Query 015565
Match_columns 404
No_of_seqs 114 out of 262
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 07:30:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015565.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015565hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07498 Rho_N: Rho terminatio 98.8 3E-09 6.4E-14 76.7 2.0 34 367-400 2-35 (43)
2 PRK12678 transcription termina 98.3 4.3E-07 9.4E-12 96.2 4.8 46 357-402 13-58 (672)
3 PRK14537 50S ribosomal protein 98.1 1.7E-06 3.7E-11 82.3 2.7 38 364-401 188-225 (230)
4 PF02037 SAP: SAP domain; Int 97.1 0.00063 1.4E-08 47.3 3.6 33 367-401 1-33 (35)
5 PF12949 HeH: HeH/LEM domain; 96.9 0.0007 1.5E-08 48.3 2.6 35 367-401 1-35 (35)
6 smart00513 SAP Putative DNA-bi 96.1 0.011 2.3E-07 40.8 4.3 33 367-401 1-33 (35)
7 TIGR00578 ku70 ATP-dependent D 93.4 0.077 1.7E-06 55.8 4.0 37 363-401 545-581 (584)
8 PF10281 Ish1: Putative stress 90.8 0.57 1.2E-05 32.9 4.6 35 367-401 1-36 (38)
9 PF10208 Armet: Degradation ar 65.6 9.7 0.00021 35.3 4.4 37 365-401 102-138 (154)
10 PF13867 SAP30_Sin3_bdg: Sin3 57.2 16 0.00034 27.8 3.5 32 370-401 1-32 (53)
11 KOG2236 Uncharacterized conser 56.9 17 0.00038 38.8 4.9 29 230-258 380-409 (483)
12 PF12720 DUF3807: Protein of u 45.6 68 0.0015 30.0 6.4 23 131-153 53-77 (172)
13 PF11705 RNA_pol_3_Rpc31: DNA- 43.0 65 0.0014 30.3 5.9 23 123-145 45-67 (233)
14 TIGR03734 PRTRC_parB PRTRC sys 41.7 9.1 0.0002 41.3 0.2 36 366-401 495-538 (554)
15 PF07766 LETM1: LETM1-like pro 40.3 29 0.00062 33.5 3.2 34 366-400 216-249 (268)
16 PF11116 DUF2624: Protein of u 36.4 35 0.00075 29.0 2.7 21 366-386 11-31 (85)
17 PF09124 Endonuc-dimeris: T4 r 29.5 61 0.0013 25.6 2.9 35 366-400 12-46 (54)
18 TIGR00280 L37a ribosomal prote 29.4 34 0.00074 29.4 1.7 24 15-38 35-60 (91)
19 PHA02571 a-gt.4 hypothetical p 28.8 1.1E+02 0.0023 27.4 4.6 28 125-152 9-36 (109)
20 cd00789 KU_like Ku-core domain 27.7 86 0.0019 30.4 4.2 42 138-183 214-255 (256)
21 smart00054 EFh EF-hand, calciu 27.6 77 0.0017 17.6 2.5 28 374-401 1-28 (29)
22 smart00417 H4 Histone H4. 27.1 54 0.0012 27.0 2.4 35 366-400 10-44 (74)
23 PLN03106 TCP2 Protein TCP2; Pr 24.1 48 0.001 35.0 1.9 19 138-156 207-225 (447)
24 PRK03976 rpl37ae 50S ribosomal 23.2 54 0.0012 28.2 1.7 24 15-38 36-61 (90)
25 PLN02347 GMP synthetase 23.0 71 0.0015 34.1 3.0 23 363-385 382-404 (536)
26 PF07946 DUF1682: Protein of u 22.2 1.5E+02 0.0032 29.4 4.7 15 164-178 300-314 (321)
27 PF07754 DUF1610: Domain of un 21.8 64 0.0014 21.8 1.5 14 25-38 9-23 (24)
28 PF01402 RHH_1: Ribbon-helix-h 21.4 1.4E+02 0.003 20.2 3.2 23 371-399 10-32 (39)
29 smart00803 TAF TATA box bindin 21.4 95 0.002 24.5 2.7 30 370-399 3-32 (65)
30 PF04760 IF2_N: Translation in 20.7 52 0.0011 24.1 1.0 19 375-399 6-24 (54)
No 1
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=98.77 E-value=3e-09 Score=76.73 Aligned_cols=34 Identities=41% Similarity=0.692 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHh
Q 015565 367 LSALKLPELRALAKSRGVKGFSKMKKAVLLELLA 400 (404)
Q Consensus 367 Ls~MtvaELK~LAKe~GIKGySkMKKaELIeaLq 400 (404)
|..|++.||++||+++||+||++|+|.|||.+|.
T Consensus 2 L~~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~Il 35 (43)
T PF07498_consen 2 LKSMTLSELREIAKELGIEGYSKMRKQELIFAIL 35 (43)
T ss_dssp HHCS-HHHHHHHHHCTT-TTGCCS-HHHHHHHHH
T ss_pred cccCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHH
Confidence 6789999999999999999999999999999984
No 2
>PRK12678 transcription termination factor Rho; Provisional
Probab=98.33 E-value=4.3e-07 Score=96.19 Aligned_cols=46 Identities=41% Similarity=0.650 Sum_probs=40.4
Q ss_pred hhhhhhccCCCCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhcC
Q 015565 357 NKQEEIENGDLSALKLPELRALAKSRGVKGFSKMKKAVLLELLAGS 402 (404)
Q Consensus 357 ~~~~~~~~~dLs~MtvaELK~LAKe~GIKGySkMKKaELIeaLq~~ 402 (404)
........++|+.|+|+||++||+++||+|+++|+|.|||++|+..
T Consensus 13 ~~~~~a~~~~LsamkL~ELr~lA~~lGI~Gts~mrK~eLI~AI~~~ 58 (672)
T PRK12678 13 DTAPRARGGGLAGMKLPELRALAKQLGIKGTSGMRKGELIAAIKEA 58 (672)
T ss_pred ccCccccCCCcccCcHHHHHHHHHHcCCcccccccHHHHHHHHHHh
Confidence 3444556678999999999999999999999999999999999753
No 3
>PRK14537 50S ribosomal protein L20/unknown domain fusion protein; Provisional
Probab=98.08 E-value=1.7e-06 Score=82.30 Aligned_cols=38 Identities=37% Similarity=0.531 Sum_probs=35.4
Q ss_pred cCCCCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 364 NGDLSALKLPELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 364 ~~dLs~MtvaELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
..+|+.|.|.||++|||++.|.||++|+|+|||+||..
T Consensus 188 ~~~l~~m~~~elk~lak~~~i~~~~~~kk~e~i~al~~ 225 (230)
T PRK14537 188 HIDLSKMLLKELKKLAKEHKIPNFNKLKKTEIIKALKK 225 (230)
T ss_pred cccHHHhhHHHHHHHHHHhCCcchhhhhHHHHHHHHHH
Confidence 34699999999999999999999999999999999964
No 4
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=97.10 E-value=0.00063 Score=47.33 Aligned_cols=33 Identities=42% Similarity=0.499 Sum_probs=28.2
Q ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 367 LSALKLPELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 367 Ls~MtvaELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
|+.|+++|||++++++||+.-++ |.+||+.|.+
T Consensus 1 l~~l~v~eLk~~l~~~gL~~~G~--K~~Li~Rl~~ 33 (35)
T PF02037_consen 1 LSKLTVAELKEELKERGLSTSGK--KAELIERLKE 33 (35)
T ss_dssp TTTSHHHHHHHHHHHTTS-STSS--HHHHHHHHHH
T ss_pred CCcCcHHHHHHHHHHCCCCCCCC--HHHHHHHHHH
Confidence 67899999999999999998444 9999999864
No 5
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=96.93 E-value=0.0007 Score=48.31 Aligned_cols=35 Identities=26% Similarity=0.357 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 367 LSALKLPELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 367 Ls~MtvaELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
+.+|||++||++-.++||.=-++.+|+|||+++++
T Consensus 1 p~sltV~~Lk~iL~~~~I~~ps~AkKaeLv~L~~~ 35 (35)
T PF12949_consen 1 PKSLTVAQLKRILDEHGIEFPSNAKKAELVALFNQ 35 (35)
T ss_dssp STT--SHHHHHHHHHHT---SSS--SHHHHHH---
T ss_pred CCcCcHHHHHHHHHHcCCCCCCCCCHHHHHHHHcC
Confidence 46899999999999999999999999999999863
No 6
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=96.13 E-value=0.011 Score=40.79 Aligned_cols=33 Identities=39% Similarity=0.493 Sum_probs=28.6
Q ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 367 LSALKLPELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 367 Ls~MtvaELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
+..|++++|+++++++||.- +. +|.+||+.|..
T Consensus 1 ~~~l~~~~Lk~~l~~~gl~~-~G-~K~~Lv~Rl~~ 33 (35)
T smart00513 1 LAKLKVSELKDELKKRGLST-SG-TKAELVDRLLE 33 (35)
T ss_pred CCcCcHHHHHHHHHHcCCCC-CC-CHHHHHHHHHH
Confidence 46899999999999999996 33 79999998864
No 7
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=93.44 E-value=0.077 Score=55.84 Aligned_cols=37 Identities=27% Similarity=0.489 Sum_probs=33.0
Q ss_pred ccCCCCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 363 ENGDLSALKLPELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 363 ~~~dLs~MtvaELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
.++.|..|||++||++++.+||++ .-||+|||+.|..
T Consensus 545 ~~~~l~kltv~~Lk~~l~~~g~~~--~~kKadLi~~i~~ 581 (584)
T TIGR00578 545 KKGTLGKLTVSVLKDFCRAYGLRS--GSKKQELLDALTK 581 (584)
T ss_pred HcCChhhccHHHHHHHHHHcCCCc--cccHHHHHHHHHH
Confidence 568999999999999999999995 4479999999864
No 8
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=90.77 E-value=0.57 Score=32.93 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=31.9
Q ss_pred CCCCCHHHHHHHHHHcCCCCCCCC-CHHHHHHHHhc
Q 015565 367 LSALKLPELRALAKSRGVKGFSKM-KKAVLLELLAG 401 (404)
Q Consensus 367 Ls~MtvaELK~LAKe~GIKGySkM-KKaELIeaLq~ 401 (404)
|.+|+-.+|++..+++||..-... +|.+||++++.
T Consensus 1 fdtWs~~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~ 36 (38)
T PF10281_consen 1 FDTWSDSDLKSWLKSHGIPVPKSAKTRDELLKLAKK 36 (38)
T ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHH
Confidence 578999999999999999998888 99999999875
No 9
>PF10208 Armet: Degradation arginine-rich protein for mis-folding; InterPro: IPR019345 This entry represents Armet proteins (aka mesencephalic astrocyte-derived neurotrophic factor or arginine-rich protein). Armet is a small protein of approximately 170 residues which contains four di-sulphide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress []. Armet from Rattus norvegicus (Rat) selectively promotes the survival of dopaminergic neurons of the ventral mid-brain. It modulates GABAergic transmission to the dopaminergic neurons of the substantia nigra, and enhances spontaneous, as well as evoked, GABAergic inhibitory postsynaptic currents in dopaminergic neurons [].; PDB: 2KVE_A 2KVD_A 2W51_A 2W50_B 2RQY_A.
Probab=65.61 E-value=9.7 Score=35.31 Aligned_cols=37 Identities=16% Similarity=0.262 Sum_probs=33.1
Q ss_pred CCCCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 365 GDLSALKLPELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 365 ~dLs~MtvaELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
.+|..|+|.+||+|-.+.|+.--+=+-|.|+|+.|..
T Consensus 102 ~Dl~KlrVk~LK~iL~~~g~~C~GC~EK~dfv~ri~e 138 (154)
T PF10208_consen 102 VDLKKLRVKQLKKILDDWGEDCKGCLEKSDFVRRIEE 138 (154)
T ss_dssp TSTTTTCHHHHHHHHHHHTTT-SS-CSHHHHHHHCHC
T ss_pred hHHhhCcHHHHHHHHHHcCCCCCCccchHHHHHHHHH
Confidence 5899999999999999999999999999999999865
No 10
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=57.18 E-value=16 Score=27.77 Aligned_cols=32 Identities=22% Similarity=0.239 Sum_probs=22.2
Q ss_pred CCHHHHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 370 LKLPELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 370 MtvaELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
|.++.|+...+..++.+...+.|.||+.+++.
T Consensus 1 L~~~tLrrY~~~~~l~~~~~~sK~qLa~~V~k 32 (53)
T PF13867_consen 1 LQTPTLRRYKKHYKLPERPRSSKEQLANAVRK 32 (53)
T ss_dssp S-HHHHHHHHHHTT----SS--HHHHHHHHHH
T ss_pred CchHHHHHHHHHhCCCCCCCCCHHHHHHHHHH
Confidence 46788999999999998889999999999853
No 11
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=56.91 E-value=17 Score=38.81 Aligned_cols=29 Identities=28% Similarity=0.535 Sum_probs=24.0
Q ss_pred CCcccCCCCccccCCCCCccc-cccccCch
Q 015565 230 VSSFTRPASNFRRRSPVTQFK-YQPVYSSE 258 (404)
Q Consensus 230 ~ssf~RP~SnFrRrSPVp~vK-~Qpv~s~e 258 (404)
.-.|.||++||-++.|++--- |+|++++-
T Consensus 380 ~~gf~rp~s~~~q~pP~~~q~~~~p~~~~~ 409 (483)
T KOG2236|consen 380 NRGFKRPRSNHGQKPPQSAQNSFHPSSSDN 409 (483)
T ss_pred ccCCCCcccccCCCCCcccccccCccccCC
Confidence 346889999999999999776 88887765
No 12
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=45.60 E-value=68 Score=30.00 Aligned_cols=23 Identities=39% Similarity=0.605 Sum_probs=20.3
Q ss_pred HHHHHHHH--HHHHHHHHHHhhhhh
Q 015565 131 EIVELFRK--VQVQLRERAAAREDK 153 (404)
Q Consensus 131 EIVELFrk--VQAqLR~Raa~keeK 153 (404)
|=|++||- +||-||+|...++.+
T Consensus 53 EQI~IFRHSEI~aL~Rere~~~e~~ 77 (172)
T PF12720_consen 53 EQIEIFRHSEIQALRRERELREEAE 77 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 67899994 899999999988887
No 13
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=42.97 E-value=65 Score=30.25 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=20.5
Q ss_pred cCCCcchHHHHHHHHHHHHHHHH
Q 015565 123 STPGPREKEIVELFRKVQVQLRE 145 (404)
Q Consensus 123 s~PGpREKEIVELFrkVQAqLR~ 145 (404)
..++++|..||.|++.+++++|.
T Consensus 45 ~~~t~~E~~~v~~~~~lr~~~~~ 67 (233)
T PF11705_consen 45 LPLTEEERYLVALKRELRERMRD 67 (233)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHh
Confidence 56778999999999999999985
No 14
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=41.72 E-value=9.1 Score=41.26 Aligned_cols=36 Identities=36% Similarity=0.419 Sum_probs=28.7
Q ss_pred CCCCCCHHHHHHHHHHcCCCC-----CCC---CCHHHHHHHHhc
Q 015565 366 DLSALKLPELRALAKSRGVKG-----FSK---MKKAVLLELLAG 401 (404)
Q Consensus 366 dLs~MtvaELK~LAKe~GIKG-----ySk---MKKaELIeaLq~ 401 (404)
=|+-||.+||..+|++.||+- |.| =||.|+|++|-.
T Consensus 495 ~l~~lTk~e~~~~~~e~G~~~~~g~~f~k~~~gkk~e~ik~ll~ 538 (554)
T TIGR03734 495 FLELLTKSEIDALADEIGLKAAMGKEFKKLRAGKKGDFIKALLA 538 (554)
T ss_pred HHHHhhHHHHHHHHHHhCHHHHhhhHHHHHHcCCcHHHHHHHhc
Confidence 477899999999999999953 333 278899999854
No 15
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=40.29 E-value=29 Score=33.52 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=24.6
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHh
Q 015565 366 DLSALKLPELRALAKSRGVKGFSKMKKAVLLELLA 400 (404)
Q Consensus 366 dLs~MtvaELK~LAKe~GIKGySkMKKaELIeaLq 400 (404)
.+..|+.+||+..|.++||.. ..+.+.+|...|.
T Consensus 216 Gv~~Ls~~EL~~Ac~~RGl~~-~~~s~~~lr~~L~ 249 (268)
T PF07766_consen 216 GVDSLSEEELQDACYERGLRS-TGLSEEELREWLK 249 (268)
T ss_dssp -GGGS-HHHHHHHHHHTT----TT--HHHHHHHHH
T ss_pred ccccCCHHHHHHHHHHhCCCc-CCCCHHHHHHHHH
Confidence 678899999999999999987 5789999998885
No 16
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=36.35 E-value=35 Score=29.01 Aligned_cols=21 Identities=19% Similarity=0.208 Sum_probs=18.9
Q ss_pred CCCCCCHHHHHHHHHHcCCCC
Q 015565 366 DLSALKLPELRALAKSRGVKG 386 (404)
Q Consensus 366 dLs~MtvaELK~LAKe~GIKG 386 (404)
-|..||..||..+||+.||+=
T Consensus 11 Kln~iT~~eLlkyskqy~i~i 31 (85)
T PF11116_consen 11 KLNNITAKELLKYSKQYNISI 31 (85)
T ss_pred HHhcCCHHHHHHHHHHhCCCC
Confidence 477899999999999999984
No 17
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=29.55 E-value=61 Score=25.64 Aligned_cols=35 Identities=31% Similarity=0.274 Sum_probs=25.7
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHh
Q 015565 366 DLSALKLPELRALAKSRGVKGFSKMKKAVLLELLA 400 (404)
Q Consensus 366 dLs~MtvaELK~LAKe~GIKGySkMKKaELIeaLq 400 (404)
.++-|+++|..+.+.++||.=--++.|++|+..-+
T Consensus 12 ~FSRl~k~eMiaem~~~G~~y~~~~tK~~Lvk~fk 46 (54)
T PF09124_consen 12 WFSRLTKPEMIAEMDSYGFEYNEKDTKAQLVKIFK 46 (54)
T ss_dssp HHHTS-HHHHHHHHHHTT----TTS-HHHHHHHHH
T ss_pred HHHhcCHHHHHHHHHHhCCcCCccccHHHHHHHHH
Confidence 46789999999999999999888999999998653
No 18
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=29.42 E-value=34 Score=29.38 Aligned_cols=24 Identities=21% Similarity=0.415 Sum_probs=21.6
Q ss_pred CCccccC--CCccCceeeeeecCCCC
Q 015565 15 EGRCLPC--MGVSGRAVAVSSCSSRG 38 (404)
Q Consensus 15 ~grcl~c--SgVs~r~~av~~css~~ 38 (404)
.-.|.+| ..|-|.++.|.-|..|+
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~ 60 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCG 60 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCC
Confidence 4569999 89999999999999998
No 19
>PHA02571 a-gt.4 hypothetical protein; Provisional
Probab=28.78 E-value=1.1e+02 Score=27.43 Aligned_cols=28 Identities=18% Similarity=0.285 Sum_probs=21.2
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHhhhh
Q 015565 125 PGPREKEIVELFRKVQVQLRERAAARED 152 (404)
Q Consensus 125 PGpREKEIVELFrkVQAqLR~Raa~kee 152 (404)
+---+-+|.|+-.++|+++++-|..+-.
T Consensus 9 ~~~~d~~~ee~~~~~q~~~e~eA~kkA~ 36 (109)
T PHA02571 9 EELTDEEVEELLSELQARNEAEAEKKAA 36 (109)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344567999999999999987765544
No 20
>cd00789 KU_like Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs are predicted to form homodimers. It is proposed that the Ku homologs are functionally associated with ATP-dependent DNA ligase and the eukaryotic-type primase, probably as components of a double-strand break repair system.
Probab=27.65 E-value=86 Score=30.42 Aligned_cols=42 Identities=19% Similarity=0.271 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHhhhhhccccccccccccccHHHHHHHHHhhhhhhc
Q 015565 138 KVQVQLRERAAAREDKKTESMQGQRKESETVDSLLKLLRKHSVEQG 183 (404)
Q Consensus 138 kVQAqLR~Raa~keeKK~Eask~Qgke~~tVDSLLkLLRKHSveQ~ 183 (404)
++++=+++++++++-+.+++... +.+.|..|+.+||+ |++|.
T Consensus 214 ~l~~li~~K~~~~~~~~~~~~~~---~~~~v~dlm~aL~~-Sl~~~ 255 (256)
T cd00789 214 ALMELIEAKIEGKAIEAAEPAPA---ASGNVVDLMEALKK-SLEAA 255 (256)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCC---CCCCHHHHHHHHHH-HHhhc
Confidence 33444455565555443332221 15799999999986 66654
No 21
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=27.60 E-value=77 Score=17.64 Aligned_cols=28 Identities=21% Similarity=0.208 Sum_probs=20.6
Q ss_pred HHHHHHHHcCCCCCCCCCHHHHHHHHhc
Q 015565 374 ELRALAKSRGVKGFSKMKKAVLLELLAG 401 (404)
Q Consensus 374 ELK~LAKe~GIKGySkMKKaELIeaLq~ 401 (404)
||+.+-+.....+-..+...||+.+|+.
T Consensus 1 ~~~~~f~~~d~~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 1 ELKEAFRLFDKDGDGKIDFEEFKDLLKA 28 (29)
T ss_pred CHHHHHHHHCCCCCCcEeHHHHHHHHHh
Confidence 3566667777777778888888888764
No 22
>smart00417 H4 Histone H4.
Probab=27.14 E-value=54 Score=26.96 Aligned_cols=35 Identities=26% Similarity=0.405 Sum_probs=31.5
Q ss_pred CCCCCCHHHHHHHHHHcCCCCCCCCCHHHHHHHHh
Q 015565 366 DLSALKLPELRALAKSRGVKGFSKMKKAVLLELLA 400 (404)
Q Consensus 366 dLs~MtvaELK~LAKe~GIKGySkMKKaELIeaLq 400 (404)
.+.+++++-++.||+.-|++-+|..=..||.++|.
T Consensus 10 ~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle 44 (74)
T smart00417 10 NIQGITKPAIRRLARRGGVKRISGLIYDETRNVLK 44 (74)
T ss_pred hhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHH
Confidence 46789999999999999999999999999888874
No 23
>PLN03106 TCP2 Protein TCP2; Provisional
Probab=24.13 E-value=48 Score=35.03 Aligned_cols=19 Identities=21% Similarity=0.368 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHhhhhhccc
Q 015565 138 KVQVQLRERAAAREDKKTE 156 (404)
Q Consensus 138 kVQAqLR~Raa~keeKK~E 156 (404)
||+|+-|||..+-+||++|
T Consensus 207 R~karerarertaKEkEkE 225 (447)
T PLN03106 207 RDKARERARERTAKEKEKE 225 (447)
T ss_pred hhHHHHHHHHhhhhhhhhh
Confidence 7888887777666665554
No 24
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=23.15 E-value=54 Score=28.15 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=21.3
Q ss_pred CCccccC--CCccCceeeeeecCCCC
Q 015565 15 EGRCLPC--MGVSGRAVAVSSCSSRG 38 (404)
Q Consensus 15 ~grcl~c--SgVs~r~~av~~css~~ 38 (404)
.-.|.+| -.|-|.++.|..|.+|+
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~ 61 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCG 61 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCC
Confidence 4579999 88999999999999997
No 25
>PLN02347 GMP synthetase
Probab=22.99 E-value=71 Score=34.15 Aligned_cols=23 Identities=30% Similarity=0.229 Sum_probs=20.5
Q ss_pred ccCCCCCCCHHHHHHHHHHcCCC
Q 015565 363 ENGDLSALKLPELRALAKSRGVK 385 (404)
Q Consensus 363 ~~~dLs~MtvaELK~LAKe~GIK 385 (404)
....|..|+.+|+|+||+++||.
T Consensus 382 ii~PL~~l~K~eVR~la~~lgl~ 404 (536)
T PLN02347 382 LIEPLKLLFKDEVRKLGRLLGVP 404 (536)
T ss_pred cccchhhCcHHHHHHHHHHcCCC
Confidence 44578999999999999999997
No 26
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=22.15 E-value=1.5e+02 Score=29.38 Aligned_cols=15 Identities=13% Similarity=0.018 Sum_probs=9.4
Q ss_pred ccccHHHHHHHHHhh
Q 015565 164 ESETVDSLLKLLRKH 178 (404)
Q Consensus 164 e~~tVDSLLkLLRKH 178 (404)
..-|.+..-|++.|-
T Consensus 300 ~~lspeeQrK~eeKe 314 (321)
T PF07946_consen 300 SKLSPEEQRKYEEKE 314 (321)
T ss_pred hcCCHHHHHHHHHHH
Confidence 455667777776553
No 27
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=21.76 E-value=64 Score=21.84 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=9.2
Q ss_pred cCce-eeeeecCCCC
Q 015565 25 SGRA-VAVSSCSSRG 38 (404)
Q Consensus 25 s~r~-~av~~css~~ 38 (404)
..|- ++.|+|..||
T Consensus 9 ~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 9 APREQAVPFPCPNCG 23 (24)
T ss_pred cCcccCceEeCCCCC
Confidence 3444 6677787776
No 28
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=21.39 E-value=1.4e+02 Score=20.17 Aligned_cols=23 Identities=26% Similarity=0.276 Sum_probs=17.8
Q ss_pred CHHHHHHHHHHcCCCCCCCCCHHHHHHHH
Q 015565 371 KLPELRALAKSRGVKGFSKMKKAVLLELL 399 (404)
Q Consensus 371 tvaELK~LAKe~GIKGySkMKKaELIeaL 399 (404)
....|.++|++.|+ .++++|..+
T Consensus 10 ~~~~l~~~a~~~g~------s~s~~ir~a 32 (39)
T PF01402_consen 10 LYERLDELAKELGR------SRSELIREA 32 (39)
T ss_dssp HHHHHHHHHHHHTS------SHHHHHHHH
T ss_pred HHHHHHHHHHHHCc------CHHHHHHHH
Confidence 35789999999884 578888765
No 29
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=21.35 E-value=95 Score=24.49 Aligned_cols=30 Identities=23% Similarity=0.310 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHcCCCCCCCCCHHHHHHHH
Q 015565 370 LKLPELRALAKSRGVKGFSKMKKAVLLELL 399 (404)
Q Consensus 370 MtvaELK~LAKe~GIKGySkMKKaELIeaL 399 (404)
++.+-++.||+..||+..|.-=..+|.+.+
T Consensus 3 ~p~~~i~ria~~~Gi~ris~~a~~~l~~~~ 32 (65)
T smart00803 3 LPKETIKDVAESLGIGNLSDEAAKLLAEDV 32 (65)
T ss_pred CCHHHHHHHHHHCCCccccHHHHHHHHHHH
Confidence 678899999999999988876666666554
No 30
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=20.66 E-value=52 Score=24.14 Aligned_cols=19 Identities=32% Similarity=0.447 Sum_probs=12.0
Q ss_pred HHHHHHHcCCCCCCCCCHHHHHHHH
Q 015565 375 LRALAKSRGVKGFSKMKKAVLLELL 399 (404)
Q Consensus 375 LK~LAKe~GIKGySkMKKaELIeaL 399 (404)
+++||+++||+. .+||+.|
T Consensus 6 V~elAk~l~v~~------~~ii~~l 24 (54)
T PF04760_consen 6 VSELAKELGVPS------KEIIKKL 24 (54)
T ss_dssp TTHHHHHHSSSH------HHHHHHH
T ss_pred HHHHHHHHCcCH------HHHHHHH
Confidence 345677777665 5666666
Done!