Query 033637
Match_columns 114
No_of_seqs 100 out of 160
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 04:33:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033637.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033637hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05669 Med31: SOH1; InterPr 100.0 2.9E-49 6.3E-54 283.8 6.6 85 27-111 1-85 (101)
2 KOG4086 Transcriptional regula 100.0 8.7E-45 1.9E-49 270.0 8.0 83 28-110 14-96 (130)
3 COG5088 SOH1 Rad5p-binding pro 100.0 3.7E-39 7.9E-44 235.4 9.3 83 28-110 14-96 (114)
4 PF05669 Med31: SOH1; InterPr 64.0 2.8 6E-05 30.6 0.5 43 56-104 15-57 (101)
5 PF12672 DUF3793: Protein of u 49.5 32 0.0007 26.3 4.2 44 38-88 67-111 (176)
6 KOG4086 Transcriptional regula 45.4 11 0.00024 28.8 1.1 14 69-82 40-53 (130)
7 smart00727 STI1 Heat shock cha 42.7 30 0.00066 19.8 2.5 20 90-109 6-29 (41)
8 PF01340 MetJ: Met Apo-repress 39.6 23 0.00051 26.1 2.0 35 78-112 22-59 (104)
9 PF05021 NPL4: NPL4 family; I 37.8 56 0.0012 27.4 4.2 59 34-92 247-305 (306)
10 cd07291 PX_SNX5 The phosphoino 36.9 24 0.00052 27.2 1.8 40 28-67 95-140 (141)
11 PF14307 Glyco_tran_WbsX: Glyc 33.2 35 0.00077 28.0 2.3 29 50-78 126-155 (345)
12 cd07292 PX_SNX6 The phosphoino 32.9 23 0.0005 27.3 1.1 39 29-67 96-140 (141)
13 PF09060 L27_N: L27_N; InterP 28.3 32 0.0007 22.5 1.0 16 87-102 27-42 (49)
14 PF02980 FokI_C: Restriction e 27.6 36 0.00079 26.4 1.4 19 77-95 9-27 (142)
15 PRK05264 transcriptional repre 27.2 50 0.0011 24.5 2.0 44 69-112 14-60 (105)
16 PRK05321 nicotinate phosphorib 26.1 1.1E+02 0.0023 26.7 4.1 38 30-68 54-92 (400)
17 cd00490 Met_repressor_MetJ Met 25.6 56 0.0012 24.1 2.0 44 69-112 13-59 (103)
18 PLN03219 uncharacterized prote 25.4 60 0.0013 24.1 2.1 46 3-51 26-74 (108)
19 PF07849 DUF1641: Protein of u 24.3 82 0.0018 19.0 2.3 20 83-102 11-30 (42)
20 smart00766 DnaG_DnaB_bind DNA 24.3 1.6E+02 0.0035 18.5 3.8 54 40-100 8-65 (125)
21 COG3060 MetJ Transcriptional r 22.9 61 0.0013 23.8 1.8 44 69-112 14-60 (105)
22 PF14947 HTH_45: Winged helix- 22.7 1.7E+02 0.0037 19.0 3.7 64 28-92 2-69 (77)
23 PF12564 TypeIII_RM_meth: Type 22.1 56 0.0012 21.6 1.3 39 40-79 9-51 (57)
No 1
>PF05669 Med31: SOH1; InterPro: IPR008831 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. This entry represents subunit Med31 of the Mediator complex. It contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant [] and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent, 0016592 mediator complex; PDB: 3FBI_D 3FBN_D.
Probab=100.00 E-value=2.9e-49 Score=283.82 Aligned_cols=85 Identities=66% Similarity=1.198 Sum_probs=70.9
Q ss_pred ccchhHHHHHHHHhhcChHHHHHHHHcccCCCHHHHHHHHHHhhhcCCCccccccChhHHHHHHhhCChHHHHHhcCchH
Q 033637 27 GRQRFLLELEFVQCLANPTYIHYLAQNRYFEDEAFIGYLKYLQYWQRPEYIKFIMYPHCLYFLELLQNANFRNAMAHPAN 106 (114)
Q Consensus 27 ~~~RFe~ELEFVQ~LANP~YL~~LA~~gy~~d~~FinYLkYL~YWk~PeYak~l~YP~cL~~L~LLq~~~FR~~i~~p~~ 106 (114)
+++|||+|||||||||||+||+|||++|||+||+|+||||||+|||+|+|+|||+||+||+||+|||+++||++|++|++
T Consensus 1 ~~~RFe~ELEFVQ~LaNp~Yl~~La~~~y~~d~~F~nYLkYL~YW~~P~Yakyl~YP~cL~~L~LLq~~~FR~~i~~~~~ 80 (101)
T PF05669_consen 1 NPTRFELELEFVQCLANPQYLNYLAQQGYFEDPAFINYLKYLQYWKRPEYAKYLVYPHCLHFLELLQNEEFRQAIANPDF 80 (101)
T ss_dssp ---HHHHHHHHHHHTTSHHHHHHHH-SGGGTSTHHHHHHHHGGGGGSTTGGGG-SSTHHHHHHH-HHHHHHHH--B-TTS
T ss_pred CcchhHHHHHHHHHhcCHHHHHHHHhcCccCCHHHHHHHHHHHHhCCCchhhhhcChHHHHHHHHHCcHHHHHHHhCCcc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhh
Q 033637 107 KVRLC 111 (114)
Q Consensus 107 ~~~l~ 111 (114)
++.+.
T Consensus 81 ~~~i~ 85 (101)
T PF05669_consen 81 AKFIM 85 (101)
T ss_dssp -----
T ss_pred cchhc
Confidence 88764
No 2
>KOG4086 consensus Transcriptional regulator SOH1 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=8.7e-45 Score=270.02 Aligned_cols=83 Identities=58% Similarity=1.124 Sum_probs=80.2
Q ss_pred cchhHHHHHHHHhhcChHHHHHHHHcccCCCHHHHHHHHHHhhhcCCCccccccChhHHHHHHhhCChHHHHHhcCchHH
Q 033637 28 RQRFLLELEFVQCLANPTYIHYLAQNRYFEDEAFIGYLKYLQYWQRPEYIKFIMYPHCLYFLELLQNANFRNAMAHPANK 107 (114)
Q Consensus 28 ~~RFe~ELEFVQ~LANP~YL~~LA~~gy~~d~~FinYLkYL~YWk~PeYak~l~YP~cL~~L~LLq~~~FR~~i~~p~~~ 107 (114)
+.|||+|||||||||||+||+||||+|||+|++|+||||||+|||+|+|+|||+||+|||||++||++.||..|++.+..
T Consensus 14 ~~RFevELEFVQ~LaNp~YLnfLaQ~g~fk~e~F~nYLkYLeYWk~PeYak~l~YP~CL~mLelL~~~~fr~~i~~~~~~ 93 (130)
T KOG4086|consen 14 RSRFEVELEFVQCLANPNYLNFLAQRGYFKDEAFVNYLKYLEYWKEPEYAKFLKYPQCLHMLELLQSEQFRDEISNAQLA 93 (130)
T ss_pred CcchhhhHHHHHHhcChHHHHHHHHcccccCHHHHHHHHHHHHhcCccHHHHHhhHhHHHHHHHhccHHHHHHHhhhHHH
Confidence 55999999999999999999999999999999999999999999999999999999999999999999999999999887
Q ss_pred Hhh
Q 033637 108 VRL 110 (114)
Q Consensus 108 ~~l 110 (114)
+.+
T Consensus 94 k~l 96 (130)
T KOG4086|consen 94 KFL 96 (130)
T ss_pred HHh
Confidence 765
No 3
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=100.00 E-value=3.7e-39 Score=235.36 Aligned_cols=83 Identities=47% Similarity=0.871 Sum_probs=80.0
Q ss_pred cchhHHHHHHHHhhcChHHHHHHHHcccCCCHHHHHHHHHHhhhcCCCccccccChhHHHHHHhhCChHHHHHhcCchHH
Q 033637 28 RQRFLLELEFVQCLANPTYIHYLAQNRYFEDEAFIGYLKYLQYWQRPEYIKFIMYPHCLYFLELLQNANFRNAMAHPANK 107 (114)
Q Consensus 28 ~~RFe~ELEFVQ~LANP~YL~~LA~~gy~~d~~FinYLkYL~YWk~PeYak~l~YP~cL~~L~LLq~~~FR~~i~~p~~~ 107 (114)
.+|||+||||||+||||+||++|+|+|+|+|++|.+||+||+|||.|||+|||+||+||+||++|+++.||..+.+.++.
T Consensus 14 ~sRFE~ELEFvQ~L~Np~Yl~~Ltq~~~fese~F~~YL~YlEYWr~PeYs~fivYP~CL~iL~lLn~~~~~~~vs~~~l~ 93 (114)
T COG5088 14 DSRFEVELEFVQSLANPQYLTLLTQQQIFESENFKNYLKYLEYWRNPEYSQFIVYPNCLFILKLLNGFMESAIVSEDGLL 93 (114)
T ss_pred CchhHHHHHHHHHhcCHHHHHHHHHhhhhcCHHHHHHHHHHHHhhCCcccceeechhHHHHHHHhcchhHhhhhhhhHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999998887
Q ss_pred Hhh
Q 033637 108 VRL 110 (114)
Q Consensus 108 ~~l 110 (114)
+.+
T Consensus 94 ~~l 96 (114)
T COG5088 94 EGL 96 (114)
T ss_pred Hhh
Confidence 765
No 4
>PF05669 Med31: SOH1; InterPro: IPR008831 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. This entry represents subunit Med31 of the Mediator complex. It contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant [] and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent, 0016592 mediator complex; PDB: 3FBI_D 3FBN_D.
Probab=63.96 E-value=2.8 Score=30.65 Aligned_cols=43 Identities=19% Similarity=0.643 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCccccccChhHHHHHHhhCChHHHHHhcCc
Q 033637 56 FEDEAFIGYLKYLQYWQRPEYIKFIMYPHCLYFLELLQNANFRNAMAHP 104 (114)
Q Consensus 56 ~~d~~FinYLkYL~YWk~PeYak~l~YP~cL~~L~LLq~~~FR~~i~~p 104 (114)
+.+|..++||..=.||++|.+..||+| |+--..|+.-+-|.-|
T Consensus 15 LaNp~Yl~~La~~~y~~d~~F~nYLkY------L~YW~~P~Yakyl~YP 57 (101)
T PF05669_consen 15 LANPQYLNYLAQQGYFEDPAFINYLKY------LQYWKRPEYAKYLVYP 57 (101)
T ss_dssp TTSHHHHHHHH-SGGGTSTHHHHHHHH------GGGGGSTTGGGG-SST
T ss_pred hcCHHHHHHHHhcCccCCHHHHHHHHH------HHHhCCCchhhhhcCh
Confidence 556777777776689999998877766 3333445544444444
No 5
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=49.51 E-value=32 Score=26.30 Aligned_cols=44 Identities=23% Similarity=0.442 Sum_probs=35.2
Q ss_pred HHhhcChHHHHHHHHcccCCCHHHHHHHHHHh-hhcCCCccccccChhHHHH
Q 033637 38 VQCLANPTYIHYLAQNRYFEDEAFIGYLKYLQ-YWQRPEYIKFIMYPHCLYF 88 (114)
Q Consensus 38 VQ~LANP~YL~~LA~~gy~~d~~FinYLkYL~-YWk~PeYak~l~YP~cL~~ 88 (114)
-..|++|.--.+|.+-|| .+..+.++|..|. =|+.-+ +||-+.+
T Consensus 67 ~~~L~~~~~~~fL~~~GY-~~~~~~~~L~~L~~R~~~~~------FPHEIGi 111 (176)
T PF12672_consen 67 ERYLSDPEVRSFLKSYGY-PDSSLEDCLEHLKKRFESGE------FPHEIGI 111 (176)
T ss_pred HHHHCCHHHHHHHHHCCc-CCCCHHHHHHHHHHHhcCCC------CCchhHh
Confidence 368999999999999999 9999999999993 343332 7776655
No 6
>KOG4086 consensus Transcriptional regulator SOH1 [Transcription; Replication, recombination and repair]
Probab=45.38 E-value=11 Score=28.83 Aligned_cols=14 Identities=14% Similarity=0.819 Sum_probs=9.0
Q ss_pred hhhcCCCccccccC
Q 033637 69 QYWQRPEYIKFIMY 82 (114)
Q Consensus 69 ~YWk~PeYak~l~Y 82 (114)
.|||.+.+..||+|
T Consensus 40 g~fk~e~F~nYLkY 53 (130)
T KOG4086|consen 40 GYFKDEAFVNYLKY 53 (130)
T ss_pred ccccCHHHHHHHHH
Confidence 57777766666555
No 7
>smart00727 STI1 Heat shock chaperonin-binding motif.
Probab=42.68 E-value=30 Score=19.84 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=9.3
Q ss_pred HhhCChHHHHHhc----CchHHHh
Q 033637 90 ELLQNANFRNAMA----HPANKVR 109 (114)
Q Consensus 90 ~LLq~~~FR~~i~----~p~~~~~ 109 (114)
.++++|.|+..+. ||+.+..
T Consensus 6 ~~l~~P~~~~~l~~~~~nP~~~~~ 29 (41)
T smart00727 6 LRLQNPQVQSLLQDMQQNPDMLAQ 29 (41)
T ss_pred HHHcCHHHHHHHHHHHHCHHHHHH
Confidence 3344555555544 5544433
No 8
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=39.59 E-value=23 Score=26.08 Aligned_cols=35 Identities=26% Similarity=0.298 Sum_probs=25.6
Q ss_pred ccccChhHHHHHHhhCChHHHHHhcC---chHHHhhhh
Q 033637 78 KFIMYPHCLYFLELLQNANFRNAMAH---PANKVRLCC 112 (114)
Q Consensus 78 k~l~YP~cL~~L~LLq~~~FR~~i~~---p~~~~~l~~ 112 (114)
|=|+----|++|++|.+|.-|+.+.| ..+.+.||.
T Consensus 22 kkiTVSIP~kVLkvLtdERTrRQvnNLRHATNSeLLcE 59 (104)
T PF01340_consen 22 KKITVSIPLKVLKVLTDERTRRQVNNLRHATNSELLCE 59 (104)
T ss_dssp EEEEEEEEHHHHHHHHHHHHHHHHTTBSS-SHHHHHHH
T ss_pred heeeEeeeHHHHHHHhhHHHHHHHhhhhhcccHHHHHH
Confidence 44444445899999999999999876 456677764
No 9
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=37.81 E-value=56 Score=27.43 Aligned_cols=59 Identities=10% Similarity=0.111 Sum_probs=39.6
Q ss_pred HHHHHHhhcChHHHHHHHHcccCCCHHHHHHHHHHhhhcCCCccccccChhHHHHHHhh
Q 033637 34 ELEFVQCLANPTYIHYLAQNRYFEDEAFIGYLKYLQYWQRPEYIKFIMYPHCLYFLELL 92 (114)
Q Consensus 34 ELEFVQ~LANP~YL~~LA~~gy~~d~~FinYLkYL~YWk~PeYak~l~YP~cL~~L~LL 92 (114)
.-.|++.|+|=|.|-||+..+.|.+..+..=++-..==......++..=|+...++.+|
T Consensus 247 ~~~~~~~lsDFHLLlfL~~~~il~~~d~~~L~~av~~~d~~~~~~~~~~~~w~tl~~il 305 (306)
T PF05021_consen 247 SQPFLERLSDFHLLLFLATMDILDKEDMPLLCEAVRERDEEAAYQLSESEGWQTLIAIL 305 (306)
T ss_pred cchHhhhcccHHHHHHHHhCCCCCHHHHHHHHHHHHhcCHHHHHHhhcChHHHHHHHHh
Confidence 36899999999999999999999988888777666421122233333334444444444
No 10
>cd07291 PX_SNX5 The phosphoinositide binding Phox Homology domain of Sorting Nexin 5. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting
Probab=36.92 E-value=24 Score=27.16 Aligned_cols=40 Identities=20% Similarity=0.440 Sum_probs=25.4
Q ss_pred cchhHHHHHHHHhh----c-ChHHHHHHHHcc-cCCCHHHHHHHHH
Q 033637 28 RQRFLLELEFVQCL----A-NPTYIHYLAQNR-YFEDEAFIGYLKY 67 (114)
Q Consensus 28 ~~RFe~ELEFVQ~L----A-NP~YL~~LA~~g-y~~d~~FinYLkY 67 (114)
+.|.++|.|.+... | .-.||+=+|+.- .-.|+.|..||.|
T Consensus 95 ~~r~~~~~~~~~~~kk~~a~lE~fL~Ria~HP~l~~d~~f~~FLe~ 140 (141)
T cd07291 95 KMKQELEAEYLAVFKKTVQVHEVFLQRLSSHPSLSKDRNFHIFLEY 140 (141)
T ss_pred HHHHHhhhhhhhHHHHHHHHHHHHHHHHhhCCeeccCcchhhhccC
Confidence 34555565554322 2 345888888764 5678889888865
No 11
>PF14307 Glyco_tran_WbsX: Glycosyltransferase WbsX
Probab=33.22 E-value=35 Score=28.00 Aligned_cols=29 Identities=31% Similarity=0.781 Sum_probs=22.6
Q ss_pred HHHcccCCCHHHHHHHHHH-hhhcCCCccc
Q 033637 50 LAQNRYFEDEAFIGYLKYL-QYWQRPEYIK 78 (114)
Q Consensus 50 LA~~gy~~d~~FinYLkYL-~YWk~PeYak 78 (114)
|..+.|-....+.++.+|| .|+++|-|.|
T Consensus 126 l~~q~y~~~~d~~~~~~~l~~~F~D~rYik 155 (345)
T PF14307_consen 126 LIEQKYSGEDDWKEHFRYLLPYFKDPRYIK 155 (345)
T ss_pred cccccCCchhHHHHHHHHHHHHhCCCCcee
Confidence 4556777666677777777 8999999987
No 12
>cd07292 PX_SNX6 The phosphoinositide binding Phox Homology domain of Sorting Nexin 6. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transfo
Probab=32.86 E-value=23 Score=27.31 Aligned_cols=39 Identities=21% Similarity=0.362 Sum_probs=25.9
Q ss_pred chhHHHHHHHHhh-----cChHHHHHHHHcc-cCCCHHHHHHHHH
Q 033637 29 QRFLLELEFVQCL-----ANPTYIHYLAQNR-YFEDEAFIGYLKY 67 (114)
Q Consensus 29 ~RFe~ELEFVQ~L-----ANP~YL~~LA~~g-y~~d~~FinYLkY 67 (114)
.|.++|.|.+... +.-.||+-+|+.- .-.|+.|..||.|
T Consensus 96 ~~~~l~~~~~~~~kk~~a~~E~Fl~Ria~HP~l~~D~~f~~FLe~ 140 (141)
T cd07292 96 MKQELEAEYLAIFKKTVAMHEVFLCRVAAHPILRKDLNFHVFLEY 140 (141)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccCcchhheecc
Confidence 4555666655433 3346888887775 4578899998877
No 13
>PF09060 L27_N: L27_N; InterPro: IPR015145 The L27_N domain plays a role in the biogenesis of tight junctions and in the establishment of cell polarity in epithelial cells. Each L27_N domain consists of three alpha-helices, the first two of which form an antiparallel coiled-coil. Two L27 domains come together to form a four-helical bundle with the antiparallel coiled-coils formed by the first two helices. The third helix of each domain forms another coiled-coil packing at one end of the four-helix bundle, creating a large hydrophobic interface: the hydrophobic interactions are the major force that drives heterodimer formation []. ; PDB: 1Y76_B 3UIT_B 1VF6_C.
Probab=28.33 E-value=32 Score=22.47 Aligned_cols=16 Identities=50% Similarity=0.862 Sum_probs=12.3
Q ss_pred HHHHhhCChHHHHHhc
Q 033637 87 YFLELLQNANFRNAMA 102 (114)
Q Consensus 87 ~~L~LLq~~~FR~~i~ 102 (114)
-+|.||++++|+.+.+
T Consensus 27 lllqLl~~~dFq~A~~ 42 (49)
T PF09060_consen 27 LLLQLLQNSDFQNAFK 42 (49)
T ss_dssp HHHHHHH-HHHHHHHH
T ss_pred HHHHHHhhHhHHHHHH
Confidence 3688999999998864
No 14
>PF02980 FokI_C: Restriction endonuclease FokI, catalytic domain; InterPro: IPR004233 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition (IPR004234 from INTERPRO) and cleavage functions, respectively. The catalytic domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. The catalytic domain is sequestered in a 'piggyback' fashion by the recognition domain [].; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=27.64 E-value=36 Score=26.36 Aligned_cols=19 Identities=26% Similarity=0.422 Sum_probs=15.3
Q ss_pred cccccChhHHHHHHhhCCh
Q 033637 77 IKFIMYPHCLYFLELLQNA 95 (114)
Q Consensus 77 ak~l~YP~cL~~L~LLq~~ 95 (114)
-.+|.||.+-.+|.||++.
T Consensus 9 ~alLsYPpA~rvL~lL~~~ 27 (142)
T PF02980_consen 9 EALLSYPPAARVLSLLGEN 27 (142)
T ss_dssp HHHTT-HHHHHHHHHHTT-
T ss_pred HHHhcCCcHHHHHHHHHHh
Confidence 4678999999999999873
No 15
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=27.18 E-value=50 Score=24.46 Aligned_cols=44 Identities=23% Similarity=0.283 Sum_probs=32.4
Q ss_pred hhhcCCCccccccChhHHHHHHhhCChHHHHHhcC---chHHHhhhh
Q 033637 69 QYWQRPEYIKFIMYPHCLYFLELLQNANFRNAMAH---PANKVRLCC 112 (114)
Q Consensus 69 ~YWk~PeYak~l~YP~cL~~L~LLq~~~FR~~i~~---p~~~~~l~~ 112 (114)
+.=|.-+=+|=|+----+.+|+.|.++.-|+.+.| ..+.+.||.
T Consensus 14 EHGkKseqVKKiTVSIP~kVLkiLTdERTRRQvnNLRHATNSELLCE 60 (105)
T PRK05264 14 EHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCE 60 (105)
T ss_pred HcChhhhhheeeeEeeeHHHHHHHhhHHHHHHHhhhhhcccHHHHHH
Confidence 34445555676766667999999999999999876 456677764
No 16
>PRK05321 nicotinate phosphoribosyltransferase; Provisional
Probab=26.07 E-value=1.1e+02 Score=26.71 Aligned_cols=38 Identities=18% Similarity=0.427 Sum_probs=25.3
Q ss_pred hhHHHHHHHHhhc-ChHHHHHHHHcccCCCHHHHHHHHHH
Q 033637 30 RFLLELEFVQCLA-NPTYIHYLAQNRYFEDEAFIGYLKYL 68 (114)
Q Consensus 30 RFe~ELEFVQ~LA-NP~YL~~LA~~gy~~d~~FinYLkYL 68 (114)
-.+.+++++..|. ...=+.||++.++|++ +|+.||+-.
T Consensus 54 gl~~~i~~l~~l~ft~eei~yL~~~~~~~~-~fl~~L~~f 92 (400)
T PRK05321 54 EIREQLDHLCTLRLTDDELDYLRGLPFFKP-DFLDWLRLF 92 (400)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHhCCCCCH-HHHHHHHhC
Confidence 4566777777665 5666788888787764 566655543
No 17
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=25.57 E-value=56 Score=24.08 Aligned_cols=44 Identities=23% Similarity=0.283 Sum_probs=32.3
Q ss_pred hhhcCCCccccccChhHHHHHHhhCChHHHHHhcC---chHHHhhhh
Q 033637 69 QYWQRPEYIKFIMYPHCLYFLELLQNANFRNAMAH---PANKVRLCC 112 (114)
Q Consensus 69 ~YWk~PeYak~l~YP~cL~~L~LLq~~~FR~~i~~---p~~~~~l~~ 112 (114)
+.=|.-|-+|=|+----|.+|+.|.++.-|+.+.| ..+.+.||.
T Consensus 13 EhGkKseqVKKiTVsIP~kVLkiLTdERTRRQvnnlRHATNSELLCE 59 (103)
T cd00490 13 EHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCE 59 (103)
T ss_pred HcChhhhhheeeeEeeeHHHHHHHhhHHHHHHHhhhhhcccHHHHHH
Confidence 33445555666766667999999999999999876 456677764
No 18
>PLN03219 uncharacterized protein; Provisional
Probab=25.41 E-value=60 Score=24.06 Aligned_cols=46 Identities=22% Similarity=0.463 Sum_probs=27.3
Q ss_pred CCCCCCcCCCCCCCCC---CCCCCCccccchhHHHHHHHHhhcChHHHHHHH
Q 033637 3 ASKDNEEASDAPSSPK---KVYKDPDDGRQRFLLELEFVQCLANPTYIHYLA 51 (114)
Q Consensus 3 ~~~~~~~~~~~p~~p~---~~~~~~~~~~~RFe~ELEFVQ~LANP~YL~~LA 51 (114)
+|.+++....+..+|+ +.+-..++.+.||.+-++ .|.+|-+..-|.
T Consensus 26 ~~~~~~~~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~---yL~hP~F~~LL~ 74 (108)
T PLN03219 26 SSSPSSSTTTSGLVPKGHVAVYVGEQMEKKRFVVPIS---YLNHPLFREFLN 74 (108)
T ss_pred CCCCccCCCCCCCCCCCeEEEEECCCCCceEEEEEHH---HcCChHHHHHHH
Confidence 4455555555444444 222222234789999988 677888777774
No 19
>PF07849 DUF1641: Protein of unknown function (DUF1641); InterPro: IPR012440 Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long.
Probab=24.27 E-value=82 Score=19.02 Aligned_cols=20 Identities=10% Similarity=0.242 Sum_probs=16.2
Q ss_pred hhHHHHHHhhCChHHHHHhc
Q 033637 83 PHCLYFLELLQNANFRNAMA 102 (114)
Q Consensus 83 P~cL~~L~LLq~~~FR~~i~ 102 (114)
+.-+.++++|.||+.++.|.
T Consensus 11 ~gl~gl~~~l~DpdvqrgL~ 30 (42)
T PF07849_consen 11 VGLFGLLRALRDPDVQRGLG 30 (42)
T ss_pred CCHHHHHHHHcCHHHHHHHH
Confidence 35678999999999998764
No 20
>smart00766 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. DnaG_DnaB_bind defines a domain of primase required for functional interaction with DnaB that attracts primase to the replication fork. DnaG_DnaB_bind is responsible for the interaction between DnaG and DnaB.
Probab=24.26 E-value=1.6e+02 Score=18.54 Aligned_cols=54 Identities=15% Similarity=0.169 Sum_probs=33.3
Q ss_pred hhcChHHHHHHHHc---ccCCCHHHHHHHHHHhh-hcCCCccccccChhHHHHHHhhCChHHHHH
Q 033637 40 CLANPTYIHYLAQN---RYFEDEAFIGYLKYLQY-WQRPEYIKFIMYPHCLYFLELLQNANFRNA 100 (114)
Q Consensus 40 ~LANP~YL~~LA~~---gy~~d~~FinYLkYL~Y-Wk~PeYak~l~YP~cL~~L~LLq~~~FR~~ 100 (114)
.|.||..+.++... .-|.+|.+....+++.+ +..|. +..-.+++-+.++.++..
T Consensus 8 ll~~P~l~~~v~~~~~~~~f~~~~~~~l~~~l~~~~~~~~-------~~~~~l~~~~~~~~~~~~ 65 (125)
T smart00766 8 LLQNPELASLVPDLLTLEDFTHPGLALLAELLATCRGNPG-------LTTGQLLEHWRDTPYEEL 65 (125)
T ss_pred HHHCHHHHhhCCCchhhhhcccccHHHHHHHHHHHHcCCC-------CcHHHHHHHHcCChHHHH
Confidence 57789988888533 35788877777777753 45543 234456666655444443
No 21
>COG3060 MetJ Transcriptional regulator of met regulon [Transcription / Amino acid transport and metabolism]
Probab=22.94 E-value=61 Score=23.85 Aligned_cols=44 Identities=23% Similarity=0.283 Sum_probs=32.4
Q ss_pred hhhcCCCccccccChhHHHHHHhhCChHHHHHhcC---chHHHhhhh
Q 033637 69 QYWQRPEYIKFIMYPHCLYFLELLQNANFRNAMAH---PANKVRLCC 112 (114)
Q Consensus 69 ~YWk~PeYak~l~YP~cL~~L~LLq~~~FR~~i~~---p~~~~~l~~ 112 (114)
+.=|.-+-+|-|+----|++|++|.++.-|+.+.| ..+.+.||.
T Consensus 14 ehgkkseqvkkitvsip~kvl~ilt~ertrrq~~nlrhatnsellce 60 (105)
T COG3060 14 EHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCE 60 (105)
T ss_pred hcchhhhhhheeeEeeeHHHHHHHhhHHHHHHHHhhhhhhhHHHHHH
Confidence 34455566677777667999999999999998765 456666664
No 22
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=22.67 E-value=1.7e+02 Score=19.04 Aligned_cols=64 Identities=19% Similarity=0.219 Sum_probs=39.1
Q ss_pred cchhHHHHHHHHhh-cChHHHHHHHHcccCCCHHHHHHHHHHh---hhcCCCccccccChhHHHHHHhh
Q 033637 28 RQRFLLELEFVQCL-ANPTYIHYLAQNRYFEDEAFIGYLKYLQ---YWQRPEYIKFIMYPHCLYFLELL 92 (114)
Q Consensus 28 ~~RFe~ELEFVQ~L-ANP~YL~~LA~~gy~~d~~FinYLkYL~---YWk~PeYak~l~YP~cL~~L~LL 92 (114)
++|.++=.+.+.++ .++.=...|+..--+.-..|..||++|. +-+. .-..|..=|-...+|+.+
T Consensus 2 Rs~~~Ii~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 2 RSRLEIIFDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK-KDGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp TTTTHHHHHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE-ETTEEEE-HHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC-CCCEEEECccHHHHHHHH
Confidence 45667767777777 6677777887777788888888888883 3222 334455555556666655
No 23
>PF12564 TypeIII_RM_meth: Type III restriction/modification enzyme methylation subunit; InterPro: IPR022221 This domain family is found in bacteria, and is approximately 60 amino acids in length. It is found in association with PF01555 from PFAM. There are two completely conserved residues (F and S) that may be functionally important. It is found in bacterial phage resistance proteins, in particular in the methylation subunit of the type III restriction/modification enzyme complex [].
Probab=22.05 E-value=56 Score=21.57 Aligned_cols=39 Identities=26% Similarity=0.565 Sum_probs=27.7
Q ss_pred hhcChH----HHHHHHHcccCCCHHHHHHHHHHhhhcCCCcccc
Q 033637 40 CLANPT----YIHYLAQNRYFEDEAFIGYLKYLQYWQRPEYIKF 79 (114)
Q Consensus 40 ~LANP~----YL~~LA~~gy~~d~~FinYLkYL~YWk~PeYak~ 79 (114)
.|+|+. |..-++..-.|+...|+.+|.|=+||-. .|-+|
T Consensus 9 LL~~~~ik~~Ff~~i~g~~iF~~~~f~~~l~~keyl~~-SyT~y 51 (57)
T PF12564_consen 9 LLSNELIKEHFFKKIDGVLIFKKNKFIEFLEYKEYLPD-SYTKY 51 (57)
T ss_pred HHcCHHHHHHHHHHhCCeEEeeHHHHHHHHHHHhhhhh-hHHHh
Confidence 455654 4444444567999999999999999977 44443
Done!