Query 028676
Match_columns 205
No_of_seqs 121 out of 627
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 15:14:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3274 Uncharacterized conser 100.0 2.6E-57 5.6E-62 380.9 15.5 180 9-192 25-206 (210)
2 PF01871 AMMECR1: AMMECR1; In 100.0 3.7E-57 8.1E-62 376.2 14.5 148 18-178 23-171 (171)
3 TIGR00296 uncharacterized prot 100.0 6.1E-55 1.3E-59 371.1 15.1 146 22-181 38-193 (200)
4 PRK00801 hypothetical protein; 100.0 1.2E-54 2.6E-59 369.6 14.7 147 21-181 37-189 (201)
5 COG2078 AMMECR1 Uncharacterize 100.0 3.8E-50 8.2E-55 340.9 14.6 151 21-181 37-193 (203)
6 PRK03881 hypothetical protein; 100.0 2.9E-44 6.4E-49 336.5 14.4 135 24-177 331-467 (467)
7 cd01760 RBD Ubiquitin-like dom 34.0 48 0.001 24.0 2.9 25 133-157 14-38 (72)
8 COG3044 Predicted ATPase of th 27.4 71 0.0015 31.4 3.6 62 53-118 64-127 (554)
9 PF00853 Runt: Runt domain; I 26.6 48 0.001 27.1 2.0 73 27-111 51-125 (135)
10 TIGR02396 diverge_rpsU rpsU-di 24.3 55 0.0012 27.5 2.1 26 130-157 9-34 (184)
11 TIGR03687 pupylate_cterm ubiqu 23.3 63 0.0014 20.5 1.6 14 140-153 19-32 (33)
12 PF06102 DUF947: Domain of unk 22.1 41 0.00089 28.1 0.9 13 69-81 32-44 (168)
13 KOG1612 Exosomal 3'-5' exoribo 21.3 1E+02 0.0022 28.2 3.2 41 56-99 147-187 (288)
14 cd01817 RGS12_RBD Ubiquitin do 21.3 1.2E+02 0.0027 22.3 3.1 25 133-157 14-38 (73)
No 1
>KOG3274 consensus Uncharacterized conserved protein, AMMECR1 [Function unknown]
Probab=100.00 E-value=2.6e-57 Score=380.90 Aligned_cols=180 Identities=57% Similarity=0.978 Sum_probs=165.4
Q ss_pred hhhhhcc--ccccCCCCCCCccceEEEEEEeccCCCCcceeeecccCcccHHHHHHHHHHHhhhcCCCCCCCCcCcCCCc
Q 028676 9 IYATVLD--YVLVCCFSYSGFSPLFVTWKKVVNGGEPRLRGCIGTLEARCLINGFKDYALTSALKDRRFPPIQARELPSL 86 (205)
Q Consensus 9 ~~~~~~~--~~~~~~~~~~~~~g~FVTl~~~~~~~~~~LRGCIGt~~p~pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L 86 (205)
+|+++-. -+-++|.-.+...|+||||++ |.+.+||||||||+++||+.++.+||+.|||+|.||+||+.+||++|
T Consensus 25 l~~~ln~~k~p~~~~~~~~~~~PLFvtwk~---g~dkrLRGCIGTFsam~L~~Gl~eYaltsAl~DsRF~PIsr~ELp~L 101 (210)
T KOG3274|consen 25 LYAHLNNEKSPSLPPDFRNRLYPLFVTWKK---GHDKRLRGCIGTFSAMPLHSGLREYALTSALKDSRFPPISREELPSL 101 (210)
T ss_pred hhhhhccccCCCcchhhhccCcceeEEecc---CCCcccccceeehhhcchhhhHHHHHHHHHhhcccCCCCChhhcCce
Confidence 4565552 233366677788999999996 44689999999999999999999999999999999999999999999
Q ss_pred eEEEEeecCccccCCccCCccCceeeEEEEeCCCCCCcceeeeeccchhccCCCHHHHHHHHHHHcCCCCCCcccccCcE
Q 028676 87 ECTVSILTDFETANNYLDWEVGTHGLIIEFTDPEYSTRRSATYLPEVAAHEGWTKVEAIDSLMRKAGFSGPITESLRKRI 166 (205)
Q Consensus 87 ~ieVSvLs~~e~~~d~~d~~~G~hGlii~~~~~~~g~~~~atfLPqVa~Eq~w~~eefl~~L~~KAGl~~~~~~~~~~~i 166 (205)
.|+||+|++||++.|+.||++|+|||.|+|.+ ..|..++|||||+||.|||||++|++++|++||||.+.|++.+++.|
T Consensus 102 ~CsvslL~nFE~i~d~lDWevG~HGIrieF~~-e~g~krsATyLPeVa~EQgWd~~eTidsLirKaGY~g~It~~~r~~I 180 (210)
T KOG3274|consen 102 QCSVSLLTNFEDIFDYLDWEVGVHGIRIEFTN-ETGTKRSATYLPEVAAEQGWDQIETIDSLIRKAGYKGPITEELRKSI 180 (210)
T ss_pred EEEEEeeccchhcccccceeeccceEEEEEEc-CCCcEeeeeecccchhhcCCcHHHHHHHHHHhcCCCCccCHHHHhhe
Confidence 99999999999999999999999999999987 34799999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEEEEeehHHHHHHHHhhcC
Q 028676 167 RLTRYQSTLFALHYSDYASYVKTTRG 192 (205)
Q Consensus 167 ~v~ryq~~~~~~~~~ey~~~~~~~~~ 192 (205)
+++||++++++++|.||++.++++..
T Consensus 181 ~ltRY~S~k~~~~Y~EY~~~~q~~~~ 206 (210)
T KOG3274|consen 181 KLTRYRSEKISITYEEYLAYLQHHGA 206 (210)
T ss_pred eeeEeeceeeeeeHHHHHHHHHhhcC
Confidence 99999999999999999999999753
No 2
>PF01871 AMMECR1: AMMECR1; InterPro: IPR002733 The contiguous gene deletion syndrome is characterised by Alport syndrome (A), mental retardation (M), midface hypoplasia (M), and elliptocytosis (E), as well as generalized hypoplasia and cardiac abnormalities. It is caused by a deletion in Xq22.3, comprising several genes including AMME chromosomal region gene 1 (AMMECR1), which encodes a protein with a nuclear location and presently unknown function. The C-terminal region of AMMECR1 (from residue 122 to 333) is well conserved, and homologues appear in species ranging from bacteria and archaea to eukaryotes. The high level of conservation of the AMMECR1 domain points to a basic cellular function, potentially in either the transcription, replication, repair or translation machinery [, ]. The AMMECR1 domain contains a 6-amino-acid motif (LRGCIG) that might be functionally important since it is strikingly conserved throughout evolution []. The AMMECR1 domain consists of two distinct subdomains of different sizes. The large subdomain, which contains both the N- and C-terminal regions, consists of five alpha-helices and five beta-strands. These five beta-strands form an antiparallel beta-sheet. The small subdomain consists of four alpha-helices and three beta-strands, and these beta-strands also form an antiparallel beta-sheet. The conserved 'LRGCIG' motif is located at beta(2) and its N-terminal loop, and most of the side chains of these residues point toward the interface of the two subdomains. The two subdomains are connected by only two loops, and the interaction between the two subdomains is not strong. Thus, these subdomains may move dynamically when the substrate enters the cleft. The size of the cleft suggests that the substrate is large, e.g., the substrate may be a nucleic acid or protein. However, the inner side of the cleft is not filled with positively charged residues, and therefore it is unlikely that negatively charged nucleic acids such as DNA or RNA interact at this site []. ; PDB: 1WSC_B 1VAJ_A 1ZQ7_D.
Probab=100.00 E-value=3.7e-57 Score=376.17 Aligned_cols=148 Identities=40% Similarity=0.627 Sum_probs=120.9
Q ss_pred ccCCCCCCCccceEEEEEEeccCCCCcceeeecccCc-ccHHHHHHHHHHHhhhcCCCCCCCCcCcCCCceEEEEeecCc
Q 028676 18 LVCCFSYSGFSPLFVTWKKVVNGGEPRLRGCIGTLEA-RCLINGFKDYALTSALKDRRFPPIQARELPSLECTVSILTDF 96 (205)
Q Consensus 18 ~~~~~~~~~~~g~FVTl~~~~~~~~~~LRGCIGt~~p-~pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvLs~~ 96 (205)
...++.+.+++||||||++ +|+|||||||++| +||+++|++||++|||+||||+||+++||++|+||||||++|
T Consensus 23 ~~~~~~l~~~~g~FVTl~~-----~g~LRGCIGt~~p~~~L~~~v~~~A~~AA~~DpRF~Pl~~~El~~l~ieVSvL~~~ 97 (171)
T PF01871_consen 23 PPLPPELSEPRGVFVTLKK-----DGELRGCIGTFEPVRPLAEDVIENAIAAAFEDPRFPPLTPSELPELSIEVSVLSPP 97 (171)
T ss_dssp CT--GGGGSBEEEEEEEEE-----CCCEEEEEEESSSESBHHHHHHHHHHHHHHT-TTS----GGGGGGEEEEEEEE---
T ss_pred CCCChhhcCceeEEEEEEE-----CCEEEEEeccCCcchhHHHHHHHHHHHHhhCCCCCCCCCHHHHcccEEEEEeccCc
Confidence 4456778889999999999 5899999999999 999999999999999999999999999999999999999999
Q ss_pred cccCCccCCccCceeeEEEEeCCCCCCcceeeeeccchhccCCCHHHHHHHHHHHcCCCCCCcccccCcEEEEEEEEEEE
Q 028676 97 ETANNYLDWEVGTHGLIIEFTDPEYSTRRSATYLPEVAAHEGWTKVEAIDSLMRKAGFSGPITESLRKRIRLTRYQSTLF 176 (205)
Q Consensus 97 e~~~d~~d~~~G~hGlii~~~~~~~g~~~~atfLPqVa~Eq~w~~eefl~~L~~KAGl~~~~~~~~~~~i~v~ryq~~~~ 176 (205)
++++++.+|+||+|||+|++ ++++||||||||.||+||+++||++||+|||++.+ .|.+++++++|||+++|
T Consensus 98 ~~i~~~~~~~~g~~Glil~~------~~~~~~~LPqVa~E~~w~~~~fl~~l~~KAG~~~~--~w~~~~~~~~rf~~~~f 169 (171)
T PF01871_consen 98 EPISDPEDWEPGRHGLILEF------GGYRGTFLPQVAWEQGWDPEEFLRHLCRKAGLPPD--AWKSPDIKLYRFQAEVF 169 (171)
T ss_dssp EE--GGGG--TTT-EEEEEE------TTEEEEE-THHHHHTT--HHHHHHHHHHHTTS-TT--CCCTTTSEEEEE-EEEE
T ss_pred EEcCCHHHcccCcceeEEEe------cCcceEECCCchhhcCCCHHHHHHHHHHHCCCCcc--ccccCCeEEEEEEEEEE
Confidence 99999999999999999999 89999999999999999999999999999999974 34488999999999999
Q ss_pred Ee
Q 028676 177 AL 178 (205)
Q Consensus 177 ~~ 178 (205)
+|
T Consensus 170 ~E 171 (171)
T PF01871_consen 170 SE 171 (171)
T ss_dssp EE
T ss_pred eC
Confidence 86
No 3
>TIGR00296 uncharacterized protein, PH0010 family. Members of this functionally uncharacterized protein family have been crystallized from Pyrococcus Horikoshii, Methanosarcina Mazei, and Sulfolobus Tokodaii.
Probab=100.00 E-value=6.1e-55 Score=371.13 Aligned_cols=146 Identities=37% Similarity=0.599 Sum_probs=134.9
Q ss_pred CCCCCccceEEEEEEeccCCCCc--ceeeecccCc-ccHHHHHHHHHHHhhhcCCCCCCCCcCcCCCceEEEEeecCccc
Q 028676 22 FSYSGFSPLFVTWKKVVNGGEPR--LRGCIGTLEA-RCLINGFKDYALTSALKDRRFPPIQARELPSLECTVSILTDFET 98 (205)
Q Consensus 22 ~~~~~~~g~FVTl~~~~~~~~~~--LRGCIGt~~p-~pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvLs~~e~ 98 (205)
..+.+++||||||++ +++ |||||||+.| +||+++|++||++|||+||||+||+++||++|+||||||+++++
T Consensus 38 ~~l~~~~g~FVTl~~-----~~~~~LRGCIGs~~p~~pL~~~v~~~A~~AA~~DpRF~Pl~~~EL~~l~ieVSvL~~~e~ 112 (200)
T TIGR00296 38 IVFNEKRGVFITLKK-----KGNKHLRGCIGTPEPVMPLIEAIEEAAISAATEDPRFPPVQLEELDDIKVEVSILTPPET 112 (200)
T ss_pred hhhCCcccEEEEEEE-----CCCcCCCcccccCCCcccHHHHHHHHHHHHHcCCCCCCCCChHHhCCcEEEEEeCCCCEE
Confidence 456889999999998 356 9999999999 99999999999999999999999999999999999999999999
Q ss_pred cC------CccCCccCceeeEEEEeCCCCCCcceeeeeccchhccCCCHHHHHHHHHHHcCCCCCCccccc-CcEEEEEE
Q 028676 99 AN------NYLDWEVGTHGLIIEFTDPEYSTRRSATYLPEVAAHEGWTKVEAIDSLMRKAGFSGPITESLR-KRIRLTRY 171 (205)
Q Consensus 99 ~~------d~~d~~~G~hGlii~~~~~~~g~~~~atfLPqVa~Eq~w~~eefl~~L~~KAGl~~~~~~~~~-~~i~v~ry 171 (205)
++ ++.+|+||+|||+|++ +.++||||||||.||+||+++||.+||+|||+++ +.|. +.++++||
T Consensus 113 i~~~~~~~~~~~~~~G~hGlii~~------g~~~gt~LPqVa~E~~wd~~~fl~~l~~KAGl~~---d~w~~~~~~v~rf 183 (200)
T TIGR00296 113 IFVGGPKDYPFDIEIGRHGLIVEF------GPKRGLLLPQVAVEYGWDAEEFLANLCMKAGLPP---DCFLTYGIEVYRF 183 (200)
T ss_pred cccCCccccHHHcccccceEEEEE------CCccEEECCccHhhcCCCHHHHHHHHHHhCCCCc---cccccCCcEEEEE
Confidence 93 5678999999999999 7999999999999999999999999999999999 4455 47999999
Q ss_pred EEEEEEeehH
Q 028676 172 QSTLFALHYS 181 (205)
Q Consensus 172 q~~~~~~~~~ 181 (205)
++++|++...
T Consensus 184 ~~~~f~E~~~ 193 (200)
T TIGR00296 184 EGQIFEEFEP 193 (200)
T ss_pred EEEEEEecCC
Confidence 9999997643
No 4
>PRK00801 hypothetical protein; Provisional
Probab=100.00 E-value=1.2e-54 Score=369.63 Aligned_cols=147 Identities=29% Similarity=0.420 Sum_probs=137.8
Q ss_pred CCCCCCccceEEEEEEeccCCCCcceeeecccCc-ccHHHHHHHHHHHhhhcCCCCCCCCcCcCCCceEEEEeecCcccc
Q 028676 21 CFSYSGFSPLFVTWKKVVNGGEPRLRGCIGTLEA-RCLINGFKDYALTSALKDRRFPPIQARELPSLECTVSILTDFETA 99 (205)
Q Consensus 21 ~~~~~~~~g~FVTl~~~~~~~~~~LRGCIGt~~p-~pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvLs~~e~~ 99 (205)
|..+.+++||||||++ +|+|||||||+.| +||+++|++||++|||+||||+||+++||++|.||||||++++++
T Consensus 37 ~~~l~~~~g~FVTl~~-----~g~LRGCIGs~~p~~pL~~~v~~~A~~AA~~DpRF~Pl~~~EL~~l~ieVSvLs~~e~i 111 (201)
T PRK00801 37 PPVFWEKRGVFVTLNK-----HGVLRGCIGFPYPDSPLVEAIIDSAISAATRDPRFPPVKLEEMDEITVEVTVLTPPELI 111 (201)
T ss_pred CHhHcccccEEEEEEE-----CCeeccccCCCCCcccHHHHHHHHHHHHHcCCCCCCCCChHHhCCcEEEEEEcCCCEEc
Confidence 3457889999999998 5899999999999 999999999999999999999999999999999999999999999
Q ss_pred CC-----ccCCccCceeeEEEEeCCCCCCcceeeeeccchhccCCCHHHHHHHHHHHcCCCCCCcccccCcEEEEEEEEE
Q 028676 100 NN-----YLDWEVGTHGLIIEFTDPEYSTRRSATYLPEVAAHEGWTKVEAIDSLMRKAGFSGPITESLRKRIRLTRYQST 174 (205)
Q Consensus 100 ~d-----~~d~~~G~hGlii~~~~~~~g~~~~atfLPqVa~Eq~w~~eefl~~L~~KAGl~~~~~~~~~~~i~v~ryq~~ 174 (205)
++ +.+|+||+|||+|++ +.++||||||||+|||||+++||++||+||||++ +.|.++++++||+++
T Consensus 112 ~~~~~~l~~~~~~G~~Glii~~------g~~~g~~LPqV~~e~~wd~~efl~~l~~KAGl~~---d~w~~~~~v~rf~~~ 182 (201)
T PRK00801 112 EGPPEELPEKIEVGRHGLIVKK------GIYSGLLLPQVAPEWGFDSEEFLSHTCLKAGLPP---DCWLDDAEVYRFEGQ 182 (201)
T ss_pred cCcchhhHHhccccceEEEEEe------CCccEEECCcchhhcCCCHHHHHHHHHHhcCCCc---cccccCcEEEEEEEE
Confidence 75 578999999999999 7999999999999999999999999999999998 567779999999999
Q ss_pred EEEeehH
Q 028676 175 LFALHYS 181 (205)
Q Consensus 175 ~~~~~~~ 181 (205)
+|++.-.
T Consensus 183 ~f~E~~p 189 (201)
T PRK00801 183 IFKEEEP 189 (201)
T ss_pred EEEccCC
Confidence 9998654
No 5
>COG2078 AMMECR1 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.8e-50 Score=340.91 Aligned_cols=151 Identities=33% Similarity=0.487 Sum_probs=141.0
Q ss_pred CCCCCCccceEEEEEEeccCCCCcceeeecccCc-ccHHHHHHHHHHHhhhcCCCCCCCCcCcCCCceEEEEeecCcccc
Q 028676 21 CFSYSGFSPLFVTWKKVVNGGEPRLRGCIGTLEA-RCLINGFKDYALTSALKDRRFPPIQARELPSLECTVSILTDFETA 99 (205)
Q Consensus 21 ~~~~~~~~g~FVTl~~~~~~~~~~LRGCIGt~~p-~pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvLs~~e~~ 99 (205)
+..+++++|+||||++.+ ++++||||||++.| .||+++++++|+.||++||||+||+.+||+++.||||||++|+++
T Consensus 37 ~~~~~~k~gvFvTl~~~~--~~~~LRGCIG~~~p~~~l~~ai~~~Ai~AA~~DPRF~pv~~~EL~~i~veV~iLt~pe~i 114 (203)
T COG2078 37 PKLFQEKRGVFVTLEKYS--PDGELRGCIGTPEPVKPLAEAIIKAAIEAALSDPRFPPVSLEELDDIVVEVTILTPPEEI 114 (203)
T ss_pred chhhhhccceEEEEEEeC--CCCceeeecccCcccCcHHHHHHHHHHHHHhcCCCCCCCChhHhcceEEEEEEcCCCeec
Confidence 467899999999999965 24799999999999 899999999999999999999999999999999999999999999
Q ss_pred CCc-----cCCccCceeeEEEEeCCCCCCcceeeeeccchhccCCCHHHHHHHHHHHcCCCCCCcccccCcEEEEEEEEE
Q 028676 100 NNY-----LDWEVGTHGLIIEFTDPEYSTRRSATYLPEVAAHEGWTKVEAIDSLMRKAGFSGPITESLRKRIRLTRYQST 174 (205)
Q Consensus 100 ~d~-----~d~~~G~hGlii~~~~~~~g~~~~atfLPqVa~Eq~w~~eefl~~L~~KAGl~~~~~~~~~~~i~v~ryq~~ 174 (205)
++. .+|++|+|||++.+ +.++|++||||++|++||+++||+++|.||||+++ +|..+++++++|+++
T Consensus 115 ~~~p~~~p~~ie~G~~Gliv~~------g~~sgllLPqV~vE~~w~~eefL~~~c~KAGlp~~--~w~~~~~~iy~F~~~ 186 (203)
T COG2078 115 DVPPEERPEDIEVGRHGLIVEK------GIYSGLLLPQVPVEYRWDVEEFLEHTCEKAGLPGD--CWLDEDVKIYRFEAQ 186 (203)
T ss_pred CCCchhChhheeecceEEEEec------CCcceeecCccccccCCCHHHHHHHHHHHcCCCcc--cccccCceEEEEEEE
Confidence 754 68999999999999 89999999999999999999999999999999996 667779999999999
Q ss_pred EEEeehH
Q 028676 175 LFALHYS 181 (205)
Q Consensus 175 ~~~~~~~ 181 (205)
+|+++..
T Consensus 187 If~E~~p 193 (203)
T COG2078 187 IFKEKEP 193 (203)
T ss_pred EEEecCC
Confidence 9999865
No 6
>PRK03881 hypothetical protein; Provisional
Probab=100.00 E-value=2.9e-44 Score=336.51 Aligned_cols=135 Identities=28% Similarity=0.469 Sum_probs=125.4
Q ss_pred CCCccceEEEEEEeccCCCCcceeeecccCc-c-cHHHHHHHHHHHhhhcCCCCCCCCcCcCCCceEEEEeecCccccCC
Q 028676 24 YSGFSPLFVTWKKVVNGGEPRLRGCIGTLEA-R-CLINGFKDYALTSALKDRRFPPIQARELPSLECTVSILTDFETANN 101 (205)
Q Consensus 24 ~~~~~g~FVTl~~~~~~~~~~LRGCIGt~~p-~-pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvLs~~e~~~d 101 (205)
++++.||||||++ +|+|||||||++| + ||.++|++||++|||+||||+||+++||++|.||||||+++|++++
T Consensus 331 ~~~~~g~FVTl~~-----~g~LRGCIG~~~p~~~~L~~~v~~~a~~AA~~DpRF~pl~~~El~~l~i~VsvL~~~~~~~~ 405 (467)
T PRK03881 331 LNRRAGVFVSLKK-----DGELRGCIGTIFPTRENIAEEIIRNAISAGTEDPRFPPVEEDELDDLVYSVDVLTEPEPVSS 405 (467)
T ss_pred hCCcccEEEEEEE-----CCeeeeeeeecCCCcchHHHHHHHHHHHHhcCCCCCCCCChHHhCCeEEEEEEcCCCeECCC
Confidence 6889999999998 4899999999999 4 8999999999999999999999999999999999999999999999
Q ss_pred ccCCccCceeeEEEEeCCCCCCcceeeeeccchhccCCCHHHHHHHHHHHcCCCCCCcccccCcEEEEEEEEEEEE
Q 028676 102 YLDWEVGTHGLIIEFTDPEYSTRRSATYLPEVAAHEGWTKVEAIDSLMRKAGFSGPITESLRKRIRLTRYQSTLFA 177 (205)
Q Consensus 102 ~~d~~~G~hGlii~~~~~~~g~~~~atfLPqVa~Eq~w~~eefl~~L~~KAGl~~~~~~~~~~~i~v~ryq~~~~~ 177 (205)
+.+|+||+|||+|++ +.++||||||| |+.+++++||+++|+|||++++ +.++++||++++|.
T Consensus 406 ~~~~~~g~~Gli~~~------~~~~g~~LP~v--~~~~~~~~fl~~~~~KaGl~~~------~~~~~~~f~~~~~~ 467 (467)
T PRK03881 406 LDELDPKRYGVIVRS------GRRRGLLLPDL--EGVDTVEEQLSIALRKAGIDPD------EDVEIERFEVVRHK 467 (467)
T ss_pred HHHcCCccceEEEEE------CCccEEECCCC--CCCCCHHHHHHHHHHhcCCCCC------CCeEEEEEEEEEeC
Confidence 999999999999999 78999999999 4434559999999999999995 24999999999873
No 7
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=34.01 E-value=48 Score=24.01 Aligned_cols=25 Identities=16% Similarity=0.312 Sum_probs=21.0
Q ss_pred chhccCCCHHHHHHHHHHHcCCCCC
Q 028676 133 VAAHEGWTKVEAIDSLMRKAGFSGP 157 (205)
Q Consensus 133 Va~Eq~w~~eefl~~L~~KAGl~~~ 157 (205)
|.+..|-+..+.|+.+|+|-|+.+.
T Consensus 14 V~vrpg~ti~d~L~~~c~kr~l~~~ 38 (72)
T cd01760 14 VPVRPGMSVRDVLAKACKKRGLNPE 38 (72)
T ss_pred EEECCCCCHHHHHHHHHHHcCCCHH
Confidence 4445677999999999999999974
No 8
>COG3044 Predicted ATPase of the ABC class [General function prediction only]
Probab=27.42 E-value=71 Score=31.40 Aligned_cols=62 Identities=23% Similarity=0.328 Sum_probs=39.7
Q ss_pred CcccHHHHHHHHHHHhhhcCCCCCCCCcCcCCC--ceEEEEeecCccccCCccCCccCceeeEEEEeC
Q 028676 53 EARCLINGFKDYALTSALKDRRFPPIQARELPS--LECTVSILTDFETANNYLDWEVGTHGLIIEFTD 118 (205)
Q Consensus 53 ~p~pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~--L~ieVSvLs~~e~~~d~~d~~~G~hGlii~~~~ 118 (205)
.|.|+.+.|.++-+. -++|-|+.=.++.. -.-|-|.+-.....-+..-|-+|+|++++++..
T Consensus 64 a~~p~iEeikr~~~~----~~dfyplag~~~~~~k~l~epstvI~~~~~l~~~lw~~gk~n~~lR~~~ 127 (554)
T COG3044 64 APVPLIEEIKRYQMA----ARDFYPLAGAEFSGAKQLNEPSTVISGQTVLDSTLWLFGKHNIELRFRM 127 (554)
T ss_pred CcccHHHHHHHHHhh----cccccccccchhhcccccCCCceeEecccccCCcccccCccceEEeecc
Confidence 348999999998554 58999999888711 111111111222223455699999999999843
No 9
>PF00853 Runt: Runt domain; InterPro: IPR013524 The AML1 gene is rearranged by the t(8;21) translocation in acute myeloid leukemia []. The gene is highly similar to the Drosophila melanogaster segmentation gene runt and to the mouse transcription factor PEBP2 alpha subunit gene []. The region of shared similarity, known as the Runt domain, is responsible for DNA-binding and protein-protein interaction. In addition to the highly-conserved Runt domain, the AML-1 gene product carries a putative ATP-binding site (GRSGRGKS), and has a C-terminal region rich in proline and serine residues. The protein (known as acute myeloid leukemia 1 protein, oncogene AML-1, core-binding factor (CBF), alpha-B subunit, etc.) binds to the core site, 5'-pygpyggt-3', of a number of enhancers and promoters. The protein is a heterodimer of alpha- and beta-subunits. The alpha-subunit binds DNA as a monomer, and appears to have a role in the development of normal hematopoiesis. CBF is a nuclear protein expressed in numerous tissue types, except brain and heart; highest levels have been found to occur in thymus, bone marrow and peripheral blood. This domain occurs towards the N terminus of the proteins in this entry.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1E50_E 1LJM_A 1CO1_A 1H9D_C 1CMO_A 1EAO_B 1HJC_D 1HJB_F 2J6W_B 1EAN_A ....
Probab=26.61 E-value=48 Score=27.12 Aligned_cols=73 Identities=19% Similarity=0.220 Sum_probs=45.2
Q ss_pred ccceEEEEEEeccCC-CCcceeeecccCcccHHHHHHHHHHHhhhcCCCCCCCCcCcCCCceEEEEeecCccccCCcc-C
Q 028676 27 FSPLFVTWKKVVNGG-EPRLRGCIGTLEARCLINGFKDYALTSALKDRRFPPIQARELPSLECTVSILTDFETANNYL-D 104 (205)
Q Consensus 27 ~~g~FVTl~~~~~~~-~~~LRGCIGt~~p~pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvLs~~e~~~d~~-d 104 (205)
+-|.-||+.--+..+ ..+||.|.-....+ .|-|+|=||-.-+-. =++..++|+|.+.+-.+..+. .
T Consensus 51 ~DGT~Vtv~AGNDEn~~aElRN~tavmknq-----------vA~FnDLRFvGRSGR-GKsFtltItv~t~PpqvAty~~A 118 (135)
T PF00853_consen 51 PDGTLVTVMAGNDENYCAELRNATAVMKNQ-----------VARFNDLRFVGRSGR-GKSFTLTITVFTNPPQVATYHRA 118 (135)
T ss_dssp STTEEEEEEEEESSCSSBBEES-EEEEETT-----------EEEESS-EECST-TT-TSEEEEEEEE-SSS-EEEEECCE
T ss_pred CCCcEEEEEecCCchhhhhhhchhhhhhcc-----------cccccccccccccCC-ccceEEEEEEeCCCchHHhheee
Confidence 568899998744321 37999998766553 357999999884433 467888999998887665442 2
Q ss_pred CccCcee
Q 028676 105 WEVGTHG 111 (205)
Q Consensus 105 ~~~G~hG 111 (205)
+.+-+||
T Consensus 119 IKVTVDG 125 (135)
T PF00853_consen 119 IKVTVDG 125 (135)
T ss_dssp EEEESS-
T ss_pred EEEEecC
Confidence 4444443
No 10
>TIGR02396 diverge_rpsU rpsU-divergently transcribed protein. This uncharacterized protein is found in a number of Alphaproteobacteria and, with N-terminal regions long enough to be transit peptides, in eukaryotes. This phylogeny suggests mitochondrial derivation. In several Alphaproteobacteria, the gene for this protein is encoded divergently from rpsU, the gene for ribosomal protein S21. S21 is unusual in being encoded outside the usual long ribosomal protein operons, but rather in contexts that suggest regulation of the initiation of protein translation.
Probab=24.35 E-value=55 Score=27.48 Aligned_cols=26 Identities=38% Similarity=0.586 Sum_probs=21.2
Q ss_pred eccchhccCCCHHHHHHHHHHHcCCCCC
Q 028676 130 LPEVAAHEGWTKVEAIDSLMRKAGFSGP 157 (205)
Q Consensus 130 LPqVa~Eq~w~~eefl~~L~~KAGl~~~ 157 (205)
|+.|+ +.||+ ++.|...++.+|++..
T Consensus 9 l~~vp-~~Gwt-~~al~~aa~~lgl~~~ 34 (184)
T TIGR02396 9 LEHVP-FLGWT-NEALLLAARELGYSDS 34 (184)
T ss_pred HHhhh-hcCCC-HHHHHHHHHHcCCCHH
Confidence 56665 89999 5678889999999964
No 11
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=23.32 E-value=63 Score=20.47 Aligned_cols=14 Identities=21% Similarity=0.432 Sum_probs=12.9
Q ss_pred CHHHHHHHHHHHcC
Q 028676 140 TKVEAIDSLMRKAG 153 (205)
Q Consensus 140 ~~eefl~~L~~KAG 153 (205)
+.++|++.-.+|+|
T Consensus 19 NAe~FV~~fVQKGG 32 (33)
T TIGR03687 19 NAEEFVRGFVQKGG 32 (33)
T ss_pred hHHHHHHHHHHccC
Confidence 78999999999998
No 12
>PF06102 DUF947: Domain of unknown function (DUF947); InterPro: IPR009292 This is a family of eukaryotic proteins with unknown function.
Probab=22.15 E-value=41 Score=28.08 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=10.2
Q ss_pred hhcCCCCCCCCcC
Q 028676 69 ALKDRRFPPIQAR 81 (205)
Q Consensus 69 A~~DpRF~Pl~~~ 81 (205)
-..||||.|+.-.
T Consensus 32 ~~rDPRFd~~~G~ 44 (168)
T PF06102_consen 32 KRRDPRFDSLSGE 44 (168)
T ss_pred CCCCCCcCccccc
Confidence 5789999988543
No 13
>KOG1612 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis]
Probab=21.31 E-value=1e+02 Score=28.20 Aligned_cols=41 Identities=24% Similarity=0.210 Sum_probs=27.8
Q ss_pred cHHHHHHHHHHHhhhcCCCCCCCCcCcCCCceEEEEeecCcccc
Q 028676 56 CLINGFKDYALTSALKDRRFPPIQARELPSLECTVSILTDFETA 99 (205)
Q Consensus 56 pL~~~v~~~Ai~AA~~DpRF~Pl~~~EL~~L~ieVSvLs~~e~~ 99 (205)
.+.+ .+..|+.||+++.|||-+.-.+-+.. ++.++-+.++.
T Consensus 147 n~~d-AiS~Ai~~AL~~T~lPkv~v~~dd~~--~~~i~~s~~~Y 187 (288)
T KOG1612|consen 147 NLLD-AISIAIYAALNNTRLPKVIVAFDDDG--EVEILLSDEEY 187 (288)
T ss_pred CHHH-HHHHHHHHHHhcccCCccccccccCC--ceeeccCcccc
Confidence 3444 66789999999999998877665444 44444444443
No 14
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=21.30 E-value=1.2e+02 Score=22.31 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=21.0
Q ss_pred chhccCCCHHHHHHHHHHHcCCCCC
Q 028676 133 VAAHEGWTKVEAIDSLMRKAGFSGP 157 (205)
Q Consensus 133 Va~Eq~w~~eefl~~L~~KAGl~~~ 157 (205)
|..-.|.+-.+.|..+|+|-|+...
T Consensus 14 V~vrpG~ti~d~L~kllekRgl~~~ 38 (73)
T cd01817 14 VPTRPGESIRDLLSGLCEKRGINYA 38 (73)
T ss_pred EEecCCCCHHHHHHHHHHHcCCChh
Confidence 4455677999999999999999974
Done!