Query 013093
Match_columns 449
No_of_seqs 168 out of 580
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 00:20:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013093hhsearch_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 1.3E-27 2.8E-32 195.3 3.9 62 388-449 1-62 (75)
2 cd08035 LARP_4 La RNA-binding 99.9 2.5E-27 5.5E-32 193.7 4.5 62 388-449 1-62 (75)
3 cd08038 LARP_2 La RNA-binding 99.9 1.5E-26 3.2E-31 188.3 4.7 61 389-449 2-62 (73)
4 cd08037 LARP_1 La RNA-binding 99.9 1.6E-26 3.4E-31 188.1 4.6 61 389-449 2-62 (73)
5 cd08034 LARP_1_2 La RNA-bindin 99.9 5E-26 1.1E-30 185.1 4.5 62 388-449 1-62 (73)
6 cd08032 LARP_7 La RNA-binding 99.9 1.1E-25 2.3E-30 186.8 5.8 65 385-449 3-69 (82)
7 cd08031 LARP_4_5_like La RNA-b 99.9 7.8E-26 1.7E-30 184.7 4.6 61 389-449 2-62 (75)
8 cd08028 LARP_3 La RNA-binding 99.9 2.9E-25 6.4E-30 184.0 5.4 65 385-449 2-67 (82)
9 cd08033 LARP_6 La RNA-binding 99.9 2.7E-25 5.9E-30 182.3 4.9 61 389-449 2-64 (77)
10 smart00715 LA Domain in the RN 99.9 4.3E-25 9.4E-30 181.9 4.9 65 385-449 1-66 (80)
11 PF05383 La: La domain; Inter 99.9 6.2E-25 1.4E-29 172.6 3.5 58 391-448 1-61 (61)
12 cd07323 LAM LA motif RNA-bindi 99.9 2.3E-24 5.1E-29 175.3 4.7 61 389-449 2-62 (75)
13 cd08029 LA_like_fungal La-moti 99.9 3.9E-24 8.3E-29 175.0 4.5 60 389-449 2-63 (76)
14 cd08030 LA_like_plant La-motif 99.9 1.1E-23 2.3E-28 177.6 4.3 62 388-449 2-77 (90)
15 KOG2590 RNA-binding protein LA 99.7 3.8E-16 8.2E-21 162.5 22.4 57 388-449 301-357 (448)
16 KOG1855 Predicted RNA-binding 99.7 1.3E-18 2.9E-23 178.6 4.2 66 384-449 137-204 (484)
17 KOG2591 c-Mpl binding protein, 99.7 4.9E-17 1.1E-21 171.2 5.1 65 385-449 94-158 (684)
18 KOG4213 RNA-binding protein La 99.5 1.2E-14 2.7E-19 136.4 4.1 65 385-449 11-77 (205)
19 COG5193 LHP1 La protein, small 99.2 6.4E-12 1.4E-16 129.2 1.7 60 389-448 272-331 (438)
20 COG5193 LHP1 La protein, small 98.4 5.6E-08 1.2E-12 100.6 0.8 58 391-448 75-141 (438)
21 KOG2590 RNA-binding protein LA 90.8 0.045 9.7E-07 58.5 -1.5 71 378-448 88-163 (448)
22 KOG2278 RNA:NAD 2'-phosphotran 85.1 0.72 1.6E-05 44.6 2.8 38 409-446 24-61 (207)
23 PF01885 PTS_2-RNA: RNA 2'-pho 78.6 1.3 2.9E-05 42.0 2.1 35 413-447 26-60 (186)
24 KOG4849 mRNA cleavage factor I 77.4 75 0.0016 34.2 14.4 47 312-360 280-327 (498)
25 PRK00819 RNA 2'-phosphotransfe 68.4 4.4 9.6E-05 38.6 2.9 56 388-447 6-61 (179)
26 KOG0921 Dosage compensation co 56.4 73 0.0016 38.1 10.0 11 251-261 1225-1235(1282)
27 PF04963 Sigma54_CBD: Sigma-54 51.8 5.2 0.00011 37.9 0.2 57 384-445 14-73 (194)
28 PTZ00315 2'-phosphotransferase 46.4 16 0.00034 40.9 2.9 56 388-448 378-434 (582)
29 PRK12469 RNA polymerase factor 45.0 13 0.00029 40.5 2.0 62 384-446 122-186 (481)
30 PF09421 FRQ: Frequency clock 42.6 17 0.00036 42.9 2.4 34 414-447 473-506 (989)
31 KOG1924 RhoA GTPase effector D 41.6 67 0.0015 37.7 6.8 11 403-413 652-662 (1102)
32 KOG2253 U1 snRNP complex, subu 40.3 17 0.00037 41.1 2.0 28 404-431 51-78 (668)
33 KOG3973 Uncharacterized conser 36.8 1.4E+02 0.003 32.2 7.8 9 209-217 384-392 (465)
34 PRK05932 RNA polymerase factor 36.1 24 0.00052 38.1 2.2 57 384-445 100-159 (455)
35 KOG4301 Beta-dystrobrevin [Cyt 35.5 16 0.00035 38.9 0.8 58 389-448 142-216 (434)
36 TIGR02395 rpoN_sigma RNA polym 34.5 14 0.0003 39.5 0.2 57 384-445 75-134 (429)
37 KOG1924 RhoA GTPase effector D 28.4 92 0.002 36.7 5.2 8 378-385 644-651 (1102)
38 cd05140 Barstar_AU1054-like Ba 20.8 79 0.0017 26.8 2.3 59 384-446 11-73 (86)
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=1.3e-27 Score=195.30 Aligned_cols=62 Identities=23% Similarity=0.371 Sum_probs=60.1
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 388 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 388 ~~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++.|++||||||||+||++|.||+++||+||||||++||+|||||+||+|+++|++|||.|+
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=2.5e-27 Score=193.69 Aligned_cols=62 Identities=27% Similarity=0.387 Sum_probs=60.2
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 388 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 388 ~~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
+++|++||||||||+||++|.||+++||.||||||++|++|||||+||.|+++|++||+.|+
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=1.5e-26 Score=188.33 Aligned_cols=61 Identities=39% Similarity=0.608 Sum_probs=59.8
Q ss_pred HHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 389 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|++||||||||+||++|.||+++|+.||||||++|++|||||+|+.|+++|++||+.|+
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 7899999999999999999999999999999999999999999999999999999999985
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=1.6e-26 Score=188.15 Aligned_cols=61 Identities=41% Similarity=0.635 Sum_probs=59.8
Q ss_pred HHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 389 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|++||||||||+||++|.||+++|+.||||||++|++|||||+||.|+++|++||+.|+
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 6899999999999999999999999999999999999999999999999999999999995
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=5e-26 Score=185.08 Aligned_cols=62 Identities=40% Similarity=0.614 Sum_probs=60.1
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 388 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 388 ~~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
+++|++||||||||+||++|.||+++|+.||||||++|++|+|||+|+.|+++|++||+.|+
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=1.1e-25 Score=186.80 Aligned_cols=65 Identities=28% Similarity=0.526 Sum_probs=62.6
Q ss_pred HHHHHHHHhhhhhhcCCCCcCcchHHHhhhC--CCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 385 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD--DQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 385 ~~L~~~I~kQIEYYFSDeNL~kD~FLr~~Md--~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|+++|++||||||||+||++|.||+++|+ .||||||++|++|||||+||.|+++|++||+.|+
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 5789999999999999999999999999996 7999999999999999999999999999999985
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=7.8e-26 Score=184.69 Aligned_cols=61 Identities=33% Similarity=0.535 Sum_probs=59.6
Q ss_pred HHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 389 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|++||||||||+||++|.||+++|+.||||+|++|++|||||+||.|+++|++||+.|+
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=2.9e-25 Score=184.03 Aligned_cols=65 Identities=35% Similarity=0.641 Sum_probs=62.3
Q ss_pred HHHHHHHHhhhhhhcCCCCcCcchHHHhhhC-CCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 385 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 385 ~~L~~~I~kQIEYYFSDeNL~kD~FLr~~Md-~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|.++|++||||||||+||++|+||+++|+ +||||||++|++|||||+|+.|.++|++||+.|+
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 4689999999999999999999999999997 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=2.7e-25 Score=182.30 Aligned_cols=61 Identities=38% Similarity=0.644 Sum_probs=59.1
Q ss_pred HHHHhhhhhhcCCCCcCcchHHHhhh--CCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 389 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL~kD~FLr~~M--d~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|++||||||||+||++|.||+++| +.||||||++|++|||||+|+.|+++|++||+.|+
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 78999999999999999999999999999999985
No 10
>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function.
Probab=99.91 E-value=4.3e-25 Score=181.93 Aligned_cols=65 Identities=38% Similarity=0.652 Sum_probs=62.3
Q ss_pred HHHHHHHHhhhhhhcCCCCcCcchHHHhhhCC-CCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 385 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDD-QGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 385 ~~L~~~I~kQIEYYFSDeNL~kD~FLr~~Md~-dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
+++.++|++||||||||+||++|.||+++|+. ||||||++|++|+|||+|+.|+++|++||+.|.
T Consensus 1 ~~~~~~i~~QvEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~ 66 (80)
T smart00715 1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSP 66 (80)
T ss_pred ChHHHHHHHHHHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCC
Confidence 36889999999999999999999999999987 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=6.2e-25 Score=172.57 Aligned_cols=58 Identities=40% Similarity=0.736 Sum_probs=53.6
Q ss_pred HHhhhhhhcCCCCcCcchHHHhhhCC--CCcEehhhhccchhhhhcc-CCHHHHHHHhhcC
Q 013093 391 LIHQIDYYFSDANLVKDEFLKSNMDD--QGWVPITLIASFPRVSFYS-QISYFLITCSQFS 448 (449)
Q Consensus 391 I~kQIEYYFSDeNL~kD~FLr~~Md~--dG~VPI~lIasFnRVK~LT-~d~~~IleALr~S 448 (449)
|++||||||||+||++|+||+++|+. ||||||++|++|+|||+|+ .|+++|++|||+|
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 9999999999988
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=175.34 Aligned_cols=61 Identities=44% Similarity=0.749 Sum_probs=59.4
Q ss_pred HHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 389 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|++||||||||+||++|.||+++|++||||||++|++|+|||+|+.|.++|++||+.|.
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 6899999999999999999999999999999999999999999999999999999999984
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=3.9e-24 Score=175.01 Aligned_cols=60 Identities=35% Similarity=0.622 Sum_probs=57.2
Q ss_pred HHHHhhhhhhcCCCCcCcchHHHhhh--CCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 389 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL~kD~FLr~~M--d~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
++|++||||||||+||++|.||+++| +.||||||++|++|+|||+|+.+ ++|++||+.|.
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 69999999999999999999966 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=1.1e-23 Score=177.55 Aligned_cols=62 Identities=31% Similarity=0.516 Sum_probs=58.5
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHHhhh--CCCCcEehhhhccchhhhhccC------------CHHHHHHHhhcCC
Q 013093 388 AAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQ------------ISYFLITCSQFSL 449 (449)
Q Consensus 388 ~~~I~kQIEYYFSDeNL~kD~FLr~~M--d~dG~VPI~lIasFnRVK~LT~------------d~~~IleALr~St 449 (449)
+++|++||||||||+||++|+||+++| +.||||+|++|++|||||+|+. |+++|++||+.|+
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 689999999999999999999999999 7899999999999999999985 3789999999985
No 15
>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]
Probab=99.73 E-value=3.8e-16 Score=162.50 Aligned_cols=57 Identities=33% Similarity=0.578 Sum_probs=52.8
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 388 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 388 ~~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
.+.|.+|||||||.|||++|.||+++| |+|.||++|+||+.|+.|+++|++|||+|.
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 368899999999999999999999876 669999999999999999999999999873
No 16
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=99.73 E-value=1.3e-18 Score=178.61 Aligned_cols=66 Identities=36% Similarity=0.637 Sum_probs=63.0
Q ss_pred cHHHHHHHHhhhhhhcCCCCcCcchHHHhhh--CCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 384 EPSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 384 e~~L~~~I~kQIEYYFSDeNL~kD~FLr~~M--d~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
-++|..+|++||||||||+||.+|.||.++| +.+|||+|++|++|||||+||.|+.+|.+|||+|.
T Consensus 137 sedl~~kIv~QVEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~ 204 (484)
T KOG1855|consen 137 SEDLAAKIVDQVEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSS 204 (484)
T ss_pred cHHHHHHHHHHhheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcc
Confidence 3588999999999999999999999999999 68999999999999999999999999999999883
No 17
>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]
Probab=99.66 E-value=4.9e-17 Score=171.16 Aligned_cols=65 Identities=32% Similarity=0.552 Sum_probs=63.5
Q ss_pred HHHHHHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 385 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 385 ~~L~~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
.+|++.|++|||||||.|||..|.||+.+||+|.||||.+||+|++|++||+|+++|+|+||+|+
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=99.50 E-value=1.2e-14 Score=136.40 Aligned_cols=65 Identities=35% Similarity=0.683 Sum_probs=61.4
Q ss_pred HHHHHHHHhhhhhhcCCCCcCcchHHHhhh--CCCCcEehhhhccchhhhhccCCHHHHHHHhhcCC
Q 013093 385 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVSFYSQISYFLITCSQFSL 449 (449)
Q Consensus 385 ~~L~~~I~kQIEYYFSDeNL~kD~FLr~~M--d~dG~VPI~lIasFnRVK~LT~d~~~IleALr~St 449 (449)
+.|.++|.+||||||.|-||.||.||+++| ..+|||||.+++.|+|+..|++|++.|++||+.|.
T Consensus 11 a~lE~kii~qleyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ksk 77 (205)
T KOG4213|consen 11 AALEAKIIHQLEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKSK 77 (205)
T ss_pred hHHHHhhhhhhhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhCH
Confidence 467789999999999999999999999999 38999999999999999999999999999999883
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=99.17 E-value=6.4e-12 Score=129.16 Aligned_cols=60 Identities=28% Similarity=0.555 Sum_probs=57.1
Q ss_pred HHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcC
Q 013093 389 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFS 448 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~S 448 (449)
..|++|||||||.+||+.|.|||++|+++||||+.+|..|.|++.+..|.++|+.|||.+
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=98.42 E-value=5.6e-08 Score=100.65 Aligned_cols=58 Identities=34% Similarity=0.574 Sum_probs=55.3
Q ss_pred HHhhhhhhcC-----CCCcCcchHHHhhhC----CCCcEehhhhccchhhhhccCCHHHHHHHhhcC
Q 013093 391 LIHQIDYYFS-----DANLVKDEFLKSNMD----DQGWVPITLIASFPRVSFYSQISYFLITCSQFS 448 (449)
Q Consensus 391 I~kQIEYYFS-----DeNL~kD~FLr~~Md----~dG~VPI~lIasFnRVK~LT~d~~~IleALr~S 448 (449)
+..|+||||| |.|+.+|+||+..-. .+|||+|.+|++|+|||.++..++.|..||++|
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 9999999999 999999999999873 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=90.75 E-value=0.045 Score=58.53 Aligned_cols=71 Identities=24% Similarity=0.190 Sum_probs=62.4
Q ss_pred CCCCCCcHHHHHHHHh--hhhhhcCCCCcCcchHHHhhhCCCC---cEehhhhccchhhhhccCCHHHHHHHhhcC
Q 013093 378 VLMPVPEPSLAAMLIH--QIDYYFSDANLVKDEFLKSNMDDQG---WVPITLIASFPRVSFYSQISYFLITCSQFS 448 (449)
Q Consensus 378 ~~~P~~e~~L~~~I~k--QIEYYFSDeNL~kD~FLr~~Md~dG---~VPI~lIasFnRVK~LT~d~~~IleALr~S 448 (449)
..++.+...|.+.+.. +++|||+..++.+|.|++..++..| +.+|+.+..|.++..++++...+..+++.|
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 4555666677777766 9999999999999999999999888 999999999999999999999988887764
No 22
>KOG2278 consensus RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis]
Probab=85.09 E-value=0.72 Score=44.62 Aligned_cols=38 Identities=16% Similarity=0.171 Sum_probs=33.1
Q ss_pred HHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhh
Q 013093 409 FLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQ 446 (449)
Q Consensus 409 FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr 446 (449)
-++=+|+.||||+|+.|++.|+.|...-.+++|.++++
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=78.60 E-value=1.3 Score=42.02 Aligned_cols=35 Identities=17% Similarity=0.132 Sum_probs=23.7
Q ss_pred hhCCCCcEehhhhccchhhhhccCCHHHHHHHhhc
Q 013093 413 NMDDQGWVPITLIASFPRVSFYSQISYFLITCSQF 447 (449)
Q Consensus 413 ~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~ 447 (449)
.||.||||.|+.|+...+++.+..+.+.|.++++.
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 58999999999999999998877778888877764
No 24
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=77.44 E-value=75 Score=34.21 Aligned_cols=47 Identities=28% Similarity=0.440 Sum_probs=27.5
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCceeeeCCCCccc
Q 013093 312 QPQRGPPRGF-VRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMPVEA 360 (449)
Q Consensus 312 ~~q~~~pr~f-~RPppp~~~~f~~p~p~~pf~~P~~~~~~yy~p~~p~~~ 360 (449)
+||.+++.+| +||+...++..|+++|+-.-+.|+. .-+|+|++..+.
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 4555556677 8888888878888776543333222 125666555333
No 25
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=68.37 E-value=4.4 Score=38.63 Aligned_cols=56 Identities=14% Similarity=0.177 Sum_probs=33.6
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHHhhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhc
Q 013093 388 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQF 447 (449)
Q Consensus 388 ~~~I~kQIEYYFSDeNL~kD~FLr~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~ 447 (449)
..+|-|-|-|-+--. =.-+.=.||.+|||+|+.|+...+.+....+.+.|.+.++.
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 01112268999999999999876654333456677666654
No 26
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=56.44 E-value=73 Score=38.14 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.2
Q ss_pred CCCCCCCCCCc
Q 013093 251 SNWDARPVGGF 261 (449)
Q Consensus 251 ~~~~~~~~~gf 261 (449)
+++..-.+|||
T Consensus 1225 ~GyrGvsrgGf 1235 (1282)
T KOG0921|consen 1225 NGYRGVSRGGF 1235 (1282)
T ss_pred CCCccccCCcc
Confidence 34444445555
No 27
>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=51.82 E-value=5.2 Score=37.89 Aligned_cols=57 Identities=23% Similarity=0.232 Sum_probs=31.2
Q ss_pred cHHHHHHHHhhhhhhcCCCC-cCcchHHHhhhCCCCcEe--hhhhccchhhhhccCCHHHHHHHh
Q 013093 384 EPSLAAMLIHQIDYYFSDAN-LVKDEFLKSNMDDQGWVP--ITLIASFPRVSFYSQISYFLITCS 445 (449)
Q Consensus 384 e~~L~~~I~kQIEYYFSDeN-L~kD~FLr~~Md~dG~VP--I~lIasFnRVK~LT~d~~~IleAL 445 (449)
++.|.+.|..||...+-++. ..-=.||...+|++||+. +..|+ +.+..+.+.|.+||
T Consensus 14 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia-----~~l~~~~~~v~~~l 73 (194)
T PF04963_consen 14 EESLYEHLLEQLNLSPLSEEEREIAEYLIDNLDDDGYLTESLEEIA-----EELGVSEEEVEKAL 73 (194)
T ss_dssp -----HHHHHHHHHH---TCCHHHHHHHCCCBTTTSTCSS-HHHHH-----HHCTS-HHHHHHHH
T ss_pred ccCHHHHHHHHHcCcccCHHHHHHHHHHHHcCCCCCccCCCHHHHH-----HHhCCCHHHHHHHH
Confidence 55889999999998754433 333567777789999985 44553 23334445554444
No 28
>PTZ00315 2'-phosphotransferase; Provisional
Probab=46.40 E-value=16 Score=40.91 Aligned_cols=56 Identities=9% Similarity=-0.042 Sum_probs=36.7
Q ss_pred HHHHHhhhhhhcCCCCcCcchHHH-hhhCCCCcEehhhhccchhhhhccCCHHHHHHHhhcC
Q 013093 388 AAMLIHQIDYYFSDANLVKDEFLK-SNMDDQGWVPITLIASFPRVSFYSQISYFLITCSQFS 448 (449)
Q Consensus 388 ~~~I~kQIEYYFSDeNL~kD~FLr-~~Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~S 448 (449)
..+|-|-|-|-+- ..---. =.||.+|||.|+.|+.-.+.+....+.+.|.+.++..
T Consensus 378 ~~~lSK~LS~lLR-----H~pe~~GL~ld~~Gwv~vd~LL~~~~~~~~~~t~e~i~~VV~~n 434 (582)
T PTZ00315 378 LVTYSKFMSRLLR-----HKADQWRVPITSNGYVLLDDILRQPPMRNDPVSVQDVARVVRDS 434 (582)
T ss_pred HHHHHHHHHHHHc-----CCHhhcCCCcCCCCCEEHHHHHHHHHhcCCCCCHHHHHHHHHcC
Confidence 3466777765422 111000 1468999999999999888776555677887777653
No 29
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=44.98 E-value=13 Score=40.49 Aligned_cols=62 Identities=18% Similarity=0.226 Sum_probs=41.1
Q ss_pred cHHHHHHHHhhhhhhcCCCCc-CcchHHHhhhCCCCcE--ehhhhccchhhhhccCCHHHHHHHhh
Q 013093 384 EPSLAAMLIHQIDYYFSDANL-VKDEFLKSNMDDQGWV--PITLIASFPRVSFYSQISYFLITCSQ 446 (449)
Q Consensus 384 e~~L~~~I~kQIEYYFSDeNL-~kD~FLr~~Md~dG~V--PI~lIasFnRVK~LT~d~~~IleALr 446 (449)
.+.|.+.|..||..++-++.- .-=.||...+|++||+ ++..|+.-.. +.|..+.+.|.+||+
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 6777764322 223445555555553
No 30
>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=42.60 E-value=17 Score=42.90 Aligned_cols=34 Identities=18% Similarity=0.410 Sum_probs=31.3
Q ss_pred hCCCCcEehhhhccchhhhhccCCHHHHHHHhhc
Q 013093 414 MDDQGWVPITLIASFPRVSFYSQISYFLITCSQF 447 (449)
Q Consensus 414 Md~dG~VPI~lIasFnRVK~LT~d~~~IleALr~ 447 (449)
.|.+|||-|.|||+.-.|--|..+.++|..||.+
T Consensus 473 pDaeGWVYLNLL~NmAQLHiiNVTPdFVRsAV~E 506 (989)
T PF09421_consen 473 PDAEGWVYLNLLCNMAQLHIINVTPDFVRSAVSE 506 (989)
T ss_pred cccccceehHHHHHHHHHHhhccCHHHHHHHHHh
Confidence 4799999999999999999999999999999863
No 31
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=41.55 E-value=67 Score=37.74 Aligned_cols=11 Identities=18% Similarity=0.359 Sum_probs=6.2
Q ss_pred CcCcchHHHhh
Q 013093 403 NLVKDEFLKSN 413 (449)
Q Consensus 403 NL~kD~FLr~~ 413 (449)
-|..|.+|-++
T Consensus 652 k~en~dlfakL 662 (1102)
T KOG1924|consen 652 KLENDDLFAKL 662 (1102)
T ss_pred hccchHHHHHH
Confidence 45566666554
No 32
>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]
Probab=40.28 E-value=17 Score=41.11 Aligned_cols=28 Identities=36% Similarity=0.447 Sum_probs=18.7
Q ss_pred cCcchHHHhhhCCCCcEehhhhccchhh
Q 013093 404 LVKDEFLKSNMDDQGWVPITLIASFPRV 431 (449)
Q Consensus 404 L~kD~FLr~~Md~dG~VPI~lIasFnRV 431 (449)
++-+.|+++.+..-|||++..++.|-.+
T Consensus 51 ~~s~~~~~~il~~~g~v~s~kr~~fgf~ 78 (668)
T KOG2253|consen 51 LVSQEFWKSILAKSGFVPSWKRDKFGFC 78 (668)
T ss_pred hhhHHHHHHHHhhCCcchhhhhhhhccc
Confidence 4556677777777777777766665443
No 33
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=36.78 E-value=1.4e+02 Score=32.25 Aligned_cols=9 Identities=22% Similarity=0.231 Sum_probs=4.6
Q ss_pred CCCCCCCCC
Q 013093 209 PTQPPPPPP 217 (449)
Q Consensus 209 ~~~p~p~~~ 217 (449)
+-+|+.+++
T Consensus 384 yqqp~~~~~ 392 (465)
T KOG3973|consen 384 YQQPQQQQQ 392 (465)
T ss_pred CcCchhhhh
Confidence 445555554
No 34
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=36.08 E-value=24 Score=38.09 Aligned_cols=57 Identities=18% Similarity=0.183 Sum_probs=37.6
Q ss_pred cHHHHHHHHhhhhhhcCC-CCcCcchHHHhhhCCCCcE--ehhhhccchhhhhccCCHHHHHHHh
Q 013093 384 EPSLAAMLIHQIDYYFSD-ANLVKDEFLKSNMDDQGWV--PITLIASFPRVSFYSQISYFLITCS 445 (449)
Q Consensus 384 e~~L~~~I~kQIEYYFSD-eNL~kD~FLr~~Md~dG~V--PI~lIasFnRVK~LT~d~~~IleAL 445 (449)
+..|.+.|..||.+++-+ .-..==.||...+|++||+ ++..|+.- |..+.+.|.+||
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 447889999999987443 3333446788888999998 55666432 223455555554
No 35
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=35.53 E-value=16 Score=38.87 Aligned_cols=58 Identities=14% Similarity=0.197 Sum_probs=46.2
Q ss_pred HHHHhhhhhhcCCCCc--------CcchHHHhhhC---------CCCcEehhhhccchhhhhccCCHHHHHHHhhcC
Q 013093 389 AMLIHQIDYYFSDANL--------VKDEFLKSNMD---------DQGWVPITLIASFPRVSFYSQISYFLITCSQFS 448 (449)
Q Consensus 389 ~~I~kQIEYYFSDeNL--------~kD~FLr~~Md---------~dG~VPI~lIasFnRVK~LT~d~~~IleALr~S 448 (449)
.||+.|+.|.||-.|= .+|.||++++. .-||-.+..=.-|.|=|+.+ ++..+++|..+
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 5899999999987764 47999999984 56888888888888887765 67777777654
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=34.54 E-value=14 Score=39.53 Aligned_cols=57 Identities=19% Similarity=0.265 Sum_probs=38.0
Q ss_pred cHHHHHHHHhhhhhh-cCCCCcCcchHHHhhhCCCCcEe--hhhhccchhhhhccCCHHHHHHHh
Q 013093 384 EPSLAAMLIHQIDYY-FSDANLVKDEFLKSNMDDQGWVP--ITLIASFPRVSFYSQISYFLITCS 445 (449)
Q Consensus 384 e~~L~~~I~kQIEYY-FSDeNL~kD~FLr~~Md~dG~VP--I~lIasFnRVK~LT~d~~~IleAL 445 (449)
...|.+.|..||.++ |++.-..==.||...+|++||+. +..|+.- |..+.+.|.+||
T Consensus 75 ~~sL~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~-----l~~~~~~ve~~l 134 (429)
T TIGR02395 75 TESLFEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEIDLEEIADE-----LEVSEEEVEKVL 134 (429)
T ss_pred CCCHHHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHH-----cCCCHHHHHHHH
Confidence 447889999999987 44344444568888999999985 5666432 223455555444
No 37
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=28.38 E-value=92 Score=36.70 Aligned_cols=8 Identities=25% Similarity=0.243 Sum_probs=3.6
Q ss_pred CCCCCCcH
Q 013093 378 VLMPVPEP 385 (449)
Q Consensus 378 ~~~P~~e~ 385 (449)
.|+-+.|+
T Consensus 644 FWvkv~Ed 651 (1102)
T KOG1924|consen 644 FWVKVNED 651 (1102)
T ss_pred eeeecchh
Confidence 34444444
No 38
>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=20.76 E-value=79 Score=26.77 Aligned_cols=59 Identities=15% Similarity=0.248 Sum_probs=36.0
Q ss_pred cHHHHHHHHhhhhh--hcCCCCcCcchHHHhhhCCCCcEehhhh-ccchhhhh-ccCCHHHHHHHhh
Q 013093 384 EPSLAAMLIHQIDY--YFSDANLVKDEFLKSNMDDQGWVPITLI-ASFPRVSF-YSQISYFLITCSQ 446 (449)
Q Consensus 384 e~~L~~~I~kQIEY--YFSDeNL~kD~FLr~~Md~dG~VPI~lI-asFnRVK~-LT~d~~~IleALr 446 (449)
.+++.+.|+++++| ||.. || | =|..-|....|.|..++ ..++..++ +-.++..|++|++
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 3 35555655566554332 33343433 3355666777665
Done!