Query 028341
Match_columns 210
No_of_seqs 144 out of 285
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 10:00:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028341.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028341hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4259 Putative nucleic acid- 99.8 3.7E-19 8E-24 156.2 9.9 125 54-183 108-259 (260)
2 KOG4259 Putative nucleic acid- 99.5 4.1E-14 8.8E-19 124.6 7.8 87 73-162 148-259 (260)
3 KOG1861 Leucine permease trans 14.7 1.1E+02 0.0024 30.8 1.9 23 164-186 230-252 (540)
4 PF02042 RWP-RK: RWP-RK domain 11.3 1.4E+02 0.0029 21.1 1.1 12 127-138 31-42 (52)
5 PF06884 DUF1264: Protein of u 11.3 2E+02 0.0044 24.9 2.4 12 127-138 146-157 (171)
6 PF10642 Tom5: Mitochondrial i 10.9 2.5E+02 0.0055 19.6 2.4 19 89-107 2-21 (49)
7 PF05673 DUF815: Protein of un 6.9 4.5E+02 0.0097 24.0 2.9 9 131-139 206-214 (249)
8 PF04081 DNA_pol_delta_4: DNA 6.8 3.1E+02 0.0068 22.6 1.7 38 75-113 60-100 (124)
9 PF12824 MRP-L20: Mitochondria 6.2 3.3E+02 0.0072 23.0 1.6 14 146-159 135-148 (164)
10 PF13331 DUF4093: Domain of un 6.1 1.2E+03 0.026 17.6 4.5 11 128-138 68-78 (87)
No 1
>KOG4259 consensus Putative nucleic acid-binding protein Hcc-1/proliferation associated cytokine-inducible protein, contains SAP domain [Cell cycle control, cell division, chromosome partitioning]
Probab=99.79 E-value=3.7e-19 Score=156.19 Aligned_cols=125 Identities=34% Similarity=0.421 Sum_probs=80.5
Q ss_pred CCCCCcceeccCCCCCCCCCCCCChHHHHHHHHh---hhCCCCCCCH---HHHHHHHHhhhCCCCCCCC-------C---
Q 028341 54 GNDSKTAVTITAVSPVSGDADLVTDTQKKIRRAE---RFGMPVQMSE---EEKRNTRAERFGTGSKTQG-------S--- 117 (210)
Q Consensus 54 ~~~~kk~vkIt~~~~~~~~~~~lSd~EKk~~RAe---RFGip~~lse---~eKkk~RAeRFGl~~~~~~-------s--- 117 (210)
...++++|.|+++. -............|++ ||+.|+++-+ .+++.+||+||||+..... +
T Consensus 108 ~~~Eks~v~~tstg----k~~E~paet~~~srae~~~rf~~Pvvae~k~a~e~laaRAkRFgIp~d~t~i~sadnKas~a 183 (260)
T KOG4259|consen 108 ISKEKSQVPETSTG----KEAEEPAETTEESRAEVSNRFSSPVVAEEKTAQEKLAARAKRFGIPVDDTQIKSADNKASSA 183 (260)
T ss_pred hhhccccccccccc----cccccchhhhhhhhcccccccCCCcccccccchHHHHHHHHhcCCCCchHHHHhhccchhhh
Confidence 44577777777743 1123344555666666 7777665533 3666777777776643210 0
Q ss_pred -----CcccchHHHHHHHHHHhhCCCCCCC--cc---hHHHHHHHHhhhcCCCCCCCchHHHHH-HHHHhccCCCCC
Q 028341 118 -----EVSKTSEELKRKARAERFGLPVPSS--VS---EEEAKRKARLARFAPYPKTDSVEEDKR-KARALRFSKTSS 183 (210)
Q Consensus 118 -----~~~K~~eeeKlKkRAERFG~~~~~~--~~---~eeeKkkkRaERFG~~~~~d~~ee~Kk-kkRaeRFg~~~~ 183 (210)
........+++|.||+|||+++++. .. +-..|+++|++|||. .-.+...|+|+ ++|+||||+..+
T Consensus 184 ~~fG~~~~~p~a~dklk~rAqrfg~~v~s~Sr~s~~de~~~kl~arkkRfgg-titde~tEAKKaRaRaERFgtA~~ 259 (260)
T KOG4259|consen 184 ANFGNKIQQPLASDKLKNRAQRFGPQVRSNSRSSQRDENAPKLSARKKRFGG-TITDEPTEAKKARARAERFGTAAK 259 (260)
T ss_pred hhcCCcccchhhhHHHHHHHHhcCCCCCcccccCccccccchhhhhHHhcCC-CCCCchhhHHHHHHHHHHhcccCC
Confidence 0111245679999999999999865 12 223599999999994 23455677777 999999998765
No 2
>KOG4259 consensus Putative nucleic acid-binding protein Hcc-1/proliferation associated cytokine-inducible protein, contains SAP domain [Cell cycle control, cell division, chromosome partitioning]
Probab=99.50 E-value=4.1e-14 Score=124.65 Aligned_cols=87 Identities=37% Similarity=0.524 Sum_probs=61.6
Q ss_pred CCCCChHHHHHHHHhhhCCCCCC-----------------------CHHHHHHHHHhhhCCCCCCCCCCcccch-HHHHH
Q 028341 73 ADLVTDTQKKIRRAERFGMPVQM-----------------------SEEEKRNTRAERFGTGSKTQGSEVSKTS-EELKR 128 (210)
Q Consensus 73 ~~~lSd~EKk~~RAeRFGip~~l-----------------------se~eKkk~RAeRFGl~~~~~~s~~~K~~-eeeKl 128 (210)
.-+.+.++++.+||+|||||+.. -..++++.||+|||+..+.. +..++.. ..-+|
T Consensus 148 ae~k~a~e~laaRAkRFgIp~d~t~i~sadnKas~a~~fG~~~~~p~a~dklk~rAqrfg~~v~s~-Sr~s~~de~~~kl 226 (260)
T KOG4259|consen 148 AEEKTAQEKLAARAKRFGIPVDDTQIKSADNKASSAANFGNKIQQPLASDKLKNRAQRFGPQVRSN-SRSSQRDENAPKL 226 (260)
T ss_pred cccccchHHHHHHHHhcCCCCchHHHHhhccchhhhhhcCCcccchhhhHHHHHHHHhcCCCCCcc-cccCccccccchh
Confidence 44566778999999999999632 13789999999999986532 2222211 22489
Q ss_pred HHHHHhhCCCCCCCcchHHHHH-HHHhhhcCCCCC
Q 028341 129 KARAERFGLPVPSSVSEEEAKR-KARLARFAPYPK 162 (210)
Q Consensus 129 KkRAERFG~~~~~~~~~eeeKk-kkRaERFG~~~~ 162 (210)
++|++|||-..- ....+.|+ ++|+||||++++
T Consensus 227 ~arkkRfggtit--de~tEAKKaRaRaERFgtA~~ 259 (260)
T KOG4259|consen 227 SARKKRFGGTIT--DEPTEAKKARARAERFGTAAK 259 (260)
T ss_pred hhhHHhcCCCCC--CchhhHHHHHHHHHHhcccCC
Confidence 999999993322 23456666 999999998653
No 3
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=14.66 E-value=1.1e+02 Score=30.80 Aligned_cols=23 Identities=52% Similarity=0.582 Sum_probs=17.4
Q ss_pred CchHHHHHHHHHhccCCCCCCcc
Q 028341 164 DSVEEDKRKARALRFSKTSSSSV 186 (210)
Q Consensus 164 d~~ee~KkkkRaeRFg~~~~~~~ 186 (210)
..|++++++.|+.||....+.+.
T Consensus 230 ~~d~e~rr~~Ra~RF~~~~s~s~ 252 (540)
T KOG1861|consen 230 GSDEEARRKRRARRFSQGGSRST 252 (540)
T ss_pred CchHHHHHHHHHHHHhhcccccc
Confidence 56888889999999976666443
No 4
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=11.33 E-value=1.4e+02 Score=21.06 Aligned_cols=12 Identities=42% Similarity=0.827 Sum_probs=7.1
Q ss_pred HHHHHHHhhCCC
Q 028341 127 KRKARAERFGLP 138 (210)
Q Consensus 127 KlKkRAERFG~~ 138 (210)
.+|++.-++||.
T Consensus 31 ~LKr~CR~~GI~ 42 (52)
T PF02042_consen 31 TLKRRCRRLGIP 42 (52)
T ss_pred HHHHHHHHcCCC
Confidence 356666666664
No 5
>PF06884 DUF1264: Protein of unknown function (DUF1264); InterPro: IPR010686 This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.
Probab=11.29 E-value=2e+02 Score=24.94 Aligned_cols=12 Identities=50% Similarity=0.736 Sum_probs=6.8
Q ss_pred HHHHHHHhhCCC
Q 028341 127 KRKARAERFGLP 138 (210)
Q Consensus 127 KlKkRAERFG~~ 138 (210)
-.+.|=+|||+.
T Consensus 146 lv~~RD~r~gv~ 157 (171)
T PF06884_consen 146 LVKERDERFGVD 157 (171)
T ss_pred HHHHHHHhcCCC
Confidence 345566666654
No 6
>PF10642 Tom5: Mitochondrial import receptor subunit or translocase; InterPro: IPR019603 This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore []. Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Probab=10.87 E-value=2.5e+02 Score=19.56 Aligned_cols=19 Identities=47% Similarity=0.597 Sum_probs=12.2
Q ss_pred hCC-CCCCCHHHHHHHHHhh
Q 028341 89 FGM-PVQMSEEEKRNTRAER 107 (210)
Q Consensus 89 FGi-p~~lse~eKkk~RAeR 107 (210)
||. +..+|++|++...++-
T Consensus 2 Fgg~~~qpS~eE~k~~e~~A 21 (49)
T PF10642_consen 2 FGGPPPQPSEEEIKAAEAQA 21 (49)
T ss_pred CCCCCCCCCHHHHHHHHHHH
Confidence 666 3456777777766653
No 7
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=6.94 E-value=4.5e+02 Score=23.96 Aligned_cols=9 Identities=56% Similarity=0.958 Sum_probs=4.4
Q ss_pred HHHhhCCCC
Q 028341 131 RAERFGLPV 139 (210)
Q Consensus 131 RAERFG~~~ 139 (210)
=++++|+..
T Consensus 206 ~~~~~g~~~ 214 (249)
T PF05673_consen 206 YAERYGLEL 214 (249)
T ss_pred HHHHcCCCC
Confidence 445555544
No 8
>PF04081 DNA_pol_delta_4: DNA polymerase delta, subunit 4 ; InterPro: IPR007218 DNA polymerase is responsible for effective DNA replication. The function of the delta subunit 4 of DNA polymerase is not yet known.; GO: 0006260 DNA replication, 0005634 nucleus
Probab=6.84 E-value=3.1e+02 Score=22.63 Aligned_cols=38 Identities=21% Similarity=0.382 Sum_probs=21.0
Q ss_pred CCChHHHHHH---HHhhhCCCCCCCHHHHHHHHHhhhCCCCC
Q 028341 75 LVTDTQKKIR---RAERFGMPVQMSEEEKRNTRAERFGTGSK 113 (210)
Q Consensus 75 ~lSd~EKk~~---RAeRFGip~~lse~eKkk~RAeRFGl~~~ 113 (210)
.++..++.+. -.-.||-..-+| --++=.||++|||+.|
T Consensus 60 ~~~~~e~~Lr~FDl~~~yGPC~Git-Rl~RW~RA~~lgL~PP 100 (124)
T PF04081_consen 60 DLSQHEKILRQFDLSSQYGPCIGIT-RLERWERAKRLGLNPP 100 (124)
T ss_pred hhhHHHHHHHHhccccccCCccCch-HHHHHHHHHHcCCCCC
Confidence 3455554443 123344332232 3456789999999865
No 9
>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=6.23 E-value=3.3e+02 Score=23.04 Aligned_cols=14 Identities=36% Similarity=0.503 Sum_probs=7.3
Q ss_pred HHHHHHHHhhhcCC
Q 028341 146 EEAKRKARLARFAP 159 (210)
Q Consensus 146 eeeKkkkRaERFG~ 159 (210)
.+.++....+|.|.
T Consensus 135 ~~~~le~~k~rWg~ 148 (164)
T PF12824_consen 135 MEARLEAIKSRWGP 148 (164)
T ss_pred HHHHHHHHHHhccH
Confidence 34445555556664
No 10
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=6.06 E-value=1.2e+03 Score=17.57 Aligned_cols=11 Identities=27% Similarity=0.440 Sum_probs=5.5
Q ss_pred HHHHHHhhCCC
Q 028341 128 RKARAERFGLP 138 (210)
Q Consensus 128 lKkRAERFG~~ 138 (210)
+.+|...||+.
T Consensus 68 llkrLN~f~it 78 (87)
T PF13331_consen 68 LLKRLNMFGIT 78 (87)
T ss_pred HHHHHHHcCCC
Confidence 44555555554
Done!