Query 031673
Match_columns 155
No_of_seqs 120 out of 191
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 03:48:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031673.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031673hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3318 Predicted membrane pro 100.0 7.6E-56 1.6E-60 353.1 12.0 144 9-152 5-149 (178)
2 PF06417 DUF1077: Protein of u 100.0 7.3E-50 1.6E-54 306.3 9.5 101 52-152 4-108 (124)
3 PF05328 CybS: CybS; InterPro 50.8 1.1E+02 0.0025 23.5 7.7 114 28-151 4-120 (132)
4 PF12037 DUF3523: Domain of un 39.6 15 0.00033 32.0 1.2 42 105-146 210-253 (276)
5 KOG0527 HMG-box transcription 38.9 9.6 0.00021 33.9 -0.1 9 76-84 66-74 (331)
6 PF04244 DPRP: Deoxyribodipyri 33.2 13 0.00028 31.1 -0.3 35 2-39 164-198 (224)
7 PLN02720 complex II 29.3 43 0.00093 26.6 2.1 19 134-152 109-127 (140)
8 cd00084 HMG-box High Mobility 27.1 24 0.00051 22.2 0.2 10 76-85 4-13 (66)
9 PF10032 Pho88: Phosphate tran 25.5 73 0.0016 26.3 2.9 28 117-145 22-49 (192)
10 cd01390 HMGB-UBF_HMG-box HMGB- 22.4 33 0.00071 21.8 0.2 10 76-85 4-13 (66)
No 1
>KOG3318 consensus Predicted membrane protein [Function unknown]
Probab=100.00 E-value=7.6e-56 Score=353.13 Aligned_cols=144 Identities=44% Similarity=0.769 Sum_probs=128.7
Q ss_pred CCCCcceecccCCCCCCCCCCCCCCCCCCCCCCCCcchhhhhhhhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhCCc
Q 031673 9 GSGRRWAVDFTDNSTTPSTRDIADPPGFSRASQDQDDSTLSRQKKDAEANWKSQKAWEVAQAPFKNLMMMGFMMWMAGST 88 (155)
Q Consensus 9 ~~~~kW~~dl~~~~~~~~~~~lp~PpGy~~~~~~~~~~~~~~~~~~~~~~Lk~KkaWeiA~~P~K~ipMn~FMmyMsGns 88 (155)
+.+.+|++++++.....++.++|+||||.+++...++++.+.+++++.+.|+.|||||+|++|+||||||+|||||+|||
T Consensus 5 ~~~~~Wa~~~~~~~~~~nsd~~~~PpGf~~~s~~~~~s~~a~r~~d~~~~L~~kkaWdiAl~P~K~iPMN~FmmYMaGns 84 (178)
T KOG3318|consen 5 GEKLDWAVEFSDQSTVPNSDSIPSPPGFSRKSLVQQTSAEADRKKDQEATLVLKKAWDIALGPLKNIPMNLFMMYMAGNS 84 (178)
T ss_pred ccccchHHHhCCcccCCcccCCCCCCCccccccccchHHHHhhhhhHHHHHHHHHHHHHhhChHhhccHHHHHHHHcCCc
Confidence 45789999999976554566789999999886554444444555677789999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHHHHhhhcccccccccccc-ccchhhHHHHHHHHHHHHHHHHHhhccccc
Q 031673 89 VHLFSIGITFSALWQPISALQGVGKVFEPYKDSK-VDLLGPKLLFIALNLGGLALGVWKVRIHYT 152 (155)
Q Consensus 89 iqIFsImmv~m~~~~Pikai~~~~~~F~~~e~~~-~~~~~~klvyv~~ql~~l~lglyK~~smg~ 152 (155)
|||||||||+|++|||||||++++++|++||+++ .+++.+|++||++|+++++||+||||+||-
T Consensus 85 vsIFpIMm~~Mml~~PikAl~st~stFkp~eg~~~~q~~~~~lvy~l~nL~~~~lgvyKlqsMGL 149 (178)
T KOG3318|consen 85 VSIFPIMMVLMMLWRPIKALFSTGSTFKPFEGNKASQLFMAKLVYLLGNLGGLALGVYKLQSMGL 149 (178)
T ss_pred eEEeHHHHHHHHHHHHHHHHHhhhhhcccccCCchhhhHHHHHHHHHHhhhHHHHHHHhhhhcCC
Confidence 9999999999999999999999999999999976 789999999999999999999999999994
No 2
>PF06417 DUF1077: Protein of unknown function (DUF1077); InterPro: IPR009445 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=100.00 E-value=7.3e-50 Score=306.25 Aligned_cols=101 Identities=37% Similarity=0.645 Sum_probs=96.5
Q ss_pred hhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhCCccchHHHHHHHHHHHHHHHHhhhcccccccccccc----ccchh
Q 031673 52 KKDAEANWKSQKAWEVAQAPFKNLMMMGFMMWMAGSTVHLFSIGITFSALWQPISALQGVGKVFEPYKDSK----VDLLG 127 (155)
Q Consensus 52 ~~~~~~~Lk~KkaWeiA~~P~K~ipMn~FMmyMsGnsiqIFsImmv~m~~~~Pikai~~~~~~F~~~e~~~----~~~~~ 127 (155)
+++++++|++|||||+|++|+||||||+|||||||||+||||||||+|+++||||||+++|++|++||++. .++++
T Consensus 4 ~~~~~~~L~~KkAWeiA~~P~K~ipMn~FMmyMsGnsi~IFsIm~v~m~~~~Pikai~~~~~~F~~~~~~~~~~~~~~~~ 83 (124)
T PF06417_consen 4 SKEQQDALKVKKAWEIALGPAKSIPMNLFMMYMSGNSIQIFSIMMVGMLLWNPIKAIFSVNQAFKPFEGDSNDNRSQLLL 83 (124)
T ss_pred cHHHHHHHHHHHHHHHHhhHHHhhhHHHHHHHHhCCcchhhhHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhHHH
Confidence 45678899999999999999999999999999999999999999999999999999999999999998863 48999
Q ss_pred hHHHHHHHHHHHHHHHHHhhccccc
Q 031673 128 PKLLFIALNLGGLALGVWKVRIHYT 152 (155)
Q Consensus 128 ~klvyv~~ql~~l~lglyK~~smg~ 152 (155)
+|++||+||++++++|+||||+||-
T Consensus 84 ~kl~yvl~ql~~l~~gl~K~~~MGL 108 (124)
T PF06417_consen 84 QKLVYVLCQLLGLALGLYKCNSMGL 108 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHccC
Confidence 9999999999999999999999994
No 3
>PF05328 CybS: CybS; InterPro: IPR007992 This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulphur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the haem-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterised by the development of benign, vascularised tumours in the head and neck [].; GO: 0005506 iron ion binding, 0020037 heme binding, 0006099 tricarboxylic acid cycle, 0005740 mitochondrial envelope, 0016021 integral to membrane; PDB: 3AE7_D 3AEB_D 3AEC_D 3AE6_D 3AE4_D 3AE3_D 3AEG_D 3SFD_D 3AE9_D 1ZOY_D ....
Probab=50.85 E-value=1.1e+02 Score=23.54 Aligned_cols=114 Identities=16% Similarity=0.175 Sum_probs=51.5
Q ss_pred CCCCCCCCCCCCCCCCcchhhhhhhhhHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHhCCccchHHHHHHHHHHHHHHHH
Q 031673 28 RDIADPPGFSRASQDQDDSTLSRQKKDAEANWKSQKAWEVAQAPFKNLMMMGFMMWMAGSTVHLFSIGITFSALWQPISA 107 (155)
Q Consensus 28 ~~lp~PpGy~~~~~~~~~~~~~~~~~~~~~~Lk~KkaWeiA~~P~K~ipMn~FMmyMsGnsiqIFsImmv~m~~~~Pika 107 (155)
+.+|.|||+..+.........+....+.-.+....|+..+++-|+--+|. ++|+ .-+++=....+.=|+-+
T Consensus 4 ~~~p~~p~~v~~tvn~~~~~p~~~~~~gs~hW~~ER~~a~~Llpl~~~~~------~~gs---~~~~~D~~La~~l~~H~ 74 (132)
T PF05328_consen 4 KTLPQPPGGVSGTVNDAYPPPAPSKSHGSYHWKFERIVAAALLPLIPAAF------ASGS---PNPVMDYLLAVALPLHS 74 (132)
T ss_dssp ------------------------TTHHHHHHHHHHHHHHHHHHHHHHHH------HS------SHHHHHHHHHHHHHHH
T ss_pred cccccccccccccccccCCCCCCCCCCcceeeHHHHHHHHHHHHHHHHHH------HhcC---CcHHHHHHHHHHHHHHH
Confidence 46788998886533211111111122334578888999999988865553 3343 34555555666667777
Q ss_pred hhhccccccccccc-cccchhhHHHHHH--HHHHHHHHHHHhhcccc
Q 031673 108 LQGVGKVFEPYKDS-KVDLLGPKLLFIA--LNLGGLALGVWKVRIHY 151 (155)
Q Consensus 108 i~~~~~~F~~~e~~-~~~~~~~klvyv~--~ql~~l~lglyK~~smg 151 (155)
-++.++....+-.. ... ..+|++=.+ +-.+..+.|||++|.-+
T Consensus 75 h~G~~svI~DYip~~v~~-~~~~~a~~~l~~~s~~~l~Gl~~~~~~d 120 (132)
T PF05328_consen 75 HIGFESVITDYIPKRVFG-KLHKLAMWLLYAGSALTLAGLYYFNTND 120 (132)
T ss_dssp HHHHHHHHHHHS-----S-HHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred HHhhhhhhhhhccccccc-hHHHHHHHHHHHHHHHHHHHheEEEecC
Confidence 77877777666331 112 233332211 22345567999998754
No 4
>PF12037 DUF3523: Domain of unknown function (DUF3523); InterPro: IPR021911 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with PF00004 from PFAM. This domain has a conserved LER sequence motif.
Probab=39.58 E-value=15 Score=32.03 Aligned_cols=42 Identities=26% Similarity=0.314 Sum_probs=27.6
Q ss_pred HHHhhhccccccccccccccch--hhHHHHHHHHHHHHHHHHHh
Q 031673 105 ISALQGVGKVFEPYKDSKVDLL--GPKLLFIALNLGGLALGVWK 146 (155)
Q Consensus 105 ikai~~~~~~F~~~e~~~~~~~--~~klvyv~~ql~~l~lglyK 146 (155)
-+.|-++|.+|..+.++-..++ ..|++-.++-+.+|++|||=
T Consensus 210 ~t~lesI~t~f~~lg~G~~~lltD~~kl~~~vgg~T~LA~GvYt 253 (276)
T PF12037_consen 210 ETVLESINTTFSHLGEGFRALLTDRDKLTTTVGGLTALAAGVYT 253 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHH
Confidence 3445567777777765322222 25788888888888888884
No 5
>KOG0527 consensus HMG-box transcription factor [Transcription]
Probab=38.94 E-value=9.6 Score=33.95 Aligned_cols=9 Identities=44% Similarity=0.959 Sum_probs=8.2
Q ss_pred HHHHHHHHH
Q 031673 76 MMMGFMMWM 84 (155)
Q Consensus 76 pMn~FMmyM 84 (155)
|||+||.|=
T Consensus 66 PMNAFMVWS 74 (331)
T KOG0527|consen 66 PMNAFMVWS 74 (331)
T ss_pred Ccchhhhhh
Confidence 999999994
No 6
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=33.16 E-value=13 Score=31.06 Aligned_cols=35 Identities=31% Similarity=0.594 Sum_probs=11.3
Q ss_pred CCCCCCCCCCCcceecccCCCCCCCCCCCCCCCCCCCC
Q 031673 2 EKGKGVMGSGRRWAVDFTDNSTTPSTRDIADPPGFSRA 39 (155)
Q Consensus 2 ~~~~~~~~~~~kW~~dl~~~~~~~~~~~lp~PpGy~~~ 39 (155)
|.|+|++ -||.+|-.+-.+-+....+|.|+-|.+.
T Consensus 164 ~~g~P~G---GkWnfD~eNRk~~p~~~~~P~~~~~~~d 198 (224)
T PF04244_consen 164 EDGKPVG---GKWNFDAENRKKLPKGIPIPEPPRFEPD 198 (224)
T ss_dssp ETTEEGG---GSS--GGGS-------TTS---------
T ss_pred CCCCcCC---CcCCCChhhccCCCCCCCCCCCCCCCCC
Confidence 3454444 5999999874433344578888888763
No 7
>PLN02720 complex II
Probab=29.25 E-value=43 Score=26.62 Aligned_cols=19 Identities=11% Similarity=0.097 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHhhccccc
Q 031673 134 ALNLGGLALGVWKVRIHYT 152 (155)
Q Consensus 134 ~~ql~~l~lglyK~~smg~ 152 (155)
..+++...++|||+++|++
T Consensus 109 G~EvAnh~lqLYk~d~m~a 127 (140)
T PLN02720 109 GQEVANHWLQLYKFDTMAA 127 (140)
T ss_pred hHHHHHHHHHHHhccccch
Confidence 4567788899999999986
No 8
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=27.11 E-value=24 Score=22.18 Aligned_cols=10 Identities=0% Similarity=0.368 Sum_probs=8.0
Q ss_pred HHHHHHHHHh
Q 031673 76 MMMGFMMWMA 85 (155)
Q Consensus 76 pMn~FMmyMs 85 (155)
|+|.||+|+.
T Consensus 4 p~~af~~f~~ 13 (66)
T cd00084 4 PLSAYFLFSQ 13 (66)
T ss_pred CCcHHHHHHH
Confidence 7888888874
No 9
>PF10032 Pho88: Phosphate transport (Pho88); InterPro: IPR019263 This entry represents proteins involved in inorganic phosphate transport, as well as telomere length regulation and maintenance [, , , ].
Probab=25.50 E-value=73 Score=26.29 Aligned_cols=28 Identities=18% Similarity=0.278 Sum_probs=22.2
Q ss_pred ccccccccchhhHHHHHHHHHHHHHHHHH
Q 031673 117 PYKDSKVDLLGPKLLFIALNLGGLALGVW 145 (155)
Q Consensus 117 ~~e~~~~~~~~~klvyv~~ql~~l~lgly 145 (155)
.||+. ..+...+++|+++|++.+++-+|
T Consensus 22 d~~dP-~v~~~vR~~y~~s~~i~~~~y~y 49 (192)
T PF10032_consen 22 DFEDP-QVLFYVRIAYVASQLIILGVYLY 49 (192)
T ss_pred CCCCH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34543 44677899999999999999887
No 10
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=22.43 E-value=33 Score=21.78 Aligned_cols=10 Identities=0% Similarity=0.368 Sum_probs=7.8
Q ss_pred HHHHHHHHHh
Q 031673 76 MMMGFMMWMA 85 (155)
Q Consensus 76 pMn~FMmyMs 85 (155)
|+|.||+|+.
T Consensus 4 p~saf~~f~~ 13 (66)
T cd01390 4 PLSAYFLFSQ 13 (66)
T ss_pred CCcHHHHHHH
Confidence 7788888864
Done!