Query psy11729
Match_columns 281
No_of_seqs 150 out of 735
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 17:23:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11729hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00567 3mg DNA-3-methyladen 100.0 8.4E-83 1.8E-87 564.0 19.6 190 18-268 1-192 (192)
2 PF02245 Pur_DNA_glyco: Methyl 100.0 1.6E-79 3.4E-84 539.9 16.1 182 19-266 1-184 (184)
3 PRK00802 3-methyladenine DNA g 100.0 9.5E-79 2.1E-83 536.7 18.7 183 17-268 4-188 (188)
4 cd00540 AAG Alkyladenine DNA g 100.0 8.4E-77 1.8E-81 520.8 18.2 177 22-261 1-179 (179)
5 COG2094 Mpg 3-methyladenine DN 100.0 7E-75 1.5E-79 514.7 17.0 192 17-275 5-199 (200)
6 KOG4486|consensus 100.0 9E-74 2E-78 512.0 12.5 202 15-276 56-257 (261)
7 cd01733 LSm10 The eukaryotic S 71.6 11 0.00024 29.2 5.3 38 24-61 7-44 (78)
8 PF12006 DUF3500: Protein of u 66.6 2.6 5.6E-05 40.6 0.9 97 18-118 54-154 (313)
9 cd01725 LSm2 The eukaryotic Sm 65.8 12 0.00025 29.2 4.3 32 30-61 5-36 (81)
10 cd01721 Sm_D3 The eukaryotic S 65.7 13 0.00028 28.1 4.4 42 28-69 2-44 (70)
11 cd01726 LSm6 The eukaryotic Sm 63.4 15 0.00032 27.4 4.3 34 28-61 2-35 (67)
12 cd01723 LSm4 The eukaryotic Sm 61.7 20 0.00043 27.4 4.8 35 27-61 2-36 (76)
13 COG2451 Ribosomal protein L35A 57.9 16 0.00036 30.3 4.0 40 22-61 32-72 (100)
14 cd01724 Sm_D1 The eukaryotic S 56.8 24 0.00052 28.1 4.7 42 29-70 4-46 (90)
15 PF01423 LSM: LSM domain ; In 56.6 24 0.00051 25.5 4.3 29 32-60 4-32 (67)
16 smart00651 Sm snRNP Sm protein 52.3 29 0.00063 25.0 4.2 30 32-61 4-33 (67)
17 cd01722 Sm_F The eukaryotic Sm 50.3 41 0.00089 25.1 4.8 35 27-61 2-36 (68)
18 cd00600 Sm_like The eukaryotic 46.9 41 0.0009 23.7 4.2 29 32-60 2-30 (63)
19 PRK00737 small nuclear ribonuc 37.2 1E+02 0.0022 23.2 5.3 36 26-61 4-39 (72)
20 COG1958 LSM1 Small nuclear rib 35.2 80 0.0017 24.0 4.5 36 27-62 8-43 (79)
21 cd01731 archaeal_Sm1 The archa 34.5 86 0.0019 23.2 4.4 33 29-61 3-35 (68)
22 KOG3172|consensus 30.0 65 0.0014 27.4 3.4 26 35-60 14-39 (119)
23 PF06718 DUF1203: Protein of u 29.8 58 0.0013 27.5 3.1 50 38-102 64-113 (117)
24 PRK04337 50S ribosomal protein 26.6 1.1E+02 0.0023 25.0 3.9 32 26-57 30-61 (87)
25 PRK05753 nucleoside diphosphat 22.4 1.8E+02 0.004 24.6 4.9 31 29-60 94-128 (137)
26 cd04328 RNAP_I_Rpa43_N RNAP_I_ 22.1 80 0.0017 24.5 2.4 54 15-69 17-76 (89)
No 1
>TIGR00567 3mg DNA-3-methyladenine glycosylase (3mg). This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine.
Probab=100.00 E-value=8.4e-83 Score=563.99 Aligned_cols=190 Identities=44% Similarity=0.779 Sum_probs=175.0
Q ss_pred CChhhhCCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCceEEEEEccCce
Q psy11729 18 LDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTYGMY 97 (281)
Q Consensus 18 L~~~Ff~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~~YVY~~YGmh 97 (281)
|+++||++|+++||++||||+|||+.++|..++|||||||||+|++|+|||||+|+||+||++||++|||+|||+|||||
T Consensus 1 l~~~Ff~~~~~~vA~~LLGk~Lv~~~~~g~~~~grIvEtEAY~G~~D~A~Ha~~grrT~Rn~~mfg~~G~~YVY~~YGmh 80 (192)
T TIGR00567 1 MPPEFFQQDAVTLAPRLLGQLLVRRLDKGTEVRGRIVETEAYMGPEDSAAHSRGGRQTPRTRGMFGPPGRLYVYIIYGMH 80 (192)
T ss_pred CCHHHhcCCHHHHHHHhCCCEEEEECCCCcEEEEEEEEEecccCCCCccccccCCCCCcchHHHccCCceEEEEEecCCE
Confidence 67899999999999999999999999888666899999999999999999999998899999999999999999999999
Q ss_pred eeeeeeecCCC--cEEEEcccccCCChHHHHHhhccccccccccccCCCCCCCCCCcccccccCCCChhhHHHhhhhhcc
Q psy11729 98 HCFNLSSQESG--GAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQT 175 (281)
Q Consensus 98 ~clNIvt~~~g--~AVLIRAlEP~~G~~~M~~~R~~~~~~~~~~k~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 175 (281)
|||||||+.+| +||||||+||++|++.|+++|+. .
T Consensus 81 ~~lNvVt~~~g~p~aVLIRA~ep~~G~~~m~~~R~~------~------------------------------------- 117 (192)
T TIGR00567 81 YMLNVVAAPEGVPAAVLIRALEPLEGLELMRERRGR------S------------------------------------- 117 (192)
T ss_pred EEEEEEECCCCCccEEEEEeccccCchHHHHHhcCC------C-------------------------------------
Confidence 99999998664 99999999999999999999864 1
Q ss_pred cCCCCCCCCCccccCCCCcccCChhHHHHHhcCCcccccCcCCCCCCceEEecCCCCCCCcEeeeccccccCcccccccc
Q psy11729 176 LSSNDWDQPNKKSKLQDRDLCNGPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKAK 255 (281)
Q Consensus 176 ~~~~~~~~~~~~~~~~~~~L~nGPGKLc~ALgI~~~~~ng~~L~~~~~l~i~~~~~~~~~~I~~s~RIGI~~~~~ew~~~ 255 (281)
...++|||||||||||||||++ +||.+|+++++|||+++.. +.+|++||||||++++ ||+++
T Consensus 118 --------------~~~~~L~nGPGkL~~ALgI~~~-~ng~~l~~~~~l~i~~~~~--~~~i~~t~RIGI~~a~-~~~~~ 179 (192)
T TIGR00567 118 --------------LKDRELTNGPGKLCQALGITMS-FNGRDLIQPSALWLERGPL--EHSAPAGPRVGIDYAG-EWDIK 179 (192)
T ss_pred --------------ccccccccCHHHHHHHhCCCHH-HCCCcccCCCceEEecCCC--CCceeeeCcccccCcc-ccccC
Confidence 1236799999999999999999 9999998765799996642 3479999999999998 99999
Q ss_pred ceeeEECCCeeec
Q psy11729 256 LLRFYILGNKCVS 268 (281)
Q Consensus 256 p~RFyi~gn~~VS 268 (281)
|||||++||||||
T Consensus 180 pwRf~v~~n~~VS 192 (192)
T TIGR00567 180 PWRFYVTGNPWVS 192 (192)
T ss_pred CcEEEECCCcccC
Confidence 9999999999998
No 2
>PF02245 Pur_DNA_glyco: Methylpurine-DNA glycosylase (MPG); InterPro: IPR003180 Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA []. Its action is induced by alkylating chemotherapeutics, as well as deaminated and lipid peroxidation-induced purine adducts []. MPG without an N-terminal extension excises hypoxanthine with one-third of the efficiency of full-length MPG under similar conditions, suggesting that is function may largely be attributable to the N-terminal extension [].; GO: 0003677 DNA binding, 0003905 alkylbase DNA N-glycosylase activity, 0006284 base-excision repair; PDB: 1BNK_A 1F6O_A 3QI5_A 3UBY_B 1F4R_A 1EWN_A.
Probab=100.00 E-value=1.6e-79 Score=539.86 Aligned_cols=182 Identities=48% Similarity=0.879 Sum_probs=150.5
Q ss_pred ChhhhCCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCceEEEEEccCcee
Q psy11729 19 DQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTYGMYH 98 (281)
Q Consensus 19 ~~~Ff~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~~YVY~~YGmh~ 98 (281)
|++||++|+++||++||||+|||+.++|. ++|||||||||+|.+|||||||+| +|+||++||++|||+|||++|||||
T Consensus 1 p~~Ff~r~~~~vA~~LLG~~Lv~~~~~~~-~~grIvEtEAY~g~~D~AsHa~~g-~T~Rn~~mf~~~G~~YVY~~YGmh~ 78 (184)
T PF02245_consen 1 PRDFFDRDTVEVARDLLGKVLVRRIPGGE-LSGRIVETEAYLGPEDPASHAYRG-RTPRNEVMFGPPGHAYVYLIYGMHH 78 (184)
T ss_dssp --HHHSSBHHHHHHHCTT-EEEEE-TTS--EEEEEEEEEEE-STT-TTSTTGGG---STTGGGGSSTTBEEEEEETTTEE
T ss_pred CcchhccCHHHHHHHhCCCEEEEEeCCCe-EEEEEEEEeeccCCCCCcccccCC-CCcccHHHcCCCCEEEEEEecCCee
Confidence 58999999999999999999999998776 899999999999999999999999 8999999999999999999999999
Q ss_pred eeeeeecCCC--cEEEEcccccCCChHHHHHhhccccccccccccCCCCCCCCCCcccccccCCCChhhHHHhhhhhccc
Q psy11729 99 CFNLSSQESG--GAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTL 176 (281)
Q Consensus 99 clNIvt~~~g--~AVLIRAlEP~~G~~~M~~~R~~~~~~~~~~k~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~ 176 (281)
||||||+++| +||||||+||++|++.|+++|+. +
T Consensus 79 clNivt~~~g~~~aVLIRAieP~~G~~~m~~~R~~------~-------------------------------------- 114 (184)
T PF02245_consen 79 CLNIVTGPEGVPEAVLIRAIEPLEGIELMRARRGG------K-------------------------------------- 114 (184)
T ss_dssp EEEEE-BSTT---EEEEEEEEEEE-HHHHHHHHHH------H--------------------------------------
T ss_pred EEeEEecCCCceEEEEEEeccccCCHHHHHHhcCC------C--------------------------------------
Confidence 9999998765 99999999999999999999986 1
Q ss_pred CCCCCCCCCccccCCCCcccCChhHHHHHhcCCcccccCcCCCCCCceEEecCCCCCCCcEeeeccccccCccccccccc
Q psy11729 177 SSNDWDQPNKKSKLQDRDLCNGPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKAKL 256 (281)
Q Consensus 177 ~~~~~~~~~~~~~~~~~~L~nGPGKLc~ALgI~~~~~ng~~L~~~~~l~i~~~~~~~~~~I~~s~RIGI~~~~~ew~~~p 256 (281)
+.++|||||||||||||||++ +||.+|+.++.|||++. ...+.+|++||||||+ +|+++|
T Consensus 115 --------------~~~~L~~GPGkL~~ALgI~~~-~~g~~l~~~~~l~i~~~-~~~~~~I~~t~RIGI~----~~~~~p 174 (184)
T PF02245_consen 115 --------------RDKNLTNGPGKLCQALGIDRE-LNGLDLCGDPSLWIEGD-GVPPEEIVATPRIGIS----EWADKP 174 (184)
T ss_dssp --------------HGGGSSSSHHHHHHHTT--GG-GTT-BTTT-SSEEEEE--SB-CSGEEEEE-STSG----CTTCSC
T ss_pred --------------CccccccCHHHHHHHhCCCHH-HCCcccCCCCceEEccC-CCCCCCEEEcCCcccC----ccccCC
Confidence 356899999999999999999 99999998877999333 3457799999999999 688999
Q ss_pred eeeEECCCee
Q psy11729 257 LRFYILGNKC 266 (281)
Q Consensus 257 ~RFyi~gn~~ 266 (281)
||||++||||
T Consensus 175 wRF~v~gnp~ 184 (184)
T PF02245_consen 175 WRFYVKGNPF 184 (184)
T ss_dssp EEEEETT-T-
T ss_pred ceeEeCCCCC
Confidence 9999999997
No 3
>PRK00802 3-methyladenine DNA glycosylase; Reviewed
Probab=100.00 E-value=9.5e-79 Score=536.70 Aligned_cols=183 Identities=44% Similarity=0.792 Sum_probs=166.6
Q ss_pred cCChhhhCCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCceEEEEEccCc
Q psy11729 17 CLDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTYGM 96 (281)
Q Consensus 17 ~L~~~Ff~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~~YVY~~YGm 96 (281)
+|+++||++|+++||++||||+|||+ | .++|||||||||+|.+|+|||||+| +|+||++||++|||+|||+||||
T Consensus 4 ~l~~~Ff~~~~~~vA~~LLGk~Lv~~---~-~~~grIvETEAY~G~~D~A~Ha~~g-rT~Rn~~mf~~~G~~YVY~~YG~ 78 (188)
T PRK00802 4 PLPREFFARDALEVARDLLGKVLVHE---G-GVSGRIVETEAYIGADDPASHSYRG-RTPRTEVMFGPPGHAYVYFIYGM 78 (188)
T ss_pred ccCHHHHCCCHHHHHHHhCCCEEEEC---C-EEEEEEEEEecccCCCCccccccCC-CChhhHHHcCCCceEEEEEecCc
Confidence 68999999999999999999999997 4 5899999999999999999999999 79999999999999999999999
Q ss_pred eeeeeeeecCC--CcEEEEcccccCCChHHHHHhhccccccccccccCCCCCCCCCCcccccccCCCChhhHHHhhhhhc
Q psy11729 97 YHCFNLSSQES--GGAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQ 174 (281)
Q Consensus 97 h~clNIvt~~~--g~AVLIRAlEP~~G~~~M~~~R~~~~~~~~~~k~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~ 174 (281)
||||||||+.+ ++||||||+||+.|++.|+++|+. +
T Consensus 79 h~~lNvVt~~~g~~~aVLIRA~ep~~g~~~m~~~R~~------~------------------------------------ 116 (188)
T PRK00802 79 HHCLNVVCGPEGTGAAVLIRALEPLEGIALMRRRRGG------K------------------------------------ 116 (188)
T ss_pred eeEEEEEECCCCCccEEEEEeccccccHHHHHHhccc------C------------------------------------
Confidence 99999999755 599999999999999999999853 1
Q ss_pred ccCCCCCCCCCccccCCCCcccCChhHHHHHhcCCcccccCcCCCCCCceEEecCCCCCCCcEeeeccccccCccccccc
Q psy11729 175 TLSSNDWDQPNKKSKLQDRDLCNGPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKA 254 (281)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~L~nGPGKLc~ALgI~~~~~ng~~L~~~~~l~i~~~~~~~~~~I~~s~RIGI~~~~~ew~~ 254 (281)
.+.++|||||||||||||||++ +||.+|+.+.+|||++.. .+.+|++||||||++ |++
T Consensus 117 ---------------~~~~~L~nGPGkL~~AlgI~~~-~~g~~l~~~~~l~i~~~~--~~~~i~~t~RIGI~~----~~~ 174 (188)
T PRK00802 117 ---------------RPEKNLCNGPGKLCKALGITLA-DNGADLFDASPLYIEDGK--EPPEIVAGPRIGISK----ARD 174 (188)
T ss_pred ---------------CcccccccCHHHHHHHhCCCHH-HCCCcccCCCCEEEecCC--CCCcEEEeCccccCc----ccc
Confidence 1457899999999999999999 999999855579999643 245899999999994 568
Q ss_pred cceeeEECCCeeec
Q psy11729 255 KLLRFYILGNKCVS 268 (281)
Q Consensus 255 ~p~RFyi~gn~~VS 268 (281)
+||||||+||||||
T Consensus 175 ~pwRf~i~~~~~VS 188 (188)
T PRK00802 175 LPWRFWIPGSPFVS 188 (188)
T ss_pred CCeEEEECCCcccC
Confidence 99999999999998
No 4
>cd00540 AAG Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with the other BER glycosylases and is structurally quite distinct from them.
Probab=100.00 E-value=8.4e-77 Score=520.79 Aligned_cols=177 Identities=46% Similarity=0.802 Sum_probs=161.8
Q ss_pred hhCCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCceEEEEEccCceeeee
Q psy11729 22 FFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTYGMYHCFN 101 (281)
Q Consensus 22 Ff~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~~YVY~~YGmh~clN 101 (281)
||++|+++||++||||+|||++++ .+++|||||||||+|++|+|||||+|| |+||.+||++|||+|||+|||||||||
T Consensus 1 f~~~~~~~vA~~LLGk~Lv~~~~~-~~~~grIvEtEAY~G~~D~A~Ha~~gr-~~~~~~mfg~~G~~YVY~~YG~h~~lN 78 (179)
T cd00540 1 FFNRDTVEVARDLLGKVLVRRLPG-GILSGRIVETEAYLGPEDPASHAYRGR-TTRRTVMFGPPGHAYVYLIYGMHWCLN 78 (179)
T ss_pred CCCCCHHHHHHHhCCCEEEEECCC-CEEEEEEEEEeccCCCCCccccccCCC-CccchhhccCCceEEEEeecCCEEEEE
Confidence 899999999999999999999864 568999999999999999999999996 555669999999999999999999999
Q ss_pred eeecCC--CcEEEEcccccCCChHHHHHhhccccccccccccCCCCCCCCCCcccccccCCCChhhHHHhhhhhcccCCC
Q psy11729 102 LSSQES--GGAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQTLSSN 179 (281)
Q Consensus 102 Ivt~~~--g~AVLIRAlEP~~G~~~M~~~R~~~~~~~~~~k~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~ 179 (281)
|||+.+ ++||||||+||+.|++.|+++|+. +
T Consensus 79 vVt~~~g~~~aVLIRAiEp~~G~~~m~~~R~~------~----------------------------------------- 111 (179)
T cd00540 79 VVTGPEGEPAAVLIRALEPLEGLELMRERRGG------K----------------------------------------- 111 (179)
T ss_pred EEECCCCCccEEEEEeeccccchhhHHhccCC------C-----------------------------------------
Confidence 999865 599999999999999999999975 1
Q ss_pred CCCCCCccccCCCCcccCChhHHHHHhcCCcccccCcCCCCCCceEEecCCCCCCCcEeeeccccccCccccccccceee
Q psy11729 180 DWDQPNKKSKLQDRDLCNGPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKAKLLRF 259 (281)
Q Consensus 180 ~~~~~~~~~~~~~~~L~nGPGKLc~ALgI~~~~~ng~~L~~~~~l~i~~~~~~~~~~I~~s~RIGI~~~~~ew~~~p~RF 259 (281)
..++|||||||||||||||++ +||.+|++++.|||+++.. .+.+|++||||||++++ ||+++||||
T Consensus 112 -----------~~~~L~nGPGkL~~AlgI~~~-~ng~~l~~~~~l~i~~~~~-~~~~i~~~~RIGI~~a~-e~~~~pwRf 177 (179)
T cd00540 112 -----------RKRDLTNGPGKLCQALGIDKS-LNGADLTDSSPLWLEDGGP-PPEEIVATPRIGIDYAG-EWADLPWRF 177 (179)
T ss_pred -----------ccCeeccChHHHHHHhCCcHH-HCCCccCCCCcEEEecCCC-CCCCEEEeCccccCCCC-ccccCCcee
Confidence 236899999999999999999 9999999756799998764 45689999999999998 999999999
Q ss_pred EE
Q psy11729 260 YI 261 (281)
Q Consensus 260 yi 261 (281)
||
T Consensus 178 ~i 179 (179)
T cd00540 178 YV 179 (179)
T ss_pred eC
Confidence 96
No 5
>COG2094 Mpg 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=100.00 E-value=7e-75 Score=514.73 Aligned_cols=192 Identities=42% Similarity=0.686 Sum_probs=177.5
Q ss_pred cCChhhhCCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCceEEEEEccCc
Q psy11729 17 CLDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTYGM 96 (281)
Q Consensus 17 ~L~~~Ff~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~~YVY~~YGm 96 (281)
.||.+||++|++.||++||||.|+|+. +|..++|+|||||||.|++|+|||||+|+ |+||++||++|||+|||++|||
T Consensus 5 ~~p~~F~~rd~~~vAr~LLG~~lv~~~-~g~~~~g~IVEtEAY~G~~D~A~Ha~~Gr-T~R~~aMf~~~G~~YvY~~~G~ 82 (200)
T COG2094 5 PLPRSFFARDTLVVARELLGKTLVRRI-GGLTTSGRIVETEAYLGPDDPACHAYRGR-TKRNRAMFGPPGHAYVYRIYGM 82 (200)
T ss_pred cCCHhhhccCHHHHHHHhcCcEEEEec-CCcEEEEEEEEEeEecCCCchhhhhccCc-CcccHhhccCCceEEEEEEecc
Confidence 489999999999999999999999997 45568999999999999999999999995 9999999999999999999999
Q ss_pred eeeeeeeecCCC--cEEEEcccccCCChHHHHHhhccccccccccccCCCCCCCCCCcccccccCCCChhhHHHhhhhhc
Q psy11729 97 YHCFNLSSQESG--GAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQ 174 (281)
Q Consensus 97 h~clNIvt~~~g--~AVLIRAlEP~~G~~~M~~~R~~~~~~~~~~k~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~ 174 (281)
|+||||||.++| +||||||+||++|++.|.++|+. +
T Consensus 83 h~~lNvv~~~eG~p~aVLIRAieP~eg~~~m~~rR~~------~------------------------------------ 120 (200)
T COG2094 83 HYCLNVVTGPEGIPAAVLIRAIEPEEGIEPMRQRRGV------R------------------------------------ 120 (200)
T ss_pred EEEEEEEecCCCCcceEEEEeeccccccchhhhccCc------c------------------------------------
Confidence 999999999877 79999999999999999999986 1
Q ss_pred ccCCCCCCCCCccccCCCCcccCChhHHHHHhcCCcccccCcCCCCCCc-eEEecCCCCCCCcEeeeccccccCcccccc
Q psy11729 175 TLSSNDWDQPNKKSKLQDRDLCNGPSKLCISMDITIEYLNKRHICESEE-MWVQDLDCESNITIVESSRIGIGDFAKEWK 253 (281)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~L~nGPGKLc~ALgI~~~~~ng~~L~~~~~-l~i~~~~~~~~~~I~~s~RIGI~~~~~ew~ 253 (281)
..++|||||||||+|||||++ +||.++...++ ||++.+. .+..|++++||||+++.
T Consensus 121 ----------------~~~~l~nGPgkLc~ALgI~~~-~~g~~l~~~~~~l~l~~~~--~~~~i~~~~RIGI~~~~---- 177 (200)
T COG2094 121 ----------------VLRLLTNGPGKLCKALGITRE-DNGADLINPSEPLWLELGK--TPFAISAGARIGISKAT---- 177 (200)
T ss_pred ----------------ccchhccCchHHHHHhCCCHH-HcCCcccCCCCceEEecCC--CCcceeeeccccccccc----
Confidence 257899999999999999999 99999887665 9999877 46789999999999995
Q ss_pred ccceeeEECCCeeecCCchhhh
Q psy11729 254 AKLLRFYILGNKCVSKTDKKME 275 (281)
Q Consensus 254 ~~p~RFyi~gn~~VS~~~k~~~ 275 (281)
|+|||||++||+|||+.++..+
T Consensus 178 ~~pwRF~i~g~~~vS~~r~~~~ 199 (200)
T COG2094 178 DKPWRFYITGNPFVSRRRRSQR 199 (200)
T ss_pred cCceEEEecCCceeeecccCCC
Confidence 8999999999999999887654
No 6
>KOG4486|consensus
Probab=100.00 E-value=9e-74 Score=511.99 Aligned_cols=202 Identities=45% Similarity=0.787 Sum_probs=190.6
Q ss_pred cccCChhhhCCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCceEEEEEcc
Q psy11729 15 ANCLDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTY 94 (281)
Q Consensus 15 ~~~L~~~Ff~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~~YVY~~Y 94 (281)
++.|+.+||++|++++|+.|||+.|+|+++ |+++.|||||||||+|++|+|||+..|++||||++|||+|||+|||+||
T Consensus 56 m~~mgpEFFqipA~~LArrlLG~~l~RR~~-g~~~~gRIvEtEAYlgPeD~AcHsRgGr~TPRn~~mFmk~Gt~YVY~iY 134 (261)
T KOG4486|consen 56 MMDMGPEFFQIPASQLARRLLGKMLCRRIE-GRTTKGRIVETEAYLGPEDKACHSRGGRRTPRNSAMFMKAGTCYVYRIY 134 (261)
T ss_pred HhhcChhhhcCchHHHHHHHHHHHHhhhcC-CceeeeeEEeeeeecCcchhhhhhcCCccCCCcccccccCceEEEEEee
Confidence 457899999999999999999999999996 7889999999999999999999999999999999999999999999999
Q ss_pred CceeeeeeeecCCCcEEEEcccccCCChHHHHHhhccccccccccccCCCCCCCCCCcccccccCCCChhhHHHhhhhhc
Q psy11729 95 GMYHCFNLSSQESGGAVLIRSLEPVHGLDIMNRLRNQFNENQNKSKRNNHLPNSQNNEETHSQSNRNSPAKKQKLIKSKQ 174 (281)
Q Consensus 95 Gmh~clNIvt~~~g~AVLIRAlEP~~G~~~M~~~R~~~~~~~~~~k~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~~~ 174 (281)
|||+|||||++|.|++|||||+||+.|++.|+.+|+. +
T Consensus 135 G~y~c~NIss~G~GA~VLiRalePl~G~ETmreRrG~------~------------------------------------ 172 (261)
T KOG4486|consen 135 GRYECFNISSVGAGAGVLVRALEPLCGVETMRERRGG------R------------------------------------ 172 (261)
T ss_pred eehheeeeeccccceEEeeeccCcccchHHHHHhcCC------C------------------------------------
Confidence 9999999999999999999999999999999999886 2
Q ss_pred ccCCCCCCCCCccccCCCCcccCChhHHHHHhcCCcccccCcCCCCCCceEEecCCCCCCCcEeeeccccccCccccccc
Q psy11729 175 TLSSNDWDQPNKKSKLQDRDLCNGPSKLCISMDITIEYLNKRHICESEEMWVQDLDCESNITIVESSRIGIGDFAKEWKA 254 (281)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~L~nGPGKLc~ALgI~~~~~ng~~L~~~~~l~i~~~~~~~~~~I~~s~RIGI~~~~~ew~~ 254 (281)
.++++||||||||||||||+++ +|..+|..++.+|++++....+.+|+.++|+||++++ ||+.
T Consensus 173 ---------------~kdr~L~nGPsKlcQALgi~~e-~d~~~La~~e~~wLe~G~e~~~p~Vvag~RVGi~~Ag-Ew~~ 235 (261)
T KOG4486|consen 173 ---------------VKDRDLANGPSKLCQALGITRE-IDKEWLAGSEKIWLEEGREVADPEVVAGRRVGIRNAG-EWEE 235 (261)
T ss_pred ---------------cCChhhhcCcHHHHHHhccccc-cccccccCCCcEeeecCCCCCchhheeccccccchhh-hhhh
Confidence 3678999999999999999999 9999999988999999955567799999999999999 9999
Q ss_pred cceeeEECCCeeecCCchhhhh
Q psy11729 255 KLLRFYILGNKCVSKTDKKMES 276 (281)
Q Consensus 255 ~p~RFyi~gn~~VS~~~k~~~~ 276 (281)
+|||||+.||||||..+..++.
T Consensus 236 k~lRFyVrd~PWvS~~~r~~~~ 257 (261)
T KOG4486|consen 236 KKLRFYVRDNPWVSCIRRRELG 257 (261)
T ss_pred hceEEEEcCCcceecchhhhcc
Confidence 9999999999999998877654
No 7
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=71.63 E-value=11 Score=29.23 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=33.4
Q ss_pred CCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 24 DQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 24 ~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
.+....+=+.|.|+.+...+.+|..+.|.+++++.|+-
T Consensus 7 ~~tl~~~L~~l~g~~V~VeLKng~~~~G~L~~vD~~MN 44 (78)
T cd01733 7 ENTLIILLQGLQGKVVTVELRNETTVTGRIASVDAFMN 44 (78)
T ss_pred hchHHHHHHHCCCCEEEEEECCCCEEEEEEEEEcCCce
Confidence 45556677899999999999999999999999999984
No 8
>PF12006 DUF3500: Protein of unknown function (DUF3500); InterPro: IPR021889 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 335 to 438 amino acids in length. This protein has a conserved GHH sequence motif. This protein has two completely conserved G residues that may be functionally important.
Probab=66.57 E-value=2.6 Score=40.56 Aligned_cols=97 Identities=18% Similarity=0.076 Sum_probs=65.4
Q ss_pred CChhhhCCCHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCce--EEEEEccC
Q psy11729 18 LDQAFFDQPCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGT--IYVYFTYG 95 (281)
Q Consensus 18 L~~~Ff~r~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~--~YVY~~YG 95 (281)
|..+.+..+-..+|..||=..|- +.|-...-.|.+.|.|++......=...+ .-.-+-++||.|+. -+-+.++|
T Consensus 54 l~l~~lt~~Qr~~a~~lL~~~LS---~~Gy~k~~~im~~d~~L~~~~~~~~~~~~-~~~Y~~~ifG~Ps~~~~Wg~~f~G 129 (313)
T PF12006_consen 54 LRLDDLTDEQRKAALALLKAALS---PEGYEKARGIMRLDDVLGELEGGSPTIRD-PESYYFAIFGTPSTTGPWGWQFEG 129 (313)
T ss_pred cchHhCCHHHHHHHHHHHHHhcC---HHHHHHHHHHHHHHHHHHHhhcCCcccCC-CCceEEEEecCCCCCCCeeEEecc
Confidence 55566777777888888888876 24532234688999999765443322223 35567899999998 78899999
Q ss_pred ceeeeeeeecCCC--cEEEEccccc
Q psy11729 96 MYHCFNLSSQESG--GAVLIRSLEP 118 (281)
Q Consensus 96 mh~clNIvt~~~g--~AVLIRAlEP 118 (281)
.|-|+|++-.+.. ..=..-|.||
T Consensus 130 HHlsln~~~~~~~v~~tP~F~Ga~P 154 (313)
T PF12006_consen 130 HHLSLNCTFVGGQVSITPTFFGAEP 154 (313)
T ss_pred cEEEEEEEEeCCCEEECceeeCCCC
Confidence 9999999764332 2223445555
No 9
>cd01725 LSm2 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm2 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=65.84 E-value=12 Score=29.18 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=28.6
Q ss_pred HHHhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 30 LANALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 30 vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
.=+.|.|+.+...+.+|..+.|++++++.|+-
T Consensus 5 fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MN 36 (81)
T cd01725 5 FFKTLVGKEVTVELKNDLSIRGTLHSVDQYLN 36 (81)
T ss_pred HHHhCCCCEEEEEECCCcEEEEEEEEECCCcc
Confidence 34678999999999999999999999999984
No 10
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=65.73 E-value=13 Score=28.09 Aligned_cols=42 Identities=21% Similarity=0.394 Sum_probs=33.9
Q ss_pred HHHHHhccCCeEEEEecCCcEEEEEEEEecccCCCC-CCcccc
Q psy11729 28 IDLANALLGKYLVRRLSCGTLLIGKIVETESYLGVE-DRASHS 69 (281)
Q Consensus 28 ~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~~-D~AsHa 69 (281)
.++-+.++|+....++.+|..+.|.++.++.|.--. |.|.+.
T Consensus 2 ~~~L~~~~g~~V~VeLk~g~~~~G~L~~~D~~MNl~L~~~~~~ 44 (70)
T cd01721 2 IKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVT 44 (70)
T ss_pred hHHHhhCCCCEEEEEECCCcEEEEEEEEEcCCceeEEEEEEEE
Confidence 355678899999999999999999999999998532 555543
No 11
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=63.43 E-value=15 Score=27.35 Aligned_cols=34 Identities=21% Similarity=0.442 Sum_probs=29.8
Q ss_pred HHHHHhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 28 IDLANALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 28 ~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
.++=+.++|+.+..++.+|..+.|.++..+.|+-
T Consensus 2 ~~~L~~~~~~~V~V~Lk~g~~~~G~L~~~D~~mN 35 (67)
T cd01726 2 SEFLKAIIGRPVVVKLNSGVDYRGILACLDGYMN 35 (67)
T ss_pred HHHHHhhCCCeEEEEECCCCEEEEEEEEEcccee
Confidence 4566788999999999999999999999999874
No 12
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=61.71 E-value=20 Score=27.40 Aligned_cols=35 Identities=14% Similarity=0.305 Sum_probs=31.0
Q ss_pred HHHHHHhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 27 CIDLANALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 27 ~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
++++=+.++|+.+...+.+|..+.|.++..+.|+-
T Consensus 2 Pl~~L~~~~g~~V~VeLkng~~~~G~L~~~D~~mN 36 (76)
T cd01723 2 PLSLLKTAQNHPMLVELKNGETYNGHLVNCDNWMN 36 (76)
T ss_pred chHHHHhcCCCEEEEEECCCCEEEEEEEEEcCCCc
Confidence 35677889999999999999999999999999874
No 13
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=57.88 E-value=16 Score=30.30 Aligned_cols=40 Identities=25% Similarity=0.333 Sum_probs=32.2
Q ss_pred hhCCCHHHHHHhccCCeEEEEecC-CcEEEEEEEEecccCC
Q psy11729 22 FFDQPCIDLANALLGKYLVRRLSC-GTLLIGKIVETESYLG 61 (281)
Q Consensus 22 Ff~r~~~~vA~~LLGk~Lvr~~~~-G~~l~grIVETEAY~G 61 (281)
+-.-+..+=|+.+||+..+.+.+. |.++.|+|+-|-.-.|
T Consensus 32 i~gv~s~~eA~~y~gk~v~yk~~~~G~Vi~G~V~R~HGnsG 72 (100)
T COG2451 32 IEGVDSPEEAQFYLGKRVCYKYRSSGRVIKGKVVRTHGNSG 72 (100)
T ss_pred EecCCCHHHHHhhhccEEEEEeCCCCcEEEEEEEEecCCcc
Confidence 344566788999999999988877 8999999999865444
No 14
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=56.77 E-value=24 Score=28.15 Aligned_cols=42 Identities=14% Similarity=0.208 Sum_probs=33.2
Q ss_pred HHHHhccCCeEEEEecCCcEEEEEEEEecccCCC-CCCccccC
Q psy11729 29 DLANALLGKYLVRRLSCGTLLIGKIVETESYLGV-EDRASHSY 70 (281)
Q Consensus 29 ~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~-~D~AsHay 70 (281)
.+-+.|.|+.+...+.+|..+.|.+++++.|+-- -+.|....
T Consensus 4 ~fL~~l~g~~V~VeLKng~~~~G~L~~vD~~MNl~L~~a~~~~ 46 (90)
T cd01724 4 RFLMKLTNETVTIELKNGTIVHGTITGVDPSMNTHLKNVKLTL 46 (90)
T ss_pred HHHHhCCCCEEEEEECCCCEEEEEEEEEcCceeEEEEEEEEEc
Confidence 4557889999999999999999999999999842 13354443
No 15
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=56.63 E-value=24 Score=25.54 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=26.7
Q ss_pred HhccCCeEEEEecCCcEEEEEEEEecccC
Q psy11729 32 NALLGKYLVRRLSCGTLLIGKIVETESYL 60 (281)
Q Consensus 32 ~~LLGk~Lvr~~~~G~~l~grIVETEAY~ 60 (281)
++++|+.+...+.+|..+.|.++....|.
T Consensus 4 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~~ 32 (67)
T PF01423_consen 4 QKLIGKRVRVELKNGRTYRGTLVSFDQFM 32 (67)
T ss_dssp HHTTTSEEEEEETTSEEEEEEEEEEETTE
T ss_pred HHhCCcEEEEEEeCCEEEEEEEEEeechh
Confidence 67899999999999999999999999886
No 16
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=52.25 E-value=29 Score=25.01 Aligned_cols=30 Identities=20% Similarity=0.409 Sum_probs=27.0
Q ss_pred HhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 32 NALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 32 ~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
++++|+.++..+.+|..+.|.++.++.|.-
T Consensus 4 ~~~~~~~V~V~l~~g~~~~G~L~~~D~~~N 33 (67)
T smart00651 4 KKLIGKRVLVELKNGREYRGTLKGFDQFMN 33 (67)
T ss_pred HHhCCcEEEEEECCCcEEEEEEEEECcccc
Confidence 578999999999999999999999999863
No 17
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=50.30 E-value=41 Score=25.07 Aligned_cols=35 Identities=29% Similarity=0.445 Sum_probs=29.8
Q ss_pred HHHHHHhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 27 CIDLANALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 27 ~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
+..+=+.++|+.+...+.+|..+.|.++..+.|.-
T Consensus 2 p~~~L~~~~g~~V~V~Lk~g~~~~G~L~~~D~~mN 36 (68)
T cd01722 2 PKPFLNDLTGKPVIVKLKWGMEYKGTLVSVDSYMN 36 (68)
T ss_pred HHHHHHHcCCCEEEEEECCCcEEEEEEEEECCCEE
Confidence 34566788999999999999999999999988863
No 18
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=46.92 E-value=41 Score=23.75 Aligned_cols=29 Identities=31% Similarity=0.519 Sum_probs=25.9
Q ss_pred HhccCCeEEEEecCCcEEEEEEEEecccC
Q psy11729 32 NALLGKYLVRRLSCGTLLIGKIVETESYL 60 (281)
Q Consensus 32 ~~LLGk~Lvr~~~~G~~l~grIVETEAY~ 60 (281)
+.++|+.+...+.+|..+.|.++..+.|.
T Consensus 2 ~~~~g~~V~V~l~~g~~~~G~L~~~D~~~ 30 (63)
T cd00600 2 KDLVGKTVRVELKDGRVLEGVLVAFDKYM 30 (63)
T ss_pred hHHCCCEEEEEECCCcEEEEEEEEECCCC
Confidence 46899999999999999999999998884
No 19
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=37.17 E-value=1e+02 Score=23.22 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=30.3
Q ss_pred CHHHHHHhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 26 PCIDLANALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 26 ~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
.+..+=..++|+.+...+.+|..+.|.++..+.|.-
T Consensus 4 ~P~~~L~~~~~k~V~V~lk~g~~~~G~L~~~D~~mN 39 (72)
T PRK00737 4 RPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMN 39 (72)
T ss_pred chHHHHHHhCCCEEEEEECCCCEEEEEEEEEcccce
Confidence 345666778999999999999999999999998864
No 20
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=35.21 E-value=80 Score=24.02 Aligned_cols=36 Identities=22% Similarity=0.414 Sum_probs=31.1
Q ss_pred HHHHHHhccCCeEEEEecCCcEEEEEEEEecccCCC
Q psy11729 27 CIDLANALLGKYLVRRLSCGTLLIGKIVETESYLGV 62 (281)
Q Consensus 27 ~~~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G~ 62 (281)
+..+-+.++|+.+...+.+|..+.|+.+....|.--
T Consensus 8 ~~~~l~~~~~~~V~V~lk~g~~~~G~L~~~D~~mNl 43 (79)
T COG1958 8 PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNL 43 (79)
T ss_pred cHHHHHHhhCCEEEEEECCCCEEEEEEEEEccceeE
Confidence 456778889999999999999999999999988743
No 21
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=34.52 E-value=86 Score=23.17 Aligned_cols=33 Identities=18% Similarity=0.310 Sum_probs=27.9
Q ss_pred HHHHhccCCeEEEEecCCcEEEEEEEEecccCC
Q psy11729 29 DLANALLGKYLVRRLSCGTLLIGKIVETESYLG 61 (281)
Q Consensus 29 ~vA~~LLGk~Lvr~~~~G~~l~grIVETEAY~G 61 (281)
++=+.++|+.+...+.+|..+.|.+.....|.-
T Consensus 3 ~~L~~~~~~~V~V~l~~g~~~~G~L~~~D~~mN 35 (68)
T cd01731 3 DVLKDSLNKPVLVKLKGGKEVRGRLKSYDQHMN 35 (68)
T ss_pred HHHHHhcCCEEEEEECCCCEEEEEEEEECCcce
Confidence 445678999999999999999999988888764
No 22
>KOG3172|consensus
Probab=30.00 E-value=65 Score=27.43 Aligned_cols=26 Identities=23% Similarity=0.446 Sum_probs=23.2
Q ss_pred cCCeEEEEecCCcEEEEEEEEecccC
Q psy11729 35 LGKYLVRRLSCGTLLIGKIVETESYL 60 (281)
Q Consensus 35 LGk~Lvr~~~~G~~l~grIVETEAY~ 60 (281)
=|.++...+..|.++.|+.+|.|-|.
T Consensus 14 qGhIVt~Et~tGe~YRGkliEaeDnm 39 (119)
T KOG3172|consen 14 QGHIVTVETKTGEVYRGKLIEAEDNM 39 (119)
T ss_pred cCcEEEEEecCCceeeeeeEEecccc
Confidence 48888888888999999999999886
No 23
>PF06718 DUF1203: Protein of unknown function (DUF1203); InterPro: IPR009593 This family consists of several hypothetical bacterial proteins of around 155 residues in length. Family members are present in Rhizobium, Agrobacterium and Streptomyces species.
Probab=29.76 E-value=58 Score=27.50 Aligned_cols=50 Identities=22% Similarity=0.359 Sum_probs=37.4
Q ss_pred eEEEEecCCcEEEEEEEEecccCCCCCCccccCCCCCCCccccccCCCceEEEEEccCceeeeee
Q psy11729 38 YLVRRLSCGTLLIGKIVETESYLGVEDRASHSYNNRRTPRNEPMYMKPGTIYVYFTYGMYHCFNL 102 (281)
Q Consensus 38 ~Lvr~~~~G~~l~grIVETEAY~G~~D~AsHay~gkrT~Rn~~MFg~~G~~YVY~~YGmh~clNI 102 (281)
.|..+..+|.++.|++||... -.++-+.||..|.+.||-.=+.-|-||..
T Consensus 64 ~lR~Y~a~~~iv~g~v~~g~~---------------~~~~l~~~fa~p~VayVHvr~a~~GCf~~ 113 (117)
T PF06718_consen 64 SLRAYDADGRIVTGRVVEGAD---------------IEARLAELFADPEVAYVHVRNARNGCFAC 113 (117)
T ss_pred EEEeEcCCCCEEeeeEEcchh---------------HHHHHHHHhcCCCceEEEeeccCCCeEEE
Confidence 344455667788899998765 13445779999999999988877778765
No 24
>PRK04337 50S ribosomal protein L35Ae; Validated
Probab=26.58 E-value=1.1e+02 Score=25.02 Aligned_cols=32 Identities=25% Similarity=0.390 Sum_probs=26.6
Q ss_pred CHHHHHHhccCCeEEEEecCCcEEEEEEEEec
Q psy11729 26 PCIDLANALLGKYLVRRLSCGTLLIGKIVETE 57 (281)
Q Consensus 26 ~~~~vA~~LLGk~Lvr~~~~G~~l~grIVETE 57 (281)
++.+-|..+|||.++...+.|.++.|+|+-+-
T Consensus 30 ~~~~~a~fylGKrv~yvyk~grviwGKItR~H 61 (87)
T PRK04337 30 DDREEAAKLIGRKVIWKDPTGNKYVGKIVRVH 61 (87)
T ss_pred CCHHHHHhhcCceEEEEeCCCCEEEEEEEeee
Confidence 44577899999999988888888999998654
No 25
>PRK05753 nucleoside diphosphate kinase regulator; Provisional
Probab=22.45 E-value=1.8e+02 Score=24.64 Aligned_cols=31 Identities=29% Similarity=0.320 Sum_probs=23.3
Q ss_pred HHHHhccCCe----EEEEecCCcEEEEEEEEecccC
Q psy11729 29 DLANALLGKY----LVRRLSCGTLLIGKIVETESYL 60 (281)
Q Consensus 29 ~vA~~LLGk~----Lvr~~~~G~~l~grIVETEAY~ 60 (281)
.++++|||+. +....++|....-+|++.| |.
T Consensus 94 PlG~ALlG~~~Gd~v~v~~p~G~~~~~~I~~I~-y~ 128 (137)
T PRK05753 94 PVGAALLGLSVGQSIDWPLPGGKETHLEVLEVE-YQ 128 (137)
T ss_pred HHHHHHcCCCCCCEEEEECCCCCEEEEEEEEEE-eC
Confidence 5899999974 4555778854566899998 75
No 26
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=22.06 E-value=80 Score=24.52 Aligned_cols=54 Identities=15% Similarity=0.131 Sum_probs=35.9
Q ss_pred cccCChhhhCCCHHHHHHhccCCeEEEEecC--CcEEEE-EEEEe-c--ccCCCCCCcccc
Q psy11729 15 ANCLDQAFFDQPCIDLANALLGKYLVRRLSC--GTLLIG-KIVET-E--SYLGVEDRASHS 69 (281)
Q Consensus 15 ~~~L~~~Ff~r~~~~vA~~LLGk~Lvr~~~~--G~~l~g-rIVET-E--AY~G~~D~AsHa 69 (281)
.-+|+..+|..+...+..+|..+++ ++.++ |-+++- -|... + |+...+|++.|.
T Consensus 17 ~v~l~P~~~~~~~~~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~ 76 (89)
T cd04328 17 YVSLAPKYLGNPLTGIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFV 76 (89)
T ss_pred EEEECchhhcCHhHHHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeCCCcEEEE
Confidence 3468899999887788888888888 77765 333321 25555 3 666566666664
Done!