Query psy1064
Match_columns 107
No_of_seqs 57 out of 59
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 23:38:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1064.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1064hhsearch_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 7.8E-46 1.7E-50 255.8 9.3 91 16-106 1-91 (91)
2 PF04417 DUF501: Protein of un 77.2 1 2.2E-05 33.1 0.7 25 48-72 27-55 (139)
3 PF07494 Reg_prop: Two compone 49.8 10 0.00022 19.6 1.0 9 16-24 15-23 (24)
4 PF09784 L31: Mitochondrial ri 46.6 20 0.00043 25.6 2.5 33 17-53 7-39 (103)
5 KOG0197|consensus 35.7 15 0.00033 32.2 0.6 43 16-58 219-264 (468)
6 COG1507 Uncharacterized conser 28.4 18 0.00038 27.8 -0.2 16 48-63 50-65 (167)
7 PF00140 Sigma70_r1_2: Sigma-7 26.4 43 0.00093 19.0 1.3 15 53-67 13-27 (37)
8 KOG0485|consensus 25.5 1.2E+02 0.0025 24.9 4.0 71 17-95 96-167 (268)
9 KOG0194|consensus 22.2 77 0.0017 27.8 2.5 43 16-58 170-224 (474)
10 PF06212 GRIM-19: GRIM-19 prot 22.0 1.6E+02 0.0034 21.5 3.8 29 39-67 56-84 (130)
11 cd00086 homeodomain Homeodomai 21.2 1.8E+02 0.0038 16.6 5.7 46 29-83 6-51 (59)
12 PRK13291 metal-dependent hydro 21.2 1.1E+02 0.0024 22.5 2.9 50 21-70 8-70 (173)
13 cd05043 PTK_Ryk Pseudokinase d 21.2 70 0.0015 23.4 1.8 44 16-59 19-72 (280)
14 KOG0493|consensus 20.9 87 0.0019 26.3 2.5 55 39-98 258-312 (342)
15 PF09008 Head_binding: Head bi 20.9 38 0.00082 24.6 0.4 17 16-32 28-44 (114)
No 1
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=100.00 E-value=7.8e-46 Score=255.82 Aligned_cols=91 Identities=35% Similarity=0.513 Sum_probs=84.6
Q ss_pred CCceeeeccccccccCHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCCCchHhh
Q psy1064 16 KGNIFRGKYRIVEPVTHLRKAIKIEEFKIEERNMFLLRHPYLTEEEELVHLKDLERNENFRRERRALKLQKFIKHTKLTD 95 (107)
Q Consensus 16 ~G~~w~GK~R~~~~vs~~~k~~~~~~l~~E~en~~~Ls~PYlT~EqE~g~~~~l~~r~~~~~~~~~~~~~Kf~~H~ti~d 95 (107)
+|+|||||||+|++||.++|++|+++|+||||||||||+||||+|||+||++++....+.+..+.+++.+|||+|+||+|
T Consensus 1 pG~~w~GKhR~~r~vt~~~k~~~~~~le~E~eN~~~Ls~PYLT~EQE~gh~~e~r~~k~~~~~~~~~~~~kf~~h~~i~d 80 (91)
T PF14978_consen 1 PGKQWIGKHRRPRKVTWQMKENMIRRLEIEEENMYWLSRPYLTAEQEYGHAKERRKEKAFFEWIKEKKRSKFPPHKTIAD 80 (91)
T ss_pred CCCcccCcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHcchHHHHhHHHHHHHHHHHHHHccCCCcccHHH
Confidence 39999999999999999999999999999999999999999999999999995544226778888888999999999999
Q ss_pred hhhccccccCC
Q psy1064 96 HLSDLRYQDKW 106 (107)
Q Consensus 96 ~L~hL~v~~~W 106 (107)
||+||||+++|
T Consensus 81 ~L~hL~v~~~W 91 (91)
T PF14978_consen 81 RLNHLNVTKKW 91 (91)
T ss_pred HHhhhcccCCC
Confidence 99999999999
No 2
>PF04417 DUF501: Protein of unknown function (DUF501); InterPro: IPR007511 This is a family of uncharacterised bacterial proteins.
Probab=77.24 E-value=1 Score=33.06 Aligned_cols=25 Identities=28% Similarity=0.490 Sum_probs=17.9
Q ss_pred HHHHHhcCCCCHHHHh----hhhHHHHHH
Q psy1064 48 NMFLLRHPYLTEEEEL----VHLKDLERN 72 (107)
Q Consensus 48 n~~~Ls~PYlT~EqE~----g~~~~l~~r 72 (107)
+.|||+.|||+.+-+. |..++++.+
T Consensus 27 TlfwLtcP~L~~~isrLE~~G~i~~l~~~ 55 (139)
T PF04417_consen 27 TLFWLTCPYLVKAISRLEAEGGIAELEER 55 (139)
T ss_pred ccHhhcCHHHHHHHHHHHhcCHHHHHHHH
Confidence 5799999999977554 666655544
No 3
>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=49.80 E-value=10 Score=19.62 Aligned_cols=9 Identities=44% Similarity=1.088 Sum_probs=7.9
Q ss_pred CCceeeecc
Q psy1064 16 KGNIFRGKY 24 (107)
Q Consensus 16 ~G~~w~GK~ 24 (107)
+|++|+|+.
T Consensus 15 ~G~lWigT~ 23 (24)
T PF07494_consen 15 DGNLWIGTY 23 (24)
T ss_dssp TSCEEEEET
T ss_pred CcCEEEEeC
Confidence 699999975
No 4
>PF09784 L31: Mitochondrial ribosomal protein L31; InterPro: IPR016340 This group represents a predicted mitochondrial ribosomal protein L31, fungal type [, ].
Probab=46.56 E-value=20 Score=25.64 Aligned_cols=33 Identities=12% Similarity=0.089 Sum_probs=28.5
Q ss_pred CceeeeccccccccCHHHHHHHHHHHHHHHHHHHHHh
Q psy1064 17 GNIFRGKYRIVEPVTHLRKAIKIEEFKIEERNMFLLR 53 (107)
Q Consensus 17 G~~w~GK~R~~~~vs~~~k~~~~~~l~~E~en~~~Ls 53 (107)
|..|.. |..+|...|.+.++||...-+|.--|.
T Consensus 7 GlLWK~----pwRlS~~qK~r~R~Rlr~VD~vi~~l~ 39 (103)
T PF09784_consen 7 GLLWKI----PWRLSSPQKARQRKRLRAVDSVIDTLY 39 (103)
T ss_pred ceeecC----CCCCChHHHHHHHHHHHHHHHHHHHHH
Confidence 777754 678999999999999999999987776
No 5
>KOG0197|consensus
Probab=35.72 E-value=15 Score=32.16 Aligned_cols=43 Identities=28% Similarity=0.252 Sum_probs=33.2
Q ss_pred CCceeeeccccccccCHHHHH--HHH-HHHHHHHHHHHHHhcCCCC
Q psy1064 16 KGNIFRGKYRIVEPVTHLRKA--IKI-EEFKIEERNMFLLRHPYLT 58 (107)
Q Consensus 16 ~G~~w~GK~R~~~~vs~~~k~--~~~-~~l~~E~en~~~Ls~PYlT 58 (107)
+|.||-|+++.-.+|...... +|. +.|.+|++.|+=|+||-|-
T Consensus 219 FG~V~~g~~~~~~~vavk~ik~~~m~~~~f~~Ea~iMk~L~H~~lV 264 (468)
T KOG0197|consen 219 FGEVWLGKWNGSTKVAVKTIKEGSMSPEAFLREAQIMKKLRHEKLV 264 (468)
T ss_pred cceEEEEEEcCCCcccceEEeccccChhHHHHHHHHHHhCcccCeE
Confidence 699999999988777733221 233 6788999999999999874
No 6
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=28.40 E-value=18 Score=27.83 Aligned_cols=16 Identities=31% Similarity=0.634 Sum_probs=13.1
Q ss_pred HHHHHhcCCCCHHHHh
Q psy1064 48 NMFLLRHPYLTEEEEL 63 (107)
Q Consensus 48 n~~~Ls~PYlT~EqE~ 63 (107)
.-|||.+|-||+|.+.
T Consensus 50 Tly~lt~P~L~kaaSr 65 (167)
T COG1507 50 TLYYLTHPVLTKAASR 65 (167)
T ss_pred ceeeecChHHHHHHHH
Confidence 3489999999988876
No 7
>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=26.42 E-value=43 Score=18.99 Aligned_cols=15 Identities=47% Similarity=0.620 Sum_probs=12.1
Q ss_pred hcCCCCHHHHhhhhH
Q psy1064 53 RHPYLTEEEELVHLK 67 (107)
Q Consensus 53 s~PYlT~EqE~g~~~ 67 (107)
+.|=||+|||...+.
T Consensus 13 ~~~LLt~eeE~~LA~ 27 (37)
T PF00140_consen 13 RYPLLTAEEEIELAR 27 (37)
T ss_dssp HS-EETTHHHHHHHH
T ss_pred CCCCCCHHHHHHHHH
Confidence 579999999998877
No 8
>KOG0485|consensus
Probab=25.51 E-value=1.2e+02 Score=24.92 Aligned_cols=71 Identities=15% Similarity=0.020 Sum_probs=46.7
Q ss_pred CceeeeccccccccC-HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCCCchHhh
Q psy1064 17 GNIFRGKYRIVEPVT-HLRKAIKIEEFKIEERNMFLLRHPYLTEEEELVHLKDLERNENFRRERRALKLQKFIKHTKLTD 95 (107)
Q Consensus 17 G~~w~GK~R~~~~vs-~~~k~~~~~~l~~E~en~~~Ls~PYlT~EqE~g~~~~l~~r~~~~~~~~~~~~~Kf~~H~ti~d 95 (107)
|.. .|-.|+-++=| +.+-+ +..||-+.|--.| |+..+-.+.++.|..-+--+.-|.+.++.|+|-|.+.++
T Consensus 96 g~~-~g~~RKKktRTvFSraQ--V~qLEs~Fe~krY-----LSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 96 GNG-LGDDRKKKTRTVFSRAQ--VFQLESTFELKRY-----LSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred CCc-ccccccccchhhhhHHH--HHHHHHHHHHHhh-----hhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 444 66677776666 44445 6677777776554 555555677777776666666677777888887665543
No 9
>KOG0194|consensus
Probab=22.18 E-value=77 Score=27.77 Aligned_cols=43 Identities=33% Similarity=0.492 Sum_probs=32.6
Q ss_pred CCceeeeccccccc-----cC-------HHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy1064 16 KGNIFRGKYRIVEP-----VT-------HLRKAIKIEEFKIEERNMFLLRHPYLT 58 (107)
Q Consensus 16 ~G~~w~GK~R~~~~-----vs-------~~~k~~~~~~l~~E~en~~~Ls~PYlT 58 (107)
+|.||.|+.+..-. |. .......+.+|..||+.|.=|.||++.
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 69999997776421 21 224455689999999999999999875
No 10
>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=21.99 E-value=1.6e+02 Score=21.53 Aligned_cols=29 Identities=31% Similarity=0.297 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCHHHHhhhhH
Q psy1064 39 IEEFKIEERNMFLLRHPYLTEEEELVHLK 67 (107)
Q Consensus 39 ~~~l~~E~en~~~Ls~PYlT~EqE~g~~~ 67 (107)
++++.+|...--.--.|+|.+|+...-.+
T Consensus 56 ~r~~~~E~~~ar~al~PlLqAE~DR~~lr 84 (130)
T PF06212_consen 56 RRELKREKRWARIALLPLLQAEEDRRYLR 84 (130)
T ss_pred HHHHHHHHHHhHHHHhHHHHHHHHHHHHH
Confidence 56778888888788899999999998777
No 11
>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=21.21 E-value=1.8e+02 Score=16.56 Aligned_cols=46 Identities=22% Similarity=0.167 Sum_probs=29.0
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHhhhhHHHHHHHHHHHHHHHHh
Q psy1064 29 PVTHLRKAIKIEEFKIEERNMFLLRHPYLTEEEELVHLKDLERNENFRRERRALK 83 (107)
Q Consensus 29 ~vs~~~k~~~~~~l~~E~en~~~Ls~PYlT~EqE~g~~~~l~~r~~~~~~~~~~~ 83 (107)
..|......|..-|+ .+||.+.++-...++.++--...+..|...+
T Consensus 6 ~~~~~~~~~Le~~f~---------~~~~P~~~~~~~la~~~~l~~~qV~~WF~nr 51 (59)
T cd00086 6 RFTPEQLEELEKEFE---------KNPYPSREEREELAKELGLTERQVKIWFQNR 51 (59)
T ss_pred cCCHHHHHHHHHHHH---------hCCCCCHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 345555554444333 3999999988888887765555555555444
No 12
>PRK13291 metal-dependent hydrolase; Provisional
Probab=21.19 E-value=1.1e+02 Score=22.49 Aligned_cols=50 Identities=22% Similarity=0.236 Sum_probs=34.7
Q ss_pred eeccccccccCHHHHHHHHHHHHHHHHH---------HHHHhcCCC----CHHHHhhhhHHHH
Q psy1064 21 RGKYRIVEPVTHLRKAIKIEEFKIEERN---------MFLLRHPYL----TEEEELVHLKDLE 70 (107)
Q Consensus 21 ~GK~R~~~~vs~~~k~~~~~~l~~E~en---------~~~Ls~PYl----T~EqE~g~~~~l~ 70 (107)
|||+-.|.+||....+..++.|+.-.+. .-.|..+|- |.-|=.||..+.+
T Consensus 8 ~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~~l~~lsee~l~~~~~~gkWSi~Evl~HL~D~e 70 (173)
T PRK13291 8 IGQFQYPEEITEEQIQEWIAEIEALPNELRAAVSGLSDEQLDTPYREGGWTVRQVVHHVADSH 70 (173)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHcCCCCCCCCcHHHHHHHHHHHH
Confidence 9999999999999999999888765432 223444443 3444458887543
No 13
>cd05043 PTK_Ryk Pseudokinase domain of Ryk (Receptor related to tyrosine kinase). Protein Tyrosine Kinase (PTK) family; Receptor related to tyrosine kinase (Ryk); pseudokinase domain. The PTKc (catalytic domain) family to which this subfamily belongs, is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ryk is a receptor tyr kinase (RTK) containing an extracellular region with two leucine-rich motifs, a transmembrane segment, and an intracellular inactive pseudokinase domain. The extracellular region of Ryk shows homology to the N-terminal domain of Wnt inhibitory factor-1 (WIF) and serves as the ligand (Wnt) binding domain of Ryk. Ryk is expressed in many different tissues both during development and in adults, suggesting a widespread function. It
Probab=21.17 E-value=70 Score=23.39 Aligned_cols=44 Identities=23% Similarity=0.246 Sum_probs=29.0
Q ss_pred CCceeeecccc----------ccccCHHHHHHHHHHHHHHHHHHHHHhcCCCCH
Q psy1064 16 KGNIFRGKYRI----------VEPVTHLRKAIKIEEFKIEERNMFLLRHPYLTE 59 (107)
Q Consensus 16 ~G~~w~GK~R~----------~~~vs~~~k~~~~~~l~~E~en~~~Ls~PYlT~ 59 (107)
.|.+|.|.+.. ++.+.......-.+.+..|.+.+.-|+||.+..
T Consensus 19 ~g~V~~~~~~~~~~~~~~~v~~k~~~~~~~~~~~~~~~~e~~~l~~l~h~ni~~ 72 (280)
T cd05043 19 FGRIFYGILIDEKPGKEEEVFVKTVKDHASEIQVTLLLQESCLLYGLSHQNILP 72 (280)
T ss_pred CceEEEEEEecCCCCceeEEEEEEccCCCCHHHHHHHHHHHHHHHhCCCCCCCe
Confidence 48899997655 122222223344677888888888889998664
No 14
>KOG0493|consensus
Probab=20.94 E-value=87 Score=26.34 Aligned_cols=55 Identities=25% Similarity=0.219 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCCCchHhhhhh
Q psy1064 39 IEEFKIEERNMFLLRHPYLTEEEELVHLKDLERNENFRRERRALKLQKFIKHTKLTDHLS 98 (107)
Q Consensus 39 ~~~l~~E~en~~~Ls~PYlT~EqE~g~~~~l~~r~~~~~~~~~~~~~Kf~~H~ti~d~L~ 98 (107)
.+||..|.+-- =|||...-...+.||...+.-+.-|.+.+++|.|+-.-+...|.
T Consensus 258 L~RLK~EF~en-----RYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la 312 (342)
T KOG0493|consen 258 LQRLKAEFQEN-----RYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLA 312 (342)
T ss_pred HHHHHHHHhhh-----hhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchh
Confidence 67888887653 46676544455556676667667777777888886666655554
No 15
>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=20.90 E-value=38 Score=24.63 Aligned_cols=17 Identities=24% Similarity=0.278 Sum_probs=12.1
Q ss_pred CCceeeeccccccccCH
Q psy1064 16 KGNIFRGKYRIVEPVTH 32 (107)
Q Consensus 16 ~G~~w~GK~R~~~~vs~ 32 (107)
+|++||||---+...+.
T Consensus 28 ~GKiYIGk~~tDP~~p~ 44 (114)
T PF09008_consen 28 NGKIYIGKAGTDPTNPG 44 (114)
T ss_dssp TEEEEEESTTS-TTSGG
T ss_pred CCcEEEecCCCCCCCCC
Confidence 69999999776665543
Done!