Query 025199
Match_columns 256
No_of_seqs 158 out of 1114
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:34:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025199hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0432 Uncharacterized conser 100.0 5.7E-54 1.2E-58 358.9 16.1 133 61-198 1-135 (137)
2 TIGR00149 TIGR00149_YbjQ secon 100.0 1.2E-50 2.6E-55 336.1 16.0 128 67-199 2-130 (132)
3 PF01894 UPF0047: Uncharacteri 100.0 4.8E-50 1E-54 326.9 12.8 118 78-199 1-118 (118)
4 KOG3267 Uncharacterized conser 100.0 7.8E-43 1.7E-47 285.9 10.7 137 65-201 1-137 (138)
5 COG3292 Predicted periplasmic 26.2 32 0.0007 36.2 1.1 20 169-188 215-234 (671)
6 cd04904 ACT_AAAH ACT domain of 16.2 1.2E+02 0.0026 22.3 2.1 21 109-131 3-23 (74)
7 cd04931 ACT_PAH ACT domain of 15.6 97 0.0021 24.3 1.6 17 114-131 21-37 (90)
8 smart00036 CNH Domain found in 15.0 1.4E+02 0.003 27.6 2.7 25 164-188 5-31 (302)
9 PF15054 DUF4535: Domain of un 14.9 4E+02 0.0087 19.0 4.4 30 100-129 3-33 (46)
10 PF03460 NIR_SIR_ferr: Nitrite 14.6 1E+02 0.0022 21.9 1.4 18 170-187 38-55 (69)
No 1
>COG0432 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.7e-54 Score=358.89 Aligned_cols=133 Identities=41% Similarity=0.701 Sum_probs=126.9
Q ss_pred CeEEEEEEEecCCCC-eEEeCcHHHHHHHhhhhcCCccceEEEEeccceEEEEEeccCCcchHHHHHHHHhhhCCCCCCC
Q 025199 61 PRWAQKTVTLPPLRR-GCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSA 139 (256)
Q Consensus 61 M~~~q~tItV~T~gr-g~~DIT~eV~~~V~~~~SgIknGlv~Vfv~HTTAsLtInEnaDP~v~~DL~~~LerLVP~~~~~ 139 (256)
|+|+|++|+|+|+++ +++|||++|+++|++ |||++|+|+||++||||||+||| +||+|++||+++|++|+|++.
T Consensus 1 m~~~~~~l~v~T~~r~~~vdIT~ev~~~v~e--sgv~~Gl~~vf~~HtTaal~inE-~ep~l~~Di~~~l~~lvP~~~-- 75 (137)
T COG0432 1 MKVYQKELTVSTKRRIEFVDITDEVEKFVRE--SGVKNGLLLVFVPHTTAALTINE-AEPGLKEDIERFLEKLVPEGA-- 75 (137)
T ss_pred CceEEEEEEEeccCccceEEchHHHHHHHHH--cCCccceEEEEecCcceEEEEec-CCCcHHHHHHHHHHHhCCCCC--
Confidence 789999999999987 999999999999998 99999999999999999999999 699999999999999999985
Q ss_pred CceeCccCCCCchhhhhhhccCceEEEEeeCCeecccCcceEEEEecCCCCc-eEEEEEE
Q 025199 140 SWKHTLEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRV-KELHGCM 198 (256)
Q Consensus 140 ~Y~H~~eG~dN~~AHLKSsLlG~SlTVPV~dGkL~LGTWQgIyL~EfDgpR~-RkV~v~~ 198 (256)
.|+|+.+|+|||+|||||+|+|+|++|||.||+|.|||||+|||+||||||. |+|++-+
T Consensus 76 ~Y~H~~~~~Dn~~aHlkasllG~S~~iPv~~GrL~LGTWQ~I~~~E~dg~r~~R~v~v~i 135 (137)
T COG0432 76 GYRHDEEGPDNAPAHLKASLLGPSLTIPVINGRLVLGTWQGIFLVEFDGPRHRRRVVVKI 135 (137)
T ss_pred CcccccCCCCchHHHHHHHhcCceEEEEEeCCeEceecccEEEEEEecCCCCccEEEEEE
Confidence 5999999999999999999999999999999999999999999999999999 6666543
No 2
>TIGR00149 TIGR00149_YbjQ secondary thiamine-phosphate synthase enzyme. Members of this protein family have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamin phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of this enzyme remains unknown.
Probab=100.00 E-value=1.2e-50 Score=336.14 Aligned_cols=128 Identities=38% Similarity=0.635 Sum_probs=119.7
Q ss_pred EEEecCCC-CeEEeCcHHHHHHHhhhhcCCccceEEEEeccceEEEEEeccCCcchHHHHHHHHhhhCCCCCCCCceeCc
Q 025199 67 TVTLPPLR-RGCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHTL 145 (256)
Q Consensus 67 tItV~T~g-rg~~DIT~eV~~~V~~~~SgIknGlv~Vfv~HTTAsLtInEnaDP~v~~DL~~~LerLVP~~~~~~Y~H~~ 145 (256)
+|++.|.+ ++++|||++|+++|++ ||+++|+|+||++||||||++|||+||+++.||+++|+||+|++. +|+|+
T Consensus 2 ~~~~~t~~~~~~~dIT~~V~~~v~~--s~i~~G~~~v~~~HTTa~l~inE~~dp~l~~Dl~~~l~~lvP~~~--~y~H~- 76 (132)
T TIGR00149 2 ELLLKTTKRVELIDITSEIEAVLQS--SGVKDGLLLVYVPHTTASLTINENADPDVLHDIERFFERLVPDDG--NYEHD- 76 (132)
T ss_pred EEEEEcCCCCeEEEChHHHHHHHHH--cCCcccEEEEEeCCCcEEEEEecCCCccHHHHHHHHHHHHCCCCC--Ccccc-
Confidence 46777765 6999999999999998 999999999999999999999999999999999999999999874 69997
Q ss_pred cCCCCchhhhhhhccCceEEEEeeCCeecccCcceEEEEecCCCCceEEEEEEe
Q 025199 146 EGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRVKELHGCML 199 (256)
Q Consensus 146 eG~dN~~AHLKSsLlG~SlTVPV~dGkL~LGTWQgIyL~EfDgpR~RkV~v~~i 199 (256)
+++|||+|||||+|+|+|++|||.||+|.|||||+|||+||||||+|+|+|.++
T Consensus 77 ~~~~n~~aHlka~L~G~s~tipi~dG~L~LGtwQ~I~l~E~Dg~r~R~v~v~i~ 130 (132)
T TIGR00149 77 EGDDNMDAHIKSSLLGTSQHVPVENGRLQLGTWQGIFFAEFDGPRTRRIIVKVQ 130 (132)
T ss_pred CCCCCHHHHHHHHhcCccEEEEEeCCEEcccCccEEEEEECCCCCCcEEEEEEE
Confidence 889999999999999999999999999999999999999999999999666554
No 3
>PF01894 UPF0047: Uncharacterised protein family UPF0047; InterPro: IPR001602 This family contains small uncharacterised proteins of 14 to 16 kDa mainly from bacteria although the signatures also occur in a hypothetical protein from archaea and from yeast.; PDB: 1VPH_E 2P6C_A 2CU5_A 1VMJ_A 1XBF_B 1VMH_A 1VE0_A 2P6H_B 1VMF_C.
Probab=100.00 E-value=4.8e-50 Score=326.90 Aligned_cols=118 Identities=42% Similarity=0.766 Sum_probs=104.7
Q ss_pred EeCcHHHHHHHhhhhcCCccceEEEEeccceEEEEEeccCCcchHHHHHHHHhhhCCCCCCCCceeCccCCCCchhhhhh
Q 025199 78 HLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHTLEGPDDMPAHIKS 157 (256)
Q Consensus 78 ~DIT~eV~~~V~~~~SgIknGlv~Vfv~HTTAsLtInEnaDP~v~~DL~~~LerLVP~~~~~~Y~H~~eG~dN~~AHLKS 157 (256)
+|||++|+++|++ |++++|+|+||++||||||+||||+||++++||+++|+||+|++. .|+|+.+|++||+||+||
T Consensus 1 idIT~~V~~~v~~--s~i~~Gl~~v~~~HTTaal~inE~~dp~v~~Dl~~~l~~lvP~~~--~y~H~~~~~~n~~aHlks 76 (118)
T PF01894_consen 1 IDITEEVREAVEE--SGIRNGLVHVFVPHTTAALTINENADPDVRRDLLEALERLVPEDD--PYRHNEEGPDNAPAHLKS 76 (118)
T ss_dssp EE-HHHHHHHHHH--HT-SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHS-TTS--T-GGGCTT-STHHHHHHH
T ss_pred CcchHHHHHHHHH--hCCcceEEEEEeCCCeEEEEEeecCChhHHHhHHHHHHHhCCCCC--ceEeCCccccCccHHHHH
Confidence 6999999999998 999999999999999999999999999999999999999999984 799999999999999999
Q ss_pred hccCceEEEEeeCCeecccCcceEEEEecCCCCceEEEEEEe
Q 025199 158 SMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRVKELHGCML 199 (256)
Q Consensus 158 sLlG~SlTVPV~dGkL~LGTWQgIyL~EfDgpR~RkV~v~~i 199 (256)
+|+|+|++|||.||+|.|||||+|||+||||||+|+|++-+|
T Consensus 77 ~l~G~S~~vpv~~G~L~LGtwQ~I~l~E~dgpr~R~v~v~i~ 118 (118)
T PF01894_consen 77 SLIGPSLTVPVHDGKLALGTWQGIYLVEFDGPRERTVVVQIM 118 (118)
T ss_dssp HHH-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEEEE
T ss_pred HhcCCeEEEEEECCEEccCCcCEEEEEECCCCCeEEEEEEEC
Confidence 999999999999999999999999999999999999998775
No 4
>KOG3267 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7.8e-43 Score=285.92 Aligned_cols=137 Identities=58% Similarity=1.012 Sum_probs=128.3
Q ss_pred EEEEEecCCCCeEEeCcHHHHHHHhhhhcCCccceEEEEeccceEEEEEeccCCcchHHHHHHHHhhhCCCCCCCCceeC
Q 025199 65 QKTVTLPPLRRGCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHT 144 (256)
Q Consensus 65 q~tItV~T~grg~~DIT~eV~~~V~~~~SgIknGlv~Vfv~HTTAsLtInEnaDP~v~~DL~~~LerLVP~~~~~~Y~H~ 144 (256)
|++|++...++|||.||+++.+.++++++.+..|++++|.+||+|+|+||||+||+++.|++.+|+|+||++.+.+|+|+
T Consensus 1 qk~itl~~~~kg~~iit~~ilkeir~dl~~fn~g~~~~fiqhtsaaltinen~d~d~qad~~~~ldkivpe~nsa~~rht 80 (138)
T KOG3267|consen 1 QKIITLDPLRKGCHIITNDILKEIREDLKDFNCGLAHFFIQHTSAALTINENWDADTQADMEDFLDKIVPEGNSAGWRHT 80 (138)
T ss_pred CceEecCcccCccEEecHHHHHHHHHHHhhccccceeeeeeccceeeEecccCCcchhhhHHHHHHhhCcCCCCcccccc
Confidence 57899998889999999999999988889999999999999999999999999999999999999999999877789999
Q ss_pred ccCCCCchhhhhhhccCceEEEEeeCCeecccCcceEEEEecCCCCceEEEEEEeec
Q 025199 145 LEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRVKELHGCMLLL 201 (256)
Q Consensus 145 ~eG~dN~~AHLKSsLlG~SlTVPV~dGkL~LGTWQgIyL~EfDgpR~RkV~v~~i~~ 201 (256)
.||+||||||+||+|+|+++||||.+|+|.|||||+|+|+||++.++-+.+||-|-|
T Consensus 81 ~eg~ddmpahikssl~g~qltipit~gklslgtwq~i~l~e~r~~p~ar~iv~ti~g 137 (138)
T KOG3267|consen 81 AEGLDDMPAHIKSSLFGCQLTIPITKGKLSLGTWQDIQLAEFRDAPHARRIVCTIIG 137 (138)
T ss_pred ccCcccchhhhhhccccceEEEEeccCeecccccccchhhhhhcCCcccEEEEEEec
Confidence 999999999999999999999999999999999999999999987765556676654
No 5
>COG3292 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=26.22 E-value=32 Score=36.19 Aligned_cols=20 Identities=35% Similarity=0.578 Sum_probs=18.4
Q ss_pred eCCeecccCcceEEEEecCC
Q 025199 169 TDGQLNMGTWQGMFTLTHNG 188 (256)
Q Consensus 169 ~dGkL~LGTWQgIyL~EfDg 188 (256)
..|+|-.|||||||+.|-.|
T Consensus 215 ~qg~LWVGTdqGv~~~e~~G 234 (671)
T COG3292 215 VQGRLWVGTDQGVYLQEAEG 234 (671)
T ss_pred hcCcEEEEeccceEEEchhh
Confidence 47999999999999999887
No 6
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=16.23 E-value=1.2e+02 Score=22.25 Aligned_cols=21 Identities=0% Similarity=0.137 Sum_probs=15.0
Q ss_pred EEEEEeccCCcchHHHHHHHHhh
Q 025199 109 ASLTINENYDSDVRDDTETFLNK 131 (256)
Q Consensus 109 AsLtInEnaDP~v~~DL~~~Ler 131 (256)
-.+++ .+ +|+.+.+++..|.+
T Consensus 3 l~f~l-~~-~pG~L~~vL~~f~~ 23 (74)
T cd04904 3 LIFSL-KE-EVGALARALKLFEE 23 (74)
T ss_pred EEEEe-CC-CCcHHHHHHHHHHH
Confidence 33444 44 79999999888875
No 7
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=15.63 E-value=97 Score=24.27 Aligned_cols=17 Identities=0% Similarity=0.044 Sum_probs=13.4
Q ss_pred eccCCcchHHHHHHHHhh
Q 025199 114 NENYDSDVRDDTETFLNK 131 (256)
Q Consensus 114 nEnaDP~v~~DL~~~Ler 131 (256)
..+ +|+.+.+++..|.+
T Consensus 21 l~~-~pGsL~~vL~~Fa~ 37 (90)
T cd04931 21 LKE-EVGALAKVLRLFEE 37 (90)
T ss_pred cCC-CCcHHHHHHHHHHH
Confidence 354 79999999888875
No 8
>smart00036 CNH Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. Unpublished observations.
Probab=14.98 E-value=1.4e+02 Score=27.61 Aligned_cols=25 Identities=32% Similarity=0.439 Sum_probs=20.3
Q ss_pred EEEEeeCC--eecccCcceEEEEecCC
Q 025199 164 LTIPITDG--QLNMGTWQGMFTLTHNG 188 (256)
Q Consensus 164 lTVPV~dG--kL~LGTWQgIyL~EfDg 188 (256)
.+.|+..+ .|.+||=+|||+.+.++
T Consensus 5 ~~~~~~~~~~~lL~GTe~Gly~~~~~~ 31 (302)
T smart00036 5 WNHPITCDGKWLLVGTEEGLYVLNISD 31 (302)
T ss_pred EccccccCCcEEEEEeCCceEEEEccc
Confidence 45567655 89999999999999775
No 9
>PF15054 DUF4535: Domain of unknown function (DUF4535)
Probab=14.94 E-value=4e+02 Score=19.01 Aligned_cols=30 Identities=27% Similarity=0.319 Sum_probs=21.6
Q ss_pred EEEEeccceEEEEEeccCC-cchHHHHHHHH
Q 025199 100 AHLFLLHTSASLTINENYD-SDVRDDTETFL 129 (256)
Q Consensus 100 v~Vfv~HTTAsLtInEnaD-P~v~~DL~~~L 129 (256)
+.-|..+|-++|.+.-|++ |++.+=+.+.+
T Consensus 3 ~fsF~~G~~~GiY~AQNY~VPnv~kl~~~~~ 33 (46)
T PF15054_consen 3 LFSFGAGTYTGIYVAQNYEVPNVKKLAETGL 33 (46)
T ss_pred eEEEeeccEEEEEeeecccCCchHHHHHHHH
Confidence 4568889999999988876 77755344333
No 10
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=14.61 E-value=1e+02 Score=21.87 Aligned_cols=18 Identities=22% Similarity=0.270 Sum_probs=14.9
Q ss_pred CCeecccCcceEEEEecC
Q 025199 170 DGQLNMGTWQGMFTLTHN 187 (256)
Q Consensus 170 dGkL~LGTWQgIyL~EfD 187 (256)
+|.+.|.+||+|+|...+
T Consensus 38 ~~~irlT~~Q~l~l~~v~ 55 (69)
T PF03460_consen 38 DGEIRLTTRQNLQLRGVP 55 (69)
T ss_dssp TSEEEEETTSCEEEEEEE
T ss_pred CCeEEECCCCeEEEeCCC
Confidence 578999999999987654
Done!