Query 008506
Match_columns 563
No_of_seqs 217 out of 624
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 13:01:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008506.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008506hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2591 c-Mpl binding protein, 100.0 8.7E-41 1.9E-45 355.6 7.7 154 295-471 92-247 (684)
2 cd08037 LARP_1 La RNA-binding 100.0 6.1E-30 1.3E-34 213.4 6.0 72 301-372 2-73 (73)
3 cd08038 LARP_2 La RNA-binding 100.0 9.4E-30 2E-34 212.3 6.3 72 301-372 2-73 (73)
4 cd08036 LARP_5 La RNA-binding 100.0 1.5E-29 3.3E-34 211.6 4.7 71 301-371 2-74 (75)
5 cd08035 LARP_4 La RNA-binding 100.0 2.6E-29 5.7E-34 210.5 5.9 72 300-371 1-74 (75)
6 cd08034 LARP_1_2 La RNA-bindin 100.0 3.3E-29 7.1E-34 208.9 6.3 73 300-372 1-73 (73)
7 cd08032 LARP_7 La RNA-binding 99.9 3.6E-28 7.9E-33 206.7 7.4 76 297-372 3-82 (82)
8 cd08033 LARP_6 La RNA-binding 99.9 8.4E-28 1.8E-32 202.2 6.5 72 301-372 2-77 (77)
9 smart00715 LA Domain in the RN 99.9 1.1E-27 2.4E-32 202.5 6.8 76 298-373 2-80 (80)
10 cd08031 LARP_4_5_like La RNA-b 99.9 1.4E-27 3.1E-32 200.0 6.3 71 301-371 2-74 (75)
11 cd08028 LARP_3 La RNA-binding 99.9 3.4E-27 7.3E-32 200.7 7.0 76 297-372 2-82 (82)
12 cd08029 LA_like_fungal La-moti 99.9 1E-26 2.2E-31 195.2 5.9 71 301-372 2-76 (76)
13 cd07323 LAM LA motif RNA-bindi 99.9 2.7E-26 5.8E-31 191.7 6.3 72 301-372 2-75 (75)
14 cd08030 LA_like_plant La-motif 99.9 3.3E-26 7.1E-31 197.7 5.8 73 300-372 2-90 (90)
15 PF05383 La: La domain; Inter 99.9 1.6E-23 3.4E-28 169.0 4.6 58 303-360 1-61 (61)
16 KOG1855 Predicted RNA-binding 99.8 7.1E-22 1.5E-26 207.2 7.3 102 296-401 137-242 (484)
17 KOG2590 RNA-binding protein LA 99.7 2.3E-15 4.9E-20 160.9 17.6 80 300-384 301-381 (448)
18 KOG4213 RNA-binding protein La 99.5 6.6E-15 1.4E-19 141.4 4.3 76 297-372 11-92 (205)
19 COG5193 LHP1 La protein, small 99.3 4.1E-13 8.9E-18 141.1 2.1 86 300-385 271-380 (438)
20 COG5193 LHP1 La protein, small 98.5 1.6E-08 3.4E-13 107.2 0.6 72 303-374 75-160 (438)
21 KOG2590 RNA-binding protein LA 97.9 6.6E-06 1.4E-10 89.2 3.8 248 298-561 96-378 (448)
22 PF09421 FRQ: Frequency clock 91.1 1.7 3.7E-05 52.0 11.4 49 326-374 473-524 (989)
23 PF01885 PTS_2-RNA: RNA 2'-pho 90.5 0.37 8.1E-06 47.1 4.7 52 325-376 26-84 (186)
24 PRK00819 RNA 2'-phosphotransfe 89.6 0.55 1.2E-05 46.0 5.0 55 325-379 27-83 (179)
25 KOG2278 RNA:NAD 2'-phosphotran 83.1 0.93 2E-05 45.0 2.7 41 322-362 25-65 (207)
26 KOG1924 RhoA GTPase effector D 65.2 34 0.00074 41.0 9.5 15 296-310 727-741 (1102)
27 COG1859 KptA RNA:NAD 2'-phosph 63.9 9.3 0.0002 38.8 4.3 54 325-378 53-108 (211)
28 PTZ00315 2'-phosphotransferase 54.6 16 0.00036 41.9 4.7 54 325-378 399-460 (582)
29 PF05918 API5: Apoptosis inhib 42.8 8.1 0.00018 44.1 0.0 25 183-207 517-541 (556)
30 KOG0132 RNA polymerase II C-te 40.4 3.2E+02 0.007 33.2 12.0 11 368-378 807-817 (894)
31 KOG3973 Uncharacterized conser 28.2 2.7E+02 0.0058 31.0 8.3 27 183-210 357-383 (465)
32 PF04963 Sigma54_CBD: Sigma-54 24.7 63 0.0014 31.7 2.8 59 296-359 14-75 (194)
33 KOG1924 RhoA GTPase effector D 23.6 1.6E+02 0.0035 35.7 6.1 13 346-358 797-809 (1102)
34 KOG0921 Dosage compensation co 21.0 2.4E+02 0.0052 35.1 6.9 9 189-197 1213-1221(1282)
No 1
>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]
Probab=100.00 E-value=8.7e-41 Score=355.59 Aligned_cols=154 Identities=28% Similarity=0.399 Sum_probs=146.4
Q ss_pred hHHHHHHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCCeeecCC
Q 008506 295 ETLALKANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGDKVRRRD 374 (563)
Q Consensus 295 e~~~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~dKVRRR~ 374 (563)
...+|++.|++|||||||.+||..|.||+.+||+|.||||.+||.|+.|++||+|++||+|+||.|+.||||++..|.|.
T Consensus 92 ls~~~kq~lk~qlEy~fSreNlssD~YL~sQMDSDqyVPI~tva~~~~i~klttDvdLI~Evlresp~VqvDekgekVrp 171 (684)
T KOG2591|consen 92 LSRDLKQLLKKQLEYYFSRENLSSDRYLISQMDSDQYVPINTVANFPEIMKLTTDVDLIVEVLRESPNVQVDEKGEKVRP 171 (684)
T ss_pred cchhHHHHHHHHHHHhhccccccchhhhhhhcccccccchhhhccchhhhhhccchHHHHHHHhcCCCceeccCcccccc
Confidence 34489999999999999999999999999999999999999999999999999999999999999999999976555557
Q ss_pred CCCcccccccccccCCcccCccccccccccccccCCCCCCCCCCCCCcccccccCCCCcccCCCCCCCcccccCCCCCcc
Q 008506 375 EWSKWIPASVEQTMSSTAQTSQSQSAENPVDSIGNGDINKDNKREMPKENVGFSSNTGNLMENVPPSFDSVEIEPDNGEE 454 (563)
Q Consensus 375 ~w~kwv~~s~e~~~~S~~~~~~~~pieev~~~f~n~~~~~~n~~~~~~~~~efa~n~~~~~~~~~~~~~~~~~~~da~~~ 454 (563)
..++||+|++| |+++++||+|++||+ ++||| ++++|||++||+ ||||||+|+|||+|
T Consensus 172 ~~kRcIvilRE--------Ipettp~e~Vk~lf~-----~encP--k~iscefa~N~n--------WyITfesd~DAQqA 228 (684)
T KOG2591|consen 172 NHKRCIVILRE--------IPETTPIEVVKALFK-----GENCP--KVISCEFAHNDN--------WYITFESDTDAQQA 228 (684)
T ss_pred CcceeEEEEee--------cCCCChHHHHHHHhc-----cCCCC--CceeeeeeecCc--------eEEEeecchhHHHH
Confidence 88999999999 999999999999999 77899 999999999999 99999999999999
Q ss_pred ccc--ccccccCCCCcccc
Q 008506 455 HCD--EFLLLDDGKPAFSA 471 (563)
Q Consensus 455 ~~~--~~~~~~~~kp~~~~ 471 (563)
|+| ||+|+|+|||||.-
T Consensus 229 ykylreevk~fqgKpImAR 247 (684)
T KOG2591|consen 229 YKYLREEVKTFQGKPIMAR 247 (684)
T ss_pred HHHHHHHHHhhcCcchhhh
Confidence 999 99999999999983
No 2
>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=6.1e-30 Score=213.39 Aligned_cols=72 Identities=44% Similarity=0.787 Sum_probs=70.8
Q ss_pred HHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCCeeec
Q 008506 301 ANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGDKVRR 372 (563)
Q Consensus 301 ~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~dKVRR 372 (563)
+.|++||||||||+||++|.|||++|++||||||++|++|||||+||.|+++|++||+.|+.|||+++||||
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 679999999999999999999999999999999999999999999999999999999999999999999996
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=99.96 E-value=9.4e-30 Score=212.25 Aligned_cols=72 Identities=49% Similarity=0.821 Sum_probs=70.9
Q ss_pred HHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCCeeec
Q 008506 301 ANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGDKVRR 372 (563)
Q Consensus 301 ~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~dKVRR 372 (563)
++|++||||||||+||++|.|||++|+.||||||++|++|||||+|+.|+++|++||+.|+.|||++|+|||
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 689999999999999999999999999999999999999999999999999999999999999999999996
No 4
>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=99.95 E-value=1.5e-29 Score=211.58 Aligned_cols=71 Identities=39% Similarity=0.678 Sum_probs=68.1
Q ss_pred HHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcC--Ceee
Q 008506 301 ANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQG--DKVR 371 (563)
Q Consensus 301 ~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~--dKVR 371 (563)
+.|++||||||||+||++|.|||++||+||||||++||+|+|||+||+|+++|++||++|+.|||++ +|||
T Consensus 2 e~i~kQvEyYFS~~NL~~D~fLr~~md~~g~Vpi~~ia~F~rik~Lt~D~~lI~~aL~~S~~vevse~g~kVR 74 (75)
T cd08036 2 ELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVR 74 (75)
T ss_pred hhhhcceeeeechhhccccHHHHHHhccCCCEehHHHhccHHHHHhcCCHHHHHHHHhhCCeEEECCCCCccC
Confidence 6799999999999999999999999999999999999999999999999999999999999999975 4777
No 5
>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=99.95 E-value=2.6e-29 Score=210.53 Aligned_cols=72 Identities=43% Similarity=0.721 Sum_probs=68.7
Q ss_pred HHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eee
Q 008506 300 KANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVR 371 (563)
Q Consensus 300 ~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVR 371 (563)
+++|++||||||||+||++|.||+++||+||||||++||+|+|||+||.|+++|++||+.|+.|||++| |||
T Consensus 1 ~e~i~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpi~~iasF~rik~lt~d~~~I~~AL~~S~~levsedg~kVR 74 (75)
T cd08035 1 RECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVR 74 (75)
T ss_pred ChHHHhhHHhhcCHhhcccCHHHHHhhCcCCCEehHHHhccHHHHHhcCCHHHHHHHHHcCCeEEEcCCCCccC
Confidence 368999999999999999999999999999999999999999999999999999999999999999754 777
No 6
>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=99.95 E-value=3.3e-29 Score=208.92 Aligned_cols=73 Identities=51% Similarity=0.823 Sum_probs=71.1
Q ss_pred HHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCCeeec
Q 008506 300 KANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGDKVRR 372 (563)
Q Consensus 300 ~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~dKVRR 372 (563)
+++|++||||||||+||+||.|||++|+.+|||||++|++|+|||+|+.|+++|++||+.|+.|||+++||||
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 3689999999999999999999999999999999999999999999999999999999999999999999996
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=3.6e-28 Score=206.66 Aligned_cols=76 Identities=36% Similarity=0.679 Sum_probs=72.4
Q ss_pred HHHHHHHHHHhhhhcCCCCcCcchHHHHhhc--CCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eeec
Q 008506 297 LALKANIVKQIEYYFSDENLQNDHYLISLMD--AQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVRR 372 (563)
Q Consensus 297 ~~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD--~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVRR 372 (563)
.+|+++|++||||||||+||++|.||+++|+ .||||||++|++|||||+||.|+++|++||+.|+.|||++| +|||
T Consensus 3 ~~l~~~I~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VRR 82 (82)
T cd08032 3 KQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIRR 82 (82)
T ss_pred HHHHHHHHHHHHhhcchhhcccCHHHHHHhcCCCCCCEeHHHHhcchHHHHHcCCHHHHHHHHhcCCEEEEcCCCCccCC
Confidence 5899999999999999999999999999996 79999999999999999999999999999999999999865 7876
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=99.94 E-value=8.4e-28 Score=202.24 Aligned_cols=72 Identities=49% Similarity=0.812 Sum_probs=68.8
Q ss_pred HHHHHHhhhhcCCCCcCcchHHHHhh--cCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eeec
Q 008506 301 ANIVKQIEYYFSDENLQNDHYLISLM--DAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVRR 372 (563)
Q Consensus 301 ~~I~kQIEYYFSDeNL~kD~FLRk~M--D~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVRR 372 (563)
++|++||||||||+||++|.|||++| +.||||||++|++|+|||+|+.|.++|++||+.|..|||++| +|||
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~l~~d~~~I~~Al~~S~~lev~~d~~~VRR 77 (77)
T cd08033 2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVRR 77 (77)
T ss_pred hHHHhHHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhcchHHHHHcCCHHHHHHHHHhCCeEEEcCCCCccCC
Confidence 67999999999999999999999999 789999999999999999999999999999999999999865 7876
No 9
>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function.
Probab=99.94 E-value=1.1e-27 Score=202.52 Aligned_cols=76 Identities=55% Similarity=0.887 Sum_probs=72.4
Q ss_pred HHHHHHHHHhhhhcCCCCcCcchHHHHhhcC-CCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eeecC
Q 008506 298 ALKANIVKQIEYYFSDENLQNDHYLISLMDA-QGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVRRR 373 (563)
Q Consensus 298 ~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD~-dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVRRR 373 (563)
++.++|++||||||||+||++|.|||++|+. +|||||++|++|+|||+|+.|.++|++||+.|..|||++| +|||+
T Consensus 2 ~~~~~i~~QvEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~~lel~~d~~~VRR~ 80 (80)
T smart00715 2 ELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR 80 (80)
T ss_pred hHHHHHHHHHHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCeeCcC
Confidence 6889999999999999999999999999987 9999999999999999999999999999999999999865 78874
No 10
>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=99.94 E-value=1.4e-27 Score=199.99 Aligned_cols=71 Identities=46% Similarity=0.819 Sum_probs=68.1
Q ss_pred HHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eee
Q 008506 301 ANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVR 371 (563)
Q Consensus 301 ~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVR 371 (563)
++|++||||||||+||++|.||+++|++||||||++|++|+|||+||.|+++|++||+.|+.|||++| +||
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~m~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VR 74 (75)
T cd08031 2 ELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEKVR 74 (75)
T ss_pred hHHHHHHHHHcCHhhhccCHHHHHHhCCCCCEEHHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCccC
Confidence 68999999999999999999999999999999999999999999999999999999999999999966 565
No 11
>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=3.4e-27 Score=200.69 Aligned_cols=76 Identities=41% Similarity=0.755 Sum_probs=71.6
Q ss_pred HHHHHHHHHHhhhhcCCCCcCcchHHHHhhc-CCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCC--ceEEcCC--eee
Q 008506 297 LALKANIVKQIEYYFSDENLQNDHYLISLMD-AQGWVPIAIIADFKRVKRMSTDLPFILDALQNSS--TVEAQGD--KVR 371 (563)
Q Consensus 297 ~~L~~~I~kQIEYYFSDeNL~kD~FLRk~MD-~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~--~VEV~~d--KVR 371 (563)
++|..+|++||||||||+||++|.|||++|+ +||||||++|++|+|||+|+.|.++|++||+.|+ .|||++| +||
T Consensus 2 ~~l~~~I~~QvEfYFSd~NL~~D~fLr~~m~~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~~~lev~~d~~~VR 81 (82)
T cd08028 2 DDLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKIR 81 (82)
T ss_pred hHHHHHHHHHHHhhcCHhhhccCHHHHHHHhccCCCEEhHHHhCChhHHHhcCCHHHHHHHHHhCCCCEEEEcCCCCccC
Confidence 3689999999999999999999999999997 5999999999999999999999999999999999 9999866 677
Q ss_pred c
Q 008506 372 R 372 (563)
Q Consensus 372 R 372 (563)
|
T Consensus 82 R 82 (82)
T cd08028 82 R 82 (82)
T ss_pred C
Confidence 5
No 12
>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=99.93 E-value=1e-26 Score=195.22 Aligned_cols=71 Identities=45% Similarity=0.800 Sum_probs=66.9
Q ss_pred HHHHHHhhhhcCCCCcCcchHHHHhh--cCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eeec
Q 008506 301 ANIVKQIEYYFSDENLQNDHYLISLM--DAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVRR 372 (563)
Q Consensus 301 ~~I~kQIEYYFSDeNL~kD~FLRk~M--D~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVRR 372 (563)
++|++||||||||+||++|.|||++| +.||||||++|++|+|||+|+.+ ++|++||+.|+.|||++| +|||
T Consensus 2 ~~I~~QvEfYFSd~NL~~D~fLr~~~~~~~~G~Vpl~~i~~F~rmk~l~~~-~~i~~Al~~S~~lev~~d~~~VRR 76 (76)
T cd08029 2 EEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPL-EAVVEALRESELLEVSEDGENVRR 76 (76)
T ss_pred hHHHhhHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhCchHHHHcCCH-HHHHHHHHhCCeEEEeCCCCcccC
Confidence 57999999999999999999999999 69999999999999999999976 999999999999999865 7886
No 13
>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=2.7e-26 Score=191.72 Aligned_cols=72 Identities=58% Similarity=0.999 Sum_probs=68.9
Q ss_pred HHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eeec
Q 008506 301 ANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVRR 372 (563)
Q Consensus 301 ~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVRR 372 (563)
++|++||||||||+||++|.||+++|+++|||||++|++|+|||+|+.|.++|++||+.|..|||+++ +|||
T Consensus 2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~g~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~s~~lel~~~~~~Vrr 75 (75)
T cd07323 2 EKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR 75 (75)
T ss_pred hHHHhhhHhccCHhhhCcCHHHHHhcCCCCCEEHHHHhCchHHHHHcCCHHHHHHHHHhCCeEEEeCCCCccCC
Confidence 57999999999999999999999999999999999999999999999999999999999999999965 6775
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=99.92 E-value=3.3e-26 Score=197.73 Aligned_cols=73 Identities=34% Similarity=0.681 Sum_probs=67.9
Q ss_pred HHHHHHHhhhhcCCCCcCcchHHHHhh--cCCCcEehhhhhcchhHhhhcC------------CHHHHHHHHhcCCceEE
Q 008506 300 KANIVKQIEYYFSDENLQNDHYLISLM--DAQGWVPIAIIADFKRVKRMST------------DLPFILDALQNSSTVEA 365 (563)
Q Consensus 300 ~~~I~kQIEYYFSDeNL~kD~FLRk~M--D~dG~VPIslIasFnRVK~LT~------------Di~lI~eALr~S~~VEV 365 (563)
+++|++||||||||+||++|.||+++| +.||||||++|++|||||+|+. |+++|++||+.|..|||
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 678999999999999999999999999 7899999999999999999985 37899999999999999
Q ss_pred cCC--eeec
Q 008506 366 QGD--KVRR 372 (563)
Q Consensus 366 ~~d--KVRR 372 (563)
++| +|||
T Consensus 82 seD~~~VRR 90 (90)
T cd08030 82 SEDGKRVGR 90 (90)
T ss_pred cCCCCccCC
Confidence 976 5665
No 15
>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=99.88 E-value=1.6e-23 Score=169.03 Aligned_cols=58 Identities=55% Similarity=0.986 Sum_probs=53.4
Q ss_pred HHHHhhhhcCCCCcCcchHHHHhhcC--CCcEehhhhhcchhHhhhc-CCHHHHHHHHhcC
Q 008506 303 IVKQIEYYFSDENLQNDHYLISLMDA--QGWVPIAIIADFKRVKRMS-TDLPFILDALQNS 360 (563)
Q Consensus 303 I~kQIEYYFSDeNL~kD~FLRk~MD~--dG~VPIslIasFnRVK~LT-~Di~lI~eALr~S 360 (563)
|++||||||||+||++|.||+++|+. ||||||++|++|+|||+|+ .|+++|++||+.|
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 16
>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]
Probab=99.85 E-value=7.1e-22 Score=207.22 Aligned_cols=102 Identities=37% Similarity=0.657 Sum_probs=92.9
Q ss_pred HHHHHHHHHHHhhhhcCCCCcCcchHHHHhh--cCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCC--eee
Q 008506 296 TLALKANIVKQIEYYFSDENLQNDHYLISLM--DAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGD--KVR 371 (563)
Q Consensus 296 ~~~L~~~I~kQIEYYFSDeNL~kD~FLRk~M--D~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~d--KVR 371 (563)
.++|..+|++||||||||+||.+|.||.++| +.+|||||++|++|||||+||.|..+|..|||.|..|+|++| |||
T Consensus 137 sedl~~kIv~QVEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~kL~vseDgkKVr 216 (484)
T KOG1855|consen 137 SEDLAAKIVDQVEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSSKLEVSEDGKKVR 216 (484)
T ss_pred cHHHHHHHHHHhheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcceEEEccCCceee
Confidence 3689999999999999999999999999999 689999999999999999999999999999999999999865 999
Q ss_pred cCCCCCcccccccccccCCcccCccccccc
Q 008506 372 RRDEWSKWIPASVEQTMSSTAQTSQSQSAE 401 (563)
Q Consensus 372 RR~~w~kwv~~s~e~~~~S~~~~~~~~pie 401 (563)
|-.++..+ .+...+|++.+.++++.+
T Consensus 217 RisPlp~~----~~eel~srtivaenLP~D 242 (484)
T KOG1855|consen 217 RISPLPEF----DEEELPSRTIVAENLPLD 242 (484)
T ss_pred ecCCCCCc----cccccccceEEEecCCcc
Confidence 98876655 345678999998888876
No 17
>KOG2590 consensus RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones; Translation, ribosomal structure and biogenesis]
Probab=99.66 E-value=2.3e-15 Score=160.87 Aligned_cols=80 Identities=45% Similarity=0.728 Sum_probs=73.1
Q ss_pred HHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCCeeec-CCCCCc
Q 008506 300 KANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGDKVRR-RDEWSK 378 (563)
Q Consensus 300 ~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~dKVRR-R~~w~k 378 (563)
.+-|.+|||||||.|||++|.||++ +||+|.||++|+||+.|+.|+++|++||+.+..||+..|-+|| +..|..
T Consensus 301 ~~~~~~~ie~~FSeE~~~~d~~n~~-----k~~~l~~ia~F~r~ad~s~d~nli~~alr~s~ive~~~d~~~r~~~~~g~ 375 (448)
T KOG2590|consen 301 IAFIQEPIEFYFSEENLQRDRFNRE-----KFVPLRVIAKFKRVADLSSDINLILAALRNSLIVEETGDLERRGGDRWGN 375 (448)
T ss_pred ccccccccccccchHHHhhhhhhhc-----ccchhhhhhhhhhhhhcccCHHHHHHHHhhhhhhhccchhhhcccccccc
Confidence 4558999999999999999999987 5677999999999999999999999999999999999999988 888999
Q ss_pred cccccc
Q 008506 379 WIPASV 384 (563)
Q Consensus 379 wv~~s~ 384 (563)
|+....
T Consensus 376 ~~~ra~ 381 (448)
T KOG2590|consen 376 HVSRAK 381 (448)
T ss_pred eecccc
Confidence 986554
No 18
>KOG4213 consensus RNA-binding protein La [RNA processing and modification]
Probab=99.52 E-value=6.6e-15 Score=141.42 Aligned_cols=76 Identities=43% Similarity=0.782 Sum_probs=70.1
Q ss_pred HHHHHHHHHHhhhhcCCCCcCcchHHHHhh--cCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCC--ceEEcCCe--e
Q 008506 297 LALKANIVKQIEYYFSDENLQNDHYLISLM--DAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSS--TVEAQGDK--V 370 (563)
Q Consensus 297 ~~L~~~I~kQIEYYFSDeNL~kD~FLRk~M--D~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~--~VEV~~dK--V 370 (563)
+.|-++|+.||||||.|-||.||.|||.++ ..+|||||.+++.|+|+.+|++|++.|++||+.|. +++|++|+ +
T Consensus 11 a~lE~kii~qleyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ksk~~l~eisedk~k~ 90 (205)
T KOG4213|consen 11 AALEAKIIHQLEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKSKAELMEISEDKTKI 90 (205)
T ss_pred hHHHHhhhhhhhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhCHHhhhhhhhchhhh
Confidence 578888999999999999999999999999 48999999999999999999999999999999985 78999875 5
Q ss_pred ec
Q 008506 371 RR 372 (563)
Q Consensus 371 RR 372 (563)
||
T Consensus 91 rr 92 (205)
T KOG4213|consen 91 RR 92 (205)
T ss_pred hc
Confidence 55
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=99.32 E-value=4.1e-13 Score=141.13 Aligned_cols=86 Identities=35% Similarity=0.624 Sum_probs=72.3
Q ss_pred HHHHHHHhhhhcCCCCcCcchHHHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcC-----------------Cc
Q 008506 300 KANIVKQIEYYFSDENLQNDHYLISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNS-----------------ST 362 (563)
Q Consensus 300 ~~~I~kQIEYYFSDeNL~kD~FLRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S-----------------~~ 362 (563)
...|+.|||||||.+||+.|.|||++|+.+||||+++|..|.|.+++..|.++|+.|||.+ ..
T Consensus 271 I~a~k~QiEyYFseenl~~d~~lrkk~~kaGf~plsfi~kf~Rn~Sf~gd~nLilaa~ke~v~n~a~~~~~~~~~~~~d~ 350 (438)
T COG5193 271 IMAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEVVQNKATNHLEIALGSIEDA 350 (438)
T ss_pred hhhHHhhhHhhhhHHhhhhhhHHHhhhhhcccccHhhhhhhhhccccCCchhhhHHHHHHHhhhhhhhhhhhhhhccchh
Confidence 4456679999999999999999999999999999999999999999999999999999987 11
Q ss_pred --eEEc----CC-eeecCCCCCcccccccc
Q 008506 363 --VEAQ----GD-KVRRRDEWSKWIPASVE 385 (563)
Q Consensus 363 --VEV~----~d-KVRRR~~w~kwv~~s~e 385 (563)
.+.+ ++ .++||..|..|++..-+
T Consensus 351 ~~~~~k~~sp~~~~f~rkk~wSewl~e~~~ 380 (438)
T COG5193 351 QKNEAKDFSPGKKYFIRKKEWSEWLMESNF 380 (438)
T ss_pred hhccccccCcchhhhhhhhhhhhhhccccc
Confidence 1111 12 47889999999987553
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=98.55 E-value=1.6e-08 Score=107.15 Aligned_cols=72 Identities=33% Similarity=0.628 Sum_probs=64.6
Q ss_pred HHHHhhhhcC-----CCCcCcchHHHHhh----cCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcC---CceEEcC--C
Q 008506 303 IVKQIEYYFS-----DENLQNDHYLISLM----DAQGWVPIAIIADFKRVKRMSTDLPFILDALQNS---STVEAQG--D 368 (563)
Q Consensus 303 I~kQIEYYFS-----DeNL~kD~FLRk~M----D~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S---~~VEV~~--d 368 (563)
+.+|+||||| |.|+.+|.||+..- ..+|||||.+|++|+||+.++..++.|..||+.| .+++++. .
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 8899999999 99999999999865 2599999999999999999999999999999999 7889874 4
Q ss_pred eeecCC
Q 008506 369 KVRRRD 374 (563)
Q Consensus 369 KVRRR~ 374 (563)
++||++
T Consensus 155 n~~r~~ 160 (438)
T COG5193 155 NKNRTE 160 (438)
T ss_pred cccccc
Confidence 666654
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=97.92 E-value=6.6e-06 Score=89.17 Aligned_cols=248 Identities=13% Similarity=0.092 Sum_probs=145.5
Q ss_pred HHHHHHH--HHhhhhcCCCCcCcchHHHHhhcCCC---cEehhhhhcchhHhhhcCCHHHHHHHHhcCCceEEcCCeeec
Q 008506 298 ALKANIV--KQIEYYFSDENLQNDHYLISLMDAQG---WVPIAIIADFKRVKRMSTDLPFILDALQNSSTVEAQGDKVRR 372 (563)
Q Consensus 298 ~L~~~I~--kQIEYYFSDeNL~kD~FLRk~MD~dG---~VPIslIasFnRVK~LT~Di~lI~eALr~S~~VEV~~dKVRR 372 (563)
.|.+++. |+++|||+..++.+|.|++..|+..| +.+|+.+..|.++..++++...++..++.|...+....+.|+
T Consensus 96 ~l~e~~~~~k~~s~~~~~~~~~~~~~~~~k~~~t~~~~~~~~S~~~~s~~~~~~s~n~~~~~~~~~~sa~~~~~~~~~~~ 175 (448)
T KOG2590|consen 96 PLKEYSKSDKKKSWPASKPFTPRDSFKGSKPTNTGNGTFLPISKISSSGPVSGGSANNSNIRGPLKGSASSNPVPNNSRA 175 (448)
T ss_pred cccccccccccccCcccCCCCccccccCCCccccCCCccCCCccccccccccCcccccccccCcCCCCCcCCcCcccccc
Confidence 4455554 49999999999999999999999888 999999999999999999999999999999889999999999
Q ss_pred CCCCCcccccccccccCCcccCccccccccccccccCCCCCCCCCCCCCcccccccCCCCcccCCCCCCCcccccCCCCC
Q 008506 373 RDEWSKWIPASVEQTMSSTAQTSQSQSAENPVDSIGNGDINKDNKREMPKENVGFSSNTGNLMENVPPSFDSVEIEPDNG 452 (563)
Q Consensus 373 R~~w~kwv~~s~e~~~~S~~~~~~~~pieev~~~f~n~~~~~~n~~~~~~~~~efa~n~~~~~~~~~~~~~~~~~~~da~ 452 (563)
|..-++|...... ....+. +++.+..+..+. .++.-....+..+-.=.++.+. .+..=.++.+.-++.
T Consensus 176 ~~~~qr~~~~~~~-~~~~~~-~d~~~~t~~~n~------~~~~~~~~~~~~n~~~~~~~~s----s~~q~~k~~~~~~~~ 243 (448)
T KOG2590|consen 176 KPLNQRWPDSSPS-SGGVRD-GDFKQLTNNPNS------VPGQRGQNQHHDNSSQNPHHNS----SGFQRVKNMNGNSNH 243 (448)
T ss_pred ccccccCCCCCCC-CcCccc-cchhhhhcCcCC------CCccccccccccccCcCCCCCC----CCccchhhcccCccc
Confidence 9999999865441 222221 344333332111 1111111011111111111110 000000111111111
Q ss_pred cccc------------------------cccccccCCCCccccCCCCCcccccccccccccCCCccccCccccccccccc
Q 008506 453 EEHC------------------------DEFLLLDDGKPAFSAENGDSRTSLSESDMKFSNLGTNHNISSEDLSQRTESA 508 (563)
Q Consensus 453 ~~~~------------------------~~~~~~~~~kp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 (563)
..+. .--.+...+.|+...-+- .--.+..+- ...-.+.--+-|++..+.+.-.
T Consensus 244 ~q~~~G~~~~~~~l~~~~~~~~k~~~~~~~~~~~~~~~p~~~~~~~-~~~s~~pi~--~~~~~~~~~ie~~FSeE~~~~d 320 (448)
T KOG2590|consen 244 YQYSRGFSNSLPDLGNQNRNRVKNSSYRPAPQKSQSGEPIQPGDKN-QIPSVQPIG--NVIAFIQEPIEFYFSEENLQRD 320 (448)
T ss_pred cccCCCcCCccccccCcccccccccccccchhhcCCCCccccCccc-cCCCccccc--ccccccccccccccchHHHhhh
Confidence 1111 011222222232220000 000000000 0122233345567777777777
Q ss_pred cccccC------CccccccchhhhhhhhcccccccccccchhhhhhhhhcccccccCcC
Q 008506 509 RFGDYG------TQGLERSSTVAVQNLIELSNDFANTFMLDEELEIEQKTMKKDDLSAH 561 (563)
Q Consensus 509 ~~~~~~------~~~~~~~s~~~~~n~~~~s~df~~tfmldeelele~~~~~~~~~s~~ 561 (563)
.++..+ ++++...+++.. |+..|..||.+++++||+++||++--++.+++..
T Consensus 321 ~~n~~k~~~l~~ia~F~r~ad~s~-d~nli~~alr~s~ive~~~d~~~r~~~~~g~~~~ 378 (448)
T KOG2590|consen 321 RFNREKFVPLRVIAKFKRVADLSS-DINLILAALRNSLIVEETGDLERRGGDRWGNHVS 378 (448)
T ss_pred hhhhcccchhhhhhhhhhhhhccc-CHHHHHHHHhhhhhhhccchhhhcccccccceec
Confidence 777766 667766666665 8889999999999999999999995555555443
No 22
>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=91.12 E-value=1.7 Score=52.02 Aligned_cols=49 Identities=24% Similarity=0.546 Sum_probs=43.4
Q ss_pred hcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhc-CCceEEc--CCeeecCC
Q 008506 326 MDAQGWVPIAIIADFKRVKRMSTDLPFILDALQN-SSTVEAQ--GDKVRRRD 374 (563)
Q Consensus 326 MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~-S~~VEV~--~dKVRRR~ 374 (563)
.|.+|||-|.|||+.-.+--|..+-+.|+.||.. |+.+||+ +-|||=|-
T Consensus 473 pDaeGWVYLNLL~NmAQLHiiNVTPdFVRsAV~E~StKfQLSpDGrKIRWRG 524 (989)
T PF09421_consen 473 PDAEGWVYLNLLCNMAQLHIINVTPDFVRSAVSEKSTKFQLSPDGRKIRWRG 524 (989)
T ss_pred cccccceehHHHHHHHHHHhhccCHHHHHHHHHhcccceeeCCCCCeeeecC
Confidence 3789999999999999999999999999999985 8899997 45999664
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=90.51 E-value=0.37 Score=47.13 Aligned_cols=52 Identities=21% Similarity=0.359 Sum_probs=35.4
Q ss_pred hhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCc--eEEc-----CCeeecCCCC
Q 008506 325 LMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSST--VEAQ-----GDKVRRRDEW 376 (563)
Q Consensus 325 ~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~--VEV~-----~dKVRRR~~w 376 (563)
.||++|||+|..|+...+.+.+..+.+.|.+++++.+. .|+. +.+||.+...
T Consensus 26 ~~d~~G~v~v~dLL~~~~~~~~~~t~~~i~~vV~~~~K~Rfel~~~~~~~~~IRA~qGH 84 (186)
T PF01885_consen 26 VMDPDGWVSVDDLLRALRFKGLWVTEEDIREVVETDDKQRFELRYEDPGGWRIRANQGH 84 (186)
T ss_dssp ---TT--EEHHHHHHHHHHT-TT--HHHHHHHHHH-SS--EEEE-----TTEEEESS--
T ss_pred ccCCCCCEeHHHHHHHHHHcCCCCCHHHHHHHHhhCCCCCeeEEcccccCceEEECCCC
Confidence 37899999999999999999888788999999998764 6666 6789977543
No 24
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=89.62 E-value=0.55 Score=45.98 Aligned_cols=55 Identities=20% Similarity=0.326 Sum_probs=42.6
Q ss_pred hhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCc--eEEcCCeeecCCCCCcc
Q 008506 325 LMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSST--VEAQGDKVRRRDEWSKW 379 (563)
Q Consensus 325 ~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~--VEV~~dKVRRR~~w~kw 379 (563)
.||++|||+|..|+...+.+....+.+.|.+++++.+. .|+++++||.+....-.
T Consensus 27 ~ld~~G~v~v~~Ll~~~~~~~~~~t~~~l~~vV~~d~K~Rf~l~~~~IRA~qGHSi~ 83 (179)
T PRK00819 27 TLDEEGWVDIDALIEALAKAYKWVTRELLEAVVESDDKGRFEISGDRIRARQGHSVD 83 (179)
T ss_pred ccCCCCCEEHHHHHHHHHHccCCCCHHHHHHHHHcCCCcceEecCceEEeccCcCCc
Confidence 46899999999999877654333467899999998875 66778899988765443
No 25
>KOG2278 consensus RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis]
Probab=83.08 E-value=0.93 Score=44.98 Aligned_cols=41 Identities=15% Similarity=0.291 Sum_probs=35.7
Q ss_pred HHHhhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCc
Q 008506 322 LISLMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSST 362 (563)
Q Consensus 322 LRk~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~ 362 (563)
++=+|+.||||+|..|++.++.|.+.-.+++|.++++.-..
T Consensus 25 ~~L~m~~dGfvpv~~lL~lnq~r~~~~t~ddi~riVk~ndK 65 (207)
T KOG2278|consen 25 LRLNMRGDGFVPVEDLLNLNQFRGANHTIDDIRRIVKRNDK 65 (207)
T ss_pred hcccccCCCceEHHHHhccchhcccCCcHHHHHHHHhcccc
Confidence 34467899999999999999999999889999999987653
No 26
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=65.23 E-value=34 Score=40.99 Aligned_cols=15 Identities=7% Similarity=0.104 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHhhhh
Q 008506 296 TLALKANIVKQIEYY 310 (563)
Q Consensus 296 ~~~L~~~I~kQIEYY 310 (563)
++-|.+.++.||-=|
T Consensus 727 e~vLse~~iqnLik~ 741 (1102)
T KOG1924|consen 727 EDVLSESMIQNLIKH 741 (1102)
T ss_pred HHHHHHHHHHHHHHh
Confidence 445555555555443
No 27
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=63.92 E-value=9.3 Score=38.82 Aligned_cols=54 Identities=20% Similarity=0.271 Sum_probs=42.6
Q ss_pred hhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCc--eEEcCCeeecCCCCCc
Q 008506 325 LMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSST--VEAQGDKVRRRDEWSK 378 (563)
Q Consensus 325 ~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~--VEV~~dKVRRR~~w~k 378 (563)
.||.+||+.|+-|+.--|-+----|.++|..+++..+. .++.+.+||.+..|.-
T Consensus 53 ~lD~~Gwa~i~~l~~~~~k~~~~~~~~~l~~iV~~d~K~Rf~l~~~~IRA~yGHSi 108 (211)
T COG1859 53 RLDEEGWADIDELLEGLRKAGRWLTRELLLAVVATDDKGRFELKEGKIRARYGHSI 108 (211)
T ss_pred eeccccchhHHHHHHHHHhhccCCCHHHHHHHHhcCCCceeEecccceeeccCcce
Confidence 35899999999888766654333467888888888775 7888999999999983
No 28
>PTZ00315 2'-phosphotransferase; Provisional
Probab=54.56 E-value=16 Score=41.95 Aligned_cols=54 Identities=13% Similarity=0.174 Sum_probs=41.9
Q ss_pred hhcCCCcEehhhhhcchhHhhhcCCHHHHHHHHhcCCc--eEEc-----C-CeeecCCCCCc
Q 008506 325 LMDAQGWVPIAIIADFKRVKRMSTDLPFILDALQNSST--VEAQ-----G-DKVRRRDEWSK 378 (563)
Q Consensus 325 ~MD~dG~VPIslIasFnRVK~LT~Di~lI~eALr~S~~--VEV~-----~-dKVRRR~~w~k 378 (563)
.||++|||.|..|+.-.+.+...-+.+.|.+++++.+. .++. + .+||.+....-
T Consensus 399 ~ld~~Gwv~vd~LL~~~~~~~~~~t~e~i~~VV~~ndK~RF~l~~~~~~~~~~IRA~QGHSi 460 (582)
T PTZ00315 399 PITSNGYVLLDDILRQPPMRNDPVSVQDVARVVRDSDKQRFKLAYGAADGRLYIRANQGHSI 460 (582)
T ss_pred CcCCCCCEEHHHHHHHHHhcCCCCCHHHHHHHHHcCCCCceEEeccCCCCceEEEeccCccc
Confidence 36899999999999988887665678999999998874 5564 1 25888776653
No 29
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=42.82 E-value=8.1 Score=44.11 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC
Q 008506 183 PPRGDPNASVANFPNRRPNTQEPGG 207 (563)
Q Consensus 183 ~pRGD~~~~~~n~g~~R~~~qgRGg 207 (563)
+|||.+.++-++++.+|||.||||+
T Consensus 517 ~p~~k~ss~~~~~~~~~g~gr~rg~ 541 (556)
T PF05918_consen 517 PPSGKYSSNGGNSGRGRGGGRGRGR 541 (556)
T ss_dssp -------------------------
T ss_pred CCCCCCcCCCCCCCCCCCCCCCCCC
Confidence 4566666666554444555555553
No 30
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=40.44 E-value=3.2e+02 Score=33.15 Aligned_cols=11 Identities=27% Similarity=0.540 Sum_probs=5.7
Q ss_pred CeeecCCCCCc
Q 008506 368 DKVRRRDEWSK 378 (563)
Q Consensus 368 dKVRRR~~w~k 378 (563)
++-|||.+|.+
T Consensus 807 ~~~rrR~~r~~ 817 (894)
T KOG0132|consen 807 REHRRRSDRDR 817 (894)
T ss_pred ccccccCcccc
Confidence 34566664443
No 31
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=28.19 E-value=2.7e+02 Score=31.02 Aligned_cols=27 Identities=19% Similarity=0.185 Sum_probs=16.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 008506 183 PPRGDPNASVANFPNRRPNTQEPGGHMN 210 (563)
Q Consensus 183 ~pRGD~~~~~~n~g~~R~~~qgRGgH~N 210 (563)
..||-....++.+|++|+| .||||-.+
T Consensus 357 g~Rgg~Gg~~gGrGgGRGg-gG~GGGgg 383 (465)
T KOG3973|consen 357 GSRGGSGGNWGGRGGGRGG-GGRGGGGG 383 (465)
T ss_pred CCCCCCCCCCCCCCCCCCC-CCCCCCCC
Confidence 3466555566777778874 55655443
No 32
>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=24.65 E-value=63 Score=31.67 Aligned_cols=59 Identities=20% Similarity=0.292 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhhhhcCCCCc-CcchHHHHhhcCCCcEe--hhhhhcchhHhhhcCCHHHHHHHHhc
Q 008506 296 TLALKANIVKQIEYYFSDENL-QNDHYLISLMDAQGWVP--IAIIADFKRVKRMSTDLPFILDALQN 359 (563)
Q Consensus 296 ~~~L~~~I~kQIEYYFSDeNL-~kD~FLRk~MD~dG~VP--IslIasFnRVK~LT~Di~lI~eALr~ 359 (563)
...|.+.|..||...+.++.. .-=.||...+|++||+. +..|+ +.+..+.+.|.++|+.
T Consensus 14 ~~sL~e~L~~Ql~~~~l~~~~~~ia~~lI~~LD~~GyL~~~~~eia-----~~l~~~~~~v~~~l~~ 75 (194)
T PF04963_consen 14 EESLYEHLLEQLNLSPLSEEEREIAEYLIDNLDDDGYLTESLEEIA-----EELGVSEEEVEKALEL 75 (194)
T ss_dssp -----HHHHHHHHHH---TCCHHHHHHHCCCBTTTSTCSS-HHHHH-----HHCTS-HHHHHHHHHH
T ss_pred ccCHHHHHHHHHcCcccCHHHHHHHHHHHHcCCCCCccCCCHHHHH-----HHhCCCHHHHHHHHHH
Confidence 458999999999987544432 22455666678999975 44443 2333455555555543
No 33
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=23.64 E-value=1.6e+02 Score=35.70 Aligned_cols=13 Identities=15% Similarity=0.263 Sum_probs=7.0
Q ss_pred hcCCHHHHHHHHh
Q 008506 346 MSTDLPFILDALQ 358 (563)
Q Consensus 346 LT~Di~lI~eALr 358 (563)
+.-||-.|..||+
T Consensus 797 iKP~i~avt~ACE 809 (1102)
T KOG1924|consen 797 IKPDIVAVTAACE 809 (1102)
T ss_pred cChHHHHHHHHHH
Confidence 3345555555655
No 34
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=20.98 E-value=2.4e+02 Score=35.05 Aligned_cols=9 Identities=22% Similarity=0.324 Sum_probs=4.2
Q ss_pred CCCCCCCCC
Q 008506 189 NASVANFPN 197 (563)
Q Consensus 189 ~~~~~n~g~ 197 (563)
++||+|||.
T Consensus 1213 ~~~~~~~Ga 1221 (1282)
T KOG0921|consen 1213 PSARANYGA 1221 (1282)
T ss_pred CCCCCCccc
Confidence 344455544
Done!