Query 041888
Match_columns 326
No_of_seqs 117 out of 223
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 11:44:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041888.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041888hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01568 A_thal_3678 uncharac 100.0 9.4E-34 2E-38 217.4 7.9 65 259-323 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 5.4E-32 1.2E-36 203.6 7.4 59 265-323 1-59 (59)
3 smart00544 MA3 Domain in DAP-5 70.5 5.9 0.00013 31.1 3.5 44 272-317 1-44 (113)
4 PF06375 BLVR: Bovine leukaemi 58.9 3.4 7.4E-05 36.9 0.2 11 135-145 66-76 (154)
5 KOG1920 IkappaB kinase complex 47.9 60 0.0013 37.6 7.4 34 288-321 1184-1217(1265)
6 PF02979 NHase_alpha: Nitrile 40.3 48 0.001 31.0 4.5 48 269-316 5-53 (188)
7 PRK10072 putative transcriptio 37.5 51 0.0011 27.1 3.8 30 266-295 4-42 (96)
8 PF14551 MCM_N: MCM N-terminal 35.8 79 0.0017 24.6 4.5 51 272-322 18-74 (121)
9 PF02847 MA3: MA3 domain; Int 34.3 62 0.0013 25.2 3.8 41 272-314 1-41 (113)
10 PF09177 Syntaxin-6_N: Syntaxi 31.4 1.8E+02 0.004 23.1 6.0 32 267-306 1-32 (97)
11 PF10273 WGG: Pre-rRNA-process 29.6 76 0.0016 25.2 3.5 37 264-300 28-64 (82)
12 PF04994 TfoX_C: TfoX C-termin 27.1 81 0.0018 25.0 3.3 31 274-304 13-45 (81)
13 PF10278 Med19: Mediator of RN 25.6 45 0.00097 30.8 1.8 37 95-131 97-133 (178)
14 KOG3571 Dishevelled 3 and rela 25.5 26 0.00056 37.4 0.3 21 210-230 204-225 (626)
15 cd00982 gltB_C gltb_C. This do 24.3 90 0.002 30.0 3.7 59 256-317 179-241 (251)
16 PF09388 SpoOE-like: Spo0E lik 24.0 1.9E+02 0.0041 20.3 4.4 32 270-301 7-44 (45)
17 KOG2422 Uncharacterized conser 23.8 31 0.00067 37.3 0.5 22 257-281 271-292 (665)
18 PF13945 NST1: Salt tolerance 22.5 38 0.00082 31.4 0.8 10 289-298 156-165 (190)
19 PRK10548 flagellar biosynthesi 22.3 1.2E+02 0.0026 26.0 3.7 54 269-322 11-72 (121)
20 PF08887 GAD-like: GAD-like do 21.7 32 0.00069 28.9 0.1 45 274-318 34-92 (109)
21 PF10415 FumaraseC_C: Fumarase 20.2 1E+02 0.0022 23.0 2.5 27 274-300 26-52 (55)
No 1
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=100.00 E-value=9.4e-34 Score=217.40 Aligned_cols=65 Identities=51% Similarity=0.830 Sum_probs=63.0
Q ss_pred EEEEeecCChHHHHHHHHHHHHHhcCCC-ChhHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHhcc
Q 041888 259 FAVVKSSSDPYNDFRTSMVEMIVEKQIF-AAKDLEQLLQCFLSLNSHHHHRIILEVFTEIWEALFS 323 (326)
Q Consensus 259 vAVVK~S~DPY~DFR~SMvEMI~ekgi~-d~~dLEELL~CYLsLNsk~hH~~Iv~AF~DLw~~Lfs 323 (326)
|||+|+|.|||.|||+||+|||+++|+. +|++|||||+|||+||+++||++|++||+|||.+||+
T Consensus 1 vAv~k~S~DPy~DFr~SM~EMI~~~~i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~AF~dl~~~L~~ 66 (66)
T TIGR01568 1 VAVAKESDDPYEDFRRSMEEMIEERELEADWKELEELLACYLDLNPKKSHRFIVRAFVDILSALLS 66 (66)
T ss_pred CeeeeCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHhC
Confidence 6999999999999999999999999996 6999999999999999999999999999999999985
No 2
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=99.97 E-value=5.4e-32 Score=203.57 Aligned_cols=59 Identities=61% Similarity=1.015 Sum_probs=57.9
Q ss_pred cCChHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHhcc
Q 041888 265 SSDPYNDFRTSMVEMIVEKQIFAAKDLEQLLQCFLSLNSHHHHRIILEVFTEIWEALFS 323 (326)
Q Consensus 265 S~DPY~DFR~SMvEMI~ekgi~d~~dLEELL~CYLsLNsk~hH~~Iv~AF~DLw~~Lfs 323 (326)
|.|||+|||+||+|||+|+|+.+|++|||||+|||+||+++||++||+||+|||.+||+
T Consensus 1 S~DP~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~dv~~~l~s 59 (59)
T PF04844_consen 1 SSDPYEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPEHHKFIVEAFVDVWVELFS 59 (59)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHhC
Confidence 78999999999999999999999999999999999999999999999999999999985
No 3
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=70.52 E-value=5.9 Score=31.11 Aligned_cols=44 Identities=18% Similarity=0.435 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 041888 272 FRTSMVEMIVEKQIFAAKDLEQLLQCFLSLNSHHHHRIILEVFTEI 317 (326)
Q Consensus 272 FR~SMvEMI~ekgi~d~~dLEELL~CYLsLNsk~hH~~Iv~AF~DL 317 (326)
||+++...|.+- .+..|++|...|.+.||.+++|..++...+..
T Consensus 1 ~~k~i~~~l~ey--~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~ 44 (113)
T smart00544 1 LKKKIFLIIEEY--LSSGDTDEAVHCLLELKLPEQHHEVVKVLLTC 44 (113)
T ss_pred ChhHHHHHHHHH--HHcCCHHHHHHHHHHhCCCcchHHHHHHHHHH
Confidence 455666665432 23358888889999999776666666554443
No 4
>PF06375 BLVR: Bovine leukaemia virus receptor (BLVR); InterPro: IPR010474 Bovine leukemia virus (BLV) is one of the most common infectious cattle viruses, with between 30 and 40% of cows in the United States being infected. It is closely related to the human T-cell leukaemia virus type 1 (HTLV-1) and has highly conserved envelope glycoprotein functional domains []. BLV is an oncogenic C-type retrovirus, which results in the animals developing a malignant lymphoma. BLV, like the human and simian T cell leukaemia viruses, is a deltaretrovirus. 182 residues at the amino-terminal of the BLV envelope glycoprotein surface unit encompass the receptor-binding domain. The metabolic activity in B cells, T cells, and thymocytes is indicated by the expression of the BLV-binding receptor []. A candidate gene of the receptor (BLVR) is related, but unique, to a gene family of the delta subunit of the adaptor protein (AP) complex 3, AP-3 []. The AP-3 complex is not clathrin-associated but is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. ; PDB: 4AFI_B.
Probab=58.94 E-value=3.4 Score=36.94 Aligned_cols=11 Identities=18% Similarity=0.250 Sum_probs=4.4
Q ss_pred ccccccccccc
Q 041888 135 LFYYGCNKEKK 145 (326)
Q Consensus 135 ~~~~~~~~~k~ 145 (326)
+.|..-..++.
T Consensus 66 dkYl~~~~~~~ 76 (154)
T PF06375_consen 66 DKYLKQQQERR 76 (154)
T ss_dssp SSEEESST---
T ss_pred HHHHHHHHhhh
Confidence 46665444443
No 5
>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]
Probab=47.86 E-value=60 Score=37.58 Aligned_cols=34 Identities=21% Similarity=0.521 Sum_probs=30.6
Q ss_pred hhHHHHHHHHHHhcCCCCchhhHHHHHHHHHHHh
Q 041888 288 AKDLEQLLQCFLSLNSHHHHRIILEVFTEIWEAL 321 (326)
Q Consensus 288 ~~dLEELL~CYLsLNsk~hH~~Iv~AF~DLw~~L 321 (326)
.+++..||.|...+|-.+.-..+-++|.++...|
T Consensus 1184 r~E~~~Ll~~l~~~g~~eqa~~Lq~~f~ev~~~i 1217 (1265)
T KOG1920|consen 1184 RNELKRLLEVLVTFGMDEQARALQKAFDEVLQAI 1217 (1265)
T ss_pred cHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999977654
No 6
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=40.26 E-value=48 Score=30.98 Aligned_cols=48 Identities=10% Similarity=0.359 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHhcCCCChhHHHHHHHHHHhc-CCCCchhhHHHHHHH
Q 041888 269 YNDFRTSMVEMIVEKQIFAAKDLEQLLQCFLSL-NSHHHHRIILEVFTE 316 (326)
Q Consensus 269 Y~DFR~SMvEMI~ekgi~d~~dLEELL~CYLsL-Nsk~hH~~Iv~AF~D 316 (326)
++.--+.+++++.|+|+.+.++++.++..|-+. .+..--++|-+|.+|
T Consensus 5 ~~~~~~al~~ll~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~D 53 (188)
T PF02979_consen 5 IAARVRALESLLIEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTD 53 (188)
T ss_dssp HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCC
Confidence 344456788999999999999999999999998 666666777777766
No 7
>PRK10072 putative transcriptional regulator; Provisional
Probab=37.47 E-value=51 Score=27.13 Aligned_cols=30 Identities=20% Similarity=0.400 Sum_probs=23.2
Q ss_pred CChHHHHHHHHHHHHHhcCC-----C----ChhHHHHHH
Q 041888 266 SDPYNDFRTSMVEMIVEKQI-----F----AAKDLEQLL 295 (326)
Q Consensus 266 ~DPY~DFR~SMvEMI~ekgi-----~----d~~dLEELL 295 (326)
.||..|..+||.|||.++|- . ...+|.+|.
T Consensus 4 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~eik~LR 42 (96)
T PRK10072 4 KDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLR 42 (96)
T ss_pred CCHHHHHHHHHHHHHHhcCCccceeecccCChHHHHHHH
Confidence 69999999999999997662 1 456676663
No 8
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=35.78 E-value=79 Score=24.57 Aligned_cols=51 Identities=24% Similarity=0.272 Sum_probs=38.3
Q ss_pred HHHHHHHHHHhcC---CCChhHHHH---HHHHHHhcCCCCchhhHHHHHHHHHHHhc
Q 041888 272 FRTSMVEMIVEKQ---IFAAKDLEQ---LLQCFLSLNSHHHHRIILEVFTEIWEALF 322 (326)
Q Consensus 272 FR~SMvEMI~ekg---i~d~~dLEE---LL~CYLsLNsk~hH~~Iv~AF~DLw~~Lf 322 (326)
+++.+.+|+..+. ..++++|.+ -|+-.|.-|+.++..++-+|..+++..++
T Consensus 18 Y~~~l~~~~~~~~~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~a~~~~~~~~~ 74 (121)
T PF14551_consen 18 YMDQLREMIQRNKKSLYVDLDDLREFDPDLAEALIENPYRYLPLFEEALKEVVKELF 74 (121)
T ss_dssp CHHHHHHHHHHT-SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHTT-
T ss_pred HHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3556666766533 237788765 78889999999999999999999988653
No 9
>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=34.33 E-value=62 Score=25.18 Aligned_cols=41 Identities=20% Similarity=0.553 Sum_probs=19.7
Q ss_pred HHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCCCchhhHHHHH
Q 041888 272 FRTSMVEMIVEKQIFAAKDLEQLLQCFLSLNSHHHHRIILEVF 314 (326)
Q Consensus 272 FR~SMvEMI~ekgi~d~~dLEELL~CYLsLNsk~hH~~Iv~AF 314 (326)
||+.+-..|.|- ..-.|.+|...|-..||.+.+|..++...
T Consensus 1 ~rk~i~~~l~ey--~~~~d~~ea~~~l~el~~~~~~~~vv~~~ 41 (113)
T PF02847_consen 1 LRKKIFSILMEY--FSSGDVDEAVECLKELKLPSQHHEVVKVI 41 (113)
T ss_dssp HHHHHHHHHHHH--HHHT-HHHHHHHHHHTT-GGGHHHHHHHH
T ss_pred ChHHHHHHHHHH--hcCCCHHHHHHHHHHhCCCccHHHHHHHH
Confidence 445555555431 12235666666666666665555444433
No 10
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=31.41 E-value=1.8e+02 Score=23.07 Aligned_cols=32 Identities=22% Similarity=0.372 Sum_probs=26.6
Q ss_pred ChHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHhcCCCCc
Q 041888 267 DPYNDFRTSMVEMIVEKQIFAAKDLEQLLQCFLSLNSHHH 306 (326)
Q Consensus 267 DPY~DFR~SMvEMI~ekgi~d~~dLEELL~CYLsLNsk~h 306 (326)
|||-++++-..+.| +.|+.|+.-|+.+.....
T Consensus 1 DPF~~v~~ev~~sl--------~~l~~~~~~~~~~~~~~~ 32 (97)
T PF09177_consen 1 DPFFVVKDEVQSSL--------DRLESLYRRWQRLRSDTS 32 (97)
T ss_dssp -HHHHHHHHHHHHH--------HHHHHHHHHHHHHTTHCC
T ss_pred CCcHHHHHHHHHHH--------HHHHHHHHHHHHhcccCC
Confidence 89999999998888 778999999999876654
No 11
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=29.60 E-value=76 Score=25.20 Aligned_cols=37 Identities=22% Similarity=0.286 Sum_probs=30.0
Q ss_pred ecCChHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHh
Q 041888 264 SSSDPYNDFRTSMVEMIVEKQIFAAKDLEQLLQCFLS 300 (326)
Q Consensus 264 ~S~DPY~DFR~SMvEMI~ekgi~d~~dLEELL~CYLs 300 (326)
.|.+-...|...+.++..++...+.++||++|.-||.
T Consensus 28 ~s~~K~~~l~~~i~~~f~~~~~~~~~~le~~L~~~m~ 64 (82)
T PF10273_consen 28 DSQEKADWLAEVIVDWFTENKDPDADDLEDFLEDIMD 64 (82)
T ss_pred cHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 4666777888888888888777779999999998883
No 12
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=27.11 E-value=81 Score=24.98 Aligned_cols=31 Identities=23% Similarity=0.455 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCCChhHHHHH--HHHHHhcCCC
Q 041888 274 TSMVEMIVEKQIFAAKDLEQL--LQCFLSLNSH 304 (326)
Q Consensus 274 ~SMvEMI~ekgi~d~~dLEEL--L~CYLsLNsk 304 (326)
--|++|..+-||.+.++|+++ .+||+.|-..
T Consensus 13 ~~~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~ 45 (81)
T PF04994_consen 13 PKSERMLAKVGIHTVEDLRELGAVEAYLRLKAS 45 (81)
T ss_dssp HHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH
Confidence 458899999999999999998 6788887654
No 13
>PF10278 Med19: Mediator of RNA pol II transcription subunit 19 ; InterPro: IPR019403 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. Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=25.62 E-value=45 Score=30.79 Aligned_cols=37 Identities=16% Similarity=0.257 Sum_probs=17.3
Q ss_pred cccccCcceecccccCCCCCCCCCcCCCCCCCCCCCC
Q 041888 95 VSEQYSPFALTTTTSNSSDNHNGHVMCPPASPTSPFN 131 (326)
Q Consensus 95 ~s~~~~pf~~~~~~~~~~~~~~~~~~cpp~sp~~~~n 131 (326)
|-|+|.-+........-.+-++.+..=.|..+..+..
T Consensus 97 lPE~yr~~~~~~P~~k~K~Khk~~~~k~~~~~~~~~d 133 (178)
T PF10278_consen 97 LPEQYRLLHQQPPKKKHKHKHKKHRHKDPEDQDADSD 133 (178)
T ss_pred CchHHhhhhccCcchhhhcccccccccCCCCcccccc
Confidence 5677765533322222233444544334555555543
No 14
>KOG3571 consensus Dishevelled 3 and related proteins [General function prediction only]
Probab=25.48 E-value=26 Score=37.45 Aligned_cols=21 Identities=52% Similarity=0.664 Sum_probs=10.2
Q ss_pred cccCC-CCCCcccccccccccc
Q 041888 210 TLSSD-SSGSSLHRRHRSLRKK 230 (326)
Q Consensus 210 SfSSD-SS~s~~~r~~r~~~~k 230 (326)
|.+.| ||-+...|+++++++|
T Consensus 204 s~~Td~ss~srl~~r~K~rrrk 225 (626)
T KOG3571|consen 204 SSSTDQSSVSRLHRRKKRRRRK 225 (626)
T ss_pred cccccchhHHHHHHHHHHhhhh
Confidence 45556 5555455544444333
No 15
>cd00982 gltB_C gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites appear to occur in other domains within the protein, and not the domain in this CD. This particular domain has no known function, but it likely has a structural role as it interacts with the amidotransferase and FMN-binding domains of gltS.
Probab=24.34 E-value=90 Score=30.02 Aligned_cols=59 Identities=19% Similarity=0.260 Sum_probs=41.6
Q ss_pred cceEEEEeecCChHHHHHHH-HHHHHHhcCCC---ChhHHHHHHHHHHhcCCCCchhhHHHHHHHH
Q 041888 256 KDSFAVVKSSSDPYNDFRTS-MVEMIVEKQIF---AAKDLEQLLQCFLSLNSHHHHRIILEVFTEI 317 (326)
Q Consensus 256 ~eSvAVVK~S~DPY~DFR~S-MvEMI~ekgi~---d~~dLEELL~CYLsLNsk~hH~~Iv~AF~DL 317 (326)
..+++++. ||-.+|.+- -.|||.-..+. ++++|++||..|+..-..+..+.||+-|.+.
T Consensus 179 ~gG~iyv~---~~~~~~~~~~n~~~V~~~~l~~~~d~~~l~~ll~~h~~~t~s~~a~~iL~~~~~~ 241 (251)
T cd00982 179 SGGVAYVL---DEDGDFEKKVNHEMVDLERLEDAEDEEQLKELIEEHVEYTGSEKAKEILANWEAY 241 (251)
T ss_pred CCCEEEEE---CCcCChhhhcCHhhEeeccCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHH
Confidence 35666665 666677532 23566543343 6788999999999998888888888877654
No 16
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=23.99 E-value=1.9e+02 Score=20.33 Aligned_cols=32 Identities=19% Similarity=0.452 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHhcCCCCh------hHHHHHHHHHHhc
Q 041888 270 NDFRTSMVEMIVEKQIFAA------KDLEQLLQCFLSL 301 (326)
Q Consensus 270 ~DFR~SMvEMI~ekgi~d~------~dLEELL~CYLsL 301 (326)
+.-|.-|.+++...|+.++ .+|-+|+..|..+
T Consensus 7 e~~R~~L~~~~~~~~l~~~~vl~~Sq~LD~lI~~y~~~ 44 (45)
T PF09388_consen 7 EELRQELNELAEKKGLTDPEVLELSQELDKLINEYQKL 44 (45)
T ss_dssp HHHHHHHHHHHHHCCTTCHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhh
Confidence 3568899999999999887 4688888888653
No 17
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.83 E-value=31 Score=37.30 Aligned_cols=22 Identities=18% Similarity=0.406 Sum_probs=11.4
Q ss_pred ceEEEEeecCChHHHHHHHHHHHHH
Q 041888 257 DSFAVVKSSSDPYNDFRTSMVEMIV 281 (326)
Q Consensus 257 eSvAVVK~S~DPY~DFR~SMvEMI~ 281 (326)
+.|+++.. ..||. ..|..+|-.
T Consensus 271 n~v~~lL~-ssPYH--vdsLLqva~ 292 (665)
T KOG2422|consen 271 NNVLILLI-SSPYH--VDSLLQVAD 292 (665)
T ss_pred cceeeeec-cCCcc--hhHHHHHHH
Confidence 34444444 44986 455555544
No 18
>PF13945 NST1: Salt tolerance down-regulator
Probab=22.46 E-value=38 Score=31.37 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=6.4
Q ss_pred hHHHHHHHHH
Q 041888 289 KDLEQLLQCF 298 (326)
Q Consensus 289 ~dLEELL~CY 298 (326)
++||.|...|
T Consensus 156 ~ele~ly~~~ 165 (190)
T PF13945_consen 156 EELERLYDAY 165 (190)
T ss_pred HHHHHHHHHH
Confidence 5677766555
No 19
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=22.25 E-value=1.2e+02 Score=25.98 Aligned_cols=54 Identities=7% Similarity=0.048 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHhcCCCChhHHHHHHHHHHhc------C--CCCchhhHHHHHHHHHHHhc
Q 041888 269 YNDFRTSMVEMIVEKQIFAAKDLEQLLQCFLSL------N--SHHHHRIILEVFTEIWEALF 322 (326)
Q Consensus 269 Y~DFR~SMvEMI~ekgi~d~~dLEELL~CYLsL------N--sk~hH~~Iv~AF~DLw~~Lf 322 (326)
|.+--..-.+|++...-.+||+|=+|-..|+.+ + +......+.+.+.+|...+.
T Consensus 11 Yq~I~~lS~~ML~aA~~g~Wd~Li~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL 72 (121)
T PRK10548 11 WQQILTLSQSMLRLATEGQWDELIEQEVAYVQAVEEIAHLTIPPDISTVMQEQLRPMLRQIL 72 (121)
T ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHH
Confidence 667777888999999999999999999999865 1 23456667777777766543
No 20
>PF08887 GAD-like: GAD-like domain; InterPro: IPR014983 This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain IPR004115 from INTERPRO.
Probab=21.71 E-value=32 Score=28.87 Aligned_cols=45 Identities=18% Similarity=0.296 Sum_probs=36.5
Q ss_pred HHHHHHHHhcCCC----------ChhHHHHHHHHHHh----cCCCCchhhHHHHHHHHH
Q 041888 274 TSMVEMIVEKQIF----------AAKDLEQLLQCFLS----LNSHHHHRIILEVFTEIW 318 (326)
Q Consensus 274 ~SMvEMI~ekgi~----------d~~dLEELL~CYLs----LNsk~hH~~Iv~AF~DLw 318 (326)
+.+.+.-.+.|.. ++++.+++|..-|. +....+|.+.+.||-||+
T Consensus 34 ~~Ll~~W~~~G~g~~~dG~f~~vnP~dy~~vl~~~~~~~~~~~~~~~~~ia~tAFGdl~ 92 (109)
T PF08887_consen 34 DELLEYWKEYGFGGYGDGLFWLVNPDDYEDVLDEWLGGTPLFDPDNYIPIARTAFGDLY 92 (109)
T ss_pred HHHHHHHHHcCCchhcCcEEEEECHHHHHHHHHHHhcCCccccCceEEEEEEcccccEE
Confidence 4566666666543 68999999999886 788999999999999975
No 21
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=20.18 E-value=1e+02 Score=22.97 Aligned_cols=27 Identities=22% Similarity=0.390 Sum_probs=20.4
Q ss_pred HHHHHHHHhcCCCChhHHHHHHHHHHh
Q 041888 274 TSMVEMIVEKQIFAAKDLEQLLQCFLS 300 (326)
Q Consensus 274 ~SMvEMI~ekgi~d~~dLEELL~CYLs 300 (326)
+|..|.+.+.|+.+.+++++||.-..-
T Consensus 26 ~svre~v~~~g~lt~ee~d~ll~p~~m 52 (55)
T PF10415_consen 26 RSVREVVLEEGLLTEEELDELLDPERM 52 (55)
T ss_dssp --HHHHHHHTTSS-HHHHHHHTSHHHH
T ss_pred CCHHHHHHHcCCCCHHHHHHHcCHHHc
Confidence 578899999999999999999865443
Done!