Query 010207
Match_columns 515
No_of_seqs 160 out of 244
Neff 6.6
Searched_HMMs 46136
Date Thu Mar 28 22:18:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010207.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010207hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05327 RRN3: RNA polymerase 100.0 3E-119 7E-124 987.7 26.9 479 15-514 2-553 (563)
2 KOG2434 RNA polymerase I trans 100.0 2.6E-69 5.6E-74 566.6 25.9 441 12-514 3-469 (500)
3 PF03810 IBN_N: Importin-beta 78.6 11 0.00024 29.8 7.2 41 330-370 14-63 (77)
4 KOG1824 TATA-binding protein-i 70.9 1.1E+02 0.0024 36.5 14.9 137 83-240 171-317 (1233)
5 PF02854 MIF4G: MIF4G domain; 58.8 18 0.0004 33.6 5.3 128 80-218 31-163 (209)
6 PF07560 DUF1539: Domain of Un 54.8 29 0.00062 31.3 5.4 46 330-378 67-112 (126)
7 PF04931 DNA_pol_phi: DNA poly 53.0 36 0.00077 39.9 7.3 30 201-230 604-633 (784)
8 PF04388 Hamartin: Hamartin pr 51.2 1E+02 0.0023 35.5 10.6 136 21-185 16-154 (668)
9 PF12348 CLASP_N: CLASP N term 46.3 1.4E+02 0.0029 28.8 9.3 99 99-210 65-163 (228)
10 smart00543 MIF4G Middle domain 40.5 2.5E+02 0.0054 25.9 9.9 119 84-218 34-155 (200)
11 PF01602 Adaptin_N: Adaptin N 30.8 1.7E+02 0.0037 31.8 7.9 130 78-231 331-465 (526)
12 KOG1077 Vesicle coat complex A 30.3 9.1E+02 0.02 28.4 13.2 155 68-239 405-577 (938)
13 KOG2259 Uncharacterized conser 23.2 6.1E+02 0.013 29.4 10.2 100 102-231 388-490 (823)
14 PF02847 MA3: MA3 domain; Int 23.0 4.6E+02 0.01 22.1 10.2 35 83-118 33-67 (113)
15 PF12074 DUF3554: Domain of un 22.0 2.8E+02 0.0061 28.7 7.3 76 330-408 204-284 (339)
16 KOG1991 Nuclear transport rece 21.5 1.5E+03 0.033 27.5 13.7 206 23-238 282-519 (1010)
17 PF10206 WRW: Mitochondrial F1 21.0 2.9E+02 0.0064 24.1 5.9 61 354-416 37-97 (104)
No 1
>PF05327 RRN3: RNA polymerase I specific transcription initiation factor RRN3; InterPro: IPR007991 This family consists of several eukaryotic proteins which are homologous to the Saccharomyces cerevisiae RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in the S. cerevisiae [] RNA polymerase I complex within the nucleolus. In mammalian cells, the phosphorylation state of Rrn3 regulates rDNA transcription by determining the steady-state concentration of the Rrn3 [].; PDB: 3TJ1_B.
Probab=100.00 E-value=3e-119 Score=987.69 Aligned_cols=479 Identities=36% Similarity=0.599 Sum_probs=353.0
Q ss_pred cccCcCChHHHHHHHHHHHHHhhcCCchHHHHHHHHh-ccCCCCCcchHHHHHHHHHHHHccccccCccchHHHHHHHHc
Q 010207 15 MEDVNISDLELVYHVREALTSVQSGDNDNYNQLVAVM-HLSGRLDPDNRALLETSLKALSGAVSYIDISHHESLLVSIFG 93 (515)
Q Consensus 15 ~~~~~~s~~~~~~~V~~aL~~~~~Gd~~~Y~~L~~~l-~~~~~~~~~~~~~l~~~L~aL~~~Vs~Ld~~~~~~LV~ail~ 93 (515)
++|++||+++++.+|++||+++++||+++|++|+++| .+.+.++++++++|..||++|++|||+||.+ |++||++||+
T Consensus 2 ~~~~~~s~~~~~~~V~~AL~~~~~Gd~~~Y~~L~~~l~~~~~~~d~~~~~~l~~~L~~L~~~Vs~Ld~~-~~~LV~ail~ 80 (563)
T PF05327_consen 2 KNDVEFSDEMYKSFVRSALESHEKGDSSQYDELVEQLSDPSESKDAISVSQLIRWLKALSSCVSLLDSS-CKQLVEAILS 80 (563)
T ss_dssp -------HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHS-TT-TTS--HHHHHHHHHHHHHGGGGG-SC-CHHHHHHHHT
T ss_pred CchhhhCHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcccccCcccccHHHHHHHHHHHHHHHHHhhhH-HHHHHHHHHc
Confidence 5789999999999999999999999999999999999 6777888888999999999999999999976 9999999999
Q ss_pred CCCcCCChhHHHHHHHHHHHHHhcccCcHHHHHHHHhhccCCCcccccccCCCCCc-hhhhhhHHHHHHHHHHHHhHcCC
Q 010207 94 MSMWNYDPDVMDALKGLIISLAASNGKYVDSCLTMLVSNFTPPSYFLDKLKEPHGL-ERKHQVLSRVHAALKSIFDLVPL 172 (515)
Q Consensus 94 ~~~W~~~~~~v~~y~~Fl~~Lvsa~~~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~-~~~~~~~~~~H~~L~~Il~lvP~ 172 (515)
+.||.++++++++|++|+++||||||+|++.|++|||++|.|++.....+ ++.+ .+++++++++|.+|++|+++||+
T Consensus 81 ~~W~~~~~~~v~~y~~Fl~~Lvsa~~~yl~~vl~~LV~~f~p~~~~~~~~--~~~~~~~~~~~~~~vH~~L~~Il~lvP~ 158 (563)
T PF05327_consen 81 LNWLGRDEDFVEAYIQFLINLVSAQPKYLSPVLSMLVKNFIPPPSSIAEW--PGCPPEKRREIYERVHDALQKILRLVPT 158 (563)
T ss_dssp -TGGGS-HHHHHHHHHHHHHHHHH-GGGHHHHHHHHHHGGGS-HHHHHH-----------------HHHHHHHHHHH-GG
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhccCCCcccccc--chhhhhhhhhhHHHHHHHHHHHHHHcCC
Confidence 96558888999999999999999999999999999999999987643322 3333 47788999999999999999999
Q ss_pred ChhhhHHHHHhcCCCCcCccccccchhhhHHHHHHhhhccchhhHHHHHHHHHHHHHHhhcccccc--ccccccccccc-
Q 010207 173 APTRLLPIVVQRMPTVHNKHERLKMIVVYMENTLKLESSAMGELVRSTLLMAVVDRLIDLDMEIGW--DDILHDDFSKG- 249 (515)
Q Consensus 173 a~~~L~~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~~y~~~p~L~~~il~lIi~rli~iDVei~~--ddi~~d~~~~~- 249 (515)
++++|.++|+++|||+++++. .|++|++|+|+|++|+ |+||++||++||+||++|||||+. ||+++++ .++
T Consensus 159 s~~~L~~~l~~~FP~~~~~~~---~~~~Yv~NlL~l~~Y~--P~L~~~Il~lIi~rLi~iDVeiq~~~ddidd~~-~~~~ 232 (563)
T PF05327_consen 159 SPSFLIPILVQNFPHKRKSKD---EHVNYVRNLLRLTEYC--PELRSDILSLIIERLIKIDVEIQIELDDIDDEE-EEDL 232 (563)
T ss_dssp GHHHHHHHHHHTS--TTS-HH---HHHHHHHHHHHHHCC---GGGHHHHHHHHHHHHHHHHHHHHHHHHCH---------
T ss_pred CHHHHHHHHHHcCcCCCCChH---HHHHHHHHHHHHHcch--HHHHHHHHHHHHHHHHHHhcccccCccchhhhh-hhhh
Confidence 999999999999999999984 5599999999999998 999999999999999999996654 6764433 222
Q ss_pred -----------cccccchhhhhhcccccccCCCCCCCchhhcccchhhHHHHHHHHHHHHHHHhhhhccCCc--------
Q 010207 250 -----------IFEMELEDVEEAADDAEQVGDELPSGSLSRKSLSGNLIAELLDSLMVLTFEHLESCEGTGR-------- 310 (515)
Q Consensus 250 -----------if~me~dd~~~~~~d~e~~~de~~~~~~~~~~~~~~~~a~kLD~lm~~lf~~l~~~~~~~~-------- 310 (515)
+|+|++++++++ +.++++..+++..+..+++++++|||+||.++|+|+++|+.+++
T Consensus 233 ~~~~~~~~~~~~~~~d~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~kLD~im~~lf~~l~~~~~~~~~~~~~~~~ 307 (563)
T PF05327_consen 233 FEEEEDDEEDDVFDMDEDDDDDS-----SIDDEDESDEEERRTEDIDEMAEKLDSIMDLLFEYLDSCFTNGSLDEGNADS 307 (563)
T ss_dssp -------------------------------------------HHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHSSTHHH
T ss_pred hhhccCccccccccccccccccc-----ccccccccchhhhhHhhHHHHHHHHHHHHHHHHHHHHHhccCCccchhHHHH
Confidence 333322221111 01112222223445567999999999999999999999876543
Q ss_pred --------------------cceeeeeeeecCCccchhHHHHHHHHHHHhcCCCChhhhhhHHHHHHHHHhhhccCCHHH
Q 010207 311 --------------------LIEFVMFYACALDPENCGLRFATMLADVFVSGLYPPLTRMSAVSYLASFLSRARFLSPCF 370 (515)
Q Consensus 311 --------------------l~~FllFy~cs~~~~~~~~~F~~~L~~~~~~~~~~~~~R~aAaaYLaSflARAk~v~~~~ 370 (515)
+.||||||+||++|++++ +|+++||+++++|++|+++||+||+|||||||||||||.++
T Consensus 308 lf~~Ll~~F~~~ILpT~~sr~vQFl~Fy~~s~~~~~~~-~Fl~~L~~~~~~~~~~~~~R~~A~~YlaSflaRAk~v~~~~ 386 (563)
T PF05327_consen 308 LFNTLLSIFESHILPTHKSRHVQFLLFYFCSLDPELAD-AFLSFLWKIAFDPNQPPVTRQAAAAYLASFLARAKFVPLST 386 (563)
T ss_dssp HHHHHHHHHHHTCCCC-S-SSTTHHHHHHHTTSHHHHH-HHHHHHHHHHH-SSS-HHHHHHHHHHHHHHHHHBTT--HHH
T ss_pred HHHHHHHHHHHHccCCCccchHHHHHHHHHHcCchHHH-HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcCCHHH
Confidence 445999999999999986 99999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhCC----CCCCCchhHHHHHHHHHHHHHhhhccccccCchhhhhhhccc--hhHhhccCCCC
Q 010207 371 IVSLLKRLVDWCLEYCNILGG----DINPKAHRVFYSGCQAIMYVLCFRMRSIMDIPRLKSQLLLMP--LETVLKHDLNP 444 (515)
Q Consensus 371 v~~~l~~L~~w~~~Y~~~~~~----~~~~~~h~~FYs~cQA~~YIfCFR~~dL~~~~~~~~~l~~~~--l~rii~s~LNP 444 (515)
|+.++++|++||++|++++++ ++++++|++|||+|||+|||||||||+|+..++...++++++ |+|+|+|||||
T Consensus 387 v~~~l~~L~~w~~~y~~~~~~~~~~~~~~~~h~~FYs~~QAi~YifcFR~~~l~~~~~~~~~~~~l~~~l~r~v~s~lnP 466 (563)
T PF05327_consen 387 VRSVLSYLCDWLHDYIDEQESSSNAGPDLKRHGVFYSVCQAIFYIFCFRWRDLLASPKDLEWLQSLDKFLQRIVTSKLNP 466 (563)
T ss_dssp HHHHHHHHHHHHHHHHHHHGGGTTSSS-GGGGHHHHHHHHHHHHHHHHHGGGG--B-TTS-BGGGHHHHHHHHHHSTT-H
T ss_pred HHHHHHHHHHHHHHHHHHhccccccCCChhhhhhHHHHHHHHHHHHHHhHHHhccCCCcchHHHHHHHHHHHHhcCCCCC
Confidence 999999999999999998875 347899999999999999999999999997665555555555 99999999999
Q ss_pred cccccHHHHHHHHHHhhhcccceeecccccchhhhhhhh----hccCC-------------------cccCcccCCCCCC
Q 010207 445 LKVCLPSVVSEFLQQSKAARLFTVSETFVFNDLLESELS----RAFGG-------------------LERLDMFFPFDPC 501 (515)
Q Consensus 445 Lk~C~p~VV~~Fa~ia~~~~l~y~~~~~~~~~~~e~~~~----~~~~~-------------------~~~Ld~fFPFDPy 501 (515)
||+|+|+||.+||+||+++|++||+ +++|+|.+ ...|+ .++||+|||||||
T Consensus 467 Lk~C~~~Vv~~Fa~ia~~~~l~yc~------~iie~n~r~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~fFPFDPy 540 (563)
T PF05327_consen 467 LKVCSPSVVREFARIARHLQLVYCY------SIIERNKRSRLSSFRSSSSGMRSRRERPSAAWNESPRQPLDSFFPFDPY 540 (563)
T ss_dssp HHHS-HHHHHHHHHHHHHTTS---H------HHHHHHHHHHHH---------------------HHHHHHHHH--TTS--
T ss_pred cCccCHHHHHHHHHHHHHcCcchHH------HHHHhhhhhhhhhccCcccccccccccccccccccccCcCccCCCCCcc
Confidence 9999999999999999999999997 45666533 22221 1359999999999
Q ss_pred CcccccccccccC
Q 010207 502 LLKKSDRFANATL 514 (515)
Q Consensus 502 ~L~~S~~~I~p~~ 514 (515)
+||+|++||+|+|
T Consensus 541 ~L~~S~~~i~~~Y 553 (563)
T PF05327_consen 541 LLPRSKRFIEPLY 553 (563)
T ss_dssp -SHHHHHHHGGGB
T ss_pred cchhhHhhcchhc
Confidence 9999999999998
No 2
>KOG2434 consensus RNA polymerase I transcription factor [Transcription]
Probab=100.00 E-value=2.6e-69 Score=566.55 Aligned_cols=441 Identities=43% Similarity=0.626 Sum_probs=372.7
Q ss_pred ccccccCcCChHHHHHHHHHHHHHhhcCCchHHHHHHHHhccCCCCCcchHHHHHHHHHHHHccccccCccchHHHHHHH
Q 010207 12 SHEMEDVNISDLELVYHVREALTSVQSGDNDNYNQLVAVMHLSGRLDPDNRALLETSLKALSGAVSYIDISHHESLLVSI 91 (515)
Q Consensus 12 ~~~~~~~~~s~~~~~~~V~~aL~~~~~Gd~~~Y~~L~~~l~~~~~~~~~~~~~l~~~L~aL~~~Vs~Ld~~~~~~LV~ai 91 (515)
++.+++..++++..+.-|+.++.....|++..|.++..++.-.+. ..+..+++..+++.|++.+.+||...|..|+..+
T Consensus 3 ~~~v~~~~~~~~~~v~t~~~~~~s~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~l~~~~~~ida~~~~~l~~i~ 81 (500)
T KOG2434|consen 3 SESVDKKDLSDSTLVPTVRKALTSFESGDSDLYSRLVQVMLLKKN-ALDQVAQLETLLKLLSQFVACIDALHHNTLLLIL 81 (500)
T ss_pred chhhhhhhhccccccchhhhhhccccccchHhhhhHHHHHhhhhc-cCcHHHHHHHHHHHHHhhHHhhcccchhHHHHHH
Confidence 345678889999999999999999999999999999998883222 3366788888999999999999988777766555
Q ss_pred HcCCCcCCChhHHHHHHHHHHHHHhcccCcHHHHHHHHhhccCCCcccccccCCCCCchhhhhhHHHHHHHHHHHHhHcC
Q 010207 92 FGMSMWNYDPDVMDALKGLIISLAASNGKYVDSCLTMLVSNFTPPSYFLDKLKEPHGLERKHQVLSRVHAALKSIFDLVP 171 (515)
Q Consensus 92 l~~~~W~~~~~~v~~y~~Fl~~Lvsa~~~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~~~~~~~~~~~H~~L~~Il~lvP 171 (515)
. .|..++.++.++..|++.|++++++|+.+|+.|+|.+| |++...+ ..+.++++|.+|++|+++||
T Consensus 82 ~---~~~~~~sv~~~~~~~l~~l~~~~~~~l~~c~~~lv~~~-~~~~v~~----------~~~~fe~~H~al~~v~r~vP 147 (500)
T KOG2434|consen 82 S---LRSHRGSVIEALLNLLISLAVTSGKFLSPCLSMLVSNL-SQPSVTE----------QIEHFERAHAALKYILRLVP 147 (500)
T ss_pred H---hhcCCchHHHHHHHHHHHHHHhCCchHHHHHHHHHHhC-Ccchhhh----------hHHHHHHHHHHHHHHHHHcc
Confidence 4 46888899999999999999999999999999999999 7765332 26789999999999999999
Q ss_pred CChhhhHHHHHhcCCCCcCccccccchhhhHHHHHHhhhccchhhHHHHHHHHHHHHHHhhccccccccccccccccccc
Q 010207 172 LAPTRLLPIVVQRMPTVHNKHERLKMIVVYMENTLKLESSAMGELVRSTLLMAVVDRLIDLDMEIGWDDILHDDFSKGIF 251 (515)
Q Consensus 172 ~a~~~L~~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~~y~~~p~L~~~il~lIi~rli~iDVei~~ddi~~d~~~~~if 251 (515)
++|++|.|+|.+.||+++++...+ ++|++|+|++.+|. |.++.+||++|++|++++||++.+|| ++.|.|
T Consensus 148 ~~~~~l~~~L~~~~p~~~k~~~~~---~~YvsNll~l~~y~--~~l~~~ile~vierl~~~Dv~~~~dd-----s~~~~~ 217 (500)
T KOG2434|consen 148 LAPSFLLPILAQVMPKKDKKDRTL---VTYVSNLLKLENYG--PSIGKDILEAVIERLIDLDVEIETDD-----SSSGMF 217 (500)
T ss_pred CchhhHHHHHHHHccccccchhhH---HHHHhHHHHHHhhh--hHHHHHHHHHHHHHHHhhceeeeecc-----cccccc
Confidence 999999999999999999998666 99999999999985 99999999999999999999887776 677899
Q ss_pred cccchhhhhhcccccccCCCCCCCchhhcccchhhHHHHHHHHHHHHHHHhhhhccCCccc-------------------
Q 010207 252 EMELEDVEEAADDAEQVGDELPSGSLSRKSLSGNLIAELLDSLMVLTFEHLESCEGTGRLI------------------- 312 (515)
Q Consensus 252 ~me~dd~~~~~~d~e~~~de~~~~~~~~~~~~~~~~a~kLD~lm~~lf~~l~~~~~~~~l~------------------- 312 (515)
+|+.++..+.+--+ +++-.. ..+-..++..++.+||.+|...|.|++.|.++++++
T Consensus 218 d~~~~~~~~~e~~~---G~~~~~--~~~~t~~~~~~s~~ld~~l~~~~~~l~s~~~~~~l~~vf~~l~~~fe~~vL~t~~ 292 (500)
T KOG2434|consen 218 DMETDDAEELETFS---GMERNQ--ANPVTIGITRLSTLLDKLLVESFRHLESCLNDGSLDEVFNTLLNEFENTVLNTVA 292 (500)
T ss_pred ccccchHHHHHhhc---cccccc--cchhhhhhHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHhHHHhhhHHHH
Confidence 99887766543110 111111 111234678899999999999999999998887544
Q ss_pred ----eeeeeeeecCCccchhHHHHHHHHHHHhcCCCChhhhhhHHHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHhhh
Q 010207 313 ----EFVMFYACALDPENCGLRFATMLADVFVSGLYPPLTRMSAVSYLASFLSRARFLSPCFIVSLLKRLVDWCLEYCNI 388 (515)
Q Consensus 313 ----~FllFy~cs~~~~~~~~~F~~~L~~~~~~~~~~~~~R~aAaaYLaSflARAk~v~~~~v~~~l~~L~~w~~~Y~~~ 388 (515)
||+|||+||+++++ +++|++.||++.++|+.|..+||+|+ +|+++++.|++.|+.+
T Consensus 293 ~~~~qf~~fy~~sld~~~-~~~fL~~L~~v~~~~~~pa~tr~~a~-------------------~~l~~l~~w~~~Yv~~ 352 (500)
T KOG2434|consen 293 TRFVQFLIFYACSLDETL-EEAFLSKLWKVCLSPNNPAETRQAAA-------------------TCLELLVIWLDIYVIE 352 (500)
T ss_pred hhhhheEEEeecccchHH-HHHHHHHHHHHHhCcccHHHHHhhhh-------------------HHHHHHHHHHHHHHHh
Confidence 49999999999775 56999999999999999999999998 2999999999999999
Q ss_pred hCCCCCC---CchhHHHHHHHHHHHHHhhhccccccCchhhhhhhccchhHhhccCCCCcccccHHHHHHHHHHhhhccc
Q 010207 389 LGGDINP---KAHRVFYSGCQAIMYVLCFRMRSIMDIPRLKSQLLLMPLETVLKHDLNPLKVCLPSVVSEFLQQSKAARL 465 (515)
Q Consensus 389 ~~~~~~~---~~h~~FYs~cQA~~YIfCFR~~dL~~~~~~~~~l~~~~l~rii~s~LNPLk~C~p~VV~~Fa~ia~~~~l 465 (515)
++.+..+ .+|++|||+|||+||+|||||+.++..++..+--+.++++|+++|+|||||+|+|+||.+|+++|+++||
T Consensus 353 ~~~~~~~~g~~~h~~fysgcqa~~y~f~fR~~~~~~~~~~~~~e~~~~f~riv~s~lnPlk~c~~~vv~~F~~ia~~~~l 432 (500)
T KOG2434|consen 353 LSKGTKPIGLMKHSVFYSGCQAEFYRFCFRYRHLVKDDDSEELEQEMEFERIVSSKLNPLKYCSPSVVLQFAAIANALTL 432 (500)
T ss_pred hcccccccchhhcccccccCcceeeeeeeeehhhcccCchhhhccccchhhhhccccccccccCHHHHHHHHhhcCcceE
Confidence 9886666 9999999999999999999999999987765422458999999999999999999999999999999999
Q ss_pred ceeecccccchhhhhhhhhccCCcccCcccCCCCCCCcccccccccccC
Q 010207 466 FTVSETFVFNDLLESELSRAFGGLERLDMFFPFDPCLLKKSDRFANATL 514 (515)
Q Consensus 466 ~y~~~~~~~~~~~e~~~~~~~~~~~~Ld~fFPFDPy~L~~S~~~I~p~~ 514 (515)
+||++.+++.+..+....+++|| |.|++|+.+|.|++
T Consensus 433 ~~~~~iie~~~~~~~~~~r~~~d------------~~lk~ss~~~~p~~ 469 (500)
T KOG2434|consen 433 FYCFSIIEFNDLQISELSRAFGD------------CLLKESSSFISPNF 469 (500)
T ss_pred EEEchhhhccchhhhhhhhhccc------------hhhhhcccccCchh
Confidence 99985443333323333444443 99999999999986
No 3
>PF03810 IBN_N: Importin-beta N-terminal domain; InterPro: IPR001494 Karyopherins are a group of proteins involved in transporting molecules through the pores of the nuclear envelope. Karyopherins, which may act as importins or exportins, are part of the Importin-beta super-family, which all share a similar three-dimensional structure. Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins [, ], which is important for importin-beta mediated transport. Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. As a result, the N-terminal auto-inhibitory region on importin-alpha is free to loop back and bind to the major NLS-binding site, causing the cargo to be released []. There are additional release factors as well. This entry represents the N-terminal domain of karyopherins that is important for the binding of the Ran protein []. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport; PDB: 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 1IBR_D 1QGR_A 3LWW_A 1F59_A 2Q5D_A ....
Probab=78.59 E-value=11 Score=29.84 Aligned_cols=41 Identities=20% Similarity=0.174 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhcCCCChhhhhhHHHHHHHHHhhh-c--------cCCHHH
Q 010207 330 RFATMLADVFVSGLYPPLTRMSAVSYLASFLSRA-R--------FLSPCF 370 (515)
Q Consensus 330 ~F~~~L~~~~~~~~~~~~~R~aAaaYLaSflARA-k--------~v~~~~ 370 (515)
.|...|++++.+++.+..+|+.|+-||=-.|.|- + .+|.+.
T Consensus 14 ~~~~~l~~il~~~~~~~~~R~~A~i~LKn~I~~~W~~~~~~~~~~~~~~~ 63 (77)
T PF03810_consen 14 GFWQYLLQILSSNSQDPEVRQLAAILLKNLIKKNWSPSKQKGWSQLPEEE 63 (77)
T ss_dssp CHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHSGGHHHHHHHHGSSHHH
T ss_pred hHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHcCchhhccCCCCCCHHH
Confidence 4889999999999999999999999999999988 6 677764
No 4
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=70.89 E-value=1.1e+02 Score=36.52 Aligned_cols=137 Identities=12% Similarity=0.143 Sum_probs=73.3
Q ss_pred chHHHHHHHHcCCCcCC-ChhHHHHHHHHHHHHHhcccCcH-HHHHHHHhhccCCCcccccccCCCCCchhhhhhHHHHH
Q 010207 83 HHESLLVSIFGMSMWNY-DPDVMDALKGLIISLAASNGKYV-DSCLTMLVSNFTPPSYFLDKLKEPHGLERKHQVLSRVH 160 (515)
Q Consensus 83 ~~~~LV~ail~~~~W~~-~~~~v~~y~~Fl~~Lvsa~~~y~-~~vl~~LV~~F~p~~~~~~~~~~~~~~~~~~~~~~~~H 160 (515)
.|..+.+.++ +.... +..+++.-+..|+.|+++-+..+ ..+..-|.+++.++.. -......-
T Consensus 171 fh~~il~~l~--~ql~s~R~aVrKkai~~l~~la~~~~~~ly~~li~~Ll~~L~~~~q--------------~~~~rt~I 234 (1233)
T KOG1824|consen 171 FHLSILKCLL--PQLQSPRLAVRKKAITALGHLASSCNRDLYVELIEHLLKGLSNRTQ--------------MSATRTYI 234 (1233)
T ss_pred hHHHHHHHHh--hcccChHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCCCc--------------hHHHHHHH
Confidence 5788887776 34544 34599999999999998876554 5666777777765422 01112233
Q ss_pred HHHHHHHhH----cCCChhhhHHHHHhcCCCCcCccccccchhhhHHHHHH-hhhccchhhHHHHHHHHHHHHHH---hh
Q 010207 161 AALKSIFDL----VPLAPTRLLPIVVQRMPTVHNKHERLKMIVVYMENTLK-LESSAMGELVRSTLLMAVVDRLI---DL 232 (515)
Q Consensus 161 ~~L~~Il~l----vP~a~~~L~~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~-l~~y~~~p~L~~~il~lIi~rli---~i 232 (515)
.+|..|.+- +-+..+.+.|.+.++=-......+.+ ..|.--.|. ...|| |.=-..+|..|++-++ .-
T Consensus 235 q~l~~i~r~ag~r~~~h~~~ivp~v~~y~~~~e~~dDEL---rE~~lQale~fl~rc--p~ei~p~~pei~~l~l~yisY 309 (1233)
T KOG1824|consen 235 QCLAAICRQAGHRFGSHLDKIVPLVADYCNKIEEDDDEL---REYCLQALESFLRRC--PKEILPHVPEIINLCLSYISY 309 (1233)
T ss_pred HHHHHHHHHhcchhhcccchhhHHHHHHhcccccCcHHH---HHHHHHHHHHHHHhC--hhhhcccchHHHHHHHHHhcc
Confidence 334444332 23344455565555443333333334 444333332 23344 6555555555555554 45
Q ss_pred cccccccc
Q 010207 233 DMEIGWDD 240 (515)
Q Consensus 233 DVei~~dd 240 (515)
|=|..-|+
T Consensus 310 DPNy~yd~ 317 (1233)
T KOG1824|consen 310 DPNYNYDT 317 (1233)
T ss_pred CCCCCCCC
Confidence 55555443
No 5
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=58.76 E-value=18 Score=33.63 Aligned_cols=128 Identities=13% Similarity=0.126 Sum_probs=78.3
Q ss_pred CccchHHHHHHHHcCCCcCCChhHHHHHHHHHHHHHhccc-CcHHHHHHHHhhccCCCcccccccCCCCCc-hhhhhhHH
Q 010207 80 DISHHESLLVSIFGMSMWNYDPDVMDALKGLIISLAASNG-KYVDSCLTMLVSNFTPPSYFLDKLKEPHGL-ERKHQVLS 157 (515)
Q Consensus 80 d~~~~~~LV~ail~~~~W~~~~~~v~~y~~Fl~~Lvsa~~-~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~-~~~~~~~~ 157 (515)
+......+++.|+. .|...+.+...|.+++..|....+ .+...+++.+.+.|..+.. .... ........
T Consensus 31 ~~~~~~~i~~~i~~--~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~~f~~~~~-------~~~~~~~~~~~~~ 101 (209)
T PF02854_consen 31 DPETLKEIVKLIFE--KAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQEEFEERYS-------NEELEENRQSSKQ 101 (209)
T ss_dssp CHHHHHHHHHHHHH--HHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHT--------HHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHhh--hhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHhhh-------hhhHHHHHHHHHH
Confidence 33445678888875 577778999999999999999999 8999999999999985210 0000 11222335
Q ss_pred HHHHHHHHHHhHcCC---ChhhhHHHHHhcCCCCcCccccccchhhhHHHHHHhhhccchhhHH
Q 010207 158 RVHAALKSIFDLVPL---APTRLLPIVVQRMPTVHNKHERLKMIVVYMENTLKLESSAMGELVR 218 (515)
Q Consensus 158 ~~H~~L~~Il~lvP~---a~~~L~~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~~y~~~p~L~ 218 (515)
+....++.|..++-. ..+.+..++..-......... .......++-++.+..++ |+.++
T Consensus 102 ~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~-~~~~~~~ie~~~~lL~~~-G~~l~ 163 (209)
T PF02854_consen 102 RRRGNIRFLAELFNFGVVSEKIIFDILRELLSDGTDECQ-PPPDEENIECLCTLLKTC-GKKLE 163 (209)
T ss_dssp HHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSHHCC-HHTCHHHHHHHHHHHHHH-HHHHH
T ss_pred HHhhhhhHHHhhHhhccccchhHHHHHHHHHhccccccc-CCCcHhHHHHHHHHHHHH-HHHHh
Confidence 566677766666543 455666666554443322000 000145666666666553 56666
No 6
>PF07560 DUF1539: Domain of Unknown Function (DUF1539); InterPro: IPR011436 This domain is found in a small number of Chlamydia proteins of unknown function. It occurs together with IPR013044 from INTERPRO.
Probab=54.77 E-value=29 Score=31.34 Aligned_cols=46 Identities=15% Similarity=0.301 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhcCCCChhhhhhHHHHHHHHHhhhccCCHHHHHHHHHHH
Q 010207 330 RFATMLADVFVSGLYPPLTRMSAVSYLASFLSRARFLSPCFIVSLLKRL 378 (515)
Q Consensus 330 ~F~~~L~~~~~~~~~~~~~R~aAaaYLaSflARAk~v~~~~v~~~l~~L 378 (515)
..+-.|...+.||+.|...++.++.|+|||=-|++ +.-+..+.+.|
T Consensus 67 ~~m~~l~~aL~dp~Is~erK~~~l~yIaSya~~c~---pTW~evi~rel 112 (126)
T PF07560_consen 67 STMHQLIKALQDPTISKERKREALNYIASYADACP---PTWVEVIFREL 112 (126)
T ss_pred HHHHHHHHHhcCCCCChHHHHHHHHHHHHHhccCc---hhHHHHHHHHH
Confidence 45556777788999999999999999999976543 44344444333
No 7
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=52.95 E-value=36 Score=39.91 Aligned_cols=30 Identities=13% Similarity=0.045 Sum_probs=15.4
Q ss_pred hHHHHHHhhhccchhhHHHHHHHHHHHHHH
Q 010207 201 YMENTLKLESSAMGELVRSTLLMAVVDRLI 230 (515)
Q Consensus 201 Yv~NlL~l~~y~~~p~L~~~il~lIi~rli 230 (515)
++|.+-...=-.+||.+...-|.+|++-|-
T Consensus 604 llR~~~~~vf~~~~~~~t~~~l~~ll~vl~ 633 (784)
T PF04931_consen 604 LLRKVSEQVFEAFCPHLTESGLQLLLDVLD 633 (784)
T ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHhc
Confidence 334333333333456666666666666553
No 8
>PF04388 Hamartin: Hamartin protein; InterPro: IPR007483 This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein IPR003913 from INTERPRO. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterised by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation in either TSC1 or TSC2 tumour suppressor genes. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin IPR003913 from INTERPRO. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking [].
Probab=51.21 E-value=1e+02 Score=35.47 Aligned_cols=136 Identities=18% Similarity=0.190 Sum_probs=83.3
Q ss_pred ChHHHHHHHHHHHHHhhcCCc--hHHHHHHHHhccCCCCCcchHHHHHHHHHHHHccccccCccchHHHHHHHHcCCCcC
Q 010207 21 SDLELVYHVREALTSVQSGDN--DNYNQLVAVMHLSGRLDPDNRALLETSLKALSGAVSYIDISHHESLLVSIFGMSMWN 98 (515)
Q Consensus 21 s~~~~~~~V~~aL~~~~~Gd~--~~Y~~L~~~l~~~~~~~~~~~~~l~~~L~aL~~~Vs~Ld~~~~~~LV~ail~~~~W~ 98 (515)
+|....++|+.++.+....+. .--+.|++-+-.... .+ .+..|. .+....+..|...| ..|-
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~y~~~t~s------~~---~~~il~----~~~~P~~K~~~~~l---~~~~ 79 (668)
T PF04388_consen 16 NDLSVLEEIKALLQELLNSDREPWLVNGLVDYYLSTNS------QR---ALEILV----GVQEPHDKHLFDKL---NDYF 79 (668)
T ss_pred CchhhHHHHHHHHHHHhhccchHHHHHHHHHHHhhcCc------HH---HHHHHH----hcCCccHHHHHHHH---HHHH
Confidence 455577888888888876653 344555555433221 11 123333 22223335555443 2465
Q ss_pred CChhHHHHHHHHHHHHHhcccCcHHHHHH-HHhhccCCCcccccccCCCCCchhhhhhHHHHHHHHHHHHhHcCCChhhh
Q 010207 99 YDPDVMDALKGLIISLAASNGKYVDSCLT-MLVSNFTPPSYFLDKLKEPHGLERKHQVLSRVHAALKSIFDLVPLAPTRL 177 (515)
Q Consensus 99 ~~~~~v~~y~~Fl~~Lvsa~~~y~~~vl~-~LV~~F~p~~~~~~~~~~~~~~~~~~~~~~~~H~~L~~Il~lvP~a~~~L 177 (515)
..++.+-.-+.+|+.+|..||.|+..++. -|+.++.--- ..+....-++.||.-|+.++|..|+.+
T Consensus 80 ~~~~~Rl~~L~Ll~~~v~~qp~~l~~i~~t~Lf~~LLk~L-------------~~D~~~~~~~~al~~LimlLP~ip~~l 146 (668)
T PF04388_consen 80 VKPSYRLQALTLLGHFVRSQPPWLYKILQTPLFKSLLKCL-------------QFDTSITVVSSALLVLIMLLPHIPSSL 146 (668)
T ss_pred cCchhHHHHHHHHHHHHhcCCchHHHHhcChhHHHHHHHH-------------hhcccHHHHHHHHHHHHHHhccccchh
Confidence 66778888889999999999999987663 3444332000 011223568999999999999999888
Q ss_pred HHHHHhcC
Q 010207 178 LPIVVQRM 185 (515)
Q Consensus 178 ~~~l~~~F 185 (515)
.+.|-.-|
T Consensus 147 ~~~L~~Lf 154 (668)
T PF04388_consen 147 GPHLPDLF 154 (668)
T ss_pred hHHHHHHH
Confidence 88776544
No 9
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=46.32 E-value=1.4e+02 Score=28.75 Aligned_cols=99 Identities=16% Similarity=0.185 Sum_probs=59.1
Q ss_pred CChhHHHHHHHHHHHHHhcccCcHHHHHHHHhhccCCCcccccccCCCCCchhhhhhHHHHHHHHHHHHhHcCCChhhhH
Q 010207 99 YDPDVMDALKGLIISLAASNGKYVDSCLTMLVSNFTPPSYFLDKLKEPHGLERKHQVLSRVHAALKSIFDLVPLAPTRLL 178 (515)
Q Consensus 99 ~~~~~v~~y~~Fl~~Lvsa~~~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~~~~~~~~~~~H~~L~~Il~lvP~a~~~L~ 178 (515)
.+..+++.-+.++..|+..-+..+.+.+..++..+..--. +.+..+.+.++.+|..|.+.+|..+..+.
T Consensus 65 ~Rs~v~~~A~~~l~~l~~~l~~~~~~~~~~~l~~Ll~~~~-----------~~~~~i~~~a~~~L~~i~~~~~~~~~~~~ 133 (228)
T PF12348_consen 65 LRSKVSKTACQLLSDLARQLGSHFEPYADILLPPLLKKLG-----------DSKKFIREAANNALDAIIESCSYSPKILL 133 (228)
T ss_dssp H---HHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHHGGG--------------HHHHHHHHHHHHHHHTTS-H--HHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHc-----------cccHHHHHHHHHHHHHHHHHCCcHHHHHH
Confidence 3445777777888888777666666666555554432110 12335668899999999999997777889
Q ss_pred HHHHhcCCCCcCccccccchhhhHHHHHHhhh
Q 010207 179 PIVVQRMPTVHNKHERLKMIVVYMENTLKLES 210 (515)
Q Consensus 179 ~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~~ 210 (515)
+.+....-|++..... .-..|+.+++.-..
T Consensus 134 ~~l~~~~~~Kn~~vR~--~~~~~l~~~l~~~~ 163 (228)
T PF12348_consen 134 EILSQGLKSKNPQVRE--ECAEWLAIILEKWG 163 (228)
T ss_dssp HHHHHHTT-S-HHHHH--HHHHHHHHHHTT--
T ss_pred HHHHHHHhCCCHHHHH--HHHHHHHHHHHHcc
Confidence 9999999987644321 12567777766543
No 10
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=40.48 E-value=2.5e+02 Score=25.89 Aligned_cols=119 Identities=17% Similarity=0.152 Sum_probs=72.5
Q ss_pred hHHHHHHHHcCCCcCCChhHHHHHHHHHHHHHhcccCcHHHHHHHHhhccCCCcccccccCCCCCchhhhhhHHHHHHHH
Q 010207 84 HESLLVSIFGMSMWNYDPDVMDALKGLIISLAASNGKYVDSCLTMLVSNFTPPSYFLDKLKEPHGLERKHQVLSRVHAAL 163 (515)
Q Consensus 84 ~~~LV~ail~~~~W~~~~~~v~~y~~Fl~~Lvsa~~~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~~~~~~~~~~~H~~L 163 (515)
-..+++.++. .|...+.++..|..++..|....+.+...+++.++..|..... ..+.....+....+
T Consensus 34 ~~~l~~~i~~--~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~~~~f~~~~e-----------~~~~~~~~~~~~~i 100 (200)
T smart00543 34 RKYILELIFE--KAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEFEKGLE-----------SEEESDKQRRLGLV 100 (200)
T ss_pred HHHHHHHHHH--HHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHHHhhhhHHhHH
Confidence 4577777775 5777788999999999999998899999999999998874211 00111223445555
Q ss_pred HHHHhHcC---CChhhhHHHHHhcCCCCcCccccccchhhhHHHHHHhhhccchhhHH
Q 010207 164 KSIFDLVP---LAPTRLLPIVVQRMPTVHNKHERLKMIVVYMENTLKLESSAMGELVR 218 (515)
Q Consensus 164 ~~Il~lvP---~a~~~L~~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~~y~~~p~L~ 218 (515)
+.|..++. ...+.+..++..-...-..+... .....++-++.+..++ |+.+.
T Consensus 101 ~fl~eL~~~~~i~~~~i~~~l~~ll~~~~~~~~~--~~~~~ve~l~~lL~~~-G~~l~ 155 (200)
T smart00543 101 RFLGELYNFQVLTSKIILELLKELLNDLTKLDPP--RSDFSVECLLSLLPTC-GKDLE 155 (200)
T ss_pred HHHHHHHHcccCcHHHHHHHHHHHHhccCCCCCC--CcHHHHHHHHHHHHHh-hHHHc
Confidence 55554443 34456677776666543322100 0134556666665554 44444
No 11
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=30.75 E-value=1.7e+02 Score=31.80 Aligned_cols=130 Identities=14% Similarity=0.196 Sum_probs=82.3
Q ss_pred ccCccchHHHHHHHHcCCCcCCChhHHHHHHHHHHHHHhcccCcHHHHHHHHhhccCCCcccccccCCCCCchhhhhhHH
Q 010207 78 YIDISHHESLLVSIFGMSMWNYDPDVMDALKGLIISLAASNGKYVDSCLTMLVSNFTPPSYFLDKLKEPHGLERKHQVLS 157 (515)
Q Consensus 78 ~Ld~~~~~~LV~ail~~~~W~~~~~~v~~y~~Fl~~Lvsa~~~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~~~~~~~~~ 157 (515)
..+..-...+|+.+++.-.....+++.+..+.-++.++...+.-...+++.+++-+..... .+..
T Consensus 331 l~~~~n~~~Il~eL~~~l~~~~d~~~~~~~i~~I~~la~~~~~~~~~~v~~l~~ll~~~~~---------------~~~~ 395 (526)
T PF01602_consen 331 LANESNVKEILDELLKYLSELSDPDFRRELIKAIGDLAEKFPPDAEWYVDTLLKLLEISGD---------------YVSN 395 (526)
T ss_dssp H--HHHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHGSSHHHHHHHHHHHHHCTGG---------------GCHC
T ss_pred cccccchhhHHHHHHHHHHhccchhhhhhHHHHHHHHHhccCchHHHHHHHHHHhhhhccc---------------cccc
Confidence 3343434567777776421233556999999999999999998888888888886663321 0112
Q ss_pred HHHHHHHHHHhHcCCChhhhHHHHHhcCCCCcCccccccchhhhHHHHHHhhhccchhhHHH-----HHHHHHHHHHHh
Q 010207 158 RVHAALKSIFDLVPLAPTRLLPIVVQRMPTVHNKHERLKMIVVYMENTLKLESSAMGELVRS-----TLLMAVVDRLID 231 (515)
Q Consensus 158 ~~H~~L~~Il~lvP~a~~~L~~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~~y~~~p~L~~-----~il~lIi~rli~ 231 (515)
.+-..+..++.-.|.........+.+.++.... ....+.++|+.+- |+..... +++..++++...
T Consensus 396 ~~~~~i~~ll~~~~~~~~~~l~~L~~~l~~~~~--------~~~~~~~~wilGE-y~~~~~~~~~~~~~~~~l~~~~~~ 465 (526)
T PF01602_consen 396 EIINVIRDLLSNNPELREKILKKLIELLEDISS--------PEALAAAIWILGE-YGELIENTESAPDILRSLIENFIE 465 (526)
T ss_dssp HHHHHHHHHHHHSTTTHHHHHHHHHHHHTSSSS--------HHHHHHHHHHHHH-HCHHHTTTTHHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHhhcChhhhHHHHHHHHHHHHHhhH--------HHHHHHHHhhhcc-cCCcccccccHHHHHHHHHHhhcc
Confidence 233445556677898888888888888887222 3457888888764 4444443 566666655543
No 12
>KOG1077 consensus Vesicle coat complex AP-2, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.26 E-value=9.1e+02 Score=28.36 Aligned_cols=155 Identities=12% Similarity=0.135 Sum_probs=83.9
Q ss_pred HHHHHHccccccCccchHHHHH--HHHcCCCcCCChhHHHHHHHHHHHHHhcccCcHH-HHHHHHhhccCCCcccccccC
Q 010207 68 SLKALSGAVSYIDISHHESLLV--SIFGMSMWNYDPDVMDALKGLIISLAASNGKYVD-SCLTMLVSNFTPPSYFLDKLK 144 (515)
Q Consensus 68 ~L~aL~~~Vs~Ld~~~~~~LV~--ail~~~~W~~~~~~v~~y~~Fl~~Lvsa~~~y~~-~vl~~LV~~F~p~~~~~~~~~ 144 (515)
.+..|-+.....|..--+.+|- |||. .....+-. =|+.-+.+|..--|.|.+ .|-.-+|+=.+....++
T Consensus 405 IV~elLqYL~tAd~sireeivlKvAILa-EKyAtDy~---WyVdviLqLiriagd~vsdeVW~RvvQiVvNnedlq---- 476 (938)
T KOG1077|consen 405 IVAELLQYLETADYSIREEIVLKVAILA-EKYATDYS---WYVDVILQLIRIAGDYVSDEVWYRVVQIVVNNEDLQ---- 476 (938)
T ss_pred HHHHHHHHHhhcchHHHHHHHHHHHHHH-HHhcCCcc---hhHHHHHHHHHHhcccccHHHHHHhheeEecchhhh----
Confidence 4555555555566443344433 5664 23322222 144444455554556664 33344444222221111
Q ss_pred CCCCchhh-hhh--HHHHHHHHHHHHhHc------------CCChhhhHHHHHhcCCCCcCccccccchhhhHHHHHHhh
Q 010207 145 EPHGLERK-HQV--LSRVHAALKSIFDLV------------PLAPTRLLPIVVQRMPTVHNKHERLKMIVVYMENTLKLE 209 (515)
Q Consensus 145 ~~~~~~~~-~~~--~~~~H~~L~~Il~lv------------P~a~~~L~~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~ 209 (515)
+...++ .+- -..+|+.+-+.-.++ -.+|..+..+|.++|+-..-.+. .--+.-.+++.
T Consensus 477 --~yaak~~fe~Lq~~a~hE~mVKvggyiLGEfg~LIa~~prss~~~qFsllh~K~~~~s~~tr-----~lLLtTyiKl~ 549 (938)
T KOG1077|consen 477 --GYAAKRLFEYLQKPACHENMVKVGGYILGEFGNLIADDPRSSPAVQFSLLHEKLHLCSPVTR-----ALLLTTYIKLI 549 (938)
T ss_pred --HHHHHHHHHHHhhhHHHHHHHHhhhhhhhhhhhhhcCCCCCChHHHHHHHHHHhccCChhHH-----HHHHHHHHHHH
Confidence 111111 111 135777765543333 35788999999999996554442 33334444555
Q ss_pred hccchhhHHHHHHHHHHHHHHhhccccccc
Q 010207 210 SSAMGELVRSTLLMAVVDRLIDLDMEIGWD 239 (515)
Q Consensus 210 ~y~~~p~L~~~il~lIi~rli~iDVei~~d 239 (515)
.-. |+++..|+..-=...--+|||+|-.
T Consensus 550 nl~--PEi~~~v~~vFq~~~n~~D~ElQqR 577 (938)
T KOG1077|consen 550 NLF--PEIKSNVQKVFQLYSNLIDVELQQR 577 (938)
T ss_pred hhC--hhhhHHHHHHHHhhcccCCHHHHHH
Confidence 555 9999999998877777799999863
No 13
>KOG2259 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.20 E-value=6.1e+02 Score=29.42 Aligned_cols=100 Identities=21% Similarity=0.174 Sum_probs=61.5
Q ss_pred hHHHHHHHHHHHHHhcccCcHHHHHHHHhhccCCCcccccccCCCCCchhhhhhHHHHHHHHHHHHhHcCCCh---hhhH
Q 010207 102 DVMDALKGLIISLAASNGKYVDSCLTMLVSNFTPPSYFLDKLKEPHGLERKHQVLSRVHAALKSIFDLVPLAP---TRLL 178 (515)
Q Consensus 102 ~~v~~y~~Fl~~Lvsa~~~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~~~~~~~~~~~H~~L~~Il~lvP~a~---~~L~ 178 (515)
+++++-+.=++.|+.+.|.|...++.-||..|...- +.+....-.+|..|...+-.-. ..++
T Consensus 388 EVR~AAV~Sl~~La~ssP~FA~~aldfLvDMfNDE~---------------~~VRL~ai~aL~~Is~~l~i~eeql~~il 452 (823)
T KOG2259|consen 388 EVRRAAVASLCSLATSSPGFAVRALDFLVDMFNDEI---------------EVVRLKAIFALTMISVHLAIREEQLRQIL 452 (823)
T ss_pred HHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHhccHH---------------HHHHHHHHHHHHHHHHHheecHHHHHHHH
Confidence 367788888999999999999999999999987321 2222333444454444432222 2334
Q ss_pred HHHHhcCCCCcCccccccchhhhHHHHHHhhhccchhhHHHHHHHHHHHHHHh
Q 010207 179 PIVVQRMPTVHNKHERLKMIVVYMENTLKLESSAMGELVRSTLLMAVVDRLID 231 (515)
Q Consensus 179 ~~l~~~FP~~~~~~~~~~~h~~Yv~NlL~l~~y~~~p~L~~~il~lIi~rli~ 231 (515)
..|....|.. ..=+|+||..+.+. ..+.+.+.+.+|++
T Consensus 453 ~~L~D~s~dv----------Re~l~elL~~~~~~-----d~~~i~m~v~~lL~ 490 (823)
T KOG2259|consen 453 ESLEDRSVDV----------REALRELLKNARVS-----DLECIDMCVAHLLK 490 (823)
T ss_pred HHHHhcCHHH----------HHHHHHHHHhcCCC-----cHHHHHHHHHHHHH
Confidence 4444444421 34567777777653 44566666666664
No 14
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=22.99 E-value=4.6e+02 Score=22.06 Aligned_cols=35 Identities=11% Similarity=0.158 Sum_probs=25.2
Q ss_pred chHHHHHHHHcCCCcCCChhHHHHHHHHHHHHHhcc
Q 010207 83 HHESLLVSIFGMSMWNYDPDVMDALKGLIISLAASN 118 (515)
Q Consensus 83 ~~~~LV~ail~~~~W~~~~~~v~~y~~Fl~~Lvsa~ 118 (515)
.|..+|..++.. -...++...+.|..++..|+..+
T Consensus 33 ~~~~vv~~~l~~-~le~~~~~r~~~~~Ll~~L~~~~ 67 (113)
T PF02847_consen 33 QHHEVVKVILEC-ALEEKKSYREYYSKLLSHLCKRK 67 (113)
T ss_dssp GHHHHHHHHHHH-HHTSSHHHHHHHHHHHHHHHHTT
T ss_pred cHHHHHHHHHHH-HhhccHHHHHHHHHHHHHHHhcC
Confidence 456777777763 45566778888888888887654
No 15
>PF12074 DUF3554: Domain of unknown function (DUF3554); InterPro: IPR022716 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 287 to 356 amino acids in length. This domain is found associated with PF02985 from PFAM.
Probab=21.96 E-value=2.8e+02 Score=28.70 Aligned_cols=76 Identities=18% Similarity=0.127 Sum_probs=54.5
Q ss_pred HHHHHHHHHHhcCCCChhhhhhHHHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHhhhh----C-CCCCCCchhHHHHH
Q 010207 330 RFATMLADVFVSGLYPPLTRMSAVSYLASFLSRARFLSPCFIVSLLKRLVDWCLEYCNIL----G-GDINPKAHRVFYSG 404 (515)
Q Consensus 330 ~F~~~L~~~~~~~~~~~~~R~aAaaYLaSflARAk~v~~~~v~~~l~~L~~w~~~Y~~~~----~-~~~~~~~h~~FYs~ 404 (515)
.+...++-.+++++.++.+|+.|..-+...++|-.-+ +-..++..+-+|+..-.... . .......|.++-++
T Consensus 204 ~~~~a~i~ll~s~~~~~~vR~~A~~~l~~l~~~~~~~---l~~~li~~l~~~l~~~~~~~~~s~~~~~~~~~~~~v~~ai 280 (339)
T PF12074_consen 204 AWAQAFIYLLCSSNVSWKVRRAALSALKKLYASNPEL---LSKSLISGLWKWLSSSETGDKESSAENSSDKNLSPVLSAI 280 (339)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHhChHH---HHHHHHHHHHHHHHhccccccccccccccccccccchHHH
Confidence 6888888999999999999999999999888876554 55667777788877554221 1 11122456777777
Q ss_pred HHHH
Q 010207 405 CQAI 408 (515)
Q Consensus 405 cQA~ 408 (515)
|++.
T Consensus 281 ~~~~ 284 (339)
T PF12074_consen 281 CLAP 284 (339)
T ss_pred Hhhh
Confidence 7754
No 16
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.50 E-value=1.5e+03 Score=27.47 Aligned_cols=206 Identities=14% Similarity=0.124 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhhcCCchHHHHHHHHhccCCCCCcchHHHHHHHHHHHHccccccC-----ccchHHHHHHHHcCCC-
Q 010207 23 LELVYHVREALTSVQSGDNDNYNQLVAVMHLSGRLDPDNRALLETSLKALSGAVSYID-----ISHHESLLVSIFGMSM- 96 (515)
Q Consensus 23 ~~~~~~V~~aL~~~~~Gd~~~Y~~L~~~l~~~~~~~~~~~~~l~~~L~aL~~~Vs~Ld-----~~~~~~LV~ail~~~~- 96 (515)
+++++|-.--+.++..|=-.-+=+++++.+. ..+-++.+ |.-.|..|.+|||.-+ ..+-..+++.++ +|.
T Consensus 282 ~~y~~Fa~~f~~n~~~~ile~~lk~l~~~~~-~~yls~rv--l~~~l~fl~~~Vs~~~twkll~PHl~~ii~~vI-FPlm 357 (1010)
T KOG1991|consen 282 PEYKEFAQMFLKNFAQGILEVFLKILEQWRQ-QLYLSDRV--LYYLLNFLEQCVSHASTWKLLKPHLQVIIQDVI-FPLM 357 (1010)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cccCCHHH--HHHHHHHHHHhccHHHHHHHhhhHHHHHHHHhh-hhhc
Q ss_pred ---------c-CCChhHHHHHH--------------HHHHHHHhcc-cCcHHHHHHHHhhccCCCcccccccCCCCCchh
Q 010207 97 ---------W-NYDPDVMDALK--------------GLIISLAASN-GKYVDSCLTMLVSNFTPPSYFLDKLKEPHGLER 151 (515)
Q Consensus 97 ---------W-~~~~~~v~~y~--------------~Fl~~Lvsa~-~~y~~~vl~~LV~~F~p~~~~~~~~~~~~~~~~ 151 (515)
| +.+.++++.+. .|+..+|+-+ ..=+...+.-+++=|+.... ...|...++
T Consensus 358 c~~d~deelwe~DP~EYiR~~~Di~ed~~sp~~Aa~~~l~~~~~KR~ke~l~k~l~F~~~Il~~~~~----~~~~~~~~r 433 (1010)
T KOG1991|consen 358 CFNDEDEELWEEDPYEYIRKKFDIFEDGYSPDTAALDFLTTLVSKRGKETLPKILSFIVDILTRYKE----ASPPNKNPR 433 (1010)
T ss_pred CCCcccHHHHhcCHHHHHHhcCchhcccCCCcHHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhhcc----cCCCccChh
Q ss_pred hhhhHHHHHHHHHHHHhHcCCChhhhHHHHHhc-CCCCcCccccccchhhhHHHHHHhhhccchhhHHHHHHHHHHHHHH
Q 010207 152 KHQVLSRVHAALKSIFDLVPLAPTRLLPIVVQR-MPTVHNKHERLKMIVVYMENTLKLESSAMGELVRSTLLMAVVDRLI 230 (515)
Q Consensus 152 ~~~~~~~~H~~L~~Il~lvP~a~~~L~~~l~~~-FP~~~~~~~~~~~h~~Yv~NlL~l~~y~~~p~L~~~il~lIi~rli 230 (515)
+.+---|.-.+|..+|.==-.-.+.+-..|+.+ ||....+.-.+++..+|+-+.+.=.+... |..-.++++++...|.
T Consensus 434 qkdGAL~~vgsl~~~L~K~s~~~~~mE~flv~hVfP~f~s~~g~Lrarac~vl~~~~~~df~d-~~~l~~ale~t~~~l~ 512 (1010)
T KOG1991|consen 434 QKDGALRMVGSLASILLKKSPYKSQMEYFLVNHVFPEFQSPYGYLRARACWVLSQFSSIDFKD-PNNLSEALELTHNCLL 512 (1010)
T ss_pred hhhhHHHHHHHHHHHHccCCchHHHHHHHHHHHhhHhhcCchhHHHHHHHHHHHHHHhccCCC-hHHHHHHHHHHHHHhc
Q ss_pred hhcccccc
Q 010207 231 DLDMEIGW 238 (515)
Q Consensus 231 ~iDVei~~ 238 (515)
. |-++++
T Consensus 513 ~-d~~lPV 519 (1010)
T KOG1991|consen 513 N-DNELPV 519 (1010)
T ss_pred c-CCcCch
No 17
>PF10206 WRW: Mitochondrial F1F0-ATP synthase, subunit f; InterPro: IPR019344 This entry represents small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known.
Probab=21.02 E-value=2.9e+02 Score=24.14 Aligned_cols=61 Identities=18% Similarity=0.256 Sum_probs=43.7
Q ss_pred HHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHhhhhCCCCCCCchhHHHHHHHHHHHHHhhhc
Q 010207 354 SYLASFLSRARFLSPCFIVSLLKRLVDWCLEYCNILGGDINPKAHRVFYSGCQAIMYVLCFRM 416 (515)
Q Consensus 354 aYLaSflARAk~v~~~~v~~~l~~L~~w~~~Y~~~~~~~~~~~~h~~FYs~cQA~~YIfCFR~ 416 (515)
+=|.|-++|=.+=|..++..+-.-.-.|-++|++-.++++. ....+-+..=+++|++-|.+
T Consensus 37 gELpsW~~rRd~sP~~~~~a~sR~~wry~~KYi~~Kr~gia--~~~~v~~g~~~~~Y~~~Y~~ 97 (104)
T PF10206_consen 37 GELPSWLSRRDKSPSGIAGAFSRGYWRYQHKYINVKRGGIA--PFFQVLAGYMVFSYCINYKH 97 (104)
T ss_pred chhHHHHhhccCCHHHHHHHHHHHHHHHHHhhhceecCCcc--hhHHHHHHHHHHHHHHhhcH
Confidence 56889999977777777777777778899999986665333 34445555556777776643
Done!