Query 021396
Match_columns 313
No_of_seqs 33 out of 35
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 02:37:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021396.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021396hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12298 Bot1p: Eukaryotic mit 98.9 4E-10 8.7E-15 99.6 1.1 132 104-243 14-151 (172)
2 PF12824 MRP-L20: Mitochondria 95.5 0.004 8.7E-08 55.2 0.1 45 106-152 85-129 (164)
3 PF06784 UPF0240: Uncharacteri 90.6 0.15 3.3E-06 45.8 1.9 30 117-148 128-157 (179)
4 PF06413 Neugrin: Neugrin; In 79.6 0.37 8E-06 44.8 -1.3 43 104-148 8-50 (225)
5 PF12178 INCENP_N: Chromosome 44.3 17 0.00038 26.1 1.8 12 147-158 27-38 (38)
6 PF04255 DUF433: Protein of un 28.8 46 0.00099 24.3 2.0 23 127-149 31-54 (56)
7 TIGR00600 rad2 DNA excision re 28.5 18 0.00039 40.7 -0.1 45 197-251 190-241 (1034)
8 PF08620 RPAP1_C: RPAP1-like, 27.2 97 0.0021 24.7 3.7 37 117-153 28-66 (73)
9 PF08576 DUF1764: Eukaryotic p 25.6 27 0.00058 28.5 0.4 21 252-272 61-82 (102)
10 PF09098 Dehyd-heme_bind: Quin 18.6 3.5 7.6E-05 37.6 -6.6 65 205-269 32-124 (167)
No 1
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=98.89 E-value=4e-10 Score=99.61 Aligned_cols=132 Identities=15% Similarity=0.053 Sum_probs=94.9
Q ss_pred CCCCCCCCccccccccCCCCCCcccchHHHHhHhhHhhhhHHHHHHHhHHHHHHHHhhCCCCCCCCcccHHHHHhh----
Q 021396 104 NNNEGKHHVNSSVGLGAEGSGDKLYSLESIKKDYRLKKQRIHAALWLKEIEKQEEAKLDTHGPHHHHHDIDRLLDT---- 179 (313)
Q Consensus 104 ~~~~~~~aKteMY~lh~e~~~p~~ytVe~LAkdYRirkQRVhAILwLKEiE~~ee~k~g~~~~~~~~ddie~Llds---- 179 (313)
..+.+...|++||.++.++ +.||.+||..|+|..|||.|||.||+||++-.+....... .........
T Consensus 14 ~~~lse~~r~~Iy~~~~~~----~~sv~~vS~~ygi~~~RV~AIvrLkeiE~~~~~~~k~l~~----~~~~~m~~Mlp~~ 85 (172)
T PF12298_consen 14 NPVLSEELREQIYEDVMQD----GKSVREVSQKYGIKIQRVEAIVRLKEIEKRWKNKGKPLAT----PYARAMERMLPVF 85 (172)
T ss_pred CCcCCHHHHHHHHHHHHhC----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHhcccChhhH----HHHHHHHHHhccC
Confidence 3556667799999999999 4599999999999999999999999999987443333222 111111111
Q ss_pred --hhhccccCCCCccccccCCCCCccccCCCCCcccccCCCchhhhhhhHHHHHHHHHHHHhhhhh
Q 021396 180 --CSEIFDSTNDDLDNAKIPSSSEFKNKPDGWETTAKEQDGNVWEMSQREEDILLQEFDRRIAYCK 243 (313)
Q Consensus 180 --~~e~F~s~n~E~Hv~~lP~~p~FKv~P~Gwd~tak~~d~~~wEiS~kEe~iLlqEF~rRl~yNk 243 (313)
...+..-..+|+|+..+.....|..+++..+-+..|....+-...+.+--..+++|....+...
T Consensus 86 ~~~~~~~~E~~~ei~v~~~t~~q~F~~vsES~~F~p~DAak~~~~~Pa~~~~~~~~~~~~~~~~~~ 151 (172)
T PF12298_consen 86 KPQSQRPHENINEIPVHSLTMQQRFLPVSESEPFTPVDAAKAFELEPADETLEKLEEIGEESEIHE 151 (172)
T ss_pred CCccccCCCchhccCcccccCCceeEecCCCcccchhhHHHhccCCCccchhcchhhhhchHhhcC
Confidence 1112333456889988988999999999999998888877655666666667777766644443
No 2
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=95.46 E-value=0.004 Score=55.17 Aligned_cols=45 Identities=9% Similarity=0.070 Sum_probs=39.6
Q ss_pred CCCCCCccccccccCCCCCCcccchHHHHhHhhHhhhhHHHHHHHhH
Q 021396 106 NEGKHHVNSSVGLGAEGSGDKLYSLESIKKDYRLKKQRIHAALWLKE 152 (313)
Q Consensus 106 ~~~~~aKteMY~lh~e~~~p~~ytVe~LAkdYRirkQRVhAILwLKE 152 (313)
...++...+|+.|.++| |.+||+..|||.|.|-.+.|+.+.....
T Consensus 85 ~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 85 HLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred cCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 34455578999999999 9999999999999999999999988764
No 3
>PF06784 UPF0240: Uncharacterised protein family (UPF0240); InterPro: IPR009622 This is a group of proteins of unknown function.
Probab=90.62 E-value=0.15 Score=45.75 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=26.8
Q ss_pred cccCCCCCCcccchHHHHhHhhHhhhhHHHHH
Q 021396 117 GLGAEGSGDKLYSLESIKKDYRLKKQRIHAAL 148 (313)
Q Consensus 117 ~lh~e~~~p~~ytVe~LAkdYRirkQRVhAIL 148 (313)
..|+.+ |++||+|.||.+|.|...=|.+||
T Consensus 128 ~~Hq~~--P~~WtaekIA~eY~L~~~dv~~iL 157 (179)
T PF06784_consen 128 NNHQLD--PETWTAEKIAQEYKLDEKDVKNIL 157 (179)
T ss_pred HHhccC--ccccCHHHHHHHhCCCHHHHHHHH
Confidence 347777 999999999999999999988887
No 4
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=79.64 E-value=0.37 Score=44.83 Aligned_cols=43 Identities=12% Similarity=0.245 Sum_probs=35.8
Q ss_pred CCCCCCCCccccccccCCCCCCcccchHHHHhHhhHhhhhHHHHH
Q 021396 104 NNNEGKHHVNSSVGLGAEGSGDKLYSLESIKKDYRLKKQRIHAAL 148 (313)
Q Consensus 104 ~~~~~~~aKteMY~lh~e~~~p~~ytVe~LAkdYRirkQRVhAIL 148 (313)
++.....|+.++-.||+++ |+.|||+.||+.|+|=-.=|--||
T Consensus 8 ~k~Ls~~~~~~ir~L~~~~--p~~~t~~~Lae~F~vspe~irrIL 50 (225)
T PF06413_consen 8 PKKLSREAMEQIRYLHKED--PEEWTVERLAESFKVSPEAIRRIL 50 (225)
T ss_pred CCCCCHHHHHHHHHHHHhC--ccccCHHHHHhhCCCCHHHHHHHH
Confidence 3455566788899999999 999999999999998776666666
No 5
>PF12178 INCENP_N: Chromosome passenger complex (CPC) protein INCENP N terminal; InterPro: IPR022006 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. INCENP is a regulatory protein in the chromosome passenger complex. It is involved in regulation of the catalytic protein Aurora B. It performs this function in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N-terminal domain is the domain involved in formation of this three helical bundle. ; PDB: 2QFA_C.
Probab=44.26 E-value=17 Score=26.08 Aligned_cols=12 Identities=42% Similarity=1.008 Sum_probs=10.2
Q ss_pred HHHHhHHHHHHH
Q 021396 147 ALWLKEIEKQEE 158 (313)
Q Consensus 147 ILwLKEiE~~ee 158 (313)
.+||.||+++++
T Consensus 27 ~vWLeEI~eeA~ 38 (38)
T PF12178_consen 27 MVWLEEIQEEAE 38 (38)
T ss_dssp HHHHHHHHHHHH
T ss_pred hHHHHHHHHhcC
Confidence 689999999764
No 6
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=28.84 E-value=46 Score=24.33 Aligned_cols=23 Identities=43% Similarity=0.381 Sum_probs=17.2
Q ss_pred ccchHHHHhHhh-HhhhhHHHHHH
Q 021396 127 LYSLESIKKDYR-LKKQRIHAALW 149 (313)
Q Consensus 127 ~ytVe~LAkdYR-irkQRVhAILw 149 (313)
+||++.++++|. |-.+-|.|+|.
T Consensus 31 G~s~eeI~~~yp~Lt~~~i~aAl~ 54 (56)
T PF04255_consen 31 GESPEEIAEDYPSLTLEDIRAALA 54 (56)
T ss_dssp T--HHHHHHHSTT--HHHHHHHHH
T ss_pred CCCHHHHHHHCCCCCHHHHHHHHH
Confidence 789999999998 99999999875
No 7
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.50 E-value=18 Score=40.70 Aligned_cols=45 Identities=18% Similarity=0.378 Sum_probs=29.2
Q ss_pred CCCCCccccCCCCCcccccCCCchhh-------hhhhHHHHHHHHHHHHhhhhhcccccchh
Q 021396 197 PSSSEFKNKPDGWETTAKEQDGNVWE-------MSQREEDILLQEFDRRIAYCKFQIASFIK 251 (313)
Q Consensus 197 P~~p~FKv~P~Gwd~tak~~d~~~wE-------iS~kEe~iLlqEF~rRl~yNk~kiag~Ik 251 (313)
|.+++|+.+|. ..-|| .|..==+-|-.=|-++|+|++|||-++.|
T Consensus 190 ~~S~~F~sLP~----------~~qyeILs~lRlrSRlRmeQLeemfpdSmDFSkFQIkrv~k 241 (1034)
T TIGR00600 190 IESEEFSSLPP----------EVKHEILTDMKLFTKRRRTLFEAMPENSMDFSQYQLKGLLK 241 (1034)
T ss_pred CCCHHHHhCCH----------HHHHHHHHHHHHHHHHHHHHHhhcCCCchhhhHHHHHHHHH
Confidence 45578888876 12343 22221255666688999999999987654
No 8
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 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 C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=27.23 E-value=97 Score=24.70 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=28.4
Q ss_pred cccCCCCCCcccchHHHHhHhh--HhhhhHHHHHHHhHH
Q 021396 117 GLGAEGSGDKLYSLESIKKDYR--LKKQRIHAALWLKEI 153 (313)
Q Consensus 117 ~lh~e~~~p~~ytVe~LAkdYR--irkQRVhAILwLKEi 153 (313)
--|.++..-.+||+..|+--=| |-.||+.|+=-|-.|
T Consensus 28 hhHg~~p~~aGYTi~El~~L~RSsv~~QR~~al~~L~~I 66 (73)
T PF08620_consen 28 HHHGEDPEAAGYTIQELFHLSRSSVPSQRCIALQTLGRI 66 (73)
T ss_pred cccCCCCCcCCcCHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence 3466665556899999988766 789999998777655
No 9
>PF08576 DUF1764: Eukaryotic protein of unknown function (DUF1764); InterPro: IPR013885 This entry consists of eukaryotic proteins of unknown function, including many hypothetical proteins.
Probab=25.58 E-value=27 Score=28.48 Aligned_cols=21 Identities=43% Similarity=0.605 Sum_probs=16.9
Q ss_pred hccccccCCCCCce-eEEEEcC
Q 021396 252 THIFSRRRPIDGWK-YMIEEIG 272 (313)
Q Consensus 252 ~h~~SRRRP~~GW~-~mVe~LG 272 (313)
.-...|||-++||. |..++||
T Consensus 61 ~~~~~rrrteDGl~IYt~eEL~ 82 (102)
T PF08576_consen 61 RESKPRRRTEDGLPIYTEEELG 82 (102)
T ss_pred cccccccccCCCceEecHHHhC
Confidence 33448899999997 7788998
No 10
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=18.57 E-value=3.5 Score=37.57 Aligned_cols=65 Identities=20% Similarity=0.407 Sum_probs=38.1
Q ss_pred cCCCCCcccccCCCc-hhhhhhhHHHHHHHHHHHHhhhhhcccccc-----------------------hhhccccc---
Q 021396 205 KPDGWETTAKEQDGN-VWEMSQREEDILLQEFDRRIAYCKFQIASF-----------------------IKTHIFSR--- 257 (313)
Q Consensus 205 ~P~Gwd~tak~~d~~-~wEiS~kEe~iLlqEF~rRl~yNk~kiag~-----------------------Ik~h~~SR--- 257 (313)
-|+||+.|.+-+--. -=.||.-|..-+|+-+....--.-.+++++ .+||.+.|
T Consensus 32 TPEGW~mTV~RM~~~hGl~Is~eer~avVkYLAd~~GLap~Et~~~ry~~er~~~~~e~~~~e~~~~~C~rCHs~aR~~l 111 (167)
T PF09098_consen 32 TPEGWDMTVKRMQRVHGLPISPEERRAVVKYLADTQGLAPSETAPVRYALERRPNTVEQFPNEEITQMCARCHSGARVAL 111 (167)
T ss_dssp -HHHHHHHHHHHHHHC-----HHHHHHHHHHHHHHT---CGGCTT-CCCCCT-TT-----SCHHHHHHHSSSS-THHHHT
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHccCCCchhhcchhhhhhcCcchhhcccchHHHHHHHHhhhhhHHHH
Confidence 388999887766422 128999999999988776543332222211 46998877
Q ss_pred -cCCCCCceeEEE
Q 021396 258 -RRPIDGWKYMIE 269 (313)
Q Consensus 258 -RRP~~GW~~mVe 269 (313)
||+.+-|..+|.
T Consensus 112 QrRt~~eW~~lv~ 124 (167)
T PF09098_consen 112 QRRTAEEWEKLVH 124 (167)
T ss_dssp EEE-HHHHHHHHH
T ss_pred hhCCHHHHHHHHH
Confidence 899999987764
Done!