Query 012704
Match_columns 458
No_of_seqs 170 out of 587
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 05:26:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08036 LARP_5 La RNA-binding 99.9 1.7E-27 3.7E-32 195.0 3.7 62 397-458 1-62 (75)
2 cd08035 LARP_4 La RNA-binding 99.9 3.2E-27 7E-32 193.5 4.4 62 397-458 1-62 (75)
3 cd08038 LARP_2 La RNA-binding 99.9 1.4E-26 3E-31 188.9 4.6 61 398-458 2-62 (73)
4 cd08037 LARP_1 La RNA-binding 99.9 1.5E-26 3.3E-31 188.7 4.5 61 398-458 2-62 (73)
5 cd08034 LARP_1_2 La RNA-bindin 99.9 4.7E-26 1E-30 185.6 4.5 62 397-458 1-62 (73)
6 cd08032 LARP_7 La RNA-binding 99.9 9.5E-26 2.1E-30 187.5 5.7 65 394-458 3-69 (82)
7 cd08031 LARP_4_5_like La RNA-b 99.9 6.9E-26 1.5E-30 185.4 4.6 61 398-458 2-62 (75)
8 cd08028 LARP_3 La RNA-binding 99.9 2.7E-25 5.8E-30 184.7 5.4 65 394-458 2-67 (82)
9 cd08033 LARP_6 La RNA-binding 99.9 2.6E-25 5.5E-30 182.9 4.9 61 398-458 2-64 (77)
10 smart00715 LA Domain in the RN 99.9 4E-25 8.8E-30 182.5 4.9 64 395-458 2-66 (80)
11 PF05383 La: La domain; Inter 99.9 5.3E-25 1.1E-29 173.4 3.6 58 400-457 1-61 (61)
12 cd07323 LAM LA motif RNA-bindi 99.9 2.3E-24 4.9E-29 175.8 4.8 61 398-458 2-62 (75)
13 cd08029 LA_like_fungal La-moti 99.9 3.6E-24 7.7E-29 175.6 4.4 60 398-458 2-63 (76)
14 cd08030 LA_like_plant La-motif 99.9 1.2E-23 2.5E-28 177.8 4.2 62 397-458 2-77 (90)
15 KOG1855 Predicted RNA-binding 99.7 1.6E-18 3.5E-23 178.4 4.1 65 394-458 138-204 (484)
16 KOG2590 RNA-binding protein LA 99.7 8E-16 1.7E-20 160.4 22.5 57 397-458 301-357 (448)
17 KOG2591 c-Mpl binding protein, 99.6 2.6E-16 5.7E-21 166.1 5.1 65 394-458 94-158 (684)
18 KOG4213 RNA-binding protein La 99.5 3.2E-15 6.9E-20 140.6 4.0 64 394-457 11-76 (205)
19 COG5193 LHP1 La protein, small 99.2 6.5E-12 1.4E-16 129.4 1.8 60 398-457 272-331 (438)
20 COG5193 LHP1 La protein, small 98.4 4.7E-08 1E-12 101.4 0.8 58 400-457 75-141 (438)
21 KOG2590 RNA-binding protein LA 90.3 0.054 1.2E-06 58.1 -1.4 71 387-457 88-163 (448)
22 KOG2278 RNA:NAD 2'-phosphotran 84.5 0.8 1.7E-05 44.4 2.8 38 418-455 24-61 (207)
23 PF01885 PTS_2-RNA: RNA 2'-pho 79.2 1.4 3E-05 42.1 2.3 35 422-456 26-60 (186)
24 KOG0921 Dosage compensation co 76.9 15 0.00032 43.6 9.8 11 260-270 1225-1235(1282)
25 KOG4849 mRNA cleavage factor I 69.2 19 0.0004 38.7 7.8 47 321-369 280-327 (498)
26 PRK00819 RNA 2'-phosphotransfe 68.1 4.7 0.0001 38.5 3.0 56 397-456 6-61 (179)
27 KOG4307 RNA binding protein RB 50.9 81 0.0017 36.7 9.1 76 324-422 822-902 (944)
28 PF04963 Sigma54_CBD: Sigma-54 47.8 7.3 0.00016 37.0 0.5 58 392-454 13-73 (194)
29 PTZ00315 2'-phosphotransferase 46.6 16 0.00034 41.0 2.9 55 397-456 378-433 (582)
30 KOG1924 RhoA GTPase effector D 43.3 61 0.0013 38.1 6.8 12 411-422 651-662 (1102)
31 PF09421 FRQ: Frequency clock 41.0 19 0.00041 42.6 2.5 34 423-456 473-506 (989)
32 PRK12469 RNA polymerase factor 40.0 17 0.00038 39.7 2.0 62 393-455 122-186 (481)
33 KOG3973 Uncharacterized conser 38.3 1.3E+02 0.0027 32.6 7.8 9 218-226 384-392 (465)
34 KOG4301 Beta-dystrobrevin [Cyt 33.4 23 0.00049 37.9 1.5 58 398-457 142-216 (434)
35 PRK05932 RNA polymerase factor 32.4 30 0.00064 37.5 2.2 57 393-454 100-159 (455)
36 TIGR02395 rpoN_sigma RNA polym 30.3 18 0.00039 38.8 0.1 43 393-435 75-120 (429)
37 KOG1924 RhoA GTPase effector D 29.7 1E+02 0.0022 36.5 5.8 8 387-394 644-651 (1102)
38 KOG2253 U1 snRNP complex, subu 24.1 45 0.00099 38.0 1.9 24 414-437 52-75 (668)
39 cd05140 Barstar_AU1054-like Ba 23.9 64 0.0014 27.4 2.3 59 393-455 11-73 (86)
40 COG1508 RpoN DNA-directed RNA 20.9 70 0.0015 35.0 2.4 44 393-437 89-133 (444)
No 1
>cd08036 LARP_5 La RNA-binding domain of La-related protein 5. This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.94 E-value=1.7e-27 Score=195.02 Aligned_cols=62 Identities=23% Similarity=0.371 Sum_probs=60.0
Q ss_pred HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++.|++||||||||+||++|.||+++||+||||||++||+|||||+||+|+++|++|||+|+
T Consensus 1 ~e~i~kQvEyYFS~~NL~~D~fLr~~md~~g~Vpi~~ia~F~rik~Lt~D~~lI~~aL~~S~ 62 (75)
T cd08036 1 RELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLP 62 (75)
T ss_pred ChhhhcceeeeechhhccccHHHHHHhccCCCEehHHHhccHHHHHhcCCHHHHHHHHhhCC
Confidence 36899999999999999999999999999999999999999999999999999999999985
No 2
>cd08035 LARP_4 La RNA-binding domain of La-related protein 4. This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.93 E-value=3.2e-27 Score=193.51 Aligned_cols=62 Identities=27% Similarity=0.387 Sum_probs=60.1
Q ss_pred HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
+++|++||||||||+||++|.||+++|+.||||||++|++|||||+||+|+++|++||+.|+
T Consensus 1 ~e~i~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpi~~iasF~rik~lt~d~~~I~~AL~~S~ 62 (75)
T cd08035 1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSP 62 (75)
T ss_pred ChHHHhhHHhhcCHhhcccCHHHHHhhCcCCCEehHHHhccHHHHHhcCCHHHHHHHHHcCC
Confidence 37899999999999999999999999999999999999999999999999999999999985
No 3
>cd08038 LARP_2 La RNA-binding domain of La-related protein 2. This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.93 E-value=1.4e-26 Score=188.95 Aligned_cols=61 Identities=39% Similarity=0.608 Sum_probs=59.8
Q ss_pred HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|++||||||||+||++|.||+++|+.||||||++|++|||||+||.|+++|++||+.|+
T Consensus 2 e~I~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~ia~F~rmk~lt~d~~~I~~Al~~S~ 62 (73)
T cd08038 2 EYIKRQIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDST 62 (73)
T ss_pred hHHHhhHHhhcchhhhccCHHHHHHhCCCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCC
Confidence 6899999999999999999999999999999999999999999999999999999999985
No 4
>cd08037 LARP_1 La RNA-binding domain of La-related protein 1. This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.93 E-value=1.5e-26 Score=188.68 Aligned_cols=61 Identities=41% Similarity=0.635 Sum_probs=59.7
Q ss_pred HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|++||||||||+||++|.||+++|+.||||||++|++|||||+||.|+++|++||+.|+
T Consensus 2 ~~I~~QvEyYFSd~NL~~D~fLr~~md~dG~Vpi~~ia~F~rmk~Lt~d~~~I~~Al~~S~ 62 (73)
T cd08037 2 DYIKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSK 62 (73)
T ss_pred hHHHHHHHHhccHhhhccCHHHHHHhccCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCC
Confidence 6899999999999999999999999999999999999999999999999999999999985
No 5
>cd08034 LARP_1_2 La RNA-binding domain proteins similar to La-related proteins 1 and 2. This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.92 E-value=4.7e-26 Score=185.62 Aligned_cols=62 Identities=40% Similarity=0.614 Sum_probs=60.1
Q ss_pred HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
+++|++||||||||+||++|.||+++|+.||||||++|++|||||+||.|+++|++||+.|+
T Consensus 1 ~~~i~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~ 62 (73)
T cd08034 1 KEYIKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDST 62 (73)
T ss_pred ChHHHhhHHhhcCHhhhccCHHHHHHcCCCCCEeHHHHhccHHHHHHcCCHHHHHHHHHcCC
Confidence 36899999999999999999999999999999999999999999999999999999999985
No 6
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=99.92 E-value=9.5e-26 Score=187.46 Aligned_cols=65 Identities=28% Similarity=0.526 Sum_probs=62.6
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchHhHhhcC--CCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD--DQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md--~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
.+|+++|++||||||||+||++|.||+++|+ .||||||++|++|||||+||.|+++|++||+.|+
T Consensus 3 ~~l~~~I~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~ 69 (82)
T cd08032 3 KQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSS 69 (82)
T ss_pred HHHHHHHHHHHHhhcchhhcccCHHHHHHhcCCCCCCEeHHHHhcchHHHHHcCCHHHHHHHHhcCC
Confidence 5889999999999999999999999999996 7999999999999999999999999999999984
No 7
>cd08031 LARP_4_5_like La RNA-binding domain of proteins similar to La-related proteins 4 and 5. This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.92 E-value=6.9e-26 Score=185.42 Aligned_cols=61 Identities=33% Similarity=0.535 Sum_probs=59.6
Q ss_pred HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|++||||||||+||++|.||+++|+.||||+|++|++|||||+||.|+++|++||+.|+
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~m~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~ 62 (75)
T cd08031 2 ELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESP 62 (75)
T ss_pred hHHHHHHHHHcCHhhhccCHHHHHHhCCCCCEEHHHHhCchhHHHHcCCHHHHHHHHHhCC
Confidence 6899999999999999999999999999999999999999999999999999999999985
No 8
>cd08028 LARP_3 La RNA-binding domain of La-related protein 3. This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).
Probab=99.91 E-value=2.7e-25 Score=184.66 Aligned_cols=65 Identities=35% Similarity=0.641 Sum_probs=62.2
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchHhHhhcC-CCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md-~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|.++|++||||||||+||++|.||+++|+ .||||+|++|++|||||+||.|+++|++||+.|+
T Consensus 2 ~~l~~~I~~QvEfYFSd~NL~~D~fLr~~m~~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~ 67 (82)
T cd08028 2 DDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSK 67 (82)
T ss_pred hHHHHHHHHHHHhhcCHhhhccCHHHHHHHhccCCCEEhHHHhCChhHHHhcCCHHHHHHHHHhCC
Confidence 3689999999999999999999999999997 5999999999999999999999999999999985
No 9
>cd08033 LARP_6 La RNA-binding domain of La-related protein 6. This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.91 E-value=2.6e-25 Score=182.88 Aligned_cols=61 Identities=38% Similarity=0.644 Sum_probs=59.1
Q ss_pred HHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|++||||||||+||++|.||+++| +.||||||++|++|||||+||.|+++|++||+.|+
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~l~~d~~~I~~Al~~S~ 64 (77)
T cd08033 2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSS 64 (77)
T ss_pred hHHHhHHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhcchHHHHHcCCHHHHHHHHHhCC
Confidence 68999999999999999999999999 68999999999999999999999999999999985
No 10
>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function.
Probab=99.91 E-value=4e-25 Score=182.51 Aligned_cols=64 Identities=39% Similarity=0.664 Sum_probs=61.9
Q ss_pred HHHHHHHhhhhhhcCcCCcCcchHhHhhcCC-CCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 395 SLAAMLIHQIDYYFSDANLVKDEFLKSNMDD-QGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 395 ~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md~-dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
+++++|++||||||||+||++|.||+++|+. ||||||++|++|||||+|+.|+++|++||+.|.
T Consensus 2 ~~~~~i~~QvEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~ 66 (80)
T smart00715 2 ELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSP 66 (80)
T ss_pred hHHHHHHHHHHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCC
Confidence 6889999999999999999999999999987 999999999999999999999999999999984
No 11
>PF05383 La: La domain; InterPro: IPR006630 Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La. The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome []. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor []. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation []. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis []. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif []. Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [].; PDB: 1S29_A 1YTY_B 2VOO_B 1S7A_A 2VOP_A 2VON_B 1ZH5_B 2VOD_A 2CQK_A.
Probab=99.90 E-value=5.3e-25 Score=173.35 Aligned_cols=58 Identities=40% Similarity=0.736 Sum_probs=53.6
Q ss_pred HHhhhhhhcCcCCcCcchHhHhhcCC--CCcEehhhhccchhhhhcc-CCHHHHHHHhhhC
Q 012704 400 LIHQIDYYFSDANLVKDEFLKSNMDD--QGWVPITLIASFPRVSFYS-QISYFLITCSQFS 457 (458)
Q Consensus 400 I~kQIEYYFSDeNL~kD~FLrk~Md~--dGwVPIslIasFnRVK~LT-~Di~~Il~ALr~S 457 (458)
|++||||||||+||++|+||+++|+. ||||||++|++|||||+|+ .|+++|++||++|
T Consensus 1 I~~QvEfYFSd~NL~~D~fL~~~~~~~~~g~Vpi~~i~~F~r~k~l~~~~~~~I~~al~~S 61 (61)
T PF05383_consen 1 IKKQVEFYFSDENLPRDKFLRSQMDSNPDGWVPISTILSFNRMKALTNTDIELIVDALRDS 61 (61)
T ss_dssp HHHHHHHHTSHHHHCC-HHHHHHHCTTTTTBEEHHHHTTSHHHHHH--S-HHHHHHHHHTS
T ss_pred ChhHHHHhcCHHHhCcCHHHHHHHHhcCCCcEeHHHHHchHHHHHHhcCCHHHHHHHHHcC
Confidence 79999999999999999999999986 9999999999999999999 9999999999987
No 12
>cd07323 LAM LA motif RNA-binding domain. This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.90 E-value=2.3e-24 Score=175.83 Aligned_cols=61 Identities=44% Similarity=0.749 Sum_probs=59.4
Q ss_pred HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|++||||||||+||++|.||+++|+++|||||++|++|||||+|+.|.++|++||+.|.
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~g~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~s~ 62 (75)
T cd07323 2 EKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSS 62 (75)
T ss_pred hHHHhhhHhccCHhhhCcCHHHHHhcCCCCCEEHHHHhCchHHHHHcCCHHHHHHHHHhCC
Confidence 6899999999999999999999999999999999999999999999999999999999884
No 13
>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen. This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.89 E-value=3.6e-24 Score=175.60 Aligned_cols=60 Identities=35% Similarity=0.622 Sum_probs=57.1
Q ss_pred HHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|++||||||||+||++|.|||++| +.||||||++|++|||||+||.+ ++|++||+.|.
T Consensus 2 ~~I~~QvEfYFSd~NL~~D~fLr~~~~~~~~G~Vpl~~i~~F~rmk~l~~~-~~i~~Al~~S~ 63 (76)
T cd08029 2 EEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPL-EAVVEALRESE 63 (76)
T ss_pred hHHHhhHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhCchHHHHcCCH-HHHHHHHHhCC
Confidence 58999999999999999999999999 69999999999999999999965 99999999984
No 14
>cd08030 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen. This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=99.88 E-value=1.2e-23 Score=177.75 Aligned_cols=62 Identities=31% Similarity=0.516 Sum_probs=58.3
Q ss_pred HHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccC------------CHHHHHHHhhhCC
Q 012704 397 AAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQ------------ISYFLITCSQFSL 458 (458)
Q Consensus 397 ~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~------------Di~~Il~ALr~St 458 (458)
+++|++||||||||+||++|+||+++| +.||||+|++|++|||||+||. |+++|++||+.|+
T Consensus 2 ~~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~V~i~~i~~F~rmk~l~~~~~~~~~~~~~~~~~~I~~ALk~S~ 77 (90)
T cd08030 2 KEKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKAVAEALRTST 77 (90)
T ss_pred hHHHHHHHHcccchhhcccCHHHHHHhccCCCCCEehHHHhcChHHHHHhhcccccccccchhHHHHHHHHHccCC
Confidence 589999999999999999999999999 6899999999999999999985 3789999999985
No 15
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=99.73 E-value=1.6e-18 Score=178.43 Aligned_cols=65 Identities=37% Similarity=0.645 Sum_probs=62.4
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
++|..+|.+||||||||+||.+|.||.++| +.+|||+|++|++|||||+||.|+.+|.+|||+|.
T Consensus 138 edl~~kIv~QVEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~ 204 (484)
T KOG1855|consen 138 EDLAAKIVDQVEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSS 204 (484)
T ss_pred HHHHHHHHHHhheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcc
Confidence 588999999999999999999999999999 69999999999999999999999999999999883
No 16
>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=8e-16 Score=160.41 Aligned_cols=57 Identities=33% Similarity=0.578 Sum_probs=52.8
Q ss_pred HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
.+.|.+|||||||.|||++|.||+++| |+|.||++|+||+.|+.|+++|++|||+|.
T Consensus 301 ~~~~~~~ie~~FSeE~~~~d~~n~~k~-----~~l~~ia~F~r~ad~s~d~nli~~alr~s~ 357 (448)
T KOG2590|consen 301 IAFIQEPIEFYFSEENLQRDRFNREKF-----VPLRVIAKFKRVADLSSDINLILAALRNSL 357 (448)
T ss_pred ccccccccccccchHHHhhhhhhhccc-----chhhhhhhhhhhhhcccCHHHHHHHHhhhh
Confidence 367899999999999999999999876 669999999999999999999999999873
No 17
>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]
Probab=99.62 E-value=2.6e-16 Score=166.06 Aligned_cols=65 Identities=32% Similarity=0.552 Sum_probs=63.4
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhCC
Q 012704 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 458 (458)
Q Consensus 394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~St 458 (458)
.+|++.|++|||||||.+||..|+||+.+||+|-||||.+||.|++|++||+|+++|+|+||+|+
T Consensus 94 ~~~kq~lk~qlEy~fSreNlssD~YL~sQMDSDqyVPI~tva~~~~i~klttDvdLI~Evlresp 158 (684)
T KOG2591|consen 94 RDLKQLLKKQLEYYFSRENLSSDRYLISQMDSDQYVPINTVANFPEIMKLTTDVDLIVEVLRESP 158 (684)
T ss_pred hhHHHHHHHHHHHhhccccccchhhhhhhcccccccchhhhccchhhhhhccchHHHHHHHhcCC
Confidence 39999999999999999999999999999999999999999999999999999999999999985
No 18
>KOG4213 consensus RNA-binding protein La [RNA processing and modification]
Probab=99.54 E-value=3.2e-15 Score=140.61 Aligned_cols=64 Identities=36% Similarity=0.705 Sum_probs=61.2
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchHhHhhc--CCCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012704 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFS 457 (458)
Q Consensus 394 ~~L~~~I~kQIEYYFSDeNL~kD~FLrk~M--d~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S 457 (458)
+.|.++|++||||||+|.||.||.||+++| .++|||||.+++.|||+..|++|++.|++||++|
T Consensus 11 a~lE~kii~qleyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ks 76 (205)
T KOG4213|consen 11 AALEAKIIHQLEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKS 76 (205)
T ss_pred hHHHHhhhhhhhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhC
Confidence 477889999999999999999999999999 3899999999999999999999999999999987
No 19
>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]
Probab=99.18 E-value=6.5e-12 Score=129.40 Aligned_cols=60 Identities=28% Similarity=0.555 Sum_probs=57.0
Q ss_pred HHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012704 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFS 457 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S 457 (458)
..|++|||||||.+||+.|.|||++|+++||||+++|..|.|++.|..|.++|+.|||.+
T Consensus 272 ~a~k~QiEyYFseenl~~d~~lrkk~~kaGf~plsfi~kf~Rn~Sf~gd~nLilaa~ke~ 331 (438)
T COG5193 272 MAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEV 331 (438)
T ss_pred hhHHhhhHhhhhHHhhhhhhHHHhhhhhcccccHhhhhhhhhccccCCchhhhHHHHHHH
Confidence 567779999999999999999999999999999999999999999999999999999875
No 20
>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]
Probab=98.44 E-value=4.7e-08 Score=101.41 Aligned_cols=58 Identities=34% Similarity=0.574 Sum_probs=55.2
Q ss_pred HHhhhhhhcC-----cCCcCcchHhHhhcC----CCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012704 400 LIHQIDYYFS-----DANLVKDEFLKSNMD----DQGWVPITLIASFPRVSFYSQISYFLITCSQFS 457 (458)
Q Consensus 400 I~kQIEYYFS-----DeNL~kD~FLrk~Md----~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S 457 (458)
+..|+||||| |.|+.+|+||+.+-. .+|||+|..|++|+|||.++..++.|..|||+|
T Consensus 75 ~l~qvE~~fS~s~~~d~n~~~dk~~ktta~Kn~~~~kwVpIkt~~tfn~~k~~gs~~~~v~~a~rks 141 (438)
T COG5193 75 TLKQVEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKS 141 (438)
T ss_pred cccceeEEeeccccccccccchhhhccccccccCCCCceeeeeeeeeccccccCCchhhhhhhhhcC
Confidence 8999999999 999999999999863 599999999999999999999999999999988
No 21
>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]
Probab=90.28 E-value=0.054 Score=58.09 Aligned_cols=71 Identities=24% Similarity=0.190 Sum_probs=61.4
Q ss_pred CCCCCCcHHHHHHHHh--hhhhhcCcCCcCcchHhHhhcCCCC---cEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012704 387 VLMPVPEPSLAAMLIH--QIDYYFSDANLVKDEFLKSNMDDQG---WVPITLIASFPRVSFYSQISYFLITCSQFS 457 (458)
Q Consensus 387 ~~~P~~e~~L~~~I~k--QIEYYFSDeNL~kD~FLrk~Md~dG---wVPIslIasFnRVK~LT~Di~~Il~ALr~S 457 (458)
..++.+...|.+.+.. +++|||+-.++.+|.|+...++..| +.+|+.+..|.++..++++...+..+++.|
T Consensus 88 ~~~~~ps~~l~e~~~~~k~~s~~~~~~~~~~~~~~~~k~~~t~~~~~~~~S~~~~s~~~~~~s~n~~~~~~~~~~s 163 (448)
T KOG2590|consen 88 QVISVPSPPLKEYSKSDKKKSWPASKPFTPRDSFKGSKPTNTGNGTFLPISKISSSGPVSGGSANNSNIRGPLKGS 163 (448)
T ss_pred cccccccccccccccccccccCcccCCCCccccccCCCccccCCCccCCCccccccccccCcccccccccCcCCCC
Confidence 4455556667776666 9999999999999999999999888 999999999999999999998888887764
No 22
>KOG2278 consensus RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis]
Probab=84.51 E-value=0.8 Score=44.42 Aligned_cols=38 Identities=16% Similarity=0.171 Sum_probs=32.8
Q ss_pred HhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhh
Q 012704 418 FLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQ 455 (458)
Q Consensus 418 FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr 455 (458)
-++=+|+.||||+|+.|++.|+.|...-.+++|.++++
T Consensus 24 ~~~L~m~~dGfvpv~~lL~lnq~r~~~~t~ddi~riVk 61 (207)
T KOG2278|consen 24 ELRLNMRGDGFVPVEDLLNLNQFRGANHTIDDIRRIVK 61 (207)
T ss_pred HhcccccCCCceEHHHHhccchhcccCCcHHHHHHHHh
Confidence 35667899999999999999999998877888888775
No 23
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.
Probab=79.18 E-value=1.4 Score=42.07 Aligned_cols=35 Identities=17% Similarity=0.132 Sum_probs=23.3
Q ss_pred hcCCCCcEehhhhccchhhhhccCCHHHHHHHhhh
Q 012704 422 NMDDQGWVPITLIASFPRVSFYSQISYFLITCSQF 456 (458)
Q Consensus 422 ~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~ 456 (458)
.||+||||.|+.|+...+++.+..+.+.|.+.++.
T Consensus 26 ~~d~~G~v~v~dLL~~~~~~~~~~t~~~i~~vV~~ 60 (186)
T PF01885_consen 26 VMDPDGWVSVDDLLRALRFKGLWVTEEDIREVVET 60 (186)
T ss_dssp ---TT--EEHHHHHHHHHHT-TT--HHHHHHHHHH
T ss_pred ccCCCCCEeHHHHHHHHHHcCCCCCHHHHHHHHhh
Confidence 58999999999999999998877677777777764
No 24
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=76.91 E-value=15 Score=43.63 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.2
Q ss_pred CCCCCCCCCCc
Q 012704 260 SNWDARPVGGF 270 (458)
Q Consensus 260 ~~~~~~~~ggf 270 (458)
+++..-.+|||
T Consensus 1225 ~GyrGvsrgGf 1235 (1282)
T KOG0921|consen 1225 NGYRGVSRGGF 1235 (1282)
T ss_pred CCCccccCCcc
Confidence 34444445555
No 25
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=69.23 E-value=19 Score=38.65 Aligned_cols=47 Identities=28% Similarity=0.440 Sum_probs=27.3
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCceeEeCCCCccc
Q 012704 321 QPQRGPPRGF-VRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEA 369 (458)
Q Consensus 321 ~~q~~~pr~f-~RPppp~~~~f~~p~p~~pf~~p~~~~~~yy~p~~p~~~ 369 (458)
+||.+++.+| +||+..-++..|+++|+-.-+.|+. .-+|+|++..+.
T Consensus 280 qq~p~pp~~~ppRP~m~l~phl~gppPga~pPaph~--NpaffpPP~~~s 327 (498)
T KOG4849|consen 280 QQQPQPPMGQPPRPMMQLSPHLMGPPPGAGPPAPHN--NPAFFPPPQLGS 327 (498)
T ss_pred ccCCCCCCCCCCCcccccCcccCCCCCCCCCCCccc--CcccCCCCCcCc
Confidence 3455556667 7888777777888776543333222 125666655443
No 26
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=68.08 E-value=4.7 Score=38.52 Aligned_cols=56 Identities=14% Similarity=0.177 Sum_probs=32.9
Q ss_pred HHHHHhhhhhhcCcCCcCcchHhHhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhh
Q 012704 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQF 456 (458)
Q Consensus 397 ~~~I~kQIEYYFSDeNL~kD~FLrk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~ 456 (458)
..+|-|-|-|-+--. =.-+.=.||++|||+|+.|+...+.+....+.+.|.+.++.
T Consensus 6 ~~~lSK~LS~lLRH~----p~~~GL~ld~~G~v~v~~Ll~~~~~~~~~~t~~~l~~vV~~ 61 (179)
T PRK00819 6 LEKLSKFLSGVLRHK----PEAIGLTLDEEGWVDIDALIEALAKAYKWVTRELLEAVVES 61 (179)
T ss_pred HHHHHHHHHHHHCCC----HHHcCCccCCCCCEEHHHHHHHHHHccCCCCHHHHHHHHHc
Confidence 345666666553311 01112258999999999999876654322345666665543
No 27
>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]
Probab=50.93 E-value=81 Score=36.73 Aligned_cols=76 Identities=22% Similarity=0.285 Sum_probs=39.9
Q ss_pred CCCCCCCCCCCCCCC----CCCCCCCCCCCCCCCCC-CCceeEeCCCCccccccccCCCCCCCCCCCCCCCCCCcHHHHH
Q 012704 324 RGPPRGFVRPAPPNA----AAFAPPQPMRPFPNPMG-FPEFIYIPPMPVEAAALRGVTGMPPFIPPAPVLMPVPEPSLAA 398 (458)
Q Consensus 324 ~~~pr~f~RPppp~~----~~f~~p~p~~pf~~p~~-~~~~yy~p~~p~~~~~~~g~~~~~P~~~~~p~~~P~~e~~L~~ 398 (458)
.++-++|.|+=|+.. ..|-++-| .+...|.. |.+.+--|.+-+-. +++| ||. .
T Consensus 822 ~~gf~pg~rggpp~~g~gpg~~~g~~p-~~~~~P~~~~~~~~~~pGp~V~~--~~n~----Pf~---------------v 879 (944)
T KOG4307|consen 822 DGGFRPGFRGGPPGRGGGPGGFQGGSP-GDDSQPSQELMELIKSPGPRVLS--CNNF----PFD---------------V 879 (944)
T ss_pred cCCcCCccCCCCCCCCCCCCCCCCCCC-CCCCCChHHHHHhcCCCCCeEEE--ecCC----Ccc---------------c
Confidence 344566777544422 23433332 23334443 44445556554544 7887 773 3
Q ss_pred HHHhhhhhhcCcCCcCcchHhHhh
Q 012704 399 MLIHQIDYYFSDANLVKDEFLKSN 422 (458)
Q Consensus 399 ~I~kQIEYYFSDeNL~kD~FLrk~ 422 (458)
.|...||| |+|.-|..|.-.++.
T Consensus 880 ~l~dI~~F-F~dY~~~p~sI~~r~ 902 (944)
T KOG4307|consen 880 TLEDIVEF-FNDYEPDPNSIRIRR 902 (944)
T ss_pred cHHHHHHH-hcccccCCCceeEee
Confidence 44445564 678888877654443
No 28
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=47.76 E-value=7.3 Score=37.01 Aligned_cols=58 Identities=22% Similarity=0.229 Sum_probs=31.3
Q ss_pred CcHHHHHHHHhhhhhhcCcCC-cCcchHhHhhcCCCCcEe--hhhhccchhhhhccCCHHHHHHHh
Q 012704 392 PEPSLAAMLIHQIDYYFSDAN-LVKDEFLKSNMDDQGWVP--ITLIASFPRVSFYSQISYFLITCS 454 (458)
Q Consensus 392 ~e~~L~~~I~kQIEYYFSDeN-L~kD~FLrk~Md~dGwVP--IslIasFnRVK~LT~Di~~Il~AL 454 (458)
.++.|.+.|..||...+-++. ..-=.||...+|++||+. +..|+ +.+..+.+.|.+||
T Consensus 13 ~~~sL~e~L~~Ql~~~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia-----~~l~~~~~~v~~~l 73 (194)
T PF04963_consen 13 AEESLYEHLLEQLNLSPLSEEEREIAEYLIDNLDDDGYLTESLEEIA-----EELGVSEEEVEKAL 73 (194)
T ss_dssp ------HHHHHHHHHH---TCCHHHHHHHCCCBTTTSTCSS-HHHHH-----HHCTS-HHHHHHHH
T ss_pred cccCHHHHHHHHHcCcccCHHHHHHHHHHHHcCCCCCccCCCHHHHH-----HHhCCCHHHHHHHH
Confidence 355889999999998755443 333567778889999985 44554 22334444454444
No 29
>PTZ00315 2'-phosphotransferase; Provisional
Probab=46.62 E-value=16 Score=41.04 Aligned_cols=55 Identities=7% Similarity=-0.019 Sum_probs=35.5
Q ss_pred HHHHHhhhhhhcCcCCcCcchHh-HhhcCCCCcEehhhhccchhhhhccCCHHHHHHHhhh
Q 012704 397 AAMLIHQIDYYFSDANLVKDEFL-KSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQF 456 (458)
Q Consensus 397 ~~~I~kQIEYYFSDeNL~kD~FL-rk~Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~ 456 (458)
..+|-|-|-|-+- ..--- .=.||++|||.|+.|+.-.+.+....+.+.|.+.++.
T Consensus 378 ~~~lSK~LS~lLR-----H~pe~~GL~ld~~Gwv~vd~LL~~~~~~~~~~t~e~i~~VV~~ 433 (582)
T PTZ00315 378 LVTYSKFMSRLLR-----HKADQWRVPITSNGYVLLDDILRQPPMRNDPVSVQDVARVVRD 433 (582)
T ss_pred HHHHHHHHHHHHc-----CCHhhcCCCcCCCCCEEHHHHHHHHHhcCCCCCHHHHHHHHHc
Confidence 3466677765432 11100 0146899999999999988877654567777776654
No 30
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=43.32 E-value=61 Score=38.14 Aligned_cols=12 Identities=17% Similarity=0.321 Sum_probs=6.6
Q ss_pred CCcCcchHhHhh
Q 012704 411 ANLVKDEFLKSN 422 (458)
Q Consensus 411 eNL~kD~FLrk~ 422 (458)
+-|..|.+|-++
T Consensus 651 dk~en~dlfakL 662 (1102)
T KOG1924|consen 651 DKLENDDLFAKL 662 (1102)
T ss_pred hhccchHHHHHH
Confidence 345566665554
No 31
>PF09421 FRQ: Frequency clock protein; InterPro: IPR018554 The frequency clock protein, is the central component of the frq-based circadian negative feedback loop, regulates various aspects of the circadian clock in Neurospora crassa []. This protein has been shown to interact with itself via a coiled-coil [].
Probab=41.00 E-value=19 Score=42.61 Aligned_cols=34 Identities=18% Similarity=0.410 Sum_probs=31.0
Q ss_pred cCCCCcEehhhhccchhhhhccCCHHHHHHHhhh
Q 012704 423 MDDQGWVPITLIASFPRVSFYSQISYFLITCSQF 456 (458)
Q Consensus 423 Md~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~ 456 (458)
.|.+|||-|.|||+.-.|--|..+-++|..||.+
T Consensus 473 pDaeGWVYLNLL~NmAQLHiiNVTPdFVRsAV~E 506 (989)
T PF09421_consen 473 PDAEGWVYLNLLCNMAQLHIINVTPDFVRSAVSE 506 (989)
T ss_pred cccccceehHHHHHHHHHHhhccCHHHHHHHHHh
Confidence 3789999999999999999999999999999864
No 32
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=39.96 E-value=17 Score=39.67 Aligned_cols=62 Identities=18% Similarity=0.226 Sum_probs=41.1
Q ss_pred cHHHHHHHHhhhhhhcCcCCc-CcchHhHhhcCCCCcE--ehhhhccchhhhhccCCHHHHHHHhh
Q 012704 393 EPSLAAMLIHQIDYYFSDANL-VKDEFLKSNMDDQGWV--PITLIASFPRVSFYSQISYFLITCSQ 455 (458)
Q Consensus 393 e~~L~~~I~kQIEYYFSDeNL-~kD~FLrk~Md~dGwV--PIslIasFnRVK~LT~Di~~Il~ALr 455 (458)
+..|.+.|..||..++-+..- .-=.||...+|++||+ ++..|+.-.. +.|..+.+.|.+||+
T Consensus 122 ~~sL~~~L~~Ql~~~~~~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~~~-~~l~~~~~~ve~vL~ 186 (481)
T PRK12469 122 EPTLHEHLHDALRLYFLTERDREIARTIIDALDDDGYLRQDLSELAEAAD-PELGLSEQELEVALR 186 (481)
T ss_pred CCCHHHHHHHHHhccCCCHHHHHHHHHHHhhCCCCCCCCCCHHHHHhccc-cccCCCHHHHHHHHH
Confidence 347889999999988666543 2234899999999997 6777764321 223345555555553
No 33
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=38.27 E-value=1.3e+02 Score=32.62 Aligned_cols=9 Identities=22% Similarity=0.231 Sum_probs=4.7
Q ss_pred CCCCCCCCC
Q 012704 218 PTQPPPPPP 226 (458)
Q Consensus 218 ~~~p~p~~~ 226 (458)
+-+|+.+++
T Consensus 384 yqqp~~~~~ 392 (465)
T KOG3973|consen 384 YQQPQQQQQ 392 (465)
T ss_pred CcCchhhhh
Confidence 445555554
No 34
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=33.41 E-value=23 Score=37.88 Aligned_cols=58 Identities=14% Similarity=0.197 Sum_probs=46.3
Q ss_pred HHHHhhhhhhcCcCCc--------CcchHhHhhcC---------CCCcEehhhhccchhhhhccCCHHHHHHHhhhC
Q 012704 398 AMLIHQIDYYFSDANL--------VKDEFLKSNMD---------DQGWVPITLIASFPRVSFYSQISYFLITCSQFS 457 (458)
Q Consensus 398 ~~I~kQIEYYFSDeNL--------~kD~FLrk~Md---------~dGwVPIslIasFnRVK~LT~Di~~Il~ALr~S 457 (458)
.+|+.|+.|.||-.|= .+|.||++.+. .-||-.+..-.-|-|=|+.+ ++..+++|..+
T Consensus 142 gk~~dklryIfs~isds~gim~~i~~~~fl~evlslpT~v~e~psfg~te~~a~~cf~qqrKv~--Ln~fldtl~sd 216 (434)
T KOG4301|consen 142 GKIKDKLRYIFSLISDSRGIMQEIQRDQFLHEVLSLPTAVFEGPSFGYTELSARLCFLQQRKVE--LNQFLDTLMSD 216 (434)
T ss_pred chHHHHHHHHHHHHccchHHHHHHHHHHHHHHHHcCCchhhcCCCcchHHHHHHHHHHHHHHHH--HHHHHHHHhcC
Confidence 5889999999987763 47999999984 56888888888898888876 66777777654
No 35
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=32.41 E-value=30 Score=37.49 Aligned_cols=57 Identities=18% Similarity=0.170 Sum_probs=37.7
Q ss_pred cHHHHHHHHhhhhhhcCcCC-cCcchHhHhhcCCCCcE--ehhhhccchhhhhccCCHHHHHHHh
Q 012704 393 EPSLAAMLIHQIDYYFSDAN-LVKDEFLKSNMDDQGWV--PITLIASFPRVSFYSQISYFLITCS 454 (458)
Q Consensus 393 e~~L~~~I~kQIEYYFSDeN-L~kD~FLrk~Md~dGwV--PIslIasFnRVK~LT~Di~~Il~AL 454 (458)
+..|.+.|..||.+++-++. ..==.||...+|++||+ ++..|+.- |..+.+.|.+||
T Consensus 100 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~-----l~~~~~~v~~~l 159 (455)
T PRK05932 100 TESLQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTEDLEEIAES-----LGVELDEVEAVL 159 (455)
T ss_pred CCCHHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHH-----cCCCHHHHHHHH
Confidence 34788999999999854433 33356788888999998 56666432 223445555544
No 36
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=30.28 E-value=18 Score=38.80 Aligned_cols=43 Identities=23% Similarity=0.380 Sum_probs=32.1
Q ss_pred cHHHHHHHHhhhhhhcCc-CCcCcchHhHhhcCCCCcEe--hhhhc
Q 012704 393 EPSLAAMLIHQIDYYFSD-ANLVKDEFLKSNMDDQGWVP--ITLIA 435 (458)
Q Consensus 393 e~~L~~~I~kQIEYYFSD-eNL~kD~FLrk~Md~dGwVP--IslIa 435 (458)
+..|.+.|..||.+++-+ .-..==.||...+|++||+. +..|+
T Consensus 75 ~~sL~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~~~~eia 120 (429)
T TIGR02395 75 TESLFEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEIDLEEIA 120 (429)
T ss_pred CCCHHHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHH
Confidence 448889999999988443 44444568888999999985 56664
No 37
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=29.75 E-value=1e+02 Score=36.47 Aligned_cols=8 Identities=25% Similarity=0.243 Sum_probs=3.7
Q ss_pred CCCCCCcH
Q 012704 387 VLMPVPEP 394 (458)
Q Consensus 387 ~~~P~~e~ 394 (458)
.|+-+.|+
T Consensus 644 FWvkv~Ed 651 (1102)
T KOG1924|consen 644 FWVKVNED 651 (1102)
T ss_pred eeeecchh
Confidence 34444444
No 38
>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]
Probab=24.10 E-value=45 Score=38.01 Aligned_cols=24 Identities=38% Similarity=0.533 Sum_probs=11.9
Q ss_pred CcchHhHhhcCCCCcEehhhhccc
Q 012704 414 VKDEFLKSNMDDQGWVPITLIASF 437 (458)
Q Consensus 414 ~kD~FLrk~Md~dGwVPIslIasF 437 (458)
+-+.|+++.+..-|||++-.++.|
T Consensus 52 ~s~~~~~~il~~~g~v~s~kr~~f 75 (668)
T KOG2253|consen 52 VSQEFWKSILAKSGFVPSWKRDKF 75 (668)
T ss_pred hhHHHHHHHHhhCCcchhhhhhhh
Confidence 334455555555555554444443
No 39
>cd05140 Barstar_AU1054-like Barstar_AU1054-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor AU1054 found in Burkholderia cenocepacia. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=23.85 E-value=64 Score=27.42 Aligned_cols=59 Identities=15% Similarity=0.248 Sum_probs=36.3
Q ss_pred cHHHHHHHHhhhhh--hcCcCCcCcchHhHhhcCCCCcEehhhh-ccchhhhh-ccCCHHHHHHHhh
Q 012704 393 EPSLAAMLIHQIDY--YFSDANLVKDEFLKSNMDDQGWVPITLI-ASFPRVSF-YSQISYFLITCSQ 455 (458)
Q Consensus 393 e~~L~~~I~kQIEY--YFSDeNL~kD~FLrk~Md~dGwVPIslI-asFnRVK~-LT~Di~~Il~ALr 455 (458)
.+++.+.|+++++| ||+. || | =|...|....|.|..++ ..++..++ +-.++..|++|++
T Consensus 11 ~~~l~~~l~~~l~fP~~fG~-N~--D-Al~D~lt~~~~lP~~i~~~~~~~~~~~~~~~~~~l~e~l~ 73 (86)
T cd05140 11 ERELHELLKECLGFPGWYGC-NW--D-AFWDAITGLVSMPPVLRFVGWSQFKRRLPRDAELLKECLD 73 (86)
T ss_pred HHHHHHHHHHHcCCchhhcC-CH--H-HHHHHHcCCccCCCEEEEeChHHHHHHCHHHHHHHHHHHH
Confidence 45889999999998 7776 44 2 35666666666654332 33343433 3345666666665
No 40
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=20.93 E-value=70 Score=35.04 Aligned_cols=44 Identities=16% Similarity=0.333 Sum_probs=32.4
Q ss_pred cHHHHHHHHhhhhhhcCcCCcCc-chHhHhhcCCCCcEehhhhccc
Q 012704 393 EPSLAAMLIHQIDYYFSDANLVK-DEFLKSNMDDQGWVPITLIASF 437 (458)
Q Consensus 393 e~~L~~~I~kQIEYYFSDeNL~k-D~FLrk~Md~dGwVPIslIasF 437 (458)
...|.+.+..||...|..+.=.. =.||...+|++||+.++ +..+
T Consensus 89 ~~tL~e~L~~Ql~~~~~s~~e~~Ia~~lI~~Ldd~GYl~~~-le~~ 133 (444)
T COG1508 89 TKTLSEYLLEQLRLLPLSDTERAIATYLIDALDDEGYLTES-LEEI 133 (444)
T ss_pred ccCHHHHHHHHHhhcCCChHHHHHHHHHHhhcCcCCCcccC-HHHH
Confidence 34789999999999887664322 35677778999998777 4444
Done!