Query psy4920
Match_columns 111
No_of_seqs 55 out of 57
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 21:14:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4920.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4920hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2390|consensus 98.8 7.3E-09 1.6E-13 92.7 4.9 64 40-109 192-256 (669)
2 cd00928 Cyt_c_Oxidase_VIIa Cyt 64.4 11 0.00024 24.7 3.3 32 48-84 21-52 (55)
3 PF06812 ImpA-rel_N: ImpA-rela 40.3 61 0.0013 20.3 3.8 41 60-100 21-61 (62)
4 PF05476 PET122: PET122; Inte 27.3 48 0.001 27.9 2.1 43 45-89 29-73 (267)
5 PF00178 Ets: Ets-domain; Int 25.7 1E+02 0.0022 21.1 3.2 18 83-100 55-72 (85)
6 PRK04358 hypothetical protein; 24.2 71 0.0015 26.1 2.5 24 76-99 91-114 (217)
7 TIGR03875 RNA_lig_partner RNA 23.4 76 0.0017 25.8 2.5 24 76-99 87-110 (206)
8 PF04214 DUF411: Protein of un 21.3 46 0.00099 22.7 0.8 15 94-108 55-69 (70)
9 COG5215 KAP95 Karyopherin (imp 21.2 19 0.00042 34.1 -1.4 67 28-101 75-150 (858)
10 PHA02046 hypothetical protein 21.2 77 0.0017 23.2 2.0 19 83-101 19-37 (99)
No 1
>KOG2390|consensus
Probab=98.77 E-value=7.3e-09 Score=92.71 Aligned_cols=64 Identities=17% Similarity=0.167 Sum_probs=57.7
Q ss_pred ccchhhcccCcCCCCCchHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhcCccccCC-CCCCccc
Q psy4920 40 DVTQEGLSGLKSCPPDGLVWRLAICSSHALYSMGGAKSFAHVWFEFVQELRYRWENSLRIPGV-KKKSLEA 109 (111)
Q Consensus 40 ~~~~e~~~~iKSAP~dSL~~RLAl~~~~c~~~~GGlravAhLW~EFV~ELRyrWEn~~~IPgl-~~~~p~~ 109 (111)
+.+++.+.+.++||++| .|++..+.+++|++.+|++|.+||.|+||+|+++..||+. ..++||.
T Consensus 192 ~~~~n~~n~~~~ap~~s------~~Ll~~~~~~~t~~~~a~~w~a~v~e~r~~w~~~s~ipw~~a~~~PDl 256 (669)
T KOG2390|consen 192 AHELNMLNAASMAPNQS------DDLLVNNVKLDTLFNYANPWSANVFEARYKWAKKSTIPWRLAIALPDL 256 (669)
T ss_pred chhhhhhhHhhcCCCch------hHHHHHhhhccchhhhhhHHHHHHHHHHHHHhhcCcCCcccccCCCcc
Confidence 34588889999999999 6677778899999999999999999999999999999987 8899986
No 2
>cd00928 Cyt_c_Oxidase_VIIa Cytochrome c oxidase subunit VIIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIIa has two tissue-specific isoforms that are expressed in a developmental manner. VIIa-H is expressed in heart and skeletal muscle but not smooth muscle. VIIa-L is expressed in liver and non-muscle tissues.
Probab=64.38 E-value=11 Score=24.71 Aligned_cols=32 Identities=19% Similarity=0.262 Sum_probs=26.6
Q ss_pred cCcCCCCCchHHHHHHHHHhhhccccchHHHHHHHHH
Q psy4920 48 GLKSCPPDGLVWRLAICSSHALYSMGGAKSFAHVWFE 84 (111)
Q Consensus 48 ~iKSAP~dSL~~RLAl~~~~c~~~~GGlravAhLW~E 84 (111)
++|.-|.|.+.+|+.+.+|.+ |+-+...+|..
T Consensus 21 ~LKGG~~D~~LYr~Tm~L~~v-----G~~~~~~~l~~ 52 (55)
T cd00928 21 HLKGGVVDRILYRLTMALTVV-----GTGYSLYLLYM 52 (55)
T ss_pred EecCCchhHHHHHHHHHHHHH-----hHHHHHHHHHH
Confidence 499999999999999988875 77777766654
No 3
>PF06812 ImpA-rel_N: ImpA-related N-terminal; InterPro: IPR010657 This entry represents a conserved region located towards the N-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans []. Note that many members are hypothetical proteins.
Probab=40.27 E-value=61 Score=20.34 Aligned_cols=41 Identities=20% Similarity=0.234 Sum_probs=30.4
Q ss_pred HHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhcCcccc
Q psy4920 60 RLAICSSHALYSMGGAKSFAHVWFEFVQELRYRWENSLRIP 100 (111)
Q Consensus 60 RLAl~~~~c~~~~GGlravAhLW~EFV~ELRyrWEn~~~IP 100 (111)
|++..++.+....+|+.|++.==.-+..=+..+||...|-|
T Consensus 21 rv~~~l~~a~~~~~g~~gl~~gl~ll~~ll~~~W~~l~P~~ 61 (62)
T PF06812_consen 21 RVAVWLTEALLRLEGLAGLAEGLELLADLLENYWDSLHPQL 61 (62)
T ss_pred HHHHHHHHHHHHccChhHHHHHHHHHHHHHHHCCcccCCCC
Confidence 56666666666788999888877777777788998877644
No 4
>PF05476 PET122: PET122; InterPro: IPR008732 The nuclear PET122 gene of Saccharomyces cerevisiae encodes a mitochondrial-localised protein that activates initiation of translation of the mitochondrial mRNA from the COX3 gene, which encodes subunit III of cytochrome c oxidase [].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation, 0005740 mitochondrial envelope
Probab=27.30 E-value=48 Score=27.92 Aligned_cols=43 Identities=19% Similarity=0.403 Sum_probs=30.9
Q ss_pred hcccCcCCCCCchHHHHHHHH-Hh-hhccccchHHHHHHHHHHHHHH
Q psy4920 45 GLSGLKSCPPDGLVWRLAICS-SH-ALYSMGGAKSFAHVWFEFVQEL 89 (111)
Q Consensus 45 ~~~~iKSAP~dSL~~RLAl~~-~~-c~~~~GGlravAhLW~EFV~EL 89 (111)
.++.+++-|.++.-+.|--.. +. | ..|-+..|+.+|+.||+-.
T Consensus 29 vL~~~R~~p~~emd~~fLq~yL~~S~--qwgHv~Si~yIW~k~Vmr~ 73 (267)
T PF05476_consen 29 VLAELRQIPVDEMDYSFLQLYLARSC--QWGHVPSIDYIWYKYVMRR 73 (267)
T ss_pred HHHHHHcCcHhHhhHHHHHHHHHHHH--HHhcchHHHHHHHHHHhhc
Confidence 345677788888877764322 22 4 5677899999999999754
No 5
>PF00178 Ets: Ets-domain; InterPro: IPR000418 Transcription factors are protein molecules that bind to specific DNA sequences in the genome, resulting in the induction or inhibition of gene transcription []. The ets oncogene is such a factor, possessing a region of 85-90 amino acids known as the ETS (erythroblast transformation specific) domain [, , ]. This domain is rich in positively-charged and aromatic residues, and binds to purine-rich segments of DNA. The ETS domain has been identified in other transcription factors such as PU.1, human erg, human elf-1, human elk-1, GA binding protein, and a number of others [, , ]. It is generally localized at the C terminus of the protein, with the exception of ELF-1, ELK-1, ELK-3, ELK-4 and ERF where it is found at the N terminus. NMR-analysis of the structure of the Ets domains revealed that it contains three alpha-helixes (1-3) and four-stranded beta-sheets (1-4) arranged in the order alpha1-beta1-beta2-alpha2-alpha3-beta3-beta4 forming a winged helix-turn-helix (wHTH) topology []. The third alpha-helix is responsive to contact to the major groove of the DNA. Different members of the Ets family proteins display distinct DNA binding specificities. The Ets domains and the flanking amino acid sequences of the proteins influence the binding affinity, and the alteration of a single amino acid in the Ets domain can change its DNA binding specificities. Avian leukemia virus E26 is a replication defective retrovirus that induces a mixed erythroid/myeloid leukemia in chickens.This virus carries two distinct oncogenes: v-myb and v-ets. The ets portion of this oncogene is required for the induction of erythroblastosis. V-ets and c-ets-1, its cellular progenitor, have been shown [] to be nuclear DNA-binding proteins. Ets-1 differs slightly from v-ets at its carboxy-terminal region. In most species where it has been sequenced, c-ets-1 exists in various isoforms generated by alternative splicing and differential phosphorylation.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DUX_F 4AVP_B 1HBX_G 1BC7_C 1K6O_A 1BC8_C 1PUE_E 1FLI_A 2DAO_A 1WWX_A ....
Probab=25.70 E-value=1e+02 Score=21.15 Aligned_cols=18 Identities=17% Similarity=0.340 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHhcCcccc
Q psy4920 83 FEFVQELRYRWENSLRIP 100 (111)
Q Consensus 83 ~EFV~ELRyrWEn~~~IP 100 (111)
..+-+-||++.++++.-+
T Consensus 55 eklsR~LR~yy~k~il~k 72 (85)
T PF00178_consen 55 EKLSRALRYYYKKGILEK 72 (85)
T ss_dssp HHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhhCCeEEe
Confidence 568899999999998754
No 6
>PRK04358 hypothetical protein; Provisional
Probab=24.17 E-value=71 Score=26.08 Aligned_cols=24 Identities=29% Similarity=0.695 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCccc
Q psy4920 76 KSFAHVWFEFVQELRYRWENSLRI 99 (111)
Q Consensus 76 ravAhLW~EFV~ELRyrWEn~~~I 99 (111)
+==|.+-+|||.|||.|-+.+..|
T Consensus 91 ~IPA~i~ye~I~~mR~RInkGLRV 114 (217)
T PRK04358 91 KIPAEIFYEYIEDMRERINKGLRV 114 (217)
T ss_pred eccHHHHHHHHHHHHHHHhcchHH
Confidence 334678899999999999988765
No 7
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=23.38 E-value=76 Score=25.75 Aligned_cols=24 Identities=33% Similarity=0.718 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCccc
Q psy4920 76 KSFAHVWFEFVQELRYRWENSLRI 99 (111)
Q Consensus 76 ravAhLW~EFV~ELRyrWEn~~~I 99 (111)
+==|.+-+|||.|||.|-+.+..|
T Consensus 87 ~IPA~i~ye~I~e~R~RInkGLRV 110 (206)
T TIGR03875 87 KIPAEIFYEYIEEVRERIDKGLRV 110 (206)
T ss_pred eccHHHHHHHHHHHHHHHhcchhH
Confidence 334678999999999999888765
No 8
>PF04214 DUF411: Protein of unknown function, DUF; InterPro: IPR007332 The function of the members of this bacterial protein family is unknown. Some members may be involved in conferring cation resistance.
Probab=21.26 E-value=46 Score=22.73 Aligned_cols=15 Identities=27% Similarity=0.445 Sum_probs=12.5
Q ss_pred hcCccccCCCCCCcc
Q psy4920 94 ENSLRIPGVKKKSLE 108 (111)
Q Consensus 94 En~~~IPgl~~~~p~ 108 (111)
=.++.+|||+-+||-
T Consensus 55 ~~GlavPGMP~GSPG 69 (70)
T PF04214_consen 55 ARGLAVPGMPAGSPG 69 (70)
T ss_pred ceEEeCCCCCCCCCC
Confidence 457899999999983
No 9
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=21.16 E-value=19 Score=34.14 Aligned_cols=67 Identities=13% Similarity=0.185 Sum_probs=43.6
Q ss_pred ccccceeeeeccccchhhcccCcCC---CCCchHHHHHHHHHhhhccccchHHHHH------HHHHHHHHHHHHHhcCcc
Q psy4920 28 SESIGCQIIKQDDVTQEGLSGLKSC---PPDGLVWRLAICSSHALYSMGGAKSFAH------VWFEFVQELRYRWENSLR 98 (111)
Q Consensus 28 ~~~~g~~~~~~~~~~~e~~~~iKSA---P~dSL~~RLAl~~~~c~~~~GGlravAh------LW~EFV~ELRyrWEn~~~ 98 (111)
-+++||+--|.. -.-|.-.++|+- -..|-..|++..++. =+.+||. +|.+|..||+-..-...+
T Consensus 75 ~~~~~~~qrW~~-~~~E~k~qvK~~al~aL~s~epr~~~~Aaq------l~aaIA~~Elp~~~wp~lm~~mv~nvg~eqp 147 (858)
T COG5215 75 ELQKGCSQRWLG-MRHESKEQVKGMALRALKSPEPRFCTMAAQ------LLAAIARMELPNSLWPGLMEEMVRNVGDEQP 147 (858)
T ss_pred HHHHHHHHhhcc-CCHHHHHHHHHHHHHHhcCCccHHHHHHHH------HHHHHHHhhCccccchHHHHHHHHhccccCc
Confidence 467788776765 444444455541 233445689887765 3555653 899999999987766666
Q ss_pred ccC
Q psy4920 99 IPG 101 (111)
Q Consensus 99 IPg 101 (111)
.-|
T Consensus 148 ~~~ 150 (858)
T COG5215 148 VSG 150 (858)
T ss_pred hHh
Confidence 554
No 10
>PHA02046 hypothetical protein
Probab=21.16 E-value=77 Score=23.25 Aligned_cols=19 Identities=21% Similarity=0.494 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHhcCccccC
Q psy4920 83 FEFVQELRYRWENSLRIPG 101 (111)
Q Consensus 83 ~EFV~ELRyrWEn~~~IPg 101 (111)
..+.+|++|+=||-+++|.
T Consensus 19 ~~l~~e~~~~re~eiPlpa 37 (99)
T PHA02046 19 TAIEREFKWYRENDIPLPA 37 (99)
T ss_pred HHHHHHHHHHHhcCCCCch
Confidence 5688999999999999996
Done!