Query psy843
Match_columns 109
No_of_seqs 70 out of 72
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 18:38:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy843.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/843hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10210 MRP-S32: Mitochondria 100.0 2.2E-54 4.7E-59 304.8 8.5 96 8-106 1-96 (96)
2 KOG4106|consensus 100.0 4.2E-47 9E-52 277.2 8.6 98 8-109 27-125 (125)
3 PF13540 RCC1_2: Regulator of 78.7 2.1 4.5E-05 23.7 2.1 14 11-25 10-23 (30)
4 PF01436 NHL: NHL repeat; Int 75.9 2.8 6.1E-05 22.7 2.1 17 9-25 3-19 (28)
5 PF06009 Laminin_II: Laminin D 58.5 5.3 0.00011 28.9 1.1 20 12-31 110-129 (138)
6 PF13186 SPASM: Iron-sulfur cl 57.3 6.5 0.00014 23.2 1.2 19 9-27 4-22 (64)
7 cd08556 GDPD Glycerophosphodie 54.8 8.1 0.00017 27.1 1.5 15 12-27 33-47 (189)
8 COG1724 Predicted RNA binding 48.2 12 0.00027 25.2 1.5 17 16-32 35-52 (66)
9 PF03009 GDPD: Glycerophosphor 47.4 13 0.00028 26.8 1.6 15 12-27 30-44 (256)
10 TIGR02608 delta_60_rpt delta-6 44.9 19 0.00041 23.0 2.0 16 10-25 3-18 (55)
11 cd01747 GATase1_Glutamyl_Hydro 43.9 94 0.002 24.9 6.2 13 25-38 210-222 (273)
12 cd08582 GDPD_like_2 Glyceropho 42.6 16 0.00035 27.4 1.6 17 12-29 33-49 (233)
13 cd08562 GDPD_EcUgpQ_like Glyce 41.5 17 0.00036 26.9 1.5 17 12-29 33-49 (229)
14 cd08567 GDPD_SpGDE_like Glycer 39.4 19 0.00042 27.1 1.6 17 12-29 35-51 (263)
15 cd08563 GDPD_TtGDE_like Glycer 38.8 19 0.00042 27.0 1.5 17 12-29 35-51 (230)
16 PF07676 PD40: WD40-like Beta 38.6 27 0.00059 19.2 1.8 12 12-23 13-24 (39)
17 PF08432 Vfa1: AAA-ATPase Vps4 38.3 19 0.00041 27.3 1.4 25 10-34 5-29 (182)
18 PF09561 RE_HpaII: HpaII restr 36.8 22 0.00047 30.6 1.7 14 13-27 296-309 (355)
19 PF06004 DUF903: Bacterial pro 36.7 31 0.00067 21.8 2.0 13 12-24 2-14 (50)
20 cd08560 GDPD_EcGlpQ_like_1 Gly 33.1 27 0.00058 29.4 1.6 16 12-28 51-66 (356)
21 KOG1784|consensus 32.3 34 0.00074 24.7 1.8 13 14-26 15-27 (96)
22 cd08579 GDPD_memb_like Glycero 31.3 30 0.00066 25.7 1.5 16 12-28 33-48 (220)
23 PF14132 DUF4299: Domain of un 31.1 35 0.00075 28.6 1.9 28 12-41 213-240 (304)
24 cd08601 GDPD_SaGlpQ_like Glyce 30.8 34 0.00074 26.1 1.7 16 12-28 35-50 (256)
25 PHA03141 helicase-primase prim 30.8 37 0.00081 24.7 1.8 18 13-32 40-57 (101)
26 cd08561 GDPD_cytoplasmic_ScUgp 30.7 31 0.00068 26.2 1.5 15 12-27 33-47 (249)
27 PF06739 SBBP: Beta-propeller 29.4 80 0.0017 18.2 2.8 25 8-32 13-38 (38)
28 cd08572 GDPD_GDE5_like Glycero 28.5 41 0.00088 26.9 1.9 16 12-28 42-57 (293)
29 cd08559 GDPD_periplasmic_GlpQ_ 28.2 36 0.00077 27.1 1.5 15 12-27 35-49 (296)
30 cd08604 GDPD_SHV3_repeat_2 Gly 28.1 36 0.00077 27.4 1.5 14 12-26 35-48 (300)
31 cd08600 GDPD_EcGlpQ_like Glyce 28.0 37 0.0008 27.6 1.6 16 12-28 35-50 (318)
32 cd08571 GDPD_SHV3_plant Glycer 27.8 37 0.00079 27.4 1.5 16 12-28 35-50 (302)
33 PF09875 DUF2102: Uncharacteri 27.6 45 0.00098 24.3 1.8 29 72-100 48-79 (104)
34 cd08602 GDPD_ScGlpQ1_like Glyc 27.5 39 0.00084 27.4 1.6 15 12-27 35-49 (309)
35 KOG4131|consensus 27.0 26 0.00055 29.4 0.5 15 14-28 62-76 (272)
36 cd08566 GDPD_AtGDE_like Glycer 26.0 42 0.00091 25.8 1.5 15 12-27 35-49 (240)
37 PRK11143 glpQ glycerophosphodi 25.9 42 0.00091 28.0 1.6 16 12-28 61-76 (355)
38 PRK09454 ugpQ cytoplasmic glyc 25.8 43 0.00093 25.7 1.5 14 12-26 42-55 (249)
39 cd08574 GDPD_GDE_2_3_6 Glycero 24.9 48 0.001 25.7 1.7 15 12-27 36-50 (252)
40 cd08583 PI-PLCc_GDPD_SF_unchar 24.8 45 0.00097 25.2 1.4 15 12-27 35-49 (237)
41 cd08603 GDPD_SHV3_repeat_1 Gly 24.6 47 0.001 27.5 1.6 15 12-27 37-51 (299)
42 smart00199 SCY Intercrine alph 24.4 56 0.0012 20.2 1.6 18 11-29 32-49 (59)
43 PF15641 Tox-MPTase5: Metallop 24.0 14 0.00031 26.9 -1.3 17 28-44 22-38 (109)
44 cd08578 GDPD_NUC-2_fungi Putat 24.0 56 0.0012 26.9 2.0 15 12-27 35-49 (300)
45 cd08568 GDPD_TmGDE_like Glycer 24.0 51 0.0011 24.7 1.6 15 12-27 34-48 (226)
46 cd08570 GDPD_YPL206cp_fungi Gl 23.7 52 0.0011 24.8 1.6 15 12-27 33-47 (234)
47 PF09631 Sen15: Sen15 protein; 23.5 66 0.0014 22.0 1.9 13 13-25 77-89 (101)
48 cd08606 GDPD_YPL110cp_fungi Gl 23.3 61 0.0013 25.2 2.0 16 12-28 44-59 (286)
49 KOG1765|consensus 23.1 70 0.0015 25.4 2.2 69 16-98 65-133 (181)
50 PF12967 DUF3855: Domain of Un 23.1 48 0.001 25.5 1.3 25 64-89 121-145 (158)
51 KOG1407|consensus 22.9 65 0.0014 27.5 2.2 21 10-30 254-285 (313)
52 cd08607 GDPD_GDE5 Glycerophosp 22.4 64 0.0014 25.1 1.9 15 12-27 41-55 (290)
53 KOG2747|consensus 21.9 58 0.0013 28.5 1.7 14 70-83 330-343 (396)
54 PF00400 WD40: WD domain, G-be 21.6 1.1E+02 0.0024 15.9 2.3 16 9-24 13-28 (39)
55 cd08581 GDPD_like_1 Glyceropho 21.6 61 0.0013 24.8 1.6 16 12-28 33-48 (229)
56 KOG2284|consensus 21.5 87 0.0019 28.8 2.8 51 32-85 483-534 (728)
57 cd08575 GDPD_GDE4_like Glycero 20.9 63 0.0014 25.2 1.6 16 12-28 35-50 (264)
58 cd08573 GDPD_GDE1 Glycerophosp 20.3 65 0.0014 25.1 1.6 16 12-28 33-48 (258)
59 cd08605 GDPD_GDE5_like_1_plant 20.3 75 0.0016 24.7 1.9 15 12-27 45-59 (282)
60 cd08585 GDPD_like_3 Glyceropho 20.0 64 0.0014 24.9 1.5 16 12-28 40-55 (237)
No 1
>PF10210 MRP-S32: Mitochondrial 28S ribosomal protein S32; InterPro: IPR019346 This entry represents a family of short proteins; each approximately 100 amino acid residues in length. They are identified as the mitochondrial 28S ribosomal proteins S32.
Probab=100.00 E-value=2.2e-54 Score=304.80 Aligned_cols=96 Identities=41% Similarity=0.739 Sum_probs=92.0
Q ss_pred cccceeeeecCCcEEEEecCCCCCCcccccCCCCCCCCCchhHHHHHHHHHHHHhhcCCChhhhHHHHhhhhccccCccc
Q psy843 8 PLTHKIAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWF 87 (109)
Q Consensus 8 ~l~~~iavTsDG~tIVcwHP~~~fPYEhTKPIp~~d~~~~~~~lk~~~lk~~l~~~k~k~~e~~~eELsKmfyTTKHRWy 87 (109)
+++.+|||||||+|||||||+++||||||||||++++..+++++++|+|++.+++|+.+++|++||||||||||||||||
T Consensus 1 ~c~~~iavT~dG~tIVcwHP~~~fPYEhTKPip~~~~~~~~~~~~d~~lk~~l~~~~~~~~~p~~eeLskmfyTTKHrWy 80 (96)
T PF10210_consen 1 NCKVEIAVTSDGRTIVCWHPEKDFPYEHTKPIPRPDPVSSNEETHDQILKARLSKFKKKKPEPVIEELSKMFYTTKHRWY 80 (96)
T ss_pred CceeeEEEecCCCEEEEeCCCCCCCcccccCCCCCCCCcchhhhhhHHHHHHHHhhhccCccchHHHHHHhhCCCCcccc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhhhhcCCCCCCCC
Q psy843 88 PVRKMRQKKRYFKPLIPDR 106 (109)
Q Consensus 88 Pr~q~~~rr~k~~p~p~DR 106 (109)
|+| ++||+|+|| |+||
T Consensus 81 Pr~--r~~r~k~~p-p~~r 96 (96)
T PF10210_consen 81 PRG--RDRRAKKTP-PKDR 96 (96)
T ss_pred ccc--ccccccCCC-CCCC
Confidence 999 699999999 6665
No 2
>KOG4106|consensus
Probab=100.00 E-value=4.2e-47 Score=277.23 Aligned_cols=98 Identities=33% Similarity=0.592 Sum_probs=91.1
Q ss_pred cccceeeeecCCcEEEEecCCCCCCcccccCCCCCCCCCchhHHHHHHHHHHHHhhcCCCh-hhhHHHHhhhhccccCcc
Q psy843 8 PLTHKIAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKE-EFVRQDLMNITFTNKHRW 86 (109)
Q Consensus 8 ~l~~~iavTsDG~tIVcwHP~~~fPYEhTKPIp~~d~~~~~~~lk~~~lk~~l~~~k~k~~-e~~~eELsKmfyTTKHRW 86 (109)
+||++||||+||||||||||+++||||||||||++++.++|+++|||++++.+++++...+ +++++|||+|||||||||
T Consensus 27 ~lve~vavt~nGRTIvawHP~~~~PYEhTkPip~~s~~~~savvkdq~lkt~~~ak~s~~pe~p~~~eL~~~f~TtKHrW 106 (125)
T KOG4106|consen 27 RLVEKVAVTANGRTIVAWHPPQHFPYEHTKPIPLGSLTKKSAVVKDQSLKTSAAAKASSIPEEPVNAELKDIFYTTKHRW 106 (125)
T ss_pred ceeeeEEEecCCcEEEEecCCCCCCcccCCCCCCCccccchhhHHHHHHHHHHHHHHhhCCcchHHHHHHHHHhhhcccc
Confidence 4899999999999999999999999999999999999999999999999999999877775 778899999999999999
Q ss_pred ccchhhhhhhhcCCCCCCCCCCC
Q psy843 87 FPVRKMRQKKRYFKPLIPDREYL 109 (109)
Q Consensus 87 yPr~q~~~rr~k~~p~p~DR~yl 109 (109)
|||+ |++|+++++ +|+||+
T Consensus 107 ypr~--R~~r~r~~~--~p~p~r 125 (125)
T KOG4106|consen 107 YPRT--REERLRNVA--APIPRR 125 (125)
T ss_pred ccch--HHHHHhcCC--CCCCCC
Confidence 9999 777778888 888875
No 3
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=78.68 E-value=2.1 Score=23.65 Aligned_cols=14 Identities=57% Similarity=1.260 Sum_probs=10.9
Q ss_pred ceeeeecCCcEEEEe
Q psy843 11 HKIAITADGTTVVCW 25 (109)
Q Consensus 11 ~~iavTsDG~tIVcw 25 (109)
..+||++|| .+.||
T Consensus 10 ht~al~~~g-~v~~w 23 (30)
T PF13540_consen 10 HTCALTSDG-EVYCW 23 (30)
T ss_dssp EEEEEE-TT-EEEEE
T ss_pred EEEEEEcCC-CEEEE
Confidence 468999999 68888
No 4
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=75.87 E-value=2.8 Score=22.68 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=14.5
Q ss_pred ccceeeeecCCcEEEEe
Q psy843 9 LTHKIAITADGTTVVCW 25 (109)
Q Consensus 9 l~~~iavTsDG~tIVcw 25 (109)
.+..||+.+||..+||=
T Consensus 3 ~P~gvav~~~g~i~VaD 19 (28)
T PF01436_consen 3 YPHGVAVDSDGNIYVAD 19 (28)
T ss_dssp SEEEEEEETTSEEEEEE
T ss_pred CCcEEEEeCCCCEEEEE
Confidence 46789999999999984
No 5
>PF06009 Laminin_II: Laminin Domain II; InterPro: IPR010307 It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure [].; GO: 0007155 cell adhesion, 0005604 basement membrane; PDB: 2WJS_A.
Probab=58.51 E-value=5.3 Score=28.87 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=5.4
Q ss_pred eeeeecCCcEEEEecCCCCC
Q psy843 12 KIAITADGTTVVCWHPEQPF 31 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~~~f 31 (109)
.|+|+.||.++|.|+|..+.
T Consensus 110 kV~m~F~g~s~velrpp~~l 129 (138)
T PF06009_consen 110 KVSMKFNGNSGVELRPPINL 129 (138)
T ss_dssp --B-------EEEE----S-
T ss_pred eeeeEECCCceeeeCCCCCH
Confidence 57899999999999997654
No 6
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=57.31 E-value=6.5 Score=23.15 Aligned_cols=19 Identities=26% Similarity=0.396 Sum_probs=15.0
Q ss_pred ccceeeeecCCcEEEEecC
Q psy843 9 LTHKIAITADGTTVVCWHP 27 (109)
Q Consensus 9 l~~~iavTsDG~tIVcwHP 27 (109)
.-..++|++||.+..|-+.
T Consensus 4 ~~~~~~I~~dG~v~pC~~~ 22 (64)
T PF13186_consen 4 GWNSLYIDPDGDVYPCCHD 22 (64)
T ss_pred cCeEEEEeeCccEEeCCCC
Confidence 3467899999999999433
No 7
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=54.81 E-value=8.1 Score=27.15 Aligned_cols=15 Identities=33% Similarity=0.629 Sum_probs=12.8
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|.+|.|| ++||+|-
T Consensus 33 Dv~~tkDg-~~vv~Hd 47 (189)
T cd08556 33 DVQLTKDG-VLVVIHD 47 (189)
T ss_pred EeeEcCCC-CEEEEcC
Confidence 57789999 6888998
No 8
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=48.22 E-value=12 Score=25.23 Aligned_cols=17 Identities=35% Similarity=0.753 Sum_probs=13.6
Q ss_pred ecC-CcEEEEecCCCCCC
Q psy843 16 TAD-GTTVVCWHPEQPFP 32 (109)
Q Consensus 16 TsD-G~tIVcwHP~~~fP 32 (109)
-+| |+++|-.||..|+|
T Consensus 35 Hp~~~~vtVP~Hp~~dl~ 52 (66)
T COG1724 35 HPDGGRVTVPFHPGEDLP 52 (66)
T ss_pred cCCCCEEEecCCCccccC
Confidence 345 78888899999876
No 9
>PF03009 GDPD: Glycerophosphoryl diester phosphodiesterase family; InterPro: IPR004129 Glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol) all of which are are hydrolysed by this enzyme.; GO: 0008889 glycerophosphodiester phosphodiesterase activity, 0006071 glycerol metabolic process; PDB: 3I10_A 2P76_H 2OOG_F 3KS6_D 3KS5_A 2PZ0_B 1YDY_B 1T8Q_A 1O1Z_A 3L12_B ....
Probab=47.39 E-value=13 Score=26.83 Aligned_cols=15 Identities=33% Similarity=0.669 Sum_probs=9.8
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|+|| .+||+|-
T Consensus 30 Dv~lTkDg-~~Vv~HD 44 (256)
T PF03009_consen 30 DVQLTKDG-VPVVFHD 44 (256)
T ss_dssp EEEE-TTS--EEE-SS
T ss_pred cccccCCc-eeEeccC
Confidence 46799999 8888886
No 10
>TIGR02608 delta_60_rpt delta-60 repeat domain. This domain occurs in tandem repeats, as many as 13, in proteins from Bdellovibrio bacteriovorus, Azotobacter vinelandii, Geobacter sulfurreducens, Pirellula sp. 1, Myxococcus xanthus, and others, many of which are Deltaproteobacteria. The periodicity of the repeat ranges from about 57 to 61 amino acids, and a core region of about 54 is represented by this model and seed alignment.
Probab=44.93 E-value=19 Score=22.96 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=13.4
Q ss_pred cceeeeecCCcEEEEe
Q psy843 10 THKIAITADGTTVVCW 25 (109)
Q Consensus 10 ~~~iavTsDG~tIVcw 25 (109)
+..|++-+||+.||+=
T Consensus 3 ~~~~~~q~DGkIlv~G 18 (55)
T TIGR02608 3 AYAVAVQSDGKILVAG 18 (55)
T ss_pred eEEEEECCCCcEEEEE
Confidence 4678999999999863
No 11
>cd01747 GATase1_Glutamyl_Hydrolase Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. gamma-Glutamyl Hydrolase catalyzes the cleavage of the gamma-glutamyl chain of folylpoly-gamma-glutamyl substrates and is a central enzyme in folyl and antifolyl poly-gamma-glutamate metabolism. GATase activity involves the removal of the ammonia group from a glutamate molecule and its subsequent transfer to a specific substrate, thus creating a new carbon-nitrogen group on the substrate. gamma-Glutamyl hydrolases belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site.
Probab=43.88 E-value=94 Score=24.88 Aligned_cols=13 Identities=38% Similarity=0.989 Sum_probs=10.6
Q ss_pred ecCCCCCCcccccC
Q psy843 25 WHPEQPFPYEHSLP 38 (109)
Q Consensus 25 wHP~~~fPYEhTKP 38 (109)
||||.. +||...-
T Consensus 210 FHPEks-~few~~~ 222 (273)
T cd01747 210 WHPEKN-AFEWKKS 222 (273)
T ss_pred cCCCcc-ccccccc
Confidence 699988 8998763
No 12
>cd08582 GDPD_like_2 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=42.64 E-value=16 Score=27.44 Aligned_cols=17 Identities=35% Similarity=0.745 Sum_probs=13.4
Q ss_pred eeeeecCCcEEEEecCCC
Q psy843 12 KIAITADGTTVVCWHPEQ 29 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~~ 29 (109)
.|.+|.|| ++||+|-..
T Consensus 33 Dv~lTkDg-~~Vv~HD~~ 49 (233)
T cd08582 33 DVRLTKDG-ELVCVHDPT 49 (233)
T ss_pred EEEEccCC-CEEEecCCc
Confidence 47789999 888889543
No 13
>cd08562 GDPD_EcUgpQ_like Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), UgpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two distinct GP-GDEs. UgpQ gene from the E. coli ugp operon codes for a cytosolic phosphodiesterase GlpQ, which is the prototype of this family. Various glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG)
Probab=41.49 E-value=17 Score=26.90 Aligned_cols=17 Identities=29% Similarity=0.622 Sum_probs=13.5
Q ss_pred eeeeecCCcEEEEecCCC
Q psy843 12 KIAITADGTTVVCWHPEQ 29 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~~ 29 (109)
.|.+|+|| .+|++|-..
T Consensus 33 Dv~~TkDg-~lvv~HD~~ 49 (229)
T cd08562 33 DVKLSGDG-TLVLIHDDT 49 (229)
T ss_pred EEeECCCC-CEEEEcCCC
Confidence 47789999 888888653
No 14
>cd08567 GDPD_SpGDE_like Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter pomeroyi (SpGDE). It shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=39.44 E-value=19 Score=27.13 Aligned_cols=17 Identities=29% Similarity=0.571 Sum_probs=13.2
Q ss_pred eeeeecCCcEEEEecCCC
Q psy843 12 KIAITADGTTVVCWHPEQ 29 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~~ 29 (109)
.|.+|.|| ++||+|-..
T Consensus 35 DV~~TkDg-~~Vv~HD~~ 51 (263)
T cd08567 35 DLVLTKDG-VIVVSHDPK 51 (263)
T ss_pred EEEEcCCC-CEEEeCCCc
Confidence 47899999 778888653
No 15
>cd08563 GDPD_TtGDE_like Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase (TtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Despite the fact that most of GDPD family members exist as the monomer, TtGDE can function as a dimeric unit. Its catalytic mechanism is based on the general base-acid catalysis, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 3.1.4.11). A divalent metal cation is required for the enzyme activity of TtGDE.
Probab=38.83 E-value=19 Score=26.96 Aligned_cols=17 Identities=35% Similarity=0.614 Sum_probs=13.6
Q ss_pred eeeeecCCcEEEEecCCC
Q psy843 12 KIAITADGTTVVCWHPEQ 29 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~~ 29 (109)
.|.+|.|| ++||+|-..
T Consensus 35 DV~~TkDg-~~Vv~HD~~ 51 (230)
T cd08563 35 DVHLTKDG-QLVVIHDET 51 (230)
T ss_pred EeeEcCCC-CEEEECCCC
Confidence 57899999 888888654
No 16
>PF07676 PD40: WD40-like Beta Propeller Repeat; InterPro: IPR011659 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This region appears to be related to the IPR001680 from INTERPRO repeat. This model is likely to miss copies within a sequence.; PDB: 2HQS_D 1C5K_A 2IVZ_A 2W8B_D 3IAX_A 1CRZ_A 1N6F_D 1N6D_C 1N6E_C 1K32_A ....
Probab=38.64 E-value=27 Score=19.16 Aligned_cols=12 Identities=25% Similarity=0.318 Sum_probs=9.0
Q ss_pred eeeeecCCcEEE
Q psy843 12 KIAITADGTTVV 23 (109)
Q Consensus 12 ~iavTsDG~tIV 23 (109)
..++++||+.||
T Consensus 13 ~p~~SpDGk~i~ 24 (39)
T PF07676_consen 13 SPAWSPDGKYIY 24 (39)
T ss_dssp EEEE-TTSSEEE
T ss_pred CEEEecCCCEEE
Confidence 567899999887
No 17
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=38.32 E-value=19 Score=27.31 Aligned_cols=25 Identities=20% Similarity=0.421 Sum_probs=20.1
Q ss_pred cceeeeecCCcEEEEecCCCCCCcc
Q psy843 10 THKIAITADGTTVVCWHPEQPFPYE 34 (109)
Q Consensus 10 ~~~iavTsDG~tIVcwHP~~~fPYE 34 (109)
.+.||.++-..++|||=|+..+=|-
T Consensus 5 ~RkVa~~~~k~C~IC~KpsttVL~t 29 (182)
T PF08432_consen 5 HRKVAETDAKACFICYKPSTTVLIT 29 (182)
T ss_pred eeeeccCCCCceeEecCCCceEEec
Confidence 3678999999999999998655543
No 18
>PF09561 RE_HpaII: HpaII restriction endonuclease; InterPro: IPR019062 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This family includes HpaII, which recognises the double-stranded sequence CCGG and cleaves after C-1.
Probab=36.80 E-value=22 Score=30.58 Aligned_cols=14 Identities=43% Similarity=1.016 Sum_probs=11.1
Q ss_pred eeeecCCcEEEEecC
Q psy843 13 IAITADGTTVVCWHP 27 (109)
Q Consensus 13 iavTsDG~tIVcwHP 27 (109)
|.|..|| -|||||=
T Consensus 296 ivV~~dG-evlcYHi 309 (355)
T PF09561_consen 296 IVVKEDG-EVLCYHI 309 (355)
T ss_pred EEEeCCC-CEEEEEe
Confidence 6688888 5699994
No 19
>PF06004 DUF903: Bacterial protein of unknown function (DUF903); InterPro: IPR010305 This family consists of several small bacterial proteins several of which are classified as putative lipoproteins. The function of this family is unknown.; PDB: 2RB6_B 3BDU_F 2RA2_F 2RD1_C 3FIF_H 2JN0_A 2K57_A.
Probab=36.72 E-value=31 Score=21.81 Aligned_cols=13 Identities=38% Similarity=0.549 Sum_probs=10.5
Q ss_pred eeeeecCCcEEEE
Q psy843 12 KIAITADGTTVVC 24 (109)
Q Consensus 12 ~iavTsDG~tIVc 24 (109)
.+.-|.||++||+
T Consensus 2 yvi~t~dG~~i~t 14 (50)
T PF06004_consen 2 YVITTNDGRTIVT 14 (50)
T ss_dssp EEEEETTSEEEEE
T ss_pred cEEEeCCCcEEEe
Confidence 3567899999995
No 20
>cd08560 GDPD_EcGlpQ_like_1 Glycerophosphodiester phosphodiesterase domain similar to Escherichia coli periplasmic phosphodiesterase (GlpQ) include uncharacterized proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and their hypothetical homologs. Members in this subfamily show high sequence similarity to Escherichia coli periplasmic phosphodiesterase GlpQ, which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=33.11 E-value=27 Score=29.37 Aligned_cols=16 Identities=31% Similarity=0.711 Sum_probs=13.5
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|.+|.|| .+||+|=.
T Consensus 51 DV~lTkDg-~lVV~HD~ 66 (356)
T cd08560 51 DVTFTKDR-ELVCRHSQ 66 (356)
T ss_pred EeeEccCC-cEEEECCC
Confidence 57899999 88889974
No 21
>KOG1784|consensus
Probab=32.31 E-value=34 Score=24.66 Aligned_cols=13 Identities=38% Similarity=0.429 Sum_probs=10.9
Q ss_pred eeecCCcEEEEec
Q psy843 14 AITADGTTVVCWH 26 (109)
Q Consensus 14 avTsDG~tIVcwH 26 (109)
.+|.|||+||.--
T Consensus 15 vIt~DGr~ivgsL 27 (96)
T KOG1784|consen 15 VITNDGRVIVGSL 27 (96)
T ss_pred EEecCCeEEEEEe
Confidence 5899999999753
No 22
>cd08579 GDPD_memb_like Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial glycerophosphodiester phosphodiesterases. In addition to a C-terminal GDPD domain, most members in this family have an N-terminus that functions as a membrane anchor.
Probab=31.29 E-value=30 Score=25.72 Aligned_cols=16 Identities=31% Similarity=0.457 Sum_probs=12.6
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|+|| .+||+|-.
T Consensus 33 DV~~T~Dg-~~vv~HD~ 48 (220)
T cd08579 33 DVQETKDG-QFVVMHDA 48 (220)
T ss_pred EeeEcCCC-CEEEEcCC
Confidence 46789999 77888864
No 23
>PF14132 DUF4299: Domain of unknown function (DUF4299)
Probab=31.05 E-value=35 Score=28.58 Aligned_cols=28 Identities=18% Similarity=0.234 Sum_probs=20.7
Q ss_pred eeeeecCCcEEEEecCCCCCCcccccCCCC
Q psy843 12 KIAITADGTTVVCWHPEQPFPYEHSLPLPV 41 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~~~fPYEhTKPIp~ 41 (109)
-=++|.|.+||.-+.|+++| +....+..
T Consensus 213 ~YtLte~v~TILP~kP~v~~--~~~e~~~~ 240 (304)
T PF14132_consen 213 VYTLTEGVDTILPYKPSVEF--ENVEIVKN 240 (304)
T ss_pred EEEEcCCCCEEecCCCCCCc--ccccccCC
Confidence 34799999999999995554 45555555
No 24
>cd08601 GDPD_SaGlpQ_like Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) from Staphylococcus aureus, Bacillus subtilis and similar proteins. Members in this family show very high sequence similarity to Escherichia coli periplasmic phosphodiesterase GlpQ, which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=30.85 E-value=34 Score=26.13 Aligned_cols=16 Identities=38% Similarity=0.679 Sum_probs=11.6
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|+|| .+|++|-.
T Consensus 35 DV~lTkDg-~~Vv~HD~ 50 (256)
T cd08601 35 DLQMTKDG-VLVAMHDE 50 (256)
T ss_pred EeeECCCC-eEEEeCCC
Confidence 47789999 66666653
No 25
>PHA03141 helicase-primase primase subunit; Provisional
Probab=30.81 E-value=37 Score=24.67 Aligned_cols=18 Identities=44% Similarity=1.200 Sum_probs=13.4
Q ss_pred eeeecCCcEEEEecCCCCCC
Q psy843 13 IAITADGTTVVCWHPEQPFP 32 (109)
Q Consensus 13 iavTsDG~tIVcwHP~~~fP 32 (109)
..+|.+| =+|||+..+.|
T Consensus 40 fi~T~~G--p~cW~~~~~lP 57 (101)
T PHA03141 40 FLLTTEG--PVCWHQKLPLP 57 (101)
T ss_pred EEEeCCc--ceEecCCCCCC
Confidence 4578888 47999986554
No 26
>cd08561 GDPD_cytoplasmic_ScUgpQ2_like Glycerophosphodiester phosphodiesterase domain of Streptomyces coelicolor cytoplasmic phosphodiesterases UgpQ2 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized cytoplasmic phosphodiesterases which predominantly exist in bacteria. The prototype of this family is a putative cytoplasmic phosphodiesterase encoded by gene ulpQ2 (SCO1419) in the Streptomyces coelicolor genome. It is distantly related to the Escherichia coli cytoplasmic phosphodiesterases UgpQ that catalyzes the hydrolysis of glycerophosphodiesters at the inner side of the cytoplasmic membrane to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=30.75 E-value=31 Score=26.21 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.0
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|.+|.|| .+||+|-
T Consensus 33 Dv~~TkDg-~~Vv~HD 47 (249)
T cd08561 33 DVHATKDG-VLVVIHD 47 (249)
T ss_pred EeeECCCC-CEEEECC
Confidence 46789999 8888884
No 27
>PF06739 SBBP: Beta-propeller repeat; InterPro: IPR010620 This family is related to IPR001680 from INTERPRO and is likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller.
Probab=29.43 E-value=80 Score=18.21 Aligned_cols=25 Identities=24% Similarity=0.363 Sum_probs=18.7
Q ss_pred cccceeeeecCCcEEEEecCCC-CCC
Q psy843 8 PLTHKIAITADGTTVVCWHPEQ-PFP 32 (109)
Q Consensus 8 ~l~~~iavTsDG~tIVcwHP~~-~fP 32 (109)
.-...|||.++|...|+=.=.. +||
T Consensus 13 ~~~~~IavD~~GNiYv~G~T~~~~fp 38 (38)
T PF06739_consen 13 DYGNGIAVDSNGNIYVTGYTNGNDFP 38 (38)
T ss_pred eeEEEEEECCCCCEEEEEeecCCCCC
Confidence 4577899999999998855444 554
No 28
>cd08572 GDPD_GDE5_like Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE5-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase GDE5-like proteins. GDE5 is widely expressed in mammalian tissues, with highest expression in spinal chord. Although its biological function remains unclear, mammalian GDE5 shows higher sequence homology to fungal and plant glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46) than to other bacterial and mammalian GP-GDEs. It may also hydrolyze glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=28.54 E-value=41 Score=26.87 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=12.7
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|.|| .+||+|=.
T Consensus 42 DV~lTkDG-~lVv~HD~ 57 (293)
T cd08572 42 DVQLTKDG-VPVIYHDF 57 (293)
T ss_pred EEEEccCC-eEEEEcCC
Confidence 46789999 88888853
No 29
>cd08559 GDPD_periplasmic_GlpQ_like Periplasmic glycerophosphodiester phosphodiesterase domain (GlpQ) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in bacterial and eukaryotic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ. GP-GDEs are involved in glycerol metabolism and catalyze the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. In E. coli, there are two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the glp operon codes for a periplasmic phosphodiesterase GlpQ. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI),
Probab=28.23 E-value=36 Score=27.06 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=12.0
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| .+||.|=
T Consensus 35 DV~lTkDg-~lVv~HD 49 (296)
T cd08559 35 DLVMTKDG-VLVARHD 49 (296)
T ss_pred eeEEccCC-CEEEecc
Confidence 47789999 7788884
No 30
>cd08604 GDPD_SHV3_repeat_2 Glycerophosphodiester phosphodiesterase domain repeat 2 of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) repeat 2 present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play important an role in cell wall organization. The prototype of this family is a glycosylphosphatidylinositol (GPI) anchored protein SHV3 encoded by shaven3 (shv3) gene from Arabidopsis thaliana. Members in this family show sequence homology to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Both, SHV3 and SVLs, have two tandemly repeated GDPD domains whose biochemical functions remain unclear. The residues essential for interactions with the substrates and calcium ions in bacterial GP
Probab=28.09 E-value=36 Score=27.41 Aligned_cols=14 Identities=21% Similarity=0.653 Sum_probs=11.6
Q ss_pred eeeeecCCcEEEEec
Q psy843 12 KIAITADGTTVVCWH 26 (109)
Q Consensus 12 ~iavTsDG~tIVcwH 26 (109)
.|.+|.|| .+||.|
T Consensus 35 DV~lTkDG-~lVv~H 48 (300)
T cd08604 35 SVQMSKDG-VPFCLD 48 (300)
T ss_pred eeeEcCCC-CEEEec
Confidence 47899999 777888
No 31
>cd08600 GDPD_EcGlpQ_like Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli periplasmic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), GlpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the E. coli glp operon codes for a periplasmic phosphodiesterase GlpQ, which is the prototype of this family. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GP
Probab=27.97 E-value=37 Score=27.62 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=13.1
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|.|| .+||+|-.
T Consensus 35 DV~lTkDg-~lVv~HD~ 50 (318)
T cd08600 35 DVVLTKDD-KLVVIHDH 50 (318)
T ss_pred eeeECcCC-cEEEeCCc
Confidence 46789999 88889964
No 32
>cd08571 GDPD_SHV3_plant Glycerophosphodiester phosphodiesterase domain of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase (GDPD) domain present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play an important role in cell wall organization. The prototype of this family is a glycosylphosphatidylinositol (GPI) anchored protein SHV3 encoded by shaven3 (shv3) gene from Arabidopsis thaliana. Members in this family show sequence homology to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Both, SHV3 and SVLs, have two tandemly repeated GDPD domains whose biochemical functions remain unclear. The residues essential for interactions with the substrates and calcium ions in bacterial GP-GDEs are not conserv
Probab=27.82 E-value=37 Score=27.43 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=12.7
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|.+|.|| .+||.|-.
T Consensus 35 DV~lTkDg-~lVv~HD~ 50 (302)
T cd08571 35 DVQLTKDG-VPICLPSI 50 (302)
T ss_pred eeeEcCCC-cEEEeCCc
Confidence 47799999 78888853
No 33
>PF09875 DUF2102: Uncharacterized protein conserved in archaea (DUF2102); InterPro: IPR012025 The exact functionof this protein unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=27.60 E-value=45 Score=24.32 Aligned_cols=29 Identities=17% Similarity=0.171 Sum_probs=21.0
Q ss_pred HHHHhhhhcc---ccCccccchhhhhhhhcCC
Q psy843 72 RQDLMNITFT---NKHRWFPVRKMRQKKRYFK 100 (109)
Q Consensus 72 ~eELsKmfyT---TKHRWyPr~q~~~rr~k~~ 100 (109)
++++.+|-.+ +|-||||.|.-|+.|+..-
T Consensus 48 i~~iR~ld~~~IF~KdRGFppgD~RRCRa~rg 79 (104)
T PF09875_consen 48 IEEIRKLDPNHIFVKDRGFPPGDPRRCRATRG 79 (104)
T ss_pred HHHHHhhCCCceEeecCCCCCCccHHhhhccC
Confidence 4566665433 6999999998888887754
No 34
>cd08602 GDPD_ScGlpQ1_like Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of putative bacterial and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ, as well as plant glycerophosphodiester phosphodiesterases (GP-PDEs), all of which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. The prototypes of this family include putative secreted phosphodiesterase encoded by gene glpQ1 (SCO1565) from the pho regulon in Streptomyces coelicolor genome, and in plants, two distinct Arabidopsis thaliana genes, AT5G08030 and AT1G74210, coding putative GP-PDEs from the cell walls and vacuoles, respectively.
Probab=27.53 E-value=39 Score=27.37 Aligned_cols=15 Identities=33% Similarity=0.784 Sum_probs=12.2
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| .+||+|=
T Consensus 35 DVqlTkDg-~lVv~HD 49 (309)
T cd08602 35 DLVSTKDG-VLICRHE 49 (309)
T ss_pred eeeECCCC-cEEEeCC
Confidence 46789999 7888885
No 35
>KOG4131|consensus
Probab=27.02 E-value=26 Score=29.36 Aligned_cols=15 Identities=27% Similarity=0.733 Sum_probs=12.9
Q ss_pred eeecCCcEEEEecCC
Q psy843 14 AITADGTTVVCWHPE 28 (109)
Q Consensus 14 avTsDG~tIVcwHP~ 28 (109)
|+-+++.-||+|||-
T Consensus 62 a~ek~~e~IvAYHP~ 76 (272)
T KOG4131|consen 62 ALEKNAESIVAYHPP 76 (272)
T ss_pred HHHhCCceeEeecCc
Confidence 366999999999994
No 36
>cd08566 GDPD_AtGDE_like Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (AtGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homolgoues. Members in this family shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. AtGDE exists as a hexamer that is a trimer of dimers, which is unique among current known GDPD family members. However, it remains unclear if the hexamer plays a physiological role in AtGDE enzymatic function.
Probab=25.98 E-value=42 Score=25.78 Aligned_cols=15 Identities=33% Similarity=0.490 Sum_probs=11.2
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|.+|+|| .+|++|-
T Consensus 35 DV~~T~Dg-~~vv~HD 49 (240)
T cd08566 35 DVRRTKDG-VLVLMHD 49 (240)
T ss_pred EeeEcCCC-CEEEECC
Confidence 47789999 6666674
No 37
>PRK11143 glpQ glycerophosphodiester phosphodiesterase; Provisional
Probab=25.92 E-value=42 Score=27.98 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=13.0
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|.|| ++||+|-.
T Consensus 61 DV~lTkDg-~lVv~HD~ 76 (355)
T PRK11143 61 DLVMTKDD-QLVVLHDH 76 (355)
T ss_pred eeeEccCC-cEEEeCCc
Confidence 46789999 88899963
No 38
>PRK09454 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase; Provisional
Probab=25.83 E-value=43 Score=25.73 Aligned_cols=14 Identities=29% Similarity=0.577 Sum_probs=10.8
Q ss_pred eeeeecCCcEEEEec
Q psy843 12 KIAITADGTTVVCWH 26 (109)
Q Consensus 12 ~iavTsDG~tIVcwH 26 (109)
.|-+|.|| .+|++|
T Consensus 42 DV~lT~Dg-~lVV~H 55 (249)
T PRK09454 42 DAKLSADG-EIFLLH 55 (249)
T ss_pred EeeECCCC-CEEEEC
Confidence 46789999 566677
No 39
>cd08574 GDPD_GDE_2_3_6 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2, GDE3, GDE6-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase domain-containing protein subtype 5 (GDE2), subtype 2 (GDE3), subtype 1 (GDE6), and their eukaryotic homologs. Mammalian GDE2, GDE3, and GDE6 show very high sequence similarity to each other and have been classified into the same family. Although they are all transmembrane proteins, based on different pattern of tissue distribution, these enzymes might display diverse cellular functions. Mammalian GDE2 is primarily expressed in mature neurons. It selectively hydrolyzes glycerophosphocholine (GPC) and mainly functions in a complex with an antioxidant scavenger peroxiredoxin1 (Prdx1) to control motor neuron differentiation in the spinal cord. Mammalian GDE3 is specifically expressed in bo
Probab=24.88 E-value=48 Score=25.68 Aligned_cols=15 Identities=27% Similarity=0.443 Sum_probs=11.2
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| .+||.|=
T Consensus 36 DV~lTkDg-~lVV~HD 50 (252)
T cd08574 36 DVTISYDG-VPFLMHD 50 (252)
T ss_pred EEeEccCC-cEEEeCC
Confidence 46789999 6667774
No 40
>cd08583 PI-PLCc_GDPD_SF_unchar1 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=24.85 E-value=45 Score=25.24 Aligned_cols=15 Identities=33% Similarity=0.725 Sum_probs=12.0
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| .+|++|=
T Consensus 35 DV~lTkDg-~lVv~HD 49 (237)
T cd08583 35 DLSLTSDG-VLVARHS 49 (237)
T ss_pred EeeEccCC-CEEEEEC
Confidence 46689999 7888884
No 41
>cd08603 GDPD_SHV3_repeat_1 Glycerophosphodiester phosphodiesterase domain repeat 1 of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) repeat 1 present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play an important role in cell wall organization. The prototype of this family is a glycosylphosphatidylinositol (GPI) anchored protein SHV3 encoded by shaven3 (shv3) gene from Arabidopsis thaliana. Members in this family show sequence homology to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Both, SHV3 and SVLs, have two tandemly repeated GDPD domains whose biochemical functions remain unclear. The residues essential for interactions with the substrates and calcium ions in bacterial GP
Probab=24.58 E-value=47 Score=27.53 Aligned_cols=15 Identities=27% Similarity=0.625 Sum_probs=12.6
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|.+|.|| ..||.|=
T Consensus 37 DV~lTkDg-vlVv~HD 51 (299)
T cd08603 37 DLQLTKDG-VGICLPD 51 (299)
T ss_pred EeeECcCC-cEEEeCC
Confidence 67899999 8888884
No 42
>smart00199 SCY Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). Family of cytokines involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response.
Probab=24.36 E-value=56 Score=20.21 Aligned_cols=18 Identities=33% Similarity=0.519 Sum_probs=12.6
Q ss_pred ceeeeecCCcEEEEecCCC
Q psy843 11 HKIAITADGTTVVCWHPEQ 29 (109)
Q Consensus 11 ~~iavTsDG~tIVcwHP~~ 29 (109)
.=|..|..|+. ||.+|+.
T Consensus 32 avIf~tk~g~~-~C~dP~~ 49 (59)
T smart00199 32 AVIFTTKKGRK-VCADPKA 49 (59)
T ss_pred cEEEEEeCCCE-EecCCCh
Confidence 34566667865 8999974
No 43
>PF15641 Tox-MPTase5: Metallopeptidase toxin 5
Probab=24.05 E-value=14 Score=26.85 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=11.4
Q ss_pred CCCCCcccccCCCCCCC
Q psy843 28 EQPFPYEHSLPLPVTEQ 44 (109)
Q Consensus 28 ~~~fPYEhTKPIp~~d~ 44 (109)
+.||||=.--=+|+-.+
T Consensus 22 ~edf~~l~lt~~p~y~~ 38 (109)
T PF15641_consen 22 SEDFPYLNLTHIPQYNY 38 (109)
T ss_pred HhhcccccceeccccCh
Confidence 57888876666666333
No 44
>cd08578 GDPD_NUC-2_fungi Putative glycerophosphodiester phosphodiesterase domain of ankyrin repeat protein NUC-2 and similar proteins. This subfamily corresponds to a putative glycerophosphodiester phosphodiesterase domain (GDPD) present in Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81. Some uncharecaterized NUC-2 sequence homologs are also included in this family. NUC-2 plays an important role in the phosphate-regulated signal transduction pathway in Neurospora crassa. It shows high similarity to a cyclin-dependent kinase inhibitory protein PHO81, which is part of the phosphate regulatory cascade in S. cerevisiae. Both NUC-2 and PHO81 have multi-domain architecture, including an SPX N-terminal domain following by several ankyrin repeats and a putative C-terminal GDPD domain with unknown function. Although the putative GDPD domain displays sequence homology to that of bacterial glycerophos
Probab=24.03 E-value=56 Score=26.85 Aligned_cols=15 Identities=33% Similarity=0.410 Sum_probs=11.6
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| +.|+||=
T Consensus 35 DVqLTkDg-vpVV~HD 49 (300)
T cd08578 35 KVCVLKDG-TPVVAPE 49 (300)
T ss_pred EEEECcCC-EEEEECC
Confidence 46689999 7777773
No 45
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=23.96 E-value=51 Score=24.73 Aligned_cols=15 Identities=33% Similarity=0.581 Sum_probs=11.0
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| .+|++|-
T Consensus 34 DV~lT~Dg-~~Vv~HD 48 (226)
T cd08568 34 DVWLTKDG-KLVVLHD 48 (226)
T ss_pred EEEEcCCC-CEEEECC
Confidence 46789999 5666773
No 46
>cd08570 GDPD_YPL206cp_fungi Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL206cp and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL206cp and uncharacterized hypothetical homologs existing in fungi. The product of S. cerevisiae ORF YPL206c (PGC1), YPL206cp (Pgc1p), displays homology to bacterial and mammalian glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. S. cerevisiae YPL206cp is an integral membrane protein with a single GDPD domain following by a short hydrophobic C-terminal tail that may function as a membrane anchor. This protein plays an essential role in the regulation of the cardiolipin (CL) biosynthetic pathway in yeast by removing the excess phosphatidylglycerol (PG) content of membranes via a phospholip
Probab=23.68 E-value=52 Score=24.81 Aligned_cols=15 Identities=40% Similarity=0.594 Sum_probs=11.7
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| .+|++|-
T Consensus 33 Dv~lTkDg-~~vv~HD 47 (234)
T cd08570 33 DVHLTKDG-VVVISHD 47 (234)
T ss_pred EeeEccCC-cEEEeCC
Confidence 46789999 7778884
No 47
>PF09631 Sen15: Sen15 protein; InterPro: IPR018593 The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly []. ; PDB: 2GW6_B.
Probab=23.48 E-value=66 Score=22.02 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=8.5
Q ss_pred eeeecCCcEEEEe
Q psy843 13 IAITADGTTVVCW 25 (109)
Q Consensus 13 iavTsDG~tIVcw 25 (109)
||+.+|.+|||=|
T Consensus 77 LAiv~~DsTiVYY 89 (101)
T PF09631_consen 77 LAIVDDDSTIVYY 89 (101)
T ss_dssp EEEE-TTS-EEEE
T ss_pred EEEEcCCCCEEEE
Confidence 6777777899966
No 48
>cd08606 GDPD_YPL110cp_fungi Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL110cp and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL110cp and other uncharacterized fungal homologs. The product of S. cerevisiae ORF YPL110c (GDE1), YPL110cp (Gde1p), displays homology to bacterial and mammalian glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. S. cerevisiae YPL110cp has been characterized as a cytoplasmic glycerophosphocholine (GPC)-specific phosphodiesterase that selectively hydrolyzes GPC, not glycerophosphoinositol (GPI), to generate choline and glycerolphosphate. YPL110cp has multi-domain architecture, including not only C-terminal GDPD, but also an SPX N-terminal domain along with several ankyrin repeats, which imp
Probab=23.32 E-value=61 Score=25.23 Aligned_cols=16 Identities=25% Similarity=0.306 Sum_probs=11.7
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|.|| ++|++|-.
T Consensus 44 DV~lTkDg-~~VV~HD~ 59 (286)
T cd08606 44 DVQLTKDL-VPVIYHDF 59 (286)
T ss_pred EEEEccCC-EEEEeCCC
Confidence 46789999 66667754
No 49
>KOG1765|consensus
Probab=23.09 E-value=70 Score=25.39 Aligned_cols=69 Identities=26% Similarity=0.342 Sum_probs=39.6
Q ss_pred ecCCcEEEEecCCCCCCcccccCCCCCCCCCchhHHHHHHHHHHHHhhcCCChhhhHHHHhhhhccccCccccchhhhhh
Q psy843 16 TADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWFPVRKMRQK 95 (109)
Q Consensus 16 TsDG~tIVcwHP~~~fPYEhTKPIp~~d~~~~~~~lk~~~lk~~l~~~k~k~~e~~~eELsKmfyTTKHRWyPr~q~~~r 95 (109)
|.+| ||.--|+.-.+.---||||++-+ +++=+-.....+.-+.++.+.+-.|-|. .|-|+-.|+++
T Consensus 65 t~e~--vv~qLPe~Tt~LPReK~lPr~k~-----~TkWe~FAr~KGI~krKk~~lV~DEasg-------ew~pr~GY~~~ 130 (181)
T KOG1765|consen 65 TEEG--VVVQLPEPTTRLPREKPLPRPKP-----ETKWERFARKKGIEKRKKEKLVYDEASG-------EWKPRWGYKRK 130 (181)
T ss_pred cccc--eeEeCCCccccCccccCCCCCCC-----ccHHHHHHHHcCcchhhccCcceecccc-------ccccccCcccc
Confidence 4455 45555666555556689998766 4443332222222133334455677776 89998888776
Q ss_pred hhc
Q psy843 96 KRY 98 (109)
Q Consensus 96 r~k 98 (109)
...
T Consensus 131 ndd 133 (181)
T KOG1765|consen 131 NDD 133 (181)
T ss_pred ccc
Confidence 543
No 50
>PF12967 DUF3855: Domain of Unknown Function with PDB structure (DUF3855); InterPro: IPR024482 This domain forms an unusual alpha/beta fold where a six-stranded antiparallel beta-sheet is wrapped around a central alpha-helix, flanked by an additional alpha-helix and a small sub-domain consisting of a single beta-strand and a two-stranded antiparallel beta-sheet []. It shows weak structural similarities to phosphoribosylformylglycinamidine synthases and some thioesterase superfamily members, but its function is unknown.; PDB: 1O22_A.
Probab=23.06 E-value=48 Score=25.45 Aligned_cols=25 Identities=32% Similarity=0.539 Sum_probs=16.1
Q ss_pred cCCChhhhHHHHhhhhccccCccccc
Q psy843 64 KPKKEEFVRQDLMNITFTNKHRWFPV 89 (109)
Q Consensus 64 k~k~~e~~~eELsKmfyTTKHRWyPr 89 (109)
|+|...-+.+|.||-||-|| .|=|-
T Consensus 121 k~knr~e~v~~fmkyffesk-gw~pg 145 (158)
T PF12967_consen 121 KSKNRNEVVEEFMKYFFESK-GWNPG 145 (158)
T ss_dssp TT--HHHHHHHHHHHHHHHT-T--GG
T ss_pred hhccHHHHHHHHHHHHHhcc-CCCCC
Confidence 55554456799999999998 57653
No 51
>KOG1407|consensus
Probab=22.91 E-value=65 Score=27.48 Aligned_cols=21 Identities=43% Similarity=0.819 Sum_probs=15.1
Q ss_pred cceeeeecCCcEE-----------EEecCCCC
Q psy843 10 THKIAITADGTTV-----------VCWHPEQP 30 (109)
Q Consensus 10 ~~~iavTsDG~tI-----------VcwHP~~~ 30 (109)
.=.||-+.+|..+ |+|||...
T Consensus 254 ~IDIA~vetGd~~~eI~~~~~t~tVAWHPk~~ 285 (313)
T KOG1407|consen 254 FIDIAEVETGDRVWEIPCEGPTFTVAWHPKRP 285 (313)
T ss_pred eEEeEecccCCeEEEeeccCCceeEEecCCCc
Confidence 3457777777765 89999754
No 52
>cd08607 GDPD_GDE5 Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative mammalian GDE5 and similar proteins. Mammalian GDE5 is widely expressed in mammalian tissues, with highest expression in the spinal chord. Although its biological function remains unclear, mammalian GDE5 shows higher sequence homology to fungal and plant glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46) than to other bacterial and mammalian GP-GDEs. It may also hydrolyze glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. In addition to C-terminal GDPD domain, all members in this subfamily have a starch binding domain (CBM20) in the N-terminus, which suggests these proteins may play a distinct role in glycerol metabolism.
Probab=22.41 E-value=64 Score=25.09 Aligned_cols=15 Identities=27% Similarity=0.437 Sum_probs=11.1
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.|| ++|++|-
T Consensus 41 DV~lTkDg-~~VV~HD 55 (290)
T cd08607 41 DVQLTKDL-VPVVYHD 55 (290)
T ss_pred EEEEccCC-eEEEEcC
Confidence 46789999 6666774
No 53
>KOG2747|consensus
Probab=21.90 E-value=58 Score=28.51 Aligned_cols=14 Identities=7% Similarity=-0.052 Sum_probs=11.7
Q ss_pred hhHHHHhhhhcccc
Q psy843 70 FVRQDLMNITFTNK 83 (109)
Q Consensus 70 ~~~eELsKmfyTTK 83 (109)
+.|.|||++|.-+.
T Consensus 330 isI~~iS~~Tgi~~ 343 (396)
T KOG2747|consen 330 ISIKEISKETGIRP 343 (396)
T ss_pred ccHHHHHHhhCCCH
Confidence 88999999987654
No 54
>PF00400 WD40: WD domain, G-beta repeat; InterPro: IPR019781 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.; PDB: 2ZKQ_a 3CFV_B 3CFS_B 1PEV_A 1NR0_A 1VYH_T 3RFH_A 3O2Z_T 3FRX_C 3U5G_g ....
Probab=21.64 E-value=1.1e+02 Score=15.91 Aligned_cols=16 Identities=25% Similarity=0.347 Sum_probs=9.5
Q ss_pred ccceeeeecCCcEEEE
Q psy843 9 LTHKIAITADGTTVVC 24 (109)
Q Consensus 9 l~~~iavTsDG~tIVc 24 (109)
-+..|++.++|..|++
T Consensus 13 ~i~~i~~~~~~~~~~s 28 (39)
T PF00400_consen 13 SINSIAWSPDGNFLAS 28 (39)
T ss_dssp SEEEEEEETTSSEEEE
T ss_pred cEEEEEEeccccccee
Confidence 4556666666666554
No 55
>cd08581 GDPD_like_1 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=21.58 E-value=61 Score=24.76 Aligned_cols=16 Identities=31% Similarity=0.721 Sum_probs=12.4
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|.|| .+|+.|-.
T Consensus 33 DV~lTkDg-~~Vv~HD~ 48 (229)
T cd08581 33 DVQLSADG-VPVVFHDD 48 (229)
T ss_pred eeeECCCC-cEEEECCC
Confidence 46789999 77788864
No 56
>KOG2284|consensus
Probab=21.52 E-value=87 Score=28.80 Aligned_cols=51 Identities=27% Similarity=0.365 Sum_probs=31.3
Q ss_pred CcccccCCCCCCCCCchhHHHHHHHHHHHHhhcCCC-hhhhHHHHhhhhccccCc
Q psy843 32 PYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKK-EEFVRQDLMNITFTNKHR 85 (109)
Q Consensus 32 PYEhTKPIp~~d~~~~~~~lk~~~lk~~l~~~k~k~-~e~~~eELsKmfyTTKHR 85 (109)
-||.|--+|.+|+..+..+ ..++.... ..|.-+. -+++++|.- .|||.||.
T Consensus 483 gyefts~~~~td~~~s~~l-nn~f~~~i-~nf~~pq~l~~~iq~fe-~fyt~~~~ 534 (728)
T KOG2284|consen 483 GYEFTSSWPLTDPQLSTNL-NNQFAQDI-ANFHLPQILQPVIQEFE-KFYTGKHN 534 (728)
T ss_pred CceecccCCCCChhhcccc-chhHHHHH-HhccchHHHHHHHHHHH-HHhccccC
Confidence 5999999999888665433 33333322 3343332 356667664 59999884
No 57
>cd08575 GDPD_GDE4_like Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function is not elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests mammalian GDE4 may play some distinct role from other members of mammalian GDEs family. Also included in this subfamily are uncharacterized mammalian glycerophosphodiester phosphodiesterase domain-containing protein 3 (GDPD3) and similar proteins which display very high sequence homology to mammalian GDE4.
Probab=20.90 E-value=63 Score=25.17 Aligned_cols=16 Identities=38% Similarity=0.646 Sum_probs=11.9
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|+|| .+|++|=.
T Consensus 35 DV~lT~Dg-~~Vv~HD~ 50 (264)
T cd08575 35 DVQLTKDG-QVVVFHDW 50 (264)
T ss_pred EEEECCCC-CEEEEcCC
Confidence 46789999 67777754
No 58
>cd08573 GDPD_GDE1 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE1 (also known as MIR16, membrane interacting protein of RGS16) and their metazoan homologs. GDE1 is widely expressed in mammalian tissues, including the heart, brain, liver, and kidney. It shows sequence homology to bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), which catalyzes the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. GDE1 has been characterized as GPI-GDE (EC 3.1.4.44) that selectively hydrolyzes extracellular glycerophosphoinositol (GPI) to generate glycerol phosphate and inositol. It functions as an integral membrane-bound glycoprotein interacting with regulator of G protein signaling protein RGS16, and is modulated by G
Probab=20.31 E-value=65 Score=25.13 Aligned_cols=16 Identities=31% Similarity=0.518 Sum_probs=12.1
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|.|| .+||.|-.
T Consensus 33 DV~lTkDg-~~Vv~HD~ 48 (258)
T cd08573 33 DLEFTKDG-VPVLMHDD 48 (258)
T ss_pred EeeECCCC-cEEEECCC
Confidence 46789999 67777753
No 59
>cd08605 GDPD_GDE5_like_1_plant Glycerophosphodiester phosphodiesterase domain of uncharacterized plant glycerophosphodiester phosphodiesterase-like proteins similar to mammalian GDE5. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized plant glycerophosphodiester phosphodiesterase (GP-PDE)-like proteins. Members in this family show very high sequence homology to mammalian glycerophosphodiester phosphodiesterase GDE5 and are distantly related to plant GP-PDEs.
Probab=20.31 E-value=75 Score=24.75 Aligned_cols=15 Identities=40% Similarity=0.882 Sum_probs=10.2
Q ss_pred eeeeecCCcEEEEecC
Q psy843 12 KIAITADGTTVVCWHP 27 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP 27 (109)
.|-+|.||. +|++|-
T Consensus 45 DV~lTkDg~-~VV~HD 59 (282)
T cd08605 45 DVQVTRDGV-PVIWHD 59 (282)
T ss_pred EEEECcCCe-EEEECC
Confidence 467899995 555554
No 60
>cd08585 GDPD_like_3 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity with Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=20.02 E-value=64 Score=24.88 Aligned_cols=16 Identities=44% Similarity=0.848 Sum_probs=11.6
Q ss_pred eeeeecCCcEEEEecCC
Q psy843 12 KIAITADGTTVVCWHPE 28 (109)
Q Consensus 12 ~iavTsDG~tIVcwHP~ 28 (109)
.|-+|.|| .+|++|=.
T Consensus 40 DV~lT~Dg-~lVv~HD~ 55 (237)
T cd08585 40 DVQLTADG-EVVVFHDD 55 (237)
T ss_pred EeeECCCC-CEEEeccc
Confidence 46789999 66677743
Done!