Query psy12066
Match_columns 164
No_of_seqs 78 out of 80
Neff 2.1
Searched_HMMs 46136
Date Fri Aug 16 17:48:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12066.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12066hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3841|consensus 100.0 3.5E-39 7.7E-44 287.5 7.7 108 7-126 34-144 (455)
2 smart00426 TEA TEA domain. 100.0 2.8E-31 6.2E-36 188.7 3.0 66 57-123 1-68 (68)
3 PF01285 TEA: TEA/ATTS domain 99.9 1.6E-28 3.5E-33 216.8 0.4 81 55-138 45-134 (431)
4 TIGR01557 myb_SHAQKYF myb-like 68.8 4.5 9.7E-05 27.5 2.2 20 60-79 4-23 (57)
5 cd06407 PB1_NLP A PB1 domain i 57.7 6.1 0.00013 28.3 1.3 38 51-88 41-79 (82)
6 PF00515 TPR_1: Tetratricopept 56.5 9.9 0.00021 21.1 1.8 16 64-79 18-33 (34)
7 COG2877 KdsA 3-deoxy-D-manno-o 55.1 7 0.00015 34.9 1.5 28 76-103 153-180 (279)
8 PF13926 DUF4211: Domain of un 48.6 21 0.00046 27.2 3.1 20 58-81 88-107 (153)
9 PF00249 Myb_DNA-binding: Myb- 47.6 24 0.00053 21.8 2.7 21 60-80 2-22 (48)
10 PF07719 TPR_2: Tetratricopept 46.7 26 0.00056 18.9 2.5 16 65-80 19-34 (34)
11 PF12218 End_N_terminal: N ter 44.9 25 0.00055 25.7 2.8 44 67-138 10-55 (67)
12 smart00028 TPR Tetratricopepti 36.5 42 0.00091 15.6 2.1 16 64-79 18-33 (34)
13 KOG4132|consensus 36.3 15 0.00033 32.5 0.7 52 63-114 63-134 (260)
14 PF10488 PP1c_bdg: Phosphatase 31.3 76 0.0016 28.7 4.2 27 10-36 82-108 (307)
15 PF00877 NLPC_P60: NlpC/P60 fa 29.5 43 0.00093 23.2 1.9 26 138-163 46-77 (105)
16 PF15163 Meiosis_expr: Meiosis 28.4 37 0.00079 25.4 1.5 16 60-75 5-20 (77)
17 cd08867 START_STARD4_5_6-like 25.8 1.7E+02 0.0036 22.8 4.8 77 66-145 7-87 (206)
18 PF00665 rve: Integrase core d 24.8 49 0.0011 22.2 1.5 41 63-105 49-89 (120)
19 PRK10424 ilvG operon leader pe 23.3 26 0.00057 22.5 -0.1 7 75-81 18-24 (32)
20 PF07533 BRK: BRK domain; Int 23.2 40 0.00087 22.3 0.8 28 107-134 13-46 (46)
21 PF11330 DUF3132: Protein of u 22.8 62 0.0014 25.7 1.9 17 144-160 76-94 (124)
22 PF08302 tRNA_lig_CPD: Fungal 21.3 62 0.0013 27.4 1.7 16 63-78 27-43 (257)
23 PRK01388 arginine deiminase; P 21.0 94 0.002 28.1 2.9 32 130-162 201-232 (406)
24 PF00778 DIX: DIX domain; Int 20.9 35 0.00075 25.0 0.2 34 122-159 46-80 (84)
25 smart00678 WWE Domain in Delte 20.5 61 0.0013 21.5 1.3 10 63-72 20-29 (73)
26 PF13230 GATase_4: Glutamine a 20.2 42 0.00091 28.2 0.5 28 127-154 230-258 (271)
No 1
>KOG3841|consensus
Probab=100.00 E-value=3.5e-39 Score=287.48 Aligned_cols=108 Identities=44% Similarity=0.641 Sum_probs=85.9
Q ss_pred cccccccccCCCcCCCCCCCCCCCCCCCCCCCCccccCCCCcccccc-ccCCCCCCCChhHHHHHHHHHHhcCCCCccee
Q psy12066 7 FGLVTGTISSPWTPGSAAVPPGADTNGSGGDSKHALDVGDLDDDKDL-AAADAEGVWSPDIEQSFQEALAIYPPCGRRKI 85 (164)
Q Consensus 7 ~~~~~gTIsspWTp~~~g~p~g~~w~~~~s~~~~~~~~~~~~~~~~~-~~~d~e~VWs~DIEqAF~EALaIyPp~GRrKI 85 (164)
.+-+|++..+.|++.+.|.+||+. +.. +++..++.. .+.|+|+||||||||||||||+||||||||||
T Consensus 34 ~ag~a~~n~~q~~~~~~~~g~~s~--~~~---------~p~~~~~~~D~~~daegvWSpdIEqsFqEALaiyppcGrrKI 102 (455)
T KOG3841|consen 34 VAGAAGDNIPQWELVNTGLGAGSA--DLK---------GPEAKDKFTDNQRDAEGVWSPDIEQSFQEALAIYPPCGRRKI 102 (455)
T ss_pred hccccccCCcCceecCCCCCCCcc--ccC---------CccccccCCccccccccccChhHHHHHHHHHhhcCCCCceeE
Confidence 455677888999998887654432 111 111112221 13399999999999999999999999999999
Q ss_pred eeCCCCcccccchhhhhccccccCCCccccc--chhhhHHHhh
Q psy12066 86 ILSDEGKMYETVGTFGRKKNPTKGGKGAVGG--IDLMGFLKAQ 126 (164)
Q Consensus 86 iLSdeGK~yGRNELIa~YI~~~tgGK~R~~~--~~l~~~lK~~ 126 (164)
|||||||||||||||||||++| |||+|||+ ++|+|+|++.
T Consensus 103 ilsdegkmyGRNELIarYIKlr-tgktRTrKQVSSHIQVlarr 144 (455)
T KOG3841|consen 103 ILSDEGKMYGRNELIARYIKLR-TGKTRTRKQVSSHIQVLARR 144 (455)
T ss_pred EEccCccccchHHHHHHHHHHh-cCCchhHHHHHHHHHHHHHH
Confidence 9999999999999999999976 59999988 7899999875
No 2
>smart00426 TEA TEA domain.
Probab=99.96 E-value=2.8e-31 Score=188.67 Aligned_cols=66 Identities=62% Similarity=0.960 Sum_probs=61.0
Q ss_pred CCCCCCChhHHHHHHHHHHhcCCCCcceeeeCCCCcccccchhhhhccccccCCCccccc--chhhhHH
Q psy12066 57 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYETVGTFGRKKNPTKGGKGAVGG--IDLMGFL 123 (164)
Q Consensus 57 d~e~VWs~DIEqAF~EALaIyPp~GRrKIiLSdeGK~yGRNELIa~YI~~~tgGK~R~~~--~~l~~~l 123 (164)
|.++|||+|||+||.|||++|||||+|||+++++|||||||||||+||+. +|||.||++ ++|+|+|
T Consensus 1 dg~~vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs~YI~~-~tGk~Rt~KQVsShIQvl 68 (68)
T smart00426 1 DAEGVWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKL-RTGKTRTRKQVSSHIQVL 68 (68)
T ss_pred CCCCcCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHHHHHHH-HhCCccchhhhcchheeC
Confidence 67899999999999999999999999999999999999999999999995 569999988 6677764
No 3
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=99.94 E-value=1.6e-28 Score=216.75 Aligned_cols=81 Identities=46% Similarity=0.719 Sum_probs=45.2
Q ss_pred cCCCCCCCChhHHHHHHHHHHhcCCCCcceeeeCCCCcccccchhhhhccccccCCCccccc--chhhhHHHh----h--
Q psy12066 55 AADAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYETVGTFGRKKNPTKGGKGAVGG--IDLMGFLKA----Q-- 126 (164)
Q Consensus 55 ~~d~e~VWs~DIEqAF~EALaIyPp~GRrKIiLSdeGK~yGRNELIa~YI~~~tgGK~R~~~--~~l~~~lK~----~-- 126 (164)
+.++++||++|||+||+|||+|||||||||| +++|||||||||||+||+.+ |||.||++ .+|+|+|++ .
T Consensus 45 ~~~~~~vw~~~~e~af~~al~~~~~~g~~k~--~~~~~~~grn~li~~yi~~~-tg~~rt~kqvsshiqvl~~~~~~~~k 121 (431)
T PF01285_consen 45 DGDGEGVWPPDIEQAFQEALAIYPPCGRRKL--SDEGKMYGRNELISDYIKLK-TGKTRTRKQVSSHIQVLKREIQNKLK 121 (431)
T ss_dssp -GGGS--S-HHHHHHHHHHHHHS-SSS---H--HHH-----THHHHHHHHHHH-HS----SHHHHHHHHHHTT-------
T ss_pred CCCCCCCCCHHHHHHHHHHHHhCCCCCCccc--ccccccccchhHHHHHHHHH-hCcccchhHHHHHHHHHHHHHhhccc
Confidence 5789999999999999999999999999995 77999999999999999965 59999988 678888821 1
Q ss_pred -hccccccccccc
Q psy12066 127 -RYEGRELWEELP 138 (164)
Q Consensus 127 -r~e~~~~W~~l~ 138 (164)
....++.|..|.
T Consensus 122 ~~~~kd~~l~~l~ 134 (431)
T PF01285_consen 122 DQTAKDKALQSLI 134 (431)
T ss_dssp -------------
T ss_pred ccccccHHHHhhh
Confidence 133666776664
No 4
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=68.82 E-value=4.5 Score=27.47 Aligned_cols=20 Identities=25% Similarity=0.496 Sum_probs=17.6
Q ss_pred CCCChhHHHHHHHHHHhcCC
Q psy12066 60 GVWSPDIEQSFQEALAIYPP 79 (164)
Q Consensus 60 ~VWs~DIEqAF~EALaIyPp 79 (164)
-.|++|.++.|.+|+..+..
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~ 23 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGG 23 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCC
Confidence 47999999999999999853
No 5
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=57.70 E-value=6.1 Score=28.31 Aligned_cols=38 Identities=24% Similarity=0.406 Sum_probs=27.3
Q ss_pred cccccCCCCCCCChh-HHHHHHHHHHhcCCCCcceeeeC
Q psy12066 51 KDLAAADAEGVWSPD-IEQSFQEALAIYPPCGRRKIILS 88 (164)
Q Consensus 51 ~~~~~~d~e~VWs~D-IEqAF~EALaIyPp~GRrKIiLS 88 (164)
-.++=.|+|+-|..= =.+=++||++|+..+++++|+|+
T Consensus 41 f~LkY~Ddegd~v~ltsd~DL~eai~i~~~~~~~~v~l~ 79 (82)
T cd06407 41 FDLKYLDDDEEWVLLTCDADLEECIDVYRSSGSHTIRLL 79 (82)
T ss_pred eEEEEECCCCCeEEeecHHHHHHHHHHHHHCCCCeEEEE
Confidence 344445666777532 23448899999999999999985
No 6
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=56.51 E-value=9.9 Score=21.09 Aligned_cols=16 Identities=25% Similarity=0.416 Sum_probs=13.2
Q ss_pred hhHHHHHHHHHHhcCC
Q psy12066 64 PDIEQSFQEALAIYPP 79 (164)
Q Consensus 64 ~DIEqAF~EALaIyPp 79 (164)
++-.++|++||+|.|.
T Consensus 18 ~~A~~~~~~al~~~p~ 33 (34)
T PF00515_consen 18 EEALEYYQRALELDPD 33 (34)
T ss_dssp HHHHHHHHHHHHHSTT
T ss_pred hHHHHHHHHHHHHCcC
Confidence 3557899999999985
No 7
>COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]
Probab=55.07 E-value=7 Score=34.85 Aligned_cols=28 Identities=18% Similarity=0.283 Sum_probs=24.6
Q ss_pred hcCCCCcceeeeCCCCcccccchhhhhc
Q psy12066 76 IYPPCGRRKIILSDEGKMYETVGTFGRK 103 (164)
Q Consensus 76 IyPp~GRrKIiLSdeGK~yGRNELIa~Y 103 (164)
-.-.+|..||+|.++|-+||=|-|++|.
T Consensus 153 K~~~~gn~~v~lcERG~sFGYnnLV~DM 180 (279)
T COG2877 153 KFLETGNNKVILCERGASFGYNNLVVDM 180 (279)
T ss_pred HHHhcCCCcEEEEeccCccCcchhHHHh
Confidence 3345899999999999999999999985
No 8
>PF13926 DUF4211: Domain of unknown function (DUF4211)
Probab=48.62 E-value=21 Score=27.23 Aligned_cols=20 Identities=40% Similarity=0.961 Sum_probs=15.9
Q ss_pred CCCCCChhHHHHHHHHHHhcCCCC
Q psy12066 58 AEGVWSPDIEQSFQEALAIYPPCG 81 (164)
Q Consensus 58 ~e~VWs~DIEqAF~EALaIyPp~G 81 (164)
...+|+++ |.+||..||.+-
T Consensus 88 ~ss~W~~~----f~~aL~~~P~l~ 107 (153)
T PF13926_consen 88 SSSAWKPD----FKKALETYPELS 107 (153)
T ss_pred eeccCCHH----HHHHHHHCCCeE
Confidence 34578765 999999999883
No 9
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=47.57 E-value=24 Score=21.84 Aligned_cols=21 Identities=24% Similarity=0.518 Sum_probs=17.6
Q ss_pred CCCChhHHHHHHHHHHhcCCC
Q psy12066 60 GVWSPDIEQSFQEALAIYPPC 80 (164)
Q Consensus 60 ~VWs~DIEqAF~EALaIyPp~ 80 (164)
+.|+++=++.|.+|+..+++.
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~ 22 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKD 22 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTT
T ss_pred CCCCHHHHHHHHHHHHHhCCc
Confidence 579999999999999999876
No 10
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=46.72 E-value=26 Score=18.92 Aligned_cols=16 Identities=25% Similarity=0.422 Sum_probs=12.9
Q ss_pred hHHHHHHHHHHhcCCC
Q psy12066 65 DIEQSFQEALAIYPPC 80 (164)
Q Consensus 65 DIEqAF~EALaIyPp~ 80 (164)
+-.+.|++||++.|.+
T Consensus 19 ~A~~~~~~al~l~p~~ 34 (34)
T PF07719_consen 19 EAIEYFEKALELDPNN 34 (34)
T ss_dssp HHHHHHHHHHHHSTTS
T ss_pred HHHHHHHHHHHHCcCC
Confidence 4567899999999963
No 11
>PF12218 End_N_terminal: N terminal extension of bacteriophage endosialidase; InterPro: IPR024429 This entry represents the N-terminal extension domain of endosialidases which is approximately 70 amino acids in length. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain [].; PDB: 3JU4_A 3GVL_A 3GVK_B 3GVJ_A 1V0E_B 1V0F_E.
Probab=44.89 E-value=25 Score=25.71 Aligned_cols=44 Identities=32% Similarity=0.421 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcCCCCcceeeeCCCCcccccchh--hhhccccccCCCcccccchhhhHHHhhhccccccccccc
Q psy12066 67 EQSFQEALAIYPPCGRRKIILSDEGKMYETVGT--FGRKKNPTKGGKGAVGGIDLMGFLKAQRYEGRELWEELP 138 (164)
Q Consensus 67 EqAF~EALaIyPp~GRrKIiLSdeGK~yGRNEL--Ia~YI~~~tgGK~R~~~~~l~~~lK~~r~e~~~~W~~l~ 138 (164)
.+||-+||+.-|.. +||=. .|..|-=|.| |++|+. .+++|||++
T Consensus 10 t~A~~a~l~a~~~g--~~IDg--~GlTykVs~lPd~srf~N------------------------~rF~~eri~ 55 (67)
T PF12218_consen 10 TAAITAALEASPVG--RKIDG--AGLTYKVSSLPDISRFKN------------------------ARFVYERIP 55 (67)
T ss_dssp HHHHHHHHHHS-TT--S-EE---TT-EEEESS---GGGEES-------------------------EEEE-SST
T ss_pred HHHHHHHHhccCCC--eEEec--CCceEEEeeCccHHhhcc------------------------ceEEEeecC
Confidence 47899999988753 56644 5777766655 555544 678999986
No 12
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=36.47 E-value=42 Score=15.64 Aligned_cols=16 Identities=19% Similarity=0.403 Sum_probs=11.6
Q ss_pred hhHHHHHHHHHHhcCC
Q psy12066 64 PDIEQSFQEALAIYPP 79 (164)
Q Consensus 64 ~DIEqAF~EALaIyPp 79 (164)
++....|++|+.+.|.
T Consensus 18 ~~a~~~~~~~~~~~~~ 33 (34)
T smart00028 18 DEALEYYEKALELDPN 33 (34)
T ss_pred HHHHHHHHHHHccCCC
Confidence 3456678888888774
No 13
>KOG4132|consensus
Probab=36.32 E-value=15 Score=32.51 Aligned_cols=52 Identities=23% Similarity=0.129 Sum_probs=37.9
Q ss_pred ChhHHHHHHHHHH--hcCC--------------C----CcceeeeCCCCcccccchhhhhccccccCCCccc
Q psy12066 63 SPDIEQSFQEALA--IYPP--------------C----GRRKIILSDEGKMYETVGTFGRKKNPTKGGKGAV 114 (164)
Q Consensus 63 s~DIEqAF~EALa--IyPp--------------~----GRrKIiLSdeGK~yGRNELIa~YI~~~tgGK~R~ 114 (164)
||-.-+|..|||. .-+- . =||++-|.-+|+-||+-|..||||--..++|+.-
T Consensus 63 SpR~VEa~~eaL~q~~tel~~~w~a~~vYtVG~aT~~si~~~~~l~T~Ge~~gNa~~LaD~Ive~~~~~~al 134 (260)
T KOG4132|consen 63 SPRCVEALNEALIQTETELKAAWLAKHVYTVGPATHASIRRLGFLNTHGEDAGNAEILADLIVETFTDKRAL 134 (260)
T ss_pred ChHHHHHHHHHhccccchhhhHHhhcceeeeccccHHHHHHhcCccccccccccHHHHhHhhhhcCCCcccC
Confidence 5677777777776 1111 1 1566667779999999999999999877777654
No 14
>PF10488 PP1c_bdg: Phosphatase-1 catalytic subunit binding region; InterPro: IPR019523 This entry represents the conserved C terminus of the regulatory subunit (15A and 15B) of protein phosphatase 1. This C-terminal domain appears to be a binding region for the catalytic subunit (PP1C) of protein phosphatase-1, which may in some circumstances also be retroviral in origin since it is found in both herpes simplex virus and in mouse and man. This domain is found in Gadd-34 apoptosis-associated proteins as well as the constitutive repressor of eIF2-alpha phosphorylation/protein phosphatase 1, regulatory (inhibitor) subunit 15b, otherwise known as CReP. Diverse stressful conditions are associated with phosphorylation of the alpha-subunit of eukaryotic translation initiation factor 2 (eIF2-alpha) on serine 51. This signaling event, which is conserved from yeast to mammals, negatively regulates the guanine nucleotide exchange factor, eIF2-B and inhibits the recycling of eIF2 to its active GTP bound form. In mammalian cells eIF2-alpha phosphorylation emerges as an important event in stress signaling that impacts on gene expression at both the translational and transcriptional levels [].
Probab=31.34 E-value=76 Score=28.70 Aligned_cols=27 Identities=22% Similarity=0.216 Sum_probs=20.5
Q ss_pred ccccccCCCcCCCCCCCCCCCCCCCCC
Q psy12066 10 VTGTISSPWTPGSAAVPPGADTNGSGG 36 (164)
Q Consensus 10 ~~gTIsspWTp~~~g~p~g~~w~~~~s 36 (164)
-..||.++|||....++-..+|++..+
T Consensus 82 fta~iqt~~~~~~~~~~~e~d~s~~~~ 108 (307)
T PF10488_consen 82 FTATIQTAATPVPKDPSSEKDLSDKSD 108 (307)
T ss_pred ccccccccccCCCCCCccccccccccc
Confidence 357899999998888765667766555
No 15
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=29.51 E-value=43 Score=23.18 Aligned_cols=26 Identities=38% Similarity=0.677 Sum_probs=19.7
Q ss_pred cccceeecCcceeeec------eEEEEeccCC
Q psy12066 138 PVGRAELRGGDVLWEG------EVVMYLGKGR 163 (164)
Q Consensus 138 ~~~~~~~~~~~~~~~~------~~~~~~~~~~ 163 (164)
.+-..+++-||+++-. -|.||+|.++
T Consensus 46 ~~~~~~~~pGDlif~~~~~~~~Hvgiy~g~~~ 77 (105)
T PF00877_consen 46 RVPISELQPGDLIFFKGGGGISHVGIYLGDGK 77 (105)
T ss_dssp HEEGGG-TTTEEEEEEGTGGEEEEEEEEETTE
T ss_pred ccchhcCCcccEEEEeCCccCCEeEEEEeCCe
Confidence 4667889999988754 5999998875
No 16
>PF15163 Meiosis_expr: Meiosis-expressed
Probab=28.38 E-value=37 Score=25.43 Aligned_cols=16 Identities=25% Similarity=0.576 Sum_probs=12.2
Q ss_pred CCCChhHHHHHHHHHH
Q psy12066 60 GVWSPDIEQSFQEALA 75 (164)
Q Consensus 60 ~VWs~DIEqAF~EALa 75 (164)
-.||++||.||.=-+|
T Consensus 5 K~Ws~evE~~yRfQ~A 20 (77)
T PF15163_consen 5 KKWSEEVENAYRFQQA 20 (77)
T ss_pred cccCHHHHHHHHHHHc
Confidence 3799999999764444
No 17
>cd08867 START_STARD4_5_6-like Lipid-binding START domain of mammalian STARD4, -5, -6, and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD4, -5, and -6. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD4 plays an important role in steroidogenesis, trafficking cholesterol into mitochondria. It specifically binds cholesterol, and demonstrates limited binding to another sterol, 7a-hydroxycholesterol. STARD4 and STARD5 are ubiquitously expressed, with highest levels in liver and kidney. STRAD5 functions in the kidney within the proximal tubule cells where it is associated with the Endoplasmic Reticulum (ER), and may participate in ER-associated cholesterol transport. It binds cholesterol and 25-hydroxycholesterol. Expression
Probab=25.84 E-value=1.7e+02 Score=22.83 Aligned_cols=77 Identities=12% Similarity=-0.034 Sum_probs=44.6
Q ss_pred HHHHHHHHHHhcCCCCcceeeeCCCC-cccccchhhhhc---cccccCCCcccccchhhhHHHhhhcccccccccccccc
Q psy12066 66 IEQSFQEALAIYPPCGRRKIILSDEG-KMYETVGTFGRK---KNPTKGGKGAVGGIDLMGFLKAQRYEGRELWEELPVGR 141 (164)
Q Consensus 66 IEqAF~EALaIyPp~GRrKIiLSdeG-K~yGRNELIa~Y---I~~~tgGK~R~~~~~l~~~lK~~r~e~~~~W~~l~~~~ 141 (164)
+++|-+|+|.|.-.....|+..+.+| +.|=|. .+.| ++ +--|-.-..-.+++.+|..+..+.+..|+......
T Consensus 7 ~~~~~~~~~~~~~~~~~W~~~~~~~~i~v~~~~--~~~~~~~~~-k~~~~i~~~~~~v~~~l~d~~~~~r~~Wd~~~~~~ 83 (206)
T cd08867 7 AEKLANEALQYINDTDGWKVLKTVKNITVSWKP--STEFTGHLY-RAEGIVDALPEKVIDVIIPPCGGLRLKWDKSLKHY 83 (206)
T ss_pred HHHHHHHHHHHhcCcCCcEEEEcCCCcEEEEec--CCCCCCEEE-EEEEEEcCCHHHHHHHHHhcCccccccccccccce
Confidence 67889999999988777777655433 444331 0111 11 11111111225666777655578889998776655
Q ss_pred eeec
Q psy12066 142 AELR 145 (164)
Q Consensus 142 ~~~~ 145 (164)
..|.
T Consensus 84 ~~le 87 (206)
T cd08867 84 EVLE 87 (206)
T ss_pred EEEE
Confidence 5444
No 18
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=24.82 E-value=49 Score=22.24 Aligned_cols=41 Identities=12% Similarity=0.174 Sum_probs=28.3
Q ss_pred ChhHHHHHHHHHHhcCCCCcceeeeCCCCcccccchhhhhccc
Q psy12066 63 SPDIEQSFQEALAIYPPCGRRKIILSDEGKMYETVGTFGRKKN 105 (164)
Q Consensus 63 s~DIEqAF~EALaIyPp~GRrKIiLSdeGK~yGRNELIa~YI~ 105 (164)
..++-++|.+++..+..+. -+++.||.|+.|-.+ .+..+..
T Consensus 49 ~~~~~~~l~~~~~~~~~~~-p~~i~tD~g~~f~~~-~~~~~~~ 89 (120)
T PF00665_consen 49 AEAALRALKRAIEKRGGRP-PRVIRTDNGSEFTSH-AFEAWCK 89 (120)
T ss_dssp HHHHHHHHHHHHHHHS-SE--SEEEEESCHHHHSH-HHHHHHH
T ss_pred ccccccccccccccccccc-ceecccccccccccc-hhhhHHH
Confidence 3678888888888887766 567789999988544 4444444
No 19
>PRK10424 ilvG operon leader peptide; Provisional
Probab=23.26 E-value=26 Score=22.48 Aligned_cols=7 Identities=71% Similarity=1.701 Sum_probs=5.5
Q ss_pred HhcCCCC
Q psy12066 75 AIYPPCG 81 (164)
Q Consensus 75 aIyPp~G 81 (164)
-|+||||
T Consensus 18 iiippcg 24 (32)
T PRK10424 18 IIIPPCG 24 (32)
T ss_pred EEecCch
Confidence 3789996
No 20
>PF07533 BRK: BRK domain; InterPro: IPR006576 BRK is a domain of unknown function found only in the metazoa and in association with CHROMO domain (IPR000953 from INTERPRO) and DEAD/DEAH box helicase domain (IPR011545 from INTERPRO).; GO: 0005515 protein binding, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2DL6_A 2CKA_A 2V0F_A 2V0E_A 2CKC_A.
Probab=23.23 E-value=40 Score=22.26 Aligned_cols=28 Identities=32% Similarity=0.548 Sum_probs=19.2
Q ss_pred ccCCCccccc-----chhhhHHHhh-hccccccc
Q psy12066 107 TKGGKGAVGG-----IDLMGFLKAQ-RYEGRELW 134 (164)
Q Consensus 107 ~tgGK~R~~~-----~~l~~~lK~~-r~e~~~~W 134 (164)
+++||.-++. .+|.++|+.+ .|+-.|.|
T Consensus 13 ~~tGk~l~G~~AP~~~~L~~WL~~~P~y~V~P~w 46 (46)
T PF07533_consen 13 RKTGKRLTGDEAPKLKELEEWLEEHPGYEVAPRW 46 (46)
T ss_dssp TTTTEEE-CCCS-BCCCHHHHHHH-TTEEESHHH
T ss_pred CCCCCCcccccCcCHHHHHHHHHHCcCceeCCCC
Confidence 5677777654 8999999977 66666655
No 21
>PF11330 DUF3132: Protein of unknown function (DUF3132); InterPro: IPR021479 This entry is represented by the Citrus psorosis virus, 54kDa protein; it is a family of uncharacterised viral proteins.
Probab=22.79 E-value=62 Score=25.65 Aligned_cols=17 Identities=65% Similarity=0.872 Sum_probs=13.8
Q ss_pred ecCcceeee--ceEEEEec
Q psy12066 144 LRGGDVLWE--GEVVMYLG 160 (164)
Q Consensus 144 ~~~~~~~~~--~~~~~~~~ 160 (164)
-.|.|||-| |||||.|.
T Consensus 76 tagddvllekdgevvmild 94 (124)
T PF11330_consen 76 TAGDDVLLEKDGEVVMILD 94 (124)
T ss_pred ccCCeEEEecCCcEEEEEe
Confidence 457889875 99999985
No 22
>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=21.30 E-value=62 Score=27.42 Aligned_cols=16 Identities=38% Similarity=0.708 Sum_probs=13.3
Q ss_pred ChhHHHHHHHHHH-hcC
Q psy12066 63 SPDIEQSFQEALA-IYP 78 (164)
Q Consensus 63 s~DIEqAF~EALa-IyP 78 (164)
+++|++||+.||. --|
T Consensus 27 ~e~id~A~~~Al~~Ykp 43 (257)
T PF08302_consen 27 DEEIDEAFQKALNEYKP 43 (257)
T ss_pred HHHHHHHHHHHHhhCCC
Confidence 3789999999999 444
No 23
>PRK01388 arginine deiminase; Provisional
Probab=21.00 E-value=94 Score=28.10 Aligned_cols=32 Identities=38% Similarity=0.676 Sum_probs=22.9
Q ss_pred cccccccccccceeecCcceeeeceEEEEeccC
Q psy12066 130 GRELWEELPVGRAELRGGDVLWEGEVVMYLGKG 162 (164)
Q Consensus 130 ~~~~W~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (164)
+-+.|.+.. +.+-+.||||+|-|.-+.++|-+
T Consensus 201 ~~~i~~~~~-~~~~iEGGDvl~l~~~~l~IG~s 232 (406)
T PRK01388 201 DVPVWDDRH-GNATLEGGDVLVLGKGVVAIGMS 232 (406)
T ss_pred CceEEecCC-CCCCCccceEEEECCCEEEEEec
Confidence 457775433 66779999999999766666644
No 24
>PF00778 DIX: DIX domain; InterPro: IPR001158 Dishevelled (Dsh) protein is an important component of the Wnt signal-transduction pathway. It has three relatively conserved domains: DIX, PDZ and DEP. The DIX domain of Dvl-1 (a mammalian Dishevelled homologue) shares 37% identity with the C-terminal region of Axin. Dsh can interact with the Axin/APC/GSK3/beta-catenin complex, and may thus modulate its activity []. The Wnt signalling pathway is conserved in various species from Caenorhabditis elegans to mammals, and plays important roles in development, cellular proliferation, and differentiation. The molecular mechanisms by which the Wnt signal regulates cellular functions are becoming increasingly well understood. Wnt stabilises cytoplasmic beta-catenin, which stimulates the expression of genes including c-myc, c-jun, fra-1, and cyclin D1. Axin and its homologue Axil are components of the Wnt signalling pathway that negatively regulate this pathway. Other components of the Wnt signalling pathway, including Dvl, glycogen synthase kinase-3beta (GSK-3beta), beta-catenin, and adenomatous polyposis coli (APC), interact with Axin, and the phosphorylation and stability of beta-catenin are regulated in the Axin complex. Axil has similar functions to Axin. Thus, Axin and Axil act as scaffold proteins in the Wnt signalling pathway, thereby modulating the Wnt-dependent cellular functions [].; GO: 0004871 signal transducer activity, 0007275 multicellular organismal development, 0005622 intracellular; PDB: 1WSP_B 2D5G_A 3PZ7_A 3PZ8_H.
Probab=20.95 E-value=35 Score=25.01 Aligned_cols=34 Identities=26% Similarity=0.314 Sum_probs=22.6
Q ss_pred HHHhhhcccc-cccccccccceeecCcceeeeceEEEEe
Q psy12066 122 FLKAQRYEGR-ELWEELPVGRAELRGGDVLWEGEVVMYL 159 (164)
Q Consensus 122 ~lK~~r~e~~-~~W~~l~~~~~~~~~~~~~~~~~~~~~~ 159 (164)
|.|....|+. .-|+++.--.+-| .+|||.||+.+
T Consensus 46 fFK~~~~d~~~~V~eEi~dD~~~L----P~~eGkI~~~v 80 (84)
T PF00778_consen 46 FFKSLDPDFGCVVKEEITDDDDIL----PLFEGKIVAKV 80 (84)
T ss_dssp EEEEEETTTETEEEEEE-STTSB-------BTTEEEEEE
T ss_pred EEEEeCCCCCeeeEEEEcCCcccc----cccCCEEEEEE
Confidence 3455555655 7899988887777 68999999876
No 25
>smart00678 WWE Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis.
Probab=20.52 E-value=61 Score=21.55 Aligned_cols=10 Identities=40% Similarity=0.723 Sum_probs=7.2
Q ss_pred ChhHHHHHHH
Q psy12066 63 SPDIEQSFQE 72 (164)
Q Consensus 63 s~DIEqAF~E 72 (164)
+.+||+||++
T Consensus 20 ~~~IE~ay~~ 29 (73)
T smart00678 20 SEDIEEAYAA 29 (73)
T ss_pred HHHHHHHHHc
Confidence 4677888875
No 26
>PF13230 GATase_4: Glutamine amidotransferases class-II; PDB: 3MDN_D.
Probab=20.24 E-value=42 Score=28.24 Aligned_cols=28 Identities=29% Similarity=0.541 Sum_probs=7.6
Q ss_pred hccccccccccccccee-ecCcceeeece
Q psy12066 127 RYEGRELWEELPVGRAE-LRGGDVLWEGE 154 (164)
Q Consensus 127 r~e~~~~W~~l~~~~~~-~~~~~~~~~~~ 154 (164)
.+..++.|++++.|..- ++.|.|++.+.
T Consensus 230 PLt~~e~W~~vp~g~~l~~~~G~v~~~~~ 258 (271)
T PF13230_consen 230 PLTDDEDWEPVPPGSLLVFRDGEVVARSK 258 (271)
T ss_dssp ----SS--EE--SSEEEE-----------
T ss_pred cCCCCCCeEEcCCCcEEEEeccccccccc
Confidence 45567789999999876 78899988764
Done!