Query psy1833
Match_columns 105
No_of_seqs 56 out of 58
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 17:32:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1833.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1833hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14978 MRP-63: Mitochondrial 100.0 1.9E-43 4.2E-48 243.2 8.7 87 16-104 1-89 (91)
2 PF04417 DUF501: Protein of un 60.5 3.4 7.4E-05 30.2 0.4 16 48-63 27-42 (139)
3 KOG0197|consensus 55.4 8.7 0.00019 33.5 2.1 42 16-58 219-264 (468)
4 COG1507 Uncharacterized conser 34.8 17 0.00036 27.9 0.6 21 48-68 50-74 (167)
5 PF07494 Reg_prop: Two compone 34.6 21 0.00045 18.3 0.8 9 16-24 15-23 (24)
6 cd00086 homeodomain Homeodomai 34.1 94 0.002 17.7 3.8 35 50-84 18-52 (59)
7 KOG0848|consensus 31.5 30 0.00064 28.9 1.6 39 20-69 198-236 (317)
8 KOG0485|consensus 29.5 81 0.0018 25.7 3.7 71 17-95 96-167 (268)
9 PF00140 Sigma70_r1_2: Sigma-7 25.6 41 0.0009 19.0 1.1 16 53-68 13-28 (37)
10 PF09008 Head_binding: Head bi 24.4 28 0.0006 25.3 0.2 13 16-28 28-40 (114)
11 PF06212 GRIM-19: GRIM-19 prot 23.2 1.5E+02 0.0032 21.6 3.8 30 39-68 56-85 (130)
12 KOG0194|consensus 21.3 81 0.0018 27.5 2.5 43 16-58 170-224 (474)
13 PF15114 UPF0640: Uncharacteri 20.2 40 0.00087 22.5 0.3 24 1-25 1-25 (69)
No 1
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=100.00 E-value=1.9e-43 Score=243.19 Aligned_cols=87 Identities=32% Similarity=0.440 Sum_probs=81.4
Q ss_pred CCceeeccccccccch--hhhhhhhHHHHHHHHHHHHHHhcCCCCHHHhhhhhHHHhHHHHHHHHHHHHHHcCCCCCchH
Q psy1833 16 KGNIFRGKYRIVEPVT--HLRKAIKIEEFKIEERNMFLLRHPYLTEEEELVHLKDLDRNENFRRERRALKLQKFIKHTKL 93 (105)
Q Consensus 16 ~G~~w~GK~R~~~~vS--~k~~~~~~~~le~E~enm~~Ls~PYLT~EqE~gh~~el~~r~~~~~~~~~~~~~Kf~~H~ti 93 (105)
+|+|||||||+|++|| ++++| +++|+||||||||||+||||+|||+||+++++...+.++.+++++++|||+|+||
T Consensus 1 pG~~w~GKhR~~r~vt~~~k~~~--~~~le~E~eN~~~Ls~PYLT~EQE~gh~~e~r~~k~~~~~~~~~~~~kf~~h~~i 78 (91)
T PF14978_consen 1 PGKQWIGKHRRPRKVTWQMKENM--IRRLEIEEENMYWLSRPYLTAEQEYGHAKERRKEKAFFEWIKEKKRSKFPPHKTI 78 (91)
T ss_pred CCCcccCcCCCcCCCCHHHHHHH--HHHHHHHHHHHHHHcCCcccHHHHcchHHHHhHHHHHHHHHHHHHHccCCCcccH
Confidence 3999999999999999 99999 9999999999999999999999999999996554478888888889999999999
Q ss_pred hhhhccCCCCC
Q psy1833 94 TDHLSDRGKPL 104 (105)
Q Consensus 94 ~d~L~hL~~~~ 104 (105)
+|||+||||+-
T Consensus 79 ~d~L~hL~v~~ 89 (91)
T PF14978_consen 79 ADRLNHLNVTK 89 (91)
T ss_pred HHHHhhhcccC
Confidence 99999999984
No 2
>PF04417 DUF501: Protein of unknown function (DUF501); InterPro: IPR007511 This is a family of uncharacterised bacterial proteins.
Probab=60.46 E-value=3.4 Score=30.21 Aligned_cols=16 Identities=31% Similarity=0.584 Sum_probs=12.5
Q ss_pred HHHHHhcCCCCHHHhh
Q psy1833 48 NMFLLRHPYLTEEEEL 63 (105)
Q Consensus 48 nm~~Ls~PYLT~EqE~ 63 (105)
+.|||+.|||+.+-+.
T Consensus 27 TlfwLtcP~L~~~isr 42 (139)
T PF04417_consen 27 TLFWLTCPYLVKAISR 42 (139)
T ss_pred ccHhhcCHHHHHHHHH
Confidence 4699999999976544
No 3
>KOG0197|consensus
Probab=55.41 E-value=8.7 Score=33.53 Aligned_cols=42 Identities=29% Similarity=0.296 Sum_probs=33.5
Q ss_pred CCceeeccccccccch---hhh-hhhhHHHHHHHHHHHHHHhcCCCC
Q psy1833 16 KGNIFRGKYRIVEPVT---HLR-KAIKIEEFKIEERNMFLLRHPYLT 58 (105)
Q Consensus 16 ~G~~w~GK~R~~~~vS---~k~-~~~~~~~le~E~enm~~Ls~PYLT 58 (105)
+|.||-|+|+.-.+|+ -+. .| --+.|.+|++.|+=|+||-|-
T Consensus 219 FG~V~~g~~~~~~~vavk~ik~~~m-~~~~f~~Ea~iMk~L~H~~lV 264 (468)
T KOG0197|consen 219 FGEVWLGKWNGSTKVAVKTIKEGSM-SPEAFLREAQIMKKLRHEKLV 264 (468)
T ss_pred cceEEEEEEcCCCcccceEEecccc-ChhHHHHHHHHHHhCcccCeE
Confidence 6999999999887777 233 33 137788999999999999874
No 4
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=34.81 E-value=17 Score=27.89 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=16.2
Q ss_pred HHHHHhcCCCCHHHhh----hhhHH
Q psy1833 48 NMFLLRHPYLTEEEEL----VHLKD 68 (105)
Q Consensus 48 nm~~Ls~PYLT~EqE~----gh~~e 68 (105)
.-|||.+|-||+|.+. |-.++
T Consensus 50 Tly~lt~P~L~kaaSrLEs~gymke 74 (167)
T COG1507 50 TLYYLTHPVLTKAASRLESTGYMKE 74 (167)
T ss_pred ceeeecChHHHHHHHHHHHhhHHHH
Confidence 3589999999999876 55555
No 5
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=34.57 E-value=21 Score=18.31 Aligned_cols=9 Identities=44% Similarity=1.088 Sum_probs=7.6
Q ss_pred CCceeeccc
Q psy1833 16 KGNIFRGKY 24 (105)
Q Consensus 16 ~G~~w~GK~ 24 (105)
+|++|+|-+
T Consensus 15 ~G~lWigT~ 23 (24)
T PF07494_consen 15 DGNLWIGTY 23 (24)
T ss_dssp TSCEEEEET
T ss_pred CcCEEEEeC
Confidence 699999965
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=34.14 E-value=94 Score=17.71 Aligned_cols=35 Identities=20% Similarity=0.136 Sum_probs=25.0
Q ss_pred HHHhcCCCCHHHhhhhhHHHhHHHHHHHHHHHHHH
Q psy1833 50 FLLRHPYLTEEEELVHLKDLDRNENFRRERRALKL 84 (105)
Q Consensus 50 ~~Ls~PYLT~EqE~gh~~el~~r~~~~~~~~~~~~ 84 (105)
.+..+||.+.++-..-+++++--...+..|...++
T Consensus 18 ~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR 52 (59)
T cd00086 18 EFEKNPYPSREEREELAKELGLTERQVKIWFQNRR 52 (59)
T ss_pred HHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34449999999998888888755565555555543
No 7
>KOG0848|consensus
Probab=31.55 E-value=30 Score=28.91 Aligned_cols=39 Identities=21% Similarity=0.295 Sum_probs=24.8
Q ss_pred eeccccccccchhhhhhhhHHHHHHHHHHHHHHhcCCCCHHHhhhhhHHH
Q psy1833 20 FRGKYRIVEPVTHLRKAIKIEEFKIEERNMFLLRHPYLTEEEELVHLKDL 69 (105)
Q Consensus 20 w~GK~R~~~~vS~k~~~~~~~~le~E~enm~~Ls~PYLT~EqE~gh~~el 69 (105)
..-|||-|| +=-+|||.|-|=+ ..+|+|.-.-+.-++-|
T Consensus 198 TkDKYRvVY--------TDhQRLELEKEfh---~SryITirRKSELA~~L 236 (317)
T KOG0848|consen 198 TKDKYRVVY--------TDHQRLELEKEFH---TSRYITIRRKSELAATL 236 (317)
T ss_pred cccceeEEe--------cchhhhhhhhhhc---cccceeeehhHHHHHhh
Confidence 455777776 1146777777644 46899977666555443
No 8
>KOG0485|consensus
Probab=29.49 E-value=81 Score=25.74 Aligned_cols=71 Identities=17% Similarity=0.053 Sum_probs=46.9
Q ss_pred Cceeeccccccccch-hhhhhhhHHHHHHHHHHHHHHhcCCCCHHHhhhhhHHHhHHHHHHHHHHHHHHcCCCCCchHhh
Q psy1833 17 GNIFRGKYRIVEPVT-HLRKAIKIEEFKIEERNMFLLRHPYLTEEEELVHLKDLDRNENFRRERRALKLQKFIKHTKLTD 95 (105)
Q Consensus 17 G~~w~GK~R~~~~vS-~k~~~~~~~~le~E~enm~~Ls~PYLT~EqE~gh~~el~~r~~~~~~~~~~~~~Kf~~H~ti~d 95 (105)
|.. .|..|+-++-| .-+.- +..||-+.|--. ||+..+-.+-++.|+--|-.+.-|.+.++.|++-|.+-++
T Consensus 96 g~~-~g~~RKKktRTvFSraQ--V~qLEs~Fe~kr-----YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 96 GNG-LGDDRKKKTRTVFSRAQ--VFQLESTFELKR-----YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred CCc-ccccccccchhhhhHHH--HHHHHHHHHHHh-----hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 445 78888777777 33444 567777776555 5555556677777777777777777777777776665443
No 9
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=25.65 E-value=41 Score=19.01 Aligned_cols=16 Identities=44% Similarity=0.576 Sum_probs=12.7
Q ss_pred hcCCCCHHHhhhhhHH
Q psy1833 53 RHPYLTEEEELVHLKD 68 (105)
Q Consensus 53 s~PYLT~EqE~gh~~e 68 (105)
+.|=||+|||...+..
T Consensus 13 ~~~LLt~eeE~~LA~~ 28 (37)
T PF00140_consen 13 RYPLLTAEEEIELARR 28 (37)
T ss_dssp HS-EETTHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHH
Confidence 5799999999987766
No 10
>PF09008 Head_binding: Head binding; InterPro: IPR009093 This entry represents the N-terminal domain of the Bacteriophage P22, Gp9, tailspike protein (TSP). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The tailspike protein of Salmonella bacteriophage P22 is a viral adhesion protein that mediates attachment of the viral protein to host cell-surface lipopolysaccharide. The tailspike protein displays both receptor binding and destroying properties, inactivating the receptor by endoglycosidase activity. The N-terminal, head-binding domain mediates the non-covalent attachment of the six homotrimeric tailspike molecules to the DNA injection apparatus []. The N-terminal domain of the P22 tailspike protein shows significant sequence similarity to the N-terminal domain of the Shigella phage Sf6 tailspike protein [].; GO: 0009405 pathogenesis; PDB: 2XC1_C 1LKT_D 2VFQ_A 2VFO_A 2VFN_A 2VFP_A 2VKY_B 2VFM_A 2VNL_A 2VBK_A ....
Probab=24.42 E-value=28 Score=25.27 Aligned_cols=13 Identities=31% Similarity=0.450 Sum_probs=9.8
Q ss_pred CCceeeccccccc
Q psy1833 16 KGNIFRGKYRIVE 28 (105)
Q Consensus 16 ~G~~w~GK~R~~~ 28 (105)
+|++||||---+.
T Consensus 28 ~GKiYIGk~~tDP 40 (114)
T PF09008_consen 28 NGKIYIGKAGTDP 40 (114)
T ss_dssp TEEEEEESTTS-T
T ss_pred CCcEEEecCCCCC
Confidence 6999999976444
No 11
>PF06212 GRIM-19: GRIM-19 protein; InterPro: IPR009346 This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-beta and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity [].
Probab=23.16 E-value=1.5e+02 Score=21.56 Aligned_cols=30 Identities=30% Similarity=0.284 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCHHHhhhhhHH
Q psy1833 39 IEEFKIEERNMFLLRHPYLTEEEELVHLKD 68 (105)
Q Consensus 39 ~~~le~E~enm~~Ls~PYLT~EqE~gh~~e 68 (105)
++++.+|...--.--.|+|.+|+...-++.
T Consensus 56 ~r~~~~E~~~ar~al~PlLqAE~DR~~lr~ 85 (130)
T PF06212_consen 56 RRELKREKRWARIALLPLLQAEEDRRYLRR 85 (130)
T ss_pred HHHHHHHHHHhHHHHhHHHHHHHHHHHHHH
Confidence 567777877777778999999999876666
No 12
>KOG0194|consensus
Probab=21.33 E-value=81 Score=27.54 Aligned_cols=43 Identities=35% Similarity=0.546 Sum_probs=32.5
Q ss_pred CCceeecccccc-----ccch---hh----hhhhhHHHHHHHHHHHHHHhcCCCC
Q psy1833 16 KGNIFRGKYRIV-----EPVT---HL----RKAIKIEEFKIEERNMFLLRHPYLT 58 (105)
Q Consensus 16 ~G~~w~GK~R~~-----~~vS---~k----~~~~~~~~le~E~enm~~Ls~PYLT 58 (105)
+|.+|.|+++.. .+|. .+ ...+-+++|..||+.|.=|.||++.
T Consensus 170 FGeV~~G~l~~~~~~~~~~VAvK~~k~~~~~~~~~~~e~m~EArvMr~l~H~NVV 224 (474)
T KOG0194|consen 170 FGEVFKGKLKLKNGFKVVPVAVKTTKGSSELTKEQIKEFMKEARVMRQLNHPNVV 224 (474)
T ss_pred ccEEEEEEEEecCCceeeeeEEEeecccccccHHHHHHHHHHHHHHHhCCCCCEE
Confidence 699999999964 2133 22 2233489999999999999999875
No 13
>PF15114 UPF0640: Uncharacterised protein family UPF0640
Probab=20.21 E-value=40 Score=22.48 Aligned_cols=24 Identities=33% Similarity=0.470 Sum_probs=17.4
Q ss_pred CcchHHHHhc-cCCCCCCceeecccc
Q psy1833 1 MHLTQILLRG-ARKYPKGNIFRGKYR 25 (105)
Q Consensus 1 M~LT~~L~~~-~~~ip~G~~w~GK~R 25 (105)
|++....+++ +..+| |++-.|-||
T Consensus 1 M~~~s~~i~~ll~~~P-GK~~fG~YR 25 (69)
T PF15114_consen 1 MFLRSRRIRRLLDLWP-GKRRFGIYR 25 (69)
T ss_pred CchhHHHHHHHHHHCC-Cccccchhh
Confidence 6664444443 56889 999999999
Done!