Query 025523
Match_columns 251
No_of_seqs 128 out of 189
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 06:42:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025523.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025523hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3169 RNA polymerase II tran 100.0 4.1E-59 8.9E-64 407.3 15.7 179 20-204 1-189 (208)
2 PF04934 Med6: MED6 mediator s 100.0 8.2E-54 1.8E-58 356.8 -10.2 129 28-156 1-137 (140)
3 COG5097 MED6 RNA polymerase II 100.0 1E-42 2.2E-47 301.7 12.1 137 25-161 6-150 (210)
4 PF13162 DUF3997: Protein of u 29.1 78 0.0017 26.3 3.7 30 93-122 43-81 (115)
5 PF01213 CAP_N: Adenylate cycl 24.4 73 0.0016 30.4 3.1 27 140-166 184-213 (312)
6 PF08650 DASH_Dad4: DASH compl 19.7 2E+02 0.0044 22.2 4.1 27 130-156 9-35 (72)
7 PF08479 POTRA_2: POTRA domain 19.7 73 0.0016 23.2 1.7 49 114-162 4-54 (76)
8 PF02191 OLF: Olfactomedin-lik 18.4 2.9E+02 0.0063 25.3 5.6 22 83-104 122-143 (250)
9 PF00278 Orn_DAP_Arg_deC: Pyri 18.3 1E+02 0.0022 23.6 2.3 30 98-127 6-35 (116)
10 PF13590 DUF4136: Domain of un 17.3 1.2E+02 0.0026 24.1 2.5 19 184-202 133-151 (151)
No 1
>KOG3169 consensus RNA polymerase II transcriptional regulation mediator [Transcription]
Probab=100.00 E-value=4.1e-59 Score=407.25 Aligned_cols=179 Identities=34% Similarity=0.547 Sum_probs=152.7
Q ss_pred CCCCCCCceeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCC--CChhhhhhcCCceeEEeeecCCceE
Q 025523 20 PPGTDMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHP--LDISQLSKMTGIEYMLSEVMEPHLF 97 (251)
Q Consensus 20 ~p~~d~~~i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~--l~~~~L~~m~GiEY~l~~~~ep~Lf 97 (251)
++.+|+++|+||||+|++.++|+++|||||||+|||||++||||+||||++.+ +..++|.+|.||||+|.|++||.||
T Consensus 1 ~~~~~l~~isw~dp~wi~~~~L~~~nVLdYFs~sPFYd~scNNe~lkMQ~qf~~~~~~e~L~~m~GieYvl~~~~~P~Lf 80 (208)
T KOG3169|consen 1 PMEDDLLSISWRDPEWIQSKGLRTENVLDYFSSSPFYDKSCNNEVLKMQTQFRGRDLEEHLFSMVGIEYVLLHSREPILF 80 (208)
T ss_pred CCCCCccceeeeCcccccccCCCcchHHHHhhcCccccccccHHHHHHHHHHhccchHHHHhhCcCeEEEEEecCCCeEE
Confidence 35789999999999999999999999999999999999999999999997652 3468999999999999999999999
Q ss_pred EEEEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCcCCCCCC---CCCC
Q 025523 98 VIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYVDAENDG---GTPL 171 (251)
Q Consensus 98 VIrKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~~~~~~~---~~~~ 171 (251)
|||||+|+++++++||++||||||+|||||++|+|++|||++++++|++||+++.++.+ .+||+|..... ++++
T Consensus 81 VIrKQ~R~n~tev~PLa~YYII~g~VYqAPd~ysiv~sRml~a~~~lqsa~~e~~~~~rynP~kGy~~~~~s~~~~~~~~ 160 (208)
T KOG3169|consen 81 VIRKQRRHNPTEVIPLADYYIINGNVYQAPDLYSIVQSRMLNAVYQLQSAFDEAMSYRRYNPSKGYTWRFLSKSLEDSKD 160 (208)
T ss_pred EEehhhcCCCccceeeeeEEEECceeeeCccHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCcccccCCchhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999988 89999854433 1122
Q ss_pred CCCCCCC--CcchHHHhhHHHHHHHHHHhCCCCCC
Q 025523 172 HSKAGKE--TIDLKEVKRVDQILASLQRKLPPAPP 204 (251)
Q Consensus 172 ~~k~~~e--~~~~fQ~~RvD~lL~~L~~kfPp~~~ 204 (251)
..|+.++ ....+| |++.|..+||+..+
T Consensus 161 ~~~~~~~~~~~~~~s------l~n~~~~~~p~~~~ 189 (208)
T KOG3169|consen 161 LDNKNEIFNKFKKSS------LLNALYSFSPEDFS 189 (208)
T ss_pred ccccccccccchhHH------HHhhccccCCCccc
Confidence 2222221 122223 78888877775533
No 2
>PF04934 Med6: MED6 mediator sub complex component; InterPro: IPR007018 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Regulation of mRNA synthesis requires intermediary proteins that transduce regulatory signals from upstream transcriptional activator proteins to basal transcription machinery at the core promoter. Three types of intermediary factors that enable the basal transcription machinery to respond to transcriptional activator proteins bound to regulatory DNA sequences have been identified: (i) TAFIIs, which associate with TATA-binding protein (TBP) to form TFIID; (ii) mediator, which associates with RNA polymerase II to form a holo-polymerase; and (iii) coactivators such as human upstream stimulatory activity (USA), mammalian CBP/P300, yeast ADA complex, and HMG proteins. The interaction of these multiprotein complexes with activators and general transcription factors is essential for transcriptional regulation. This family of proteins represent the transcriptional mediator protein subunit 6 that is required for activation of many RNA polymerase II promoters and which are conserved from yeast to humans []..; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3RJ1_N.
Probab=100.00 E-value=8.2e-54 Score=356.83 Aligned_cols=129 Identities=49% Similarity=0.785 Sum_probs=55.2
Q ss_pred eeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCCC--------ChhhhhhcCCceeEEeeecCCceEEE
Q 025523 28 ICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPL--------DISQLSKMTGIEYMLSEVMEPHLFVI 99 (251)
Q Consensus 28 i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~l--------~~~~L~~m~GiEY~l~~~~ep~LfVI 99 (251)
|+||||+||++++||.+||||||++|||||++||||+||||++++. .+++|++|.|+||+|+|++||+||||
T Consensus 1 i~w~dp~~l~~~~l~~~nvL~YF~~SPFyd~~snNe~lrmQ~~~~~~~~~~~~~~~~~L~~m~GiEY~l~~~~eP~l~vI 80 (140)
T PF04934_consen 1 IQWRDPEWLQQNGLNSNNVLDYFSESPFYDRTSNNEVLRMQRQFNQQNLPTREAFEQQLRNMKGIEYVLAHVQEPGLFVI 80 (140)
T ss_dssp -------SHHHHHH---STTSSTTTHHHH----SSSSSSTTTSHHHTT-SSSHHHHHTTTS-------------------
T ss_pred CcccCHHHHHhcCCChhHHHHHHccCcccCCCCCCceeeeccccCccccchhHHHHHHHhhcCCeEEEEeccCCCCEEEE
Confidence 7999999999999999999999999999999999999999987532 23579999999999999999999999
Q ss_pred EEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025523 100 RKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE 156 (251)
Q Consensus 100 rKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~ 156 (251)
|||+|+++++++||++||||||+|||||||++||++||++++++|++||+.+.++.+
T Consensus 81 ~Kq~r~~~~~~~~la~YYIi~g~IYqAPsl~~vl~sRl~~~~~~l~~a~~~~~~~~~ 137 (140)
T PF04934_consen 81 RKQRRQSPDEVTPLAYYYIINGNIYQAPSLYSVLSSRLLSAVSSLSKAFDEANSMSR 137 (140)
T ss_dssp -------------------------------SSSSSTTTHHHHHHHHHHHTT-----
T ss_pred EEeeccCCCcceEeEEEEEECCEEEeCCCHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 999999999999999999999999999999999999999999999999999988654
No 3
>COG5097 MED6 RNA polymerase II transcriptional regulation mediator [Transcription]
Probab=100.00 E-value=1e-42 Score=301.71 Aligned_cols=137 Identities=31% Similarity=0.513 Sum_probs=127.0
Q ss_pred CCceeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCC-CCh----hhhhhcCCceeEEeeecCCceEEE
Q 025523 25 MTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHP-LDI----SQLSKMTGIEYMLSEVMEPHLFVI 99 (251)
Q Consensus 25 ~~~i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~-l~~----~~L~~m~GiEY~l~~~~ep~LfVI 99 (251)
+++|+|+||+||+.+||..+||||||+.|||||++||||+||||+..+ ||. ++|+.+.|++||+.|+.||.||||
T Consensus 6 l~siqw~~pew~qs~gLrteNVLeYFs~SPFydk~sNNeilKMQ~QF~~LdL~ql~~~l~~l~g~~~V~ss~rep~lwVI 85 (210)
T COG5097 6 LTSIQWVDPEWLQSKGLRTENVLEYFSGSPFYDKSSNNEILKMQTQFRGLDLGQLSKLLSMLGGFYEVESSNREPTLWVI 85 (210)
T ss_pred ccceeecCHHHHhccCCcchhHHHHhcCCCccccccchHHHHHHHHhhccChHHHHHHHHhccCEEEEEecCCCCcEEEE
Confidence 889999999999999999999999999999999999999999998543 553 557788999999999999999999
Q ss_pred EEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCc
Q 025523 100 RKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYV 161 (251)
Q Consensus 100 rKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~ 161 (251)
|||+|++.++++||.+|||+|.+|||||+.|+|+++||++++++|+++++.+...-+ ..||.
T Consensus 86 rKq~r~n~~e~~pl~~Y~i~g~NIY~aPt~y~i~~~Rm~~s~y~lns~l~~~~~~~~fnP~~g~~ 150 (210)
T COG5097 86 RKQYRHNDTEETPLMYYIIHGHNIYAAPTNYSIYRCRMGDSMYQLNSFLDRMMEKRRFNPFSGPK 150 (210)
T ss_pred ehhhhcCCcccccceEEEEecCceeeCcchhhhhhhhhhhhHHHHHHHHHHHHHhhccCCCCCCC
Confidence 999999999999999999999999999999999999999999999999999888655 55654
No 4
>PF13162 DUF3997: Protein of unknown function (DUF3997)
Probab=29.08 E-value=78 Score=26.28 Aligned_cols=30 Identities=20% Similarity=0.304 Sum_probs=18.6
Q ss_pred CCceEEEEEee-ecCCCcc--------ccceeEEEEcCe
Q 025523 93 EPHLFVIRKQK-RDGPEKV--------TPMLTYYVLDGS 122 (251)
Q Consensus 93 ep~LfVIrKQ~-R~s~~~v--------~pLa~YYIi~G~ 122 (251)
-...|||+||+ ....+.. ..+..||||+=+
T Consensus 43 ~dd~yIiaKq~p~~~~d~~~~~~~~~~~~~e~Y~IId~~ 81 (115)
T PF13162_consen 43 YDDDYIIAKQKPEIKSDPNNPKSYIYNKSSEEYWIIDKK 81 (115)
T ss_pred cCCeeEEEEccccccCCCCCccceeccCCCceEEEEEcC
Confidence 35789999998 4433211 133469999643
No 5
>PF01213 CAP_N: Adenylate cyclase associated (CAP) N terminal; InterPro: IPR013992 Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways [, , , ]. In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly [, ]. In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity. All CAPs appear to contain a C-terminal actin-binding domain that regulates actin remodelling in response to cellular signals and is required for normal cellular morphology, cell division, growth and locomotion in eukaryotes. CAP directly regulates actin filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localisation and the establishment of cell polarity. Actin exists both as globular (G) (monomeric) actin subunits and assembled into filamentous (F) actin. In cells, actin cycles between these two forms. Proteins that bind F-actin often regulate F-actin assembly and its interaction with other proteins, while proteins that interact with G-actin often control the availability of unpolymerised actin. CAPs bind G-actin. In addition to actin-binding, CAPs can have additional roles, and may act as bifunctional proteins. In Saccharomyces cerevisiae (Baker's yeast), CAP is a component of the adenylyl cyclase complex (Cyr1p) that serves as an effector of Ras during normal cell signalling. S. cerevisiae CAP functions to expose adenylate cyclase binding sites to Ras, thereby enabling adenylate cyclase to be activated by Ras regulatory signals. In Schizosaccharomyces pombe (Fission yeast), CAP is also required for adenylate cyclase activity, but not through the Ras pathway. In both organisms, the N-terminal domain is responsible for adenylate cyclase activation, but the S cerevisiae and S. pombe N-termini cannot complement one another. Yeast CAPs are unique among the CAP family of proteins, because they are the only ones to directly interact with and activate adenylate cyclase []. S. cerevisiae CAP has four major domains. In addition to the N-terminal adenylate cyclase-interacting domain, and the C-terminal actin-binding domain, it possesses two other domains: a proline-rich domain that interacts with Src homology 3 (SH3) domains of specific proteins, and a domain that is responsible for CAP oligomerisation to form multimeric complexes (although oligomerisation appears to involve the N- and C-terminal domains as well). The proline-rich domain interacts with profilin, a protein that catalyses nucleotide exchange on G-actin monomers and promotes addition to barbed ends of filamentous F-actin []. Since CAP can bind profilin via a proline-rich domain, and G-actin via a C-terminal domain, it has been suggested that a ternary G-actin/CAP/profilin complex could be formed. This entry represents the N-terminal domain of CAP proteins. This domain has an all-alpha structure consisting of six helices in a bundle with a left-handed twist and an up-and-down topology [].; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1TJF_B 1S0P_A.
Probab=24.42 E-value=73 Score=30.44 Aligned_cols=27 Identities=4% Similarity=0.008 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHhh---hcCCcCCCCC
Q 025523 140 ALHYIQKAFTTAASKLE---KIGYVDAEND 166 (251)
Q Consensus 140 a~~~L~kaf~~~~s~~~---~~GY~~~~~~ 166 (251)
-+..+-..|+.+..|+. ..|-.|+...
T Consensus 184 Wvks~~~l~~~L~~YVke~httGl~WN~~G 213 (312)
T PF01213_consen 184 WVKSFKALLKELQAYVKEHHTTGLSWNPKG 213 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHSTTS----TTS
T ss_pred HHHHHHHHHHHHHHHHHHhCccCcccCCcc
Confidence 34455667777778776 7888886544
No 6
>PF08650 DASH_Dad4: DASH complex subunit Dad4; InterPro: IPR013959 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=19.74 E-value=2e+02 Score=22.19 Aligned_cols=27 Identities=15% Similarity=0.177 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025523 130 CNVFSARIGRALHYIQKAFTTAASKLE 156 (251)
Q Consensus 130 ~sVl~sRl~sa~~~L~kaf~~~~s~~~ 156 (251)
.++|-+||.+.+..|+.|+.++...++
T Consensus 9 Q~~LLsRIi~NvekLNEsv~~lN~~l~ 35 (72)
T PF08650_consen 9 QSNLLSRIIGNVEKLNESVAELNQELE 35 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999998877764
No 7
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=19.70 E-value=73 Score=23.23 Aligned_cols=49 Identities=16% Similarity=0.267 Sum_probs=33.1
Q ss_pred eeEEEEcCeEeeCCchhHHHHHHHHH--HHHHHHHHHHHHHHHhhhcCCcC
Q 025523 114 LTYYVLDGSIYQAPQLCNVFSARIGR--ALHYIQKAFTTAASKLEKIGYVD 162 (251)
Q Consensus 114 a~YYIi~G~IYQAPsl~sVl~sRl~s--a~~~L~kaf~~~~s~~~~~GY~~ 162 (251)
....+-|..++-...+..++..-+.. .+..|+++.+.+..+++.+||..
T Consensus 4 ~~i~~~G~~~~~~~~l~~~~~~~~g~~l~~~~l~~~~~~l~~~y~~~GY~~ 54 (76)
T PF08479_consen 4 KGIRFEGNTLLPEEELQAILAPYIGRCLTLADLQQLADALTNYYREKGYIT 54 (76)
T ss_dssp -EEEEES-TSSSCCHHHHHHGGGTTSBB-HHHHHHHHHHHHHHHHHTT-TT
T ss_pred EEEEEECCCcCCHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHcCceE
Confidence 34456666777777777777655544 35678888888889999999963
No 8
>PF02191 OLF: Olfactomedin-like domain; InterPro: IPR003112 The olfactomedin-domain was first identified in olfactomedin, an extracellular matrix protein of the olfactory neuroepithelium []. Members of this extracellular domain-family have since been shown to be present in several metazoan proteins, such as latrophilins, myocilins, optimedins and noelins, the latter being involved in the generation of neural crest cells. Myocilin is of considerable interest, as mutations in its olfactomedin-domain can lead to glaucoma []. The olfactomedin-domains in myocilin and optimedin are essential for the interaction between these two proteins [].; GO: 0005515 protein binding
Probab=18.45 E-value=2.9e+02 Score=25.32 Aligned_cols=22 Identities=27% Similarity=0.215 Sum_probs=14.5
Q ss_pred CceeEEeeecCCceEEEEEeee
Q 025523 83 GIEYMLSEVMEPHLFVIRKQKR 104 (251)
Q Consensus 83 GiEY~l~~~~ep~LfVIrKQ~R 104 (251)
|--|+-..+.|.|||||.--..
T Consensus 122 ~~t~iD~AvDE~GLWvIYat~~ 143 (250)
T PF02191_consen 122 GYTDIDFAVDENGLWVIYATED 143 (250)
T ss_pred CCceEEEEEcCCCEEEEEecCC
Confidence 3344444568999999965543
No 9
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=18.30 E-value=1e+02 Score=23.65 Aligned_cols=30 Identities=20% Similarity=0.377 Sum_probs=15.9
Q ss_pred EEEEeeecCCCccccceeEEEEcCeEeeCC
Q 025523 98 VIRKQKRDGPEKVTPMLTYYVLDGSIYQAP 127 (251)
Q Consensus 98 VIrKQ~R~s~~~v~pLa~YYIi~G~IYQAP 127 (251)
||.|+.+...+....-..+|++++.+|+++
T Consensus 6 Vi~~k~~~~~~~~~~~~~~~~vd~G~~~~~ 35 (116)
T PF00278_consen 6 VIGVKRRRDSDLKNKKRRWYYVDDGVYGSF 35 (116)
T ss_dssp EEEEEEETT---HCTTEEEEEESS-TTTCC
T ss_pred EEEEEEcCCCccccceeeEEEEeCChhhCh
Confidence 556665554322222344666999999984
No 10
>PF13590 DUF4136: Domain of unknown function (DUF4136)
Probab=17.28 E-value=1.2e+02 Score=24.13 Aligned_cols=19 Identities=11% Similarity=0.399 Sum_probs=17.1
Q ss_pred HHhhHHHHHHHHHHhCCCC
Q 025523 184 EVKRVDQILASLQRKLPPA 202 (251)
Q Consensus 184 Q~~RvD~lL~~L~~kfPp~ 202 (251)
-..+++.++..++++|||.
T Consensus 133 ~~~~i~~~V~~i~~~fP~~ 151 (151)
T PF13590_consen 133 REEAIPKAVNKIFEQFPPK 151 (151)
T ss_pred HHHHHHHHHHHHHHhCCCC
Confidence 6778999999999999984
Done!