Query psy17767
Match_columns 64
No_of_seqs 110 out of 325
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 22:19:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17767.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17767hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0938|consensus 99.7 5.9E-17 1.3E-21 119.1 6.4 56 1-56 371-428 (446)
2 KOG0937|consensus 99.5 4.5E-14 9.7E-19 105.0 6.5 60 1-60 347-409 (424)
3 PF00928 Adap_comp_sub: Adapto 98.7 2.3E-08 5E-13 67.8 5.7 51 2-52 187-239 (262)
4 KOG2740|consensus 93.0 0.13 2.9E-06 38.8 3.6 47 4-51 349-396 (418)
5 KOG2677|consensus 78.2 3.5 7.6E-05 33.7 3.9 48 4-51 823-871 (922)
6 PF10291 muHD: Muniscin C-term 68.7 14 0.0003 25.9 4.7 37 7-47 189-227 (257)
7 PF11604 CusF_Ec: Copper bindi 54.1 18 0.00038 20.5 2.6 30 13-43 13-44 (70)
8 PF07795 DUF1635: Protein of u 52.1 5.3 0.00011 28.0 0.2 21 20-40 155-177 (214)
9 PF00942 CBM_3: Cellulose bind 43.8 28 0.00061 20.1 2.4 19 29-47 15-39 (86)
10 COG4834 Uncharacterized protei 29.5 21 0.00045 26.4 0.3 18 31-48 307-326 (334)
11 PF12991 DUF3875: Domain of un 24.3 76 0.0016 17.8 1.9 17 25-41 26-46 (54)
12 cd08342 HPPD_N_like N-terminal 23.7 77 0.0017 18.9 2.1 23 39-64 113-136 (136)
13 PRK09838 periplasmic copper-bi 22.6 53 0.0012 20.6 1.2 23 21-43 66-90 (115)
14 PF14400 Transglut_i_TM: Inact 21.6 2.6E+02 0.0056 18.6 4.6 18 27-44 32-49 (165)
15 COG3700 AphA Acid phosphatase 20.8 66 0.0014 22.7 1.5 19 25-43 60-82 (237)
No 1
>KOG0938|consensus
Probab=99.68 E-value=5.9e-17 Score=119.09 Aligned_cols=56 Identities=46% Similarity=0.718 Sum_probs=50.5
Q ss_pred CCCCcEEEEEEEEEecccc-ccccCCCCCeEEEEEee-cccccceEeEEEEeeecccC
Q psy17767 1 MAGMKETQLSAEIELLETD-TKKKWTRPPISMNFEVP-FAPSGFKVSHLSEILILLLS 56 (64)
Q Consensus 1 ~~G~~E~~L~a~v~L~s~~-~~~~~~~pPI~l~FeIP-~t~SGLqVryLkV~e~~~~~ 56 (64)
|.|.+|.+|+|+++|.++. +.+.|.+|||+|+|||| |+.|||.||||||.|+..-+
T Consensus 371 f~G~tE~tlsAevels~Tt~nkq~WtrPPIsleFeV~MFt~SGL~VrylkV~e~~Sk~ 428 (446)
T KOG0938|consen 371 FNGLTESTLSAEVELSDTTQNKQQWTRPPISLEFEVPMFTNSGLVVRYLKVSEKDSKH 428 (446)
T ss_pred cCCcccceeEEEEEeccCccccccccCCCceeEEeeeeecCCceEEEEEEEecccCCC
Confidence 6899999999999997765 78899999999999999 99999999999999954433
No 2
>KOG0937|consensus
Probab=99.50 E-value=4.5e-14 Score=104.95 Aligned_cols=60 Identities=30% Similarity=0.369 Sum_probs=53.0
Q ss_pred CCCCcEEEEEEEEEeccccccc-cC-CCCCeEEEEEee-cccccceEeEEEEeeecccCCCCC
Q psy17767 1 MAGMKETQLSAEIELLETDTKK-KW-TRPPISMNFEVP-FAPSGFKVSHLSEILILLLSPEGP 60 (64)
Q Consensus 1 ~~G~~E~~L~a~v~L~s~~~~~-~~-~~pPI~l~FeIP-~t~SGLqVryLkV~e~~~~~~~~~ 60 (64)
|+||.|+.++|++.+++....+ .| +.+||+|+|+|| ||+||+||||||+.|+.+.+.++|
T Consensus 347 ~~gg~e~~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~~T~SgiqVrylki~ep~~~y~s~~ 409 (424)
T KOG0937|consen 347 FVGGKEYSLRARMDLPSEEHEEQCTEGLGPIKVKFEIPYFTVSGIQVRYLKIIEPKSQYQSLP 409 (424)
T ss_pred ccCCceEEEEEeecCCccccCCCCcccCCceEEEEEecccccCCeEEEEEEecccccCCCccc
Confidence 5799999999999998865555 35 699999999999 999999999999999888887776
No 3
>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents the C-terminal domain of the mu subunit from various clathrin adaptors (AP1, AP2 and AP3) []. The C-teminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors []. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear []. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1H6E_A 3L81_A 1W63_V 4EMZ_A 4EN2_A 2VGL_M 3ML6_F 2PR9_A 2JKT_M 1I31_A ....
Probab=98.74 E-value=2.3e-08 Score=67.84 Aligned_cols=51 Identities=31% Similarity=0.561 Sum_probs=36.6
Q ss_pred CCCcEEEEEEEEEecccccc-ccCCCCCeEEEEEee-cccccceEeEEEEeee
Q psy17767 2 AGMKETQLSAEIELLETDTK-KKWTRPPISMNFEVP-FAPSGFKVSHLSEILI 52 (64)
Q Consensus 2 ~G~~E~~L~a~v~L~s~~~~-~~~~~pPI~l~FeIP-~t~SGLqVryLkV~e~ 52 (64)
.|++++.|++.+++...... ..|..+||+|+|++| +++|||+|++|+|.+.
T Consensus 187 ~~~~~~~l~~~l~~~~~~~~~~~~~~~pi~v~F~~~~~~~Sgl~V~~l~v~~~ 239 (262)
T PF00928_consen 187 PGGSESTLSGTLEFSSPSSVPSDWSFFPISVEFTIPGYTLSGLKVRSLDVVNE 239 (262)
T ss_dssp ETSEEEEEEEEEEEEEECCSS-S-----EEEEEEESTSETTT-EEEEEEEE-S
T ss_pred cCcccccEEEEEEecCCCcccccccceeEEEEEEeCCcccCCCEEEEEEeEec
Confidence 57889999999999653332 245799999999999 9999999999999873
No 4
>KOG2740|consensus
Probab=93.01 E-value=0.13 Score=38.78 Aligned_cols=47 Identities=30% Similarity=0.311 Sum_probs=36.0
Q ss_pred CcEEEEEEEEEeccccccccCCCCCeEEEEEee-cccccceEeEEEEee
Q psy17767 4 MKETQLSAEIELLETDTKKKWTRPPISMNFEVP-FAPSGFKVSHLSEIL 51 (64)
Q Consensus 4 ~~E~~L~a~v~L~s~~~~~~~~~pPI~l~FeIP-~t~SGLqVryLkV~e 51 (64)
|+-..|++.+.+.. ...+..+.|-++++|+|. -++|||.|..|++..
T Consensus 349 g~lp~Lkg~~~~e~-~~sk~~~l~t~~Lqykiqg~alsglkVe~Ldm~~ 396 (418)
T KOG2740|consen 349 GKLPVLKGTINLEP-GFSKKVDLPTLSLQYKIQGQALSGLKVERLDMYG 396 (418)
T ss_pred CcccccccccccCC-CCCccccCcccceeeeeeeeeccceEEEeeeecC
Confidence 44455666666653 334555799999999999 999999999999854
No 5
>KOG2677|consensus
Probab=78.25 E-value=3.5 Score=33.72 Aligned_cols=48 Identities=19% Similarity=0.156 Sum_probs=37.0
Q ss_pred CcEEEEEEEEEeccccccccCCCCCeEEEEEee-cccccceEeEEEEee
Q psy17767 4 MKETQLSAEIELLETDTKKKWTRPPISMNFEVP-FAPSGFKVSHLSEIL 51 (64)
Q Consensus 4 ~~E~~L~a~v~L~s~~~~~~~~~pPI~l~FeIP-~t~SGLqVryLkV~e 51 (64)
+.-|-|.+.++|.+-..-...=.|=.+++|.+| -++|.-.||.+-|..
T Consensus 823 ~hpHcl~c~lELgSd~evPs~f~p~~~V~FsmP~t~aS~t~VRSisVE~ 871 (922)
T KOG2677|consen 823 GHPHCLFCHLELGSDREVPSRFAPHVNVEFSMPTTSASKTSVRSISVED 871 (922)
T ss_pred CCCeeEEEEEeccccccCchhhccccceeeeccccccccceeeeeeccc
Confidence 445679999999763222222367889999999 999999999999865
No 6
>PF10291 muHD: Muniscin C-terminal mu homology domain; InterPro: IPR018808 The muniscins are a family of endocytic adaptors that is conserved from yeast to humans.This C-terminal domain is structurally similar to mu homology domains, and is the region of the muniscin proteins involved in the interactions with the endocytic adaptor-scaffold proteins Ede1-eps15. This interaction influences muniscin localisation. The muniscins provide a combined adaptor-membrane-tubulation activity that is important for regulating endocytosis.; PDB: 3G9H_A.
Probab=68.75 E-value=14 Score=25.87 Aligned_cols=37 Identities=19% Similarity=0.226 Sum_probs=22.3
Q ss_pred EEEEEEEEeccccccccCCCCCeEEEEEee--cccccceEeEE
Q psy17767 7 TQLSAEIELLETDTKKKWTRPPISMNFEVP--FAPSGFKVSHL 47 (64)
Q Consensus 7 ~~L~a~v~L~s~~~~~~~~~pPI~l~FeIP--~t~SGLqVryL 47 (64)
..|.|+|.+..... ..++|.++|++- -+.||+.|.-.
T Consensus 189 ~kL~ARf~~~~~~~----~p~~v~vkF~~~~~~~~sg~~i~~~ 227 (257)
T PF10291_consen 189 GKLIARFMTSGGPS----RPGGVEVKFEIEGGSTLSGLGISLV 227 (257)
T ss_dssp EEEEEEEEESS--------SS-EEEEEEE---S-SS----EEE
T ss_pred ceEEEEEECCCCCC----CCceEEEEEEEcCCCcccCcEEEEe
Confidence 68999999865211 578999999998 77999888766
No 7
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=54.14 E-value=18 Score=20.51 Aligned_cols=30 Identities=23% Similarity=0.467 Sum_probs=17.0
Q ss_pred EEeccccccccCCCCCeEEEEEee--cccccce
Q psy17767 13 IELLETDTKKKWTRPPISMNFEVP--FAPSGFK 43 (64)
Q Consensus 13 v~L~s~~~~~~~~~pPI~l~FeIP--~t~SGLq 43 (64)
+++.. ..-..|..|+..|+|.+. -..+||+
T Consensus 13 iti~H-~pIp~l~wpaMTM~F~v~~~~~l~~l~ 44 (70)
T PF11604_consen 13 ITISH-EPIPELGWPAMTMDFPVADPVDLAGLK 44 (70)
T ss_dssp EEEEE---BCCCTB-SEEEEEE--TTSEESS-S
T ss_pred EEEec-CccccCCCCCeEEEEEcCChhhhhcCC
Confidence 44433 334568899999999997 6667664
No 8
>PF07795 DUF1635: Protein of unknown function (DUF1635); InterPro: IPR012862 The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long.
Probab=52.09 E-value=5.3 Score=27.99 Aligned_cols=21 Identities=29% Similarity=0.789 Sum_probs=15.2
Q ss_pred ccccCCCCCeEE-EEEee-cccc
Q psy17767 20 TKKKWTRPPISM-NFEVP-FAPS 40 (64)
Q Consensus 20 ~~~~~~~pPI~l-~FeIP-~t~S 40 (64)
....|..||-.+ .|+|| ++++
T Consensus 155 PLP~WRnPPP~l~s~~IPpv~i~ 177 (214)
T PF07795_consen 155 PLPQWRNPPPQLQSFEIPPVSIK 177 (214)
T ss_pred CCccccCCCCccccccCCCcccc
Confidence 346799887765 59999 7754
No 9
>PF00942 CBM_3: Cellulose binding domain; InterPro: IPR001956 This domain is involved in cellulose binding [] and is found associated with a wide range of bacterial glycosyl hydrolases. The structure for this domain is known []; it forms a beta sandwich.; GO: 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 2L8A_A 4TF4_B 3TF4_B 1JS4_A 1TF4_B 1NBC_A 2YLK_A 3ZQX_A 2XFG_B 2XBT_A ....
Probab=43.81 E-value=28 Score=20.08 Aligned_cols=19 Identities=26% Similarity=0.494 Sum_probs=11.6
Q ss_pred eEEEEEe-----e-cccccceEeEE
Q psy17767 29 ISMNFEV-----P-FAPSGFKVSHL 47 (64)
Q Consensus 29 I~l~FeI-----P-~t~SGLqVryL 47 (64)
|++.|+| | ...|.|.|||-
T Consensus 15 i~~~~~i~Ntg~~~i~Ls~l~iRYy 39 (86)
T PF00942_consen 15 IEPKFKIKNTGWPAIDLSDLKIRYY 39 (86)
T ss_dssp EEEEEEEEETSSS-EEGGGEEEEEE
T ss_pred EEEEEEEEECCCCCEEcCCEEEEEE
Confidence 4555555 3 56677777764
No 10
>COG4834 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.53 E-value=21 Score=26.44 Aligned_cols=18 Identities=28% Similarity=0.571 Sum_probs=16.5
Q ss_pred EEEEee--cccccceEeEEE
Q psy17767 31 MNFEVP--FAPSGFKVSHLS 48 (64)
Q Consensus 31 l~FeIP--~t~SGLqVryLk 48 (64)
+.|.|| |-.||..|||=|
T Consensus 307 ~rfdVPge~r~~GV~~R~Pk 326 (334)
T COG4834 307 LRFDVPGEYRYSGVEFRYPK 326 (334)
T ss_pred ccccCCceeeeccEEEecch
Confidence 899999 999999999865
No 11
>PF12991 DUF3875: Domain of unknown function, B. Theta Gene description (DUF3875); InterPro: IPR024451 This domain of unknown function is found in proteins from Bacteroidetes, including the conjugation system ATPase, TraG.
Probab=24.29 E-value=76 Score=17.81 Aligned_cols=17 Identities=35% Similarity=0.589 Sum_probs=13.9
Q ss_pred CCCCeEEEEEe--e--ccccc
Q psy17767 25 TRPPISMNFEV--P--FAPSG 41 (64)
Q Consensus 25 ~~pPI~l~FeI--P--~t~SG 41 (64)
+.+-|.+-|++ | ||+|+
T Consensus 26 k~gDiTv~f~v~LPEiFtls~ 46 (54)
T PF12991_consen 26 KNGDITVAFRVELPEIFTLSE 46 (54)
T ss_pred cCCCEEEEEEecCCeeEEech
Confidence 46788999988 7 99886
No 12
>cd08342 HPPD_N_like N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS). HppD and HmaS are non-heme iron-dependent dioxygenases, which modify a common substrate, 4-hydroxyphenylpyruvate (HPP), but yield different products. HPPD catalyzes the second reaction in tyrosine catabolism, the conversion of HPP to homogentisate (2,5-dihydroxyphenylacetic acid, HG). HmaS converts HPP to 4-hydroxymandelate, a committed step in the formation of hydroxyphenylglycerine, a structural component of nonproteinogenic macrocyclic peptide antibiotics, such as vancomycin. If the emphasis is on catalytic chemistry, HPPD and HmaS are classified as members of a large family of alpha-keto acid dependent mononuclear non-heme iron oxygenases most of which require Fe(II), molecular oxygen, and an alpha-keto acid (typically alpha-ketoglutarate) to either oxygenate or oxidize a third substrate. Both enzymes are exceptions in that they require two, instead of three, su
Probab=23.65 E-value=77 Score=18.91 Aligned_cols=23 Identities=26% Similarity=0.228 Sum_probs=12.5
Q ss_pred cccceEeEEEEeeeccc-CCCCCCCCC
Q psy17767 39 PSGFKVSHLSEILILLL-SPEGPGFEP 64 (64)
Q Consensus 39 ~SGLqVryLkV~e~~~~-~~~~~~~~~ 64 (64)
..|..|..++ +.-+ -|-+|||||
T Consensus 113 p~G~~ie~~~---~~~~~~~~~~~~~~ 136 (136)
T cd08342 113 YGDSLHTLVD---RKGYKGPFLPGFEP 136 (136)
T ss_pred cCCcEEEEEe---cCCCCCccCCCCCC
Confidence 4555554443 3333 355699987
No 13
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=22.64 E-value=53 Score=20.61 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=17.6
Q ss_pred cccCCCCCeEEEEEee--cccccce
Q psy17767 21 KKKWTRPPISMNFEVP--FAPSGFK 43 (64)
Q Consensus 21 ~~~~~~pPI~l~FeIP--~t~SGLq 43 (64)
-..|..|+..|+|.++ --+.+|+
T Consensus 66 Ip~l~wPaMTM~F~v~~~~~l~~lk 90 (115)
T PRK09838 66 IPAVNWPEMTMRFTITPQTKMSEIK 90 (115)
T ss_pred cccCCCCCccccccCCChhhhccCC
Confidence 4568899999999997 5455554
No 14
>PF14400 Transglut_i_TM: Inactive transglutaminase fused to 7 transmembrane helices
Probab=21.58 E-value=2.6e+02 Score=18.65 Aligned_cols=18 Identities=22% Similarity=0.671 Sum_probs=13.5
Q ss_pred CCeEEEEEeecccccceE
Q psy17767 27 PPISMNFEVPFAPSGFKV 44 (64)
Q Consensus 27 pPI~l~FeIP~t~SGLqV 44 (64)
.|+.++|-+|.+..|+.|
T Consensus 32 ~pvkvsl~lP~~~pgf~i 49 (165)
T PF14400_consen 32 GPVKVSLALPDTQPGFTI 49 (165)
T ss_pred CCEEEEEcCCCCCCCeEE
Confidence 389999999866666654
No 15
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=20.77 E-value=66 Score=22.74 Aligned_cols=19 Identities=42% Similarity=1.008 Sum_probs=15.6
Q ss_pred CCCCeEEEEEee----cccccce
Q psy17767 25 TRPPISMNFEVP----FAPSGFK 43 (64)
Q Consensus 25 ~~pPI~l~FeIP----~t~SGLq 43 (64)
.+|||.+.|.|. |+.-|++
T Consensus 60 G~~Pi~VsFDIDDTvLFsSp~F~ 82 (237)
T COG3700 60 GRPPIAVSFDIDDTVLFSSPGFW 82 (237)
T ss_pred CCCCeeEeeccCCeeEecccccc
Confidence 599999999996 7766654
Done!