Query 030570
Match_columns 175
No_of_seqs 86 out of 88
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 15:44:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030570.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030570hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03143 nudix hydrolase; Prov 100.0 1.6E-43 3.5E-48 307.2 17.9 140 33-174 19-158 (291)
2 KOG3041 Nucleoside diphosphate 99.2 2.5E-11 5.5E-16 103.5 7.1 99 45-174 5-103 (225)
3 PRK15009 GDP-mannose pyrophosp 95.7 0.12 2.7E-06 42.5 9.6 51 119-171 16-70 (191)
4 PRK10729 nudF ADP-ribose pyrop 95.0 0.27 5.9E-06 40.8 9.6 51 119-172 19-75 (202)
5 TIGR00052 nudix-type nucleosid 91.5 2 4.4E-05 35.0 9.1 37 133-171 33-69 (185)
6 PRK11762 nudE adenosine nucleo 88.5 2.9 6.4E-05 33.5 7.7 40 131-173 32-73 (185)
7 PF13355 DUF4101: Protein of u 78.6 8.3 0.00018 29.5 6.1 52 64-116 16-67 (117)
8 cd01723 LSm4 The eukaryotic Sm 47.9 97 0.0021 21.9 7.0 45 101-150 22-68 (76)
9 cd01728 LSm1 The eukaryotic Sm 45.5 1.1E+02 0.0024 21.9 7.3 18 133-150 54-71 (74)
10 cd01721 Sm_D3 The eukaryotic S 45.4 1E+02 0.0022 21.5 6.1 39 109-152 28-68 (70)
11 TIGR02222 chap_CsaA export-rel 43.3 34 0.00074 25.9 3.5 34 142-175 72-106 (107)
12 PRK10089 tRNA-binding protein; 41.2 40 0.00086 25.6 3.5 34 142-175 77-111 (112)
13 cd01724 Sm_D1 The eukaryotic S 38.6 1.6E+02 0.0035 21.8 6.4 38 109-150 29-67 (90)
14 cd01733 LSm10 The eukaryotic S 38.1 95 0.0021 22.4 5.0 36 109-148 37-73 (78)
15 PF14356 DUF4403: Domain of un 35.5 2.1E+02 0.0045 26.3 7.8 71 57-146 248-319 (427)
16 PF10296 DUF2404: Putative int 34.7 66 0.0014 23.2 3.7 38 75-113 10-48 (91)
17 cd01732 LSm5 The eukaryotic Sm 34.5 50 0.0011 23.8 3.0 15 137-151 59-73 (76)
18 cd01726 LSm6 The eukaryotic Sm 33.7 1.3E+02 0.0029 20.6 4.9 11 138-148 54-64 (67)
19 cd01727 LSm8 The eukaryotic Sm 31.5 1.6E+02 0.0034 20.7 5.1 17 134-150 53-69 (74)
20 PF01863 DUF45: Protein of unk 31.3 1.6E+02 0.0034 23.3 5.7 63 49-118 4-66 (205)
21 PF12123 Amidase02_C: N-acetyl 30.1 96 0.0021 20.9 3.6 34 47-88 5-38 (45)
22 PF04612 T2SM: Type II secreti 28.8 1.5E+02 0.0033 22.7 5.0 49 59-127 108-156 (160)
23 cd01718 Sm_E The eukaryotic Sm 28.5 48 0.001 24.4 2.1 14 137-150 64-77 (79)
24 cd00600 Sm_like The eukaryotic 28.0 1.7E+02 0.0038 18.9 5.3 19 132-150 44-62 (63)
25 cd01730 LSm3 The eukaryotic Sm 27.6 56 0.0012 23.5 2.3 14 136-149 66-79 (82)
26 COG4326 Spo0M Sporulation cont 27.6 1.9E+02 0.0042 25.9 6.0 64 73-146 148-217 (270)
27 cd02800 tRNA_bind_EcMetRS_like 27.3 1.1E+02 0.0025 22.4 4.0 43 132-175 56-104 (105)
28 COG1958 LSM1 Small nuclear rib 24.8 2.5E+02 0.0055 19.7 5.8 15 136-150 63-77 (79)
29 PF05688 DUF824: Salmonella re 24.0 91 0.002 21.1 2.7 21 121-142 15-35 (47)
30 cd01720 Sm_D2 The eukaryotic S 23.9 66 0.0014 23.9 2.1 12 138-149 71-82 (87)
31 TIGR00399 metG_C_term methiony 22.8 1.5E+02 0.0033 23.4 4.1 44 132-175 87-136 (137)
32 cd01731 archaeal_Sm1 The archa 22.7 2.6E+02 0.0056 19.1 6.9 45 101-150 21-66 (68)
33 CHL00123 rps6 ribosomal protei 22.7 86 0.0019 23.3 2.6 42 58-116 8-49 (97)
34 PF11761 CbiG_mid: Cobalamin b 22.1 6.4 0.00014 27.3 -3.4 37 110-152 3-39 (93)
35 cd01719 Sm_G The eukaryotic Sm 22.0 84 0.0018 22.2 2.3 16 138-153 54-69 (72)
36 PRK10707 putative NUDIX hydrol 21.7 1.4E+02 0.003 24.6 3.8 28 144-172 30-60 (190)
37 PF14789 THDPS_M: Tetrahydrodi 21.1 78 0.0017 21.0 1.8 26 84-115 15-40 (41)
38 smart00632 Aamy_C Aamy_C domai 21.0 2.1E+02 0.0045 20.1 4.2 8 117-124 17-24 (81)
39 PRK09731 putative general secr 20.9 2.8E+02 0.006 23.3 5.5 48 57-124 124-171 (178)
40 PRK13665 hypothetical protein; 20.5 1.3E+02 0.0028 27.8 3.6 57 59-119 170-231 (316)
41 smart00651 Sm snRNP Sm protein 20.4 77 0.0017 21.0 1.8 17 134-150 49-65 (67)
42 cd01729 LSm7 The eukaryotic Sm 20.1 89 0.0019 22.6 2.1 15 136-150 62-76 (81)
No 1
>PLN03143 nudix hydrolase; Provisional
Probab=100.00 E-value=1.6e-43 Score=307.23 Aligned_cols=140 Identities=75% Similarity=1.064 Sum_probs=130.7
Q ss_pred eEeecCCCCCCCCceeEEEecCCCCCCeEEEeCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeee
Q 030570 33 VCSKMPTESSPSPLTHSITIPSQLSQPVHVVAAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVD 112 (175)
Q Consensus 33 ~~~km~~~~~~~~~~~t~tlp~~~~~~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD 112 (175)
+++||+++++ ++|+|||||+++.++|+|+++||++++|++++++|++|++|+++|++|+++|++++|+||+|+||+||
T Consensus 19 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~vd 96 (291)
T PLN03143 19 KEASSSSSSS--PLTHSITLPGQPGQPVLVVAAPGISSSDFRKAIDSSLFRQWLKNLQSESGILAYGSMSLKQVLIQGVD 96 (291)
T ss_pred ehhccCCCCC--CceeEEEccCCCCCceeEecCCCCCHHHHHhHhcChHHHHHHHHhhhccccccCCCceeEEEEEEEEe
Confidence 3444444444 79999999998889999999999999999999999999999999999999999999999999999999
Q ss_pred eecceeeEEEEEEEEeecCCCceeccEEEeecCeeEEEEEEecCCCeEEEEEeeecccCCCC
Q 030570 113 MFGKRIGFLKFKADIFCKETGQKVPGIVFARGPAVAVLILLDSEGETYAILTEQVVFLYLSL 174 (175)
Q Consensus 113 ~FG~RvGFvKl~ADv~~~~~G~klPG~VFLRG~SVamLviL~~~~EkyvVLT~QpRIpaGSl 174 (175)
|||+||||+|+++|+.+.++|+++||+||+||++||||+++.+++++|+|||+|+|+|+|.+
T Consensus 97 ~fg~~~gflkv~~d~~~l~~G~~~~~~v~~rg~aVaVL~~l~~~ge~~VlLVrQ~R~pvg~~ 158 (291)
T PLN03143 97 MFGKRIGFLKFKADIIDKETGQKVPGIVFARGPAVAVLILLESEGETYAVLTEQVRVPVGKF 158 (291)
T ss_pred cccCceeEEEEEEEEEECCCCCEeeEEEEEcCCeEEEEEEEeCCCCEEEEEEEeEecCCCcE
Confidence 99999999999999998789999999999999999999999888999999999999999864
No 2
>KOG3041 consensus Nucleoside diphosphate-sugar hydrolase of the MutT (NUDIX) family [Replication, recombination and repair]
Probab=99.22 E-value=2.5e-11 Score=103.51 Aligned_cols=99 Identities=34% Similarity=0.314 Sum_probs=74.5
Q ss_pred CceeEEEecCCCCCCeEEEeCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeecceeeEEEEE
Q 030570 45 PLTHSITIPSQLSQPVHVVAAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGKRIGFLKFK 124 (175)
Q Consensus 45 ~~~~t~tlp~~~~~~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~RvGFvKl~ 124 (175)
++| ++++|++.+.++-++...+. .++.. -... .|= -.=..|++|.+| |+||+
T Consensus 5 ~~~-~i~l~sq~ne~~~ss~~~kp--~~i~~---~~~i-e~~-----------~kWi~Lkkv~~q--D~~GK-------- 56 (225)
T KOG3041|consen 5 SLT-SITLPSQPNEPTMSSATGKP--SKIIE---VEDI-ESD-----------GKWIRLKKVLYQ--DPTGK-------- 56 (225)
T ss_pred cce-eeeccCCCCCceeecccCCc--hheee---eecc-cCC-----------ccEEEEEEEEEE--cCCCc--------
Confidence 355 99999987666666665433 22222 1111 010 112569999999 99998
Q ss_pred EEEeecCCCceeccEEEeecCeeEEEEEEecCCCeEEEEEeeecccCCCC
Q 030570 125 ADIFCKETGQKVPGIVFARGPAVAVLILLDSEGETYAILTEQVVFLYLSL 174 (175)
Q Consensus 125 ADv~~~~~G~klPG~VFLRG~SVamLviL~~~~EkyvVLT~QpRIpaGSl 174 (175)
+.+.+.+++.++ ++.|+++||||.+|+.+|+.|+||+.|-|+|.|.+
T Consensus 57 --ir~wes~~Rttr-~ea~~dgVaIl~il~~dG~~~ivL~kQfRpP~Gk~ 103 (225)
T KOG3041|consen 57 --IRDWESVQRTTR-VEARADGVAILAILESDGKPYIVLVKQFRPPTGKI 103 (225)
T ss_pred --eeeeehheeccc-ccccCCeEEEEEEEecCCcEEEEEEEeecCCCCcE
Confidence 444479999999 99999999999999999999999999999999975
No 3
>PRK15009 GDP-mannose pyrophosphatase NudK; Provisional
Probab=95.68 E-value=0.12 Score=42.48 Aligned_cols=51 Identities=14% Similarity=0.301 Sum_probs=36.6
Q ss_pred eEEEEEEEEee--cCCCceecc--EEEeecCeeEEEEEEecCCCeEEEEEeeecccC
Q 030570 119 GFLKFKADIFC--KETGQKVPG--IVFARGPAVAVLILLDSEGETYAILTEQVVFLY 171 (175)
Q Consensus 119 GFvKl~ADv~~--~~~G~klPG--~VFLRG~SVamLviL~~~~EkyvVLT~QpRIpa 171 (175)
+|+++.-+..+ .++|...+. .++-+|++|+||+.- +++..+||+.|.|.|+
T Consensus 16 ~~~~v~~~~~~~~~pdG~~~~~~r~vv~~~~~v~Vl~~~--~~~~~vvLvrQyR~~v 70 (191)
T PRK15009 16 NYFTLHNITYDLTRKDGEVIRHKREVYDRGNGATILLYN--AKKKTVVLIRQFRVAT 70 (191)
T ss_pred CeEEEEEEEEEEECCCCCccceEEEEEEECCEEEEEEEE--CCCCEEEEEEcccccc
Confidence 56666554321 278886443 688999999988763 3355799999999997
No 4
>PRK10729 nudF ADP-ribose pyrophosphatase NudF; Provisional
Probab=95.03 E-value=0.27 Score=40.76 Aligned_cols=51 Identities=24% Similarity=0.290 Sum_probs=36.6
Q ss_pred eEEEEEE---EEeecCCCc---eeccEEEeecCeeEEEEEEecCCCeEEEEEeeecccCC
Q 030570 119 GFLKFKA---DIFCKETGQ---KVPGIVFARGPAVAVLILLDSEGETYAILTEQVVFLYL 172 (175)
Q Consensus 119 GFvKl~A---Dv~~~~~G~---klPG~VFLRG~SVamLviL~~~~EkyvVLT~QpRIpaG 172 (175)
||+++.. +... ++|. ...-.++-++++|+||.+.. ++..+||+.|.|.|++
T Consensus 19 ~~~~v~~~~~~~~~-~~G~~~~~~~~~vv~~~~~V~il~~~~--~~~~vlLvrQyR~~~~ 75 (202)
T PRK10729 19 GFFSLDLYRFRHRL-FNGEMSGEVRREIFERGHAAVLLPFDP--VRDEVVLIEQIRIAAY 75 (202)
T ss_pred CeEEEEEEEEEEEe-cCCccccEEeEEEEEcCCeEEEEEEEC--CCCEEEEEEeeecccc
Confidence 5655543 3222 4676 56668899999999988752 3347999999999985
No 5
>TIGR00052 nudix-type nucleoside diphosphatase, YffH/AdpP family.
Probab=91.47 E-value=2 Score=35.00 Aligned_cols=37 Identities=27% Similarity=0.330 Sum_probs=30.5
Q ss_pred CceeccEEEeecCeeEEEEEEecCCCeEEEEEeeecccC
Q 030570 133 GQKVPGIVFARGPAVAVLILLDSEGETYAILTEQVVFLY 171 (175)
Q Consensus 133 G~klPG~VFLRG~SVamLviL~~~~EkyvVLT~QpRIpa 171 (175)
+..+.-.++-+|++|+||++-. ++..++|+.|.|.|+
T Consensus 33 ~~~~~~~~v~~~~~v~vl~~~~--~~~~vlLvrq~R~~~ 69 (185)
T TIGR00052 33 SIRVTREIYDRGNAAAVLLYDP--KKDTVVLIEQFRIAA 69 (185)
T ss_pred CceEEEEEEEcCCeEEEEEEEC--CCCEEEEEECceeee
Confidence 3678888999999999987753 456899999999876
No 6
>PRK11762 nudE adenosine nucleotide hydrolase NudE; Provisional
Probab=88.50 E-value=2.9 Score=33.46 Aligned_cols=40 Identities=13% Similarity=0.015 Sum_probs=25.1
Q ss_pred CCCceeccEEEe--ecCeeEEEEEEecCCCeEEEEEeeecccCCC
Q 030570 131 ETGQKVPGIVFA--RGPAVAVLILLDSEGETYAILTEQVVFLYLS 173 (175)
Q Consensus 131 ~~G~klPG~VFL--RG~SVamLviL~~~~EkyvVLT~QpRIpaGS 173 (175)
++|....=.+.. ++++|+|+.+. ++..++|+.|.|.+.+.
T Consensus 32 ~~G~~~~~~~v~~~~~~~v~v~~~~---~~~~vlLvrq~r~~~~~ 73 (185)
T PRK11762 32 SNGVERVYERMRPSGRGAVMIVPIL---DDDTLLLIREYAAGTER 73 (185)
T ss_pred CCCCEEEEEEEecCCCCEEEEEEEe---CCCEEEEEEeecCCCCC
Confidence 677653322222 23567777765 34579999999987764
No 7
>PF13355 DUF4101: Protein of unknown function (DUF4101)
Probab=78.58 E-value=8.3 Score=29.54 Aligned_cols=52 Identities=15% Similarity=0.172 Sum_probs=38.2
Q ss_pred eCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeecc
Q 030570 64 AAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGK 116 (175)
Q Consensus 64 ~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~ 116 (175)
|.|.-+-+.|..++.-+.+++|.++-+.-.+....-.|+ .++.|.+|+.|..
T Consensus 16 lg~~~~~~~L~~vl~g~ll~~w~~~a~~~~~~g~y~~y~-~~~~I~sv~~~~~ 67 (117)
T PF13355_consen 16 LGPPHDIDSLSEVLTGPLLSQWQDRAQWLKANGWYWEYD-HKLKIDSVEVFSD 67 (117)
T ss_pred hCCCcchhHHHHHhhHHHHHHHHHHHHHHHHcCCeEEEe-eeeEEEEEEEcCC
Confidence 445556678888899999999999987532222222466 8999999999973
No 8
>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=47.94 E-value=97 Score=21.90 Aligned_cols=45 Identities=16% Similarity=0.136 Sum_probs=27.3
Q ss_pred eeEeEEEEeeeeeecceeeEEEEEEEEeecCCCceec--cEEEeecCeeEEE
Q 030570 101 MLLKQVLIQGVDMFGKRIGFLKFKADIFCKETGQKVP--GIVFARGPAVAVL 150 (175)
Q Consensus 101 y~Lr~I~IQsVD~FG~RvGFvKl~ADv~~~~~G~klP--G~VFLRG~SVamL 150 (175)
..++.+. .+||-| +-.+.-.|...+ ++|++.. |.||+||-++-..
T Consensus 22 ~~~~G~L-~~~D~~---mNi~L~~~~~~~-~~g~~~~~~~~v~IRG~~I~~i 68 (76)
T cd01723 22 ETYNGHL-VNCDNW---MNIHLREVICTS-KDGDKFWKMPECYIRGNTIKYL 68 (76)
T ss_pred CEEEEEE-EEEcCC---CceEEEeEEEEC-CCCcEeeeCCcEEEeCCEEEEE
Confidence 4444443 344443 444444555554 7888764 6899999997654
No 9
>cd01728 LSm1 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. LSm1 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=45.54 E-value=1.1e+02 Score=21.90 Aligned_cols=18 Identities=39% Similarity=0.619 Sum_probs=14.4
Q ss_pred CceeccEEEeecCeeEEE
Q 030570 133 GQKVPGIVFARGPAVAVL 150 (175)
Q Consensus 133 G~klPG~VFLRG~SVamL 150 (175)
++.-=|.+++||.+|.++
T Consensus 54 ~~~~lG~~viRG~~V~~i 71 (74)
T cd01728 54 GDIPRGIFIIRGENVVLL 71 (74)
T ss_pred ceeEeeEEEEECCEEEEE
Confidence 345569999999999875
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=45.40 E-value=1e+02 Score=21.48 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=22.8
Q ss_pred eeeeeecceeeEEEEEEEEeecCCCc--eeccEEEeecCeeEEEEE
Q 030570 109 QGVDMFGKRIGFLKFKADIFCKETGQ--KVPGIVFARGPAVAVLIL 152 (175)
Q Consensus 109 QsVD~FG~RvGFvKl~ADv~~~~~G~--klPG~VFLRG~SVamLvi 152 (175)
++||-| .-...-.|.... .+|+ ++ |.+|+||-.|-.+++
T Consensus 28 ~~~D~~---MNl~L~~~~~~~-~~g~~~~~-~~v~IRG~nI~~v~l 68 (70)
T cd01721 28 IEAEDN---MNCQLKDVTVTA-RDGRVSQL-EQVYIRGSKIRFFIL 68 (70)
T ss_pred EEEcCC---ceeEEEEEEEEC-CCCcEeEc-CcEEEeCCEEEEEEe
Confidence 445543 334444454443 4554 44 899999999865543
No 11
>TIGR02222 chap_CsaA export-related chaperone CsaA. This model describes Bacillus subtilis CsaA, an export-related chaperone that interacts with the Sec system, and related proteins from a number of other bacteria and archaea. The crystal structure is known for the homodimer from Thermus thermophilus.
Probab=43.25 E-value=34 Score=25.87 Aligned_cols=34 Identities=12% Similarity=0.008 Sum_probs=26.3
Q ss_pred eecC-eeEEEEEEecCCCeEEEEEeeecccCCCCC
Q 030570 142 ARGP-AVAVLILLDSEGETYAILTEQVVFLYLSLI 175 (175)
Q Consensus 142 LRG~-SVamLviL~~~~EkyvVLT~QpRIpaGSl~ 175 (175)
+||- |=||+++-.+++++..+++...-+|.|+-|
T Consensus 72 ~~G~~S~gMil~~~~~~~~~~l~~~~~~~~~G~~v 106 (107)
T TIGR02222 72 IAGFLSEVLVLGVIDEQGRVVLLQPDRPVPNGTKI 106 (107)
T ss_pred eCCccccEEEEEEECCCCeEEEecCCCCCCCcCCc
Confidence 3454 889988876655578899999999999854
No 12
>PRK10089 tRNA-binding protein; Provisional
Probab=41.22 E-value=40 Score=25.62 Aligned_cols=34 Identities=12% Similarity=0.074 Sum_probs=26.1
Q ss_pred eecC-eeEEEEEEecCCCeEEEEEeeecccCCCCC
Q 030570 142 ARGP-AVAVLILLDSEGETYAILTEQVVFLYLSLI 175 (175)
Q Consensus 142 LRG~-SVamLviL~~~~EkyvVLT~QpRIpaGSl~ 175 (175)
+||- |=|||++-.+++.+..+++.+.-+|.|+-|
T Consensus 77 ~~G~~S~gmil~~~~~~~~~~l~~p~~~~~~G~~i 111 (112)
T PRK10089 77 IAGFMSEVLVLGFEDEDGEVVLLTPDRPVPNGVKL 111 (112)
T ss_pred ecCccccEEEEEEEcCCCeEEEecCCCCCCCcCCc
Confidence 3564 889999887655567788888889999854
No 13
>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=38.56 E-value=1.6e+02 Score=21.77 Aligned_cols=38 Identities=18% Similarity=0.219 Sum_probs=23.5
Q ss_pred eeeeeecceeeEEEEEEEEeecCCCceec-cEEEeecCeeEEE
Q 030570 109 QGVDMFGKRIGFLKFKADIFCKETGQKVP-GIVFARGPAVAVL 150 (175)
Q Consensus 109 QsVD~FG~RvGFvKl~ADv~~~~~G~klP-G~VFLRG~SVamL 150 (175)
++||-| .-...=.|.... .+|.... |.||+||-+|=-+
T Consensus 29 ~~vD~~---MNl~L~~a~~~~-~~~~~~~~~~v~IRG~nI~yi 67 (90)
T cd01724 29 TGVDPS---MNTHLKNVKLTL-KGRNPVPLDTLSIRGNNIRYF 67 (90)
T ss_pred EEEcCc---eeEEEEEEEEEc-CCCceeEcceEEEeCCEEEEE
Confidence 455544 344444555554 4556554 9999999988544
No 14
>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=38.07 E-value=95 Score=22.37 Aligned_cols=36 Identities=22% Similarity=0.369 Sum_probs=22.8
Q ss_pred eeeeeecceeeEEEEEEEEeecCCCceec-cEEEeecCeeE
Q 030570 109 QGVDMFGKRIGFLKFKADIFCKETGQKVP-GIVFARGPAVA 148 (175)
Q Consensus 109 QsVD~FG~RvGFvKl~ADv~~~~~G~klP-G~VFLRG~SVa 148 (175)
.+||-| .-...-.|...+ ++|.+.. |-+|+||-.|=
T Consensus 37 ~~vD~~---MNl~L~~~~~~~-~~~~~~~~~~v~IRG~nI~ 73 (78)
T cd01733 37 ASVDAF---MNIRLAKVTIID-RNGKQVQVEEIMVTGRNIR 73 (78)
T ss_pred EEEcCC---ceeEEEEEEEEc-CCCceeECCcEEEECCEEE
Confidence 444443 345555666664 5666544 99999998863
No 15
>PF14356 DUF4403: Domain of unknown function (DUF4403)
Probab=35.54 E-value=2.1e+02 Score=26.29 Aligned_cols=71 Identities=13% Similarity=0.163 Sum_probs=41.6
Q ss_pred CCCeEEEeCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCC-eeEeEEEEeeeeeecceeeEEEEEEEEeecCCCce
Q 030570 57 SQPVHVVAAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGD-MLLKQVLIQGVDMFGKRIGFLKFKADIFCKETGQK 135 (175)
Q Consensus 57 ~~~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~-y~Lr~I~IQsVD~FG~RvGFvKl~ADv~~~~~G~k 135 (175)
...+.|.++-.++=+++.+ ++.+ ++.-+.- + -.-++|+|++|+++| .=+-+.+.+++.- +
T Consensus 248 ~~~~~i~l~~~i~y~~i~~---------~l~~---~l~gk~f-~~~~~~~v~v~~v~v~g-~~~rl~i~~~~~g-----~ 308 (427)
T PF14356_consen 248 PGGFRINLPADIPYAEINK---------LLTK---QLAGKTF-SFSGGKKVTVKSVSVYG-SGDRLVIALDVTG-----S 308 (427)
T ss_pred CCcEEEEEEEEcCHHHHHH---------HHHH---HHcCCcc-ccCCCceEEEEEEEEEe-cCCcEEEEEEEEE-----E
Confidence 4557777777666666554 3333 2211000 1 234689999999999 3333445555542 1
Q ss_pred eccEEEeecCe
Q 030570 136 VPGIVFARGPA 146 (175)
Q Consensus 136 lPG~VFLRG~S 146 (175)
+.|.+.|.|-=
T Consensus 309 ~~G~i~l~G~P 319 (427)
T PF14356_consen 309 LNGTIYLSGRP 319 (427)
T ss_pred EEEEEEEEEEE
Confidence 78888888854
No 16
>PF10296 DUF2404: Putative integral membrane protein conserved region (DUF2404); InterPro: IPR019411 This is entry represents a domain of unknown function found in mitochondrial distribution and morphology proteins Mdm12 and Mdm34, and in maintenance of mitochondrial morphology protein Mmm1. These proteins are components of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria [].
Probab=34.72 E-value=66 Score=23.22 Aligned_cols=38 Identities=16% Similarity=0.254 Sum_probs=25.9
Q ss_pred hhccChhHHHHHHH-HhhhcccccCCCeeEeEEEEeeeee
Q 030570 75 CAVESTLFKQWLKN-LQSETGILANGDMLLKQVLIQGVDM 113 (175)
Q Consensus 75 ~a~~~~~Fk~Wl~~-L~~sl~~~~~~~y~Lr~I~IQsVD~ 113 (175)
+......|++|+.+ |++.|.... -|.-|.+|.|+++|+
T Consensus 10 ~~~~t~~~~~~i~~~L~~kL~~i~-~P~fl~~i~v~~~~l 48 (91)
T PF10296_consen 10 DFRRTEAFRDKIKEKLQKKLNKIK-LPSFLDEISVTELDL 48 (91)
T ss_pred HHhcCHHHHHHHHHHHHHHHcccc-CCCccCcEEEEEEEC
Confidence 34457788888766 666555433 345569999999986
No 17
>cd01732 LSm5 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=34.54 E-value=50 Score=23.79 Aligned_cols=15 Identities=13% Similarity=0.397 Sum_probs=12.8
Q ss_pred ccEEEeecCeeEEEE
Q 030570 137 PGIVFARGPAVAVLI 151 (175)
Q Consensus 137 PG~VFLRG~SVamLv 151 (175)
-|.+|+||.+|.++.
T Consensus 59 lg~v~iRG~nV~~i~ 73 (76)
T cd01732 59 LDQILLNGNNICMLV 73 (76)
T ss_pred cCeEEEeCCeEEEEE
Confidence 499999999998763
No 18
>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=33.67 E-value=1.3e+02 Score=20.60 Aligned_cols=11 Identities=45% Similarity=0.649 Sum_probs=9.5
Q ss_pred cEEEeecCeeE
Q 030570 138 GIVFARGPAVA 148 (175)
Q Consensus 138 G~VFLRG~SVa 148 (175)
|.||+||.++-
T Consensus 54 ~~v~IRG~~I~ 64 (67)
T cd01726 54 GDAFIRGNNVL 64 (67)
T ss_pred CCEEEECCEEE
Confidence 89999999874
No 19
>cd01727 LSm8 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. LSm8 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=31.52 E-value=1.6e+02 Score=20.67 Aligned_cols=17 Identities=41% Similarity=0.620 Sum_probs=13.6
Q ss_pred ceeccEEEeecCeeEEE
Q 030570 134 QKVPGIVFARGPAVAVL 150 (175)
Q Consensus 134 ~klPG~VFLRG~SVamL 150 (175)
+..-|.+++||..|.++
T Consensus 53 ~~~lG~~~iRG~~I~~i 69 (74)
T cd01727 53 QVVLGLYIIRGDNIAVV 69 (74)
T ss_pred eeEeceEEECCCEEEEE
Confidence 34459999999999765
No 20
>PF01863 DUF45: Protein of unknown function DUF45; InterPro: IPR002725 Members of this family are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.
Probab=31.26 E-value=1.6e+02 Score=23.27 Aligned_cols=63 Identities=11% Similarity=0.161 Sum_probs=39.2
Q ss_pred EEEecCCCCCCeEEEeCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeeccee
Q 030570 49 SITIPSQLSQPVHVVAAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGKRI 118 (175)
Q Consensus 49 t~tlp~~~~~~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~Rv 118 (175)
.+.+... ..|.|++|++.|++++++.+. .-+.|+.+-..+... ..-...-++=..+.+||++.
T Consensus 4 ~l~v~~d--g~i~V~aP~~~s~~~I~~fl~--~~~~WI~~~~~~~~~---~~~~~~~~~g~~~~~~G~~~ 66 (205)
T PF01863_consen 4 RLRVDPD--GEIVVSAPPRVSKEEIERFLR--SKRDWILKKLQKFQN---RPPSRQYIDGEKIYLLGKPY 66 (205)
T ss_pred EEEEcCC--CEEEEEECCCCCHHHHHHHHH--HHHHHHHHHHHHHHh---ccccccccccceEEEeccEE
Confidence 4455442 679999999999999998644 457899886665432 11111122334456678653
No 21
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=30.10 E-value=96 Score=20.88 Aligned_cols=34 Identities=24% Similarity=0.444 Sum_probs=19.6
Q ss_pred eeEEEecCCCCCCeEEEeCCCCChhhhhhhccChhHHHHHHH
Q 030570 47 THSITIPSQLSQPVHVVAAPGLSESDFRCAVESTLFKQWLKN 88 (175)
Q Consensus 47 ~~t~tlp~~~~~~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~ 88 (175)
++.|++... ...+...+.++|.++|.+ |+.|+++
T Consensus 5 ~~ki~~~~~--~Gl~y~vT~~~s~~~L~k------~~~wld~ 38 (45)
T PF12123_consen 5 TAKIIFQSK--DGLPYFVTDPLSDAELDK------FTAWLDE 38 (45)
T ss_dssp -EEEEE-T---TS-EEEEE----HHHHHH------HHHHHHH
T ss_pred EEEEEEecC--CCcEEEEeCCCCHHHHHH------HHHHHHh
Confidence 566777652 457777788899988874 8999886
No 22
>PF04612 T2SM: Type II secretion system (T2SS), protein M; InterPro: IPR007690 General secretion pathway (GSP) protein M is a membrane protein involved in the export of proteins in bacteria. It consists of a short cytosolic N-terminal domain, a transmembrane domain, and a C-terminal periplasmic domain. The precise function of this protein is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers [],; GO: 0006858 extracellular transport; PDB: 1UV7_A.
Probab=28.80 E-value=1.5e+02 Score=22.68 Aligned_cols=49 Identities=20% Similarity=0.375 Sum_probs=28.3
Q ss_pred CeEEEeCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeecceeeEEEEEEEE
Q 030570 59 PVHVVAAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGKRIGFLKFKADI 127 (175)
Q Consensus 59 ~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~RvGFvKl~ADv 127 (175)
.|.|.+.. ..+..+-.|+..|+.+ .+..+.+++|...| .-|.|+..+..
T Consensus 108 ~v~v~l~~----------v~~~~L~~WL~~l~~~------~gi~v~~l~l~~~~----~~g~v~~~~~l 156 (160)
T PF04612_consen 108 RVQVWLEN----------VSFDQLLQWLQQLEQQ------HGISVTQLSLTRAD----EPGLVSVRLTL 156 (160)
T ss_dssp EEEEEE------------B-HHHHHHHHHHHHHH------S--EEEEEEEEE----------EEEEEEE
T ss_pred EEEEEEec----------CCHHHHHHHHHHHHHh------CCcEEEEEEEEEcC----CCCEEEEEEEE
Confidence 57777632 2377888999999964 36788888877665 66777776654
No 23
>cd01718 Sm_E 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 subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming 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=28.51 E-value=48 Score=24.35 Aligned_cols=14 Identities=14% Similarity=0.534 Sum_probs=12.1
Q ss_pred ccEEEeecCeeEEE
Q 030570 137 PGIVFARGPAVAVL 150 (175)
Q Consensus 137 PG~VFLRG~SVamL 150 (175)
-|.+|+||.+|.++
T Consensus 64 lG~iliRGnnV~~I 77 (79)
T cd01718 64 LGRILLKGDNITLI 77 (79)
T ss_pred cCcEEEeCCEEEEE
Confidence 39999999999874
No 24
>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=27.96 E-value=1.7e+02 Score=18.90 Aligned_cols=19 Identities=32% Similarity=0.593 Sum_probs=14.7
Q ss_pred CCceeccEEEeecCeeEEE
Q 030570 132 TGQKVPGIVFARGPAVAVL 150 (175)
Q Consensus 132 ~G~klPG~VFLRG~SVamL 150 (175)
....--|.+|+||..|..+
T Consensus 44 ~~~~~~~~~~irG~~I~~I 62 (63)
T cd00600 44 GKKRVLGLVLIRGDNVRLV 62 (63)
T ss_pred CcEEECCeEEEECCEEEEE
Confidence 4456679999999998754
No 25
>cd01730 LSm3 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. LSm3 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=27.62 E-value=56 Score=23.45 Aligned_cols=14 Identities=29% Similarity=0.503 Sum_probs=11.6
Q ss_pred eccEEEeecCeeEE
Q 030570 136 VPGIVFARGPAVAV 149 (175)
Q Consensus 136 lPG~VFLRG~SVam 149 (175)
--|.+|+||.+|-.
T Consensus 66 ~lg~~~iRGd~Vv~ 79 (82)
T cd01730 66 NIPMLFVRGDSVIL 79 (82)
T ss_pred EcCeEEEeCCEEEE
Confidence 34999999999865
No 26
>COG4326 Spo0M Sporulation control protein [General function prediction only]
Probab=27.56 E-value=1.9e+02 Score=25.95 Aligned_cols=64 Identities=20% Similarity=0.290 Sum_probs=42.0
Q ss_pred hhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeecceeeEEEEEEEEeecCC-Cce---e--ccEEEeecCe
Q 030570 73 FRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGKRIGFLKFKADIFCKET-GQK---V--PGIVFARGPA 146 (175)
Q Consensus 73 l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~RvGFvKl~ADv~~~~~-G~k---l--PG~VFLRG~S 146 (175)
...+..-|-...=++.+++- +|.||+++-...-+||++.-||-= -+.. ++ |.- + =.+||.+|+-
T Consensus 148 ~l~Vr~hP~m~~vl~AiE~l-------GfrL~~vdCEqa~yF~~a~PFVQE-fEFv--PTtG~yr~~ldElEivf~l~~d 217 (270)
T COG4326 148 ILTVRPHPMMDGVLSAIEAL-------GFRLRQVDCEQAKYFGGALPFVQE-FEFV--PTTGPYRGRLDELEIVFYLDPD 217 (270)
T ss_pred eEEEecchHHHHHHHHHHhh-------ccEeeeccccccccccccccceeE-EEEe--ccCCcccccchheEEEEEECcc
Confidence 33444566666667777763 799999999999999999888752 1211 12 211 1 1478888875
No 27
>cd02800 tRNA_bind_EcMetRS_like tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine transfer RNAs (tRNAmet). AaTrbp111 is structure-specific molecular chaperone recognizing the L-shape of the tRNA fold. AaTrbp111 plays a role in nuclear trafficking of tRNAs. The functional unit of EcMetRs and AaTrbp111 is a homodimer, this domain acts as the dimerization domain.
Probab=27.31 E-value=1.1e+02 Score=22.38 Aligned_cols=43 Identities=19% Similarity=0.190 Sum_probs=30.3
Q ss_pred CCceeccEEEe-----ec-CeeEEEEEEecCCCeEEEEEeeecccCCCCC
Q 030570 132 TGQKVPGIVFA-----RG-PAVAVLILLDSEGETYAILTEQVVFLYLSLI 175 (175)
Q Consensus 132 ~G~klPG~VFL-----RG-~SVamLviL~~~~EkyvVLT~QpRIpaGSl~ 175 (175)
.|.++++.+-+ || .|=|||+...++ ++-.+++.++-+|.|+-|
T Consensus 56 ~g~~v~~~~nl~~~~~~Gv~S~GMl~s~~~~-~~~~l~~~~~~~~~G~~i 104 (105)
T cd02800 56 VGKKVVVVANLKPRKLRGVESQGMILAAEDG-GKLKLLTPDEEVEPGSRV 104 (105)
T ss_pred ccCceEeEeeECCccCCCeEeceEEEEecCC-CeEEEEeCCCCCCCcCCc
Confidence 46666665543 23 466899888666 666788889999999864
No 28
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=24.78 E-value=2.5e+02 Score=19.69 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=12.3
Q ss_pred eccEEEeecCeeEEE
Q 030570 136 VPGIVFARGPAVAVL 150 (175)
Q Consensus 136 lPG~VFLRG~SVamL 150 (175)
+-|.+|+||..|-.+
T Consensus 63 ~~~~~~IRG~~I~~I 77 (79)
T COG1958 63 LGGEVLIRGDNIVLI 77 (79)
T ss_pred eccEEEEECCcEEEE
Confidence 566999999988765
No 29
>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=23.98 E-value=91 Score=21.09 Aligned_cols=21 Identities=19% Similarity=0.392 Sum_probs=16.8
Q ss_pred EEEEEEEeecCCCceeccEEEe
Q 030570 121 LKFKADIFCKETGQKVPGIVFA 142 (175)
Q Consensus 121 vKl~ADv~~~~~G~klPG~VFL 142 (175)
|.+.+.+.| .+|..+|+.-|-
T Consensus 15 I~ltVt~kd-a~G~pv~n~~f~ 35 (47)
T PF05688_consen 15 IPLTVTVKD-ANGNPVPNAPFT 35 (47)
T ss_pred EEEEEEEEC-CCCCCcCCceEE
Confidence 567778887 699999998774
No 30
>cd01720 Sm_D2 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 D2 heterodimerizes with subunit D1 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 D2, 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=23.85 E-value=66 Score=23.92 Aligned_cols=12 Identities=33% Similarity=0.606 Sum_probs=10.5
Q ss_pred cEEEeecCeeEE
Q 030570 138 GIVFARGPAVAV 149 (175)
Q Consensus 138 G~VFLRG~SVam 149 (175)
|.||+||.+|-.
T Consensus 71 g~v~iRGd~Vv~ 82 (87)
T cd01720 71 SKMFLRGDSVIL 82 (87)
T ss_pred ccEEEeCCEEEE
Confidence 999999999854
No 31
>TIGR00399 metG_C_term methionyl-tRNA synthetase C-terminal region/beta chain. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (E. coli, B. subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. Proteins hit by this model should called methionyl-tRNA synthetase beta chain if and only if the model metG hits a separate protein not also hit by this model.
Probab=22.77 E-value=1.5e+02 Score=23.42 Aligned_cols=44 Identities=16% Similarity=0.211 Sum_probs=31.3
Q ss_pred CCceeccEEE-----eec-CeeEEEEEEecCCCeEEEEEeeecccCCCCC
Q 030570 132 TGQKVPGIVF-----ARG-PAVAVLILLDSEGETYAILTEQVVFLYLSLI 175 (175)
Q Consensus 132 ~G~klPG~VF-----LRG-~SVamLviL~~~~EkyvVLT~QpRIpaGSl~ 175 (175)
-|.++++.+- +|| .|=|||+...+++.+-.+|+..+=+|.|+-|
T Consensus 87 ~G~~v~~~~nlkp~k~~Gv~S~GMlls~~~~~~~~~l~~~~~~~~~G~~i 136 (137)
T TIGR00399 87 VGKKVIVVANLKPAKLFGVKSEGMILAAEDDGKVLFLLSPDQEAIAGERI 136 (137)
T ss_pred CCCEEEeeEEecCccCCCeEeccEEEEEecCCCeEEEecCCCCCCCcCCc
Confidence 4667766443 233 5778999887666567888888889999754
No 32
>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=22.71 E-value=2.6e+02 Score=19.07 Aligned_cols=45 Identities=18% Similarity=0.174 Sum_probs=24.3
Q ss_pred eeEeEEEEeeeeeecceeeEEEEEEEEeecCCCcee-ccEEEeecCeeEEE
Q 030570 101 MLLKQVLIQGVDMFGKRIGFLKFKADIFCKETGQKV-PGIVFARGPAVAVL 150 (175)
Q Consensus 101 y~Lr~I~IQsVD~FG~RvGFvKl~ADv~~~~~G~kl-PG~VFLRG~SVamL 150 (175)
-.++.+. .++|-| .-.+.-.|.-.. .++++. =|.+|+||.+|-+.
T Consensus 21 ~~~~G~L-~~~D~~---mNlvL~~~~e~~-~~~~~~~lg~~~iRG~~I~~i 66 (68)
T cd01731 21 KEVRGRL-KSYDQH---MNLVLEDAEEID-DGEPVRKYGRVVIRGDNVLFI 66 (68)
T ss_pred CEEEEEE-EEECCc---ceEEEeeEEEEe-cCCeEeEcCcEEEeCCEEEEE
Confidence 3444443 444443 344444554443 233332 28999999998764
No 33
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=22.66 E-value=86 Score=23.29 Aligned_cols=42 Identities=19% Similarity=0.184 Sum_probs=25.8
Q ss_pred CCeEEEeCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeecc
Q 030570 58 QPVHVVAAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGK 116 (175)
Q Consensus 58 ~~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~ 116 (175)
+-.-+.+.|++++++...+ ...--+.+.+ ..-+|..+|.||+
T Consensus 8 YE~~~Il~p~l~e~~~~~~-----~~~~~~~i~~------------~gg~i~~~~~wG~ 49 (97)
T CHL00123 8 YETMYLLKPDLNEEELLKW-----IENYKKLLRK------------RGAKNISVQNRGK 49 (97)
T ss_pred eeEEEEECCCCCHHHHHHH-----HHHHHHHHHH------------CCCEEEEEEeecC
Confidence 4466788999999988752 1122222222 2346777889995
No 34
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=22.08 E-value=6.4 Score=27.34 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=22.4
Q ss_pred eeeeecceeeEEEEEEEEeecCCCceeccEEEeecCeeEEEEE
Q 030570 110 GVDMFGKRIGFLKFKADIFCKETGQKVPGIVFARGPAVAVLIL 152 (175)
Q Consensus 110 sVD~FG~RvGFvKl~ADv~~~~~G~klPG~VFLRG~SVamLvi 152 (175)
++|+||++.|... .| .+.-|---+.++.|..|++..=
T Consensus 3 AvD~la~~~g~~i-----~~-~~~~k~vsaalv~g~~V~~~~~ 39 (93)
T PF11761_consen 3 AVDLLARELGWRI-----EN-REAVKRVSAALVNGEPVALYQD 39 (93)
T ss_pred CcchhhhhCCCEE-----cC-HHHHHHHHHHHHCCCEEEEEEe
Confidence 6899998877765 21 3334444555666666665544
No 35
>cd01719 Sm_G 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 subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming 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=22.04 E-value=84 Score=22.22 Aligned_cols=16 Identities=38% Similarity=0.671 Sum_probs=13.9
Q ss_pred cEEEeecCeeEEEEEE
Q 030570 138 GIVFARGPAVAVLILL 153 (175)
Q Consensus 138 G~VFLRG~SVamLviL 153 (175)
|.+|+||.+|.++=.|
T Consensus 54 g~v~IRG~~I~~i~~~ 69 (72)
T cd01719 54 GMVVIRGNSIVMLEAL 69 (72)
T ss_pred ceEEECCCEEEEEEcc
Confidence 8999999999887655
No 36
>PRK10707 putative NUDIX hydrolase; Provisional
Probab=21.73 E-value=1.4e+02 Score=24.56 Aligned_cols=28 Identities=11% Similarity=0.068 Sum_probs=15.9
Q ss_pred cCeeEEEEEEecCCCeEEEEEe---eecccCC
Q 030570 144 GPAVAVLILLDSEGETYAILTE---QVVFLYL 172 (175)
Q Consensus 144 G~SVamLviL~~~~EkyvVLT~---QpRIpaG 172 (175)
.+|+.|+.+. .+++..++|+. |.|-+.|
T Consensus 30 ~~aavvl~l~-~~~~~~vLl~~R~~~~r~~~G 60 (190)
T PRK10707 30 RQAAVLIPIV-RRPQPTLLLTQRSIHLRKHAG 60 (190)
T ss_pred CCeEEEEEEE-ECCCCEEEEEEeCCcccCCCC
Confidence 4455555544 44455677776 6775544
No 37
>PF14789 THDPS_M: Tetrahydrodipicolinate N-succinyltransferase middle; PDB: 3R5A_F 3R5B_A 3R5C_B 3R5D_D 3FSY_C 3FSX_A 2RIJ_A.
Probab=21.09 E-value=78 Score=20.98 Aligned_cols=26 Identities=15% Similarity=0.234 Sum_probs=12.9
Q ss_pred HHHHHHhhhcccccCCCeeEeEEEEeeeeeec
Q 030570 84 QWLKNLQSETGILANGDMLLKQVLIQGVDMFG 115 (175)
Q Consensus 84 ~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG 115 (175)
.|++..+.+|.. .+ +.++|.+||-|=
T Consensus 15 ~~~~~~r~~lr~--~g----~~~~V~~VDKFP 40 (41)
T PF14789_consen 15 EDFEENRLRLRA--RG----RPLTVYSVDKFP 40 (41)
T ss_dssp HHHHHHHHHHHH--TT--------EEEEESS-
T ss_pred HHHHHHHHHHHh--CC----CCcEEEEEcCCC
Confidence 455555554432 11 348999999883
No 38
>smart00632 Aamy_C Aamy_C domain.
Probab=20.98 E-value=2.1e+02 Score=20.05 Aligned_cols=8 Identities=25% Similarity=0.605 Sum_probs=3.9
Q ss_pred eeeEEEEE
Q 030570 117 RIGFLKFK 124 (175)
Q Consensus 117 RvGFvKl~ 124 (175)
..||+-+.
T Consensus 17 ~~g~VaiN 24 (81)
T smart00632 17 SKGFVAIN 24 (81)
T ss_pred CeEEEEEE
Confidence 34555443
No 39
>PRK09731 putative general secretion pathway protein YghD; Provisional
Probab=20.91 E-value=2.8e+02 Score=23.35 Aligned_cols=48 Identities=15% Similarity=0.315 Sum_probs=31.2
Q ss_pred CCCeEEEeCCCCChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeecceeeEEEEE
Q 030570 57 SQPVHVVAAPGLSESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGKRIGFLKFK 124 (175)
Q Consensus 57 ~~~V~V~~~pgls~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~RvGFvKl~ 124 (175)
+..|.|.+.+- .|..+-.||+.|+.. .+..+..++|.. ++.=|+|+++
T Consensus 124 Ge~vQVwld~v----------~F~~ll~WL~~L~~q------~GV~V~~ldl~~----~~~pG~V~V~ 171 (178)
T PRK09731 124 GENIQVWIEPV----------VFNDLLNWLNALDEK------YALRVTQIDVSA----AEKPGMVNVQ 171 (178)
T ss_pred CCEEEEEECCC----------CHHHHHHHHHHHHHh------cCceEEEEeeec----CCCCCEEEEE
Confidence 35688888552 388999999999874 234444444332 4566777763
No 40
>PRK13665 hypothetical protein; Provisional
Probab=20.51 E-value=1.3e+02 Score=27.80 Aligned_cols=57 Identities=21% Similarity=0.294 Sum_probs=37.7
Q ss_pred CeEEEeCCCC-----ChhhhhhhccChhHHHHHHHHhhhcccccCCCeeEeEEEEeeeeeecceee
Q 030570 59 PVHVVAAPGL-----SESDFRCAVESTLFKQWLKNLQSETGILANGDMLLKQVLIQGVDMFGKRIG 119 (175)
Q Consensus 59 ~V~V~~~pgl-----s~e~l~~a~~~~~Fk~Wl~~L~~sl~~~~~~~y~Lr~I~IQsVD~FG~RvG 119 (175)
+|--...+|+ |.+.+.++++.|-- +++.--+.++-+..-|++-+|+|-+||. |++||
T Consensus 170 TIiARVGEgIVttIGSa~~hk~VLEnPd~---ISk~VL~kGLDagTAFeIlSIDIADvdV-G~NIG 231 (316)
T PRK13665 170 TIIARVGEGIVSTIGSSESHKEVLENPDS---ISKTVLSKGLDAGTAFEILSIDIADVDV-GKNIG 231 (316)
T ss_pred eeEeeecCceeecccCcchHHHHhcCHHH---HHHHHHhccCCcCceeEEEEEeeecccc-chhhc
Confidence 3444445553 56777778888854 3333333445455679999999999996 77777
No 41
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=20.44 E-value=77 Score=21.02 Aligned_cols=17 Identities=29% Similarity=0.671 Sum_probs=13.6
Q ss_pred ceeccEEEeecCeeEEE
Q 030570 134 QKVPGIVFARGPAVAVL 150 (175)
Q Consensus 134 ~klPG~VFLRG~SVamL 150 (175)
..--|.+|+||.+|...
T Consensus 49 ~~~~~~~~IrG~~I~~i 65 (67)
T smart00651 49 KRKLGLVFIRGNNIVYI 65 (67)
T ss_pred EeEeCCEEEcCCEEEEE
Confidence 44568999999998765
No 42
>cd01729 LSm7 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. LSm7 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=20.07 E-value=89 Score=22.59 Aligned_cols=15 Identities=33% Similarity=0.671 Sum_probs=12.6
Q ss_pred eccEEEeecCeeEEE
Q 030570 136 VPGIVFARGPAVAVL 150 (175)
Q Consensus 136 lPG~VFLRG~SVamL 150 (175)
--|.+|+||..|.++
T Consensus 62 ~lG~v~iRG~nV~~i 76 (81)
T cd01729 62 QLGLVVCRGTSVVLI 76 (81)
T ss_pred EccEEEEcCCEEEEE
Confidence 349999999999765
Done!