidence 356667788899999999999999999999988865544
No 15
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=63.29 E-value=4.1 Score=34.09 Aligned_cols=16 Identities=25% Similarity=0.231 Sum_probs=13.8
Q ss_pred hHHHHhhhhcCcccCc
Q psy16114 126 EITLTRMRIGHTRLTH 141 (202)
Q Consensus 126 ~~~L~qlRTGH~~l~h 141 (202)
...|.||||.|-+.+|
T Consensus 213 vGALsqLrTehrPCtY 228 (311)
T PF15322_consen 213 VGALSQLRTEHRPCTY 228 (311)
T ss_pred cchhhhhhhccCCccc
Confidence 4579999999999984
No 16
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=54.23 E-value=18 Score=25.55 Aligned_cols=27 Identities=7% Similarity=0.160 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHhCCCceEEEEecc
Q psy16114 23 PLVSKAYSCWDLLTSNNKDVRFMWCPS 49 (202)
Q Consensus 23 ~~~~~i~~~~~~l~~~~~~i~l~WvPg 49 (202)
..+..|.+.+..+..+|..|++.|.--
T Consensus 60 k~l~~i~~~Le~~~~~g~~V~v~Wyyd 86 (99)
T PF09345_consen 60 KALMDIFDLLEDAAQKGGKVTVNWYYD 86 (99)
T ss_pred HHHHHHHHHHHHHHhcCCcEEEEEEEC
Confidence 356778888888899999999999863
No 17
>COG2875 CobM Precorrin-4 methylase [Coenzyme metabolism]
Probab=38.95 E-value=48 Score=27.35 Aligned_cols=31 Identities=10% Similarity=0.009 Sum_probs=26.2
Q ss_pred cCCCHHHH-HHHHHHHHHHhCCCceEEEEecccC
Q psy16114 19 KFTNPLVS-KAYSCWDLLTSNNKDVRFMWCPSHC 51 (202)
Q Consensus 19 ~~~~~~~~-~i~~~~~~l~~~~~~i~l~WvPgH~ 51 (202)
+||+|-+. .+.+++.+|...|....+ |||=+
T Consensus 82 hSGDpsiYgA~~EQm~~L~~~gI~yev--vPGVs 113 (254)
T COG2875 82 HSGDPSIYGALAEQMRELEALGIPYEV--VPGVS 113 (254)
T ss_pred ecCChhHHHHHHHHHHHHHHcCCCeEE--eCCch
Confidence 89999766 799999999998887776 78766
No 18
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=38.36 E-value=15 Score=20.45 Aligned_cols=15 Identities=33% Similarity=0.919 Sum_probs=12.0
Q ss_pred Ccc-CCCCCcccccc-cccc
Q psy16114 152 NCP-CGEHLSVRHIL-TCHR 169 (202)
Q Consensus 152 ~C~-Cg~~et~~H~l-~Cp~ 169 (202)
.|- |+... |++ +||.
T Consensus 10 ~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 10 VCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred EeecCCCCC---ccHhHCCC
Confidence 577 88654 999 9997
No 19
>KOG4602|consensus
Probab=37.34 E-value=17 Score=30.13 Aligned_cols=21 Identities=29% Similarity=0.619 Sum_probs=18.0
Q ss_pred CCCcc-CCCCCcccccc-ccccc
Q psy16114 150 PPNCP-CGEHLSVRHIL-TCHRH 170 (202)
Q Consensus 150 ~~~C~-Cg~~et~~H~l-~Cp~~ 170 (202)
+-.|+ ||...+-.|.+ +||..
T Consensus 268 ~YVCPiCGATgDnAHTiKyCPl~ 290 (318)
T KOG4602|consen 268 SYVCPICGATGDNAHTIKYCPLA 290 (318)
T ss_pred hhcCccccccCCcccceeccccc
Confidence 45699 99988999999 99973
No 20
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=36.60 E-value=24 Score=22.49 Aligned_cols=19 Identities=32% Similarity=0.738 Sum_probs=12.8
Q ss_pred cCCCCCCCcc-CCC--CCcccc
Q psy16114 145 FTKTDPPNCP-CGE--HLSVRH 163 (202)
Q Consensus 145 ~~~~~~~~C~-Cg~--~et~~H 163 (202)
|...+.|.|+ |+. .+...+
T Consensus 34 Fs~~~~p~CPlC~s~M~~~~r~ 55 (59)
T PF14169_consen 34 FSFEEEPVCPLCKSPMVSGTRM 55 (59)
T ss_pred cccCCCccCCCcCCccccceee
Confidence 3456789999 996 445444
No 21
>TIGR01506 ribC_arch riboflavin synthase. This archaeal protein catalyzes the same reaction, the final step in riboflavin biosynthesis, as bacterial riboflavin biosynthesis alpha chain. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain.
Probab=35.58 E-value=37 Score=25.91 Aligned_cols=32 Identities=9% Similarity=-0.031 Sum_probs=22.8
Q ss_pred HHHHHHh--CCCceEEEEecccCCCccchhhhhhhc
Q psy16114 31 CWDLLTS--NNKDVRFMWCPSHCGIRGNEDVDQAAR 64 (202)
Q Consensus 31 ~~~~l~~--~~~~i~l~WvPgH~gI~GNE~AD~~Ak 64 (202)
+++.|+. .+..|.+.||||=-.||- .|.++++
T Consensus 18 A~~~L~~~g~g~~i~v~~VPGa~EiP~--aak~l~~ 51 (151)
T TIGR01506 18 AIDELRKHTAGIKIIRRTVPGIKDLPV--AAKKLLE 51 (151)
T ss_pred HHHHHHhcCCCCeEEEEECCcHhHHHH--HHHHHHh
Confidence 4455665 788899999999766653 4556665
No 22
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=35.57 E-value=36 Score=25.99 Aligned_cols=34 Identities=15% Similarity=0.238 Sum_probs=24.2
Q ss_pred HHHHHHHhCC---CceEEEEecccCCCccchhhhhhhcC
Q psy16114 30 SCWDLLTSNN---KDVRFMWCPSHCGIRGNEDVDQAARN 65 (202)
Q Consensus 30 ~~~~~l~~~~---~~i~l~WvPgH~gI~GNE~AD~~Ak~ 65 (202)
.++..|...| ..|.+.||||=-.||- .|.++++.
T Consensus 33 ga~~~l~~~gv~~~~i~v~~VPGa~EiP~--a~~~l~~~ 69 (154)
T PRK00061 33 GALDALKRHGVSEENIDVVRVPGAFEIPL--AAKKLAES 69 (154)
T ss_pred HHHHHHHHcCCCccceEEEECCCHHHHHH--HHHHHHHc
Confidence 3455788788 6799999999766653 45566654
No 23
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=34.95 E-value=45 Score=25.11 Aligned_cols=34 Identities=9% Similarity=0.194 Sum_probs=25.3
Q ss_pred HHHHHHHhCCC---ceEEEEecccCCCccchhhhhhhcC
Q psy16114 30 SCWDLLTSNNK---DVRFMWCPSHCGIRGNEDVDQAARN 65 (202)
Q Consensus 30 ~~~~~l~~~~~---~i~l~WvPgH~gI~GNE~AD~~Ak~ 65 (202)
.++..|...|. +|...||||=-.+| =.|.++++.
T Consensus 24 ~a~~~l~~~g~~~~~i~~~~VPGa~ElP--~a~~~l~~~ 60 (144)
T PF00885_consen 24 GALEELKRHGVAEENIEVIRVPGAFELP--LAAKRLAES 60 (144)
T ss_dssp HHHHHHHHTTTTGGCEEEEEESSGGGHH--HHHHHHHHC
T ss_pred HHHHHHHHcCCCccceEEEEcCCHHHHH--HHHHHHhcc
Confidence 35567888887 89999999986555 356777765
No 24
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=33.17 E-value=41 Score=25.90 Aligned_cols=33 Identities=12% Similarity=0.106 Sum_probs=22.7
Q ss_pred HHHHHHhCC---CceEEEEecccCCCccchhhhhhhcC
Q psy16114 31 CWDLLTSNN---KDVRFMWCPSHCGIRGNEDVDQAARN 65 (202)
Q Consensus 31 ~~~~l~~~~---~~i~l~WvPgH~gI~GNE~AD~~Ak~ 65 (202)
++..|...| .+|.+.||||=-.||- .|.++|+.
T Consensus 32 A~~~l~~~G~~~~~i~v~~VPGA~EiP~--~a~~l~~~ 67 (158)
T PRK12419 32 FVAEIAARGGAASQVDIFDVPGAFEIPL--HAQTLAKT 67 (158)
T ss_pred HHHHHHHcCCCccceEEEECCcHHHHHH--HHHHHHhc
Confidence 344677777 5699999999765553 45666664
No 25
>PRK06455 riboflavin synthase; Provisional
Probab=31.51 E-value=48 Score=25.42 Aligned_cols=32 Identities=9% Similarity=0.006 Sum_probs=20.8
Q ss_pred HHHHHHh--CCCceEEEEecccCCCccchhhhhhhc
Q psy16114 31 CWDLLTS--NNKDVRFMWCPSHCGIRGNEDVDQAAR 64 (202)
Q Consensus 31 ~~~~l~~--~~~~i~l~WvPgH~gI~GNE~AD~~Ak 64 (202)
+++.|+. .+.+|.+.||||=-.||- .|.++++
T Consensus 20 Ai~~L~~~g~~~~I~v~~VPGa~ELP~--aakkL~~ 53 (155)
T PRK06455 20 AIDELRKLDPSAKIIRYTVPGIKDLPV--AAKKLIE 53 (155)
T ss_pred HHHHHHhcCCCCceEEEECCCHHHHHH--HHHHHHh
Confidence 3445555 557899999998655542 3555554
No 26
>KOG1402|consensus
Probab=31.11 E-value=69 Score=28.01 Aligned_cols=60 Identities=23% Similarity=0.173 Sum_probs=44.1
Q ss_pred CCChHHHHHHHHcccCCCHHHHHHHHHHHHHHhCCCc------------eEE-----EEecccCCCccchhhhhhhc
Q psy16114 5 GNGFISALSALSNIKFTNPLVSKAYSCWDLLTSNNKD------------VRF-----MWCPSHCGIRGNEDVDQAAR 64 (202)
Q Consensus 5 ~~~s~sal~al~~~~~~~~~~~~i~~~~~~l~~~~~~------------i~l-----~WvPgH~gI~GNE~AD~~Ak 64 (202)
-+|++||.+|......-+.++....+..+.|...+.- |+. .=.|-.+|.++||.|=+||+
T Consensus 61 ylDflsaysaVnqGhchpki~~aLqeq~~kLtlssrafYnd~~~~f~~~vt~lf~~~kvlpmnTGaEa~Eta~KLaR 137 (427)
T KOG1402|consen 61 YLDFLSAYSAVNQGHCHPKIIKALQEQADKLTLSSRAFYNDVLGEFAEYVTKLFGYDKVLPMNTGAEAVETACKLAR 137 (427)
T ss_pred hhhhhhhhhhcccCCCCHHHHHHHHHHHhHhhhhhHHHhhhhHHHHHHHHHHhcCcceeeecccchhHHHHHHHHHH
Confidence 3899999999988777777776777777766544421 110 12688999999999999998
No 27
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=30.57 E-value=52 Score=24.80 Aligned_cols=33 Identities=12% Similarity=0.324 Sum_probs=23.5
Q ss_pred HHHHHHhCCCc---eEEEEecccCCCccchhhhhhhcC
Q psy16114 31 CWDLLTSNNKD---VRFMWCPSHCGIRGNEDVDQAARN 65 (202)
Q Consensus 31 ~~~~l~~~~~~---i~l~WvPgH~gI~GNE~AD~~Ak~ 65 (202)
+...|...|.. |.+.||||=-.|| =.|+++|+.
T Consensus 29 a~~~l~~~gv~~~~i~v~~VPGa~EiP--~a~~~l~~s 64 (141)
T PLN02404 29 ALETFKRYSVKEENIDVVWVPGSFEIP--VVAQRLAKS 64 (141)
T ss_pred HHHHHHHcCCCccceEEEEcCcHHHHH--HHHHHHHhc
Confidence 34467777764 8999999986666 356677764
No 28
>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=30.28 E-value=36 Score=16.07 Aligned_cols=15 Identities=47% Similarity=1.094 Sum_probs=10.0
Q ss_pred Ccc-CCCCCcccccc-cccc
Q psy16114 152 NCP-CGEHLSVRHIL-TCHR 169 (202)
Q Consensus 152 ~C~-Cg~~et~~H~l-~Cp~ 169 (202)
.|- ||+ ..|+. +||.
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 465 764 46888 8873
No 29
>KOG3243|consensus
Probab=30.15 E-value=62 Score=24.18 Aligned_cols=32 Identities=16% Similarity=0.343 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHhCCCceEEEEecccCCCc
Q psy16114 23 PLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIR 54 (202)
Q Consensus 23 ~~~~~i~~~~~~l~~~~~~i~l~WvPgH~gI~ 54 (202)
+++--..+......-+--+|.+.||||--.++
T Consensus 34 ~LvkGAiEtm~~~~V~eenI~ie~VPGS~Elp 65 (158)
T KOG3243|consen 34 LLVKGAIETMKKYSVREENIEIEWVPGSFELP 65 (158)
T ss_pred HHHHHHHHHHHHhCcchhceeEEEcCCceecc
Confidence 34444444444444455679999999987665
No 30
>PF15216 TSLP: Thymic stromal lymphopoietin
Probab=28.60 E-value=17 Score=26.44 Aligned_cols=12 Identities=25% Similarity=0.520 Sum_probs=10.9
Q ss_pred EEecccCCCccc
Q psy16114 45 MWCPSHCGIRGN 56 (202)
Q Consensus 45 ~WvPgH~gI~GN 56 (202)
.|+||++++.-|
T Consensus 80 ~~CPGyse~QiN 91 (124)
T PF15216_consen 80 NYCPGYSETQIN 91 (124)
T ss_pred HhCCCcchhhcc
Confidence 589999999988
No 31
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=28.48 E-value=41 Score=21.70 Aligned_cols=15 Identities=40% Similarity=0.853 Sum_probs=9.7
Q ss_pred cCCCCCCCcc-CCCCC
Q psy16114 145 FTKTDPPNCP-CGEHL 159 (202)
Q Consensus 145 ~~~~~~~~C~-Cg~~e 159 (202)
+--.+...|| ||..+
T Consensus 13 l~~~d~e~CP~Cgs~~ 28 (64)
T COG2093 13 LTPEDTEICPVCGSTD 28 (64)
T ss_pred cCCCCCccCCCCCCcc
Confidence 3345556699 99753
No 32
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=27.99 E-value=60 Score=24.32 Aligned_cols=33 Identities=18% Similarity=0.362 Sum_probs=22.9
Q ss_pred HHHHHHhCCCc---eEEEEecccCCCccchhhhhhhcC
Q psy16114 31 CWDLLTSNNKD---VRFMWCPSHCGIRGNEDVDQAARN 65 (202)
Q Consensus 31 ~~~~l~~~~~~---i~l~WvPgH~gI~GNE~AD~~Ak~ 65 (202)
++..|+..|.. |.+.||||=-.||- .|.++++.
T Consensus 22 a~~~l~~~g~~~~~i~v~~VPGa~EiP~--a~~~l~~~ 57 (138)
T TIGR00114 22 AIDALKRLGAEVDNIDVIWVPGAFELPL--AVKKLAET 57 (138)
T ss_pred HHHHHHHcCCCccceEEEECCcHHHHHH--HHHHHHhc
Confidence 34567777754 78999999866653 46677764
No 33
>KOG1994|consensus
Probab=27.61 E-value=31 Score=28.17 Aligned_cols=30 Identities=20% Similarity=0.288 Sum_probs=21.6
Q ss_pred HHHHhhhhcCcccCcccccCCCCCCCcc-CCC-CCcccccc-ccccc
Q psy16114 127 ITLTRMRIGHTRLTHGFIFTKTDPPNCP-CGE-HLSVRHIL-TCHRH 170 (202)
Q Consensus 127 ~~L~qlRTGH~~l~h~~~~~~~~~~~C~-Cg~-~et~~H~l-~Cp~~ 170 (202)
.++.-||.||.+ |- ||. ..|.+.++ .||--
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 345567777655 44 995 78999999 99964
No 34
>PF14090 HTH_39: Helix-turn-helix domain
Probab=27.05 E-value=53 Score=21.27 Aligned_cols=39 Identities=15% Similarity=0.175 Sum_probs=24.3
Q ss_pred ChHHHHHHHHcccCCCHHHHHHHHHHHHHHhCCCceEEEEeccc
Q psy16114 7 GFISALSALSNIKFTNPLVSKAYSCWDLLTSNNKDVRFMWCPSH 50 (202)
Q Consensus 7 ~s~sal~al~~~~~~~~~~~~i~~~~~~l~~~~~~i~l~WvPgH 50 (202)
++++.+.|+....... .-..|.+|+..|..|.-.|++..
T Consensus 14 ~~it~~ea~~~~gi~~-----~~aRI~eLR~~G~~I~t~~~~~~ 52 (70)
T PF14090_consen 14 GSITTLEARRELGIMR-----LAARISELRKKGYPIVTEWVTVP 52 (70)
T ss_pred CCcCHHHHHHHcCCCC-----HHHHHHHHHHcCCeeeEEEEEee
Confidence 4455555555553333 23345679999999999996543
No 35
>PRK12568 glycogen branching enzyme; Provisional
Probab=26.94 E-value=84 Score=30.25 Aligned_cols=33 Identities=12% Similarity=0.059 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhCCCceEEEEecccCCCccch
Q psy16114 25 VSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNE 57 (202)
Q Consensus 25 ~~~i~~~~~~l~~~~~~i~l~WvPgH~gI~GNE 57 (202)
..+....++.+..+|..|-|-|||.|++-.++.
T Consensus 318 ~~dfk~lV~~~H~~Gi~VIlD~V~nH~~~d~~~ 350 (730)
T PRK12568 318 PDGFAQFVDACHRAGIGVILDWVSAHFPDDAHG 350 (730)
T ss_pred HHHHHHHHHHHHHCCCEEEEEeccccCCccccc
Confidence 567888999999999999999999999865543
No 36
>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=26.45 E-value=11 Score=23.54 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=11.0
Q ss_pred hhhcCcccCcccccCCCCCCCccCCC
Q psy16114 132 MRIGHTRLTHGFIFTKTDPPNCPCGE 157 (202)
Q Consensus 132 lRTGH~~l~h~~~~~~~~~~~C~Cg~ 157 (202)
--+|||+. |+--+-....|.|+|+.
T Consensus 18 ~CSGHGr~-flDg~~~dG~p~CECn~ 42 (56)
T PF04863_consen 18 SCSGHGRA-FLDGLIADGSPVCECNS 42 (56)
T ss_dssp --TTSEE---TTS-EETTEE--EE-T
T ss_pred CcCCCCee-eeccccccCCccccccC
Confidence 46899987 33222245669999884
No 37
>PF10580 Neuromodulin_N: Gap junction protein N-terminal region; InterPro: IPR018947 Neuromodulin is a component of the motile growth cones. It is membrane protein whose expression is widely correlated with successful axon elongation []. It is a crucial component of an effective regeneration response in the nervous system []. Although its function is uncertain, the N-terminal region is well conserved and contains both a calmodulin binding domain, and sites for acylation, membrane attachment and protein kinase C phosphorylation. Structure predictions suggest that the C-terminal region may exist as an extended, negatively-charged rod with some similarity to the side arms of neurofilaments, indicating that the biological role of neuromodulin may depend on its ability to form a dynamic membrane-cytoplasm-calmodulin complex []. This entry represents the neuromodulin N-terminal domain.
Probab=25.49 E-value=56 Score=17.84 Aligned_cols=20 Identities=20% Similarity=0.202 Sum_probs=15.1
Q ss_pred EecccCCCccchhhhhhhcC
Q psy16114 46 WCPSHCGIRGNEDVDQAARN 65 (202)
Q Consensus 46 WvPgH~gI~GNE~AD~~Ak~ 65 (202)
-+-.+..++-||.||+-...
T Consensus 4 c~r~tk~VEKNeeadQkieq 23 (32)
T PF10580_consen 4 CIRRTKPVEKNEEADQKIEQ 23 (32)
T ss_pred eeeccccccccchhhhhhhh
Confidence 34556678999999987764
No 38
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, 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), 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=24.19 E-value=37 Score=18.83 Aligned_cols=10 Identities=50% Similarity=1.454 Sum_probs=6.5
Q ss_pred CCCCcc-CCCC
Q psy16114 149 DPPNCP-CGEH 158 (202)
Q Consensus 149 ~~~~C~-Cg~~ 158 (202)
.+..|+ ||..
T Consensus 17 ~p~~CP~Cg~~ 27 (34)
T cd00729 17 APEKCPICGAP 27 (34)
T ss_pred CCCcCcCCCCc
Confidence 456787 8753
No 39
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=23.04 E-value=46 Score=15.65 Aligned_cols=14 Identities=29% Similarity=0.306 Sum_probs=9.4
Q ss_pred CCCCCCChHHHHHH
Q psy16114 1 MCPKGNGFISALSA 14 (202)
Q Consensus 1 ~~~~~~~s~sal~a 14 (202)
+|++.|.+.+++..
T Consensus 5 ~C~~~~~~~~~l~~ 18 (24)
T PF13894_consen 5 ICGKSFRSKSELRQ 18 (24)
T ss_dssp STS-EESSHHHHHH
T ss_pred CCCCcCCcHHHHHH
Confidence 48888888877653
No 40
>PHA02446 hypothetical protein
Probab=22.89 E-value=37 Score=24.83 Aligned_cols=21 Identities=29% Similarity=0.816 Sum_probs=14.6
Q ss_pred CCCcc-CCCCC----------cccccc-ccccc
Q psy16114 150 PPNCP-CGEHL----------SVRHIL-TCHRH 170 (202)
Q Consensus 150 ~~~C~-Cg~~e----------t~~H~l-~Cp~~ 170 (202)
-..|+ ||+.. -++.+| +||.-
T Consensus 62 ~q~cp~cg~dawv~~~g~~eahpd~l~qecpls 94 (166)
T PHA02446 62 QQQCPLCGQDAWVIHTGIVEAHPDKLLQECPLS 94 (166)
T ss_pred hhcCCCcccceeEeecCccccCcHHHHHhCCCC
Confidence 35799 99532 345678 99975
No 41
>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=22.64 E-value=30 Score=18.83 Aligned_cols=18 Identities=39% Similarity=0.969 Sum_probs=5.2
Q ss_pred CCcc-CCCCC-cccccc-ccc
Q psy16114 151 PNCP-CGEHL-SVRHIL-TCH 168 (202)
Q Consensus 151 ~~C~-Cg~~e-t~~H~l-~Cp 168 (202)
|.|+ |+... =.+..+ .||
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp 23 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCP 23 (30)
T ss_dssp ---TTT-----EE-SSSEEET
T ss_pred CCCCCCCCcceeccCCEEeCC
Confidence 6788 98532 233334 554
No 42
>PF11658 DUF3260: Protein of unknown function (DUF3260); InterPro: IPR017744 This protein was identified by the partial phylogenetic profiling algorithm [] as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation [].
Probab=22.26 E-value=1.3e+02 Score=27.55 Aligned_cols=33 Identities=24% Similarity=0.483 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHhCCCceEEEEeccc-CCCccc
Q psy16114 24 LVSKAYSCWDLLTSNNKDVRFMWCPSH-CGIRGN 56 (202)
Q Consensus 24 ~~~~i~~~~~~l~~~~~~i~l~WvPgH-~gI~GN 56 (202)
+..++..-+.+|.+.|.+|.++-||-| .++.|.
T Consensus 381 Llddl~~F~~~Le~SgR~v~vv~VPEHGAAlrGD 414 (518)
T PF11658_consen 381 LLDDLDRFFDELEKSGRKVMVVVVPEHGAALRGD 414 (518)
T ss_pred HHHHHHHHHHHHHHcCCcEEEEEecCcccccccc
Confidence 566788888999999999999999999 556664
No 43
>PF02810 SEC-C: SEC-C motif; InterPro: IPR004027 The SEC-C motif found in the C terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif is predicted to chelate zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif. It is predicted to be a potential nucleic acid binding domain.; PDB: 1OZB_J 1TM6_A 2I9W_A 2JQ5_A.
Probab=22.17 E-value=55 Score=16.24 Aligned_cols=9 Identities=44% Similarity=1.239 Sum_probs=6.7
Q ss_pred CCCccCCCC
Q psy16114 150 PPNCPCGEH 158 (202)
Q Consensus 150 ~~~C~Cg~~ 158 (202)
+..|+||..
T Consensus 2 n~~CpCgSg 10 (21)
T PF02810_consen 2 NDPCPCGSG 10 (21)
T ss_dssp TSBTTTSCS
T ss_pred CCcCcCCCC
Confidence 467999964
No 44
>KOG2879|consensus
Probab=22.07 E-value=49 Score=27.86 Aligned_cols=21 Identities=38% Similarity=1.054 Sum_probs=17.5
Q ss_pred CCCCCcc-CCCCCcccccc-ccc
Q psy16114 148 TDPPNCP-CGEHLSVRHIL-TCH 168 (202)
Q Consensus 148 ~~~~~C~-Cg~~et~~H~l-~Cp 168 (202)
+++-+|+ ||+.-|+-|+. -|.
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~ 259 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCG 259 (298)
T ss_pred cCCceeeccCCCCCCCeeecccc
Confidence 4567899 99999999988 786
No 45
>PRK14706 glycogen branching enzyme; Provisional
Probab=21.06 E-value=1.2e+02 Score=28.62 Aligned_cols=31 Identities=16% Similarity=0.135 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHhCCCceEEEEecccCCCcc
Q psy16114 25 VSKAYSCWDLLTSNNKDVRFMWCPSHCGIRG 55 (202)
Q Consensus 25 ~~~i~~~~~~l~~~~~~i~l~WvPgH~gI~G 55 (202)
..+....+..+..+|..|-|-|||.|.|-.+
T Consensus 216 ~~~~~~lv~~~H~~gi~VilD~v~nH~~~~~ 246 (639)
T PRK14706 216 PEDFKYLVNHLHGLGIGVILDWVPGHFPTDE 246 (639)
T ss_pred HHHHHHHHHHHHHCCCEEEEEecccccCcch
Confidence 5678889999999999999999999987543
No 46
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.86 E-value=42 Score=16.91 Aligned_cols=13 Identities=38% Similarity=0.455 Sum_probs=10.5
Q ss_pred CCCCCChHHHHHH
Q psy16114 2 CPKGNGFISALSA 14 (202)
Q Consensus 2 ~~~~~~s~sal~a 14 (202)
|.+.|++++++.+
T Consensus 7 C~~~F~~~~~l~~ 19 (27)
T PF13912_consen 7 CGKTFSSLSALRE 19 (27)
T ss_dssp TTEEESSHHHHHH
T ss_pred cCCccCChhHHHH
Confidence 7888888888765
No 47
>smart00642 Aamy Alpha-amylase domain.
Probab=20.55 E-value=1.6e+02 Score=22.43 Aligned_cols=29 Identities=10% Similarity=-0.066 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhCCCceEEEEecccCCC
Q psy16114 25 VSKAYSCWDLLTSNNKDVRFMWCPSHCGI 53 (202)
Q Consensus 25 ~~~i~~~~~~l~~~~~~i~l~WvPgH~gI 53 (202)
..+....+..++++|..|-+-.||-|++.
T Consensus 69 ~~d~~~lv~~~h~~Gi~vilD~V~NH~~~ 97 (166)
T smart00642 69 MEDFKELVDAAHARGIKVILDVVINHTSD 97 (166)
T ss_pred HHHHHHHHHHHHHCCCEEEEEECCCCCCC
Confidence 46788889999999999999999999987
Done!