Query psy16727
Match_columns 210
No_of_seqs 149 out of 993
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 20:27:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1944|consensus 100.0 1.3E-40 2.8E-45 280.9 12.6 165 28-196 47-218 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.9 6.8E-25 1.5E-29 152.8 5.5 68 123-190 1-68 (68)
3 smart00071 Galanin Galanin. Ga 50.6 5.5 0.00012 29.2 0.1 8 3-10 12-19 (103)
4 PF00140 Sigma70_r1_2: Sigma-7 37.1 23 0.00049 21.2 1.4 19 17-36 2-20 (37)
5 PF01296 Galanin: Galanin; In 29.6 19 0.00041 20.5 0.1 7 4-10 1-7 (29)
6 PRK09609 hypothetical protein; 26.8 1.7E+02 0.0038 26.2 5.7 53 41-97 58-110 (312)
7 PF03818 MadM: Malonate/sodium 22.5 1.9E+02 0.0041 19.5 3.9 34 24-60 5-38 (60)
8 PF10929 DUF2811: Protein of u 21.4 1.3E+02 0.0028 20.1 2.9 29 50-81 12-42 (57)
9 cd02577 PSTD1 PSTD1: Pseudouri 18.8 2.1E+02 0.0045 25.6 4.7 30 161-190 228-258 (319)
10 PF03988 DUF347: Repeat of Unk 18.1 2.9E+02 0.0063 17.9 4.5 45 33-89 5-49 (55)
No 1
>KOG1944|consensus
Probab=100.00 E-value=1.3e-40 Score=280.93 Aligned_cols=165 Identities=39% Similarity=0.758 Sum_probs=156.0
Q ss_pred hhchhhhhhchhhhHHHHH-HHHHHHHhhhhcCCC--CCccchhhHHHHHHHhhh-hchhhhHHHHHHHHhhch---HHH
Q psy16727 28 GLGDVIAQSLAVHNFTSLM-GLGDVIAQTFIDGKQ--LTQINPMRTLQYSVVGLV-VGPTVGKWYRILEGIYGK---EAV 100 (210)
Q Consensus 28 ~~~Pl~tk~~~~~ts~~l~-~~gD~laQ~i~~~~~--~~~~D~~R~~r~~~~G~~-~gP~~h~wy~~Ld~~~p~---~~~ 100 (210)
..+|++++++ +++.+. ..||+++|.++..++ .+.+|+.|++||+++|++ .||..|+||+.||+++|. .++
T Consensus 47 ~~~~~l~~~i---~~~~~~~~~~d~~~q~~~~~~~~~~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~L~~~~p~~~~~~~ 123 (222)
T KOG1944|consen 47 SLYPLLTKAI---TTSLLLAAAGDVISQSLEGRSKKLFQTLDLTRTLRMGIFGFLFVGPTLHYWYRLLSKLFPKKTLITV 123 (222)
T ss_pred hhhhHHHHHH---HHHHHHHHhchhhhhhhhhhcccccccccHHHHHHHHhhhhheeccchhHHHHHHHHHccCccHHHH
Confidence 4689899999 888888 999999999988765 578999999999999987 999999999999999998 899
Q ss_pred HHHHHHhhhhhhHHHHHHHHHHHHhhcCCCHHHHHHHHHhhhHHHHhhccccchHHHhhhhhcccccchhHHHHHHHHHH
Q psy16727 101 VKKVLTDQLIFSPVFIAILVTSLNLLQGLSWDEAVTKVQNSYFDILLTGYQIWPAVQVVNFYFIPIQYRVLLVQAVAVVW 180 (210)
Q Consensus 101 l~Kvl~Dq~v~~P~~~~~f~~~~~~leg~~~~~~~~~lk~~~~~~~~~~~~vWp~~q~iNF~~VP~~~Rvlf~n~v~~~W 180 (210)
++|++.||++++|+.+.+|+.+++++||++.++..++++++++|+++++|++||++|++||++||+++|++++|+++++|
T Consensus 124 ~~kvl~dql~~~P~~~~~ff~~~~~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~inF~~VP~~~rvl~~~~vsl~W 203 (222)
T KOG1944|consen 124 VKKVLLDQLVFAPLFIVVFFLLMGLLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQFINFRLVPLQYRVLFVNIVSLVW 203 (222)
T ss_pred HHHHHHhhhhhchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhheecchhheeeeEEccccceehhhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCcccccc
Q psy16727 181 NTYLSWKLNSTTVEAT 196 (210)
Q Consensus 181 n~yLS~~~~~~~~~~~ 196 (210)
|+|||+++++. ++..
T Consensus 204 ~~~Ls~~~~~~-~~~~ 218 (222)
T KOG1944|consen 204 NTYLSYKNASL-VELA 218 (222)
T ss_pred HHHHHHHhhcc-cccc
Confidence 99999999988 5443
No 2
>PF04117 Mpv17_PMP22: Mpv17 / PMP22 family ; InterPro: IPR007248 The 22 kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information []. Mpv17 is a closely related peroxisomal protein involved in the development of early-onset glomerulosclerosis []. A member of this family found in Saccharomyces cerevisiae (Baker's yeast) is an integral membrane protein of the inner mitochondrial membrane and has been suggested to play a role in mitochondrial function during heat shock [].; GO: 0016021 integral to membrane
Probab=99.91 E-value=6.8e-25 Score=152.80 Aligned_cols=68 Identities=43% Similarity=0.925 Sum_probs=66.4
Q ss_pred HHhhcCCCHHHHHHHHHhhhHHHHhhccccchHHHhhhhhcccccchhHHHHHHHHHHHHHHHhhhcC
Q psy16727 123 LNLLQGLSWDEAVTKVQNSYFDILLTGYQIWPAVQVVNFYFIPIQYRVLLVQAVAVVWNTYLSWKLNS 190 (210)
Q Consensus 123 ~~~leg~~~~~~~~~lk~~~~~~~~~~~~vWp~~q~iNF~~VP~~~Rvlf~n~v~~~Wn~yLS~~~~~ 190 (210)
|+++||++++++.+++|++++++++++|++|||+|++||.|||+++|++|+|+++++||+|||+++||
T Consensus 1 Mg~l~g~s~~~~~~~l~~~~~~~~~~~~~~Wp~~~~vnF~~vP~~~Rv~~~~~v~~~W~~~LS~~~~r 68 (68)
T PF04117_consen 1 MGLLEGKSWEEIKEKLKRDYWPTLKASWKFWPPAQIVNFRYVPPHYRVLFVNVVSFFWNTYLSYIANR 68 (68)
T ss_pred CCcccCCCHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHhcccChhhhhhhhhhHHHHHHHHHHHHhcC
Confidence 57899999999999999999999999999999999999999999999999999999999999999986
No 3
>smart00071 Galanin Galanin. Galanin [1,2,3] is a neuropeptide that controls various biological activities: it regulates the release growth hormone, inhibits the release of insulin and somatostatin, contracts smooth muscle of the gastrointestinal and genitourinary tract and may be involved in the control of adrenal secretion
Probab=50.59 E-value=5.5 Score=29.20 Aligned_cols=8 Identities=25% Similarity=0.401 Sum_probs=6.7
Q ss_pred cccccchh
Q psy16727 3 RRYYLGTY 10 (210)
Q Consensus 3 ~~~~~~~~ 10 (210)
|||||||+
T Consensus 12 Rgwtlnsa 19 (103)
T smart00071 12 RGWTLNSA 19 (103)
T ss_pred cCceeccC
Confidence 89999885
No 4
>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=37.11 E-value=23 Score=21.22 Aligned_cols=19 Identities=11% Similarity=0.335 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHhhchhhhhh
Q psy16727 17 QEVGVYIASLMGLGDVIAQS 36 (210)
Q Consensus 17 ~~~~~y~~~~l~~~Pl~tk~ 36 (210)
+.++.|+ +.+.++|++|.-
T Consensus 2 D~l~~Yl-~ei~~~~LLt~e 20 (37)
T PF00140_consen 2 DSLRLYL-KEIGRYPLLTAE 20 (37)
T ss_dssp HHHHHHH-HHHHHS-EETTH
T ss_pred cHHHHHH-HHHcCCCCCCHH
Confidence 4678888 688999999864
No 5
>PF01296 Galanin: Galanin; InterPro: IPR008174 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. Galanin is a 29 amino acid peptide processed from a larger precursor protein. Except in human, galanin is C-terminally amidated. Its sequence is highly conserved and the first 14 residues are identical in all currently known sequences.; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=29.61 E-value=19 Score=20.53 Aligned_cols=7 Identities=14% Similarity=0.235 Sum_probs=4.6
Q ss_pred ccccchh
Q psy16727 4 RYYLGTY 10 (210)
Q Consensus 4 ~~~~~~~ 10 (210)
||||||+
T Consensus 1 gwtlnsa 7 (29)
T PF01296_consen 1 GWTLNSA 7 (29)
T ss_pred Ccccccc
Confidence 5777764
No 6
>PRK09609 hypothetical protein; Provisional
Probab=26.83 E-value=1.7e+02 Score=26.19 Aligned_cols=53 Identities=23% Similarity=0.226 Sum_probs=43.0
Q ss_pred hHHHHHHHHHHHHhhhhcCCCCCccchhhHHHHHHHhhhhchhhhHHHHHHHHhhch
Q psy16727 41 NFTSLMGLGDVIAQTFIDGKQLTQINPMRTLQYSVVGLVVGPTVGKWYRILEGIYGK 97 (210)
Q Consensus 41 ts~~l~~~gD~laQ~i~~~~~~~~~D~~R~~r~~~~G~~~gP~~h~wy~~Ld~~~p~ 97 (210)
.+++.++++|++.=.+.. ..+.+.=++.-++.|++.|-+..+.|+.+.++|.+
T Consensus 58 ~G~ivG~lsDLLs~li~p----G~ffPgFTLsa~l~GlI~Glf~~~~fk~~~~~f~~ 110 (312)
T PRK09609 58 VGFFTGLLSDLISFLFVP----GVYHPYYTLAAMVYGFIPGIVGWFFFKFGKKFFGK 110 (312)
T ss_pred HHHHHHHHHHHHHHHhcC----CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 567788899999866642 35788888888888888999999999999998876
No 7
>PF03818 MadM: Malonate/sodium symporter MadM subunit; InterPro: IPR018402 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM.The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity.
Probab=22.49 E-value=1.9e+02 Score=19.55 Aligned_cols=34 Identities=9% Similarity=0.149 Sum_probs=30.6
Q ss_pred HHHHhhchhhhhhchhhhHHHHHHHHHHHHhhhhcCC
Q psy16727 24 ASLMGLGDVIAQSLAVHNFTSLMGLGDVIAQTFIDGK 60 (210)
Q Consensus 24 ~~~l~~~Pl~tk~~~~~ts~~l~~~gD~laQ~i~~~~ 60 (210)
.+.++++.++|.=. .-|+++.++..++-++..+|
T Consensus 5 ~~vl~~ngLitaFa---~vG~~m~~S~~lS~~LT~Gr 38 (60)
T PF03818_consen 5 EKVLTKNGLITAFA---VVGIIMWVSYWLSKKLTRGR 38 (60)
T ss_pred HHHHhhCchHHHHH---HHHHHHHHHHHHHHHHhCCC
Confidence 46788999999999 99999999999999998876
No 8
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=21.36 E-value=1.3e+02 Score=20.13 Aligned_cols=29 Identities=14% Similarity=0.260 Sum_probs=20.7
Q ss_pred HHHHhhhhcCCCCCccchhhHHHHHHHhhh--hc
Q psy16727 50 DVIAQTFIDGKQLTQINPMRTLQYSVVGLV--VG 81 (210)
Q Consensus 50 D~laQ~i~~~~~~~~~D~~R~~r~~~~G~~--~g 81 (210)
+.+.+.++...+ +|-.|.+.-++.|++ +|
T Consensus 12 ~~m~~fie~hP~---WDQ~Rl~~aALa~FL~QnG 42 (57)
T PF10929_consen 12 QAMKDFIETHPN---WDQYRLFQAALAGFLLQNG 42 (57)
T ss_pred HHHHHHHHcCCC---chHHHHHHHHHHHHHHHcC
Confidence 344555666554 777899999999988 66
No 9
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=18.80 E-value=2.1e+02 Score=25.56 Aligned_cols=30 Identities=27% Similarity=0.485 Sum_probs=24.7
Q ss_pred hhcccccchhHHHHH-HHHHHHHHHHhhhcC
Q psy16727 161 FYFIPIQYRVLLVQA-VAVVWNTYLSWKLNS 190 (210)
Q Consensus 161 F~~VP~~~Rvlf~n~-v~~~Wn~yLS~~~~~ 190 (210)
|.-+|...|.+|++. .|.+||-.+|..-..
T Consensus 228 l~~iP~~lr~myvhAYQSylfN~~lS~Ri~~ 258 (319)
T cd02577 228 FLALPKNLRRMFVHAYQSYLFNEILSERIEE 258 (319)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345999999998885 899999999986643
No 10
>PF03988 DUF347: Repeat of Unknown Function (DUF347) ; InterPro: IPR007136 This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan.
Probab=18.14 E-value=2.9e+02 Score=17.85 Aligned_cols=45 Identities=22% Similarity=0.341 Sum_probs=28.1
Q ss_pred hhhhchhhhHHHHHHHHHHHHhhhhcCCCCCccchhhHHHHHHHhhhhchhhhHHHH
Q psy16727 33 IAQSLAVHNFTSLMGLGDVIAQTFIDGKQLTQINPMRTLQYSVVGLVVGPTVGKWYR 89 (210)
Q Consensus 33 ~tk~~~~~ts~~l~~~gD~laQ~i~~~~~~~~~D~~R~~r~~~~G~~~gP~~h~wy~ 89 (210)
+++.+ +...-...||.++|. .+........+++.+..-....||+
T Consensus 5 ~a~il---t~~lGt~~~D~l~~~---------lglg~~~~~~~~~~~l~~~~~~~~~ 49 (55)
T PF03988_consen 5 IAKIL---TTTLGTTAGDFLSKT---------LGLGYLISTLIFAALLAVVLALWYR 49 (55)
T ss_pred HHHHH---HHHhHHHHHHHHHhc---------cCccHHHHHHHHHHHHHHHHHHHHH
Confidence 45666 777788899999994 2334555555566653334445553
Done!