Query psy17940
Match_columns 81
No_of_seqs 102 out of 138
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 18:13:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17940hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07718 Coatamer_beta_C: Coat 99.0 1.9E-10 4.2E-15 80.2 2.7 48 24-81 1-48 (140)
2 KOG1058|consensus 98.9 5E-10 1.1E-14 94.8 3.1 72 1-81 642-713 (948)
3 PF05186 Dpy-30: Dpy-30 motif; 20.7 22 0.00049 19.8 -0.7 10 23-32 24-33 (42)
4 smart00394 RIIa RIIalpha, Regu 20.0 27 0.00058 18.6 -0.5 10 22-31 16-25 (38)
5 PF02197 RIIa: Regulatory subu 15.5 32 0.0007 18.6 -0.8 10 23-32 17-26 (38)
6 PF05662 YadA_stalk: Coiled st 14.1 69 0.0015 15.7 0.2 12 23-34 10-21 (21)
7 PF13257 DUF4048: Domain of un 13.6 1.3E+02 0.0027 23.1 1.6 17 48-64 99-115 (253)
8 PRK13895 conjugal transfer pro 13.0 76 0.0016 22.5 0.3 18 17-34 14-31 (144)
9 PF12196 hNIFK_binding: FHA Ki 5.6 3E+02 0.0065 15.6 0.7 8 26-33 32-39 (41)
10 PF03683 UPF0175: Uncharacteri 5.3 2.8E+02 0.006 16.7 0.5 30 27-56 47-76 (76)
No 1
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised 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 []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=99.00 E-value=1.9e-10 Score=80.24 Aligned_cols=48 Identities=40% Similarity=0.481 Sum_probs=37.5
Q ss_pred CCCCceeecccccccCCCCCCchhhhHhHHHHHhccCCCcccccccCCCccccccCCC
Q psy17940 24 QPDDPISFLELSSARGSEFGGTENVFELSLNQALIGSGPAAAQTQAADPSGASKLNKM 81 (81)
Q Consensus 24 Q~DD~I~FrQL~~~~~~~~~~~ed~~e~dL~~A~g~~~~~~~~~~~~~~~~~SKLnKV 81 (81)
||||+|+||||+++ ......++++++||.+|+|... .. ..+.|||+||
T Consensus 1 q~D~~i~f~ql~~~--~~~~~~~~~~~~dl~~a~g~~~-----~~---~~~~skL~kv 48 (140)
T PF07718_consen 1 QPDDLISFRQLKGK--KALSGDEDDFEDDLSRATGSID-----KS---EDFSSKLNKV 48 (140)
T ss_pred CCCCcEeheccccC--ccccccchhhhhhHHHhhCCcc-----cc---chhhhhhccE
Confidence 89999999999887 4444455789999999998543 23 4557999986
No 2
>KOG1058|consensus
Probab=98.93 E-value=5e-10 Score=94.78 Aligned_cols=72 Identities=38% Similarity=0.421 Sum_probs=52.6
Q ss_pred CchhhhHHHHHhhhhhhCCCCCCCCCCceeecccccccCCCCCCchhhhHhHHHHHhccCCCcccccccCCCccccccCC
Q psy17940 1 MLEAKSQEEASTQKAKEKPGHKVQPDDPISFLELSSARGSEFGGTENVFELSLNQALIGSGPAAAQTQAADPSGASKLNK 80 (81)
Q Consensus 1 mL~ak~~e~~~~~k~~~~~~~~vQ~DD~I~FrQL~~~~~~~~~~~ed~~e~dL~~A~g~~~~~~~~~~~~~~~~~SKLnK 80 (81)
|+.++..+++...+. +..+..+||||||+|+||++. .+....+|.|++||.+|+|... ... +.+.+|||+|
T Consensus 642 m~~~~~~~~~~~~~~-~~~~~~~~~ddpI~f~q~~~~--~s~~~~en~fe~~L~~A~g~~~-----~~~-~~s~~sKL~k 712 (948)
T KOG1058|consen 642 MIDAKKKRRKEELLK-KSQKTTAQPDDPINFRQLRSG--RSDERGENQFEEDLVQATGDAQ-----KAE-DGSPASKLNK 712 (948)
T ss_pred HhhHHHHHHHHHHHh-hhccccCCCCCccchHhhccc--chhhhhhhHHHHHHHHHhcccc-----ccc-cCCcHHHhhc
Confidence 566766666654444 567788999999999999864 3434478899999999999664 332 2333799999
Q ss_pred C
Q psy17940 81 M 81 (81)
Q Consensus 81 V 81 (81)
|
T Consensus 713 V 713 (948)
T KOG1058|consen 713 V 713 (948)
T ss_pred e
Confidence 7
No 3
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=20.71 E-value=22 Score=19.79 Aligned_cols=10 Identities=60% Similarity=1.245 Sum_probs=6.6
Q ss_pred CCCCCceeec
Q psy17940 23 VQPDDPISFL 32 (81)
Q Consensus 23 vQ~DD~I~Fr 32 (81)
.+|+|||.|.
T Consensus 24 ~rP~DPi~~L 33 (42)
T PF05186_consen 24 ERPEDPIEFL 33 (42)
T ss_dssp H--SSHHHHH
T ss_pred HCCCChHHHH
Confidence 5789999885
No 4
>smart00394 RIIa RIIalpha, Regulatory subunit portion of type II PKA R-subunit. RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).
Probab=19.96 E-value=27 Score=18.55 Aligned_cols=10 Identities=40% Similarity=0.876 Sum_probs=7.9
Q ss_pred CCCCCCceee
Q psy17940 22 KVQPDDPISF 31 (81)
Q Consensus 22 ~vQ~DD~I~F 31 (81)
..||+|+|.|
T Consensus 16 ~~qP~d~~~f 25 (38)
T smart00394 16 RAQPSDLVQF 25 (38)
T ss_pred HHCCCcHHHH
Confidence 3589999977
No 5
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=15.47 E-value=32 Score=18.61 Aligned_cols=10 Identities=50% Similarity=0.800 Sum_probs=4.9
Q ss_pred CCCCCceeec
Q psy17940 23 VQPDDPISFL 32 (81)
Q Consensus 23 vQ~DD~I~Fr 32 (81)
.||+|++.|-
T Consensus 17 ~qP~Di~~F~ 26 (38)
T PF02197_consen 17 EQPDDILQFA 26 (38)
T ss_dssp H--S-HHHHH
T ss_pred HCCCcHHHHH
Confidence 4889988763
No 6
>PF05662 YadA_stalk: Coiled stalk of trimeric autotransporter adhesin; InterPro: IPR008635 This short motif is found in invasins and haemagglutinins, normally associated with the Hep_Hag repeat (IPR008640 from INTERPRO).; GO: 0009405 pathogenesis, 0019867 outer membrane; PDB: 3NTN_A 3PR7_A 1P9H_A 3D9X_A 3LAA_A 3LA9_A 3EMO_C.
Probab=14.13 E-value=69 Score=15.75 Aligned_cols=12 Identities=17% Similarity=0.354 Sum_probs=8.0
Q ss_pred CCCCCceeeccc
Q psy17940 23 VQPDDPISFLEL 34 (81)
Q Consensus 23 vQ~DD~I~FrQL 34 (81)
+..-|.++|.||
T Consensus 10 ~~~tDAVN~~QL 21 (21)
T PF05662_consen 10 TNDTDAVNVSQL 21 (21)
T ss_dssp TTTTSB-BHHHH
T ss_pred CCCccceecccC
Confidence 355688888887
No 7
>PF13257 DUF4048: Domain of unknown function (DUF4048)
Probab=13.63 E-value=1.3e+02 Score=23.08 Aligned_cols=17 Identities=29% Similarity=0.503 Sum_probs=14.4
Q ss_pred hhHhHHHHHhccCCCcc
Q psy17940 48 VFELSLNQALIGSGPAA 64 (81)
Q Consensus 48 ~~e~dL~~A~g~~~~~~ 64 (81)
.|-+||-|||-|+.+|.
T Consensus 99 TFvEDIRQATVGDEpIn 115 (253)
T PF13257_consen 99 TFVEDIRQATVGDEPIN 115 (253)
T ss_pred HHHHHHHHhhccccccC
Confidence 68999999999997553
No 8
>PRK13895 conjugal transfer protein TraM; Provisional
Probab=12.97 E-value=76 Score=22.50 Aligned_cols=18 Identities=44% Similarity=0.591 Sum_probs=15.6
Q ss_pred hCCCCCCCCCCceeeccc
Q psy17940 17 EKPGHKVQPDDPISFLEL 34 (81)
Q Consensus 17 ~~~~~~vQ~DD~I~FrQL 34 (81)
.+++.++-.||||...|-
T Consensus 14 ~KHGIal~rDDPILilqT 31 (144)
T PRK13895 14 AKHGIAVGRDDPILILQT 31 (144)
T ss_pred HHcCcccCCCCCchhHHH
Confidence 478889999999998876
No 9
>PF12196 hNIFK_binding: FHA Ki67 binding domain of hNIFK; InterPro: IPR021043 This entry represents eukaryotic proteins that contain a domain of approximately 40 amino acids in length. These proteins are found in association with PF00076 from PFAM. There are two conserved sequence motifs: TPVCTP and LERRKS. This domain is found on the human nucleolar protein hNIFK. It binds to the fork-head-associated domain of human Ki67. High-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230. This interaction is involved in cell cycle regulation []. ; PDB: 2AFF_B.
Probab=5.56 E-value=3e+02 Score=15.63 Aligned_cols=8 Identities=50% Similarity=0.771 Sum_probs=5.8
Q ss_pred CCceeecc
Q psy17940 26 DDPISFLE 33 (81)
Q Consensus 26 DD~I~FrQ 33 (81)
||-|.|.|
T Consensus 32 D~EIv~K~ 39 (41)
T PF12196_consen 32 DDEIVFKQ 39 (41)
T ss_dssp S-SEEESS
T ss_pred CCeeEecc
Confidence 78899986
No 10
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=5.32 E-value=2.8e+02 Score=16.74 Aligned_cols=30 Identities=33% Similarity=0.381 Sum_probs=16.6
Q ss_pred CceeecccccccCCCCCCchhhhHhHHHHH
Q psy17940 27 DPISFLELSSARGSEFGGTENVFELSLNQA 56 (81)
Q Consensus 27 D~I~FrQL~~~~~~~~~~~ed~~e~dL~~A 56 (81)
....|.++-+.+|-....++++++.||..|
T Consensus 47 s~~eF~~~L~~~gI~~~~~~eel~~dle~a 76 (76)
T PF03683_consen 47 SRWEFLELLKERGIPINYDEEELEEDLETA 76 (76)
T ss_pred CHHHHHHHHHHCCCCCCCCHHHHHHHHHhC
Confidence 346677774442333344566777777543
Done!