Query 001216
Match_columns 1122
No_of_seqs 30 out of 32
Neff 2.0
Searched_HMMs 46136
Date Thu Mar 28 18:57:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001216hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03465 HpnD squalene syntha 42.3 21 0.00046 37.3 2.9 58 269-326 112-174 (266)
2 PF13406 SLT_2: Transglycosyla 40.8 3.2 6.8E-05 44.9 -3.4 59 159-217 120-182 (262)
3 PF13986 DUF4224: Domain of un 35.2 13 0.00028 31.3 0.0 27 1-27 1-27 (47)
4 cd00683 Trans_IPPS_HH Trans-Is 35.0 38 0.00083 35.2 3.4 59 268-326 119-183 (265)
5 PF06685 DUF1186: Protein of u 29.9 1.2E+02 0.0025 33.2 6.1 60 293-359 19-87 (249)
6 PF13410 GST_C_2: Glutathione 29.5 1.4E+02 0.003 24.4 5.2 44 650-695 2-45 (69)
7 PF02985 HEAT: HEAT repeat; I 24.5 29 0.00062 25.9 0.3 27 1026-1052 2-28 (31)
8 TIGR02282 MltB lytic murein tr 21.9 16 0.00034 40.5 -2.1 53 162-214 119-175 (290)
9 PRK04998 hypothetical protein; 19.6 73 0.0016 29.4 1.9 30 482-511 28-59 (88)
10 PRK00907 hypothetical protein; 18.4 84 0.0018 29.9 2.1 31 481-511 29-63 (92)
No 1
>TIGR03465 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.
Probab=42.33 E-value=21 Score=37.29 Aligned_cols=58 Identities=28% Similarity=0.367 Sum_probs=43.1
Q ss_pred hhccCchhhHHHHhhhccCCCCCC---ChhHHHHHHHHHHHHH-hhhhhhc-cCCCcchhhHH
Q 001216 269 YAFATPSATQRLLLGLLEAPPSWA---PDALDAAVQLVELLRA-AEEYATG-IKLPRNWMHLH 326 (1122)
Q Consensus 269 YaiAtPsATQRLLlGLLEAPpSWA---PDALDAAVQLVELLRA-AEdYasg-~rLPrNWmhlH 326 (1122)
|+=.|-++.-++++.++..+...+ -++|=.|.||+.+||. .||...| +-||+.||.-|
T Consensus 112 Y~~~vAg~vg~l~~~llg~~~~~~~~~a~~lG~AlqltnilRdv~eD~~~gR~ylP~~~l~~~ 174 (266)
T TIGR03465 112 YCDRVAGAVGRLSARIFGATDARTLEYAHHLGRALQLTNILRDVGEDARRGRIYLPAEELQRF 174 (266)
T ss_pred HHHHhHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHhHHHHhCCCeecCHHHHHHc
Confidence 455666778889999987554332 1245668999999998 8999877 67999998655
No 2
>PF13406 SLT_2: Transglycosylase SLT domain; PDB: 1LTM_A 1D0L_A 1QDT_A 1D0K_A 1D0M_A 1QDR_A 1QUT_A 1QUS_A 4ANR_A.
Probab=40.79 E-value=3.2 Score=44.86 Aligned_cols=59 Identities=34% Similarity=0.310 Sum_probs=32.6
Q ss_pred cccccccccccccccccccc-CCCCCCc-cccCCCCCCCCCcccCCCc-cee-ecCCeeEEee
Q 001216 159 LGIRSDYFRWCSGVMGKYAA-GELKPPT-IASSRGSGKHPQLMLSTPR-WAV-ANGAGVILSV 217 (1122)
Q Consensus 159 lgirsDYFRWC~gVmGKYAa-gelkppt-ta~srgsgKHPQLmpSTPr-WAV-ANGAgVIlSV 217 (1122)
-+-|++|||-----.=+++- |.+.|-+ .+|.-|.=-|||.|||+=+ ++| .||-|.|==.
T Consensus 120 ~~rR~~~f~~EL~a~L~~~~~~~~~~~~l~GS~AGAmG~~QFmPSs~~~yavD~dgDG~~Dl~ 182 (262)
T PF13406_consen 120 DYRRADFFRKELIAALKIADRGGIDPETLKGSWAGAMGQPQFMPSSYLKYAVDGDGDGRIDLW 182 (262)
T ss_dssp C-GGHHHHHHHHHHHHHHHHHCT--CCC-EE-TT--BTTTTB-HHHHHHH---TTSSS---TT
T ss_pred cccHHHHHHHHHHHHHHHHHcCCCChhhcCCCcccCcCCCCcCHHHHHHhCcCCCCCCCcCCC
Confidence 34677887654333333444 6677766 5688888899999999976 999 8999988433
No 3
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=35.18 E-value=13 Score=31.29 Aligned_cols=27 Identities=26% Similarity=0.217 Sum_probs=25.3
Q ss_pred CchhHHHHHHHHHhhCCCCccchhhhh
Q 001216 1 MLLTRYILVQLIRSHYPHKERRLFDDV 27 (1122)
Q Consensus 1 ~~~~~~~iaeli~~~yPske~~l~ddv 27 (1122)
|+||++||.||..-.+|+++.+-|+.-
T Consensus 1 ~fLT~~El~elTG~k~~~~Q~~~L~~~ 27 (47)
T PF13986_consen 1 EFLTDEELQELTGYKRPSKQIRWLRRN 27 (47)
T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHC
Confidence 789999999999999999999999984
No 4
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes
Probab=35.00 E-value=38 Score=35.21 Aligned_cols=59 Identities=31% Similarity=0.417 Sum_probs=42.1
Q ss_pred hhhccCchhhHHHHhhhccC-CCCCCCh---hHHHHHHHHHHHHH-hhhhhhc-cCCCcchhhHH
Q 001216 268 YYAFATPSATQRLLLGLLEA-PPSWAPD---ALDAAVQLVELLRA-AEEYATG-IKLPRNWMHLH 326 (1122)
Q Consensus 268 YYaiAtPsATQRLLlGLLEA-PpSWAPD---ALDAAVQLVELLRA-AEdYasg-~rLPrNWmhlH 326 (1122)
.|+-.+-++.-++++-++-. .+.+..+ .|=.|.||+.+||. .||.+.| +-||+.||.-|
T Consensus 119 ~Y~~~vAg~vg~l~~~i~~~~~~~~~~~~A~~lG~AlqltnilRdv~eD~~~gR~YlP~d~l~~~ 183 (265)
T cd00683 119 EYCYYVAGVVGLMLLRVFGASSDEAALERARALGLALQLTNILRDVGEDARRGRIYLPREELARF 183 (265)
T ss_pred HHHHHhHHHHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCcCCHHHHHHc
Confidence 45666667888888888865 2322222 34458999999985 6777766 67999998766
No 5
>PF06685 DUF1186: Protein of unknown function (DUF1186); InterPro: IPR010602 This family consists of several hypothetical bacterial proteins of around 250 residues in length and is found in several Chlamydia and Anabaena species. The function of this family is unknown.
Probab=29.93 E-value=1.2e+02 Score=33.24 Aligned_cols=60 Identities=27% Similarity=0.337 Sum_probs=38.3
Q ss_pred ChhHHHHHH--------HHHHHHHhhhhhhccCCCcch-hhHHHHHHhhhHHhhhhhhHHhHHHHHHHHhhcCCcc
Q 001216 293 PDALDAAVQ--------LVELLRAAEEYATGIKLPRNW-MHLHFLRAIGVAMSMRAGIAADAAAALLFRILSQPAL 359 (1122)
Q Consensus 293 PDALDAAVQ--------LVELLRAAEdYasg~rLPrNW-mhlHFLRaiGtAmsMraGiAaDaAAAllFRilsqpaL 359 (1122)
-+||++|++ |.++|..|.+.+.-.---.+| .|+|-++.+|-... ..|-.+++|+++||--
T Consensus 19 ~~al~~A~~~~e~i~P~Ll~~Le~a~~~~~e~~~~~~~~~~~~a~~LLaq~re-------~~A~~~li~l~~~~~~ 87 (249)
T PF06685_consen 19 REALEAAIEQREEITPELLKILEDAIERANELLDDEEYNLHFYALYLLAQFRE-------ERALPPLIRLFSQDDD 87 (249)
T ss_pred HHHHHHHHHCHHHhhHHHHHHHHHHHHhHHHhccCcchHHHHHHHHHHHHHhh-------hhhHHHHHHHHcCCcc
Confidence 368888886 333444444333222222454 69999999887654 4467889999999854
No 6
>PF13410 GST_C_2: Glutathione S-transferase, C-terminal domain; PDB: 4DEJ_H 3IC8_A 2JL4_A 2V6K_B 3CBU_B 1JLW_B 3F6D_B 3G7I_A 3F63_A 3G7J_B ....
Probab=29.52 E-value=1.4e+02 Score=24.42 Aligned_cols=44 Identities=23% Similarity=0.210 Sum_probs=35.6
Q ss_pred chhHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCChHHHHHHHHHH
Q 001216 650 SSIESAIHHTHRILTILEALFSLKPSSIGTSWGYSSNEIVAAAMVA 695 (1122)
Q Consensus 650 Ngi~SAv~HTrRiL~ILEALfSLKPSSVGTswsYSSNEIVAAAMVA 695 (1122)
..+..+..+.++.|..||..+.=+|.-.|. .+|.=||..+.++.
T Consensus 2 ~~~~~~~~~~~~~l~~le~~L~~~~fl~G~--~~s~aD~~l~~~l~ 45 (69)
T PF13410_consen 2 AAVERARAQLEAALDALEDHLADGPFLFGD--RPSLADIALAPFLW 45 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTSSBTTBS--S--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCCC--CCCHHHHHHHHHHH
Confidence 467889999999999999999999988888 67777887776654
No 7
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=24.54 E-value=29 Score=25.90 Aligned_cols=27 Identities=30% Similarity=0.485 Sum_probs=21.8
Q ss_pred ccceeecccCCchhhhhhhHHHHHHhh
Q 001216 1026 LPATIRCLSHPSAHVRALSTSVLRDFL 1052 (1122)
Q Consensus 1026 LpATvRCLSHpSAhVRAlS~SVLRdIl 1052 (1122)
||..+.+|++|+..||.....-|-+|.
T Consensus 2 lp~l~~~l~D~~~~VR~~a~~~l~~i~ 28 (31)
T PF02985_consen 2 LPILLQLLNDPSPEVRQAAAECLGAIA 28 (31)
T ss_dssp HHHHHHHHT-SSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 466778999999999999888887765
No 8
>TIGR02282 MltB lytic murein transglycosylase B. This family consists of lytic murein transglycosylases (murein hydrolases) in the family of MltB, which is a membrane-bound lipoprotein in Escherichia coli. The N-terminal lipoprotein modification motif is conserved in about half the members of this family. The term Slt35 describes a naturally occurring soluble fragment of MltB. Members of this family never contain the putative peptidoglycan binding domain described by Pfam model pfam01471, which is associated with several classes of bacterial cell wall lytic enzymes.
Probab=21.87 E-value=16 Score=40.48 Aligned_cols=53 Identities=36% Similarity=0.446 Sum_probs=35.5
Q ss_pred ccccccccccccccccc-CCCCCCc-cccCCCCCCCCCcccCCC-cceee-cCCeeE
Q 001216 162 RSDYFRWCSGVMGKYAA-GELKPPT-IASSRGSGKHPQLMLSTP-RWAVA-NGAGVI 214 (1122)
Q Consensus 162 rsDYFRWC~gVmGKYAa-gelkppt-ta~srgsgKHPQLmpSTP-rWAVA-NGAgVI 214 (1122)
|++|||-----.=|... |.+.|-. .+|.-|.=-|||.||||= +++|. ||-|.+
T Consensus 119 R~~ff~~EL~aaL~i~~~~~~~~~~l~GS~aGAmG~~QFmPss~~~yavD~dgDG~~ 175 (290)
T TIGR02282 119 RATFFRGELGQFLLLAREEQLDPLTLKGSYAGAMGYPQFMPSSYRQYAVDFDGDGHI 175 (290)
T ss_pred HHHHHHHHHHHHHHHHHhcCCChHhcCCCcccccCCcccCHHHHHHhCcCCCCCCCc
Confidence 77777754211123333 6676655 457888889999999995 48885 677764
No 9
>PRK04998 hypothetical protein; Provisional
Probab=19.55 E-value=73 Score=29.35 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=23.8
Q ss_pred HHHHHHHHHhccCCCCC--Cchhccccccccc
Q 001216 482 FVATVEAIIKRTFPPES--SPENTRRARHLSG 511 (1122)
Q Consensus 482 FvATVeAIL~RTFP~es--s~Eq~rk~r~~~~ 511 (1122)
|++.|.+|+++.+|... +..++|++||.+.
T Consensus 28 ~~~~v~~v~~~~~~~~~~~~~r~S~~GkY~Sv 59 (88)
T PRK04998 28 LVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSV 59 (88)
T ss_pred HHHHHHHHHHHhCCCCCCceEccCCCCEEEEE
Confidence 89999999999999873 2245678898775
No 10
>PRK00907 hypothetical protein; Provisional
Probab=18.36 E-value=84 Score=29.89 Aligned_cols=31 Identities=6% Similarity=0.010 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhccCCC--CCCc--hhccccccccc
Q 001216 481 IFVATVEAIIKRTFPP--ESSP--ENTRRARHLSG 511 (1122)
Q Consensus 481 IFvATVeAIL~RTFP~--ess~--Eq~rk~r~~~~ 511 (1122)
-|..+|.+|+++.+|. +.+. ..++|+||.+.
T Consensus 29 ~l~~~V~~vv~~h~p~~~~~~i~~r~Ss~GkY~Sv 63 (92)
T PRK00907 29 GLETELPRLLAATGVELLQERISWKHSSSGKYVSV 63 (92)
T ss_pred hHHHHHHHHHHHhCCCCCcCcEEeccCCCCEEEEE
Confidence 4899999999999983 3332 45779999875
Done!