Query psy842
Match_columns 111
No_of_seqs 70 out of 72
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 18:25:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy842.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/842hhsearch_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 2.5E-54 5.4E-59 305.2 8.5 96 10-108 1-96 (96)
2 KOG4106|consensus 100.0 4.8E-47 1E-51 277.4 8.6 97 11-111 28-125 (125)
3 PF13540 RCC1_2: Regulator of 79.4 2 4.3E-05 23.8 2.2 14 13-27 10-23 (30)
4 PF01436 NHL: NHL repeat; Int 69.4 4.7 0.0001 21.9 2.0 17 11-27 3-19 (28)
5 PF07676 PD40: WD40-like Beta 60.4 5.9 0.00013 22.0 1.3 12 14-25 13-24 (39)
6 PF06009 Laminin_II: Laminin D 55.2 6.1 0.00013 28.6 1.0 20 14-33 110-129 (138)
7 cd08556 GDPD Glycerophosphodie 53.9 8.6 0.00019 27.1 1.6 15 14-29 33-47 (189)
8 PF13186 SPASM: Iron-sulfur cl 52.1 9.6 0.00021 22.5 1.4 18 12-29 5-22 (64)
9 COG4118 Phd Antitoxin of toxin 49.0 20 0.00043 24.7 2.7 29 2-31 15-43 (84)
10 cd01747 GATase1_Glutamyl_Hydro 48.2 74 0.0016 25.6 6.2 13 27-40 210-222 (273)
11 COG1724 Predicted RNA binding 47.1 13 0.00028 25.2 1.5 18 17-34 34-52 (66)
12 PF03009 GDPD: Glycerophosphor 45.4 14 0.0003 26.8 1.5 15 14-29 30-44 (256)
13 cd08582 GDPD_like_2 Glyceropho 41.1 18 0.00039 27.3 1.6 17 14-31 33-49 (233)
14 cd08562 GDPD_EcUgpQ_like Glyce 39.6 19 0.00041 26.7 1.5 17 14-31 33-49 (229)
15 PF02604 PhdYeFM_antitox: Anti 39.2 33 0.00072 21.4 2.4 24 2-25 14-37 (75)
16 cd08567 GDPD_SpGDE_like Glycer 38.1 21 0.00046 27.0 1.6 17 14-31 35-51 (263)
17 cd08563 GDPD_TtGDE_like Glycer 37.7 21 0.00045 26.9 1.5 17 14-31 35-51 (230)
18 PF09561 RE_HpaII: HpaII restr 37.2 22 0.00047 30.7 1.7 15 14-29 295-309 (355)
19 KOG1784|consensus 37.2 32 0.0007 24.9 2.3 13 16-28 15-27 (96)
20 PF06004 DUF903: Bacterial pro 36.5 28 0.00061 22.1 1.8 12 15-26 3-14 (50)
21 TIGR01552 phd_fam prevent-host 36.4 34 0.00073 20.2 2.0 24 2-26 12-35 (52)
22 TIGR02608 delta_60_rpt delta-6 33.7 36 0.00078 21.7 1.9 15 13-27 4-18 (55)
23 PF09875 DUF2102: Uncharacteri 33.5 31 0.00067 25.2 1.8 19 84-102 61-79 (104)
24 cd08560 GDPD_EcGlpQ_like_1 Gly 31.8 29 0.00064 29.2 1.6 16 14-30 51-66 (356)
25 PHA03141 helicase-primase prim 31.5 39 0.00084 24.6 2.0 19 14-34 39-57 (101)
26 PF14132 DUF4299: Domain of un 30.4 36 0.00078 28.6 1.9 27 15-43 214-240 (304)
27 cd08579 GDPD_memb_like Glycero 30.0 33 0.00072 25.6 1.5 16 14-30 33-48 (220)
28 cd08561 GDPD_cytoplasmic_ScUgp 29.5 34 0.00074 26.1 1.5 15 14-29 33-47 (249)
29 cd08601 GDPD_SaGlpQ_like Glyce 29.4 37 0.00081 26.0 1.8 16 14-30 35-50 (256)
30 cd08572 GDPD_GDE5_like Glycero 28.3 42 0.00091 26.9 1.9 16 14-30 42-57 (293)
31 cd08559 GDPD_periplasmic_GlpQ_ 27.4 38 0.00082 27.0 1.5 15 14-29 35-49 (296)
32 KOG1559|consensus 27.3 1.2E+02 0.0025 26.1 4.4 13 74-86 311-323 (340)
33 cd08602 GDPD_ScGlpQ1_like Glyc 27.3 40 0.00087 27.4 1.7 15 14-29 35-49 (309)
34 cd08600 GDPD_EcGlpQ_like Glyce 27.1 39 0.00085 27.5 1.6 16 14-30 35-50 (318)
35 cd08604 GDPD_SHV3_repeat_2 Gly 26.8 39 0.00085 27.3 1.5 14 14-28 35-48 (300)
36 cd08571 GDPD_SHV3_plant Glycer 26.4 40 0.00088 27.3 1.5 16 14-30 35-50 (302)
37 PF15641 Tox-MPTase5: Metallop 26.0 14 0.0003 27.0 -1.1 17 30-46 22-38 (109)
38 PRK11143 glpQ glycerophosphodi 25.3 45 0.00097 27.9 1.6 16 14-30 61-76 (355)
39 PRK09454 ugpQ cytoplasmic glyc 24.9 46 0.001 25.7 1.5 15 14-29 42-56 (249)
40 smart00199 SCY Intercrine alph 24.8 58 0.0013 20.2 1.7 17 14-31 33-49 (59)
41 cd08566 GDPD_AtGDE_like Glycer 24.7 46 0.001 25.6 1.5 16 14-30 35-50 (240)
42 KOG4131|consensus 24.3 28 0.0006 29.2 0.2 15 16-30 62-76 (272)
43 cd08578 GDPD_NUC-2_fungi Putat 24.2 57 0.0012 26.9 2.0 15 14-29 35-49 (300)
44 cd08583 PI-PLCc_GDPD_SF_unchar 24.0 48 0.001 25.2 1.5 15 14-29 35-49 (237)
45 cd08574 GDPD_GDE_2_3_6 Glycero 23.9 53 0.0011 25.6 1.7 15 14-29 36-50 (252)
46 cd08603 GDPD_SHV3_repeat_1 Gly 23.3 52 0.0011 27.3 1.7 15 14-29 37-51 (299)
47 cd08568 GDPD_TmGDE_like Glycer 23.0 56 0.0012 24.6 1.6 15 14-29 34-48 (226)
48 cd08606 GDPD_YPL110cp_fungi Gl 23.0 64 0.0014 25.2 2.0 16 14-30 44-59 (286)
49 KOG1407|consensus 22.9 66 0.0014 27.5 2.2 19 14-32 256-285 (313)
50 PF06739 SBBP: Beta-propeller 22.7 1.2E+02 0.0026 17.5 2.7 23 12-34 15-38 (38)
51 PF08432 Vfa1: AAA-ATPase Vps4 22.7 50 0.0011 25.1 1.3 23 14-36 7-29 (182)
52 PF12967 DUF3855: Domain of Un 22.6 49 0.0011 25.4 1.2 26 65-91 120-145 (158)
53 cd08570 GDPD_YPL206cp_fungi Gl 22.6 58 0.0012 24.7 1.7 15 14-29 33-47 (234)
54 cd08607 GDPD_GDE5 Glycerophosp 22.3 66 0.0014 25.1 2.0 15 14-29 41-55 (290)
55 PRK04057 30S ribosomal protein 22.2 52 0.0011 26.1 1.4 24 1-24 85-110 (203)
56 COG4703 Uncharacterized protei 22.1 42 0.00092 23.2 0.8 25 1-26 1-35 (74)
57 PF09631 Sen15: Sen15 protein; 22.0 76 0.0016 21.8 2.0 25 3-27 60-89 (101)
58 PF14569 zf-UDP: Zinc-binding 20.9 35 0.00076 23.9 0.2 23 11-34 15-37 (80)
59 PF04939 RRS1: Ribosome biogen 20.7 1.6E+02 0.0035 22.7 3.8 79 3-98 40-119 (164)
60 cd08581 GDPD_like_1 Glyceropho 20.6 66 0.0014 24.6 1.6 16 14-30 33-48 (229)
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=2.5e-54 Score=305.21 Aligned_cols=96 Identities=41% Similarity=0.739 Sum_probs=92.1
Q ss_pred cccceeEEeeCCcEEEEecCCCCCCcccccCCCCCCCCCchhHHHHHHHHHHHHhhcCCchhhhHHHHhhhhcccccccc
Q psy842 10 PLTHKIAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWF 89 (111)
Q Consensus 10 s~~~~iavTsDG~tIVcwHP~~~fPYEhTKPIp~~d~~~~~~~lk~~~lk~~l~~~k~k~~~~~~eELskmf~TTKHrWy 89 (111)
+++++||||+||+|||||||+++||||||||||++++..+++++++|+|++.+++|+.+++|++||||||||||||||||
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 47889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhhhhcCCCCCCCC
Q psy842 90 PVRKMRQKKRYFKPLIPDR 108 (111)
Q Consensus 90 Pr~q~~~rr~k~~p~p~DR 108 (111)
||| ++||+|+|| |+||
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=4.8e-47 Score=277.42 Aligned_cols=97 Identities=33% Similarity=0.601 Sum_probs=89.8
Q ss_pred ccceeEEeeCCcEEEEecCCCCCCcccccCCCCCCCCCchhHHHHHHHHHHHHhhcCCch-hhhHHHHhhhhcccccccc
Q psy842 11 LTHKIAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKE-EFVRQDLMNITFTNKHRWF 89 (111)
Q Consensus 11 ~~~~iavTsDG~tIVcwHP~~~fPYEhTKPIp~~d~~~~~~~lk~~~lk~~l~~~k~k~~-~~~~eELskmf~TTKHrWy 89 (111)
|+++||||+||||||||||+++||||||||||++++.++|+++|||++++.+++++...+ +++++|||+||||||||||
T Consensus 28 lve~vavt~nGRTIvawHP~~~~PYEhTkPip~~s~~~~savvkdq~lkt~~~ak~s~~pe~p~~~eL~~~f~TtKHrWy 107 (125)
T KOG4106|consen 28 LVEKVAVTANGRTIVAWHPPQHFPYEHTKPIPLGSLTKKSAVVKDQSLKTSAAAKASSIPEEPVNAELKDIFYTTKHRWY 107 (125)
T ss_pred eeeeEEEecCCcEEEEecCCCCCCcccCCCCCCCccccchhhHHHHHHHHHHHHHHhhCCcchHHHHHHHHHhhhccccc
Confidence 677999999999999999999999999999999999999999999999999999877775 7788999999999999999
Q ss_pred cchhhhhhhhcCCCCCCCCCCC
Q psy842 90 PVRKMRQKKRYFKPLIPDREYL 111 (111)
Q Consensus 90 Pr~q~~~rr~k~~p~p~DR~yl 111 (111)
||+ |+.|+++++ +|+||+
T Consensus 108 pr~--R~~r~r~~~--~p~p~r 125 (125)
T KOG4106|consen 108 PRT--REERLRNVA--APIPRR 125 (125)
T ss_pred cch--HHHHHhcCC--CCCCCC
Confidence 999 777777887 888774
No 3
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=79.36 E-value=2 Score=23.77 Aligned_cols=14 Identities=57% Similarity=1.260 Sum_probs=10.9
Q ss_pred ceeEEeeCCcEEEEe
Q psy842 13 HKIAITADGTTVVCW 27 (111)
Q Consensus 13 ~~iavTsDG~tIVcw 27 (111)
..+||++|| .+.||
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 378999999 78888
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=69.44 E-value=4.7 Score=21.86 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=14.0
Q ss_pred ccceeEEeeCCcEEEEe
Q psy842 11 LTHKIAITADGTTVVCW 27 (111)
Q Consensus 11 ~~~~iavTsDG~tIVcw 27 (111)
....||+.+||..+||=
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 35679999999999983
No 5
>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=60.37 E-value=5.9 Score=21.99 Aligned_cols=12 Identities=25% Similarity=0.318 Sum_probs=9.6
Q ss_pred eeEEeeCCcEEE
Q psy842 14 KIAITADGTTVV 25 (111)
Q Consensus 14 ~iavTsDG~tIV 25 (111)
..++++||+.||
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 778999999987
No 6
>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=55.24 E-value=6.1 Score=28.63 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=5.5
Q ss_pred eeEEeeCCcEEEEecCCCCC
Q psy842 14 KIAITADGTTVVCWHPEQPF 33 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~~f 33 (111)
.|+|+.||.++|-|+|..+.
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 78999999999999997654
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=53.92 E-value=8.6 Score=27.12 Aligned_cols=15 Identities=33% Similarity=0.629 Sum_probs=13.4
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|.+|.|| ++||+|-
T Consensus 33 Dv~~tkDg-~~vv~Hd 47 (189)
T cd08556 33 DVQLTKDG-VLVVIHD 47 (189)
T ss_pred EeeEcCCC-CEEEEcC
Confidence 78899999 6888998
No 8
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=52.07 E-value=9.6 Score=22.49 Aligned_cols=18 Identities=28% Similarity=0.499 Sum_probs=14.5
Q ss_pred cceeEEeeCCcEEEEecC
Q psy842 12 THKIAITADGTTVVCWHP 29 (111)
Q Consensus 12 ~~~iavTsDG~tIVcwHP 29 (111)
...++|++||.+..|-+.
T Consensus 5 ~~~~~I~~dG~v~pC~~~ 22 (64)
T PF13186_consen 5 WNSLYIDPDGDVYPCCHD 22 (64)
T ss_pred CeEEEEeeCccEEeCCCC
Confidence 457899999999999433
No 9
>COG4118 Phd Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=49.02 E-value=20 Score=24.67 Aligned_cols=29 Identities=34% Similarity=0.440 Sum_probs=21.2
Q ss_pred hhhhhhhccccceeEEeeCCcEEEEecCCC
Q psy842 2 SSLLRRLVPLTHKIAITADGTTVVCWHPEQ 31 (111)
Q Consensus 2 ~~l~rr~~s~~~~iavTsDG~tIVcwHP~~ 31 (111)
|.||+|... .++|.||..|+.|+=-=|-.
T Consensus 15 S~lL~rV~a-GEev~IT~~G~PVArivp~~ 43 (84)
T COG4118 15 SELLRRVRA-GEEVIITKRGRPVARLVPLA 43 (84)
T ss_pred HHHHHHHhC-CCEEEEeeCCeEEEEEeecC
Confidence 667777654 66899999999887554433
No 10
>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=48.18 E-value=74 Score=25.56 Aligned_cols=13 Identities=38% Similarity=0.989 Sum_probs=10.6
Q ss_pred ecCCCCCCcccccC
Q psy842 27 WHPEQPFPYEHSLP 40 (111)
Q Consensus 27 wHP~~~fPYEhTKP 40 (111)
||||.. +||...-
T Consensus 210 FHPEks-~few~~~ 222 (273)
T cd01747 210 WHPEKN-AFEWKKS 222 (273)
T ss_pred cCCCcc-ccccccc
Confidence 799988 8997763
No 11
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=47.06 E-value=13 Score=25.19 Aligned_cols=18 Identities=33% Similarity=0.672 Sum_probs=14.1
Q ss_pred EeeC-CcEEEEecCCCCCC
Q psy842 17 ITAD-GTTVVCWHPEQPFP 34 (111)
Q Consensus 17 vTsD-G~tIVcwHP~~~fP 34 (111)
.-+| |+++|-.||..|.|
T Consensus 34 kHp~~~~vtVP~Hp~~dl~ 52 (66)
T COG1724 34 KHPDGGRVTVPFHPGEDLP 52 (66)
T ss_pred EcCCCCEEEecCCCccccC
Confidence 3455 78888889999876
No 12
>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=45.42 E-value=14 Score=26.76 Aligned_cols=15 Identities=33% Similarity=0.669 Sum_probs=10.5
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
-|-+|+|| .+||+|-
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 78899999 8888886
No 13
>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=41.14 E-value=18 Score=27.29 Aligned_cols=17 Identities=35% Similarity=0.745 Sum_probs=14.0
Q ss_pred eeEEeeCCcEEEEecCCC
Q psy842 14 KIAITADGTTVVCWHPEQ 31 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~ 31 (111)
.|.+|.|| ++||+|-..
T Consensus 33 Dv~lTkDg-~~Vv~HD~~ 49 (233)
T cd08582 33 DVRLTKDG-ELVCVHDPT 49 (233)
T ss_pred EEEEccCC-CEEEecCCc
Confidence 78899999 888899544
No 14
>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=39.62 E-value=19 Score=26.74 Aligned_cols=17 Identities=29% Similarity=0.622 Sum_probs=14.1
Q ss_pred eeEEeeCCcEEEEecCCC
Q psy842 14 KIAITADGTTVVCWHPEQ 31 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~ 31 (111)
.|.+|+|| .+|++|-..
T Consensus 33 Dv~~TkDg-~lvv~HD~~ 49 (229)
T cd08562 33 DVKLSGDG-TLVLIHDDT 49 (229)
T ss_pred EEeECCCC-CEEEEcCCC
Confidence 78899999 888888653
No 15
>PF02604 PhdYeFM_antitox: Antitoxin Phd_YefM, type II toxin-antitoxin system; InterPro: IPR006442 This entry is represented by Bacteriophage P1, prevent-host-death protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins is characterised by a region of about 55 amino acids toward the N-terminal end of bacterial proteins which are themselves only 85 amino acids, or thereabouts, in length. The best-characterised member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (IPR006440 from INTERPRO) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. ; PDB: 3DBO_A 2ODK_B 3G5O_D 2A6Q_B 3D55_C 3OEI_E 3CTO_C 3K33_D 3KH2_F 3HS2_C ....
Probab=39.16 E-value=33 Score=21.37 Aligned_cols=24 Identities=29% Similarity=0.364 Sum_probs=16.2
Q ss_pred hhhhhhhccccceeEEeeCCcEEE
Q psy842 2 SSLLRRLVPLTHKIAITADGTTVV 25 (111)
Q Consensus 2 ~~l~rr~~s~~~~iavTsDG~tIV 25 (111)
+.++.+...-.+.|+||.+|+-.+
T Consensus 14 ~~~l~~v~~~~~pv~It~~g~~~~ 37 (75)
T PF02604_consen 14 SELLDEVEEGEEPVIITKNGKPVA 37 (75)
T ss_dssp HHHHHHHHHCT-EEEEEETTEEEE
T ss_pred HHHHHHHHcCCCeEEEEECCCCCe
Confidence 345555555555699999998754
No 16
>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=38.11 E-value=21 Score=27.03 Aligned_cols=17 Identities=29% Similarity=0.571 Sum_probs=13.8
Q ss_pred eeEEeeCCcEEEEecCCC
Q psy842 14 KIAITADGTTVVCWHPEQ 31 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~ 31 (111)
.|.+|.|| ++||+|-..
T Consensus 35 DV~~TkDg-~~Vv~HD~~ 51 (263)
T cd08567 35 DLVLTKDG-VIVVSHDPK 51 (263)
T ss_pred EEEEcCCC-CEEEeCCCc
Confidence 78999999 788888653
No 17
>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=37.73 E-value=21 Score=26.90 Aligned_cols=17 Identities=35% Similarity=0.614 Sum_probs=14.1
Q ss_pred eeEEeeCCcEEEEecCCC
Q psy842 14 KIAITADGTTVVCWHPEQ 31 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~ 31 (111)
.|-+|.|| ++||+|-..
T Consensus 35 DV~~TkDg-~~Vv~HD~~ 51 (230)
T cd08563 35 DVHLTKDG-QLVVIHDET 51 (230)
T ss_pred EeeEcCCC-CEEEECCCC
Confidence 78899999 888888654
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=37.19 E-value=22 Score=30.69 Aligned_cols=15 Identities=40% Similarity=0.902 Sum_probs=11.9
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
=|.|..|| -|||||=
T Consensus 295 yivV~~dG-evlcYHi 309 (355)
T PF09561_consen 295 YIVVKEDG-EVLCYHI 309 (355)
T ss_pred EEEEeCCC-CEEEEEe
Confidence 47788888 5699994
No 19
>KOG1784|consensus
Probab=37.18 E-value=32 Score=24.85 Aligned_cols=13 Identities=38% Similarity=0.429 Sum_probs=10.9
Q ss_pred EEeeCCcEEEEec
Q psy842 16 AITADGTTVVCWH 28 (111)
Q Consensus 16 avTsDG~tIVcwH 28 (111)
.+|.|||+||.--
T Consensus 15 vIt~DGr~ivgsL 27 (96)
T KOG1784|consen 15 VITNDGRVIVGSL 27 (96)
T ss_pred EEecCCeEEEEEe
Confidence 5899999999753
No 20
>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=36.53 E-value=28 Score=22.05 Aligned_cols=12 Identities=42% Similarity=0.653 Sum_probs=10.0
Q ss_pred eEEeeCCcEEEE
Q psy842 15 IAITADGTTVVC 26 (111)
Q Consensus 15 iavTsDG~tIVc 26 (111)
+.-|.||++||+
T Consensus 3 vi~t~dG~~i~t 14 (50)
T PF06004_consen 3 VITTNDGRTIVT 14 (50)
T ss_dssp EEEETTSEEEEE
T ss_pred EEEeCCCcEEEe
Confidence 557899999995
No 21
>TIGR01552 phd_fam prevent-host-death family protein. This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family.
Probab=36.39 E-value=34 Score=20.21 Aligned_cols=24 Identities=29% Similarity=0.411 Sum_probs=16.0
Q ss_pred hhhhhhhccccceeEEeeCCcEEEE
Q psy842 2 SSLLRRLVPLTHKIAITADGTTVVC 26 (111)
Q Consensus 2 ~~l~rr~~s~~~~iavTsDG~tIVc 26 (111)
+.++.+...-. .|.||.+|+.++-
T Consensus 12 ~~~l~~v~~~~-pv~It~~g~~~av 35 (52)
T TIGR01552 12 GELLKRVRDGE-PVTITKRGRPVAV 35 (52)
T ss_pred HHHHHHHHCCC-CEEEEECCcceEE
Confidence 34555554434 8999999985553
No 22
>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=33.68 E-value=36 Score=21.72 Aligned_cols=15 Identities=27% Similarity=0.437 Sum_probs=12.5
Q ss_pred ceeEEeeCCcEEEEe
Q psy842 13 HKIAITADGTTVVCW 27 (111)
Q Consensus 13 ~~iavTsDG~tIVcw 27 (111)
..+++-+|||.||+=
T Consensus 4 ~~~~~q~DGkIlv~G 18 (55)
T TIGR02608 4 YAVAVQSDGKILVAG 18 (55)
T ss_pred EEEEECCCCcEEEEE
Confidence 468999999999863
No 23
>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=33.49 E-value=31 Score=25.23 Aligned_cols=19 Identities=26% Similarity=0.200 Sum_probs=16.0
Q ss_pred cccccccchhhhhhhhcCC
Q psy842 84 NKHRWFPVRKMRQKKRYFK 102 (111)
Q Consensus 84 TKHrWyPr~q~~~rr~k~~ 102 (111)
+|-||||.|.-|++|+..-
T Consensus 61 ~KdRGFppgD~RRCRa~rg 79 (104)
T PF09875_consen 61 VKDRGFPPGDPRRCRATRG 79 (104)
T ss_pred eecCCCCCCccHHhhhccC
Confidence 4999999998888888754
No 24
>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=31.75 E-value=29 Score=29.21 Aligned_cols=16 Identities=31% Similarity=0.711 Sum_probs=13.9
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|.+|.|| .+||+|=.
T Consensus 51 DV~lTkDg-~lVV~HD~ 66 (356)
T cd08560 51 DVTFTKDR-ELVCRHSQ 66 (356)
T ss_pred EeeEccCC-cEEEECCC
Confidence 78999999 88889974
No 25
>PHA03141 helicase-primase primase subunit; Provisional
Probab=31.55 E-value=39 Score=24.62 Aligned_cols=19 Identities=42% Similarity=1.101 Sum_probs=14.2
Q ss_pred eeEEeeCCcEEEEecCCCCCC
Q psy842 14 KIAITADGTTVVCWHPEQPFP 34 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~~fP 34 (111)
-..+|.+| =+|||++-+.|
T Consensus 39 ~fi~T~~G--p~cW~~~~~lP 57 (101)
T PHA03141 39 LFLLTTEG--PVCWHQKLPLP 57 (101)
T ss_pred eEEEeCCc--ceEecCCCCCC
Confidence 45688888 57999976554
No 26
>PF14132 DUF4299: Domain of unknown function (DUF4299)
Probab=30.37 E-value=36 Score=28.56 Aligned_cols=27 Identities=15% Similarity=0.240 Sum_probs=20.4
Q ss_pred eEEeeCCcEEEEecCCCCCCcccccCCCC
Q psy842 15 IAITADGTTVVCWHPEQPFPYEHSLPLPV 43 (111)
Q Consensus 15 iavTsDG~tIVcwHP~~~fPYEhTKPIp~ 43 (111)
=++|.|.+||.-+.|+++ |+....+..
T Consensus 214 YtLte~v~TILP~kP~v~--~~~~e~~~~ 240 (304)
T PF14132_consen 214 YTLTEGVDTILPYKPSVE--FENVEIVKN 240 (304)
T ss_pred EEEcCCCCEEecCCCCCC--cccccccCC
Confidence 478999999999999554 455555555
No 27
>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=30.01 E-value=33 Score=25.61 Aligned_cols=16 Identities=31% Similarity=0.457 Sum_probs=13.2
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|-+|.|| .+||+|-.
T Consensus 33 DV~~T~Dg-~~vv~HD~ 48 (220)
T cd08579 33 DVQETKDG-QFVVMHDA 48 (220)
T ss_pred EeeEcCCC-CEEEEcCC
Confidence 78899999 77888864
No 28
>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=29.53 E-value=34 Score=26.11 Aligned_cols=15 Identities=33% Similarity=0.536 Sum_probs=12.8
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|.+|.|| .+||+|-
T Consensus 33 Dv~~TkDg-~~Vv~HD 47 (249)
T cd08561 33 DVHATKDG-VLVVIHD 47 (249)
T ss_pred EeeECCCC-CEEEECC
Confidence 78899999 8888884
No 29
>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=29.40 E-value=37 Score=25.99 Aligned_cols=16 Identities=38% Similarity=0.679 Sum_probs=12.1
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|-+|+|| .+|++|-.
T Consensus 35 DV~lTkDg-~~Vv~HD~ 50 (256)
T cd08601 35 DLQMTKDG-VLVAMHDE 50 (256)
T ss_pred EeeECCCC-eEEEeCCC
Confidence 68899999 66666753
No 30
>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=28.28 E-value=42 Score=26.88 Aligned_cols=16 Identities=31% Similarity=0.534 Sum_probs=13.4
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|-+|.|| ++||+|=.
T Consensus 42 DV~lTkDG-~lVv~HD~ 57 (293)
T cd08572 42 DVQLTKDG-VPVIYHDF 57 (293)
T ss_pred EEEEccCC-eEEEEcCC
Confidence 68899999 88888853
No 31
>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=27.39 E-value=38 Score=26.99 Aligned_cols=15 Identities=33% Similarity=0.638 Sum_probs=12.6
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| ++||.|=
T Consensus 35 DV~lTkDg-~lVv~HD 49 (296)
T cd08559 35 DLVMTKDG-VLVARHD 49 (296)
T ss_pred eeEEccCC-CEEEecc
Confidence 78899999 7788884
No 32
>KOG1559|consensus
Probab=27.30 E-value=1.2e+02 Score=26.09 Aligned_cols=13 Identities=23% Similarity=0.358 Sum_probs=9.9
Q ss_pred HHHHhhhhccccc
Q psy842 74 RQDLMNITFTNKH 86 (111)
Q Consensus 74 ~eELskmf~TTKH 86 (111)
.++||.+.|.=|-
T Consensus 311 ekvlsnLIYnykP 323 (340)
T KOG1559|consen 311 EKVLSNLIYNYKP 323 (340)
T ss_pred HHHHHHHHhccCc
Confidence 4889999986553
No 33
>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=27.28 E-value=40 Score=27.40 Aligned_cols=15 Identities=33% Similarity=0.784 Sum_probs=12.8
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| .+||+|=
T Consensus 35 DVqlTkDg-~lVv~HD 49 (309)
T cd08602 35 DLVSTKDG-VLICRHE 49 (309)
T ss_pred eeeECCCC-cEEEeCC
Confidence 68899999 7888885
No 34
>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=27.14 E-value=39 Score=27.55 Aligned_cols=16 Identities=25% Similarity=0.472 Sum_probs=13.7
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|.+|.|| .+||+|-.
T Consensus 35 DV~lTkDg-~lVv~HD~ 50 (318)
T cd08600 35 DVVLTKDD-KLVVIHDH 50 (318)
T ss_pred eeeECcCC-cEEEeCCc
Confidence 68899999 88889964
No 35
>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=26.78 E-value=39 Score=27.26 Aligned_cols=14 Identities=21% Similarity=0.653 Sum_probs=12.1
Q ss_pred eeEEeeCCcEEEEec
Q psy842 14 KIAITADGTTVVCWH 28 (111)
Q Consensus 14 ~iavTsDG~tIVcwH 28 (111)
.|.+|.|| .+||.|
T Consensus 35 DV~lTkDG-~lVv~H 48 (300)
T cd08604 35 SVQMSKDG-VPFCLD 48 (300)
T ss_pred eeeEcCCC-CEEEec
Confidence 78899999 777888
No 36
>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=26.40 E-value=40 Score=27.28 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=13.2
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|.+|.|| .+||.|-.
T Consensus 35 DV~lTkDg-~lVv~HD~ 50 (302)
T cd08571 35 DVQLTKDG-VPICLPSI 50 (302)
T ss_pred eeeEcCCC-cEEEeCCc
Confidence 68899999 78888854
No 37
>PF15641 Tox-MPTase5: Metallopeptidase toxin 5
Probab=26.02 E-value=14 Score=26.96 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=11.3
Q ss_pred CCCCCcccccCCCCCCC
Q psy842 30 EQPFPYEHSLPLPVTEQ 46 (111)
Q Consensus 30 ~~~fPYEhTKPIp~~d~ 46 (111)
+.||||=.--=||+-.+
T Consensus 22 ~edf~~l~lt~~p~y~~ 38 (109)
T PF15641_consen 22 SEDFPYLNLTHIPQYNY 38 (109)
T ss_pred HhhcccccceeccccCh
Confidence 57888876666666333
No 38
>PRK11143 glpQ glycerophosphodiester phosphodiesterase; Provisional
Probab=25.25 E-value=45 Score=27.92 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=13.7
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|-+|.|| ++||+|-.
T Consensus 61 DV~lTkDg-~lVv~HD~ 76 (355)
T PRK11143 61 DLVMTKDD-QLVVLHDH 76 (355)
T ss_pred eeeEccCC-cEEEeCCc
Confidence 68899999 88899963
No 39
>PRK09454 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase; Provisional
Probab=24.87 E-value=46 Score=25.65 Aligned_cols=15 Identities=27% Similarity=0.523 Sum_probs=11.8
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| .+|++|=
T Consensus 42 DV~lT~Dg-~lVV~HD 56 (249)
T PRK09454 42 DAKLSADG-EIFLLHD 56 (249)
T ss_pred EeeECCCC-CEEEECC
Confidence 78899999 5667773
No 40
>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=24.80 E-value=58 Score=20.21 Aligned_cols=17 Identities=35% Similarity=0.565 Sum_probs=11.8
Q ss_pred eeEEeeCCcEEEEecCCC
Q psy842 14 KIAITADGTTVVCWHPEQ 31 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~ 31 (111)
=|..|.+|+. ||.+|+.
T Consensus 33 vIf~tk~g~~-~C~dP~~ 49 (59)
T smart00199 33 VIFTTKKGRK-VCADPKA 49 (59)
T ss_pred EEEEEeCCCE-EecCCCh
Confidence 3455667765 8999974
No 41
>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=24.67 E-value=46 Score=25.64 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=12.1
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|.+|+|| .+|++|-.
T Consensus 35 DV~~T~Dg-~~vv~HD~ 50 (240)
T cd08566 35 DVRRTKDG-VLVLMHDD 50 (240)
T ss_pred EeeEcCCC-CEEEECCC
Confidence 78899999 66666743
No 42
>KOG4131|consensus
Probab=24.32 E-value=28 Score=29.22 Aligned_cols=15 Identities=27% Similarity=0.733 Sum_probs=12.4
Q ss_pred EEeeCCcEEEEecCC
Q psy842 16 AITADGTTVVCWHPE 30 (111)
Q Consensus 16 avTsDG~tIVcwHP~ 30 (111)
++-+++.-||+|||-
T Consensus 62 a~ek~~e~IvAYHP~ 76 (272)
T KOG4131|consen 62 ALEKNAESIVAYHPP 76 (272)
T ss_pred HHHhCCceeEeecCc
Confidence 355889999999994
No 43
>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=24.17 E-value=57 Score=26.92 Aligned_cols=15 Identities=33% Similarity=0.410 Sum_probs=12.2
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| +.|+||=
T Consensus 35 DVqLTkDg-vpVV~HD 49 (300)
T cd08578 35 KVCVLKDG-TPVVAPE 49 (300)
T ss_pred EEEECcCC-EEEEECC
Confidence 67899999 7777773
No 44
>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=24.01 E-value=48 Score=25.16 Aligned_cols=15 Identities=33% Similarity=0.725 Sum_probs=12.7
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| .+|++|=
T Consensus 35 DV~lTkDg-~lVv~HD 49 (237)
T cd08583 35 DLSLTSDG-VLVARHS 49 (237)
T ss_pred EeeEccCC-CEEEEEC
Confidence 67899999 8888885
No 45
>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=23.87 E-value=53 Score=25.56 Aligned_cols=15 Identities=27% Similarity=0.443 Sum_probs=11.8
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| .+||.|=
T Consensus 36 DV~lTkDg-~lVV~HD 50 (252)
T cd08574 36 DVTISYDG-VPFLMHD 50 (252)
T ss_pred EEeEccCC-cEEEeCC
Confidence 68899999 6667774
No 46
>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=23.32 E-value=52 Score=27.35 Aligned_cols=15 Identities=27% Similarity=0.625 Sum_probs=12.9
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|.+|.|| +.||.|=
T Consensus 37 DV~lTkDg-vlVv~HD 51 (299)
T cd08603 37 DLQLTKDG-VGICLPD 51 (299)
T ss_pred EeeECcCC-cEEEeCC
Confidence 78899999 8888884
No 47
>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=22.97 E-value=56 Score=24.62 Aligned_cols=15 Identities=33% Similarity=0.581 Sum_probs=11.6
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| .+|+.|-
T Consensus 34 DV~lT~Dg-~~Vv~HD 48 (226)
T cd08568 34 DVWLTKDG-KLVVLHD 48 (226)
T ss_pred EEEEcCCC-CEEEECC
Confidence 68899999 5666773
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=22.96 E-value=64 Score=25.21 Aligned_cols=16 Identities=25% Similarity=0.306 Sum_probs=12.3
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|-+|.|| ++|++|-.
T Consensus 44 DV~lTkDg-~~VV~HD~ 59 (286)
T cd08606 44 DVQLTKDL-VPVIYHDF 59 (286)
T ss_pred EEEEccCC-EEEEeCCC
Confidence 78899999 66667754
No 49
>KOG1407|consensus
Probab=22.86 E-value=66 Score=27.49 Aligned_cols=19 Identities=47% Similarity=0.982 Sum_probs=15.2
Q ss_pred eeEEeeCCcEE-----------EEecCCCC
Q psy842 14 KIAITADGTTV-----------VCWHPEQP 32 (111)
Q Consensus 14 ~iavTsDG~tI-----------VcwHP~~~ 32 (111)
.||-+.+|..+ |+|||...
T Consensus 256 DIA~vetGd~~~eI~~~~~t~tVAWHPk~~ 285 (313)
T KOG1407|consen 256 DIAEVETGDRVWEIPCEGPTFTVAWHPKRP 285 (313)
T ss_pred EeEecccCCeEEEeeccCCceeEEecCCCc
Confidence 68888888876 99999754
No 50
>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=22.68 E-value=1.2e+02 Score=17.51 Aligned_cols=23 Identities=26% Similarity=0.404 Sum_probs=17.2
Q ss_pred cceeEEeeCCcEEEEecCCC-CCC
Q psy842 12 THKIAITADGTTVVCWHPEQ-PFP 34 (111)
Q Consensus 12 ~~~iavTsDG~tIVcwHP~~-~fP 34 (111)
...|||.++|...|+=.=.. +||
T Consensus 15 ~~~IavD~~GNiYv~G~T~~~~fp 38 (38)
T PF06739_consen 15 GNGIAVDSNGNIYVTGYTNGNDFP 38 (38)
T ss_pred EEEEEECCCCCEEEEEeecCCCCC
Confidence 45899999999998855444 554
No 51
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=22.66 E-value=50 Score=25.12 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=18.2
Q ss_pred eeEEeeCCcEEEEecCCCCCCcc
Q psy842 14 KIAITADGTTVVCWHPEQPFPYE 36 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~~~fPYE 36 (111)
.||.++-..++|||=|+..+=|-
T Consensus 7 kVa~~~~k~C~IC~KpsttVL~t 29 (182)
T PF08432_consen 7 KVAETDAKACFICYKPSTTVLIT 29 (182)
T ss_pred eeccCCCCceeEecCCCceEEec
Confidence 57888888899999998655443
No 52
>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=22.60 E-value=49 Score=25.44 Aligned_cols=26 Identities=31% Similarity=0.520 Sum_probs=16.4
Q ss_pred hcCCchhhhHHHHhhhhcccccccccc
Q psy842 65 FKPKKEEFVRQDLMNITFTNKHRWFPV 91 (111)
Q Consensus 65 ~k~k~~~~~~eELskmf~TTKHrWyPr 91 (111)
.|+|...-+.+|.||-||-|| .|=|-
T Consensus 120 vk~knr~e~v~~fmkyffesk-gw~pg 145 (158)
T PF12967_consen 120 VKSKNRNEVVEEFMKYFFESK-GWNPG 145 (158)
T ss_dssp STT--HHHHHHHHHHHHHHHT-T--GG
T ss_pred hhhccHHHHHHHHHHHHHhcc-CCCCC
Confidence 355555556799999999998 46553
No 53
>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=22.59 E-value=58 Score=24.68 Aligned_cols=15 Identities=40% Similarity=0.594 Sum_probs=12.4
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| .+|++|-
T Consensus 33 Dv~lTkDg-~~vv~HD 47 (234)
T cd08570 33 DVHLTKDG-VVVISHD 47 (234)
T ss_pred EeeEccCC-cEEEeCC
Confidence 67889999 7778884
No 54
>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=22.32 E-value=66 Score=25.10 Aligned_cols=15 Identities=27% Similarity=0.437 Sum_probs=11.7
Q ss_pred eeEEeeCCcEEEEecC
Q psy842 14 KIAITADGTTVVCWHP 29 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP 29 (111)
.|-+|.|| ++|++|-
T Consensus 41 DV~lTkDg-~~VV~HD 55 (290)
T cd08607 41 DVQLTKDL-VPVVYHD 55 (290)
T ss_pred EEEEccCC-eEEEEcC
Confidence 68899999 6666774
No 55
>PRK04057 30S ribosomal protein S3Ae; Validated
Probab=22.24 E-value=52 Score=26.08 Aligned_cols=24 Identities=38% Similarity=0.473 Sum_probs=19.0
Q ss_pred ChhhhhhhccccceeE--EeeCCcEE
Q psy842 1 MSSLLRRLVPLTHKIA--ITADGTTV 24 (111)
Q Consensus 1 ~~~l~rr~~s~~~~ia--vTsDG~tI 24 (111)
+.||.||-+|+.+.+. .|.||-.+
T Consensus 85 lrSlVrk~~S~Ie~~vdvkTkDGy~l 110 (203)
T PRK04057 85 LRSLVRRRTSKIDAIVDVTTKDGYKV 110 (203)
T ss_pred HHhHhccCceeEEEEEEEEcCCCCEE
Confidence 3589999999999554 69999653
No 56
>COG4703 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.14 E-value=42 Score=23.21 Aligned_cols=25 Identities=40% Similarity=0.663 Sum_probs=14.7
Q ss_pred Chhhhh---hhccccc-------eeEEeeCCcEEEE
Q psy842 1 MSSLLR---RLVPLTH-------KIAITADGTTVVC 26 (111)
Q Consensus 1 ~~~l~r---r~~s~~~-------~iavTsDG~tIVc 26 (111)
||+|++ ||.++++ .-.+-.|| ++||
T Consensus 1 ~ShLl~IinRL~~m~edggn~k~~rnFEr~G-~vv~ 35 (74)
T COG4703 1 MSHLLGIINRLEAMQEDGGNEKRQRNFERNG-EVVC 35 (74)
T ss_pred CcHHHHHHHHHHHHHhccCCchhhhhhhcCC-EEEE
Confidence 677765 7776666 12344566 5555
No 57
>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=21.95 E-value=76 Score=21.76 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=14.6
Q ss_pred hhhhhhcccc---c--eeEEeeCCcEEEEe
Q psy842 3 SLLRRLVPLT---H--KIAITADGTTVVCW 27 (111)
Q Consensus 3 ~l~rr~~s~~---~--~iavTsDG~tIVcw 27 (111)
.+|-+|.+.. . -||+.+|.+|||=|
T Consensus 60 ~~f~~l~~~~~~~~ri~LAiv~~DsTiVYY 89 (101)
T PF09631_consen 60 EVFDSLPNPSGDPKRILLAIVDDDSTIVYY 89 (101)
T ss_dssp HHHHHHHHHCT---EEEEEEE-TTS-EEEE
T ss_pred HHHHHhcccCCCCcEEEEEEEcCCCCEEEE
Confidence 4555555432 2 57888888899966
No 58
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=20.95 E-value=35 Score=23.94 Aligned_cols=23 Identities=30% Similarity=0.595 Sum_probs=10.0
Q ss_pred ccceeEEeeCCcEEEEecCCCCCC
Q psy842 11 LTHKIAITADGTTVVCWHPEQPFP 34 (111)
Q Consensus 11 ~~~~iavTsDG~tIVcwHP~~~fP 34 (111)
..+.|++|.||..+|+-| +--||
T Consensus 15 CGD~VGl~~~Ge~FVAC~-eC~fP 37 (80)
T PF14569_consen 15 CGDDVGLTENGEVFVACH-ECAFP 37 (80)
T ss_dssp S--B--B-SSSSB--S-S-SS---
T ss_pred ccCccccCCCCCEEEEEc-ccCCc
Confidence 445899999999999988 35555
No 59
>PF04939 RRS1: Ribosome biogenesis regulatory protein (RRS1); InterPro: IPR007023 This is a family of eukaryotic ribosomal biogenesis regulatory proteins.; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=20.69 E-value=1.6e+02 Score=22.70 Aligned_cols=79 Identities=19% Similarity=0.325 Sum_probs=46.4
Q ss_pred hhhhhhccccceeEEeeCCcEEEEecCCCCCCcccccCCCCCCCCCchhHHHHHHHHHHHHhhcCCchhhhHHHHhhhhc
Q psy842 3 SLLRRLVPLTHKIAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVRQDLMNITF 82 (111)
Q Consensus 3 ~l~rr~~s~~~~iavTsDG~tIVcwHP~~~fPYEhTKPIp~~d~~~~~~~lk~~~lk~~l~~~k~k~~~~~~eELskmf~ 82 (111)
.|+-+|-+| .+.-++|| +|+-=|...+.-=--||||.+-+ .++=+.-....+ +....=++|.|
T Consensus 40 ~Lin~l~~L--p~~~~~~g--~~~~LP~p~t~LPReKplPk~K~-----~TkWE~FA~~KG--------I~K~Kk~~lv~ 102 (164)
T PF04939_consen 40 LLINQLFEL--PTERTEDG--VLAKLPEPTTRLPREKPLPKPKP-----PTKWEKFAKKKG--------IKKRKKSKLVY 102 (164)
T ss_pred HHHHHHHhC--CceecCCC--eEEECCCCCccCcccCCCCCCCC-----CChHHHHHHHcC--------CccccCcCccc
Confidence 466666667 44455777 77777777777777789998665 344332221111 12222344444
Q ss_pred -ccccccccchhhhhhh
Q psy842 83 -TNKHRWFPVRKMRQKK 98 (111)
Q Consensus 83 -TTKHrWyPr~q~~~rr 98 (111)
-....|-||-.|....
T Consensus 103 DE~~~eW~prwGyk~~n 119 (164)
T PF04939_consen 103 DEETGEWVPRWGYKRAN 119 (164)
T ss_pred cccccchhhcccccccc
Confidence 3457899998775544
No 60
>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=20.59 E-value=66 Score=24.65 Aligned_cols=16 Identities=31% Similarity=0.721 Sum_probs=13.1
Q ss_pred eeEEeeCCcEEEEecCC
Q psy842 14 KIAITADGTTVVCWHPE 30 (111)
Q Consensus 14 ~iavTsDG~tIVcwHP~ 30 (111)
.|-+|.|| .+|+.|-.
T Consensus 33 DV~lTkDg-~~Vv~HD~ 48 (229)
T cd08581 33 DVQLSADG-VPVVFHDD 48 (229)
T ss_pred eeeECCCC-cEEEECCC
Confidence 78899999 77788864
Done!