Query 032114
Match_columns 147
No_of_seqs 113 out of 586
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 09:46:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032114.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032114hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1278 Endosomal membrane pro 100.0 4E-39 8.6E-44 281.6 11.5 120 23-146 17-137 (628)
2 KOG1277 Endosomal membrane pro 100.0 1.3E-30 2.8E-35 224.6 9.5 109 36-146 26-137 (593)
3 PF02990 EMP70: Endomembrane p 99.9 7.5E-26 1.6E-30 199.7 6.3 82 64-147 1-83 (521)
4 PLN02288 mannose-6-phosphate i 57.9 6.5 0.00014 34.4 1.8 29 28-57 256-284 (394)
5 smart00767 DCD DCD is a plant 57.1 9 0.00019 28.7 2.2 70 53-138 33-110 (132)
6 PF10539 Dev_Cell_Death: Devel 48.2 15 0.00033 27.4 2.2 72 53-138 31-110 (130)
7 PRK15131 mannose-6-phosphate i 43.1 13 0.00028 32.3 1.3 29 28-57 242-270 (389)
8 PF07240 Turandot: Stress-indu 43.0 16 0.00034 25.4 1.5 29 119-147 27-55 (85)
9 PF04423 Rad50_zn_hook: Rad50 39.3 16 0.00035 22.4 1.0 22 112-134 23-44 (54)
10 PF15180 NPBW: Neuropeptides B 39.0 24 0.00052 26.0 2.0 21 29-50 18-38 (120)
11 PF05688 DUF824: Salmonella re 32.2 51 0.0011 20.3 2.4 29 43-71 8-36 (47)
12 COG3112 Uncharacterized protei 31.2 16 0.00035 26.7 0.0 45 33-77 55-105 (121)
13 COG0099 RpsM Ribosomal protein 31.0 51 0.0011 24.3 2.6 22 118-139 46-67 (121)
14 PF01157 Ribosomal_L21e: Ribos 30.2 36 0.00077 24.2 1.6 27 42-70 31-57 (99)
15 PF10731 Anophelin: Thrombin i 28.9 69 0.0015 21.0 2.6 15 33-48 23-37 (65)
16 cd00114 LIGANc NAD+ dependent 26.8 67 0.0015 27.0 3.0 29 118-146 79-113 (307)
17 PF12158 DUF3592: Protein of u 26.4 60 0.0013 23.0 2.3 19 42-60 90-108 (148)
18 smart00532 LIGANc Ligase N fam 25.4 69 0.0015 28.4 2.9 29 118-146 81-115 (441)
19 COG1482 ManA Phosphomannose is 25.1 51 0.0011 28.1 2.0 37 28-68 163-199 (312)
20 COG2139 RPL21A Ribosomal prote 24.6 61 0.0013 23.1 2.0 28 41-70 30-57 (98)
21 PRK04306 50S ribosomal protein 23.3 59 0.0013 23.1 1.7 27 42-70 33-59 (98)
22 cd04472 S1_PNPase S1_PNPase: P 21.3 98 0.0021 18.7 2.3 18 42-59 43-60 (68)
No 1
>KOG1278 consensus Endosomal membrane proteins, EMP70 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4e-39 Score=281.60 Aligned_cols=120 Identities=42% Similarity=0.739 Sum_probs=113.7
Q ss_pred HHHHhhcccceeeccCCCCCCCCCCCceEEEEeecccCCCCccccccccCCCCCCCCccccccccccccccCeeecCCce
Q 032114 23 VFFFFQSSCLGFYLRDNYPHKHVVSDPLSVKVNSITSIDTKMPFSYYSLSFCKPQEGVKDSAENRGELLMGDRIENSPYR 102 (147)
Q Consensus 23 ~~~~~~~~~~af~lpg~~p~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~LPfC~p~~~~~~~~~sLGeiL~GDri~~S~y~ 102 (147)
+.++++.+ .|||+||++|.+|+.||+|+++|||++|.++|.||+||++|||+|+ ++++++|||||+|+||||+||||+
T Consensus 17 ~~~~~~~~-~~FylpG~aPv~f~~gd~i~l~vnklts~~t~lpY~YY~~~Fc~p~-~i~~~~EnLGeVl~GDRi~nSPy~ 94 (628)
T KOG1278|consen 17 VSLLLSTS-SAFYLPGVAPVNFCSGDPIELKVNKLTSSRTQLPYEYYSLPFCRPE-KIKKQSENLGEVLRGDRIENSPYK 94 (628)
T ss_pred HHHHHhcc-cceecCCcCCccCCCCCceEEEEEEeeccccccCcccccccccCcc-ccCCcccchhceeccCcccCCCce
Confidence 34444546 8999999999999999999999999999999999999999999998 789999999999999999999999
Q ss_pred EEecccccce-eeccccCCCHHHHHHHHHHHhhcceEEEEeecCC
Q 032114 103 FKTYTNETDI-FFCKTDPLSKDNFELLKRRIDEMYQVFFFFRVRS 146 (147)
Q Consensus 103 i~f~~n~~~c-~lC~~~~l~~~~~~~l~~~I~~~Y~~~~~iD~l~ 146 (147)
++|++|++ | .+|. .++++++++.++++|+++|++||+|||||
T Consensus 95 ~~m~e~~~-C~~lC~-~k~~~~~~~~l~~~I~~~Y~v~wivDnlP 137 (628)
T KOG1278|consen 95 FKMLENQP-CETLCA-TKLDKEDAKLLKKLIREGYVVNWIVDNLP 137 (628)
T ss_pred EecccCCc-chhhhc-ccCCHHHHHHHHHHHhhccEeeeeecCCc
Confidence 99999999 9 9998 58999999999999999999999999998
No 2
>KOG1277 consensus Endosomal membrane proteins, EMP70 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=1.3e-30 Score=224.59 Aligned_cols=109 Identities=23% Similarity=0.441 Sum_probs=101.8
Q ss_pred ccCCCCCCCCCCCceEEEEeecccC-CCCccccccccCCCCCC-CCccccccccccccccCeeecCCceEEecccccce-
Q 032114 36 LRDNYPHKHVVSDPLSVKVNSITSI-DTKMPFSYYSLSFCKPQ-EGVKDSAENRGELLMGDRIENSPYRFKTYTNETDI- 112 (147)
Q Consensus 36 lpg~~p~~Y~~Gd~V~v~vNkl~s~-~t~~~Y~Yy~LPfC~p~-~~~~~~~~sLGeiL~GDri~~S~y~i~f~~n~~~c- 112 (147)
-.....|.|++||+|++||||++|+ |+||+|.||+||||.++ +++++++|+|||+|.|||++.|+|+|+|+.|++ .
T Consensus 26 ~ade~dh~Yk~~e~VvLw~NkVGPyhNpqETY~YfsLPfC~g~~~~i~hk~etLGEvL~G~eL~~s~y~ikF~~~v~-~~ 104 (593)
T KOG1277|consen 26 RADESDHRYKDGEEVVLWMNKVGPYHNPQETYRYFSLPFCSGSKESISHKHETLGEVLQGDELEFSGYEIKFRDNVE-KE 104 (593)
T ss_pred cccccccccccCCeeEEEEeccCCCCChhhhceeeccceecCCCcccchhhhhHHhhhCCceeeecceeeeecccCC-ce
Confidence 3455679999999999999999999 99999999999999853 268889999999999999999999999999999 7
Q ss_pred eeccccCCCHHHHHHHHHHHhhcceEEEEeecCC
Q 032114 113 FFCKTDPLSKDNFELLKRRIDEMYQVFFFFRVRS 146 (147)
Q Consensus 113 ~lC~~~~l~~~~~~~l~~~I~~~Y~~~~~iD~l~ 146 (147)
++|. +++++++++.|+++|++.|++||++||||
T Consensus 105 v~C~-~~L~~e~v~~f~~AI~~~Yyfqmy~DdlP 137 (593)
T KOG1277|consen 105 VYCE-KKLSEEKVKAFRYAIENDYYFQMYIDDLP 137 (593)
T ss_pred eeeh-hhcCHHHHHHHHHHHHhhheeeeeecCce
Confidence 9998 79999999999999999999999999998
No 3
>PF02990 EMP70: Endomembrane protein 70; InterPro: IPR004240 The transmembrane 9 superfamily protein (TM9SF) may function as a channel or small molecule transporter. Proteins in this group are endosomal integral membrane proteins.; GO: 0016021 integral to membrane
Probab=99.92 E-value=7.5e-26 Score=199.65 Aligned_cols=82 Identities=40% Similarity=0.812 Sum_probs=77.6
Q ss_pred ccccccccCCCCCCCCccccccccccccccCeeecCCceEEecccccce-eeccccCCCHHHHHHHHHHHhhcceEEEEe
Q 032114 64 MPFSYYSLSFCKPQEGVKDSAENRGELLMGDRIENSPYRFKTYTNETDI-FFCKTDPLSKDNFELLKRRIDEMYQVFFFF 142 (147)
Q Consensus 64 ~~Y~Yy~LPfC~p~~~~~~~~~sLGeiL~GDri~~S~y~i~f~~n~~~c-~lC~~~~l~~~~~~~l~~~I~~~Y~~~~~i 142 (147)
+|||||+||||+|+++++++++||||+|.|||+++|||+++|++|++ | .+|+ ++++++|+++++++|+++|++||+|
T Consensus 1 l~Y~Yy~lPfC~P~~~~~~~~~slGevL~Gdr~~~S~y~i~f~~~~~-c~~lC~-~~l~~~~~~~l~~~I~~~Y~~~~~v 78 (521)
T PF02990_consen 1 LPYDYYDLPFCRPEEGIEHKSESLGEVLRGDRIQNSPYEIKFLQNVT-CKVLCK-KTLTKEDVKKLKEAIENNYRVEMYV 78 (521)
T ss_pred CCccccCCCCcCCCCccccccCCHHHHhccCceecCceEEEEecCcc-hhhccC-ccCCHHHHHHHHHHHHHhheeeEEe
Confidence 59999999999997337888999999999999999999999999999 9 9998 6999999999999999999999999
Q ss_pred ecCCC
Q 032114 143 RVRSS 147 (147)
Q Consensus 143 D~l~~ 147 (147)
||||.
T Consensus 79 D~LP~ 83 (521)
T PF02990_consen 79 DDLPI 83 (521)
T ss_pred cCceE
Confidence 99984
No 4
>PLN02288 mannose-6-phosphate isomerase
Probab=57.94 E-value=6.5 Score=34.36 Aligned_cols=29 Identities=21% Similarity=0.291 Sum_probs=25.4
Q ss_pred hcccceeeccCCCCCCCCCCCceEEEEeec
Q 032114 28 QSSCLGFYLRDNYPHKHVVSDPLSVKVNSI 57 (147)
Q Consensus 28 ~~~~~af~lpg~~p~~Y~~Gd~V~v~vNkl 57 (147)
... +|.|+|--.||.|-.|+-|++++|+=
T Consensus 256 ~PG-eaifl~ag~~HAYl~G~~vE~MA~SD 284 (394)
T PLN02288 256 NPG-EALYLGANEPHAYLSGECIECMATSD 284 (394)
T ss_pred CCC-CEEEecCCCCceecCCCeEEeeecCC
Confidence 456 78999999999999999999998753
No 5
>smart00767 DCD DCD is a plant specific domain in proteins involved in development and programmed cell death. The domain is shared by several proteins in the Arabidopsis and the rice genomes, which otherwise show a different protein architecture. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone.
Probab=57.07 E-value=9 Score=28.71 Aligned_cols=70 Identities=16% Similarity=0.121 Sum_probs=40.3
Q ss_pred EEeecccCCCCccccccc--cC--C--CCCCCCcccccccc-ccccccCeeecCCceEEecccccce-eeccccCCCHHH
Q 032114 53 KVNSITSIDTKMPFSYYS--LS--F--CKPQEGVKDSAENR-GELLMGDRIENSPYRFKTYTNETDI-FFCKTDPLSKDN 124 (147)
Q Consensus 53 ~vNkl~s~~t~~~Y~Yy~--LP--f--C~p~~~~~~~~~sL-GeiL~GDri~~S~y~i~f~~n~~~c-~lC~~~~l~~~~ 124 (147)
.|-+|++--+..-|+|-. |. | ++.. ..|| =....|++-..=|.+++|..... | +|. ++
T Consensus 33 ~V~~IkpG~~LFLfn~~~r~L~GifeA~S~G------~~ni~p~Af~~~~~s~fPaQVrf~i~~~-C~PL~------E~- 98 (132)
T smart00767 33 FVRNIKPGLPLFLYNYDTRKLHGIFEATSFG------GLNIDPNAFEGKKESRFPAQVRFRIRKD-CKPLP------ES- 98 (132)
T ss_pred hhheeCCCCEEEEEecCCceeeeEEEeccCC------cCCcChhHhcCCCCCccCcEEEEEEeee-ecCCC------HH-
Confidence 456777777777788753 22 2 1211 1122 13344554223356788876666 5 554 43
Q ss_pred HHHHHHHHhhcceE
Q 032114 125 FELLKRRIDEMYQV 138 (147)
Q Consensus 125 ~~~l~~~I~~~Y~~ 138 (147)
.|+.+|.++|..
T Consensus 99 --~f~~aI~~nY~~ 110 (132)
T smart00767 99 --EFRSAILENYDG 110 (132)
T ss_pred --HHHHHHHHhCcC
Confidence 399999999976
No 6
>PF10539 Dev_Cell_Death: Development and cell death domain; InterPro: IPR013989 The DCD (Development and Cell Death) domain is found in plant proteins involved in development and cell death. The DCD domain is an ~130 amino acid long stretch that contains several mostly invariable motifs. These include a FGLP and a LFL motif at the N terminus and a PAQV and a PLxE motif towards the C terminus of the domain. The DCD domain is present in proteins with different architectures. Some of these proteins contain additional recognizable motifs, like the KELCH repeats or the ParB domain []. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone. The predicted secondary structure of the DCD domain is mostly composed of beta strands and confined by an alpha-helix at the N- and at the C terminus []. Proteins known to contain a DCD domain are listed below: Carrot B2 protein. Pea Gda-1 protein. Soybean N-rich protein (NRP).
Probab=48.20 E-value=15 Score=27.37 Aligned_cols=72 Identities=19% Similarity=0.158 Sum_probs=42.3
Q ss_pred EEeecccCCCCccccccc--cC--CCCCCCCcccccccc-ccccccCeeecCC--ceEEecccccce-eeccccCCCHHH
Q 032114 53 KVNSITSIDTKMPFSYYS--LS--FCKPQEGVKDSAENR-GELLMGDRIENSP--YRFKTYTNETDI-FFCKTDPLSKDN 124 (147)
Q Consensus 53 ~vNkl~s~~t~~~Y~Yy~--LP--fC~p~~~~~~~~~sL-GeiL~GDri~~S~--y~i~f~~n~~~c-~lC~~~~l~~~~ 124 (147)
.|-+|+|-.+..=|+|-. |- | .. ...-..|| -.+..|+.-..|+ .+++|..... | +|-.
T Consensus 31 ~V~~I~pG~~LFLfn~~~r~L~Gif-eA---~S~G~~ni~p~Af~~~~~~~~~fPAQVrf~i~~~-C~PL~E-------- 97 (130)
T PF10539_consen 31 FVKKIKPGMPLFLFNYSDRKLYGIF-EA---TSDGGMNIEPYAFSGSGSGESPFPAQVRFRIRWD-CPPLPE-------- 97 (130)
T ss_pred HHheeCCCCEEEEEEcCCCEEEEEE-Ee---cCCCccCcChhhhCCCCCCCcccceEEEEEEeee-eecCCH--------
Confidence 356788888888888854 22 2 11 11112233 2344454444454 5677877666 6 6654
Q ss_pred HHHHHHHHhhcceE
Q 032114 125 FELLKRRIDEMYQV 138 (147)
Q Consensus 125 ~~~l~~~I~~~Y~~ 138 (147)
..++.+|+++|.-
T Consensus 98 -~~fk~aI~~Ny~~ 110 (130)
T PF10539_consen 98 -SQFKPAIKDNYYD 110 (130)
T ss_pred -HHHHHHHHHhCCC
Confidence 6788999998875
No 7
>PRK15131 mannose-6-phosphate isomerase; Provisional
Probab=43.14 E-value=13 Score=32.31 Aligned_cols=29 Identities=24% Similarity=0.266 Sum_probs=25.2
Q ss_pred hcccceeeccCCCCCCCCCCCceEEEEeec
Q 032114 28 QSSCLGFYLRDNYPHKHVVSDPLSVKVNSI 57 (147)
Q Consensus 28 ~~~~~af~lpg~~p~~Y~~Gd~V~v~vNkl 57 (147)
... +++|+|.-.||.|-.|+-|++..|+=
T Consensus 242 ~pG-eaifipAg~~HAyl~G~~iEima~SD 270 (389)
T PRK15131 242 NPG-EAMFLFAETPHAYLQGVALEVMANSD 270 (389)
T ss_pred CCC-CEEEeCCCCCeEEcCCeEEEEEecCC
Confidence 346 78999999999999999999997754
No 8
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=43.00 E-value=16 Score=25.38 Aligned_cols=29 Identities=14% Similarity=0.118 Sum_probs=23.6
Q ss_pred CCCHHHHHHHHHHHhhcceEEEEeecCCC
Q 032114 119 PLSKDNFELLKRRIDEMYQVFFFFRVRSS 147 (147)
Q Consensus 119 ~l~~~~~~~l~~~I~~~Y~~~~~iD~l~~ 147 (147)
.++.++.+++.+.|++.=..+..|||.|+
T Consensus 27 ~L~~~~r~~~d~~i~~y~~~~~lVDGvPa 55 (85)
T PF07240_consen 27 PLTPQDRQRIDRFIRRYKEENNLVDGVPA 55 (85)
T ss_pred CCCHHHHHHHHHHHHHHHHHhhcccCcCC
Confidence 58899989988888865555559999996
No 9
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=39.33 E-value=16 Score=22.45 Aligned_cols=22 Identities=18% Similarity=0.416 Sum_probs=13.7
Q ss_pred eeeccccCCCHHHHHHHHHHHhh
Q 032114 112 IFFCKTDPLSKDNFELLKRRIDE 134 (147)
Q Consensus 112 c~lC~~~~l~~~~~~~l~~~I~~ 134 (147)
|++|. +.++++....|.+.++.
T Consensus 23 CPlC~-r~l~~e~~~~li~~~~~ 44 (54)
T PF04423_consen 23 CPLCG-RPLDEEHRQELIKKYKS 44 (54)
T ss_dssp -TTT---EE-HHHHHHHHHHHHH
T ss_pred CCCCC-CCCCHHHHHHHHHHHHH
Confidence 69998 69999887776665543
No 10
>PF15180 NPBW: Neuropeptides B and W
Probab=39.02 E-value=24 Score=26.00 Aligned_cols=21 Identities=14% Similarity=0.148 Sum_probs=18.0
Q ss_pred cccceeeccCCCCCCCCCCCce
Q 032114 29 SSCLGFYLRDNYPHKHVVSDPL 50 (147)
Q Consensus 29 ~~~~af~lpg~~p~~Y~~Gd~V 50 (147)
.. .|+|-+-..|+.|..|-.-
T Consensus 18 Pa-~AWYK~~agP~yysVGRAs 38 (120)
T PF15180_consen 18 PA-EAWYKQAAGPSYYSVGRAS 38 (120)
T ss_pred cc-chhhccccCCcceehhhHH
Confidence 57 7999999999999998543
No 11
>PF05688 DUF824: Salmonella repeat of unknown function (DUF824); InterPro: IPR008542 This family consists of a series of repeated sequences (of around 180 residues) which are found in Salmonella typhimurium, Salmonella typhi and Escherichia coli. These repeats are almost always found with this entry. The repeats are associated with RatA and RatB, the coding sequences of which are found in the pathogeneicity island of Salmonella. The sequences may be determinants of pathogenicity [, ].
Probab=32.22 E-value=51 Score=20.27 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=21.9
Q ss_pred CCCCCCceEEEEeecccCCCCcccccccc
Q 032114 43 KHVVSDPLSVKVNSITSIDTKMPFSYYSL 71 (147)
Q Consensus 43 ~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~L 71 (147)
.-+.||.|++.|-.-.+.....||-++.|
T Consensus 8 kaK~Ge~I~ltVt~kda~G~pv~n~~f~l 36 (47)
T PF05688_consen 8 KAKVGETIPLTVTVKDANGNPVPNAPFTL 36 (47)
T ss_pred heecCCeEEEEEEEECCCCCCcCCceEEE
Confidence 45789999999888877655677776654
No 12
>COG3112 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.18 E-value=16 Score=26.70 Aligned_cols=45 Identities=18% Similarity=0.370 Sum_probs=35.6
Q ss_pred eeeccCCCCCCCCCCCceEEEEeecccC--C-CCccccccc---cCCCCCC
Q 032114 33 GFYLRDNYPHKHVVSDPLSVKVNSITSI--D-TKMPFSYYS---LSFCKPQ 77 (147)
Q Consensus 33 af~lpg~~p~~Y~~Gd~V~v~vNkl~s~--~-t~~~Y~Yy~---LPfC~p~ 77 (147)
.+.++|..-.-+-.||+|-|.+|.+.=. . --.-+.||+ |.||...
T Consensus 55 ~~~~~G~Eytl~~~geEVmVraN~L~~e~de~lE~df~yYDeESla~CG~e 105 (121)
T COG3112 55 EWQLAGHEYTLWMDGEEVMVRANQLAFEGDEELEEDFNYYDEESLALCGTE 105 (121)
T ss_pred hheecCcEEEEEEcCceeeeecchhccccchhhhcccccccHHHHHhhchH
Confidence 5889999988889999999999998643 2 235678884 8899653
No 13
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=30.97 E-value=51 Score=24.35 Aligned_cols=22 Identities=27% Similarity=0.428 Sum_probs=19.2
Q ss_pred cCCCHHHHHHHHHHHhhcceEE
Q 032114 118 DPLSKDNFELLKRRIDEMYQVF 139 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~~Y~~~ 139 (147)
..++++|++.+++.|++.|.++
T Consensus 46 ~eLteeei~~ir~~i~~~~~ve 67 (121)
T COG0099 46 GELTEEEIERLRDAIQNKYLVE 67 (121)
T ss_pred ccCCHHHHHHHHHHHHhcCeeh
Confidence 4689999999999999988764
No 14
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=30.22 E-value=36 Score=24.20 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=12.9
Q ss_pred CCCCCCCceEEEEeecccCCCCccccccc
Q 032114 42 HKHVVSDPLSVKVNSITSIDTKMPFSYYS 70 (147)
Q Consensus 42 ~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~ 70 (147)
+.|..||.|.|.+|-- ...-+|+.+|.
T Consensus 31 ~~yk~GD~V~I~id~s--v~kGmPh~~yH 57 (99)
T PF01157_consen 31 QEYKVGDKVDIKIDPS--VHKGMPHKRYH 57 (99)
T ss_dssp ----TT-EEEE---TT--SSSSS--GGGT
T ss_pred HHccCCCEEEEEecCc--cccCCCcceEC
Confidence 7899999999997643 35578988886
No 15
>PF10731 Anophelin: Thrombin inhibitor from mosquito; InterPro: IPR018932 Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen. The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite. The inhibitor acts by blocking the exosite, rather than by interacting with the active site. The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing.
Probab=28.87 E-value=69 Score=20.95 Aligned_cols=15 Identities=20% Similarity=0.129 Sum_probs=11.2
Q ss_pred eeeccCCCCCCCCCCC
Q 032114 33 GFYLRDNYPHKHVVSD 48 (147)
Q Consensus 33 af~lpg~~p~~Y~~Gd 48 (147)
.-|.||..| +|.+.+
T Consensus 23 PQYa~GeeP-~YDEdd 37 (65)
T PF10731_consen 23 PQYAPGEEP-SYDEDD 37 (65)
T ss_pred cccCCCCCC-CcCccc
Confidence 469999998 676643
No 16
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=26.84 E-value=67 Score=27.01 Aligned_cols=29 Identities=17% Similarity=0.219 Sum_probs=25.2
Q ss_pred cCCCHHHHHHHHHHHhh------cceEEEEeecCC
Q 032114 118 DPLSKDNFELLKRRIDE------MYQVFFFFRVRS 146 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~------~Y~~~~~iD~l~ 146 (147)
+.++.+++..|.+.+.+ .|.++.-|||++
T Consensus 79 k~~~~~el~~~~~r~~~~~~~~~~~~vepKiDGls 113 (307)
T cd00114 79 NAFDEEELRAFDERIKRFLGEEPAYVVEPKIDGLS 113 (307)
T ss_pred ccCCHHHHHHHHHHHHHhcCCCCcEEEEEeccceE
Confidence 46788999999999974 799999999985
No 17
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=26.37 E-value=60 Score=23.04 Aligned_cols=19 Identities=21% Similarity=0.169 Sum_probs=14.2
Q ss_pred CCCCCCCceEEEEeecccC
Q 032114 42 HKHVVSDPLSVKVNSITSI 60 (147)
Q Consensus 42 ~~Y~~Gd~V~v~vNkl~s~ 60 (147)
..|+.||+|+|++|.=.|.
T Consensus 90 ~~~~~G~~V~V~Y~P~~P~ 108 (148)
T PF12158_consen 90 PKYPIGDTVTVYYNPNNPE 108 (148)
T ss_pred ccCCCcCEEEEEECCcCCC
Confidence 4588888888887766555
No 18
>smart00532 LIGANc Ligase N family.
Probab=25.41 E-value=69 Score=28.43 Aligned_cols=29 Identities=21% Similarity=0.276 Sum_probs=25.3
Q ss_pred cCCCHHHHHHHHHHHhh------cceEEEEeecCC
Q 032114 118 DPLSKDNFELLKRRIDE------MYQVFFFFRVRS 146 (147)
Q Consensus 118 ~~l~~~~~~~l~~~I~~------~Y~~~~~iD~l~ 146 (147)
+.++.+++..|.+.|++ .|.++.-+||++
T Consensus 81 k~~~~~el~~f~~~~~~~~~~~~~~~~epKiDGls 115 (441)
T smart00532 81 NAFDEDELRAFDERIEKALGSPFAYVVEPKIDGLS 115 (441)
T ss_pred ccCCHHHHHHHHHHHHHhcCCCceEEEEEecccEE
Confidence 47899999999999876 589999999985
No 19
>COG1482 ManA Phosphomannose isomerase [Carbohydrate transport and metabolism]
Probab=25.12 E-value=51 Score=28.06 Aligned_cols=37 Identities=24% Similarity=0.261 Sum_probs=28.3
Q ss_pred hcccceeeccCCCCCCCCCCCceEEEEeecccCCCCccccc
Q 032114 28 QSSCLGFYLRDNYPHKHVVSDPLSVKVNSITSIDTKMPFSY 68 (147)
Q Consensus 28 ~~~~~af~lpg~~p~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Y 68 (147)
.+. +++|+|.-.||.|..|.-+++..|+ .++.--|+|
T Consensus 163 kpG-e~~fl~Agt~HA~~~G~~lEvmqnS---DntyR~yd~ 199 (312)
T COG1482 163 KPG-EAFFLPAGTPHAYLKGLVLEVMQNS---DNTYRVYDT 199 (312)
T ss_pred CCC-CEEEecCCCceeeccceEEEEEecC---ccEEEcccc
Confidence 346 7899999999999999888998764 344444444
No 20
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=24.57 E-value=61 Score=23.06 Aligned_cols=28 Identities=18% Similarity=0.422 Sum_probs=21.7
Q ss_pred CCCCCCCCceEEEEeecccCCCCccccccc
Q 032114 41 PHKHVVSDPLSVKVNSITSIDTKMPFSYYS 70 (147)
Q Consensus 41 p~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~ 70 (147)
-.+|.+||.|.|.+|- |...-+|+.+|.
T Consensus 30 l~ey~~Gd~V~I~Idp--Sv~kGmPh~rf~ 57 (98)
T COG2139 30 LQEYKVGDKVHIDIDP--SVHKGMPHPRFQ 57 (98)
T ss_pred HhhccCCCEEEEEeCc--ccccCCCCcccc
Confidence 4789999999998764 334568888876
No 21
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=23.29 E-value=59 Score=23.08 Aligned_cols=27 Identities=11% Similarity=0.305 Sum_probs=21.3
Q ss_pred CCCCCCCceEEEEeecccCCCCccccccc
Q 032114 42 HKHVVSDPLSVKVNSITSIDTKMPFSYYS 70 (147)
Q Consensus 42 ~~Y~~Gd~V~v~vNkl~s~~t~~~Y~Yy~ 70 (147)
..|+.||.|.|.+|--- ..-+|+.+|.
T Consensus 33 ~~y~~Gd~V~I~~d~sv--~kGmPh~~yh 59 (98)
T PRK04306 33 QEFEEGDKVHIVIDPSV--HKGMPHPRFH 59 (98)
T ss_pred HhccCCCEEEEEecCce--ecCCcccccc
Confidence 78999999999987433 4468988886
No 22
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=21.27 E-value=98 Score=18.70 Aligned_cols=18 Identities=28% Similarity=0.298 Sum_probs=15.4
Q ss_pred CCCCCCCceEEEEeeccc
Q 032114 42 HKHVVSDPLSVKVNSITS 59 (147)
Q Consensus 42 ~~Y~~Gd~V~v~vNkl~s 59 (147)
..|+.||.|.+.+.++.+
T Consensus 43 ~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 43 DVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred HccCCCCEEEEEEEEECC
Confidence 358999999999988876
Done!