Query psy987
Match_columns 114
No_of_seqs 93 out of 95
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 21:44:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy987.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/987hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05641 Agenet: Agenet domain 98.3 1.7E-06 3.8E-11 56.1 5.5 50 4-53 5-65 (68)
2 smart00743 Agenet Tudor-like d 98.0 2.3E-05 5E-10 49.0 5.8 49 5-53 8-58 (61)
3 PF11717 Tudor-knot: RNA bindi 96.4 0.0077 1.7E-07 37.5 4.4 39 11-49 12-54 (55)
4 cd04508 TUDOR Tudor domains ar 96.4 0.012 2.6E-07 34.6 5.0 43 6-50 4-48 (48)
5 smart00333 TUDOR Tudor domain. 95.9 0.028 6E-07 34.0 5.1 46 6-53 9-55 (57)
6 smart00561 MBT Present in Dros 95.4 0.077 1.7E-06 36.7 6.3 49 4-52 34-84 (96)
7 PF02820 MBT: mbt repeat; Int 93.6 0.4 8.7E-06 31.1 6.2 42 11-52 10-53 (73)
8 PF06003 SMN: Survival motor n 93.0 0.24 5.2E-06 39.9 5.3 41 11-53 81-123 (264)
9 PF00567 TUDOR: Tudor domain; 87.5 1.9 4.1E-05 28.2 5.1 41 10-52 63-104 (121)
10 PF02736 Myosin_N: Myosin N-te 71.4 18 0.00039 21.2 5.8 25 10-34 8-32 (42)
11 smart00557 IG_FLMN Filamin-typ 70.4 12 0.00026 24.8 4.6 33 2-34 32-64 (93)
12 KOG2039|consensus 65.0 12 0.00025 35.2 4.8 48 4-53 701-749 (875)
13 PF09465 LBR_tudor: Lamin-B re 64.7 12 0.00025 24.1 3.4 22 13-34 20-43 (55)
14 PF00630 Filamin: Filamin/ABP2 60.2 33 0.00071 22.2 5.1 33 2-34 42-78 (101)
15 cd05162 PWWP The PWWP domain, 57.2 16 0.00034 23.9 3.2 38 14-53 15-63 (87)
16 cd05841 BS69_related The PWWP 55.6 18 0.00039 24.7 3.3 38 14-52 21-58 (83)
17 PF12148 DUF3590: Protein of u 55.6 30 0.00064 23.9 4.4 43 10-52 7-57 (85)
18 PF00855 PWWP: PWWP domain; I 51.0 54 0.0012 20.8 4.9 37 13-51 14-58 (86)
19 cd05835 Dnmt3b_related The PWW 50.1 18 0.00039 24.2 2.6 41 7-51 10-58 (87)
20 PLN00104 MYST -like histone ac 46.0 39 0.00084 29.7 4.6 43 10-52 65-115 (450)
21 PF11623 DUF3252: Protein of u 43.1 56 0.0012 20.8 3.8 27 16-42 20-48 (53)
22 PF07039 DUF1325: SGF29 tudor- 42.9 37 0.00079 24.6 3.5 21 14-34 87-110 (130)
23 PF15057 DUF4537: Domain of un 41.4 49 0.0011 23.6 3.9 25 10-34 9-34 (124)
24 COG3390 Uncharacterized protei 39.7 16 0.00034 28.9 1.1 44 6-51 57-101 (196)
25 PF14319 Zn_Tnp_IS91: Transpos 38.1 30 0.00065 24.3 2.3 21 92-112 85-105 (111)
26 PF12318 FAD-SLDH: Membrane bo 37.8 20 0.00044 27.0 1.5 24 14-38 117-143 (168)
27 cd04452 S1_IF2_alpha S1_IF2_al 37.7 84 0.0018 19.2 4.1 23 12-34 3-25 (76)
28 COG3031 PulC Type II secretory 34.1 11 0.00024 31.1 -0.5 39 16-54 129-168 (275)
29 cd05834 HDGF_related The PWWP 33.7 41 0.00089 22.4 2.3 43 7-53 12-59 (83)
30 PF07653 SH3_2: Variant SH3 do 33.1 31 0.00068 20.5 1.5 15 6-20 24-40 (55)
31 cd06080 MUM1_like Mutated mela 32.2 57 0.0012 22.0 2.8 24 13-36 14-39 (80)
32 PF12945 YcgR_2: Flagellar pro 30.8 1.4E+02 0.003 18.7 4.9 34 3-36 6-42 (87)
33 PF02576 DUF150: Uncharacteris 30.2 2E+02 0.0044 20.4 6.1 35 11-45 99-135 (141)
34 PRK14639 hypothetical protein; 29.0 2.3E+02 0.0049 20.7 5.8 29 5-33 90-118 (140)
35 COG5301 Phage-related tail fib 28.5 57 0.0012 29.5 2.9 33 13-45 84-116 (587)
36 cd05698 S1_Rrp5_repeat_hs6_sc5 28.2 1.3E+02 0.0028 18.1 3.8 52 13-68 1-56 (70)
37 PF05304 DUF728: Protein of un 28.0 75 0.0016 22.6 2.9 19 12-32 44-62 (103)
38 smart00326 SH3 Src homology 3 27.7 76 0.0016 17.6 2.5 17 6-22 27-44 (58)
39 COG1959 Predicted transcriptio 27.0 23 0.0005 26.0 0.2 16 4-19 54-69 (150)
40 KOG3023|consensus 26.9 32 0.0007 28.5 1.1 24 87-114 198-221 (285)
41 PF03137 OATP: Organic Anion T 26.8 21 0.00046 31.2 0.0 9 13-21 226-234 (539)
42 cd03713 EFG_mtEFG_C EFG_mtEFG_ 26.6 94 0.002 19.5 3.0 40 62-101 3-47 (78)
43 PF08605 Rad9_Rad53_bind: Fung 26.5 1E+02 0.0022 22.6 3.6 56 9-68 18-81 (131)
44 KOG0644|consensus 24.0 48 0.001 31.9 1.7 26 10-35 994-1029(1113)
45 PF03869 Arc: Arc-like DNA bin 23.7 54 0.0012 20.0 1.4 17 93-109 3-19 (50)
46 PF15436 PGBA_N: Plasminogen-b 23.6 78 0.0017 25.3 2.6 91 17-112 47-146 (218)
47 PF11213 DUF3006: Protein of u 23.0 2.1E+02 0.0047 18.2 5.4 49 17-72 1-53 (71)
48 cd00174 SH3 Src homology 3 dom 22.6 1.1E+02 0.0024 16.7 2.5 16 6-21 24-40 (54)
49 PF14247 DUF4344: Domain of un 22.3 49 0.0011 26.2 1.3 15 3-17 38-54 (220)
50 cd05840 SPBC215_ISWI_like The 21.9 71 0.0015 21.7 1.9 42 7-52 10-65 (93)
51 TIGR00242 mraZ protein. Member 21.3 57 0.0012 23.6 1.4 15 98-112 86-100 (142)
52 PRK15095 FKBP-type peptidyl-pr 21.1 3.4E+02 0.0074 19.9 5.7 47 5-51 98-146 (156)
53 cd05707 S1_Rrp5_repeat_sc11 S1 20.9 2.1E+02 0.0045 17.2 3.7 21 14-34 2-22 (68)
54 smart00293 PWWP domain with co 20.8 1.8E+02 0.0038 18.0 3.4 40 7-50 10-61 (63)
55 PF04452 Methyltrans_RNA: RNA 20.7 2.6E+02 0.0056 21.3 5.0 30 5-34 22-51 (225)
56 cd02858 Esterase_N_term Estera 20.5 1.3E+02 0.0027 19.6 2.8 20 13-32 39-58 (85)
57 PF00018 SH3_1: SH3 domain; I 20.3 1.3E+02 0.0028 17.2 2.5 17 6-22 22-39 (48)
58 TIGR02010 IscR iron-sulfur clu 20.3 75 0.0016 22.4 1.8 17 3-19 53-69 (135)
No 1
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=98.31 E-value=1.7e-06 Score=56.09 Aligned_cols=50 Identities=32% Similarity=0.409 Sum_probs=36.1
Q ss_pred ceeeeecC----CCcEEeEEEEEEeCC-eEEEEEccCcce------eeeeecCccccCCCC
Q psy987 4 LEVEVCGE----NGAYYKVIVKMIKGD-FHVVEYLGCQST------FTEIVPPERMRQKNT 53 (114)
Q Consensus 4 l~VEv~g~----ngawwkA~Vk~vkgd-~~vV~f~~w~~~------~~eiv~~~RLrp~n~ 53 (114)
-.|||+.. .|+||.|+|.+..++ .+.|+|.+...+ .++.|+..+|||.++
T Consensus 5 ~~VEV~s~e~g~~gaWf~a~V~~~~~~~~~~V~Y~~~~~~~~~~~~l~e~V~~~~iRP~pP 65 (68)
T PF05641_consen 5 DEVEVSSDEDGFRGAWFPATVLKENGDDKYLVEYDDLPDEDGESPPLKEWVDARRIRPCPP 65 (68)
T ss_dssp -EEEEEE-SBTT--EEEEEEEEEEETT-EEEEEETT-SS--------EEEEEGGGEEE---
T ss_pred CEEEEEEcCCCCCcEEEEEEEEEeCCCcEEEEEECCcccccccccccEEEechheEECcCc
Confidence 36888864 689999999999999 999999763322 789999999999875
No 2
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=98.00 E-value=2.3e-05 Score=49.00 Aligned_cols=49 Identities=24% Similarity=0.386 Sum_probs=41.0
Q ss_pred eeeeec-CCCcEEeEEEEEEeC-CeEEEEEccCcceeeeeecCccccCCCC
Q psy987 5 EVEVCG-ENGAYYKVIVKMIKG-DFHVVEYLGCQSTFTEIVPPERMRQKNT 53 (114)
Q Consensus 5 ~VEv~g-~ngawwkA~Vk~vkg-d~~vV~f~~w~~~~~eiv~~~RLrp~n~ 53 (114)
.||++= ++|+||.|+|..+.+ +.+.|.|.+.....++.|+..+|||.+.
T Consensus 8 ~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~ 58 (61)
T smart00743 8 RVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPP 58 (61)
T ss_pred EEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCC
Confidence 477775 488999999999999 8899999974455689999999999864
No 3
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=96.40 E-value=0.0077 Score=37.53 Aligned_cols=39 Identities=28% Similarity=0.519 Sum_probs=34.4
Q ss_pred CCCcEEeEEEEEEeCC----eEEEEEccCcceeeeeecCcccc
Q psy987 11 ENGAYYKVIVKMIKGD----FHVVEYLGCQSTFTEIVPPERMR 49 (114)
Q Consensus 11 ~ngawwkA~Vk~vkgd----~~vV~f~~w~~~~~eiv~~~RLr 49 (114)
.+|.||.|+|.+++.+ .|.|-|.||+..+.+=++.+||+
T Consensus 12 ~~~~~y~A~I~~~r~~~~~~~YyVHY~g~nkR~DeWV~~~~i~ 54 (55)
T PF11717_consen 12 KDGQWYEAKILDIREKNGEPEYYVHYQGWNKRLDEWVPESRIR 54 (55)
T ss_dssp TTTEEEEEEEEEEEECTTCEEEEEEETTSTGCC-EEEETTTEE
T ss_pred CCCcEEEEEEEEEEecCCCEEEEEEcCCCCCCceeeecHHHcc
Confidence 5889999999999887 49999999999999999998885
No 4
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=96.39 E-value=0.012 Score=34.58 Aligned_cols=43 Identities=21% Similarity=0.307 Sum_probs=32.5
Q ss_pred eeeecC-CCcEEeEEEEEEe-CCeEEEEEccCcceeeeeecCccccC
Q psy987 6 VEVCGE-NGAYYKVIVKMIK-GDFHVVEYLGCQSTFTEIVPPERMRQ 50 (114)
Q Consensus 6 VEv~g~-ngawwkA~Vk~vk-gd~~vV~f~~w~~~~~eiv~~~RLrp 50 (114)
+-++-+ .|.||.|+|..+. ++.+.|.|..... .+.++...|||
T Consensus 4 c~a~~~~d~~wyra~V~~~~~~~~~~V~f~DyG~--~~~v~~~~l~~ 48 (48)
T cd04508 4 CLAKYSDDGKWYRAKITSILSDGKVEVFFVDYGN--TEVVPLSDLRP 48 (48)
T ss_pred EEEEECCCCeEEEEEEEEECCCCcEEEEEEcCCC--cEEEeHHHcCC
Confidence 334444 4999999999999 8899999998554 35577767764
No 5
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=95.93 E-value=0.028 Score=34.04 Aligned_cols=46 Identities=24% Similarity=0.485 Sum_probs=34.9
Q ss_pred eeeecCCCcEEeEEEEEEeC-CeEEEEEccCcceeeeeecCccccCCCC
Q psy987 6 VEVCGENGAYYKVIVKMIKG-DFHVVEYLGCQSTFTEIVPPERMRQKNT 53 (114)
Q Consensus 6 VEv~g~ngawwkA~Vk~vkg-d~~vV~f~~w~~~~~eiv~~~RLrp~n~ 53 (114)
|.++-+.|.||.|+|..+.+ ..+.|.|..... .+-|+.+.||+.+.
T Consensus 9 ~~a~~~d~~wyra~I~~~~~~~~~~V~f~D~G~--~~~v~~~~l~~l~~ 55 (57)
T smart00333 9 VAARWEDGEWYRARIIKVDGEQLYEVFFIDYGN--EEVVPPSDLRPLPE 55 (57)
T ss_pred EEEEeCCCCEEEEEEEEECCCCEEEEEEECCCc--cEEEeHHHeecCCC
Confidence 33343789999999999999 899999998444 35666777777653
No 6
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=95.36 E-value=0.077 Score=36.75 Aligned_cols=49 Identities=12% Similarity=0.080 Sum_probs=37.9
Q ss_pred ceeeeecCCCcEEeEEEEEEeCCeEEEEEccCcceeeee--ecCccccCCC
Q psy987 4 LEVEVCGENGAYYKVIVKMIKGDFHVVEYLGCQSTFTEI--VPPERMRQKN 52 (114)
Q Consensus 4 l~VEv~g~ngawwkA~Vk~vkgd~~vV~f~~w~~~~~ei--v~~~RLrp~n 52 (114)
|++--..+++.+|.|.|.++.|..+.|.|++|+..|.+- +..-+|.|..
T Consensus 34 LEavD~~~~~~i~vAtV~~v~g~~l~v~~dg~~~~~D~W~~~~S~~I~PvG 84 (96)
T smart00561 34 LEAVDPRNPSLICVATVVEVKGYRLLLHFDGWDDKYDFWCDADSPDIHPVG 84 (96)
T ss_pred EEEECCCCCceEEEEEEEEEECCEEEEEEccCCCcCCEEEECCCCCcccCc
Confidence 444445667899999999999999999999999875444 4555666663
No 7
>PF02820 MBT: mbt repeat; InterPro: IPR004092 The function of the malignant brain tumor (MBT) repeat is unknown, but is found in a number of nuclear proteins involved in transcriptional repression. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function. The crystal structure of the two MBT repeats of human SCM-like 2 protein has been reported. Each repeat consists of an extended "arm" and a globular core. The arm of the first repeat packs against the core of the second repeat and vice versa. The structure of the core-interacting part of each arm consists of an N-terminal alpha-helix and a turn of 310 helix connected by a short beta-strand. The core consists of an Src homology 3-like five-stranded beta-barrel followed by a C-terminal alpha-helix and another short beta-strand. Each arm interacts with its partner core in a similar way, with the orientation of the N-terminal helix relative to the barrel varying slightly. There are also extensive interactions between the two barrels [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P0K_A 3F70_B 3CEY_A 2VYT_A 2BIV_A 1OI1_A 3OQ5_A 2RJE_B 2RJD_A 2RI3_A ....
Probab=93.57 E-value=0.4 Score=31.10 Aligned_cols=42 Identities=14% Similarity=0.146 Sum_probs=33.4
Q ss_pred CCCcEEeEEEEEEeCCeEEEEEccCcceeee--eecCccccCCC
Q psy987 11 ENGAYYKVIVKMIKGDFHVVEYLGCQSTFTE--IVPPERMRQKN 52 (114)
Q Consensus 11 ~ngawwkA~Vk~vkgd~~vV~f~~w~~~~~e--iv~~~RLrp~n 52 (114)
++..+|.|.|..+.|+.+.|.|.+|+..+.+ -++.-+|-|..
T Consensus 10 ~~~~~~vAtV~~v~g~~l~v~~dg~~~~~d~w~~~~S~~i~PvG 53 (73)
T PF02820_consen 10 NPSLICVATVVKVCGGRLLVRYDGWDDDYDFWCHIDSPRIFPVG 53 (73)
T ss_dssp ECCEEEEEEEEEEETTEEEEEETTSTGGGEEEEETTSTTEEETT
T ss_pred CCCeEEEEEEEEEeCCEEEEEEcCCCCCccEEEECCCCCeeecc
Confidence 3678999999999999999999999975554 44556666663
No 8
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=92.96 E-value=0.24 Score=39.88 Aligned_cols=41 Identities=24% Similarity=0.434 Sum_probs=35.1
Q ss_pred CCCcEEeEEEEEEeCC--eEEEEEccCcceeeeeecCccccCCCC
Q psy987 11 ENGAYYKVIVKMIKGD--FHVVEYLGCQSTFTEIVPPERMRQKNT 53 (114)
Q Consensus 11 ~ngawwkA~Vk~vkgd--~~vV~f~~w~~~~~eiv~~~RLrp~n~ 53 (114)
+.|.||.|.|..|.++ .++|.|.++.. ++.|...-|+|...
T Consensus 81 ~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn--~e~v~l~dL~~~~~ 123 (264)
T PF06003_consen 81 EDGQYYPATIESIDEEDGTCVVVFTGYGN--EEEVNLSDLKPSEG 123 (264)
T ss_dssp TTSSEEEEEEEEEETTTTEEEEEETTTTE--EEEEEGGGEEETT-
T ss_pred CCCCEEEEEEEEEcCCCCEEEEEEcccCC--eEeeehhhhccccc
Confidence 5788999999999974 89999999876 58999999998864
No 9
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=87.51 E-value=1.9 Score=28.19 Aligned_cols=41 Identities=22% Similarity=0.342 Sum_probs=31.4
Q ss_pred cCCCcEEeEEE-EEEeCCeEEEEEccCcceeeeeecCccccCCC
Q psy987 10 GENGAYYKVIV-KMIKGDFHVVEYLGCQSTFTEIVPPERMRQKN 52 (114)
Q Consensus 10 g~ngawwkA~V-k~vkgd~~vV~f~~w~~~~~eiv~~~RLrp~n 52 (114)
.+.|.||.|.| ....++.+.|.|-.... ++.++...|++.+
T Consensus 63 ~~~~~w~Ra~I~~~~~~~~~~V~~iD~G~--~~~v~~~~l~~l~ 104 (121)
T PF00567_consen 63 SEDGRWYRAVITVDIDENQYKVFLIDYGN--TEKVSASDLRPLP 104 (121)
T ss_dssp TTTSEEEEEEEEEEECTTEEEEEETTTTE--EEEEEGGGEEE--
T ss_pred ecCCceeeEEEEEecccceeEEEEEecCc--eEEEcHHHhhhhC
Confidence 34789999999 88888999999997444 4557777888776
No 10
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=71.44 E-value=18 Score=21.16 Aligned_cols=25 Identities=16% Similarity=0.066 Sum_probs=22.4
Q ss_pred cCCCcEEeEEEEEEeCCeEEEEEcc
Q psy987 10 GENGAYYKVIVKMIKGDFHVVEYLG 34 (114)
Q Consensus 10 g~ngawwkA~Vk~vkgd~~vV~f~~ 34 (114)
=+.-||=+|.|+...|+.++|+-.+
T Consensus 8 D~~egfv~g~I~~~~g~~vtV~~~~ 32 (42)
T PF02736_consen 8 DPKEGFVKGEIIEEEGDKVTVKTED 32 (42)
T ss_dssp ESSSSEEEEEEEEEESSEEEEEETT
T ss_pred CCcccEEEEEEEEEcCCEEEEEECC
Confidence 3456799999999999999999998
No 11
>smart00557 IG_FLMN Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).
Probab=70.36 E-value=12 Score=24.76 Aligned_cols=33 Identities=39% Similarity=0.358 Sum_probs=29.0
Q ss_pred CcceeeeecCCCcEEeEEEEEEeCCeEEEEEcc
Q psy987 2 DELEVEVCGENGAYYKVIVKMIKGDFHVVEYLG 34 (114)
Q Consensus 2 ~~l~VEv~g~ngawwkA~Vk~vkgd~~vV~f~~ 34 (114)
++|.|.+.+..|.=-.+.|++.+++.|.|.|.-
T Consensus 32 ~~~~v~i~~p~g~~~~~~v~d~~dGty~v~y~P 64 (93)
T smart00557 32 GELEVEVTGPSGKKVPVEVKDNGDGTYTVSYTP 64 (93)
T ss_pred CcEEEEEECCCCCeeEeEEEeCCCCEEEEEEEe
Confidence 468899999888788999999999999999964
No 12
>KOG2039|consensus
Probab=65.00 E-value=12 Score=35.23 Aligned_cols=48 Identities=19% Similarity=0.320 Sum_probs=38.3
Q ss_pred ceeeeecCCCcEEeEEEEEEeC-CeEEEEEccCcceeeeeecCccccCCCC
Q psy987 4 LEVEVCGENGAYYKVIVKMIKG-DFHVVEYLGCQSTFTEIVPPERMRQKNT 53 (114)
Q Consensus 4 l~VEv~g~ngawwkA~Vk~vkg-d~~vV~f~~w~~~~~eiv~~~RLrp~n~ 53 (114)
+-+.=.+.-|.||.|.|+.|.+ +.+.|-|.+.-+ ++.++..||+|.++
T Consensus 701 ~c~A~y~~D~qwyRa~i~~V~~~~~~~V~yiDygn--~E~lp~~~l~~lp~ 749 (875)
T KOG2039|consen 701 LCVAKYSLDGQWYRALIVEVLDPESMEVFYIDYGN--IETLPFVRLKPLPP 749 (875)
T ss_pred eeeeeeccccceeeeeeeeeccCcceeEEEEecCc--ccccccccccCCCh
Confidence 3333344468899999999999 999999987554 58899999999884
No 13
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=64.74 E-value=12 Score=24.05 Aligned_cols=22 Identities=32% Similarity=0.264 Sum_probs=19.1
Q ss_pred CcEEeEEEEE--EeCCeEEEEEcc
Q psy987 13 GAYYKVIVKM--IKGDFHVVEYLG 34 (114)
Q Consensus 13 gawwkA~Vk~--vkgd~~vV~f~~ 34 (114)
..||+|+|.. .+.+.+.|.|..
T Consensus 20 ~lYYe~kV~~~d~~~~~y~V~Y~D 43 (55)
T PF09465_consen 20 SLYYEGKVLSYDSKSDRYTVLYED 43 (55)
T ss_dssp S-EEEEEEEEEETTTTEEEEEETT
T ss_pred CcEEEEEEEEecccCceEEEEEcC
Confidence 3499999998 889999999987
No 14
>PF00630 Filamin: Filamin/ABP280 repeat; InterPro: IPR017868 The many different actin cross-linking proteins share a common architecture, consisting of a globular actin-binding domain and an extended rod. Whereas their actin-binding domains consist of two calponin homology domains (see IPR001715 from INTERPRO), their rods fall into three families. The rod domain of the family including the Dictyostelium discoideum (Slime mould) gelation factor (ABP120) and human filamin (ABP280) is constructed from tandem repeats of a 100-residue motif that is glycine and proline rich []. The gelation factor's rod contains 6 copies of the repeat, whereas filamin has a rod constructed from 24 repeats. The resolution of the 3D structure of rod repeats from the gelation factor has shown that they consist of a beta-sandwich, formed by two beta-sheets arranged in an immunoglobulin-like fold [, ]. Because conserved residues that form the core of the repeats are preserved in filamin, the repeat structure should be common to the members of the gelation factor/filamin family. The head to tail homodimerisation is crucial to the function of the ABP120 and ABP280 proteins. This interaction involves a small portion at the distal end of the rod domains. For the gelation factor it has been shown that the carboxy-terminal repeat 6 dimerises through a double edge-to-edge extension of the beta-sheet and that repeat 5 contributes to dimerisation to some extent [, , ].; PDB: 2DI9_A 2EEC_A 2DIC_A 2EEA_A 2DMC_A 2EE9_A 2D7O_A 2D7N_A 2K7P_A 2NQC_A ....
Probab=60.17 E-value=33 Score=22.21 Aligned_cols=33 Identities=24% Similarity=0.212 Sum_probs=28.0
Q ss_pred CcceeeeecCCCc----EEeEEEEEEeCCeEEEEEcc
Q psy987 2 DELEVEVCGENGA----YYKVIVKMIKGDFHVVEYLG 34 (114)
Q Consensus 2 ~~l~VEv~g~nga----wwkA~Vk~vkgd~~vV~f~~ 34 (114)
+++.|.+.+.+|. --.+.|.+.+++.|.|.|.-
T Consensus 42 ~~~~v~i~~p~~~~~~~~~~~~v~~~~~G~y~v~y~p 78 (101)
T PF00630_consen 42 DEFQVTITSPDGKEEPVPVPVEVIDNGDGTYTVSYTP 78 (101)
T ss_dssp SEEEEEEESSSSESS--EEEEEEEEESSSEEEEEEEE
T ss_pred ceeEEEEeCCCCCccccccceEEEECCCCEEEEEEEe
Confidence 4678999998887 67788999999999999964
No 15
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=57.23 E-value=16 Score=23.89 Aligned_cols=38 Identities=21% Similarity=0.331 Sum_probs=25.8
Q ss_pred cEEeEEEEEEeC-----------CeEEEEEccCcceeeeeecCccccCCCC
Q psy987 14 AYYKVIVKMIKG-----------DFHVVEYLGCQSTFTEIVPPERMRQKNT 53 (114)
Q Consensus 14 awwkA~Vk~vkg-----------d~~vV~f~~w~~~~~eiv~~~RLrp~n~ 53 (114)
-||.|.|.+... +.+.|.|-+ +.+| --++..+|.|-..
T Consensus 15 pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg-~~~~-~wv~~~~l~pf~~ 63 (87)
T cd05162 15 PWWPALVVDPPKDSKKAKKKAKEGKVLVLFFG-DKTF-AWVGAERLKPFTE 63 (87)
T ss_pred CCCCEEEccccccchhhhccCCCCEEEEEEeC-CCcE-EEeCccceeeccc
Confidence 499999976654 688888887 3333 4456666766653
No 16
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=55.65 E-value=18 Score=24.66 Aligned_cols=38 Identities=16% Similarity=0.325 Sum_probs=27.7
Q ss_pred cEEeEEEEEEeCCeEEEEEccCcceeeeeecCccccCCC
Q psy987 14 AYYKVIVKMIKGDFHVVEYLGCQSTFTEIVPPERMRQKN 52 (114)
Q Consensus 14 awwkA~Vk~vkgd~~vV~f~~w~~~~~eiv~~~RLrp~n 52 (114)
-||.|+|-...+..+-|.|-+...++ --|+...|-|-+
T Consensus 21 p~WPAkV~~~~~~~~~V~FFG~t~~~-a~v~~~~i~~~~ 58 (83)
T cd05841 21 PYWPAKVMRVEDNQVDVRFFGGQHDR-AWIPSNNIQPIS 58 (83)
T ss_pred CCCCEEEeecCCCeEEEEEcCCCCCe-EEEehHHeeehh
Confidence 39999999999999999999855554 334444555444
No 17
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=55.63 E-value=30 Score=23.90 Aligned_cols=43 Identities=12% Similarity=0.205 Sum_probs=29.3
Q ss_pred cCCCcEEeEEEEEEeCC--------eEEEEEccCcceeeeeecCccccCCC
Q psy987 10 GENGAYYKVIVKMIKGD--------FHVVEYLGCQSTFTEIVPPERMRQKN 52 (114)
Q Consensus 10 g~ngawwkA~Vk~vkgd--------~~vV~f~~w~~~~~eiv~~~RLrp~n 52 (114)
-++|||.-|.|..+--. .|=|.|+.....-.+.++..-+||..
T Consensus 7 ~~~gAWfEa~i~~i~~~~~~~~e~viYhIkyddype~gvv~~~~~~iRpRA 57 (85)
T PF12148_consen 7 RNMGAWFEAQIVTITKKCMSDDEDVIYHIKYDDYPENGVVEMRSKDIRPRA 57 (85)
T ss_dssp TTT-EEEEEEEEEEEES-SSSSTTEEEEEEETT-GGG-EEEEEGGGEEE--
T ss_pred CCCcceEEEEEEEeeccCCCCCCCEEEEEEeccCCCcCceeccccccccee
Confidence 35899999999766542 67899998666666778888888876
No 18
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=51.04 E-value=54 Score=20.79 Aligned_cols=37 Identities=16% Similarity=0.277 Sum_probs=25.6
Q ss_pred CcEEeEEEEEE--------eCCeEEEEEccCcceeeeeecCccccCC
Q psy987 13 GAYYKVIVKMI--------KGDFHVVEYLGCQSTFTEIVPPERMRQK 51 (114)
Q Consensus 13 gawwkA~Vk~v--------kgd~~vV~f~~w~~~~~eiv~~~RLrp~ 51 (114)
..||.|+|.+. .++.+.|.|-+-. ++ --+...+|.|-
T Consensus 14 ~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg~~-~~-~wv~~~~i~~f 58 (86)
T PF00855_consen 14 YPWWPARVCDPDEKSKKKRKDGHVLVRFFGDN-DY-AWVKPSNIKPF 58 (86)
T ss_dssp SEEEEEEEEECCHCTSCSSSSTEEEEEETTTT-EE-EEEEGGGEEEC
T ss_pred CCCCceEEeecccccccCCCCCEEEEEecCCC-CE-EEECHHHhhCh
Confidence 45999999888 4678999998744 44 34445555544
No 19
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=50.08 E-value=18 Score=24.22 Aligned_cols=41 Identities=20% Similarity=0.294 Sum_probs=25.4
Q ss_pred eeecCCCcEEeEEEEEEeCC--------eEEEEEccCcceeeeeecCccccCC
Q psy987 7 EVCGENGAYYKVIVKMIKGD--------FHVVEYLGCQSTFTEIVPPERMRQK 51 (114)
Q Consensus 7 Ev~g~ngawwkA~Vk~vkgd--------~~vV~f~~w~~~~~eiv~~~RLrp~ 51 (114)
.+.|-+ ||.|+|.....+ .+.|.|-+ +.++ --++..+|-|-
T Consensus 10 K~kg~p--wWP~~V~~~~~~~~~~~~~~~~~V~fFG-s~~~-a~v~~~~l~pf 58 (87)
T cd05835 10 KIKGFP--WWPGRVVSITVTSKRPPVVGMRWVTWFG-SGTF-SEVSVDKLSPF 58 (87)
T ss_pred ecCCCC--CCCeEEechhhcccccCCCCeEEEEEeC-CCCE-eEECHHHCcCh
Confidence 445544 999999877554 37888877 3333 34455555554
No 20
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=46.05 E-value=39 Score=29.75 Aligned_cols=43 Identities=21% Similarity=0.147 Sum_probs=35.3
Q ss_pred cCCCcEEeEEEEEEeC--------CeEEEEEccCcceeeeeecCccccCCC
Q psy987 10 GENGAYYKVIVKMIKG--------DFHVVEYLGCQSTFTEIVPPERMRQKN 52 (114)
Q Consensus 10 g~ngawwkA~Vk~vkg--------d~~vV~f~~w~~~~~eiv~~~RLrp~n 52 (114)
++.|.|+.|.|-.+.. -.|-|-|.+|+...-+=|+.+||...+
T Consensus 65 ~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~rLdls~ 115 (450)
T PLN00104 65 RFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLEQLDLDT 115 (450)
T ss_pred CCCCCEEEEEEEEEeccCCCCCCCceEEEEEecCCccHhhccCHhhccccc
Confidence 3468899999988875 259999999998888899999996544
No 21
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=43.08 E-value=56 Score=20.82 Aligned_cols=27 Identities=19% Similarity=0.172 Sum_probs=22.1
Q ss_pred EeEEEEEEeCCeEEEEEcc--Ccceeeee
Q psy987 16 YKVIVKMIKGDFHVVEYLG--CQSTFTEI 42 (114)
Q Consensus 16 wkA~Vk~vkgd~~vV~f~~--w~~~~~ei 42 (114)
|.++|..+-++-+.|=|++ |+.--++.
T Consensus 20 y~G~VQRvsdgkaaVLFEGGnWdKlvTf~ 48 (53)
T PF11623_consen 20 YEGFVQRVSDGKAAVLFEGGNWDKLVTFR 48 (53)
T ss_dssp -EEEEEEEETTEEEEEEEETTEEEEEEEE
T ss_pred heEEEEEeeCCeEEEEecCCCceEEEEEE
Confidence 7899999999999999998 98654443
No 22
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=42.93 E-value=37 Score=24.61 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=18.3
Q ss_pred cEEeEEEEEE---eCCeEEEEEcc
Q psy987 14 AYYKVIVKMI---KGDFHVVEYLG 34 (114)
Q Consensus 14 awwkA~Vk~v---kgd~~vV~f~~ 34 (114)
+||+|.|... +.+.|.+.|++
T Consensus 87 ~FY~A~V~~~p~~~~~~y~l~Fed 110 (130)
T PF07039_consen 87 CFYPATVVSPPKKKSGEYKLKFED 110 (130)
T ss_dssp EEEEEEEEEE-SSTTS-EEEEECT
T ss_pred eEEEEEEEeCCCCCCCcEEEEEeC
Confidence 5999999998 88899999997
No 23
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=41.39 E-value=49 Score=23.61 Aligned_cols=25 Identities=32% Similarity=0.433 Sum_probs=20.7
Q ss_pred cCCCcEEeEEEEEE-eCCeEEEEEcc
Q psy987 10 GENGAYYKVIVKMI-KGDFHVVEYLG 34 (114)
Q Consensus 10 g~ngawwkA~Vk~v-kgd~~vV~f~~ 34 (114)
-++|-||.|.|+.. .++-++|+|.+
T Consensus 9 ~~DG~YY~GtV~~~~~~~~~lV~f~~ 34 (124)
T PF15057_consen 9 EEDGFYYPGTVKKCVSSGQFLVEFDD 34 (124)
T ss_pred CCCCcEEeEEEEEccCCCEEEEEECC
Confidence 35899999999776 78899999954
No 24
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.68 E-value=16 Score=28.93 Aligned_cols=44 Identities=25% Similarity=0.371 Sum_probs=35.3
Q ss_pred eeeecCCCcEEeEEEEEEeCCeEEEEEcc-CcceeeeeecCccccCC
Q psy987 6 VEVCGENGAYYKVIVKMIKGDFHVVEYLG-CQSTFTEIVPPERMRQK 51 (114)
Q Consensus 6 VEv~g~ngawwkA~Vk~vkgd~~vV~f~~-w~~~~~eiv~~~RLrp~ 51 (114)
.|-.|+.+.+|++.|-|=-|-|+| |.| .||+-+.-+..++.+-.
T Consensus 57 k~~i~ed~~~~R~rVvDpTGsF~V--yag~yqPEa~a~l~~ve~~~~ 101 (196)
T COG3390 57 KEGIGEDREYWRIRVVDPTGSFYV--YAGQYQPEAKAFLEDVEVPDL 101 (196)
T ss_pred ccCcCCcccEEEEEEecCCceEEE--EcCCCChHHHHHHHhccCCce
Confidence 344566688999999999999998 999 99987777777776543
No 25
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=38.11 E-value=30 Score=24.33 Aligned_cols=21 Identities=10% Similarity=0.176 Sum_probs=16.3
Q ss_pred CceeEEEecCchhHHHhhhcc
Q psy987 92 KTFHKFDIEVPLDVQELGLMR 112 (114)
Q Consensus 92 ~~f~k~~~~vpedlre~~~~~ 112 (114)
-..+++..+||.+||.++..+
T Consensus 85 ~~y~HvVFTlP~~L~~~~~~n 105 (111)
T PF14319_consen 85 VPYFHVVFTLPHELRPLFRQN 105 (111)
T ss_pred CCeEEEEEcCcHHHHHHHHHC
Confidence 457788888888888887654
No 26
>PF12318 FAD-SLDH: Membrane bound FAD containing D-sorbitol dehydrogenase ; InterPro: IPR024651 There are two types of membrane-bound D-sorbitol dehydrogenase: PQQ-SLDH (pyrroloquinoline quinone sorbitol dehydrogenase) and FAD-SLDH (FAD-containing sorbitol dehydrogenase). FAD-SLDH is involved in oxidation of D-sorbitol to L-sorbose and consists of a large, small and cytochrome c subunits []. This entry represents the small subunit of the FAD-containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria and contains a conserved ALM sequence motif. The role of the small subunit is unknown. Gluconate dehydrogenases and fructose dehydrogenases are also included in this entry.
Probab=37.77 E-value=20 Score=26.96 Aligned_cols=24 Identities=42% Similarity=0.405 Sum_probs=18.3
Q ss_pred cEEeEEEEEEeCCeEEEEEcc---Ccce
Q psy987 14 AYYKVIVKMIKGDFHVVEYLG---CQST 38 (114)
Q Consensus 14 awwkA~Vk~vkgd~~vV~f~~---w~~~ 38 (114)
|||.|.|-.-+ +--+|+|++ |+++
T Consensus 117 aWY~G~vg~~~-~a~~VaY~~ALm~~~~ 143 (168)
T PF12318_consen 117 AWYLGVVGDGK-DARVVAYEEALMYQPT 143 (168)
T ss_pred HeeeEEEecCC-CceEEehHHhhccHHh
Confidence 59999997666 666779986 6654
No 27
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=37.65 E-value=84 Score=19.21 Aligned_cols=23 Identities=30% Similarity=0.192 Sum_probs=20.8
Q ss_pred CCcEEeEEEEEEeCCeEEEEEcc
Q psy987 12 NGAYYKVIVKMIKGDFHVVEYLG 34 (114)
Q Consensus 12 ngawwkA~Vk~vkgd~~vV~f~~ 34 (114)
.|..+.|.|+.+....+.|+..+
T Consensus 3 ~G~~~~g~V~~v~~~g~~v~l~~ 25 (76)
T cd04452 3 EGELVVVTVKSIADMGAYVSLLE 25 (76)
T ss_pred CCCEEEEEEEEEEccEEEEEEcC
Confidence 57899999999999999999974
No 28
>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]
Probab=34.11 E-value=11 Score=31.06 Aligned_cols=39 Identities=23% Similarity=0.319 Sum_probs=35.5
Q ss_pred EeEEEEEEeCCeEEEEEcc-CcceeeeeecCccccCCCCC
Q psy987 16 YKVIVKMIKGDFHVVEYLG-CQSTFTEIVPPERMRQKNTN 54 (114)
Q Consensus 16 wkA~Vk~vkgd~~vV~f~~-w~~~~~eiv~~~RLrp~n~n 54 (114)
|+|++|.|..|.+++++.| -..+++.-....++++.+++
T Consensus 129 ~~a~ik~Vn~drVife~~G~~e~~~k~~~~~~~~~~v~p~ 168 (275)
T COG3031 129 YKALIKKVNNDRVIFEKNGVEELEFKVTKGEKSLTQVNPT 168 (275)
T ss_pred hHHHHHhhcCceEEEEcCCeeeeccccccCCcccccCCCC
Confidence 5699999999999999999 66799999999999999875
No 29
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=33.69 E-value=41 Score=22.42 Aligned_cols=43 Identities=19% Similarity=0.217 Sum_probs=28.9
Q ss_pred eeecCCCcEEeEEEEEEe-----CCeEEEEEccCcceeeeeecCccccCCCC
Q psy987 7 EVCGENGAYYKVIVKMIK-----GDFHVVEYLGCQSTFTEIVPPERMRQKNT 53 (114)
Q Consensus 7 Ev~g~ngawwkA~Vk~vk-----gd~~vV~f~~w~~~~~eiv~~~RLrp~n~ 53 (114)
.++|-+ ||.|+|-+.. +..+.|.|-+.. ++ --++...|-|-..
T Consensus 12 K~kGyp--~WPa~I~~~~~~~~~~~~~~V~FfGt~-~~-a~v~~~~l~pf~~ 59 (83)
T cd05834 12 KVKGYP--AWPARVDEPEDWKPPGKKYPVYFFGTH-ET-AFLKPEDLFPYTE 59 (83)
T ss_pred ecCCCC--CCCEEEecccccCCCCCEEEEEEeCCC-CE-eEECHHHceeccc
Confidence 455644 9999998887 578999998733 33 2356666655543
No 30
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=33.07 E-value=31 Score=20.53 Aligned_cols=15 Identities=13% Similarity=0.244 Sum_probs=11.7
Q ss_pred eeee--cCCCcEEeEEE
Q psy987 6 VEVC--GENGAYYKVIV 20 (114)
Q Consensus 6 VEv~--g~ngawwkA~V 20 (114)
|+|- .++++||++..
T Consensus 24 i~v~~~~~~~~ww~~~~ 40 (55)
T PF07653_consen 24 IEVLGEKDDDGWWLGEN 40 (55)
T ss_dssp EEEEEEECSTSEEEEEE
T ss_pred EEEEEeecCCCEEEEEE
Confidence 6665 55789999987
No 31
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=32.17 E-value=57 Score=21.98 Aligned_cols=24 Identities=17% Similarity=0.364 Sum_probs=18.5
Q ss_pred CcEEeEEEEEEe--CCeEEEEEccCc
Q psy987 13 GAYYKVIVKMIK--GDFHVVEYLGCQ 36 (114)
Q Consensus 13 gawwkA~Vk~vk--gd~~vV~f~~w~ 36 (114)
.-||.|+|.++. ...+.|.|-+-.
T Consensus 14 ~P~WPa~I~~~~~~~~k~~V~FfG~~ 39 (80)
T cd06080 14 YPWWPAVIKSISRKKQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEeeecCCCCEEEEEEeCCC
Confidence 349999999885 457888888744
No 32
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=30.84 E-value=1.4e+02 Score=18.69 Aligned_cols=34 Identities=24% Similarity=0.387 Sum_probs=23.1
Q ss_pred cceeeeecCCC--cEEeEEEEEEeCC-eEEEEEccCc
Q psy987 3 ELEVEVCGENG--AYYKVIVKMIKGD-FHVVEYLGCQ 36 (114)
Q Consensus 3 ~l~VEv~g~ng--awwkA~Vk~vkgd-~~vV~f~~w~ 36 (114)
.+.+|+...+| ..|+.+|-++.+| .+.|+...++
T Consensus 6 ~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P~~~ 42 (87)
T PF12945_consen 6 KIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMPMEK 42 (87)
T ss_dssp EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE---CC
T ss_pred EEEEEEECCCCceEEEEEEEEEECCCCEEEEEcCccC
Confidence 46677755544 4799999999999 8888887433
No 33
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=30.16 E-value=2e+02 Score=20.42 Aligned_cols=35 Identities=9% Similarity=-0.012 Sum_probs=23.4
Q ss_pred CCCcEEeEEEEEEeCCeEEEEEccC-c-ceeeeeecC
Q psy987 11 ENGAYYKVIVKMIKGDFHVVEYLGC-Q-STFTEIVPP 45 (114)
Q Consensus 11 ~ngawwkA~Vk~vkgd~~vV~f~~w-~-~~~~eiv~~ 45 (114)
++..+|.|++..+.++.+++++.+- + .+.+.+++.
T Consensus 99 ~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~ 135 (141)
T PF02576_consen 99 NGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSD 135 (141)
T ss_dssp SS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS-
T ss_pred CCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHH
Confidence 3456999999999999999999863 2 244444443
No 34
>PRK14639 hypothetical protein; Provisional
Probab=28.97 E-value=2.3e+02 Score=20.67 Aligned_cols=29 Identities=10% Similarity=0.139 Sum_probs=23.3
Q ss_pred eeeeecCCCcEEeEEEEEEeCCeEEEEEc
Q psy987 5 EVEVCGENGAYYKVIVKMIKGDFHVVEYL 33 (114)
Q Consensus 5 ~VEv~g~ngawwkA~Vk~vkgd~~vV~f~ 33 (114)
.|.|.-.++..|.|++..+.++.++++..
T Consensus 90 ~v~v~l~~~~~~~G~L~~~~~~~i~l~~~ 118 (140)
T PRK14639 90 LVKITTNEKEKFEGKIVSVDDENITLENL 118 (140)
T ss_pred EEEEEECCCcEEEEEEEEEeCCEEEEEEc
Confidence 35565556789999999999999998763
No 35
>COG5301 Phage-related tail fibre protein [General function prediction only]
Probab=28.49 E-value=57 Score=29.51 Aligned_cols=33 Identities=12% Similarity=0.324 Sum_probs=28.5
Q ss_pred CcEEeEEEEEEeCCeEEEEEccCcceeeeeecC
Q psy987 13 GAYYKVIVKMIKGDFHVVEYLGCQSTFTEIVPP 45 (114)
Q Consensus 13 gawwkA~Vk~vkgd~~vV~f~~w~~~~~eiv~~ 45 (114)
|+||.--|--.-.|.-+|.+-||.++|+--.+.
T Consensus 84 GGwwiREvGlfDadG~liavgncPeSYKpqm~e 116 (587)
T COG5301 84 GGWWIREVGLFDADGKLIAVGNCPESYKPQMEE 116 (587)
T ss_pred cceEEEEeeeecCCCCEEEEccCCccccccccC
Confidence 569999999999999999999999999655443
No 36
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.18 E-value=1.3e+02 Score=18.13 Aligned_cols=52 Identities=12% Similarity=0.220 Sum_probs=32.1
Q ss_pred CcEEeEEEEEEeCCeEEEEEcc-CcceeeeeecCccccC---CCCCCCCCCCceEEEEEc
Q psy987 13 GAYYKVIVKMIKGDFHVVEYLG-CQSTFTEIVPPERMRQ---KNTNPPIDAKTFHKFDIE 68 (114)
Q Consensus 13 gawwkA~Vk~vkgd~~vV~f~~-w~~~~~eiv~~~RLrp---~n~n~pm~K~~F~~ie~~ 68 (114)
|.=+.|+|+.+....+.|++.+ ++. .++...|.. .+....+..|+-.++.+.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~g----li~~s~l~~~~~~~~~~~~~~G~~i~v~v~ 56 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKG----FLPKSELSEAFIKDPEEHFRVGQVVKVKVL 56 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEE----EEEHHHcChhhcCCHHHcccCCCEEEEEEE
Confidence 4457899999999999999986 443 222222321 112234666777766655
No 37
>PF05304 DUF728: Protein of unknown function (DUF728); InterPro: IPR007968 This entry is represented by the Tobacco rattle virus, 16kDa protein; it is a family of uncharacterised viral proteins.
Probab=28.01 E-value=75 Score=22.63 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=13.6
Q ss_pred CCcEEeEEEEEEeCCeEEEEE
Q psy987 12 NGAYYKVIVKMIKGDFHVVEY 32 (114)
Q Consensus 12 ngawwkA~Vk~vkgd~~vV~f 32 (114)
|||||.|.+ |..+++-|-|
T Consensus 44 NCGWf~~i~--v~~~~~eVY~ 62 (103)
T PF05304_consen 44 NCGWFPAIS--VNDDTFEVYF 62 (103)
T ss_pred CCCceEEEE--EeccEEeeee
Confidence 899999986 4566655544
No 38
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=27.69 E-value=76 Score=17.55 Aligned_cols=17 Identities=12% Similarity=0.253 Sum_probs=12.1
Q ss_pred eeeecC-CCcEEeEEEEE
Q psy987 6 VEVCGE-NGAYYKVIVKM 22 (114)
Q Consensus 6 VEv~g~-ngawwkA~Vk~ 22 (114)
|++.+. +++||.++...
T Consensus 27 v~v~~~~~~~w~~~~~~~ 44 (58)
T smart00326 27 ITVLEKSDDGWWKGRLGR 44 (58)
T ss_pred EEEEEcCCCCeEEEEeCC
Confidence 555555 78899997654
No 39
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=26.99 E-value=23 Score=25.98 Aligned_cols=16 Identities=31% Similarity=0.391 Sum_probs=12.3
Q ss_pred ceeeeecCCCcEEeEE
Q psy987 4 LEVEVCGENGAYYKVI 19 (114)
Q Consensus 4 l~VEv~g~ngawwkA~ 19 (114)
|.-=+||.+|||.+|+
T Consensus 54 lV~S~rG~~GGy~Lar 69 (150)
T COG1959 54 LVKSVRGKGGGYRLAR 69 (150)
T ss_pred CEEeecCCCCCccCCC
Confidence 3344789999999986
No 40
>KOG3023|consensus
Probab=26.95 E-value=32 Score=28.51 Aligned_cols=24 Identities=21% Similarity=0.292 Sum_probs=17.9
Q ss_pred CCCCCCceeEEEecCchhHHHhhhccCC
Q psy987 87 PPIDAKTFHKFDIEVPLDVQELGLMRDL 114 (114)
Q Consensus 87 ~pi~~~~f~k~~~~vpedlre~~~~~~~ 114 (114)
--++=+++.+ ||.||+++|...|+
T Consensus 198 nqVnL~~cCv----vPpdLqafa~~hdi 221 (285)
T KOG3023|consen 198 NQVNLGQCCV----VPPDLQAFADRHDI 221 (285)
T ss_pred ceeecccccc----CCHHHHHHhhhcce
Confidence 4444556554 89999999999885
No 41
>PF03137 OATP: Organic Anion Transporter Polypeptide (OATP) family; InterPro: IPR004156 This family consists of several eukaryotic Organic-Anion-Transporting Polypeptides (OATPs). Several have been identified mostly in human and rat. Different OATPs vary in tissue distribution and substrate specificity. Since the numbering of different OATPs in particular species was based originally on the order of discovery, similarly numbered OATPs in humans and rats did not necessarily correspond in function, tissue distribution and substrate specificity (in spite of the name, some OATPs also transport organic cations and neutral molecules) so a scheme of using digits for rat OATPs and letters for human ones was introduced []. Prostaglandin transporter (PGT) proteins are also considered to be OATP family members. In addition, the methotrexate transporter OATK is closely related to OATPs. This family also includes several predicted proteins from Caenorhabditis elegans and Drosophila melanogaster. This similarity was not previously noted. Note: Members of this family are described (in the UniProtKB/Swiss-Prot database) as belonging to the SLC21 family of transporters.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 3MRR_P.
Probab=26.82 E-value=21 Score=31.20 Aligned_cols=9 Identities=22% Similarity=0.464 Sum_probs=0.0
Q ss_pred CcEEeEEEE
Q psy987 13 GAYYKVIVK 21 (114)
Q Consensus 13 gawwkA~Vk 21 (114)
||||++++-
T Consensus 226 GAWWLGfli 234 (539)
T PF03137_consen 226 GAWWLGFLI 234 (539)
T ss_dssp ---------
T ss_pred HHHHHHHHH
Confidence 899999974
No 42
>cd03713 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide
Probab=26.59 E-value=94 Score=19.54 Aligned_cols=40 Identities=18% Similarity=0.201 Sum_probs=22.0
Q ss_pred eEEEEEccCccHHHH----HhhcCCC-CCCCCCCCCceeEEEecC
Q psy987 62 FHKFDIEVPLDQSDW----LISKNGK-NTNPPIDAKTFHKFDIEV 101 (114)
Q Consensus 62 F~~ie~~vP~dl~Ei----~~r~r~~-n~n~pi~~~~f~k~~~~v 101 (114)
++.++|.+|+++..- +.+-|.. .+..+++.....++.+++
T Consensus 3 i~~~~I~~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~~~iP~ 47 (78)
T cd03713 3 IMKVEVTVPEEYMGDVIGDLSSRRGQILGTESRGGWKVIKAEVPL 47 (78)
T ss_pred EEEEEEEcCHHHHHHHHHHHHHcCCceEceeccCCcEEEEEEcCH
Confidence 678999999875332 2332222 223455555555555554
No 43
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=26.53 E-value=1e+02 Score=22.56 Aligned_cols=56 Identities=16% Similarity=0.097 Sum_probs=36.5
Q ss_pred ecCCCcEEeEEEEEEeCCe--EEEEEccCcceeeeeecCccccCCCC------CCCCCCCceEEEEEc
Q psy987 9 CGENGAYYKVIVKMIKGDF--HVVEYLGCQSTFTEIVPPERMRQKNT------NPPIDAKTFHKFDIE 68 (114)
Q Consensus 9 ~g~ngawwkA~Vk~vkgd~--~vV~f~~w~~~~~eiv~~~RLrp~n~------n~pm~K~~F~~ie~~ 68 (114)
+|-|.++|.|.+.....+. +.|.|+... .-+...-++.... +-.+.|.++.++-+.
T Consensus 18 ~~~~~~yYPa~~~~~~~~~~~~~V~Fedg~----~~i~~~dv~~LDlRIGD~Vkv~~~k~~yiV~Gl~ 81 (131)
T PF08605_consen 18 AGYNLKYYPATCVGSGVDRDRSLVRFEDGT----YEIKNEDVKYLDLRIGDTVKVDGPKVTYIVVGLE 81 (131)
T ss_pred ecCCCeEeeEEEEeecCCCCeEEEEEecCc----eEeCcccEeeeeeecCCEEEECCCCccEEEEEee
Confidence 4558899999998887766 999999533 2233333444542 124567777766666
No 44
>KOG0644|consensus
Probab=24.00 E-value=48 Score=31.95 Aligned_cols=26 Identities=23% Similarity=0.385 Sum_probs=20.2
Q ss_pred cCCCcEEeEEEEEEeC----------CeEEEEEccC
Q psy987 10 GENGAYYKVIVKMIKG----------DFHVVEYLGC 35 (114)
Q Consensus 10 g~ngawwkA~Vk~vkg----------d~~vV~f~~w 35 (114)
||.|+||-|.|-.++- +-|.|.|++-
T Consensus 994 ~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~~ 1029 (1113)
T KOG0644|consen 994 EEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDNT 1029 (1113)
T ss_pred CcCCceeeeeeeeccCCCCCCCCCcceeEEEEecCC
Confidence 5789999999988875 3477777654
No 45
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=23.67 E-value=54 Score=19.95 Aligned_cols=17 Identities=18% Similarity=0.356 Sum_probs=13.1
Q ss_pred ceeEEEecCchhHHHhh
Q psy987 93 TFHKFDIEVPLDVQELG 109 (114)
Q Consensus 93 ~f~k~~~~vpedlre~~ 109 (114)
+-.+|+|.+|++|++.-
T Consensus 3 ~~~~f~lRlP~~l~~~l 19 (50)
T PF03869_consen 3 KDPQFNLRLPEELKEKL 19 (50)
T ss_dssp CSEEEEEECEHHHHHHH
T ss_pred CCCceeeECCHHHHHHH
Confidence 34689999999987643
No 46
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=23.60 E-value=78 Score=25.28 Aligned_cols=91 Identities=11% Similarity=-0.045 Sum_probs=48.0
Q ss_pred eEEEEEEeCCeEEEEEccCcceeeeeecCccccCCCCCCCCCCCceE-EEEEccC--ccHHHHHhhc----CCCCCCCCC
Q psy987 17 KVIVKMIKGDFHVVEYLGCQSTFTEIVPPERMRQKNTNPPIDAKTFH-KFDIEVP--LDQSDWLISK----NGKNTNPPI 89 (114)
Q Consensus 17 kA~Vk~vkgd~~vV~f~~w~~~~~eiv~~~RLrp~n~n~pm~K~~F~-~ie~~vP--~dl~Ei~~r~----r~~n~n~pi 89 (114)
.|.|..++++...+.|.-.+.=-|.-++.-++-|... -.+.=+.|| +.-+-.| +.|.+|-+.. ..|-|.
T Consensus 47 ~a~V~~~~~g~A~~kf~~fd~L~Q~aLP~p~~~pk~G-D~vil~~~Y~rallIAPn~e~Y~~i~~~~~~i~fihpDl--- 122 (218)
T PF15436_consen 47 RAVVISKKNGVAKAKFSVFDSLKQDALPTPKMVPKKG-DEVILNYLYNRALLIAPNQETYEKIKSSYPNINFIHPDL--- 122 (218)
T ss_pred EEEEEEecCCeeEEEEeehhhhhhhcCCCCccccCCC-CEEEEeecccceEEEcCCHHHHHHHHHhCCCceEecHHH---
Confidence 3667888899999998654433333333333333321 233444566 5445567 4455553321 112221
Q ss_pred CCCc--eeEEEecCchhHHHhhhcc
Q psy987 90 DAKT--FHKFDIEVPLDVQELGLMR 112 (114)
Q Consensus 90 ~~~~--f~k~~~~vpedlre~~~~~ 112 (114)
=++- ..+. -+.++|+|++|...
T Consensus 123 ~aa~L~~~g~-~P~~~dfrkfc~~~ 146 (218)
T PF15436_consen 123 FAAFLSENGH-DPTREDFRKFCNQY 146 (218)
T ss_pred HHHHHHhcCC-CCCHHHHHHHHHHh
Confidence 1111 1243 78899999999754
No 47
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=22.98 E-value=2.1e+02 Score=18.24 Aligned_cols=49 Identities=27% Similarity=0.369 Sum_probs=36.0
Q ss_pred eEEEEEEeCCeEEEEEccCcceeeeeecCccccCCCCCCCCCCCceEEE----EEccCcc
Q psy987 17 KVIVKMIKGDFHVVEYLGCQSTFTEIVPPERMRQKNTNPPIDAKTFHKF----DIEVPLD 72 (114)
Q Consensus 17 kA~Vk~vkgd~~vV~f~~w~~~~~eiv~~~RLrp~n~n~pm~K~~F~~i----e~~vP~d 72 (114)
||.|--+-|+.+|+...+-+ -...++..+||+-- .-|+...+ .+.+...
T Consensus 1 k~ivDRiE~~~AVl~~~~~~--~~~~vp~~~LP~~~-----keGDvl~i~~~~~~~~d~e 53 (71)
T PF11213_consen 1 KAIVDRIEGDYAVLELEDGE--KEIDVPRSRLPEGA-----KEGDVLEIGEDGSIEIDPE 53 (71)
T ss_pred CeEEEEEeCCEEEEEECCCe--EEEEEEHHHCCCCC-----CcccEEEECCCceEEECHH
Confidence 57888899999999998755 35778888887543 36887777 6665543
No 48
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=22.61 E-value=1.1e+02 Score=16.71 Aligned_cols=16 Identities=13% Similarity=0.318 Sum_probs=10.5
Q ss_pred eeeecC-CCcEEeEEEE
Q psy987 6 VEVCGE-NGAYYKVIVK 21 (114)
Q Consensus 6 VEv~g~-ngawwkA~Vk 21 (114)
|.|... +++||.+...
T Consensus 24 v~v~~~~~~~w~~~~~~ 40 (54)
T cd00174 24 IEVLEKSDDGWWEGRLL 40 (54)
T ss_pred EEEEEcCCCCeEEEEEC
Confidence 445544 6779998753
No 49
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=22.31 E-value=49 Score=26.20 Aligned_cols=15 Identities=40% Similarity=1.117 Sum_probs=12.3
Q ss_pred cceeee--ecCCCcEEe
Q psy987 3 ELEVEV--CGENGAYYK 17 (114)
Q Consensus 3 ~l~VEv--~g~ngawwk 17 (114)
+|+|.. ||+.|+||=
T Consensus 38 ~l~i~~~~CGe~nA~yd 54 (220)
T PF14247_consen 38 DLTIRFAECGEDNAFYD 54 (220)
T ss_pred CeEEEEeecCCCCCccC
Confidence 567777 999999994
No 50
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=21.93 E-value=71 Score=21.74 Aligned_cols=42 Identities=17% Similarity=0.184 Sum_probs=23.4
Q ss_pred eeecCCCcEEeEEEEE--------------EeCCeEEEEEccCcceeeeeecCccccCCC
Q psy987 7 EVCGENGAYYKVIVKM--------------IKGDFHVVEYLGCQSTFTEIVPPERMRQKN 52 (114)
Q Consensus 7 Ev~g~ngawwkA~Vk~--------------vkgd~~vV~f~~w~~~~~eiv~~~RLrp~n 52 (114)
-++|-+ ||.|+|.+ .++..+.|.|-+ +.+| -=++..+|.|..
T Consensus 10 K~~GyP--wWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg-~~~~-~Wv~~~~l~pl~ 65 (93)
T cd05840 10 KVKGFP--AWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFP-DGDY-YWVPNKDLKPLT 65 (93)
T ss_pred eCCCCC--CCCEEECChHHCCHHHHhcccCCCCCeEEEEEeC-CCcE-EEEChhhcccCC
Confidence 455644 99999954 234567777765 2233 223455555443
No 51
>TIGR00242 mraZ protein. Members of this family contain two tandem copies of a domain described by pfam02381. This protein often is found with other genes of the dcw (division cell wall) gene cluster, including mraW, ftsI, murE, murF, ftsW, murG, etc.
Probab=21.33 E-value=57 Score=23.64 Aligned_cols=15 Identities=0% Similarity=0.147 Sum_probs=12.5
Q ss_pred EecCchhHHHhhhcc
Q psy987 98 DIEVPLDVQELGLMR 112 (114)
Q Consensus 98 ~~~vpedlre~~~~~ 112 (114)
.|-+|+.||++|...
T Consensus 86 Ri~iP~~lr~~a~l~ 100 (142)
T TIGR00242 86 RVLIANNLRNHAKLE 100 (142)
T ss_pred eEeCCHHHHHHhCCC
Confidence 577899999999765
No 52
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=21.13 E-value=3.4e+02 Score=19.89 Aligned_cols=47 Identities=13% Similarity=0.118 Sum_probs=33.0
Q ss_pred eeeeecCCCcEEeEEEEEEeCCeEEEEEcc--CcceeeeeecCccccCC
Q psy987 5 EVEVCGENGAYYKVIVKMIKGDFHVVEYLG--CQSTFTEIVPPERMRQK 51 (114)
Q Consensus 5 ~VEv~g~ngawwkA~Vk~vkgd~~vV~f~~--w~~~~~eiv~~~RLrp~ 51 (114)
.++.-+.+|..-.++|+.+-++.++|.|.. -.-+.++-+....+||.
T Consensus 98 ~~~~~~~~G~~~~~~V~~i~~~~v~vD~NHPLAGk~L~f~v~i~~v~~a 146 (156)
T PRK15095 98 IMLFTAMDGSEMPGVIREINGDSITVDFNHPLAGQTVHFDIEVLEIDPA 146 (156)
T ss_pred EEEEECCCCCEEEEEEEEEcCCEEEEECCCcCCCCEEEEEEEEEEeccC
Confidence 355667778888999999999999999965 22344555555555554
No 53
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.87 E-value=2.1e+02 Score=17.24 Aligned_cols=21 Identities=19% Similarity=-0.009 Sum_probs=18.3
Q ss_pred cEEeEEEEEEeCCeEEEEEcc
Q psy987 14 AYYKVIVKMIKGDFHVVEYLG 34 (114)
Q Consensus 14 awwkA~Vk~vkgd~~vV~f~~ 34 (114)
.=+.|+|+.+.+..+.|++.+
T Consensus 2 ~~v~g~V~~v~~~Gv~V~l~~ 22 (68)
T cd05707 2 DVVRGFVKNIANNGVFVTLGR 22 (68)
T ss_pred CEEEEEEEEEECccEEEEeCC
Confidence 457899999999999999975
No 54
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=20.76 E-value=1.8e+02 Score=17.97 Aligned_cols=40 Identities=13% Similarity=0.230 Sum_probs=22.5
Q ss_pred eeecCCCcEEeEEEEEEe------------CCeEEEEEccCcceeeeeecCccccC
Q psy987 7 EVCGENGAYYKVIVKMIK------------GDFHVVEYLGCQSTFTEIVPPERMRQ 50 (114)
Q Consensus 7 Ev~g~ngawwkA~Vk~vk------------gd~~vV~f~~w~~~~~eiv~~~RLrp 50 (114)
.+.|-+ ||.|+|-.-. +..+.|.|-+=. ++ --++..+|.|
T Consensus 10 K~~G~p--~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg~~-~~-awv~~~~l~p 61 (63)
T smart00293 10 KMKGFP--WWPALVVSPKETPDNIRKRKRFENLYPVLFFGDK-DT-AWISSSKLFP 61 (63)
T ss_pred ECCCCC--CCCeEEcCcccCChhHhhccCCCCEEEEEEeCCC-CE-EEECccceee
Confidence 455544 9999995443 346777776511 22 3455555544
No 55
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=20.71 E-value=2.6e+02 Score=21.33 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=25.8
Q ss_pred eeeeecCCCcEEeEEEEEEeCCeEEEEEcc
Q psy987 5 EVEVCGENGAYYKVIVKMIKGDFHVVEYLG 34 (114)
Q Consensus 5 ~VEv~g~ngawwkA~Vk~vkgd~~vV~f~~ 34 (114)
.|+|.-.+|.-|.|.|..+....+.+.-..
T Consensus 22 ~i~v~dg~g~~~~a~i~~i~~~~~~~~i~~ 51 (225)
T PF04452_consen 22 SIEVFDGDGGEYRAEITEISKKSATLRILE 51 (225)
T ss_dssp EEEEEESSSEEEEEEEEEEESSEEEEEEEE
T ss_pred EEEEEECCCCEEEEEEEECcCcEEEEEEee
Confidence 478888899999999999999999777653
No 56
>cd02858 Esterase_N_term Esterase N-terminal domain. Esterases catalyze the hydrolysis of organic esters to release an alcohol or thiol and acid. The term can be applied to enzymes that hydrolyze carboxylate, phosphate and sulphate esters, but is more often restricted to the first class of substrate. The N-terminus of esterase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=20.45 E-value=1.3e+02 Score=19.62 Aligned_cols=20 Identities=5% Similarity=0.124 Sum_probs=13.4
Q ss_pred CcEEeEEEEEEeCCeEEEEE
Q psy987 13 GAYYKVIVKMIKGDFHVVEY 32 (114)
Q Consensus 13 gawwkA~Vk~vkgd~~vV~f 32 (114)
.|||.+.+..+++.++.-.|
T Consensus 39 ~G~W~~~v~~l~~g~Y~Y~~ 58 (85)
T cd02858 39 AGVWSVTTGPLAPGIYTYSF 58 (85)
T ss_pred CeEEEEEECCCCCcEEEEEE
Confidence 35888888777777764444
No 57
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=20.31 E-value=1.3e+02 Score=17.24 Aligned_cols=17 Identities=24% Similarity=0.409 Sum_probs=10.9
Q ss_pred eeeec-CCCcEEeEEEEE
Q psy987 6 VEVCG-ENGAYYKVIVKM 22 (114)
Q Consensus 6 VEv~g-~ngawwkA~Vk~ 22 (114)
++|.. ++.+||+++...
T Consensus 22 i~v~~~~~~~Ww~~~~~~ 39 (48)
T PF00018_consen 22 IEVLEKSDDGWWKVRNES 39 (48)
T ss_dssp EEEEEESSSSEEEEEETT
T ss_pred EEEEEecCCCEEEEEECC
Confidence 34444 466899998653
No 58
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=20.30 E-value=75 Score=22.38 Aligned_cols=17 Identities=29% Similarity=0.255 Sum_probs=13.0
Q ss_pred cceeeeecCCCcEEeEE
Q psy987 3 ELEVEVCGENGAYYKVI 19 (114)
Q Consensus 3 ~l~VEv~g~ngawwkA~ 19 (114)
.|..-.+|.+|||.+|+
T Consensus 53 glv~s~~G~~Ggy~l~~ 69 (135)
T TIGR02010 53 GLVKSVRGPGGGYQLGR 69 (135)
T ss_pred CceEEEeCCCCCEeccC
Confidence 34556789999999886
Done!