Query 044560
Match_columns 68
No_of_seqs 94 out of 96
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 04:28:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044560.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044560hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3426 NADH:ubiquinone oxidor 100.0 5E-31 1.1E-35 174.4 5.2 57 3-68 68-124 (124)
2 PF05347 Complex1_LYR: Complex 91.9 0.12 2.6E-06 28.7 1.7 19 3-21 40-58 (59)
3 PF13232 Complex1_LYR_1: Compl 81.6 1.8 4E-05 24.3 2.5 20 3-22 40-59 (61)
4 PF05020 zf-NPL4: NPL4 family, 38.8 11 0.00024 25.9 0.2 26 7-32 122-147 (147)
5 PF00191 Annexin: Annexin; In 35.9 49 0.0011 18.1 2.5 29 4-32 16-44 (66)
6 PF08621 RPAP1_N: RPAP1-like, 27.4 50 0.0011 18.5 1.6 14 5-18 32-45 (49)
7 PF03130 HEAT_PBS: PBS lyase H 26.5 53 0.0012 15.6 1.4 11 3-13 12-22 (27)
8 PF04818 CTD_bind: RNA polymer 25.0 72 0.0016 17.7 2.0 17 15-31 45-61 (64)
9 PHA00456 hypothetical protein 22.7 71 0.0015 17.1 1.5 16 16-31 18-33 (34)
10 KOG3801 Uncharacterized conser 21.6 1.1E+02 0.0023 19.8 2.5 22 2-23 45-66 (94)
11 cd01671 CARD Caspase activatio 20.9 1.6E+02 0.0035 16.5 3.0 25 7-31 48-72 (80)
12 PF09547 Spore_IV_A: Stage IV 20.7 59 0.0013 26.4 1.4 16 49-64 24-39 (492)
No 1
>KOG3426 consensus NADH:ubiquinone oxidoreductase, NDUFA6/B14 subunit [Energy production and conversion]
Probab=99.97 E-value=5e-31 Score=174.43 Aligned_cols=57 Identities=46% Similarity=0.824 Sum_probs=54.8
Q ss_pred ccchhHHHHHHHhhHHHHHHHHHHhhcccchhhhhhcCCCccccCCCCCCCCcchHHHHHhhcCCC
Q 044560 3 LVNVQVIDMLLFKGTEELNNILEHAKQRHHVIGQYVLGPQGLVQDLDPKDQGLSSFLKNFYKSNYF 68 (68)
Q Consensus 3 VtD~rVID~Lv~KG~~EL~e~~~~wKQ~~Hvm~~~~~~~~~~~~~~g~~~~~~sdFL~kFy~G~~~ 68 (68)
||||||||+||+||+|||+|++.+|||+||||+||..| +++|+|+|||||||.|+||
T Consensus 68 vTD~rViDlLV~kg~~elkeiv~~~kqr~Him~y~f~e---------n~d~kptDFLskF~~g~~~ 124 (124)
T KOG3426|consen 68 VTDPRVIDLLVIKGMEELKEIVDHWKQRHHIMRYYFTE---------NKDPKPTDFLSKFYTGNYF 124 (124)
T ss_pred cCCchhhhHHHHhhHHHHHHHHHHHhCchHHHHHhhcc---------cCCCCchhHHHHHhccCCC
Confidence 89999999999999999999999999999999998866 7899999999999999997
No 2
>PF05347 Complex1_LYR: Complex 1 protein (LYR family); InterPro: IPR008011 This family of short proteins includes proteins from the NADH-ubiquinone oxidoreductase complex I. The family includes the B14 subunit from bovine NADH-ubiquinone oxidoreductase B14 subunit Q02366 from SWISSPROT, and the B22 subunit from the human enzyme Q9Y6M9 from SWISSPROT. The family has been named LYR after a highly conserved tripeptide motif close to the N terminus of these proteins. Members of this family also found in yeast which do contain this complex. In these organisms they are believed to be be required for iron-sulphur custer biogenesis.
Probab=91.94 E-value=0.12 Score=28.70 Aligned_cols=19 Identities=42% Similarity=0.506 Sum_probs=17.9
Q ss_pred ccchhHHHHHHHhhHHHHH
Q 044560 3 LVNVQVIDMLLFKGTEELN 21 (68)
Q Consensus 3 VtD~rVID~Lv~KG~~EL~ 21 (68)
+|||..|+.|+-+|+++|+
T Consensus 40 ~~d~~~I~~~l~~g~~~l~ 58 (59)
T PF05347_consen 40 ETDPEKIEELLKKGEEELE 58 (59)
T ss_pred CCCHHHHHHHHHHHHHHhc
Confidence 7899999999999999986
No 3
>PF13232 Complex1_LYR_1: Complex1_LYR-like
Probab=81.61 E-value=1.8 Score=24.29 Aligned_cols=20 Identities=30% Similarity=0.393 Sum_probs=18.6
Q ss_pred ccchhHHHHHHHhhHHHHHH
Q 044560 3 LVNVQVIDMLLFKGTEELNN 22 (68)
Q Consensus 3 VtD~rVID~Lv~KG~~EL~e 22 (68)
+|||.-|+-++-+|+.+|..
T Consensus 40 ~td~~~i~~~l~~~~~~L~~ 59 (61)
T PF13232_consen 40 VTDPEKIAKLLKEGRKELEL 59 (61)
T ss_pred CCCHHHHHHHHHHHHHHHHH
Confidence 78999999999999999976
No 4
>PF05020 zf-NPL4: NPL4 family, putative zinc binding region; InterPro: IPR007716 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome []. This region of the protein contains possibly two zinc binding motifs. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing.
Probab=38.83 E-value=11 Score=25.92 Aligned_cols=26 Identities=23% Similarity=0.399 Sum_probs=23.1
Q ss_pred hHHHHHHHhhHHHHHHHHHHhhcccc
Q 044560 7 QVIDMLLFKGTEELNNILEHAKQRHH 32 (68)
Q Consensus 7 rVID~Lv~KG~~EL~e~~~~wKQ~~H 32 (68)
|-||.+-|-..+++.+.++.|.+.+|
T Consensus 122 R~VDhVeF~n~~iv~~Fl~~WR~tG~ 147 (147)
T PF05020_consen 122 RHVDHVEFENPEIVNRFLDYWRKTGH 147 (147)
T ss_pred ccccceeecCHHHHHHHHHHHHhcCC
Confidence 56888889999999999999998876
No 5
>PF00191 Annexin: Annexin; InterPro: IPR018502 The annexins (or lipocortins) are a family of proteins that bind to phospholipids in a calcium-dependent manner []. They are distributed ubiquitously in different tissues and cell types of higher and lower eukaryotes, including mammals, fish, birds, Drosophila melanogaster (Fruit fly), Xenopus laevis (African clawed frog), Caenorhabditis elegans , Dictyostelium discoideum (Slime mold) and Neurospora crassa [, ]. Annexins are absent from yeasts and prokaryotes []. The plant annexins are somewhat distinct from those found in other taxa []. Most eukaryotic species have 1-20 annexin (ANX) genes. All annexins share a core domain made up of four similar repeats, each approximately 70 amino acids long []. Each individual annexin repeat (sometimes referred to as endonexin folds) is folded into five alpha-helices, and in turn are wound into a right-handed super-helix; they usually contain a characteristic 'type 2' motif for binding calcium ions with the sequence 'GxGT-[38 residues]-D/E'. Animal and fungal annexins also have variable amino-terminal domains. The core domains of most vertebrate annexins have been analysed by X-ray crystallography, revealing conservation of their secondary and tertiary structures despite only 45-55% amino-acid identity among individual members. The four repeats pack into a structure that resembles a flattened disc, with a slightly convex surface on which the Ca 2+ -binding loops are located and a concave surface at which the amino and carboxyl termini come into close apposition. Annexins are traditionally thought of as calcium-dependent phospholipid-binding proteins, but recent work suggests a more complex set of functions. The famiy has been linked with inhibition of phospholipase activity, exocytosis and endoctyosis, signal transduction, organisation of the extracellular matrix, resistance to reactive oxygen species and DNA replication [].; GO: 0005509 calcium ion binding, 0005544 calcium-dependent phospholipid binding; PDB: 1N44_A 1BC1_A 2IE6_A 2H0M_A 1A8B_A 2H0K_A 1BCW_A 1BCZ_A 1N42_A 1BC0_A ....
Probab=35.91 E-value=49 Score=18.09 Aligned_cols=29 Identities=17% Similarity=0.211 Sum_probs=24.1
Q ss_pred cchhHHHHHHHhhHHHHHHHHHHhhcccc
Q 044560 4 VNVQVIDMLLFKGTEELNNILEHAKQRHH 32 (68)
Q Consensus 4 tD~rVID~Lv~KG~~EL~e~~~~wKQ~~H 32 (68)
.+..+|++|.-+...+++++.+.+++.+.
T Consensus 16 de~~li~Il~~rs~~ql~~i~~~Y~~~~g 44 (66)
T PF00191_consen 16 DEDVLIEILCTRSPAQLRAIKQAYKKKYG 44 (66)
T ss_dssp THHHHHHHHHHSTHHHHHHHHHHHHHHHS
T ss_pred ChhHhhhHHhhhcccccceeehhhhhhhH
Confidence 45568999999999999999988877543
No 6
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=27.35 E-value=50 Score=18.53 Aligned_cols=14 Identities=14% Similarity=0.370 Sum_probs=11.8
Q ss_pred chhHHHHHHHhhHH
Q 044560 5 NVQVIDMLLFKGTE 18 (68)
Q Consensus 5 D~rVID~Lv~KG~~ 18 (68)
||.+|++|.-++..
T Consensus 32 dP~li~~L~~R~~~ 45 (49)
T PF08621_consen 32 DPKLIEFLKKRANK 45 (49)
T ss_pred CHHHHHHHHHhhhc
Confidence 89999999888753
No 7
>PF03130 HEAT_PBS: PBS lyase HEAT-like repeat; InterPro: IPR004155 These proteins contain a short bi-helical repeat that is related to HEAT. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. These proteins include the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/Flyase P31967 from SWISSPROT, P31968 from SWISSPROT, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin []. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six) []. All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerisation reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase []. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted []. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif [].; PDB: 1TE4_A.
Probab=26.48 E-value=53 Score=15.61 Aligned_cols=11 Identities=18% Similarity=0.332 Sum_probs=8.3
Q ss_pred ccchhHHHHHH
Q 044560 3 LVNVQVIDMLL 13 (68)
Q Consensus 3 VtD~rVID~Lv 13 (68)
+.|++.|+.|+
T Consensus 12 igd~~ai~~L~ 22 (27)
T PF03130_consen 12 IGDPRAIPALI 22 (27)
T ss_dssp G-SHHHHHHHH
T ss_pred cCCHHHHHHHH
Confidence 57889999886
No 8
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=24.98 E-value=72 Score=17.69 Aligned_cols=17 Identities=12% Similarity=0.268 Sum_probs=13.2
Q ss_pred hhHHHHHHHHHHhhccc
Q 044560 15 KGTEELNNILEHAKQRH 31 (68)
Q Consensus 15 KG~~EL~e~~~~wKQ~~ 31 (68)
+.+.-+..+++.|++|.
T Consensus 45 ~~~~kv~rll~iW~~r~ 61 (64)
T PF04818_consen 45 EVRKKVQRLLNIWEERN 61 (64)
T ss_dssp HHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHhhCCC
Confidence 34667888999999874
No 9
>PHA00456 hypothetical protein
Probab=22.71 E-value=71 Score=17.06 Aligned_cols=16 Identities=13% Similarity=0.241 Sum_probs=12.4
Q ss_pred hHHHHHHHHHHhhccc
Q 044560 16 GTEELNNILEHAKQRH 31 (68)
Q Consensus 16 G~~EL~e~~~~wKQ~~ 31 (68)
|...++|.-|.||-|.
T Consensus 18 ~~~~Y~ely~lWk~Rg 33 (34)
T PHA00456 18 ANDAYQELYNLWKRRG 33 (34)
T ss_pred ccHHHHHHHHHHHHcc
Confidence 4567888889999874
No 10
>KOG3801 consensus Uncharacterized conserved protein BCN92 [RNA processing and modification]
Probab=21.63 E-value=1.1e+02 Score=19.79 Aligned_cols=22 Identities=18% Similarity=0.191 Sum_probs=18.6
Q ss_pred cccchhHHHHHHHhhHHHHHHH
Q 044560 2 ILVNVQVIDMLLFKGTEELNNI 23 (68)
Q Consensus 2 ~VtD~rVID~Lv~KG~~EL~e~ 23 (68)
-++||..|+-|+-+|+-.|+-+
T Consensus 45 n~~Dp~e~~~l~~eakk~Levi 66 (94)
T KOG3801|consen 45 NVCDPAEIKKLYKEAKKQLEVI 66 (94)
T ss_pred ccCCHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999888653
No 11
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.87 E-value=1.6e+02 Score=16.49 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=16.4
Q ss_pred hHHHHHHHhhHHHHHHHHHHhhccc
Q 044560 7 QVIDMLLFKGTEELNNILEHAKQRH 31 (68)
Q Consensus 7 rVID~Lv~KG~~EL~e~~~~wKQ~~ 31 (68)
+.+|+|.-||..-.......-+..+
T Consensus 48 ~Lld~l~~kg~~af~~F~~~L~~~~ 72 (80)
T cd01671 48 KLLDILPRKGPKAFQSFLQALQETD 72 (80)
T ss_pred HHHHHHHhcChHHHHHHHHHHHhcC
Confidence 4677777777777766666555443
No 12
>PF09547 Spore_IV_A: Stage IV sporulation protein A (spore_IV_A); InterPro: IPR014201 This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=20.66 E-value=59 Score=26.40 Aligned_cols=16 Identities=38% Similarity=0.733 Sum_probs=13.9
Q ss_pred CCCCCCcchHHHHHhh
Q 044560 49 DPKDQGLSSFLKNFYK 64 (68)
Q Consensus 49 g~~~~~~sdFL~kFy~ 64 (68)
|+...++|+|.++|..
T Consensus 24 GPVRTGKSTFIKRFMe 39 (492)
T PF09547_consen 24 GPVRTGKSTFIKRFME 39 (492)
T ss_pred cCcccCchhHHHHHHH
Confidence 4788899999999975
Done!