Query 028374
Match_columns 210
No_of_seqs 162 out of 1132
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 10:31:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028374.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028374hhsearch_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 2.8E-56 6.1E-61 362.1 16.8 135 61-209 1-137 (137)
2 TIGR00149 TIGR00149_YbjQ secon 100.0 1.8E-53 3.8E-58 343.9 16.2 130 67-210 2-132 (132)
3 PF01894 UPF0047: Uncharacteri 100.0 1.5E-51 3.2E-56 327.1 13.0 118 78-208 1-118 (118)
4 KOG3267 Uncharacterized conser 100.0 2E-47 4.2E-52 302.8 11.1 138 65-210 1-138 (138)
5 COG3292 Predicted periplasmic 26.3 33 0.00072 34.9 1.2 19 177-195 215-233 (671)
6 PF03460 NIR_SIR_ferr: Nitrite 17.9 91 0.002 21.4 1.8 17 178-194 38-54 (69)
7 PF14438 SM-ATX: Ataxin 2 SM d 16.7 1.5E+02 0.0033 21.1 2.8 28 161-192 4-31 (77)
8 cd07999 GH7_CBH_EG Glycosyl hy 16.1 1.6E+02 0.0034 28.5 3.3 36 166-201 114-150 (386)
9 PF11743 DUF3301: Protein of u 15.6 1.9E+02 0.0041 22.1 3.2 29 178-209 57-86 (97)
10 PF00688 TGFb_propeptide: TGF- 15.5 2.4E+02 0.0052 23.2 4.0 40 62-103 162-201 (238)
No 1
>COG0432 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.8e-56 Score=362.08 Aligned_cols=135 Identities=44% Similarity=0.750 Sum_probs=129.7
Q ss_pred CeEEEEEEEecCCCC-eEEeccHHHHHHHHhhccCcccceEEEEecccceEEEEeccCCchhHHHHHHHHHHhCCCcccc
Q 028374 61 PRWAQKTVTLPPLRR-GCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPELYFV 139 (210)
Q Consensus 61 m~~~~~titv~T~~r-g~~dIT~eV~~~V~~~~SgI~~Glv~Vf~~HTTAsLtInEn~Dp~v~~Dl~~~L~rLvP~~~~~ 139 (210)
|.|+|++|+|+|++| +++|||++|+++|++ |||++|+|+||++||||||+||| +||+|++||+++|++++|+
T Consensus 1 m~~~~~~l~v~T~~r~~~vdIT~ev~~~v~e--sgv~~Gl~~vf~~HtTaal~inE-~ep~l~~Di~~~l~~lvP~---- 73 (137)
T COG0432 1 MKVYQKELTVSTKRRIEFVDITDEVEKFVRE--SGVKNGLLLVFVPHTTAALTINE-AEPGLKEDIERFLEKLVPE---- 73 (137)
T ss_pred CceEEEEEEEeccCccceEEchHHHHHHHHH--cCCccceEEEEecCcceEEEEec-CCCcHHHHHHHHHHHhCCC----
Confidence 789999999999999 999999999999999 99999999999999999999999 7999999999999999999
Q ss_pred ccccCCCCCCCCCCCCCCCchhhhhhhccCceEEEEEeCCeeecCCcceEEEEEecCCCCC-eEEEEEEec
Q 028374 140 SLLQGRSASWKHTLEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTP-RKVVITLNG 209 (210)
Q Consensus 140 ~~~~~~~~~Y~H~~eG~dn~~AHIKssL~G~SltIPV~dGkL~LGtWQ~I~l~E~~dgpr~-R~V~v~v~G 209 (210)
+..|+|+.+|+|||+|||||+|+|+|++|||.||+|.|||||+|||+||| +||. |+|+++++|
T Consensus 74 ------~~~Y~H~~~~~Dn~~aHlkasllG~S~~iPv~~GrL~LGTWQ~I~~~E~d-g~r~~R~v~v~i~g 137 (137)
T COG0432 74 ------GAGYRHDEEGPDNAPAHLKASLLGPSLTIPVINGRLVLGTWQGIFLVEFD-GPRHRRRVVVKIIG 137 (137)
T ss_pred ------CCCcccccCCCCchHHHHHHHhcCceEEEEEeCCeEceecccEEEEEEec-CCCCccEEEEEEcC
Confidence 56799999999999999999999999999999999999999999999995 5555 999999987
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=1.8e-53 Score=343.93 Aligned_cols=130 Identities=41% Similarity=0.736 Sum_probs=123.1
Q ss_pred EEEecCCCC-eEEeccHHHHHHHHhhccCcccceEEEEecccceEEEEeccCCchhHHHHHHHHHHhCCCccccccccCC
Q 028374 67 TVTLPPLRR-GCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPELYFVSLLQGR 145 (210)
Q Consensus 67 titv~T~~r-g~~dIT~eV~~~V~~~~SgI~~Glv~Vf~~HTTAsLtInEn~Dp~v~~Dl~~~L~rLvP~~~~~~~~~~~ 145 (210)
++++.|.++ +++|||++|+++|++ ||+++|+|+||++||||||++|||+||+|+.||+++|+||||+
T Consensus 2 ~~~~~t~~~~~~~dIT~~V~~~v~~--s~i~~G~~~v~~~HTTa~l~inE~~dp~l~~Dl~~~l~~lvP~---------- 69 (132)
T TIGR00149 2 ELLLKTTKRVELIDITSEIEAVLQS--SGVKDGLLLVYVPHTTASLTINENADPDVLHDIERFFERLVPD---------- 69 (132)
T ss_pred EEEEEcCCCCeEEEChHHHHHHHHH--cCCcccEEEEEeCCCcEEEEEecCCCccHHHHHHHHHHHHCCC----------
Confidence 467777655 999999999999999 9999999999999999999999999999999999999999998
Q ss_pred CCCCCCCCCCCCCchhhhhhhccCceEEEEEeCCeeecCCcceEEEEEecCCCCCeEEEEEEecC
Q 028374 146 SASWKHTLEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTPRKVVITLNGI 210 (210)
Q Consensus 146 ~~~Y~H~~eG~dn~~AHIKssL~G~SltIPV~dGkL~LGtWQ~I~l~E~~dgpr~R~V~v~v~Ge 210 (210)
+..|+|+ +++|||+|||||+|+|+|++|||.||+|.||+||+|||||| |+||+|+|+|+++||
T Consensus 70 ~~~y~H~-~~~~n~~aHlka~L~G~s~tipi~dG~L~LGtwQ~I~l~E~-Dg~r~R~v~v~i~Ge 132 (132)
T TIGR00149 70 DGNYEHD-EGDDNMDAHIKSSLLGTSQHVPVENGRLQLGTWQGIFFAEF-DGPRTRRIIVKVQGE 132 (132)
T ss_pred CCCcccc-CCCCCHHHHHHHHhcCccEEEEEeCCEEcccCccEEEEEEC-CCCCCcEEEEEEEeC
Confidence 4569998 88999999999999999999999999999999999999999 699999999999997
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=1.5e-51 Score=327.13 Aligned_cols=118 Identities=47% Similarity=0.834 Sum_probs=105.0
Q ss_pred EeccHHHHHHHHhhccCcccceEEEEecccceEEEEeccCCchhHHHHHHHHHHhCCCccccccccCCCCCCCCCCCCCC
Q 028374 78 HLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPELYFVSLLQGRSASWKHTLEGPD 157 (210)
Q Consensus 78 ~dIT~eV~~~V~~~~SgI~~Glv~Vf~~HTTAsLtInEn~Dp~v~~Dl~~~L~rLvP~~~~~~~~~~~~~~Y~H~~eG~d 157 (210)
+|||++|+++|++ ||+++|+|+||++||||||+||||+||+|++||+++|+||||+ +..|+|+.+|++
T Consensus 1 idIT~~V~~~v~~--s~i~~Gl~~v~~~HTTaal~inE~~dp~v~~Dl~~~l~~lvP~----------~~~y~H~~~~~~ 68 (118)
T PF01894_consen 1 IDITEEVREAVEE--SGIRNGLVHVFVPHTTAALTINENADPDVRRDLLEALERLVPE----------DDPYRHNEEGPD 68 (118)
T ss_dssp EE-HHHHHHHHHH--HT-SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHS-T----------TST-GGGCTT-S
T ss_pred CcchHHHHHHHHH--hCCcceEEEEEeCCCeEEEEEeecCChhHHHhHHHHHHHhCCC----------CCceEeCCcccc
Confidence 7999999999999 9999999999999999999999999999999999999999999 568999999999
Q ss_pred CchhhhhhhccCceEEEEEeCCeeecCCcceEEEEEecCCCCCeEEEEEEe
Q 028374 158 DMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTPRKVVITLN 208 (210)
Q Consensus 158 n~~AHIKssL~G~SltIPV~dGkL~LGtWQ~I~l~E~~dgpr~R~V~v~v~ 208 (210)
||+||+||+|+|+|++|||.||+|.||+||+|||||| ||||+|+|+|+||
T Consensus 69 n~~aHlks~l~G~S~~vpv~~G~L~LGtwQ~I~l~E~-dgpr~R~v~v~i~ 118 (118)
T PF01894_consen 69 NAPAHLKSSLIGPSLTVPVHDGKLALGTWQGIYLVEF-DGPRERTVVVQIM 118 (118)
T ss_dssp THHHHHHHHHH-SEEEEEEETTEE---TTEEEEEEES-S-SSEEEEEEEEE
T ss_pred CccHHHHHHhcCCeEEEEEECCEEccCCcCEEEEEEC-CCCCeEEEEEEEC
Confidence 9999999999999999999999999999999999999 5699999999986
No 4
>KOG3267 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2e-47 Score=302.79 Aligned_cols=138 Identities=66% Similarity=1.141 Sum_probs=133.3
Q ss_pred EEEEEecCCCCeEEeccHHHHHHHHhhccCcccceEEEEecccceEEEEeccCCchhHHHHHHHHHHhCCCccccccccC
Q 028374 65 QKTVTLPPLRRGCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPELYFVSLLQG 144 (210)
Q Consensus 65 ~~titv~T~~rg~~dIT~eV~~~V~~~~SgI~~Glv~Vf~~HTTAsLtInEn~Dp~v~~Dl~~~L~rLvP~~~~~~~~~~ 144 (210)
|++|++...++|||.||+++.+.++++++....|++|+|.+||+|+|+||||+||+++.|++.+|+|+||+ +
T Consensus 1 qk~itl~~~~kg~~iit~~ilkeir~dl~~fn~g~~~~fiqhtsaaltinen~d~d~qad~~~~ldkivpe--------~ 72 (138)
T KOG3267|consen 1 QKIITLDPLRKGCHIITNDILKEIREDLKDFNCGLAHFFIQHTSAALTINENWDADTQADMEDFLDKIVPE--------G 72 (138)
T ss_pred CceEecCcccCccEEecHHHHHHHHHHHhhccccceeeeeeccceeeEecccCCcchhhhHHHHHHhhCcC--------C
Confidence 57899999899999999999999988889999999999999999999999999999999999999999999 5
Q ss_pred CCCCCCCCCCCCCCchhhhhhhccCceEEEEEeCCeeecCCcceEEEEEecCCCCCeEEEEEEecC
Q 028374 145 RSASWKHTLEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTPRKVVITLNGI 210 (210)
Q Consensus 145 ~~~~Y~H~~eG~dn~~AHIKssL~G~SltIPV~dGkL~LGtWQ~I~l~E~~dgpr~R~V~v~v~Ge 210 (210)
+..+|+|..||+||||||+||+|+|+++||||.+|||.|||||+|+|+|||+.|+.|+|+++++|.
T Consensus 73 nsa~~rht~eg~ddmpahikssl~g~qltipit~gklslgtwq~i~l~e~r~~p~ar~iv~ti~gi 138 (138)
T KOG3267|consen 73 NSAGWRHTAEGLDDMPAHIKSSLFGCQLTIPITKGKLSLGTWQDIQLAEFRDAPHARRIVCTIIGI 138 (138)
T ss_pred CCccccccccCcccchhhhhhccccceEEEEeccCeecccccccchhhhhhcCCcccEEEEEEecC
Confidence 568999999999999999999999999999999999999999999999999999999999999984
No 5
>COG3292 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=26.28 E-value=33 Score=34.93 Aligned_cols=19 Identities=42% Similarity=0.636 Sum_probs=16.8
Q ss_pred eCCeeecCCcceEEEEEec
Q 028374 177 TDGQLNMGTWQGIWLCEHR 195 (210)
Q Consensus 177 ~dGkL~LGtWQ~I~l~E~~ 195 (210)
.+|+|-.|||||||+.|-+
T Consensus 215 ~qg~LWVGTdqGv~~~e~~ 233 (671)
T COG3292 215 VQGRLWVGTDQGVYLQEAE 233 (671)
T ss_pred hcCcEEEEeccceEEEchh
Confidence 3799999999999999963
No 6
>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=17.93 E-value=91 Score=21.41 Aligned_cols=17 Identities=29% Similarity=0.411 Sum_probs=14.5
Q ss_pred CCeeecCCcceEEEEEe
Q 028374 178 DGQLNMGTWQGIWLCEH 194 (210)
Q Consensus 178 dGkL~LGtWQ~I~l~E~ 194 (210)
+|.+.|.+||+|+|...
T Consensus 38 ~~~irlT~~Q~l~l~~v 54 (69)
T PF03460_consen 38 DGEIRLTTRQNLQLRGV 54 (69)
T ss_dssp TSEEEEETTSCEEEEEE
T ss_pred CCeEEECCCCeEEEeCC
Confidence 58899999999998765
No 7
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=16.68 E-value=1.5e+02 Score=21.08 Aligned_cols=28 Identities=18% Similarity=0.525 Sum_probs=22.7
Q ss_pred hhhhhhccCceEEEEEeCCeeecCCcceEEEE
Q 028374 161 AHIKSSMFGCTLTIPITDGQLNMGTWQGIWLC 192 (210)
Q Consensus 161 AHIKssL~G~SltIPV~dGkL~LGtWQ~I~l~ 192 (210)
-|+-+.|+|..+.|=+.||.. ++|||-.
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~----yeGif~s 31 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSV----YEGIFHS 31 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-E----EEEEEEE
T ss_pred HHHHHhCcCCEEEEEECCCCE----EEEEEEe
Confidence 478899999999999999986 6777643
No 8
>cd07999 GH7_CBH_EG Glycosyl hydrolase family 7. Glycosyl hydrolase family 7 contains eukaryotic endoglucanases (EGs) and cellobiohydrolases (CBHs) that hydrolyze glycosidic bonds using a double-displacement mechanism. This leads to a net retention of the conformation at the anomeric carbon. Both enzymes work synergistically in the degradation of cellulose,which is the main component of plant cell wall, and is composed of beta-1,4 linked glycosyl units. EG cleaves the beta-1,4 linkages of cellulose and CBH cleaves off cellobiose disaccharide units from the reducing end of the chain. In general, the O-glycosyl hydrolases are a widespread group of enzymes that hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycoside hydrolase family 7.
Probab=16.13 E-value=1.6e+02 Score=28.54 Aligned_cols=36 Identities=19% Similarity=0.355 Sum_probs=31.8
Q ss_pred hccCceEEEEEeCCeeecCCcceEEEEEec-CCCCCe
Q 028374 166 SMFGCTLTIPITDGQLNMGTWQGIWLCEHR-DAPTPR 201 (210)
Q Consensus 166 sL~G~SltIPV~dGkL~LGtWQ~I~l~E~~-dgpr~R 201 (210)
.|+|..+|+=|.-.+|-.|---.+||+|.+ ||.+.|
T Consensus 114 ~Llg~EftFDVD~S~LpCGlNgALYfveMdadGg~s~ 150 (386)
T cd07999 114 KLLGQEFTFDVDMSNLPCGMNGALYLSEMDADGGMSK 150 (386)
T ss_pred EecCCeeEEEeecccCCccccceeeeeeecCCCCccc
Confidence 589999999999999999999999999997 565544
No 9
>PF11743 DUF3301: Protein of unknown function (DUF3301); InterPro: IPR021732 This family is conserved in Proteobacteria, but the function is not known.
Probab=15.63 E-value=1.9e+02 Score=22.11 Aligned_cols=29 Identities=21% Similarity=0.483 Sum_probs=20.3
Q ss_pred CCeeecCCcceEEEEEec-CCCCCeEEEEEEec
Q 028374 178 DGQLNMGTWQGIWLCEHR-DAPTPRKVVITLNG 209 (210)
Q Consensus 178 dGkL~LGtWQ~I~l~E~~-dgpr~R~V~v~v~G 209 (210)
+|++ .|+.+|-+||- +|..+.+=.|...|
T Consensus 57 ~g~~---~~~r~y~FEFS~~G~~ry~G~l~m~G 86 (97)
T PF11743_consen 57 RGRL---RWRRVYQFEFSSDGEDRYQGELVMLG 86 (97)
T ss_pred CCCe---EEEEEEEEEEeCCChhcceEEEEEEC
Confidence 5666 47999999995 66655555555555
No 10
>PF00688 TGFb_propeptide: TGF-beta propeptide; InterPro: IPR001111 The transforming growth factor beta, N terminus (TGFb) domain is present in a variety of proteins which include the transforming growth factor beta, decapentaplegic proteins and bone morphogenetic proteins. Transforming growth factor beta is a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types. The decapentaplegic protein acts as an extracellular morphogen responsible for the proper development of the embryonic dorsal hypoderm, for viability of larvae and for cell viability of the epithelial cells in the imaginal disks. Bone morphogenetic protein induces cartilage and bone formation and may be responsible for epithelial osteogenesis in some organisms.; GO: 0008083 growth factor activity, 0040007 growth; PDB: 3RJR_A.
Probab=15.50 E-value=2.4e+02 Score=23.19 Aligned_cols=40 Identities=15% Similarity=0.044 Sum_probs=22.4
Q ss_pred eEEEEEEEecCCCCeEEeccHHHHHHHHhhccCcccceEEEE
Q 028374 62 RWAQKTVTLPPLRRGCHLITPKIVKEIAQDLSEFKCGLAHLF 103 (210)
Q Consensus 62 ~~~~~titv~T~~rg~~dIT~eV~~~V~~~~SgI~~Glv~Vf 103 (210)
.+..+.+.....+.-..|||..|++|+.. .....|+..-.
T Consensus 162 ~l~s~~v~~~~~gW~~~dvt~~v~~W~~~--~~~n~gl~l~~ 201 (238)
T PF00688_consen 162 LLDSRTVDPSDSGWVSFDVTSAVRRWLRN--PEKNLGLELEV 201 (238)
T ss_dssp EEEEEEE---S--EEEEE-HHHHHHHHH-----S-EEEEEEE
T ss_pred eeeeeeeccccCCceeEhHHHHHHHHHhC--CCCCccEEEEE
Confidence 34555566666677889999999999997 55567866544
Done!