Query psy13404
Match_columns 167
No_of_seqs 113 out of 173
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 18:36:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12619 MCM2_N: Mini-chromoso 99.9 2.9E-25 6.3E-30 178.1 7.8 93 65-157 26-128 (156)
2 KOG0477|consensus 99.6 2.9E-16 6.3E-21 149.5 4.7 73 34-122 21-93 (854)
3 PF07225 NDUF_B4: NADH-ubiquin 50.2 24 0.00052 28.0 3.7 30 94-124 12-41 (125)
4 PF03700 Sorting_nexin: Sortin 17.8 90 0.002 25.0 1.9 12 67-78 23-34 (129)
5 PF04270 Strep_his_triad: Stre 17.2 1.4E+02 0.003 20.5 2.5 19 101-119 35-53 (53)
6 PF08909 DUF1854: Domain of un 14.7 1.3E+02 0.0029 24.1 2.1 22 100-121 36-57 (133)
7 PF15234 LAT: Linker for activ 12.1 3.5E+02 0.0076 23.6 4.1 27 80-106 169-196 (230)
8 PF09444 MRC1: MRC1-like domai 6.8 9.6E+02 0.021 19.5 4.5 6 76-81 41-46 (145)
9 KOG4330|consensus 5.3 5.2E+02 0.011 22.4 2.2 11 33-43 63-73 (206)
10 PF06183 DinI: DinI-like famil 4.7 4.6E+02 0.0099 18.3 1.3 18 104-121 1-18 (65)
No 1
>PF12619 MCM2_N: Mini-chromosome maintenance protein 2; InterPro: IPR008045 The MCM2-7 complex consists of six closely related proteins that are highly conserved throughout the eukaryotic kingdom. During late mitosis and G1, replication origins are 'licensed' for replication by loading the minichromosome maintenance (MCM) 2-7 proteins pre-replicative complex essential for initiating and elongating replication forks during S phase. The components of the MCM2-7 complex in Homo sapiens (Human) (EBI-913604 from INTACT) are: . DNA replication licensing factor MCM2, P49736 from SWISSPROT, IPR008045 from INTERPRO DNA replication licensing factor MCM3, P25205 from SWISSPROT, IPR008046 from INTERPRO DNA replication licensing factor MCM4, P33991 from SWISSPROT, IPR008047 from INTERPRO DNA replication licensing factor MCM5, P33992 from SWISSPROT, IPR008048 from INTERPRO DNA replication licensing factor MCM6, Q14566 from SWISSPROT, IPR008049 from INTERPRO DNA replication licensing factor MCM7, P33993 from SWISSPROT, IPR008050 from INTERPRO Studies in Xenopus eggs have showed the 6 MCM proteins to form hexamers, where each class is present in equal stoichiometry []. The initiation of DNA synthesis in eukaryotes requires the binding of origin recognition complex (ORC) - a complex of six subunits - to the autonomously replicating sequences (ARS) of replication origins [], the recruitment of CDC6 and binding of the MCM protein complex to the ARS to form the prereplicative complex (pre-RC) []. DNA synthesis is subsequently initiated by the activation of pre-RC by CDC7 and CDC28 protein kinases []. MCM proteins associate with chromatin during G1 phase and dissociate again during S phase, remaining unbound until the end of mitosis []. Periodic chromatin association of the MCM complex ensures that DNA synthesis from replication origins is initiated only once during the cell cycle, avoiding over-replication of parts of the genome. Elongation of replication forks away from individual replication origins results in displacement of the MCM-containing complex from chromatin. Budding yeast MCM proteins are translocated in and out of the nucleus during each cell cycle. However, fission yeast MCMs, like those in metazoans, are constitutively nuclear. The six classes of MCM protein together share a conserved 200 amino acid residue domain, while sequences within the same class show more extensive similarity outside this region. The conserved central domain is similar to the A motif of the Walker-type NTP-binding domain; it also shares similarity with ATPase domains of prokaryotic NtrC-related transcription regulators. The ATP-binding motif is thought to mediate ATP-dependent opening of double-stranded DNA at replication origins. In addition to the central region, MCM2, 4, 6 and 7 contain a zinc-finger-type motif thought to have a role in mediating protein-protein interactions []. Moreover, a conserved alpha-helical structure in the C-terminal region has been noted; this comprises a conserved heptad repeat and a putative four-helix bundle. Most of the MCM proteins contain acidic regions, or alternately repeated clusters of acidic and basic residues. In addition to its role in initiation of DNA replication, MCM2 is able to inhibit the MCM4,6,7 helicase. Studies on murine MCM2 indicate that its C terminus is required for interaction with MCM4, as well as for inhibition of the DNA helicase activity of the MCM4,6,7 complex. The N-terminal region, which contains an H3-binding domain and a region required for nuclear localisation, is required for the phosphorylation by CDC7 kinase. ; GO: 0003677 DNA binding, 0005524 ATP binding, 0006270 DNA-dependent DNA replication initiation, 0005634 nucleus
Probab=99.92 E-value=2.9e-25 Score=178.08 Aligned_cols=93 Identities=53% Similarity=0.871 Sum_probs=75.9
Q ss_pred ccccccccccccchhhccCCCCCCCccCCCCCCC-cccccCCHHHHHHHHHHHHHhHHHHHcCC--CCCCcccccCCC-c
Q psy13404 65 EDEGSGEELFGDNLENDYRPMPALDRYDHDQLDD-SDYSVISADARAEAERALRRRDREQAMGG--RRGDADLLYESD-E 140 (167)
Q Consensus 65 eEEEeGEDLfgDnmE~DYr~~pElD~Yd~~gLDD-~dyeemd~~~RRaaE~~L~rRDr~~~r~~--~R~~~~ll~DdD-d 140 (167)
+++++|+||||+||++||+++++||+|+..+||| .+|++|++++||+||++|++||+..++.. +|+.++||++++ +
T Consensus 26 eEEeeGEDLfgDnme~DYr~~~elD~Yd~~~lDDe~dy~~md~~~RraaE~~L~~RDr~~~~~~~~rr~~p~~~~ddddd 105 (156)
T PF12619_consen 26 EEEEEGEDLFGDNMERDYRPNPELDRYDEDGLDDESDYEEMDPAARRAAERELNRRDREEGRRRGRRRRMPAAFLDDDDD 105 (156)
T ss_pred ccccccchhcccCHHHHhccCcccCccccCCCCchhhcccCCHHHHHHHHHHHHHHHHHHhhhccccccccccccccccc
Confidence 5678999999999999999999999999999998 59999999999999999999999988642 244455555554 3
Q ss_pred ccc------hHHHHHHHHHHhhc
Q psy13404 141 DEE------APRRKRRAAERAAE 157 (167)
Q Consensus 141 ddd------~p~RRRR~~eraae 157 (167)
++. +++||||++++++.
T Consensus 106 dd~~~~l~~~~rRRR~~~d~~~d 128 (156)
T PF12619_consen 106 DDEDFDLPVQRRRRRRRYDEAAD 128 (156)
T ss_pred ccccccccccchhhHHHhhhhcc
Confidence 332 23788888888653
No 2
>KOG0477|consensus
Probab=99.61 E-value=2.9e-16 Score=149.49 Aligned_cols=73 Identities=47% Similarity=0.796 Sum_probs=65.7
Q ss_pred cCCCCCCCCCCCCCCCccccccCCCCCCCCCccccccccccccchhhccCCCCCCCccCCCCCCCcccccCCHHHHHHHH
Q psy13404 34 VDEEAPFENEENFNDGDSDIIGAGSPLRVEDEDEGSGEELFGDNLENDYRPMPALDRYDHDQLDDSDYSVISADARAEAE 113 (167)
Q Consensus 34 ~~~~~p~~~~~~~ede~e~l~gd~~~~~~~deEEEeGEDLfgDnmE~DYr~~pElD~Yd~~gLDD~dyeemd~~~RRaaE 113 (167)
...++|.++ +|++|.+ ++||++||||||++|++||++++++|+|+.+ ||| ++.+|+...|++|+
T Consensus 21 ~~~~~~~g~--~f~~e~e------------~~eee~ge~l~~d~me~Dy~~~~e~d~yd~~-~dd-~~~el~~~~r~a~~ 84 (854)
T KOG0477|consen 21 DALTSPPGD--PFEDEEE------------DEEEEEGEDLFGDGMERDYRAMPELDQYDAE-LDD-DVEELSLSDRRAAD 84 (854)
T ss_pred ccCCCCCCC--CCCCccc------------chhhhhhhhhhccchhhhhccChhhhhcccc-ccc-cHhhhchhhHHHHH
Confidence 477888884 9999977 2667889999999999999999999999998 988 59999999999999
Q ss_pred HHHHHhHHH
Q psy13404 114 RALRRRDRE 122 (167)
Q Consensus 114 ~~L~rRDr~ 122 (167)
+.|++||+.
T Consensus 85 ~~l~~rd~~ 93 (854)
T KOG0477|consen 85 ADLRERDRG 93 (854)
T ss_pred hHHhhhhcC
Confidence 999999993
No 3
>PF07225 NDUF_B4: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4); InterPro: IPR009866 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family contains human NADH-ubiquinone oxidoreductase subunit NDUFB4 and related sequences.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=50.16 E-value=24 Score=28.00 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=25.8
Q ss_pred CCCCCcccccCCHHHHHHHHHHHHHhHHHHH
Q psy13404 94 DQLDDSDYSVISADARAEAERALRRRDREQA 124 (167)
Q Consensus 94 ~gLDD~dyeemd~~~RRaaE~~L~rRDr~~~ 124 (167)
..||-.+| ++|++.|+++..++..|.++.+
T Consensus 12 ~~l~p~eY-~~SpE~r~a~~eR~a~Ra~Lk~ 41 (125)
T PF07225_consen 12 KTLDPAEY-DVSPEERRAQQERAAIRARLKR 41 (125)
T ss_pred CCCCHhhc-CCCHHHHHHHHHHHHHHHHHHH
Confidence 45677889 9999999999999999998654
No 4
>PF03700 Sorting_nexin: Sorting nexin, N-terminal domain ; InterPro: IPR005329 SNXs are hydrophilic molecules that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domains (IPR001683 from INTERPRO) or through protein-protein interactions with membrane-associated protein complexes []. Indeed, several of the SNXs require several targeting motifs for their appropriate cellular localization. In almost every case studied, mammalian SNXs can be shown to have a role in protein sorting, with the most commonly used experimental model being plasma-membrane receptor endocytosis and sorting through the endosomal pathway. However, it is equally probable that SNXs sort vesicles that are not derived from the plasma membrane, and have a function in the accurate targeting of these vesicles and their cargo. The N-terminal domain appears to be specific to sorting nexins 1 and 2. SNX1 is both membrane-associated and cytosolic, where it probably exists as a tetramer in large protein complexes and may hetero-oligomerize with SNX2.; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport
Probab=17.79 E-value=90 Score=24.98 Aligned_cols=12 Identities=25% Similarity=0.739 Sum_probs=8.4
Q ss_pred ccccccccccch
Q psy13404 67 EGSGEELFGDNL 78 (167)
Q Consensus 67 EEeGEDLfgDnm 78 (167)
.++|||||--+.
T Consensus 23 ~deGEDiFt~~~ 34 (129)
T PF03700_consen 23 DDEGEDIFTSAV 34 (129)
T ss_pred cccccccccccc
Confidence 467899986544
No 5
>PF04270 Strep_his_triad: Streptococcal histidine triad protein ; InterPro: IPR006270 This entry represents a repeated sequence region that includes a His-X-X-His-X-His (histidine triad) motif, which is found in family of Streptococcal proteins. Members of the family are suggested to cleave human complement component 3, and family member PhpA has been shown in vaccine studies to be a protective antigen in mice []. ; PDB: 2CS7_C.
Probab=17.24 E-value=1.4e+02 Score=20.54 Aligned_cols=19 Identities=26% Similarity=0.158 Sum_probs=14.6
Q ss_pred cccCCHHHHHHHHHHHHHh
Q psy13404 101 YSVISADARAEAERALRRR 119 (167)
Q Consensus 101 yeemd~~~RRaaE~~L~rR 119 (167)
+..||+.++.+|++-|+.+
T Consensus 35 k~dLs~~E~~aA~~~~~~K 53 (53)
T PF04270_consen 35 KSDLSASELKAAQAYLAGK 53 (53)
T ss_dssp GGGS-HHHHHHHHHHHH--
T ss_pred hhhCCHHHHHHHHHHHhcC
Confidence 6799999999999988764
No 6
>PF08909 DUF1854: Domain of unknown function (DUF1854); InterPro: IPR015005 These protein is functionally uncharacterised. It is found at the C terminus of a number of ATP transporter proteins suggesting it may be involved in ligand binding.
Probab=14.70 E-value=1.3e+02 Score=24.09 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=19.6
Q ss_pred ccccCCHHHHHHHHHHHHHhHH
Q psy13404 100 DYSVISADARAEAERALRRRDR 121 (167)
Q Consensus 100 dyeemd~~~RRaaE~~L~rRDr 121 (167)
+++.|+++.|..+|.+|..|.-
T Consensus 36 ~l~~L~~~~r~lle~eLa~R~f 57 (133)
T PF08909_consen 36 DLDDLPEESRALLEEELARREF 57 (133)
T ss_pred ChhHCCHHHHHHHHHHHHhCCC
Confidence 4778999999999999999865
No 7
>PF15234 LAT: Linker for activation of T-cells
Probab=12.11 E-value=3.5e+02 Score=23.60 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=14.1
Q ss_pred hccCCCCCCCccCCCCCCC-cccccCCH
Q psy13404 80 NDYRPMPALDRYDHDQLDD-SDYSVISA 106 (167)
Q Consensus 80 ~DYr~~pElD~Yd~~gLDD-~dyeemd~ 106 (167)
.||..-++-..-...-||- .+|-+.+.
T Consensus 169 eDYVNVpeseesa~aSLdGSrEYVNVsq 196 (230)
T PF15234_consen 169 EDYVNVPESEESAEASLDGSREYVNVSQ 196 (230)
T ss_pred ccccccCCccccccccccCccceEecch
Confidence 4666555554444444555 45665554
No 8
>PF09444 MRC1: MRC1-like domain; InterPro: IPR018564 This putative domain is found in the most conserved region in mediator of replication checkpoint protein 1. This protein is a component of the replisome and is required for Rad3-dependent activation of the checkpoint kinase Cds1 in response to replication fork arrest [].
Probab=6.84 E-value=9.6e+02 Score=19.48 Aligned_cols=6 Identities=17% Similarity=0.584 Sum_probs=2.8
Q ss_pred cchhhc
Q psy13404 76 DNLEND 81 (167)
Q Consensus 76 DnmE~D 81 (167)
..|-.|
T Consensus 41 e~MIDD 46 (145)
T PF09444_consen 41 EKMIDD 46 (145)
T ss_pred HHHhcc
Confidence 445444
No 9
>KOG4330|consensus
Probab=5.29 E-value=5.2e+02 Score=22.35 Aligned_cols=11 Identities=36% Similarity=0.582 Sum_probs=5.2
Q ss_pred ccCCCCCCCCC
Q psy13404 33 DVDEEAPFENE 43 (167)
Q Consensus 33 ~~~~~~p~~~~ 43 (167)
...+.+||++.
T Consensus 63 ~~~epsp~~~~ 73 (206)
T KOG4330|consen 63 ATLEPSPFGNQ 73 (206)
T ss_pred hhcCCCCcchh
Confidence 33455555443
No 10
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=4.71 E-value=4.6e+02 Score=18.29 Aligned_cols=18 Identities=28% Similarity=0.296 Sum_probs=12.9
Q ss_pred CCHHHHHHHHHHHHHhHH
Q psy13404 104 ISADARAEAERALRRRDR 121 (167)
Q Consensus 104 md~~~RRaaE~~L~rRDr 121 (167)
|...+.-+++.+|.+|=.
T Consensus 1 lp~ga~~AL~~EL~kRl~ 18 (65)
T PF06183_consen 1 LPAGALEALESELTKRLH 18 (65)
T ss_dssp --TTHHHHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHHH
Confidence 456778899999998744
Done!