Query 012097
Match_columns 471
No_of_seqs 190 out of 620
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 08:36:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012097.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012097hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd08037 LARP_1 La RNA-binding 100.0 8.5E-31 1.8E-35 214.2 5.1 72 398-469 2-73 (73)
2 cd08038 LARP_2 La RNA-binding 100.0 1.4E-30 3E-35 213.0 5.3 72 398-469 2-73 (73)
3 cd08036 LARP_5 La RNA-binding 100.0 1.1E-30 2.3E-35 214.5 4.2 71 398-468 2-72 (75)
4 cd08035 LARP_4 La RNA-binding 100.0 2E-30 4.3E-35 213.1 5.2 71 397-467 1-71 (75)
5 cd08034 LARP_1_2 La RNA-bindin 100.0 5.6E-30 1.2E-34 209.3 5.2 73 397-469 1-73 (73)
6 cd08031 LARP_4_5_like La RNA-b 100.0 4.4E-29 9.6E-34 204.9 5.2 71 398-468 2-72 (75)
7 cd08032 LARP_7 La RNA-binding 100.0 8.4E-29 1.8E-33 206.4 6.4 74 394-467 3-78 (82)
8 cd08033 LARP_6 La RNA-binding 99.9 2E-28 4.3E-33 201.9 5.6 70 398-467 2-73 (77)
9 smart00715 LA Domain in the RN 99.9 3.3E-28 7.1E-33 201.6 5.6 74 394-467 1-75 (80)
10 cd08028 LARP_3 La RNA-binding 99.9 4.4E-28 9.6E-33 201.9 5.9 75 394-468 2-79 (82)
11 cd08029 LA_like_fungal La-moti 99.9 2.4E-27 5.3E-32 194.9 5.0 69 398-467 2-72 (76)
12 cd07323 LAM LA motif RNA-bindi 99.9 5.1E-27 1.1E-31 192.0 5.5 70 398-467 2-71 (75)
13 cd08030 LA_like_plant La-motif 99.9 4.9E-27 1.1E-31 198.8 4.9 72 397-468 2-87 (90)
14 PF05383 La: La domain; Inter 99.9 1.7E-24 3.6E-29 171.1 3.2 58 400-457 1-61 (61)
15 KOG1855 Predicted RNA-binding 99.8 6.3E-21 1.4E-25 196.6 4.8 75 393-467 137-213 (484)
16 KOG2590 RNA-binding protein LA 99.8 1.2E-17 2.6E-22 174.5 22.6 68 397-469 301-368 (448)
17 KOG2591 c-Mpl binding protein, 99.7 7.1E-19 1.5E-23 185.8 5.8 75 394-468 94-168 (684)
18 KOG4213 RNA-binding protein La 99.6 2.5E-16 5.5E-21 148.3 3.1 74 394-467 11-88 (205)
19 COG5193 LHP1 La protein, small 99.2 5.5E-12 1.2E-16 130.3 1.4 60 398-457 272-331 (438)
20 COG5193 LHP1 La protein, small 98.7 5.7E-09 1.2E-13 108.4 1.8 68 400-467 75-154 (438)
21 KOG2590 RNA-binding protein LA 93.7 0.012 2.5E-07 63.3 -1.5 81 389-469 90-175 (448)
22 PF01885 PTS_2-RNA: RNA 2'-pho 91.3 0.18 3.9E-06 48.2 3.2 48 422-469 26-80 (186)
23 PRK00819 RNA 2'-phosphotransfe 91.1 0.24 5.2E-06 47.3 3.9 49 422-470 27-77 (179)
24 PF09421 FRQ: Frequency clock 89.5 0.33 7.1E-06 56.6 3.9 46 423-468 473-521 (989)
25 KOG2278 RNA:NAD 2'-phosphotran 86.2 0.66 1.4E-05 45.1 3.1 40 419-458 25-64 (207)
26 KOG0921 Dosage compensation co 77.5 14 0.0003 44.0 9.8 11 260-270 1225-1235(1282)
27 KOG4849 mRNA cleavage factor I 76.4 80 0.0017 34.2 14.3 44 321-366 280-324 (498)
28 PTZ00315 2'-phosphotransferase 68.3 5.6 0.00012 44.6 4.0 42 422-463 399-442 (582)
29 COG1859 KptA RNA:NAD 2'-phosph 65.4 5.8 0.00013 39.4 3.1 48 422-469 53-102 (211)
30 PF04963 Sigma54_CBD: Sigma-54 50.9 7 0.00015 37.3 0.9 58 393-455 14-74 (194)
31 KOG2253 U1 snRNP complex, subu 49.5 7.6 0.00016 44.0 1.0 53 413-467 51-103 (668)
32 KOG3973 Uncharacterized conser 38.4 1.2E+02 0.0027 32.8 7.8 9 218-226 384-392 (465)
33 PRK12469 RNA polymerase factor 37.9 14 0.0003 40.6 0.8 62 394-456 123-187 (481)
34 PF05204 Hom_end: Homing endon 32.8 3.2 6.9E-05 36.9 -4.1 28 405-432 4-31 (110)
35 PRK05932 RNA polymerase factor 31.1 22 0.00047 38.6 1.0 59 393-456 100-161 (455)
36 TIGR02395 rpoN_sigma RNA polym 29.1 19 0.00042 38.7 0.2 59 393-456 75-136 (429)
37 KOG4301 Beta-dystrobrevin [Cyt 26.2 29 0.00063 37.2 0.8 60 397-458 141-217 (434)
38 KOG1924 RhoA GTPase effector D 24.8 3.8E+02 0.0083 32.2 9.2 9 459-467 722-730 (1102)
39 PF11641 Antigen_Bd37: Glycosy 21.5 76 0.0017 31.7 2.6 51 394-455 5-59 (224)
No 1
>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=99.96 E-value=8.5e-31 Score=214.23 Aligned_cols=72 Identities=46% Similarity=0.764 Sum_probs=70.8
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcccc
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLFID 469 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDkiR~ 469 (471)
++|++||||||||+||++|.|||++|+.||||||++|++|||||+||.|+++|++||+.|++|||++|+||+
T Consensus 2 ~~I~~QvEyYFSd~NL~~D~fLr~~md~dG~Vpi~~ia~F~rmk~Lt~d~~~I~~Al~~S~~vev~~~~~r~ 73 (73)
T cd08037 2 DYIKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEIIDMKIRR 73 (73)
T ss_pred hHHHHHHHHhccHhhhccCHHHHHHhccCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEecchhcC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999995
No 2
>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=99.96 E-value=1.4e-30 Score=212.99 Aligned_cols=72 Identities=47% Similarity=0.743 Sum_probs=70.8
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcccc
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLFID 469 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDkiR~ 469 (471)
++|++||||||||+||++|.|||++|+.||||||++|++|||||+|+.|+++|++||+.|+.|||++|+||+
T Consensus 2 e~I~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~ia~F~rmk~lt~d~~~I~~Al~~S~~ve~~~~~~r~ 73 (73)
T cd08038 2 EYIKRQIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVDQKIRR 73 (73)
T ss_pred hHHHhhHHhhcchhhhccCHHHHHHhCCCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEeCCcccC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999995
No 3
>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=99.96 E-value=1.1e-30 Score=214.47 Aligned_cols=71 Identities=31% Similarity=0.544 Sum_probs=68.6
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCccc
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLFI 468 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDkiR 468 (471)
+.|++||||||||+||++|+|||++||.||||||++|++|||||+||.|+++|++||+.|++|||++|+.+
T Consensus 2 e~i~kQvEyYFS~~NL~~D~fLr~~md~~g~Vpi~~ia~F~rik~Lt~D~~lI~~aL~~S~~vevse~g~k 72 (75)
T cd08036 2 ELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEK 72 (75)
T ss_pred hhhhcceeeeechhhccccHHHHHHhccCCCEehHHHhccHHHHHhcCCHHHHHHHHhhCCeEEECCCCCc
Confidence 68999999999999999999999999999999999999999999999999999999999999999888753
No 4
>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=99.96 E-value=2e-30 Score=213.07 Aligned_cols=71 Identities=39% Similarity=0.583 Sum_probs=68.8
Q ss_pred HHHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 397 ~~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
+++|++||||||||+||++|.||+++||.||||||++|++|||||+||.|+++|++||+.|++|||+||+.
T Consensus 1 ~e~i~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpi~~iasF~rik~lt~d~~~I~~AL~~S~~levsedg~ 71 (75)
T cd08035 1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGE 71 (75)
T ss_pred ChHHHhhHHhhcCHhhcccCHHHHHhhCcCCCEehHHHhccHHHHHhcCCHHHHHHHHHcCCeEEEcCCCC
Confidence 36899999999999999999999999999999999999999999999999999999999999999998876
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=99.96 E-value=5.6e-30 Score=209.27 Aligned_cols=73 Identities=48% Similarity=0.733 Sum_probs=71.0
Q ss_pred HHHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcccc
Q 012097 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLFID 469 (471)
Q Consensus 397 ~~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDkiR~ 469 (471)
+++|++||||||||+||+||.||+++|+.+|||||++|++|+|||+|+.|.++|++||+.|+.|||++|+||+
T Consensus 1 ~~~i~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~lev~e~kvR~ 73 (73)
T cd08034 1 KEYIKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELVDEKVRC 73 (73)
T ss_pred ChHHHhhHHhhcCHhhhccCHHHHHHcCCCCCEeHHHHhccHHHHHHcCCHHHHHHHHHcCCeEEEecCeecC
Confidence 3689999999999999999999999999999999999999999999999999999999999999999999985
No 6
>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=99.95 E-value=4.4e-29 Score=204.87 Aligned_cols=71 Identities=42% Similarity=0.670 Sum_probs=69.2
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCccc
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLFI 468 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDkiR 468 (471)
++|++||||||||+||+||+||+++|+.||||+|++|++|||||+||.|.++|++||+.|+.|||++|+.|
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~m~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~ 72 (75)
T cd08031 2 ELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEK 72 (75)
T ss_pred hHHHHHHHHHcCHhhhccCHHHHHHhCCCCCEEHHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999875
No 7
>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=99.95 E-value=8.4e-29 Score=206.37 Aligned_cols=74 Identities=36% Similarity=0.631 Sum_probs=71.4
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchhhhhccC--CCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD--DQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 394 ~~L~~~I~kQIEYYFSD~NL~kD~FLR~~Md--~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
.+|+++|++||||||||+||++|+||+++|+ .||||||++|++|||||+||.|+++|++||+.|++|||++|+.
T Consensus 3 ~~l~~~I~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~ 78 (82)
T cd08032 3 KQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGT 78 (82)
T ss_pred HHHHHHHHHHHHhhcchhhcccCHHHHHHhcCCCCCCEeHHHHhcchHHHHHcCCHHHHHHHHhcCCEEEEcCCCC
Confidence 4789999999999999999999999999996 7999999999999999999999999999999999999999876
No 8
>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=99.95 E-value=2e-28 Score=201.91 Aligned_cols=70 Identities=41% Similarity=0.699 Sum_probs=67.9
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhcc--CCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~M--d~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
++|++||||||||+||++|+||+++| +.||||||++|++|||||+|+.|.++|++||+.|+.|||++|+.
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~l~~d~~~I~~Al~~S~~lev~~d~~ 73 (77)
T cd08033 2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGK 73 (77)
T ss_pred hHHHhHHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhcchHHHHHcCCHHHHHHHHHhCCeEEEcCCCC
Confidence 68999999999999999999999999 78999999999999999999999999999999999999999865
No 9
>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function.
Probab=99.95 E-value=3.3e-28 Score=201.56 Aligned_cols=74 Identities=46% Similarity=0.793 Sum_probs=71.5
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchhhhhccCC-CccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDD-QGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 394 ~~L~~~I~kQIEYYFSD~NL~kD~FLR~~Md~-dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
++++++|++||||||||+||+||.|||++|+. +|||||++|++|+|||+|+.|.++|++||+.|..|||++|+.
T Consensus 1 ~~~~~~i~~QvEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~~lel~~d~~ 75 (80)
T smart00715 1 EELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGL 75 (80)
T ss_pred ChHHHHHHHHHHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCC
Confidence 36889999999999999999999999999987 999999999999999999999999999999999999999986
No 10
>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=99.94 E-value=4.4e-28 Score=201.94 Aligned_cols=75 Identities=39% Similarity=0.729 Sum_probs=71.6
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchhhhhccC-CCccEehhhhccchhhhhhccCHHHHHHHHhcCC--cEEEcCCccc
Q 012097 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMD-DQGWVPITLIASFPRVKNLTSNIQLILDSLRTST--VVEVQSYLFI 468 (471)
Q Consensus 394 ~~L~~~I~kQIEYYFSD~NL~kD~FLR~~Md-~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~--~LEVseDkiR 468 (471)
++|..+|++||||||||+||++|+|||++|+ +||||||++|++|||||+|+.|.++|++||+.|+ +|||++|+.+
T Consensus 2 ~~l~~~I~~QvEfYFSd~NL~~D~fLr~~m~~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~~~lev~~d~~~ 79 (82)
T cd08028 2 DDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTK 79 (82)
T ss_pred hHHHHHHHHHHHhhcCHhhhccCHHHHHHHhccCCCEEhHHHhCChhHHHhcCCHHHHHHHHHhCCCCEEEEcCCCCc
Confidence 4689999999999999999999999999997 6999999999999999999999999999999999 9999999863
No 11
>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=99.94 E-value=2.4e-27 Score=194.91 Aligned_cols=69 Identities=36% Similarity=0.649 Sum_probs=66.1
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhcc--CCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~M--d~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
++|++||||||||+||++|+|||++| +.||||||++|++|+|||+|+.+ ++|++||+.|++|||++|+.
T Consensus 2 ~~I~~QvEfYFSd~NL~~D~fLr~~~~~~~~G~Vpl~~i~~F~rmk~l~~~-~~i~~Al~~S~~lev~~d~~ 72 (76)
T cd08029 2 EEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPL-EAVVEALRESELLEVSEDGE 72 (76)
T ss_pred hHHHhhHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhCchHHHHcCCH-HHHHHHHHhCCeEEEeCCCC
Confidence 58999999999999999999999999 69999999999999999999965 99999999999999999976
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=99.93 E-value=5.1e-27 Score=192.02 Aligned_cols=70 Identities=56% Similarity=0.929 Sum_probs=67.8
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
++|++||||||||+||++|.||+++|+++|||||++|++|+|||+|+.|.++|++||+.|..|||++|+.
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~g~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~s~~lel~~~~~ 71 (75)
T cd07323 2 EKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGT 71 (75)
T ss_pred hHHHhhhHhccCHhhhCcCHHHHHhcCCCCCEEHHHHhCchHHHHHcCCHHHHHHHHHhCCeEEEeCCCC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999754
No 13
>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=99.93 E-value=4.9e-27 Score=198.83 Aligned_cols=72 Identities=35% Similarity=0.636 Sum_probs=68.0
Q ss_pred HHHHHhhhhhhcCcCCcCcchhhhhcc--CCCccEehhhhccchhhhhhcc------------CHHHHHHHHhcCCcEEE
Q 012097 397 AAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTS------------NIQLILDSLRTSTVVEV 462 (471)
Q Consensus 397 ~~~I~kQIEYYFSD~NL~kD~FLR~~M--d~dG~VPIslIasFnRVK~LT~------------D~~lI~eALr~S~~LEV 462 (471)
+++|++||||||||+||++|+||+++| +.||||+|++|++|||||+|+. ++++|++||+.|++|||
T Consensus 2 ~~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~V~i~~i~~F~rmk~l~~~~~~~~~~~~~~~~~~I~~ALk~S~~lev 81 (90)
T cd08030 2 KEKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKAVAEALRTSTLLKV 81 (90)
T ss_pred hHHHHHHHHcccchhhcccCHHHHHHhccCCCCCEehHHHhcChHHHHHhhcccccccccchhHHHHHHHHHccCCEEEE
Confidence 589999999999999999999999999 7899999999999999999985 37899999999999999
Q ss_pred cCCccc
Q 012097 463 QSYLFI 468 (471)
Q Consensus 463 seDkiR 468 (471)
++|+.|
T Consensus 82 seD~~~ 87 (90)
T cd08030 82 SEDGKR 87 (90)
T ss_pred cCCCCc
Confidence 999874
No 14
>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=99.89 E-value=1.7e-24 Score=171.14 Aligned_cols=58 Identities=55% Similarity=1.016 Sum_probs=53.3
Q ss_pred HHhhhhhhcCcCCcCcchhhhhccCC--CccEehhhhccchhhhhhc-cCHHHHHHHHhcC
Q 012097 400 LIHQIDYYFSDANLVKDEFLKSNMDD--QGWVPITLIASFPRVKNLT-SNIQLILDSLRTS 457 (471)
Q Consensus 400 I~kQIEYYFSD~NL~kD~FLR~~Md~--dG~VPIslIasFnRVK~LT-~D~~lI~eALr~S 457 (471)
|++||||||||+||++|+||+++|+. ||||||++|++|+|||+|+ .|+++|++||+.|
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 8999999999987
No 15
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=99.82 E-value=6.3e-21 Score=196.57 Aligned_cols=75 Identities=44% Similarity=0.742 Sum_probs=72.0
Q ss_pred cHHHHHHHHhhhhhhcCcCCcCcchhhhhcc--CCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 393 EPSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 393 e~~L~~~I~kQIEYYFSD~NL~kD~FLR~~M--d~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
-++|..+|++||||||||+||.+|.||.++| |.+|||+|++|++|||||+||.|+.+|.+|||.|.+|||+||+.
T Consensus 137 sedl~~kIv~QVEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~kL~vseDgk 213 (484)
T KOG1855|consen 137 SEDLAAKIVDQVEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSSKLEVSEDGK 213 (484)
T ss_pred cHHHHHHHHHHhheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcceEEEccCCc
Confidence 3699999999999999999999999999999 69999999999999999999999999999999999999999954
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=99.79 E-value=1.2e-17 Score=174.52 Aligned_cols=68 Identities=41% Similarity=0.677 Sum_probs=64.0
Q ss_pred HHHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcccc
Q 012097 397 AAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLFID 469 (471)
Q Consensus 397 ~~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDkiR~ 469 (471)
.+.|.+|||||||.||||+|.||+++| |+|.||++|+||+.|+.|+++|++||+.+.+||+..|.+|+
T Consensus 301 ~~~~~~~ie~~FSeE~~~~d~~n~~k~-----~~l~~ia~F~r~ad~s~d~nli~~alr~s~ive~~~d~~~r 368 (448)
T KOG2590|consen 301 IAFIQEPIEFYFSEENLQRDRFNREKF-----VPLRVIAKFKRVADLSSDINLILAALRNSLIVEETGDLERR 368 (448)
T ss_pred ccccccccccccchHHHhhhhhhhccc-----chhhhhhhhhhhhhcccCHHHHHHHHhhhhhhhccchhhhc
Confidence 367889999999999999999999876 66999999999999999999999999999999999999987
No 17
>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]
Probab=99.75 E-value=7.1e-19 Score=185.77 Aligned_cols=75 Identities=39% Similarity=0.649 Sum_probs=72.5
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCccc
Q 012097 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLFI 468 (471)
Q Consensus 394 ~~L~~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDkiR 468 (471)
.+|++.|++|||||||.+||..|+||+.+||+|.||||.+||.|++|++||+|++||+|+||+|+.|||+|++.|
T Consensus 94 ~~~kq~lk~qlEy~fSreNlssD~YL~sQMDSDqyVPI~tva~~~~i~klttDvdLI~Evlresp~VqvDekgek 168 (684)
T KOG2591|consen 94 RDLKQLLKKQLEYYFSRENLSSDRYLISQMDSDQYVPINTVANFPEIMKLTTDVDLIVEVLRESPNVQVDEKGEK 168 (684)
T ss_pred hhHHHHHHHHHHHhhccccccchhhhhhhcccccccchhhhccchhhhhhccchHHHHHHHhcCCCceeccCccc
Confidence 399999999999999999999999999999999999999999999999999999999999999999999998763
No 18
>KOG4213 consensus RNA-binding protein La [RNA processing and modification]
Probab=99.60 E-value=2.5e-16 Score=148.33 Aligned_cols=74 Identities=38% Similarity=0.781 Sum_probs=69.7
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchhhhhcc--CCCccEehhhhccchhhhhhccCHHHHHHHHhcCC--cEEEcCCcc
Q 012097 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNM--DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTST--VVEVQSYLF 467 (471)
Q Consensus 394 ~~L~~~I~kQIEYYFSD~NL~kD~FLR~~M--d~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~--~LEVseDki 467 (471)
.+|.++|++||||||.|.||.||.|||++| ..+|||||.+++.|+|+..|++|++.|++||+.|. ++||++|+.
T Consensus 11 a~lE~kii~qleyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ksk~~l~eisedk~ 88 (205)
T KOG4213|consen 11 AALEAKIIHQLEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKSKAELMEISEDKT 88 (205)
T ss_pred hHHHHhhhhhhhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhCHHhhhhhhhchh
Confidence 478899999999999999999999999999 48999999999999999999999999999999886 799999975
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=5.5e-12 Score=130.32 Aligned_cols=60 Identities=33% Similarity=0.664 Sum_probs=57.1
Q ss_pred HHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcC
Q 012097 398 AMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTS 457 (471)
Q Consensus 398 ~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S 457 (471)
..|+.|||||||.+|||.|.|||++|+++||||+++|..|.|++.+..|.++|+.|||.+
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 467779999999999999999999999999999999999999999999999999999976
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=98.68 E-value=5.7e-09 Score=108.38 Aligned_cols=68 Identities=43% Similarity=0.692 Sum_probs=63.6
Q ss_pred HHhhhhhhcC-----cCCcCcchhhhhcc----CCCccEehhhhccchhhhhhccCHHHHHHHHhcC---CcEEEcCCcc
Q 012097 400 LIHQIDYYFS-----DANLVKDEFLKSNM----DDQGWVPITLIASFPRVKNLTSNIQLILDSLRTS---TVVEVQSYLF 467 (471)
Q Consensus 400 I~kQIEYYFS-----D~NL~kD~FLR~~M----d~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S---~~LEVseDki 467 (471)
+++|+||||| |.|+.+|+||+..- ..+|||+|.+|++|+|||.++..+..|..||+.| .++||+.++.
T Consensus 75 ~l~qvE~~fS~s~~~d~n~~~dk~~ktta~Kn~~~~kwVpIkt~~tfn~~k~~gs~~~~v~~a~rks~~~rv~e~Sssgs 154 (438)
T COG5193 75 TLKQVEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLDARVLEVSSSGS 154 (438)
T ss_pred cccceeEEeeccccccccccchhhhccccccccCCCCceeeeeeeeeccccccCCchhhhhhhhhcCcccceeeeccccc
Confidence 8999999999 99999999999875 2599999999999999999999999999999999 7999998865
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=93.72 E-value=0.012 Score=63.25 Aligned_cols=81 Identities=22% Similarity=0.219 Sum_probs=69.7
Q ss_pred CCCCcHHHHHHHHh--hhhhhcCcCCcCcchhhhhccCCCc---cEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEc
Q 012097 389 MPVPEPSLAAMLIH--QIDYYFSDANLVKDEFLKSNMDDQG---WVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQ 463 (471)
Q Consensus 389 ~P~~e~~L~~~I~k--QIEYYFSD~NL~kD~FLR~~Md~dG---~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVs 463 (471)
++.+...|.+.+.. +++|||+..++.+|.|++..++..| |.+|+.+..|.++..++++...++..++.|...+..
T Consensus 90 ~~~ps~~l~e~~~~~k~~s~~~~~~~~~~~~~~~~k~~~t~~~~~~~~S~~~~s~~~~~~s~n~~~~~~~~~~sa~~~~~ 169 (448)
T KOG2590|consen 90 ISVPSPPLKEYSKSDKKKSWPASKPFTPRDSFKGSKPTNTGNGTFLPISKISSSGPVSGGSANNSNIRGPLKGSASSNPV 169 (448)
T ss_pred cccccccccccccccccccCcccCCCCccccccCCCccccCCCccCCCccccccccccCcccccccccCcCCCCCcCCcC
Confidence 34444566666665 9999999999999999999999888 999999999999999999999999999998877777
Q ss_pred CCcccc
Q 012097 464 SYLFID 469 (471)
Q Consensus 464 eDkiR~ 469 (471)
..+.|+
T Consensus 170 ~~~~~~ 175 (448)
T KOG2590|consen 170 PNNSRA 175 (448)
T ss_pred cccccc
Confidence 666654
No 22
>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=91.29 E-value=0.18 Score=48.16 Aligned_cols=48 Identities=23% Similarity=0.318 Sum_probs=33.9
Q ss_pred ccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCc--EEEc-----CCcccc
Q 012097 422 NMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQ-----SYLFID 469 (471)
Q Consensus 422 ~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~--LEVs-----eDkiR~ 469 (471)
.||.+|||.|+.|+...+++.+.-+.+.|.+++++..+ .|+. +++||.
T Consensus 26 ~~d~~G~v~v~dLL~~~~~~~~~~t~~~i~~vV~~~~K~Rfel~~~~~~~~~IRA 80 (186)
T PF01885_consen 26 VMDPDGWVSVDDLLRALRFKGLWVTEEDIREVVETDDKQRFELRYEDPGGWRIRA 80 (186)
T ss_dssp ---TT--EEHHHHHHHHHHT-TT--HHHHHHHHHH-SS--EEEE-----TTEEEE
T ss_pred ccCCCCCEeHHHHHHHHHHcCCCCCHHHHHHHHhhCCCCCeeEEcccccCceEEE
Confidence 37899999999999999999877789999999998764 6777 777775
No 23
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=91.14 E-value=0.24 Score=47.34 Aligned_cols=49 Identities=14% Similarity=0.213 Sum_probs=39.0
Q ss_pred ccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCc--EEEcCCccccC
Q 012097 422 NMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQSYLFIDS 470 (471)
Q Consensus 422 ~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~--LEVseDkiR~~ 470 (471)
.||.+|||+|+.|+...+.+...-+.+.|.+++++..+ .|+++++||..
T Consensus 27 ~ld~~G~v~v~~Ll~~~~~~~~~~t~~~l~~vV~~d~K~Rf~l~~~~IRA~ 77 (179)
T PRK00819 27 TLDEEGWVDIDALIEALAKAYKWVTRELLEAVVESDDKGRFEISGDRIRAR 77 (179)
T ss_pred ccCCCCCEEHHHHHHHHHHccCCCCHHHHHHHHHcCCCcceEecCceEEec
Confidence 47899999999999877654333578999999998764 78888888864
No 24
>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=89.51 E-value=0.33 Score=56.57 Aligned_cols=46 Identities=15% Similarity=0.344 Sum_probs=41.2
Q ss_pred cCCCccEehhhhccchhhhhhccCHHHHHHHHhc-CCcEEEcCC--ccc
Q 012097 423 MDDQGWVPITLIASFPRVKNLTSNIQLILDSLRT-STVVEVQSY--LFI 468 (471)
Q Consensus 423 Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~-S~~LEVseD--kiR 468 (471)
.|.+|||-|.|||+.-.|--|..+.++|+.||.+ |++|||+.| |||
T Consensus 473 pDaeGWVYLNLL~NmAQLHiiNVTPdFVRsAV~E~StKfQLSpDGrKIR 521 (989)
T PF09421_consen 473 PDAEGWVYLNLLCNMAQLHIINVTPDFVRSAVSEKSTKFQLSPDGRKIR 521 (989)
T ss_pred cccccceehHHHHHHHHHHhhccCHHHHHHHHHhcccceeeCCCCCeee
Confidence 4789999999999999999998999999999985 899999977 455
No 25
>KOG2278 consensus RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis]
Probab=86.18 E-value=0.66 Score=45.12 Aligned_cols=40 Identities=20% Similarity=0.395 Sum_probs=35.3
Q ss_pred hhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCC
Q 012097 419 LKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTST 458 (471)
Q Consensus 419 LR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~ 458 (471)
++=+|+.||||+|+.|++.|+.|-....+++|.++++.-.
T Consensus 25 ~~L~m~~dGfvpv~~lL~lnq~r~~~~t~ddi~riVk~nd 64 (207)
T KOG2278|consen 25 LRLNMRGDGFVPVEDLLNLNQFRGANHTIDDIRRIVKRND 64 (207)
T ss_pred hcccccCCCceEHHHHhccchhcccCCcHHHHHHHHhccc
Confidence 3446789999999999999999999888999999998754
No 26
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=77.46 E-value=14 Score=43.98 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=5.3
Q ss_pred CCCCCCCCCCc
Q 012097 260 SNWDARPVGGF 270 (471)
Q Consensus 260 ~~~~~~~~~gf 270 (471)
+++..-.+|||
T Consensus 1225 ~GyrGvsrgGf 1235 (1282)
T KOG0921|consen 1225 NGYRGVSRGGF 1235 (1282)
T ss_pred CCCccccCCcc
Confidence 34444445555
No 27
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=76.44 E-value=80 Score=34.22 Aligned_cols=44 Identities=32% Similarity=0.510 Sum_probs=26.6
Q ss_pred CCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCceeecCCCC
Q 012097 321 QPQRGPPRGF-VRPAPPNAAAFAPPQPMRPFPNPMGFPEFIYIPPMP 366 (471)
Q Consensus 321 ~~q~~~pr~f-~RPppp~~~~f~~p~p~~p~~~P~~~p~~yy~P~~~ 366 (471)
+||.+++.+| +||+..-++..|+++|+..-+.|+.-+ .|+|++.
T Consensus 280 qq~p~pp~~~ppRP~m~l~phl~gppPga~pPaph~Np--affpPP~ 324 (498)
T KOG4849|consen 280 QQQPQPPMGQPPRPMMQLSPHLMGPPPGAGPPAPHNNP--AFFPPPQ 324 (498)
T ss_pred ccCCCCCCCCCCCcccccCcccCCCCCCCCCCCcccCc--ccCCCCC
Confidence 4455556677 777777777788888765444443322 4555543
No 28
>PTZ00315 2'-phosphotransferase; Provisional
Probab=68.32 E-value=5.6 Score=44.62 Aligned_cols=42 Identities=19% Similarity=0.291 Sum_probs=35.3
Q ss_pred ccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCc--EEEc
Q 012097 422 NMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQ 463 (471)
Q Consensus 422 ~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~--LEVs 463 (471)
.||.+|||.|+.|+.-.+.+...-+.+.|.+++++..+ .|+.
T Consensus 399 ~ld~~Gwv~vd~LL~~~~~~~~~~t~e~i~~VV~~ndK~RF~l~ 442 (582)
T PTZ00315 399 PITSNGYVLLDDILRQPPMRNDPVSVQDVARVVRDSDKQRFKLA 442 (582)
T ss_pred CcCCCCCEEHHHHHHHHHhcCCCCCHHHHHHHHHcCCCCceEEe
Confidence 36899999999999988877665689999999998764 6776
No 29
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=65.36 E-value=5.8 Score=39.38 Aligned_cols=48 Identities=19% Similarity=0.240 Sum_probs=37.5
Q ss_pred ccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCc--EEEcCCcccc
Q 012097 422 NMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTV--VEVQSYLFID 469 (471)
Q Consensus 422 ~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~--LEVseDkiR~ 469 (471)
+||.+||+.|+.|+.--|-+----|.++|..+++..++ .||.+.+||.
T Consensus 53 ~lD~~Gwa~i~~l~~~~~k~~~~~~~~~l~~iV~~d~K~Rf~l~~~~IRA 102 (211)
T COG1859 53 RLDEEGWADIDELLEGLRKAGRWLTRELLLAVVATDDKGRFELKEGKIRA 102 (211)
T ss_pred eeccccchhHHHHHHHHHhhccCCCHHHHHHHHhcCCCceeEecccceee
Confidence 36899999999888775554333468999999998775 8899988875
No 30
>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=50.94 E-value=7 Score=37.27 Aligned_cols=58 Identities=26% Similarity=0.358 Sum_probs=31.9
Q ss_pred cHHHHHHHHhhhhhhcCcCC-cCcchhhhhccCCCccEe--hhhhccchhhhhhccCHHHHHHHHh
Q 012097 393 EPSLAAMLIHQIDYYFSDAN-LVKDEFLKSNMDDQGWVP--ITLIASFPRVKNLTSNIQLILDSLR 455 (471)
Q Consensus 393 e~~L~~~I~kQIEYYFSD~N-L~kD~FLR~~Md~dG~VP--IslIasFnRVK~LT~D~~lI~eALr 455 (471)
++.|.+.|+.||...+-++. ..-=.||...+|++||+. +..|+ +.+..+.+.|.++|+
T Consensus 14 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia-----~~l~~~~~~v~~~l~ 74 (194)
T PF04963_consen 14 EESLYEHLLEQLNLSPLSEEEREIAEYLIDNLDDDGYLTESLEEIA-----EELGVSEEEVEKALE 74 (194)
T ss_dssp -----HHHHHHHHHH---TCCHHHHHHHCCCBTTTSTCSS-HHHHH-----HHCTS-HHHHHHHHH
T ss_pred ccCHHHHHHHHHcCcccCHHHHHHHHHHHHcCCCCCccCCCHHHHH-----HHhCCCHHHHHHHHH
Confidence 46899999999998755443 333567888889999975 44443 223344444444444
No 31
>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]
Probab=49.51 E-value=7.6 Score=44.05 Aligned_cols=53 Identities=26% Similarity=0.241 Sum_probs=34.9
Q ss_pred cCcchhhhhccCCCccEehhhhccchhhhhhccCHHHHHHHHhcCCcEEEcCCcc
Q 012097 413 LVKDEFLKSNMDDQGWVPITLIASFPRVKNLTSNIQLILDSLRTSTVVEVQSYLF 467 (471)
Q Consensus 413 L~kD~FLR~~Md~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~~LEVseDki 467 (471)
++-+.|+++.+..-|||++..++.|-.+--+ +...++.|++..+.+.++++++
T Consensus 51 ~~s~~~~~~il~~~g~v~s~kr~~fgf~~f~--~~~~~~ra~r~~t~~~~~~~kl 103 (668)
T KOG2253|consen 51 LVSQEFWKSILAKSGFVPSWKRDKFGFCEFL--KHIGDLRASRLLTELNIDDQKL 103 (668)
T ss_pred hhhHHHHHHHHhhCCcchhhhhhhhcccchh--hHHHHHHHHHHhcccCCCcchh
Confidence 4556778887888888888888776654332 2444556666666666666654
No 32
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=38.41 E-value=1.2e+02 Score=32.76 Aligned_cols=9 Identities=22% Similarity=0.231 Sum_probs=4.7
Q ss_pred CCCCCCCCC
Q 012097 218 PTQPPPPPP 226 (471)
Q Consensus 218 ~~~~~p~~~ 226 (471)
+-+|+.+++
T Consensus 384 yqqp~~~~~ 392 (465)
T KOG3973|consen 384 YQQPQQQQQ 392 (465)
T ss_pred CcCchhhhh
Confidence 445555554
No 33
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=37.85 E-value=14 Score=40.62 Aligned_cols=62 Identities=21% Similarity=0.290 Sum_probs=41.5
Q ss_pred HHHHHHHHhhhhhhcCcCCc-CcchhhhhccCCCccE--ehhhhccchhhhhhccCHHHHHHHHhc
Q 012097 394 PSLAAMLIHQIDYYFSDANL-VKDEFLKSNMDDQGWV--PITLIASFPRVKNLTSNIQLILDSLRT 456 (471)
Q Consensus 394 ~~L~~~I~kQIEYYFSD~NL-~kD~FLR~~Md~dG~V--PIslIasFnRVK~LT~D~~lI~eALr~ 456 (471)
..|.+.|..||.+++-+..- .-=.||...+|++||+ ++..|+.-.+ +.|..+.+.|.+||+.
T Consensus 123 ~sL~~~L~~Ql~~~~~~~~~~~ia~~lI~~LD~~GyL~~~~~eia~~~~-~~l~~~~~~ve~vL~~ 187 (481)
T PRK12469 123 PTLHEHLHDALRLYFLTERDREIARTIIDALDDDGYLRQDLSELAEAAD-PELGLSEQELEVALRL 187 (481)
T ss_pred CCHHHHHHHHHhccCCCHHHHHHHHHHHhhCCCCCCCCCCHHHHHhccc-cccCCCHHHHHHHHHH
Confidence 47899999999988666543 2234888899999997 6666654311 1233456666666554
No 34
>PF05204 Hom_end: Homing endonuclease; InterPro: IPR007869 Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce [] revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This domain corresponds to the C-terminal domain, which has structural similarity to IPR001767 from INTERPRO.; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0030908 protein splicing; PDB: 1LWT_A 1UM2_B 1JVA_B 1VDE_A 1EF0_B 1DFA_A 1LWS_A 1GPP_A.
Probab=32.81 E-value=3.2 Score=36.94 Aligned_cols=28 Identities=25% Similarity=0.528 Sum_probs=21.4
Q ss_pred hhhcCcCCcCcchhhhhccCCCccEehh
Q 012097 405 DYYFSDANLVKDEFLKSNMDDQGWVPIT 432 (471)
Q Consensus 405 EYYFSD~NL~kD~FLR~~Md~dG~VPIs 432 (471)
+||.++.=..|-.||-.+||.||||.-.
T Consensus 4 ~~l~~es~~vReafLAGLiDsdG~v~~~ 31 (110)
T PF05204_consen 4 SFLLSESIEVREAFLAGLIDSDGYVKEP 31 (110)
T ss_dssp CCCCCTHHHHHHHHHHHHHHHHEECCST
T ss_pred hHHhhCCHHHHHHHHhhEEECCCCccCC
Confidence 3555666666778999999999998655
No 35
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=31.13 E-value=22 Score=38.62 Aligned_cols=59 Identities=20% Similarity=0.300 Sum_probs=38.7
Q ss_pred cHHHHHHHHhhhhhhcCcCC-cCcchhhhhccCCCccE--ehhhhccchhhhhhccCHHHHHHHHhc
Q 012097 393 EPSLAAMLIHQIDYYFSDAN-LVKDEFLKSNMDDQGWV--PITLIASFPRVKNLTSNIQLILDSLRT 456 (471)
Q Consensus 393 e~~L~~~I~kQIEYYFSD~N-L~kD~FLR~~Md~dG~V--PIslIasFnRVK~LT~D~~lI~eALr~ 456 (471)
+..|.+.|..||.+++-+.. ..==.||...+|++||+ ++..|+.- |..+.+.|.+||+.
T Consensus 100 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~-----l~~~~~~v~~~l~~ 161 (455)
T PRK05932 100 TESLQDHLLEQIELTPFSETDRAIATYIIDALDDEGYLTEDLEEIAES-----LGVELDEVEAVLKR 161 (455)
T ss_pred CCCHHHHHHHHHcccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHH-----cCCCHHHHHHHHHH
Confidence 34888999999998854433 33356788889999998 55665432 22345555555543
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=29.12 E-value=19 Score=38.72 Aligned_cols=59 Identities=20% Similarity=0.314 Sum_probs=39.2
Q ss_pred cHHHHHHHHhhhhhhc-CcCCcCcchhhhhccCCCccEe--hhhhccchhhhhhccCHHHHHHHHhc
Q 012097 393 EPSLAAMLIHQIDYYF-SDANLVKDEFLKSNMDDQGWVP--ITLIASFPRVKNLTSNIQLILDSLRT 456 (471)
Q Consensus 393 e~~L~~~I~kQIEYYF-SD~NL~kD~FLR~~Md~dG~VP--IslIasFnRVK~LT~D~~lI~eALr~ 456 (471)
...|.+.|..||.+++ ++.-..==.||...+|++||+. +..|+.- |..+.+.|.+||+.
T Consensus 75 ~~sL~e~L~~Ql~~~~~~~~~~~ia~~iI~~LD~~GyL~~~~~eia~~-----l~~~~~~ve~~l~~ 136 (429)
T TIGR02395 75 TESLFEHLLEQLDLQLFTERDRKIALYIIDNLDEDGYLEIDLEEIADE-----LEVSEEEVEKVLEL 136 (429)
T ss_pred CCCHHHHHHHHHhccCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHH-----cCCCHHHHHHHHHH
Confidence 3488999999999884 4344444567888999999985 5555432 22355555555543
No 37
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=26.20 E-value=29 Score=37.24 Aligned_cols=60 Identities=18% Similarity=0.420 Sum_probs=45.8
Q ss_pred HHHHHhhhhhhcCcCC--------cCcchhhhhccC---------CCccEehhhhccchhhhhhccCHHHHHHHHhcCC
Q 012097 397 AAMLIHQIDYYFSDAN--------LVKDEFLKSNMD---------DQGWVPITLIASFPRVKNLTSNIQLILDSLRTST 458 (471)
Q Consensus 397 ~~~I~kQIEYYFSD~N--------L~kD~FLR~~Md---------~dG~VPIslIasFnRVK~LT~D~~lI~eALr~S~ 458 (471)
-.||+.|+.|.||-.| ..+|.||++.+. .-||-.+..-..|.|=|+.+ ++..+++|..+.
T Consensus 141 ~gk~~dklryIfs~isds~gim~~i~~~~fl~evlslpT~v~e~psfg~te~~a~~cf~qqrKv~--Ln~fldtl~sdp 217 (434)
T KOG4301|consen 141 GGKIKDKLRYIFSLISDSRGIMQEIQRDQFLHEVLSLPTAVFEGPSFGYTELSARLCFLQQRKVE--LNQFLDTLMSDP 217 (434)
T ss_pred cchHHHHHHHHHHHHccchHHHHHHHHHHHHHHHHcCCchhhcCCCcchHHHHHHHHHHHHHHHH--HHHHHHHHhcCC
Confidence 3588999999999776 357899998763 46888888888898887754 666667766553
No 38
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=24.80 E-value=3.8e+02 Score=32.17 Aligned_cols=9 Identities=22% Similarity=0.512 Sum_probs=5.4
Q ss_pred cEEEcCCcc
Q 012097 459 VVEVQSYLF 467 (471)
Q Consensus 459 ~LEVseDki 467 (471)
+|||++|-+
T Consensus 722 ILevne~vL 730 (1102)
T KOG1924|consen 722 ILEVNEDVL 730 (1102)
T ss_pred HhhccHHHH
Confidence 467776643
No 39
>PF11641 Antigen_Bd37: Glycosylphosphatidylinositol-anchored merozoite surface protein; InterPro: IPR021669 This family of proteins represents the core region of Bd37, a surface antigen of B.divergens which is GPI-anchored at the surface of the merozoite. The structure of the protein consists of mainly alpha folds and has three sub domains []. ; PDB: 2JO7_A.
Probab=21.50 E-value=76 Score=31.67 Aligned_cols=51 Identities=18% Similarity=0.210 Sum_probs=34.3
Q ss_pred HHHHHHHHhhhhhhcCcCCcCcchhhhhccCCCccEehhhhccchhhhh----hccCHHHHHHHHh
Q 012097 394 PSLAAMLIHQIDYYFSDANLVKDEFLKSNMDDQGWVPITLIASFPRVKN----LTSNIQLILDSLR 455 (471)
Q Consensus 394 ~~L~~~I~kQIEYYFSD~NL~kD~FLR~~Md~dG~VPIslIasFnRVK~----LT~D~~lI~eALr 455 (471)
++|+..++.|=| +||.+.|+++|-+-|--|..|=||-. |..|-+.|.+|-+
T Consensus 5 e~lr~Elk~qRE-----------~~Ls~Ii~sdGp~tIlqLid~LRiidtDlLlkVD~~~V~kAG~ 59 (224)
T PF11641_consen 5 EELRKELKGQRE-----------RVLSTIIDSDGPFTILQLIDYLRIIDTDLLLKVDQAKVKKAGE 59 (224)
T ss_dssp HHHHHHHHHHHH-----------HHHHHHHH--S---TTHHHHHHHHHHHHTTT---HHHHHHHHH
T ss_pred HHHHHHHHHHHH-----------HHHHHHHccCCCeeHHHHHHHHHHhccchhhccCHHHHHHHHH
Confidence 478888888855 89999999999999999999999876 2346666666644
Done!