Query 039493
Match_columns 749
No_of_seqs 137 out of 172
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 10:14:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039493hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07990 NABP: Nucleic acid bi 100.0 8E-108 2E-112 871.0 26.7 381 303-722 1-385 (385)
2 KOG1488 Translational represso 99.1 1.4E-10 2.9E-15 130.1 8.8 60 689-748 141-201 (503)
3 smart00025 Pumilio Pumilio-lik 94.4 0.007 1.5E-07 43.4 -1.0 25 724-748 2-26 (36)
4 PF00806 PUF: Pumilio-family R 94.1 0.01 2.2E-07 43.9 -0.7 25 723-747 1-25 (35)
5 COG5099 RNA-binding protein of 87.4 0.28 6.1E-06 59.3 1.7 29 719-747 433-462 (777)
6 cd07920 Pumilio Pumilio-family 41.0 5.4 0.00012 42.0 -1.6 25 723-747 79-103 (322)
7 cd06395 PB1_Map2k5 PB1 domain 23.7 16 0.00034 33.6 -1.4 29 90-121 55-86 (91)
8 PF07508 Recombinase: Recombin 22.4 64 0.0014 28.4 2.2 40 94-133 45-98 (102)
9 PF10775 ATP_sub_h: ATP syntha 22.3 40 0.00087 29.8 0.8 28 706-733 16-43 (67)
10 PF13630 SdpI: SdpI/YhfL prote 20.9 48 0.001 28.1 1.0 20 116-135 12-31 (76)
11 cd07920 Pumilio Pumilio-family 20.8 24 0.00052 37.2 -1.0 24 724-747 44-67 (322)
No 1
>PF07990 NABP: Nucleic acid binding protein NABP; InterPro: IPR012940 This domain occurs in some putative nucleic acid binding proteins. One of these proteins has been partially characterised [] and contains two putative phosphorylation sites and a possible dimerisation / leucine zipper domain.
Probab=100.00 E-value=8.5e-108 Score=870.96 Aligned_cols=381 Identities=65% Similarity=1.045 Sum_probs=368.1
Q ss_pred cCCCCCCCCCCccccccCCCCCCCCCCCcCCCCCCCCchHHHHHHhcCCccCCCCCCCcCCCCchhHHHhHhhhhccccC
Q 039493 303 RAPSPCPTAIGSGRVGASEKRGMTSSNSFSGVSSGINESADLVAALSGMNLSTNGVLNEDNQLPSQIEQDIENHQNYLHG 382 (749)
Q Consensus 303 R~psp~lppiG~~~~~~~~k~~~~~s~~~~~~ss~~~e~adl~salsglnlS~~~~~~~e~~~~sq~q~~~~~q~~~~~~ 382 (749)
|||||||||||+ |+.+.|||++.++++|++++|+++|+|||+|||||||||+++++++|+|+|+|+|+|||||++|+|+
T Consensus 1 R~PSp~lpPIG~-Rv~s~eKk~~~g~~sfn~~SS~~~e~aDlvAALSGLNLS~~~~~~ee~~~qSqlqqdvdnqq~~lf~ 79 (385)
T PF07990_consen 1 RAPSPCLPPIGV-RVGSVEKKNNGGSSSFNGVSSGINESADLVAALSGLNLSGNRAADEENHMQSQLQQDVDNQQDFLFN 79 (385)
T ss_pred CCCCCCCCCccc-cccchhcccccCCcccccccCCCCcHHHHHHHHhcCCcCcCccccccccchHHHHHHHHHhhhhhhc
Confidence 899999999999 9999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccchhhhhhcccCCCCCCCCCCcCCCcccchhhccCCCCCCCCcccccccccccccCCCCCCCCcccCCCCCcc
Q 039493 383 IQGGQNHIKQNKYMKKSDSGNLQMPPGLQSAKMSYSDLAKSNGGGLDLNNASLLTDRRVELQKPAVPTSNSYLKGSPTST 462 (749)
Q Consensus 383 ~~~~~~~~~q~~~~~~~~~~~~~~~~~~q~~~~~y~~~~~~~~~~~~~n~~kl~~d~Q~~l~~~~~~~~~~y~~~~~~s~ 462 (749)
+|++|+|++||.|++++|++|+++ +++++..+++.++|+|++.+++
T Consensus 80 ~q~~q~~~~Qq~~~~~se~~~l~~----------------------------------~e~~~a~~~~~~s~~~~~~~s~ 125 (385)
T PF07990_consen 80 VQGGQNQGNQQSYMKKSESGHLNA----------------------------------PELQKAAFPSGNSYFKNSNASK 125 (385)
T ss_pred CccchhhhhhHHHhhccchhhccc----------------------------------cccccccCCCccccccCCCccc
Confidence 999999999999999999999974 3567778888999999999999
Q ss_pred cCCCCCCCCCCcCCCCCCCCCCCCccCCCCchhhhcccCCCCCCCccchhhhhhhhccCCCCCcccCCCCCCCCcccccc
Q 039493 463 LNGGGGLNSQYQNVDNLPNYGLGGYALSPSMASVMAGQLGAGNLPPLYENVAAASAMAVPGMDSRVLGGGFASGQNLSAT 542 (749)
Q Consensus 463 ~s~~g~~~~~YqNl~~~~~yg~~GY~~n~~~~s~m~~~~~~g~~p~~f~~~a~asa~a~pg~~sr~~g~~~~s~~nl~~~ 542 (749)
++.++..+..||+++. ++|.++||++||++++||.+++++|++|++||+++++++++.+++|+|++|+++.++.+ ++.
T Consensus 126 ~~~~g~~~~~~q~~~~-~n~~~~gy~~n~~~~s~~~~~~~~gn~p~~fd~~~~~s~~~~~~~~s~~~g~~~~s~~~-~~~ 203 (385)
T PF07990_consen 126 LSGGGGSPFPYQNSDN-PNSSFGGYALNPALPSMMASQLNNGNIPPLFDNSAAASALASPGMDSRSLGGGLDSGGN-QGA 203 (385)
T ss_pred ccCCCCCCCcccCCCc-ccccccccccCccchhhhhccccCCCCCccccccccchhhccCCCcccccCCccccccc-ccc
Confidence 9999998999999665 78888999999999999999999999999999999999999999999999999999998 788
Q ss_pred cccccccccccCCCCCCCCCCCCChhhHhhhccch-HHHHHhhcCCCCcCCcCCCCCccchHHHHHHhhhcccccccccC
Q 039493 543 SESHNLNRAGSQMGGGALQFPFVDPVYLQYLRSSE-YAAQLAALNDPSVDRNFLGNSYMNLLELQKAYLGVLLSPQKSQY 621 (749)
Q Consensus 543 sd~~nl~r~g~q~~~~~lQ~p~~DP~Y~QYlq~~~-~~~~~a~~~dP~~~Rn~~g~s~~dl~~~QKayl~~lLs~QK~Qy 621 (749)
+|+|||+|+|||++|.+||+||+||+|+||||++| +++++++++||+++|||+|++|+|++++|||||++||++||+||
T Consensus 204 ~d~~~l~r~gnq~~g~~lq~~~~DP~Y~Qylq~~~~aa~~~a~~~dP~~~R~~~G~s~~dl~~~qKayl~~lL~~QK~Qy 283 (385)
T PF07990_consen 204 SDGQNLNRFGNQVAGSALQSPFVDPLYLQYLQAPEYAAQQAAAQNDPSVDRNYMGSSYMDLLGLQKAYLEALLAQQKSQY 283 (385)
T ss_pred cchhhhhhhcccccCcccCCCCCCchHHHHhccccchhhhhhccCCcccccCCcCccccchHHHHHHHHHHHHHHHHHhh
Confidence 99999999999997799999999999999999999 88899999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccc-ccccCCCCCCCCCcccC--C
Q 039493 622 GGPLGSKSSGSNHHGYCGTPGFGLGMSYPGSPLANPVIPNSPVGPGSPIRHNDPNLRFA-GMRNLAGGVMGPWHLDA--S 698 (749)
Q Consensus 622 ~~p~l~Ks~G~~~~~Y~G~P~~G~~M~YpgSpl~sPvlp~sp~g~gsP~~~g~rn~r~~-~~Rn~~Gg~~gsw~~~~--~ 698 (749)
|+|+ .|+ |+++++|||+|.||++|+||||||++||||+||+|+|+||||+||+|||+ +|||++||++|+||.|+ +
T Consensus 284 ~~P~-~~~-~~~n~~y~gnp~~G~gm~Y~gsplaspvlPsspvG~gsp~r~~er~~R~~s~mRn~~GG~~GsW~~d~g~~ 361 (385)
T PF07990_consen 284 GVPL-KKS-GSMNHGYYGNPSYGLGMPYPGSPLASPVLPSSPVGPGSPLRHNERNMRFPSGMRNSSGGSMGSWHSDAGGN 361 (385)
T ss_pred CCcc-ccC-CCCCCCCCCCCCccccCCCCCCCCcCCCCCCCCCCCCCCCcCCccccccCccccccccccccccccccccc
Confidence 9999 776 88999999999999999999999999999999999999999999999999 99999999999999999 7
Q ss_pred CCCccccchHHHhhhCCCCceeec
Q 039493 699 MDESFGSSLLEEFKSNKTKCFELS 722 (749)
Q Consensus 699 ~~~~~~s~lLeefr~nk~k~~EL~ 722 (749)
+|+++.|.||||||+||+|+|||+
T Consensus 362 ~d~~~~sSlLEEFKsNKtr~FELS 385 (385)
T PF07990_consen 362 MDENFASSLLEEFKSNKTRSFELS 385 (385)
T ss_pred ccccchhHHHHHHhcCCccceecC
Confidence 999999999999999999999995
No 2
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=99.11 E-value=1.4e-10 Score=130.13 Aligned_cols=60 Identities=27% Similarity=0.291 Sum_probs=53.5
Q ss_pred CCCCCcccCCCCCccccchHHHhhhC-CCCceeecccccceeEeecCcccchhhhhhhhcc
Q 039493 689 VMGPWHLDASMDESFGSSLLEEFKSN-KTKCFELSEIAGHVVEFRYAMLLAHLMLHFSAVL 748 (749)
Q Consensus 689 ~~gsw~~~~~~~~~~~s~lLeefr~n-k~k~~EL~DI~GhvvEFs~DQ~GSRFIQ~~~~~~ 748 (749)
+...|++....+...++.+||+++++ +.+.+++.||.||+|||++||||||||||+++..
T Consensus 141 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~v~f~~Dq~GsrfiQqkl~~~ 201 (503)
T KOG1488|consen 141 STNNSNSSDSSNSTGPSFLLDPFRSNSLSKTLELVDIPGHLVEFAKDQHGSRFIQQKLETA 201 (503)
T ss_pred cccccCCcccCCCCCCCccccccccccccccccccccCCCceeecCCcccchHHHHhcccc
Confidence 55667777766777889999999999 8899999999999999999999999999999864
No 3
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=94.42 E-value=0.007 Score=43.37 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=22.0
Q ss_pred cccceeEeecCcccchhhhhhhhcc
Q 039493 724 IAGHVVEFRYAMLLAHLMLHFSAVL 748 (749)
Q Consensus 724 I~GhvvEFs~DQ~GSRFIQ~~~~~~ 748 (749)
+.+|++|+|.|+||+|+||+.+...
T Consensus 2 ~~~~~~~l~~~~~g~~viqk~l~~~ 26 (36)
T smart00025 2 IKGHLLELSKDQYGNRVVQKLLEHA 26 (36)
T ss_pred chHHHHHHHhcchhhHHHHHHHHHC
Confidence 5789999999999999999987643
No 4
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....
Probab=94.11 E-value=0.01 Score=43.91 Aligned_cols=25 Identities=20% Similarity=0.173 Sum_probs=22.4
Q ss_pred ccccceeEeecCcccchhhhhhhhc
Q 039493 723 EIAGHVVEFRYAMLLAHLMLHFSAV 747 (749)
Q Consensus 723 DI~GhvvEFs~DQ~GSRFIQ~~~~~ 747 (749)
.|.+|+++.|.|+||+|.||+.+.+
T Consensus 1 ~i~~~~~~l~~d~~Gn~VvQk~le~ 25 (35)
T PF00806_consen 1 EIKGNLVELSKDQYGNYVVQKCLEH 25 (35)
T ss_dssp CHTTTHHHHHTSTTHHHHHHHHHHH
T ss_pred ChHHHHHHHHhccccCHHHHHHHHH
Confidence 3789999999999999999998765
No 5
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=87.39 E-value=0.28 Score=59.30 Aligned_cols=29 Identities=7% Similarity=0.063 Sum_probs=26.3
Q ss_pred eeecccccceeEee-cCcccchhhhhhhhc
Q 039493 719 FELSEIAGHVVEFR-YAMLLAHLMLHFSAV 747 (749)
Q Consensus 719 ~EL~DI~GhvvEFs-~DQ~GSRFIQ~~~~~ 747 (749)
.-..||+++..+|+ +||||+||||++|++
T Consensus 433 ~s~~~~l~~~~~~~~~Dq~g~r~LQk~Lds 462 (777)
T COG5099 433 VSATDILGPSIIVSCKDQHGSRFLQKLLDS 462 (777)
T ss_pred ccccccccCccccccCCcHHHHHHHHHhcc
Confidence 45679999999999 999999999999976
No 6
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=41.05 E-value=5.4 Score=41.96 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=17.2
Q ss_pred ccccceeEeecCcccchhhhhhhhc
Q 039493 723 EIAGHVVEFRYAMLLAHLMLHFSAV 747 (749)
Q Consensus 723 DI~GhvvEFs~DQ~GSRFIQ~~~~~ 747 (749)
.|.||+++.|.|+||+|+||+-+..
T Consensus 79 ~~~~~~~~l~~~~~g~~vlqkll~~ 103 (322)
T cd07920 79 KILGHVVRLSLDMYGCRVIQKLLES 103 (322)
T ss_pred HHHHHHHHHcccchhHHHHHHHHHh
Confidence 3457777777777777777765543
No 7
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=23.73 E-value=16 Score=33.59 Aligned_cols=29 Identities=48% Similarity=0.744 Sum_probs=21.5
Q ss_pred CCCChhhhccCcccceeeccCC---CCCCCCCCCC
Q 039493 90 GFSSEEELRSDPAYLSYYYSNV---NLNPRLPPPL 121 (749)
Q Consensus 90 ~~~seeelRsdPAYl~YYYSnv---nLNPRLPPPL 121 (749)
.+-|+||+. |.++||++-+ -.|--||+||
T Consensus 55 TVRSDeEm~---AMlsyy~~~~~E~~~~g~~~~PL 86 (91)
T cd06395 55 TVRSDEEMK---AMLSYYCSTVMEQQVNGQLIEPL 86 (91)
T ss_pred EecchHHHH---HHHHHHHHHHHHHHhccCCCCCc
Confidence 477899998 8999998744 3455567776
No 8
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=22.44 E-value=64 Score=28.39 Aligned_cols=40 Identities=25% Similarity=0.451 Sum_probs=28.3
Q ss_pred hhhhccCcccceeeccCCCC------C--------CCCCCCCCChhhHHHHHHh
Q 039493 94 EEELRSDPAYLSYYYSNVNL------N--------PRLPPPLLSKEDWRFAQRL 133 (749)
Q Consensus 94 eeelRsdPAYl~YYYSnvnL------N--------PRLPPPLlSkEdwR~aqRl 133 (749)
=..|..+|+|+.++.-+..- + +--=|||||+|.|.-+|..
T Consensus 45 v~~iL~np~y~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IIs~~~f~~vq~~ 98 (102)
T PF07508_consen 45 VRRILRNPAYAGYRVYNKRERKKRKRKPKEDWIVVEGYHPPIISEEEFERVQKK 98 (102)
T ss_pred HHHHHhhhhccceEEeeecccchhccCCCCceEEEECCCCCccCHHHHHHHHHH
Confidence 34667789998877666554 1 1123799999999999954
No 9
>PF10775 ATP_sub_h: ATP synthase complex subunit h; InterPro: IPR019711 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit H found in the F0 complex of F-ATPases from fungal mitochondria. Subunit H is homologous to the mammalian factor F6, and is essential for the correct assembly and/or functioning of F-ATPases, since yeast cells lacking it are not able to grow on non-fermentable carbon sources. Subunit H occupies a central place in the peripheral stalk between the F1 sector and the membrane [].
Probab=22.26 E-value=40 Score=29.78 Aligned_cols=28 Identities=25% Similarity=0.371 Sum_probs=24.7
Q ss_pred chHHHhhhCCCCceeecccccceeEeec
Q 039493 706 SLLEEFKSNKTKCFELSEIAGHVVEFRY 733 (749)
Q Consensus 706 ~lLeefr~nk~k~~EL~DI~GhvvEFs~ 733 (749)
--|-|+|+-|.....-.|+.|||.+|+.
T Consensus 16 LYLkELKayKp~p~~~~d~~g~Vk~f~~ 43 (67)
T PF10775_consen 16 LYLKELKAYKPPPISADDAEGQVKKFSL 43 (67)
T ss_pred HHHHHHHhcCCCCCCchhHHhccccCCC
Confidence 4688999999988889999999999974
No 10
>PF13630 SdpI: SdpI/YhfL protein family
Probab=20.87 E-value=48 Score=28.10 Aligned_cols=20 Identities=40% Similarity=0.753 Sum_probs=16.5
Q ss_pred CCCCCCCChhhHHHHHHhhC
Q 039493 116 RLPPPLLSKEDWRFAQRLRG 135 (749)
Q Consensus 116 RLPPPLlSkEdwR~aqRl~~ 135 (749)
|.|-=|-|+|.|+.|||+-+
T Consensus 12 Rt~~t~~s~~~W~~a~r~~g 31 (76)
T PF13630_consen 12 RTPWTMKSDENWKKAHRFAG 31 (76)
T ss_pred eChHHhCCHHHHHHHHHHHH
Confidence 55666789999999999875
No 11
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=20.84 E-value=24 Score=37.21 Aligned_cols=24 Identities=21% Similarity=0.137 Sum_probs=16.8
Q ss_pred cccceeEeecCcccchhhhhhhhc
Q 039493 724 IAGHVVEFRYAMLLAHLMLHFSAV 747 (749)
Q Consensus 724 I~GhvvEFs~DQ~GSRFIQ~~~~~ 747 (749)
|.+|+++.+.|+||+++||+-+.+
T Consensus 44 l~~~~~~l~~~~~g~~vvq~~l~~ 67 (322)
T cd07920 44 ILPHVVELMVDPFGNYVIQKLFEH 67 (322)
T ss_pred HHHhHHHHhcCccccHHHHHHHHh
Confidence 567777777777777777766543
Done!