Query 007265
Match_columns 610
No_of_seqs 139 out of 264
Neff 4.5
Searched_HMMs 46136
Date Thu Mar 28 21:13:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007265.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007265hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2318 Uncharacterized conser 100.0 3E-147 7E-152 1181.9 26.2 563 25-609 10-605 (650)
2 COG5638 Uncharacterized conser 100.0 2E-133 4E-138 1042.5 24.8 528 27-608 11-580 (622)
3 PF08159 NUC153: NUC153 domain 99.3 4.4E-13 9.5E-18 95.5 -0.8 29 570-598 1-29 (30)
4 cd00590 RRM RRM (RNA recogniti 93.4 0.48 1E-05 36.3 7.5 66 177-290 1-66 (74)
5 PLN03134 glycine-rich RNA-bind 93.0 0.33 7.2E-06 46.0 7.2 79 173-298 32-110 (144)
6 TIGR01649 hnRNP-L_PTB hnRNP-L/ 90.2 1.2 2.6E-05 49.7 8.9 75 173-300 273-347 (481)
7 PF14259 RRM_6: RNA recognitio 89.8 1.4 2.9E-05 35.3 6.7 65 178-290 1-65 (70)
8 TIGR01649 hnRNP-L_PTB hnRNP-L/ 89.4 0.96 2.1E-05 50.5 7.4 75 175-300 96-170 (481)
9 TIGR01648 hnRNP-R-Q heterogene 88.8 1.1 2.4E-05 51.7 7.5 73 174-299 232-304 (578)
10 smart00360 RRM RNA recognition 88.1 2.1 4.5E-05 32.4 6.4 63 181-290 2-64 (71)
11 TIGR01642 U2AF_lg U2 snRNP aux 88.0 1.7 3.6E-05 48.0 8.1 69 173-291 173-249 (509)
12 TIGR01642 U2AF_lg U2 snRNP aux 87.0 2.3 5E-05 46.9 8.4 79 173-300 293-371 (509)
13 smart00362 RRM_2 RNA recogniti 86.2 4.9 0.00011 30.5 7.5 65 177-290 1-65 (72)
14 PF00076 RRM_1: RNA recognitio 83.3 6.5 0.00014 30.7 7.2 66 178-291 1-66 (70)
15 TIGR01659 sex-lethal sex-letha 81.6 14 0.00031 40.1 11.3 122 174-301 106-272 (346)
16 PF08159 NUC153: NUC153 domain 77.3 0.91 2E-05 33.0 0.4 15 53-67 1-15 (30)
17 TIGR01628 PABP-1234 polyadenyl 75.9 6.6 0.00014 44.3 7.0 70 174-291 284-353 (562)
18 KOG2318 Uncharacterized conser 75.6 1.1 2.5E-05 51.3 0.8 30 50-80 10-39 (650)
19 TIGR01622 SF-CC1 splicing fact 74.5 16 0.00035 39.9 9.3 80 174-302 185-264 (457)
20 TIGR01661 ELAV_HUD_SF ELAV/HuD 73.2 14 0.0003 38.6 8.1 79 174-301 268-346 (352)
21 KOG2321 WD40 repeat protein [G 72.4 1.6 3.5E-05 50.2 1.0 29 568-596 480-508 (703)
22 TIGR01661 ELAV_HUD_SF ELAV/HuD 71.2 13 0.00027 39.0 7.3 80 174-300 88-167 (352)
23 PLN03213 repressor of silencin 68.3 15 0.00032 42.1 7.2 67 173-290 8-76 (759)
24 TIGR01628 PABP-1234 polyadenyl 62.6 16 0.00034 41.4 6.4 71 175-293 88-158 (562)
25 TIGR01648 hnRNP-R-Q heterogene 56.0 28 0.00061 40.5 7.0 69 174-290 57-125 (578)
26 TIGR01645 half-pint poly-U bin 55.9 29 0.00062 40.8 7.0 73 174-293 106-178 (612)
27 PF13893 RRM_5: RNA recognitio 50.4 20 0.00043 27.8 3.3 26 265-290 22-47 (56)
28 TIGR01645 half-pint poly-U bin 49.1 50 0.0011 38.9 7.5 73 174-293 203-275 (612)
29 PLN03120 nucleic acid binding 47.8 67 0.0014 34.1 7.5 69 175-294 4-72 (260)
30 TIGR01622 SF-CC1 splicing fact 45.2 79 0.0017 34.6 8.0 71 173-291 87-157 (457)
31 smart00361 RRM_1 RNA recogniti 38.9 37 0.0008 27.8 3.3 26 266-291 39-64 (70)
32 KOG1832 HIV-1 Vpr-binding prot 38.3 17 0.00036 44.4 1.6 7 90-96 1392-1398(1516)
33 PF07576 BRAP2: BRCA1-associat 35.9 41 0.00089 31.1 3.4 28 264-291 54-81 (110)
34 PF12583 TPPII_N: Tripeptidyl 30.5 23 0.00051 34.1 1.0 30 248-284 73-102 (139)
35 KOG2321 WD40 repeat protein [G 27.1 34 0.00075 39.9 1.7 23 45-67 474-496 (703)
36 COG0724 RNA-binding proteins ( 25.8 3.2E+02 0.007 25.7 7.8 79 175-300 115-193 (306)
37 KOG0123 Polyadenylate-binding 25.5 1.2E+02 0.0026 33.4 5.4 68 178-295 79-146 (369)
38 KOG1456 Heterogeneous nuclear 25.5 53 0.0011 36.7 2.6 36 266-301 161-196 (494)
39 PF11767 SET_assoc: Histone ly 25.0 64 0.0014 27.4 2.5 40 252-293 19-62 (66)
40 KOG0130 RNA-binding protein RB 23.2 59 0.0013 31.8 2.2 36 266-301 116-151 (170)
41 PF07988 LMSTEN: LMSTEN motif; 23.1 43 0.00093 26.7 1.0 18 516-533 24-41 (48)
42 PF04911 ATP-synt_J: ATP synth 22.3 27 0.00058 28.8 -0.2 19 575-593 30-48 (54)
No 1
>KOG2318 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.1e-147 Score=1181.94 Aligned_cols=563 Identities=45% Similarity=0.726 Sum_probs=407.6
Q ss_pred CCCCcccccCCCCCCCCCCCcCCCcccccccccccccCcCCCCCCCCccCCCCCCCCccCchhhhhhhhccccccccCch
Q 007265 25 IITDSRFASVHSDPRFQNVPKQKSKVAIDSRFDRMFTDKNFASSTAPFDKRGKPKKNLKTSKSSLQHYYRIEAEDKKSDE 104 (610)
Q Consensus 25 ~~~D~RFa~i~~DPRFr~~~kk~~KVkiD~RF~~mf~D~~F~~~~a~vDKyGRki~~~~~~~~~L~kfY~~e~ee~~~~~ 104 (610)
||.||||+++||||||+++|++++||+||+||++||+|+.|.++ +.||+|||||++ +++.+|+.||+|++-.....+
T Consensus 10 v~~D~RF~~~~tDPrF~~~~~~d~KvkiDkRF~~m~~dk~fk~~-~~VDk~gr~~~~--~t~~dlref~eldd~~ek~~E 86 (650)
T KOG2318|consen 10 VVIDPRFASALTDPRFSRMPKVDRKVKIDKRFQGMFMDKKFKLK-SAVDKYGRPINK--STKEDLREFYELDDFDEKSGE 86 (650)
T ss_pred ccccHHHHhhhcChhhcccccccchhhhhhhhccccchhhhhhc-chhhhcCCcccc--cchhhhHHHhhhccchhcccc
Confidence 89999999999999999999999999999999999999999984 789999999986 458999999999863221100
Q ss_pred ---------hHHH--HHHh----hccccccHHHHHH-hhhcCCCCCCC-CCCccccCCCCCCcc--ccc-ccCCCCCccc
Q 007265 105 ---------DEEI--EEEE----RRNETDSESELKE-AADVSSGSGTE-EEDDDDVSESTTDDE--EED-VDFDEGPEEE 164 (610)
Q Consensus 105 ---------~~~~--~~ee----~~~~~~~e~e~~~-~~~~~~~s~~~-sss~~d~~~~d~e~~--~e~-~~~~~~~e~e 164 (610)
..+. .+++ ...++..+.++.. +...+|+.-.+ |+|+ +++ |+++++ ++. ..++-+ .+.
T Consensus 87 es~~~esde~sEi~d~~~e~~a~~~seE~~~~~~k~~lD~ar~E~~~s~s~SS-dE~-Se~E~E~eede~e~~d~a-~~~ 163 (650)
T KOG2318|consen 87 ESLKDESDEESEINDEEEEDSAEEESEEESDDELKRALDSARGEGNVSDSESS-DED-SEDESEDEEDEKEISDLA-NLD 163 (650)
T ss_pred ccccccccchhhhhhhhhhhhhhhhhhhcccchhhhhcccccccccccccccc-ccc-ccccccCchhhhhhhhhc-ccC
Confidence 0000 0000 0000111112211 22222322222 2222 221 111111 111 111111 111
Q ss_pred cccCCCCCCCCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCC-CccCCCCCC---
Q 007265 165 EEAIPEIDNETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPV-GLFDSQNEN--- 240 (610)
Q Consensus 165 ~e~~p~~~~~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~-~l~~~~~~~--- 240 (610)
.+..|..+++|+||||||||||||+|.|||||||||||+||+|+||.||||+||++||++|+|+||| .||......
T Consensus 164 pE~~~~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s 243 (650)
T KOG2318|consen 164 PEENPVLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKES 243 (650)
T ss_pred cccccccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCccc
Confidence 2223566789999999999999999999999999999999999999999999999999999999997 688654321
Q ss_pred -CCCCCchhhhHHHHHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccccCCCCccCCCCccccccCC
Q 007265 241 -SDDEDNDEIDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFIPDTMEFKYPPRDVATEAP 319 (610)
Q Consensus 241 -~e~~~~e~~d~e~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRFVPDd~~F~~~prd~ct~~P 319 (610)
.+.+.+++|++++||+|||+|||||||||+|||+.||.+||.+|||+|||+|||+||||||||||+|++.|||+|+++|
T Consensus 244 ~sD~ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIPDdm~Fddd~rd~cseap 323 (650)
T KOG2318|consen 244 ESDDEEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIPDDMTFDDDPRDECSEAP 323 (650)
T ss_pred ccchhhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecCCCCccccccHhHhhhcc
Confidence 2445567899999999999999999999999999999999999999999999999999999999999988999999999
Q ss_pred CC-CCCCccccccccccccccccCCCchHHHHHHHhhCChhHHHhHHHHHHhcCCCCCCcccccch--hhhhhhhhHHHH
Q 007265 320 AN-YGGLDFFTKALQHSNVQLSWDDDEPDRVKTLKRKFNADQVAELELKEFLASDESETDDEDDNV--ADEQSDKKSKKQ 396 (610)
Q Consensus 320 ~~-Ykp~~F~T~ALqhSkVkLTWDe~d~~R~k~~~r~f~~~el~e~D~kaYLASdsse~dde~~~~--~~~~~~~~~k~~ 396 (610)
.+ |+|..|+|+|||||+|+||||+++|+|++++.++|+..+|+++||++||||++|++++.++.+ .......+....
T Consensus 324 ~~~Ykpk~Fst~Alq~s~vkltWDE~d~~R~~l~~~kf~~~~l~d~d~~~~laS~~sde~d~d~~~~e~~~~l~s~d~~k 403 (650)
T KOG2318|consen 324 GNGYKPKDFSTRALQHSKVKLTWDETDPHRKKLFNEKFNGEELEDLDFSAYLASSDSDEEDGDEAESEVDNKLKSKDDQK 403 (650)
T ss_pred ccccCchhhhHHHHHhccccccccccCHHHHHHHHHhhcchhhhhchHHHhhcCCcccccchhhHhHHHHHHhhcccccc
Confidence 87 999999999999999999999999999999999999999999999999999777665543211 111111111123
Q ss_pred HHHHHHHhCCCCCCCCCCCCCCceEEEEe-CCcchhhHHHhhhhcCCCCChHHHHHHHHHHHHHHhhhhcccCCCCcccc
Q 007265 397 DKYRALLESGDGSDEDGEEDGQDMEVTFN-TGLEDISKRILEKKDKKSETIWEAYLRKRREKKKAGKNKSKYSSDDEASD 475 (610)
Q Consensus 397 ~kyr~LL~~~~~~~~~~~~~~~dmEITf~-pgL~~~~~~~~~~~~~~~eT~~EkylrK~kekkk~rk~k~k~~~e~~~~~ 475 (610)
.+|++.-... ..+.+.++..++|||||+ |+++.... ..+.++.+||||+|+|+++||+++||.+.+........
T Consensus 404 dk~~~~sk~e-~~ekk~ke~~~dmE~t~~~~~~e~~~~---k~k~kk~~t~~E~~~~k~~Ekk~~rK~~~~~ke~~~~~- 478 (650)
T KOG2318|consen 404 DKFLANSKEE-EKEKKEKENDGDMEVTFVTDDFEGFNN---KQKDKKEETPIEKYKRKRKEKKRARKKKGKLKEIKDEK- 478 (650)
T ss_pred chhhhhcccc-chhhhcccccccceeEecCchhhcccc---ccccccccChHHHHHHHhhhhHHHHHHhhhhhhhhhhh-
Confidence 3333333211 111222456899999999 67765443 23556789999999999999999999765543211111
Q ss_pred cCccccCCCCcccccCCCCCCCcccCCCCcchhhhhhcchHHHhhcHHHHHHhhccccCccCCCCCCCCch----hhccc
Q 007265 476 TDREAIEEPDDFFVEEPKGKKGEEAGGNHRREEKEQQDTDKEATASTAELELLLADDKGAENGLKGYNMKP----KKRKG 551 (610)
Q Consensus 476 ~~~~~~~~~D~FF~~e~~~k~~kk~~~~k~k~~~~~~~~~~e~~~~kaELELLm~dd~~~~~~~~hF~mk~----kK~K~ 551 (610)
....+.+..+|||.........|| +++.+....+..+++++++|||||||+++.+ ++ ||.+ .++|+
T Consensus 479 ~~~~d~d~~~~~~~~k~k~~~~KK-----~kk~~~~~eE~~~~k~~~~ElElLl~d~d~~-d~----n~~kil~~e~~kk 548 (650)
T KOG2318|consen 479 GLGSDKDEKDDYFKDKFKQENPKK-----KKKGKKTKEEDAEAKRQEKELELLLMDEDAD-DE----NMNKILKIEKKKK 548 (650)
T ss_pred cccccccccCccchhhhhhccccc-----cccccccchhhhhhhhhHHHHHHHhcccccc-ch----hHHHHHHHHHHHh
Confidence 134455667888887554311111 1122223556667888999999999988754 22 5542 11111
Q ss_pred cCCCCCCCCCCCCCCCCCCchhhccccCCCcccCCCCcCcccchHHHHHHHHhhhccC
Q 007265 552 KKGKEVPDEDKIPTADYDDPRFSALFTSPLFALDPTDPQFKRYEILYGINQFISFQGR 609 (610)
Q Consensus 552 kk~k~~~~e~~~~~iDv~DpRF~alf~sh~FaIDPTnP~FKkT~am~~il~~~~~~~~ 609 (610)
|+++-.. +.....++|+||||+|||+||.||||||+||||+|++|.+||.+.++|++
T Consensus 549 k~~~l~k-~~~ie~~~l~D~RFsAlftsh~yaiDPt~p~FK~tk~m~kil~ek~Kr~k 605 (650)
T KOG2318|consen 549 KKKKLKK-EDNIEEANLNDPRFSALFTSHAYAIDPTDPHFKGTKTMEKILEEKSKRRK 605 (650)
T ss_pred hhhhhcc-hhhccccccccHHHHHHhcccccccCCCCccccchHHHHHHHHHHhccch
Confidence 1111111 23345899999999999999999999999999999999999999999553
No 2
>COG5638 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.8e-133 Score=1042.45 Aligned_cols=528 Identities=38% Similarity=0.605 Sum_probs=394.0
Q ss_pred CCcccccCCCCCCCCCCCcCCCcccccccccccccCcCCCCCCCCccCCCCCCCCccCchhhhhhhhccccccccCchhH
Q 007265 27 TDSRFASVHSDPRFQNVPKQKSKVAIDSRFDRMFTDKNFASSTAPFDKRGKPKKNLKTSKSSLQHYYRIEAEDKKSDEDE 106 (610)
Q Consensus 27 ~D~RFa~i~~DPRFr~~~kk~~KVkiD~RF~~mf~D~~F~~~~a~vDKyGRki~~~~~~~~~L~kfY~~e~ee~~~~~~~ 106 (610)
.||||++||+||||.+.+++..||+||.||++ .|..|++ +++||+|||||+. +...+++.+||+++.+.++..+--
T Consensus 11 ~d~rf~~v~sdprf~~~k~~n~kvkvd~rf~k--~d~d~k~-~a~vdrygr~l~q-dk~~~e~dr~~e~e~e~~e~sei~ 86 (622)
T COG5638 11 ADPRFQSVHSDPRFSRLKRGNFKVKVDERFKK--EDKDFKT-TASVDRYGRPLNQ-DKATKEIDRLYELENESSESSEIT 86 (622)
T ss_pred CCccccccccCccccccccCCceeehhhhhcc--ccccchh-hhhhhhhCCcccc-chhHHHHHHHHHhhcccccccccc
Confidence 59999999999999999999999999999995 8999997 6999999999984 467899999999987644321100
Q ss_pred HHHHHhhccccccHHHHH-HhhhcCCCCCCCCCCccccCCCCCCcccccccCCCCCccccc--cCCCCCCCCceeEEecc
Q 007265 107 EIEEEERRNETDSESELK-EAADVSSGSGTEEEDDDDVSESTTDDEEEDVDFDEGPEEEEE--AIPEIDNETHRLAIVNM 183 (610)
Q Consensus 107 ~~~~ee~~~~~~~e~e~~-~~~~~~~~s~~~sss~~d~~~~d~e~~~e~~~~~~~~e~e~e--~~p~~~~~T~RlAvvN~ 183 (610)
...+..+-.. ++- .+...+++.-++.|.++++ ++.+++ ++-..++-+. .+|..+.+|+|||||||
T Consensus 87 ~~~~v~~a~~-----el~dey~~a~~e~~~s~sess~e--s~~ESe-----eE~~~EisE~ag~~pe~G~~tkrLAvVnm 154 (622)
T COG5638 87 DNEEVASASS-----ELTDEYDPARGEGIISTSESSDE--SREESE-----EEKANEISEKAGAVPEEGNPTKRLAVVNM 154 (622)
T ss_pred cchhhhhccc-----cCCccccccCCcceecccccCcc--hhhhhh-----hhhhhhhhhhccCccCCCCcccceeEeec
Confidence 0000000000 000 0001111111111111111 111111 1112233222 26777899999999999
Q ss_pred CCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCC-CccCCCCCC----------------------
Q 007265 184 DWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPV-GLFDSQNEN---------------------- 240 (610)
Q Consensus 184 DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~-~l~~~~~~~---------------------- 240 (610)
|||||.|+|||++|+||||+||.|.+|+||||+||++||+.|.|+||| .||......
T Consensus 155 DWd~v~a~DLf~~fsSf~P~ggkl~kV~iypsefGkeRm~~e~vqGpprdif~~~d~~~ssqk~~~dn~~sd~d~g~d~~ 234 (622)
T COG5638 155 DWDRVDAKDLFKIFSSFLPYGGKLSKVKIYPSEFGKERMAAEHVQGPPRDIFTPADNQPSSQKFGDDNVFSDRDAGEDAL 234 (622)
T ss_pred ccccchHHHHHHHHHhhCCCCCccceeEechhhhhHHHHhHhhccCCchhhccccccCcchhccCCccchhhhhcchhhh
Confidence 999999999999999999999999999999999999999999999999 588533110
Q ss_pred CCCCCchhhhHHHHHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccccCCCCccCCCCccccccCCC
Q 007265 241 SDDEDNDEIDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFIPDTMEFKYPPRDVATEAPA 320 (610)
Q Consensus 241 ~e~~~~e~~d~e~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRFVPDd~~F~~~prd~ct~~P~ 320 (610)
.+.+-+.+||+.+||||||+|||||||||+|+++.|+++||..|||+|||+|||+||||||||+|+|++..|++||.+|.
T Consensus 235 ~Egd~g~e~d~~~lrqyqlerlryYyAvvec~d~~tsK~iY~~CDG~Eye~san~~DLRfvPD~~tfddd~re~ct~~p~ 314 (622)
T COG5638 235 IEGDRGNEFDMVKLRQYQLERLRYYYAVVECEDIETSKNIYSACDGVEYENSANVLDLRFVPDSLTFDDDSREVCTKAPE 314 (622)
T ss_pred hhcccccchhHHHHHHHHhhhheeEEEEEEeccchhhHHHHhccCccccccccceeeeeecCCCcccccchHhhhhcccc
Confidence 12233568999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccccccccccccccccCCCchHHHHHHHhhCChhHHHhHHHHHHhcCCCCCCcccccchhhhhhhhhHHHHHHHH
Q 007265 321 NYGGLDFFTKALQHSNVQLSWDDDEPDRVKTLKRKFNADQVAELELKEFLASDESETDDEDDNVADEQSDKKSKKQDKYR 400 (610)
Q Consensus 321 ~Ykp~~F~T~ALqhSkVkLTWDe~d~~R~k~~~r~f~~~el~e~D~kaYLASdsse~dde~~~~~~~~~~~~~k~~~kyr 400 (610)
+|.|.+|+|+|||||+|+||||++||.|+.+..++||..+|.++||+|||||..|++++.. -.+.+|.
T Consensus 315 ~y~p~~f~tdalqhs~vklswd~~~~~r~dl~k~AFt~~~i~d~dFsay~as~~sde~d~~------------v~es~~q 382 (622)
T COG5638 315 KYEPRDFVTDALQHSKVKLSWDAEDPHRKDLCKEAFTDDGIRDKDFSAYTASKLSDEDDDS------------VMESKMQ 382 (622)
T ss_pred ccCcccchhhhhhhcccccccccCCchHHHHHHHhhcccccccchHHHHhhhhcccccchH------------HHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999665544321 1456677
Q ss_pred HHHhCCC-----CCC---CCCCCCCCceEEEEeCCcchhhHHHhhhhcCCCCChHHHHHHHHHHHHHHhhh-hcccCCCC
Q 007265 401 ALLESGD-----GSD---EDGEEDGQDMEVTFNTGLEDISKRILEKKDKKSETIWEAYLRKRREKKKAGKN-KSKYSSDD 471 (610)
Q Consensus 401 ~LL~~~~-----~~~---~~~~~~~~dmEITf~pgL~~~~~~~~~~~~~~~eT~~EkylrK~kekkk~rk~-k~k~~~e~ 471 (610)
.|+.+.. .+. ..++.+.++|+|||+|+|...... ....+.+||+|+|.||.+|++++||+ +.|....+
T Consensus 383 kL~s~~~~DFg~nS~~~~~~D~~e~~eme~tft~~l~~~ne~---~s~dk~Ettiek~~rk~~Er~~~rKe~qlk~~k~~ 459 (622)
T COG5638 383 KLFSEKEIDFGLNSELVDMSDDGENGEMEDTFTSHLPASNES---ESDDKLETTIEKLDRKLRERQENRKERQLKKTKDD 459 (622)
T ss_pred HHhhhcccccccccccCCcCcccccccccceeccCCcCcccc---ccchhhhhHHHHHHHHHHHHHHHHHHHhhhhhccc
Confidence 7765311 111 112345789999999999754322 12346789999999999999999995 44444322
Q ss_pred cccccCccccCCCCcccccCCCCCCCcccCCCCcchhhhhhcchHHHhhcHHHHHHhhccccCccCCCCCCCCch-----
Q 007265 472 EASDTDREAIEEPDDFFVEEPKGKKGEEAGGNHRREEKEQQDTDKEATASTAELELLLADDKGAENGLKGYNMKP----- 546 (610)
Q Consensus 472 ~~~~~~~~~~~~~D~FF~~e~~~k~~kk~~~~k~k~~~~~~~~~~e~~~~kaELELLm~dd~~~~~~~~hF~mk~----- 546 (610)
. +++ .+.+++.-.+|+++ ...+.+..+++++||||||++|+... .+.||+|+.
T Consensus 460 s-------d~d-----------~Kdk~~S~nkk~~~---~~~~Ie~~a~sk~eleli~~dd~d~e-qldhfdm~~ilkae 517 (622)
T COG5638 460 S-------DVD-----------LKDKKESINKKNKK---GKHAIERTAASKEELELIKADDEDDE-QLDHFDMKSILKAE 517 (622)
T ss_pred h-------hhh-----------hhhhHhhhcccccc---chhhccchhhhhHHHHhhhccccchh-hhccchHHHHHHHH
Confidence 1 111 11111110111222 22233447899999999998877553 578999973
Q ss_pred --hhccccCCCCCCCCCCCCCCCCCCchhhccccCCCcccCCCCcCcccchHHHHHHHHhhhcc
Q 007265 547 --KKRKGKKGKEVPDEDKIPTADYDDPRFSALFTSPLFALDPTDPQFKRYEILYGINQFISFQG 608 (610)
Q Consensus 547 --kK~K~kk~k~~~~e~~~~~iDv~DpRF~alf~sh~FaIDPTnP~FKkT~am~~il~~~~~~~ 608 (610)
|++++-+++....+ ..|..|+.||||.|||++|.||||||||+||+|.||++||.+-++|.
T Consensus 518 k~k~~rk~kkk~~~le-egF~~D~~DpRF~aifedhnFaiDPT~PefK~t~~m~kImdE~rkR~ 580 (622)
T COG5638 518 KFKKNRKLKKKASNLE-EGFVFDPKDPRFVAIFEDHNFAIDPTHPEFKKTGGMKKIMDEKRKRL 580 (622)
T ss_pred HHhhhhhhhhhhhccc-cccccCCCCcchhhhcccCccccCCCCccccccccHHHHHHHHHHHH
Confidence 23222233344444 36899999999999999999999999999999999999999988764
No 3
>PF08159 NUC153: NUC153 domain; InterPro: IPR012580 This small domain is found in a novel nucleolar family [].; GO: 0005634 nucleus
Probab=99.27 E-value=4.4e-13 Score=95.53 Aligned_cols=29 Identities=52% Similarity=0.985 Sum_probs=28.1
Q ss_pred CchhhccccCCCcccCCCCcCcccchHHH
Q 007265 570 DPRFSALFTSPLFALDPTDPQFKRYEILY 598 (610)
Q Consensus 570 DpRF~alf~sh~FaIDPTnP~FKkT~am~ 598 (610)
||||++||++|+|+||||||+||+|++|.
T Consensus 1 D~RF~~lf~~~dF~ID~t~~~yk~~~~~~ 29 (30)
T PF08159_consen 1 DPRFKALFEDPDFAIDPTSPEYKKTNPME 29 (30)
T ss_pred CchHHHhhCCcccccCCCCHHHHhhCccc
Confidence 89999999999999999999999999986
No 4
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=93.39 E-value=0.48 Score=36.35 Aligned_cols=66 Identities=26% Similarity=0.295 Sum_probs=55.5
Q ss_pred eeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHHHH
Q 007265 177 RLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRA 256 (610)
Q Consensus 177 RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~LR~ 256 (610)
+|-|.|+.|+ +...+|.-+|..| |.|..+.++++..+ .|
T Consensus 1 ~i~i~~l~~~-~~~~~i~~~~~~~----g~i~~~~~~~~~~~----------~~-------------------------- 39 (74)
T cd00590 1 TLFVGNLPPD-VTEEDLRELFSKF----GKVESVRIVRDKDT----------KS-------------------------- 39 (74)
T ss_pred CEEEeCCCCc-cCHHHHHHHHHhc----CCEEEEEEeeCCCC----------Cc--------------------------
Confidence 4778999998 8889999999998 78999999986654 11
Q ss_pred HHhhcccceEEEEEeCCHHHHHHHHHhcCccccc
Q 007265 257 YEKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (610)
Q Consensus 257 YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E 290 (610)
.-||.|+|.|++.|...++.++|+-+.
T Consensus 40 -------~~~~~v~f~s~~~a~~a~~~~~~~~~~ 66 (74)
T cd00590 40 -------KGFAFVEFEDEEDAEKALEALNGKELG 66 (74)
T ss_pred -------ceEEEEEECCHHHHHHHHHHhCCCeEC
Confidence 348999999999999999999998743
No 5
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=93.00 E-value=0.33 Score=45.98 Aligned_cols=79 Identities=19% Similarity=0.313 Sum_probs=61.6
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHH
Q 007265 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (610)
Q Consensus 173 ~~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e 252 (610)
..+++|=|-||.|+ ++..||.-+|..| |.|.+|.|-..-. .|
T Consensus 32 ~~~~~lfVgnL~~~-~te~~L~~~F~~~----G~I~~v~i~~d~~----------tg----------------------- 73 (144)
T PLN03134 32 LMSTKLFIGGLSWG-TDDASLRDAFAHF----GDVVDAKVIVDRE----------TG----------------------- 73 (144)
T ss_pred CCCCEEEEeCCCCC-CCHHHHHHHHhcC----CCeEEEEEEecCC----------CC-----------------------
Confidence 46889999999998 7999999999987 7899998843110 00
Q ss_pred HHHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccc
Q 007265 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDL 298 (610)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDL 298 (610)
+.| =||+|+|.+.+.|...+.+++|.++.-....+++
T Consensus 74 --------~~k-GfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~ 110 (144)
T PLN03134 74 --------RSR-GFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP 110 (144)
T ss_pred --------Ccc-eEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence 011 3899999999999999999999988765544443
No 6
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=90.18 E-value=1.2 Score=49.72 Aligned_cols=75 Identities=15% Similarity=0.214 Sum_probs=64.0
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHH
Q 007265 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (610)
Q Consensus 173 ~~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e 252 (610)
..++.|=|-||+|+.|...+|+.||+.| |.|.+|.|.+.- .
T Consensus 273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~y----G~V~~vki~~~~-----------~------------------------ 313 (481)
T TIGR01649 273 GPGSVLMVSGLHQEKVNCDRLFNLFCVY----GNVERVKFMKNK-----------K------------------------ 313 (481)
T ss_pred CCCCEEEEeCCCCCCCCHHHHHHHHHhc----CCeEEEEEEeCC-----------C------------------------
Confidence 4678999999999999999999999987 899999986530 0
Q ss_pred HHHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 007265 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (610)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRF 300 (610)
=||.|+|.+++.|......++|..+. +..|-+.|
T Consensus 314 ------------g~afV~f~~~~~A~~Ai~~lng~~l~--g~~l~v~~ 347 (481)
T TIGR01649 314 ------------ETALIEMADPYQAQLALTHLNGVKLF--GKPLRVCP 347 (481)
T ss_pred ------------CEEEEEECCHHHHHHHHHHhCCCEEC--CceEEEEE
Confidence 28999999999999999999999884 56666665
No 7
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=89.82 E-value=1.4 Score=35.34 Aligned_cols=65 Identities=25% Similarity=0.274 Sum_probs=50.3
Q ss_pred eEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHHHHH
Q 007265 178 LAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAY 257 (610)
Q Consensus 178 lAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~LR~Y 257 (610)
|=|-||.|. +...||+.+|+.| |.|..|.+..+.=|
T Consensus 1 v~i~nlp~~-~~~~~l~~~f~~~----g~v~~v~~~~~~~~--------------------------------------- 36 (70)
T PF14259_consen 1 VYISNLPPS-TTEEDLRNFFSRF----GPVEKVRLIKNKDG--------------------------------------- 36 (70)
T ss_dssp EEEESSTTT---HHHHHHHCTTS----SBEEEEEEEESTTS---------------------------------------
T ss_pred CEEeCCCCC-CCHHHHHHHHHhc----CCcceEEEEeeecc---------------------------------------
Confidence 457899995 9999999998886 46889988743101
Q ss_pred HhhcccceEEEEEeCCHHHHHHHHHhcCccccc
Q 007265 258 EKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (610)
Q Consensus 258 Ql~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E 290 (610)
..+-||.|+|.|.+.|..+++.++|+.+.
T Consensus 37 ----~~~~~a~v~f~~~~~a~~al~~~~~~~~~ 65 (70)
T PF14259_consen 37 ----QSRGFAFVEFSSEEDAKRALELLNGKEID 65 (70)
T ss_dssp ----SEEEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred ----ccCCEEEEEeCCHHHHHHHHHHCCCcEEC
Confidence 23678999999999999999999988774
No 8
>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).
Probab=89.40 E-value=0.96 Score=50.45 Aligned_cols=75 Identities=19% Similarity=0.354 Sum_probs=59.8
Q ss_pred CceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHH
Q 007265 175 THRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKL 254 (610)
Q Consensus 175 T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~L 254 (610)
..+|-|.||+|. |...+|..+|+.| |.|.+|.|++.. |
T Consensus 96 ~~~v~v~nl~~~-vt~~~L~~~F~~~----G~V~~v~i~~~~------------~------------------------- 133 (481)
T TIGR01649 96 VLRVIVENPMYP-ITLDVLYQIFNPY----GKVLRIVTFTKN------------N------------------------- 133 (481)
T ss_pred eEEEEEcCCCCC-CCHHHHHHHHhcc----CCEEEEEEEecC------------C-------------------------
Confidence 457899999985 9999999999966 899999986421 0
Q ss_pred HHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 007265 255 RAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (610)
Q Consensus 255 R~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRF 300 (610)
+ +||.|+|.+++.|.+.-..++|.++...++.|-+.|
T Consensus 134 --------~-~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~ 170 (481)
T TIGR01649 134 --------V-FQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEY 170 (481)
T ss_pred --------c-eEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEE
Confidence 0 369999999999999999999999965444444444
No 9
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=88.80 E-value=1.1 Score=51.68 Aligned_cols=73 Identities=22% Similarity=0.211 Sum_probs=61.0
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
.++.|=|.||+| ++...+|..+|+.|.| |.|.+|.|- .
T Consensus 232 ~~k~LfVgNL~~-~~tee~L~~~F~~f~~--G~I~rV~~~-----------------r---------------------- 269 (578)
T TIGR01648 232 KVKILYVRNLMT-TTTEEIIEKSFSEFKP--GKVERVKKI-----------------R---------------------- 269 (578)
T ss_pred cccEEEEeCCCC-CCCHHHHHHHHHhcCC--CceEEEEee-----------------c----------------------
Confidence 467899999999 5999999999999966 799998651 0
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccccccccccc
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLR 299 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLR 299 (610)
=||.|+|.+.+.|.+...+++|.++.-....+++-
T Consensus 270 -----------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A 304 (578)
T TIGR01648 270 -----------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA 304 (578)
T ss_pred -----------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence 07999999999999999999999987765555544
No 10
>smart00360 RRM RNA recognition motif.
Probab=88.06 E-value=2.1 Score=32.36 Aligned_cols=63 Identities=29% Similarity=0.335 Sum_probs=47.7
Q ss_pred eccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHHHHHHhh
Q 007265 181 VNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAYEKS 260 (610)
Q Consensus 181 vN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~LR~YQl~ 260 (610)
.|+.|. +...||..+|+.| |.|..|.|++... .|.+
T Consensus 2 ~~l~~~-~~~~~l~~~f~~~----g~v~~~~i~~~~~----------~~~~----------------------------- 37 (71)
T smart00360 2 GNLPPD-VTEEELRELFSKF----GKIESVRLVRDKD----------TGKS----------------------------- 37 (71)
T ss_pred CCCCcc-cCHHHHHHHHHhh----CCEeEEEEEeCCC----------CCCC-----------------------------
Confidence 456554 6778999999854 6888898887542 1111
Q ss_pred cccceEEEEEeCCHHHHHHHHHhcCccccc
Q 007265 261 RLRYYYAVVECDSSATADYLYRACDGVEFE 290 (610)
Q Consensus 261 RLRYYYAVvecdS~~TA~~IY~ecDG~E~E 290 (610)
.-||.|+|.+.+.|..+...++|..+.
T Consensus 38 ---~~~a~v~f~~~~~a~~a~~~~~~~~~~ 64 (71)
T smart00360 38 ---KGFAFVEFESEEDAEKALEALNGKELD 64 (71)
T ss_pred ---CceEEEEeCCHHHHHHHHHHcCCCeeC
Confidence 138999999999999999999988874
No 11
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=87.99 E-value=1.7 Score=47.99 Aligned_cols=69 Identities=13% Similarity=0.246 Sum_probs=52.8
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhhccC--------CCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCC
Q 007265 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLP--------KDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDE 244 (610)
Q Consensus 173 ~~T~RlAvvN~DWD~i~A~DL~vlf~SF~P--------~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~ 244 (610)
...+||=|.||.|+ ++-.+|..+|+.|+. +++.|.+|.|-.+
T Consensus 173 ~~~r~lyVgnLp~~-~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~----------------------------- 222 (509)
T TIGR01642 173 RQARRLYVGGIPPE-FVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKE----------------------------- 222 (509)
T ss_pred ccccEEEEeCCCCC-CCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCC-----------------------------
Confidence 35789999999996 888999999998742 2445655554210
Q ss_pred CchhhhHHHHHHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccc
Q 007265 245 DNDEIDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFER 291 (610)
Q Consensus 245 ~~e~~d~e~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~ 291 (610)
+ -||.|+|.+++.|.... +++|+.|.-
T Consensus 223 ------------------k-g~afVeF~~~e~A~~Al-~l~g~~~~g 249 (509)
T TIGR01642 223 ------------------K-NFAFLEFRTVEEATFAM-ALDSIIYSN 249 (509)
T ss_pred ------------------C-CEEEEEeCCHHHHhhhh-cCCCeEeeC
Confidence 0 28999999999999988 699988754
No 12
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=86.98 E-value=2.3 Score=46.90 Aligned_cols=79 Identities=22% Similarity=0.288 Sum_probs=61.0
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHH
Q 007265 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (610)
Q Consensus 173 ~~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e 252 (610)
+.+++|-|-||.|. +...+|..+|+.| |.|..|.|..-. ..|.
T Consensus 293 ~~~~~l~v~nlp~~-~~~~~l~~~f~~~----G~i~~~~~~~~~----------~~g~---------------------- 335 (509)
T TIGR01642 293 DSKDRIYIGNLPLY-LGEDQIKELLESF----GDLKAFNLIKDI----------ATGL---------------------- 335 (509)
T ss_pred CCCCEEEEeCCCCC-CCHHHHHHHHHhc----CCeeEEEEEecC----------CCCC----------------------
Confidence 46789999999996 8999999999998 678888875210 0111
Q ss_pred HHHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 007265 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (610)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRF 300 (610)
-.-||.|+|.+.+.|......|+|+.+.- ..|-+++
T Consensus 336 ----------~~g~afv~f~~~~~a~~A~~~l~g~~~~~--~~l~v~~ 371 (509)
T TIGR01642 336 ----------SKGYAFCEYKDPSVTDVAIAALNGKDTGD--NKLHVQR 371 (509)
T ss_pred ----------cCeEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEE
Confidence 13489999999999999999999999864 3444444
No 13
>smart00362 RRM_2 RNA recognition motif.
Probab=86.16 E-value=4.9 Score=30.46 Aligned_cols=65 Identities=28% Similarity=0.286 Sum_probs=49.9
Q ss_pred eeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHHHH
Q 007265 177 RLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRA 256 (610)
Q Consensus 177 RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~LR~ 256 (610)
||-|.|+.| ++...+|..+|.. -|.|..|.|++.. |.+
T Consensus 1 ~v~i~~l~~-~~~~~~l~~~~~~----~g~v~~~~~~~~~------------~~~------------------------- 38 (72)
T smart00362 1 TLFVGNLPP-DVTEEDLKELFSK----FGPIESVKIPKDT------------GKS------------------------- 38 (72)
T ss_pred CEEEcCCCC-cCCHHHHHHHHHh----cCCEEEEEEecCC------------CCC-------------------------
Confidence 467888877 4677888888874 3578888888764 211
Q ss_pred HHhhcccceEEEEEeCCHHHHHHHHHhcCccccc
Q 007265 257 YEKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (610)
Q Consensus 257 YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E 290 (610)
.=||.|+|.+...|......++|..+.
T Consensus 39 -------~~~~~v~f~~~~~a~~a~~~~~~~~~~ 65 (72)
T smart00362 39 -------KGFAFVEFESEEDAEKAIEALNGTKLG 65 (72)
T ss_pred -------CceEEEEeCCHHHHHHHHHHhCCcEEC
Confidence 137999999999999999999997774
No 14
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=83.26 E-value=6.5 Score=30.66 Aligned_cols=66 Identities=27% Similarity=0.327 Sum_probs=51.3
Q ss_pred eEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHHHHH
Q 007265 178 LAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAY 257 (610)
Q Consensus 178 lAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~LR~Y 257 (610)
|=|.||.|+ +...+|.-+|+.| |.|..|.|.+. ..|+.
T Consensus 1 l~v~nlp~~-~t~~~l~~~f~~~----g~i~~~~~~~~-----------~~~~~-------------------------- 38 (70)
T PF00076_consen 1 LYVGNLPPD-VTEEELRDFFSQF----GKIESIKVMRN-----------SSGKS-------------------------- 38 (70)
T ss_dssp EEEESETTT-SSHHHHHHHHHTT----STEEEEEEEEE-----------TTSSE--------------------------
T ss_pred cEEcCCCCc-CCHHHHHHHHHHh----hhccccccccc-----------ccccc--------------------------
Confidence 347788875 5668999999886 67888888876 11221
Q ss_pred HhhcccceEEEEEeCCHHHHHHHHHhcCcccccc
Q 007265 258 EKSRLRYYYAVVECDSSATADYLYRACDGVEFER 291 (610)
Q Consensus 258 Ql~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~ 291 (610)
.=||+|+|.+.+.|..+.++++|..+.-
T Consensus 39 ------~~~a~V~F~~~~~a~~a~~~l~g~~~~~ 66 (70)
T PF00076_consen 39 ------KGYAFVEFESEEDAEKALEELNGKKING 66 (70)
T ss_dssp ------EEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred ------cceEEEEEcCHHHHHHHHHHcCCCEECc
Confidence 3489999999999999999999987753
No 15
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=81.57 E-value=14 Score=40.06 Aligned_cols=122 Identities=15% Similarity=0.185 Sum_probs=77.4
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecC------------hhhHHHHHHHHh---cCCCCccCCC-
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPS------------EFGIQRMKEEEV---RGPVGLFDSQ- 237 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPS------------eFGkeRM~~Ee~---~GP~~l~~~~- 237 (610)
..++|=|-||.|+ ++..+|..+|..| |.|.+|.|-.- +|.-+.-+...+ .|-. |....
T Consensus 106 ~~~~LfVgnLp~~-~te~~L~~lF~~~----G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~-l~gr~i 179 (346)
T TIGR01659 106 SGTNLIVNYLPQD-MTDRELYALFRTI----GPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGIT-VRNKRL 179 (346)
T ss_pred CCcEEEEeCCCCC-CCHHHHHHHHHhc----CCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCc-cCCcee
Confidence 5678999999998 7999999999987 56888888432 244555444444 3321 11100
Q ss_pred -----CCC-CCC--------CCchhhhHHHHHHHH-----hhcccc----------eEEEEEeCCHHHHHHHHHhcCccc
Q 007265 238 -----NEN-SDD--------EDNDEIDEEKLRAYE-----KSRLRY----------YYAVVECDSSATADYLYRACDGVE 288 (610)
Q Consensus 238 -----~~~-~e~--------~~~e~~d~e~LR~YQ-----l~RLRY----------YYAVvecdS~~TA~~IY~ecDG~E 288 (610)
... ... .=...+..+.||.+= +.+++. =||.|+|.+.+.|...-..|+|+.
T Consensus 180 ~V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~ 259 (346)
T TIGR01659 180 KVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI 259 (346)
T ss_pred eeecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCc
Confidence 000 000 001123444555442 223222 299999999999999999999999
Q ss_pred ccccccccccccc
Q 007265 289 FERSSNKLDLRFI 301 (610)
Q Consensus 289 ~E~San~lDLRFV 301 (610)
++-....|-+++.
T Consensus 260 ~~g~~~~l~V~~a 272 (346)
T TIGR01659 260 PEGGSQPLTVRLA 272 (346)
T ss_pred cCCCceeEEEEEC
Confidence 8877667766654
No 16
>PF08159 NUC153: NUC153 domain; InterPro: IPR012580 This small domain is found in a novel nucleolar family [].; GO: 0005634 nucleus
Probab=77.26 E-value=0.91 Score=32.96 Aligned_cols=15 Identities=47% Similarity=0.895 Sum_probs=12.6
Q ss_pred cccccccccCcCCCC
Q 007265 53 DSRFDRMFTDKNFAS 67 (610)
Q Consensus 53 D~RF~~mf~D~~F~~ 67 (610)
|.||+.||++..|..
T Consensus 1 D~RF~~lf~~~dF~I 15 (30)
T PF08159_consen 1 DPRFKALFEDPDFAI 15 (30)
T ss_pred CchHHHhhCCccccc
Confidence 789999999988873
No 17
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=75.91 E-value=6.6 Score=44.35 Aligned_cols=70 Identities=21% Similarity=0.213 Sum_probs=57.2
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
.+..|-|-||+|+ |.-.+|--+|+.| |.|.+|.|....-|.-
T Consensus 284 ~~~~l~V~nl~~~-~~~~~L~~~F~~~----G~i~~~~i~~d~~g~~--------------------------------- 325 (562)
T TIGR01628 284 QGVNLYVKNLDDT-VTDEKLRELFSEC----GEITSAKVMLDEKGVS--------------------------------- 325 (562)
T ss_pred CCCEEEEeCCCCc-cCHHHHHHHHHhc----CCeEEEEEEECCCCCc---------------------------------
Confidence 5667999999996 7889999999887 7899999987533321
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccc
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFER 291 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~ 291 (610)
-=||.|+|.+++.|...-.+++|..+.-
T Consensus 326 ----------~g~gfV~f~~~~~A~~A~~~~~g~~~~g 353 (562)
T TIGR01628 326 ----------RGFGFVCFSNPEEANRAVTEMHGRMLGG 353 (562)
T ss_pred ----------CCeEEEEeCCHHHHHHHHHHhcCCeeCC
Confidence 1289999999999999999999977653
No 18
>KOG2318 consensus Uncharacterized conserved protein [Function unknown]
Probab=75.59 E-value=1.1 Score=51.26 Aligned_cols=30 Identities=37% Similarity=0.558 Sum_probs=25.8
Q ss_pred ccccccccccccCcCCCCCCCCccCCCCCCC
Q 007265 50 VAIDSRFDRMFTDKNFASSTAPFDKRGKPKK 80 (610)
Q Consensus 50 VkiD~RF~~mf~D~~F~~~~a~vDKyGRki~ 80 (610)
|.||.||+++++|++|.. ..+||..++.-+
T Consensus 10 v~~D~RF~~~~tDPrF~~-~~~~d~KvkiDk 39 (650)
T KOG2318|consen 10 VVIDPRFASALTDPRFSR-MPKVDRKVKIDK 39 (650)
T ss_pred ccccHHHHhhhcChhhcc-cccccchhhhhh
Confidence 999999999999999996 578888777554
No 19
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=74.49 E-value=16 Score=39.87 Aligned_cols=80 Identities=15% Similarity=0.293 Sum_probs=62.6
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
.+++|-|.||.+ +|.-.+|..+|+.| |.|.+|.|.....+ |..
T Consensus 185 ~~~~l~v~nl~~-~~te~~l~~~f~~~----G~i~~v~~~~d~~~----------g~~---------------------- 227 (457)
T TIGR01622 185 NFLKLYVGNLHF-NITEQELRQIFEPF----GDIEDVQLHRDPET----------GRS---------------------- 227 (457)
T ss_pred CCCEEEEcCCCC-CCCHHHHHHHHHhc----CCeEEEEEEEcCCC----------Ccc----------------------
Confidence 378999999996 58899999999865 78999998753211 111
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccccC
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFIP 302 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRFVP 302 (610)
--||.|+|.+++.|......++|+.+ .+..|-+.|.-
T Consensus 228 ----------~g~afV~f~~~e~A~~A~~~l~g~~i--~g~~i~v~~a~ 264 (457)
T TIGR01622 228 ----------KGFGFIQFHDAEEAKEALEVMNGFEL--AGRPIKVGYAQ 264 (457)
T ss_pred ----------ceEEEEEECCHHHHHHHHHhcCCcEE--CCEEEEEEEcc
Confidence 14899999999999999999999766 45667777654
No 20
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=73.19 E-value=14 Score=38.64 Aligned_cols=79 Identities=14% Similarity=0.179 Sum_probs=59.7
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
.++.|=|-||.|+ +...+|..+|+-| |.|.+|.|..- ...|..
T Consensus 268 ~~~~lfV~NL~~~-~~e~~L~~~F~~f----G~v~~v~i~~d----------~~t~~s---------------------- 310 (352)
T TIGR01661 268 AGYCIFVYNLSPD-TDETVLWQLFGPF----GAVQNVKIIRD----------LTTNQC---------------------- 310 (352)
T ss_pred CCcEEEEeCCCCC-CCHHHHHHHHHhC----CCeEEEEEeEc----------CCCCCc----------------------
Confidence 3457999999987 7999999999977 78999998631 011111
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccccccccccccc
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFI 301 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRFV 301 (610)
-=||.|+|.+++.|......++|..+.- ..|-+-|+
T Consensus 311 ----------kG~aFV~F~~~~~A~~Ai~~lnG~~~~g--r~i~V~~~ 346 (352)
T TIGR01661 311 ----------KGYGFVSMTNYDEAAMAILSLNGYTLGN--RVLQVSFK 346 (352)
T ss_pred ----------cceEEEEECCHHHHHHHHHHhCCCEECC--eEEEEEEc
Confidence 1289999999999999999999988754 44444444
No 21
>KOG2321 consensus WD40 repeat protein [General function prediction only]
Probab=72.42 E-value=1.6 Score=50.17 Aligned_cols=29 Identities=21% Similarity=0.469 Sum_probs=25.7
Q ss_pred CCCchhhccccCCCcccCCCCcCcccchH
Q 007265 568 YDDPRFSALFTSPLFALDPTDPQFKRYEI 596 (610)
Q Consensus 568 v~DpRF~alf~sh~FaIDPTnP~FKkT~a 596 (610)
+.|.||++||++++|.||-+.-+|+.-.-
T Consensus 480 LtDdRFk~mFen~dFeVDeds~ey~~l~p 508 (703)
T KOG2321|consen 480 LTDDRFKSMFENEDFEVDEDSEEYRLLAP 508 (703)
T ss_pred cchhHHHHhccCcccccCccHHHHhhhch
Confidence 67889999999999999999999987443
No 22
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=71.24 E-value=13 Score=38.96 Aligned_cols=80 Identities=19% Similarity=0.308 Sum_probs=60.8
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
...+|=|.||.+. ++..+|..+|+.| |.|..|.|.... ..|+.
T Consensus 88 ~~~~l~v~~l~~~-~~~~~l~~~f~~~----G~i~~~~~~~~~----------~~~~~---------------------- 130 (352)
T TIGR01661 88 KGANLYVSGLPKT-MTQHELESIFSPF----GQIITSRILSDN----------VTGLS---------------------- 130 (352)
T ss_pred ccceEEECCcccc-CCHHHHHHHHhcc----CCEEEEEEEecC----------CCCCc----------------------
Confidence 4568999999887 4778999999877 788888875311 11111
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRF 300 (610)
--||.|+|.+.+.|...-+.++|..+..+...|-++|
T Consensus 131 ----------~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~ 167 (352)
T TIGR01661 131 ----------KGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF 167 (352)
T ss_pred ----------CcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence 1589999999999999999999998877665555554
No 23
>PLN03213 repressor of silencing 3; Provisional
Probab=68.31 E-value=15 Score=42.12 Aligned_cols=67 Identities=22% Similarity=0.322 Sum_probs=53.4
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHH
Q 007265 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (610)
Q Consensus 173 ~~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e 252 (610)
..+-||=|-||-|+ |...||-.+|.+| |.|.+|.|- -+= | .
T Consensus 8 ~~gMRIYVGNLSyd-VTEDDLravFSeF----GsVkdVEIp-RET-----------G-R--------------------- 48 (759)
T PLN03213 8 GGGVRLHVGGLGES-VGRDDLLKIFSPM----GTVDAVEFV-RTK-----------G-R--------------------- 48 (759)
T ss_pred CcceEEEEeCCCCC-CCHHHHHHHHHhc----CCeeEEEEe-ccc-----------C-C---------------------
Confidence 47899999999996 8999999999999 899999994 221 2 0
Q ss_pred HHHHHHhhcccceEEEEEeCCH--HHHHHHHHhcCccccc
Q 007265 253 KLRAYEKSRLRYYYAVVECDSS--ATADYLYRACDGVEFE 290 (610)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecdS~--~TA~~IY~ecDG~E~E 290 (610)
=||-|++.+. ..+.+....+||.++-
T Consensus 49 ------------GFAFVEMssdddaEeeKAISaLNGAEWK 76 (759)
T PLN03213 49 ------------SFAYIDFSPSSTNSLTKLFSTYNGCVWK 76 (759)
T ss_pred ------------ceEEEEecCCcHHHHHHHHHHhcCCeec
Confidence 2777887765 6788888888888753
No 24
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=62.61 E-value=16 Score=41.37 Aligned_cols=71 Identities=24% Similarity=0.323 Sum_probs=56.9
Q ss_pred CceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHH
Q 007265 175 THRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKL 254 (610)
Q Consensus 175 T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~L 254 (610)
..+|-|.||.+ .|.-.+|+-+|+.| |.|++|.|.....|+-
T Consensus 88 ~~~vfV~nLp~-~~~~~~L~~~F~~~----G~i~~~~i~~~~~g~s---------------------------------- 128 (562)
T TIGR01628 88 VGNIFVKNLDK-SVDNKALFDTFSKF----GNILSCKVATDENGKS---------------------------------- 128 (562)
T ss_pred CCceEEcCCCc-cCCHHHHHHHHHhc----CCcceeEeeecCCCCc----------------------------------
Confidence 45799999998 57788999999987 7899998876544321
Q ss_pred HHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccccc
Q 007265 255 RAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSS 293 (610)
Q Consensus 255 R~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~Sa 293 (610)
-=||.|+|.+.+.|......++|+.+.-..
T Consensus 129 ---------kg~afV~F~~~e~A~~Ai~~lng~~~~~~~ 158 (562)
T TIGR01628 129 ---------RGYGFVHFEKEESAKAAIQKVNGMLLNDKE 158 (562)
T ss_pred ---------ccEEEEEECCHHHHHHHHHHhcccEecCce
Confidence 027999999999999999999999775543
No 25
>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.
Probab=55.98 E-value=28 Score=40.55 Aligned_cols=69 Identities=14% Similarity=0.150 Sum_probs=56.8
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
....|=|-||.| .|...+|.-+|+.| |.|..|.|....-|+-
T Consensus 57 ~~~~lFVgnLp~-~~tEd~L~~~F~~~----G~I~~vrl~~D~sG~s--------------------------------- 98 (578)
T TIGR01648 57 RGCEVFVGKIPR-DLYEDELVPLFEKA----GPIYELRLMMDFSGQN--------------------------------- 98 (578)
T ss_pred CCCEEEeCCCCC-CCCHHHHHHHHHhh----CCEEEEEEEECCCCCc---------------------------------
Confidence 457899999999 58999999999988 6899998865521211
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccc
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E 290 (610)
| =||.|+|.+.+.|...-+.++|.++.
T Consensus 99 -------R---GfaFV~F~~~e~A~~Ai~~lng~~i~ 125 (578)
T TIGR01648 99 -------R---GYAFVTFCGKEEAKEAVKLLNNYEIR 125 (578)
T ss_pred -------c---ceEEEEeCCHHHHHHHHHHcCCCeec
Confidence 1 18999999999999999999999885
No 26
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=55.94 E-value=29 Score=40.79 Aligned_cols=73 Identities=15% Similarity=0.220 Sum_probs=57.0
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
..+||=|-||.| .++-.+|..+|..| |.|.+|.|-.-.. .|
T Consensus 106 ~~~rLfVGnLp~-~~tEe~Lr~lF~~f----G~I~sV~I~~D~~----------Tg------------------------ 146 (612)
T TIGR01645 106 IMCRVYVGSISF-ELREDTIRRAFDPF----GPIKSINMSWDPA----------TG------------------------ 146 (612)
T ss_pred CCCEEEEcCCCC-CCCHHHHHHHHHcc----CCEEEEEEeecCC----------CC------------------------
Confidence 568999999999 78999999999876 6798888732100 01
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccccc
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSS 293 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~Sa 293 (610)
+. -=||.|+|.+.+.|...+.+++|..+.-..
T Consensus 147 -------ks-kGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~ 178 (612)
T TIGR01645 147 -------KH-KGFAFVEYEVPEAAQLALEQMNGQMLGGRN 178 (612)
T ss_pred -------Cc-CCeEEEEeCcHHHHHHHHHhcCCeEEecce
Confidence 00 128999999999999999999999886443
No 27
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=50.41 E-value=20 Score=27.77 Aligned_cols=26 Identities=27% Similarity=0.323 Sum_probs=23.8
Q ss_pred eEEEEEeCCHHHHHHHHHhcCccccc
Q 007265 265 YYAVVECDSSATADYLYRACDGVEFE 290 (610)
Q Consensus 265 YYAVvecdS~~TA~~IY~ecDG~E~E 290 (610)
-+|.|++.+++.|......++|..|-
T Consensus 22 ~~a~V~f~~~~~A~~a~~~l~~~~~~ 47 (56)
T PF13893_consen 22 GFAFVEFASVEDAQKAIEQLNGRQFN 47 (56)
T ss_dssp TEEEEEESSHHHHHHHHHHHTTSEET
T ss_pred CEEEEEECCHHHHHHHHHHhCCCEEC
Confidence 37999999999999999999999873
No 28
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.
Probab=49.09 E-value=50 Score=38.88 Aligned_cols=73 Identities=11% Similarity=0.204 Sum_probs=57.9
Q ss_pred CCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHH
Q 007265 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (610)
Q Consensus 174 ~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~ 253 (610)
..+||=|.||.++ |.-.||..+|+.| |.|.+|.|.+..-+ |..
T Consensus 203 ~~~rLfVgnLp~~-vteedLk~lFs~F----G~I~svrl~~D~~t----------gks---------------------- 245 (612)
T TIGR01645 203 KFNRIYVASVHPD-LSETDIKSVFEAF----GEIVKCQLARAPTG----------RGH---------------------- 245 (612)
T ss_pred ccceEEeecCCCC-CCHHHHHHHHhhc----CCeeEEEEEecCCC----------CCc----------------------
Confidence 4579999999976 7889999999988 78999998653211 100
Q ss_pred HHHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccccc
Q 007265 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSS 293 (610)
Q Consensus 254 LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~Sa 293 (610)
==||.|+|.+.+.|...-..++|+++.-.-
T Consensus 246 ----------KGfGFVeFe~~e~A~kAI~amNg~elgGr~ 275 (612)
T TIGR01645 246 ----------KGYGFIEYNNLQSQSEAIASMNLFDLGGQY 275 (612)
T ss_pred ----------CCeEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence 128999999999999999999999887443
No 29
>PLN03120 nucleic acid binding protein; Provisional
Probab=47.76 E-value=67 Score=34.09 Aligned_cols=69 Identities=17% Similarity=0.167 Sum_probs=54.6
Q ss_pred CceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHH
Q 007265 175 THRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKL 254 (610)
Q Consensus 175 T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~L 254 (610)
++.|=|.||.|. +.-.||.-+|+.| |.|.+|.|.... + +
T Consensus 4 ~rtVfVgNLs~~-tTE~dLrefFS~~----G~I~~V~I~~d~--------~----~------------------------ 42 (260)
T PLN03120 4 VRTVKVSNVSLK-ATERDIKEFFSFS----GDIEYVEMQSEN--------E----R------------------------ 42 (260)
T ss_pred CCEEEEeCCCCC-CCHHHHHHHHHhc----CCeEEEEEeecC--------C----C------------------------
Confidence 678999999999 9999999999654 899999995321 0 0
Q ss_pred HHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccc
Q 007265 255 RAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSN 294 (610)
Q Consensus 255 R~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San 294 (610)
+ =||.|+|.+.+.|...- .++|..+.-...
T Consensus 43 ------~---GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V 72 (260)
T PLN03120 43 ------S---QIAYVTFKDPQGAETAL-LLSGATIVDQSV 72 (260)
T ss_pred ------C---CEEEEEeCcHHHHHHHH-HhcCCeeCCceE
Confidence 0 18999999999999888 499988865443
No 30
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=45.17 E-value=79 Score=34.58 Aligned_cols=71 Identities=13% Similarity=0.117 Sum_probs=54.3
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHH
Q 007265 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (610)
Q Consensus 173 ~~T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e 252 (610)
...++|-|.||.|+ |.-.||..+|+.| |.|..|.|..-- ..|.
T Consensus 87 ~~~~~l~V~nlp~~-~~~~~l~~~F~~~----G~v~~v~i~~d~----------~~~~---------------------- 129 (457)
T TIGR01622 87 RDDRTVFVLQLALK-ARERDLYEFFSKV----GKVRDVQCIKDR----------NSRR---------------------- 129 (457)
T ss_pred cCCcEEEEeCCCCC-CCHHHHHHHHHhc----CCeeEEEEeecC----------CCCC----------------------
Confidence 35789999999995 8999999999987 589999885310 0010
Q ss_pred HHHHHHhhcccceEEEEEeCCHHHHHHHHHhcCcccccc
Q 007265 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFER 291 (610)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~ 291 (610)
.-=||.|+|.+++.|.+... ++|+.+.-
T Consensus 130 ----------skg~afVeF~~~e~A~~Al~-l~g~~~~g 157 (457)
T TIGR01622 130 ----------SKGVAYVEFYDVESVIKALA-LTGQMLLG 157 (457)
T ss_pred ----------cceEEEEEECCHHHHHHHHH-hCCCEECC
Confidence 12489999999999998874 88887653
No 31
>smart00361 RRM_1 RNA recognition motif.
Probab=38.87 E-value=37 Score=27.79 Aligned_cols=26 Identities=15% Similarity=0.155 Sum_probs=23.7
Q ss_pred EEEEEeCCHHHHHHHHHhcCcccccc
Q 007265 266 YAVVECDSSATADYLYRACDGVEFER 291 (610)
Q Consensus 266 YAVvecdS~~TA~~IY~ecDG~E~E~ 291 (610)
||.|+|.+.+-|......++|..|.-
T Consensus 39 ~~fV~f~~~~dA~~A~~~l~g~~~~g 64 (70)
T smart00361 39 NVYITFERSEDAARAIVDLNGRYFDG 64 (70)
T ss_pred EEEEEECCHHHHHHHHHHhCCCEECC
Confidence 69999999999999999999998753
No 32
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=38.32 E-value=17 Score=44.40 Aligned_cols=7 Identities=29% Similarity=0.553 Sum_probs=4.5
Q ss_pred hhhhccc
Q 007265 90 QHYYRIE 96 (610)
Q Consensus 90 ~kfY~~e 96 (610)
-|.|++.
T Consensus 1392 ~r~yEIG 1398 (1516)
T KOG1832|consen 1392 ARMYEIG 1398 (1516)
T ss_pred hhhhhhc
Confidence 4678773
No 33
>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []. These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.
Probab=35.87 E-value=41 Score=31.07 Aligned_cols=28 Identities=21% Similarity=0.491 Sum_probs=25.6
Q ss_pred ceEEEEEeCCHHHHHHHHHhcCcccccc
Q 007265 264 YYYAVVECDSSATADYLYRACDGVEFER 291 (610)
Q Consensus 264 YYYAVvecdS~~TA~~IY~ecDG~E~E~ 291 (610)
-|=+++.|.+...|..-|.+++|.-|-+
T Consensus 54 rymVLikF~~~~~Ad~Fy~~fNGk~Fns 81 (110)
T PF07576_consen 54 RYMVLIKFRDQESADEFYEEFNGKPFNS 81 (110)
T ss_pred eEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence 5889999999999999999999988854
No 34
>PF12583 TPPII_N: Tripeptidyl peptidase II N terminal; InterPro: IPR022232 This entry represents a region of approximately 190 amino acids in length and is found in association with PF00082 from PFAM. The members are serine peptidases belonging to MEROPS peptidase family S8A, tripeptidyl peptidase II (TPPII), clan SB. They are a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. ; PDB: 3LXU_X.
Probab=30.49 E-value=23 Score=34.10 Aligned_cols=30 Identities=20% Similarity=0.354 Sum_probs=24.7
Q ss_pred hhhHHHHHHHHhhcccceEEEEEeCCHHHHHHHHHhc
Q 007265 248 EIDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRAC 284 (610)
Q Consensus 248 ~~d~e~LR~YQl~RLRYYYAVvecdS~~TA~~IY~ec 284 (610)
+-..|+||-||..-| +.|+. +.|+.||.++
T Consensus 73 DeY~EaLRDfq~~~i------aKle~-e~Ae~vY~el 102 (139)
T PF12583_consen 73 DEYSEALRDFQCSWI------AKLEP-ENAEQVYEEL 102 (139)
T ss_dssp HHHHHHHHHHHHHHH------TTS-H-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH------HhhCH-HHHHHHHHHH
Confidence 445799999999876 67887 9999999987
No 35
>KOG2321 consensus WD40 repeat protein [General function prediction only]
Probab=27.13 E-value=34 Score=39.91 Aligned_cols=23 Identities=30% Similarity=0.668 Sum_probs=17.9
Q ss_pred cCCCcccccccccccccCcCCCC
Q 007265 45 KQKSKVAIDSRFDRMFTDKNFAS 67 (610)
Q Consensus 45 kk~~KVkiD~RF~~mf~D~~F~~ 67 (610)
++...|--|+||+.||.++.|.+
T Consensus 474 k~~~siLtDdRFk~mFen~dFeV 496 (703)
T KOG2321|consen 474 KKAPSILTDDRFKSMFENEDFEV 496 (703)
T ss_pred ccCCcccchhHHHHhccCccccc
Confidence 33445667899999999999974
No 36
>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]
Probab=25.78 E-value=3.2e+02 Score=25.69 Aligned_cols=79 Identities=22% Similarity=0.294 Sum_probs=59.6
Q ss_pred CceeEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHH
Q 007265 175 THRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKL 254 (610)
Q Consensus 175 T~RlAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~L 254 (610)
.++|-|.||.| .|.-.+|.-+|..|-| |.+|.|.-.- ..|..
T Consensus 115 ~~~l~v~nL~~-~~~~~~l~~~F~~~g~----~~~~~~~~d~----------~~~~~----------------------- 156 (306)
T COG0724 115 NNTLFVGNLPY-DVTEEDLRELFKKFGP----VKRVRLVRDR----------ETGKS----------------------- 156 (306)
T ss_pred CceEEEeCCCC-CCCHHHHHHHHHhcCc----eeEEEeeecc----------ccCcc-----------------------
Confidence 69999999996 5889999999998865 4555553321 11111
Q ss_pred HHHHhhcccceEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 007265 255 RAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (610)
Q Consensus 255 R~YQl~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRF 300 (610)
-=||.|+|.+...|..+....+|..|.-.-..+.+-.
T Consensus 157 ---------~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~ 193 (306)
T COG0724 157 ---------RGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ 193 (306)
T ss_pred ---------CceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence 2389999999999999999999999888776665543
No 37
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=25.50 E-value=1.2e+02 Score=33.45 Aligned_cols=68 Identities=26% Similarity=0.326 Sum_probs=54.0
Q ss_pred eEEeccCCCccchhhHHHHHhhccCCCCceEEEEEecChhhHHHHHHHHhcCCCCccCCCCCCCCCCCchhhhHHHHHHH
Q 007265 178 LAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAY 257 (610)
Q Consensus 178 lAvvN~DWD~i~A~DL~vlf~SF~P~gG~i~~V~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~e~~~~e~~d~e~LR~Y 257 (610)
|=|.|||=+ |.-.+|+-+|+.| |.|+||.|=--+=|
T Consensus 79 ~~i~nl~~~-~~~~~~~d~f~~~----g~ilS~kv~~~~~g--------------------------------------- 114 (369)
T KOG0123|consen 79 VFIKNLDES-IDNKSLYDTFSEF----GNILSCKVATDENG--------------------------------------- 114 (369)
T ss_pred eeecCCCcc-cCcHHHHHHHHhh----cCeeEEEEEEcCCC---------------------------------------
Confidence 888888854 7778899999988 79999987432211
Q ss_pred HhhcccceEEEEEeCCHHHHHHHHHhcCcccccccccc
Q 007265 258 EKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNK 295 (610)
Q Consensus 258 Ql~RLRYYYAVvecdS~~TA~~IY~ecDG~E~E~San~ 295 (610)
++|| .|+|+|.++|+..-+.++|+-+..-...
T Consensus 115 ----~kg~--FV~f~~e~~a~~ai~~~ng~ll~~kki~ 146 (369)
T KOG0123|consen 115 ----SKGY--FVQFESEESAKKAIEKLNGMLLNGKKIY 146 (369)
T ss_pred ----ceee--EEEeCCHHHHHHHHHHhcCcccCCCeeE
Confidence 7787 9999999999999999999987664433
No 38
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=25.50 E-value=53 Score=36.69 Aligned_cols=36 Identities=25% Similarity=0.311 Sum_probs=33.0
Q ss_pred EEEEEeCCHHHHHHHHHhcCcccccccccccccccc
Q 007265 266 YAVVECDSSATADYLYRACDGVEFERSSNKLDLRFI 301 (610)
Q Consensus 266 YAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRFV 301 (610)
-|.|||||++.|...=..++|..+-+-++.|-+-|-
T Consensus 161 QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyA 196 (494)
T KOG1456|consen 161 QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYA 196 (494)
T ss_pred eeEEeechhHHHHHHHhhcccccccccceeEEEEec
Confidence 389999999999999999999999999999987664
No 39
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=25.01 E-value=64 Score=27.39 Aligned_cols=40 Identities=33% Similarity=0.541 Sum_probs=32.9
Q ss_pred HHHHHHHhhcccc----eEEEEEeCCHHHHHHHHHhcCcccccccc
Q 007265 252 EKLRAYEKSRLRY----YYAVVECDSSATADYLYRACDGVEFERSS 293 (610)
Q Consensus 252 e~LR~YQl~RLRY----YYAVvecdS~~TA~~IY~ecDG~E~E~Sa 293 (610)
.+||+|...|.+- || |.|.+..-|..=|..|||+.+-.+-
T Consensus 19 ~~Lr~y~~~~I~~d~tGfY--IvF~~~~Ea~rC~~~~~~~~~f~y~ 62 (66)
T PF11767_consen 19 KRLRKYRWDRIRDDRTGFY--IVFNDSKEAERCFRAEDGTLFFTYR 62 (66)
T ss_pred HHHhcCCcceEEecCCEEE--EEECChHHHHHHHHhcCCCEEEEEE
Confidence 5899999999882 55 4588999999999999999876554
No 40
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=23.24 E-value=59 Score=31.81 Aligned_cols=36 Identities=28% Similarity=0.402 Sum_probs=33.5
Q ss_pred EEEEEeCCHHHHHHHHHhcCcccccccccccccccc
Q 007265 266 YAVVECDSSATADYLYRACDGVEFERSSNKLDLRFI 301 (610)
Q Consensus 266 YAVvecdS~~TA~~IY~ecDG~E~E~San~lDLRFV 301 (610)
||+||......|.+.-++++|+++..-...+|.=||
T Consensus 116 YaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv 151 (170)
T KOG0130|consen 116 YALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV 151 (170)
T ss_pred eeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence 999999999999999999999999988888887777
No 41
>PF07988 LMSTEN: LMSTEN motif; InterPro: IPR012642 Proteins containing the Wos2 domain are involved in the regulation of the cell cycle [] and are Myb-related transcriptional activators. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2AGH_A 1SB0_B.
Probab=23.06 E-value=43 Score=26.73 Aligned_cols=18 Identities=33% Similarity=0.444 Sum_probs=11.5
Q ss_pred HHHhhcHHHHHHhhcccc
Q 007265 516 KEATASTAELELLLADDK 533 (610)
Q Consensus 516 ~e~~~~kaELELLm~dd~ 533 (610)
.+.+++--|||||||.-+
T Consensus 24 pdkekrikelelllms~e 41 (48)
T PF07988_consen 24 PDKEKRIKELELLLMSAE 41 (48)
T ss_dssp ---HHHHHHHHHHHHCHH
T ss_pred hhHHHHHHHHHHHHHhhH
Confidence 344566778999998643
No 42
>PF04911 ATP-synt_J: ATP synthase j chain; InterPro: IPR006995 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o)
Probab=22.26 E-value=27 Score=28.81 Aligned_cols=19 Identities=32% Similarity=0.579 Sum_probs=16.8
Q ss_pred ccccCCCcccCCCCcCccc
Q 007265 575 ALFTSPLFALDPTDPQFKR 593 (610)
Q Consensus 575 alf~sh~FaIDPTnP~FKk 593 (610)
++-.|.+|.=||-||.|++
T Consensus 30 a~~ns~E~~NDPRNP~~~~ 48 (54)
T PF04911_consen 30 AMMNSDEFKNDPRNPRAAK 48 (54)
T ss_pred HHhcCHHHhcCCCChhhhc
Confidence 5668999999999999985
Done!