Query psy8268
Match_columns 61
No_of_seqs 102 out of 148
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 22:59:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8268.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8268hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1060|consensus 99.6 4E-17 8.7E-22 131.8 1.7 50 4-53 524-573 (968)
2 PTZ00429 beta-adaptin; Provisi 98.6 2.9E-08 6.3E-13 79.3 3.6 50 4-53 498-548 (746)
3 PF01602 Adaptin_N: Adaptin N 97.8 5.3E-06 1.1E-10 60.0 0.5 48 4-51 474-524 (526)
4 KOG1061|consensus 93.8 0.051 1.1E-06 44.6 2.7 47 5-51 481-528 (734)
5 COG5096 Vesicle coat complex, 93.2 0.049 1.1E-06 44.7 1.6 40 5-51 511-562 (757)
6 PHA02907 hypothetical protein; 60.6 6.1 0.00013 27.3 1.7 18 36-53 109-126 (182)
7 PF02985 HEAT: HEAT repeat; I 56.9 11 0.00024 18.2 1.8 21 23-44 2-22 (31)
8 PF10725 DUF2517: Protein of u 47.8 10 0.00022 22.7 1.0 11 39-49 32-42 (63)
9 PF14468 DUF4427: Protein of u 41.7 12 0.00027 25.2 0.8 26 23-48 65-90 (132)
10 smart00583 SPK domain in SET a 38.3 48 0.001 21.0 3.1 27 25-51 51-77 (114)
11 PRK10941 hypothetical protein; 36.3 42 0.0009 24.2 2.8 17 33-49 213-229 (269)
12 KOG4143|consensus 32.1 18 0.00039 26.1 0.4 34 11-44 29-65 (218)
13 PF10193 Telomere_reg-2: Telom 24.3 1.2E+02 0.0026 19.0 3.1 34 12-49 78-111 (114)
14 COG1671 Uncharacterized protei 22.6 59 0.0013 22.2 1.5 20 30-49 121-140 (150)
No 1
>KOG1060|consensus
Probab=99.64 E-value=4e-17 Score=131.76 Aligned_cols=50 Identities=60% Similarity=0.857 Sum_probs=48.3
Q ss_pred eeeeehhhhhcCchhHHHHHHHHHHhhcccCCcchhHHHHHHHHHhCCCC
Q psy8268 4 ACRRMVKLYLTNPAQTTLLCQYLLSLARYDQNYDIRDRARLLRQLLFPAP 53 (61)
Q Consensus 4 ~L~LaAKL~~~~~~~~~~l~~yvl~LakyD~~yDiRDRaRfl~~Ll~~~~ 53 (61)
+|+|+||||++++++++++++||++|++||+|||||||+||++.|+.+.+
T Consensus 524 ILnL~aKLyl~~~~~~kll~~Yv~~L~~yD~sYDiRDRaRF~r~l~~~~~ 573 (968)
T KOG1060|consen 524 ILNLSAKLYLTNIDQTKLLVQYVFELARYDLSYDIRDRARFLRQLISPLE 573 (968)
T ss_pred HHHhhhhheEechhhHHHHHHHHHHHhccCCCcchhHHHHHHHHHhccHH
Confidence 58999999999999999999999999999999999999999999998866
No 2
>PTZ00429 beta-adaptin; Provisional
Probab=98.62 E-value=2.9e-08 Score=79.26 Aligned_cols=50 Identities=24% Similarity=0.299 Sum_probs=44.6
Q ss_pred eeeeehhhhhcCchhHHHHHHHHHH-hhcccCCcchhHHHHHHHHHhCCCC
Q psy8268 4 ACRRMVKLYLTNPAQTTLLCQYLLS-LARYDQNYDIRDRARLLRQLLFPAP 53 (61)
Q Consensus 4 ~L~LaAKL~~~~~~~~~~l~~yvl~-LakyD~~yDiRDRaRfl~~Ll~~~~ 53 (61)
.|+.++|+++..|.+.+.+.++||+ ++++|.|+||||||+|+-.|+..+.
T Consensus 498 lLta~vKlfl~~p~~~~~~l~~vL~~~t~~~~d~DVRDRA~~Y~rLLs~~~ 548 (746)
T PTZ00429 498 ILSAAVKMFLRDPQGMEPQLNRVLETVTTHSDDPDVRDRAFAYWRLLSKGI 548 (746)
T ss_pred HHHHHHHHHhcCcHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHcCCC
Confidence 5788999999999888889999995 5699999999999999999998653
No 3
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 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. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin 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 []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=97.81 E-value=5.3e-06 Score=60.02 Aligned_cols=48 Identities=38% Similarity=0.508 Sum_probs=41.0
Q ss_pred eeeeehhhhhcCch--hHHHHHHHHHHhhcccC-CcchhHHHHHHHHHhCC
Q psy8268 4 ACRRMVKLYLTNPA--QTTLLCQYLLSLARYDQ-NYDIRDRARLLRQLLFP 51 (61)
Q Consensus 4 ~L~LaAKL~~~~~~--~~~~l~~yvl~LakyD~-~yDiRDRaRfl~~Ll~~ 51 (61)
.++..+|++..+|+ ....+.+++.+++++|. |+||||||+++..|+..
T Consensus 474 ilt~~~Kl~~~~~~~~~~~~i~~~~~~~~~~~s~~~evr~Ra~~y~~ll~~ 524 (526)
T PF01602_consen 474 ILTALAKLFKRNPENEVQNEILQFLLSLATEDSSDPEVRDRAREYLRLLNS 524 (526)
T ss_dssp HHHHHHHHHHHSCSTTHHHHHHHHHHCHHHHS-SSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhCCchhhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHcc
Confidence 46788999999985 34699999999999855 99999999999999864
No 4
>KOG1061|consensus
Probab=93.80 E-value=0.051 Score=44.59 Aligned_cols=47 Identities=36% Similarity=0.505 Sum_probs=43.0
Q ss_pred eeeehhhhhcCchhHHHHHHHHHHhhcccCCc-chhHHHHHHHHHhCC
Q psy8268 5 CRRMVKLYLTNPAQTTLLCQYLLSLARYDQNY-DIRDRARLLRQLLFP 51 (61)
Q Consensus 5 L~LaAKL~~~~~~~~~~l~~yvl~LakyD~~y-DiRDRaRfl~~Ll~~ 51 (61)
|+-+.|+++..|.+.+.|.+.||++|-=|.+- |+|||+=|+..+++.
T Consensus 481 Lta~ik~Fl~~p~~tq~~l~~vL~~~~~d~~~~dlrDr~l~Y~RlLs~ 528 (734)
T KOG1061|consen 481 LTAAIKLFLKKPTETQELLQGVLPLATADTDNPDLRDRGLIYWRLLSE 528 (734)
T ss_pred HHHHHHHHhcCCccHHHHHHHHHhhhhccccChhhhhhHHHHHHHhhc
Confidence 45578999999999999999999999999988 999999999999984
No 5
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=93.16 E-value=0.049 Score=44.69 Aligned_cols=40 Identities=33% Similarity=0.408 Sum_probs=30.9
Q ss_pred eeeehhhhhcCchhH------------HHHHHHHHHhhcccCCcchhHHHHHHHHHhCC
Q psy8268 5 CRRMVKLYLTNPAQT------------TLLCQYLLSLARYDQNYDIRDRARLLRQLLFP 51 (61)
Q Consensus 5 L~LaAKL~~~~~~~~------------~~l~~yvl~LakyD~~yDiRDRaRfl~~Ll~~ 51 (61)
++.++|+++.+++.. ...++|+..+ |+||||+|+..++++
T Consensus 511 l~~svkl~~~~~~~~~~~~~~~d~~v~~~~~~~v~~~-------DlRDra~my~~~lst 562 (757)
T COG5096 511 LMSSVKLIANSIRKAKQCNSELDQDVLRRCFDYVLVP-------DLRDRARMYSRLLST 562 (757)
T ss_pred HHHHHHHHHhCcHhhhhccchhccHHHHHHHhccCCh-------hHHHHHHHHHHHhcC
Confidence 567889998887543 3356666666 999999999999983
No 6
>PHA02907 hypothetical protein; Provisional
Probab=60.65 E-value=6.1 Score=27.31 Aligned_cols=18 Identities=39% Similarity=0.560 Sum_probs=14.8
Q ss_pred cchhHHHHHHHHHhCCCC
Q psy8268 36 YDIRDRARLLRQLLFPAP 53 (61)
Q Consensus 36 yDiRDRaRfl~~Ll~~~~ 53 (61)
..||||-||++.|+.--+
T Consensus 109 vkirdrlrfirklfryvg 126 (182)
T PHA02907 109 VKIRDRLRFIRKLFRYVG 126 (182)
T ss_pred hhhHHHHHHHHHHHHHhh
Confidence 579999999999986543
No 7
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=56.93 E-value=11 Score=18.19 Aligned_cols=21 Identities=29% Similarity=0.335 Sum_probs=14.4
Q ss_pred HHHHHHhhcccCCcchhHHHHH
Q psy8268 23 CQYLLSLARYDQNYDIRDRARL 44 (61)
Q Consensus 23 ~~yvl~LakyD~~yDiRDRaRf 44 (61)
...++++.. |++.+||.-|-.
T Consensus 2 lp~l~~~l~-D~~~~VR~~a~~ 22 (31)
T PF02985_consen 2 LPILLQLLN-DPSPEVRQAAAE 22 (31)
T ss_dssp HHHHHHHHT--SSHHHHHHHHH
T ss_pred HHHHHHHcC-CCCHHHHHHHHH
Confidence 345666666 999999987654
No 8
>PF10725 DUF2517: Protein of unknown function (DUF2517); InterPro: IPR019663 This entry represents proteins conserved in Proteobacteria and includes the predicted protein YbfA. The function is not known.
Probab=47.80 E-value=10 Score=22.73 Aligned_cols=11 Identities=45% Similarity=0.561 Sum_probs=8.9
Q ss_pred hHHHHHHHHHh
Q psy8268 39 RDRARLLRQLL 49 (61)
Q Consensus 39 RDRaRfl~~Ll 49 (61)
+|||||.+-|-
T Consensus 32 ~dRArfYSyLh 42 (63)
T PF10725_consen 32 SDRARFYSYLH 42 (63)
T ss_pred cchhHHHHHHH
Confidence 89999987663
No 9
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=41.71 E-value=12 Score=25.20 Aligned_cols=26 Identities=23% Similarity=0.645 Sum_probs=22.6
Q ss_pred HHHHHHhhcccCCcchhHHHHHHHHH
Q psy8268 23 CQYLLSLARYDQNYDIRDRARLLRQL 48 (61)
Q Consensus 23 ~~yvl~LakyD~~yDiRDRaRfl~~L 48 (61)
-.|++.+..+|.++++|-|..|-+.+
T Consensus 65 GRYLl~l~~~~s~~plr~kE~~ak~v 90 (132)
T PF14468_consen 65 GRYLLDLDLFDSDWPLRKKEAMAKHV 90 (132)
T ss_pred ceeeeecccccCCCchHHHHHHHHHH
Confidence 36999999999999999998886654
No 10
>smart00583 SPK domain in SET and PHD domain containing proteins and protein kinases.
Probab=38.33 E-value=48 Score=20.99 Aligned_cols=27 Identities=26% Similarity=0.196 Sum_probs=19.8
Q ss_pred HHHHhhcccCCcchhHHHHHHHHHhCC
Q psy8268 25 YLLSLARYDQNYDIRDRARLLRQLLFP 51 (61)
Q Consensus 25 yvl~LakyD~~yDiRDRaRfl~~Ll~~ 51 (61)
.+....--..+||+..|+|++-+|=.+
T Consensus 51 ~Lap~i~~~~~y~~~~kirm~Fals~~ 77 (114)
T smart00583 51 KLAPNMIKLNNYSIEERIRMMFALSGK 77 (114)
T ss_pred HHHhhHhhccCCCHHHHHHHHHhcCCc
Confidence 344444456799999999999887554
No 11
>PRK10941 hypothetical protein; Provisional
Probab=36.28 E-value=42 Score=24.20 Aligned_cols=17 Identities=41% Similarity=0.677 Sum_probs=13.5
Q ss_pred cCCcchhHHHHHHHHHh
Q psy8268 33 DQNYDIRDRARLLRQLL 49 (61)
Q Consensus 33 D~~yDiRDRaRfl~~Ll 49 (61)
|.-|++|||+-.+.+|=
T Consensus 213 ~dp~e~RDRGll~~qL~ 229 (269)
T PRK10941 213 EDPYEIRDRGLIYAQLD 229 (269)
T ss_pred CCHHHHHHHHHHHHHcC
Confidence 44599999998887763
No 12
>KOG4143|consensus
Probab=32.10 E-value=18 Score=26.06 Aligned_cols=34 Identities=26% Similarity=0.338 Sum_probs=25.8
Q ss_pred hhhcCchhHHHHHHHHHHhh---cccCCcchhHHHHH
Q psy8268 11 LYLTNPAQTTLLCQYLLSLA---RYDQNYDIRDRARL 44 (61)
Q Consensus 11 L~~~~~~~~~~l~~yvl~La---kyD~~yDiRDRaRf 44 (61)
-|+.+|+++..|++-++.|- .-|-.+||||+-|.
T Consensus 29 ~y~Fdp~~l~el~~q~i~l~~~~t~all~di~d~l~~ 65 (218)
T KOG4143|consen 29 SYVFDPEELAELARQYIGLDANHTLALLRDIVDLLRL 65 (218)
T ss_pred ceeeCHHHHHHHHHHHhccccccHHHHHHHHHHHHHh
Confidence 46778888888888777664 33567999999876
No 13
>PF10193 Telomere_reg-2: Telomere length regulation protein; InterPro: IPR019337 This entry represents a conserved domain found in a group of proteins called telomere-length regulation, or clock abnormal protein-2, which are conserved from plants to humans. These proteins regulate telomere length and contribute to silencing of sub-telomeric regions []. In vitro the protein binds to telomeric DNA repeats. ; PDB: 3O4Z_B.
Probab=24.25 E-value=1.2e+02 Score=19.01 Aligned_cols=34 Identities=21% Similarity=0.447 Sum_probs=18.5
Q ss_pred hhcCchhHHHHHHHHHHhhcccCCcchhHHHHHHHHHh
Q psy8268 12 YLTNPAQTTLLCQYLLSLARYDQNYDIRDRARLLRQLL 49 (61)
Q Consensus 12 ~~~~~~~~~~l~~yvl~LakyD~~yDiRDRaRfl~~Ll 49 (61)
.+..|+++.. |+.+. -|..+|.+..|.-++.+|-
T Consensus 78 ~v~~P~~~~~---~L~~~-f~~~~~Sl~qR~~iL~~l~ 111 (114)
T PF10193_consen 78 VVAAPEKVAP---YLTEE-FFSGDYSLQQRMSILSALS 111 (114)
T ss_dssp HHHSGGGHHH----HHHH-HTTS---THHHHHHHHHHH
T ss_pred HHHhhHHHHH---HHHHH-HhcCCCCHHHHHHHHHHHH
Confidence 4455655433 33222 2569999999999998874
No 14
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.61 E-value=59 Score=22.24 Aligned_cols=20 Identities=25% Similarity=0.318 Sum_probs=15.4
Q ss_pred hcccCCcchhHHHHHHHHHh
Q psy8268 30 ARYDQNYDIRDRARLLRQLL 49 (61)
Q Consensus 30 akyD~~yDiRDRaRfl~~Ll 49 (61)
.+.-..|-=|||.||.++|-
T Consensus 121 ~~gp~~~~~rDr~~F~~~ld 140 (150)
T COG1671 121 TGGPAAFSSRDRSRFANALD 140 (150)
T ss_pred cCCCCccChHHHHHHHHHHH
Confidence 44566788899999988763
Done!