Query psy17374
Match_columns 71
No_of_seqs 117 out of 657
Neff 7.0
Searched_HMMs 46136
Date Fri Aug 16 20:50:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17374hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03028 Dynein_heavy: Dynein 99.8 6.7E-20 1.4E-24 137.0 5.3 67 3-71 519-586 (707)
2 PF03822 NAF: NAF domain; Int 43.2 7.4 0.00016 21.5 -0.1 12 47-58 14-25 (63)
3 PF04062 P21-Arc: ARP2/3 compl 36.4 1.1E+02 0.0024 20.2 4.5 23 48-70 111-143 (175)
4 cd08871 START_STARD10-like Lip 36.1 48 0.001 21.6 2.9 38 3-41 172-209 (222)
5 PF12249 AftA_C: Arabinofurano 34.6 77 0.0017 21.0 3.6 17 25-41 82-98 (178)
6 PF09396 Thrombin_light: Throm 26.1 35 0.00076 18.0 0.7 8 54-61 8-15 (49)
7 PF03490 Varsurf_PPLC: Variant 26.0 54 0.0012 17.4 1.5 15 20-34 7-21 (51)
8 cd08868 START_STARD1_3_like Ch 25.3 39 0.00085 21.8 1.1 31 3-34 177-207 (208)
9 cd00291 SirA_YedF_YeeD SirA, Y 25.1 66 0.0014 16.7 1.8 19 49-67 1-19 (69)
10 cd08867 START_STARD4_5_6-like 24.9 59 0.0013 20.9 1.8 29 3-32 177-205 (206)
11 cd07561 Peptidase_S41_CPP_like 24.3 1.1E+02 0.0023 20.8 3.1 39 21-66 9-47 (256)
12 PF13817 DDE_Tnp_IS66_C: IS66 23.9 88 0.0019 15.4 2.0 15 20-34 12-26 (39)
13 PF01206 TusA: Sulfurtransfera 22.4 87 0.0019 16.5 1.9 18 49-66 2-19 (70)
14 cd08818 CARD_MDA5_1 Caspase ac 21.9 64 0.0014 19.0 1.4 17 50-68 63-79 (88)
15 cd03421 SirA_like_N SirA_like_ 21.9 89 0.0019 16.4 1.9 18 50-67 2-19 (67)
16 KOG2099|consensus 21.8 94 0.002 24.8 2.6 15 4-18 486-500 (843)
17 TIGR02115 potass_kdpF K+-trans 21.7 26 0.00057 16.1 -0.2 9 54-62 17-25 (26)
18 PF05209 MinC_N: Septum format 21.4 1.6E+02 0.0034 16.9 3.0 44 20-68 24-67 (99)
19 PF06868 DUF1257: Protein of u 21.3 78 0.0017 18.9 1.7 15 56-70 62-76 (105)
20 PF12392 DUF3656: Collagenase 20.8 74 0.0016 18.9 1.6 22 48-69 88-110 (122)
No 1
>PF03028 Dynein_heavy: Dynein heavy chain and region D6 of dynein motor; InterPro: IPR004273 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits, intermediate size subunits and small subunits (see IPR001372 from INTERPRO). This family represents the C-terminal region of dynein heavy chain. The dynein heavy chain also exhibits ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. ; GO: 0003777 microtubule motor activity, 0007018 microtubule-based movement, 0030286 dynein complex; PDB: 3VKG_A 3VKH_C 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A.
Probab=99.79 E-value=6.7e-20 Score=137.00 Aligned_cols=67 Identities=24% Similarity=0.383 Sum_probs=46.9
Q ss_pred CCCCCchhhhhhcc-CCCChHHHHHHHHHHHHHHHHHHhhcCCCCCCceecCCCcchhHHHHHHHHHhcC
Q psy17374 3 PNDYTPDDWQSIWS-GSGNPLLYIRSVVSRAVMVHKCYQVSSTYWRSPVDLSGLFHPHAFLSVLKQHTAR 71 (71)
Q Consensus 3 ~~~~vP~~W~~~~~-~~~~~~~w~~~l~~R~~~l~~w~~~~~~~~~~~~wLs~lF~P~~FLtA~~Q~~AR 71 (71)
..|+||..|.+.++ +++.+.+|++||++|++++++|.+..+ .|.+|||||||||++||||+||++||
T Consensus 519 ~~~~VP~~W~~~~~~s~~~l~~Wl~dL~~Rv~~l~~w~~~~~--~p~~~wLs~ff~P~aFLtAlrQ~~AR 586 (707)
T PF03028_consen 519 LKGQVPKSWLRYSYPSPKPLSSWLQDLIKRVEQLQRWASNSG--QPKSFWLSGFFNPQAFLTALRQEYAR 586 (707)
T ss_dssp HHTS--GGG--S---SS--HHHHHHHHHHHHHHHHHHHH---------B-GGGSS-HHHHHHHHHHHHHH
T ss_pred HhCCCChhHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhccC--CceEEecccccChHHHHHHHHHHHHH
Confidence 46899999998644 567779999999999999999998622 47999999999999999999999997
No 2
>PF03822 NAF: NAF domain; InterPro: IPR004041 The NAF domain is a 24 amino acid domain that is found in a plant-specific subgroup of serine-threonine protein kinases (CIPKs), that interact with calcineurin B-like calcium sensor proteins (CBLs). Whereas the N-terminal part of CIPKs comprises a conserved catalytic domain typical of Ser-Thr kinases, the much less conserved C-terminal domain appears to be unique to this subgroup of kinases. The only exception is the NAF domain that forms an 'island of conservation' in this otherwise variable region. The NAF domain has been named after the prominent conserved amino acids Asn-Ala-Phe. It represents a minimum protein interaction module that is both necessary and sufficient to mediate the interaction with the CBL calcium sensor proteins []. The secondary structure of the NAF domain is currently not known, but secondary structure computation of the C-terminal region of Arabidopsis thaliana CBL-interacting protein kinase 1 revealed a long helical structure [].; GO: 0007165 signal transduction; PDB: 2ZFD_B 2EHB_D.
Probab=43.23 E-value=7.4 Score=21.46 Aligned_cols=12 Identities=58% Similarity=0.802 Sum_probs=10.0
Q ss_pred CCceecCCCcch
Q psy17374 47 RSPVDLSGLFHP 58 (71)
Q Consensus 47 ~~~~wLs~lF~P 58 (71)
+..+||||||--
T Consensus 14 S~G~DLSgLFe~ 25 (63)
T PF03822_consen 14 SSGFDLSGLFEE 25 (63)
T ss_dssp STTTSCGGGGGC
T ss_pred ccCCChHHhcCc
Confidence 578999999954
No 3
>PF04062 P21-Arc: ARP2/3 complex ARPC3 (21 kDa) subunit; InterPro: IPR007204 The Arp2/3 complex is a seven-protein assembly that is critical for actin nucleation and branching in cells. Arp2/3 nucleates new actin filaments while bound to existing filaments, thus creating a branched network []. The complex consists of Arp2, Arp3, p41, p34, p21, p20 and p16. Subunits p34 and p20 constitute the core of the structure, with the remaining subunits located peripherally []. This entry describes the p21 subunit. Proteins such as WASp and Scar1 may mediate receptor signalling through interactions with p21-Arc, resulting in the activation of Arc2/3 complex activity [].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_J 2P9P_E 2P9N_E 2P9K_E 1TYQ_E 1U2V_E 3RSE_E 2P9U_E 3DXM_E 2P9S_E ....
Probab=36.41 E-value=1.1e+02 Score=20.21 Aligned_cols=23 Identities=22% Similarity=0.431 Sum_probs=17.5
Q ss_pred CceecCCCcch----------hHHHHHHHHHhc
Q psy17374 48 SPVDLSGLFHP----------HAFLSVLKQHTA 70 (71)
Q Consensus 48 ~~~wLs~lF~P----------~~FLtA~~Q~~A 70 (71)
..|-|+++|-+ .+||+.+||+++
T Consensus 111 ~gFpLn~~y~~P~~~~e~d~lR~Yl~QlRqElg 143 (175)
T PF04062_consen 111 PGFPLNSLYAKPANRQEADLLRQYLTQLRQELG 143 (175)
T ss_dssp TT-TTTTTS---SSHHHHHHHHHHHHHHHHHHC
T ss_pred CCCCccccccCCCChhHHHHHHHHHHHHHHHHH
Confidence 67899999995 369999999986
No 4
>cd08871 START_STARD10-like Lipid-binding START domain of mammalian STARD10 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD10 (also known as CGI-52, PTCP-like, and SDCCAG28). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD10 binds phophatidylcholine and phosphatidylethanolamine. This protein is widely expressed and is synthesized constitutively in many organs. It may function in the liver in the export of phospholipids into bile. It is concentrated in the sperm flagellum, and may play a role in energy metabolism. In the mammary gland it may participate in the enrichment of lipids in milk, and be a potential marker of differentiation. Its expression is induced in this gland during gestation and lactation. It is overe
Probab=36.06 E-value=48 Score=21.61 Aligned_cols=38 Identities=11% Similarity=0.111 Sum_probs=27.6
Q ss_pred CCCCCchhhhhhccCCCChHHHHHHHHHHHHHHHHHHhh
Q psy17374 3 PNDYTPDDWQSIWSGSGNPLLYIRSVVSRAVMVHKCYQV 41 (71)
Q Consensus 3 ~~~~vP~~W~~~~~~~~~~~~w~~~l~~R~~~l~~w~~~ 41 (71)
+.|.+|. |.-.+-....+..++.+|.+-++.+.+|...
T Consensus 172 p~G~IP~-~lvN~~~~~~~~~~l~~l~k~~~~y~~~~~~ 209 (222)
T cd08871 172 PKGSLPK-WVVNKATTKLAPKVMKKLHKAALKYPEWKAK 209 (222)
T ss_pred CCCCcCH-HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHh
Confidence 5677887 4332332334578999999999999999876
No 5
>PF12249 AftA_C: Arabinofuranosyltransferase A C terminal; InterPro: IPR020959 The arabinofuranosyltransferase enzyme AftA is involved in cell wall arabinan biosynthesis in bacteria []. It catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. As this enzyme is important for cell growth and is found in some important pathogens, such as Mycobacterium tuberculosis, it represents a potential target for the devlopment of new antibacterial drugs. This entry represents the C-terminal domain of AftA.; GO: 0016757 transferase activity, transferring glycosyl groups, 0044038 cell wall macromolecule biosynthetic process, 0005886 plasma membrane, 0016021 integral to membrane
Probab=34.65 E-value=77 Score=21.01 Aligned_cols=17 Identities=6% Similarity=0.130 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHhh
Q psy17374 25 IRSVVSRAVMVHKCYQV 41 (71)
Q Consensus 25 ~~~l~~R~~~l~~w~~~ 41 (71)
+.++-+|.+++++|.+.
T Consensus 82 LaeF~~R~~~Ie~Ws~~ 98 (178)
T PF12249_consen 82 LAEFDERNAEIESWSEL 98 (178)
T ss_pred hhhHHHHHHHHHHHhcc
Confidence 56678999999999774
No 6
>PF09396 Thrombin_light: Thrombin light chain; InterPro: IPR018992 Thrombin is a Na+-activated, allosteric serine protease that functions in blood homeostasis, inflammation and wound healing []. Thrombin (or coagulation factor II) is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, and (in complex with thrombomodulin) protein C []. Sodium binding is the major driving force behind the procoagulant, prothrombotic and signaling functions of the enzyme, but is dispensable for cleavage of the anticoagulant protein C []. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. This domain corresponds to the light chain of thrombin. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0007596 blood coagulation, 0005576 extracellular region; PDB: 3HKI_D 2OCV_A 3EDX_A 3HK6_C 2PV9_A 2PUX_A 3HK3_A 1HRT_L 1TOC_G 1ETT_L ....
Probab=26.06 E-value=35 Score=17.98 Aligned_cols=8 Identities=38% Similarity=1.036 Sum_probs=6.7
Q ss_pred CCcchhHH
Q psy17374 54 GLFHPHAF 61 (71)
Q Consensus 54 ~lF~P~~F 61 (71)
-||+|.+|
T Consensus 8 ~FFn~kTF 15 (49)
T PF09396_consen 8 TFFNPKTF 15 (49)
T ss_dssp STSTHHHH
T ss_pred cccCcccc
Confidence 58999988
No 7
>PF03490 Varsurf_PPLC: Variant-surface-glycoprotein phospholipase C; InterPro: IPR003633 Variant-surface-glycoprotein phospholipase C, by hydrolysis of the attached glycolipid, releases soluble variant surface glycoprotein containing phosphoinositol from the cell wall after lysis. It catalyses the conversion of variant-surface-glycoprotein 1,2 didecanoyl-SN-phosphatidylinositol and water to 1,2-didecanoylglycerol and the soluble variant-surface-glycoprotein. It also cleaves similar membrane anchors on some mammalian proteins.; GO: 0047396 glycosylphosphatidylinositol diacylglycerol-lyase activity, 0006650 glycerophospholipid metabolic process
Probab=26.00 E-value=54 Score=17.41 Aligned_cols=15 Identities=13% Similarity=0.173 Sum_probs=11.2
Q ss_pred ChHHHHHHHHHHHHH
Q psy17374 20 NPLLYIRSVVSRAVM 34 (71)
Q Consensus 20 ~~~~w~~~l~~R~~~ 34 (71)
.|.+|+.||...+..
T Consensus 7 ~PqSWM~DLrS~I~~ 21 (51)
T PF03490_consen 7 HPQSWMSDLRSSIGE 21 (51)
T ss_pred CcHHHHHHHHHHHhc
Confidence 578999999766553
No 8
>cd08868 START_STARD1_3_like Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD1 (also known as StAR) and STARD3 (also known as metastatic lymph node 64/MLN64). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. This STARD1-like subfamily has a high affinity for cholesterol. STARD1/StAR can reduce macrophage lipid content and inflammatory status. It plays an essential role in steroidogenic tissues: transferring the steroid precursor, cholesterol, from the outer to the inner mitochondrial membrane, across the aqueous space. Mutations in the gene encoding STARD1/StAR can cause lipid congenital adrenal hyperplasia (CAH), an autosomal recessive disorder characterized by a steroid synth
Probab=25.31 E-value=39 Score=21.79 Aligned_cols=31 Identities=10% Similarity=0.131 Sum_probs=16.1
Q ss_pred CCCCCchhhhhhccCCCChHHHHHHHHHHHHH
Q psy17374 3 PNDYTPDDWQSIWSGSGNPLLYIRSVVSRAVM 34 (71)
Q Consensus 3 ~~~~vP~~W~~~~~~~~~~~~w~~~l~~R~~~ 34 (71)
+.|.+|. |.-..-.+..+..++.+|.++++.
T Consensus 177 p~G~iP~-~lvN~~~~~~~~~~~~~Lr~~~~~ 207 (208)
T cd08868 177 LKGWLPQ-YLVDQALASVLLDFMKHLRKRIAT 207 (208)
T ss_pred CCCCCcc-eeeehhhHHHHHHHHHHHHHHHhh
Confidence 3455665 433233334456677777666543
No 9
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=25.11 E-value=66 Score=16.74 Aligned_cols=19 Identities=37% Similarity=0.475 Sum_probs=15.7
Q ss_pred ceecCCCcchhHHHHHHHH
Q psy17374 49 PVDLSGLFHPHAFLSVLKQ 67 (71)
Q Consensus 49 ~~wLs~lF~P~~FLtA~~Q 67 (71)
.+|+.|+-.|.-++.+.+.
T Consensus 1 ~lD~rg~~CP~Pl~~~~~~ 19 (69)
T cd00291 1 TLDLRGLPCPLPVLKTKKA 19 (69)
T ss_pred CccccCCcCCHHHHHHHHH
Confidence 3688999999999988764
No 10
>cd08867 START_STARD4_5_6-like Lipid-binding START domain of mammalian STARD4, -5, -6, and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD4, -5, and -6. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD4 plays an important role in steroidogenesis, trafficking cholesterol into mitochondria. It specifically binds cholesterol, and demonstrates limited binding to another sterol, 7a-hydroxycholesterol. STARD4 and STARD5 are ubiquitously expressed, with highest levels in liver and kidney. STRAD5 functions in the kidney within the proximal tubule cells where it is associated with the Endoplasmic Reticulum (ER), and may participate in ER-associated cholesterol transport. It binds cholesterol and 25-hydroxycholesterol. Expression
Probab=24.85 E-value=59 Score=20.91 Aligned_cols=29 Identities=10% Similarity=0.022 Sum_probs=14.5
Q ss_pred CCCCCchhhhhhccCCCChHHHHHHHHHHH
Q psy17374 3 PNDYTPDDWQSIWSGSGNPLLYIRSVVSRA 32 (71)
Q Consensus 3 ~~~~vP~~W~~~~~~~~~~~~w~~~l~~R~ 32 (71)
+.|.+|. |.-..-....+..|+.+|.+++
T Consensus 177 pkG~iP~-~lvn~~~~~~~~~~~~~lr~~~ 205 (206)
T cd08867 177 LRGMIPQ-SLVESAMPSNLVNFYTDLVKGV 205 (206)
T ss_pred cCCCCcH-HHHHhhhhhhHHHHHHHHHHhc
Confidence 4566665 4332223334566666665543
No 11
>cd07561 Peptidase_S41_CPP_like C-terminal processing peptidase-like; serine protease family S41. Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain.
Probab=24.34 E-value=1.1e+02 Score=20.84 Aligned_cols=39 Identities=23% Similarity=0.170 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhhcCCCCCCceecCCCcchhHHHHHHH
Q psy17374 21 PLLYIRSVVSRAVMVHKCYQVSSTYWRSPVDLSGLFHPHAFLSVLK 66 (71)
Q Consensus 21 ~~~w~~~l~~R~~~l~~w~~~~~~~~~~~~wLs~lF~P~~FLtA~~ 66 (71)
...||.++++..- -|.++ .|..-.|..+.-|++||.+++
T Consensus 9 ~~~~~~~~m~~~Y---lw~~~----~p~~~~~~~~~~p~~~~~~l~ 47 (256)
T cd07561 9 VNQWIYDVMREWY---LWYDD----IPALDDLDYFDDPEDFLESLL 47 (256)
T ss_pred HHHHHHHHHHhhh---ccccc----ccccccccccCCHHHHHHHhh
Confidence 3677766544221 35554 355566999999999999986
No 12
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=23.93 E-value=88 Score=15.38 Aligned_cols=15 Identities=33% Similarity=0.587 Sum_probs=12.8
Q ss_pred ChHHHHHHHHHHHHH
Q psy17374 20 NPLLYIRSVVSRAVM 34 (71)
Q Consensus 20 ~~~~w~~~l~~R~~~ 34 (71)
+|-.|++++..|+..
T Consensus 12 ~P~~yL~~vL~~i~~ 26 (39)
T PF13817_consen 12 NPYAYLTDVLERIPN 26 (39)
T ss_pred CHHHHHHHHHHHHcc
Confidence 578999999998875
No 13
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=22.37 E-value=87 Score=16.47 Aligned_cols=18 Identities=39% Similarity=0.571 Sum_probs=14.5
Q ss_pred ceecCCCcchhHHHHHHH
Q psy17374 49 PVDLSGLFHPHAFLSVLK 66 (71)
Q Consensus 49 ~~wLs~lF~P~~FLtA~~ 66 (71)
.+|+.|+..|.-++.+.+
T Consensus 2 ~lD~rg~~CP~Pll~~~~ 19 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKK 19 (70)
T ss_dssp EEECSS-STTHHHHHHHH
T ss_pred EEeCCCCCCCHHHHHHHH
Confidence 589999999999988765
No 14
>cd08818 CARD_MDA5_1 Caspase activation and recruitment domain found in MDA5, first repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-
Probab=21.90 E-value=64 Score=18.99 Aligned_cols=17 Identities=29% Similarity=0.425 Sum_probs=12.2
Q ss_pred eecCCCcchhHHHHHHHHH
Q psy17374 50 VDLSGLFHPHAFLSVLKQH 68 (71)
Q Consensus 50 ~wLs~lF~P~~FLtA~~Q~ 68 (71)
.|=.|.| ++||+|+++.
T Consensus 63 ~~~~GWf--~~FldAL~~~ 79 (88)
T cd08818 63 TWDPGWF--REFVTALEQG 79 (88)
T ss_pred ccCCchH--HHHHHHHHhc
Confidence 4455666 6899999874
No 15
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.86 E-value=89 Score=16.38 Aligned_cols=18 Identities=28% Similarity=0.490 Sum_probs=15.0
Q ss_pred eecCCCcchhHHHHHHHH
Q psy17374 50 VDLSGLFHPHAFLSVLKQ 67 (71)
Q Consensus 50 ~wLs~lF~P~~FLtA~~Q 67 (71)
+|+.|+..|.-++-+-+.
T Consensus 2 lD~rG~~CP~P~l~~k~a 19 (67)
T cd03421 2 IDARGLACPQPVIKTKKA 19 (67)
T ss_pred cccCCCCCCHHHHHHHHH
Confidence 688999999999887664
No 16
>KOG2099|consensus
Probab=21.77 E-value=94 Score=24.80 Aligned_cols=15 Identities=27% Similarity=0.550 Sum_probs=11.4
Q ss_pred CCCCchhhhhhccCC
Q psy17374 4 NDYTPDDWQSIWSGS 18 (71)
Q Consensus 4 ~~~vP~~W~~~~~~~ 18 (71)
+|-+|..|...+.+.
T Consensus 486 NGITPRRWL~~cnP~ 500 (843)
T KOG2099|consen 486 NGITPRRWLLLCNPG 500 (843)
T ss_pred CCcCHHHHHHhcCch
Confidence 688999999865433
No 17
>TIGR02115 potass_kdpF K+-transporting ATPase, KdpF subunit. This model describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (TIGR00680). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation.
Probab=21.74 E-value=26 Score=16.08 Aligned_cols=9 Identities=33% Similarity=0.781 Sum_probs=5.8
Q ss_pred CCcchhHHH
Q psy17374 54 GLFHPHAFL 62 (71)
Q Consensus 54 ~lF~P~~FL 62 (71)
.+++||.|.
T Consensus 17 aLl~PErF~ 25 (26)
T TIGR02115 17 ALLRPERFX 25 (26)
T ss_pred HHhCHHhcC
Confidence 467777763
No 18
>PF05209 MinC_N: Septum formation inhibitor MinC, N-terminal domain; InterPro: IPR007874 In Escherichia coli FtsZ (P0A9A6 from SWISSPROT) assembles into a Z ring at midcell. Its assembly at polar sites is prevented by the min system. MinC P18196 from SWISSPROT, a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with the MinDE proteins. MinC is an oligomer, probably a dimer []. The C-terminal half of MinC is the most conserved and interacts with MinD. The N-terminal half is thought to interact with FtsZ. MinC rapidly oscillates between the poles of the cell to destabilise FtsZ filaments that have formed before they mature into polar Z rings; GO: 0051302 regulation of cell division; PDB: 3GHF_A 1HF2_C.
Probab=21.45 E-value=1.6e+02 Score=16.90 Aligned_cols=44 Identities=14% Similarity=0.091 Sum_probs=32.1
Q ss_pred ChHHHHHHHHHHHHHHHHHHhhcCCCCCCceecCCCcchhHHHHHHHHH
Q psy17374 20 NPLLYIRSVVSRAVMVHKCYQVSSTYWRSPVDLSGLFHPHAFLSVLKQH 68 (71)
Q Consensus 20 ~~~~w~~~l~~R~~~l~~w~~~~~~~~~~~~wLs~lF~P~~FLtA~~Q~ 68 (71)
++......|..|+.+--+...+ .|-+++++++ ..+-=+.++.+.
T Consensus 24 d~~~l~~~L~~ki~~ap~FF~~----~pvvldl~~l-~~~~dl~~L~~~ 67 (99)
T PF05209_consen 24 DLDELLQALDEKIAQAPDFFKN----APVVLDLSNL-PDELDLAALVEL 67 (99)
T ss_dssp -HHHHHHHHHHHHHHTHHHCTT----TEEEEEEEEE-ETTHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhChHhHcC----CCeEEehhhc-CChhhHHHHHHH
Confidence 5688888899999888887664 2689999999 555455666554
No 19
>PF06868 DUF1257: Protein of unknown function (DUF1257); InterPro: IPR009666 This family represents Ycf35, which is encoded in algal chloroplast and in cyanobacteria. The function of these proteins are unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=21.26 E-value=78 Score=18.85 Aligned_cols=15 Identities=33% Similarity=0.468 Sum_probs=12.4
Q ss_pred cchhHHHHHHHHHhc
Q psy17374 56 FHPHAFLSVLKQHTA 70 (71)
Q Consensus 56 F~P~~FLtA~~Q~~A 70 (71)
...+.||.-+.|.||
T Consensus 62 ~~~e~fl~kl~Q~YA 76 (105)
T PF06868_consen 62 YSVERFLNKLTQRYA 76 (105)
T ss_pred CCHHHHHHHHHHHHH
Confidence 457889999999887
No 20
>PF12392 DUF3656: Collagenase ; InterPro: IPR020988 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This domain is found in a number of proteins belonging to the MEROPS peptidase family U32. Peptidase family U32 contains endopeptidases, including collagenase, from bacteria.
Probab=20.82 E-value=74 Score=18.89 Aligned_cols=22 Identities=36% Similarity=0.610 Sum_probs=18.2
Q ss_pred Cceec-CCCcchhHHHHHHHHHh
Q psy17374 48 SPVDL-SGLFHPHAFLSVLKQHT 69 (71)
Q Consensus 48 ~~~wL-s~lF~P~~FLtA~~Q~~ 69 (71)
-.+.+ .++|.|-+-|+.+|.+.
T Consensus 88 i~i~~~~~lFlP~s~LN~lRRea 110 (122)
T PF12392_consen 88 IEIDLDEGLFLPISELNELRREA 110 (122)
T ss_pred EEEEcCCCEEEEHHHHHHHHHHH
Confidence 34565 89999999999999764
Done!