Query psy11168
Match_columns 126
No_of_seqs 101 out of 427
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 19:48:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11168.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11168hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1959|consensus 100.0 3E-33 6.5E-38 238.1 5.9 121 1-126 601-729 (996)
2 PLN02701 alpha-mannosidase 100.0 1.4E-31 3E-36 236.5 15.5 122 1-126 660-790 (1050)
3 KOG1958|consensus 99.9 8.1E-26 1.8E-30 193.9 4.1 124 1-126 772-896 (1129)
4 PF07748 Glyco_hydro_38C: Glyc 99.3 1.8E-11 4E-16 99.3 11.4 121 1-126 107-241 (457)
5 PRK09819 alpha-mannosidase; Pr 93.7 1.6 3.4E-05 39.4 12.0 104 3-118 506-632 (875)
6 PF14128 DUF4295: Domain of un 68.6 6.6 0.00014 22.8 2.5 10 29-38 26-35 (47)
7 PF02762 Cbl_N3: CBL proto-onc 67.8 3 6.5E-05 26.9 1.1 14 28-41 22-35 (86)
8 COG0383 AMS1 Alpha-mannosidase 48.2 65 0.0014 29.7 6.5 55 53-114 660-720 (943)
9 cd01396 MeCP2_MBD MeCP2, MBD1, 47.8 20 0.00043 22.7 2.4 31 95-125 7-37 (77)
10 PF09121 Tower: Tower; InterP 43.4 14 0.0003 20.9 1.0 12 29-40 4-15 (42)
11 PF10411 DsbC_N: Disulfide bon 43.4 21 0.00045 21.1 1.9 13 112-124 31-43 (57)
12 COG5266 CbiK ABC-type Co2+ tra 40.8 70 0.0015 25.1 4.8 9 116-124 215-223 (264)
13 smart00084 NMU Neuromedin U. N 39.7 22 0.00049 17.9 1.3 13 28-40 13-25 (26)
14 cd00122 MBD MeCP2, MBD1, MBD2, 39.6 29 0.00062 20.7 2.1 32 94-125 5-36 (62)
15 PF02070 NMU: Neuromedin U; I 37.8 25 0.00054 17.6 1.3 13 27-39 12-24 (25)
16 PF02814 UreE_N: UreE urease a 36.0 30 0.00065 20.8 1.8 26 97-123 35-62 (65)
17 PF04376 ATE_N: Arginine-tRNA- 32.4 25 0.00055 22.2 1.1 13 28-40 44-56 (80)
18 PF12565 DUF3747: Protein of u 30.2 21 0.00045 26.5 0.5 8 117-124 91-98 (181)
19 PF01473 CW_binding_1: Putativ 26.3 47 0.001 14.9 1.2 12 113-124 7-18 (19)
20 cd01397 HAT_MBD Methyl-CpG bin 25.2 67 0.0014 20.3 2.0 33 93-125 4-36 (73)
21 PF06004 DUF903: Bacterial pro 24.2 46 0.001 19.4 1.1 29 97-125 6-36 (50)
22 PF04530 Viral_Beta_CD: Viral 22.4 30 0.00065 24.1 0.1 12 115-126 82-93 (122)
23 KOG1785|consensus 22.1 46 0.00099 28.0 1.1 50 14-65 257-311 (563)
24 PHA01516 hypothetical protein 22.1 28 0.00061 22.5 -0.1 10 117-126 48-57 (98)
25 KOG3527|consensus 21.0 44 0.00096 30.6 0.8 21 106-126 785-805 (975)
26 PRK14094 psbM photosystem II r 20.2 77 0.0017 18.4 1.5 19 104-122 24-42 (50)
No 1
>KOG1959|consensus
Probab=99.98 E-value=3e-33 Score=238.10 Aligned_cols=121 Identities=28% Similarity=0.518 Sum_probs=108.5
Q ss_pred CeeEEecCCCcEEEEEEEEEEeecCCC---CCCceeeEEeeCCCCc-cCCCCCCcEEEEeCCcEEEEEEEcC-ceEEEEE
Q psy11168 1 MKSITDKDSKYTSPINLDFVTYTSRKG---KEMSGAYLFLPRGEAK-SVPVTHPPVIIIQGPLVSMVIVELP-LVTHTVL 75 (126)
Q Consensus 1 L~si~~~~~g~~~~v~~~f~~Y~s~~~---~~~SGAYiF~P~~~~~-~~~~~~~~~~v~~G~lv~ev~~~~~-~~~~~~r 75 (126)
|++|....+|.+.+|.|+|+||.+..+ +|.|||||||| +.+. |+..+..++.|+.||||.||||.++ |++|++|
T Consensus 601 l~~v~~n~t~~t~~V~Q~f~~Y~~~~g~n~~q~SgAYiFRp-~~~~~~~~~~~vel~vv~G~LV~EVhQ~f~~wiSQviR 679 (996)
T KOG1959|consen 601 LKTVEMNQTGVTENVDQEFGYYKGYRGDNDKQASGAYIFRP-GQADIPIVSDQVELTVVDGPLVKEVHQQFNPWISQVIR 679 (996)
T ss_pred eEEEEecccCcceeeeeeeEEEEeecCCcCCccCcceEecC-CCCCccccccceEEEEecCchHHHHHHHHHHHHhheeE
Confidence 578888889999999999999998764 47899999999 5444 4556678899999999999999998 9999999
Q ss_pred EeecCCCCCCeEEEEEEe---eccCCCCeEEEEEEEeccccCCEEEecCCCCcC
Q psy11168 76 VNHVADSDDLGIDIQNLL---DIRQTVNTEVAMRLTTNIENQDVFYTDLNGYQS 126 (126)
Q Consensus 76 ly~~~~~~~~~ieie~~v---~i~~~~~kE~v~r~~t~i~n~~~FyTDsNG~em 126 (126)
||++. +++|+||.| |+.+..|||+|+||+|+|+++++||||||||||
T Consensus 680 vy~g~----~~~E~Ew~VGpIp~~d~~gkEvVtr~~t~i~S~g~fYTDSNGRe~ 729 (996)
T KOG1959|consen 680 VYEGK----NHVEFEWLVGPIPIDDGIGKEVVTRFSTEISSNGVFYTDSNGREM 729 (996)
T ss_pred ecCCC----cceEEEEEecceecCCCccceEEEEeccccccCceEEecCcHHHH
Confidence 99877 799999998 456889999999999999999999999999997
No 2
>PLN02701 alpha-mannosidase
Probab=99.97 E-value=1.4e-31 Score=236.48 Aligned_cols=122 Identities=29% Similarity=0.492 Sum_probs=107.8
Q ss_pred CeeEEecCCCcEEEEEEEEEEeecCCCCCCceeeEEeeCCCCccCCCCCCcEEEEeCCcEEEEEEEc------CceEEEE
Q psy11168 1 MKSITDKDSKYTSPINLDFVTYTSRKGKEMSGAYLFLPRGEAKSVPVTHPPVIIIQGPLVSMVIVEL------PLVTHTV 74 (126)
Q Consensus 1 L~si~~~~~g~~~~v~~~f~~Y~s~~~~~~SGAYiF~P~~~~~~~~~~~~~~~v~~G~lv~ev~~~~------~~~~~~~ 74 (126)
|++|.++.+|+...++++|.+|.+. .||||||||++++.|.....+.+.+.+|||++||++.+ +|++|++
T Consensus 660 L~si~~~~~g~~~~v~q~f~~Y~s~----~SGAYiFrP~~~~~p~~~~~~~~~v~~Gplv~eV~~~~~~~~~~s~isQ~i 735 (1050)
T PLN02701 660 LRKIKIHKNGSETVVGEEIGMYSSQ----GSGAYLFKPDGEAQPIVQAGGLVVVSEGPLVQEVHSVPKTKWEKSPLSRST 735 (1050)
T ss_pred eeEEEecccCceecceeeeeeecCC----CCcceEEcCCCCCcccCCCCceEEEEeCCEEEEEEEEeecccCCcceEEEE
Confidence 6789999999999999999999874 69999999999988754444567899999999999976 2899999
Q ss_pred EEeec-CCCCCCeEEEEEEee-cc-CCCCeEEEEEEEeccccCCEEEecCCCCcC
Q psy11168 75 LVNHV-ADSDDLGIDIQNLLD-IR-QTVNTEVAMRLTTNIENQDVFYTDLNGYQS 126 (126)
Q Consensus 75 rly~~-~~~~~~~ieie~~v~-i~-~~~~kE~v~r~~t~i~n~~~FyTDsNG~em 126 (126)
|||++ .+.++..+|+||+|+ |+ +..|||+||||+|+|+|+++||||||||||
T Consensus 736 RLY~~~~~~~~~~vE~e~~V~~ip~d~~~kEii~R~~T~i~s~~~FYTDsNG~qm 790 (1050)
T PLN02701 736 RLYHGGKSVQDLSVEKEYHVELLGHDFNDKELIVRFKTDIDNKRVFYSDLNGFQM 790 (1050)
T ss_pred EEecCCCccccceEEEEEEecCcccCCCCcEEEEEEeecccCCCeEEEcCcccee
Confidence 99996 566778999999994 33 778999999999999999999999999997
No 3
>KOG1958|consensus
Probab=99.92 E-value=8.1e-26 Score=193.89 Aligned_cols=124 Identities=40% Similarity=0.605 Sum_probs=107.9
Q ss_pred CeeEEecCCCcEEEEEEEEEEeecCCCCCCceeeEEeeCCCCcc-CCCCCCcEEEEeCCcEEEEEEEcCceEEEEEEeec
Q psy11168 1 MKSITDKDSKYTSPINLDFVTYTSRKGKEMSGAYLFLPRGEAKS-VPVTHPPVIIIQGPLVSMVIVELPLVTHTVLVNHV 79 (126)
Q Consensus 1 L~si~~~~~g~~~~v~~~f~~Y~s~~~~~~SGAYiF~P~~~~~~-~~~~~~~~~v~~G~lv~ev~~~~~~~~~~~rly~~ 79 (126)
++++..+.+++...+++.|..|+...+++.||||+|+|+|+|+| +....|.+++ +|+|++||.+.+.++.+.++ ++.
T Consensus 772 i~~~~~~~D~~~~~~q~~f~~y~~~~~~~~sgaylf~p~G~a~~~i~~~~p~v~v-~g~L~qev~~~~~~v~~~~~-~~~ 849 (1129)
T KOG1958|consen 772 IKSINSLSDNKHFESQVSFSNYGERISGDESGAYLFLPDGNAKPIIELQWPHVRV-KGPLVQEVSQFLKNVLHRLS-QNV 849 (1129)
T ss_pred hhhhhhcccCCCcccceeeccccccccCCCCceEEEccCCCCCCceecCCCeEEe-ecceeeeeccccchHHHhch-hhe
Confidence 46777888999999999999999998889999999999999999 6677788877 99999999999985544443 332
Q ss_pred CCCCCCeEEEEEEeeccCCCCeEEEEEEEeccccCCEEEecCCCCcC
Q psy11168 80 ADSDDLGIDIQNLLDIRQTVNTEVAMRLTTNIENQDVFYTDLNGYQS 126 (126)
Q Consensus 80 ~~~~~~~ieie~~v~i~~~~~kE~v~r~~t~i~n~~~FyTDsNG~em 126 (126)
.+..|..+||++.|||....|.|++|||+|++++++.||||+||+||
T Consensus 850 ~~~~G~~vei~~~vdi~~~~n~Ela~R~st~vds~~~FyTDlnG~Q~ 896 (1129)
T KOG1958|consen 850 RGYSGEEVEISNSVDIRKEDNTELAMRFSTDVDSGDLFYTDLNGMQM 896 (1129)
T ss_pred eccCCcceeeeceeecccccchhhhhhhhhcccCCceeeeccchhhh
Confidence 33355689999999999999999999999999999999999999997
No 4
>PF07748 Glyco_hydro_38C: Glycosyl hydrolases family 38 C-terminal domain; InterPro: IPR011682 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 38 GH38 from CAZY comprises enzymes with only one known activity; alpha-mannosidase (3.2.1.24 from EC) (3.2.1.114 from EC). This domain is found at the C terminus of glycosyl hydrolases from family 38.; GO: 0015923 mannosidase activity, 0006013 mannose metabolic process; PDB: 2WYI_A 2WYH_A 3LVT_A 3CZN_A 2FYV_A 3D50_A 3EJU_A 3EJS_A 3DX3_A 3BVX_A ....
Probab=99.32 E-value=1.8e-11 Score=99.35 Aligned_cols=121 Identities=26% Similarity=0.341 Sum_probs=84.1
Q ss_pred CeeEEecCCCcEEE--EEEEEEEeecCCC--------CCCceeeEEeeCCCCccCCCCCCcEEEEeCC--cEEEEEEEcC
Q psy11168 1 MKSITDKDSKYTSP--INLDFVTYTSRKG--------KEMSGAYLFLPRGEAKSVPVTHPPVIIIQGP--LVSMVIVELP 68 (126)
Q Consensus 1 L~si~~~~~g~~~~--v~~~f~~Y~s~~~--------~~~SGAYiF~P~~~~~~~~~~~~~~~v~~G~--lv~ev~~~~~ 68 (126)
|++|.++++|.... ...+|.+|....+ .+.+|||+|+|+|+......-...+ ...+. ++.++.....
T Consensus 107 i~sl~dk~~g~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~i~~~~~~-~~p~~~~~~~~~~~~~~ 185 (457)
T PF07748_consen 107 IKSLYDKKTGREYVDQDGNDFYIYEDIDGDYDISPLELQRSGAYLFVEDGPLRSSIRVEYKF-ELPKNLSLVKRSEQTGS 185 (457)
T ss_dssp EEEEEETTTS-EEEEEECEEEEEEEBTTSCTTE-SCCCGSEECCEEEEESSSEEEEEEEEEE-EEESCBECEEEESCEEE
T ss_pred EEEEEEccCCeEEEeecCCceeEeccccccccccccccccCceEEEEecCCceEEEEEEEEE-eccCCcEEEEEEEeccc
Confidence 46889999999999 9999999976432 2369999999998764310000000 01111 2344443344
Q ss_pred -ceEEEEEEeecCCCCCCeEEEEEEee-ccCCCCeEEEEEEEeccccCCEEEecCCCCcC
Q psy11168 69 -LVTHTVLVNHVADSDDLGIDIQNLLD-IRQTVNTEVAMRLTTNIENQDVFYTDLNGYQS 126 (126)
Q Consensus 69 -~~~~~~rly~~~~~~~~~ieie~~v~-i~~~~~kE~v~r~~t~i~n~~~FyTDsNG~em 126 (126)
.+.+.+|||++. +.||+++.|+ +.....+|+.++|.|+|+++..||+|.||+++
T Consensus 186 ~~i~~~i~L~~~~----~~ie~~~~vdn~~~~~~~~l~~~f~t~i~~~~~~~~~~fG~~~ 241 (457)
T PF07748_consen 186 SRITQTIRLYKGS----PRIEFETEVDNWAEDHRKELRVRFPTNIDSDEAFYDDQFGFIE 241 (457)
T ss_dssp EEEEEEEEEETTE----SSEEEEEEEEE-TTSCEEEEEEEEEES-S-TCEEEEESTTEEE
T ss_pred eEEEEEEEEecCc----eEEEEEEEecccccCCceeEEEEeecCCCCCCEEEECCCCeEE
Confidence 788999999877 7999999998 65433359999999999999999999999864
No 5
>PRK09819 alpha-mannosidase; Provisional
Probab=93.67 E-value=1.6 Score=39.35 Aligned_cols=104 Identities=20% Similarity=0.204 Sum_probs=62.8
Q ss_pred eEEecCCCcEEEEEEEEEEeecCCCCCCceeeEEeeCCCCccC--CCCCCcEEEEeCCcEEEEEEEcC------------
Q psy11168 3 SITDKDSKYTSPINLDFVTYTSRKGKEMSGAYLFLPRGEAKSV--PVTHPPVIIIQGPLVSMVIVELP------------ 68 (126)
Q Consensus 3 si~~~~~g~~~~v~~~f~~Y~s~~~~~~SGAYiF~P~~~~~~~--~~~~~~~~v~~G~lv~ev~~~~~------------ 68 (126)
+|.+|.+|... .. ++.+.- ..+..-||-|.|.-....+ ......+.+.+|++..++.....
T Consensus 506 ~l~dk~~gr~~--~~-~~~~~d--~~d~gD~yd~~p~~~d~~~~~~~~~~~~~v~~~~~~~~~~i~~~~~~p~~~~~r~~ 580 (875)
T PRK09819 506 TIVDKKSGKTY--DR-QLIIEE--NGDDGDEYDYSPPREDWVITSAEAVPSVEISHSAWQSRAVIRYRLAVPKNLEERAA 580 (875)
T ss_pred EEEECCCCcEE--ec-eEEEEe--cCcCCCCcccCCCCCCCEEeccCCcceEEEEEcCCeEEEEEEEEEeCCcChhhHhh
Confidence 46667777654 22 233322 1244558988874332222 12235678889999888776432
Q ss_pred -------ceEEEEEEeecCCCCCCeEEEEEEeeccCCCCeEEEEE--EEeccccCCEEE
Q psy11168 69 -------LVTHTVLVNHVADSDDLGIDIQNLLDIRQTVNTEVAMR--LTTNIENQDVFY 118 (126)
Q Consensus 69 -------~~~~~~rly~~~~~~~~~ieie~~v~i~~~~~kE~v~r--~~t~i~n~~~Fy 118 (126)
.+.+.++|+++. +.|++...|+. ..++..+| |.++|.+...+|
T Consensus 581 ~~~~~~~~i~~~i~L~~~s----~~i~~~~~vdw---~~~~~~Lrv~fp~~i~~~~~~~ 632 (875)
T PRK09819 581 GQKTGRMPVKLVVTLSKNS----RRIDFDVNLDN---QADDHRLRVLFPTEIASKFSLA 632 (875)
T ss_pred ccccceEEEEEEEEEecCC----CEEEEEEEEec---cccceEEEEEccCCCCCCceEc
Confidence 456888888665 78999999854 34445555 457777666443
No 6
>PF14128 DUF4295: Domain of unknown function (DUF4295)
Probab=68.59 E-value=6.6 Score=22.79 Aligned_cols=10 Identities=40% Similarity=0.650 Sum_probs=8.3
Q ss_pred CCceeeEEee
Q psy11168 29 EMSGAYLFLP 38 (126)
Q Consensus 29 ~~SGAYiF~P 38 (126)
.++|||.|.-
T Consensus 26 pKTGaYtFkE 35 (47)
T PF14128_consen 26 PKTGAYTFKE 35 (47)
T ss_pred CCCcceEEEE
Confidence 5899999963
No 7
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=67.78 E-value=3 Score=26.90 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=11.4
Q ss_pred CCCceeeEEeeCCC
Q psy11168 28 KEMSGAYLFLPRGE 41 (126)
Q Consensus 28 ~~~SGAYiF~P~~~ 41 (126)
..++|+||||+...
T Consensus 22 ~~kpGsYiFRlSCT 35 (86)
T PF02762_consen 22 RDKPGSYIFRLSCT 35 (86)
T ss_dssp TTSTTEEEEEEESS
T ss_pred hCCcccEEEeeccc
Confidence 36899999999764
No 8
>COG0383 AMS1 Alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=48.19 E-value=65 Score=29.74 Aligned_cols=55 Identities=25% Similarity=0.344 Sum_probs=40.6
Q ss_pred EEEeCCcEEEEEEEcC----ceEEEEEEeecCCCCCCeEEEEEEeeccCCCCeEEEEEEE--eccccC
Q psy11168 53 IIIQGPLVSMVIVELP----LVTHTVLVNHVADSDDLGIDIQNLLDIRQTVNTEVAMRLT--TNIENQ 114 (126)
Q Consensus 53 ~v~~G~lv~ev~~~~~----~~~~~~rly~~~~~~~~~ieie~~v~i~~~~~kE~v~r~~--t~i~n~ 114 (126)
.+..|||..+++.... -+.+.+++|++. +.++++..|| +..++..+|.. ++++++
T Consensus 660 ~~~~~~~~~~~~~~~~~~~~~i~~~i~l~~~s----~~l~~~t~vd---~q~~~~~lrv~fp~~~~s~ 720 (943)
T COG0383 660 AIENGPLVRTVRVSKELTESTITQKVTLYKGS----PRLDFKTEVD---NQVRDHRLRVLFPTDIASD 720 (943)
T ss_pred hhccccceeeeeeeeeccceEEEEEEEEecCC----ceeEEEEEEE---ccccceEEEEEeccccccc
Confidence 4678999999888654 577999999877 6899999986 44566666654 566554
No 9
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=47.75 E-value=20 Score=22.70 Aligned_cols=31 Identities=19% Similarity=0.295 Sum_probs=23.0
Q ss_pred ccCCCCeEEEEEEEeccccCCEEEecCCCCc
Q psy11168 95 IRQTVNTEVAMRLTTNIENQDVFYTDLNGYQ 125 (126)
Q Consensus 95 i~~~~~kE~v~r~~t~i~n~~~FyTDsNG~e 125 (126)
.+..|-+|+++|-...-.-.++||.+-+|..
T Consensus 7 lp~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk 37 (77)
T cd01396 7 LPPGWKRELVPRKSGSAGKFDVYYISPTGKK 37 (77)
T ss_pred CCCCCEEEEEEecCCCCCcceEEEECCCCCE
Confidence 4567889999998753334668999988864
No 10
>PF09121 Tower: Tower; InterPro: IPR015205 This domain adopts a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA []. ; PDB: 1IYJ_D 1MIU_A.
Probab=43.41 E-value=14 Score=20.88 Aligned_cols=12 Identities=33% Similarity=0.564 Sum_probs=8.2
Q ss_pred CCceeeEEeeCC
Q psy11168 29 EMSGAYLFLPRG 40 (126)
Q Consensus 29 ~~SGAYiF~P~~ 40 (126)
..+|-||||-..
T Consensus 4 ~~~G~~vFRn~R 15 (42)
T PF09121_consen 4 TPSGSYVFRNER 15 (42)
T ss_dssp -SSSSEEEE-CC
T ss_pred cCCCceEeecch
Confidence 368999999654
No 11
>PF10411 DsbC_N: Disulfide bond isomerase protein N-terminus; InterPro: IPR018950 This is the N-terminal domain of the disulphide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerisation []. DsbC is required for disulphide bond formation and functions as a disulphide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity []. ; PDB: 1EEJ_B 2IYJ_A 1TJD_A 1JZD_B 1JZO_A 1G0T_B 1T3B_A.
Probab=43.40 E-value=21 Score=21.06 Aligned_cols=13 Identities=23% Similarity=0.578 Sum_probs=10.2
Q ss_pred ccCCEEEecCCCC
Q psy11168 112 ENQDVFYTDLNGY 124 (126)
Q Consensus 112 ~n~~~FyTDsNG~ 124 (126)
.+++.||+|.+|.
T Consensus 31 ~~~~i~Y~~~dg~ 43 (57)
T PF10411_consen 31 KGGGILYVDEDGR 43 (57)
T ss_dssp -TTEEEEEETTSS
T ss_pred CCCeEEEEcCCCC
Confidence 4678999999984
No 12
>COG5266 CbiK ABC-type Co2+ transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=40.80 E-value=70 Score=25.12 Aligned_cols=9 Identities=44% Similarity=0.512 Sum_probs=6.9
Q ss_pred EEEecCCCC
Q psy11168 116 VFYTDLNGY 124 (126)
Q Consensus 116 ~FyTDsNG~ 124 (126)
.-|||+||+
T Consensus 215 ~~~TD~kG~ 223 (264)
T COG5266 215 VQFTDDKGE 223 (264)
T ss_pred EEEcCCCce
Confidence 358999994
No 13
>smart00084 NMU Neuromedin U. Neuromedin U (NmU) is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C- terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved in mammals, birds and amphibians.
Probab=39.68 E-value=22 Score=17.90 Aligned_cols=13 Identities=38% Similarity=0.800 Sum_probs=9.9
Q ss_pred CCCceeeEEeeCC
Q psy11168 28 KEMSGAYLFLPRG 40 (126)
Q Consensus 28 ~~~SGAYiF~P~~ 40 (126)
.|.-|-++|||-.
T Consensus 13 ~qsrgyFLfRPRN 25 (26)
T smart00084 13 SQSRGYFLFRPRN 25 (26)
T ss_pred cccCceEEeccCC
Confidence 4677889999953
No 14
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=39.62 E-value=29 Score=20.73 Aligned_cols=32 Identities=19% Similarity=0.309 Sum_probs=22.5
Q ss_pred eccCCCCeEEEEEEEeccccCCEEEecCCCCc
Q psy11168 94 DIRQTVNTEVAMRLTTNIENQDVFYTDLNGYQ 125 (126)
Q Consensus 94 ~i~~~~~kE~v~r~~t~i~n~~~FyTDsNG~e 125 (126)
|.+..|-+|++.|=...-.-.+++|...+|..
T Consensus 5 P~p~GW~R~~~~r~~g~~~k~dv~Y~sP~Gk~ 36 (62)
T cd00122 5 PLPPGWKRELVIRKSGSAGKGDVYYYSPCGKK 36 (62)
T ss_pred CCCCCeEEEEEEcCCCCCCcceEEEECCCCce
Confidence 45567788888887653334668888888864
No 15
>PF02070 NMU: Neuromedin U; InterPro: IPR008199 Neuromedin U (NmU) [, ] is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C-terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved.; GO: 0006940 regulation of smooth muscle contraction
Probab=37.83 E-value=25 Score=17.59 Aligned_cols=13 Identities=46% Similarity=0.902 Sum_probs=10.0
Q ss_pred CCCCceeeEEeeC
Q psy11168 27 GKEMSGAYLFLPR 39 (126)
Q Consensus 27 ~~~~SGAYiF~P~ 39 (126)
..|.-|-++|||-
T Consensus 12 ~~qsrgyFlfRPR 24 (25)
T PF02070_consen 12 GIQSRGYFLFRPR 24 (25)
T ss_pred ccccccEEEeccC
Confidence 3567788999994
No 16
>PF02814 UreE_N: UreE urease accessory protein, N-terminal domain; InterPro: IPR004029 Urease and other nickel metalloenzymes are synthesised as precursors devoid of the metalloenzyme active site. These precursors then undergo a complex post-translational maturation process that requires a number of accessory proteins. Members of this group are nickel-binding proteins required for urease metallocentre assembly []. They are believed to function as metallochaperones to deliver nickel to urease apoprotein [, ]. It has been shown by yeast two-hybrid analysis that UreE forms a dimeric complex with UreG in Helicobacter pylori []. The UreDFG-apoenzyme complex has also been shown to exist [, ] and is believed to be, with the addition of UreE, the assembly system for active urease []. The complexes, rather than the individual proteins, presumably bind to UreB via UreE/H recognition sites. The structure of Klebsiella aerogenes UreE reveals a unique two-domain architecture.The N-terminal domain is structurally related to a heat shock protein, while the C-terminal domain shows homology to the Atx1 copper metallochaperone [, ]. Significantly, the metal-binding sites in UreE and Atx1 are distinct in location and types of residues despite the relationship between these proteins and the mechanism for UreE activation of urease is proposed to be different from the thiol ligand exchange mechanism used by the copper metallochaperones. The N-terminal domain is termed the peptide-binding domain. Deletion of this domain does not eliminate enzymatic activity, and the truncated protein can still activate urease [].; GO: 0016151 nickel ion binding, 0006461 protein complex assembly, 0019627 urea metabolic process; PDB: 3NXZ_B 3TJA_B 3LA0_B 3TJ9_B 3NY0_A 3L9Z_A 3TJ8_A 1EAR_A 1EB0_A 1GMU_B ....
Probab=36.02 E-value=30 Score=20.81 Aligned_cols=26 Identities=27% Similarity=0.551 Sum_probs=17.5
Q ss_pred CCCCeEEEEEEEe--ccccCCEEEecCCC
Q psy11168 97 QTVNTEVAMRLTT--NIENQDVFYTDLNG 123 (126)
Q Consensus 97 ~~~~kE~v~r~~t--~i~n~~~FyTDsNG 123 (126)
...|.|+.+++.. .++.++.+|+| +|
T Consensus 35 t~~G~ei~i~L~r~~~L~~GDvL~~d-~g 62 (65)
T PF02814_consen 35 TDDGREIGIDLPRGTVLRDGDVLYLD-DG 62 (65)
T ss_dssp -TTS-EEEEE-SSTTT--TTEEEEEC-TS
T ss_pred CCCCCEEEEECCCCcccCCCCEEEeC-CC
Confidence 4679999999974 48999999999 54
No 17
>PF04376 ATE_N: Arginine-tRNA-protein transferase, N terminus; InterPro: IPR007471 Arginine-tRNA-protein transferase catalyses the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N terminus rule pathway of protein degradation by conjugating a destabilising amino acid to the N-terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N-terminal cysteine is sometimes modified []. In Saccharomyces cerevisiae, Cys20, 23, 94 and/or 95 are thought to be important for activity []. Of these, only Cys 94 appears to be completely conserved in this family. This entry represents the N-terminal region of the enzyme arginine-tRNA-protein transferase, found in both eukaryotic and prokaryotic enzymes.; GO: 0004057 arginyltransferase activity, 0016598 protein arginylation
Probab=32.37 E-value=25 Score=22.25 Aligned_cols=13 Identities=31% Similarity=0.577 Sum_probs=11.5
Q ss_pred CCCceeeEEeeCC
Q psy11168 28 KEMSGAYLFLPRG 40 (126)
Q Consensus 28 ~~~SGAYiF~P~~ 40 (126)
-.+||.|+|+|+-
T Consensus 44 ~RRsG~~~YrP~c 56 (80)
T PF04376_consen 44 FRRSGNYFYRPNC 56 (80)
T ss_pred CcccCCEEecCCC
Confidence 4789999999986
No 18
>PF12565 DUF3747: Protein of unknown function (DUF3747); InterPro: IPR022222 This family of proteins is found in bacteria. Proteins in this family are typically between 215 and 413 amino acids in length. There is a conserved DSNGYS sequence motif.
Probab=30.19 E-value=21 Score=26.49 Aligned_cols=8 Identities=75% Similarity=1.161 Sum_probs=7.1
Q ss_pred EEecCCCC
Q psy11168 117 FYTDLNGY 124 (126)
Q Consensus 117 FyTDsNG~ 124 (126)
-||||||+
T Consensus 91 R~tDSNGY 98 (181)
T PF12565_consen 91 RYTDSNGY 98 (181)
T ss_pred cccCCCCc
Confidence 69999996
No 19
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=26.32 E-value=47 Score=14.88 Aligned_cols=12 Identities=42% Similarity=0.897 Sum_probs=9.0
Q ss_pred cCCEEEecCCCC
Q psy11168 113 NQDVFYTDLNGY 124 (126)
Q Consensus 113 n~~~FyTDsNG~ 124 (126)
++..+|-|+||.
T Consensus 7 ~~~wYy~~~~G~ 18 (19)
T PF01473_consen 7 NGNWYYFDSDGY 18 (19)
T ss_dssp TTEEEEETTTSB
T ss_pred CCEEEEeCCCcc
Confidence 456789999983
No 20
>cd01397 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.
Probab=25.15 E-value=67 Score=20.27 Aligned_cols=33 Identities=15% Similarity=0.091 Sum_probs=23.0
Q ss_pred eeccCCCCeEEEEEEEeccccCCEEEecCCCCc
Q psy11168 93 LDIRQTVNTEVAMRLTTNIENQDVFYTDLNGYQ 125 (126)
Q Consensus 93 v~i~~~~~kE~v~r~~t~i~n~~~FyTDsNG~e 125 (126)
+|+.-.|-+|+++|=.++=..++++|...-|.-
T Consensus 4 ~Pl~~GW~Re~vir~~~~~~~~dV~Y~aPcGKk 36 (73)
T cd01397 4 VPLELGWRRETRIRGLGGRIQGEVAYYAPCGKK 36 (73)
T ss_pred CCCCCCceeEEEeccCCCCccceEEEECCCCcc
Confidence 566778889998887653334667888777753
No 21
>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=24.23 E-value=46 Score=19.42 Aligned_cols=29 Identities=14% Similarity=0.216 Sum_probs=17.9
Q ss_pred CCCCeEEEEEEEeccccCC--EEEecCCCCc
Q psy11168 97 QTVNTEVAMRLTTNIENQD--VFYTDLNGYQ 125 (126)
Q Consensus 97 ~~~~kE~v~r~~t~i~n~~--~FyTDsNG~e 125 (126)
-..|++++..=+..++... .=|+|.+|.+
T Consensus 6 t~dG~~i~t~gkP~~D~~tG~~~y~D~~G~~ 36 (50)
T PF06004_consen 6 TNDGRTIVTDGKPKYDKDTGMYSYTDADGKE 36 (50)
T ss_dssp ETTSEEEEESSEEEEETTTTEEEEEBTTS-E
T ss_pred eCCCcEEEeCCCccccCCCCcEEEECCCCCE
Confidence 3457777666555554433 5699999964
No 22
>PF04530 Viral_Beta_CD: Viral Beta C/D like family; InterPro: IPR007617 This is a family of ssRNA positive-strand viral proteins. Conserved region is found in the Beta C and Beta D transcripts.
Probab=22.41 E-value=30 Score=24.06 Aligned_cols=12 Identities=42% Similarity=0.719 Sum_probs=10.0
Q ss_pred CEEEecCCCCcC
Q psy11168 115 DVFYTDLNGYQS 126 (126)
Q Consensus 115 ~~FyTDsNG~em 126 (126)
..||-|+||.||
T Consensus 82 syfyQDLNsVei 93 (122)
T PF04530_consen 82 SYFYQDLNSVEI 93 (122)
T ss_pred chheeeccceEE
Confidence 359999999876
No 23
>KOG1785|consensus
Probab=22.11 E-value=46 Score=28.04 Aligned_cols=50 Identities=18% Similarity=0.228 Sum_probs=26.1
Q ss_pred EEEEEEEEeecCC-----CCCCceeeEEeeCCCCccCCCCCCcEEEEeCCcEEEEEE
Q psy11168 14 PINLDFVTYTSRK-----GKEMSGAYLFLPRGEAKSVPVTHPPVIIIQGPLVSMVIV 65 (126)
Q Consensus 14 ~v~~~f~~Y~s~~-----~~~~SGAYiF~P~~~~~~~~~~~~~~~v~~G~lv~ev~~ 65 (126)
+=-+.|+-|..-+ -..+.|.||||+....--.. ........|.+.+.+-+
T Consensus 257 PGYmAFLTYDEVk~RLqk~~~KpGSYIFRlSCTRlGQW--AIGYVt~dG~IlQTIP~ 311 (563)
T KOG1785|consen 257 PGYMAFLTYDEVKARLQKYIKKPGSYIFRLSCTRLGQW--AIGYVTADGNILQTIPQ 311 (563)
T ss_pred CceeEEeeHHHHHHHHHHHhcCCCceEEeeccCcccce--eEEEEcCCCceeeccCC
Confidence 3345566664221 13689999999976421110 01122456666655544
No 24
>PHA01516 hypothetical protein
Probab=22.07 E-value=28 Score=22.55 Aligned_cols=10 Identities=40% Similarity=0.517 Sum_probs=8.6
Q ss_pred EEecCCCCcC
Q psy11168 117 FYTDLNGYQS 126 (126)
Q Consensus 117 FyTDsNG~em 126 (126)
=|+..||+||
T Consensus 48 dycn~~glqm 57 (98)
T PHA01516 48 DYCNANGLQM 57 (98)
T ss_pred cccCccchhh
Confidence 4889999997
No 25
>KOG3527|consensus
Probab=20.99 E-value=44 Score=30.63 Aligned_cols=21 Identities=38% Similarity=0.442 Sum_probs=16.8
Q ss_pred EEEeccccCCEEEecCCCCcC
Q psy11168 106 RLTTNIENQDVFYTDLNGYQS 126 (126)
Q Consensus 106 r~~t~i~n~~~FyTDsNG~em 126 (126)
.+++++.-...-|||.||+|+
T Consensus 785 ~~ts~~~~~~~~~td~~g~~i 805 (975)
T KOG3527|consen 785 QETSDLPEQVEVYTDENGRQI 805 (975)
T ss_pred eecccccccccccccCCCceE
Confidence 445677777889999999985
No 26
>PRK14094 psbM photosystem II reaction center protein M; Provisional
Probab=20.22 E-value=77 Score=18.41 Aligned_cols=19 Identities=21% Similarity=0.434 Sum_probs=13.3
Q ss_pred EEEEEeccccCCEEEecCC
Q psy11168 104 AMRLTTNIENQDVFYTDLN 122 (126)
Q Consensus 104 v~r~~t~i~n~~~FyTDsN 122 (126)
++-.+|.=.+...||.|+.
T Consensus 24 ilYVkT~s~~kssf~sd~s 42 (50)
T PRK14094 24 GLFISTQDGEKSSFYSDSS 42 (50)
T ss_pred heeEEecccCccceecccc
Confidence 3444666667778999975
Done!