Query psy7199
Match_columns 146
No_of_seqs 106 out of 128
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 20:41:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7199hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4076|consensus 100.0 8.4E-31 1.8E-35 200.4 8.1 91 17-116 22-112 (121)
2 PF04667 Endosulfine: cAMP-reg 99.9 2.7E-22 5.9E-27 145.0 6.7 50 20-75 4-53 (86)
3 COG3908 Uncharacterized protei 64.9 1.1 2.5E-05 32.5 -1.4 30 57-104 15-44 (77)
4 KOG4076|consensus 60.3 9.6 0.00021 29.9 2.9 34 8-41 16-49 (121)
5 PF13838 Clathrin_H_link: Clat 43.2 16 0.00034 25.6 1.5 24 44-70 4-27 (66)
6 PF09562 RE_LlaMI: LlaMI restr 35.4 29 0.00064 30.2 2.2 41 24-66 189-246 (271)
7 PF14863 Alkyl_sulf_dimr: Alky 33.9 23 0.0005 27.6 1.3 24 44-70 68-91 (141)
8 COG3733 TynA Cu2+-containing a 27.0 19 0.00041 34.8 -0.3 15 57-71 316-330 (654)
9 KOG4612|consensus 24.5 52 0.0011 25.2 1.7 33 28-60 71-103 (105)
10 KOG2892|consensus 24.1 36 0.00078 30.5 0.9 35 26-64 137-173 (320)
11 cd09236 V_AnPalA_UmRIM20_like 21.9 55 0.0012 28.4 1.6 44 19-62 100-145 (353)
No 1
>KOG4076|consensus
Probab=99.97 E-value=8.4e-31 Score=200.35 Aligned_cols=91 Identities=48% Similarity=0.748 Sum_probs=77.1
Q ss_pred CChhhhhHHHHHHHHHHhcCCCCCCCCCchHHHHHHHhcCCCCccchhhHHhhhccCCCCCCCccCCCCCCCCCCCCCCC
Q psy7199 17 MSALEIEKAEEAKLKAKYAFKSGPAIGGHSTFLQKKLAKGQKYFDSGDYQMAKQTTGAPGGLAKQIPGSKLVPSNLGFGT 96 (146)
Q Consensus 17 ~~~~~~ek~eE~KLk~kYg~L~~kP~~g~s~~L~krLqkgrKYFDSGDYaMaKa~~~s~~~~~~~~p~~v~~~a~~~~~T 96 (146)
....++|++||.+|+++|+.+++.| ++++||+||||+||||||||||||+||++++.. .+.+ .+...+.+|
T Consensus 22 ~~~~~~ek~~epkl~~ky~~~GklP--~~sd~l~krlQkgrKyFDSGDYam~KAk~~~~~-----~~~~--~~~k~~~~t 92 (121)
T KOG4076|consen 22 TEGTSPEKKEEPKLKKKYPSYGKLP--GGSDFLRKRLQKGRKYFDSGDYAMAKAKMKNKQ-----LPTA--NPDKNNLPT 92 (121)
T ss_pred ccccChhhhhCHHHHHHHHHhCCCC--cccHHHHHHHHhcccccccchHHHHHhhccccc-----CCcc--ccccCCCCC
Confidence 4568889999999999999999999 889999999999999999999999999996532 2211 011227899
Q ss_pred CCcCCCCCCCCCCCCccccC
Q psy7199 97 GDAIPTPESVPARKTSIIQP 116 (146)
Q Consensus 97 G~~IPTPE~IP~rksSii~s 116 (146)
|++||+||+||+|+.|++++
T Consensus 93 ~~~~~~~e~~p~rk~S~~s~ 112 (121)
T KOG4076|consen 93 GDHIPTPEDLPARKPSLVSP 112 (121)
T ss_pred CCCCcCccccccccccccCC
Confidence 99999999999999999985
No 2
>PF04667 Endosulfine: cAMP-regulated phosphoprotein/endosulfine conserved region; InterPro: IPR006760 This endosulphine family includes cAMP-regulated phosphoprotein 19 (ARPP-19), alpha endosulphine and protein Igo1. No function has yet been assigned to ARPP-19 []. Endosulphine is the endogenous ligand for the ATP-dependent potassium channels which occupy a key position in the control of insulin release from the pancreatic beta cell by coupling cell polarity to metabolism []. Igo1 is required for initiation of G0 program. In the absence of stimulatory signals, cells may enter into a reversible quiescence (or G0) state that is typically characterised by low metabolic activity, including low rates of protein synthesis and transcription. Igo proteins associate with the mRNA decapping activator Dhh1, sheltering newly expressed mRNAs from degradation via the 5'-3' mRNA decay pathway, and thereby enabling their proper translation during initiation of the G0 program [].
Probab=99.87 E-value=2.7e-22 Score=145.02 Aligned_cols=50 Identities=52% Similarity=0.688 Sum_probs=44.0
Q ss_pred hhhhHHHHHHHHHHhcCCCCCCCCCchHHHHHHHhcCCCCccchhhHHhhhccCCC
Q psy7199 20 LEIEKAEEAKLKAKYAFKSGPAIGGHSTFLQKKLAKGQKYFDSGDYQMAKQTTGAP 75 (146)
Q Consensus 20 ~~~ek~eE~KLk~kYg~L~~kP~~g~s~~L~krLqkgrKYFDSGDYaMaKa~~~s~ 75 (146)
.+.+++||++|++|||+|+ +++.+|++||++ |||||||||||+||++.++
T Consensus 4 ~~~~~~eE~kl~~kYG~l~-----~~~~~L~kkl~~-rKYFDSgDyam~Ka~~~~~ 53 (86)
T PF04667_consen 4 ISSLSEEEAKLKAKYGKLP-----PKKKLLQKKLQK-RKYFDSGDYAMAKAGKKSS 53 (86)
T ss_pred cccccHHHHHHHHHcCCCC-----CCchhhhhhhcc-ccccchHHHHHHHhhcccc
Confidence 4567889999999999997 456789999998 9999999999999999543
No 3
>COG3908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.86 E-value=1.1 Score=32.50 Aligned_cols=30 Identities=37% Similarity=0.572 Sum_probs=21.7
Q ss_pred CCCccchhhHHhhhccCCCCCCCccCCCCCCCCCCCCCCCCCcCCCCC
Q psy7199 57 QKYFDSGDYQMAKQTTGAPGGLAKQIPGSKLVPSNLGFGTGDAIPTPE 104 (146)
Q Consensus 57 rKYFDSGDYaMaKa~~~s~~~~~~~~p~~v~~~a~~~~~TG~~IPTPE 104 (146)
-.|.| |||+|.+.+. .| .-.+||..||.-|
T Consensus 15 iryld-gdf~vv~~Gs------------fV-----~CAVtgk~IPlde 44 (77)
T COG3908 15 IRYLD-GDFQVVSPGS------------FV-----LCAVTGKPIPLDE 44 (77)
T ss_pred EEEec-CceEEEcCCc------------EE-----EEEecCCcccHHH
Confidence 46999 9999998876 11 1348999998643
No 4
>KOG4076|consensus
Probab=60.35 E-value=9.6 Score=29.87 Aligned_cols=34 Identities=21% Similarity=0.166 Sum_probs=25.9
Q ss_pred CCccccCCCCChhhhhHHHHHHHHHHhcCCCCCC
Q psy7199 8 EQPEFAKPNMSALEIEKAEEAKLKAKYAFKSGPA 41 (146)
Q Consensus 8 ~~pe~~kp~~~~~~~ek~eE~KLk~kYg~L~~kP 41 (146)
++.+...-....+..|..+|.++++.||+|+.+-
T Consensus 16 ~~~~~~~~~~~~ek~~epkl~~ky~~~GklP~~s 49 (121)
T KOG4076|consen 16 ETGEIETEGTSPEKKEEPKLKKKYPSYGKLPGGS 49 (121)
T ss_pred hcccccccccChhhhhCHHHHHHHHHhCCCCccc
Confidence 4554445555777888999999999999998544
No 5
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=43.21 E-value=16 Score=25.64 Aligned_cols=24 Identities=21% Similarity=0.541 Sum_probs=18.5
Q ss_pred CchHHHHHHHhcCCCCccchhhHHhhh
Q psy7199 44 GHSTFLQKKLAKGQKYFDSGDYQMAKQ 70 (146)
Q Consensus 44 g~s~~L~krLqkgrKYFDSGDYaMaKa 70 (146)
|.-+++..|.++ +|+.|||.=|.-
T Consensus 4 Gad~l~~~~F~~---l~~~g~y~eAA~ 27 (66)
T PF13838_consen 4 GADDLYVQQFNE---LFSQGQYEEAAK 27 (66)
T ss_dssp S-HHHHHHHHHH---HHHTT-HHHHHH
T ss_pred cHHHHHHHHHHH---HHHcCCHHHHHH
Confidence 677899999987 999999986643
No 6
>PF09562 RE_LlaMI: LlaMI restriction endonuclease; InterPro: IPR019063 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 []. This entry includes the restriction endonuclease LlaMI, which recognises and cleaves the double-stranded sequence CC^NGG.
Probab=35.36 E-value=29 Score=30.24 Aligned_cols=41 Identities=37% Similarity=0.430 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhcCCCC-----------------CCCCCchHHHHHHHhcCCCCccchhhH
Q psy7199 24 KAEEAKLKAKYAFKSG-----------------PAIGGHSTFLQKKLAKGQKYFDSGDYQ 66 (146)
Q Consensus 24 k~eE~KLk~kYg~L~~-----------------kP~~g~s~~L~krLqkgrKYFDSGDYa 66 (146)
+.-+.||.+||..++. +|+ -=++-.+-..+|-=|||||=|+
T Consensus 189 ~~lk~Kle~KFndkGWFkC~~~~~g~Y~~I~FG~Pi--nfd~W~~lV~~GiVfFDsGMY~ 246 (271)
T PF09562_consen 189 KCLKAKLEKKFNDKGWFKCLKNSQGCYNKICFGSPI--NFDNWINLVEKGIVFFDSGMYQ 246 (271)
T ss_pred hHHHHHHHHHhccCceeEeecCCCcceeeeecCCcc--cHHHHHHHHHccceEEeccccc
Confidence 4567899999988752 221 1244556678899999999996
No 7
>PF14863 Alkyl_sulf_dimr: Alkyl sulfatase dimerisation; PDB: 2YHE_C 2CG2_A 2CG3_A 2CFU_A 2CFZ_A.
Probab=33.87 E-value=23 Score=27.55 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=16.8
Q ss_pred CchHHHHHHHhcCCCCccchhhHHhhh
Q psy7199 44 GHSTFLQKKLAKGQKYFDSGDYQMAKQ 70 (146)
Q Consensus 44 g~s~~L~krLqkgrKYFDSGDYaMaKa 70 (146)
|+.+-|.++.++ .||.|||++|-.
T Consensus 68 GG~d~vl~~A~~---~~~~gd~~wA~~ 91 (141)
T PF14863_consen 68 GGADKVLERAQA---ALAAGDYQWAAE 91 (141)
T ss_dssp TCHHHHHHHHHH---HHHCT-HHHHHH
T ss_pred CCHHHHHHHHHH---HHHCCCHHHHHH
Confidence 456666566655 999999998754
No 8
>COG3733 TynA Cu2+-containing amine oxidase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.04 E-value=19 Score=34.84 Aligned_cols=15 Identities=40% Similarity=0.764 Sum_probs=11.9
Q ss_pred CCCccchhhHHhhhc
Q psy7199 57 QKYFDSGDYQMAKQT 71 (146)
Q Consensus 57 rKYFDSGDYaMaKa~ 71 (146)
+-+||+|||.|-+-.
T Consensus 316 K~~fD~GeYglG~l~ 330 (654)
T COG3733 316 KNAFDSGEYGLGTLT 330 (654)
T ss_pred hhcccccccCccccc
Confidence 469999999986543
No 9
>KOG4612|consensus
Probab=24.54 E-value=52 Score=25.19 Aligned_cols=33 Identities=24% Similarity=0.288 Sum_probs=22.5
Q ss_pred HHHHHHhcCCCCCCCCCchHHHHHHHhcCCCCc
Q psy7199 28 AKLKAKYAFKSGPAIGGHSTFLQKKLAKGQKYF 60 (146)
Q Consensus 28 ~KLk~kYg~L~~kP~~g~s~~L~krLqkgrKYF 60 (146)
.|=|+|+|-|..---..++.+|..|.+|||+|.
T Consensus 71 ~KRKrkhGfl~R~~s~~G~~vl~rR~lKGR~~L 103 (105)
T KOG4612|consen 71 LKRKRKHGFLARAKSKQGSKVLKRRKLKGRWFL 103 (105)
T ss_pred hhhhhhhhhhhhhcccchhHHHHHHHhcccccc
Confidence 455677777752111256788889999999885
No 10
>KOG2892|consensus
Probab=24.08 E-value=36 Score=30.53 Aligned_cols=35 Identities=26% Similarity=0.196 Sum_probs=22.4
Q ss_pred HHHHHHHHhcCCCCCCCCCchHHHHHHHhc--CCCCccchh
Q psy7199 26 EEAKLKAKYAFKSGPAIGGHSTFLQKKLAK--GQKYFDSGD 64 (146)
Q Consensus 26 eE~KLk~kYg~L~~kP~~g~s~~L~krLqk--grKYFDSGD 64 (146)
.-+.|.+|||+|.-.- --.-|+.||+| +.| |+++=
T Consensus 137 R~Aql~RkyPHL~f~~---~rgn~~trl~kld~~~-~~~~i 173 (320)
T KOG2892|consen 137 RKAQILRKYPHLHVES---IRGNLQTRLSKLDGGK-PFQAI 173 (320)
T ss_pred HHHHHHhhCCceEEEE---ecChHHHHHHhhcCCC-cchhH
Confidence 4688999999996221 22345666666 466 66653
No 11
>cd09236 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas Pa
Probab=21.87 E-value=55 Score=28.41 Aligned_cols=44 Identities=20% Similarity=0.275 Sum_probs=28.8
Q ss_pred hhhhhHHHHHHHHHHhcC--CCCCCCCCchHHHHHHHhcCCCCccc
Q psy7199 19 ALEIEKAEEAKLKAKYAF--KSGPAIGGHSTFLQKKLAKGQKYFDS 62 (146)
Q Consensus 19 ~~~~ek~eE~KLk~kYg~--L~~kP~~g~s~~L~krLqkgrKYFDS 62 (146)
..+-|..++.+++++||. ..+.|-..-..=|..++.+=+.|++.
T Consensus 100 ~L~~E~~ed~~~R~k~g~~~Wtr~~S~~~~~~l~~~~~~~~~~L~~ 145 (353)
T cd09236 100 ILDDEASEDESLRRKFGTDRWTRPDSHEANPKLYTQAAEYEGYLKQ 145 (353)
T ss_pred HHHHHHhHHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 455677888899999994 44444111134466778776778774
Done!