Query 031014
Match_columns 167
No_of_seqs 28 out of 30
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 07:57:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031014.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031014hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04530 Viral_Beta_CD: Viral 50.3 6.7 0.00015 31.4 0.6 23 81-103 70-92 (122)
2 PF15513 DUF4651: Domain of un 42.1 23 0.00049 25.4 2.2 18 18-35 3-20 (62)
3 PF09932 DUF2164: Uncharacteri 39.6 32 0.0007 25.0 2.7 20 13-32 2-21 (76)
4 KOG2435 Uncharacterized conser 38.0 21 0.00045 32.6 1.8 46 100-151 262-319 (323)
5 smart00309 PAH Pancreatic horm 35.9 91 0.002 20.2 4.0 30 5-34 3-32 (36)
6 PRK11546 zraP zinc resistance 35.1 19 0.00041 29.3 1.0 26 13-38 43-68 (143)
7 PF00140 Sigma70_r1_2: Sigma-7 33.1 32 0.00069 21.4 1.6 19 12-30 15-33 (37)
8 PF13801 Metal_resist: Heavy-m 33.1 48 0.001 22.8 2.7 25 12-36 40-64 (125)
9 PF00159 Hormone_3: Pancreatic 30.6 1.3E+02 0.0029 19.3 4.1 30 5-34 3-32 (36)
10 COG2979 Uncharacterized protei 28.5 48 0.001 29.1 2.4 21 8-28 121-141 (225)
11 cd00126 PAH Pancreatic Hormone 27.1 1.7E+02 0.0038 18.9 4.2 31 4-34 2-32 (36)
12 PF14480 DNA_pol3_a_NI: DNA po 27.0 71 0.0015 21.6 2.6 26 9-34 43-68 (76)
13 COG3866 PelB Pectate lyase [Ca 26.7 48 0.001 30.7 2.2 54 87-152 264-320 (345)
14 cd04458 CSP_CDS Cold-Shock Pro 26.1 38 0.00083 22.3 1.1 13 108-121 11-23 (65)
15 PF01213 CAP_N: Adenylate cycl 23.6 18 0.00039 32.3 -1.0 18 96-113 192-209 (312)
16 PF12101 DUF3577: Protein of u 23.3 33 0.00071 27.9 0.4 19 106-124 12-34 (137)
17 PF04391 DUF533: Protein of un 23.2 74 0.0016 26.6 2.5 22 8-29 90-111 (188)
18 cd00225 API3 Ascaris pepsin in 20.5 1.2E+02 0.0025 25.5 3.1 13 35-47 84-96 (159)
19 KOG2675 Adenylate cyclase-asso 20.5 27 0.00059 33.5 -0.6 20 96-115 196-215 (480)
20 PF03444 HrcA_DNA-bdg: Winged 20.2 47 0.001 24.6 0.7 21 96-117 47-67 (78)
21 KOG2988 60S ribosomal protein 20.1 50 0.0011 26.3 0.9 53 78-132 44-97 (112)
No 1
>PF04530 Viral_Beta_CD: Viral Beta C/D like family; InterPro: IPR007617 This is a family of ssRNA positive-strand viral proteins. Conserved region is found in the Beta C and Beta D transcripts.
Probab=50.32 E-value=6.7 Score=31.39 Aligned_cols=23 Identities=22% Similarity=0.509 Sum_probs=15.7
Q ss_pred ecCCcccchhhhhhhhccccccc
Q 031014 81 WNGSEVTEEFQETEYYKDLNRIN 103 (167)
Q Consensus 81 ~~gg~v~eEFvETeYYkdL~~ID 103 (167)
+.++-+.+.=.=++||||||+|-
T Consensus 70 ~~~~s~~~~~~~syfyQDLNsVe 92 (122)
T PF04530_consen 70 SSGGSNVDPVKGSYFYQDLNSVE 92 (122)
T ss_pred eccCcccCccccchheeeccceE
Confidence 33454444445688999999975
No 2
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=42.12 E-value=23 Score=25.40 Aligned_cols=18 Identities=22% Similarity=0.497 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHhhhhcCC
Q 031014 18 EEAKMEDEVRENFENLAP 35 (167)
Q Consensus 18 eq~~i~~evR~~Fd~~AP 35 (167)
.+++|.++||++|..|-+
T Consensus 3 kre~i~~~iR~~fs~lG~ 20 (62)
T PF15513_consen 3 KREEITAEIRQFFSQLGE 20 (62)
T ss_pred HHHHHHHHHHHHHHhcCc
Confidence 578999999999987753
No 3
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=39.56 E-value=32 Score=24.98 Aligned_cols=20 Identities=35% Similarity=0.650 Sum_probs=18.2
Q ss_pred CCCHHHHHHHHHHHHHhhhh
Q 031014 13 HLSREEEAKMEDEVRENFEN 32 (167)
Q Consensus 13 ~l~~Eeq~~i~~evR~~Fd~ 32 (167)
-|+.|+++.+..+|+.||..
T Consensus 2 ~l~ke~k~~li~~iq~yf~~ 21 (76)
T PF09932_consen 2 KLSKEEKAELIDKIQRYFAE 21 (76)
T ss_pred cCCHHHHHHHHHHHHHHHHH
Confidence 48999999999999999964
No 4
>KOG2435 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.02 E-value=21 Score=32.59 Aligned_cols=46 Identities=22% Similarity=0.269 Sum_probs=35.5
Q ss_pred cccccCc-----cCCCccceEeeccCCceeEeecCCCCCcccccccCCC-------CCCCcCCC
Q 031014 100 NRINKDH-----HTTGTGFIKMENANGKSFILAPDNDDAHHSSCKGNPA-------TNEWIPSA 151 (167)
Q Consensus 100 ~~IDKqH-----HTTGtGFIKve~~~g~~f~l~~~~~~~~~~s~k~NPA-------TNDWiPa~ 151 (167)
+-+|.|| |++|.||--+.+ .++.|.|..|-. +.+..|+ -|+|+|+.
T Consensus 262 riqDrq~e~nl~~vssig~sl~dk-~dGpF~LEIDfI-----Gv~~d~~H~EdFayE~y~~p~~ 319 (323)
T KOG2435|consen 262 RIQDRQHELNLDKVSSIGFSLADK-VDGPFFLEIDFI-----GVFTDPAHTEDFAYENYPEPNP 319 (323)
T ss_pred ceeecccccCccceeeEeEEEeec-cCCcceeeEEEE-----EEecCCCcccceeeeccccccc
Confidence 3468887 899999999998 668898887754 3455565 58899987
No 5
>smart00309 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions.
Probab=35.90 E-value=91 Score=20.18 Aligned_cols=30 Identities=20% Similarity=0.309 Sum_probs=26.8
Q ss_pred CCCCCCccCCCHHHHHHHHHHHHHhhhhcC
Q 031014 5 RRPDRSDVHLSREEEAKMEDEVRENFENLA 34 (167)
Q Consensus 5 ~rP~RSD~~l~~Eeq~~i~~evR~~Fd~~A 34 (167)
.||-|--+--++||-++--+++|.|+--+.
T Consensus 3 ~~P~~Pg~~a~~e~l~~Y~~~L~~Yinlit 32 (36)
T smart00309 3 SKPERPGDDASPEDLRQYLAALREYINLIT 32 (36)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 578888889999999999999999998765
No 6
>PRK11546 zraP zinc resistance protein; Provisional
Probab=35.07 E-value=19 Score=29.28 Aligned_cols=26 Identities=15% Similarity=0.249 Sum_probs=23.4
Q ss_pred CCCHHHHHHHHHHHHHhhhhcCCCCC
Q 031014 13 HLSREEEAKMEDEVRENFENLAPKRH 38 (167)
Q Consensus 13 ~l~~Eeq~~i~~evR~~Fd~~APKR~ 38 (167)
-|+||+|+++..-..+|++..+|-|-
T Consensus 43 ~LT~EQQa~~q~I~~~f~~~t~~LRq 68 (143)
T PRK11546 43 PLTTEQQAAWQKIHNDFYAQTSALRQ 68 (143)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 49999999999999999999988764
No 7
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=33.15 E-value=32 Score=21.41 Aligned_cols=19 Identities=26% Similarity=0.356 Sum_probs=15.7
Q ss_pred cCCCHHHHHHHHHHHHHhh
Q 031014 12 VHLSREEEAKMEDEVRENF 30 (167)
Q Consensus 12 ~~l~~Eeq~~i~~evR~~F 30 (167)
.-|++||+..++.+|+.--
T Consensus 15 ~LLt~eeE~~LA~~i~~g~ 33 (37)
T PF00140_consen 15 PLLTAEEEIELARRIRKGD 33 (37)
T ss_dssp -EETTHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHhH
Confidence 4689999999999998743
No 8
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=33.11 E-value=48 Score=22.85 Aligned_cols=25 Identities=20% Similarity=0.294 Sum_probs=20.6
Q ss_pred cCCCHHHHHHHHHHHHHhhhhcCCC
Q 031014 12 VHLSREEEAKMEDEVRENFENLAPK 36 (167)
Q Consensus 12 ~~l~~Eeq~~i~~evR~~Fd~~APK 36 (167)
.-||+|++.+|.+..++|+..+.+-
T Consensus 40 l~Lt~eQ~~~l~~~~~~~~~~~~~~ 64 (125)
T PF13801_consen 40 LNLTPEQQAKLRALMDEFRQEMRAL 64 (125)
T ss_dssp S-TTHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4699999999999999999876543
No 9
>PF00159 Hormone_3: Pancreatic hormone peptide; InterPro: IPR001955 Pancreatic hormone (PP) [] is a peptide synthesized in pancreatic islets of Langherhans, which acts as a regulator of pancreatic and gastrointestinal functions. The hormone is produced as a larger propeptide, which is enzymatically cleaved to yield the mature active peptide: this is 36 amino acids in length [] and has an amidated C terminus []. The hormone has a globular structure, residues 2-8 forming a left-handed poly-proline-II-like helix, residues 9-13 a beta turn, and 14-32 an alpha-helix,held close to the first helix by hydrophobic interactions []. Unlike glucagon, another peptide hormone, the structure of pancreatic peptide is preserved in aqueous solution []. Both N and C termini are required for activity: receptor binding and activation functions may reside in the N and C termini respectively []. Pancreatic hormone is part of a wider family of active peptides that includes: Neuropeptide Y (NPY) [], one of the most abundant peptides in the mammalian nervous system. NPY is implicated in the control of feeding and the secretion of the gonadotrophin-releasing hormone. Peptide YY (PYY) []. PPY is a gut peptide that inhibits exocrine pancreatic secretion, has a vasoconstrictory action and inhibits jejunal and colonic mobility. Various NPY and PYY-like polypeptides from fish and amphibians [, ]. Neuropeptide F (NPF) from invertebrates such as worms and snail. Skin peptide Tyr-Tyr (SPYY) from the frog Phyllomedusa bicolor. SPYY shows a large spectra of antibacterial and antifungal activity. All these peptides are 36 to 39 amino acids long. Like most active peptides, their C-terminal is amidated and they are synthesized as larger protein precursors.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1LJV_A 1BBA_A 1V1D_A 1PPT_A 2H3T_A 2H4B_A 2BF9_A 2H3S_B 1K8V_A 2DF0_A ....
Probab=30.63 E-value=1.3e+02 Score=19.34 Aligned_cols=30 Identities=23% Similarity=0.302 Sum_probs=26.5
Q ss_pred CCCCCCccCCCHHHHHHHHHHHHHhhhhcC
Q 031014 5 RRPDRSDVHLSREEEAKMEDEVRENFENLA 34 (167)
Q Consensus 5 ~rP~RSD~~l~~Eeq~~i~~evR~~Fd~~A 34 (167)
.||.|--+.-++||-++--.++|.||--+.
T Consensus 3 ~~P~~P~~~aspeel~~Y~~~L~~Y~~lvt 32 (36)
T PF00159_consen 3 SKPERPGDFASPEELAQYYAALRHYINLVT 32 (36)
T ss_dssp SSSSSSSTTSSHHHHHHHHHHHHHHHHHHT
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHc
Confidence 578888888999999999999999997665
No 10
>COG2979 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.51 E-value=48 Score=29.11 Aligned_cols=21 Identities=24% Similarity=0.547 Sum_probs=18.8
Q ss_pred CCCccCCCHHHHHHHHHHHHH
Q 031014 8 DRSDVHLSREEEAKMEDEVRE 28 (167)
Q Consensus 8 ~RSD~~l~~Eeq~~i~~evR~ 28 (167)
.+||-|++..|+++|+.+|+.
T Consensus 121 AkaDGhIDe~ERa~I~~~l~e 141 (225)
T COG2979 121 AKADGHIDEKERARIMQKLQE 141 (225)
T ss_pred HhhcCCcCHHHHHHHHHHHHH
Confidence 479999999999999988875
No 11
>cd00126 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers
Probab=27.06 E-value=1.7e+02 Score=18.86 Aligned_cols=31 Identities=19% Similarity=0.243 Sum_probs=26.1
Q ss_pred CCCCCCCccCCCHHHHHHHHHHHHHhhhhcC
Q 031014 4 VRRPDRSDVHLSREEEAKMEDEVRENFENLA 34 (167)
Q Consensus 4 ~~rP~RSD~~l~~Eeq~~i~~evR~~Fd~~A 34 (167)
..||-+--+--++||-++--.++|.|+--+.
T Consensus 2 p~~P~~Pg~~a~~eel~~Y~~~L~~Yinlit 32 (36)
T cd00126 2 PSKPENPGDDASPEELRQYLAALREYINLIT 32 (36)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHc
Confidence 3577777777889999999999999997765
No 12
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=27.02 E-value=71 Score=21.60 Aligned_cols=26 Identities=27% Similarity=0.378 Sum_probs=23.7
Q ss_pred CCccCCCHHHHHHHHHHHHHhhhhcC
Q 031014 9 RSDVHLSREEEAKMEDEVRENFENLA 34 (167)
Q Consensus 9 RSD~~l~~Eeq~~i~~evR~~Fd~~A 34 (167)
+|+..|+.+.-..+++.++..|..+|
T Consensus 43 ~~~~~l~~~~~~~~~~~l~~~F~~ia 68 (76)
T PF14480_consen 43 SSPHILPFEVYQKFEEKLKKQFSHIA 68 (76)
T ss_pred EeCCcCCHHHHHHHHHHHHHHhCCcC
Confidence 37889999999999999999998877
No 13
>COG3866 PelB Pectate lyase [Carbohydrate transport and metabolism]
Probab=26.72 E-value=48 Score=30.67 Aligned_cols=54 Identities=20% Similarity=0.437 Sum_probs=36.3
Q ss_pred cchhhhhhhhccccccccCccCCCccceEeeccCCceeEeecCCCCCcccccccCCCC---CCCcCCCC
Q 031014 87 TEEFQETEYYKDLNRINKDHHTTGTGFIKMENANGKSFILAPDNDDAHHSSCKGNPAT---NEWIPSAD 152 (167)
Q Consensus 87 ~eEFvETeYYkdL~~IDKqHHTTGtGFIKve~~~g~~f~l~~~~~~~~~~s~k~NPAT---NDWiPa~~ 152 (167)
..=|||--||.++ +-|.||++--.. .+|-.+ |..+ -..+||+++-+ +-|-|++-
T Consensus 264 AkiyvE~NyF~~~--------~~~~~f~dt~~~--~GY~~~-d~gs-y~~~s~~~~~~~~G~~w~ps~~ 320 (345)
T COG3866 264 AKIYVENNYFENG--------SEGLGFLDTKGT--SGYANQ-DSGS-YLNSSKSMSVRAGGVTWNPSSY 320 (345)
T ss_pred eEEEEecceeccC--------CCCceeeecCCc--cceEEe-ccCc-eecccCCcccccCCccCCCCCC
Confidence 5779999999987 556677765543 233332 2222 12788999888 99999873
No 14
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=26.07 E-value=38 Score=22.31 Aligned_cols=13 Identities=38% Similarity=0.810 Sum_probs=10.1
Q ss_pred CCCccceEeeccCC
Q 031014 108 TTGTGFIKMENANG 121 (167)
Q Consensus 108 TTGtGFIKve~~~g 121 (167)
.-|.|||+.+. +|
T Consensus 11 ~kGfGFI~~~~-~g 23 (65)
T cd04458 11 EKGFGFITPDD-GG 23 (65)
T ss_pred CCCeEEEecCC-CC
Confidence 46999999986 44
No 15
>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=23.61 E-value=18 Score=32.33 Aligned_cols=18 Identities=44% Similarity=0.728 Sum_probs=12.4
Q ss_pred hccccccccCccCCCccc
Q 031014 96 YKDLNRINKDHHTTGTGF 113 (167)
Q Consensus 96 YkdL~~IDKqHHTTGtGF 113 (167)
+++|-..=|+|||||--|
T Consensus 192 ~~~L~~YVke~httGl~W 209 (312)
T PF01213_consen 192 LKELQAYVKEHHTTGLSW 209 (312)
T ss_dssp HHHHHHHHHHHSTTS---
T ss_pred HHHHHHHHHHhCccCccc
Confidence 566777779999999755
No 16
>PF12101 DUF3577: Protein of unknown function (DUF3577); InterPro: IPR021960 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.
Probab=23.25 E-value=33 Score=27.89 Aligned_cols=19 Identities=37% Similarity=0.719 Sum_probs=13.8
Q ss_pred ccCCCccceEeec----cCCcee
Q 031014 106 HHTTGTGFIKMEN----ANGKSF 124 (167)
Q Consensus 106 HHTTGtGFIKve~----~~g~~f 124 (167)
=||+|-|||.-.| .+|..|
T Consensus 12 Lht~GiGYLnriR~V~~~kg~pF 34 (137)
T PF12101_consen 12 LHTTGIGYLNRIREVTPRKGDPF 34 (137)
T ss_pred EEEeeEEEeccceEccCCCCCee
Confidence 3999999998666 445545
No 17
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=23.22 E-value=74 Score=26.60 Aligned_cols=22 Identities=27% Similarity=0.528 Sum_probs=18.8
Q ss_pred CCCccCCCHHHHHHHHHHHHHh
Q 031014 8 DRSDVHLSREEEAKMEDEVREN 29 (167)
Q Consensus 8 ~RSD~~l~~Eeq~~i~~evR~~ 29 (167)
.++|-|++.+|+++|..++.+.
T Consensus 90 AkADG~ID~~Er~~I~~~l~~~ 111 (188)
T PF04391_consen 90 AKADGHIDEEERQRIEGALQEL 111 (188)
T ss_pred HHcCCCCCHHHHHHHHHHHHHh
Confidence 4789999999999998877663
No 18
>cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin.
Probab=20.53 E-value=1.2e+02 Score=25.53 Aligned_cols=13 Identities=31% Similarity=0.386 Sum_probs=10.8
Q ss_pred CCCCCCCCCCCCc
Q 031014 35 PKRHTKPQRSDYS 47 (167)
Q Consensus 35 PKR~~KP~RSE~s 47 (167)
||+|.||+=--++
T Consensus 84 Pk~PkkPsFCt~~ 96 (159)
T cd00225 84 PKAPKKPSFCSPD 96 (159)
T ss_pred CCCCCCCCcCCCC
Confidence 9999999876555
No 19
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=20.52 E-value=27 Score=33.48 Aligned_cols=20 Identities=40% Similarity=0.597 Sum_probs=14.6
Q ss_pred hccccccccCccCCCccceE
Q 031014 96 YKDLNRINKDHHTTGTGFIK 115 (167)
Q Consensus 96 YkdL~~IDKqHHTTGtGFIK 115 (167)
|-+|..-=|+|||||--+=+
T Consensus 196 ~~eL~~YVk~hhtTGl~W~~ 215 (480)
T KOG2675|consen 196 FLELQAYVKEHHTTGLVWNK 215 (480)
T ss_pred HHHHHHHHHHhccccceecC
Confidence 44566667999999976643
No 20
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.22 E-value=47 Score=24.59 Aligned_cols=21 Identities=24% Similarity=0.526 Sum_probs=14.7
Q ss_pred hccccccccCccCCCccceEee
Q 031014 96 YKDLNRINKDHHTTGTGFIKME 117 (167)
Q Consensus 96 YkdL~~IDKqHHTTGtGFIKve 117 (167)
-++|+-|+++|||.| |+|-..
T Consensus 47 Le~lGlve~~p~~s~-GriPT~ 67 (78)
T PF03444_consen 47 LEELGLVESQPHPSG-GRIPTD 67 (78)
T ss_pred HHHCCCccCCCCCCC-CCCcCH
Confidence 457888999999865 555433
No 21
>KOG2988 consensus 60S ribosomal protein L30 [Translation, ribosomal structure and biogenesis]
Probab=20.12 E-value=50 Score=26.26 Aligned_cols=53 Identities=30% Similarity=0.321 Sum_probs=38.3
Q ss_pred cEEecCC-cccchhhhhhhhccccccccCccCCCccceEeeccCCceeEeecCCCC
Q 031014 78 KLIWNGS-EVTEEFQETEYYKDLNRINKDHHTTGTGFIKMENANGKSFILAPDNDD 132 (167)
Q Consensus 78 ~Lv~~gg-~v~eEFvETeYYkdL~~IDKqHHTTGtGFIKve~~~g~~f~l~~~~~~ 132 (167)
+|+.-.. --.=-|-|-|||--|.- -.-||-+| ..|-.+.+-|+.|.+..+...
T Consensus 44 kL~~is~n~p~lrks~ieyyamlak-~~v~~~sg-~n~~lgt~~g~~fRv~v~~iv 97 (112)
T KOG2988|consen 44 KLIIISSNCPPLRKSEIEYYAMLAK-TGVHHYSG-NNVELGTACGKTFRVSVLSIV 97 (112)
T ss_pred eEEEeecCCCCcchhHHHHHHHHhc-CceeeecC-CcEeHHHHhcCeeEeeEEEEE
Confidence 5655554 33667899999998876 66666677 677777777888988766543
Done!