Query psy1832
Match_columns 111
No_of_seqs 57 out of 59
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 17:31:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1832.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1832hhsearch_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 1.6E-46 3.5E-51 260.4 9.1 91 16-106 1-91 (91)
2 PF04417 DUF501: Protein of un 66.5 2.3 5.1E-05 31.3 0.5 24 48-71 27-54 (139)
3 PF07494 Reg_prop: Two compone 52.7 8.6 0.00019 20.0 1.1 9 16-24 15-23 (24)
4 KOG0197|consensus 36.1 15 0.00033 32.4 0.6 43 16-58 219-264 (468)
5 COG1507 Uncharacterized conser 31.2 14 0.00031 28.4 -0.3 22 48-69 50-75 (167)
6 PF09784 L31: Mitochondrial ri 28.3 59 0.0013 23.4 2.5 33 17-53 7-39 (103)
7 PF09008 Head_binding: Head bi 25.8 27 0.00059 25.5 0.4 17 16-32 28-44 (114)
8 COG5321 Uncharacterized protei 23.9 26 0.00056 26.8 -0.0 20 92-111 66-85 (164)
9 PRK13291 metal-dependent hydro 23.5 92 0.002 23.0 2.9 48 21-68 8-68 (173)
10 PF00140 Sigma70_r1_2: Sigma-7 23.2 82 0.0018 17.9 2.0 15 53-67 13-27 (37)
11 KOG0194|consensus 21.8 80 0.0017 27.8 2.6 43 16-58 170-224 (474)
12 cd05043 PTK_Ryk Pseudokinase d 20.4 74 0.0016 23.4 1.8 44 16-59 19-72 (280)
No 1
>PF14978 MRP-63: Mitochondrial ribosome protein 63
Probab=100.00 E-value=1.6e-46 Score=260.44 Aligned_cols=91 Identities=35% Similarity=0.513 Sum_probs=85.6
Q ss_pred CCceeeeccccccccCHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHhhhhhHHHHHHHHHHHHHHHHHHcCCCCCcchhh
Q psy1832 16 KGNIFRGKYRIVEPVTHLRKAIKIEEFKIEERNMFLLRHPYLTEEEELVHLKDLERNENFRRERRALKLQKFIKHTKLTD 95 (111)
Q Consensus 16 ~G~~w~GK~R~~~~vs~~~k~~~~~rle~E~enm~~Ls~PYLT~EqE~gh~~~l~~r~~~~~~~~~~~~~Kf~~H~ti~d 95 (111)
||+|||||||+|++||+++|++|+++|+||||||||||+||||+|||+||++++....+.++.+++++++|||+|+||+|
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 39999999999999999999999999999999999999999999999999995554337788889988999999999999
Q ss_pred hhhhhhhhccc
Q psy1832 96 HLSDLRYQDKW 106 (111)
Q Consensus 96 ~L~hL~v~~~W 106 (111)
||+||||+++|
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=66.49 E-value=2.3 Score=31.32 Aligned_cols=24 Identities=29% Similarity=0.506 Sum_probs=16.9
Q ss_pred HHHHHhcCCCCHHHhh----hhhHHHHH
Q psy1832 48 NMFLLRHPYLTEEEEL----VHLKDLER 71 (111)
Q Consensus 48 nm~~Ls~PYLT~EqE~----gh~~~l~~ 71 (111)
+.|||+.|||+.+-+. |-.++++.
T Consensus 27 TlfwLtcP~L~~~isrLE~~G~i~~l~~ 54 (139)
T PF04417_consen 27 TLFWLTCPYLVKAISRLEAEGGIAELEE 54 (139)
T ss_pred ccHhhcCHHHHHHHHHHHhcCHHHHHHH
Confidence 5699999999976544 55554543
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=52.69 E-value=8.6 Score=19.96 Aligned_cols=9 Identities=44% Similarity=1.088 Sum_probs=7.9
Q ss_pred CCceeeecc
Q psy1832 16 KGNIFRGKY 24 (111)
Q Consensus 16 ~G~~w~GK~ 24 (111)
+|++|+|+.
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
>KOG0197|consensus
Probab=36.10 E-value=15 Score=32.35 Aligned_cols=43 Identities=28% Similarity=0.252 Sum_probs=33.6
Q ss_pred CCceeeeccccccccCHHHHH--HHH-HHHHHHHHHHHHHhcCCCC
Q psy1832 16 KGNIFRGKYRIVEPVTHLRKA--IKI-EEFKIEERNMFLLRHPYLT 58 (111)
Q Consensus 16 ~G~~w~GK~R~~~~vs~~~k~--~~~-~rle~E~enm~~Ls~PYLT 58 (111)
+|.+|-|+++.-.+|...... .|. +.|.+|++.|+=|+||-|-
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 699999999998777733222 233 6788999999999999874
No 5
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=31.23 E-value=14 Score=28.41 Aligned_cols=22 Identities=27% Similarity=0.552 Sum_probs=16.6
Q ss_pred HHHHHhcCCCCHHHhh----hhhHHH
Q psy1832 48 NMFLLRHPYLTEEEEL----VHLKDL 69 (111)
Q Consensus 48 nm~~Ls~PYLT~EqE~----gh~~~l 69 (111)
.-|||.+|-||+|.+. |-.+++
T Consensus 50 Tly~lt~P~L~kaaSrLEs~gymkem 75 (167)
T COG1507 50 TLYYLTHPVLTKAASRLESTGYMKEM 75 (167)
T ss_pred ceeeecChHHHHHHHHHHHhhHHHHH
Confidence 3599999999999877 555543
No 6
>PF09784 L31: Mitochondrial ribosomal protein L31; InterPro: IPR016340 This group represents a predicted mitochondrial ribosomal protein L31, fungal type [, ].
Probab=28.34 E-value=59 Score=23.36 Aligned_cols=33 Identities=12% Similarity=0.089 Sum_probs=28.1
Q ss_pred CceeeeccccccccCHHHHHHHHHHHHHHHHHHHHHh
Q psy1832 17 GNIFRGKYRIVEPVTHLRKAIKIEEFKIEERNMFLLR 53 (111)
Q Consensus 17 G~~w~GK~R~~~~vs~~~k~~~~~rle~E~enm~~Ls 53 (111)
|-.|.. |..+|...|.+.++||..--+|.-=|.
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 677754 677999999999999999999987776
No 7
>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=25.77 E-value=27 Score=25.49 Aligned_cols=17 Identities=24% Similarity=0.278 Sum_probs=12.0
Q ss_pred CCceeeeccccccccCH
Q psy1832 16 KGNIFRGKYRIVEPVTH 32 (111)
Q Consensus 16 ~G~~w~GK~R~~~~vs~ 32 (111)
+|++||||---+...+.
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 69999999766665443
No 8
>COG5321 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.87 E-value=26 Score=26.80 Aligned_cols=20 Identities=30% Similarity=0.710 Sum_probs=16.8
Q ss_pred chhhhhhhhhhhcccccccC
Q psy1832 92 KLTDHLSDLRYQDKWGKIRL 111 (111)
Q Consensus 92 ti~d~L~hL~v~~~Wd~~~~ 111 (111)
-|..++...+|..+|.+||+
T Consensus 66 EiKssiEDfrvDrKWpdYr~ 85 (164)
T COG5321 66 EIKSSIEDFRVDRKWPDYRL 85 (164)
T ss_pred EeecchhhhcccccCcchhh
Confidence 45677888999999999985
No 9
>PRK13291 metal-dependent hydrolase; Provisional
Probab=23.47 E-value=92 Score=23.04 Aligned_cols=48 Identities=23% Similarity=0.257 Sum_probs=33.7
Q ss_pred eeccccccccCHHHHHHHHHHHHHHHHH---------HHHHhcCCC----CHHHhhhhhHH
Q psy1832 21 RGKYRIVEPVTHLRKAIKIEEFKIEERN---------MFLLRHPYL----TEEEELVHLKD 68 (111)
Q Consensus 21 ~GK~R~~~~vs~~~k~~~~~rle~E~en---------m~~Ls~PYL----T~EqE~gh~~~ 68 (111)
|||+-.|.+||....++.++.|+.-.+. .=.|..+|- |.-|=.||..+
T Consensus 8 ~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~~l~~lsee~l~~~~~~gkWSi~Evl~HL~D 68 (173)
T PRK13291 8 IGQFQYPEEITEEQIQEWIAEIEALPNELRAAVSGLSDEQLDTPYREGGWTVRQVVHHVAD 68 (173)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHcCCCCCCCCcHHHHHHHHHH
Confidence 9999999999999999999888865432 223444443 34444588874
No 10
>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=23.22 E-value=82 Score=17.88 Aligned_cols=15 Identities=47% Similarity=0.620 Sum_probs=12.1
Q ss_pred hcCCCCHHHhhhhhH
Q psy1832 53 RHPYLTEEEELVHLK 67 (111)
Q Consensus 53 s~PYLT~EqE~gh~~ 67 (111)
+.|=||+|||..-+.
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 579999999998777
No 11
>KOG0194|consensus
Probab=21.80 E-value=80 Score=27.82 Aligned_cols=43 Identities=33% Similarity=0.492 Sum_probs=32.8
Q ss_pred CCceeeeccccccc-----cC-------HHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy1832 16 KGNIFRGKYRIVEP-----VT-------HLRKAIKIEEFKIEERNMFLLRHPYLT 58 (111)
Q Consensus 16 ~G~~w~GK~R~~~~-----vs-------~~~k~~~~~rle~E~enm~~Ls~PYLT 58 (111)
+|.+|.|+.+..-. |. .......+++|..||+.|.=|.||++.
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 69999998777422 21 224456689999999999999999875
No 12
>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=20.39 E-value=74 Score=23.43 Aligned_cols=44 Identities=20% Similarity=0.206 Sum_probs=29.0
Q ss_pred CCceeeeccccc----------cccCHHHHHHHHHHHHHHHHHHHHHhcCCCCH
Q psy1832 16 KGNIFRGKYRIV----------EPVTHLRKAIKIEEFKIEERNMFLLRHPYLTE 59 (111)
Q Consensus 16 ~G~~w~GK~R~~----------~~vs~~~k~~~~~rle~E~enm~~Ls~PYLT~ 59 (111)
.|.+|.|.+..+ +.+.......-.+.+..|.+.+.=|+||.+..
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 488999976551 12222223344677888888888889998664
Done!