Query 005276
Match_columns 704
No_of_seqs 158 out of 265
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 20:53:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005276.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005276hhsearch_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 1E-151 3E-156 1232.3 28.3 607 25-668 10-647 (650)
2 COG5638 Uncharacterized conser 100.0 2E-133 5E-138 1054.7 26.8 520 27-608 11-580 (622)
3 PF08159 NUC153: NUC153 domain 99.2 1.1E-12 2.3E-17 95.1 -1.0 29 570-598 1-29 (30)
4 PLN03134 glycine-rich RNA-bind 92.3 0.54 1.2E-05 45.4 7.8 79 173-298 32-110 (144)
5 cd00590 RRM RRM (RNA recogniti 92.3 0.78 1.7E-05 35.8 7.5 66 177-290 1-66 (74)
6 PF14259 RRM_6: RNA recognitio 88.2 2.1 4.6E-05 34.9 6.9 65 178-290 1-65 (70)
7 TIGR01649 hnRNP-L_PTB hnRNP-L/ 88.1 1.9 4.2E-05 49.0 8.8 75 173-300 273-347 (481)
8 TIGR01649 hnRNP-L_PTB hnRNP-L/ 87.8 1.4 3E-05 50.1 7.4 76 174-300 95-170 (481)
9 TIGR01648 hnRNP-R-Q heterogene 87.1 1.6 3.4E-05 51.4 7.5 73 174-299 232-304 (578)
10 TIGR01642 U2AF_lg U2 snRNP aux 86.2 2.3 5E-05 47.8 8.1 69 173-291 173-249 (509)
11 smart00360 RRM RNA recognition 86.2 2.9 6.2E-05 32.2 6.3 64 180-290 1-64 (71)
12 TIGR01642 U2AF_lg U2 snRNP aux 85.2 3 6.6E-05 46.9 8.3 79 173-300 293-371 (509)
13 smart00362 RRM_2 RNA recogniti 82.7 8 0.00017 29.8 7.5 65 177-290 1-65 (72)
14 TIGR01659 sex-lethal sex-letha 82.4 13 0.00028 41.1 11.5 122 174-301 106-272 (346)
15 PF00076 RRM_1: RNA recognitio 80.1 10 0.00022 30.2 7.4 66 178-291 1-66 (70)
16 PF08159 NUC153: NUC153 domain 76.9 0.92 2E-05 33.5 0.4 15 53-67 1-15 (30)
17 KOG2318 Uncharacterized conser 74.6 1.2 2.7E-05 51.7 0.8 30 50-80 10-39 (650)
18 TIGR01628 PABP-1234 polyadenyl 71.7 9.3 0.0002 44.0 7.0 69 174-290 284-352 (562)
19 TIGR01622 SF-CC1 splicing fact 70.2 22 0.00048 39.6 9.3 80 174-302 185-264 (457)
20 TIGR01661 ELAV_HUD_SF ELAV/HuD 66.6 17 0.00037 38.7 7.2 80 174-300 88-167 (352)
21 TIGR01661 ELAV_HUD_SF ELAV/HuD 66.2 23 0.00049 37.8 8.0 79 174-301 268-346 (352)
22 PLN03213 repressor of silencin 65.8 17 0.00036 42.3 7.1 66 173-289 8-75 (759)
23 KOG2321 WD40 repeat protein [G 64.2 2.4 5.2E-05 49.6 0.3 40 568-607 480-519 (703)
24 TIGR01628 PABP-1234 polyadenyl 56.8 22 0.00047 41.0 6.3 71 175-293 88-158 (562)
25 TIGR01645 half-pint poly-U bin 51.8 37 0.00081 40.6 7.1 73 174-293 106-178 (612)
26 TIGR01648 hnRNP-R-Q heterogene 47.2 45 0.00098 39.6 6.9 69 174-290 57-125 (578)
27 PF13893 RRM_5: RNA recognitio 46.0 25 0.00054 27.7 3.3 26 265-290 22-47 (56)
28 TIGR01645 half-pint poly-U bin 44.9 60 0.0013 38.9 7.4 73 174-293 203-275 (612)
29 KOG1832 HIV-1 Vpr-binding prot 44.3 12 0.00026 46.1 1.7 6 90-95 1392-1397(1516)
30 PLN03120 nucleic acid binding 42.1 87 0.0019 33.9 7.4 70 175-295 4-73 (260)
31 TIGR01622 SF-CC1 splicing fact 39.4 1E+02 0.0022 34.4 7.9 71 173-291 87-157 (457)
32 smart00361 RRM_1 RNA recogniti 35.1 45 0.00098 27.8 3.3 26 266-291 39-64 (70)
33 PF07576 BRAP2: BRCA1-associat 33.8 46 0.001 31.3 3.5 28 264-291 54-81 (110)
34 PF12583 TPPII_N: Tripeptidyl 28.1 28 0.0006 34.2 1.0 29 249-284 74-102 (139)
35 KOG0123 Polyadenylate-binding 24.6 1.6E+02 0.0034 33.2 6.2 67 178-294 79-145 (369)
36 PF11767 SET_assoc: Histone ly 22.2 76 0.0016 27.5 2.5 41 251-293 18-62 (66)
37 KOG1456 Heterogeneous nuclear 20.9 72 0.0016 36.3 2.6 36 266-301 161-196 (494)
38 KOG0130 RNA-binding protein RB 20.7 71 0.0015 31.8 2.2 36 266-301 116-151 (170)
39 PF04911 ATP-synt_J: ATP synth 20.2 32 0.00069 28.9 -0.2 20 575-594 30-49 (54)
40 KOG0533 RRM motif-containing p 20.2 91 0.002 33.3 3.1 40 174-218 82-121 (243)
No 1
>KOG2318 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.2e-151 Score=1232.27 Aligned_cols=607 Identities=43% Similarity=0.694 Sum_probs=427.7
Q ss_pred CCCCcccccCCCCCCCCCCCcCCCcccccccccccccCcCCCCCCCCcccCCCCCCCccCchhhhhhhhcccccccCCch
Q 005276 25 IITDSRFASVHSDPRFQNVPKQKSKVAIDSRFDRMFTDKNFASSTAPFDKRGKPKKNLKTSKSSLQHYYRIEAEDKKSDE 104 (704)
Q Consensus 25 ~~~D~RFa~i~tDPRFr~~~kk~~KVkID~RF~~mf~D~~F~~~~a~VDKyGR~i~k~~~~~~~L~kfY~le~ee~~~~~ 104 (704)
||.||||++|||||||+++|++++||+||+||++||+|+.|.+ .+.||+|||||++. ++.+|+.||+|++-.....+
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 VVIDPRFASALTDPRFSRMPKVDRKVKIDKRFQGMFMDKKFKL-KSAVDKYGRPINKS--TKEDLREFYELDDFDEKSGE 86 (650)
T ss_pred ccccHHHHhhhcChhhcccccccchhhhhhhhccccchhhhhh-cchhhhcCCccccc--chhhhHHHhhhccchhcccc
Confidence 8999999999999999999999999999999999999999998 58899999999865 38999999999863221110
Q ss_pred ---------hHHHH--HHhh----ccccccHHHHHH-hhhcCCCCCCC-CCCccCcCCCCCC-cccccccCCCCCchhcc
Q 005276 105 ---------DEEIE--EEER----RNETDSESELKE-AADVSSGSGTE-EEDDDDVSESTTD-DEEEDVDFDEGPEEEEE 166 (704)
Q Consensus 105 ---------~e~~~--~ee~----~~e~e~e~e~~~-~~~~~~~s~~e-ssss~d~~~~dee-~~~e~~~~~~~~e~e~e 166 (704)
..+.. .++. ..++..+.++.. +.-.+|+.-.+ |+||+++++++.+ ++++...++.+. +..+
T Consensus 87 es~~~esde~sEi~d~~~e~~a~~~seE~~~~~~k~~lD~ar~E~~~s~s~SSdE~Se~E~E~eede~e~~d~a~-~~pE 165 (650)
T KOG2318|consen 87 ESLKDESDEESEINDEEEEDSAEEESEEESDDELKRALDSARGEGNVSDSESSDEDSEDESEDEEDEKEISDLAN-LDPE 165 (650)
T ss_pred ccccccccchhhhhhhhhhhhhhhhhhhcccchhhhhcccccccccccccccccccccccccCchhhhhhhhhcc-cCcc
Confidence 00000 0000 000111111211 22222222222 2222121111111 111111111111 1123
Q ss_pred cCCCCCCCCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCc-cccCCCCCC----C
Q 005276 167 AIPEIDNETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPV-GLFDSQNEN----S 241 (704)
Q Consensus 167 d~p~~~~~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~-~l~~~~~~~----~ 241 (704)
..|..+++|+||||||||||||+|.|||||||||||+||+|+||.||||+||++||++|+||||| .||...... .
T Consensus 166 ~~~~~~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~s 245 (650)
T KOG2318|consen 166 ENPVLGEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESES 245 (650)
T ss_pred cccccccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCccccc
Confidence 33566789999999999999999999999999999999999999999999999999999999997 688654322 2
Q ss_pred CCCCChhhhHHHHHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccccccCCCCccCCCCccccccCCCC
Q 005276 242 DDEDNDEIDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFIPDTMEFKYPPRDVATEAPAN 321 (704)
Q Consensus 242 ~~~~~~e~d~e~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRFVPDd~~F~~~prd~ct~~P~~ 321 (704)
+.+.+++|++++||+|||+|||||||||+|||+.||.+||.+|||+|||+|||+||||||||+|+|++.|||+|+++|.+
T Consensus 246 D~ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFIPDdm~Fddd~rd~cseap~~ 325 (650)
T KOG2318|consen 246 DDEEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFIPDDMTFDDDPRDECSEAPGN 325 (650)
T ss_pred chhhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeecCCCCccccccHhHhhhcccc
Confidence 44555679999999999999999999999999999999999999999999999999999999999998899999999987
Q ss_pred -CCCCccccccccccccccccCCCchHHHHHHHhhCChhHHHhHHHHHHhcCCCCCCccccccc--hhhhhhhhHHHHHH
Q 005276 322 -YGGLDFFTKALQHSNVQLSWDDDEPDRVKTLKRKFNADQVAELELKEFLASDESETDDEDDNV--ADEQSDKKSKKQDK 398 (704)
Q Consensus 322 -Ykp~~F~T~ALqhSkVkLTWDe~d~~R~k~~~r~f~~~el~e~D~kaYLASdsse~dde~~~~--~~~~~~~k~k~~~k 398 (704)
|+|..|+|+|||||+|+||||+|+|+|++++.++|+..+|+++||++||||+++++++.++.+ .......+.....+
T Consensus 326 ~Ykpk~Fst~Alq~s~vkltWDE~d~~R~~l~~~kf~~~~l~d~d~~~~laS~~sde~d~d~~~~e~~~~l~s~d~~kdk 405 (650)
T KOG2318|consen 326 GYKPKDFSTRALQHSKVKLTWDETDPHRKKLFNEKFNGEELEDLDFSAYLASSDSDEEDGDEAESEVDNKLKSKDDQKDK 405 (650)
T ss_pred ccCchhhhHHHHHhccccccccccCHHHHHHHHHhhcchhhhhchHHHhhcCCcccccchhhHhHHHHHHhhccccccch
Confidence 999999999999999999999999999999999999999999999999999777665443211 11111111113344
Q ss_pred HHHHhhCCCCCCCCCCCCCCceEEEec-CCcchhhHHHhhhccCCCCChHHHHHHHHHHHHHHhhhhcccCCCCcccccc
Q 005276 399 YRALLESGDGSDEDGEEDGQDMEVTFN-TGLEDISKRILEKKDKKSETIWEAYLRKRREKKKAGKNKSKYSSDDEASDTD 477 (704)
Q Consensus 399 yraLL~~~~~~~~~~~~~~~dMEITf~-pgL~~~~~~~~~k~~~~~eT~~EkylrK~kEKkk~rK~k~k~~~~~~~~~~~ 477 (704)
|++.-... ..+...++..++|||||+ |+++.... ..+.+..+||||+|+|+++||+++||.+.+...-... ...
T Consensus 406 ~~~~sk~e-~~ekk~ke~~~dmE~t~~~~~~e~~~~---k~k~kk~~t~~E~~~~k~~Ekk~~rK~~~~~ke~~~~-~~~ 480 (650)
T KOG2318|consen 406 FLANSKEE-EKEKKEKENDGDMEVTFVTDDFEGFNN---KQKDKKEETPIEKYKRKRKEKKRARKKKGKLKEIKDE-KGL 480 (650)
T ss_pred hhhhcccc-chhhhcccccccceeEecCchhhcccc---ccccccccChHHHHHHHhhhhHHHHHHhhhhhhhhhh-hcc
Confidence 44433221 112223456899999999 66654432 3456778999999999999999999977653321111 113
Q ss_pred ccccCCCCcccccCCCCCCCcccCCCCcchhhhhhcchHHHhhcHHHHHHHhcccccccCCCCCCCCch----hhccccC
Q 005276 478 REAIEEPDDFFVEEPKGKKGEEAGGNHRREEKEQQDTDKEATASTAELELLLADDKGAENGLKGYNMKP----KKRKGKK 553 (704)
Q Consensus 478 ~~~~d~~D~fF~~e~~~k~~kk~~~~k~k~~~~~~~~~~e~~~~kaELELLm~dd~~~~~~~khf~mk~----kK~K~Kk 553 (704)
+..++..||||.+.+.....|| .++.+...++..+++.+.+|||||||+++.. ++ ||.+ .+.|+|+
T Consensus 481 ~~d~d~~~~~~~~k~k~~~~KK-----~kk~~~~~eE~~~~k~~~~ElElLl~d~d~~-d~----n~~kil~~e~~kkk~ 550 (650)
T KOG2318|consen 481 GSDKDEKDDYFKDKFKQENPKK-----KKKGKKTKEEDAEAKRQEKELELLLMDEDAD-DE----NMNKILKIEKKKKKK 550 (650)
T ss_pred cccccccCccchhhhhhccccc-----cccccccchhhhhhhhhHHHHHHHhcccccc-ch----hHHHHHHHHHHHhhh
Confidence 4456677889988654211111 1122233566677888899999999988754 22 5532 1111111
Q ss_pred CCCCCCCCCCCCCCCCCchhhccccCCCcccCCCCccccccHHHHHHHHHHHhhcchhhhhhhccccCCCCCCCCCCCcc
Q 005276 554 GKEVPDEDKIPTADYDDPRFSALFTSPLFALDPTDPQFKRSAVYARQIAQKKQKGDQREQVIRESTKIPTNAQMPSDDPD 633 (704)
Q Consensus 554 ~k~~~~e~~~~~iDv~DpRF~alf~sh~FAIDPTnP~FKkT~~m~~~L~ek~~kr~~~~~~e~~~~~~~~~~~~~~~~~~ 633 (704)
++-.. +..+..++|+||||+|||+||.||||||||+||+|++|.+||.++++++. .+.+.. ++...+.+
T Consensus 551 ~~l~k-~~~ie~~~l~D~RFsAlftsh~yaiDPt~p~FK~tk~m~kil~ek~Kr~k--~~~e~~---~~~~~~e~----- 619 (650)
T KOG2318|consen 551 KKLKK-EDNIEEANLNDPRFSALFTSHAYAIDPTDPHFKGTKTMEKILEEKSKRRK--NQEEKK---AADGKQEL----- 619 (650)
T ss_pred hhhcc-hhhccccccccHHHHHHhcccccccCCCCccccchHHHHHHHHHHhccch--hhcccc---ccccccch-----
Confidence 11111 33455899999999999999999999999999999999999999987442 222211 11111100
Q ss_pred ccccccccccccccchHHHHHHHHHHhhhhccccC
Q 005276 634 RHRHMKSDVSSLKRENHEVSLLVKSLKMKSKQIQL 668 (704)
Q Consensus 634 ~~~~~~~d~~~~~~~~~els~LVkSlKrK~k~~q~ 668 (704)
.. . ..+..+...++||+|||||++++|.
T Consensus 620 --~~---~--~~~~~kk~~~~~vkslk~k~~~~~~ 647 (650)
T KOG2318|consen 620 --NK---Q--ANKWRKKKRGSLVKSLKRKMKSKQS 647 (650)
T ss_pred --hh---h--cchhhhhhhhHHHHHHHHHHHhHHh
Confidence 00 0 0111223349999999999999884
No 2
>COG5638 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.4e-133 Score=1054.70 Aligned_cols=520 Identities=39% Similarity=0.642 Sum_probs=392.1
Q ss_pred CCcccccCCCCCCCCCCCcCCCcccccccccccccCcCCCCCCCCcccCCCCCCCccCchhhhhhhhcccccccCCchhH
Q 005276 27 TDSRFASVHSDPRFQNVPKQKSKVAIDSRFDRMFTDKNFASSTAPFDKRGKPKKNLKTSKSSLQHYYRIEAEDKKSDEDE 106 (704)
Q Consensus 27 ~D~RFa~i~tDPRFr~~~kk~~KVkID~RF~~mf~D~~F~~~~a~VDKyGR~i~k~~~~~~~L~kfY~le~ee~~~~~~e 106 (704)
.||||++||+||||.+.+++..||+||.||+ -.|..|+. ++.||+|||||+ ++...+++.+||+++.+.++..+
T Consensus 11 ~d~rf~~v~sdprf~~~k~~n~kvkvd~rf~--k~d~d~k~-~a~vdrygr~l~-qdk~~~e~dr~~e~e~e~~e~se-- 84 (622)
T COG5638 11 ADPRFQSVHSDPRFSRLKRGNFKVKVDERFK--KEDKDFKT-TASVDRYGRPLN-QDKATKEIDRLYELENESSESSE-- 84 (622)
T ss_pred CCccccccccCccccccccCCceeehhhhhc--cccccchh-hhhhhhhCCccc-cchhHHHHHHHHHhhcccccccc--
Confidence 5999999999999999999999999999999 47889997 699999999998 44668999999999876443210
Q ss_pred HHHHHhhccccccHHHHHHhhh--------cCCCCCC-CCCCccCcCCCCCCcccccccCCCCCchhcc--cCCCCCCCC
Q 005276 107 EIEEEERRNETDSESELKEAAD--------VSSGSGT-EEEDDDDVSESTTDDEEEDVDFDEGPEEEEE--AIPEIDNET 175 (704)
Q Consensus 107 ~~~~ee~~~e~e~e~e~~~~~~--------~~~~s~~-essss~d~~~~dee~~~e~~~~~~~~e~e~e--d~p~~~~~T 175 (704)
....+....++ .+++++. +.|.|+++ ++++.++ +..+++-+. .+|..+.+|
T Consensus 85 -----------i~~~~~v~~a~~el~dey~~a~~e~~~s~sess~e--s~~ESee-----E~~~EisE~ag~~pe~G~~t 146 (622)
T COG5638 85 -----------ITDNEEVASASSELTDEYDPARGEGIISTSESSDE--SREESEE-----EKANEISEKAGAVPEEGNPT 146 (622)
T ss_pred -----------cccchhhhhccccCCccccccCCcceecccccCcc--hhhhhhh-----hhhhhhhhhccCccCCCCcc
Confidence 00001111111 0111111 11111111 1111111 112233222 266778899
Q ss_pred ceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCc-cccCCCCCC--------------
Q 005276 176 HRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPV-GLFDSQNEN-------------- 240 (704)
Q Consensus 176 ~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~-~l~~~~~~~-------------- 240 (704)
+||||||||||||.|+|||++|+||||+||.|.+|+||||+||++||+.|.|+||| .||...+..
T Consensus 147 krLAvVnmDWd~v~a~DLf~~fsSf~P~ggkl~kV~iypsefGkeRm~~e~vqGpprdif~~~d~~~ssqk~~~dn~~sd 226 (622)
T COG5638 147 KRLAVVNMDWDRVDAKDLFKIFSSFLPYGGKLSKVKIYPSEFGKERMAAEHVQGPPRDIFTPADNQPSSQKFGDDNVFSD 226 (622)
T ss_pred cceeEeecccccchHHHHHHHHHhhCCCCCccceeEechhhhhHHHHhHhhccCCchhhccccccCcchhccCCccchhh
Confidence 99999999999999999999999999999999999999999999999999999999 588432110
Q ss_pred --------CCCCCChhhhHHHHHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccccccCCCCccCCCCc
Q 005276 241 --------SDDEDNDEIDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFIPDTMEFKYPPR 312 (704)
Q Consensus 241 --------~~~~~~~e~d~e~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRFVPDd~~F~~~pr 312 (704)
.+.+-+.+||+.+||||||+|||||||||+|+++.|+..||.+|||+|||+|||+||||||||+|+|++..|
T Consensus 227 ~d~g~d~~~Egd~g~e~d~~~lrqyqlerlryYyAvvec~d~~tsK~iY~~CDG~Eye~san~~DLRfvPD~~tfddd~r 306 (622)
T COG5638 227 RDAGEDALIEGDRGNEFDMVKLRQYQLERLRYYYAVVECEDIETSKNIYSACDGVEYENSANVLDLRFVPDSLTFDDDSR 306 (622)
T ss_pred hhcchhhhhhcccccchhHHHHHHHHhhhheeEEEEEEeccchhhHHHHhccCccccccccceeeeeecCCCcccccchH
Confidence 123445679999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCCccccccccccccccccCCCchHHHHHHHhhCChhHHHhHHHHHHhcCCCCCCccccccchhhhhhhh
Q 005276 313 DVATEAPANYGGLDFFTKALQHSNVQLSWDDDEPDRVKTLKRKFNADQVAELELKEFLASDESETDDEDDNVADEQSDKK 392 (704)
Q Consensus 313 d~ct~~P~~Ykp~~F~T~ALqhSkVkLTWDe~d~~R~k~~~r~f~~~el~e~D~kaYLASdsse~dde~~~~~~~~~~~k 392 (704)
++||.+|.+|.|.+|+|+|||||+|+||||++||.|+.+..++||..+|+++||.|||||..|++++...
T Consensus 307 e~ct~~p~~y~p~~f~tdalqhs~vklswd~~~~~r~dl~k~AFt~~~i~d~dFsay~as~~sde~d~~v---------- 376 (622)
T COG5638 307 EVCTKAPEKYEPRDFVTDALQHSKVKLSWDAEDPHRKDLCKEAFTDDGIRDKDFSAYTASKLSDEDDDSV---------- 376 (622)
T ss_pred hhhhccccccCcccchhhhhhhcccccccccCCchHHHHHHHhhcccccccchHHHHhhhhcccccchHH----------
Confidence 9999999999999999999999999999999999999999999999999999999999996554443211
Q ss_pred HHHHHHHHHHhhCCC-----CC---CCCCCCCCCceEEEecCCcchhhHHHhhhccCCCCChHHHHHHHHHHHHHHhhh-
Q 005276 393 SKKQDKYRALLESGD-----GS---DEDGEEDGQDMEVTFNTGLEDISKRILEKKDKKSETIWEAYLRKRREKKKAGKN- 463 (704)
Q Consensus 393 ~k~~~kyraLL~~~~-----~~---~~~~~~~~~dMEITf~pgL~~~~~~~~~k~~~~~eT~~EkylrK~kEKkk~rK~- 463 (704)
.+.+|..|+.+.. .+ +..++...++|||||+|+|...... ....+.+||+|+|.||.+|++++||+
T Consensus 377 --~es~~qkL~s~~~~DFg~nS~~~~~~D~~e~~eme~tft~~l~~~ne~---~s~dk~Ettiek~~rk~~Er~~~rKe~ 451 (622)
T COG5638 377 --MESKMQKLFSEKEIDFGLNSELVDMSDDGENGEMEDTFTSHLPASNES---ESDDKLETTIEKLDRKLRERQENRKER 451 (622)
T ss_pred --HHHHHHHHhhhcccccccccccCCcCcccccccccceeccCCcCcccc---ccchhhhhHHHHHHHHHHHHHHHHHHH
Confidence 3456777765321 11 1122345789999999999754332 13356789999999999999999995
Q ss_pred hcccCCCCccccccccccCCCCcccccCCCCCCCcccCCCCcchhhhhhcchHHHhhcHHHHHHHhcccccccCCCCCCC
Q 005276 464 KSKYSSDDEASDTDREAIEEPDDFFVEEPKGKKGEEAGGNHRREEKEQQDTDKEATASTAELELLLADDKGAENGLKGYN 543 (704)
Q Consensus 464 k~k~~~~~~~~~~~~~~~d~~D~fF~~e~~~k~~kk~~~~k~k~~~~~~~~~~e~~~~kaELELLm~dd~~~~~~~khf~ 543 (704)
+.|...++. +++ .|.+++ ... |+......+.+..+++++||||||+|+++.. .+.||+
T Consensus 452 qlk~~k~~s-------d~d-----------~Kdk~~-S~n--kk~~~~~~~Ie~~a~sk~eleli~~dd~d~e-qldhfd 509 (622)
T COG5638 452 QLKKTKDDS-------DVD-----------LKDKKE-SIN--KKNKKGKHAIERTAASKEELELIKADDEDDE-QLDHFD 509 (622)
T ss_pred hhhhhccch-------hhh-----------hhhhHh-hhc--cccccchhhccchhhhhHHHHhhhccccchh-hhccch
Confidence 445443221 111 111111 111 1111111233447889999999998877653 578999
Q ss_pred Cch-------hhccccCCCCCCCCCCCCCCCCCCchhhccccCCCcccCCCCccccccHHHHHHHHHHHhhc
Q 005276 544 MKP-------KKRKGKKGKEVPDEDKIPTADYDDPRFSALFTSPLFALDPTDPQFKRSAVYARQIAQKKQKG 608 (704)
Q Consensus 544 mk~-------kK~K~Kk~k~~~~e~~~~~iDv~DpRF~alf~sh~FAIDPTnP~FKkT~~m~~~L~ek~~kr 608 (704)
|+. |+.++-+++....+ +.|..|+.||||.|||++|.||||||||+||+|.+|.+|+.++++|+
T Consensus 510 m~~ilkaek~k~~rk~kkk~~~le-egF~~D~~DpRF~aifedhnFaiDPT~PefK~t~~m~kImdE~rkR~ 580 (622)
T COG5638 510 MKSILKAEKFKKNRKLKKKASNLE-EGFVFDPKDPRFVAIFEDHNFAIDPTHPEFKKTGGMKKIMDEKRKRL 580 (622)
T ss_pred HHHHHHHHHHhhhhhhhhhhhccc-cccccCCCCcchhhhcccCccccCCCCccccccccHHHHHHHHHHHH
Confidence 973 22222122332322 56899999999999999999999999999999999999999987655
No 3
>PF08159 NUC153: NUC153 domain; InterPro: IPR012580 This small domain is found in a novel nucleolar family [].; GO: 0005634 nucleus
Probab=99.22 E-value=1.1e-12 Score=95.10 Aligned_cols=29 Identities=52% Similarity=1.016 Sum_probs=27.9
Q ss_pred CchhhccccCCCcccCCCCccccccHHHH
Q 005276 570 DPRFSALFTSPLFALDPTDPQFKRSAVYA 598 (704)
Q Consensus 570 DpRF~alf~sh~FAIDPTnP~FKkT~~m~ 598 (704)
||||++||++|+||||||||+||+|.+|+
T Consensus 1 D~RF~~lf~~~dF~ID~t~~~yk~~~~~~ 29 (30)
T PF08159_consen 1 DPRFKALFEDPDFAIDPTSPEYKKTNPME 29 (30)
T ss_pred CchHHHhhCCcccccCCCCHHHHhhCccc
Confidence 89999999999999999999999999985
No 4
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=92.32 E-value=0.54 Score=45.38 Aligned_cols=79 Identities=18% Similarity=0.314 Sum_probs=61.6
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHH
Q 005276 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (704)
Q Consensus 173 ~~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e 252 (704)
..+++|=|-||.|+ +...||.-+|..| |.|.+|.|-..- ..
T Consensus 32 ~~~~~lfVgnL~~~-~te~~L~~~F~~~----G~I~~v~i~~d~--------------------~t-------------- 72 (144)
T PLN03134 32 LMSTKLFIGGLSWG-TDDASLRDAFAHF----GDVVDAKVIVDR--------------------ET-------------- 72 (144)
T ss_pred CCCCEEEEeCCCCC-CCHHHHHHHHhcC----CCeEEEEEEecC--------------------CC--------------
Confidence 46889999999998 7999999999987 789999883211 00
Q ss_pred HHHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccc
Q 005276 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDL 298 (704)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDL 298 (704)
.+.| =||+|+|.+.+.|...+.+++|.++.-....+++
T Consensus 73 -------g~~k-GfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~ 110 (144)
T PLN03134 73 -------GRSR-GFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP 110 (144)
T ss_pred -------CCcc-eEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence 0011 4899999999999999999999988765544444
No 5
>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=92.29 E-value=0.78 Score=35.82 Aligned_cols=66 Identities=26% Similarity=0.295 Sum_probs=55.4
Q ss_pred eeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHHHH
Q 005276 177 RLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRA 256 (704)
Q Consensus 177 RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~LR~ 256 (704)
+|-|.|+.|+ +...+|.-+|..| |.|..+.|+++..+ .|
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 4779999998 8889999999998 78999999886544 11
Q ss_pred HHhhccceeEEEEEeCCHHHHHHHHHhcCccccc
Q 005276 257 YEKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (704)
Q Consensus 257 YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E 290 (704)
.-||.|+|.|++.|...++.++|+-+.
T Consensus 40 -------~~~~~v~f~s~~~a~~a~~~~~~~~~~ 66 (74)
T cd00590 40 -------KGFAFVEFEDEEDAEKALEALNGKELG 66 (74)
T ss_pred -------ceEEEEEECCHHHHHHHHHHhCCCeEC
Confidence 348999999999999999999998753
No 6
>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=88.16 E-value=2.1 Score=34.86 Aligned_cols=65 Identities=25% Similarity=0.274 Sum_probs=50.4
Q ss_pred eEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHHHHH
Q 005276 178 LAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAY 257 (704)
Q Consensus 178 LAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~LR~Y 257 (704)
|=|-||.|. +...||+-+|+.| |.|..|.+....=|
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 46888888732101
Q ss_pred HhhccceeEEEEEeCCHHHHHHHHHhcCccccc
Q 005276 258 EKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (704)
Q Consensus 258 Ql~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E 290 (704)
..+-||.|+|.|.+.|..+++.++|+.+.
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 34678999999999999999999998774
No 7
>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=88.15 E-value=1.9 Score=48.98 Aligned_cols=75 Identities=15% Similarity=0.192 Sum_probs=63.8
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHH
Q 005276 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (704)
Q Consensus 173 ~~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e 252 (704)
..++.|=|-||+|+.|...+|+.||+.| |.|.+|.|.+.-
T Consensus 273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~y----G~V~~vki~~~~------------------------------------ 312 (481)
T TIGR01649 273 GPGSVLMVSGLHQEKVNCDRLFNLFCVY----GNVERVKFMKNK------------------------------------ 312 (481)
T ss_pred CCCCEEEEeCCCCCCCCHHHHHHHHHhc----CCeEEEEEEeCC------------------------------------
Confidence 4678999999999999999999999987 899999986530
Q ss_pred HHHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 005276 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (704)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRF 300 (704)
-=||.|++.+++.|......++|..+. +..|-+.|
T Consensus 313 -----------~g~afV~f~~~~~A~~Ai~~lng~~l~--g~~l~v~~ 347 (481)
T TIGR01649 313 -----------KETALIEMADPYQAQLALTHLNGVKLF--GKPLRVCP 347 (481)
T ss_pred -----------CCEEEEEECCHHHHHHHHHHhCCCEEC--CceEEEEE
Confidence 028999999999999999999999884 56666665
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=87.79 E-value=1.4 Score=50.14 Aligned_cols=76 Identities=20% Similarity=0.369 Sum_probs=60.5
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
...+|-|.||+|. |...+|+.+|+.| |.|.+|.|++.. +
T Consensus 95 ~~~~v~v~nl~~~-vt~~~L~~~F~~~----G~V~~v~i~~~~-----------------------------~------- 133 (481)
T TIGR01649 95 KVLRVIVENPMYP-ITLDVLYQIFNPY----GKVLRIVTFTKN-----------------------------N------- 133 (481)
T ss_pred ceEEEEEcCCCCC-CCHHHHHHHHhcc----CCEEEEEEEecC-----------------------------C-------
Confidence 3457899999986 9999999999966 799999986410 0
Q ss_pred HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRF 300 (704)
+ +||.|+|.+++.|.+.-..++|.++...++.|-+.|
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 369999999999999999999999875545555444
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=87.15 E-value=1.6 Score=51.43 Aligned_cols=73 Identities=22% Similarity=0.233 Sum_probs=60.9
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
..+.|=|.||+| ++...+|..+|+.|.| |.|.+|.|- . +
T Consensus 232 ~~k~LfVgNL~~-~~tee~L~~~F~~f~~--G~I~rV~~~-----------------r--------------g------- 270 (578)
T TIGR01648 232 KVKILYVRNLMT-TTTEEIIEKSFSEFKP--GKVERVKKI-----------------R--------------D------- 270 (578)
T ss_pred cccEEEEeCCCC-CCCHHHHHHHHHhcCC--CceEEEEee-----------------c--------------C-------
Confidence 457899999999 5999999999999966 799998641 0 0
Q ss_pred HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccccccccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLR 299 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLR 299 (704)
||.|+|.+.+.|.+...+++|.++.-....+++-
T Consensus 271 ------------fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A 304 (578)
T TIGR01648 271 ------------YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA 304 (578)
T ss_pred ------------eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence 7999999999999999999999987765555544
No 10
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=86.24 E-value=2.3 Score=47.78 Aligned_cols=69 Identities=13% Similarity=0.246 Sum_probs=52.5
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhcccC--------CCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCC
Q 005276 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLP--------KDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDE 244 (704)
Q Consensus 173 ~~T~RLAvvNmDWD~IrA~DL~vlf~SF~P--------~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~ 244 (704)
...+||=|.||.|+ +.-.+|..+|+.|+. +++.|..|.|-.+
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 2445555544110
Q ss_pred CChhhhHHHHHHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccc
Q 005276 245 DNDEIDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFER 291 (704)
Q Consensus 245 ~~~e~d~e~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~ 291 (704)
+ -||.|+|.+++.|...+ +++|+.|.-
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 27999999999999988 699988754
No 11
>smart00360 RRM RNA recognition motif.
Probab=86.18 E-value=2.9 Score=32.19 Aligned_cols=64 Identities=28% Similarity=0.346 Sum_probs=48.1
Q ss_pred EeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHHHHHHh
Q 005276 180 IVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAYEK 259 (704)
Q Consensus 180 vvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~LR~YQl 259 (704)
|.|+.|. +...||.-+|+.| |.|..|.|++... .|.+
T Consensus 1 i~~l~~~-~~~~~l~~~f~~~----g~v~~~~i~~~~~----------~~~~---------------------------- 37 (71)
T smart00360 1 VGNLPPD-VTEEELRELFSKF----GKIESVRLVRDKD----------TGKS---------------------------- 37 (71)
T ss_pred CCCCCcc-cCHHHHHHHHHhh----CCEeEEEEEeCCC----------CCCC----------------------------
Confidence 3466665 6778999998854 6788898887542 1111
Q ss_pred hccceeEEEEEeCCHHHHHHHHHhcCccccc
Q 005276 260 SRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (704)
Q Consensus 260 ~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E 290 (704)
.-||.|+|.+.+.|..+...++|..+.
T Consensus 38 ----~~~a~v~f~~~~~a~~a~~~~~~~~~~ 64 (71)
T smart00360 38 ----KGFAFVEFESEEDAEKALEALNGKELD 64 (71)
T ss_pred ----CceEEEEeCCHHHHHHHHHHcCCCeeC
Confidence 238999999999999999999998874
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=85.17 E-value=3 Score=46.85 Aligned_cols=79 Identities=23% Similarity=0.314 Sum_probs=61.0
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHH
Q 005276 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (704)
Q Consensus 173 ~~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e 252 (704)
+.+++|-|-||.|. |...+|.-+|..| |.|..|.|..-. ..|
T Consensus 293 ~~~~~l~v~nlp~~-~~~~~l~~~f~~~----G~i~~~~~~~~~----------~~g----------------------- 334 (509)
T TIGR01642 293 DSKDRIYIGNLPLY-LGEDQIKELLESF----GDLKAFNLIKDI----------ATG----------------------- 334 (509)
T ss_pred CCCCEEEEeCCCCC-CCHHHHHHHHHhc----CCeeEEEEEecC----------CCC-----------------------
Confidence 46789999999996 8999999999998 678888875210 011
Q ss_pred HHHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 005276 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (704)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRF 300 (704)
.-.-||.|+|.+.+.|......|+|+.+.- ..|-+++
T Consensus 335 ---------~~~g~afv~f~~~~~a~~A~~~l~g~~~~~--~~l~v~~ 371 (509)
T TIGR01642 335 ---------LSKGYAFCEYKDPSVTDVAIAALNGKDTGD--NKLHVQR 371 (509)
T ss_pred ---------CcCeEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEE
Confidence 113589999999999999999999999864 3444444
No 13
>smart00362 RRM_2 RNA recognition motif.
Probab=82.66 E-value=8 Score=29.85 Aligned_cols=65 Identities=28% Similarity=0.286 Sum_probs=49.6
Q ss_pred eeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHHHH
Q 005276 177 RLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRA 256 (704)
Q Consensus 177 RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~LR~ 256 (704)
||-|.|+.| ++...+|.-+|.. -|.|..|.|++.. |.+
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 4667888888874 3578888888664 211
Q ss_pred HHhhccceeEEEEEeCCHHHHHHHHHhcCccccc
Q 005276 257 YEKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (704)
Q Consensus 257 YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E 290 (704)
.=||.|+|.+...|......++|..+.
T Consensus 39 -------~~~~~v~f~~~~~a~~a~~~~~~~~~~ 65 (72)
T smart00362 39 -------KGFAFVEFESEEDAEKAIEALNGTKLG 65 (72)
T ss_pred -------CceEEEEeCCHHHHHHHHHHhCCcEEC
Confidence 137899999999999999999997774
No 14
>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=82.40 E-value=13 Score=41.13 Aligned_cols=122 Identities=16% Similarity=0.235 Sum_probs=76.9
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecC------------hhhHHhHHHHHh---hCCccccCCC-
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPS------------EFGIQRMKEEEV---RGPVGLFDSQ- 237 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPS------------eFGkeRM~~Ee~---~GP~~l~~~~- 237 (704)
..++|=|.||.|+ +...+|..+|..| |.|.+|.|-.- +|.-+.-+...+ .|-. |....
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 56888888431 255555444444 3321 11100
Q ss_pred -----CCCCCC---------CCChhhhHHHHHH----HH-hhccce----------eEEEEEeCCHHHHHHHHHhcCccc
Q 005276 238 -----NENSDD---------EDNDEIDEEKLRA----YE-KSRLRY----------YYAVVECDSSATADYLYRACDGVE 288 (704)
Q Consensus 238 -----~~~~~~---------~~~~e~d~e~LR~----YQ-l~RLRY----------YYAVvecDSv~TA~~IY~ecDG~E 288 (704)
...... .-...+..+.||. |- +.+++. =||.|+|.+.+.|......|+|+.
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 000000 0001133344444 42 223332 299999999999999999999999
Q ss_pred ccccccccccccc
Q 005276 289 FERSSNKLDLRFI 301 (704)
Q Consensus 289 ~E~San~lDLRFV 301 (704)
++-....|-+++.
T Consensus 260 ~~g~~~~l~V~~a 272 (346)
T TIGR01659 260 PEGGSQPLTVRLA 272 (346)
T ss_pred cCCCceeEEEEEC
Confidence 8877666766654
No 15
>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=80.12 E-value=10 Score=30.18 Aligned_cols=66 Identities=27% Similarity=0.331 Sum_probs=51.4
Q ss_pred eEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHHHHH
Q 005276 178 LAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAY 257 (704)
Q Consensus 178 LAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~LR~Y 257 (704)
|=|.||.|+ +...+|.-+|+.| |.|..|.|.+. ..|+
T Consensus 1 l~v~nlp~~-~t~~~l~~~f~~~----g~i~~~~~~~~-----------~~~~--------------------------- 37 (70)
T PF00076_consen 1 LYVGNLPPD-VTEEELRDFFSQF----GKIESIKVMRN-----------SSGK--------------------------- 37 (70)
T ss_dssp EEEESETTT-SSHHHHHHHHHTT----STEEEEEEEEE-----------TTSS---------------------------
T ss_pred cEEcCCCCc-CCHHHHHHHHHHh----hhccccccccc-----------cccc---------------------------
Confidence 347788875 5668999999876 67888888875 1122
Q ss_pred HhhccceeEEEEEeCCHHHHHHHHHhcCcccccc
Q 005276 258 EKSRLRYYYAVVECDSSATADYLYRACDGVEFER 291 (704)
Q Consensus 258 Ql~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~ 291 (704)
..=||+|+|.+.+.|..+...++|..+.-
T Consensus 38 -----~~~~a~V~F~~~~~a~~a~~~l~g~~~~~ 66 (70)
T PF00076_consen 38 -----SKGYAFVEFESEEDAEKALEELNGKKING 66 (70)
T ss_dssp -----EEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred -----ccceEEEEEcCHHHHHHHHHHcCCCEECc
Confidence 23489999999999999999999988753
No 16
>PF08159 NUC153: NUC153 domain; InterPro: IPR012580 This small domain is found in a novel nucleolar family [].; GO: 0005634 nucleus
Probab=76.86 E-value=0.92 Score=33.54 Aligned_cols=15 Identities=47% Similarity=0.895 Sum_probs=12.7
Q ss_pred cccccccccCcCCCC
Q 005276 53 DSRFDRMFTDKNFAS 67 (704)
Q Consensus 53 D~RF~~mf~D~~F~~ 67 (704)
|.||+.||+++.|.+
T Consensus 1 D~RF~~lf~~~dF~I 15 (30)
T PF08159_consen 1 DPRFKALFEDPDFAI 15 (30)
T ss_pred CchHHHhhCCccccc
Confidence 789999999998874
No 17
>KOG2318 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.58 E-value=1.2 Score=51.75 Aligned_cols=30 Identities=37% Similarity=0.558 Sum_probs=25.9
Q ss_pred ccccccccccccCcCCCCCCCCcccCCCCCC
Q 005276 50 VAIDSRFDRMFTDKNFASSTAPFDKRGKPKK 80 (704)
Q Consensus 50 VkID~RF~~mf~D~~F~~~~a~VDKyGR~i~ 80 (704)
|.||.||+++++|++|.. ..+||..++.-+
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 588888777554
No 18
>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=71.66 E-value=9.3 Score=43.97 Aligned_cols=69 Identities=22% Similarity=0.215 Sum_probs=56.1
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
.+..|-|-||+|+ |.-.+|--+|+.| |.|.+|.|....-|. .
T Consensus 284 ~~~~l~V~nl~~~-~~~~~L~~~F~~~----G~i~~~~i~~d~~g~-----------~---------------------- 325 (562)
T TIGR01628 284 QGVNLYVKNLDDT-VTDEKLRELFSEC----GEITSAKVMLDEKGV-----------S---------------------- 325 (562)
T ss_pred CCCEEEEeCCCCc-cCHHHHHHHHHhc----CCeEEEEEEECCCCC-----------c----------------------
Confidence 5667999999996 7888999999887 789999998753221 1
Q ss_pred HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E 290 (704)
-=||.|+|.+.+.|.....+++|..+.
T Consensus 326 ----------~g~gfV~f~~~~~A~~A~~~~~g~~~~ 352 (562)
T TIGR01628 326 ----------RGFGFVCFSNPEEANRAVTEMHGRMLG 352 (562)
T ss_pred ----------CCeEEEEeCCHHHHHHHHHHhcCCeeC
Confidence 128999999999999999999996654
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=70.18 E-value=22 Score=39.57 Aligned_cols=80 Identities=15% Similarity=0.293 Sum_probs=62.4
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
.+++|-|.||.+ .|.-.||..+|+.| |.|.+|.|.....+ |..
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 HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccccccC
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFIP 302 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRFVP 302 (704)
--||.|+|.+.+.|......++|+.+ .+..|-+.|.=
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 24899999999999999999999766 45666676654
No 20
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=66.59 E-value=17 Score=38.74 Aligned_cols=80 Identities=19% Similarity=0.308 Sum_probs=60.6
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
...+|=|.||.+. +...+|..+|+.| |.|..|.|..-. ..|+.
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 4778999999977 788888775211 01111
Q ss_pred HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccccccccccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRF 300 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRF 300 (704)
-.||.|+|.+.+.|...-+.++|..+..+...|-++|
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 21
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor. These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).
Probab=66.19 E-value=23 Score=37.81 Aligned_cols=79 Identities=14% Similarity=0.179 Sum_probs=59.7
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
.++.|=|-||.|+ +...+|.-+|+-| |.|.+|.|..- ...|..
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 001111
Q ss_pred HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccccccccccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNKLDLRFI 301 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRFV 301 (704)
-=||.|+|.+++.|......++|..|.- ..|-+-|+
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 22
>PLN03213 repressor of silencing 3; Provisional
Probab=65.82 E-value=17 Score=42.29 Aligned_cols=66 Identities=23% Similarity=0.321 Sum_probs=52.2
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHH
Q 005276 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (704)
Q Consensus 173 ~~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e 252 (704)
..+-||=|-||-|+ |...||-.+|.+| |.|.+|.|- -+= | .
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 211 2 0
Q ss_pred HHHHHHhhccceeEEEEEeCCH--HHHHHHHHhcCcccc
Q 005276 253 KLRAYEKSRLRYYYAVVECDSS--ATADYLYRACDGVEF 289 (704)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecDSv--~TA~~IY~ecDG~E~ 289 (704)
=||-|++.+. ..+.+....+||.++
T Consensus 49 ------------GFAFVEMssdddaEeeKAISaLNGAEW 75 (759)
T PLN03213 49 ------------SFAYIDFSPSSTNSLTKLFSTYNGCVW 75 (759)
T ss_pred ------------ceEEEEecCCcHHHHHHHHHHhcCCee
Confidence 2677777665 678888888888875
No 23
>KOG2321 consensus WD40 repeat protein [General function prediction only]
Probab=64.20 E-value=2.4 Score=49.58 Aligned_cols=40 Identities=25% Similarity=0.478 Sum_probs=32.4
Q ss_pred CCCchhhccccCCCcccCCCCccccccHHHHHHHHHHHhh
Q 005276 568 YDDPRFSALFTSPLFALDPTDPQFKRSAVYARQIAQKKQK 607 (704)
Q Consensus 568 v~DpRF~alf~sh~FAIDPTnP~FKkT~~m~~~L~ek~~k 607 (704)
|.|.||++||++++|-||-+.-+|+.-.-+..-+.+++.+
T Consensus 480 LtDdRFk~mFen~dFeVDeds~ey~~l~pv~s~~~~k~~k 519 (703)
T KOG2321|consen 480 LTDDRFKSMFENEDFEVDEDSEEYRLLAPVASKMSKKQPK 519 (703)
T ss_pred cchhHHHHhccCcccccCccHHHHhhhchhhhhhhccchh
Confidence 6789999999999999999999999887765444444433
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=56.80 E-value=22 Score=41.04 Aligned_cols=71 Identities=24% Similarity=0.317 Sum_probs=56.7
Q ss_pred CceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHH
Q 005276 175 THRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKL 254 (704)
Q Consensus 175 T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~L 254 (704)
..+|-|.||.+ .|.-.+|+-+|+.| |.|++|.|...+.|+ .
T Consensus 88 ~~~vfV~nLp~-~~~~~~L~~~F~~~----G~i~~~~i~~~~~g~-----------s----------------------- 128 (562)
T TIGR01628 88 VGNIFVKNLDK-SVDNKALFDTFSKF----GNILSCKVATDENGK-----------S----------------------- 128 (562)
T ss_pred CCceEEcCCCc-cCCHHHHHHHHHhc----CCcceeEeeecCCCC-----------c-----------------------
Confidence 45799999998 56788999999987 789999887554332 0
Q ss_pred HHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccccc
Q 005276 255 RAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSS 293 (704)
Q Consensus 255 R~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~Sa 293 (704)
-=||.|+|.+.+.|......++|+.+.-..
T Consensus 129 ---------kg~afV~F~~~e~A~~Ai~~lng~~~~~~~ 158 (562)
T TIGR01628 129 ---------RGYGFVHFEKEESAKAAIQKVNGMLLNDKE 158 (562)
T ss_pred ---------ccEEEEEECCHHHHHHHHHHhcccEecCce
Confidence 127999999999999999999999775543
No 25
>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=51.77 E-value=37 Score=40.60 Aligned_cols=73 Identities=15% Similarity=0.232 Sum_probs=57.0
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
..+||=|-||.| .+.-.+|..+|..| |.|.+|.|-.-.. .|
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 78999999999976 6798888732100 01
Q ss_pred HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSS 293 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~Sa 293 (704)
+ .-=||.|+|.+.+.|...+.+++|+.+.-..
T Consensus 147 -------k-skGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~ 178 (612)
T TIGR01645 147 -------K-HKGFAFVEYEVPEAAQLALEQMNGQMLGGRN 178 (612)
T ss_pred -------C-cCCeEEEEeCcHHHHHHHHHhcCCeEEecce
Confidence 0 0128999999999999999999999886443
No 26
>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=47.25 E-value=45 Score=39.62 Aligned_cols=69 Identities=14% Similarity=0.136 Sum_probs=56.5
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
....|=|-||.| .|...+|.-+|+.| |.|..|.|....-|+ .
T Consensus 57 ~~~~lFVgnLp~-~~tEd~L~~~F~~~----G~I~~vrl~~D~sG~-----------s---------------------- 98 (578)
T TIGR01648 57 RGCEVFVGKIPR-DLYEDELVPLFEKA----GPIYELRLMMDFSGQ-----------N---------------------- 98 (578)
T ss_pred CCCEEEeCCCCC-CCCHHHHHHHHHhh----CCEEEEEEEECCCCC-----------c----------------------
Confidence 457899999999 58999999999988 689988886542111 0
Q ss_pred HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFE 290 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E 290 (704)
| =||.|++.+.+.|...-+.++|.++.
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 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=45.97 E-value=25 Score=27.75 Aligned_cols=26 Identities=27% Similarity=0.323 Sum_probs=23.8
Q ss_pred eEEEEEeCCHHHHHHHHHhcCccccc
Q 005276 265 YYAVVECDSSATADYLYRACDGVEFE 290 (704)
Q Consensus 265 YYAVvecDSv~TA~~IY~ecDG~E~E 290 (704)
-+|.|++.+++.|......++|..|-
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=44.93 E-value=60 Score=38.92 Aligned_cols=73 Identities=11% Similarity=0.204 Sum_probs=57.9
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHH
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEK 253 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~ 253 (704)
..+||=|.||.++ |.-.||.-+|+.| |.|.+|.|.+..-+ |..
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 HHHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccccc
Q 005276 254 LRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSS 293 (704)
Q Consensus 254 LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~Sa 293 (704)
==||.|+|.+.+.|...-..++|.++.-.-
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
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=44.25 E-value=12 Score=46.14 Aligned_cols=6 Identities=33% Similarity=0.689 Sum_probs=4.0
Q ss_pred hhhhcc
Q 005276 90 QHYYRI 95 (704)
Q Consensus 90 ~kfY~l 95 (704)
-|.|++
T Consensus 1392 ~r~yEI 1397 (1516)
T KOG1832|consen 1392 ARMYEI 1397 (1516)
T ss_pred hhhhhh
Confidence 366877
No 30
>PLN03120 nucleic acid binding protein; Provisional
Probab=42.13 E-value=87 Score=33.87 Aligned_cols=70 Identities=17% Similarity=0.165 Sum_probs=55.0
Q ss_pred CceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHH
Q 005276 175 THRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKL 254 (704)
Q Consensus 175 T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~L 254 (704)
++.|=|.||.|. +.-.||.-+|+.| |.|.+|.|.... + +
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 9999999999655 899999995310 0 0
Q ss_pred HHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccccccc
Q 005276 255 RAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSNK 295 (704)
Q Consensus 255 R~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San~ 295 (704)
+ =||.|+|.+.+.|...- .++|..+.-....
T Consensus 43 ------~---GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~ 73 (260)
T PLN03120 43 ------S---QIAYVTFKDPQGAETAL-LLSGATIVDQSVT 73 (260)
T ss_pred ------C---CEEEEEeCcHHHHHHHH-HhcCCeeCCceEE
Confidence 0 18999999999999888 4999888654433
No 31
>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=39.45 E-value=1e+02 Score=34.35 Aligned_cols=71 Identities=13% Similarity=0.111 Sum_probs=54.3
Q ss_pred CCCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHH
Q 005276 173 NETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEE 252 (704)
Q Consensus 173 ~~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e 252 (704)
...++|-|.||.|+ |.-.||+.+|+.| |.|..|.|..-- ..|
T Consensus 87 ~~~~~l~V~nlp~~-~~~~~l~~~F~~~----G~v~~v~i~~d~----------~~~----------------------- 128 (457)
T TIGR01622 87 RDDRTVFVLQLALK-ARERDLYEFFSKV----GKVRDVQCIKDR----------NSR----------------------- 128 (457)
T ss_pred cCCcEEEEeCCCCC-CCHHHHHHHHHhc----CCeeEEEEeecC----------CCC-----------------------
Confidence 35789999999995 8999999999987 589999885310 001
Q ss_pred HHHHHHhhccceeEEEEEeCCHHHHHHHHHhcCcccccc
Q 005276 253 KLRAYEKSRLRYYYAVVECDSSATADYLYRACDGVEFER 291 (704)
Q Consensus 253 ~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~ 291 (704)
..-=||.|+|.+++.|.+... ++|+.+.-
T Consensus 129 ---------~skg~afVeF~~~e~A~~Al~-l~g~~~~g 157 (457)
T TIGR01622 129 ---------RSKGVAYVEFYDVESVIKALA-LTGQMLLG 157 (457)
T ss_pred ---------CcceEEEEEECCHHHHHHHHH-hCCCEECC
Confidence 112489999999999999874 88887653
No 32
>smart00361 RRM_1 RNA recognition motif.
Probab=35.05 E-value=45 Score=27.82 Aligned_cols=26 Identities=15% Similarity=0.155 Sum_probs=23.7
Q ss_pred EEEEEeCCHHHHHHHHHhcCcccccc
Q 005276 266 YAVVECDSSATADYLYRACDGVEFER 291 (704)
Q Consensus 266 YAVvecDSv~TA~~IY~ecDG~E~E~ 291 (704)
||.|+|.+.+-|......++|..|.-
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 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=33.77 E-value=46 Score=31.34 Aligned_cols=28 Identities=21% Similarity=0.491 Sum_probs=25.6
Q ss_pred eeEEEEEeCCHHHHHHHHHhcCcccccc
Q 005276 264 YYYAVVECDSSATADYLYRACDGVEFER 291 (704)
Q Consensus 264 YYYAVvecDSv~TA~~IY~ecDG~E~E~ 291 (704)
-|-+++.|.+...|..-|.+++|.-|-+
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=28.06 E-value=28 Score=34.25 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=24.2
Q ss_pred hhHHHHHHHHhhccceeEEEEEeCCHHHHHHHHHhc
Q 005276 249 IDEEKLRAYEKSRLRYYYAVVECDSSATADYLYRAC 284 (704)
Q Consensus 249 ~d~e~LR~YQl~RLRYYYAVvecDSv~TA~~IY~ec 284 (704)
-.+|.||-||.+-| +-|+. +.|+.||.++
T Consensus 74 eY~EaLRDfq~~~i------aKle~-e~Ae~vY~el 102 (139)
T PF12583_consen 74 EYSEALRDFQCSWI------AKLEP-ENAEQVYEEL 102 (139)
T ss_dssp HHHHHHHHHHHHHH------TTS-H-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH------HhhCH-HHHHHHHHHH
Confidence 45799999999876 67888 9999999987
No 35
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=24.56 E-value=1.6e+02 Score=33.16 Aligned_cols=67 Identities=25% Similarity=0.310 Sum_probs=53.1
Q ss_pred eEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhhHHhHHHHHhhCCccccCCCCCCCCCCCChhhhHHHHHHH
Q 005276 178 LAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFGIQRMKEEEVRGPVGLFDSQNENSDDEDNDEIDEEKLRAY 257 (704)
Q Consensus 178 LAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFGkeRM~~Ee~~GP~~l~~~~~~~~~~~~~~e~d~e~LR~Y 257 (704)
|=|+|||=+ |.-.+|+-+|+.| |.|+|+.|=--+= +
T Consensus 79 ~~i~nl~~~-~~~~~~~d~f~~~----g~ilS~kv~~~~~----------------------------g----------- 114 (369)
T KOG0123|consen 79 VFIKNLDES-IDNKSLYDTFSEF----GNILSCKVATDEN----------------------------G----------- 114 (369)
T ss_pred eeecCCCcc-cCcHHHHHHHHhh----cCeeEEEEEEcCC----------------------------C-----------
Confidence 888888854 7778899999988 7999998732111 1
Q ss_pred HhhccceeEEEEEeCCHHHHHHHHHhcCccccccccc
Q 005276 258 EKSRLRYYYAVVECDSSATADYLYRACDGVEFERSSN 294 (704)
Q Consensus 258 Ql~RLRYYYAVvecDSv~TA~~IY~ecDG~E~E~San 294 (704)
++|| .|+|+|.++|...-+.++|+.+..-.-
T Consensus 115 ----~kg~--FV~f~~e~~a~~ai~~~ng~ll~~kki 145 (369)
T KOG0123|consen 115 ----SKGY--FVQFESEESAKKAIEKLNGMLLNGKKI 145 (369)
T ss_pred ----ceee--EEEeCCHHHHHHHHHHhcCcccCCCee
Confidence 7788 999999999999999999987765433
No 36
>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=22.24 E-value=76 Score=27.47 Aligned_cols=41 Identities=32% Similarity=0.537 Sum_probs=33.2
Q ss_pred HHHHHHHHhhccce----eEEEEEeCCHHHHHHHHHhcCcccccccc
Q 005276 251 EEKLRAYEKSRLRY----YYAVVECDSSATADYLYRACDGVEFERSS 293 (704)
Q Consensus 251 ~e~LR~YQl~RLRY----YYAVvecDSv~TA~~IY~ecDG~E~E~Sa 293 (704)
..+||.|...|.+- || |.|.+..-|..=|..|||+.+-.+-
T Consensus 18 K~~Lr~y~~~~I~~d~tGfY--IvF~~~~Ea~rC~~~~~~~~~f~y~ 62 (66)
T PF11767_consen 18 KKRLRKYRWDRIRDDRTGFY--IVFNDSKEAERCFRAEDGTLFFTYR 62 (66)
T ss_pred HHHHhcCCcceEEecCCEEE--EEECChHHHHHHHHhcCCCEEEEEE
Confidence 36899999999882 55 4488999999999999999876543
No 37
>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]
Probab=20.91 E-value=72 Score=36.26 Aligned_cols=36 Identities=25% Similarity=0.311 Sum_probs=32.8
Q ss_pred EEEEEeCCHHHHHHHHHhcCcccccccccccccccc
Q 005276 266 YAVVECDSSATADYLYRACDGVEFERSSNKLDLRFI 301 (704)
Q Consensus 266 YAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRFV 301 (704)
-|.|||||++.|...-..++|..+-+-++.|-+-|-
T Consensus 161 QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyA 196 (494)
T KOG1456|consen 161 QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYA 196 (494)
T ss_pred eeEEeechhHHHHHHHhhcccccccccceeEEEEec
Confidence 389999999999999999999999999999877664
No 38
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=20.67 E-value=71 Score=31.85 Aligned_cols=36 Identities=28% Similarity=0.402 Sum_probs=33.4
Q ss_pred EEEEEeCCHHHHHHHHHhcCcccccccccccccccc
Q 005276 266 YAVVECDSSATADYLYRACDGVEFERSSNKLDLRFI 301 (704)
Q Consensus 266 YAVvecDSv~TA~~IY~ecDG~E~E~San~lDLRFV 301 (704)
||+||......|.+.-++++|+++..-...+|.=||
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 39
>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=20.21 E-value=32 Score=28.94 Aligned_cols=20 Identities=30% Similarity=0.557 Sum_probs=17.2
Q ss_pred ccccCCCcccCCCCcccccc
Q 005276 575 ALFTSPLFALDPTDPQFKRS 594 (704)
Q Consensus 575 alf~sh~FAIDPTnP~FKkT 594 (704)
++..|.+|.=||-||.|++.
T Consensus 30 a~~ns~E~~NDPRNP~~~~~ 49 (54)
T PF04911_consen 30 AMMNSDEFKNDPRNPRAAKG 49 (54)
T ss_pred HHhcCHHHhcCCCChhhhcc
Confidence 56789999999999999843
No 40
>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]
Probab=20.16 E-value=91 Score=33.33 Aligned_cols=40 Identities=20% Similarity=0.362 Sum_probs=32.1
Q ss_pred CCceeEEeccCCCccchhhHHHHHhcccCCCCceEEEEEecChhh
Q 005276 174 ETHRLAIVNMDWRHVKAVDLLVILSSFLPKDGQILSVAVYPSEFG 218 (704)
Q Consensus 174 ~T~RLAvvNmDWD~IrA~DL~vlf~SF~P~gG~I~sV~IYPSeFG 218 (704)
-..+|.|+||+..-|. .||+-||..|. .+.+|.|-+=+.|
T Consensus 82 ~~~~v~v~NL~~~V~~-~Dl~eLF~~~~----~~~r~~vhy~~~G 121 (243)
T KOG0533|consen 82 RSTKVNVSNLPYGVID-ADLKELFAEFG----ELKRVAVHYDRAG 121 (243)
T ss_pred CcceeeeecCCcCcch-HHHHHHHHHhc----cceEEeeccCCCC
Confidence 3468999999998665 69999999996 6778888776554
Done!