Query psy13896
Match_columns 171
No_of_seqs 55 out of 57
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 23:12:11 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13896.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13896hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2219|consensus 100.0 2.8E-43 6.1E-48 331.9 12.0 139 12-170 595-740 (864)
2 KOG2219|consensus 98.6 2.9E-08 6.3E-13 95.9 2.5 48 121-170 664-715 (864)
3 PF06823 DUF1236: Protein of u 53.1 14 0.0003 26.2 2.5 20 98-118 40-60 (65)
4 TIGR00228 ruvC crossover junct 29.2 34 0.00073 28.0 1.6 17 112-128 4-21 (156)
5 PF00568 WH1: WH1 domain; Int 23.7 3.1E+02 0.0067 20.3 7.2 29 100-128 9-43 (111)
6 COG0806 RimM RimM protein, req 23.2 98 0.0021 25.7 3.2 33 81-114 104-138 (174)
7 PF07151 DUF1391: Protein of u 22.6 85 0.0018 21.6 2.3 20 74-93 1-20 (49)
8 COG0817 RuvC Holliday junction 21.9 48 0.001 27.7 1.2 17 112-128 3-20 (160)
9 TIGR02583 DevR_archaea CRISPR- 21.8 1.3E+02 0.0028 26.9 3.9 41 31-71 216-257 (286)
10 PF06017 Myosin_TH1: Myosin ta 21.3 4.2E+02 0.009 21.5 6.5 35 79-113 47-81 (199)
11 TIGR01637 phage_arpU phage tra 20.5 1.6E+02 0.0035 22.0 3.7 38 28-67 2-39 (132)
12 PF14593 PH_3: PH domain; PDB: 20.5 2.1E+02 0.0046 21.8 4.4 37 80-116 10-47 (104)
No 1
>KOG2219|consensus
Probab=100.00 E-value=2.8e-43 Score=331.92 Aligned_cols=139 Identities=46% Similarity=0.765 Sum_probs=135.2
Q ss_pred cceeeeecC------CceeeeecCCchhHHHHHHHHHHHHHHHHHHHHcCCccccccCCCCCceeEecceecCCCCceeE
Q psy13896 12 KKISIFFSP------GIDFTKRLACGGVERAKRAIRVFLHIRELCLLLAGEQETQLPLTDYRSCVQVDSVLDLTNSDLIG 85 (171)
Q Consensus 12 ~~~sil~~p------gi~f~kRLPcg~~Er~rraIrvffllR~L~l~L~ge~etqLPLt~~~~~Vkv~d~LdLnnsdLI~ 85 (171)
-+++||+|| |++|+||||||++||+|||||+||++|++++++.||.|++|||++.+.+|++||+|||||||||+
T Consensus 595 ~~~~illppt~tpltgld~~krlP~ge~ek~r~~i~~y~~lR~lerdf~ge~es~lplt~~~~lv~~dn~i~l~nsdLia 674 (864)
T KOG2219|consen 595 MDHEILLPPTGTPLTGLDFSKRLPCGEVEKVRRAIRVYFFLRGLERDFSGEAESSLPLTGWIVLVDPDNVIDLNNSDLIA 674 (864)
T ss_pred cccceecCCCCCCccCceeeccCCCchHHHHhhhhhhhhhhhhhhHhhcCCccccCCCCCceeeecCcceeeccCCCcee
Confidence 468999999 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEeCCCCCceEEEEEEEeeeEEEEEecCC-ccceEEEEEEeecCcceecCCCceeEEEeEEEeEEEeeeCCCceeeeE
Q psy13896 86 CHVVRGGAGGSRVHRFLVVNDVQVILVEPDT-RVGWGVVKLAGEYPGVGCGAGGSRVHRFLVVNDVQVILVEPDTRVGWG 164 (171)
Q Consensus 86 C~Vv~~~~~~~~~~RfLvvd~~QliLVEPDs-~lGwGVVkfvg~~~~i~Ct~~~~~~~rflvld~~Q~ilvepDSRlgwg 164 (171)
|||+.++ |.++.|||++|..||||||||+ ++|||||||+|. +||.++..++.|||.+|+
T Consensus 675 Ctvv~kd--g~~~~rfL~id~~qL~LvePd~kr~gw~vvkf~Gl------------------lqd~~i~g~~dDsr~lhi 734 (864)
T KOG2219|consen 675 CTVVIKD--GHPRWRFLVIDPLQLILVEPDTKRLGWGVVKFVGL------------------LQDRWILGDRDDSRSLHI 734 (864)
T ss_pred eEEeccC--CCceeEEEEecchhceeeccchhhcchheeeeeee------------------ecceEEecccCcccceeE
Confidence 9999999 8899999999999999999999 999999999999 999999999999999999
Q ss_pred EEEecc
Q psy13896 165 VVKLAG 170 (171)
Q Consensus 165 vvkf~G 170 (171)
+++-++
T Consensus 735 tv~~~a 740 (864)
T KOG2219|consen 735 TVHMVA 740 (864)
T ss_pred EEeccC
Confidence 998754
No 2
>KOG2219|consensus
Probab=98.56 E-value=2.9e-08 Score=95.89 Aligned_cols=48 Identities=46% Similarity=0.830 Sum_probs=40.9
Q ss_pred EEEEEEeecCcceecC---CCceeEEEeEEEeEEEeeeCCCc-eeeeEEEEecc
Q psy13896 121 GVVKLAGEYPGVGCGA---GGSRVHRFLVVNDVQVILVEPDT-RVGWGVVKLAG 170 (171)
Q Consensus 121 GVVkfvg~~~~i~Ct~---~~~~~~rflvld~~Q~ilvepDS-Rlgwgvvkf~G 170 (171)
+++.--.+ =++|++ ++....|||++|-+||++||||+ |+||+++||+|
T Consensus 664 ~i~l~nsd--LiaCtvv~kdg~~~~rfL~id~~qL~LvePd~kr~gw~vvkf~G 715 (864)
T KOG2219|consen 664 VIDLNNSD--LIACTVVIKDGHPRWRFLVIDPLQLILVEPDTKRLGWGVVKFVG 715 (864)
T ss_pred eeeccCCC--ceeeEEeccCCCceeEEEEecchhceeeccchhhcchheeeeee
Confidence 44444444 479995 77899999999999999999999 89999999998
No 3
>PF06823 DUF1236: Protein of unknown function (DUF1236); InterPro: IPR009642 This family contains a number of hypothetical bacterial proteins of unknown function. Some family members contain more than one copy of the region represented by this family.
Probab=53.09 E-value=14 Score=26.24 Aligned_cols=20 Identities=50% Similarity=0.931 Sum_probs=17.0
Q ss_pred EEEEEEEeeeEEEEEecCC-cc
Q psy13896 98 VHRFLVVNDVQVILVEPDT-RV 118 (171)
Q Consensus 98 ~~RfLvvd~~QliLVEPDs-~l 118 (171)
--||..+++ |.++|||+| ++
T Consensus 40 ~Y~Y~~v~~-~~ViVdP~Tr~V 60 (65)
T PF06823_consen 40 GYRYVVVND-RIVIVDPRTRRV 60 (65)
T ss_pred CceEEEECC-EEEEEcCCCCEE
Confidence 458999999 999999999 53
No 4
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=29.17 E-value=34 Score=27.99 Aligned_cols=17 Identities=29% Similarity=0.882 Sum_probs=14.3
Q ss_pred EecCC-ccceEEEEEEee
Q psy13896 112 VEPDT-RVGWGVVKLAGE 128 (171)
Q Consensus 112 VEPDs-~lGwGVVkfvg~ 128 (171)
++|-+ +.||||+...|.
T Consensus 4 IDPGl~~tG~gvi~~~~~ 21 (156)
T TIGR00228 4 IDPGSRVTGYGVIRQVGR 21 (156)
T ss_pred ECcccccccEEEEEecCC
Confidence 78988 999999986554
No 5
>PF00568 WH1: WH1 domain; InterPro: IPR000697 The EVH1 (WH1, RanBP1-WASP) domain is found in multi-domain proteins implicated in a diverse range of signalling, nuclear transport and cytoskeletal events. This domain of around 115 amino acids is present in species ranging from yeast to mammals. Many EVH1-containing proteins associate with actin-based structures and play a role in cytoskeletal organisation. EVH1 domains recognise and bind the proline-rich motif FPPPP with low-affinity, further interactions then form between flanking residues [][]. WASP family proteins contain a EVH1 (WH1) in their N-terminals which bind proline-rich sequences in the WASP interacting protein. Proteins of the RanBP1 family contain a WH1 domain in their N-terminal region, which seems to bind a different sequence motif present in the C-terminal part of RanGTP protein [,]. Tertiary structure of the WH1 domain of the Mena protein revealed structure similarities with the pleckstrin homology (PH) domain. The overall fold consists of a compact parallel beta-sandwich, closed along one edge by a long alpha-helix. A highly conserved cluster of three surface-exposed aromatic side-chains forms the recognition site for the molecules target ligands. [].; GO: 0005515 protein binding; PDB: 1I2H_A 1DDV_A 1DDW_A 1EGX_A 3SYX_A 1TJ6_B 1XOD_B 1EVH_A 1I7A_B 2JP2_A ....
Probab=23.74 E-value=3.1e+02 Score=20.30 Aligned_cols=29 Identities=34% Similarity=0.464 Sum_probs=22.9
Q ss_pred EEEEEeeeEEEEEecCC-c-----cceEEEEEEee
Q psy13896 100 RFLVVNDVQVILVEPDT-R-----VGWGVVKLAGE 128 (171)
Q Consensus 100 RfLvvd~~QliLVEPDs-~-----lGwGVVkfvg~ 128 (171)
..++.-..|+...+|++ + -+.|+|.++-+
T Consensus 9 ~~i~~~vA~v~~~~p~~~~~W~~~~~~g~v~~v~d 43 (111)
T PF00568_consen 9 QSIATAVAQVYQADPDTKRQWSPVKGTGVVCFVKD 43 (111)
T ss_dssp EEEEEEEEEEEEEETTTSESEEESSSEEEEEEEEE
T ss_pred eEEEEEEEEEEEEEcCCCCcEeeCCeEEEEEEEEE
Confidence 57788889999999988 4 55577777766
No 6
>COG0806 RimM RimM protein, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]
Probab=23.16 E-value=98 Score=25.68 Aligned_cols=33 Identities=33% Similarity=0.492 Sum_probs=25.6
Q ss_pred CceeEEEEEeCCCCCc--eEEEEEEEeeeEEEEEec
Q psy13896 81 SDLIGCHVVRGGAGGS--RVHRFLVVNDVQVILVEP 114 (171)
Q Consensus 81 sdLI~C~Vv~~~~~~~--~~~RfLvvd~~QliLVEP 114 (171)
+|||+|+|++.+ +.. ++.-++..-...++.|+.
T Consensus 104 ~DLiG~~V~~~~-g~~lG~V~~i~~~Ga~Dvl~V~~ 138 (174)
T COG0806 104 HDLIGLEVVTED-GELLGKVTEILETGANDVLVVKA 138 (174)
T ss_pred EeecCcEEEcCC-CcEEEEEEEEeeCCCccEEEEEe
Confidence 799999999988 222 556777777778888875
No 7
>PF07151 DUF1391: Protein of unknown function (DUF1391); InterPro: IPR009821 This family consists of several Enterobacterial proteins of around 50 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi where they are often known as YdfA. The function of this family is unknown.
Probab=22.57 E-value=85 Score=21.65 Aligned_cols=20 Identities=25% Similarity=0.459 Sum_probs=17.2
Q ss_pred ceecCCCCceeEEEEEeCCC
Q psy13896 74 SVLDLTNSDLIGCHVVRGGA 93 (171)
Q Consensus 74 d~LdLnnsdLI~C~Vv~~~~ 93 (171)
|.|||.|++-.-|-|...+.
T Consensus 1 ~tidlgnneslv~gvfpn~d 20 (49)
T PF07151_consen 1 DTIDLGNNESLVCGVFPNQD 20 (49)
T ss_pred CcccccCCcceEEeEeeCCC
Confidence 67999999999999987764
No 8
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=21.91 E-value=48 Score=27.67 Aligned_cols=17 Identities=35% Similarity=0.993 Sum_probs=13.4
Q ss_pred EecCC-ccceEEEEEEee
Q psy13896 112 VEPDT-RVGWGVVKLAGE 128 (171)
Q Consensus 112 VEPDs-~lGwGVVkfvg~ 128 (171)
++|-+ +.||||+.--|.
T Consensus 3 IDPGl~~~G~gvI~~~~~ 20 (160)
T COG0817 3 IDPGLRRTGYGVIEVEGR 20 (160)
T ss_pred cCCCccccceEEEEccCC
Confidence 58988 999999875543
No 9
>TIGR02583 DevR_archaea CRISPR-associated regulatory protein, Csa2 family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This model represents one such family, typified by MJ0381 of Methanococcus jannaschii. This archaeal clade is a member of the DevR family (TIGR01875) which includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa2, for CRISPR/Cas Subtype Protein 2.
Probab=21.81 E-value=1.3e+02 Score=26.94 Aligned_cols=41 Identities=17% Similarity=0.170 Sum_probs=29.8
Q ss_pred chhHHHHHHHHHHHH-HHHHHHHHcCCccccccCCCCCceeE
Q psy13896 31 GGVERAKRAIRVFLH-IRELCLLLAGEQETQLPLTDYRSCVQ 71 (171)
Q Consensus 31 g~~Er~rraIrvffl-lR~L~l~L~ge~etqLPLt~~~~~Vk 71 (171)
-+.||++|.-...-. ++-|+....+..++.||+......|.
T Consensus 216 ~~~eR~~Rvka~LdAl~~~L~~~~GAk~sr~lP~~~~~~~Vv 257 (286)
T TIGR02583 216 DENERKRRIEAALKALLPMLSGYFGAKLARFLPVVKVEELVV 257 (286)
T ss_pred CHHHHHHHHHHHHHHHHHHhhhhhhhhhcccCcceeeeEEEE
Confidence 367888888666666 46666666777899999977666663
No 10
>PF06017 Myosin_TH1: Myosin tail; InterPro: IPR010926 These proteins share a region of sequence similarity with the tail of myosin (for example O00159 from SWISSPROT). Myosins act as molecular motors. ; GO: 0003774 motor activity, 0016459 myosin complex
Probab=21.33 E-value=4.2e+02 Score=21.48 Aligned_cols=35 Identities=20% Similarity=0.265 Sum_probs=29.7
Q ss_pred CCCceeEEEEEeCCCCCceEEEEEEEeeeEEEEEe
Q psy13896 79 TNSDLIGCHVVRGGAGGSRVHRFLVVNDVQVILVE 113 (171)
Q Consensus 79 nnsdLI~C~Vv~~~~~~~~~~RfLvvd~~QliLVE 113 (171)
+..=+.+|.|.--++.+..+.|.|++.+..+++++
T Consensus 47 ~e~vlFs~~v~K~nr~~K~~~R~livT~~~iY~l~ 81 (199)
T PF06017_consen 47 DEKVLFSDRVQKYNRRNKPQPRILIVTDKAIYLLD 81 (199)
T ss_pred CcceEEEEEEEEecCCCCccceEEEEeCCeEEEEE
Confidence 33678899988777767788999999999999996
No 11
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=20.48 E-value=1.6e+02 Score=22.02 Aligned_cols=38 Identities=11% Similarity=0.080 Sum_probs=25.2
Q ss_pred cCCchhHHHHHHHHHHHHHHHHHHHHcCCccccccCCCCC
Q psy13896 28 LACGGVERAKRAIRVFLHIRELCLLLAGEQETQLPLTDYR 67 (171)
Q Consensus 28 LPcg~~Er~rraIrvffllR~L~l~L~ge~etqLPLt~~~ 67 (171)
||.=+.++++++.+-|| +++-.-.....+..+|+..|+
T Consensus 2 ~p~ID~~kT~~~v~~~L--~~y~~~~~~~~~~~~~~~sp~ 39 (132)
T TIGR01637 2 FPEIDEKKTRANVKRFL--EDYRRLRRIAGRSLTPKLSPS 39 (132)
T ss_pred CCcccHHHHHHHHHHHH--HHHHHHHHHcCCcccCccCcc
Confidence 56677899999999998 554444444444566665544
No 12
>PF14593 PH_3: PH domain; PDB: 1W1H_D 1W1D_A 1W1G_A 2VKI_A.
Probab=20.46 E-value=2.1e+02 Score=21.78 Aligned_cols=37 Identities=11% Similarity=0.254 Sum_probs=25.4
Q ss_pred CCceeEEEEEeCCCCCc-eEEEEEEEeeeEEEEEecCC
Q psy13896 80 NSDLIGCHVVRGGAGGS-RVHRFLVVNDVQVILVEPDT 116 (171)
Q Consensus 80 nsdLI~C~Vv~~~~~~~-~~~RfLvvd~~QliLVEPDs 116 (171)
++-++-|..+.+..|=. +.|-|+..|.-+|+.|+|++
T Consensus 10 ge~Il~~g~v~K~kgl~~kkR~liLTd~PrL~Yvdp~~ 47 (104)
T PF14593_consen 10 GELILKQGYVKKRKGLFAKKRQLILTDGPRLFYVDPKK 47 (104)
T ss_dssp T--EEEEEEEEEEETTEEEEEEEEEETTTEEEEEETTT
T ss_pred CCeEEEEEEEEEeeceEEEEEEEEEccCCEEEEEECCC
Confidence 56677888887774333 44555677777999999987
Done!