Query 031331
Match_columns 161
No_of_seqs 159 out of 1314
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 12:35:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031331.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031331hhsearch_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 5.2E-46 1.1E-50 348.7 15.6 156 1-159 1-156 (1153)
2 PLN03194 putative disease resi 100.0 9.1E-46 2E-50 282.4 13.2 132 11-159 24-157 (187)
3 smart00255 TIR Toll - interleu 99.9 8.7E-27 1.9E-31 170.0 12.9 137 13-151 1-139 (140)
4 PF01582 TIR: TIR domain; Int 99.9 1.7E-28 3.7E-33 180.7 3.5 132 16-147 1-140 (141)
5 PF13676 TIR_2: TIR domain; PD 99.8 5.2E-20 1.1E-24 128.0 5.0 87 16-108 1-87 (102)
6 KOG3678 SARM protein (with ste 99.1 5.4E-10 1.2E-14 96.2 8.1 93 9-107 608-709 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.8 1.6E-08 3.5E-13 73.5 5.5 90 14-108 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 98.0 3.5E-05 7.5E-10 56.8 8.2 64 15-78 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.2 0.0012 2.6E-08 47.9 5.8 87 15-106 1-101 (125)
10 PF13271 DUF4062: Domain of un 94.7 0.1 2.3E-06 34.7 5.4 67 15-82 1-68 (83)
11 COG4916 Uncharacterized protei 91.6 0.28 6.1E-06 39.9 4.1 100 9-114 173-281 (329)
12 COG4271 Predicted nucleotide-b 89.7 1.1 2.4E-05 35.2 5.7 97 15-117 84-200 (233)
13 PF05014 Nuc_deoxyrib_tr: Nucl 89.2 3.2 7E-05 28.8 7.5 66 27-93 13-87 (113)
14 PF14258 DUF4350: Domain of un 85.8 5.3 0.00011 25.2 6.4 61 31-103 8-68 (70)
15 PF09441 Abp2: ARS binding pro 74.2 0.97 2.1E-05 34.2 -0.1 57 81-147 54-111 (175)
16 cd00860 ThrRS_anticodon ThrRS 73.3 12 0.00026 24.1 5.2 60 14-77 2-61 (91)
17 cd00738 HGTP_anticodon HGTP an 70.9 14 0.00031 23.9 5.1 60 14-77 2-64 (94)
18 PF03129 HGTP_anticodon: Antic 67.2 13 0.00028 24.4 4.3 48 27-77 15-62 (94)
19 PF14359 DUF4406: Domain of un 63.6 35 0.00077 23.1 5.9 61 31-93 19-84 (92)
20 cd00858 GlyRS_anticodon GlyRS 63.0 20 0.00044 25.1 4.8 61 13-78 26-88 (121)
21 KOG2792 Putative cytochrome C 62.0 12 0.00026 30.6 3.8 31 82-112 153-187 (280)
22 PF09419 PGP_phosphatase: Mito 57.5 20 0.00042 27.3 4.1 68 36-108 35-112 (168)
23 COG1658 Small primase-like pro 56.8 24 0.00053 25.6 4.3 54 14-68 30-83 (127)
24 PF03720 UDPG_MGDP_dh_C: UDP-g 55.3 15 0.00032 25.3 2.9 54 22-75 11-75 (106)
25 TIGR00334 5S_RNA_mat_M5 ribonu 53.0 37 0.00079 26.1 4.9 50 27-79 35-84 (174)
26 cd02426 Pol_gamma_b_Cterm C-te 52.2 12 0.00025 27.0 2.1 33 27-59 43-79 (128)
27 cd07363 45_DOPA_Dioxygenase Th 50.7 88 0.0019 25.0 7.1 69 27-97 80-150 (253)
28 cd02042 ParA ParA and ParB of 48.9 71 0.0015 21.1 5.5 64 16-79 3-74 (104)
29 COG0710 AroD 3-dehydroquinate 47.1 81 0.0018 25.3 6.3 69 27-99 78-146 (231)
30 cd00532 MGS-like MGS-like doma 46.2 59 0.0013 22.4 4.9 60 16-77 2-77 (112)
31 cd01241 PH_Akt Akt pleckstrin 45.8 19 0.00041 24.6 2.2 17 134-150 86-102 (102)
32 cd00861 ProRS_anticodon_short 45.6 46 0.001 21.6 4.1 49 27-78 17-65 (94)
33 cd01424 MGS_CPS_II Methylglyox 44.8 75 0.0016 21.6 5.2 61 15-77 2-76 (110)
34 COG4916 Uncharacterized protei 44.5 30 0.00065 28.5 3.4 98 11-111 4-107 (329)
35 PF00875 DNA_photolyase: DNA p 42.4 90 0.002 22.8 5.7 94 31-131 56-151 (165)
36 cd01251 PH_centaurin_alpha Cen 41.7 28 0.00061 23.8 2.6 19 134-152 84-102 (103)
37 PRK08155 acetolactate synthase 41.4 65 0.0014 28.7 5.5 49 1-67 1-49 (564)
38 PF01990 ATP-synt_F: ATP synth 41.3 1.1E+02 0.0023 20.5 5.4 47 33-81 9-55 (95)
39 COG0415 PhrB Deoxyribodipyrimi 40.8 99 0.0021 27.4 6.4 90 31-129 58-151 (461)
40 COG0400 Predicted esterase [Ge 40.0 61 0.0013 25.3 4.5 55 9-64 142-198 (207)
41 TIGR00418 thrS threonyl-tRNA s 39.5 61 0.0013 28.9 5.1 61 12-76 469-529 (563)
42 cd00859 HisRS_anticodon HisRS 37.6 1E+02 0.0022 19.1 5.0 59 14-76 2-60 (91)
43 COG1168 MalY Bifunctional PLP- 37.2 82 0.0018 27.2 5.1 46 58-103 148-195 (388)
44 PF11074 DUF2779: Domain of un 36.1 33 0.00071 24.9 2.3 32 58-91 62-93 (130)
45 PF02310 B12-binding: B12 bind 36.0 1.4E+02 0.003 20.2 7.1 69 30-106 17-86 (121)
46 cd03364 TOPRIM_DnaG_primases T 36.0 40 0.00087 21.6 2.5 27 40-67 44-70 (79)
47 cd07373 2A5CPDO_A The alpha su 35.2 2.4E+02 0.0052 22.7 8.1 77 27-106 90-173 (271)
48 cd01423 MGS_CPS_I_III Methylgl 34.7 52 0.0011 22.7 3.1 29 16-46 3-31 (116)
49 PF10087 DUF2325: Uncharacteri 34.0 1.4E+02 0.0031 19.8 5.3 59 28-87 10-69 (97)
50 PF03437 BtpA: BtpA family; I 34.0 53 0.0011 26.7 3.4 108 33-147 133-253 (254)
51 cd01266 PH_Gab Gab (Grb2-assoc 33.0 40 0.00086 23.1 2.3 17 134-150 92-108 (108)
52 cd06371 PBP1_sensory_GC_DEF_li 32.9 2.1E+02 0.0045 23.9 7.0 52 28-79 147-201 (382)
53 cd04142 RRP22 RRP22 subfamily. 32.6 1.9E+02 0.0042 21.8 6.3 54 60-116 74-130 (198)
54 cd01238 PH_Tec Tec pleckstrin 32.6 37 0.00081 23.3 2.1 16 134-149 91-106 (106)
55 PRK11784 tRNA 2-selenouridine 32.3 2.7E+02 0.0057 23.6 7.5 103 25-148 191-298 (345)
56 cd01219 PH_FGD FGD (faciogenit 32.2 44 0.00096 22.7 2.4 18 134-151 83-100 (101)
57 PF03709 OKR_DC_1_N: Orn/Lys/A 32.0 1.7E+02 0.0038 20.2 6.1 70 29-110 5-75 (115)
58 CHL00201 syh histidine-tRNA sy 31.7 1.1E+02 0.0024 26.4 5.3 61 12-76 324-384 (430)
59 cd06352 PBP1_NPR_GC_like Ligan 30.9 2.8E+02 0.006 22.8 7.4 41 27-68 152-195 (389)
60 PRK12325 prolyl-tRNA synthetas 30.9 72 0.0016 27.7 4.0 63 13-79 345-410 (439)
61 cd06340 PBP1_ABC_ligand_bindin 30.3 1.4E+02 0.0031 24.3 5.5 63 16-78 147-209 (347)
62 PRK14938 Ser-tRNA(Thr) hydrola 29.8 1.1E+02 0.0023 26.6 4.7 59 13-75 274-332 (387)
63 PF13289 SIR2_2: SIR2-like dom 29.6 1.1E+02 0.0023 21.3 4.1 11 29-39 76-86 (143)
64 cd01252 PH_cytohesin Cytohesin 29.3 47 0.001 23.3 2.2 24 134-157 97-121 (125)
65 COG0683 LivK ABC-type branched 29.3 2.2E+02 0.0047 23.7 6.5 70 15-84 150-219 (366)
66 cd06366 PBP1_GABAb_receptor Li 29.1 3E+02 0.0065 22.2 7.2 51 16-67 138-191 (350)
67 cd06342 PBP1_ABC_LIVBP_like Ty 28.6 2E+02 0.0042 22.9 6.0 58 16-74 138-196 (334)
68 PRK09194 prolyl-tRNA synthetas 28.3 50 0.0011 29.7 2.6 64 12-79 467-533 (565)
69 PF09837 DUF2064: Uncharacteri 27.5 2.3E+02 0.0049 20.0 6.7 85 11-105 8-95 (122)
70 cd00138 PLDc Phospholipase D. 27.2 1.1E+02 0.0023 22.2 3.9 38 28-65 21-64 (176)
71 PF00762 Ferrochelatase: Ferro 27.1 3.3E+02 0.0072 22.6 7.2 80 28-107 73-158 (316)
72 cd01244 PH_RasGAP_CG9209 RAS_G 27.1 52 0.0011 22.6 2.0 16 134-149 83-98 (98)
73 smart00233 PH Pleckstrin homol 27.1 63 0.0014 20.0 2.3 16 135-150 86-101 (102)
74 KOG3043 Predicted hydrolase re 27.0 1.6E+02 0.0034 23.8 4.9 77 66-144 37-114 (242)
75 COG0276 HemH Protoheme ferro-l 26.7 3.9E+02 0.0083 22.5 7.4 78 29-108 74-161 (320)
76 cd01260 PH_CNK Connector enhan 26.7 56 0.0012 21.5 2.1 15 134-148 81-95 (96)
77 PF00350 Dynamin_N: Dynamin fa 26.5 2.4E+02 0.0052 20.0 6.2 46 58-106 120-165 (168)
78 PF08132 AdoMetDC_leader: S-ad 26.5 57 0.0012 19.8 1.8 24 3-26 10-33 (54)
79 PF10579 Rapsyn_N: Rapsyn N-te 26.3 41 0.00089 22.5 1.3 20 135-154 22-41 (80)
80 PF10443 RNA12: RNA12 protein; 26.3 1.2E+02 0.0026 26.6 4.5 51 102-152 365-431 (431)
81 cd03411 Ferrochelatase_N Ferro 26.2 2.6E+02 0.0057 20.4 6.0 64 28-93 72-142 (159)
82 cd06370 PBP1_Speract_GC_like L 26.1 2.1E+02 0.0046 23.9 6.0 27 27-53 150-176 (404)
83 TIGR03556 photolyase_8HDF deox 25.9 3.3E+02 0.0071 23.9 7.2 83 31-120 58-142 (471)
84 PLN02449 ferrochelatase 25.3 3.8E+02 0.0083 23.9 7.5 78 29-108 165-252 (485)
85 cd06335 PBP1_ABC_ligand_bindin 25.1 2.1E+02 0.0044 23.3 5.6 19 27-45 152-170 (347)
86 cd06386 PBP1_NPR_C_like Ligand 25.1 3.7E+02 0.0079 22.4 7.2 39 30-68 157-195 (387)
87 PF03618 Kinase-PPPase: Kinase 25.0 2.9E+02 0.0064 22.4 6.3 30 76-105 213-242 (255)
88 cd01257 PH_IRS Insulin recepto 25.0 63 0.0014 22.2 2.1 16 134-149 86-101 (101)
89 cd01857 HSR1_MMR1 HSR1/MMR1. 24.5 2.6E+02 0.0055 19.6 5.4 16 60-75 5-20 (141)
90 PF12146 Hydrolase_4: Putative 24.4 1.6E+02 0.0036 18.9 4.0 34 13-47 16-49 (79)
91 cd00154 Rab Rab family. Rab G 24.1 2.4E+02 0.0051 19.1 5.6 29 52-80 57-86 (159)
92 PRK14799 thrS threonyl-tRNA sy 24.1 1.4E+02 0.0031 26.9 4.7 60 13-76 438-497 (545)
93 cd00862 ProRS_anticodon_zinc P 24.0 93 0.002 24.0 3.1 51 13-63 10-67 (202)
94 TIGR00640 acid_CoA_mut_C methy 24.0 2.8E+02 0.006 19.9 8.4 86 16-108 5-90 (132)
95 PF03808 Glyco_tran_WecB: Glyc 23.8 3.1E+02 0.0067 20.4 6.7 73 28-107 35-109 (172)
96 TIGR01101 V_ATP_synt_F vacuola 23.8 1.1E+02 0.0025 21.7 3.3 27 54-80 46-72 (115)
97 cd01235 PH_SETbf Set binding f 23.7 75 0.0016 20.9 2.3 16 134-149 85-100 (101)
98 PF03358 FMN_red: NADPH-depend 23.4 2.7E+02 0.0059 19.6 6.1 79 27-108 17-115 (152)
99 cd02986 DLP Dim1 family, Dim1- 23.0 1.2E+02 0.0027 21.5 3.3 46 66-118 13-61 (114)
100 PRK12305 thrS threonyl-tRNA sy 23.0 1.6E+02 0.0035 26.3 4.8 60 13-76 476-535 (575)
101 cd06379 PBP1_iGluR_NMDA_NR1 N- 22.7 2.2E+02 0.0049 23.4 5.4 15 28-42 169-183 (377)
102 PRK00413 thrS threonyl-tRNA sy 22.7 1.7E+02 0.0037 26.5 5.0 61 13-77 539-599 (638)
103 KOG1136 Predicted cleavage and 22.6 1.4E+02 0.003 25.8 4.0 45 63-107 191-241 (501)
104 cd06361 PBP1_GPC6A_like Ligand 22.6 2.3E+02 0.0049 24.0 5.5 20 26-45 185-204 (403)
105 PF13662 Toprim_4: Toprim doma 22.3 55 0.0012 21.0 1.3 28 40-68 47-74 (81)
106 PLN02530 histidine-tRNA ligase 22.3 2E+02 0.0044 25.3 5.3 61 12-76 400-460 (487)
107 PF07429 Glyco_transf_56: 4-al 22.2 1.1E+02 0.0024 26.2 3.4 49 33-84 300-350 (360)
108 PRK07933 thymidylate kinase; V 22.2 1.6E+02 0.0035 22.7 4.2 30 17-46 2-33 (213)
109 cd03028 GRX_PICOT_like Glutare 22.2 53 0.0011 21.7 1.3 29 63-93 4-34 (90)
110 PRK15057 UDP-glucose 6-dehydro 22.2 1.4E+02 0.003 25.5 4.1 51 22-72 310-365 (388)
111 PF00169 PH: PH domain; Inter 22.0 96 0.0021 19.6 2.5 17 134-150 87-103 (104)
112 COG2130 Putative NADP-dependen 21.8 2.1E+02 0.0045 24.3 4.9 60 13-80 196-256 (340)
113 cd02951 SoxW SoxW family; SoxW 21.7 2.7E+02 0.0059 18.9 5.1 30 57-88 3-33 (125)
114 PRK05225 ketol-acid reductoiso 21.5 56 0.0012 29.1 1.6 29 117-148 307-335 (487)
115 cd04141 Rit_Rin_Ric Rit/Rin/Ri 21.5 3.2E+02 0.007 19.7 7.1 55 60-116 67-121 (172)
116 cd04893 ACT_GcvR_1 ACT domains 21.5 81 0.0018 20.1 2.0 30 16-46 2-31 (77)
117 COG1058 CinA Predicted nucleot 21.4 1.3E+02 0.0027 24.5 3.5 42 30-75 23-67 (255)
118 cd06367 PBP1_iGluR_NMDA N-term 21.4 3.7E+02 0.008 21.9 6.4 24 20-43 143-166 (362)
119 COG2342 Predicted extracellula 21.2 1.6E+02 0.0035 24.5 4.0 44 58-107 33-79 (300)
120 TIGR00409 proS_fam_II prolyl-t 21.2 69 0.0015 29.0 2.1 62 13-78 473-537 (568)
121 PRK02228 V-type ATP synthase s 21.0 2.1E+02 0.0046 19.5 4.1 43 36-80 14-56 (100)
122 COG0125 Tmk Thymidylate kinase 21.0 1.4E+02 0.0031 23.2 3.7 98 16-114 4-141 (208)
123 PRK03991 threonyl-tRNA synthet 20.8 1.9E+02 0.0041 26.5 4.8 44 13-57 499-543 (613)
124 PF15409 PH_8: Pleckstrin homo 20.8 91 0.002 21.2 2.2 15 135-149 74-88 (89)
125 cd01246 PH_oxysterol_bp Oxyste 20.5 89 0.0019 19.8 2.1 15 134-148 76-90 (91)
126 PRK08350 hypothetical protein; 20.1 1E+02 0.0022 26.2 2.8 32 12-43 280-311 (341)
127 PF15410 PH_9: Pleckstrin homo 20.1 99 0.0021 21.6 2.4 16 135-150 103-118 (119)
128 TIGR03026 NDP-sugDHase nucleot 20.0 1.9E+02 0.0041 24.7 4.5 57 18-74 321-384 (411)
No 1
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=5.2e-46 Score=348.66 Aligned_cols=156 Identities=46% Similarity=0.747 Sum_probs=147.6
Q ss_pred CCCCCCCCCCCCcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeeccccc
Q 031331 1 MASSSRSHSAQSKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYAS 80 (161)
Q Consensus 1 m~~~~~s~~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 80 (161)
||+||||+ +.++|||||||||+|+|++|++||+.+|.++||++|.|+++.+|+.|.+++.+||++|+++|||||++|+.
T Consensus 1 ~~~~~~~~-~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~ 79 (1153)
T PLN03210 1 MASSSSSS-RNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYAS 79 (1153)
T ss_pred CCCCCCCC-CCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCccc
Confidence 77777655 57899999999999999999999999999999999998889999999999999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHhhCCceeeeEEeecCcccccccccchHHHHHHHHHhcCCChHHHHHHHHHHHHhhcccceeecC
Q 031331 81 SKWCLDELVEILECKNMNGQTVVPVFYQVDPSDVRNQTGCFADAFVEHEEQFKNMPEKVQIWRAVLTEASNLSGWYSMN 159 (161)
Q Consensus 81 S~wc~~El~~~~~~~~~~~~~viPIfy~v~p~~v~~~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~v~~~~G~~~~~ 159 (161)
|.||++||++|++|+++.++.|+||||+|+|+||++|+|.||++|.+++++. +++++++||+||++|++++||++.+
T Consensus 80 s~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~~ 156 (1153)
T PLN03210 80 SSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQN 156 (1153)
T ss_pred chHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecCC
Confidence 9999999999999999999999999999999999999999999999988764 4789999999999999999999864
No 2
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=9.1e-46 Score=282.43 Aligned_cols=132 Identities=32% Similarity=0.564 Sum_probs=122.6
Q ss_pred CCcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCc-ccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHH
Q 031331 11 QSKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEE-LSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELV 89 (161)
Q Consensus 11 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~ 89 (161)
..+|||||||+|+|+|++|++||+.+|+++||++|+|+. +.+|+.|.++|.+||++|+++|+||||+|+.|.||++||+
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~ 103 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELA 103 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHH
Confidence 578999999999999999999999999999999999987 9999999999999999999999999999999999999999
Q ss_pred HHHHHHhhCCceeeeEEeecCccccccc-ccchHHHHHHHHHhcCCChHHHHHHHHHHHHhhcccceeecC
Q 031331 90 EILECKNMNGQTVVPVFYQVDPSDVRNQ-TGCFADAFVEHEEQFKNMPEKVQIWRAVLTEASNLSGWYSMN 159 (161)
Q Consensus 90 ~~~~~~~~~~~~viPIfy~v~p~~v~~~-~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~v~~~~G~~~~~ 159 (161)
+|+++. ..||||||+|+|++|++| .|. .+.+++++||.||++|++++|+++..
T Consensus 104 ~I~e~~----~~ViPIFY~VdPsdVr~q~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~~ 157 (187)
T PLN03194 104 LIMESK----KRVIPIFCDVKPSQLRVVDNGT-------------CPDEEIRRFNWALEEAKYTVGLTFDS 157 (187)
T ss_pred HHHHcC----CEEEEEEecCCHHHhhccccCC-------------CCHHHHHHHHHHHHHHhccccccCCC
Confidence 999863 489999999999999997 332 24689999999999999999998754
No 3
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.95 E-value=8.7e-27 Score=169.98 Aligned_cols=137 Identities=36% Similarity=0.684 Sum_probs=117.2
Q ss_pred cccEEEcCcc-CcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHH
Q 031331 13 KYDVFLSFRG-EDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEI 91 (161)
Q Consensus 13 ~ydVFISy~~-~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~ 91 (161)
+|||||||++ ++....|+.+|...|...|+.+|.|+....|... .+|.++|++|+++|+|+||+|+.|+||..|+..+
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~-~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a 79 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDL-EEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA 79 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccchH-HHHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence 5999999999 4555789999999999999999998764333333 3999999999999999999999999999999999
Q ss_pred HHHHhh-CCceeeeEEeecCcccccccccchHHHHHHHHHhcCCChHHHHHHHHHHHHhhc
Q 031331 92 LECKNM-NGQTVVPVFYQVDPSDVRNQTGCFADAFVEHEEQFKNMPEKVQIWRAVLTEASN 151 (161)
Q Consensus 92 ~~~~~~-~~~~viPIfy~v~p~~v~~~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~v~~ 151 (161)
+++... ...+||||+++..|+++.++.+.++..+..+..++..+..+ +.|+.++..+.+
T Consensus 80 ~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 80 LENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 987654 67899999999889999999999999998887777654444 899999988764
No 4
>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=99.94 E-value=1.7e-28 Score=180.74 Aligned_cols=132 Identities=33% Similarity=0.588 Sum_probs=115.4
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcC--CeeeeecCc-ccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHH
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRK--NIKTFIDEE-LSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEIL 92 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~--gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~ 92 (161)
|||||++.+.+..|+.+|.++|+++ |+++|++++ +.+|..+.++|.++|++|+++|+|||++|+.|+||+.||..++
T Consensus 1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~ 80 (141)
T PF01582_consen 1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL 80 (141)
T ss_dssp EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence 8999999433688999999999999 999999876 9999999999999999999999999999999999999999999
Q ss_pred HHHhhCC--ceeeeEEeecCccccc-ccccchHHHHHHHHHhcCCC--hHHHHHHHHHHH
Q 031331 93 ECKNMNG--QTVVPVFYQVDPSDVR-NQTGCFADAFVEHEEQFKNM--PEKVQIWRAVLT 147 (161)
Q Consensus 93 ~~~~~~~--~~viPIfy~v~p~~v~-~~~~~f~~~f~~~~~~~~~~--~~~~~~W~~al~ 147 (161)
++....+ ..|+||||++.+++++ .+.+.|+..|.....-...+ .++...|++++.
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 9987654 8999999999999999 79999999998776655433 578999999975
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.80 E-value=5.2e-20 Score=127.98 Aligned_cols=87 Identities=26% Similarity=0.571 Sum_probs=75.3
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHH
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECK 95 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~ 95 (161)
|||||+++| ..++..|...|+++|+++|+|.++.+|+.+.+.|.++|++|+++|+++|++|..|+||..|+..+.
T Consensus 1 VFIS~~~~D--~~~a~~l~~~L~~~g~~v~~d~~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~--- 75 (102)
T PF13676_consen 1 VFISYSSED--REFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAW--- 75 (102)
T ss_dssp EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHH---
T ss_pred eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHH---
Confidence 899999999 479999999999999999999779999999999999999999999999999999999999999883
Q ss_pred hhCCceeeeEEee
Q 031331 96 NMNGQTVVPVFYQ 108 (161)
Q Consensus 96 ~~~~~~viPIfy~ 108 (161)
+.+.+||||.++
T Consensus 76 -~~~~~iipv~~~ 87 (102)
T PF13676_consen 76 -KRGKPIIPVRLD 87 (102)
T ss_dssp -CTSESEEEEECS
T ss_pred -HCCCEEEEEEEC
Confidence 345699999954
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.06 E-value=5.4e-10 Score=96.24 Aligned_cols=93 Identities=20% Similarity=0.458 Sum_probs=76.1
Q ss_pred CCCCcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCc-ccCcccchHHHHHhhhcCcEEEEEeecccc----cC--
Q 031331 9 SAQSKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEE-LSRGDEISQAVLNAMKGSKISVIIFSKRYA----SS-- 81 (161)
Q Consensus 9 ~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~----~S-- 81 (161)
+.+++.||||||+..- ...+++-|.-.|+-+|++||+|-+ +..|. +.+.+.+.|...+.+|+|++||.+ +.
T Consensus 608 ~~skq~DVFISYRRst-GnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~n 685 (832)
T KOG3678|consen 608 MLSKQIDVFISYRRST-GNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDDN 685 (832)
T ss_pred cccCCcceEEEeeccc-cHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhcccc
Confidence 4567899999998764 578999999999999999999988 88886 567899999999999999999976 33
Q ss_pred --hhhHHHHHHHHHHHhhCCceeeeEEe
Q 031331 82 --KWCLDELVEILECKNMNGQTVVPVFY 107 (161)
Q Consensus 82 --~wc~~El~~~~~~~~~~~~~viPIfy 107 (161)
.|...||..+++| +..|||||-
T Consensus 686 CeDWVHKEl~~Afe~----~KNIiPI~D 709 (832)
T KOG3678|consen 686 CEDWVHKELKCAFEH----QKNIIPIFD 709 (832)
T ss_pred HHHHHHHHHHHHHHh----cCCeeeeec
Confidence 4555566655555 448999984
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=98.75 E-value=1.6e-08 Score=73.52 Aligned_cols=90 Identities=23% Similarity=0.453 Sum_probs=48.6
Q ss_pred ccEEEcCccCcCcccHHHHHHHHHhcC-------Ceee-ee---------cCc-ccCcccchHHHHHhhhcCcEEEEEee
Q 031331 14 YDVFLSFRGEDTRDNFTSHLHAAFCRK-------NIKT-FI---------DEE-LSRGDEISQAVLNAMKGSKISVIIFS 75 (161)
Q Consensus 14 ydVFISy~~~D~r~~fv~~L~~~L~~~-------gi~~-f~---------d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S 75 (161)
|.|||||++.|. ...+..|...+... .+.. |. +.. ....+.|...|.+.|.+|.++||+++
T Consensus 1 ~~vFIS~~~~d~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig 79 (130)
T PF08937_consen 1 YKVFISYSHDDD-DWYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG 79 (130)
T ss_dssp ----------TH-H-HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred CCccccccccCc-HHHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence 579999999984 23677777777652 2211 11 111 22334788999999999999999999
Q ss_pred cccccChhhHHHHHHHHHHHhhCCceeeeEEee
Q 031331 76 KRYASSKWCLDELVEILECKNMNGQTVVPVFYQ 108 (161)
Q Consensus 76 ~~y~~S~wc~~El~~~~~~~~~~~~~viPIfy~ 108 (161)
++-..|.|+..|+..+++ .+..||.|.+.
T Consensus 80 ~~T~~s~wV~~EI~~A~~----~~~~Ii~V~~~ 108 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALK----KGKPIIGVYLP 108 (130)
T ss_dssp TT----HHHHHHHHHHTT----T---EEEEETT
T ss_pred CCcccCcHHHHHHHHHHH----CCCCEEEEECC
Confidence 999999999999998865 56688888753
No 8
>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=98.03 E-value=3.5e-05 Score=56.81 Aligned_cols=64 Identities=16% Similarity=0.294 Sum_probs=51.9
Q ss_pred cEEEcCccCcCc-ccHHHHHHHHHhcC-CeeeeecCc-cc--CcccchHHHHHhhhcCcEEEEEeeccc
Q 031331 15 DVFLSFRGEDTR-DNFTSHLHAAFCRK-NIKTFIDEE-LS--RGDEISQAVLNAMKGSKISVIIFSKRY 78 (161)
Q Consensus 15 dVFISy~~~D~r-~~fv~~L~~~L~~~-gi~~f~d~~-~~--~G~~i~~~i~~aI~~S~~~Ivv~S~~y 78 (161)
-|||||+++... ...|..|...|++. |+.|.+|.. .. ++..+..=+.+.+++++.+|+|+||.+
T Consensus 2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~ 70 (150)
T PF08357_consen 2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY 70 (150)
T ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence 499999986543 46799999999999 999999986 52 355666677888999999999999544
No 9
>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=97.17 E-value=0.0012 Score=47.93 Aligned_cols=87 Identities=14% Similarity=0.163 Sum_probs=63.5
Q ss_pred cEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCc-ccCcccchHHHHHhhhcCcEEEEEeecccc-------------c
Q 031331 15 DVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEE-LSRGDEISQAVLNAMKGSKISVIIFSKRYA-------------S 80 (161)
Q Consensus 15 dVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~-------------~ 80 (161)
.|||.|+ .| ...+..+...|+..|+.+-+-.. ...|..+.+.+.+.+.+++.+|++++|+=. .
T Consensus 1 kVFIvhg-~~--~~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~a 77 (125)
T PF10137_consen 1 KVFIVHG-RD--LAAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRA 77 (125)
T ss_pred CEEEEeC-CC--HHHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCcccccccc
Confidence 3899998 55 26788899999977877655333 789999999999999999999999998522 1
Q ss_pred ChhhHHHHHHHHHHHhhCCceeeeEE
Q 031331 81 SKWCLDELVEILECKNMNGQTVVPVF 106 (161)
Q Consensus 81 S~wc~~El~~~~~~~~~~~~~viPIf 106 (161)
-...+.|+..++... +..+++-+.
T Consensus 78 R~NVifE~G~f~g~L--Gr~rv~~l~ 101 (125)
T PF10137_consen 78 RQNVIFELGLFIGKL--GRERVFILV 101 (125)
T ss_pred ccceeehhhHHHhhc--CcceEEEEE
Confidence 234567887776543 233555443
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=94.74 E-value=0.1 Score=34.72 Aligned_cols=67 Identities=21% Similarity=0.217 Sum_probs=49.3
Q ss_pred cEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcc-cCcccchHHHHHhhhcCcEEEEEeecccccCh
Q 031331 15 DVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEEL-SRGDEISQAVLNAMKGSKISVIIFSKRYASSK 82 (161)
Q Consensus 15 dVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~-~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~ 82 (161)
.||||-.-.|.. .--..|...|.+.|..+..-+.+ ..+....+.+.+.|++|+++|.++-..|-..+
T Consensus 1 rVFiSSt~~Dl~-~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~~ 68 (83)
T PF13271_consen 1 RVFISSTFRDLK-EERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSVP 68 (83)
T ss_pred CEEEecChhhHH-HHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCCC
Confidence 389998777752 33466777887777766543332 34566677899999999999999999997643
No 11
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=91.55 E-value=0.28 Score=39.94 Aligned_cols=100 Identities=19% Similarity=0.196 Sum_probs=67.2
Q ss_pred CCCCcccEEEcCccCcCcccHHHHHHHHHh--cCCeeeeecCc----ccCcccchHHHHHhhh--cCcEEEEEeeccccc
Q 031331 9 SAQSKYDVFLSFRGEDTRDNFTSHLHAAFC--RKNIKTFIDEE----LSRGDEISQAVLNAMK--GSKISVIIFSKRYAS 80 (161)
Q Consensus 9 ~~~~~ydVFISy~~~D~r~~fv~~L~~~L~--~~gi~~f~d~~----~~~G~~i~~~i~~aI~--~S~~~Ivv~S~~y~~ 80 (161)
...+.||+=+||.|+- ..+|+....+++ ..-+..|+|-. +-+|+ +. .++.-+. .|+..+|.+..||..
T Consensus 173 ~~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~-~~L~~~Y~~rC~~~~VF~~~~Y~~ 248 (329)
T COG4916 173 SSEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LV-STLDPGYDIRCVVTTVFNTGSYIC 248 (329)
T ss_pred ccccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCcc-HH-HhcccccCceEEEEEEEeCCceEE
Confidence 3467899999999996 479999999998 33455677754 34443 22 3333333 577788888999999
Q ss_pred ChhhHHHHHHHHHHHhhCCceeeeEEe-ecCcccc
Q 031331 81 SKWCLDELVEILECKNMNGQTVVPVFY-QVDPSDV 114 (161)
Q Consensus 81 S~wc~~El~~~~~~~~~~~~~viPIfy-~v~p~~v 114 (161)
..||.-|...+-.-. .-....||.| .++.+-+
T Consensus 249 K~~c~~E~~~~r~~~--~~d~~~rI~~~~~d~~a~ 281 (329)
T COG4916 249 KSTCHIEGLEGRLNP--ILDTGFRIKYLYADNIAI 281 (329)
T ss_pred eeeeccchhhccccc--cccccceEEEEecCCccc
Confidence 999999977653221 1235667766 3444443
No 12
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=89.67 E-value=1.1 Score=35.16 Aligned_cols=97 Identities=15% Similarity=0.156 Sum_probs=65.8
Q ss_pred cEEEcCccCcCcccHHHHHHHHHhc-C-CeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccc--------cC---
Q 031331 15 DVFLSFRGEDTRDNFTSHLHAAFCR-K-NIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYA--------SS--- 81 (161)
Q Consensus 15 dVFISy~~~D~r~~fv~~L~~~L~~-~-gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~--------~S--- 81 (161)
.|||-|+++ ..+.....+|.+ . =..+|.|.-+..|..+.+.+.+-|.++..+|++.+|+=. ..
T Consensus 84 kvFvv~ghd----~iArael~allrd~~l~~vi~d~~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~p 159 (233)
T COG4271 84 KVFVVSGHD----AIARAELEALLRDWKLEPVILDGLFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAFP 159 (233)
T ss_pred eEEEEeccH----HHHHHHHHHHhhccccceEEecCcccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhccc
Confidence 899999765 367666667763 2 345677776889999999999999999999999999844 11
Q ss_pred ---hhhHHHHHHHHHHHhhCCceeeeEEee----cCccccccc
Q 031331 82 ---KWCLDELVEILECKNMNGQTVVPVFYQ----VDPSDVRNQ 117 (161)
Q Consensus 82 ---~wc~~El~~~~~~~~~~~~~viPIfy~----v~p~~v~~~ 117 (161)
.....||...+-.. ++.+|+-+.-+ --|||+...
T Consensus 160 raRqNVifELGm~mgrL--gRkrv~Il~k~~envelPSDi~Gv 200 (233)
T COG4271 160 RARQNVIFELGMFMGRL--GRKRVMILMKRDENVELPSDIAGV 200 (233)
T ss_pred cccccchhhHhhHHhhc--ccceEEEEecccccccCccccCce
Confidence 22566777766543 23344433321 246666543
No 13
>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=89.20 E-value=3.2 Score=28.80 Aligned_cols=66 Identities=12% Similarity=0.091 Sum_probs=49.7
Q ss_pred ccHHHHHHHHHhcCCeeeeecCc--cc-------CcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHH
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEE--LS-------RGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILE 93 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~--~~-------~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~ 93 (161)
..+...+.+.|+.+|+.+|...+ .. ....|.+.-.++|++|+++|+++...- .+.-+..|+..+..
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~a 87 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYA 87 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHH
Confidence 57889999999999999987553 21 223455566789999999999998766 55678889988765
No 14
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=85.76 E-value=5.3 Score=25.22 Aligned_cols=61 Identities=13% Similarity=0.121 Sum_probs=38.6
Q ss_pred HHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceee
Q 031331 31 SHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVV 103 (161)
Q Consensus 31 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~vi 103 (161)
..|+..|++.|+.+=.... ..+++....-++++++|.+.-+. -.++..+.+..+.++..||
T Consensus 8 ~a~~~~L~~~g~~v~~~~~----------~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~v~~G~~lvl 68 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWRK----------PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEWVEAGNTLVL 68 (70)
T ss_pred HHHHHHHHHCCCeeEEecc----------cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHHHHcCCEEEE
Confidence 4577788888988843221 12344557889999999966554 3555555565555555554
No 15
>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=74.21 E-value=0.97 Score=34.16 Aligned_cols=57 Identities=21% Similarity=0.395 Sum_probs=36.2
Q ss_pred ChhhHHHHHHHHHHHhhCCceeeeEEeecCcccccc-cccchHHHHHHHHHhcCCChHHHHHHHHHHH
Q 031331 81 SKWCLDELVEILECKNMNGQTVVPVFYQVDPSDVRN-QTGCFADAFVEHEEQFKNMPEKVQIWRAVLT 147 (161)
Q Consensus 81 S~wc~~El~~~~~~~~~~~~~viPIfy~v~p~~v~~-~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~ 147 (161)
|.|.+.||..-++..+-+.=.=+.+.++|+|-++.. |+ .+++..+.-++++|+.|++
T Consensus 54 s~~~Lf~LI~k~~~keikTW~~La~~LGVepp~~ek~qS----------tQKvqQYaVRLKRWM~aMH 111 (175)
T PF09441_consen 54 STFTLFELIRKLESKEIKTWAQLALELGVEPPDPEKGQS----------TQKVQQYAVRLKRWMRAMH 111 (175)
T ss_pred hHHHHHHHHHHHhhhhHhHHHHHHHHhCCCCCCcccccc----------hHHHHHHHHHHHHHHHHhh
Confidence 468888887665543322223344567888888764 32 2344445688999999975
No 16
>cd00860 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=73.35 E-value=12 Score=24.12 Aligned_cols=60 Identities=7% Similarity=0.174 Sum_probs=36.9
Q ss_pred ccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecc
Q 031331 14 YDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKR 77 (161)
Q Consensus 14 ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (161)
++|+|...+++. ...+-.+...|++.|+.+-+|.. +..+...+..|-+.---.++++.++
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~---~~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLR---NEKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEECcc
Confidence 677776655442 45678899999999999988653 3345555555543322344444443
No 17
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=70.89 E-value=14 Score=23.91 Aligned_cols=60 Identities=13% Similarity=0.194 Sum_probs=38.2
Q ss_pred ccEEEcCccC---cCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecc
Q 031331 14 YDVFLSFRGE---DTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKR 77 (161)
Q Consensus 14 ydVFISy~~~---D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (161)
++|+|-..++ . -...+-.+...|++.|+.+-+|.. +..+...+..+-..---.++++.++
T Consensus 2 ~~v~ii~~~~~~~~-~~~~a~~~~~~Lr~~g~~v~~~~~---~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVE-AREYAQKLLNALLANGIRVLYDDR---ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHH-HHHHHHHHHHHHHHCCCEEEecCC---CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 5666655433 2 245778899999999999988653 3455555555544433466667663
No 18
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=67.16 E-value=13 Score=24.43 Aligned_cols=48 Identities=15% Similarity=0.238 Sum_probs=31.9
Q ss_pred ccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecc
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKR 77 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (161)
..++.+|...|.+.||.+.+|.. +..+...+..|-..=--.++|+.++
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~---~~~~~k~~~~a~~~g~p~~iiiG~~ 62 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDS---DKSLGKQIKYADKLGIPFIIIIGEK 62 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESS---SSTHHHHHHHHHHTTESEEEEEEHH
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCchhHHHHHHhhcCCeEEEEECch
Confidence 46789999999999999998763 3444445555554333355555544
No 19
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=63.58 E-value=35 Score=23.11 Aligned_cols=61 Identities=11% Similarity=0.025 Sum_probs=40.9
Q ss_pred HHHHHHHhcCCeeeeecCcc--cCcccchH---HHHHhhhcCcEEEEEeecccccChhhHHHHHHHHH
Q 031331 31 SHLHAAFCRKNIKTFIDEEL--SRGDEISQ---AVLNAMKGSKISVIIFSKRYASSKWCLDELVEILE 93 (161)
Q Consensus 31 ~~L~~~L~~~gi~~f~d~~~--~~G~~i~~---~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~ 93 (161)
......|+.+|..|.-.-.+ ..|.++.+ .-...|.+|+.. ++=|+.-+|.=|.-|...+.+
T Consensus 19 ~~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i--~~l~gWe~S~GA~~E~~~A~~ 84 (92)
T PF14359_consen 19 NAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAI--YMLPGWENSRGARLEHELAKK 84 (92)
T ss_pred HHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEE--EEcCCcccCcchHHHHHHHHH
Confidence 45788889999777543223 45544443 334556677743 344999999999999988754
No 20
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=63.03 E-value=20 Score=25.09 Aligned_cols=61 Identities=5% Similarity=-0.054 Sum_probs=40.9
Q ss_pred cccEEEcCcc--CcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeeccc
Q 031331 13 KYDVFLSFRG--EDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRY 78 (161)
Q Consensus 13 ~ydVFISy~~--~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 78 (161)
.+||||-.-+ ++ ....+..|...|+++|+++-+|.. ..+...+..|-+.---.++++.++-
T Consensus 26 p~~v~Ii~~~~~~~-~~~~a~~la~~LR~~gi~v~~d~~----~sl~kqlk~A~k~g~~~~iiiG~~e 88 (121)
T cd00858 26 PIKVAVLPLVKRDE-LVEIAKEISEELRELGFSVKYDDS----GSIGRRYARQDEIGTPFCVTVDFDT 88 (121)
T ss_pred CcEEEEEecCCcHH-HHHHHHHHHHHHHHCCCEEEEeCC----CCHHHHHHHhHhcCCCEEEEECcCc
Confidence 5788887765 32 245677899999999999988652 4566666666554444566666553
No 21
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=61.98 E-value=12 Score=30.61 Aligned_cols=31 Identities=35% Similarity=0.609 Sum_probs=22.8
Q ss_pred hhhHHHHHHHHHHHh----hCCceeeeEEeecCcc
Q 031331 82 KWCLDELVEILECKN----MNGQTVVPVFYQVDPS 112 (161)
Q Consensus 82 ~wc~~El~~~~~~~~----~~~~~viPIfy~v~p~ 112 (161)
.-|-+||.++....+ ..+..++|||.-++|.
T Consensus 153 DICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 153 DICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred CcChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 458999988765432 3566778999999994
No 22
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=57.50 E-value=20 Score=27.28 Aligned_cols=68 Identities=32% Similarity=0.331 Sum_probs=44.0
Q ss_pred HHhcCCeeeee-cCc--c-cCc-ccchHHHHHhhhcCcE-----EEEEeecccccChhhHHHHHHHHHHHhhCCceeeeE
Q 031331 36 AFCRKNIKTFI-DEE--L-SRG-DEISQAVLNAMKGSKI-----SVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPV 105 (161)
Q Consensus 36 ~L~~~gi~~f~-d~~--~-~~G-~~i~~~i~~aI~~S~~-----~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPI 105 (161)
.|.+.||+..+ |.+ + .|. +.+.+++.+.+++++. .|+|+|.+-.++.---.+-+..++. ..+ |||
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~--~lg---Ipv 109 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEK--ALG---IPV 109 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHH--hhC---CcE
Confidence 48899999764 666 4 344 5777888888888773 4899999986665322333333332 223 888
Q ss_pred Eee
Q 031331 106 FYQ 108 (161)
Q Consensus 106 fy~ 108 (161)
+..
T Consensus 110 l~h 112 (168)
T PF09419_consen 110 LRH 112 (168)
T ss_pred EEe
Confidence 754
No 23
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=56.83 E-value=24 Score=25.60 Aligned_cols=54 Identities=15% Similarity=0.193 Sum_probs=40.4
Q ss_pred ccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCc
Q 031331 14 YDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSK 68 (161)
Q Consensus 14 ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~ 68 (161)
.++|+-..+.=....+++.|..+++.+|+-++.|.+ .+|+.|...|.+.+.++.
T Consensus 30 ~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D-~~Ge~Irk~l~~~l~~~~ 83 (127)
T COG1658 30 AGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD-RKGERIRKKLKEYLPGAK 83 (127)
T ss_pred CceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC-cchHHHHHHHHHHhcccc
Confidence 456665544321246788999999999999999875 579999988888888744
No 24
>PF03720 UDPG_MGDP_dh_C: UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain; InterPro: IPR014027 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the C-terminal substrate-binding domain of these enzymes. Structural studies indicate that this domain forms an incomplete dinucleotide binding fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3GG2_D 1DLI_A 1DLJ_A 2Y0E_D 2Y0D_B 2Y0C_D 1MV8_B 1MUU_A 1MFZ_C 3TDK_B ....
Probab=55.28 E-value=15 Score=25.26 Aligned_cols=54 Identities=17% Similarity=0.285 Sum_probs=33.8
Q ss_pred cCcCcccHHHHHHHHHhcCCeeeeecCc-cc----------CcccchHHHHHhhhcCcEEEEEee
Q 031331 22 GEDTRDNFTSHLHAAFCRKNIKTFIDEE-LS----------RGDEISQAVLNAMKGSKISVIIFS 75 (161)
Q Consensus 22 ~~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~----------~G~~i~~~i~~aI~~S~~~Ivv~S 75 (161)
..|.|.+=+-.|...|..+|+.+...+- +. .|-...+.+.++++.+++.|+.-.
T Consensus 11 ~~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~ 75 (106)
T PF03720_consen 11 TDDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATD 75 (106)
T ss_dssp SS--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS-
T ss_pred CcccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEec
Confidence 4578888899999999999999876432 21 122334467888888887665544
No 25
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=53.01 E-value=37 Score=26.07 Aligned_cols=50 Identities=16% Similarity=0.269 Sum_probs=39.7
Q ss_pred ccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccc
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYA 79 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 79 (161)
..-...|..+.+.+|+-+|.|.+ .+|+.|...|.+.+-++..+- ++..++
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD-~~GekIRk~i~~~vp~~khaf--i~~~~a 84 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPD-FPGEKIRKKIEQHLPGYENCF--IPKHLA 84 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCC-CchHHHHHHHHHHCCCCeEEe--eeHHhc
Confidence 45677888888999999999986 589999999999998887543 454444
No 26
>cd02426 Pol_gamma_b_Cterm C-terminal domain of mitochondrial DNA polymerase gamma B subunit, which is required for processivity. Polymerase gamma replicates and repairs mitochondrial DNA. The c-terminal domain of its B subunit is strikingly similar to the anticodon-binding domain of glycyl tRNA synthetase.
Probab=52.25 E-value=12 Score=26.98 Aligned_cols=33 Identities=6% Similarity=0.041 Sum_probs=25.8
Q ss_pred ccHHHHHHHHHhcCCeeeeecCc-c---cCcccchHH
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEE-L---SRGDEISQA 59 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~-~---~~G~~i~~~ 59 (161)
...+..|+..|+..|+.++.|.+ - .+|..+.+.
T Consensus 43 ~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~~~~ 79 (128)
T cd02426 43 RDLCQGLKNELREAGLSVWPGYLETQHSSLEQLLDKY 79 (128)
T ss_pred HHHHHHHHHHHHHcCCEEEeccCcccccCHHHHHHhh
Confidence 56789999999999999998876 2 466666544
No 27
>cd07363 45_DOPA_Dioxygenase The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine. This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine (4,5-DOPA). The reaction results in the opening of the cyclic ring between carbons 4 and 5 and producing an unstable seco-DOPA that rearranges to betalamic acid. 4,5-DOPA Dioxygenase is a key enzyme in the biosynthetic pathway of the plant pigment betalain. Homologs of DODA are present not only in betalain-producing plants but also in bacteria and archaea. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated ca
Probab=50.66 E-value=88 Score=24.96 Aligned_cols=69 Identities=14% Similarity=0.065 Sum_probs=48.8
Q ss_pred ccHHHHHHHHHhcCCeeeeecCc--ccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhh
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEE--LSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNM 97 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~--~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~ 97 (161)
..++.+|.+.|..+|+.+-.+.+ +..|--+. +.-...+.++-||.+|-+...+..-..+|.++++..+.
T Consensus 80 ~eLa~~i~~~l~~~gi~~~~~~~~~lDHG~~vP--L~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l~~ 150 (253)
T cd07363 80 PELAERVAELLKAAGIPARLDPERGLDHGAWVP--LKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPLRD 150 (253)
T ss_pred HHHHHHHHHHHHhcCCCccccCCcCCcccHHHH--HHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhhhh
Confidence 47999999999999998765432 44454332 22223345788999999888777777899998876543
No 28
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=48.94 E-value=71 Score=21.08 Aligned_cols=64 Identities=14% Similarity=0.221 Sum_probs=41.3
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeee-cCc-------ccCcccchHHHHHhhhcCcEEEEEeecccc
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFI-DEE-------LSRGDEISQAVLNAMKGSKISVIIFSKRYA 79 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~-d~~-------~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 79 (161)
+|.|..|--.+..++.+|...|.++|.++.. |-+ +.-+..+.+....++..|+..|+++.++..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~ 74 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL 74 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH
Confidence 4566655544567789999999988988765 322 111122344455788888888888877644
No 29
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=47.11 E-value=81 Score=25.26 Aligned_cols=69 Identities=20% Similarity=0.225 Sum_probs=45.5
Q ss_pred ccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCC
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNG 99 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~ 99 (161)
......|....+.+| .-|+|=++..++....++...-.+-. +|+|-+...+.+.++|+..++..+...+
T Consensus 78 ~~~i~ll~~la~~~~-~d~iDiEl~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~ 146 (231)
T COG0710 78 EEYIELLKKLAELNG-PDYIDIELSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLG 146 (231)
T ss_pred HHHHHHHHHHHhhcC-CCEEEEEccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhC
Confidence 345666666666666 56777663333322234444333333 8899999999999999999998876555
No 30
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=46.22 E-value=59 Score=22.41 Aligned_cols=60 Identities=22% Similarity=0.243 Sum_probs=38.1
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeeecCc--------------ccCccc-chHHHHHhhhc-CcEEEEEeecc
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEE--------------LSRGDE-ISQAVLNAMKG-SKISVIIFSKR 77 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~--------------~~~G~~-i~~~i~~aI~~-S~~~Ivv~S~~ 77 (161)
||||-+..| +.. ...+...|...|++++--.. +..+.. =.+++.+.|.+ -++-+||..|+
T Consensus 2 i~isv~d~~-K~~-~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn~~~ 77 (112)
T cd00532 2 VFLSVSDHV-KAM-LVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEccc-HHH-HHHHHHHHHHCCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 788887666 233 44677777788888763211 111100 12578888888 88888888776
No 31
>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=45.84 E-value=19 Score=24.62 Aligned_cols=17 Identities=18% Similarity=0.470 Sum_probs=14.3
Q ss_pred CChHHHHHHHHHHHHhh
Q 031331 134 NMPEKVQIWRAVLTEAS 150 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v~ 150 (161)
++++..+.|..||..|+
T Consensus 86 ~s~ee~~eWi~ai~~v~ 102 (102)
T cd01241 86 ESPEEREEWIHAIQTVA 102 (102)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 46789999999999874
No 32
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=45.59 E-value=46 Score=21.56 Aligned_cols=49 Identities=12% Similarity=0.147 Sum_probs=30.4
Q ss_pred ccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeeccc
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRY 78 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 78 (161)
...+..|...|++.|+++.+|.. +..+...+..|-..---.++++.++-
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~---~~~l~k~i~~a~~~g~~~~iiiG~~e 65 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDR---NERPGVKFADADLIGIPYRIVVGKKS 65 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCCcccchhHHHhcCCCEEEEECCch
Confidence 35788899999999999998764 22344444444333333455555443
No 33
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=44.82 E-value=75 Score=21.61 Aligned_cols=61 Identities=20% Similarity=0.298 Sum_probs=35.9
Q ss_pred cEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCc----c-cCcc---------cchHHHHHhhhcCcEEEEEeecc
Q 031331 15 DVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEE----L-SRGD---------EISQAVLNAMKGSKISVIIFSKR 77 (161)
Q Consensus 15 dVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~----~-~~G~---------~i~~~i~~aI~~S~~~Ivv~S~~ 77 (161)
.||+|.+..| + .-...+...|.+.|+++|--.. + ..|- .=.+++.+.|++-++.+||-.++
T Consensus 2 ~vl~s~~~~~-k-~~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn~~~ 76 (110)
T cd01424 2 TVFISVADRD-K-PEAVEIAKRLAELGFKLVATEGTAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVINTPS 76 (110)
T ss_pred eEEEEEEcCc-H-hHHHHHHHHHHHCCCEEEEchHHHHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEECCC
Confidence 3889998776 3 3344777788788888875221 0 0110 01245666777666666666554
No 34
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=44.48 E-value=30 Score=28.47 Aligned_cols=98 Identities=17% Similarity=0.375 Sum_probs=70.0
Q ss_pred CCcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecC--c-ccCcccchHHHHHhhh--cCcEEEEEeecccccChhhH
Q 031331 11 QSKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDE--E-LSRGDEISQAVLNAMK--GSKISVIIFSKRYASSKWCL 85 (161)
Q Consensus 11 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~--~-~~~G~~i~~~i~~aI~--~S~~~Ivv~S~~y~~S~wc~ 85 (161)
+.++.+=+||.++|. .+++...+-|..+|+.+|+|- + -..|..+.+- +..|. ..-+++...|.+|-...|..
T Consensus 4 ~~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~~-~~e~~q~~~~~~~~f~~~~~~r~~~~~ 80 (329)
T COG4916 4 NVQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFEEANLWGKNLYDY-LSEIYQDKALFTIMFISEHYSRKMWTN 80 (329)
T ss_pred chheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHHH-HHHHHhhhhHHHhhhhhccccCcCCCc
Confidence 345677899999993 789999999999999998863 2 2345555422 22333 35567888999999999999
Q ss_pred HHHHHHHHHHh-hCCceeeeEEeecCc
Q 031331 86 DELVEILECKN-MNGQTVVPVFYQVDP 111 (161)
Q Consensus 86 ~El~~~~~~~~-~~~~~viPIfy~v~p 111 (161)
-|+..++...+ +....++|-.++..|
T Consensus 81 ~~~~~~~a~~~~~~~~~~~~~~~~~~~ 107 (329)
T COG4916 81 HERQAMQARAFQEHQEYILPARFDETP 107 (329)
T ss_pred HHHHHHHHHHhhhccEEehhhhhccCC
Confidence 99988766543 455678888876444
No 35
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=42.39 E-value=90 Score=22.76 Aligned_cols=94 Identities=16% Similarity=0.234 Sum_probs=49.8
Q ss_pred HHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEE--ee
Q 031331 31 SHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVF--YQ 108 (161)
Q Consensus 31 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIf--y~ 108 (161)
..|...|++.|+...+- .|+ ..+.+.+-+++..+.-|++...|..-. ...-..+.+...+.+..+.-+- +=
T Consensus 56 ~~L~~~L~~~g~~L~v~----~g~-~~~~l~~l~~~~~~~~V~~~~~~~~~~--~~rd~~v~~~l~~~~i~~~~~~~~~L 128 (165)
T PF00875_consen 56 ADLQESLRKLGIPLLVL----RGD-PEEVLPELAKEYGATAVYFNEEYTPYE--RRRDERVRKALKKHGIKVHTFDDHTL 128 (165)
T ss_dssp HHHHHHHHHTTS-EEEE----ESS-HHHHHHHHHHHHTESEEEEE---SHHH--HHHHHHHHHHHHHTTSEEEEE--SSS
T ss_pred HHHHHHHHhcCcceEEE----ecc-hHHHHHHHHHhcCcCeeEeccccCHHH--HHHHHHHHHHHHhcceEEEEECCcEE
Confidence 56788888889987662 243 233555666777788888998887622 2222222222333333332221 12
Q ss_pred cCcccccccccchHHHHHHHHHh
Q 031331 109 VDPSDVRNQTGCFADAFVEHEEQ 131 (161)
Q Consensus 109 v~p~~v~~~~~~f~~~f~~~~~~ 131 (161)
+.|.++....|..-..|....++
T Consensus 129 ~~~~~i~~~~~~~~~vFtpf~k~ 151 (165)
T PF00875_consen 129 VPPDDIPKKDGEPYKVFTPFRKK 151 (165)
T ss_dssp S-HHHCHSTTSSSHSSHHHHHHH
T ss_pred EeccccccCCCCCcccHHHHHHH
Confidence 67888887777666666554443
No 36
>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=41.72 E-value=28 Score=23.78 Aligned_cols=19 Identities=11% Similarity=0.225 Sum_probs=16.0
Q ss_pred CChHHHHHHHHHHHHhhcc
Q 031331 134 NMPEKVQIWRAVLTEASNL 152 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v~~~ 152 (161)
.+++..+.|.+||..|-+.
T Consensus 84 ~s~~e~~~Wi~ai~~v~~~ 102 (103)
T cd01251 84 ETEQDRREWIAAFQNVLSR 102 (103)
T ss_pred CCHHHHHHHHHHHHHHhcC
Confidence 4678899999999998764
No 37
>PRK08155 acetolactate synthase catalytic subunit; Validated
Probab=41.42 E-value=65 Score=28.69 Aligned_cols=49 Identities=20% Similarity=0.186 Sum_probs=31.2
Q ss_pred CCCCCCCCCCCCcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcC
Q 031331 1 MASSSRSHSAQSKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGS 67 (161)
Q Consensus 1 m~~~~~s~~~~~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S 67 (161)
||||.+++.... ..-.+.|...|++.|++..+ -.||+.+. .+.+++.++
T Consensus 1 ~~~~~~~~~~~~--------------~~~~~~l~~~L~~~GV~~vF---gvpG~~~~-~l~dal~~~ 49 (564)
T PRK08155 1 MASSGTTSTRKR--------------FTGAELIVRLLERQGIRIVT---GIPGGAIL-PLYDALSQS 49 (564)
T ss_pred CCCCCCCccCCc--------------ccHHHHHHHHHHHcCCCEEE---eCCCcccH-HHHHHHhcc
Confidence 888877664333 13467788888888887554 34676655 355666554
No 38
>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=41.31 E-value=1.1e+02 Score=20.47 Aligned_cols=47 Identities=15% Similarity=0.253 Sum_probs=34.6
Q ss_pred HHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccC
Q 031331 33 LHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASS 81 (161)
Q Consensus 33 L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S 81 (161)
+..-|+-.|+..+... ...+...+.+.+.++...+.|++++++++..
T Consensus 9 ~v~gFrLaGv~~~~~~--~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~ 55 (95)
T PF01990_consen 9 TVLGFRLAGVEGVYVN--TDPEEAEEALKELLKDEDVGIIIITEDLAEK 55 (95)
T ss_dssp HHHHHHHTTSEEEEES--HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT
T ss_pred HHHHHHHcCCCCccCC--CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH
Confidence 4455667799888754 1234566677777888999999999998873
No 39
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=40.78 E-value=99 Score=27.39 Aligned_cols=90 Identities=20% Similarity=0.340 Sum_probs=54.6
Q ss_pred HHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHH-HhhCCceeeeEEee-
Q 031331 31 SHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILEC-KNMNGQTVVPVFYQ- 108 (161)
Q Consensus 31 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~-~~~~~~~viPIfy~- 108 (161)
..|.++|...|+++++-. |+.. +.+.+-+++..+..|+....| ..| ..+-..++.. ..+.+..+.- |.+
T Consensus 58 ~~L~~~L~~~gi~L~v~~----~~~~-~~l~~~~~~~~~~~v~~n~~~--~~~-~~~rD~al~~~l~~~gi~~~~-~~d~ 128 (461)
T COG0415 58 QALQQSLAELGIPLLVRE----GDPE-QVLPELAKQLAATTVFWNRDY--EEW-ERQRDAALAQPLTEVGIAVHS-FWDA 128 (461)
T ss_pred HHHHHHHHHcCCceEEEe----CCHH-HHHHHHHHHhCcceEEeeeee--chh-HHHHHHHHHHHHHhcCceEEE-eccc
Confidence 458888889999998743 4433 245555666667777777888 333 3333333433 3344444443 433
Q ss_pred --cCcccccccccchHHHHHHHH
Q 031331 109 --VDPSDVRNQTGCFADAFVEHE 129 (161)
Q Consensus 109 --v~p~~v~~~~~~f~~~f~~~~ 129 (161)
..|.+|+.+.|..-+.|....
T Consensus 129 ~l~~p~~~~t~~~~~y~vfT~F~ 151 (461)
T COG0415 129 LLHEPGEVRTGSGEPYKVFTPFY 151 (461)
T ss_pred cccCHhhccCCCCCCccccchHH
Confidence 689999998886655554443
No 40
>COG0400 Predicted esterase [General function prediction only]
Probab=40.04 E-value=61 Score=25.34 Aligned_cols=55 Identities=18% Similarity=0.146 Sum_probs=39.6
Q ss_pred CCCCcccEEEcCccCcC--cccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhh
Q 031331 9 SAQSKYDVFLSFRGEDT--RDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAM 64 (161)
Q Consensus 9 ~~~~~ydVFISy~~~D~--r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI 64 (161)
+.....-|||+|-..|. -.....+|.+.|+..|..++... ...|=.+.++-.+++
T Consensus 142 ~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~-~~~GH~i~~e~~~~~ 198 (207)
T COG0400 142 PDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRW-HEGGHEIPPEELEAA 198 (207)
T ss_pred cccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEE-ecCCCcCCHHHHHHH
Confidence 34567889999988885 24577899999999999997644 445656655444444
No 41
>TIGR00418 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..
Probab=39.53 E-value=61 Score=28.86 Aligned_cols=61 Identities=10% Similarity=0.202 Sum_probs=41.4
Q ss_pred CcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeec
Q 031331 12 SKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSK 76 (161)
Q Consensus 12 ~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (161)
...||+|-.-+++. ...+..|...|+++|++|-+|.. +.++...+..|-+.---.++|+.+
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~---~~sl~~q~k~A~~~g~~~~iiiG~ 529 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR---NERLGKKIREAQKQKIPYMLVVGD 529 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHhcCCCEEEEEch
Confidence 45788887655543 46788999999999999988763 455666666665543345555554
No 42
>cd00859 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=37.56 E-value=1e+02 Score=19.15 Aligned_cols=59 Identities=20% Similarity=0.215 Sum_probs=33.1
Q ss_pred ccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeec
Q 031331 14 YDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSK 76 (161)
Q Consensus 14 ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (161)
.||||...+++. ..-+-.+...|+++|+++.++.. +..+...+..+-..--..++++.+
T Consensus 2 ~~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~---~~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 2 VDVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYG---GRKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred CcEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecC---CCCHHHHHHHHHHcCCCEEEEEcH
Confidence 367776544432 23467889999999999977542 123333444443332234455554
No 43
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=37.25 E-value=82 Score=27.23 Aligned_cols=46 Identities=22% Similarity=0.289 Sum_probs=36.9
Q ss_pred HHHHHhhhcCc-EEEEEeecccc-cChhhHHHHHHHHHHHhhCCceee
Q 031331 58 QAVLNAMKGSK-ISVIIFSKRYA-SSKWCLDELVEILECKNMNGQTVV 103 (161)
Q Consensus 58 ~~i~~aI~~S~-~~Ivv~S~~y~-~S~wc~~El~~~~~~~~~~~~~vi 103 (161)
+.+.+++.+.+ ...++.+|+=. ..-|-.+||.++.+...+.+.+||
T Consensus 148 ~~LE~~~~~~~vkl~iLCnPHNP~Grvwt~eeL~~i~elc~kh~v~VI 195 (388)
T COG1168 148 DALEKAFVDERVKLFILCNPHNPTGRVWTKEELRKIAELCLRHGVRVI 195 (388)
T ss_pred HHHHHHHhcCCccEEEEeCCCCCCCccccHHHHHHHHHHHHHcCCEEE
Confidence 57888998887 67777788765 678999999999997777776666
No 44
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=36.07 E-value=33 Score=24.87 Aligned_cols=32 Identities=25% Similarity=0.510 Sum_probs=17.0
Q ss_pred HHHHHhhhcCcEEEEEeecccccChhhHHHHHHH
Q 031331 58 QAVLNAMKGSKISVIIFSKRYASSKWCLDELVEI 91 (161)
Q Consensus 58 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~ 91 (161)
..+.++|..-.-.|+|++..|-++ |+.||..+
T Consensus 62 ~~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~ 93 (130)
T PF11074_consen 62 EALIKAIGSIYGSIVVYNKSFEKT--RLKELAEL 93 (130)
T ss_pred HHHHHHhhhhcCeEEEechHHHHH--HHHHHHHH
Confidence 344444443334566666655543 66676654
No 45
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=35.96 E-value=1.4e+02 Score=20.19 Aligned_cols=69 Identities=13% Similarity=0.116 Sum_probs=41.8
Q ss_pred HHHHHHHHhcCCeeee-ecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEE
Q 031331 30 TSHLHAAFCRKNIKTF-IDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVF 106 (161)
Q Consensus 30 v~~L~~~L~~~gi~~f-~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIf 106 (161)
...|...|+++|+.+- +|-...+ +++.+.+.+.+--++.+|-.+. |...++..+.+..+..+..+.-|+
T Consensus 17 l~~la~~l~~~G~~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~---~~~~~~~~l~~~~k~~~p~~~iv~ 86 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDANVPP-----EELVEALRAERPDVVGISVSMT---PNLPEAKRLARAIKERNPNIPIVV 86 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSS---THHHHHHHHHHHHHTTCTTSEEEE
T ss_pred HHHHHHHHHHCCCeEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCc---CcHHHHHHHHHHHHhcCCCCEEEE
Confidence 4678899999999984 4443222 5777777777777777776533 344555555555444443433333
No 46
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=35.96 E-value=40 Score=21.58 Aligned_cols=27 Identities=15% Similarity=0.209 Sum_probs=14.1
Q ss_pred CCeeeeecCcccCcccchHHHHHhhhcC
Q 031331 40 KNIKTFIDEELSRGDEISQAVLNAMKGS 67 (161)
Q Consensus 40 ~gi~~f~d~~~~~G~~i~~~i~~aI~~S 67 (161)
+.+.+|+|.+ .+|..-...+.+.+..-
T Consensus 44 ~~vii~~D~D-~aG~~a~~~~~~~l~~~ 70 (79)
T cd03364 44 KEVILAFDGD-EAGQKAALRALELLLKL 70 (79)
T ss_pred CeEEEEECCC-HHHHHHHHHHHHHHHHC
Confidence 4566666664 44554444454444443
No 47
>cd07373 2A5CPDO_A The alpha subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO) catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the alpha subunit, which does not contain a potential metal binding site and may not possess catalytic activity.
Probab=35.16 E-value=2.4e+02 Score=22.72 Aligned_cols=77 Identities=13% Similarity=0.101 Sum_probs=52.7
Q ss_pred ccHHHHHHHHHhcCCeeee-ecCc---ccCcccchHHHHHhh--hcCcEEEEEeecccccChhhHHHHHHHHHH-HhhCC
Q 031331 27 DNFTSHLHAAFCRKNIKTF-IDEE---LSRGDEISQAVLNAM--KGSKISVIIFSKRYASSKWCLDELVEILEC-KNMNG 99 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f-~d~~---~~~G~~i~~~i~~aI--~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~-~~~~~ 99 (161)
..++..|.+.|.+.|+.+- .+.. +..|--+. +.-+ ...++-||.+|.+..-+.....+|-+++.. .++.+
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA---CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH---HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 5799999999999999885 5542 44443222 1223 245676788998887777788899998884 55555
Q ss_pred ceeeeEE
Q 031331 100 QTVVPVF 106 (161)
Q Consensus 100 ~~viPIf 106 (161)
.+|+=|-
T Consensus 167 ~rV~iIg 173 (271)
T cd07373 167 KRVAVVG 173 (271)
T ss_pred CeEEEEE
Confidence 6766553
No 48
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=34.69 E-value=52 Score=22.72 Aligned_cols=29 Identities=7% Similarity=0.092 Sum_probs=22.2
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeee
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFI 46 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~ 46 (161)
||||....| +. -...+...|...|++++-
T Consensus 3 vlisv~~~d-k~-~~~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYS-KP-ELLPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCccc-ch-hHHHHHHHHHHCCCEEEE
Confidence 899998776 33 445788888888998875
No 49
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.99 E-value=1.4e+02 Score=19.83 Aligned_cols=59 Identities=7% Similarity=0.131 Sum_probs=37.3
Q ss_pred cHHHHHHHHHhcCCeeeeecCcccCc-ccchHHHHHhhhcCcEEEEEeecccccChhhHHH
Q 031331 28 NFTSHLHAAFCRKNIKTFIDEELSRG-DEISQAVLNAMKGSKISVIIFSKRYASSKWCLDE 87 (161)
Q Consensus 28 ~fv~~L~~~L~~~gi~~f~d~~~~~G-~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~E 87 (161)
.....+...+++.|...-.. .-..| ..-...+...|.++++.|++..--.-...|...+
T Consensus 10 ~~~~~~~~~~~~~G~~~~~h-g~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~ 69 (97)
T PF10087_consen 10 DRERRYKRILEKYGGKLIHH-GRDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKK 69 (97)
T ss_pred ccHHHHHHHHHHcCCEEEEE-ecCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHH
Confidence 34677888898888875433 11112 1222357888999998888776666565565444
No 50
>PF03437 BtpA: BtpA family; InterPro: IPR005137 Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. It consists of 11 subunits, ~100 chlorophyll a molecules, 2 phylloquinones, and 3 Fe4S4-clusters. The three dimensional structure of the PSI complex has been resolved at 2.5 A [], which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA [], Ycf3 [, ], and Ycf4 (IPR003359 from INTERPRO) []. Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. These gene products are therefore involved either in the stabilisation or in the assembly of the PSI complex. However, their exact roles remain unknown. The BtpA protein appears to act at the level of PSI stabilisation []. It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane [, ]. Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain []. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids []. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners []. Ycf3 contains a number of tetratrico peptide repeats (TPR, IPR001440 from INTERPRO); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions.
Probab=33.98 E-value=53 Score=26.66 Aligned_cols=108 Identities=14% Similarity=0.229 Sum_probs=63.9
Q ss_pred HHHHHhcCCeeeeecCcc-----cCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEEe
Q 031331 33 LHAAFCRKNIKTFIDEEL-----SRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVFY 107 (161)
Q Consensus 33 L~~~L~~~gi~~f~d~~~-----~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIfy 107 (161)
.+..|... +++|.|-.. -.+.++.+....+++.+..=-+++|-.-...+=-+.++..+- +.. . +|||.
T Consensus 133 ~R~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr---~~~--~-~PVlv 205 (254)
T PF03437_consen 133 YRKRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVR---EAV--P-VPVLV 205 (254)
T ss_pred HHHHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHH---hcC--C-CCEEE
Confidence 34444455 899876432 234567677777777777766677766554443444444432 211 2 99999
Q ss_pred --ecCccccccccc----ch-HHHHHHHHH-hcCCChHHHHHHHHHHH
Q 031331 108 --QVDPSDVRNQTG----CF-ADAFVEHEE-QFKNMPEKVQIWRAVLT 147 (161)
Q Consensus 108 --~v~p~~v~~~~~----~f-~~~f~~~~~-~~~~~~~~~~~W~~al~ 147 (161)
++.++.+.++.. .. |-.|.+... .-..|.+++++.++++.
T Consensus 206 GSGvt~~Ni~~~l~~ADG~IVGS~~K~~G~~~n~VD~~Rv~~fm~~v~ 253 (254)
T PF03437_consen 206 GSGVTPENIAEYLSYADGAIVGSYFKKDGKWENPVDPERVRRFMEAVK 253 (254)
T ss_pred ecCCCHHHHHHHHHhCCEEEEeeeeeeCCEeCCcCCHHHHHHHHHHhh
Confidence 488888876532 11 333433222 11357899999998875
No 51
>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=33.02 E-value=40 Score=23.10 Aligned_cols=17 Identities=12% Similarity=0.425 Sum_probs=14.5
Q ss_pred CChHHHHHHHHHHHHhh
Q 031331 134 NMPEKVQIWRAVLTEAS 150 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v~ 150 (161)
++++.++.|..||.+|+
T Consensus 92 ~s~ee~~~Wi~~I~~~~ 108 (108)
T cd01266 92 KNEEEMTLWVNCICKLC 108 (108)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 46889999999998874
No 52
>cd06371 PBP1_sensory_GC_DEF_like Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phyloge
Probab=32.91 E-value=2.1e+02 Score=23.91 Aligned_cols=52 Identities=6% Similarity=0.173 Sum_probs=29.5
Q ss_pred cHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcC---cEEEEEeecccc
Q 031331 28 NFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGS---KISVIIFSKRYA 79 (161)
Q Consensus 28 ~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~ 79 (161)
.....|.+.|+..|+.+-....+.+++.-...+++.|+.. ++.|+.....+.
T Consensus 147 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~d~~~~L~~lk~~~~~~viv~~~~~~~~ 201 (382)
T cd06371 147 ETAQKLASALRAHGLPVGLVTSMGPDEKGAREALKKVRSADRVRVVIMCMHSVLI 201 (382)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEecCCHHHHHHHHHHHhcCCCcEEEEEEeecccc
Confidence 4567788888888887644333555543334556666653 444444444444
No 53
>cd04142 RRP22 RRP22 subfamily. RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated.
Probab=32.64 E-value=1.9e+02 Score=21.79 Aligned_cols=54 Identities=9% Similarity=0.126 Sum_probs=32.6
Q ss_pred HHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhC---CceeeeEEeecCcccccc
Q 031331 60 VLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMN---GQTVVPVFYQVDPSDVRN 116 (161)
Q Consensus 60 i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~---~~~viPIfy~v~p~~v~~ 116 (161)
...+++.++++|+|++.+ ++.-++++...++..... ...-+||+.-....|+..
T Consensus 74 ~~~~~~~ad~iilv~D~~---~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~ 130 (198)
T cd04142 74 RFRGLRNSRAFILVYDIC---SPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQR 130 (198)
T ss_pred HHhhhccCCEEEEEEECC---CHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccccc
Confidence 456689999999999975 344455554444332211 123367777556666644
No 54
>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=32.59 E-value=37 Score=23.29 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=13.4
Q ss_pred CChHHHHHHHHHHHHh
Q 031331 134 NMPEKVQIWRAVLTEA 149 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v 149 (161)
.+++..+.|..||..|
T Consensus 91 ~s~~er~~WI~ai~~~ 106 (106)
T cd01238 91 PTEELRKRWIKALKQV 106 (106)
T ss_pred CCHHHHHHHHHHHHhC
Confidence 3578899999999875
No 55
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=32.30 E-value=2.7e+02 Score=23.55 Aligned_cols=103 Identities=17% Similarity=0.228 Sum_probs=59.9
Q ss_pred CcccHHHHHHHHHhcCC--eeeeecCc-ccCcc-cchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCc
Q 031331 25 TRDNFTSHLHAAFCRKN--IKTFIDEE-LSRGD-EISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQ 100 (161)
Q Consensus 25 ~r~~fv~~L~~~L~~~g--i~~f~d~~-~~~G~-~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~ 100 (161)
+.+.|-+.|..+|.... -.+|+..+ -..|. .+.+.+.++++++.+.++-.|... -+..+++-...
T Consensus 191 sQ~~Fe~~l~~~l~~~~~~~~i~vE~Es~~IG~~~lP~~l~~~m~~~~~v~i~~~~e~--------Rv~~l~~~Y~~--- 259 (345)
T PRK11784 191 SQKDFENLLAEALLKLDPARPIVVEDESRRIGRVHLPEALYEAMQQAPIVVVEAPLEE--------RVERLLEDYVL--- 259 (345)
T ss_pred chHHHHHHHHHHHHcCCCCCeEEEEeccccccCccCCHHHHHHHhhCCEEEEECCHHH--------HHHHHHHHhhh---
Confidence 45789999999997644 36777555 45564 677899999999987655433211 01111111000
Q ss_pred eeeeEEeecCccc-ccccccchHHHHHHHHHhcCCChHHHHHHHHHHHH
Q 031331 101 TVVPVFYQVDPSD-VRNQTGCFADAFVEHEEQFKNMPEKVQIWRAVLTE 148 (161)
Q Consensus 101 ~viPIfy~v~p~~-v~~~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~ 148 (161)
..+.+ .......+.+++..+.++.+ .+++++|..+|..
T Consensus 260 --------~~~~~~~~~~~~~l~~~l~~i~k~lg--~~~~~~~~~~~~~ 298 (345)
T PRK11784 260 --------RMHAAGFQAYPEYLAEALQRIRKRLG--GERYQELLALLDA 298 (345)
T ss_pred --------hhhhhhhhccHHHHHHHHHHHHHhcC--HHHHHHHHHHHHc
Confidence 00000 00122345666677777765 6888888888774
No 56
>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=32.24 E-value=44 Score=22.66 Aligned_cols=18 Identities=6% Similarity=0.180 Sum_probs=15.1
Q ss_pred CChHHHHHHHHHHHHhhc
Q 031331 134 NMPEKVQIWRAVLTEASN 151 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v~~ 151 (161)
.+++...+|++||+.+.+
T Consensus 83 ~s~eEk~~W~~ai~~~i~ 100 (101)
T cd01219 83 RTQKEKNDWVQAIFSIID 100 (101)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 468899999999998764
No 57
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=31.95 E-value=1.7e+02 Score=20.18 Aligned_cols=70 Identities=17% Similarity=0.222 Sum_probs=41.6
Q ss_pred HHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhh-cCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEEe
Q 031331 29 FTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMK-GSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVFY 107 (161)
Q Consensus 29 fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~-~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIfy 107 (161)
-+..|..+|++.|+.+-.-.. .+.....++ .+++.-+|+|-+ .. -.++...+++..+. ...=||||.
T Consensus 5 ~~~~l~~~L~~~~~~vv~~~~-------~dd~~~~i~~~~~i~avvi~~d-~~---~~~~~~~ll~~i~~-~~~~iPVFl 72 (115)
T PF03709_consen 5 ASRELAEALEQRGREVVDADS-------TDDALAIIESFTDIAAVVISWD-GE---EEDEAQELLDKIRE-RNFGIPVFL 72 (115)
T ss_dssp HHHHHHHHHHHTTTEEEEESS-------HHHHHHHHHCTTTEEEEEEECH-HH---HHHHHHHHHHHHHH-HSTT-EEEE
T ss_pred HHHHHHHHHHHCCCEEEEeCC-------hHHHHHHHHhCCCeeEEEEEcc-cc---cchhHHHHHHHHHH-hCCCCCEEE
Confidence 467899999988988765331 123444455 589999999977 11 11222333333332 235689998
Q ss_pred ecC
Q 031331 108 QVD 110 (161)
Q Consensus 108 ~v~ 110 (161)
-.+
T Consensus 73 ~~~ 75 (115)
T PF03709_consen 73 LAE 75 (115)
T ss_dssp EES
T ss_pred Eec
Confidence 655
No 58
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=31.68 E-value=1.1e+02 Score=26.42 Aligned_cols=61 Identities=18% Similarity=0.231 Sum_probs=39.7
Q ss_pred CcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeec
Q 031331 12 SKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSK 76 (161)
Q Consensus 12 ~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (161)
...||+|.+-+++. ...+-.+...|+++|+++-+|- .+..+...+..|-+.--..++|+.+
T Consensus 324 ~~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~---~~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 324 QSIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDL---SSSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEee---CCCCHHHHHHHHHHcCCCEEEEEec
Confidence 34789998755432 3557789999999999987654 2344555666665544345555655
No 59
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=30.94 E-value=2.8e+02 Score=22.78 Aligned_cols=41 Identities=12% Similarity=0.037 Sum_probs=22.9
Q ss_pred ccHHHHHHHHHhcCCeeeeecCcccCc---ccchHHHHHhhhcCc
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEELSRG---DEISQAVLNAMKGSK 68 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~~~~G---~~i~~~i~~aI~~S~ 68 (161)
...+..+.++|++.|+.+-....+.++ ..+...+ +.|..+.
T Consensus 152 ~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l-~~i~~~~ 195 (389)
T cd06352 152 FFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEIL-QDIKRRS 195 (389)
T ss_pred HHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHH-HHhhhcc
Confidence 455677777887778776433334444 3444444 4455444
No 60
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=30.87 E-value=72 Score=27.70 Aligned_cols=63 Identities=16% Similarity=0.092 Sum_probs=39.2
Q ss_pred cccEEEcCcc--CcCcccHHHHHHHHHhcCCeeeeecCc-ccCcccchHHHHHhhhcCcEEEEEeecccc
Q 031331 13 KYDVFLSFRG--EDTRDNFTSHLHAAFCRKNIKTFIDEE-LSRGDEISQAVLNAMKGSKISVIIFSKRYA 79 (161)
Q Consensus 13 ~ydVFISy~~--~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 79 (161)
.++|+|---. .+.....+..|...|.+.|+.+.+|.. -..|..+.+ +-..---.++|+.++-.
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~ki~~----a~~~giP~~iiVG~~e~ 410 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGAKFAT----MDLIGLPWQIIVGPKGL 410 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhHHHHH----HHHcCCCEEEEECCccc
Confidence 4788776432 222346788999999999999999875 445554443 32222225566665543
No 61
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=30.28 E-value=1.4e+02 Score=24.28 Aligned_cols=63 Identities=8% Similarity=0.024 Sum_probs=34.3
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeeccc
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRY 78 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 78 (161)
|.+-+...+-....+..+...|++.|+.+-....+.+++.=.......|..++.-+|++.-..
T Consensus 147 v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~~~i~~l~~~~~d~v~~~~~~ 209 (347)
T cd06340 147 VALVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPANARDLTSEVLKLKAANPDAILPASYT 209 (347)
T ss_pred EEEEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCCCcchHHHHHHHHhcCCCEEEEcccc
Confidence 555554333234566777778888888775443355554333344455665555555554433
No 62
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=29.81 E-value=1.1e+02 Score=26.55 Aligned_cols=59 Identities=17% Similarity=0.166 Sum_probs=38.3
Q ss_pred cccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEee
Q 031331 13 KYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFS 75 (161)
Q Consensus 13 ~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S 75 (161)
.++|+|-.-+++. ...+..|...|+++|+++.+|.. +..+...+..|-+.---.++++.
T Consensus 274 P~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl~---srSLgKQiK~AdK~GaPfvIIIG 332 (387)
T PRK14938 274 PIQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDDL---DDSLGNKIRRAGTEWIPFVIIIG 332 (387)
T ss_pred cceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEEC
Confidence 4677776655542 45678899999999999988763 44566666666543333444444
No 63
>PF13289 SIR2_2: SIR2-like domain
Probab=29.57 E-value=1.1e+02 Score=21.29 Aligned_cols=11 Identities=18% Similarity=0.365 Sum_probs=5.0
Q ss_pred HHHHHHHHHhc
Q 031331 29 FTSHLHAAFCR 39 (161)
Q Consensus 29 fv~~L~~~L~~ 39 (161)
+-..|...|..
T Consensus 76 ~~~~l~~~l~~ 86 (143)
T PF13289_consen 76 FPNFLRSLLRS 86 (143)
T ss_pred HHHHHHHHHcC
Confidence 34444545533
No 64
>cd01252 PH_cytohesin Cytohesin Pleckstrin homology (PH) domain. Cytohesin Pleckstrin homology (PH) domain. Cytohesin is an ARF-Guanine nucleotide Exchange Factor (GEF), which has a Sec7-type Arf-GEFdomain and a pleckstrin homology domain. It specifically binds phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4, 5)P3) via its PH domain and it acts as a PI 3-kinase effector mediating biological responses such as cell adhesion and membrane trafficking. PH domains are only found in eukaryotes. They 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=29.30 E-value=47 Score=23.31 Aligned_cols=24 Identities=8% Similarity=0.101 Sum_probs=17.3
Q ss_pred CChHHHHHHHHHHHHhhc-ccceee
Q 031331 134 NMPEKVQIWRAVLTEASN-LSGWYS 157 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v~~-~~G~~~ 157 (161)
.+++..+.|..||..+.. -+++.+
T Consensus 97 ~s~~e~~~Wi~al~~~~~~~~~~~~ 121 (125)
T cd01252 97 ANDEEMDEWIKSIKASISPNPFYEM 121 (125)
T ss_pred CCHHHHHHHHHHHHHHHhcCchHHH
Confidence 468899999999998763 334443
No 65
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=29.27 E-value=2.2e+02 Score=23.65 Aligned_cols=70 Identities=11% Similarity=0.090 Sum_probs=42.0
Q ss_pred cEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhh
Q 031331 15 DVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWC 84 (161)
Q Consensus 15 dVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc 84 (161)
.|+|-+....-.+.+...+.+.|+.+|..+-.+....+++.-...+...|..+..-+|++...+....-.
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~ 219 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVVEEVYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALF 219 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCCCChHHHHHHHHhcCCCEEEECCCCccchHH
Confidence 4555555554456788888888888888633333355554334566666666665566666555544333
No 66
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=29.10 E-value=3e+02 Score=22.19 Aligned_cols=51 Identities=20% Similarity=0.237 Sum_probs=27.7
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCc---ccchHHHHHhhhcC
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRG---DEISQAVLNAMKGS 67 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G---~~i~~~i~~aI~~S 67 (161)
|.+-|...+....++..+...|++.|+.+-....+.+| ..+.+. ...|..+
T Consensus 138 v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~~-l~~i~~~ 191 (350)
T cd06366 138 VATIYEDDDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDA-LKKLKEK 191 (350)
T ss_pred EEEEEEcCcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHHH-HHHHhcC
Confidence 33334333323456777888888888876544435555 244433 4445443
No 67
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=28.63 E-value=2e+02 Score=22.88 Aligned_cols=58 Identities=17% Similarity=0.235 Sum_probs=30.7
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCc-ccchHHHHHhhhcCcEEEEEe
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRG-DEISQAVLNAMKGSKISVIIF 74 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G-~~i~~~i~~aI~~S~~~Ivv~ 74 (161)
|.+-|...+.....+..|...|+..|+++-....+.+| ..+. .+...|.++..-+|++
T Consensus 138 v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~d~~-~~l~~i~~~~~~~vi~ 196 (334)
T cd06342 138 VAIIDDKTAYGQGLADEFKKALKAAGGKVVAREGTTDGATDFS-AILTKIKAANPDAVFF 196 (334)
T ss_pred EEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEecCCCCCccHH-HHHHHHHhcCCCEEEE
Confidence 44434333333456677778888888876543335555 3343 4444555544333333
No 68
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=28.25 E-value=50 Score=29.68 Aligned_cols=64 Identities=17% Similarity=0.240 Sum_probs=41.3
Q ss_pred CcccEEEcCcc-C-cCcccHHHHHHHHHhcCCeeeeecCc-ccCcccchHHHHHhhhcCcEEEEEeecccc
Q 031331 12 SKYDVFLSFRG-E-DTRDNFTSHLHAAFCRKNIKTFIDEE-LSRGDEISQAVLNAMKGSKISVIIFSKRYA 79 (161)
Q Consensus 12 ~~ydVFISy~~-~-D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 79 (161)
..++|+|---+ + +.-...+..|+..|+..|+.+.+|++ -.+|..+.+.-..+ .. .++++.++..
T Consensus 467 aP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~~~ad~~G---iP-~~iiiG~~e~ 533 (565)
T PRK09194 467 APFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKFADADLIG---IP-HRIVVGDRGL 533 (565)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHHHHHHhcC---CC-EEEEEcCccc
Confidence 35889887543 2 22246788999999999999999876 55666555433222 23 4555555533
No 69
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=27.47 E-value=2.3e+02 Score=20.03 Aligned_cols=85 Identities=15% Similarity=0.275 Sum_probs=42.2
Q ss_pred CCcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcC---cEEEEEeecccccChhhHHH
Q 031331 11 QSKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGS---KISVIIFSKRYASSKWCLDE 87 (161)
Q Consensus 11 ~~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~~S~wc~~E 87 (161)
...+|++|.|.+...+ .....+ ....++.++. +.|..+.+.+.++++.. .-.|+++..+-.. -+...
T Consensus 8 ~~~~~~~l~~~~~~~~-~~~~~~---~~~~~~~~~~----Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~--l~~~~ 77 (122)
T PF09837_consen 8 ADGADVVLAYTPDGDH-AAFRQL---WLPSGFSFFP----QQGGDLGERMANAFQQAARGYEPVVLIGSDCPD--LTPDD 77 (122)
T ss_dssp TSSSEEEEEE----TT-HHHHHH---HH-TTSEEEE------SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT----HHH
T ss_pred CCCcCEEEEEcCCccH-HHHhcc---ccCCCCEEee----cCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCC--CCHHH
Confidence 3468999999887643 333332 3334555543 35666666666665544 2267777766654 34556
Q ss_pred HHHHHHHHhhCCceeeeE
Q 031331 88 LVEILECKNMNGQTVVPV 105 (161)
Q Consensus 88 l~~~~~~~~~~~~~viPI 105 (161)
|..+.+..+....++-|-
T Consensus 78 l~~A~~~L~~~d~VlgPa 95 (122)
T PF09837_consen 78 LEQAFEALQRHDVVLGPA 95 (122)
T ss_dssp HHHHHHHTTT-SEEEEEB
T ss_pred HHHHHHHhccCCEEEeec
Confidence 667777665555555553
No 70
>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=27.21 E-value=1.1e+02 Score=22.17 Aligned_cols=38 Identities=26% Similarity=0.247 Sum_probs=17.9
Q ss_pred cHHHHHHHHHhcCCeeeeecCc-ccC-----cccchHHHHHhhh
Q 031331 28 NFTSHLHAAFCRKNIKTFIDEE-LSR-----GDEISQAVLNAMK 65 (161)
Q Consensus 28 ~fv~~L~~~L~~~gi~~f~d~~-~~~-----G~~i~~~i~~aI~ 65 (161)
.+...+.+.+.+..-.+++-.. +.+ +..+.+.|.++.+
T Consensus 21 ~~~~~i~~~I~~A~~~I~i~~~~~~~~~~~~~~~l~~~L~~a~~ 64 (176)
T cd00138 21 SDLDALLEAISNAKKSIYIASFYLSPLITEYGPVILDALLAAAR 64 (176)
T ss_pred hHHHHHHHHHHhhheEEEEEEeEecccccccchHHHHHHHHHHH
Confidence 3445555555544434443222 333 4455555555555
No 71
>PF00762 Ferrochelatase: Ferrochelatase; InterPro: IPR001015 Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc. Ferrochelatase catalyses the last step in haem biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protohaem [, ]. In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane. The X-ray structure of Bacillus subtilis and human ferrochelatase have been solved [, ]. The human enzyme exists as a homodimer. Each subunit contains one [2Fe-2S] cluster. The monomer is folded into two similar domains, each with a four-stranded parallel beta-sheet flanked by an alpha-helix in a beta-alpha-beta motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the [2Fe-2S] cluster and in stabilisation of the homodimer. Ferrochelatase seems to have a structurally conserved core region that is common to the enzyme from bacteria, plants and mammals. Porphyrin binds in the identified cleft; this cleft also includes the metal-binding site of the enzyme. It is likely that the structure of the cleft region will have different conformations upon substrate binding and release [].; GO: 0004325 ferrochelatase activity, 0006783 heme biosynthetic process; PDB: 2QD3_B 2HRE_C 3HCN_B 2PNJ_A 2QD1_C 1HRK_A 2QD4_B 3AQI_B 2HRC_B 3HCO_B ....
Probab=27.09 E-value=3.3e+02 Score=22.57 Aligned_cols=80 Identities=20% Similarity=0.271 Sum_probs=42.6
Q ss_pred cHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhh---cCcEEEEEeecccccC--hhhHHHHHHHHHHH-hhCCce
Q 031331 28 NFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMK---GSKISVIIFSKRYASS--KWCLDELVEILECK-NMNGQT 101 (161)
Q Consensus 28 ~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~---~S~~~Ivv~S~~y~~S--~wc~~El~~~~~~~-~~~~~~ 101 (161)
..+..|...|...|..+-..--+.-|.+...+..+.+. -.++.++.+.|.|..+ .-+++++..++... ..-..+
T Consensus 73 ~qa~~l~~~L~~~~~~~~V~~amry~~P~i~~~l~~l~~~g~~~ivvlPLyPqyS~~ttgs~~~~~~~~~~~~~~~~~~~ 152 (316)
T PF00762_consen 73 RQAEALQQRLDERGVDVEVYYAMRYGPPSIEDALEELKADGVDRIVVLPLYPQYSSSTTGSYLDEVERALKKSRPNPKVR 152 (316)
T ss_dssp HHHHHHHHHHHHH-EEEEEEEEESSSSSBHHHHHHHHHHTT-SEEEEEESSSS--TTTHHHHHHHHHHHHHHTHSSSEEE
T ss_pred HHHHHHHHHHHhcCCCeeEEEEeccCCCCHHHHHHHHHHcCCCeEEEEeCCCchhHhhHHHHHHHHHHHHHhcCCCCeEE
Confidence 35666777776654332222225667666666666666 3467888889999854 44677777776542 112234
Q ss_pred eeeEEe
Q 031331 102 VVPVFY 107 (161)
Q Consensus 102 viPIfy 107 (161)
+|+=|+
T Consensus 153 ~i~~~~ 158 (316)
T PF00762_consen 153 FIPSFY 158 (316)
T ss_dssp EE---T
T ss_pred EeCCcc
Confidence 555443
No 72
>cd01244 PH_RasGAP_CG9209 RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. This protein consists of two C2 domains, followed by a RasGAP domain, a PH domain and a BTK 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, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=27.08 E-value=52 Score=22.55 Aligned_cols=16 Identities=19% Similarity=0.420 Sum_probs=13.2
Q ss_pred CChHHHHHHHHHHHHh
Q 031331 134 NMPEKVQIWRAVLTEA 149 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v 149 (161)
.+++..+.|..||.+|
T Consensus 83 ~s~~E~~~Wi~al~k~ 98 (98)
T cd01244 83 EAPVEATDWLNALEKQ 98 (98)
T ss_pred CCHHHHHHHHHHHhcC
Confidence 3578889999999875
No 73
>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=27.07 E-value=63 Score=19.99 Aligned_cols=16 Identities=25% Similarity=0.366 Sum_probs=13.8
Q ss_pred ChHHHHHHHHHHHHhh
Q 031331 135 MPEKVQIWRAVLTEAS 150 (161)
Q Consensus 135 ~~~~~~~W~~al~~v~ 150 (161)
+++..++|..+|..+.
T Consensus 86 s~~~~~~W~~~i~~~~ 101 (102)
T smart00233 86 SEEEREEWVDALRKAI 101 (102)
T ss_pred CHHHHHHHHHHHHHhh
Confidence 5789999999998765
No 74
>KOG3043 consensus Predicted hydrolase related to dienelactone hydrolase [General function prediction only]
Probab=27.01 E-value=1.6e+02 Score=23.83 Aligned_cols=77 Identities=17% Similarity=0.136 Sum_probs=50.3
Q ss_pred cCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEEeecCcccccccccchHHHHHHHHH-hcCCChHHHHHHHH
Q 031331 66 GSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVFYQVDPSDVRNQTGCFADAFVEHEE-QFKNMPEKVQIWRA 144 (161)
Q Consensus 66 ~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIfy~v~p~~v~~~~~~f~~~f~~~~~-~~~~~~~~~~~W~~ 144 (161)
.+...|++|+.=|--+.--..|....+.+. +=..++|=||..+|-....|...+..-+..+.- ....+-..+.+|.+
T Consensus 37 ~~~~~li~i~DvfG~~~~n~r~~Adk~A~~--Gy~v~vPD~~~Gdp~~~~~~~~~~~~w~~~~~~~~~~~~i~~v~k~lk 114 (242)
T KOG3043|consen 37 SSKKVLIVIQDVFGFQFPNTREGADKVALN--GYTVLVPDFFRGDPWSPSLQKSERPEWMKGHSPPKIWKDITAVVKWLK 114 (242)
T ss_pred CCCeEEEEEEeeeccccHHHHHHHHHHhcC--CcEEEcchhhcCCCCCCCCChhhhHHHHhcCCcccchhHHHHHHHHHH
Confidence 345799999999988766666665554432 345899999999999988887665544443311 11112346677766
No 75
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=26.70 E-value=3.9e+02 Score=22.54 Aligned_cols=78 Identities=22% Similarity=0.369 Sum_probs=46.8
Q ss_pred HHHHHHHHHhcC----CeeeeecCcccCcccchHHHHHhhhcC---cEEEEEeecccccCh--hhHHHHHHHHHHHhh-C
Q 031331 29 FTSHLHAAFCRK----NIKTFIDEELSRGDEISQAVLNAMKGS---KISVIIFSKRYASSK--WCLDELVEILECKNM-N 98 (161)
Q Consensus 29 fv~~L~~~L~~~----gi~~f~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~~S~--wc~~El~~~~~~~~~-~ 98 (161)
....+..+|+.+ .++|++- +.-|.+..++..+.+.+. +++++.+.|.|-.|. -..+++..+++..+. -
T Consensus 74 ~T~~q~~~L~~~L~~~~~~V~~a--mry~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~~~~~~ 151 (320)
T COG0276 74 ITRAQAAALEERLDLPDFKVYLA--MRYGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKELRGQP 151 (320)
T ss_pred HHHHHHHHHHHHhCCCCccEEEe--ecCCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHhcCCCC
Confidence 344455555443 4555542 455666666767666643 467778888887543 356677777765442 2
Q ss_pred CceeeeEEee
Q 031331 99 GQTVVPVFYQ 108 (161)
Q Consensus 99 ~~~viPIfy~ 108 (161)
....||-||+
T Consensus 152 ~i~~I~~~~~ 161 (320)
T COG0276 152 KISTIPDYYD 161 (320)
T ss_pred ceEEecCccC
Confidence 3467777765
No 76
>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=26.67 E-value=56 Score=21.53 Aligned_cols=15 Identities=13% Similarity=0.324 Sum_probs=12.6
Q ss_pred CChHHHHHHHHHHHH
Q 031331 134 NMPEKVQIWRAVLTE 148 (161)
Q Consensus 134 ~~~~~~~~W~~al~~ 148 (161)
++++.+++|..||..
T Consensus 81 ~s~~e~~~Wi~ai~~ 95 (96)
T cd01260 81 ETLDDLSQWVNHLIT 95 (96)
T ss_pred CCHHHHHHHHHHHHh
Confidence 467899999999975
No 77
>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=26.51 E-value=2.4e+02 Score=20.00 Aligned_cols=46 Identities=2% Similarity=0.070 Sum_probs=30.9
Q ss_pred HHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEE
Q 031331 58 QAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVF 106 (161)
Q Consensus 58 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIf 106 (161)
.-+.+.+..+++.|+|++.+- .|...+...+.+..+....+.+-|+
T Consensus 120 ~~~~~~~~~~d~vi~V~~~~~---~~~~~~~~~l~~~~~~~~~~~i~V~ 165 (168)
T PF00350_consen 120 EITEEYLPKADVVIFVVDANQ---DLTESDMEFLKQMLDPDKSRTIFVL 165 (168)
T ss_dssp HHHHHHHSTTEEEEEEEETTS---TGGGHHHHHHHHHHTTTCSSEEEEE
T ss_pred HHHHHhhccCCEEEEEeccCc---ccchHHHHHHHHHhcCCCCeEEEEE
Confidence 557788899999999997665 4555566666655555555555543
No 78
>PF08132 AdoMetDC_leader: S-adenosyl-l-methionine decarboxylase leader peptide; InterPro: IPR012511 This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzyme in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5, leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism [].
Probab=26.49 E-value=57 Score=19.75 Aligned_cols=24 Identities=42% Similarity=0.414 Sum_probs=17.9
Q ss_pred CCCCCCCCCCcccEEEcCccCcCc
Q 031331 3 SSSRSHSAQSKYDVFLSFRGEDTR 26 (161)
Q Consensus 3 ~~~~s~~~~~~ydVFISy~~~D~r 26 (161)
||||++...-.|++=+.|+=+|.|
T Consensus 10 ssssss~~s~~yeaPLgYsIEDvR 33 (54)
T PF08132_consen 10 SSSSSSSNSLFYEAPLGYSIEDVR 33 (54)
T ss_pred ccccccccceEEeccccceeeecc
Confidence 344555556789999999999986
No 79
>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=26.29 E-value=41 Score=22.48 Aligned_cols=20 Identities=20% Similarity=0.461 Sum_probs=16.7
Q ss_pred ChHHHHHHHHHHHHhhcccc
Q 031331 135 MPEKVQIWRAVLTEASNLSG 154 (161)
Q Consensus 135 ~~~~~~~W~~al~~v~~~~G 154 (161)
..+-+.+|+.||.++.+..+
T Consensus 22 ~~~Al~~W~~aL~k~~~~~~ 41 (80)
T PF10579_consen 22 TQQALQKWRKALEKITDRED 41 (80)
T ss_pred HHHHHHHHHHHHhhcCChHH
Confidence 46789999999999988654
No 80
>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]. It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].
Probab=26.29 E-value=1.2e+02 Score=26.64 Aligned_cols=51 Identities=18% Similarity=0.246 Sum_probs=35.0
Q ss_pred eeeEEe-ecCcccccccccchHHHHHHHHHhc---------------CCChHHHHHHHHHHHHhhcc
Q 031331 102 VVPVFY-QVDPSDVRNQTGCFADAFVEHEEQF---------------KNMPEKVQIWRAVLTEASNL 152 (161)
Q Consensus 102 viPIfy-~v~p~~v~~~~~~f~~~f~~~~~~~---------------~~~~~~~~~W~~al~~v~~~ 152 (161)
+|-|-. +..|+.|+...+.|..+|..+.+.. .....++.+|.+-|..++++
T Consensus 365 LItv~~~~G~p~~I~pGkPvy~aAF~~L~~D~~l~~~~d~~~~~~li~~e~~~I~k~E~EL~~L~~i 431 (431)
T PF10443_consen 365 LITVTTDNGRPSTIRPGKPVYRAAFKRLVNDKVLSARMDLAYLKKLIKIENKKIKKYEEELRKLGKI 431 (431)
T ss_pred cEEEEecCCcCCeeECCChhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 344443 5678888888899999998764411 11245788888888877654
No 81
>cd03411 Ferrochelatase_N Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=26.23 E-value=2.6e+02 Score=20.42 Aligned_cols=64 Identities=22% Similarity=0.369 Sum_probs=35.5
Q ss_pred cHHHHHHHHHhcCC--eeeeecCcccCcccchHHHHHhhhc---CcEEEEEeecccccC--hhhHHHHHHHHH
Q 031331 28 NFTSHLHAAFCRKN--IKTFIDEELSRGDEISQAVLNAMKG---SKISVIIFSKRYASS--KWCLDELVEILE 93 (161)
Q Consensus 28 ~fv~~L~~~L~~~g--i~~f~d~~~~~G~~i~~~i~~aI~~---S~~~Ivv~S~~y~~S--~wc~~El~~~~~ 93 (161)
..+..|.+.|.+.+ +.++.- +.-|.+..++..+.+.+ .++.++-+.|.|..+ .-+.+++...+.
T Consensus 72 ~q~~~l~~~L~~~~~~~~v~~a--mry~~P~i~~~l~~l~~~g~~~iivlPl~P~~S~~Tt~s~~~~~~~~~~ 142 (159)
T cd03411 72 AQAEALEKALDERGIDVKVYLA--MRYGPPSIEEALEELKADGVDRIVVLPLYPQYSASTTGSYLDEVERALK 142 (159)
T ss_pred HHHHHHHHHHhccCCCcEEEeh--HhcCCCCHHHHHHHHHHcCCCEEEEEECCcccccccHHHHHHHHHHHHH
Confidence 34566666776543 333332 44555544444444432 566777788887743 446666666554
No 82
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=26.06 E-value=2.1e+02 Score=23.95 Aligned_cols=27 Identities=15% Similarity=-0.060 Sum_probs=16.7
Q ss_pred ccHHHHHHHHHhcCCeeeeecCcccCc
Q 031331 27 DNFTSHLHAAFCRKNIKTFIDEELSRG 53 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~d~~~~~G 53 (161)
...+..+...|++.|+.+-....+.++
T Consensus 150 ~~~~~~~~~~~~~~g~~iv~~~~~~~~ 176 (404)
T cd06370 150 SSVFETLKEEAELRNITISHVEYYADF 176 (404)
T ss_pred HHHHHHHHHHHHHcCCEEEEEEEECCC
Confidence 346666777777778776543335454
No 83
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=25.92 E-value=3.3e+02 Score=23.87 Aligned_cols=83 Identities=13% Similarity=0.205 Sum_probs=46.7
Q ss_pred HHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEE--ee
Q 031331 31 SHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVF--YQ 108 (161)
Q Consensus 31 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIf--y~ 108 (161)
..|...|+..|++.++- .|+.. +.+.+-+++..+.-|++..+|..-.-..+ ..+.+.....+..+.-.- +-
T Consensus 58 ~~L~~~L~~~G~~L~v~----~G~p~-~vl~~l~~~~~~~~V~~~~~~~~~~~~rd--~~v~~~l~~~~i~~~~~~~~~l 130 (471)
T TIGR03556 58 QELQQRYQQAGSQLLIL----QGDPV-QLIPQLAQQLGAKAVYWNLDVEPYGRKRD--RAVAAALKEAGIAVVTLWDQLL 130 (471)
T ss_pred HHHHHHHHHCCCCeEEE----ECCHH-HHHHHHHHHcCCCEEEEecccCHHHHHHH--HHHHHHHHHCCCEEEEeCCcEE
Confidence 45778888889988763 34433 34555556678888889998876332222 222232333333332210 12
Q ss_pred cCcccccccccc
Q 031331 109 VDPSDVRNQTGC 120 (161)
Q Consensus 109 v~p~~v~~~~~~ 120 (161)
+.|.+|....|.
T Consensus 131 ~~p~~i~~~~~~ 142 (471)
T TIGR03556 131 HSPDEILTGSGN 142 (471)
T ss_pred ECccccccCCCC
Confidence 468888765553
No 84
>PLN02449 ferrochelatase
Probab=25.34 E-value=3.8e+02 Score=23.92 Aligned_cols=78 Identities=22% Similarity=0.338 Sum_probs=45.7
Q ss_pred HHHHHHHHHhcCC--eeeeecCcccCcccchHHHHHhhhc---CcEEEEEeeccccc--ChhhHHHHHHHHHHHhh---C
Q 031331 29 FTSHLHAAFCRKN--IKTFIDEELSRGDEISQAVLNAMKG---SKISVIIFSKRYAS--SKWCLDELVEILECKNM---N 98 (161)
Q Consensus 29 fv~~L~~~L~~~g--i~~f~d~~~~~G~~i~~~i~~aI~~---S~~~Ivv~S~~y~~--S~wc~~El~~~~~~~~~---~ 98 (161)
-+..|.++|.+.| +.|++ -+.-|.+..++..+.+.+ .++.++.+-|.|.. +.-+++.+..++..... -
T Consensus 165 Qa~~Lq~~L~~~~~~~~V~~--aMRY~~P~iedal~~l~~~G~~~iVvLPLYPQyS~sTtgSs~~~l~~~~~~~~~~~~~ 242 (485)
T PLN02449 165 QAEALAKALEAKNLPAKVYV--GMRYWHPFTEEAIDQIKADGITKLVVLPLYPQFSISTSGSSLRLLESIFREDEYLVNM 242 (485)
T ss_pred HHHHHHHHHhccCCCeEEEE--hhhcCCCCHHHHHHHHHhcCCCeEEEEECCcccccccHHHHHHHHHHHHhhcccccCC
Confidence 4556777776655 45554 245566666666666653 45677778888764 34566777666543221 1
Q ss_pred CceeeeEEee
Q 031331 99 GQTVVPVFYQ 108 (161)
Q Consensus 99 ~~~viPIfy~ 108 (161)
..++||=||+
T Consensus 243 ~~~~I~~~~~ 252 (485)
T PLN02449 243 QHTVIPSWYQ 252 (485)
T ss_pred eeEEeccccC
Confidence 2356666654
No 85
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=25.09 E-value=2.1e+02 Score=23.31 Aligned_cols=19 Identities=21% Similarity=0.308 Sum_probs=11.8
Q ss_pred ccHHHHHHHHHhcCCeeee
Q 031331 27 DNFTSHLHAAFCRKNIKTF 45 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f 45 (161)
...+..+...|++.|+.+-
T Consensus 152 ~~~~~~~~~~~~~~G~~v~ 170 (347)
T cd06335 152 RSNRKDLTAALAARGLKPV 170 (347)
T ss_pred hhHHHHHHHHHHHcCCeeE
Confidence 4456666666666676653
No 86
>cd06386 PBP1_NPR_C_like Ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANPCNPBNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation.
Probab=25.08 E-value=3.7e+02 Score=22.42 Aligned_cols=39 Identities=15% Similarity=0.112 Sum_probs=22.1
Q ss_pred HHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCc
Q 031331 30 TSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSK 68 (161)
Q Consensus 30 v~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~ 68 (161)
+..|.+.|+..|+.+-.......++.-..++.+.|+++.
T Consensus 157 ~~~l~~~~~~~gi~v~~~~~~~~~~~d~~~~l~~ik~~~ 195 (387)
T cd06386 157 LEGVHHVFQEEGYHMSIYPFDETKDLDLDEIIRAIQASE 195 (387)
T ss_pred HHHHHHHHHhcCceEEEEecCCCCcccHHHHHHHHHhcC
Confidence 677788888888776543323334333345555555444
No 87
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=25.04 E-value=2.9e+02 Score=22.42 Aligned_cols=30 Identities=23% Similarity=0.128 Sum_probs=23.2
Q ss_pred cccccChhhHHHHHHHHHHHhhCCceeeeE
Q 031331 76 KRYASSKWCLDELVEILECKNMNGQTVVPV 105 (161)
Q Consensus 76 ~~y~~S~wc~~El~~~~~~~~~~~~~viPI 105 (161)
.+|++-.-|.+||..+-+-+++.+-.||=|
T Consensus 213 s~Ya~~~~i~~El~~A~~l~~~~~~pvIdv 242 (255)
T PF03618_consen 213 SSYADLERIEEELEYAERLFRKLGCPVIDV 242 (255)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCEEEC
Confidence 578888999999999888777666665543
No 88
>cd01257 PH_IRS Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. PH domains are only found in eukaryotes, and are often involved in targeting proteins to the plasma membrane via lipid binding. 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 cytoskeletal associated molecules and in lipid associated enzymes. The IRS PH domain targets IRS molecules to the plasma membrane, usually in response to insulin stimulation.
Probab=24.99 E-value=63 Score=22.25 Aligned_cols=16 Identities=19% Similarity=0.302 Sum_probs=13.4
Q ss_pred CChHHHHHHHHHHHHh
Q 031331 134 NMPEKVQIWRAVLTEA 149 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v 149 (161)
++++..++|..||.++
T Consensus 86 ese~E~~~Wi~~i~~~ 101 (101)
T cd01257 86 ENEAEQDSWYQALLEL 101 (101)
T ss_pred CCHHHHHHHHHHHhhC
Confidence 4688999999999874
No 89
>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=24.45 E-value=2.6e+02 Score=19.64 Aligned_cols=16 Identities=25% Similarity=0.316 Sum_probs=7.0
Q ss_pred HHHhhhcCcEEEEEee
Q 031331 60 VLNAMKGSKISVIIFS 75 (161)
Q Consensus 60 i~~aI~~S~~~Ivv~S 75 (161)
+.++|+++++.++|+.
T Consensus 5 ~~~~i~~aD~vl~ViD 20 (141)
T cd01857 5 LWRVVERSDIVVQIVD 20 (141)
T ss_pred HHHHHhhCCEEEEEEE
Confidence 3344444444444444
No 90
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=24.44 E-value=1.6e+02 Score=18.94 Aligned_cols=34 Identities=15% Similarity=0.105 Sum_probs=26.1
Q ss_pred cccEEEcCccCcCcccHHHHHHHHHhcCCeeeeec
Q 031331 13 KYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFID 47 (161)
Q Consensus 13 ~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d 47 (161)
+--|+|+|--.+ ....-.+|...|.++|+.|+.-
T Consensus 16 k~~v~i~HG~~e-h~~ry~~~a~~L~~~G~~V~~~ 49 (79)
T PF12146_consen 16 KAVVVIVHGFGE-HSGRYAHLAEFLAEQGYAVFAY 49 (79)
T ss_pred CEEEEEeCCcHH-HHHHHHHHHHHHHhCCCEEEEE
Confidence 567899985443 3455678999999999999973
No 91
>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=24.15 E-value=2.4e+02 Score=19.11 Aligned_cols=29 Identities=7% Similarity=0.252 Sum_probs=20.7
Q ss_pred Ccc-cchHHHHHhhhcCcEEEEEeeccccc
Q 031331 52 RGD-EISQAVLNAMKGSKISVIIFSKRYAS 80 (161)
Q Consensus 52 ~G~-~i~~~i~~aI~~S~~~Ivv~S~~y~~ 80 (161)
||. .+.......+++++..|+|++.+-..
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~~ 86 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNRE 86 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCHH
Confidence 443 34445667788999999999986544
No 92
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=24.07 E-value=1.4e+02 Score=26.85 Aligned_cols=60 Identities=17% Similarity=0.272 Sum_probs=38.2
Q ss_pred cccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeec
Q 031331 13 KYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSK 76 (161)
Q Consensus 13 ~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (161)
..+|+|-.-+++ -...+..|...|+++|+++-+|.. +..+...+..|-..---.++|+.+
T Consensus 438 P~qV~Iipi~e~-~~~~A~~Ia~~LR~~GirVelD~~---~~~lgkkir~A~k~gip~viIIG~ 497 (545)
T PRK14799 438 SVQVRVLPITDE-VNEYAEKVLNDMRKRRIRAEIDYA---GETLSKRIKNAYDQGVPYILIVGK 497 (545)
T ss_pred CceEEEEEcCHH-HHHHHHHHHHHHHhCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEECh
Confidence 467877665443 246788899999999999988763 445555555554432234444443
No 93
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=24.00 E-value=93 Score=23.98 Aligned_cols=51 Identities=14% Similarity=0.145 Sum_probs=34.9
Q ss_pred cccEEEcCccCc--C---cccHHHHHHHHHhcCCeeeeecCc--ccCcccchHHHHHh
Q 031331 13 KYDVFLSFRGED--T---RDNFTSHLHAAFCRKNIKTFIDEE--LSRGDEISQAVLNA 63 (161)
Q Consensus 13 ~ydVFISy~~~D--~---r~~fv~~L~~~L~~~gi~~f~d~~--~~~G~~i~~~i~~a 63 (161)
.++|+|---+.+ . -...+..|...|...||++-+|.+ ..+|..+...-..+
T Consensus 10 P~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~~~ae~~G 67 (202)
T cd00862 10 PIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFNDWELKG 67 (202)
T ss_pred CceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHHHHHHhCC
Confidence 477777643322 0 135788999999999999999875 47887776544333
No 94
>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=23.95 E-value=2.8e+02 Score=19.87 Aligned_cols=86 Identities=9% Similarity=0.071 Sum_probs=50.8
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHH
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEILECK 95 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~ 95 (161)
|+|.=-+.|.+..=.+-+...|+..|+.|-.-. ++.-.+++.++..+.+.-++++|--..... ..+..+++..
T Consensus 5 v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg----~~~s~e~~v~aa~e~~adii~iSsl~~~~~---~~~~~~~~~L 77 (132)
T TIGR00640 5 ILVAKMGQDGHDRGAKVIATAYADLGFDVDVGP----LFQTPEEIARQAVEADVHVVGVSSLAGGHL---TLVPALRKEL 77 (132)
T ss_pred EEEEeeCCCccHHHHHHHHHHHHhCCcEEEECC----CCCCHHHHHHHHHHcCCCEEEEcCchhhhH---HHHHHHHHHH
Confidence 455444445432223445667788999985422 233345677778888888888887665533 3344444444
Q ss_pred hhCCceeeeEEee
Q 031331 96 NMNGQTVVPVFYQ 108 (161)
Q Consensus 96 ~~~~~~viPIfy~ 108 (161)
++.+..-+||+.+
T Consensus 78 ~~~g~~~i~vivG 90 (132)
T TIGR00640 78 DKLGRPDILVVVG 90 (132)
T ss_pred HhcCCCCCEEEEe
Confidence 4444446778876
No 95
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=23.85 E-value=3.1e+02 Score=20.35 Aligned_cols=73 Identities=15% Similarity=0.236 Sum_probs=35.3
Q ss_pred cHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcC--cEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeE
Q 031331 28 NFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGS--KISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPV 105 (161)
Q Consensus 28 ~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S--~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPI 105 (161)
+|+..|....+++|.++|+ +-..+...+.+.+.+.+. .+-|+-..+-|. ...|...+++..+..+-.++=|
T Consensus 35 dl~~~l~~~~~~~~~~ifl---lG~~~~~~~~~~~~l~~~yP~l~ivg~~~g~f----~~~~~~~i~~~I~~~~pdiv~v 107 (172)
T PF03808_consen 35 DLFPDLLRRAEQRGKRIFL---LGGSEEVLEKAAANLRRRYPGLRIVGYHHGYF----DEEEEEAIINRINASGPDIVFV 107 (172)
T ss_pred HHHHHHHHHHHHcCCeEEE---EeCCHHHHHHHHHHHHHHCCCeEEEEecCCCC----ChhhHHHHHHHHHHcCCCEEEE
Confidence 4666677777777777766 222233334444445544 344443333333 2234444444444444444444
Q ss_pred Ee
Q 031331 106 FY 107 (161)
Q Consensus 106 fy 107 (161)
-+
T Consensus 108 gl 109 (172)
T PF03808_consen 108 GL 109 (172)
T ss_pred EC
Confidence 33
No 96
>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=23.80 E-value=1.1e+02 Score=21.66 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=21.1
Q ss_pred ccchHHHHHhhhcCcEEEEEeeccccc
Q 031331 54 DEISQAVLNAMKGSKISVIIFSKRYAS 80 (161)
Q Consensus 54 ~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 80 (161)
+.+.+.+.+.+...++.|++++.++++
T Consensus 46 eei~~~~~~~l~~~digIIlIte~~a~ 72 (115)
T TIGR01101 46 SEIEDCFNRFLKRDDIAIILINQHIAE 72 (115)
T ss_pred HHHHHHHHHHhhcCCeEEEEEcHHHHH
Confidence 455666666688899999999998775
No 97
>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=23.69 E-value=75 Score=20.90 Aligned_cols=16 Identities=13% Similarity=0.393 Sum_probs=13.4
Q ss_pred CChHHHHHHHHHHHHh
Q 031331 134 NMPEKVQIWRAVLTEA 149 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v 149 (161)
++++..+.|..||..+
T Consensus 85 ~s~~e~~~Wi~ai~~~ 100 (101)
T cd01235 85 ENINEAQRWKEKIQQC 100 (101)
T ss_pred CCHHHHHHHHHHHHhh
Confidence 4578899999999875
No 98
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=23.42 E-value=2.7e+02 Score=19.58 Aligned_cols=79 Identities=14% Similarity=0.181 Sum_probs=45.7
Q ss_pred ccHHHHHHHHHhcCCeeeee-c-Ccc-cC-----------cccchHHHHHhhhcCcEEEEEeecccccChhhHHHHHHHH
Q 031331 27 DNFTSHLHAAFCRKNIKTFI-D-EEL-SR-----------GDEISQAVLNAMKGSKISVIIFSKRYASSKWCLDELVEIL 92 (161)
Q Consensus 27 ~~fv~~L~~~L~~~gi~~f~-d-~~~-~~-----------G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~ 92 (161)
..++..+.+.|++.|+.+-+ + .+. .| -..-.+++.+.+.+++ .||+.||.|..+.- -.+..++
T Consensus 17 ~~l~~~~~~~l~~~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD-~iI~~sP~y~~~~s--~~lK~~l 93 (152)
T PF03358_consen 17 RKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEAD-GIIFASPVYNGSVS--GQLKNFL 93 (152)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSS-EEEEEEEEBTTBE---HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCC-eEEEeecEEcCcCC--hhhhHHH
Confidence 45778888888887876532 1 111 11 1223357788888999 67788999986532 1233334
Q ss_pred HHH------hhCCceeeeEEee
Q 031331 93 ECK------NMNGQTVVPVFYQ 108 (161)
Q Consensus 93 ~~~------~~~~~~viPIfy~ 108 (161)
++. .-.+..+.+|-..
T Consensus 94 D~~~~~~~~~~~~K~~~~i~~~ 115 (152)
T PF03358_consen 94 DRLSCWFRRALRGKPVAIIAVG 115 (152)
T ss_dssp HTHHHTHTTTTTTSEEEEEEEE
T ss_pred HHhccccccccCCCEEEEEEEe
Confidence 433 1235566666443
No 99
>cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif.
Probab=22.97 E-value=1.2e+02 Score=21.49 Aligned_cols=46 Identities=24% Similarity=0.222 Sum_probs=25.1
Q ss_pred cCcEEEEEeecccccChhhH--HHHHHHHHHHhh-CCceeeeEEeecCcccccccc
Q 031331 66 GSKISVIIFSKRYASSKWCL--DELVEILECKNM-NGQTVVPVFYQVDPSDVRNQT 118 (161)
Q Consensus 66 ~S~~~Ivv~S~~y~~S~wc~--~El~~~~~~~~~-~~~~viPIfy~v~p~~v~~~~ 118 (161)
+.+..|+-|+. +||. ..+..+++.... -... -+||.|+.+++....
T Consensus 13 ~~klVVVdF~a-----~WC~pCk~mdp~l~ela~~~~~~--~~f~kVDVDev~dva 61 (114)
T cd02986 13 AEKVLVLRFGR-----DEDAVCLQLDDILSKTSHDLSKM--ASIYLVDVDKVPVYT 61 (114)
T ss_pred CCCEEEEEEeC-----CCChhHHHHHHHHHHHHHHccCc--eEEEEEeccccHHHH
Confidence 45666666665 5663 245455544322 2222 567887777776543
No 100
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=22.96 E-value=1.6e+02 Score=26.33 Aligned_cols=60 Identities=10% Similarity=0.221 Sum_probs=38.0
Q ss_pred cccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeec
Q 031331 13 KYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSK 76 (161)
Q Consensus 13 ~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (161)
.+||+|---+++ -...+..|...|.+.||++-+|.. +..+...+..|-..---.++|+.+
T Consensus 476 p~~v~Ii~~~~~-~~~~a~~i~~~Lr~~gi~v~~d~~---~~~l~kk~~~A~~~g~p~~iivG~ 535 (575)
T PRK12305 476 PVQVVIIPVADA-HNEYAEEVAKKLRAAGIRVEVDTS---NERLNKKIRNAQKQKIPYMLVVGD 535 (575)
T ss_pred CccEEEEEeChH-HHHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHhcCCCEEEEEec
Confidence 467888664443 245688899999999999988763 334555555554433334555554
No 101
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=22.71 E-value=2.2e+02 Score=23.42 Aligned_cols=15 Identities=7% Similarity=0.155 Sum_probs=9.7
Q ss_pred cHHHHHHHHHhcCCe
Q 031331 28 NFTSHLHAAFCRKNI 42 (161)
Q Consensus 28 ~fv~~L~~~L~~~gi 42 (161)
..+..+.+.|+..|+
T Consensus 169 ~~~~~~~~~~~~~g~ 183 (377)
T cd06379 169 AAQKRFETLLEEREI 183 (377)
T ss_pred HHHHHHHHHHHhcCC
Confidence 355666666666676
No 102
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=22.69 E-value=1.7e+02 Score=26.48 Aligned_cols=61 Identities=8% Similarity=0.138 Sum_probs=39.5
Q ss_pred cccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeecc
Q 031331 13 KYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKR 77 (161)
Q Consensus 13 ~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 77 (161)
..||+|-.-++.. ...+..|...|+++|++|-+|.. +..+...+..|-..---.++|+.++
T Consensus 539 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~---~~~l~kki~~A~~~g~~~~iiiG~~ 599 (638)
T PRK00413 539 PVQVVVLPITDKH-ADYAKEVAKKLKAAGIRVEVDLR---NEKIGYKIREAQLQKVPYMLVVGDK 599 (638)
T ss_pred cceEEEEEeChhH-HHHHHHHHHHHHhCCCEEEEECC---CCCHhHHHHHhhccCCCEEEEEcch
Confidence 4678877654432 45788899999999999988763 4445555555544333355566553
No 103
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=22.64 E-value=1.4e+02 Score=25.82 Aligned_cols=45 Identities=27% Similarity=0.600 Sum_probs=32.3
Q ss_pred hhhcCcEEEEEeecccc----cChhhHH-HHH-HHHHHHhhCCceeeeEEe
Q 031331 63 AMKGSKISVIIFSKRYA----SSKWCLD-ELV-EILECKNMNGQTVVPVFY 107 (161)
Q Consensus 63 aI~~S~~~Ivv~S~~y~----~S~wc~~-El~-~~~~~~~~~~~~viPIfy 107 (161)
.|..+|--++|--..|+ .|..|.+ |+. +..+|...+|..+||||-
T Consensus 191 ~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvFA 241 (501)
T KOG1136|consen 191 WIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVFA 241 (501)
T ss_pred hhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEeee
Confidence 45667766666555676 4888876 554 456788889999999995
No 104
>cd06361 PBP1_GPC6A_like Ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor. This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses.
Probab=22.61 E-value=2.3e+02 Score=24.04 Aligned_cols=20 Identities=0% Similarity=-0.207 Sum_probs=13.5
Q ss_pred cccHHHHHHHHHhcCCeeee
Q 031331 26 RDNFTSHLHAAFCRKNIKTF 45 (161)
Q Consensus 26 r~~fv~~L~~~L~~~gi~~f 45 (161)
....+..+.++|++.|+.+-
T Consensus 185 G~~~~~~f~~~~~~~GicIa 204 (403)
T cd06361 185 GRSALETFIIQAEANGVCIA 204 (403)
T ss_pred HHHHHHHHHHHHHHCCeEEE
Confidence 34566777777777777653
No 105
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=22.30 E-value=55 Score=21.03 Aligned_cols=28 Identities=14% Similarity=0.267 Sum_probs=17.6
Q ss_pred CCeeeeecCcccCcccchHHHHHhhhcCc
Q 031331 40 KNIKTFIDEELSRGDEISQAVLNAMKGSK 68 (161)
Q Consensus 40 ~gi~~f~d~~~~~G~~i~~~i~~aI~~S~ 68 (161)
+.+-+++|.+ .+|+.....+.+.+....
T Consensus 47 ~~Vii~~D~D-~~G~~~a~~i~~~l~~~g 74 (81)
T PF13662_consen 47 KEVIIAFDND-KAGEKAAQKIAKKLLPLG 74 (81)
T ss_dssp SEEEEEEESS-HHHHHHHHHHHHHHG---
T ss_pred ceEEEEeCcC-HHHHHHHHHHHHHHHhhc
Confidence 6677777775 477777777777665433
No 106
>PLN02530 histidine-tRNA ligase
Probab=22.26 E-value=2e+02 Score=25.30 Aligned_cols=61 Identities=10% Similarity=0.035 Sum_probs=40.7
Q ss_pred CcccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeec
Q 031331 12 SKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSK 76 (161)
Q Consensus 12 ~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 76 (161)
...||+|.+-+++. ...+-.+...|+++|+++-+|-. +..+...+..|-+.--..|+++.+
T Consensus 400 ~~~dVlVi~~~~~~-~~~A~~ia~~LR~~Gi~vevd~~---~~~l~k~ik~A~k~g~~~iviiG~ 460 (487)
T PLN02530 400 HQVDDVVFALDEDL-QGAAAGVASRLREKGRSVDLVLE---PKKLKWVFKHAERIGAKRLVLVGA 460 (487)
T ss_pred CCCcEEEEEcChHH-HHHHHHHHHHHHHCCCeEEEecC---CCCHHHHHHHHHHCCCCEEEEEch
Confidence 34689998755543 35678899999999999977542 244555666666544445666664
No 107
>PF07429 Glyco_transf_56: 4-alpha-L-fucosyltransferase glycosyl transferase group 56; InterPro: IPR009993 This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc [].; GO: 0008417 fucosyltransferase activity, 0009246 enterobacterial common antigen biosynthetic process, 0009276 Gram-negative-bacterium-type cell wall
Probab=22.23 E-value=1.1e+02 Score=26.22 Aligned_cols=49 Identities=12% Similarity=0.295 Sum_probs=26.4
Q ss_pred HHHHHhcCCeeeeecCc-ccCcccchHHHHHhhhcC-cEEEEEeecccccChhh
Q 031331 33 LHAAFCRKNIKTFIDEE-LSRGDEISQAVLNAMKGS-KISVIIFSKRYASSKWC 84 (161)
Q Consensus 33 L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S-~~~Ivv~S~~y~~S~wc 84 (161)
+.+.|..+|+.|+++.+ +.. ..+. +..+.+... +..|..|+|||.+ .|.
T Consensus 300 ~~~~l~~~~ipVlf~~d~L~~-~~v~-ea~rql~~~dk~~iaFf~pny~~-~w~ 350 (360)
T PF07429_consen 300 FWQDLKEQGIPVLFYGDELDE-ALVR-EAQRQLANVDKQQIAFFAPNYLQ-GWR 350 (360)
T ss_pred HHHHHHhCCCeEEeccccCCH-HHHH-HHHHHHhhCcccceeeeCCchHH-HHH
Confidence 56667777887776544 322 1121 222323322 2356688899887 453
No 108
>PRK07933 thymidylate kinase; Validated
Probab=22.23 E-value=1.6e+02 Score=22.69 Aligned_cols=30 Identities=20% Similarity=0.314 Sum_probs=22.6
Q ss_pred EEcCccCcC--cccHHHHHHHHHhcCCeeeee
Q 031331 17 FLSFRGEDT--RDNFTSHLHAAFCRKNIKTFI 46 (161)
Q Consensus 17 FISy~~~D~--r~~fv~~L~~~L~~~gi~~f~ 46 (161)
||.+-|-|. +.+.+..|.+.|+.+|++|..
T Consensus 2 ~IviEG~dGsGKST~~~~L~~~L~~~g~~v~~ 33 (213)
T PRK07933 2 LIAIEGVDGAGKRTLTEALRAALEARGRSVAT 33 (213)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence 677766663 357888999999998887653
No 109
>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=22.22 E-value=53 Score=21.65 Aligned_cols=29 Identities=28% Similarity=0.430 Sum_probs=16.7
Q ss_pred hhhcCcEEEEEeecccccChhhHH--HHHHHHH
Q 031331 63 AMKGSKISVIIFSKRYASSKWCLD--ELVEILE 93 (161)
Q Consensus 63 aI~~S~~~Ivv~S~~y~~S~wc~~--El~~~~~ 93 (161)
.|++.+ |+|||+.+.+.+||.. .+..+++
T Consensus 4 ~i~~~~--vvvf~k~~~~~~~Cp~C~~ak~~L~ 34 (90)
T cd03028 4 LIKENP--VVLFMKGTPEEPRCGFSRKVVQILN 34 (90)
T ss_pred hhccCC--EEEEEcCCCCCCCCcHHHHHHHHHH
Confidence 444444 5667887777777653 4444443
No 110
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=22.15 E-value=1.4e+02 Score=25.54 Aligned_cols=51 Identities=8% Similarity=0.172 Sum_probs=36.3
Q ss_pred cCcCcccHHHHHHHHHhcCCeeeeecCc-ccC----cccchHHHHHhhhcCcEEEE
Q 031331 22 GEDTRDNFTSHLHAAFCRKNIKTFIDEE-LSR----GDEISQAVLNAMKGSKISVI 72 (161)
Q Consensus 22 ~~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~----G~~i~~~i~~aI~~S~~~Iv 72 (161)
..|.|.+=+-.|.+.|..+|..+-..+- +.. |-.+.++..++++.++..|+
T Consensus 310 t~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 310 SDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred CCccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 3477888888999999999988765332 221 34566777888888887653
No 111
>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=21.98 E-value=96 Score=19.59 Aligned_cols=17 Identities=18% Similarity=0.339 Sum_probs=14.2
Q ss_pred CChHHHHHHHHHHHHhh
Q 031331 134 NMPEKVQIWRAVLTEAS 150 (161)
Q Consensus 134 ~~~~~~~~W~~al~~v~ 150 (161)
.+++....|..||..+.
T Consensus 87 ~s~~~~~~W~~~i~~~~ 103 (104)
T PF00169_consen 87 ESEEERKRWIQAIQKAI 103 (104)
T ss_dssp SSHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 36789999999998874
No 112
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=21.84 E-value=2.1e+02 Score=24.27 Aligned_cols=60 Identities=27% Similarity=0.444 Sum_probs=41.0
Q ss_pred cccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhh-cCcEEEEEeeccccc
Q 031331 13 KYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMK-GSKISVIIFSKRYAS 80 (161)
Q Consensus 13 ~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~-~S~~~Ivv~S~~y~~ 80 (161)
.+|+=|.|+.+| |...|.++-- +||.+|+|. .|..+.+.....+. ..|+.++=.=..|.+
T Consensus 196 GfD~~idyk~~d----~~~~L~~a~P-~GIDvyfeN---VGg~v~DAv~~~ln~~aRi~~CG~IS~YN~ 256 (340)
T COG2130 196 GFDAGIDYKAED----FAQALKEACP-KGIDVYFEN---VGGEVLDAVLPLLNLFARIPVCGAISQYNA 256 (340)
T ss_pred CCceeeecCccc----HHHHHHHHCC-CCeEEEEEc---CCchHHHHHHHhhccccceeeeeehhhcCC
Confidence 488999997664 6666665554 699999977 57777777777776 455555444445554
No 113
>cd02951 SoxW SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to sulfate. SoxW is specifically kept in the reduced state by SoxV, which is essential in thiosulfate oxidation.
Probab=21.68 E-value=2.7e+02 Score=18.92 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=19.8
Q ss_pred hHHHHHhhhcC-cEEEEEeecccccChhhHHHH
Q 031331 57 SQAVLNAMKGS-KISVIIFSKRYASSKWCLDEL 88 (161)
Q Consensus 57 ~~~i~~aI~~S-~~~Ivv~S~~y~~S~wc~~El 88 (161)
.+++.+++++- +..+|.|....+ ++|....
T Consensus 3 ~~~~~~a~~~~~k~vlv~f~a~wC--~~C~~~~ 33 (125)
T cd02951 3 YEDLAEAAADGKKPLLLLFSQPGC--PYCDKLK 33 (125)
T ss_pred HHHHHHHHHcCCCcEEEEEeCCCC--HHHHHHH
Confidence 35677888888 777777765443 5676544
No 114
>PRK05225 ketol-acid reductoisomerase; Validated
Probab=21.55 E-value=56 Score=29.06 Aligned_cols=29 Identities=21% Similarity=0.365 Sum_probs=19.2
Q ss_pred cccchHHHHHHHHHhcCCChHHHHHHHHHHHH
Q 031331 117 QTGCFADAFVEHEEQFKNMPEKVQIWRAVLTE 148 (161)
Q Consensus 117 ~~~~f~~~f~~~~~~~~~~~~~~~~W~~al~~ 148 (161)
|+|.|.+.+..-.+ .+..++.+||+++..
T Consensus 307 ~sG~fak~~m~d~~---~~~~~l~~~r~~~~~ 335 (487)
T PRK05225 307 ISGEFSSTMMADWA---NDDKKLLTWREETGK 335 (487)
T ss_pred hccHHHHHHHHHHh---cCChHHHHHHHHhhc
Confidence 46667666644433 346789999998764
No 115
>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign
Probab=21.52 E-value=3.2e+02 Score=19.73 Aligned_cols=55 Identities=13% Similarity=0.094 Sum_probs=34.2
Q ss_pred HHHhhhcCcEEEEEeecccccChhhHHHHHHHHHHHhhCCceeeeEEeecCcccccc
Q 031331 60 VLNAMKGSKISVIIFSKRYASSKWCLDELVEILECKNMNGQTVVPVFYQVDPSDVRN 116 (161)
Q Consensus 60 i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPIfy~v~p~~v~~ 116 (161)
....+..++.+|+|++.+-..|---..++...+..... ..-+||++-....|+.+
T Consensus 67 ~~~~~~~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~--~~~~piilvgNK~Dl~~ 121 (172)
T cd04141 67 RDQYMRCGEGFIICYSVTDRHSFQEASEFKKLITRVRL--TEDIPLVLVGNKVDLES 121 (172)
T ss_pred hHHHhhcCCEEEEEEECCchhHHHHHHHHHHHHHHhcC--CCCCCEEEEEEChhhhh
Confidence 34567889999999998777665555554444433221 12367777666666654
No 116
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=21.48 E-value=81 Score=20.12 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=24.9
Q ss_pred EEEcCccCcCcccHHHHHHHHHhcCCeeeee
Q 031331 16 VFLSFRGEDTRDNFTSHLHAAFCRKNIKTFI 46 (161)
Q Consensus 16 VFISy~~~D~r~~fv~~L~~~L~~~gi~~f~ 46 (161)
+-|+..++| |.+.+..+...|.++|.++--
T Consensus 2 ~iltv~g~D-r~GiVa~vs~~la~~g~nI~d 31 (77)
T cd04893 2 LVISALGTD-RPGILNELTRAVSESGCNILD 31 (77)
T ss_pred EEEEEEeCC-CChHHHHHHHHHHHcCCCEEE
Confidence 346778898 689999999999999998743
No 117
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=21.40 E-value=1.3e+02 Score=24.55 Aligned_cols=42 Identities=17% Similarity=0.236 Sum_probs=27.8
Q ss_pred HHHHHHHHhcCCeeeeecCcccCcc---cchHHHHHhhhcCcEEEEEee
Q 031331 30 TSHLHAAFCRKNIKTFIDEELSRGD---EISQAVLNAMKGSKISVIIFS 75 (161)
Q Consensus 30 v~~L~~~L~~~gi~~f~d~~~~~G~---~i~~~i~~aI~~S~~~Ivv~S 75 (161)
+.+|.+.|...|+.+..-. ..|| .|.+.+..+++.+++ ||+|
T Consensus 23 a~~la~~L~~~G~~v~~~~--~VgD~~~~I~~~l~~a~~r~D~--vI~t 67 (255)
T COG1058 23 AAFLADELTELGVDLARIT--TVGDNPDRIVEALREASERADV--VITT 67 (255)
T ss_pred HHHHHHHHHhcCceEEEEE--ecCCCHHHHHHHHHHHHhCCCE--EEEC
Confidence 6789999999999987532 2343 455566666667554 4455
No 118
>cd06367 PBP1_iGluR_NMDA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits
Probab=21.38 E-value=3.7e+02 Score=21.89 Aligned_cols=24 Identities=4% Similarity=0.088 Sum_probs=14.4
Q ss_pred CccCcCcccHHHHHHHHHhcCCee
Q 031331 20 FRGEDTRDNFTSHLHAAFCRKNIK 43 (161)
Q Consensus 20 y~~~D~r~~fv~~L~~~L~~~gi~ 43 (161)
|...|....++..|.+.|+..|+.
T Consensus 143 ~~~~~~g~~~~~~l~~~l~~~g~~ 166 (362)
T cd06367 143 TSRDPGYRDFLDRVETTLEESFVG 166 (362)
T ss_pred EEcCcccHHHHHHHHHHHHhcccc
Confidence 433333345677777777777765
No 119
>COG2342 Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism]
Probab=21.20 E-value=1.6e+02 Score=24.49 Aligned_cols=44 Identities=25% Similarity=0.558 Sum_probs=34.3
Q ss_pred HHHHHhhhcCcEEEEEeecccc---cChhhHHHHHHHHHHHhhCCceeeeEEe
Q 031331 58 QAVLNAMKGSKISVIIFSKRYA---SSKWCLDELVEILECKNMNGQTVVPVFY 107 (161)
Q Consensus 58 ~~i~~aI~~S~~~Ivv~S~~y~---~S~wc~~El~~~~~~~~~~~~~viPIfy 107 (161)
+.-..+|.+++.-++|+-|.|. ..+|..+||.++. ..+ ++||=|
T Consensus 33 d~~~~~i~~~~f~llVVDps~~g~~~~~~~~eelr~~~----~gg--~~pIAY 79 (300)
T COG2342 33 DAYINEILNSPFDLLVVDPSYCGPFNTPWTIEELRTKA----DGG--VKPIAY 79 (300)
T ss_pred cchHHHHhcCCCcEEEEeccccCCCCCcCcHHHHHHHh----cCC--eeEEEE
Confidence 4556789999999999999776 5789999987652 233 888877
No 120
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=21.17 E-value=69 Score=28.95 Aligned_cols=62 Identities=15% Similarity=0.320 Sum_probs=38.8
Q ss_pred cccEEEcCc-cCc-CcccHHHHHHHHHhcCCeeeeecCc-ccCcccchHHHHHhhhcCcEEEEEeeccc
Q 031331 13 KYDVFLSFR-GED-TRDNFTSHLHAAFCRKNIKTFIDEE-LSRGDEISQAVLNAMKGSKISVIIFSKRY 78 (161)
Q Consensus 13 ~ydVFISy~-~~D-~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 78 (161)
.|+|=|--- .+| .-...+..|+..|+..|+.+.+|++ -.+|..+.+.-.-+| . ..+++.++.
T Consensus 473 P~qV~Iip~~~~~~~~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~dadliGi---P-~~i~vG~~~ 537 (568)
T TIGR00409 473 PYDVVIVVMNMKDEEQQQLAEELYSELLAQGVDVLLDDRNERAGVKFADSELIGI---P-LRVVVGKKN 537 (568)
T ss_pred CeEEEEEEcCCChHHHHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHHhhhhcCC---C-EEEEECCCc
Confidence 366654321 222 2356789999999999999999887 677777765433333 2 334455544
No 121
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=21.01 E-value=2.1e+02 Score=19.45 Aligned_cols=43 Identities=9% Similarity=0.301 Sum_probs=27.4
Q ss_pred HHhcCCeeeeecCcccCcccchHHHHHhhhcCcEEEEEeeccccc
Q 031331 36 AFCRKNIKTFIDEELSRGDEISQAVLNAMKGSKISVIIFSKRYAS 80 (161)
Q Consensus 36 ~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 80 (161)
.|+-.|+..+... ...+...+.+.+.+.+-++.|++++++.+.
T Consensus 14 GFrLaGi~~~~~~--~~~ee~~~~l~~l~~~~d~gII~Ite~~~~ 56 (100)
T PRK02228 14 GFRLAGIRKVYEV--PDDEKLDEAVEEVLEDDDVGILVMHDDDLE 56 (100)
T ss_pred HHHHcCCceEEee--CCHHHHHHHHHHHhhCCCEEEEEEehhHhH
Confidence 3455688644311 111345556666667788999999999776
No 122
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=20.97 E-value=1.4e+02 Score=23.25 Aligned_cols=98 Identities=17% Similarity=0.267 Sum_probs=57.0
Q ss_pred EEEcCccCcC--cccHHHHHHHHHhcCCeeeeecCcccCcccchHHHHHhhhc---------------------------
Q 031331 16 VFLSFRGEDT--RDNFTSHLHAAFCRKNIKTFIDEELSRGDEISQAVLNAMKG--------------------------- 66 (161)
Q Consensus 16 VFISy~~~D~--r~~fv~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~--------------------------- 66 (161)
.||.+-|-|. +.+.+..|.+.|+.+|+.|.+-++ +.|.++...|.+.+-+
T Consensus 4 ~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~trE-P~~~~ige~iR~~ll~~~~~~~~~~e~lLfaadR~~h~~~~i~ 82 (208)
T COG0125 4 MFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTRE-PGGTPIGEKIRELLLNGEEKLSPKAEALLFAADRAQHLEEVIK 82 (208)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC-CCCChHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4888866663 357889999999999988766442 2222222222222211
Q ss_pred --CcEEEEEeecccccChhhHHH--------HHHHHHHH-hhCCceeeeEEeecCcccc
Q 031331 67 --SKISVIIFSKRYASSKWCLDE--------LVEILECK-NMNGQTVVPVFYQVDPSDV 114 (161)
Q Consensus 67 --S~~~Ivv~S~~y~~S~wc~~E--------l~~~~~~~-~~~~~~viPIfy~v~p~~v 114 (161)
-.-.-+|++..|.-|.-+.+- ....+... ...-.+-+-+|++++|..-
T Consensus 83 pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~a 141 (208)
T COG0125 83 PALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVA 141 (208)
T ss_pred HhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHH
Confidence 011348889999988887662 22222221 1112456667889988753
No 123
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=20.82 E-value=1.9e+02 Score=26.53 Aligned_cols=44 Identities=16% Similarity=0.174 Sum_probs=31.5
Q ss_pred cccEEEcCccCcCcccHHHHHHHHHhcCCeeeeecCc-ccCcccch
Q 031331 13 KYDVFLSFRGEDTRDNFTSHLHAAFCRKNIKTFIDEE-LSRGDEIS 57 (161)
Q Consensus 13 ~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~~i~ 57 (161)
.++|+|---+++ ....+..|...|+++|+++.+|.. -..|..+.
T Consensus 499 P~qV~IIpi~e~-~~~~A~eIa~~Lr~~GirV~lDdr~~slgkKir 543 (613)
T PRK03991 499 PTQVRVIPVSER-HLDYAEEVADKLEAAGIRVDVDDRDESLGKKIR 543 (613)
T ss_pred CceEEEEEeCHH-HHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHH
Confidence 378877654443 356889999999999999999875 44444443
No 124
>PF15409 PH_8: Pleckstrin homology domain
Probab=20.75 E-value=91 Score=21.15 Aligned_cols=15 Identities=33% Similarity=0.532 Sum_probs=12.6
Q ss_pred ChHHHHHHHHHHHHh
Q 031331 135 MPEKVQIWRAVLTEA 149 (161)
Q Consensus 135 ~~~~~~~W~~al~~v 149 (161)
+++..+.|..||..+
T Consensus 74 s~~~f~~Wv~aL~~a 88 (89)
T PF15409_consen 74 SQEDFQRWVSALQKA 88 (89)
T ss_pred CHHHHHHHHHHHHhc
Confidence 578889999999864
No 125
>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=20.48 E-value=89 Score=19.79 Aligned_cols=15 Identities=33% Similarity=0.404 Sum_probs=12.4
Q ss_pred CChHHHHHHHHHHHH
Q 031331 134 NMPEKVQIWRAVLTE 148 (161)
Q Consensus 134 ~~~~~~~~W~~al~~ 148 (161)
.+++..++|..||..
T Consensus 76 ~s~~e~~~Wi~al~~ 90 (91)
T cd01246 76 NSEEERQRWVDALEL 90 (91)
T ss_pred CCHHHHHHHHHHHHh
Confidence 357889999999975
No 126
>PRK08350 hypothetical protein; Provisional
Probab=20.15 E-value=1e+02 Score=26.18 Aligned_cols=32 Identities=13% Similarity=0.118 Sum_probs=27.8
Q ss_pred CcccEEEcCccCcCcccHHHHHHHHHhcCCee
Q 031331 12 SKYDVFLSFRGEDTRDNFTSHLHAAFCRKNIK 43 (161)
Q Consensus 12 ~~ydVFISy~~~D~r~~fv~~L~~~L~~~gi~ 43 (161)
..|-+.+|||+-++...|+.+|.-+|...-|+
T Consensus 280 ~g~~~vvSHRSGETeD~~IAdLaVa~~agqIK 311 (341)
T PRK08350 280 ERITPILAEAKYESADEALPHLAVGLRCPAML 311 (341)
T ss_pred cCCeEEeecCCCCCcchhHHHHHHHhCCCccc
Confidence 35889999998888899999999999887775
No 127
>PF15410 PH_9: Pleckstrin homology domain; PDB: 1WJM_A 1BTN_A 1MPH_A.
Probab=20.11 E-value=99 Score=21.62 Aligned_cols=16 Identities=19% Similarity=0.347 Sum_probs=13.7
Q ss_pred ChHHHHHHHHHHHHhh
Q 031331 135 MPEKVQIWRAVLTEAS 150 (161)
Q Consensus 135 ~~~~~~~W~~al~~v~ 150 (161)
+++.++.|..+|+.+|
T Consensus 103 ~~~~m~~Wi~~IN~~A 118 (119)
T PF15410_consen 103 DEEEMNEWIDAINYAA 118 (119)
T ss_dssp SHHHHHHHHHHHHHH-
T ss_pred CHHHHHHHHHHHhhhc
Confidence 6899999999999876
No 128
>TIGR03026 NDP-sugDHase nucleotide sugar dehydrogenase. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively.
Probab=20.05 E-value=1.9e+02 Score=24.66 Aligned_cols=57 Identities=19% Similarity=0.306 Sum_probs=36.6
Q ss_pred EcCc--cCcCcccHHHHHHHHHhcCCeeeeecCc-ccCcc----cchHHHHHhhhcCcEEEEEe
Q 031331 18 LSFR--GEDTRDNFTSHLHAAFCRKNIKTFIDEE-LSRGD----EISQAVLNAMKGSKISVIIF 74 (161)
Q Consensus 18 ISy~--~~D~r~~fv~~L~~~L~~~gi~~f~d~~-~~~G~----~i~~~i~~aI~~S~~~Ivv~ 74 (161)
++|. ..|.|.+=+-.|.+.|.++|..|...+. ..... ...+++.+++++++..|+.-
T Consensus 321 lafK~~t~d~r~sp~~~~~~~L~~~g~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~ad~~v~~t 384 (411)
T TIGR03026 321 LAFKPNTDDVRESPALDIIELLKEKGAKVKAYDPLVPEEEVKGLPLIDDLEEALKGADALVILT 384 (411)
T ss_pred eEecCCCCccccChHHHHHHHHHhCCCEEEEECCCCChhhhhhcccCCCHHHHHhCCCEEEEec
Confidence 3553 3477888888999999999998876443 22211 11245667888888666544
Done!