Query 041961
Match_columns 122
No_of_seqs 132 out of 1087
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 12:30:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041961.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041961hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03210 Resistant to P. syrin 100.0 2E-38 4.3E-43 283.8 10.7 118 1-121 39-156 (1153)
2 PLN03194 putative disease resi 100.0 4.2E-37 9.1E-42 227.9 10.3 103 1-120 53-156 (187)
3 PF01582 TIR: TIR domain; Int 99.9 1.1E-24 2.3E-29 154.0 2.5 108 2-109 28-140 (141)
4 smart00255 TIR Toll - interleu 99.8 1.9E-18 4.1E-23 120.3 9.9 110 1-113 29-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.3 7.6E-13 1.7E-17 88.0 0.5 65 1-70 23-87 (102)
6 KOG3678 SARM protein (with ste 97.1 0.001 2.3E-08 56.6 5.4 64 1-69 638-709 (832)
7 PF08937 DUF1863: MTH538 TIR-l 96.7 0.0034 7.4E-08 43.6 4.6 52 14-69 56-107 (130)
8 PF10137 TIR-like: Predicted n 87.8 0.88 1.9E-05 31.9 3.8 38 2-39 24-61 (125)
9 PF08357 SEFIR: SEFIR domain; 87.5 1.8 3.9E-05 30.1 5.3 38 2-39 30-69 (150)
10 PF09441 Abp2: ARS binding pro 85.2 0.49 1.1E-05 34.8 1.4 59 42-109 53-111 (175)
11 PF11074 DUF2779: Domain of un 67.4 4.3 9.3E-05 28.5 2.0 39 14-54 56-94 (130)
12 PF13271 DUF4062: Domain of un 66.1 8 0.00017 24.6 2.9 29 15-43 39-67 (83)
13 PF01990 ATP-synt_F: ATP synth 62.0 14 0.00031 23.9 3.6 39 1-42 16-54 (95)
14 KOG3861 Sensory cilia assembly 58.0 44 0.00095 27.6 6.3 97 2-117 52-154 (438)
15 COG4271 Predicted nucleotide-b 53.4 16 0.00035 28.1 3.0 52 5-57 111-176 (233)
16 TIGR01101 V_ATP_synt_F vacuola 47.1 30 0.00064 23.9 3.3 46 16-71 46-91 (115)
17 KOG2792 Putative cytochrome C 42.1 18 0.0004 28.7 1.9 29 46-74 155-187 (280)
18 cd00138 PLDc Phospholipase D. 40.6 62 0.0013 22.5 4.3 43 13-55 17-64 (176)
19 TIGR03646 YtoQ_fam YtoQ family 39.6 24 0.00053 25.3 2.0 28 15-42 61-89 (144)
20 cd00154 Rab Rab family. Rab G 39.6 1E+02 0.0022 20.1 5.1 36 14-49 57-93 (159)
21 PRK02228 V-type ATP synthase s 38.7 67 0.0014 21.2 4.0 27 16-42 30-56 (100)
22 PRK05225 ketol-acid reductoiso 37.1 18 0.00039 31.0 1.2 29 79-110 307-335 (487)
23 PF05014 Nuc_deoxyrib_tr: Nucl 36.5 1.1E+02 0.0025 20.0 4.9 39 16-55 49-87 (113)
24 cd01241 PH_Akt Akt pleckstrin 36.4 35 0.00076 22.4 2.3 17 96-112 86-102 (102)
25 PF11071 DUF2872: Protein of u 35.0 29 0.00063 24.9 1.8 20 23-42 67-86 (141)
26 cd03028 GRX_PICOT_like Glutare 34.9 19 0.00041 23.0 0.8 26 31-56 8-35 (90)
27 PF14258 DUF4350: Domain of un 34.5 94 0.002 18.6 3.9 41 23-65 28-68 (70)
28 cd01251 PH_centaurin_alpha Cen 34.0 48 0.001 21.8 2.7 19 96-114 84-102 (103)
29 PF11214 Med2: Mediator comple 32.2 24 0.00052 24.1 1.0 17 40-56 68-84 (105)
30 PRK01189 V-type ATP synthase s 30.3 45 0.00098 22.4 2.1 37 1-42 20-57 (104)
31 cd01857 HSR1_MMR1 HSR1/MMR1. 29.9 1.6E+02 0.0034 19.9 4.9 35 20-55 3-37 (141)
32 PF12128 DUF3584: Protein of u 29.3 18 0.00038 34.1 -0.1 31 62-92 34-67 (1201)
33 smart00233 PH Pleckstrin homol 27.5 70 0.0015 18.8 2.5 17 96-112 85-101 (102)
34 PF08862 DUF1829: Domain of un 27.2 96 0.0021 20.1 3.2 30 5-38 58-87 (88)
35 cd01238 PH_Tec Tec pleckstrin 26.7 58 0.0013 21.5 2.1 16 96-111 91-106 (106)
36 cd01266 PH_Gab Gab (Grb2-assoc 26.7 64 0.0014 21.2 2.4 17 96-112 92-108 (108)
37 PF00169 PH: PH domain; Inter 26.7 76 0.0017 19.2 2.6 17 96-112 87-103 (104)
38 TIGR00295 conserved hypothetic 26.5 1.3E+02 0.0028 21.5 4.0 32 83-114 132-163 (164)
39 KOG1136 Predicted cleavage and 26.3 1.5E+02 0.0032 24.9 4.7 55 11-68 180-240 (501)
40 cd01260 PH_CNK Connector enhan 25.5 66 0.0014 20.4 2.2 15 96-110 81-95 (96)
41 cd01219 PH_FGD FGD (faciogenit 25.3 74 0.0016 20.8 2.4 18 96-113 83-100 (101)
42 PRK01395 V-type ATP synthase s 24.4 1.9E+02 0.0042 19.3 4.4 36 2-42 22-57 (104)
43 PF15409 PH_8: Pleckstrin homo 24.2 74 0.0016 20.9 2.2 16 96-111 73-88 (89)
44 cd01235 PH_SETbf Set binding f 22.7 87 0.0019 19.8 2.4 16 96-111 85-100 (101)
45 cd08584 PI-PLCc_GDPD_SF_unchar 22.5 1.4E+02 0.003 22.5 3.7 33 5-40 127-159 (192)
46 PRK03957 V-type ATP synthase s 21.7 1.6E+02 0.0034 19.5 3.5 27 16-42 30-56 (100)
47 PF10579 Rapsyn_N: Rapsyn N-te 21.7 59 0.0013 21.2 1.3 20 97-116 22-41 (80)
48 PF08477 Miro: Miro-like prote 21.6 1.2E+02 0.0026 19.2 2.9 27 24-53 69-95 (119)
49 TIGR00640 acid_CoA_mut_C methy 21.5 2.7E+02 0.0059 19.2 4.8 52 16-70 39-90 (132)
50 PF00350 Dynamin_N: Dynamin fa 21.0 1.8E+02 0.0038 19.8 3.8 60 5-67 104-164 (168)
51 cd01246 PH_oxysterol_bp Oxyste 20.5 96 0.0021 18.8 2.2 15 96-110 76-90 (91)
52 COG2077 Tpx Peroxiredoxin [Pos 20.0 84 0.0018 23.0 2.0 24 27-50 73-98 (158)
No 1
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=2e-38 Score=283.81 Aligned_cols=118 Identities=48% Similarity=0.835 Sum_probs=112.6
Q ss_pred CCeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceeeeeeecCCCccccccc
Q 041961 1 KKIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIIIPVFYGVSPSDVRHQT 80 (122)
Q Consensus 1 ~gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vlPVfy~v~ps~v~~q~ 80 (122)
+||++|+|+ ++++|+.|++++++||++|+++|||||++||+|+|||+||++|++|+++.+++|+||||+|+|+|||+|+
T Consensus 39 ~~i~~f~d~-~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~ 117 (1153)
T PLN03210 39 KLIIAFKDN-EIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQT 117 (1153)
T ss_pred CCCeEEccC-CccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhcc
Confidence 699999988 5999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhHHHHHHHhhcCCHHHHHHHHHHHHHhhccccccccC
Q 041961 81 GIFGLGFGKLEQQFKEQPEMVRKWRDALTESSHLAGHESTK 121 (122)
Q Consensus 81 g~f~~~f~~~~~~~~~~~~~~~~W~~AL~~v~~~~G~~~~~ 121 (122)
|.||++|.+++++. +++++++||+||++||+++||++.+
T Consensus 118 g~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~~ 156 (1153)
T PLN03210 118 GDFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQN 156 (1153)
T ss_pred chHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecCC
Confidence 99999999988753 5789999999999999999999865
No 2
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=4.2e-37 Score=227.87 Aligned_cols=103 Identities=33% Similarity=0.590 Sum_probs=95.1
Q ss_pred CCeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceeeeeeecCCCcccccc-
Q 041961 1 KKIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIIIPVFYGVSPSDVRHQ- 79 (122)
Q Consensus 1 ~gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vlPVfy~v~ps~v~~q- 79 (122)
+||+||+|+.++++|+.|.++|.+||++|+++|+|||++|++|+|||+||++|++|. ..|+||||+|+|++||+|
T Consensus 53 ~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~~I~e~~----~~ViPIFY~VdPsdVr~q~ 128 (187)
T PLN03194 53 LNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELALIMESK----KRVIPIFCDVKPSQLRVVD 128 (187)
T ss_pred CCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHHHHHHcC----CEEEEEEecCCHHHhhccc
Confidence 599999999999999999999999999999999999999999999999999999874 479999999999999997
Q ss_pred cCchhhHHHHHHHhhcCCHHHHHHHHHHHHHhhcccccccc
Q 041961 80 TGIFGLGFGKLEQQFKEQPEMVRKWRDALTESSHLAGHEST 120 (122)
Q Consensus 80 ~g~f~~~f~~~~~~~~~~~~~~~~W~~AL~~v~~~~G~~~~ 120 (122)
.|. .+.+++++||+||++|++++|+++.
T Consensus 129 ~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~ 156 (187)
T PLN03194 129 NGT-------------CPDEEIRRFNWALEEAKYTVGLTFD 156 (187)
T ss_pred cCC-------------CCHHHHHHHHHHHHHHhccccccCC
Confidence 432 2468999999999999999999764
No 3
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=99.90 E-value=1.1e-24 Score=153.99 Aligned_cols=108 Identities=32% Similarity=0.528 Sum_probs=96.6
Q ss_pred CeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccC--CceeeeeeecCCCcccc-c
Q 041961 2 KIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMK--GQIIIPVFYGVSPSDVR-H 78 (122)
Q Consensus 2 gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~--~~~vlPVfy~v~ps~v~-~ 78 (122)
|+++|++++++.+|..+.++|.++|++|+++|+|||+||++|.||++||..++++.... ..+|+||||++.++++. .
T Consensus 28 g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~~~~~~~~~~~~Il~v~~~v~~~~~~~~ 107 (141)
T PF01582_consen 28 GYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEALERLLEEGRDKLILPVFYDVSPSDVRPD 107 (141)
T ss_dssp TS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHHHHHHCSTCTTEEEEESSSS-CHHCHTH
T ss_pred CeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhhhhccccccccceeeEeccCChhhcChh
Confidence 89999999999999999999999999999999999999999999999999999988664 48999999999999999 7
Q ss_pred ccCchhhHHHHHHHhhcCC--HHHHHHHHHHHH
Q 041961 79 QTGIFGLGFGKLEQQFKEQ--PEMVRKWRDALT 109 (122)
Q Consensus 79 q~g~f~~~f~~~~~~~~~~--~~~~~~W~~AL~ 109 (122)
+++.|+..|..+......+ .++...|++++.
T Consensus 108 ~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 108 QSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 9999999998877765543 578999999976
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.78 E-value=1.9e-18 Score=120.30 Aligned_cols=110 Identities=37% Similarity=0.574 Sum_probs=91.1
Q ss_pred CCeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhcccc-CCceeeeeeecCCCcccccc
Q 041961 1 KKIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNM-KGQIIIPVFYGVSPSDVRHQ 79 (122)
Q Consensus 1 ~gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~-~~~~vlPVfy~v~ps~v~~q 79 (122)
.|+.+|.|+. .. |.....+|.++|++|++.|+|+|++|..|.||..|+..++++... ....|+||+|+..|+.+..+
T Consensus 29 ~~~~v~~d~~-~~-~~~~~~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a~~~~~~~~~~~iIPI~~~~~~~~~~~~ 106 (140)
T smart00255 29 YGLCVFIDDF-EP-GGGDLEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAALENALEEGGLRVIPIFYEVIPSDVRKQ 106 (140)
T ss_pred CCcEEEecCc-cc-ccchHHHHHHHHHHCcEEEEEECcccccChhHHHHHHHHHHHHHHcCCCeEEEEEEecChHHHHhc
Confidence 3789999975 33 333333999999999999999999999999999999999987644 67899999999999999999
Q ss_pred cCchhhHHHHHHHhhcCCHHHHHHHHHHHHHhhc
Q 041961 80 TGIFGLGFGKLEQQFKEQPEMVRKWRDALTESSH 113 (122)
Q Consensus 80 ~g~f~~~f~~~~~~~~~~~~~~~~W~~AL~~v~~ 113 (122)
.+.++..+..+...+..+..+ ..|+.++..+.+
T Consensus 107 ~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 107 PGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred ccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 999999998875555444433 789999988764
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.27 E-value=7.6e-13 Score=88.00 Aligned_cols=65 Identities=32% Similarity=0.572 Sum_probs=53.9
Q ss_pred CCeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceeeeeeec
Q 041961 1 KKIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIIIPVFYG 70 (122)
Q Consensus 1 ~gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vlPVfy~ 70 (122)
.|+++|+|. ++..|+.+.++|.++|++|+..|+++|++|..|.||..|+..+.+ .+..|+||..+
T Consensus 23 ~g~~v~~d~-~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~----~~~~iipv~~~ 87 (102)
T PF13676_consen 23 AGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK----RGKPIIPVRLD 87 (102)
T ss_dssp TT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC----TSESEEEEECS
T ss_pred cCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH----CCCEEEEEEEC
Confidence 489999997 899999999999999999999999999999999999999998843 44589999843
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=97.09 E-value=0.001 Score=56.57 Aligned_cols=64 Identities=28% Similarity=0.502 Sum_probs=52.1
Q ss_pred CCeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCcc--------CcHHHHHHHHHHHhccccCCceeeeeee
Q 041961 1 KKIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYA--------SSKWCLNELVKILDCKNMKGQIIIPVFY 69 (122)
Q Consensus 1 ~gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~--------~S~wCl~EL~~i~~~~~~~~~~vlPVfy 69 (122)
+|++||+|-+.+..|+- .+.+++.|...+.+|.|++||-. .-.|--.||.-+++|. .-|+|||=
T Consensus 638 ~GyrVFIDVdKL~AGKF-dssLlkni~aAkhFiLVLtP~sLDr~lnD~nCeDWVHKEl~~Afe~~----KNIiPI~D 709 (832)
T KOG3678|consen 638 RGYRVFIDVDKLYAGKF-DSSLLKNIQAAKHFILVLTPNSLDRLLNDDNCEDWVHKELKCAFEHQ----KNIIPIFD 709 (832)
T ss_pred cCceEEEehhhhhcccc-cHHHHHHHHhhheeEEEeCcchHHHHhccccHHHHHHHHHHHHHHhc----CCeeeeec
Confidence 58999999988998875 46899999999999999999843 3456666777777765 47999984
No 7
>PF08937 DUF1863: MTH538 TIR-like domain (DUF1863); InterPro: IPR015032 This protein adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein []. This domain is similar to the TIR domain [].; PDB: 3HYN_A.
Probab=96.68 E-value=0.0034 Score=43.62 Aligned_cols=52 Identities=29% Similarity=0.458 Sum_probs=36.4
Q ss_pred CCCcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceeeeeee
Q 041961 14 RGDEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIIIPVFY 69 (122)
Q Consensus 14 ~G~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vlPVfy 69 (122)
..+.|...|.++|..|++.||+.|++-..|+|+-.|+..+++ .+..|+-|..
T Consensus 56 ~~~~ik~~I~~~i~~s~~~IVLig~~T~~s~wV~~EI~~A~~----~~~~Ii~V~~ 107 (130)
T PF08937_consen 56 SSEYIKRKIRERIKNSSVTIVLIGPNTAKSKWVNWEIEYALK----KGKPIIGVYL 107 (130)
T ss_dssp TTTTHHHHHHHHHHTEEEEEEE--TT----HHHHHHHHHHTT----T---EEEEET
T ss_pred hHHHHHHHHHHHHhcCCEEEEEeCCCcccCcHHHHHHHHHHH----CCCCEEEEEC
Confidence 445788899999999999999999999999999999998876 4456666654
No 8
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=87.84 E-value=0.88 Score=31.88 Aligned_cols=38 Identities=21% Similarity=0.342 Sum_probs=31.4
Q ss_pred CeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecC
Q 041961 2 KIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKD 39 (122)
Q Consensus 2 gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~ 39 (122)
|+.+.+-......|..+.+.+.+.+++++.+|++++|+
T Consensus 24 ~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpD 61 (125)
T PF10137_consen 24 GLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPD 61 (125)
T ss_pred CCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEccc
Confidence 45555555566889999999999999999999999986
No 9
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=87.50 E-value=1.8 Score=30.14 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=30.6
Q ss_pred CeeEEeeCCCCCC--CCcchHHHHHHHhhccceEEEeecC
Q 041961 2 KIRTFVDDEELRR--GDEISPALLNAIQGSKISVVVFSKD 39 (122)
Q Consensus 2 gi~~f~D~~~~~~--G~~i~~~i~~aIe~S~i~IvV~S~~ 39 (122)
|+.|.+|.-+... +.....=+.++|++++.+|||.|+.
T Consensus 30 g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~ 69 (150)
T PF08357_consen 30 GIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPG 69 (150)
T ss_pred CCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccc
Confidence 8999999876643 5566667778899999999999943
No 10
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=85.24 E-value=0.49 Score=34.84 Aligned_cols=59 Identities=24% Similarity=0.420 Sum_probs=40.8
Q ss_pred CcHHHHHHHHHHHhccccCCceeeeeeecCCCcccccccCchhhHHHHHHHhhcCCHHHHHHHHHHHH
Q 041961 42 SSKWCLNELVKILDCKNMKGQIIIPVFYGVSPSDVRHQTGIFGLGFGKLEQQFKEQPEMVRKWRDALT 109 (122)
Q Consensus 42 ~S~wCl~EL~~i~~~~~~~~~~vlPVfy~v~ps~v~~q~g~f~~~f~~~~~~~~~~~~~~~~W~~AL~ 109 (122)
-|.|-|.||..-++..+-+.=.=|-+.++|+|-++.+... .++..++.-++++|+.|+.
T Consensus 53 Fs~~~Lf~LI~k~~~keikTW~~La~~LGVepp~~ek~qS---------tQKvqQYaVRLKRWM~aMH 111 (175)
T PF09441_consen 53 FSTFTLFELIRKLESKEIKTWAQLALELGVEPPDPEKGQS---------TQKVQQYAVRLKRWMRAMH 111 (175)
T ss_pred chHHHHHHHHHHHhhhhHhHHHHHHHHhCCCCCCcccccc---------hHHHHHHHHHHHHHHHHhh
Confidence 3789999999888766555445566778999888765321 2222334688899999975
No 11
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=67.43 E-value=4.3 Score=28.54 Aligned_cols=39 Identities=31% Similarity=0.463 Sum_probs=29.7
Q ss_pred CCCcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHH
Q 041961 14 RGDEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKIL 54 (122)
Q Consensus 14 ~G~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~ 54 (122)
+-..+..++.++|..-..+|+|+++.|-.+ ||.||..+.
T Consensus 56 Pr~~~~~~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~~ 94 (130)
T PF11074_consen 56 PRRELIEALIKAIGSIYGSIVVYNKSFEKT--RLKELAELF 94 (130)
T ss_pred chHHHHHHHHHHhhhhcCeEEEechHHHHH--HHHHHHHHh
Confidence 344455677778876668999999998765 999998763
No 12
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=66.09 E-value=8 Score=24.58 Aligned_cols=29 Identities=14% Similarity=0.276 Sum_probs=23.5
Q ss_pred CCcchHHHHHHHhhccceEEEeecCccCc
Q 041961 15 GDEISPALLNAIQGSKISVVVFSKDYASS 43 (122)
Q Consensus 15 G~~i~~~i~~aIe~S~i~IvV~S~~y~~S 43 (122)
+....+.+++.|++|++.|.++...|-..
T Consensus 39 ~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 39 DQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred CCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 55556688899999999999999988653
No 13
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=62.03 E-value=14 Score=23.94 Aligned_cols=39 Identities=13% Similarity=0.302 Sum_probs=28.8
Q ss_pred CCeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccC
Q 041961 1 KKIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYAS 42 (122)
Q Consensus 1 ~gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~ 42 (122)
.|+.++... ...+++...+.+.+++.++.||+++++++.
T Consensus 16 aGv~~~~~~---~~~ee~~~~l~~l~~~~~~gIIii~e~~~~ 54 (95)
T PF01990_consen 16 AGVEGVYVN---TDPEEAEEALKELLKDEDVGIIIITEDLAE 54 (95)
T ss_dssp TTSEEEEES---HSHHHHHHHHHHHHHHTTEEEEEEEHHHHT
T ss_pred cCCCCccCC---CCHHHHHHHHHHHhcCCCccEEEeeHHHHH
Confidence 377777765 113556666667777899999999999887
No 14
>KOG3861 consensus Sensory cilia assembly protein [Extracellular structures]
Probab=58.01 E-value=44 Score=27.61 Aligned_cols=97 Identities=15% Similarity=0.219 Sum_probs=59.0
Q ss_pred CeeEEeeCCCCCCCCcchHHHHHHH---hhccceEEEeecCccCcH--HHHHHHHHHHhccccCCceeeeeeec-CCCcc
Q 041961 2 KIRTFVDDEELRRGDEISPALLNAI---QGSKISVVVFSKDYASSK--WCLNELVKILDCKNMKGQIIIPVFYG-VSPSD 75 (122)
Q Consensus 2 gi~~f~D~~~~~~G~~i~~~i~~aI---e~S~i~IvV~S~~y~~S~--wCl~EL~~i~~~~~~~~~~vlPVfy~-v~ps~ 75 (122)
|++.|+--. +-+.++..=++++ -+..-+++|++-.=.++. -.++++..-....-+++.+|=||||+ -.|..
T Consensus 52 ~Vk~~i~ag---P~~~Ft~~Efevlkkyve~GGsl~vllGEGGE~rf~tnvNf~le~YGI~vN~DtVvR~vy~KyFhPKE 128 (438)
T KOG3861|consen 52 RVKIFILAG---PQDRFTEDEFEVLKKYVEVGGSLVVLLGEGGEPRFNTNVNFFLEQYGIYVNGDTVVRPVYYKYFHPKE 128 (438)
T ss_pred ceeEEEecC---cccccchhHHHHHHHHHhcCCeEEEEecCCCCccccccHHHHHHHhCeEecCCceeehhhhhccChHH
Confidence 556665432 3455544333333 245888899887655554 25677777666667788899999996 56665
Q ss_pred cccccCchhhHHHHHHHhhcCCHHHHHHHHHHHHHhhccccc
Q 041961 76 VRHQTGIFGLGFGKLEQQFKEQPEMVRKWRDALTESSHLAGH 117 (122)
Q Consensus 76 v~~q~g~f~~~f~~~~~~~~~~~~~~~~W~~AL~~v~~~~G~ 117 (122)
---..|... ..-||.|++.|..+.-+
T Consensus 129 alV~~GVvn----------------r~i~raa~K~v~~~v~~ 154 (438)
T KOG3861|consen 129 ALVGGGVVN----------------RSIWRAALKLVIEKVYY 154 (438)
T ss_pred hhhccceee----------------HHHHHHHHhhhHHHHHh
Confidence 444444332 23488888777654433
No 15
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=53.35 E-value=16 Score=28.07 Aligned_cols=52 Identities=19% Similarity=0.246 Sum_probs=39.9
Q ss_pred EEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCcc--------CcHH------HHHHHHHHHhcc
Q 041961 5 TFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYA--------SSKW------CLNELVKILDCK 57 (122)
Q Consensus 5 ~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~--------~S~w------Cl~EL~~i~~~~ 57 (122)
+|.|. -+..|..+.+.+.+-|++++.+|+++.|+=. +-.| -+.||..+|-+.
T Consensus 111 vi~d~-~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~praRqNVifELGm~mgrL 176 (233)
T COG4271 111 VILDG-LFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAFPRARQNVIFELGMFMGRL 176 (233)
T ss_pred EEecC-cccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhccccccccchhhHhhHHhhc
Confidence 56665 3789999999999999999999999999833 1223 367888877643
No 16
>TIGR01101 V_ATP_synt_F vacuolar ATP synthase F subunit. This model describes the vacuolar ATP synthase F subunit (14 kDa subunit) in eukaryotes. In some archaeal species this protein subunit is referred as G subunit
Probab=47.09 E-value=30 Score=23.92 Aligned_cols=46 Identities=15% Similarity=0.326 Sum_probs=28.6
Q ss_pred CcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceeeeeeecC
Q 041961 16 DEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIIIPVFYGV 71 (122)
Q Consensus 16 ~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vlPVfy~v 71 (122)
+++...+.+.+.+.+++||++++++++ ++...++..+ .++|....+
T Consensus 46 eei~~~~~~~l~~~digIIlIte~~a~------~i~~~I~~~~----~~~PaIieI 91 (115)
T TIGR01101 46 SEIEDCFNRFLKRDDIAIILINQHIAE------MIRHAVDAHT----RSIPAVLEI 91 (115)
T ss_pred HHHHHHHHHHhhcCCeEEEEEcHHHHH------HhHHHHHhcC----CcCCEEEEE
Confidence 344445555578899999999998876 3444444333 455555444
No 17
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=42.05 E-value=18 Score=28.72 Aligned_cols=29 Identities=31% Similarity=0.537 Sum_probs=21.2
Q ss_pred HHHHHHHHHhc---c-ccCCceeeeeeecCCCc
Q 041961 46 CLNELVKILDC---K-NMKGQIIIPVFYGVSPS 74 (122)
Q Consensus 46 Cl~EL~~i~~~---~-~~~~~~vlPVfy~v~ps 74 (122)
|-|||.++... . .+.+..++|||.-|+|.
T Consensus 155 CPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 155 CPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred ChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 88898876543 3 34566777999999994
No 18
>cd00138 PLDc Phospholipase D. Active site motifs; The PLD superfamily includes enzymes involved in signal transduction, lipid biosynthesis, endonucleases and open reading frames in pathogenic viruses and bacteria. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. The common features of the family members are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
Probab=40.65 E-value=62 Score=22.46 Aligned_cols=43 Identities=26% Similarity=0.199 Sum_probs=31.7
Q ss_pred CCCCcchHHHHHHHhhccceEEEeecCccC-----cHHHHHHHHHHHh
Q 041961 13 RRGDEISPALLNAIQGSKISVVVFSKDYAS-----SKWCLNELVKILD 55 (122)
Q Consensus 13 ~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~-----S~wCl~EL~~i~~ 55 (122)
..++.+.+.+.++|..++..|.+.+..|.. +..-++.|....+
T Consensus 17 ~~~~~~~~~i~~~I~~A~~~I~i~~~~~~~~~~~~~~~l~~~L~~a~~ 64 (176)
T cd00138 17 VGGRSDLDALLEAISNAKKSIYIASFYLSPLITEYGPVILDALLAAAR 64 (176)
T ss_pred cCcchHHHHHHHHHHhhheEEEEEEeEecccccccchHHHHHHHHHHH
Confidence 456788889999999999999999997774 4444455555543
No 19
>TIGR03646 YtoQ_fam YtoQ family protein. Members of this family are uncharacterized proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=39.61 E-value=24 Score=25.31 Aligned_cols=28 Identities=14% Similarity=0.357 Sum_probs=21.0
Q ss_pred CCcchH-HHHHHHhhccceEEEeecCccC
Q 041961 15 GDEISP-ALLNAIQGSKISVVVFSKDYAS 42 (122)
Q Consensus 15 G~~i~~-~i~~aIe~S~i~IvV~S~~y~~ 42 (122)
|-.+.. .....|++|+++||.|.+.|-.
T Consensus 61 ~a~iNaiRT~~li~~aDvvVvrFGekYKQ 89 (144)
T TIGR03646 61 AASINNIRTRKLIEKADVVIALFGEKYKQ 89 (144)
T ss_pred ccchhhHHHHHHHhhCCEEEEEechHHHH
Confidence 544431 3346899999999999999965
No 20
>cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di
Probab=39.56 E-value=1e+02 Score=20.09 Aligned_cols=36 Identities=17% Similarity=0.205 Sum_probs=22.8
Q ss_pred CCCc-chHHHHHHHhhccceEEEeecCccCcHHHHHH
Q 041961 14 RGDE-ISPALLNAIQGSKISVVVFSKDYASSKWCLNE 49 (122)
Q Consensus 14 ~G~~-i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~E 49 (122)
+|.. ........+++++..|+|++.+-..+-..+.+
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~~~~~~~~~ 93 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNRESFENLDK 93 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCHHHHHHHHH
Confidence 4433 33445667889999999999875443333333
No 21
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=38.74 E-value=67 Score=21.25 Aligned_cols=27 Identities=11% Similarity=0.363 Sum_probs=19.9
Q ss_pred CcchHHHHHHHhhccceEEEeecCccC
Q 041961 16 DEISPALLNAIQGSKISVVVFSKDYAS 42 (122)
Q Consensus 16 ~~i~~~i~~aIe~S~i~IvV~S~~y~~ 42 (122)
+++...+.+.+.+-+++||+++++++.
T Consensus 30 ee~~~~l~~l~~~~d~gII~Ite~~~~ 56 (100)
T PRK02228 30 EKLDEAVEEVLEDDDVGILVMHDDDLE 56 (100)
T ss_pred HHHHHHHHHHhhCCCEEEEEEehhHhH
Confidence 345545555567888999999999766
No 22
>PRK05225 ketol-acid reductoisomerase; Validated
Probab=37.08 E-value=18 Score=30.98 Aligned_cols=29 Identities=14% Similarity=0.205 Sum_probs=21.5
Q ss_pred ccCchhhHHHHHHHhhcCCHHHHHHHHHHHHH
Q 041961 79 QTGIFGLGFGKLEQQFKEQPEMVRKWRDALTE 110 (122)
Q Consensus 79 q~g~f~~~f~~~~~~~~~~~~~~~~W~~AL~~ 110 (122)
|+|.|.+.+..-.++ +..+..+||+++.+
T Consensus 307 ~sG~fak~~m~d~~~---~~~~l~~~r~~~~~ 335 (487)
T PRK05225 307 ISGEFSSTMMADWAN---DDKKLLTWREETGK 335 (487)
T ss_pred hccHHHHHHHHHHhc---CChHHHHHHHHhhc
Confidence 688888777655543 46789999998764
No 23
>PF05014 Nuc_deoxyrib_tr: Nucleoside 2-deoxyribosyltransferase; InterPro: IPR007710 Nucleoside 2-deoxyribosyltransferase (2.4.2.6 from EC) catalyses the cleavage of the glycosidic bonds of 2-deoxyribonucleosides. Nucleoside 2-deoxyribosyltransferases can be divided into two groups based on their substrate specificity: class I enzymes are specific for the transfer of deoxyribose between two purines, while class II enzymes will transfer the deoxyribose between either purines or pyrimidines. The structure of the class I [] and class II [] enzymes are very similar. In class I enzymes, the purine base shields the active site from solvent, which the smaller pyrimidine base cannot do, while in class II enzymes the active site is shielded by a loop (residues 48-62). Both classes of enzymes are found in various Lactobacillus species and participate in nucleoside recycling in these microorganisms. This entry represents both classes of enzymes.; GO: 0050144 nucleoside deoxyribosyltransferase activity, 0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity, 0009159 deoxyribonucleoside monophosphate catabolic process; PDB: 1S2L_A 1S2D_C 1S2I_A 1S3F_B 1S2G_C 2A0K_A 2F67_A 2F64_B 2F62_A 2F2T_A ....
Probab=36.46 E-value=1.1e+02 Score=19.98 Aligned_cols=39 Identities=18% Similarity=0.024 Sum_probs=28.7
Q ss_pred CcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHh
Q 041961 16 DEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILD 55 (122)
Q Consensus 16 ~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~ 55 (122)
..|...-.++|++|++.|+++...- .+.=...|+..+..
T Consensus 49 ~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~a 87 (113)
T PF05014_consen 49 REIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYA 87 (113)
T ss_dssp HHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHH
Confidence 4455555679999999999998766 45667789988765
No 24
>cd01241 PH_Akt Akt pleckstrin homology (PH) domain. Akt pleckstrin homology (PH) domain. Akt (Protein Kinase B (PKB)) is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase. The PH domain recruits Akt to the plasma membrane by binding to phosphoinositides (PtdIns-3,4-P2) and is required for activation. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=36.36 E-value=35 Score=22.40 Aligned_cols=17 Identities=29% Similarity=0.589 Sum_probs=14.2
Q ss_pred CCHHHHHHHHHHHHHhh
Q 041961 96 EQPEMVRKWRDALTESS 112 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v~ 112 (122)
++++..+.|..||..|+
T Consensus 86 ~s~ee~~eWi~ai~~v~ 102 (102)
T cd01241 86 ESPEEREEWIHAIQTVA 102 (102)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 46788999999998874
No 25
>PF11071 DUF2872: Protein of unknown function (DUF2872); InterPro: IPR019884 This entry represents a family of uncharacterised proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=34.95 E-value=29 Score=24.87 Aligned_cols=20 Identities=25% Similarity=0.449 Sum_probs=17.6
Q ss_pred HHHHhhccceEEEeecCccC
Q 041961 23 LNAIQGSKISVVVFSKDYAS 42 (122)
Q Consensus 23 ~~aIe~S~i~IvV~S~~y~~ 42 (122)
...|++|+++|+.|.+.|-.
T Consensus 67 ~~li~~aDvVVvrFGekYKQ 86 (141)
T PF11071_consen 67 RTLIEKADVVVVRFGEKYKQ 86 (141)
T ss_pred HHHHhhCCEEEEEechHHHH
Confidence 45789999999999999965
No 26
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=34.88 E-value=19 Score=23.01 Aligned_cols=26 Identities=31% Similarity=0.404 Sum_probs=17.5
Q ss_pred ceEEEeecCccCcHHHHH--HHHHHHhc
Q 041961 31 ISVVVFSKDYASSKWCLN--ELVKILDC 56 (122)
Q Consensus 31 i~IvV~S~~y~~S~wCl~--EL~~i~~~ 56 (122)
.-|+|||+.+.+.+||-. .+..+++.
T Consensus 8 ~~vvvf~k~~~~~~~Cp~C~~ak~~L~~ 35 (90)
T cd03028 8 NPVVLFMKGTPEEPRCGFSRKVVQILNQ 35 (90)
T ss_pred CCEEEEEcCCCCCCCCcHHHHHHHHHHH
Confidence 467788998877777753 55556653
No 27
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=34.54 E-value=94 Score=18.57 Aligned_cols=41 Identities=15% Similarity=0.272 Sum_probs=26.0
Q ss_pred HHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceee
Q 041961 23 LNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIII 65 (122)
Q Consensus 23 ~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vl 65 (122)
..+++...-.++++++.+.-+. -.++..+.+..+.++..|+
T Consensus 28 ~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~v~~G~~lvl 68 (70)
T PF14258_consen 28 YEALEADDGTLLVIGPDLRLSE--PEEAEALLEWVEAGNTLVL 68 (70)
T ss_pred HHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHHHHcCCEEEE
Confidence 4566678889999999965543 2344455554455665554
No 28
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specifici
Probab=33.96 E-value=48 Score=21.80 Aligned_cols=19 Identities=21% Similarity=0.300 Sum_probs=16.1
Q ss_pred CCHHHHHHHHHHHHHhhcc
Q 041961 96 EQPEMVRKWRDALTESSHL 114 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v~~~ 114 (122)
++++....|.+||..|-+.
T Consensus 84 ~s~~e~~~Wi~ai~~v~~~ 102 (103)
T cd01251 84 ETEQDRREWIAAFQNVLSR 102 (103)
T ss_pred CCHHHHHHHHHHHHHHhcC
Confidence 5678899999999998764
No 29
>PF11214 Med2: Mediator complex subunit 2; InterPro: IPR021017 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression [, ].
Probab=32.16 E-value=24 Score=24.14 Aligned_cols=17 Identities=24% Similarity=0.577 Sum_probs=13.8
Q ss_pred ccCcHHHHHHHHHHHhc
Q 041961 40 YASSKWCLNELVKILDC 56 (122)
Q Consensus 40 y~~S~wCl~EL~~i~~~ 56 (122)
|..|+||++.++.+-..
T Consensus 68 l~~sk~~v~~m~e~~q~ 84 (105)
T PF11214_consen 68 LNDSKWYVDTMVELKQK 84 (105)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 78899999999887543
No 30
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=30.31 E-value=45 Score=22.44 Aligned_cols=37 Identities=14% Similarity=0.205 Sum_probs=27.7
Q ss_pred CCee-EEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccC
Q 041961 1 KKIR-TFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYAS 42 (122)
Q Consensus 1 ~gi~-~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~ 42 (122)
.||. +|.-.+ ++-..++.+.+.+.++.|++++++++.
T Consensus 20 aGi~~v~~~~~-----~e~~~~~~~~l~~~~~gII~iTE~~a~ 57 (104)
T PRK01189 20 LGIGDTIEAEG-----KDLVKKFLEIFNNPKCKYIFVSESTKN 57 (104)
T ss_pred cCCceEEEcCC-----HHHHHHHHHHHhcCCeEEEEEEHHHHh
Confidence 3775 776443 222368888999999999999999876
No 31
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.
Probab=29.93 E-value=1.6e+02 Score=19.95 Aligned_cols=35 Identities=14% Similarity=0.116 Sum_probs=22.3
Q ss_pred HHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHh
Q 041961 20 PALLNAIQGSKISVVVFSKDYASSKWCLNELVKILD 55 (122)
Q Consensus 20 ~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~ 55 (122)
.++.++|+++++.++|++-.-..+.+. .++...+.
T Consensus 3 ~~~~~~i~~aD~vl~ViD~~~p~~~~~-~~l~~~l~ 37 (141)
T cd01857 3 RQLWRVVERSDIVVQIVDARNPLLFRP-PDLERYVK 37 (141)
T ss_pred HHHHHHHhhCCEEEEEEEccCCcccCC-HHHHHHHH
Confidence 356788888888888887665444442 14545444
No 32
>PF12128 DUF3584: Protein of unknown function (DUF3584); InterPro: IPR021979 This family consist of uncharacterised bacterial proteins.
Probab=29.26 E-value=18 Score=34.07 Aligned_cols=31 Identities=29% Similarity=0.451 Sum_probs=21.1
Q ss_pred ceeeeeeecCCCccccccc---CchhhHHHHHHH
Q 041961 62 QIIIPVFYGVSPSDVRHQT---GIFGLGFGKLEQ 92 (122)
Q Consensus 62 ~~vlPVfy~v~ps~v~~q~---g~f~~~f~~~~~ 92 (122)
++.||+||+-+|+.|-..+ -+|.+-+..+..
T Consensus 34 LRlip~FYGa~p~rlv~k~~~rksF~~yYLP~~n 67 (1201)
T PF12128_consen 34 LRLIPFFYGADPSRLVPKTSGRKSFDDYYLPYSN 67 (1201)
T ss_pred HHHHHHhcCCCccccCCccchhhhHHHHcCCCCC
Confidence 5899999999999975444 245544444433
No 33
>smart00233 PH Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids.
Probab=27.50 E-value=70 Score=18.83 Aligned_cols=17 Identities=35% Similarity=0.552 Sum_probs=14.3
Q ss_pred CCHHHHHHHHHHHHHhh
Q 041961 96 EQPEMVRKWRDALTESS 112 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v~ 112 (122)
.+++....|..||..++
T Consensus 85 ~s~~~~~~W~~~i~~~~ 101 (102)
T smart00233 85 ESEEEREEWVDALRKAI 101 (102)
T ss_pred CCHHHHHHHHHHHHHhh
Confidence 46789999999998875
No 34
>PF08862 DUF1829: Domain of unknown function DUF1829; InterPro: IPR014961 This short protein is usually associated with IPR014960 from INTERPRO.
Probab=27.19 E-value=96 Score=20.08 Aligned_cols=30 Identities=27% Similarity=0.453 Sum_probs=23.5
Q ss_pred EEeeCCCCCCCCcchHHHHHHHhhccceEEEeec
Q 041961 5 TFVDDEELRRGDEISPALLNAIQGSKISVVVFSK 38 (122)
Q Consensus 5 ~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~ 38 (122)
++++|. -.++.+.+.+|+++..+.++-+|+
T Consensus 58 ii~ND~----e~~i~~~~~~a~~~y~I~~i~wS~ 87 (88)
T PF08862_consen 58 IILNDS----EKPISEDIINALEQYNIKPIPWSK 87 (88)
T ss_pred EEECCC----CCccCHHHHHHHHHCCCceecCCc
Confidence 555554 267888999999999999998886
No 35
>cd01238 PH_Tec Tec pleckstrin homology (PH) domain. Tec pleckstrin homology (PH) domain. Proteins in the Tec family of cytoplasmic protein tyrosine kinases that includes Bruton's tyrosine kinase (BTK), BMX, IL2-inducible T-cell kinase (Itk) and Tec. These proteins generally have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. Tec PH domains tether these proteins to membranes following the activation of PI3K and its subsequent phosphorylation of phosphoinositides. The importance of PH domain membrane anchoring is confirmed by the discovery of a mutation of a critical arginine residue in the BTK PH domain, which causes X-linked agammaglobulinemia (XLA) in humans and a related disorder is mice. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few dis
Probab=26.74 E-value=58 Score=21.51 Aligned_cols=16 Identities=25% Similarity=0.590 Sum_probs=13.5
Q ss_pred CCHHHHHHHHHHHHHh
Q 041961 96 EQPEMVRKWRDALTES 111 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v 111 (122)
.+++..+.|..||.+|
T Consensus 91 ~s~~er~~WI~ai~~~ 106 (106)
T cd01238 91 PTEELRKRWIKALKQV 106 (106)
T ss_pred CCHHHHHHHHHHHHhC
Confidence 4678899999999875
No 36
>cd01266 PH_Gab Gab (Grb2-associated binder) pleckstrin homology (PH) domain. Gab (Grb2-associated binder) pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display str
Probab=26.69 E-value=64 Score=21.21 Aligned_cols=17 Identities=12% Similarity=0.368 Sum_probs=14.7
Q ss_pred CCHHHHHHHHHHHHHhh
Q 041961 96 EQPEMVRKWRDALTESS 112 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v~ 112 (122)
++++.++.|..|+.+++
T Consensus 92 ~s~ee~~~Wi~~I~~~~ 108 (108)
T cd01266 92 KNEEEMTLWVNCICKLC 108 (108)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 56899999999998874
No 37
>PF00169 PH: PH domain; InterPro: IPR001849 The pleckstrin homology (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signalling or as constituents of the cytoskeleton [, , , , , , ]. The pleckstrin homology domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. The 3D structure of several PH domains has been determined []. All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. The loops connecting the beta-strands differ greatly in length, making the PH domain relatively difficult to detect. There are no totally invariant residues within the PH domain. Proteins reported to contain one more PH domains belong to the following families: Pleckstrin, the protein where this domain was first detected, is the major substrate of protein kinase C in platelets. Pleckstrin is one of the rare proteins to contains two PH domains. Ser/Thr protein kinases such as the Akt/Rac family, the beta-adrenergic receptor kinases, the mu isoform of PKC and the trypanosomal NrkA family. Tyrosine protein kinases belonging to the Btk/Itk/Tec subfamily. Insulin Receptor Substrate 1 (IRS-1). Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. Cytoskeletal proteins such as dynamin (see IPR001401 from INTERPRO), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 from INTERPRO), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. Mammalian phosphatidylinositol-specific phospholipase C (PI-PLC) (see IPR000909 from INTERPRO) isoforms gamma and delta. Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). C. elegans protein MIG-10. C. elegans hypothetical proteins C04D8.1, K06H7.4 and ZK632.12. S. cerevisiae hypothetical proteins YBR129c and YHR155w. ; GO: 0005515 protein binding; PDB: 1DYN_B 2DYN_B 3SNH_A 3ZYS_C 1X05_A 2I5F_A 1ZM0_B 1XX0_A 2I5C_C 3A8P_D ....
Probab=26.65 E-value=76 Score=19.17 Aligned_cols=17 Identities=24% Similarity=0.524 Sum_probs=14.7
Q ss_pred CCHHHHHHHHHHHHHhh
Q 041961 96 EQPEMVRKWRDALTESS 112 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v~ 112 (122)
++++....|..||..+.
T Consensus 87 ~s~~~~~~W~~~i~~~~ 103 (104)
T PF00169_consen 87 ESEEERKRWIQAIQKAI 103 (104)
T ss_dssp SSHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 57899999999999874
No 38
>TIGR00295 conserved hypothetical protein TIGR00295. This set of orthologs is narrowly defined, comprising proteins found in three Archaea but not in Pyrococcus horikoshii. The closest homologs are other archaeal proteins that appear to be represent distinct orthologous clusters.
Probab=26.49 E-value=1.3e+02 Score=21.52 Aligned_cols=32 Identities=19% Similarity=0.204 Sum_probs=26.2
Q ss_pred hhhHHHHHHHhhcCCHHHHHHHHHHHHHhhcc
Q 041961 83 FGLGFGKLEQQFKEQPEMVRKWRDALTESSHL 114 (122)
Q Consensus 83 f~~~f~~~~~~~~~~~~~~~~W~~AL~~v~~~ 114 (122)
..+.+.+..++++.++....+|+.+..+|.++
T Consensus 132 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (164)
T TIGR00295 132 IDEVIKKLEERLGKNHPSIERARKLKEELERL 163 (164)
T ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHHhh
Confidence 45666777788888888999999999998875
No 39
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=26.28 E-value=1.5e+02 Score=24.93 Aligned_cols=55 Identities=24% Similarity=0.538 Sum_probs=37.7
Q ss_pred CCCCCCcchHHHHHHHhhccceEEEeecCcc----CcHHHHH-HH-HHHHhccccCCceeeeee
Q 041961 11 ELRRGDEISPALLNAIQGSKISVVVFSKDYA----SSKWCLN-EL-VKILDCKNMKGQIIIPVF 68 (122)
Q Consensus 11 ~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~----~S~wCl~-EL-~~i~~~~~~~~~~vlPVf 68 (122)
.+.+...+.. ..|..+|--+.|--..|+ .|+.|.+ |+ .+..+|-..++.+++|||
T Consensus 180 nmTpDrHLGa---A~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvF 240 (501)
T KOG1136|consen 180 NMTPDRHLGA---AWIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVF 240 (501)
T ss_pred cCCcccccch---hhhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEee
Confidence 3444444442 346777777776666675 4788876 54 456789889999999999
No 40
>cd01260 PH_CNK Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK is believed to regulate the activity and the subcellular localization of RAS activated RAF. CNK is composed of N-terminal SAM and PDZ domains along with a central or C-terminal PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskelet
Probab=25.48 E-value=66 Score=20.38 Aligned_cols=15 Identities=20% Similarity=0.468 Sum_probs=12.9
Q ss_pred CCHHHHHHHHHHHHH
Q 041961 96 EQPEMVRKWRDALTE 110 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~ 110 (122)
++++.+++|..||..
T Consensus 81 ~s~~e~~~Wi~ai~~ 95 (96)
T cd01260 81 ETLDDLSQWVNHLIT 95 (96)
T ss_pred CCHHHHHHHHHHHHh
Confidence 568899999999975
No 41
>cd01219 PH_FGD FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD has a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. FGD is a guanine nucleotide exchange factor that activates the Rho GTPase Cdc42. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=25.31 E-value=74 Score=20.75 Aligned_cols=18 Identities=11% Similarity=0.217 Sum_probs=15.2
Q ss_pred CCHHHHHHHHHHHHHhhc
Q 041961 96 EQPEMVRKWRDALTESSH 113 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v~~ 113 (122)
.+++...+|.+||..+.+
T Consensus 83 ~s~eEk~~W~~ai~~~i~ 100 (101)
T cd01219 83 RTQKEKNDWVQAIFSIID 100 (101)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 467889999999998764
No 42
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=24.45 E-value=1.9e+02 Score=19.28 Aligned_cols=36 Identities=14% Similarity=0.180 Sum_probs=22.9
Q ss_pred CeeEEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCccC
Q 041961 2 KIRTFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDYAS 42 (122)
Q Consensus 2 gi~~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y~~ 42 (122)
|+.+|.-.+ .+... +.++.+.+-+++||+++++.+.
T Consensus 22 Gi~~~~v~~----~ee~~-~~i~~l~~~d~gII~Ite~~a~ 57 (104)
T PRK01395 22 GIDVFPVID----EQEAI-NTLRKLAMEDYGIIYITEQIAA 57 (104)
T ss_pred CCeeEEecC----hHHHH-HHHHHHhcCCcEEEEEcHHHHH
Confidence 676665433 24443 3334455668999999998876
No 43
>PF15409 PH_8: Pleckstrin homology domain
Probab=24.16 E-value=74 Score=20.92 Aligned_cols=16 Identities=25% Similarity=0.574 Sum_probs=13.2
Q ss_pred CCHHHHHHHHHHHHHh
Q 041961 96 EQPEMVRKWRDALTES 111 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v 111 (122)
.+++..+.|..||..+
T Consensus 73 ~s~~~f~~Wv~aL~~a 88 (89)
T PF15409_consen 73 KSQEDFQRWVSALQKA 88 (89)
T ss_pred CCHHHHHHHHHHHHhc
Confidence 4578899999999864
No 44
>cd01235 PH_SETbf Set binding factor Pleckstrin Homology (PH) domain. Set binding factor Pleckstrin Homology (PH) domain. Set binding factor is a myotubularin-related pseudo-phosphatase consisting of a Denn domain, a Gram domain, an inactive phosphatase domain, a SID motif and a C-terminal PH domain. Its PH domain is predicted to bind lipids based upon its ability to respond to phosphatidylinositol 3-kinase .
Probab=22.69 E-value=87 Score=19.75 Aligned_cols=16 Identities=13% Similarity=0.599 Sum_probs=13.5
Q ss_pred CCHHHHHHHHHHHHHh
Q 041961 96 EQPEMVRKWRDALTES 111 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~v 111 (122)
++++....|..||..+
T Consensus 85 ~s~~e~~~Wi~ai~~~ 100 (101)
T cd01235 85 ENINEAQRWKEKIQQC 100 (101)
T ss_pred CCHHHHHHHHHHHHhh
Confidence 5678899999999875
No 45
>cd08584 PI-PLCc_GDPD_SF_unchar2 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=22.50 E-value=1.4e+02 Score=22.46 Aligned_cols=33 Identities=9% Similarity=0.131 Sum_probs=27.7
Q ss_pred EEeeCCCCCCCCcchHHHHHHHhhccceEEEeecCc
Q 041961 5 TFVDDEELRRGDEISPALLNAIQGSKISVVVFSKDY 40 (122)
Q Consensus 5 ~f~D~~~~~~G~~i~~~i~~aIe~S~i~IvV~S~~y 40 (122)
||+|.- .+..+.+++.+...+...-|++.||.-
T Consensus 127 VW~D~f---~~~~~~~~~~~~~~~~~~~~c~VSpEL 159 (192)
T cd08584 127 VWIDSF---TSLWLDNDLILKLLKAGKKICLVSPEL 159 (192)
T ss_pred EEEecc---cccCCCHHHHHHHHHCCcEEEEECHHH
Confidence 788875 368888899888888999999999974
No 46
>PRK03957 V-type ATP synthase subunit F; Provisional
Probab=21.70 E-value=1.6e+02 Score=19.48 Aligned_cols=27 Identities=15% Similarity=0.414 Sum_probs=19.4
Q ss_pred CcchHHHHHHHhhccceEEEeecCccC
Q 041961 16 DEISPALLNAIQGSKISVVVFSKDYAS 42 (122)
Q Consensus 16 ~~i~~~i~~aIe~S~i~IvV~S~~y~~ 42 (122)
+.+...+.+.+++-+++||+++++++.
T Consensus 30 ee~~~~l~~l~~~~d~gII~ite~~~~ 56 (100)
T PRK03957 30 EEAKNAIKELVENDEIGIIIITERIAE 56 (100)
T ss_pred HHHHHHHHHHhhCCCeEEEEEcHHHHH
Confidence 444445555666788999999998775
No 47
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=21.68 E-value=59 Score=21.17 Aligned_cols=20 Identities=25% Similarity=0.538 Sum_probs=16.7
Q ss_pred CHHHHHHHHHHHHHhhcccc
Q 041961 97 QPEMVRKWRDALTESSHLAG 116 (122)
Q Consensus 97 ~~~~~~~W~~AL~~v~~~~G 116 (122)
...-+..|+.||..+.+.++
T Consensus 22 ~~~Al~~W~~aL~k~~~~~~ 41 (80)
T PF10579_consen 22 TQQALQKWRKALEKITDRED 41 (80)
T ss_pred HHHHHHHHHHHHhhcCChHH
Confidence 45779999999999998664
No 48
>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.
Probab=21.62 E-value=1.2e+02 Score=19.24 Aligned_cols=27 Identities=11% Similarity=0.159 Sum_probs=18.4
Q ss_pred HHHhhccceEEEeecCccCcHHHHHHHHHH
Q 041961 24 NAIQGSKISVVVFSKDYASSKWCLNELVKI 53 (122)
Q Consensus 24 ~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i 53 (122)
..++.++.+|+|++-.-. ..++++..+
T Consensus 69 ~~~~~~d~~ilv~D~s~~---~s~~~~~~~ 95 (119)
T PF08477_consen 69 FFLKKADAVILVYDLSDP---ESLEYLSQL 95 (119)
T ss_dssp HHHHHSCEEEEEEECCGH---HHHHHHHHH
T ss_pred chhhcCcEEEEEEcCCCh---HHHHHHHHH
Confidence 349999999999976543 345554433
No 49
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=21.46 E-value=2.7e+02 Score=19.22 Aligned_cols=52 Identities=21% Similarity=0.091 Sum_probs=33.1
Q ss_pred CcchHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceeeeeeec
Q 041961 16 DEISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIIIPVFYG 70 (122)
Q Consensus 16 ~~i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vlPVfy~ 70 (122)
+.-.+++.++..+++.-+|++|--..+..--+.++...++ +.+..-+||+-.
T Consensus 39 ~~s~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~L~---~~g~~~i~vivG 90 (132)
T TIGR00640 39 FQTPEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKELD---KLGRPDILVVVG 90 (132)
T ss_pred CCCHHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHHHH---hcCCCCCEEEEe
Confidence 3334577888889999999999888775444445554443 323324666654
No 50
>PF00350 Dynamin_N: Dynamin family; InterPro: IPR001401 Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another. Dynamins are large GTPases that belong to a protein superfamily [] that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins [, , , ], and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance. The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity. This entry represents the GTPase domain, containing the GTP-binding motifs that are needed for guanine-nucleotide binding and hydrolysis. The conservation of these motifs is absolute except for the the final motif in guanylate-binding proteins. The GTPase catalytic activity can be stimulated by oligomerisation of the protein, which is mediated by interactions between the GTPase domain, the middle domain and the GED.; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1JWY_B 1JX2_B 3ZVR_A 2AKA_B 3L43_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D ....
Probab=21.00 E-value=1.8e+02 Score=19.81 Aligned_cols=60 Identities=12% Similarity=0.091 Sum_probs=32.1
Q ss_pred EEeeCCCCCCCCc-chHHHHHHHhhccceEEEeecCccCcHHHHHHHHHHHhccccCCceeeee
Q 041961 5 TFVDDEELRRGDE-ISPALLNAIQGSKISVVVFSKDYASSKWCLNELVKILDCKNMKGQIIIPV 67 (122)
Q Consensus 5 ~f~D~~~~~~G~~-i~~~i~~aIe~S~i~IvV~S~~y~~S~wCl~EL~~i~~~~~~~~~~vlPV 67 (122)
+++|--.+..+.. -..-+.+.+..+++.|.|++.+-.- ...+...+.+..+......+-|
T Consensus 104 ~lvDtPG~~~~~~~~~~~~~~~~~~~d~vi~V~~~~~~~---~~~~~~~l~~~~~~~~~~~i~V 164 (168)
T PF00350_consen 104 TLVDTPGLNSTNSEHTEITEEYLPKADVVIFVVDANQDL---TESDMEFLKQMLDPDKSRTIFV 164 (168)
T ss_dssp EEEEEEEBHSSHTTTSHHHHHHHSTTEEEEEEEETTSTG---GGHHHHHHHHHHTTTCSSEEEE
T ss_pred EEEeCCccccchhhhHHHHHHhhccCCEEEEEeccCccc---chHHHHHHHHHhcCCCCeEEEE
Confidence 4555543322222 2245677789999999999776633 3334444444333333334444
No 51
>cd01246 PH_oxysterol_bp Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding protein (OSBP) Pleckstrin homology (PH) domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=20.52 E-value=96 Score=18.82 Aligned_cols=15 Identities=33% Similarity=0.552 Sum_probs=12.5
Q ss_pred CCHHHHHHHHHHHHH
Q 041961 96 EQPEMVRKWRDALTE 110 (122)
Q Consensus 96 ~~~~~~~~W~~AL~~ 110 (122)
.+.+...+|..||..
T Consensus 76 ~s~~e~~~Wi~al~~ 90 (91)
T cd01246 76 NSEEERQRWVDALEL 90 (91)
T ss_pred CCHHHHHHHHHHHHh
Confidence 467889999999975
No 52
>COG2077 Tpx Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=20.03 E-value=84 Score=23.03 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=19.0
Q ss_pred hhccceEEEeecC--ccCcHHHHHHH
Q 041961 27 QGSKISVVVFSKD--YASSKWCLNEL 50 (122)
Q Consensus 27 e~S~i~IvV~S~~--y~~S~wCl~EL 50 (122)
+-....+..+|-+ |+.+.||--|-
T Consensus 73 ~~~~~~Vl~IS~DLPFAq~RfC~aeG 98 (158)
T COG2077 73 KLGNTVVLCISMDLPFAQKRFCGAEG 98 (158)
T ss_pred ccCCcEEEEEeCCChhHHhhhhhhcC
Confidence 3455788889998 89999998653
Done!