Query 000877
Match_columns 1242
No_of_seqs 149 out of 194
Neff 3.6
Searched_HMMs 46136
Date Tue Apr 2 00:31:12 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0008 Transcription initiati 100.0 8E-171 2E-175 1521.5 37.1 908 214-1166 15-1063(1563)
2 PF12157 DUF3591: Protein of u 100.0 1E-126 3E-131 1083.9 31.5 441 564-1045 9-457 (457)
3 COG5179 TAF1 Transcription ini 100.0 2E-103 4E-108 890.3 25.3 398 546-988 315-758 (968)
4 PF09247 TBP-binding: TATA box 99.5 3.5E-16 7.5E-21 137.2 -4.5 47 28-74 10-58 (62)
5 PF02270 TFIIF_beta: Transcrip 92.1 0.26 5.6E-06 55.4 6.1 66 797-869 209-274 (275)
6 KOG0008 Transcription initiati 81.1 0.64 1.4E-05 61.2 1.0 72 518-589 315-386 (1563)
7 PF04801 Sin_N: Sin-like prote 48.6 25 0.00055 41.8 5.2 44 824-872 284-329 (421)
8 PF00240 ubiquitin: Ubiquitin 47.2 11 0.00023 33.2 1.5 35 594-628 31-65 (69)
9 KOG2905 Transcription initiati 46.1 28 0.00062 39.5 4.7 65 803-874 185-249 (254)
10 cd01798 parkin_N amino-termina 45.5 8.2 0.00018 34.5 0.5 35 595-629 35-69 (70)
11 PF12571 DUF3751: Phage tail-c 44.3 16 0.00035 38.2 2.4 63 731-794 45-117 (159)
12 PF07498 Rho_N: Rho terminatio 43.1 35 0.00076 28.9 3.8 40 1011-1055 1-40 (43)
13 PF02845 CUE: CUE domain; Int 38.7 32 0.0007 28.5 2.9 24 827-850 5-28 (42)
14 cd01807 GDX_N ubiquitin-like d 35.0 14 0.0003 33.5 0.3 35 595-629 37-71 (74)
15 smart00546 CUE Domain that may 34.1 42 0.00091 27.8 2.9 23 827-849 6-28 (43)
16 cd01809 Scythe_N Ubiquitin-lik 33.4 16 0.00035 32.1 0.4 35 595-629 37-71 (72)
17 PF07746 LigA: Aromatic-ring-o 33.2 27 0.00059 34.0 1.9 40 1009-1048 10-49 (88)
18 KOG0883 Cyclophilin type, U bo 32.0 23 0.0005 42.5 1.4 47 937-985 296-350 (518)
19 cd07922 CarBa CarBa is the A s 31.5 32 0.00069 33.2 2.0 40 1007-1046 14-53 (81)
20 KOG0881 Cyclophilin type pepti 29.7 39 0.00085 35.4 2.4 37 937-975 28-71 (164)
21 cd01797 NIRF_N amino-terminal 29.0 20 0.00044 33.4 0.3 34 595-628 39-72 (78)
22 cd01815 BMSC_UbP_N Ubiquitin-l 26.4 27 0.00059 33.2 0.6 34 596-629 41-74 (75)
23 cd01805 RAD23_N Ubiquitin-like 26.2 27 0.00058 31.5 0.5 35 595-629 39-73 (77)
24 cd01803 Ubiquitin Ubiquitin. U 25.9 26 0.00055 31.2 0.3 35 595-629 37-71 (76)
25 smart00540 LEM in nuclear memb 25.7 38 0.00082 29.4 1.3 31 1010-1040 1-31 (44)
26 PF10208 Armet: Degradation ar 25.6 44 0.00094 35.8 2.0 43 1004-1048 96-138 (154)
27 PTZ00044 ubiquitin; Provisiona 25.1 27 0.00059 31.4 0.4 35 595-629 37-71 (76)
28 cd01793 Fubi Fubi ubiquitin-li 24.7 29 0.00062 31.5 0.4 34 595-628 35-68 (74)
29 cd01800 SF3a120_C Ubiquitin-li 21.9 33 0.00071 31.5 0.2 36 594-629 33-68 (76)
30 cd01806 Nedd8 Nebb8-like ubiq 21.6 37 0.00081 30.1 0.5 35 595-629 37-71 (76)
No 1
>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=100.00 E-value=7.7e-171 Score=1521.55 Aligned_cols=908 Identities=37% Similarity=0.487 Sum_probs=743.8
Q ss_pred CCCCchhhhhccccCcchhhhhh-ccCCCCCCCCCCcceEEeeCCeEEEEehhhhccccccccCCcccccccCCccccCC
Q 000877 214 GSLGAEEEMTAGVKDYDEELADI-LKGPLDGQVSTPLPVLCVEDGKVILRFSEIFGIHEPLKKGKKRDQRYSTPKDKYNT 292 (1242)
Q Consensus 214 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~lp~l~~e~g~~il~fseif~~~ep~~~~~~~~~~~~~~~~~~~~ 292 (1242)
.++..++.|+ +.|++++..++ .-.+++-+..+|||. ++|+ | +|||+|.+|+|. ++.++.-++..+++.|++
T Consensus 15 ~v~~~ed~~d--~~dl~e~~e~~~~~~~~~~~s~~~l~~-~~~~---~-~~s~d~~~~~P~-~~~~~e~~~~~~~D~~~s 86 (1563)
T KOG0008|consen 15 SVLVKEDAMD--YSDLQEESEDEPAEFTLEFGSLTPLPT-YGDE---A-QFSEDFALMEPP-KRDMREDEYIGSRDKYIS 86 (1563)
T ss_pred cccccccccc--chhhhhhhhcccccccccccCcccCcc-cchh---h-hcchhhhhcCCC-CCCchhhccccccCcccc
Confidence 4556677788 99999998877 667788888999999 9999 4 999999999999 888889999999999999
Q ss_pred CCcccccchhHHHHhhh-cCCCcccccccccccccccccCccchhhhhhcccc---cccccchhhhccccccccCccccc
Q 000877 293 MDVSSLVEEDEEVYLKG-SGQGFPLFKEANIFQHGIFSLNDDDSELVKFGVEQ---DAATISEHDEQRKDSCICSEPMKE 368 (1242)
Q Consensus 293 ~~~~~~~e~dee~~lk~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~---~~~~~~~~~~~~~~s~~~~~p~~~ 368 (1242)
+|.+..++++|+..||+ +++..+-.+.+.-.+.++.....+.....+-|+.. ..++...+..--++||+...-.+.
T Consensus 87 ed~~~~~~~~e~t~l~d~d~~~dt~l~~I~~~~ld~~~Pvre~~~d~~~~~vl~~~~~~p~~~f~~~~r~s~~~~~~~~~ 166 (1563)
T KOG0008|consen 87 EDSSSLSGPDEETDLKDDDGKLDTPLSGIDSIDLDVPLPVRELFPDFRPSKVLRSRLFGPNKEFMGLWRDSRIMRKKLKQ 166 (1563)
T ss_pred cccccccCcchhhhhhhhccccCCchhhcccccccCCCchhhhccccCccceeccCCCCccchhhhhhHHHHhhhHhhhh
Confidence 99999999999999999 88876666666666666653322222222333322 222333888899999999999999
Q ss_pred cccCCCCcCCCCCCCCCcccCCccccccccccCCCccCcCCccccccccccc-h--hhhhhcCcc--cccCCCCcccc--
Q 000877 369 ESNVNPSVGWKSMPSPNFFPLDQHDWEENIVWDNSPAASDNSIESHEIAGAD-V--ESALMRGIE--LDTGQNNFHER-- 441 (1242)
Q Consensus 369 ~~~~~~~~~~~~~~~~~f~p~~~~~we~~i~w~~s~~~~~~~~~~~~~~~~~-~--~~~~~~~~~--~~~~~~~~~~~-- 441 (1242)
|+..+....|+|++++..+|+++++|+..|||..+|....+. |++.+.- + ...+..|.. =.+++..+--.
T Consensus 167 d~~~~~~~~~~sqls~~~~~gdk~~~~~~~i~E~~p~~~~~~---~e~~~~g~~~~~g~l~~g~~~~~vt~~~~~v~~~r 243 (1563)
T KOG0008|consen 167 DLIDENSEIGPSQLSMEVEVGDKMEWNLGIIMEPEPEICLAD---DEIKEMGSVESKGLLPPGEPMKKVTEQKPLVIEWR 243 (1563)
T ss_pred hhcccccccccccccccccccchhhhccCcccCCChHHhccc---hhhhccccccccccCCCCccccccccccccccccc
Confidence 999899999999999999999999999999999999776654 3332221 0 000111200 01111111110
Q ss_pred --cCCCCCcccccccCCCCcccccCCCCCCCCCCCcCCcccccccccccccccccccccCccCCCccchh----------
Q 000877 442 --STSPNEKDCIVNMQNSPVLSETFGSKSSSDNTSHLFTESRYHPQLLRLESQLDLDNHSHANGIKENVS---------- 509 (1242)
Q Consensus 442 --~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~hp~~lr~e~~~~~~~~~~~~~~~~~~~---------- 509 (1242)
+.+..-+... .+.+...++ ||... +-....+.+.++.|||++++|+. .||....++...
T Consensus 244 ~gp~~~~y~~~~--vP~~~~~ln-~gfk~-kqs~~~~~~~s~~~~q~~~~e~d-----~~~~~s~~~~~~l~~kqL~~e~ 314 (1563)
T KOG0008|consen 244 YGPAQIWYDMMK--VPESGMPLN-FGFKL-KQSPNESANKSRKTPQALSPESD-----ENESDSLRDAIFLSIKQLEWED 314 (1563)
T ss_pred cccceeeecccc--CCCcCCccc-cchhc-ccCccccccccCCCccccccccc-----ccccccchhhhhhhHhhcchhh
Confidence 2222222222 355666777 88875 34456678889999999999952 122211110000
Q ss_pred ---------------------------hh-------hc---------ccccccccccCcccCcccCCCCccceeeccCCC
Q 000877 510 ---------------------------IK-------LC---------QSDAVKRFSKHSLQNRDMMEGSWLDNIIWEPVD 546 (1242)
Q Consensus 510 ---------------------------~~-------~~---------~~~~~~r~s~~~~~N~dL~~g~Wld~IiWD~~~ 546 (1242)
.. ++ +..-..-|++||+.|-+|.+..|.++||||+..
T Consensus 315 ~v~~~g~~~~~k~~~~~~~~~~~gWd~~~i~tr~~~~f~~~d~~m~~~i~d~~~~~~~~~~~~~li~~~we~~~i~Daq~ 394 (1563)
T KOG0008|consen 315 DVRKDGEDVKDKVLEDENWLDLDGWDPNKIYTRNALAFNLQDSSMTFNIPDNKGYKIFPLHNDSLIYSRWEDDIIWDAQA 394 (1563)
T ss_pred hcccchHHHHHhhhhhcccccccccccccccccchhhhcccccccccccCCCccccccccccchhhhchhhhheeechhh
Confidence 00 00 011123477899999999999999999999954
Q ss_pred CCC---CCceeecCCCCcceeecccCCCCCc----------------------------------------ccccccccc
Q 000877 547 AVG---KPKLILDLQDEQMLFEILDNKDDEH----------------------------------------PLLHAGAMI 583 (1242)
Q Consensus 547 ~~~---k~KLiLDlnD~nmifei~d~kd~~~----------------------------------------l~~~A~~~~ 583 (1242)
... ...|.|| ||+++||++++.+...+ +++..|..+
T Consensus 395 ~~s~~~~~~l~L~-nD~~Lilg~~~~k~qa~~kk~~~~~~~~~~~lk~K~lls~d~~~~~~~~~~q~k~~k~rltvg~~~ 473 (1563)
T KOG0008|consen 395 MPSSLSPWVLNLD-NDENLILGIPDDKRQAKQKKSSKHSKRVFHSLKSKFLLSNDGKYQNLKQDHQSKGGKVRLTVGGLE 473 (1563)
T ss_pred ccCCCCCceEEec-CChhhhcCCcccchhcccCCCccccccccchhhhhhhhcchHHhhhhhhcccccccceeeeccccc
Confidence 322 2358888 99999999998887422 122334445
Q ss_pred ccCCCCCCCC-CCcc---ccccccccccccccccccccccCCCccccccccccccCcccccCCCCCCCCCCCCCCcccCC
Q 000877 584 ITRSAKPSDF-KPAE---SVKLFYLGKELEDHKSLADQNVRPNSLIHLIRTKIHLLPRAQKLPGENKSLRPPGAFKKKSD 659 (1242)
Q Consensus 584 i~~~~K~~~~-~P~~---~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R~k~~~~pka~r~pg~~kslrp~gaFkk~sD 659 (1242)
|-|+.++..+ -|++ ..+++|.+.....-++++..+++|+++.|+.++..|.|+++++.++..++++++++|....|
T Consensus 474 IqHS~pA~~Lr~pFykT~~~k~~lR~fHRp~~k~~~~~~~qp~~~~~vf~~lkh~kr~a~kr~~er~s~~~~~~ftmrdD 553 (1563)
T KOG0008|consen 474 IQHSLPAVNLRLPFYKTHMSKMKLRGFHRPPFKSRISGAVQPNSPHHVFSPLKHRKRKADKREGERESIGGGGEFTMRDD 553 (1563)
T ss_pred eeecchhhhccCCcccccccHHHHhhccCCchhhccccccCCCCcccccchHHHHHHHHhhCccchhccCCccceEeccc
Confidence 5555555433 2333 34456677766666788999999999999999999999999999999999999999999999
Q ss_pred cccCCCceEEEEeeccCCccccCCCcccccccccCCCCCCCCcccccccCCCCCCceEEcCCCCC--CCcceecCCCCce
Q 000877 660 LSVKDGHVFLMEYCEERPLLLSNAGMGANLCTYYQKSSPGDQAGALLCSGNNCLGNVLTLEPGDK--SPFLGDIKAGCSQ 737 (1242)
Q Consensus 660 LSlkDG~lVLmEYsEE~PpLLSNvGMgSkIiNYYRKk~~~D~~~~~lr~~k~~lGe~vvL~p~D~--SPFLG~V~PGqtv 737 (1242)
||.+||++||||||||||++|||+||||+|+|||||+++.|+.+|. .+.|+.++|.++|+ |||||.|+|||.+
T Consensus 554 Lsgkdg~v~L~EYsEE~P~~Lsn~GMaskl~nYYrK~n~~D~~~~~-----~~d~~~~vl~~eh~sp~pflG~vhPG~s~ 628 (1563)
T KOG0008|consen 554 LSGKDGHVILMEYSEEHPVLLSNAGMASKLKNYYRKKNEQDEYRPK-----LPDGEYGVLDVEHTSPSPFLGSVHPGQSL 628 (1563)
T ss_pred ccCCCCCEEEEEecccCchhhccchHHHHHHHHHhccCccccccCC-----CCcccceeEeecCCCCCCcccccCCCcch
Confidence 9999999999999999999999999999999999999999998743 46777777778887 7779999999999
Q ss_pred eeeecccccCCCCCCCCCCceEEEEEcCCCc--EEEEecCceeeccccccccccCCCCCcchhhhHHHHHHHHHHHHHHH
Q 000877 738 SSLETNMYRAPVFTHKVATTDFLLVRSAKGK--ISIRRIDKVAVVAQQEPLMEVMSPGSKNLQTYSINRMLVNVYREFSA 815 (1242)
Q Consensus 738 ~tLeNNMfRAPIFkHk~~~TDFLLIRS~~Gk--~yIReId~LfvVGQ~eP~vEVP~PhSKkvt~f~KNRLkv~iyRlf~k 815 (1242)
|+|||||||||||+|++.+||||||||++|+ ||||+|++|||||||||++|||+||||++|+|++|||+|||||+||+
T Consensus 629 qaleNNMyRAPIF~Hk~~~TDfLLiRS~~g~~r~ylR~In~IfvVGQq~Pl~EVpgPnSKk~tt~~~nrLkv~IYRlF~~ 708 (1563)
T KOG0008|consen 629 QALENNMYRAPIFKHKMQSTDFLLIRSSSGKMRYYLRNINHIFVVGQQFPLEEVPGPNSKKLTTFLRNRLKVFIYRLFWK 708 (1563)
T ss_pred HHHhhcchhcccccccCCCCcEEEEecCCCCceEEEeccCcEEEecccccccccCCCcchhHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999999886 99999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCCcccHhHHhhhCCCCcHHHHHHHHHHhhcccccCCCceeEEecCCCCCCChHHhhhhCChhhhHHHHHHHHHH
Q 000877 816 AAKRGLLPCIGVDELSVQFPNLSEAIIRKKLKECAFLRRDGNGKQVWSMKRTFHIPSEGDLRKLAYPEHVCSYESMQAGL 895 (1242)
Q Consensus 816 ~~~~~~~~rIrv~DI~k~FP~~sE~qIRKRLKEcad~qR~g~g~g~W~lKp~~rLPsEEELR~mITPE~VCayESMqAG~ 895 (1242)
+.. .++||+|++|++|||+++|++||||||+||+|+|+|++.+||++|++|++|+|++||+|||||+||+||||+||+
T Consensus 709 s~~--g~r~I~id~lsk~Fp~~se~siRKrLKecad~kR~G~~~~~W~LK~df~lp~eeelrslVtPE~vCayeSMlAge 786 (1563)
T KOG0008|consen 709 SDS--GPRRIRIDDLSKAFPDQSESSIRKRLKECADFKRDGMGKNYWVLKPDFRLPDEEELRSLVTPEQVCAYESMLAGE 786 (1563)
T ss_pred cCC--CCcceehhHHHhhCcccchHHHHHHHHHHHHHhhcCCCCCeeEecccccCCCHHHHhhhcCHHHHHHHHHHHHHH
Confidence 854 568999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCccccCccchhhhhccCchHHHHHHHhhhHHHHHhcCcchhhHHHHH-HhhcCcccceeeeeeccCCCCCCCc
Q 000877 896 YRLKHLGITQLTLPASISSAMSQLPDEAIALAAASHIERELQITPWNLSSNFVA-CTNQDRENIERLEITGVGDPSGRGL 974 (1242)
Q Consensus 896 qRLkDaGy~~lt~~~~is~a~~ql~DE~~~~~~a~~IE~ELqLAPWNlTrNFv~-At~QgKa~i~mLqL~G~GDPTGrGE 974 (1242)
|||+|+||+.... .+..++++| +++.+|++|+++||||||+|||+ |+ ||| |||+|||+||||||||
T Consensus 787 qrLkDaGyg~~~~-----~a~e~ddeE----~~~~~ie~E~~~aPWNtTrnFInqa~-~gk---~lLeltGvgDPTGcGe 853 (1563)
T KOG0008|consen 787 QRLKDAGYGEKYF-----FAPESDDEE----AAQSKIEDEVQLAPWNTTRNFINQAT-QGK---CLLELTGVGDPTGCGE 853 (1563)
T ss_pred HHHHhcCcchhhc-----ccccccchh----hhhhcchhhhccCcchhhHHHHHHHh-ccc---eeEEeecCCCCCcccC
Confidence 9999999987432 234445555 57899999999999999999995 76 677 6999999999999999
Q ss_pred eeEEEEcCCCccchhHHHHhHHhhhCCCCcccccchhhhccCHHHHHHHHHhCCCCHHHhhccCchhhhHHHHHhhHHHH
Q 000877 975 GFSYVRAAPKASVSSAMVKKKAAANRGGSTVTGTDADLRRLSMEAAREVLLKFNVPEEMIAKQTRWHRIAMIRKLSSEQA 1054 (1242)
Q Consensus 975 GFSfIR~s~K~~~~~~~~kkka~~~rg~~~VTGTDADLRKLSM~eAR~iLrkfGVpEE~IkkLtRWdrIaLVRkLSsEqA 1054 (1242)
||||||++.|+..+.. .+++++. .++|||||||||||+|..|+++|++|||+||+|++++||+||+|||++|+|+|
T Consensus 854 GFSyvRip~kpt~~k~--~~k~a~~--~~tvTgtdaDlrrl~~~~A~~vl~qf~v~EEeIak~trwe~i~~ir~~stE~A 929 (1563)
T KOG0008|consen 854 GFSYVRIPNKPTSMKE--GKKPAPA--KKTVTGTDADLRRLSLKAAKEVLRQFGVPEEEIAKLTRWERIDVIRTLSTEQA 929 (1563)
T ss_pred cceeEeccCCcccccc--ccccCCc--cCcccCCCcccccccHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhhchHHHH
Confidence 9999999999876643 2233332 37999999999999999999999999999999999999999999999999999
Q ss_pred hhhh-----------------HHHHHHHHHHHHHHHHHHHhhcc---CCCCCCCCCCC-CCchhhHHHhHHHhhhhhhhh
Q 000877 1055 ASGV-----------------QLQQQTRGKCQEIWDRQVQSLSA---ADDDEIGSDSE-HSDLDSFAGDLENLLDAEEFE 1113 (1242)
Q Consensus 1055 asGv-----------------e~QqqYkEecq~Ifd~Q~~sLSs---~d~De~eS~~e-~sD~d~~~~dlE~~L~a~~~~ 1113 (1242)
++|. ++|++||++||+||++|++.|++ .++|+++|+.+ ++|+|++++|||+||++++++
T Consensus 930 ks~~~~t~~~~f~rgnr~s~~e~qe~~re~cqri~d~qN~il~s~~~~~tD~~~s~a~~~sd~E~~~~~le~lL~~~kg~ 1009 (1563)
T KOG0008|consen 930 KSGGHETIMDKFARGNRFSFAERQEDYREKCQRIFDRQNGILESTEVFSTDPNESQAEEDSDLEEDGKDLENLLEAKKGK 1009 (1563)
T ss_pred hcCCCCchhhhhhccccchhhhhhhHHHHHHHHHHHHhhcchhcccccccCCccchhhhhhhHHHhHHHHHHHhhccccc
Confidence 9982 78999999999999999888876 45999999875 999999999999999999998
Q ss_pred hccccccccccccccccccc-cccchhhhhhhHhHhHHHHHHHHHHHHhhhhhH
Q 000877 1114 EEESNYDTKHDKVEGVKGLK-MRRRPIQVQAEEEIEDEAAEAAELCRLLMDDDE 1166 (1242)
Q Consensus 1114 ~~e~~~~~k~~~~~g~~gl~-~rr~~~~~q~~e~~e~E~~E~~eL~rll~~d~~ 1166 (1242)
+.++....+..+.+++++|+ +||++.++...+++++++.+++++++.+++...
T Consensus 1010 e~~~re~e~~eke~~~~~l~~~~~~~~~~ak~~~~~d~a~~~~~~~~~~~~~~~ 1063 (1563)
T KOG0008|consen 1010 EAESREREEQEKEDLKRLLNQERRQPRSVAKDEEIKDNASEYALNSSNLSQLLK 1063 (1563)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhcccccccccccccccccccchhhhchhhhcc
Confidence 87777888889999999999 999999988889999999999999998876553
No 2
>PF12157 DUF3591: Protein of unknown function (DUF3591); InterPro: IPR022591 This functionally uncharacterised domain is found centrally in the eukaryotic transcription initiation factor TFIID subunit 1.
Probab=100.00 E-value=1.4e-126 Score=1083.90 Aligned_cols=441 Identities=41% Similarity=0.650 Sum_probs=386.2
Q ss_pred eecccCCCCCccccccccccccCCCCCCCC-CCccccccccccccccccccccccccCCCccccccccccccCcccccCC
Q 000877 564 FEILDNKDDEHPLLHAGAMIITRSAKPSDF-KPAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIRTKIHLLPRAQKLP 642 (1242)
Q Consensus 564 fei~d~kd~~~l~~~A~~~~i~~~~K~~~~-~P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R~k~~~~pka~r~p 642 (1242)
|+.+......+++...+++.|.||.++.+| -|++++++ ...+++ ....|.+...|+..+.|.+++..+.++.
T Consensus 9 Y~~~k~~~~~kvr~t~~~~~vqHS~PA~kL~~p~ykt~l--~~~~lr-~fHRP~l~~~~~~~~~fs~~~~~kkk~~---- 81 (457)
T PF12157_consen 9 YEPLKENHQSKVRSTLGNLEVQHSLPALKLQLPFYKTHL--SKKELR-SFHRPRLKFPPGTPIVFSKLKHRKKKKD---- 81 (457)
T ss_pred hhccCccccchhhhccCCceeeeChHHHhhcccccCcCC--ChHHHH-hhcCCCCCCCCCCcccccchhhhhhhhh----
Confidence 566666556667888899999999998887 34445544 444453 3456777778888777877666543221
Q ss_pred CCCCCCCCCCCCcccCCcccCC-CceEEEEeeccCCccccCCCcccccccccCCCCCCCCcccccccCCCCCCceEEcCC
Q 000877 643 GENKSLRPPGAFKKKSDLSVKD-GHVFLMEYCEERPLLLSNAGMGANLCTYYQKSSPGDQAGALLCSGNNCLGNVLTLEP 721 (1242)
Q Consensus 643 g~~kslrp~gaFkk~sDLSlkD-G~lVLmEYsEE~PpLLSNvGMgSkIiNYYRKk~~~D~~~~~lr~~k~~lGe~vvL~p 721 (1242)
+...+.++|++++|||++| |++|||||||||||||+||||||+|+|||||++++|+.++. .++|++++|++
T Consensus 82 ---~~~~~~~~f~~~~DLS~~D~~~~vL~EYsEE~P~llsn~GM~s~i~nYyrk~~~~D~~~p~-----~~~Ge~~vl~~ 153 (457)
T PF12157_consen 82 ---KGKGGGEIFKKPSDLSLRDNGPLVLLEYSEEYPPLLSNVGMGSKIINYYRKKSAKDTSRPK-----LEIGETHVLDP 153 (457)
T ss_pred ---ccCCcccccCCcccCCCCCCCeEEEEEecccCchhhccccHHHHHHHhhcCCCcCCCCCcc-----ccCCceEEccC
Confidence 1334568999999999999 89999999999999999999999999999999999987654 47999999999
Q ss_pred CCCCCc--ceecCCCCceeeeecccccCCCCCCCCCCceEEEEEcCCC----cEEEEecCceeeccccccccccCCCCCc
Q 000877 722 GDKSPF--LGDIKAGCSQSSLETNMYRAPVFTHKVATTDFLLVRSAKG----KISIRRIDKVAVVAQQEPLMEVMSPGSK 795 (1242)
Q Consensus 722 ~D~SPF--LG~V~PGqtv~tLeNNMfRAPIFkHk~~~TDFLLIRS~~G----k~yIReId~LfvVGQ~eP~vEVP~PhSK 795 (1242)
+|.||| ||+|+||++|+||+|||||||||+|++++||||||||++| +||||+|++||||||+||+||||+||||
T Consensus 154 ~d~SPF~~lG~v~pG~~~~~l~nnm~rAPif~H~~~~TDFLliRs~~g~~~~~~ylR~I~~lf~VGQ~~P~~EVp~P~Sr 233 (457)
T PF12157_consen 154 EDKSPFWNLGSVPPGQTVQTLENNMFRAPIFKHKPPSTDFLLIRSTTGGGGSKYYLREIDHLFVVGQQEPLVEVPGPHSR 233 (457)
T ss_pred CCCCchhhCCccCCCCEeEEeecCccccCCccCCCCCCcEEEEEeCCCCCCceEEEEeCCcEEEeeccccceecCCCCch
Confidence 999999 9999999999999999999999999999999999999986 7999999999999999999999999999
Q ss_pred chhhhHHHHHHHHHHHHHHHhhhcCCCCcccHhHHhhhCCCCcHHHHHHHHHHhhcccccCCCceeEEecCCCCCCChHH
Q 000877 796 NLQTYSINRMLVNVYREFSAAAKRGLLPCIGVDELSVQFPNLSEAIIRKKLKECAFLRRDGNGKQVWSMKRTFHIPSEGD 875 (1242)
Q Consensus 796 kvt~f~KNRLkv~iyRlf~k~~~~~~~~rIrv~DI~k~FP~~sE~qIRKRLKEcad~qR~g~g~g~W~lKp~~rLPsEEE 875 (1242)
++|+|++|||+|+|||+|+++. ++||+|+||+++||++||++||||||+||+|+|+|++++||++|++++||+|++
T Consensus 234 ~~t~~~knrL~~~iyRlf~~~~----~~ri~~~di~~~Fp~~se~~iRkrLKe~~~~~R~g~~~~~W~lk~~~~lp~eee 309 (457)
T PF12157_consen 234 KVTNFSKNRLKMIIYRLFNKSQ----PRRIKVDDIKKHFPDQSESQIRKRLKEFADFQRTGDDSGWWVLKPGFRLPDEEE 309 (457)
T ss_pred hHHHHHHHHHHHHHHHHHhhcc----CCccCHHHHHHhCCCCcHHHHHHHHHHHHhccCCCCCCCeEEECCCCCCCCHHH
Confidence 9999999999999999999553 378999999999999999999999999999999999999999999999999999
Q ss_pred hhhhCChhhhHHHHHHHHHHHHHHhcCCccccCccchhhhhccCchHHHHHHHhhhHHHHHhcCcchhhHHHHHHhhcCc
Q 000877 876 LRKLAYPEHVCSYESMQAGLYRLKHLGITQLTLPASISSAMSQLPDEAIALAAASHIERELQITPWNLSSNFVACTNQDR 955 (1242)
Q Consensus 876 LR~mITPE~VCayESMqAG~qRLkDaGy~~lt~~~~is~a~~ql~DE~~~~~~a~~IE~ELqLAPWNlTrNFv~At~QgK 955 (1242)
||+|||||+||+|||||||+|||+|+||..+..... .+++|| ..|++|+++||||||+|||+|+ |||
T Consensus 310 lr~mvtPE~vC~~eSM~ag~~rL~D~G~~~~~~~~~-----~~~~~e-------~~~~~E~~laPWn~T~nFi~A~-qgk 376 (457)
T PF12157_consen 310 LRKMVTPEDVCAYESMQAGEQRLKDAGYGELSEFAR-----DEDDDE-------EKIEDELQLAPWNTTKNFINAT-QGK 376 (457)
T ss_pred HHhhCCHHHHHHHHHHHHHHHHHHhcCCcccccccc-----ccccch-------hhhhHHHhCCChHhHHHHHHHh-ccC
Confidence 999999999999999999999999999998765422 222233 2899999999999999999998 788
Q ss_pred ccceeeeeeccCCCCCCCceeEEEEcCCCccchhHHHHhHHhhhCCCCcccccchhhhccCHHHHHHHHHhCCCCHHHhh
Q 000877 956 ENIERLEITGVGDPSGRGLGFSYVRAAPKASVSSAMVKKKAAANRGGSTVTGTDADLRRLSMEAAREVLLKFNVPEEMIA 1035 (1242)
Q Consensus 956 a~i~mLqL~G~GDPTGrGEGFSfIR~s~K~~~~~~~~kkka~~~rg~~~VTGTDADLRKLSM~eAR~iLrkfGVpEE~Ik 1035 (1242)
| ||+|+|+||||||||||||||++||+++.+.... ...+..++||||+||||+|+|.+|+++|+.| +|+|+
T Consensus 377 a---~L~l~G~gDPTG~GeGfSfir~~~K~~~~~~~~~---~~~~~~~~v~gt~adlr~l~~~~~~~~~~~y---eeeI~ 447 (457)
T PF12157_consen 377 A---MLQLHGEGDPTGRGEGFSFIRTSMKPGFLKSGES---AQAKPKKTVTGTDADLRKLHMYNAAEQLRKY---EEEIK 447 (457)
T ss_pred c---EEEEecCCCCCCCCCceEEEEcCCCCCccccccc---ccccccccccCccchhccCCHHHHHHHHHHH---HHHHH
Confidence 4 9999999999999999999999999997543211 2233447999999999999999999999999 99999
Q ss_pred ccCchhhhHH
Q 000877 1036 KQTRWHRIAM 1045 (1242)
Q Consensus 1036 kLtRWdrIaL 1045 (1242)
+|.||++|+|
T Consensus 448 ~l~r~q~~~L 457 (457)
T PF12157_consen 448 KLWRWQRISL 457 (457)
T ss_pred HHHHHHHhcC
Confidence 9999999985
No 3
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=100.00 E-value=1.8e-103 Score=890.26 Aligned_cols=398 Identities=33% Similarity=0.539 Sum_probs=339.7
Q ss_pred CCCCCCceeecCCCCcceeecccCCCCCc-----------------------------------cccccccccccCCCCC
Q 000877 546 DAVGKPKLILDLQDEQMLFEILDNKDDEH-----------------------------------PLLHAGAMIITRSAKP 590 (1242)
Q Consensus 546 ~~~~k~KLiLDlnD~nmifei~d~kd~~~-----------------------------------l~~~A~~~~i~~~~K~ 590 (1242)
.++...|..|.|||+.+++-+.-.+..+. +|...+...|.|+..+
T Consensus 315 ~~~~~SK~~lNlndeKlll~~q~~~k~~qq~~f~d~~~~NeL~~KfNiSnD~~Y~iLKkthqsKvrntls~l~iqHs~pA 394 (968)
T COG5179 315 AKLKESKAPLNLNDEKLLLKRQAKPKKKQQEVFSDDKPLNELKGKFNISNDKYYGILKKTHQSKVRNTLSTLGIQHSLPA 394 (968)
T ss_pred ccccccccccccccHHhhhhhhcCchhhhhhhhccccchHHhhhhcccccchhhHHHHhhhHHHHHhhhhhhcccccchh
Confidence 34444667889999999887643332211 1222344555555555
Q ss_pred CCCCCcccccccccc---c-cccccccccccccCCCccccccccccccCcccccCCCCCCCCCCCCCCcccCCcccCCC-
Q 000877 591 SDFKPAESVKLFYLG---K-ELEDHKSLADQNVRPNSLIHLIRTKIHLLPRAQKLPGENKSLRPPGAFKKKSDLSVKDG- 665 (1242)
Q Consensus 591 ~~~~P~~~~klfY~g---k-el~~~~sl~~~~VrP~sl~h~~R~k~~~~pka~r~pg~~kslrp~gaFkk~sDLSlkDG- 665 (1242)
.++.|. ||+. + +++ +...+.|.||||+.+-|+..+.+++.+ +.+|.-+ +.|+++.|||+.|+
T Consensus 395 ~~L~~p-----fYK~~~~k~~lR-~fHRp~f~~rpgs~IvFs~l~arKR~k-----dK~K~~~--e~i~t~~elTvgDts 461 (968)
T COG5179 395 LRLDPP-----FYKNNHTKEELR-NFHRPRFMVRPGSNIVFSTLEARKRNK-----DKGKDVQ--EIIKTAGELTVGDTS 461 (968)
T ss_pred hhcCCc-----hhcccccHHHHH-hhcCCccccCCCCceeeeeeecccccC-----ccccchh--hhhccccceeccCCC
Confidence 555332 5543 2 333 466789999999999998777765333 5566655 89999999999996
Q ss_pred ceEEEEeeccCCccccCCCcccccccccCCCCCCCCcccccccCCCCCCceEEcCCCCCCCc--ceecCCCCceeeeecc
Q 000877 666 HVFLMEYCEERPLLLSNAGMGANLCTYYQKSSPGDQAGALLCSGNNCLGNVLTLEPGDKSPF--LGDIKAGCSQSSLETN 743 (1242)
Q Consensus 666 ~lVLmEYsEE~PpLLSNvGMgSkIiNYYRKk~~~D~~~~~lr~~k~~lGe~vvL~p~D~SPF--LG~V~PGqtv~tLeNN 743 (1242)
+++|||||||+|.+|+|+||+|+|+|||||++..|+.+|++ +.|+.+||+++|+||| ||.|.||..+++|+||
T Consensus 462 p~~L~EySEe~P~~Lsn~GMas~l~nYYRK~NeqDe~rPKL-----~vge~hVLdvqD~SPFwnFG~VePG~i~ptLyNn 536 (968)
T COG5179 462 PFSLFEYSEEEPFFLSNPGMASLLNNYYRKSNEQDEYRPKL-----DVGEYHVLDVQDPSPFWNFGDVEPGTIIPTLYNN 536 (968)
T ss_pred ceeeeeecccCceeecCchHHHHHHHHHHhcccccccccCC-----CcCceeecccCCCCcccCcCCCCCCcchHHHhhh
Confidence 68999999999999999999999999999999999987655 8999999999999999 8999999999999999
Q ss_pred cccCCCCCCCCCCceEEEEEcC--CC--cEEEEecCceeeccccccccccCCCCCcchhhhHHHHHHHHHHHHHHHhhhc
Q 000877 744 MYRAPVFTHKVATTDFLLVRSA--KG--KISIRRIDKVAVVAQQEPLMEVMSPGSKNLQTYSINRMLVNVYREFSAAAKR 819 (1242)
Q Consensus 744 MfRAPIFkHk~~~TDFLLIRS~--~G--k~yIReId~LfvVGQ~eP~vEVP~PhSKkvt~f~KNRLkv~iyRlf~k~~~~ 819 (1242)
|||||||+|..+.|||||||.+ -| +||||.|+|+|||||+||+.|||+||||++|.|++|||+|++||+|+.+...
T Consensus 537 mirAPvFKH~~~~TDflli~~sS~~G~~~~ylrnInhlf~vGQtFPveevpgPhSRKvt~~~knRLKm~~fRl~n~~~~g 616 (968)
T COG5179 537 MIRAPVFKHSSGGTDFLLIVESSNSGEMSLYLRNINHLFCVGQTFPVEEVPGPHSRKVTVFCKNRLKMAAFRLFNSKEGG 616 (968)
T ss_pred hhhcchhcccCCCcceEEEEccCCCCceeeehhcCcceEeccccccccccCCCcchhhHHHHhhhHHHHHHHHhhcCCCC
Confidence 9999999999999999999943 23 6999999999999999999999999999999999999999999999988653
Q ss_pred CCCCcccHhHHhhhCCCCcHHHHHHHHHHhhcccccCCCceeEEecCCCCCCChHHhhhhCChhhhHHHHHHHHHHHHHH
Q 000877 820 GLLPCIGVDELSVQFPNLSEAIIRKKLKECAFLRRDGNGKQVWSMKRTFHIPSEGDLRKLAYPEHVCSYESMQAGLYRLK 899 (1242)
Q Consensus 820 ~~~~rIrv~DI~k~FP~~sE~qIRKRLKEcad~qR~g~g~g~W~lKp~~rLPsEEELR~mITPE~VCayESMqAG~qRLk 899 (1242)
-|+++.|.+|||+|+++|+||||||||+|+|+|.+ |+|+||++..||+|+.+|+|||||+||+||||++|+|.|+
T Consensus 617 ----~l~I~ql~khFpdq~egq~Rq~lKEfm~y~kdGp~-g~W~Lk~~e~lldee~~rslvtPE~icq~ESM~~G~r~le 691 (968)
T COG5179 617 ----SLRISQLDKHFPDQSEGQKRQWLKEFMDYVKDGPD-GVWVLKPSEALLDEEDLRSLVTPENICQYESMLAGERKLE 691 (968)
T ss_pred ----ceeeehhhhhCCCcchhHHHHHHHHHHHHhhcCCC-ceEEeccccccCChhhhhhhcCHhHHHHHHHHHHHHHHHh
Confidence 49999999999999999999999999999998876 9999999999999999999999999999999999999999
Q ss_pred hcCCccccCccchhhhhccCchHHHHHHHhhhHHHHHhcCcchhhHHHHHHhhcCcccceeeeeeccCCCCCCCceeEEE
Q 000877 900 HLGITQLTLPASISSAMSQLPDEAIALAAASHIERELQITPWNLSSNFVACTNQDRENIERLEITGVGDPSGRGLGFSYV 979 (1242)
Q Consensus 900 DaGy~~lt~~~~is~a~~ql~DE~~~~~~a~~IE~ELqLAPWNlTrNFv~At~QgKa~i~mLqL~G~GDPTGrGEGFSfI 979 (1242)
|+||...- ...|+ .-++|..++||++|||||+|| |||| ||+|+|+||||||||||||+
T Consensus 692 D~g~~~~n----------~d~de--------e~~eE~ll~PW~~trNFiNat-qgra---ml~l~G~GDPtGiGEGfSF~ 749 (968)
T COG5179 692 DSGYKTVN----------EDDDE--------ENEEEMLLPPWCLTRNFINAT-QGRA---MLELSGPGDPTGIGEGFSFR 749 (968)
T ss_pred hccccccc----------cCccc--------cCHhhhCCCcchhhhhhhhhh-cCce---eEEEecCCCCcccCCcceee
Confidence 99998632 12232 235677899999999999998 8996 99999999999999999999
Q ss_pred EcCCCccch
Q 000877 980 RAAPKASVS 988 (1242)
Q Consensus 980 R~s~K~~~~ 988 (1242)
|++||.++.
T Consensus 750 ktsmKgGf~ 758 (968)
T COG5179 750 KTSMKGGFE 758 (968)
T ss_pred eeccccCcc
Confidence 999998875
No 4
>PF09247 TBP-binding: TATA box-binding protein binding; InterPro: IPR009067 In eukaryotes, the general transcription factor TFIID helps to regulate transcription by RNA polymerase II from class II promoters. TFIID consists of TATA-box-binding proteins (TBP) and TBP-associated factors (TAFIIs), which together mediate both activation and inhibition of transcription. In Drosophila, the N-terminal region of TAFII-230 (the TFIID 230kDa subunit) binds directly to TBP, thereby inhibiting the binding of TBP to the TATA box. The structure of TAFII-230 is comprised of three short helices in an irregular array, which forms the core that occupies the DNA-binding surface of TBP []. Note, the Gene3D model in this entry is hitting fewer proteins than it should and is under revision.; PDB: 1TBA_A.
Probab=99.51 E-value=3.5e-16 Score=137.23 Aligned_cols=47 Identities=53% Similarity=0.890 Sum_probs=34.3
Q ss_pred CcceeeeeecccCCCCCCccc-cccHHHHHHHHHHHh-hhcCCcccccc
Q 000877 28 GNRLLGFMFGNVDYAGDLDVD-YLDEDAKEHLAAVAD-KLGPSLTDIDV 74 (1242)
Q Consensus 28 ~~~~~gf~fgn~~~~g~l~~~-~ld~~~k~hl~~~~~-~lg~~~~~i~~ 74 (1242)
|+.|+||||||||++|+|+.+ |||+++|+||++|+. +||++|++|+.
T Consensus 10 g~~LtGflFGNId~~G~Le~D~~lD~e~K~~L~~L~~lgLgs~l~ei~~ 58 (62)
T PF09247_consen 10 GFSLTGFLFGNIDEDGQLEDDSYLDEEAKEHLSSLSALGLGSLLTEITD 58 (62)
T ss_dssp S---TTHHHH-EETTTEE--SS---TTTHHHHTT-TTTSHHHHHHTS--
T ss_pred CcceeeeeecccCCCCccccccccCHHHHHHHHHHHhcchhhHHHHHHh
Confidence 889999999999999999998 999999999999998 99999999974
No 5
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=92.14 E-value=0.26 Score=55.36 Aligned_cols=66 Identities=21% Similarity=0.401 Sum_probs=41.6
Q ss_pred hhhhHHHHHHHHHHHHHHHhhhcCCCCcccHhHHhhhCCCCcHHHHHHHHHHhhcccccCCCceeEEecCCCC
Q 000877 797 LQTYSINRMLVNVYREFSAAAKRGLLPCIGVDELSVQFPNLSEAIIRKKLKECAFLRRDGNGKQVWSMKRTFH 869 (1242)
Q Consensus 797 vt~f~KNRLkv~iyRlf~k~~~~~~~~rIrv~DI~k~FP~~sE~qIRKRLKEcad~qR~g~g~g~W~lKp~~r 869 (1242)
..-.-++-|+-.+|.+|.+. ....|++|...+ .|++.-+|+.|++.|.|.|.|...+.|.|||.|+
T Consensus 209 ~~R~~~~eL~d~lF~~Fe~~------~ywslK~L~~~t-~QP~~yLKeiL~eIa~~~k~g~~~~~w~LKpeyk 274 (275)
T PF02270_consen 209 RARMDKNELLDLLFKLFEKH------QYWSLKDLRQRT-QQPEAYLKEILEEIAVLNKRGPHKNMWELKPEYK 274 (275)
T ss_dssp -THHHHHHHHHHHHHHHHH-------S-B-HHHHHHH---S-HHHHHHHHHHH--EE--TT---EE----SS-
T ss_pred ceeCCHHHHHHHHHHHHHhC------CCCCHHHHHHHH-CCCHHHHHHHHHHHHHHhccCCcCCcEecchHHc
Confidence 33456778999999999876 358899999886 4999999999999999999998899999999885
No 6
>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=81.12 E-value=0.64 Score=61.25 Aligned_cols=72 Identities=28% Similarity=0.431 Sum_probs=62.4
Q ss_pred ccccccCcccCcccCCCCccceeeccCCCCCCCCceeecCCCCcceeecccCCCCCccccccccccccCCCC
Q 000877 518 VKRFSKHSLQNRDMMEGSWLDNIIWEPVDAVGKPKLILDLQDEQMLFEILDNKDDEHPLLHAGAMIITRSAK 589 (1242)
Q Consensus 518 ~~r~s~~~~~N~dL~~g~Wld~IiWD~~~~~~k~KLiLDlnD~nmifei~d~kd~~~l~~~A~~~~i~~~~K 589 (1242)
-.|+++.-+.-+.+..-+|++.++||.+....+.++.+++.|.+|.|+|++++..+...++++.+++.+.-+
T Consensus 315 ~v~~~g~~~~~k~~~~~~~~~~~gWd~~~i~tr~~~~f~~~d~~m~~~i~d~~~~~~~~~~~~~li~~~we~ 386 (1563)
T KOG0008|consen 315 DVRKDGEDVKDKVLEDENWLDLDGWDPNKIYTRNALAFNLQDSSMTFNIPDNKGYKIFPLHNDSLIYSRWED 386 (1563)
T ss_pred hcccchHHHHHhhhhhcccccccccccccccccchhhhcccccccccccCCCccccccccccchhhhchhhh
Confidence 346777777788888888999999999998888899999999999999999999888888888888865543
No 7
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=48.57 E-value=25 Score=41.80 Aligned_cols=44 Identities=25% Similarity=0.432 Sum_probs=38.2
Q ss_pred cccHhHHhhhCCCCc--HHHHHHHHHHhhcccccCCCceeEEecCCCCCCC
Q 000877 824 CIGVDELSVQFPNLS--EAIIRKKLKECAFLRRDGNGKQVWSMKRTFHIPS 872 (1242)
Q Consensus 824 rIrv~DI~k~FP~~s--E~qIRKRLKEcad~qR~g~g~g~W~lKp~~rLPs 872 (1242)
-+++..|++.+|.-+ +..+-+.|+.||-+.+ |.|++|..+..|.
T Consensus 284 v~~Fs~L~~ll~~~~~~~~~lL~~L~~~AvLV~-----G~WV~kS~ll~~~ 329 (421)
T PF04801_consen 284 VISFSELRKLLPSNSDTDEELLRALQQVAVLVQ-----GNWVVKSELLYPD 329 (421)
T ss_pred cccHHHHHHHhccccchHHHHHHHHHhheEEEe-----eeEEEehhhccCC
Confidence 589999999999655 7888889999998886 6899999988776
No 8
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=47.22 E-value=11 Score=33.17 Aligned_cols=35 Identities=46% Similarity=0.786 Sum_probs=31.1
Q ss_pred CCccccccccccccccccccccccccCCCcccccc
Q 000877 594 KPAESVKLFYLGKELEDHKSLADQNVRPNSLIHLI 628 (1242)
Q Consensus 594 ~P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~ 628 (1242)
-|....+|+|.|+.+.++.+|...++.+++.++++
T Consensus 31 ~~~~~~~L~~~G~~L~d~~tL~~~~i~~~~~I~l~ 65 (69)
T PF00240_consen 31 IPPEQQRLIYNGKELDDDKTLSDYGIKDGSTIHLV 65 (69)
T ss_dssp STGGGEEEEETTEEESTTSBTGGGTTSTTEEEEEE
T ss_pred cccccceeeeeeecccCcCcHHHcCCCCCCEEEEE
Confidence 35668899999999999999999999999988875
No 9
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=46.08 E-value=28 Score=39.51 Aligned_cols=65 Identities=20% Similarity=0.340 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHhhhcCCCCcccHhHHhhhCCCCcHHHHHHHHHHhhcccccCCCceeEEecCCCCCCChH
Q 000877 803 NRMLVNVYREFSAAAKRGLLPCIGVDELSVQFPNLSEAIIRKKLKECAFLRRDGNGKQVWSMKRTFHIPSEG 874 (1242)
Q Consensus 803 NRLkv~iyRlf~k~~~~~~~~rIrv~DI~k~FP~~sE~qIRKRLKEcad~qR~g~g~g~W~lKp~~rLPsEE 874 (1242)
|-+.-+.|.+|-+.. --.+.+|... ..|++.-++..|++.+.|.+.|..++.|.|||.|+=-.+|
T Consensus 185 ~evld~lFk~FEk~~------ywtlK~Lv~~-t~QP~~fLKEiL~~icv~NkKg~~k~tyeLKPEYK~~~~e 249 (254)
T KOG2905|consen 185 NEVLDMLFKAFEKYQ------YWTLKDLVEI-TKQPEAFLKEILKDICVLNKKGPYKNTYELKPEYKKYKEE 249 (254)
T ss_pred HHHHHHHHHHhhcCc------cccHHHHHHH-hcCHHHHHHHHHHHHHHHhccCcccCceecCHHHhhhhhh
Confidence 446667777775542 3556676554 7899999999999999999888889999999988654444
No 10
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=45.48 E-value=8.2 Score=34.49 Aligned_cols=35 Identities=23% Similarity=0.668 Sum_probs=31.2
Q ss_pred CccccccccccccccccccccccccCCCccccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
|....+|.|.|+.+.+..++...++.+++.+|+++
T Consensus 35 ~~~~q~Li~~G~~L~d~~~l~~~~i~~~stl~l~~ 69 (70)
T cd01798 35 PPDQLRVIFAGKELRNTTTIQECDLGQQSILHAVR 69 (70)
T ss_pred CHHHeEEEECCeECCCCCcHHHcCCCCCCEEEEEe
Confidence 55577899999999999999999999999999875
No 11
>PF12571 DUF3751: Phage tail-collar fibre protein; InterPro: IPR022225 This entry is represented by Bacteriophage HP1, Orf31. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in bacteria and viruses, and is approximately 160 amino acids in length, some annotation suggests that it may be a tail fibre protein. There are two completely conserved residues (K and W) that may be functionally important.
Probab=44.31 E-value=16 Score=38.23 Aligned_cols=63 Identities=21% Similarity=0.266 Sum_probs=46.3
Q ss_pred cCCCCceeeeecccccCCCCCCCCCCceEEEEE----cCCCcEEEEec------CceeeccccccccccCCCCC
Q 000877 731 IKAGCSQSSLETNMYRAPVFTHKVATTDFLLVR----SAKGKISIRRI------DKVAVVAQQEPLMEVMSPGS 794 (1242)
Q Consensus 731 V~PGqtv~tLeNNMfRAPIFkHk~~~TDFLLIR----S~~Gk~yIReI------d~LfvVGQ~eP~vEVP~PhS 794 (1242)
+.|...+++|.|-.+|+||-.+.+.+-+.+.+- +.-|.|+||+| ..|++||- +|...-|...+
T Consensus 45 ~~p~~~~t~L~~ev~r~~i~~~~~~n~n~v~~~~~i~~~~ggf~irEiGL~d~~G~Liai~~-~~~~~K~~~~~ 117 (159)
T PF12571_consen 45 YTPDESQTALVNEVYRAAINSVDPVNPNQVVYSAVIPSDVGGFTIREIGLFDEDGTLIAIAN-FPPTYKPATSE 117 (159)
T ss_pred CCCCccCCccccEEEEEccCccCCCCCCEEEEEEEECCccCCcEEEEEEEEccCCCEEEEEe-cCCcccccccC
Confidence 678888999999999999999866666655543 23466999999 46777876 45555555443
No 12
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=43.10 E-value=35 Score=28.87 Aligned_cols=40 Identities=18% Similarity=0.318 Sum_probs=26.2
Q ss_pred hhhccCHHHHHHHHHhCCCCHHHhhccCchhhhHHHHHhhHHHHh
Q 000877 1011 DLRRLSMEAAREVLLKFNVPEEMIAKQTRWHRIAMIRKLSSEQAA 1055 (1242)
Q Consensus 1011 DLRKLSM~eAR~iLrkfGVpEE~IkkLtRWdrIaLVRkLSsEqAa 1055 (1242)
||.++++.+++++-..+||+ -..++++=+ ||-.+...++.
T Consensus 1 eL~~~~~~eL~~iAk~lgI~--~~~~~~K~e---LI~~Il~~q~~ 40 (43)
T PF07498_consen 1 ELKSMTLSELREIAKELGIE--GYSKMRKQE---LIFAILKAQAE 40 (43)
T ss_dssp HHHCS-HHHHHHHHHCTT-T--TGCCS-HHH---HHHHHHHHHCT
T ss_pred CcccCCHHHHHHHHHHcCCC--CCCcCCHHH---HHHHHHHHHHH
Confidence 78999999999999999997 355666555 44444434433
No 13
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=38.68 E-value=32 Score=28.51 Aligned_cols=24 Identities=29% Similarity=0.526 Sum_probs=20.2
Q ss_pred HhHHhhhCCCCcHHHHHHHHHHhh
Q 000877 827 VDELSVQFPNLSEAIIRKKLKECA 850 (1242)
Q Consensus 827 v~DI~k~FP~~sE~qIRKRLKEca 850 (1242)
+..|+..||+++...|+..|+.+-
T Consensus 5 v~~L~~mFP~~~~~~I~~~L~~~~ 28 (42)
T PF02845_consen 5 VQQLQEMFPDLDREVIEAVLQANN 28 (42)
T ss_dssp HHHHHHHSSSS-HHHHHHHHHHTT
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcC
Confidence 567899999999999999998763
No 14
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=35.02 E-value=14 Score=33.46 Aligned_cols=35 Identities=37% Similarity=0.706 Sum_probs=30.8
Q ss_pred CccccccccccccccccccccccccCCCccccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
|....+|+|.|+.+.+..+|...++++++.+|++.
T Consensus 37 ~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~l~l~~ 71 (74)
T cd01807 37 PEEQQRLLFKGKALADDKRLSDYSIGPNAKLNLVV 71 (74)
T ss_pred CHHHeEEEECCEECCCCCCHHHCCCCCCCEEEEEE
Confidence 44577899999999999999999999999988863
No 15
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=34.13 E-value=42 Score=27.85 Aligned_cols=23 Identities=35% Similarity=0.619 Sum_probs=20.4
Q ss_pred HhHHhhhCCCCcHHHHHHHHHHh
Q 000877 827 VDELSVQFPNLSEAIIRKKLKEC 849 (1242)
Q Consensus 827 v~DI~k~FP~~sE~qIRKRLKEc 849 (1242)
++.|...||+++...||+-|..+
T Consensus 6 v~~L~~mFP~l~~~~I~~~L~~~ 28 (43)
T smart00546 6 LHDLKDMFPNLDEEVIKAVLEAN 28 (43)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHc
Confidence 56788999999999999999865
No 16
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=33.39 E-value=16 Score=32.07 Aligned_cols=35 Identities=34% Similarity=0.691 Sum_probs=30.5
Q ss_pred CccccccccccccccccccccccccCCCccccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
|....+|+|.|+.+.++.+|...++++++.+|+++
T Consensus 37 ~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~l~l~~ 71 (72)
T cd01809 37 PVEQQRLIYSGRVLKDDETLSEYKVEDGHTIHLVK 71 (72)
T ss_pred CHHHeEEEECCEECCCcCcHHHCCCCCCCEEEEEe
Confidence 44577889999999999999999999999988864
No 17
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=33.21 E-value=27 Score=33.97 Aligned_cols=40 Identities=18% Similarity=0.178 Sum_probs=30.8
Q ss_pred chhhhccCHHHHHHHHHhCCCCHHHhhccCchhhhHHHHH
Q 000877 1009 DADLRRLSMEAAREVLLKFNVPEEMIAKQTRWHRIAMIRK 1048 (1242)
Q Consensus 1009 DADLRKLSM~eAR~iLrkfGVpEE~IkkLtRWdrIaLVRk 1048 (1242)
+++.|.-=..+-...|.+||+++|++.-+.+++.++|++-
T Consensus 10 ~~~~r~~F~~D~~a~~~~~~Lt~eer~av~~rD~~~L~~~ 49 (88)
T PF07746_consen 10 DPENRERFLADPEAYLDEYGLTEEERQAVLDRDWLALIAL 49 (88)
T ss_dssp SHHHHHHHHH-HHHHHHCCT--HHHHHHHHCT-HHHHHHT
T ss_pred CHHHHHHHHHCHHHHHHHcCCCHHHHHHHHcCCHHHHHHC
Confidence 4667777777888899999999999999999999999853
No 18
>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=31.96 E-value=23 Score=42.52 Aligned_cols=47 Identities=30% Similarity=0.429 Sum_probs=30.2
Q ss_pred hcCcchhhHHHHHHhhcCcc-------cceeeeeeccCCCCCCC-ceeEEEEcCCCc
Q 000877 937 QITPWNLSSNFVACTNQDRE-------NIERLEITGVGDPSGRG-LGFSYVRAAPKA 985 (1242)
Q Consensus 937 qLAPWNlTrNFv~At~QgKa-------~i~mLqL~G~GDPTGrG-EGFSfIR~s~K~ 985 (1242)
-.||- ..-|||.-+.+|-- +|..++|-| |||||.| -|-|+-=-|-|.
T Consensus 296 d~~P~-aceNFI~lc~~gYYnnt~FHRsIrnFmiQG-GDPTGTG~GGeSiWgKpFkD 350 (518)
T KOG0883|consen 296 DYAPR-ACENFITLCKNGYYNNTIFHRSIRNFMIQG-GDPTGTGRGGESIWGKPFKD 350 (518)
T ss_pred CcchH-HHHHHHHHHhcccccchHHHHHHHHHeeeC-CCCCCCCCCCccccCCcccc
Confidence 34564 34689976666721 234578888 9999977 467776444443
No 19
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=31.46 E-value=32 Score=33.21 Aligned_cols=40 Identities=13% Similarity=-0.014 Sum_probs=34.7
Q ss_pred ccchhhhccCHHHHHHHHHhCCCCHHHhhccCchhhhHHH
Q 000877 1007 GTDADLRRLSMEAAREVLLKFNVPEEMIAKQTRWHRIAMI 1046 (1242)
Q Consensus 1007 GTDADLRKLSM~eAR~iLrkfGVpEE~IkkLtRWdrIaLV 1046 (1242)
++|+++|..-..+-..++..||+++|+++-|..=+..+|+
T Consensus 14 ~~dp~~rerF~~DPea~~~~~gLt~eE~~aL~~~D~~~L~ 53 (81)
T cd07922 14 FKDPGLIERFQDDPSAVFEEYGLTPAERAALREGTFGALT 53 (81)
T ss_pred hcCHHHHHHHHHCHHHHHHHcCCCHHHHHHHHccCHHHHH
Confidence 6788999999999999999999999999988877666665
No 20
>KOG0881 consensus Cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=29.66 E-value=39 Score=35.38 Aligned_cols=37 Identities=35% Similarity=0.643 Sum_probs=23.6
Q ss_pred hcCcchhhHHHHHHhhcCccc-------ceeeeeeccCCCCCCCce
Q 000877 937 QITPWNLSSNFVACTNQDREN-------IERLEITGVGDPSGRGLG 975 (1242)
Q Consensus 937 qLAPWNlTrNFv~At~QgKa~-------i~mLqL~G~GDPTGrGEG 975 (1242)
+-|| ++.+||..-.+.|--+ +.-+.+-| |||||.|-|
T Consensus 28 kHaP-~TC~NF~eLarrgYYn~v~FHRii~DFmiQG-GDPTGTGRG 71 (164)
T KOG0881|consen 28 KHAP-RTCQNFAELARRGYYNGVIFHRIIKDFMIQG-GDPTGTGRG 71 (164)
T ss_pred hcCc-HHHHHHHHHHhcccccceeeeehhhhheeec-CCCCCCCCC
Confidence 4455 5789999776655211 12356667 999987744
No 21
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=28.98 E-value=20 Score=33.40 Aligned_cols=34 Identities=44% Similarity=0.709 Sum_probs=30.6
Q ss_pred CccccccccccccccccccccccccCCCcccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLI 628 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~ 628 (1242)
|....+|+|.|+.+.+..+|...++++++.+|++
T Consensus 39 ~~~~QrLi~~Gk~L~D~~tL~~y~i~~~~~i~l~ 72 (78)
T cd01797 39 EPECQRLFYRGKQMEDGHTLFDYNVGLNDIIQLL 72 (78)
T ss_pred CHHHeEEEeCCEECCCCCCHHHcCCCCCCEEEEE
Confidence 5567899999999999999999999999998885
No 22
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=26.42 E-value=27 Score=33.20 Aligned_cols=34 Identities=29% Similarity=0.540 Sum_probs=31.1
Q ss_pred ccccccccccccccccccccccccCCCccccccc
Q 000877 596 AESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 596 ~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
....+|=|.||-+.+..+|...++++++.+|++|
T Consensus 41 ~dqQrLIy~GKiL~D~~TL~dygI~~gstlhLv~ 74 (75)
T cd01815 41 PELIDLIHCGRKLKDDQTLDFYGIQSGSTIHILR 74 (75)
T ss_pred hHHeEEEeCCcCCCCCCcHHHcCCCCCCEEEEEe
Confidence 5577889999999999999999999999999987
No 23
>cd01805 RAD23_N Ubiquitin-like domain of RAD23. RAD23 belongs to a family of adaptor molecules having affinity for both the proteasome and ubiquitinylated proteins and thought to shuttle these ubiquitinylated proteins to the proteasome for destruction. RAD23 interacts with ubiquitin through its C-terminal ubiquitin-associated domains (UBA) and with the proteasome through its N-terminal ubiquitin-like domain (UBL).
Probab=26.21 E-value=27 Score=31.47 Aligned_cols=35 Identities=29% Similarity=0.552 Sum_probs=30.0
Q ss_pred CccccccccccccccccccccccccCCCccccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
|....+|.|.|+.+.++.+|...+++.++.++++.
T Consensus 39 ~~~~q~L~~~G~~L~d~~~L~~~~i~~~~~i~~~~ 73 (77)
T cd01805 39 PPEQQKLIYSGKILKDDTTLEEYKIDEKDFVVVMV 73 (77)
T ss_pred ChhHeEEEECCEEccCCCCHHHcCCCCCCEEEEEE
Confidence 55678899999999999999999999998777654
No 24
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=25.85 E-value=26 Score=31.17 Aligned_cols=35 Identities=37% Similarity=0.751 Sum_probs=30.5
Q ss_pred CccccccccccccccccccccccccCCCccccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
|....+|+|.|+.+.+..++...++++++.+|++.
T Consensus 37 ~~~~q~L~~~g~~L~d~~~L~~~~i~~~~~i~l~~ 71 (76)
T cd01803 37 PPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71 (76)
T ss_pred CHHHeEEEECCEECCCCCcHHHcCCCCCCEEEEEE
Confidence 55578899999999999999999999999888864
No 25
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=25.68 E-value=38 Score=29.41 Aligned_cols=31 Identities=32% Similarity=0.418 Sum_probs=27.2
Q ss_pred hhhhccCHHHHHHHHHhCCCCHHHhhccCch
Q 000877 1010 ADLRRLSMEAAREVLLKFNVPEEMIAKQTRW 1040 (1242)
Q Consensus 1010 ADLRKLSM~eAR~iLrkfGVpEE~IkkLtRW 1040 (1242)
.|+..||=.|+++.|++||++---|-.-+|=
T Consensus 1 ~d~~~LSd~eL~~~L~~~G~~~gPIt~sTR~ 31 (44)
T smart00540 1 DDVDRLSDAELRAELKQYGLPPGPITDTTRK 31 (44)
T ss_pred CchhHcCHHHHHHHHHHcCCCCCCcCcchHH
Confidence 3789999999999999999999888777764
No 26
>PF10208 Armet: Degradation arginine-rich protein for mis-folding; InterPro: IPR019345 This entry represents Armet proteins (aka mesencephalic astrocyte-derived neurotrophic factor or arginine-rich protein). Armet is a small protein of approximately 170 residues which contains four di-sulphide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress []. Armet from Rattus norvegicus (Rat) selectively promotes the survival of dopaminergic neurons of the ventral mid-brain. It modulates GABAergic transmission to the dopaminergic neurons of the substantia nigra, and enhances spontaneous, as well as evoked, GABAergic inhibitory postsynaptic currents in dopaminergic neurons [].; PDB: 2KVE_A 2KVD_A 2W51_A 2W50_B 2RQY_A.
Probab=25.60 E-value=44 Score=35.80 Aligned_cols=43 Identities=12% Similarity=0.171 Sum_probs=28.3
Q ss_pred cccccchhhhccCHHHHHHHHHhCCCCHHHhhccCchhhhHHHHH
Q 000877 1004 TVTGTDADLRRLSMEAAREVLLKFNVPEEMIAKQTRWHRIAMIRK 1048 (1242)
Q Consensus 1004 ~VTGTDADLRKLSM~eAR~iLrkfGVpEE~IkkLtRWdrIaLVRk 1048 (1242)
++-=+..||.||+.+++|++|..+|++=.- =+-.|+-|..|+.
T Consensus 96 ~idl~~~Dl~KlrVk~LK~iL~~~g~~C~G--C~EK~dfv~ri~e 138 (154)
T PF10208_consen 96 KIDLSTVDLKKLRVKQLKKILDDWGEDCKG--CLEKSDFVRRIEE 138 (154)
T ss_dssp S-SCCCTSTTTTCHHHHHHHHHHHTTT-SS---CSHHHHHHHCHC
T ss_pred ccchhhhHHhhCcHHHHHHHHHHcCCCCCC--ccchHHHHHHHHH
Confidence 444456899999999999999999986321 1223554444443
No 27
>PTZ00044 ubiquitin; Provisional
Probab=25.14 E-value=27 Score=31.41 Aligned_cols=35 Identities=34% Similarity=0.646 Sum_probs=30.8
Q ss_pred CccccccccccccccccccccccccCCCccccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
|....+|+|.|+.+.+..++...+++++..+|++.
T Consensus 37 ~~~~q~L~~~g~~L~d~~~l~~~~i~~~~~i~l~~ 71 (76)
T PTZ00044 37 DVKQIRLIYSGKQMSDDLKLSDYKVVPGSTIHMVL 71 (76)
T ss_pred CHHHeEEEECCEEccCCCcHHHcCCCCCCEEEEEE
Confidence 55678999999999999999999999999888863
No 28
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=24.70 E-value=29 Score=31.54 Aligned_cols=34 Identities=24% Similarity=0.296 Sum_probs=30.4
Q ss_pred CccccccccccccccccccccccccCCCcccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLI 628 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~ 628 (1242)
|....+|.|.|+.+.+..+|...++++++.+|++
T Consensus 35 p~~~q~Li~~Gk~L~D~~tL~~~~i~~~~tl~l~ 68 (74)
T cd01793 35 DVEDQVLLLAGVPLEDDATLGQCGVEELCTLEVA 68 (74)
T ss_pred CHHHEEEEECCeECCCCCCHHHcCCCCCCEEEEE
Confidence 5567789999999999999999999999988885
No 29
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=21.89 E-value=33 Score=31.46 Aligned_cols=36 Identities=39% Similarity=0.452 Sum_probs=30.9
Q ss_pred CCccccccccccccccccccccccccCCCccccccc
Q 000877 594 KPAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 594 ~P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
-|....+|.|.|+.+.+..+|...+|+++..+|++.
T Consensus 33 ip~~~q~L~~~G~~L~d~~tL~~~~i~~g~~l~v~~ 68 (76)
T cd01800 33 MPAGKQKLQYEGIFIKDSNSLAYYNLANGTIIHLQL 68 (76)
T ss_pred CCHHHEEEEECCEEcCCCCcHHHcCCCCCCEEEEEE
Confidence 355678899999999999999999999999888753
No 30
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=21.60 E-value=37 Score=30.12 Aligned_cols=35 Identities=34% Similarity=0.671 Sum_probs=30.6
Q ss_pred CccccccccccccccccccccccccCCCccccccc
Q 000877 595 PAESVKLFYLGKELEDHKSLADQNVRPNSLIHLIR 629 (1242)
Q Consensus 595 P~~~~klfY~gkel~~~~sl~~~~VrP~sl~h~~R 629 (1242)
|....+|+|.|+.+.+..+|...++++++.+|++.
T Consensus 37 ~~~~qrL~~~g~~L~d~~tl~~~~i~~g~~i~l~~ 71 (76)
T cd01806 37 PPQQQRLIYSGKQMNDDKTAADYKLEGGSVLHLVL 71 (76)
T ss_pred ChhhEEEEECCeEccCCCCHHHcCCCCCCEEEEEE
Confidence 55578889999999999999999999999999875
Done!