Query 045972
Match_columns 299
No_of_seqs 172 out of 563
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:27:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045972.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045972hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2278 RNA:NAD 2'-phosphotran 100.0 1.1E-67 2.4E-72 462.8 11.8 203 92-299 5-207 (207)
2 PRK00819 RNA 2'-phosphotransfe 100.0 2.3E-63 5.1E-68 440.2 17.7 176 91-287 3-178 (179)
3 PF01885 PTS_2-RNA: RNA 2'-pho 100.0 5.3E-64 1.1E-68 446.2 12.2 183 90-280 1-186 (186)
4 PTZ00315 2'-phosphotransferase 100.0 1.7E-62 3.6E-67 495.4 18.5 201 91-298 375-580 (582)
5 COG1859 KptA RNA:NAD 2'-phosph 100.0 5.5E-53 1.2E-57 380.3 15.1 178 90-288 28-206 (211)
6 PF05918 API5: Apoptosis inhib 88.4 0.14 3E-06 53.3 0.0 39 49-89 515-553 (556)
7 cd08029 LA_like_fungal La-moti 88.0 0.44 9.6E-06 37.2 2.5 46 116-172 29-75 (76)
8 cd08028 LARP_3 La RNA-binding 87.2 0.63 1.4E-05 37.0 3.1 50 116-172 31-81 (82)
9 cd07323 LAM LA motif RNA-bindi 87.0 0.66 1.4E-05 36.0 3.1 48 116-172 27-74 (75)
10 cd08036 LARP_5 La RNA-binding 87.0 0.49 1.1E-05 37.2 2.3 47 116-173 27-75 (75)
11 cd08033 LARP_6 La RNA-binding 85.8 0.69 1.5E-05 36.3 2.6 48 116-172 29-76 (77)
12 cd08031 LARP_4_5_like La RNA-b 85.0 0.8 1.7E-05 35.8 2.6 48 116-172 27-74 (75)
13 cd08035 LARP_4 La RNA-binding 83.3 0.88 1.9E-05 35.7 2.2 48 116-173 27-75 (75)
14 cd01439 TCCD_inducible_PARP_li 81.4 0.83 1.8E-05 38.2 1.5 33 199-231 1-41 (121)
15 cd01341 ADP_ribosyl ADP_ribosy 77.3 1.2 2.6E-05 37.8 1.2 23 199-221 1-23 (137)
16 smart00715 LA Domain in the RN 77.2 1.8 3.8E-05 34.1 2.1 49 116-173 30-79 (80)
17 cd08034 LARP_1_2 La RNA-bindin 77.1 1.8 3.9E-05 33.7 2.0 42 116-164 27-68 (73)
18 cd08038 LARP_2 La RNA-binding 75.8 1.9 4.1E-05 33.7 1.9 41 116-163 27-67 (73)
19 cd08037 LARP_1 La RNA-binding 75.1 2.2 4.9E-05 33.2 2.1 36 116-156 27-62 (73)
20 COG3502 Uncharacterized protei 75.0 4.3 9.2E-05 34.2 3.8 90 198-292 4-102 (115)
21 PF00644 PARP: Poly(ADP-ribose 73.9 2.9 6.3E-05 37.2 2.9 21 198-218 61-81 (206)
22 cd08030 LA_like_plant La-motif 73.2 2.3 4.9E-05 34.5 1.8 16 116-131 30-45 (90)
23 PF05383 La: La domain; Inter 68.4 4.2 9.1E-05 30.3 2.2 33 117-154 27-60 (61)
24 cd08032 LARP_7 La RNA-binding 66.6 5.8 0.00013 31.5 2.8 46 117-172 35-81 (82)
25 PF09421 FRQ: Frequency clock 64.4 11 0.00024 41.9 5.3 70 98-176 444-525 (989)
26 cd01437 parp_like Poly(ADP-rib 62.4 5.2 0.00011 39.5 2.2 23 198-220 196-218 (347)
27 PF14487 DUF4433: Domain of un 60.9 9.7 0.00021 34.0 3.5 20 201-220 1-21 (205)
28 COG4907 Predicted membrane pro 48.4 15 0.00032 38.1 2.8 20 49-68 557-576 (595)
29 PF03089 RAG2: Recombination a 46.0 59 0.0013 32.0 6.3 95 172-296 86-196 (337)
30 KOG3293 Small nuclear ribonucl 45.9 20 0.00044 30.8 2.8 27 64-90 95-121 (134)
31 PF12872 OST-HTH: OST-HTH/LOTU 44.9 57 0.0012 23.9 4.9 61 94-162 3-63 (74)
32 PLN03122 Poly [ADP-ribose] pol 39.9 17 0.00036 40.0 1.8 22 199-220 653-674 (815)
33 PLN03124 poly [ADP-ribose] pol 39.9 18 0.00039 38.7 2.0 21 199-219 488-508 (643)
34 cd00052 EH Eps15 homology doma 31.5 77 0.0017 22.0 3.7 35 115-156 9-43 (67)
35 PF15633 Tox-ART-HYD1: HYD1 si 31.5 75 0.0016 26.1 3.9 68 200-274 1-85 (96)
36 KOG3973 Uncharacterized conser 29.2 45 0.00097 33.6 2.7 9 81-89 447-455 (465)
37 cd01436 Dipth_tox_like Mono-AD 28.7 33 0.00071 29.7 1.5 22 200-222 2-23 (147)
38 PF10961 DUF2763: Protein of u 27.5 91 0.002 25.2 3.7 16 32-47 33-48 (91)
39 PF12300 DUF3628: Protein of u 24.5 50 0.0011 29.7 1.9 19 60-78 51-69 (180)
40 PF05918 API5: Apoptosis inhib 24.5 25 0.00054 37.1 0.0 14 8-21 436-449 (556)
41 PLN03123 poly [ADP-ribose] pol 23.8 46 0.001 37.4 1.9 21 199-219 828-848 (981)
42 PF00036 EF-hand_1: EF hand; 23.5 71 0.0015 20.1 2.0 17 115-131 10-26 (29)
43 cd05027 S-100B S-100B: S-100B 23.4 1.1E+02 0.0024 23.9 3.5 43 116-158 20-63 (88)
44 PF13833 EF-hand_8: EF-hand do 21.4 1.9E+02 0.0042 19.6 4.1 35 118-156 1-35 (54)
No 1
>KOG2278 consensus RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-67 Score=462.80 Aligned_cols=203 Identities=63% Similarity=0.994 Sum_probs=192.6
Q ss_pred chhhHHHHHHHHHhccCCCcCCceeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEE
Q 045972 92 DKIDALGRLLTRILRHMASELNLNMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLI 171 (299)
Q Consensus 92 ~r~~~LSK~LSylLRH~pek~GL~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~I 171 (299)
+|.++|||+|||||||.|.+++|+|+.||||+|++||++++.+ ..+.|.|||++||..|+||||.|.++.++++|
T Consensus 5 ~~id~lskaLs~iLRHtA~~~~L~m~~dGfvpv~~lL~lnq~r-----~~~~t~ddi~riVk~ndKqRF~l~d~~~el~I 79 (207)
T KOG2278|consen 5 DRIDALSKALSRILRHTATELRLNMRGDGFVPVEDLLNLNQFR-----GANHTIDDIRRIVKRNDKQRFSLIDEAGELLI 79 (207)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcccccCCCceEHHHHhccchhc-----ccCCcHHHHHHHHhccccceEEeecCCCcEEE
Confidence 5677999999999999999999999999999999999987532 23578999999999999999999888889999
Q ss_pred EecCCCcccccccccccccCCCCCCCCeEEEeCchhcHHHHHHhCCCCCCCcceEeccCCCCCCceeeeeeeCCcEEEEE
Q 045972 172 RANQGHTITTVESESLLKPILSAEEVSVCVHGTYKRNLDSILESGLKRMKRLHVHFSCGLPTDGEVISGMRRDVNVLIFL 251 (299)
Q Consensus 172 RA~QGHSi~~v~~~~~L~pi~~~~~~~~LyHGT~~~~~~~I~~~GLk~M~R~hVHLs~~~~~a~~V~SG~R~~~~VlI~I 251 (299)
|||||||+++|+.+.+|.||+.|++.|.|+|||++++|++|+++||+||+|+|||||++.++|.+||||||++|+|+|||
T Consensus 80 rAnQGHSik~vq~~~~l~pi~~~s~lP~lVHGT~~k~~~~Il~sGls~m~RnHvHlspGl~~d~gVISGmRss~nvyIfI 159 (207)
T KOG2278|consen 80 RANQGHSIKTVQSEKLLKPILSPSELPVLVHGTYRKNWPSILASGLSRMNRNHVHLSPGLPGDPGVISGMRSSCNVYIFI 159 (207)
T ss_pred EecCCcceeecchhhhhcccCChhhCchheechhhhhhHHHHHhhcccccCCeeeecCCCCCCcchhhhhhccceEEEEe
Confidence 99999999999888889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ehHHHHhCCCeEEEeCCcEEEecCCCccccccceeeccccCCCCCcCC
Q 045972 252 NVRKALADGMKLYISDNKVVLTEGFDGVVPVEYFEKIESWPDRRPISF 299 (299)
Q Consensus 252 D~~kA~~dGi~Fy~S~NgViLTeG~~G~IP~~yf~kv~~~~~~~~~~~ 299 (299)
|.++|++|||+||+|+||||||+|.+|++|++||++++.|++++..+|
T Consensus 160 d~~~al~dgi~fyrS~N~ViLT~g~vgll~~~yfk~~et~~Dees~~~ 207 (207)
T KOG2278|consen 160 DIKKALEDGIAFYRSDNGVILTEGIVGLLPVKYFKKIETWPDEESIPF 207 (207)
T ss_pred cchHHHhhhhHHhhhcCceEeccCccccccHHHhccCCCCcccccCCC
Confidence 999999999999999999999999999999999999999999987765
No 2
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=100.00 E-value=2.3e-63 Score=440.16 Aligned_cols=176 Identities=34% Similarity=0.513 Sum_probs=158.1
Q ss_pred cchhhHHHHHHHHHhccCCCcCCceeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceE
Q 045972 91 KDKIDALGRLLTRILRHMASELNLNMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELL 170 (299)
Q Consensus 91 ~~r~~~LSK~LSylLRH~pek~GL~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~ 170 (299)
++++++|||+|||||||+|+++||+||+||||+|+|||++.... ++++|+++|++||++||||||+|+. .+
T Consensus 3 ~~~~~~lSK~LS~lLRH~p~~~GL~ld~~G~v~v~~Ll~~~~~~-----~~~~t~~~l~~vV~~d~K~Rf~l~~----~~ 73 (179)
T PRK00819 3 GKRLEKLSKFLSGVLRHKPEAIGLTLDEEGWVDIDALIEALAKA-----YKWVTRELLEAVVESDDKGRFEISG----DR 73 (179)
T ss_pred chhHHHHHHHHHHHHCCCHHHcCCccCCCCCEEHHHHHHHHHHc-----cCCCCHHHHHHHHHcCCCcceEecC----ce
Confidence 56789999999999999999999999999999999999986432 4579999999999999999999973 38
Q ss_pred EEecCCCcccccccccccccCCCCCCCCeEEEeCchhcHHHHHHhCCCCCCCcceEeccCCCCCCceeeeeeeCCcEEEE
Q 045972 171 IRANQGHTITTVESESLLKPILSAEEVSVCVHGTYKRNLDSILESGLKRMKRLHVHFSCGLPTDGEVISGMRRDVNVLIF 250 (299)
Q Consensus 171 IRA~QGHSi~~v~~~~~L~pi~~~~~~~~LyHGT~~~~~~~I~~~GLk~M~R~hVHLs~~~~~a~~V~SG~R~~~~VlI~ 250 (299)
|||+||||++ |+.+ +++. +.|++|||||+.++|++|+++||+||+|+|||||++.++ ++++|||+++||+|+
T Consensus 74 IRA~qGHSi~-v~~~--~~~~---~~P~~lyHGT~~~~~~~I~~~GL~pm~R~hVHLs~~~~~--a~~~G~R~~~~vil~ 145 (179)
T PRK00819 74 IRARQGHSVD-VDLD--LEED---TPPAVLYHGTSSEELDSILEEGLKPMKRHYVHLSTDIET--AREVGARHGSPVILE 145 (179)
T ss_pred EEeccCcCCc-cccC--CccC---CCCceeEeCCCHHHHHHHHHhCCCccCCCeEEecCCccc--CeEEcccCCCeEEEE
Confidence 9999999997 4443 3332 224499999999999999999999999999999999865 578999999999999
Q ss_pred EehHHHHhCCCeEEEeCCcEEEecCCCccccccceee
Q 045972 251 LNVRKALADGMKLYISDNKVVLTEGFDGVVPVEYFEK 287 (299)
Q Consensus 251 ID~~kA~~dGi~Fy~S~NgViLTeG~~G~IP~~yf~k 287 (299)
||+++|+++|++||+|+||||||++ ||++||++
T Consensus 146 Id~~~~~~~Gi~f~~s~n~V~Lt~~----VP~~y~~~ 178 (179)
T PRK00819 146 VDAECMRKRGIKFYKAENGVWLTEY----VPPEYLKE 178 (179)
T ss_pred EeHHHHHhCCCEEEEeCCCEEEeCC----CCHHHccC
Confidence 9999999999999999999999997 99999975
No 3
>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=100.00 E-value=5.3e-64 Score=446.22 Aligned_cols=183 Identities=48% Similarity=0.676 Sum_probs=117.0
Q ss_pred CcchhhHHHHHHHHHhccCCCcCCceeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEe-ecCCc
Q 045972 90 SKDKIDALGRLLTRILRHMASELNLNMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLL-EENGE 168 (299)
Q Consensus 90 ~~~r~~~LSK~LSylLRH~pek~GL~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~-~e~g~ 168 (299)
|++++++|||+|||||||+|+++||+||+||||+|+|||+++..+ +.++|+++|++||++|+||||+|. ++++.
T Consensus 1 ~~~~~~~lSK~Ls~lLRH~p~~~gL~~d~~G~v~v~dLL~~~~~~-----~~~~t~~~i~~vV~~~~K~Rfel~~~~~~~ 75 (186)
T PF01885_consen 1 NQKRDVKLSKALSYLLRHGPEKEGLVMDPDGWVSVDDLLRALRFK-----GLWVTEEDIREVVETDDKQRFELRYEDPGG 75 (186)
T ss_dssp -------HHHHHHHHHHT-TGGGT----TT--EEHHHHHHHHHHT------TT--HHHHHHHHHH-SS--EEEE-----T
T ss_pred CchhHHHHHHHHHHHhCCChhhcCCccCCCCCEeHHHHHHHHHHc-----CCCCCHHHHHHHHhhCCCCCeeEEcccccC
Confidence 578899999999999999999999999999999999999986542 456999999999999999999999 55567
Q ss_pred eEEEecCCCcccccccccccccCCC--CCCCCeEEEeCchhcHHHHHHhCCCCCCCcceEeccCCCCCCceeeeeeeCCc
Q 045972 169 LLIRANQGHTITTVESESLLKPILS--AEEVSVCVHGTYKRNLDSILESGLKRMKRLHVHFSCGLPTDGEVISGMRRDVN 246 (299)
Q Consensus 169 ~~IRA~QGHSi~~v~~~~~L~pi~~--~~~~~~LyHGT~~~~~~~I~~~GLk~M~R~hVHLs~~~~~a~~V~SG~R~~~~ 246 (299)
++|||+||||++.++. ..|++|+. ...|++|||||+.++|+.|+++||+||+|+|||||++.+ .++++|||+++|
T Consensus 76 ~~IRA~qGHSi~~v~~-~~L~~i~~~~~~~p~~lyHGT~~~~~~~I~~~GL~~m~R~hVHls~~~~--~a~~sG~R~~~~ 152 (186)
T PF01885_consen 76 WRIRANQGHSIPTVDS-LLLEPITLPEEEPPPILYHGTYRKAWPSILEEGLKPMGRNHVHLSTGPE--TAVISGMRRSCP 152 (186)
T ss_dssp TEEEESS--SS---------------SS---SEEEE--BGGGHHHHHHH-B---SSSSEEEES-HH--HHHHHHTTSSSB
T ss_pred ceEEECCCCCCccccc-cccccccCcccCCCCEEEEccchhhHHHHHHhCCCCCCCCEEEEeeccC--CceeecCCCCCe
Confidence 8999999999986654 45777653 234679999999999999999999999999999999954 468899999999
Q ss_pred EEEEEehHHHHhCCCeEEEeCCcEEEecCCCccc
Q 045972 247 VLIFLNVRKALADGMKLYISDNKVVLTEGFDGVV 280 (299)
Q Consensus 247 VlI~ID~~kA~~dGi~Fy~S~NgViLTeG~~G~I 280 (299)
|+||||+++|++|||+||+|+||||||+|++|+|
T Consensus 153 V~i~Id~~~a~~~Gi~f~~s~n~V~Lt~G~~G~~ 186 (186)
T PF01885_consen 153 VLIYIDAAKALEDGIKFYRSSNGVILTEGNDGVI 186 (186)
T ss_dssp EEEEEEHHHHHHTT---EE-SSSEEEES------
T ss_pred EEEEEcHHHHHHCCCeEEEeCCcEEEecccccCC
Confidence 9999999999999999999999999999988875
No 4
>PTZ00315 2'-phosphotransferase; Provisional
Probab=100.00 E-value=1.7e-62 Score=495.39 Aligned_cols=201 Identities=40% Similarity=0.661 Sum_probs=182.4
Q ss_pred cchhhHHHHHHHHHhccCCCcCCceeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEee--cCCc
Q 045972 91 KDKIDALGRLLTRILRHMASELNLNMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLE--ENGE 168 (299)
Q Consensus 91 ~~r~~~LSK~LSylLRH~pek~GL~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~--e~g~ 168 (299)
++++++|||+|||||||+|+++||+||++|||+|+|||++.... ..++|+++|++||++||||||+|.. +++.
T Consensus 375 ~~~~~~lSK~LS~lLRH~pe~~GL~ld~~Gwv~vd~LL~~~~~~-----~~~~t~e~i~~VV~~ndK~RF~l~~~~~~~~ 449 (582)
T PTZ00315 375 EEKLVTYSKFMSRLLRHKADQWRVPITSNGYVLLDDILRQPPMR-----NDPVSVQDVARVVRDSDKQRFKLAYGAADGR 449 (582)
T ss_pred cchHHHHHHHHHHHHcCCHhhcCCCcCCCCCEEHHHHHHHHHhc-----CCCCCHHHHHHHHHcCCCCceEEeccCCCCc
Confidence 56788999999999999999999999999999999999976421 3469999999999999999999983 2445
Q ss_pred eEEEecCCCcccccccccccccCCCCCCCCeEEEeCchhcHHHHHHhC-CCCCCCcceEeccCCCCCCceeeeeeeCCcE
Q 045972 169 LLIRANQGHTITTVESESLLKPILSAEEVSVCVHGTYKRNLDSILESG-LKRMKRLHVHFSCGLPTDGEVISGMRRDVNV 247 (299)
Q Consensus 169 ~~IRA~QGHSi~~v~~~~~L~pi~~~~~~~~LyHGT~~~~~~~I~~~G-Lk~M~R~hVHLs~~~~~a~~V~SG~R~~~~V 247 (299)
++|||+||||++.|+. .|.++++++++|+|||||+.++|++|+++| |+||+|+|||||++.+++.+|+||||+++||
T Consensus 450 ~~IRA~QGHSi~~V~~--~l~~~~~~~~~~~lyHGT~~~~~~sI~~~G~L~~M~R~HVHLs~~~~~~~~v~sG~R~~~~V 527 (582)
T PTZ00315 450 LYIRANQGHSIDGVEP--ELRTLTSVEEVPVAVHGTYWSAWKAIQRCGYLSTMTRQHIHFAKGLINDEQVISGMRNNVQL 527 (582)
T ss_pred eEEEeccCcccccccc--cccccCCCCCCCeEEeCCcHHHHHHHHHcCCccccCCCeEEecCCCCCcCceEeeccCCceE
Confidence 7999999999975553 367777777788999999999999999999 9999999999999999988899999999999
Q ss_pred EEEEehHHHHhCCCeEEEeCCcEEEecCC--CccccccceeeccccCCCCCcC
Q 045972 248 LIFLNVRKALADGMKLYISDNKVVLTEGF--DGVVPVEYFEKIESWPDRRPIS 298 (299)
Q Consensus 248 lI~ID~~kA~~dGi~Fy~S~NgViLTeG~--~G~IP~~yf~kv~~~~~~~~~~ 298 (299)
+||||+++|+++||+||+|+||||||+|+ +|.||++||++|++++++.+|.
T Consensus 528 li~IDa~k~~~dGi~fy~S~NgV~LT~G~~~~G~VP~~y~~~v~~r~~~~~~~ 580 (582)
T PTZ00315 528 FLYLDVAAVLADGVALYESSNGVILTPGVGHTRQLPLKYVAKVVDRSTGRTIY 580 (582)
T ss_pred EEEEEHHHHHhCCCeEEEeCCcEEEecCCCCCCccCHHHHHHHHcccCCCccC
Confidence 99999999999999999999999999995 4999999999999999888763
No 5
>COG1859 KptA RNA:NAD 2'-phosphotransferase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-53 Score=380.25 Aligned_cols=178 Identities=37% Similarity=0.538 Sum_probs=160.4
Q ss_pred CcchhhHHHHHHHHHhccCCCcCCceeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCce
Q 045972 90 SKDKIDALGRLLTRILRHMASELNLNMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGEL 169 (299)
Q Consensus 90 ~~~r~~~LSK~LSylLRH~pek~GL~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~ 169 (299)
++.+++++||+|||+|||.|+.+||.||++||+++++|+..+.+. ++++|.+.|..||++|||+||+|++ .
T Consensus 28 ~~~~~~~~SK~lS~vLRH~p~~~gl~lD~~Gwa~i~~l~~~~~k~-----~~~~~~~~l~~iV~~d~K~Rf~l~~----~ 98 (211)
T COG1859 28 NEKERVKLSKFLSGVLRHFPEAIGLRLDEEGWADIDELLEGLRKA-----GRWLTRELLLAVVATDDKGRFELKE----G 98 (211)
T ss_pred CcchhhhHHHHHHHHHhcChHHcCeeeccccchhHHHHHHHHHhh-----ccCCCHHHHHHHHhcCCCceeEecc----c
Confidence 677889999999999999999999999999999999999987543 5689999999999999999999985 3
Q ss_pred EEEecCCCcccccccccccccCCCCCCCCeEEEeCchhcHHHHHHhCCCCCCCcceEeccCCCCCCceeeeeee-CCcEE
Q 045972 170 LIRANQGHTITTVESESLLKPILSAEEVSVCVHGTYKRNLDSILESGLKRMKRLHVHFSCGLPTDGEVISGMRR-DVNVL 248 (299)
Q Consensus 170 ~IRA~QGHSi~~v~~~~~L~pi~~~~~~~~LyHGT~~~~~~~I~~~GLk~M~R~hVHLs~~~~~a~~V~SG~R~-~~~Vl 248 (299)
+|||+||||+++ +.+ ....+.|++|||||+.++|+.|+++||+||.|+|||||++..+|..| |.|+ ++||+
T Consensus 99 ~IRA~yGHSi~V-~l~-----~~~~~~p~~LyhGTs~~~l~~I~~~Gi~Pm~R~~VHLS~~~~~A~~v--g~rh~~~pVv 170 (211)
T COG1859 99 KIRARYGHSIPV-DLR-----LPEAEPPAVLYHGTSPEFLPSILEEGLKPMKRRHVHLSADYETAKQV--GLRHSGSPVV 170 (211)
T ss_pred ceeeccCcceEE-ecc-----CCCCCCCcEEEecCChhhhHHHHHhcCccccCceEEecCCHHHHHHH--hhccCCCcEE
Confidence 899999999864 222 22345567999999999999999999999999999999999887665 8788 79999
Q ss_pred EEEehHHHHhCCCeEEEeCCcEEEecCCCccccccceeec
Q 045972 249 IFLNVRKALADGMKLYISDNKVVLTEGFDGVVPVEYFEKI 288 (299)
Q Consensus 249 I~ID~~kA~~dGi~Fy~S~NgViLTeG~~G~IP~~yf~kv 288 (299)
|+||+++|+++|++||+|+|+||||+ .|||+|++.+
T Consensus 171 L~IDa~~l~~~G~~~~rs~n~V~Lt~----~VPpe~i~~~ 206 (211)
T COG1859 171 LEIDAESLREDGYKFYRSENGVYLTD----TVPPEYIKKV 206 (211)
T ss_pred EEEehHHHHhCCceEEEcCCcEEEee----ecCHHHeeec
Confidence 99999999999999999999999999 5999999974
No 6
>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=88.36 E-value=0.14 Score=53.33 Aligned_cols=39 Identities=33% Similarity=0.537 Sum_probs=0.0
Q ss_pred cCCCCCccccccccCCCCCCCCCcccccCCCCCcccCCCCC
Q 045972 49 FNQSSSSFSSFAQSSKSGGGRGRGHDIKNDGERRRSRGGGG 89 (299)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~rg~~~ 89 (299)
+++.+.-||+-..++..|+|||+++|+++ +||||||+++
T Consensus 515 y~~p~~k~ss~~~~~~~~~g~gr~rg~~~--ggg~grg~~r 553 (556)
T PF05918_consen 515 YVPPSGKYSSNGGNSGRGRGGGRGRGRRS--GGGRGRGRGR 553 (556)
T ss_dssp -----------------------------------------
T ss_pred cCCCCCCCcCCCCCCCCCCCCCCCCCCCC--CCCCCCcccc
Confidence 34445555655555333333433333333 4444555443
No 7
>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=87.96 E-value=0.44 Score=37.24 Aligned_cols=46 Identities=17% Similarity=0.365 Sum_probs=31.2
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCCC-HHHHHHHHHhCCCCceEEeecCCceEEE
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSHT-VDDIWEAVRKDNKQRFSLLEENGELLIR 172 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~vt-~edI~~VV~~ddKqRFel~~e~g~~~IR 172 (299)
.|+||||+++.|+..+.- +.+| .+.|.++++..+ --|+++++ .+||
T Consensus 29 ~~~~G~Vpl~~i~~F~rm-------k~l~~~~~i~~Al~~S~--~lev~~d~--~~VR 75 (76)
T cd08029 29 GSNNGWVPIKTIASFKRM-------RRFQPLEAVVEALRESE--LLEVSEDG--ENVR 75 (76)
T ss_pred cCCCCcEehHHHhCchHH-------HHcCCHHHHHHHHHhCC--eEEEeCCC--Cccc
Confidence 589999999999986421 2222 377888888775 46776543 3665
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=87.25 E-value=0.63 Score=36.95 Aligned_cols=50 Identities=28% Similarity=0.376 Sum_probs=35.8
Q ss_pred eC-CCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEEE
Q 045972 116 MR-SDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLIR 172 (299)
Q Consensus 116 mD-~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~IR 172 (299)
|+ .||||+++.|+..+.-+ --..+.+.|.+++...+..-.|+.+++ .+||
T Consensus 31 m~~~~G~Vpl~~i~~F~rmk-----~l~~d~~~i~~Al~~S~~~~lev~~d~--~~VR 81 (82)
T cd08028 31 IKEDDGWVPMEVMLKFNRLK-----SLSSDPEVIAKALKKSKSGLIEVSEDK--TKIR 81 (82)
T ss_pred HhccCCCEEhHHHhCChhHH-----HhcCCHHHHHHHHHhCCCCEEEEcCCC--CccC
Confidence 44 38999999999864211 112468999999999987788987643 3665
No 9
>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=87.04 E-value=0.66 Score=35.98 Aligned_cols=48 Identities=27% Similarity=0.347 Sum_probs=32.5
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEEE
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLIR 172 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~IR 172 (299)
|+++|||+++.|++...-. --..+.++|.++++..+ --|+.++ ..+||
T Consensus 27 ~~~~g~Vpl~~i~~F~r~k-----~l~~~~~~i~~Al~~s~--~lel~~~--~~~Vr 74 (75)
T cd07323 27 MDDDGWVPLSLLASFNRVK-----KLTTDVELILEALRDSS--VVEVSED--GTKVR 74 (75)
T ss_pred cCCCCCEEHHHHhCchHHH-----HHcCCHHHHHHHHHhCC--eEEEeCC--CCccC
Confidence 4899999999999864211 11356799999999886 3455443 23565
No 10
>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=87.00 E-value=0.49 Score=37.16 Aligned_cols=47 Identities=26% Similarity=0.347 Sum_probs=31.3
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCC--CHHHHHHHHHhCCCCceEEeecCCceEEEe
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSH--TVDDIWEAVRKDNKQRFSLLEENGELLIRA 173 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~v--t~edI~~VV~~ddKqRFel~~e~g~~~IRA 173 (299)
||+||||+++-+...+. .+.+ +.+.|.+++.+.+ --|++++ | .+||+
T Consensus 27 md~~g~Vpi~~ia~F~r-------ik~Lt~D~~lI~~aL~~S~--~vevse~-g-~kVRp 75 (75)
T cd08036 27 MDSDQYVPIMTVANLDH-------IKKLSTDVDLIVDVLRSLP--LVQVDEK-G-EKVRP 75 (75)
T ss_pred hccCCCEehHHHhccHH-------HHHhcCCHHHHHHHHhhCC--eEEECCC-C-CccCc
Confidence 78999999999998542 1233 4677888887764 3555543 3 36663
No 11
>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=85.75 E-value=0.69 Score=36.31 Aligned_cols=48 Identities=13% Similarity=0.252 Sum_probs=32.3
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEEE
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLIR 172 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~IR 172 (299)
.|+||||+++-++..+.-. --..+.+.|.+++...+ =.|+.+++ .+||
T Consensus 29 ~~~dG~Vpl~~i~~F~rmk-----~l~~d~~~I~~Al~~S~--~lev~~d~--~~VR 76 (77)
T cd08033 29 RNKEGYVPIKLIASFKKVK-----ALTRDWRVVAAALRRSS--KLVVSEDG--KKVR 76 (77)
T ss_pred cCCCCcEehHHHhcchHHH-----HHcCCHHHHHHHHHhCC--eEEEcCCC--CccC
Confidence 4899999999999864211 11247789999998886 25565432 3565
No 12
>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=85.04 E-value=0.8 Score=35.78 Aligned_cols=48 Identities=27% Similarity=0.354 Sum_probs=31.3
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEEE
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLIR 172 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~IR 172 (299)
|++||||+++-|+....-. .+ .-+.+.|.+.+...+. -|+.+++ .+||
T Consensus 27 m~~dG~Vpl~~i~~F~rmk----~l-t~d~~~i~~Al~~S~~--lev~ed~--~~VR 74 (75)
T cd08031 27 MDSDQYVPIWTIANFNKIK----KL-TTDIDLIVEALRESPN--VQVDEKG--EKVR 74 (75)
T ss_pred hCCCCCEEHHHHhCchhHH----HH-cCCHHHHHHHHHhCCe--EEEcCCC--CccC
Confidence 6789999999999854211 01 2367888888887752 4555432 3666
No 13
>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=83.34 E-value=0.88 Score=35.70 Aligned_cols=48 Identities=25% Similarity=0.322 Sum_probs=31.9
Q ss_pred eCCCcceeHHHHHHhhh-hcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEEEe
Q 045972 116 MRSDGFVKVEDLLKLNL-KTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLIRA 173 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~-~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~IRA 173 (299)
||+||||+++-+...+. +. -.-+.+.|.+++...++ -+++++ | .+||.
T Consensus 27 md~~G~Vpi~~iasF~rik~------lt~d~~~I~~AL~~S~~--levsed-g-~kVRp 75 (75)
T cd08035 27 MDSDQFVPIWTVANMEGIKK------LTTDMDLILDVLRSSPM--VQVDET-G-EKVRP 75 (75)
T ss_pred hCcCCCEehHHHhccHHHHH------hcCCHHHHHHHHHcCCe--EEEcCC-C-CccCc
Confidence 78999999999887432 11 12367888888888753 566543 3 36763
No 14
>cd01439 TCCD_inducible_PARP_like Poly(ADP-ribose) polymerases catalyse the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) causes pleotropic effects in mammalian species through modulating gene expression. TCCD indicible PARP (TiPARP) is a target of TCDD that may contribute to multiple responses to TCDD by modulating protein function through poly ADP-ribosylation
Probab=81.37 E-value=0.83 Score=38.19 Aligned_cols=33 Identities=21% Similarity=0.269 Sum_probs=25.4
Q ss_pred eEEEeCchhcHHHHHHhCCCCCC-C-------cceEeccCC
Q 045972 199 VCVHGTYKRNLDSILESGLKRMK-R-------LHVHFSCGL 231 (299)
Q Consensus 199 ~LyHGT~~~~~~~I~~~GLk~M~-R-------~hVHLs~~~ 231 (299)
.|||||..++|+.|.+.|+.++- . .=|+||...
T Consensus 1 ~LfHGt~~~~~~~I~~~GF~~~~~g~~~~~~G~GiYFA~~~ 41 (121)
T cd01439 1 LLFHGTSADAVEAICRHGFDRRFCGKHGTMYGKGSYFAKNA 41 (121)
T ss_pred CcccccChhhHHHHHHccCCCccCCCCCCccCCeeecccCh
Confidence 37999999999999999987762 1 136677653
No 15
>cd01341 ADP_ribosyl ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region o
Probab=77.26 E-value=1.2 Score=37.81 Aligned_cols=23 Identities=35% Similarity=0.450 Sum_probs=20.7
Q ss_pred eEEEeCchhcHHHHHHhCCCCCC
Q 045972 199 VCVHGTYKRNLDSILESGLKRMK 221 (299)
Q Consensus 199 ~LyHGT~~~~~~~I~~~GLk~M~ 221 (299)
.|+|||...+|..|+..||+++.
T Consensus 1 ~l~HGs~~~n~~~I~~~Gl~~~~ 23 (137)
T cd01341 1 FLFHGSPPGNVISILKLGLRPAS 23 (137)
T ss_pred CccccCCccchHHHhhCCCCCCC
Confidence 37999999999999999998765
No 16
>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function.
Probab=77.16 E-value=1.8 Score=34.12 Aligned_cols=49 Identities=27% Similarity=0.450 Sum_probs=31.5
Q ss_pred eCC-CcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEEEe
Q 045972 116 MRS-DGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLIRA 173 (299)
Q Consensus 116 mD~-dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~IRA 173 (299)
|++ ||||+++.|+..+.-. -...+.+.|.+++...+ --|+.++ + .+||-
T Consensus 30 ~~~~~g~Vpl~~i~~F~r~k-----~l~~d~~~i~~Al~~S~--~lel~~d-~-~~VRR 79 (80)
T smart00715 30 MDKNDGYVPISTIASFKRVK-----SLTTDVNLIVEALRSSP--KLEVSED-G-LKVRR 79 (80)
T ss_pred hccCCCCEEhHHHhCchhHH-----HHcCCHHHHHHHHHhCC--eEEEcCC-C-CeeCc
Confidence 455 9999999999864211 11245688999998884 3555443 2 46763
No 17
>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=77.08 E-value=1.8 Score=33.67 Aligned_cols=42 Identities=17% Similarity=0.334 Sum_probs=28.4
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEee
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLE 164 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~ 164 (299)
||+||||+|+-|+..+.-. .-..+.+.|.+++...+. -|+.+
T Consensus 27 m~~~G~Vpl~~i~~F~rmk-----~l~~d~~~i~~Al~~S~~--lev~e 68 (73)
T cd08034 27 MDPEGYLPIALIASFHRVQ-----ALTTDVNLILEALKDSTV--VELVD 68 (73)
T ss_pred cCCCCCEeHHHHhccHHHH-----HHcCCHHHHHHHHHcCCe--EEEec
Confidence 6899999999998854211 112467888888887762 45543
No 18
>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=75.80 E-value=1.9 Score=33.65 Aligned_cols=41 Identities=20% Similarity=0.310 Sum_probs=27.8
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEe
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLL 163 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~ 163 (299)
||++|||+++-++..+.-. --..+.+.|.+.+...+. -|+.
T Consensus 27 m~~~G~Vpl~~ia~F~rmk-----~lt~d~~~I~~Al~~S~~--ve~~ 67 (73)
T cd08038 27 MDLQGFLPISLIAGFYRVQ-----ALTTNVDLILEALKDSTE--VEIV 67 (73)
T ss_pred hCCCCCEeHHHHhcchHHH-----HhcCCHHHHHHHHHcCCe--EEEe
Confidence 6899999999999854211 112456888888887654 4444
No 19
>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=75.10 E-value=2.2 Score=33.23 Aligned_cols=36 Identities=19% Similarity=0.312 Sum_probs=25.0
Q ss_pred eCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCC
Q 045972 116 MRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDN 156 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~dd 156 (299)
||+||||+++-++..+.-. --..+.+.|.+.+...+
T Consensus 27 md~dG~Vpi~~ia~F~rmk-----~Lt~d~~~I~~Al~~S~ 62 (73)
T cd08037 27 MDEDGFLPVTLIASFHRVQ-----ALTTDISLIIKALKDSK 62 (73)
T ss_pred hccCCCEeHHHHhcchHHH-----HhcCCHHHHHHHHHcCC
Confidence 6899999999999854211 11246777888877765
No 20
>COG3502 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.04 E-value=4.3 Score=34.21 Aligned_cols=90 Identities=16% Similarity=0.179 Sum_probs=60.8
Q ss_pred CeEEEeCchhcHHHHHHhC-CCC--C--CCcceEeccCCCCCCceeeee---eeC-CcEEEEEehHHHHhCCCeEEEeCC
Q 045972 198 SVCVHGTYKRNLDSILESG-LKR--M--KRLHVHFSCGLPTDGEVISGM---RRD-VNVLIFLNVRKALADGMKLYISDN 268 (299)
Q Consensus 198 ~~LyHGT~~~~~~~I~~~G-Lk~--M--~R~hVHLs~~~~~a~~V~SG~---R~~-~~VlI~ID~~kA~~dGi~Fy~S~N 268 (299)
.++||=|....|..-++.| ... | .--+||||+...- ....- |.. .-++++||.+ ++.+.+++-.|..
T Consensus 4 ~~iykI~~~~~W~~A~~~G~f~~~svd~~dGfIH~St~~Qv---~~tAar~f~GQ~dLlLl~iD~a-aLg~~lryE~srg 79 (115)
T COG3502 4 ATIYKITPRALWAAARAAGSFEGASVDDADGFIHLSTAAQV---RETAARHFRGQADLLLLAIDPA-ALGDELRYEPSRG 79 (115)
T ss_pred ceeeeeCCHHHHHHHHHcCCcCCCCcccccceEEechHHHH---HHHHHHHhcCCcceEEEEecHH-HcCCcceeecCCC
Confidence 4899999999999999998 433 3 3459999997531 11122 222 3468899985 5788999988876
Q ss_pred cEEEecCCCccccccceeeccccC
Q 045972 269 KVVLTEGFDGVVPVEYFEKIESWP 292 (299)
Q Consensus 269 gViLTeG~~G~IP~~yf~kv~~~~ 292 (299)
| -|=+-.-|.+|.+-...+...+
T Consensus 80 g-~lFPHLYgpL~l~AV~~~~pl~ 102 (115)
T COG3502 80 G-ALFPHLYGPLPLDAVTWVAPLP 102 (115)
T ss_pred C-ccccccccccchhHheecccCC
Confidence 6 3333334667777776665544
No 21
>PF00644 PARP: Poly(ADP-ribose) polymerase catalytic domain; InterPro: IPR012317 Poly(ADP-ribose) polymerases (PARP) are a family of enzymes present in eukaryotes, which catalyze the poly(ADP-ribosyl)ation of a limited number of proteins involved in chromatin architecture, DNA repair, or in DNA metabolism, including PARP itself. PARP, also known as poly(ADP-ribose) synthetase and poly(ADP-ribose) transferase, transfers the ADP-ribose moiety from its substrate, nicotinamide adenine dinucleotide (NAD), to carboxylate groups of aspartic and glutamic residues. Whereas some PARPs might function in genome protection, others appear to play different roles in the cell, including telomere replication and cellular transport. PARP-1 is a multifunctional enzyme. The polypeptide has a highly conserved modular organisation consisting of an N-terminal DNA-binding domain, a central regulating segment, and a C-terminal or F region accommodating the catalytic centre. The F region is composed of two parts: a purely alpha-helical N- terminal domain (alpha-hd), and the mixed alpha/beta C-terminal catalytic domain bearing the putative NAD binding site. Although proteins of the PARP family are related through their PARP catalytic domain, they do not resemble each other outside of that region, but rather, they contain unique domains that distinguish them from each other and hint at their discrete functions. Domains with which the PARP catalytic domain is found associated include zinc fingers, SAP, ankyrin, BRCT, Macro, SAM, WWE and UIM domains [, , ]. The alpha-hd domain is about 130 amino acids in length and consists of an up-up-down-up-down-down motif of helices. It is thought to relay the activation signal issued on binding to damaged DNA [, ]. The PARP catalytic domain is about 230 residues in length. Its core consists of a five-stranded antiparallel beta-sheet and four-stranded mixed beta-sheet. The two sheets are consecutive and are connected via a single pair of hydrogen bonds between two strands that run at an angle of 90 degrees. These central beta-sheets are surrounded by five alpha-helices, three 3(10)-helices, and by a three- and a two-stranded beta-sheet in a 37-residue excursion between two central beta-strands [, ]. The active site, known as the 'PARP signature' is formed by a block of 50 amino acids that is strictly conserved among the vertebrates and highly conserved among all species. The 'PARP signature' is characteristic of all PARP protein family members. It is formed by a segment of conserved amino acid residues formed by a beta-sheet, an alpha-helix, a 3(10)-helix, a beta-sheet, and an alpha-helix [].; GO: 0003950 NAD+ ADP-ribosyltransferase activity; PDB: 2PQF_F 4F0D_A 1PAX_A 1EFY_A 1A26_A 2PAW_A 4PAX_A 3PAX_A 2PAX_A 3P0N_A ....
Probab=73.88 E-value=2.9 Score=37.20 Aligned_cols=21 Identities=43% Similarity=0.637 Sum_probs=19.1
Q ss_pred CeEEEeCchhcHHHHHHhCCC
Q 045972 198 SVCVHGTYKRNLDSILESGLK 218 (299)
Q Consensus 198 ~~LyHGT~~~~~~~I~~~GLk 218 (299)
.+|||||...+|..|++.||+
T Consensus 61 ~~L~HGt~~~~~~~I~~~G~~ 81 (206)
T PF00644_consen 61 RLLFHGTSAENICSILRNGFK 81 (206)
T ss_dssp EEEEEEETGGGHHHHHHHSS-
T ss_pred eEEeCCCChhhccchhcCCCc
Confidence 489999999999999999994
No 22
>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=73.20 E-value=2.3 Score=34.46 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=13.8
Q ss_pred eCCCcceeHHHHHHhh
Q 045972 116 MRSDGFVKVEDLLKLN 131 (299)
Q Consensus 116 mD~dG~V~v~dLL~~~ 131 (299)
-|+||||+++-|+..+
T Consensus 30 ~~~dG~V~i~~i~~F~ 45 (90)
T cd08030 30 EDPDGMVSLALICSFS 45 (90)
T ss_pred cCCCCCEehHHHhcCh
Confidence 4899999999999854
No 23
>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=68.37 E-value=4.2 Score=30.32 Aligned_cols=33 Identities=30% Similarity=0.563 Sum_probs=20.2
Q ss_pred CCCcceeHHHHHHhhh-hcccCCCCCCCCHHHHHHHHHh
Q 045972 117 RSDGFVKVEDLLKLNL-KTFAQIPLRSHTVDDIWEAVRK 154 (299)
Q Consensus 117 D~dG~V~v~dLL~~~~-~~~~~~~~~~vt~edI~~VV~~ 154 (299)
++||||+++.|+.... +. +...+.++|.++++.
T Consensus 27 ~~~g~Vpi~~i~~F~r~k~-----l~~~~~~~I~~al~~ 60 (61)
T PF05383_consen 27 NPDGWVPISTILSFNRMKA-----LTNTDIELIVDALRD 60 (61)
T ss_dssp TTTTBEEHHHHTTSHHHHH-----H--S-HHHHHHHHHT
T ss_pred cCCCcEeHHHHHchHHHHH-----HhcCCHHHHHHHHHc
Confidence 4599999999998542 11 111356677766653
No 24
>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=66.55 E-value=5.8 Score=31.53 Aligned_cols=46 Identities=26% Similarity=0.333 Sum_probs=29.1
Q ss_pred CCCcceeHHHHHHhhh-hcccCCCCCCCCHHHHHHHHHhCCCCceEEeecCCceEEE
Q 045972 117 RSDGFVKVEDLLKLNL-KTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEENGELLIR 172 (299)
Q Consensus 117 D~dG~V~v~dLL~~~~-~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e~g~~~IR 172 (299)
++||||+++-|+.... +. -..+.+.|.+.+...+ --|+.++ + .+||
T Consensus 35 ~~dG~Vpl~~i~~F~rmk~------lt~d~~~i~~Al~~S~--~lev~ed-~-~~VR 81 (82)
T cd08032 35 SRDGYIDISLLVSFNKMKK------LTTDGKLIARALKNSS--VVELNLE-G-TRIR 81 (82)
T ss_pred CCCCCEeHHHHhcchHHHH------HcCCHHHHHHHHhcCC--EEEEcCC-C-CccC
Confidence 4899999999998542 11 1235577888777775 2455543 2 3565
No 25
>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=64.44 E-value=11 Score=41.91 Aligned_cols=70 Identities=24% Similarity=0.294 Sum_probs=49.1
Q ss_pred HHHHHHHhcc----------CC--CcCCceeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEEeec
Q 045972 98 GRLLTRILRH----------MA--SELNLNMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSLLEE 165 (299)
Q Consensus 98 SK~LSylLRH----------~p--ek~GL~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel~~e 165 (299)
|-.|=|| || .+ +...+.+|+||||-|.-|++..+- +.-+||-+=|+..|..-..+ |+|..+
T Consensus 444 seNm~YI-RHLGl~pPell~~~~~~~~Dv~pDaeGWVYLNLL~NmAQL-----HiiNVTPdFVRsAV~E~StK-fQLSpD 516 (989)
T PF09421_consen 444 SENMEYI-RHLGLVPPELLPGQPQSIQDVHPDAEGWVYLNLLCNMAQL-----HIINVTPDFVRSAVSEKSTK-FQLSPD 516 (989)
T ss_pred hhhHHHH-HhcCCCChhccCCccccccccCcccccceehHHHHHHHHH-----HhhccCHHHHHHHHHhcccc-eeeCCC
Confidence 6777776 44 32 222467899999999999985322 24579999999999877544 999864
Q ss_pred CCceEEEecCC
Q 045972 166 NGELLIRANQG 176 (299)
Q Consensus 166 ~g~~~IRA~QG 176 (299)
| -+||=+-|
T Consensus 517 -G-rKIRWRGG 525 (989)
T PF09421_consen 517 -G-RKIRWRGG 525 (989)
T ss_pred -C-CeeeecCC
Confidence 3 26765554
No 26
>cd01437 parp_like Poly(ADP-ribose) polymerase (parp) catalytic domain catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length through interactions with telomere repeat binding factor 1.
Probab=62.40 E-value=5.2 Score=39.50 Aligned_cols=23 Identities=30% Similarity=0.431 Sum_probs=20.9
Q ss_pred CeEEEeCchhcHHHHHHhCCCCC
Q 045972 198 SVCVHGTYKRNLDSILESGLKRM 220 (299)
Q Consensus 198 ~~LyHGT~~~~~~~I~~~GLk~M 220 (299)
-.|||||...+|..|+..||..+
T Consensus 196 ~lLwHGsr~~n~~~Il~~Gl~~~ 218 (347)
T cd01437 196 KLLWHGSRLTNFVGILSQGLRIA 218 (347)
T ss_pred EEEEcCCChhhHHHHHhcCCCcC
Confidence 38999999999999999998765
No 27
>PF14487 DUF4433: Domain of unknown function (DUF4433)
Probab=60.93 E-value=9.7 Score=34.02 Aligned_cols=20 Identities=45% Similarity=0.403 Sum_probs=17.3
Q ss_pred EEeCchhcHHHHHHhC-CCCC
Q 045972 201 VHGTYKRNLDSILESG-LKRM 220 (299)
Q Consensus 201 yHGT~~~~~~~I~~~G-Lk~M 220 (299)
||=|..+++++|+++| |.+.
T Consensus 1 yH~T~i~NL~sIl~~G~L~s~ 21 (205)
T PF14487_consen 1 YHFTHIDNLPSILQNGGLLSR 21 (205)
T ss_pred CceechhhHHHHHHcCCccch
Confidence 7999999999999999 6543
No 28
>COG4907 Predicted membrane protein [Function unknown]
Probab=48.41 E-value=15 Score=38.13 Aligned_cols=20 Identities=30% Similarity=0.522 Sum_probs=10.8
Q ss_pred cCCCCCccccccccCCCCCC
Q 045972 49 FNQSSSSFSSFAQSSKSGGG 68 (299)
Q Consensus 49 ~~~~~~~~~~~~~~~~~~~~ 68 (299)
||.-++-+|+-|.|++++.+
T Consensus 557 ~~~~~raysa~a~S~~~~~~ 576 (595)
T COG4907 557 FNNLNRAYSAIASSRRSSSS 576 (595)
T ss_pred hcccchhhhcccccccCCCC
Confidence 44444666776666554433
No 29
>PF03089 RAG2: Recombination activating protein 2; InterPro: IPR004321 The variable portion of the genes encoding immunoglobulins and T cell receptors are assembled from component V, D, and J DNA segments by a site-specific recombination reaction termed V(D)J recombination. V(D)J recombination is targeted to specific sites on the chromosome by recombination signal sequences (RSSs) that flank antigen receptor gene segments. The RSS consists of a conserved heptamer (consensus, 5'-CACAGTG-3') and nonamer (consensus, 5'-ACAAAAACC-3') separated by a spacer of either 12 or 23 bp. Efficient recombination occurs between a 12-RSS and a 23-RSS, a restriction known as the 12/23 rule. V(D)J recombination can be divided into two phases, DNA cleavage and DNA joining. DNA cleavage requires two lymphocyte-specific factors, the products of the recombination activating genes, RAG1 and RAG2, which together recognise the RSSs and create double strand breaks at the RSS-coding segment junctions []. RAG-mediated DNA cleavage occurs in a synaptic complex termed the paired complex, which is constituted from two distinct RSS-RAG complexes, a 12-SC and a 23-SC (where SC stands for signal complex). The DNA cleavage reaction involves two distinct enzymatic steps, initial nicking that creates a 3'-OH between a coding segment and its RSS, followed by hairpin formation in which the newly created 3'-OH attacks a phosphodiester bond on the opposite DNA strand. This generates a blunt, 5' phosphorylated signal end containing all of the RSS elements, and a covalently sealed hairpin coding end. The second phase of V(D)J recombination, in which broken DNA fragments are processed and joined, is less well characterised. Signal ends are typically joined precisely to form a signal joint, whereas joining of the coding ends requires the hairpin structure to be opened and typically involves nucleotide addition and deletion before formation of the coding joint. The factors involved in these processes include ubiquitously expressed proteins involved in the repair of DNA double strand breaks by nonhomologous end joining, terminal deoxynucleotidyl transferase, and Artemis protein. In addition to their critical roles in RSS recognition and DNA cleavage, the RAG proteins may perform two distinct types of functions in the postcleavage phase of V(D)J. A structural function has been inferred from the finding that, after DNA cleavage in vitro, the DNA ends remain associated with the RAG proteins in a "four end" complex known as the cleaved signal complex. After release of the coding ends in vitro, and after coding joint formation in vivo, the RAG proteins remain in a stable signal end complex (SEC) containing the two signal ends. These postcleavage complexes may serve as essential scaffolds for the second phase of the reaction, with the RAG proteins acting to organise the DNA processing and joining events. The second type of RAG protein-mediated postcleavage activity is the catalysis of phosphodiester bond hydrolysis and strand transfer reactions. The RAG proteins are capable of opening hairpin coding ends in vitro. The RAG proteins also show 3' flap endonuclease activity that may contribute to coding end processing/joining and can utilise the 3' OH group on the signal ends to attack hairpin coding ends (forming hybrid or open/shut joints) or virtually any DNA duplex (forming a transposition product).; GO: 0003677 DNA binding, 0006310 DNA recombination, 0005634 nucleus
Probab=45.99 E-value=59 Score=32.05 Aligned_cols=95 Identities=19% Similarity=0.217 Sum_probs=57.3
Q ss_pred EecCCCcccccccccccccCCCCCCCCeEEEeCchhcHHHHHHhCCCCCCCcceEeccCCCCCCceeeeeeeCCcEEE-E
Q 045972 172 RANQGHTITTVESESLLKPILSAEEVSVCVHGTYKRNLDSILESGLKRMKRLHVHFSCGLPTDGEVISGMRRDVNVLI-F 250 (299)
Q Consensus 172 RA~QGHSi~~v~~~~~L~pi~~~~~~~~LyHGT~~~~~~~I~~~GLk~M~R~hVHLs~~~~~a~~V~SG~R~~~~VlI-~ 250 (299)
.|+||||+.+|.+.- +-..+..| +|.|+-+..-. .+.+- .--||+..| .
T Consensus 86 ~aRYGHt~~vV~SrG---------Kta~VlFG-----------------GRSY~P~~qRT--TenWN--sVvDC~P~VfL 135 (337)
T PF03089_consen 86 EARYGHTINVVHSRG---------KTACVLFG-----------------GRSYMPPGQRT--TENWN--SVVDCPPQVFL 135 (337)
T ss_pred cccccceEEEEEECC---------cEEEEEEC-----------------CcccCCccccc--hhhcc--eeccCCCeEEE
Confidence 699999998774321 01123333 46666655443 22331 134677644 4
Q ss_pred EehH---------HHHhCCCeEEEe---CCcEEEecC---CCccccccceeeccccCCCCC
Q 045972 251 LNVR---------KALADGMKLYIS---DNKVVLTEG---FDGVVPVEYFEKIESWPDRRP 296 (299)
Q Consensus 251 ID~~---------kA~~dGi~Fy~S---~NgViLTeG---~~G~IP~~yf~kv~~~~~~~~ 296 (299)
||.+ .-+.||..|..| ++-||+--| ..-+=||..|+.=++.+-+-|
T Consensus 136 iDleFGC~tah~lpEl~dG~SFHvslar~D~VYilGGHsl~sd~Rpp~l~rlkVdLllGSP 196 (337)
T PF03089_consen 136 IDLEFGCCTAHTLPELQDGQSFHVSLARNDCVYILGGHSLESDSRPPRLYRLKVDLLLGSP 196 (337)
T ss_pred EeccccccccccchhhcCCeEEEEEEecCceEEEEccEEccCCCCCCcEEEEEEeecCCCc
Confidence 7765 346899999976 345777766 245779999986556655544
No 30
>KOG3293 consensus Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification]
Probab=45.95 E-value=20 Score=30.79 Aligned_cols=27 Identities=37% Similarity=0.691 Sum_probs=14.4
Q ss_pred CCCCCCCCcccccCCCCCcccCCCCCC
Q 045972 64 KSGGGRGRGHDIKNDGERRRSRGGGGS 90 (299)
Q Consensus 64 ~~~~~r~~~~~~~~~~~~~~~rg~~~~ 90 (299)
-++.|||++-+-++.+.+++++|++.+
T Consensus 95 ~~~~grG~gng~~~~~~rg~~~g~~~g 121 (134)
T KOG3293|consen 95 DRGRGRGRGNGNRGGNRRGGGRGGSMG 121 (134)
T ss_pred cccCCcCCCCCCCCCCcCCCCCCCCcC
Confidence 344555555445554555565665544
No 31
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=44.85 E-value=57 Score=23.88 Aligned_cols=61 Identities=18% Similarity=0.293 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHhccCCCcCCceeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCCceEE
Q 045972 94 IDALGRLLTRILRHMASELNLNMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQRFSL 162 (299)
Q Consensus 94 ~~~LSK~LSylLRH~pek~GL~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKqRFel 162 (299)
...+-+.|--+|...+ +++||+.+.+|-....+.+.....+.+....+.++++. -..=|++
T Consensus 3 ~~~~~~~l~~ll~~~~-------~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~~l~~ll~~-~~~~~~i 63 (74)
T PF12872_consen 3 LEELKKLLRELLESQK-------GEDGWVSLSQLGQEYKKKYPDFDPRDYGFSSLSELLES-LPDVVEI 63 (74)
T ss_dssp -HHHHHHHHHHHHHTC-------TTTSSEEHHHHHHHHHHHHTT--TCCTTSSSHHHHHHT--TTTEEE
T ss_pred HHHHHHHHHHHHHhCc-------CCCceEEHHHHHHHHHHHCCCCCccccCCCcHHHHHHh-CCCeEEE
Confidence 4566677777775433 34789999999886544332223445555667777765 3344666
No 32
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=39.92 E-value=17 Score=39.96 Aligned_cols=22 Identities=27% Similarity=0.214 Sum_probs=20.6
Q ss_pred eEEEeCchhcHHHHHHhCCCCC
Q 045972 199 VCVHGTYKRNLDSILESGLKRM 220 (299)
Q Consensus 199 ~LyHGT~~~~~~~I~~~GLk~M 220 (299)
+|+||+...+|-.|+.+||+.+
T Consensus 653 LLWHGSR~tN~~gILsqGLRIA 674 (815)
T PLN03122 653 LLWCGTRSSNLLRHLAKGFLPA 674 (815)
T ss_pred EEeccchhhhHHHHhhCCCccC
Confidence 8999999999999999999854
No 33
>PLN03124 poly [ADP-ribose] polymerase; Provisional
Probab=39.86 E-value=18 Score=38.69 Aligned_cols=21 Identities=33% Similarity=0.485 Sum_probs=19.8
Q ss_pred eEEEeCchhcHHHHHHhCCCC
Q 045972 199 VCVHGTYKRNLDSILESGLKR 219 (299)
Q Consensus 199 ~LyHGT~~~~~~~I~~~GLk~ 219 (299)
+|||||...+|-.|+.+||+-
T Consensus 488 LLWHGSr~~N~~gILs~GLri 508 (643)
T PLN03124 488 LLWHGSRLTNWTGILSQGLRI 508 (643)
T ss_pred EEEcCCCcccHHHHHhccCcc
Confidence 899999999999999999873
No 34
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=31.55 E-value=77 Score=22.01 Aligned_cols=35 Identities=9% Similarity=0.050 Sum_probs=25.3
Q ss_pred eeCCCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCC
Q 045972 115 NMRSDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDN 156 (299)
Q Consensus 115 ~mD~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~dd 156 (299)
..|.+|.++.+||.+..... +++.+++.+++..-+
T Consensus 9 D~~~~G~i~~~el~~~l~~~-------g~~~~~~~~i~~~~d 43 (67)
T cd00052 9 DPDGDGLISGDEARPFLGKS-------GLPRSVLAQIWDLAD 43 (67)
T ss_pred CCCCCCcCcHHHHHHHHHHc-------CCCHHHHHHHHHHhc
Confidence 35678999999999875321 357888888876543
No 35
>PF15633 Tox-ART-HYD1: HYD1 signature containing ADP-ribosyltransferase
Probab=31.54 E-value=75 Score=26.11 Aligned_cols=68 Identities=22% Similarity=0.245 Sum_probs=40.8
Q ss_pred EEEeCchhcHHHHHHhCCCC--------CCCcceEeccCCCCCCc--------e-eeeeeeCCcEEEEEehHHHHhCCCe
Q 045972 200 CVHGTYKRNLDSILESGLKR--------MKRLHVHFSCGLPTDGE--------V-ISGMRRDVNVLIFLNVRKALADGMK 262 (299)
Q Consensus 200 LyHGT~~~~~~~I~~~GLk~--------M~R~hVHLs~~~~~a~~--------V-~SG~R~~~~VlI~ID~~kA~~dGi~ 262 (299)
|||=|+.+.++.|+++|.-+ ..-+=+.|++-.|+... + +.+-|. . =+|+||+.. +.
T Consensus 1 lyHYTs~~G~n~I~~s~~i~~~a~~p~~~~~~g~y~t~~apg~~~~~s~~~~~~~~~~~k~-t-hyieiDv~~-----L~ 73 (96)
T PF15633_consen 1 LYHYTSEKGYNGILESGIIKLKANNPKDRFGQGQYFTDIAPGKPLSLSDAFIKLGITGNKS-T-HYIEIDVSD-----LK 73 (96)
T ss_pred CccccchhhhHHhhccceEEeccCCccccCCCceEEEecCCCCcCChhHHHHhcCcccccc-e-EEEEEeccc-----ce
Confidence 69999999999999999433 22334555554443310 0 011122 2 277999854 66
Q ss_pred EEEeCCcEEEec
Q 045972 263 LYISDNKVVLTE 274 (299)
Q Consensus 263 Fy~S~NgViLTe 274 (299)
+-....+++.-.
T Consensus 74 ~v~n~~g~~~~~ 85 (96)
T PF15633_consen 74 VVKNPDGVFVEY 85 (96)
T ss_pred EEeCCCCeEEee
Confidence 666666666544
No 36
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=29.20 E-value=45 Score=33.63 Aligned_cols=9 Identities=67% Similarity=1.265 Sum_probs=4.1
Q ss_pred CcccCCCCC
Q 045972 81 RRRSRGGGG 89 (299)
Q Consensus 81 ~~~~rg~~~ 89 (299)
++||||||+
T Consensus 447 ggrgrgggg 455 (465)
T KOG3973|consen 447 GGRGRGGGG 455 (465)
T ss_pred CCCCCCCCC
Confidence 444555443
No 37
>cd01436 Dipth_tox_like Mono-ADP-ribosylating toxins catalyze the transfer of ADP_ribose from NAD+ to eukaryotic Elongation Factor 2, halting protein synthesis. A single molecule of delivered toxin is sufficient to kill a cell. These toxins share mono-ADP-ribosylating activity with a variety of bacterial toxins, such as cholera toxin and pertussis toxin. The structural core is homologous to the poly-ADP ribosylating enzymes such as the PARP enzymes and Tankyrase. Diphtheria toxin is encoded by a lysogenic bacteriophage. Both diphtheria toxin and Pseudomonas aeruginosa exotoxin A are multi-domain proteins. These domains provide a EF2 ADP_ribosylating, receptor-binding, and intracellular trafficking/transmembrane functions .
Probab=28.70 E-value=33 Score=29.72 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=19.9
Q ss_pred EEEeCchhcHHHHHHhCCCCCCC
Q 045972 200 CVHGTYKRNLDSILESGLKRMKR 222 (299)
Q Consensus 200 LyHGT~~~~~~~I~~~GLk~M~R 222 (299)
-||||...+.++|.. ||.+..+
T Consensus 2 ~YHGT~~~~~~sI~~-gI~~~~~ 23 (147)
T cd01436 2 SYHGTKPGYVDSIQK-GIQKPKS 23 (147)
T ss_pred CccccchHHHHHHHh-hccCCCC
Confidence 399999999999999 9988877
No 38
>PF10961 DUF2763: Protein of unknown function (DUF2763); InterPro: IPR024491 This entry represents an eukaryotic family of selenoproteins. It includes SelK, which seems to play an important role in protecting cells from endoplasmic reticulum stress-induced apoptosis [] and SelG, which may be involved in regulating the redox state of the cell [].
Probab=27.48 E-value=91 Score=25.16 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=10.3
Q ss_pred chheecccccccCCCC
Q 045972 32 SLFFRSVALGFMDNRN 47 (299)
Q Consensus 32 ~~~~~~~~~~~~~~~~ 47 (299)
.+||.++..+.+..+.
T Consensus 33 ~lFF~Tl~~p~~~~~~ 48 (91)
T PF10961_consen 33 VLFFQTLFSPDSSRSG 48 (91)
T ss_pred HHHHHHHhCCCccccc
Confidence 4678888877554444
No 39
>PF12300 DUF3628: Protein of unknown function (DUF3628); InterPro: IPR022077 Proteins in this entry are DEAD Box RhlB RNA Helicases found in Xanthomonadaceae bacteria.; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=24.52 E-value=50 Score=29.73 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=13.9
Q ss_pred cccCCCCCCCCCcccccCC
Q 045972 60 AQSSKSGGGRGRGHDIKND 78 (299)
Q Consensus 60 ~~~~~~~~~r~~~~~~~~~ 78 (299)
|.-.+.|+||++.|++.+.
T Consensus 51 A~E~RRGggRsg~G~RsG~ 69 (180)
T PF12300_consen 51 ADEQRRGGGRSGPGGRSGS 69 (180)
T ss_pred HHHHhhcCCCCCCCCCCCC
Confidence 6677888999987655554
No 40
>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=24.52 E-value=25 Score=37.07 Aligned_cols=14 Identities=29% Similarity=0.017 Sum_probs=3.6
Q ss_pred ceEEEeeeeecCCC
Q 045972 8 NIRILQCCHVYLPR 21 (299)
Q Consensus 8 ~~~~~~~~~~~~~~ 21 (299)
||..|..+-..=|+
T Consensus 436 NI~~lik~L~~~pP 449 (556)
T PF05918_consen 436 NILALIKDLFHNPP 449 (556)
T ss_dssp HHHHHHCC------
T ss_pred hHHHHHHHHhhCCc
Confidence 44444433333333
No 41
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=23.81 E-value=46 Score=37.39 Aligned_cols=21 Identities=33% Similarity=0.482 Sum_probs=19.8
Q ss_pred eEEEeCchhcHHHHHHhCCCC
Q 045972 199 VCVHGTYKRNLDSILESGLKR 219 (299)
Q Consensus 199 ~LyHGT~~~~~~~I~~~GLk~ 219 (299)
+|||||...+|-.|+.+||+.
T Consensus 828 LLwHGSr~~N~~gILs~GLri 848 (981)
T PLN03123 828 LLWHGSRLTNFVGILSQGLRI 848 (981)
T ss_pred EEEcCCCcccHHHHhhccCcc
Confidence 899999999999999999874
No 42
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=23.46 E-value=71 Score=20.12 Aligned_cols=17 Identities=18% Similarity=0.405 Sum_probs=13.9
Q ss_pred eeCCCcceeHHHHHHhh
Q 045972 115 NMRSDGFVKVEDLLKLN 131 (299)
Q Consensus 115 ~mD~dG~V~v~dLL~~~ 131 (299)
-.|.||+++.+|++...
T Consensus 10 D~d~dG~I~~~Ef~~~~ 26 (29)
T PF00036_consen 10 DKDGDGKIDFEEFKEMM 26 (29)
T ss_dssp STTSSSEEEHHHHHHHH
T ss_pred CCCCCCcCCHHHHHHHH
Confidence 35789999999998864
No 43
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=23.37 E-value=1.1e+02 Score=23.93 Aligned_cols=43 Identities=9% Similarity=0.047 Sum_probs=27.2
Q ss_pred eCCCc-ceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCCCC
Q 045972 116 MRSDG-FVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDNKQ 158 (299)
Q Consensus 116 mD~dG-~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~ddKq 158 (299)
.|.+| +++.+||-..+...+...-....|.++|.++++.-|+.
T Consensus 20 ~dgdG~~I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~D~n 63 (88)
T cd05027 20 REGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSD 63 (88)
T ss_pred cCCCcCEECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHhCCC
Confidence 35688 69999998875431100011236888899998766544
No 44
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=21.44 E-value=1.9e+02 Score=19.56 Aligned_cols=35 Identities=11% Similarity=0.234 Sum_probs=23.8
Q ss_pred CCcceeHHHHHHhhhhcccCCCCCCCCHHHHHHHHHhCC
Q 045972 118 SDGFVKVEDLLKLNLKTFAQIPLRSHTVDDIWEAVRKDN 156 (299)
Q Consensus 118 ~dG~V~v~dLL~~~~~~~~~~~~~~vt~edI~~VV~~dd 156 (299)
++|++..++|..++ ... +...++.+++..++..-|
T Consensus 1 ~~G~i~~~~~~~~l-~~~---g~~~~s~~e~~~l~~~~D 35 (54)
T PF13833_consen 1 KDGKITREEFRRAL-SKL---GIKDLSEEEVDRLFREFD 35 (54)
T ss_dssp SSSEEEHHHHHHHH-HHT---TSSSSCHHHHHHHHHHHT
T ss_pred CcCEECHHHHHHHH-HHh---CCCCCCHHHHHHHHHhcc
Confidence 47999999999976 321 122278888877776443
Done!