Query 018273
Match_columns 358
No_of_seqs 238 out of 727
Neff 5.7
Searched_HMMs 29240
Date Mon Mar 25 12:39:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018273.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/018273hhsearch_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 1.2E-35 4.2E-40 275.0 17.3 147 109-260 17-168 (217)
2 1w94_A MIL, probable BRIX-doma 99.9 6E-22 2.1E-26 174.9 10.9 130 130-274 1-130 (156)
3 2kxe_A DNA polymerase II small 17.5 42 0.0014 25.2 1.0 36 144-179 5-49 (75)
4 1xg7_A Hypothetical protein; s 16.6 73 0.0025 29.6 2.7 41 118-173 74-115 (250)
5 4e7p_A Response regulator; DNA 15.3 3.9E+02 0.013 20.4 6.7 58 127-184 65-122 (150)
6 3f6c_A Positive transcription 14.3 3.1E+02 0.01 20.3 5.5 31 128-158 46-76 (134)
7 3eul_A Possible nitrate/nitrit 14.2 4.2E+02 0.014 20.2 6.5 57 128-184 61-117 (152)
8 3jte_A Response regulator rece 13.9 4.1E+02 0.014 19.9 6.6 59 126-184 47-105 (143)
9 1h4v_B Histidyl-tRNA synthetas 13.3 2.4E+02 0.0081 26.9 5.5 78 128-207 328-406 (421)
10 2ohw_A YUEI protein; structura 11.9 2.7E+02 0.0092 23.1 4.7 82 116-199 23-110 (133)
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=1.2e-35 Score=275.03 Aligned_cols=147 Identities=16% Similarity=0.179 Sum_probs=127.0
Q ss_pred cccCCCCcchhhhhhhcCCCceEEEEecCCCCCcHHHHHHHHHhcCCCccccccccccHHHHHHHHHhCCCceEEEEEec
Q 018273 109 ELFAGNDADEFSSILKQGCAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIVVHTN 188 (358)
Q Consensus 109 e~~~~~~~def~~~f~~~~~PKiLITTSr~pS~r~r~f~kdL~~v~Pns~~~~R~k~~Lkdiv~~A~~~~~T~lIi~~E~ 188 (358)
+.+.++..|+|+ ++...||||||||++||.++++||+||..+|||+.|++|++++|++|++.|..++||++|||+|+
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 57889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceEEEeecCCC---c-eEEEEEeceeehhhhccCCCC-CCCCceeeecCCCCchhHHHHHHHHhcCCCCCCCC
Q 018273 189 RREPDALLIIGLPDG---P-TAHFKLSKLVLRKDIKNHGNP-TGHIPELVLNNFATRLGHRVGRLIQSLFPQSPEFR 260 (358)
Q Consensus 189 r~~p~~L~I~~lP~G---P-T~~FkI~n~~l~kdi~~~g~~-~~~~P~LIlnnF~t~lg~~i~~mf~~LFP~~p~~~ 260 (358)
+++|++|||+|+|.| | |++|+|+|+++++||+++|++ +.|+|+|+ |||++++|+++++||++|||. |.+.
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 57999999 999999999999999999999 7753
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=6e-22 Score=174.89 Aligned_cols=130 Identities=16% Similarity=0.242 Sum_probs=109.5
Q ss_pred eEEEEecCCCCCcHHHHHHHHHhcCCCccccccccccHHHHHHHHHhCCCceEEEEEecCCCCceEEEeecCCCceEEEE
Q 018273 130 KILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIVVHTNRREPDALLIIGLPDGPTAHFK 209 (358)
Q Consensus 130 KiLITTSr~pS~r~r~f~kdL~~v~Pns~~~~R~k~~Lkdiv~~A~~~~~T~lIi~~E~r~~p~~L~I~~lP~GPT~~Fk 209 (358)
|++||||++||.++++|+++|..+| |+.|++|++++|++|++.|... +|||+|++|+|++|.|+|+|.|||++|+
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 9999999999999999998543 9999999999999999999999999999
Q ss_pred EeceeehhhhccCCCCCCCCceeeecCCCCchhHHHHHHHHhcCCCCCCCCCCeEEEEEecCCeE
Q 018273 210 LSKLVLRKDIKNHGNPTGHIPELVLNNFATRLGHRVGRLIQSLFPQSPEFRGRRVVTFHNQRDFI 274 (358)
Q Consensus 210 I~n~~l~kdi~~~g~~~~~~P~LIlnnF~t~lg~~i~~mf~~LFP~~p~~~~rRVvtF~nq~d~I 274 (358)
+ |+.+.+|++... |..|...+.++.+..++.+|. ||. .+....+|++|....+++
T Consensus 76 ~-nv~l~~~~~~~~------~~~v~~~~~~~~~~~l~~~~~--~~~-~~~~~~~~~~i~~~~~~~ 130 (156)
T 1w94_A 76 F-NPSFEMKKPELA------DKAVRVSSCPPGSEGLCNLMG--LEV-DESSSRDAWSIRTDEEYA 130 (156)
T ss_dssp E-EEEECSSCCCCS------SCCCEESCCCTTCHHHHHHHT--CEE-CCSCCTTEEEEECCSSSS
T ss_pred E-ceEEcccCcccC------CceEEEecCChhHHHHHHHHC--CCc-cCCCCceEEEEEeCCCcE
Confidence 8 999999987321 445666667888888888776 344 223446788887655553
No 3
>2kxe_A DNA polymerase II small subunit; D-family, archara, helical BU transferase; HET: DNA; NMR {Pyrococcus horikoshii}
Probab=17.47 E-value=42 Score=25.18 Aligned_cols=36 Identities=25% Similarity=0.651 Sum_probs=26.1
Q ss_pred HHHHHHHHh---cC-CCcc-----ccccccccHHHHHHHHHhCCC
Q 018273 144 PAFISELLS---VI-PNSH-----YYKRGTYDLKKIIEYAKKKDF 179 (358)
Q Consensus 144 r~f~kdL~~---v~-Pns~-----~~~R~k~~Lkdiv~~A~~~~~ 179 (358)
-.|+++|.. ++ |.+. ++++|+++|-+++.+|..+|.
T Consensus 5 delVk~L~~n~YLiTPsAYyLL~~~ykkg~FsL~ELiKFAksrgt 49 (75)
T 2kxe_A 5 DEFVKGLMKNGYLITPSAYYLLVGHFNEGKFSLIELIKFAKSRET 49 (75)
T ss_dssp CHHHHHHHTTTCEECHHHHHHHHHHHHTTSSCHHHHHHHHHHHTC
T ss_pred HHHHHHHHHCCceeCchHHHHHHHHhhcccccHHHHHHHHHhcCc
Confidence 356777753 23 5443 456789999999999999883
No 4
>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=16.63 E-value=73 Score=29.57 Aligned_cols=41 Identities=17% Similarity=0.190 Sum_probs=29.0
Q ss_pred hhhhhhhcCCCceEEEEecCCCCCcHHHHHHHHHhcCCCccccccc-cccHHHHHHH
Q 018273 118 EFSSILKQGCAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRG-TYDLKKIIEY 173 (358)
Q Consensus 118 ef~~~f~~~~~PKiLITTSr~pS~r~r~f~kdL~~v~Pns~~~~R~-k~~Lkdiv~~ 173 (358)
||+.||++. .|. .++.++...++||.+-.|. ...++-|-.+
T Consensus 74 ~Fs~yfs~~-----------~~~----~l~~~~~~Fl~~S~~n~Rl~~~KikRi~k~ 115 (250)
T 1xg7_A 74 EFARYFSGR-----------EVD----SIWKAYGEFLPKSKNNRRLIEAKLNRIRKV 115 (250)
T ss_dssp HHHHHHTTC-----------CCS----CHHHHHHHHTTTCSSCCSSHHHHHHHHHHH
T ss_pred HHHHHHhcC-----------Chh----HHHHHHHHHHhhCchhHHHHHHHHHHHHHH
Confidence 899999863 222 4888999999999988885 3444444443
No 5
>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A
Probab=15.34 E-value=3.9e+02 Score=20.39 Aligned_cols=58 Identities=14% Similarity=0.083 Sum_probs=38.4
Q ss_pred CCceEEEEecCCCCCcHHHHHHHHHhcCCCccccccccccHHHHHHHHHhCCCceEEE
Q 018273 127 CAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIV 184 (358)
Q Consensus 127 ~~PKiLITTSr~pS~r~r~f~kdL~~v~Pns~~~~R~k~~Lkdiv~~A~~~~~T~lIi 184 (358)
..|-++|+--.-|......|++.|+...|+...+-=....-.+.+..|...|+.++|.
T Consensus 65 ~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~ 122 (150)
T 4e7p_A 65 ESVDIAILDVEMPVKTGLEVLEWIRSEKLETKVVVVTTFKRAGYFERAVKAGVDAYVL 122 (150)
T ss_dssp SCCSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred cCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHCCCcEEEe
Confidence 4578888877777777888888888877766543333333334555666777776654
No 6
>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}
Probab=14.32 E-value=3.1e+02 Score=20.32 Aligned_cols=31 Identities=16% Similarity=0.174 Sum_probs=21.1
Q ss_pred CceEEEEecCCCCCcHHHHHHHHHhcCCCcc
Q 018273 128 APKILITTCRFNSNRGPAFISELLSVIPNSH 158 (358)
Q Consensus 128 ~PKiLITTSr~pS~r~r~f~kdL~~v~Pns~ 158 (358)
.|-++|+--.-|......+++.|+...|+..
T Consensus 46 ~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ 76 (134)
T 3f6c_A 46 KPDIVIIDVDIPGVNGIQVLETLRKRQYSGI 76 (134)
T ss_dssp CCSEEEEETTCSSSCHHHHHHHHHHTTCCSE
T ss_pred CCCEEEEecCCCCCChHHHHHHHHhcCCCCe
Confidence 5677777666666677777777776666543
No 7
>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}
Probab=14.15 E-value=4.2e+02 Score=20.19 Aligned_cols=57 Identities=12% Similarity=0.128 Sum_probs=33.3
Q ss_pred CceEEEEecCCCCCcHHHHHHHHHhcCCCccccccccccHHHHHHHHHhCCCceEEE
Q 018273 128 APKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIV 184 (358)
Q Consensus 128 ~PKiLITTSr~pS~r~r~f~kdL~~v~Pns~~~~R~k~~Lkdiv~~A~~~~~T~lIi 184 (358)
.|-++|+--.-|......+++.|+...|+...+-=....-.+.+..|...|+.++|.
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 577777766666667777788777766665433222222233445555666665543
No 8
>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}
Probab=13.91 E-value=4.1e+02 Score=19.89 Aligned_cols=59 Identities=12% Similarity=0.036 Sum_probs=34.8
Q ss_pred CCCceEEEEecCCCCCcHHHHHHHHHhcCCCccccccccccHHHHHHHHHhCCCceEEE
Q 018273 126 GCAPKILITTCRFNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIV 184 (358)
Q Consensus 126 ~~~PKiLITTSr~pS~r~r~f~kdL~~v~Pns~~~~R~k~~Lkdiv~~A~~~~~T~lIi 184 (358)
...|-++|+-..-|......|++.|+...|+...+-=....-.+.+..|...|+.++|.
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 34677777776667777778888887766655433222222233444555666665543
No 9
>1h4v_B Histidyl-tRNA synthetase; class IIA aminoacyl-tRNA synthetase, ATP + L-histidine tRNA(His)-> AMP + PPI + L-histidyl-tRNA(His); 2.4A {Thermus thermophilus} SCOP: c.51.1.1 d.104.1.1 PDB: 1ady_A* 1adj_A
Probab=13.29 E-value=2.4e+02 Score=26.92 Aligned_cols=78 Identities=12% Similarity=0.059 Sum_probs=49.7
Q ss_pred CceEEEEecC-CCCCcHHHHHHHHHhcCCCccccccccccHHHHHHHHHhCCCceEEEEEecCCCCceEEEeecCCCceE
Q 018273 128 APKILITTCR-FNSNRGPAFISELLSVIPNSHYYKRGTYDLKKIIEYAKKKDFTSIIVVHTNRREPDALLIIGLPDGPTA 206 (358)
Q Consensus 128 ~PKiLITTSr-~pS~r~r~f~kdL~~v~Pns~~~~R~k~~Lkdiv~~A~~~~~T~lIi~~E~r~~p~~L~I~~lP~GPT~ 206 (358)
.+.|+|+.-. ........++..|+.- -.+....+ ..+++.-...|...|+..+|++.+..-....+.|-++-.|-..
T Consensus 328 p~~v~i~~~~~~~~~~a~~l~~~Lr~~-i~v~~d~~-~~~~~~~~~~a~~~g~p~~iivG~~e~~~~~v~vk~~~~~~~~ 405 (421)
T 1h4v_B 328 GPDLYLIPLTEEAVAEAFYLAEALRPR-LRAEYALA-PRKPAKGLEEALKRGAAFAGFLGEDELRAGEVTLKRLATGEQV 405 (421)
T ss_pred CCeEEEEECChHHHHHHHHHHHHHHhc-CEEEEecC-CCCHHHHHHHHHhCCCCEEEEECchHhhcCcEEEEECCCCCce
Confidence 3467776543 2233456777788765 33333333 3589999999999999999999875433334566566666443
Q ss_pred E
Q 018273 207 H 207 (358)
Q Consensus 207 ~ 207 (358)
.
T Consensus 406 ~ 406 (421)
T 1h4v_B 406 R 406 (421)
T ss_pred E
Confidence 3
No 10
>2ohw_A YUEI protein; structural genomics, PSI-2, protein structure initiative, NEW YORK SGX research center for structural genomics, nysgxrc; 1.40A {Bacillus subtilis} SCOP: d.79.8.1
Probab=11.90 E-value=2.7e+02 Score=23.05 Aligned_cols=82 Identities=16% Similarity=0.126 Sum_probs=51.1
Q ss_pred cchhhhhhhcCCCceEEEEec---CCCCCcHHHHHHHHHhcCCCccccccc---cccHHHHHHHHHhCCCceEEEEEecC
Q 018273 116 ADEFSSILKQGCAPKILITTC---RFNSNRGPAFISELLSVIPNSHYYKRG---TYDLKKIIEYAKKKDFTSIIVVHTNR 189 (358)
Q Consensus 116 ~def~~~f~~~~~PKiLITTS---r~pS~r~r~f~kdL~~v~Pns~~~~R~---k~~Lkdiv~~A~~~~~T~lIi~~E~r 189 (358)
.||=. +|-|.-.-||++.-+ -.-......|.+.|. -.|+...+-.| ...+..++.+|...||..-||=+.+.
T Consensus 23 PDEqr-~yLGtfrERV~lalt~~q~~~~~~~~~~~~~l~-~~~~~~l~ing~l~~~~~~~YiklA~~~~i~fTiV~~~~~ 100 (133)
T 2ohw_A 23 PDERH-LFLGSLRERVVLALTKGQVLRSKPYKEAEHELK-NSHNVTLLINGELQYQSYSSYIQMASRYGVPFKIVSDLQF 100 (133)
T ss_dssp HHHHH-HTTTCCGGGEEEEEEHHHHTSSSCCHHHHHHHH-TCSSEEEEEETTSCHHHHHHHHHHHHHTTCCEEEECCCSS
T ss_pred HHHHH-HhccchhhhhheeeeHHHHhchhHHHHHHHHHh-hCCCcEEEEcCCCCHHHHHHHHHHHHHcCCCeEEecCCCC
Confidence 35554 334655668877642 112223455655554 34555544443 34578889999999999998766566
Q ss_pred CCCceEEEee
Q 018273 190 REPDALLIIG 199 (358)
Q Consensus 190 ~~p~~L~I~~ 199 (358)
..|.+|+|++
T Consensus 101 ~~~~glVv~s 110 (133)
T 2ohw_A 101 HTPLGIVIAA 110 (133)
T ss_dssp CCSEEEEEEE
T ss_pred CCCeEEEEEc
Confidence 6788887754
Done!