Query 027887
Match_columns 217
No_of_seqs 159 out of 1115
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 02:58:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027887.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027887hhsearch_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 2.1E-55 4.5E-60 359.2 16.0 135 61-201 1-137 (137)
2 TIGR00149 TIGR00149_YbjQ secon 100.0 1.2E-51 2.6E-56 334.9 15.6 129 67-201 2-131 (132)
3 PF01894 UPF0047: Uncharacteri 100.0 6.8E-51 1.5E-55 324.9 12.9 117 78-198 1-117 (118)
4 KOG3267 Uncharacterized conser 100.0 1.2E-44 2.6E-49 289.2 10.4 136 65-201 1-137 (138)
5 COG3292 Predicted periplasmic 33.7 22 0.00047 36.4 1.4 20 169-188 215-234 (671)
6 smart00305 HintC Hint (Hedgeho 25.8 1.1E+02 0.0023 20.1 3.3 37 178-216 6-42 (46)
7 cd04904 ACT_AAAH ACT domain of 22.2 55 0.0012 23.4 1.4 13 177-189 40-52 (74)
8 PF03460 NIR_SIR_ferr: Nitrite 20.5 69 0.0015 22.2 1.6 18 170-187 38-55 (69)
9 cd04931 ACT_PAH ACT domain of 18.9 73 0.0016 24.3 1.6 13 177-189 54-66 (90)
10 PF15054 DUF4535: Domain of un 17.7 3.1E+02 0.0066 18.9 4.2 31 100-130 3-34 (46)
No 1
>COG0432 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.1e-55 Score=359.21 Aligned_cols=135 Identities=41% Similarity=0.687 Sum_probs=128.6
Q ss_pred CeEEEEEEEecCCCC-eEEeCcHHHHHHHHhhccCcccceEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCC
Q 027887 61 PRWAQKTVTLPPLRR-GCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSA 139 (217)
Q Consensus 61 m~~~q~titv~T~~r-~~~dIT~eV~~~V~~~~SgIk~Giv~Vfv~HTTAsLtInEn~DP~v~~Dl~~~L~rLvP~~~~~ 139 (217)
|+|+|++|+|+|++| +++|||++|+++|++ ||+++|+|+||++||||||+||| +||+|++||+++|++|+|++.
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 899999999999987 999999999999998 99999999999999999999999 699999999999999999985
Q ss_pred CceeCccCCCCcchhhhhhccCceEEEEEeCCeeeccCcceEEEEecCCCCc-eEEEEEEeec
Q 027887 140 SWKHTLEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRV-KELHGCMLLL 201 (217)
Q Consensus 140 ~Y~H~~eG~dN~~AHlKssLlG~SltIPV~dGkL~LGtWQgIyl~EfDgpr~-R~v~v~~~~g 201 (217)
.|+|+.+|+|||+|||||+|+|+|++|||.||+|.|||||+|||+||||||+ |+|++. ++|
T Consensus 76 ~Y~H~~~~~Dn~~aHlkasllG~S~~iPv~~GrL~LGTWQ~I~~~E~dg~r~~R~v~v~-i~g 137 (137)
T COG0432 76 GYRHDEEGPDNAPAHLKASLLGPSLTIPVINGRLVLGTWQGIFLVEFDGPRHRRRVVVK-IIG 137 (137)
T ss_pred CcccccCCCCchHHHHHHHhcCceEEEEEeCCeEceecccEEEEEEecCCCCccEEEEE-EcC
Confidence 5999999999999999999999999999999999999999999999999998 888654 354
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-51 Score=334.88 Aligned_cols=129 Identities=38% Similarity=0.631 Sum_probs=120.3
Q ss_pred EEEecCCC-CeEEeCcHHHHHHHHhhccCcccceEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCCCceeCc
Q 027887 67 TVTLPPLR-RGCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHTL 145 (217)
Q Consensus 67 titv~T~~-r~~~dIT~eV~~~V~~~~SgIk~Giv~Vfv~HTTAsLtInEn~DP~v~~Dl~~~L~rLvP~~~~~~Y~H~~ 145 (217)
+|++.|.+ ++++|||++|+++|++ ||+++|+|+||++||||||++|||+||+++.||+++|+||+|++. .|+|+
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 59998
Q ss_pred cCCCCcchhhhhhccCceEEEEEeCCeeeccCcceEEEEecCCCCceEEEEEEeec
Q 027887 146 EGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRVKELHGCMLLL 201 (217)
Q Consensus 146 eG~dN~~AHlKssLlG~SltIPV~dGkL~LGtWQgIyl~EfDgpr~R~v~v~~~~g 201 (217)
+++|||+||+||+|+|+|++|||.||+|.||+||+||||||||||+|+|+ ++++|
T Consensus 77 ~~~~n~~aHlka~L~G~s~tipi~dG~L~LGtwQ~I~l~E~Dg~r~R~v~-v~i~G 131 (132)
T TIGR00149 77 EGDDNMDAHIKSSLLGTSQHVPVENGRLQLGTWQGIFFAEFDGPRTRRII-VKVQG 131 (132)
T ss_pred CCCCCHHHHHHHHhcCccEEEEEeCCEEcccCccEEEEEECCCCCCcEEE-EEEEe
Confidence 88999999999999999999999999999999999999999999999965 55566
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=6.8e-51 Score=324.94 Aligned_cols=117 Identities=43% Similarity=0.765 Sum_probs=103.2
Q ss_pred EeCcHHHHHHHHhhccCcccceEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCCCceeCccCCCCcchhhhh
Q 027887 78 HLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHTLEGPDDMPAHIKS 157 (217)
Q Consensus 78 ~dIT~eV~~~V~~~~SgIk~Giv~Vfv~HTTAsLtInEn~DP~v~~Dl~~~L~rLvP~~~~~~Y~H~~eG~dN~~AHlKs 157 (217)
||||++|+++|++ ||+++|+|+||++||||||++|||+||++++||+++|+||+|++. .|+|+.+|++||+||+||
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 7999999999998 999999999999999999999999999999999999999999984 799999999999999999
Q ss_pred hccCceEEEEEeCCeeeccCcceEEEEecCCCCceEEEEEE
Q 027887 158 SMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRVKELHGCM 198 (217)
Q Consensus 158 sLlG~SltIPV~dGkL~LGtWQgIyl~EfDgpr~R~v~v~~ 198 (217)
+|+|+|++|||.||+|+||+||+|||+||||||+|+|++..
T Consensus 77 ~l~G~S~~vpv~~G~L~LGtwQ~I~l~E~dgpr~R~v~v~i 117 (118)
T PF01894_consen 77 SLIGPSLTVPVHDGKLALGTWQGIYLVEFDGPRERTVVVQI 117 (118)
T ss_dssp HHH-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEEE
T ss_pred HhcCCeEEEEEECCEEccCCcCEEEEEECCCCCeEEEEEEE
Confidence 99999999999999999999999999999999999998653
No 4
>KOG3267 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.2e-44 Score=289.17 Aligned_cols=136 Identities=59% Similarity=1.045 Sum_probs=128.3
Q ss_pred EEEEEecCCCCeEEeCcHHHHHHHHhhccCcccceEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCCCceeC
Q 027887 65 QKTVTLPPLRRGCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHT 144 (217)
Q Consensus 65 q~titv~T~~r~~~dIT~eV~~~V~~~~SgIk~Giv~Vfv~HTTAsLtInEn~DP~v~~Dl~~~L~rLvP~~~~~~Y~H~ 144 (217)
|++|++...++|||.||+++.+.++++++.+..|++++|.+||+|+|+|||||||+++.|++.+|+|+||++.+.+|+|+
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 67899998889999999999999988889999999999999999999999999999999999999999999977799999
Q ss_pred ccCCCCcchhhhhhccCceEEEEEeCCeeeccCcceEEEEecCCCCc-eEEEEEEeec
Q 027887 145 LEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGMFTLTHNGLRV-KELHGCMLLL 201 (217)
Q Consensus 145 ~eG~dN~~AHlKssLlG~SltIPV~dGkL~LGtWQgIyl~EfDgpr~-R~v~v~~~~g 201 (217)
.||+||||||+||+|+|+++||||.+|||.|||||+|+|+|||+.++ |+| ||-++|
T Consensus 81 ~eg~ddmpahikssl~g~qltipit~gklslgtwq~i~l~e~r~~p~ar~i-v~ti~g 137 (138)
T KOG3267|consen 81 AEGLDDMPAHIKSSLFGCQLTIPITKGKLSLGTWQDIQLAEFRDAPHARRI-VCTIIG 137 (138)
T ss_pred ccCcccchhhhhhccccceEEEEeccCeecccccccchhhhhhcCCcccEE-EEEEec
Confidence 99999999999999999999999999999999999999999997665 666 687776
No 5
>COG3292 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=33.72 E-value=22 Score=36.43 Aligned_cols=20 Identities=35% Similarity=0.578 Sum_probs=18.4
Q ss_pred eCCeeeccCcceEEEEecCC
Q 027887 169 TDGQLNMGTWQGMFTLTHNG 188 (217)
Q Consensus 169 ~dGkL~LGtWQgIyl~EfDg 188 (217)
.+|+|-.|||||||+.|-.|
T Consensus 215 ~qg~LWVGTdqGv~~~e~~G 234 (671)
T COG3292 215 VQGRLWVGTDQGVYLQEAEG 234 (671)
T ss_pred hcCcEEEEeccceEEEchhh
Confidence 47999999999999999887
No 6
>smart00305 HintC Hint (Hedgehog/Intein) domain C-terminal region. Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=25.78 E-value=1.1e+02 Score=20.07 Aligned_cols=37 Identities=8% Similarity=0.169 Sum_probs=21.5
Q ss_pred cceEEEEecCCCCceEEEEEEeeccccccccceeecccc
Q 027887 178 WQGMFTLTHNGLRVKELHGCMLLLTSLLTSADCVLHNCL 216 (217)
Q Consensus 178 WQgIyl~EfDgpr~R~v~v~~~~g~~~~~~~~~~~~~~~ 216 (217)
|..|.=+|..+.+ .++=..+-++--...-+.++|||.
T Consensus 6 ~~~V~~i~~~~~~--~vYd~~v~~~~~fv~ngi~~hN~~ 42 (46)
T smart00305 6 FVRVKSIEETEYT--GVYDPTVTENHNFIANGILVHNCA 42 (46)
T ss_pred EEEEEEEEEeCCc--cEEeeEeCCCCeEEECCEEEEeee
Confidence 5556666655443 555443455443333688999994
No 7
>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=22.24 E-value=55 Score=23.37 Aligned_cols=13 Identities=8% Similarity=-0.248 Sum_probs=11.6
Q ss_pred CcceEEEEecCCC
Q 027887 177 TWQGMFTLTHNGL 189 (217)
Q Consensus 177 tWQgIyl~EfDgp 189 (217)
.|+.+||+|+++.
T Consensus 40 ~~~y~Ffvd~~~~ 52 (74)
T cd04904 40 GSEYEFFVDCEVD 52 (74)
T ss_pred CceEEEEEEEEcC
Confidence 5999999999983
No 8
>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=20.49 E-value=69 Score=22.18 Aligned_cols=18 Identities=22% Similarity=0.270 Sum_probs=15.0
Q ss_pred CCeeeccCcceEEEEecC
Q 027887 170 DGQLNMGTWQGMFTLTHN 187 (217)
Q Consensus 170 dGkL~LGtWQgIyl~EfD 187 (217)
+|.+.|.+||+|+|...+
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
No 9
>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=18.91 E-value=73 Score=24.25 Aligned_cols=13 Identities=8% Similarity=-0.105 Sum_probs=11.6
Q ss_pred CcceEEEEecCCC
Q 027887 177 TWQGMFTLTHNGL 189 (217)
Q Consensus 177 tWQgIyl~EfDgp 189 (217)
.||.+||+|+++.
T Consensus 54 ~~~Y~FfVDieg~ 66 (90)
T cd04931 54 KDEYEFFINLDKK 66 (90)
T ss_pred CceEEEEEEEEcC
Confidence 4999999999975
No 10
>PF15054 DUF4535: Domain of unknown function (DUF4535)
Probab=17.71 E-value=3.1e+02 Score=18.94 Aligned_cols=31 Identities=26% Similarity=0.333 Sum_probs=22.3
Q ss_pred EEEEecccceEEEEeecCC-chhHHHHHHHHh
Q 027887 100 AHLFLLHTSASLTINENYD-SDVRDDTETFLN 130 (217)
Q Consensus 100 v~Vfv~HTTAsLtInEn~D-P~v~~Dl~~~L~ 130 (217)
+.-|..+|-++|.+.-|++ |.+.+=++++++
T Consensus 3 ~fsF~~G~~~GiY~AQNY~VPnv~kl~~~~~~ 34 (46)
T PF15054_consen 3 LFSFGAGTYTGIYVAQNYEVPNVKKLAETGLD 34 (46)
T ss_pred eEEEeeccEEEEEeeecccCCchHHHHHHHHH
Confidence 4568889999999988877 777554444443
Done!