Query 016414
Match_columns 390
No_of_seqs 218 out of 785
Neff 5.4
Searched_HMMs 29240
Date Mon Mar 25 13:11:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016414.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/016414hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2cxh_A Probable BRIX-domain ri 100.0 2.3E-35 8E-40 276.8 16.3 147 109-260 17-168 (217)
2 1w94_A MIL, probable BRIX-doma 99.9 8E-22 2.8E-26 176.4 10.2 129 130-273 1-129 (156)
3 2kxe_A DNA polymerase II small 20.4 35 0.0012 26.1 1.2 35 144-178 5-48 (75)
4 3jte_A Response regulator rece 15.2 3.9E+02 0.013 20.3 6.8 59 126-184 47-105 (143)
5 4e7p_A Response regulator; DNA 15.2 3.8E+02 0.013 20.8 6.6 59 126-184 64-122 (150)
6 1otr_A Protein CUE2; protein-p 14.9 8.1 0.00028 27.7 -3.3 18 247-264 9-26 (49)
7 3f6c_A Positive transcription 14.3 2.9E+02 0.0099 20.8 5.4 56 128-183 46-101 (134)
8 1xg7_A Hypothetical protein; s 14.3 92 0.0031 29.4 2.7 43 117-174 73-116 (250)
9 3eul_A Possible nitrate/nitrit 13.6 4.2E+02 0.014 20.5 6.4 57 128-184 61-117 (152)
10 3hdv_A Response regulator; PSI 12.3 4.7E+02 0.016 19.6 6.6 63 122-184 46-109 (136)
No 1
>2cxh_A Probable BRIX-domain ribosomal biogenesis protein; 18S rRNA, IMP4, U3 snoRNP, ribosomal biogenesis binding, structural genomics, NPPSFA; 1.80A {Aeropyrum pernix} SCOP: c.51.1.2
Probab=100.00 E-value=2.3e-35 Score=276.76 Aligned_cols=147 Identities=16% Similarity=0.179 Sum_probs=126.9
Q ss_pred hhhCCCCchhhhhhhhcCCCCeEEEEeCCCCCCcHHHHHHHHHhcCCcchhcccccccHHHHHHHHHhCCCceEEEEEec
Q 016414 109 ELFAGNDADEFSSILKQGCAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIVVHTN 188 (390)
Q Consensus 109 e~~~~~~~DEf~~~~~~~~~PKiLITTSr~pS~r~r~F~kdL~~i~PnS~~~~R~k~~Lkdiv~~A~~~g~T~lIv~~E~ 188 (390)
+.+.++..|+|. +|...||||||||++||.++++|++||..+|||+.|++|++++|++|+++|..+|||++|||+|+
T Consensus 17 ~~~~~~g~~~~~---~~~~~pKvLITTSr~pS~r~r~fakeL~~~lPns~~i~Rgk~sLkeL~e~a~~~~~tdlivV~e~ 93 (217)
T 2cxh_A 17 AGSHMLGGKGRP---SGVGGYRILVTTSRRPSPRIRSFVKDLSATIPGAFRFTRGHYSMEELAREAIIRGADRIVVVGER 93 (217)
T ss_dssp -------------------CCEEEEEESSSCCHHHHHHHHHHHTTSTTEEECCCTTCCHHHHHHHHHHTTEEEEEEEEEE
T ss_pred cccccccCcccc---cCCCCCeEEEEcCCCCCHHHHHHHHHHHHHCCCCEEeecCCcCHHHHHHHHHhCCCCEEEEEEec
Confidence 334455568887 47889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceEEEeeCCCC---c-eEEEEEeceeehhhhccCCCC-CCCCCeEEecCCCcchhHHHHHHHHhhCCCCCCCC
Q 016414 189 RREPDALLIIGLPDG---P-TAHFKLSKLVLRKDIKNHGNP-TGHIPELVLNNFATRLGHRVGRLIQSLFPQSPEFR 260 (390)
Q Consensus 189 r~~p~~L~I~~lP~G---P-T~~FkI~nv~l~kdI~~~g~~-~~~~P~LIlnnF~t~lg~~i~~mfq~LFP~~p~~~ 260 (390)
+++|++|||+|+|.| | |++|+|+|+++++||+++|++ +.|+|+|+ |||++++|+++++||++|||. |.++
T Consensus 94 rg~p~~L~~~hlP~G~~~P~Ta~F~I~nv~l~~ei~~~g~~~~~~rP~L~-~nF~t~~g~~i~~~f~~lFp~-P~~~ 168 (217)
T 2cxh_A 94 RGNPGIIRVYAVEGPERPDNIVSFIVKGVSLSRERRWGLPSLRGGEVLVA-RPLDSGVAVEFADAFVIAFHA-RLKP 168 (217)
T ss_dssp TTEEEEEEEEECCSSSCCEEEEEEEEEEEECHHHHTCCCCCCCSCCEEEE-EESSSSTHHHHHHHHHHHHCC-BSSC
T ss_pred CCCCcEEEEEECCCCCCCCcEEEEEEeeEEehhhhccCCCccCCCCceEE-eeecCchHHHHHHHHHHHcCC-CCCC
Confidence 999999999999999 9 999999999999999999976 68999999 999999999999999999998 7653
No 2
>1w94_A MIL, probable BRIX-domain ribosomal biogenesis protein; archaeal IMP4-BRIX domain, IMP4 domain; 2.0A {Methanothermobacter thermautotrophicusorganism_taxid} SCOP: c.51.1.2
Probab=99.86 E-value=8e-22 Score=176.42 Aligned_cols=129 Identities=16% Similarity=0.236 Sum_probs=107.8
Q ss_pred eEEEEeCCCCCCcHHHHHHHHHhcCCcchhcccccccHHHHHHHHHhCCCceEEEEEecCCCCceEEEeeCCCCceEEEE
Q 016414 130 KILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIVVHTNRREPDALLIIGLPDGPTAHFK 209 (390)
Q Consensus 130 KiLITTSr~pS~r~r~F~kdL~~i~PnS~~~~R~k~~Lkdiv~~A~~~g~T~lIv~~E~r~~p~~L~I~~lP~GPT~~Fk 209 (390)
|++||||++||.++++|+++|..+| |+.|++|++++|++|++.|... +|||+|++|+|++|.|+|+|.|||++|+
T Consensus 1 kilITTSr~Ps~~l~~fakeLa~~l-n~~~v~Rgk~sl~~L~~~~~~~----~iVV~e~rg~P~~l~i~hlp~gpt~~f~ 75 (156)
T 1w94_A 1 HMLLTTSRKPSQRTRSFSQRLSRIM-GWRYINRGKMSLRDVLIEARGP----VAVVSERHGNPARITFLDERGGERGYIL 75 (156)
T ss_dssp CCEEEECSSCCHHHHHHHHHHHHHH-TCEECCCTTCCHHHHHHHHSSC----EEEEEEETTEEEEEEEECTTSCEEEEEE
T ss_pred CEEEECCCCCCHHHHHHHHHHHHHh-CCEEEeeCCcCHHHHHHhcCCC----EEEEEcCCCCCCeEEEEeCCCCCEEEEE
Confidence 6899999999999999999999999 9999999999999999999544 9999999999999999999999999999
Q ss_pred EeceeehhhhccCCCCCCCCCeEEecCCCcchhHHHHHHHHhhCCCCCCCCCCeEEEEEecCCE
Q 016414 210 LSKLVLRKDIKNHGNPTGHIPELVLNNFATRLGHRVGRLIQSLFPQSPEFRGRRVVTFHNQRDF 273 (390)
Q Consensus 210 I~nv~l~kdI~~~g~~~~~~P~LIlnnF~t~lg~~i~~mfq~LFP~~p~~~~RRVVtF~nq~d~ 273 (390)
+ |+.+++|++.. .|..|...+.++.+..+..+|. ||..+ ....+|++|..+.++
T Consensus 76 ~-nv~l~~~~~~~------~~~~v~~~~~~~~~~~l~~~~~--~~~~~-~~~~~~~~i~~~~~~ 129 (156)
T 1w94_A 76 F-NPSFEMKKPEL------ADKAVRVSSCPPGSEGLCNLMG--LEVDE-SSSRDAWSIRTDEEY 129 (156)
T ss_dssp E-EEEECSSCCCC------SSCCCEESCCCTTCHHHHHHHT--CEECC-SCCTTEEEEECCSSS
T ss_pred E-ceEEcccCccc------CCceEEEecCChhHHHHHHHHC--CCccC-CCCceEEEEEeCCCc
Confidence 8 99999999621 1444666667888877777766 34432 234578888755554
No 3
>2kxe_A DNA polymerase II small subunit; D-family, archara, helical BU transferase; HET: DNA; NMR {Pyrococcus horikoshii}
Probab=20.44 E-value=35 Score=26.13 Aligned_cols=35 Identities=26% Similarity=0.691 Sum_probs=25.6
Q ss_pred HHHHHHHHh---cC-Ccch-----hcccccccHHHHHHHHHhCC
Q 016414 144 PAFISELLS---VI-PNSH-----YYKRGTYDLKKIIEYAKKKD 178 (390)
Q Consensus 144 r~F~kdL~~---i~-PnS~-----~~~R~k~~Lkdiv~~A~~~g 178 (390)
-.|+++|.. ++ |-+. ++++|+++|-+++++|+.+|
T Consensus 5 delVk~L~~n~YLiTPsAYyLL~~~ykkg~FsL~ELiKFAksrg 48 (75)
T 2kxe_A 5 DEFVKGLMKNGYLITPSAYYLLVGHFNEGKFSLIELIKFAKSRE 48 (75)
T ss_dssp CHHHHHHHTTTCEECHHHHHHHHHHHHTTSSCHHHHHHHHHHHT
T ss_pred HHHHHHHHHCCceeCchHHHHHHHHhhcccccHHHHHHHHHhcC
Confidence 356677654 23 5544 45668999999999999998
No 4
>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}
Probab=15.24 E-value=3.9e+02 Score=20.33 Aligned_cols=59 Identities=12% Similarity=0.036 Sum_probs=37.8
Q ss_pred CCCCeEEEEeCCCCCCcHHHHHHHHHhcCCcchhcccccccHHHHHHHHHhCCCceEEE
Q 016414 126 GCAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIV 184 (390)
Q Consensus 126 ~~~PKiLITTSr~pS~r~r~F~kdL~~i~PnS~~~~R~k~~Lkdiv~~A~~~g~T~lIv 184 (390)
...|-++|+-..-|......|++.|+...|+...+-=....-.+.+..|...|+.++|.
T Consensus 47 ~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~ 105 (143)
T 3jte_A 47 CNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLR 105 (143)
T ss_dssp TTTCCEEEEESCCSSSCHHHHHHHHHHHCTTCEEEEEECTTCHHHHHHHHHTTCSEEEE
T ss_pred CCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEECCCCHHHHHHHHHhCcceeEe
Confidence 45688888877777777888888888877765443322222234455566667766553
No 5
>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A
Probab=15.17 E-value=3.8e+02 Score=20.79 Aligned_cols=59 Identities=14% Similarity=0.076 Sum_probs=40.9
Q ss_pred CCCCeEEEEeCCCCCCcHHHHHHHHHhcCCcchhcccccccHHHHHHHHHhCCCceEEE
Q 016414 126 GCAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIV 184 (390)
Q Consensus 126 ~~~PKiLITTSr~pS~r~r~F~kdL~~i~PnS~~~~R~k~~Lkdiv~~A~~~g~T~lIv 184 (390)
...|-++|+--.-|......|++.|+...|+...+-=....-.+....|...|+.++|.
T Consensus 64 ~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~ 122 (150)
T 4e7p_A 64 KESVDIAILDVEMPVKTGLEVLEWIRSEKLETKVVVVTTFKRAGYFERAVKAGVDAYVL 122 (150)
T ss_dssp TSCCSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred ccCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHCCCcEEEe
Confidence 34688888887778888888999998877776544333333345556677778777664
No 6
>1otr_A Protein CUE2; protein-protein complex, cell cycle; NMR {Saccharomyces cerevisiae} SCOP: a.5.2.4
Probab=14.88 E-value=8.1 Score=27.66 Aligned_cols=18 Identities=11% Similarity=0.277 Sum_probs=12.4
Q ss_pred HHHHhhCCCCCCCCCCeE
Q 016414 247 RLIQSLFPQSPEFRGRRV 264 (390)
Q Consensus 247 ~mfq~LFP~~p~~~~RRV 264 (390)
..|+.|||.+..+..|+|
T Consensus 9 ~~L~EMFP~~~~~~ik~~ 26 (49)
T 1otr_A 9 SILMDMFPAISKSKLQVH 26 (49)
T ss_dssp HHHHHHCSSSCHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHH
Confidence 578999999775444443
No 7
>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}
Probab=14.33 E-value=2.9e+02 Score=20.79 Aligned_cols=56 Identities=9% Similarity=0.013 Sum_probs=29.8
Q ss_pred CCeEEEEeCCCCCCcHHHHHHHHHhcCCcchhcccccccHHHHHHHHHhCCCceEE
Q 016414 128 APKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSII 183 (390)
Q Consensus 128 ~PKiLITTSr~pS~r~r~F~kdL~~i~PnS~~~~R~k~~Lkdiv~~A~~~g~T~lI 183 (390)
.|-++|+-..-|......|++.|+...|+...+-=....-.+....|...|+.+++
T Consensus 46 ~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l 101 (134)
T 3f6c_A 46 KPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFV 101 (134)
T ss_dssp CCSEEEEETTCSSSCHHHHHHHHHHTTCCSEEEEEECC---CTHHHHHHTTCSEEE
T ss_pred CCCEEEEecCCCCCChHHHHHHHHhcCCCCeEEEEeCCCChHHHHHHHHhCCCEEE
Confidence 46777777666776777777777776665433222222222233444455555544
No 8
>1xg7_A Hypothetical protein; southeast collaboratory for structural genomics, secsg, hyperthermophIle, pyrococcus FU protein structure initiative; 1.88A {Pyrococcus furiosus} SCOP: a.96.1.6
Probab=14.30 E-value=92 Score=29.40 Aligned_cols=43 Identities=16% Similarity=0.142 Sum_probs=30.4
Q ss_pred hhhhhhhhcCCCCeEEEEeCCCCCCcHHHHHHHHHhcCCcchhcccc-cccHHHHHHHH
Q 016414 117 DEFSSILKQGCAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRG-TYDLKKIIEYA 174 (390)
Q Consensus 117 DEf~~~~~~~~~PKiLITTSr~pS~r~r~F~kdL~~i~PnS~~~~R~-k~~Lkdiv~~A 174 (390)
-||+.||++. .|. .++.++...++||.+..|. ...++-|-.+|
T Consensus 73 ~~Fs~yfs~~-----------~~~----~l~~~~~~Fl~~S~~n~Rl~~~KikRi~k~~ 116 (250)
T 1xg7_A 73 WEFARYFSGR-----------EVD----SIWKAYGEFLPKSKNNRRLIEAKLNRIRKVE 116 (250)
T ss_dssp HHHHHHHTTC-----------CCS----CHHHHHHHHTTTCSSCCSSHHHHHHHHHHHH
T ss_pred HHHHHHHhcC-----------Chh----HHHHHHHHHHhhCchhHHHHHHHHHHHHHHH
Confidence 3899999763 222 4788899999999998886 44455554443
No 9
>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}
Probab=13.57 E-value=4.2e+02 Score=20.52 Aligned_cols=57 Identities=12% Similarity=0.128 Sum_probs=36.5
Q ss_pred CCeEEEEeCCCCCCcHHHHHHHHHhcCCcchhcccccccHHHHHHHHHhCCCceEEE
Q 016414 128 APKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIV 184 (390)
Q Consensus 128 ~PKiLITTSr~pS~r~r~F~kdL~~i~PnS~~~~R~k~~Lkdiv~~A~~~g~T~lIv 184 (390)
.|-++|+-..-|......+++.|+...|+...+-=....-.+.+..|...|+.++|.
T Consensus 61 ~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~ 117 (152)
T 3eul_A 61 LPDVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDEPAIVYQALQQGAAGFLL 117 (152)
T ss_dssp CCSEEEEETTCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred CCCEEEEeCCCCCCCHHHHHHHHHhcCCCCeEEEEEccCCHHHHHHHHHcCCCEEEe
Confidence 578888877777777888888888877765443322233334455566667766654
No 10
>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} SCOP: c.23.1.0
Probab=12.25 E-value=4.7e+02 Score=19.65 Aligned_cols=63 Identities=10% Similarity=0.006 Sum_probs=37.5
Q ss_pred hhhcCCCCeEEEEeCCCCCCcHHHHHHHHHhc-CCcchhcccccccHHHHHHHHHhCCCceEEE
Q 016414 122 ILKQGCAPKILITTCRFNSNRGPAFISELLSV-IPNSHYYKRGTYDLKKIIEYAKKKDFTSIIV 184 (390)
Q Consensus 122 ~~~~~~~PKiLITTSr~pS~r~r~F~kdL~~i-~PnS~~~~R~k~~Lkdiv~~A~~~g~T~lIv 184 (390)
.+.....|-++|+--.-|......|++.|+.. .|+...+-=....-.+....|...|+.+++.
T Consensus 46 ~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~ 109 (136)
T 3hdv_A 46 YLHYQKRIGLMITDLRMQPESGLDLIRTIRASERAALSIIVVSGDTDVEEAVDVMHLGVVDFLL 109 (136)
T ss_dssp HHHHCTTEEEEEECSCCSSSCHHHHHHHHHTSTTTTCEEEEEESSCCHHHHHHHHHTTCSEEEE
T ss_pred HHHhCCCCcEEEEeccCCCCCHHHHHHHHHhcCCCCCCEEEEeCCCChHHHHHHHhCCcceEEe
Confidence 33333447788887777777778888888876 4654433222222234455566677766654
Done!