Query 009600
Match_columns 531
No_of_seqs 160 out of 227
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 15:04:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009600.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009600hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2330 Splicing factor 3b, su 100.0 2E-148 4E-153 1139.3 27.7 412 77-500 46-472 (500)
2 COG5182 CUS1 Splicing factor 3 100.0 3E-96 6E-101 738.2 20.3 248 145-417 117-366 (429)
3 PF04037 DUF382: Domain of unk 100.0 1.2E-73 2.6E-78 511.5 11.2 129 171-299 1-129 (129)
4 smart00581 PSP proline-rich do 99.9 4.8E-27 1E-31 184.7 5.6 54 303-356 1-54 (54)
5 PF04046 PSP: PSP; InterPro: 99.9 3.5E-24 7.7E-29 165.1 5.3 48 307-354 1-48 (48)
6 KOG2673 Uncharacterized conser 98.6 2.7E-08 5.8E-13 105.8 3.3 51 292-343 167-217 (485)
7 COG5182 CUS1 Splicing factor 3 57.8 6.9 0.00015 42.1 2.2 41 333-387 288-337 (429)
8 TIGR02697 WPE_wolbac Wolbachia 55.7 4.8 0.0001 30.4 0.5 10 199-208 1-10 (36)
9 PRK09350 poxB regulator PoxA; 44.8 7.8 0.00017 39.9 0.2 87 255-341 185-283 (306)
10 KOG2673 Uncharacterized conser 36.2 27 0.00058 39.0 2.6 42 302-344 43-84 (485)
11 cd00776 AsxRS_core Asx tRNA sy 30.3 14 0.0003 38.3 -0.7 74 266-341 214-291 (322)
12 KOG3064 RNA-binding nuclear pr 29.9 33 0.00072 36.0 2.0 13 34-46 139-151 (303)
13 PF03991 Prion_octapep: Copper 27.7 31 0.00067 18.7 0.7 7 363-369 2-8 (8)
14 COG5033 TFG3 Transcription ini 26.9 23 0.0005 36.0 0.3 42 191-236 8-85 (225)
15 PLN02850 aspartate-tRNA ligase 26.6 19 0.00042 40.2 -0.4 56 284-341 439-495 (530)
16 TIGR00457 asnS asparaginyl-tRN 24.4 21 0.00045 39.0 -0.6 74 266-341 342-418 (453)
17 cd00669 Asp_Lys_Asn_RS_core As 22.8 33 0.00071 34.9 0.5 73 268-341 160-238 (269)
18 PTZ00401 aspartyl-tRNA synthet 20.5 35 0.00077 38.5 0.2 57 283-341 458-515 (550)
19 TIGR00462 genX lysyl-tRNA synt 20.4 84 0.0018 32.4 2.8 84 258-341 183-278 (304)
No 1
>KOG2330 consensus Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=100.00 E-value=1.8e-148 Score=1139.29 Aligned_cols=412 Identities=56% Similarity=0.962 Sum_probs=352.5
Q ss_pred ccceeEEeeCCCCCCCchhHHHHHHHHhhccCCccCCCccccchhhhhhhh--hhcc-c--CCCCCchhhccCCccccCC
Q 009600 77 AEKVTVEYVPEKADLDDGLDDEFRKIFEKFSFHDAAGSEDIDKRDESAQNA--ESKK-K--ADSDTEDEEQDSQPKEKGL 151 (531)
Q Consensus 77 ~~~v~iEyv~e~~~~~d~~~~~F~~VF~kF~~~~~~~~e~~~~~~~~~~~~--~~~~-~--~~~d~~dee~~~~~~~~~l 151 (531)
..+|+|+||.+.++++ +| +||++|+..+..... .......... ..+. . ...|+ +++..++..+.+|
T Consensus 46 ~~~~~~~~v~e~~ei~-----~f-~vf~~Fk~~~~~~~~--~e~~~~~~~~e~~~~~~~~~~~ed~-~ed~~~~~~eekl 116 (500)
T KOG2330|consen 46 DKGVTIEYVDEKIEIE-----FF-DVFERFKLQEMSEKK--FEKPDHVSISEKDDEKGFVHEAEDE-DEDMKDDRIEEKL 116 (500)
T ss_pred cCCceEeeecchhhhH-----HH-HHHHHHhcccccccc--cccCCcceeeccCcccccccccchh-hhccccccchhhh
Confidence 3579999999998776 66 999999988732211 1111111111 1111 0 11111 1111222356789
Q ss_pred ChHHHHHhhcCCHHHHHhhcCCCceEEeecCCCCChHHHHHHHhcCCCccCCccccccccccccccCCCCCCCCccHHHH
Q 009600 152 SNKKKKLQRRMKIAELKQICSRPDVVEVWDATASDPKLLVFLKAYRNTVPVPRHWCQKRKFLQGKRGIEKQPFQLPDFIA 231 (531)
Q Consensus 152 Skkk~k~~~r~svaeLK~~v~~PevVE~~D~tA~DP~lLv~lKs~rNtVPVP~HW~~KR~YLsgkrgieK~pf~LP~fI~ 231 (531)
|+||+|++.|+|||+||++|.||+|||||||||.||+|||+||+|+|+||||+|||+||+||||+||||||||+||+||+
T Consensus 117 skrklRk~~r~svaeLK~~v~~pdvvE~~Dvta~dP~ll~~lK~~~n~VPVPrHW~~kr~yl~G~rg~ekppfelP~~Ik 196 (500)
T KOG2330|consen 117 SKRKLRKLLRPSVAELKQLVPYPDVVEWHDVTARDPKLLVHLKAYRNSVPVPRHWNSKRKYLSGKRGIEKPPFELPDFIK 196 (500)
T ss_pred hHHHHHHhhcccHHHHhhcCCccceeeeeccCCCChHHHHHhhhccCCCcCchhhhhhhhhhccccccCCCCccchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhChHHHHHHHHhhhhhHHHHHHHHhhhCCCCCccccchHHHHHHhhcccCCCCCCCCCcccccchhHHHhhhcCCCCCC
Q 009600 232 ATGIEKIRQAYIEKEDSKKLKQKQRERMQPKMGKMDIDYQVLHDAFFKYQTKPKLTSHGDLYHEGKEFEVKLREMKPGIL 311 (531)
Q Consensus 232 ~TGI~emR~a~~eke~~~sLKqk~RervqPKmGklDIDYqkLhDAFFk~qtKP~Lt~~GDlYYEGKe~e~~~~~~kPG~L 311 (531)
.|||++||++++|+|+.+|||+|||||||||||+|||||||||||||||||||.||.|||||||||||+..+++++||.|
T Consensus 197 ~TgI~emR~a~~e~e~~~sLk~kmRerv~PkmGkidiDyqkLhdaFFk~qtkp~lt~~Ge~yyegke~e~~~k~k~PG~i 276 (500)
T KOG2330|consen 197 KTGIQEMREALLEREAGKSLKEKMRERVRPKMGKIDIDYQKLHDAFFKWQTKPYLTKFGELYYEGKELEAMVKEKKPGDI 276 (500)
T ss_pred hcCHHHHHHHHHhhhccccHHHHHHHhhCcccccccchHHHHHHHHHhcCCCcceeecceeeecchhHHHHHhhcCccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHhCCCCCCCchHHHHHHhcCCCCCCCCCcccccCCCCCCCCCCCccCCCCCCCCCCCCCCcccccccccccCCC
Q 009600 312 SHDLKEALGMPDGAPPPWLINMQRYGPPPSYPHLKIPGLNAPIPPGASFGYHPGGWGKPPVDEYGRPLYGDVFGIHQQEQ 391 (531)
Q Consensus 312 S~eLR~ALGm~~~~pPPWl~~MQr~GpPPSYP~LkIpGLNapiP~g~~~Gyh~ggwGkppvde~g~PLyGdvfG~~~~~~ 391 (531)
|++||+||||++++||||||+|||||||||||+|||||||||||+||+||||+|||| |||++|+||||||||...++.
T Consensus 277 S~eLr~aLgmp~g~pPPWl~aMqryGpPpsYPdlkIpGLNapIPeg~s~Gyh~gGWG--pVDe~g~PLygDVfG~~~p~~ 354 (500)
T KOG2330|consen 277 SDELRIALGMPVGTPPPWLIAMQRYGPPPSYPDLKIPGLNAPIPEGCSFGYHAGGWG--PVDEFGKPLYGDVFGLNIPEH 354 (500)
T ss_pred hHHHHHHhCCCCCCCChHHHHhhhcCCCCCCCcccCCCCCCCCCcccccccccCCCc--cccccCCccchhccccccccc
Confidence 999999999999999999999999999999999999999999999999999999999 999999999999999998876
Q ss_pred CCCCCCCC-cccCccccCCcchhhhhhhhhhhh-hhhhhh--------ccCcccccCccccCCCCCCCcccccccccCCC
Q 009600 392 PNYEEEPV-DKSKHWGDLEEEEEEEEEEEEEEQ-IEEEEL--------EDGIQSVDTLSSTPTGVETPDVIDLRKQQRKE 461 (531)
Q Consensus 392 ~~~~~e~v-dk~~~WGele~eeeeeeeeeeeee-~~e~~~--------~~g~~~~sg~ss~~~g~etp~~~dlRK~~~~~ 461 (531)
.+...+.+ ++ .+||+|+++++|++||.+||| .+.++. ...+.++++++++|+|+|||+.|+|||..+.+
T Consensus 355 ~~~t~es~~~r-n~wgel~~e~~E~~EEreeee~~d~~~~~e~gg~~dp~d~~~~~~Lts~ptgiEtpd~iELRK~k~ee 433 (500)
T KOG2330|consen 355 HNGTKESEIER-NHWGELESEEEESSEEREEEEREDKNDASENGGAVDPADDIVPSGLTSFPTGIETPDAIELRKKKREE 433 (500)
T ss_pred ccccccccccc-ccccccccccchhhhhhhhhhhhhhhhhhhccccCCccccccccccccCCccccChhHHHHHhhcccc
Confidence 65544444 45 599999986555544422222 111111 11256789999999999999999999999988
Q ss_pred CCCCCceeccccccccCCCcccccccEEEcCCCccCCCC
Q 009600 462 PERPLYQVLEEKEERIAPGTLLGTTHTYVVNTGTQDKAG 500 (531)
Q Consensus 462 ~~k~LYtVl~Ek~~~~~~~~~~gS~~~Ydl~~~~~~~~g 500 (531)
+.+.|||||+||.++..+|+||||+|+|||+++++.+.+
T Consensus 434 ~~r~LYqVLpEK~t~~igg~mmgstH~Ydis~~~a~k~~ 472 (500)
T KOG2330|consen 434 ETRALYQVLPEKRTSRIGGTMMGSTHTYDISTGTADKTP 472 (500)
T ss_pred ccHHHHHhccccccccccceeeccceEEeccccccccCC
Confidence 889999999999999778889999999999999888766
No 2
>COG5182 CUS1 Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=100.00 E-value=3e-96 Score=738.17 Aligned_cols=248 Identities=44% Similarity=0.780 Sum_probs=231.2
Q ss_pred CccccCCChHHHHHhhcCCHHHHHhhcCCCceEEeecCCCCChHHHHHHHhcCCCccCCccccccccccccccCCCCCCC
Q 009600 145 QPKEKGLSNKKKKLQRRMKIAELKQICSRPDVVEVWDATASDPKLLVFLKAYRNTVPVPRHWCQKRKFLQGKRGIEKQPF 224 (531)
Q Consensus 145 ~~~~~~lSkkk~k~~~r~svaeLK~~v~~PevVE~~D~tA~DP~lLv~lKs~rNtVPVP~HW~~KR~YLsgkrgieK~pf 224 (531)
...+..||++|+||..|+++++||.+|.+|+|||||||||+||.||.+||++.|+||||+||++|++||||++++++.||
T Consensus 117 ~~~ee~ls~~k~Rk~~~~~~~qLK~~vpyp~I~Ew~D~~~~dP~~l~~~K~~~N~VPVPrHW~sk~~ylsg~~~~~~r~f 196 (429)
T COG5182 117 PYREESLSRQKKRKALQHRYEQLKLVVPYPEIFEWEDATCPDPMSLNRMKGCSNGVPVPRHWRSKSRYLSGHGYHKPRPF 196 (429)
T ss_pred ccchhhhHHHHHHHHhhhhHHHHhccCCccceeeeecCCCCChhhhhhhccCCCCCCCchhhhhhhhcccccccCCCCcc
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccHHHHHhChHHHHHHHHhhhhhHHHHHHHHhhhCCCCCccccchHHHHHHhhcccCCCCCCCCCcccccchhHHHhhh
Q 009600 225 QLPDFIAATGIEKIRQAYIEKEDSKKLKQKQRERMQPKMGKMDIDYQVLHDAFFKYQTKPKLTSHGDLYHEGKEFEVKLR 304 (531)
Q Consensus 225 ~LP~fI~~TGI~emR~a~~eke~~~sLKqk~RervqPKmGklDIDYqkLhDAFFk~qtKP~Lt~~GDlYYEGKe~e~~~~ 304 (531)
+||++|+.|||.+||+++.+.|+.|+|++++|+|||||||++||||++||||||++|+||.|+.|||+||||++++...+
T Consensus 197 elP~~I~~TgI~qmR~~~~e~ea~msLre~~RervqPkmG~ldvDy~kLhdaFF~~g~kP~L~~fGe~y~e~~n~~~~vk 276 (429)
T COG5182 197 ELPRHIIGTGIPQMRRMMREREAGMSLRERIRERVQPKMGGLDVDYRKLHDAFFSLGPKPYLSKFGEFYEEVDNDYRFVK 276 (429)
T ss_pred cchHHHhhcChHHHHHhhhhccccCcHHHHHHHhhCccccccchhHHHHHHHHHhcCCCcccccccceeeccchHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCCCCCCcccccC-CCCC-CCCCCCccCCCCCCCCCCCCCCccccc
Q 009600 305 EMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPSYPHLKIPGLN-APIP-PGASFGYHPGGWGKPPVDEYGRPLYGD 382 (531)
Q Consensus 305 ~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPSYP~LkIpGLN-apiP-~g~~~Gyh~ggwGkppvde~g~PLyGd 382 (531)
+++||.||.+||+||||++++|||||++||+||||||||+||||||| ++|| .||.|||.+-||+.|-.
T Consensus 277 ~krPG~IS~eLrealgi~~g~pPPWlf~Mq~~G~PpsYPDlkIpGlNW~~~pL~GdvyG~~~p~~h~~~~---------- 346 (429)
T COG5182 277 KKRPGAISAELREALGIDSGTPPPWLFNMQKHGMPPSYPDLKIPGLNWAPIPLEGDVYGYQPPGWHEPLF---------- 346 (429)
T ss_pred ccCCcchHHHHHHHhCCCCCCCChHHHhhhhcCCCCCCccccCCCCCCCCcccccccccccCCCcCCccC----------
Confidence 99999999999999999999999999999999999999999999999 6777 78888888888876321
Q ss_pred ccccccCCCCCCCCCCCcccCccccCCcchhhhhh
Q 009600 383 VFGIHQQEQPNYEEEPVDKSKHWGDLEEEEEEEEE 417 (531)
Q Consensus 383 vfG~~~~~~~~~~~e~vdk~~~WGele~eeeeeee 417 (531)
+++.. .+||+|.+-++++.+
T Consensus 347 --------------~~~~~-~~~gel~~fe~ee~~ 366 (429)
T COG5182 347 --------------EVGPE-TAEGELLQFEAEEIY 366 (429)
T ss_pred --------------CcCcc-hhhhhhhhccchhhc
Confidence 22333 499999876544433
No 3
>PF04037 DUF382: Domain of unknown function (DUF382) ; InterPro: IPR007180 This domain is specific to the human splicing factor 3b subunit 2 and its orthologs.; GO: 0005634 nucleus
Probab=100.00 E-value=1.2e-73 Score=511.46 Aligned_cols=129 Identities=78% Similarity=1.221 Sum_probs=128.0
Q ss_pred cCCCceEEeecCCCCChHHHHHHHhcCCCccCCccccccccccccccCCCCCCCCccHHHHHhChHHHHHHHHhhhhhHH
Q 009600 171 CSRPDVVEVWDATASDPKLLVFLKAYRNTVPVPRHWCQKRKFLQGKRGIEKQPFQLPDFIAATGIEKIRQAYIEKEDSKK 250 (531)
Q Consensus 171 v~~PevVE~~D~tA~DP~lLv~lKs~rNtVPVP~HW~~KR~YLsgkrgieK~pf~LP~fI~~TGI~emR~a~~eke~~~s 250 (531)
|.+|||||||||||+||+|||+|||++||||||+|||+||+|||||||||||||+||+||++|||++||+++.++|+++|
T Consensus 1 V~~PevVE~~D~~a~DP~lLv~lKs~rNtVPVP~HW~~Kr~YL~gkrg~eKppf~LP~~I~~TgI~emR~~~~e~e~~~s 80 (129)
T PF04037_consen 1 VPRPEVVEWHDVTAPDPRLLVHLKSYRNTVPVPRHWSQKRKYLQGKRGIEKPPFQLPDFIKDTGIEEMRQALPEKEDEKS 80 (129)
T ss_pred CCCCceEEeecCCCCChHHHHHHHhcCCCCCCCcchhhhhhhhcccccccCCCCcCCHHHHHHCcHHHHHHhhcccchhh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhCCCCCccccchHHHHHHhhcccCCCCCCCCCcccccchhH
Q 009600 251 LKQKQRERMQPKMGKMDIDYQVLHDAFFKYQTKPKLTSHGDLYHEGKEF 299 (531)
Q Consensus 251 LKqk~RervqPKmGklDIDYqkLhDAFFk~qtKP~Lt~~GDlYYEGKe~ 299 (531)
||||||||||||||+||||||+||||||+|||||.||+|||||||||||
T Consensus 81 lKqk~RervqPKmGkldIDYq~LhdAFFk~qtKP~l~~~Gd~YyEgkef 129 (129)
T PF04037_consen 81 LKQKQRERVQPKMGKLDIDYQKLHDAFFKFQTKPKLTKFGDLYYEGKEF 129 (129)
T ss_pred HHHHHHHHhCcccCcccccHHHHHHHHHhccCCCCcccccceeeccccC
Confidence 9999999999999999999999999999999999999999999999997
No 4
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=99.93 E-value=4.8e-27 Score=184.71 Aligned_cols=54 Identities=63% Similarity=1.281 Sum_probs=51.9
Q ss_pred hhcCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCCCCCCcccccCCCCCC
Q 009600 303 LREMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPSYPHLKIPGLNAPIPP 356 (531)
Q Consensus 303 ~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPSYP~LkIpGLNapiP~ 356 (531)
+++++||+||++||+||||++++|||||++||+||+|||||+|+||||||+||.
T Consensus 1 ~~~~kPG~lS~~LR~ALG~~~~~pPPWl~~Mq~~G~PPsYp~l~ipglna~ip~ 54 (54)
T smart00581 1 FKHFKPGRISDELREALGLPPGQPPPWLYRMRRLGYPPGYPRLKIPGLNAPIPL 54 (54)
T ss_pred CCCccCCcCCHHHHHHcCCCCCCCChHHHHHHHHCCCCCCcccccCCCCCCCCC
Confidence 368999999999999999999999999999999999999999999999999983
No 5
>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins.
Probab=99.90 E-value=3.5e-24 Score=165.13 Aligned_cols=48 Identities=69% Similarity=1.304 Sum_probs=47.3
Q ss_pred CCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCCCCCCcccccCCCC
Q 009600 307 KPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPSYPHLKIPGLNAPI 354 (531)
Q Consensus 307 kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPSYP~LkIpGLNapi 354 (531)
|||+||++||+||||++++|||||++||++|+|||||+++|||+|++|
T Consensus 1 kPG~lS~~LR~ALg~~~~~~PPwl~~M~~~G~PP~y~~~ki~g~n~~i 48 (48)
T PF04046_consen 1 KPGKLSDELREALGMQENDPPPWLYRMRRLGYPPGYPDLKIPGLNAPI 48 (48)
T ss_pred CCcccCHHHHHHcCCCCCCCChHHHHHHhcCCCCCCccccccCCCCCC
Confidence 799999999999999999999999999999999999999999999987
No 6
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=98.58 E-value=2.7e-08 Score=105.82 Aligned_cols=51 Identities=39% Similarity=0.793 Sum_probs=44.3
Q ss_pred ccccchhHHHhhhcCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCCCC
Q 009600 292 LYHEGKEFEVKLREMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPSYP 343 (531)
Q Consensus 292 lYYEGKe~e~~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPSYP 343 (531)
.||---+ ..+..++|||+||..||.|||+.++.||+|+++|.++|.||.|-
T Consensus 167 ry~~~te-q~re~h~KPG~lS~~~R~al~l~~~d~P~~~yRMR~lGYPPg~L 217 (485)
T KOG2673|consen 167 RYYQDTE-QGREDHFKPGVLSGNTRSALGLSPGDPPEWKYRMRRLGYPPGYL 217 (485)
T ss_pred eeeeecc-hhhhcccCCcccchhHHHhhcCCCCCchHHHHHHhhccCCchhh
Confidence 5665332 22678999999999999999999999999999999999999996
No 7
>COG5182 CUS1 Splicing factor 3b, subunit 2 [RNA processing and modification]
Probab=57.84 E-value=6.9 Score=42.15 Aligned_cols=41 Identities=29% Similarity=0.619 Sum_probs=29.2
Q ss_pred HHhcCCCCCCC-----CCcccccCCCCC----CCCCCCccCCCCCCCCCCCCCCcccccccccc
Q 009600 333 MQRYGPPPSYP-----HLKIPGLNAPIP----PGASFGYHPGGWGKPPVDEYGRPLYGDVFGIH 387 (531)
Q Consensus 333 MQr~GpPPSYP-----~LkIpGLNapiP----~g~~~Gyh~ggwGkppvde~g~PLyGdvfG~~ 387 (531)
|--+|+||+-| +++=-|+--..| +|-+||+|| |||||||..
T Consensus 288 realgi~~g~pPPWlf~Mq~~G~PpsYPDlkIpGlNW~~~p--------------L~GdvyG~~ 337 (429)
T COG5182 288 REALGIDSGTPPPWLFNMQKHGMPPSYPDLKIPGLNWAPIP--------------LEGDVYGYQ 337 (429)
T ss_pred HHHhCCCCCCCChHHHhhhhcCCCCCCccccCCCCCCCCcc--------------ccccccccc
Confidence 34456555554 566667766666 588899985 999999974
No 8
>TIGR02697 WPE_wolbac Wolbachia palindromic element (WPE) domain. This domain conceptually resembles TIGR01045, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure. Note that this model appears to work better in fragment mode.
Probab=55.69 E-value=4.8 Score=30.43 Aligned_cols=10 Identities=60% Similarity=1.438 Sum_probs=8.4
Q ss_pred CccCCccccc
Q 009600 199 TVPVPRHWCQ 208 (531)
Q Consensus 199 tVPVP~HW~~ 208 (531)
+||||+||-.
T Consensus 1 vIPV~~hwDp 10 (36)
T TIGR02697 1 VIPVPRHWDP 10 (36)
T ss_pred CcccccccCc
Confidence 5899999974
No 9
>PRK09350 poxB regulator PoxA; Provisional
Probab=44.83 E-value=7.8 Score=39.89 Aligned_cols=87 Identities=17% Similarity=0.243 Sum_probs=57.8
Q ss_pred HHhhhCCCCCc----cccchHHHHHHhhccc-CCCCCCCCCcccccchhHHHh-hhcCCCCCCcHHHH------HHhCCC
Q 009600 255 QRERMQPKMGK----MDIDYQVLHDAFFKYQ-TKPKLTSHGDLYHEGKEFEVK-LREMKPGILSHDLK------EALGMP 322 (531)
Q Consensus 255 ~RervqPKmGk----lDIDYqkLhDAFFk~q-tKP~Lt~~GDlYYEGKe~e~~-~~~~kPG~LS~eLR------~ALGm~ 322 (531)
.-..|.|++|+ +-+||=.---+|.+-. ..|.++.==|+|+.|.|+-.. ..-..|..+-.+++ .+.|+.
T Consensus 185 ~~~~ve~~l~~~~p~fi~~yP~~~~~~a~~~~~~~~~~~rfdl~i~G~Ei~nG~~el~d~~~~~~r~~~~~~~~~~~g~~ 264 (306)
T PRK09350 185 FTFGVEPNIGKEKPTFVYHFPASQAALAKISTEDHRVAERFEVYFKGIELANGFHELTDAREQRQRFEQDNRKRAARGLP 264 (306)
T ss_pred HHHHHHHhcCCCCCEEEEcCccccCccccccCCCCCeeEEEEEEECCEEEecchhhcCCHHHHHHHHHHHHHHHHhCCCC
Confidence 33577788875 4446665555554422 356677566999999986432 23455666666665 478887
Q ss_pred CCCCchHHHHHHhcCCCCC
Q 009600 323 DGAPPPWLINMQRYGPPPS 341 (531)
Q Consensus 323 ~~~pPPWl~~MQr~GpPPS 341 (531)
+....-|++.+-+||+||+
T Consensus 265 ~~~~d~~~l~a~~~G~pp~ 283 (306)
T PRK09350 265 QQPIDENLIAALEAGLPDC 283 (306)
T ss_pred cccCcHHHHHHHHcCCCCC
Confidence 7666667889989999985
No 10
>KOG2673 consensus Uncharacterized conserved protein, contains PSP domain [Function unknown]
Probab=36.19 E-value=27 Score=39.00 Aligned_cols=42 Identities=26% Similarity=0.574 Sum_probs=38.3
Q ss_pred hhhcCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCCCCC
Q 009600 302 KLREMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPSYPH 344 (531)
Q Consensus 302 ~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPSYP~ 344 (531)
....+.+|.+| ++-++|+-.+.+.||..++||+.|.|+-|-+
T Consensus 43 ~~~r~esg~i~-~qqd~l~~te~a~~~fr~~~qe~~t~s~wl~ 84 (485)
T KOG2673|consen 43 RRGRFESGVIS-EQQDLLGVTEKAFPPFRYRMQELGTPSFWLK 84 (485)
T ss_pred hhccccccccc-hHHHHhhcccccccchhhhHHhhcCchhhhh
Confidence 55789999999 8899999999999999999999999998874
No 11
>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=30.30 E-value=14 Score=38.34 Aligned_cols=74 Identities=24% Similarity=0.411 Sum_probs=49.0
Q ss_pred cccchHHHHHHhhccc--CCCCCCCCCcccccc-hhHHH-hhhcCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCC
Q 009600 266 MDIDYQVLHDAFFKYQ--TKPKLTSHGDLYHEG-KEFEV-KLREMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPS 341 (531)
Q Consensus 266 lDIDYqkLhDAFFk~q--tKP~Lt~~GDlYYEG-Ke~e~-~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPS 341 (531)
+-+||=.-.-+|+.-. ..|.++.-=|||+.| .|.-. ..+...|-.|-..+++ .|+.+... -|++.+-++|+||.
T Consensus 214 fi~~~P~~~~pfy~~~~~~~~~~~~~fdl~~~G~~El~~g~~r~~d~~~l~~r~~~-~g~~~~~~-~~yl~a~~~G~pp~ 291 (322)
T cd00776 214 FVTDYPKEIKPFYMKPDDDNPETVESFDLLMPGVGEIVGGSQRIHDYDELEERIKE-HGLDPESF-EWYLDLRKYGMPPH 291 (322)
T ss_pred EEECCccccCCceeeecCCCCCeeEEEEEEcCCCeEEeeceeecCCHHHHHHHHHH-cCCChHHH-HHHHHHHHCCCCCC
Confidence 3357666666764422 356777778999999 87632 1233455555555554 67776544 89999999999985
No 12
>KOG3064 consensus RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification]
Probab=29.94 E-value=33 Score=36.03 Aligned_cols=13 Identities=31% Similarity=0.662 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHhh
Q 009600 34 ETERRRRRRKQKK 46 (531)
Q Consensus 34 ~~~~rR~~~k~~k 46 (531)
.+..||++|.-.|
T Consensus 139 ~K~~rRE~rReeK 151 (303)
T KOG3064|consen 139 KKVERREKRREEK 151 (303)
T ss_pred hHHHHHHHHHHHH
Confidence 4455666666666
No 13
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=27.73 E-value=31 Score=18.73 Aligned_cols=7 Identities=71% Similarity=1.896 Sum_probs=4.5
Q ss_pred cCCCCCC
Q 009600 363 HPGGWGK 369 (531)
Q Consensus 363 h~ggwGk 369 (531)
|-||||.
T Consensus 2 hgG~Wgq 8 (8)
T PF03991_consen 2 HGGGWGQ 8 (8)
T ss_pred CCCcCCC
Confidence 5577774
No 14
>COG5033 TFG3 Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=26.87 E-value=23 Score=36.05 Aligned_cols=42 Identities=36% Similarity=0.438 Sum_probs=31.4
Q ss_pred HHHHhcCCCcc------------CCcccccccccccc------------------------ccCCCCCCCCccHHHHHhC
Q 009600 191 VFLKAYRNTVP------------VPRHWCQKRKFLQG------------------------KRGIEKQPFQLPDFIAATG 234 (531)
Q Consensus 191 v~lKs~rNtVP------------VP~HW~~KR~YLsg------------------------krgieK~pf~LP~fI~~TG 234 (531)
+.+|++|+++| .++||+..+-||-+ .|.|+.|||+ |..||
T Consensus 8 ~r~~t~r~Iipgea~~~~~e~~~P~r~th~w~v~v~~~g~E~~~~iv~KVifkLH~Tf~NP~Rti~~pPFe----I~EtG 83 (225)
T COG5033 8 ERLKTQRVIIPGEAKPLGNEERFPVRHTHIWLVFVRAPGKEDIATIVKKVIFKLHPTFSNPTRTIESPPFE----IKETG 83 (225)
T ss_pred EeeeeeceeccCccccCCccccCCchhhEEEEEEEeCCCCcchhhhhheeeEEeccccCCCcccccCCCcE----EEecc
Confidence 35677888888 35899999888865 4788889887 46677
Q ss_pred hH
Q 009600 235 IE 236 (531)
Q Consensus 235 I~ 236 (531)
-.
T Consensus 84 WG 85 (225)
T COG5033 84 WG 85 (225)
T ss_pred cc
Confidence 53
No 15
>PLN02850 aspartate-tRNA ligase
Probab=26.65 E-value=19 Score=40.22 Aligned_cols=56 Identities=27% Similarity=0.446 Sum_probs=37.6
Q ss_pred CCCCCCCcccccchhHHH-hhhcCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCC
Q 009600 284 PKLTSHGDLYHEGKEFEV-KLREMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPS 341 (531)
Q Consensus 284 P~Lt~~GDlYYEGKe~e~-~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPS 341 (531)
|.++.==|||+.|.|.-. ..+...|-.|-..++ +.|+++... -|++.+-+||+||.
T Consensus 439 ~~~~~~fDl~i~G~EI~~G~qr~~d~~~l~~r~~-~~g~d~~~~-~~Yl~a~~~G~pPh 495 (530)
T PLN02850 439 PKYSNSFDVFIRGEEIISGAQRVHDPELLEKRAE-ECGIDVKTI-STYIDSFRYGAPPH 495 (530)
T ss_pred CCeEEEEEEEeCCEEEeccceecCCHHHHHHHHH-HcCCChHHH-HHHHHHHHcCCCCC
Confidence 333333478888876532 123445555666655 489988766 99999999999985
No 16
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=24.43 E-value=21 Score=39.01 Aligned_cols=74 Identities=23% Similarity=0.400 Sum_probs=48.2
Q ss_pred cccchHHHHHHhhc-ccCCCCCCCCCcccccc-hhHHH-hhhcCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCC
Q 009600 266 MDIDYQVLHDAFFK-YQTKPKLTSHGDLYHEG-KEFEV-KLREMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPS 341 (531)
Q Consensus 266 lDIDYqkLhDAFFk-~qtKP~Lt~~GDlYYEG-Ke~e~-~~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPS 341 (531)
+-+||=+....|+. ....|.++.-=|+|+-| .|.-. ..+...+-.|-..++ +.||.+. .-.|++.+-+||+||.
T Consensus 342 fIt~~P~~~~pfy~~~~~~~~~~~~fDL~~~g~gEi~~gsere~~~~~l~~~~~-~~g~d~~-~~~~Yl~~~~~G~pPh 418 (453)
T TIGR00457 342 FVTNYPKDIKAFYMKLNDDGKTVAAMDLLAPGIGEIIGGSEREDDLDKLENRMK-EMGLDTD-ALNWYLDLRKYGSVPH 418 (453)
T ss_pred EEECCCcccChhhcccCCCcCceeeeeeccCCceEEeehhccCCCHHHHHHHHH-HcCCCHH-HHHHHHHHHHcCCCCC
Confidence 44466666666663 33667777777899988 46532 223444444444554 5687765 4569999999999984
No 17
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=22.83 E-value=33 Score=34.89 Aligned_cols=73 Identities=22% Similarity=0.358 Sum_probs=46.7
Q ss_pred cchHHHHHHhhccc--CCCCCCCCCcccccchhHHH-hhhcCCCCCCcHHHHHHhCCCCC---CCchHHHHHHhcCCCCC
Q 009600 268 IDYQVLHDAFFKYQ--TKPKLTSHGDLYHEGKEFEV-KLREMKPGILSHDLKEALGMPDG---APPPWLINMQRYGPPPS 341 (531)
Q Consensus 268 IDYqkLhDAFFk~q--tKP~Lt~~GDlYYEGKe~e~-~~~~~kPG~LS~eLR~ALGm~~~---~pPPWl~~MQr~GpPPS 341 (531)
+||-..--+||... ..|.++.-=|||+.|.|.-. ..+...|-.|-..+++. |+.+. .+=.|++.+-+||+||.
T Consensus 160 ~d~P~~~~~fy~~~~~~~~~~~~~fdl~~~g~Ei~~G~~r~~d~~~l~~~~~~~-~~~~~~~~~~~~~yl~a~~~G~pp~ 238 (269)
T cd00669 160 TDYPAEMHSPLASPHDVNPEIADAFDLFINGVEVGNGSSRLHDPDIQAEVFQEQ-GINKEAGMEYFEFYLKALEYGLPPH 238 (269)
T ss_pred ECCCcccCCCCCCcCCCCCCeEEEEEEeeCCEEEeeCchhcCCHHHHHHHHHHh-CcChhhccccHHHHHHHHHcCCCCC
Confidence 46665545565533 35777777799999987632 12344554555555544 55543 36789999999999984
No 18
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=20.47 E-value=35 Score=38.47 Aligned_cols=57 Identities=21% Similarity=0.269 Sum_probs=40.2
Q ss_pred CCCCCCCCcccccchhHHHh-hhcCCCCCCcHHHHHHhCCCCCCCchHHHHHHhcCCCCC
Q 009600 283 KPKLTSHGDLYHEGKEFEVK-LREMKPGILSHDLKEALGMPDGAPPPWLINMQRYGPPPS 341 (531)
Q Consensus 283 KP~Lt~~GDlYYEGKe~e~~-~~~~kPG~LS~eLR~ALGm~~~~pPPWl~~MQr~GpPPS 341 (531)
.|.++.-=|||+.|.|.-.. .+...|-.|-.+++ +.||++.. =-|++.+-+||+||.
T Consensus 458 dp~~s~~fDlf~~G~EI~sG~qR~~d~~~l~~r~~-~~G~d~~~-~~~Yl~a~~~G~PPh 515 (550)
T PTZ00401 458 DERFTNSYDMFIRGEEISSGAQRIHDPDLLLARAK-MLNVDLTP-IKEYVDSFRLGAWPH 515 (550)
T ss_pred CCCEEEEEEEEeCCEEEccchhhcCCHHHHHHHHH-HcCCCchh-hHHHHHHHHcCCCCC
Confidence 34555555899999876432 34556666777765 47988753 489999999999984
No 19
>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.
Probab=20.38 E-value=84 Score=32.45 Aligned_cols=84 Identities=19% Similarity=0.353 Sum_probs=51.3
Q ss_pred hhCCCCCc----cccchHHHHHHhhccc-CCCCCCCCCcccccchhHHHhh-hcCCCCCCcHHHH------HHhCCCCCC
Q 009600 258 RMQPKMGK----MDIDYQVLHDAFFKYQ-TKPKLTSHGDLYHEGKEFEVKL-REMKPGILSHDLK------EALGMPDGA 325 (531)
Q Consensus 258 rvqPKmGk----lDIDYqkLhDAFFk~q-tKP~Lt~~GDlYYEGKe~e~~~-~~~kPG~LS~eLR------~ALGm~~~~ 325 (531)
.|.|++|+ +-+||=.-..+|.+-. ..|.++.==|+|+.|.|+-... .-..|..+-.++. ++.|+.+..
T Consensus 183 ~ie~~~~~~~p~fi~~yP~~~~~~~~~~~~~~~~~~rfdl~~~G~Ei~~G~~el~d~~~~~~r~~~~~~~~~~~g~~~~~ 262 (304)
T TIGR00462 183 KVEPHLGFGRPTFLYDYPASQAALARISPDDPRVAERFELYIKGLELANGFHELTDAAEQRRRFEADNAERKALGLPRYP 262 (304)
T ss_pred HHHHhcCCCCCEEEEcCccccCcCccccCCCCCeeEEEEEEECCEEEeeceeecCCHHHHHHHHHHHHHHHHhCCCCcch
Confidence 44555542 3456666655554422 3566776568999998753311 1233444444443 357887766
Q ss_pred CchHHHHHHhcCCCCC
Q 009600 326 PPPWLINMQRYGPPPS 341 (531)
Q Consensus 326 pPPWl~~MQr~GpPPS 341 (531)
..-|++.+-+||+||+
T Consensus 263 ~d~~yl~~~~~G~pP~ 278 (304)
T TIGR00462 263 LDERFLAALEAGLPEC 278 (304)
T ss_pred hhHHHHHHHHcCCCCC
Confidence 6679999999999985
Done!