Query 044631
Match_columns 136
No_of_seqs 134 out of 1062
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 05:12:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044631.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044631hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03194 putative disease resi 100.0 5.1E-37 1.1E-41 226.0 11.5 109 2-115 19-127 (187)
2 PLN03210 Resistant to P. syrin 100.0 1.4E-35 3E-40 266.8 12.3 129 1-131 1-132 (1153)
3 smart00255 TIR Toll - interleu 99.9 4E-25 8.8E-30 155.1 10.5 122 9-133 1-124 (140)
4 PF01582 TIR: TIR domain; Int 99.9 9.8E-27 2.1E-31 165.0 0.6 119 12-132 1-125 (141)
5 PF13676 TIR_2: TIR domain; PD 99.8 3.9E-21 8.5E-26 128.8 4.6 87 12-106 1-87 (102)
6 KOG3678 SARM protein (with ste 99.2 5.7E-11 1.2E-15 98.6 7.7 91 8-105 611-709 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.9 5.3E-09 1.1E-13 73.2 6.3 91 10-106 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 98.4 1.7E-06 3.7E-11 61.5 8.6 65 11-76 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.5 0.00046 9.9E-09 48.3 6.7 98 11-114 1-113 (125)
10 PF13271 DUF4062: Domain of un 94.9 0.12 2.5E-06 33.2 5.8 68 11-80 1-68 (83)
11 PF05014 Nuc_deoxyrib_tr: Nucl 92.7 1.4 3.1E-05 29.5 8.1 69 23-93 13-89 (113)
12 COG4916 Uncharacterized protei 92.3 0.2 4.3E-06 39.4 3.9 95 6-105 174-273 (329)
13 COG4271 Predicted nucleotide-b 88.5 1.5 3.2E-05 33.3 5.5 97 11-114 84-199 (233)
14 cd00860 ThrRS_anticodon ThrRS 83.7 5.6 0.00012 24.8 5.8 57 10-72 2-59 (91)
15 PF03129 HGTP_anticodon: Antic 82.1 2.6 5.6E-05 26.9 3.8 47 23-74 15-61 (94)
16 cd00738 HGTP_anticodon HGTP an 81.9 6.8 0.00015 24.5 5.7 60 10-75 2-64 (94)
17 cd00858 GlyRS_anticodon GlyRS 77.0 11 0.00023 25.5 5.8 61 9-76 26-88 (121)
18 cd02042 ParA ParA and ParB of 76.0 16 0.00036 23.4 6.3 65 12-77 3-74 (104)
19 COG4916 Uncharacterized protei 70.6 5.9 0.00013 31.4 3.4 96 7-107 4-105 (329)
20 PF14258 DUF4350: Domain of un 67.3 25 0.00054 21.2 7.0 61 27-101 8-68 (70)
21 cd02426 Pol_gamma_b_Cterm C-te 63.2 7.1 0.00015 27.1 2.4 48 9-57 27-79 (128)
22 cd07363 45_DOPA_Dioxygenase Th 61.5 45 0.00098 25.6 6.9 69 23-94 80-149 (253)
23 cd00861 ProRS_anticodon_short 61.0 32 0.0007 21.5 5.1 48 23-75 17-64 (94)
24 cd00532 MGS-like MGS-like doma 58.9 38 0.00083 22.5 5.4 61 12-75 2-77 (112)
25 TIGR00334 5S_RNA_mat_M5 ribonu 58.4 18 0.0004 26.7 4.0 45 23-70 35-79 (174)
26 COG1658 Small primase-like pro 57.1 22 0.00048 24.9 4.0 55 10-67 30-84 (127)
27 TIGR00418 thrS threonyl-tRNA s 56.3 37 0.0008 29.1 6.1 61 8-74 469-529 (563)
28 PRK12325 prolyl-tRNA synthetas 55.0 26 0.00055 29.3 4.8 65 8-77 344-410 (439)
29 cd01424 MGS_CPS_II Methylglyox 54.7 53 0.0011 21.6 5.5 62 11-75 2-76 (110)
30 cd00862 ProRS_anticodon_zinc P 53.7 24 0.00053 26.2 4.1 49 8-57 9-63 (202)
31 cd07373 2A5CPDO_A The alpha su 53.1 1.1E+02 0.0023 23.8 8.3 79 23-103 90-172 (271)
32 cd08584 PI-PLCc_GDPD_SF_unchar 53.0 29 0.00062 26.1 4.3 59 11-78 103-161 (192)
33 PF10087 DUF2325: Uncharacteri 51.7 63 0.0014 20.8 5.7 59 24-85 10-69 (97)
34 cd00859 HisRS_anticodon HisRS 50.7 54 0.0012 19.7 5.5 59 10-74 2-60 (91)
35 PF01990 ATP-synt_F: ATP synth 50.4 52 0.0011 21.2 4.8 68 28-103 8-75 (95)
36 COG0276 HemH Protoheme ferro-l 50.2 1.4E+02 0.003 24.3 8.5 79 25-106 74-161 (320)
37 cd04141 Rit_Rin_Ric Rit/Rin/Ri 49.6 89 0.0019 21.9 7.1 62 50-113 58-120 (172)
38 PRK14938 Ser-tRNA(Thr) hydrola 49.1 58 0.0013 27.1 5.8 57 9-71 274-331 (387)
39 PRK03991 threonyl-tRNA synthet 49.0 28 0.00061 30.6 4.3 44 9-54 499-542 (613)
40 PRK08661 prolyl-tRNA synthetas 49.0 31 0.00068 29.2 4.4 47 9-56 287-339 (477)
41 PF03358 FMN_red: NADPH-depend 48.8 85 0.0018 21.5 6.7 80 23-106 17-115 (152)
42 PRK09194 prolyl-tRNA synthetas 48.2 22 0.00048 30.7 3.4 66 7-77 466-533 (565)
43 cd01423 MGS_CPS_I_III Methylgl 47.2 33 0.00072 22.8 3.6 29 12-43 3-31 (116)
44 PF03720 UDPG_MGDP_dh_C: UDP-g 46.4 18 0.0004 23.9 2.2 57 18-75 11-77 (106)
45 cd00154 Rab Rab family. Rab G 45.6 83 0.0018 20.7 5.5 30 50-79 57-87 (159)
46 cd03364 TOPRIM_DnaG_primases T 45.6 34 0.00075 21.1 3.3 26 37-64 44-69 (79)
47 COG0400 Predicted esterase [Ge 45.1 51 0.0011 24.8 4.7 52 8-62 145-198 (207)
48 KOG1136 Predicted cleavage and 43.7 72 0.0016 26.5 5.5 58 46-106 179-242 (501)
49 PLN03194 putative disease resi 42.1 83 0.0018 23.6 5.2 64 37-104 25-88 (187)
50 PF14359 DUF4406: Domain of un 41.7 98 0.0021 20.2 6.9 63 27-92 19-85 (92)
51 PF09837 DUF2064: Uncharacteri 41.1 1.1E+02 0.0025 20.8 7.5 82 9-102 10-94 (122)
52 KOG1673 Ras GTPases [General f 40.9 1.2E+02 0.0027 22.4 5.9 66 40-108 68-133 (205)
53 CHL00201 syh histidine-tRNA sy 40.6 77 0.0017 26.4 5.5 60 9-74 325-384 (430)
54 PF09419 PGP_phosphatase: Mito 39.9 59 0.0013 23.8 4.2 68 32-105 35-111 (168)
55 PRK12305 thrS threonyl-tRNA sy 39.1 98 0.0021 26.6 6.0 61 8-74 475-535 (575)
56 PF00762 Ferrochelatase: Ferro 38.9 2E+02 0.0044 23.0 7.7 93 24-129 73-173 (316)
57 TIGR01101 V_ATP_synt_F vacuola 38.8 57 0.0012 22.4 3.7 45 52-106 46-90 (115)
58 PRK00413 thrS threonyl-tRNA sy 38.5 94 0.002 27.1 5.9 60 9-74 539-598 (638)
59 COG2130 Putative NADP-dependen 38.4 74 0.0016 25.9 4.8 61 9-79 196-257 (340)
60 cd04127 Rab27A Rab27a subfamil 37.8 1.4E+02 0.003 20.7 6.8 26 54-79 76-101 (180)
61 PRK14799 thrS threonyl-tRNA sy 37.6 90 0.0019 27.1 5.5 57 9-71 438-495 (545)
62 cd01867 Rab8_Rab10_Rab13_like 37.1 1.4E+02 0.003 20.5 7.5 27 52-78 63-89 (167)
63 cd01864 Rab19 Rab19 subfamily. 36.8 1.4E+02 0.003 20.4 7.2 30 50-79 60-90 (165)
64 PRK02228 V-type ATP synthase s 36.3 1.3E+02 0.0027 19.8 5.0 65 30-103 12-77 (100)
65 PF02310 B12-binding: B12 bind 35.9 1.2E+02 0.0027 19.6 5.9 57 26-89 17-74 (121)
66 cd04142 RRP22 RRP22 subfamily. 35.7 1.1E+02 0.0025 22.2 5.3 53 58-113 74-129 (198)
67 PLN02530 histidine-tRNA ligase 35.7 1.1E+02 0.0024 26.0 5.7 60 9-74 401-460 (487)
68 cd01868 Rab11_like Rab11-like. 35.1 1.4E+02 0.0031 20.2 6.5 54 57-113 68-121 (165)
69 COG1058 CinA Predicted nucleot 34.8 55 0.0012 25.7 3.5 42 25-70 22-66 (255)
70 PRK12435 ferrochelatase; Provi 34.6 2.4E+02 0.0052 22.5 8.8 52 24-79 61-119 (311)
71 PLN02449 ferrochelatase 34.4 3E+02 0.0066 23.7 8.3 79 24-106 164-252 (485)
72 COG0289 DapB Dihydrodipicolina 33.6 1.7E+02 0.0038 23.1 6.1 73 9-91 69-141 (266)
73 PF00350 Dynamin_N: Dynamin fa 33.3 1.5E+02 0.0032 20.3 5.3 46 56-104 120-165 (168)
74 PF01113 DapB_N: Dihydrodipico 33.2 98 0.0021 20.9 4.2 31 9-44 67-97 (124)
75 cd00138 PLDc Phospholipase D. 33.2 77 0.0017 22.1 3.9 23 52-74 20-42 (176)
76 cd01857 HSR1_MMR1 HSR1/MMR1. 33.1 1.5E+02 0.0033 20.0 5.3 17 58-74 5-21 (141)
77 PF08477 Miro: Miro-like prote 33.0 21 0.00045 23.1 0.8 21 59-79 68-88 (119)
78 TIGR00409 proS_fam_II prolyl-t 33.0 38 0.00083 29.4 2.6 48 9-57 473-522 (568)
79 COG0710 AroD 3-dehydroquinate 32.8 2E+02 0.0043 22.2 6.2 76 23-104 78-155 (231)
80 PRK12444 threonyl-tRNA synthet 32.6 1.4E+02 0.003 26.2 6.0 62 8-74 540-601 (639)
81 PRK10569 NAD(P)H-dependent FMN 31.6 2.1E+02 0.0045 21.0 6.4 82 24-109 18-111 (191)
82 COG3613 Nucleoside 2-deoxyribo 31.5 2.2E+02 0.0047 21.1 6.0 77 24-105 20-106 (172)
83 PF03481 SUA5: Putative GTP-bi 30.4 55 0.0012 22.3 2.6 55 9-65 67-123 (125)
84 KOG2792 Putative cytochrome C 29.7 49 0.0011 26.2 2.4 31 81-111 154-188 (280)
85 cd04175 Rap1 Rap1 subgroup. T 28.0 2E+02 0.0043 19.5 7.0 30 50-79 57-87 (164)
86 PF01976 DUF116: Protein of un 27.9 2.3E+02 0.0051 20.3 5.9 64 26-106 75-139 (158)
87 PLN03110 Rab GTPase; Provision 27.2 2.5E+02 0.0055 20.5 7.7 26 54-79 74-99 (216)
88 cd04140 ARHI_like ARHI subfami 27.2 2.1E+02 0.0045 19.5 6.3 21 59-79 67-87 (165)
89 PF13662 Toprim_4: Toprim doma 27.1 50 0.0011 20.4 1.8 25 37-63 47-71 (81)
90 KOG1014 17 beta-hydroxysteroid 26.9 1.2E+02 0.0027 24.5 4.3 60 9-72 73-132 (312)
91 PF02900 LigB: Catalytic LigB 26.8 1.6E+02 0.0034 22.6 4.9 78 23-103 96-179 (272)
92 PRK15057 UDP-glucose 6-dehydro 26.6 1.3E+02 0.0029 24.7 4.7 51 19-70 311-365 (388)
93 cd04106 Rab23_lke Rab23-like s 26.4 2.1E+02 0.0045 19.2 6.7 28 50-77 59-87 (162)
94 cd04114 Rab30 Rab30 subfamily. 26.4 2.1E+02 0.0046 19.3 7.8 30 50-79 64-94 (169)
95 COG1168 MalY Bifunctional PLP- 26.4 1.4E+02 0.003 25.0 4.6 46 56-101 148-195 (388)
96 cd04170 EF-G_bact Elongation f 26.3 2.9E+02 0.0063 20.9 6.5 74 50-132 72-146 (268)
97 KOG1954 Endocytosis/signaling 26.3 2E+02 0.0042 24.5 5.4 77 47-126 164-240 (532)
98 PRK08350 hypothetical protein; 26.1 66 0.0014 26.3 2.7 32 8-40 280-311 (341)
99 COG0576 GrpE Molecular chapero 25.6 1.7E+02 0.0037 21.8 4.7 47 26-78 124-177 (193)
100 PLN02924 thymidylate kinase 25.4 2.4E+02 0.0051 21.2 5.5 41 1-42 6-48 (220)
101 TIGR02298 HpaD_Fe 3,4-dihydrox 25.1 3.4E+02 0.0073 21.3 7.7 78 23-103 96-178 (282)
102 cd04128 Spg1 Spg1p. Spg1p (se 25.1 2.6E+02 0.0056 19.9 6.6 26 54-79 62-87 (182)
103 TIGR00408 proS_fam_I prolyl-tR 25.0 1.1E+02 0.0025 25.8 4.0 46 9-55 282-332 (472)
104 COG3845 ABC-type uncharacteriz 25.0 3.1E+02 0.0067 23.8 6.5 78 28-106 120-199 (501)
105 PF00071 Ras: Ras family; Int 25.0 2.2E+02 0.0048 19.1 7.6 55 53-107 60-114 (162)
106 cd04168 TetM_like Tet(M)-like 24.6 3.1E+02 0.0067 20.7 7.3 75 50-133 72-147 (237)
107 smart00175 RAB Rab subfamily o 24.5 2.2E+02 0.0048 19.0 6.7 39 50-91 57-96 (164)
108 PF01915 Glyco_hydro_3_C: Glyc 24.2 3E+02 0.0065 20.3 9.2 85 23-112 46-146 (227)
109 PLN02775 Probable dihydrodipic 24.1 3.7E+02 0.0081 21.4 6.8 72 9-91 79-151 (286)
110 PLN02908 threonyl-tRNA synthet 24.1 2E+02 0.0043 25.6 5.5 60 9-74 589-648 (686)
111 PF05636 HIGH_NTase1: HIGH Nuc 23.7 1E+02 0.0022 25.6 3.4 47 60-111 25-80 (388)
112 cd05008 SIS_GlmS_GlmD_1 SIS (S 23.7 1.3E+02 0.0028 19.7 3.4 26 13-42 52-77 (126)
113 TIGR03567 FMN_reduc_SsuE FMN r 22.3 2.5E+02 0.0055 19.8 5.0 55 24-80 17-80 (171)
114 cd07371 2A5CPDO_AB The alpha a 22.2 3.7E+02 0.0081 20.7 8.0 78 23-103 87-169 (268)
115 PLN03108 Rab family protein; P 22.0 3.2E+02 0.0069 19.8 7.7 21 59-79 73-93 (210)
116 cd06340 PBP1_ABC_ligand_bindin 21.8 3.9E+02 0.0084 20.8 6.4 61 11-74 146-207 (347)
117 TIGR00177 molyb_syn molybdenum 21.8 1.4E+02 0.0031 20.6 3.5 46 23-71 26-73 (144)
118 PRK13762 tRNA-modifying enzyme 21.7 2.8E+02 0.0062 22.2 5.6 38 10-48 131-168 (322)
119 cd01865 Rab3 Rab3 subfamily. 21.5 2.7E+02 0.0059 18.9 6.4 20 59-78 68-87 (165)
120 PF14528 LAGLIDADG_3: LAGLIDAD 21.3 1.6E+02 0.0035 17.7 3.3 31 11-44 21-51 (77)
121 PRK14495 putative molybdopteri 21.2 3.4E+02 0.0073 23.2 6.0 29 13-43 6-34 (452)
122 COG2342 Predicted extracellula 21.0 1.5E+02 0.0031 23.9 3.6 44 56-105 33-79 (300)
123 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 21.0 2.8E+02 0.006 18.8 7.5 30 50-79 59-89 (166)
124 TIGR03026 NDP-sugDHase nucleot 21.0 1.9E+02 0.0041 23.7 4.5 53 19-72 328-384 (411)
125 PRK05569 flavodoxin; Provision 20.9 2.7E+02 0.0059 18.7 7.8 47 23-79 16-62 (141)
126 cd06386 PBP1_NPR_C_like Ligand 20.9 3.4E+02 0.0074 21.7 6.0 39 26-66 157-195 (387)
127 PF02337 Gag_p10: Retroviral G 20.6 88 0.0019 20.6 2.0 19 23-42 8-26 (90)
128 cd05017 SIS_PGI_PMI_1 The memb 20.4 1.7E+02 0.0037 19.3 3.6 26 13-42 49-74 (119)
129 PF09152 DUF1937: Domain of un 20.3 2.2E+02 0.0048 19.6 4.0 64 29-93 32-108 (116)
130 PF04244 DPRP: Deoxyribodipyri 20.3 3.7E+02 0.008 20.4 5.7 68 10-81 63-133 (224)
131 KOG0095 GTPase Rab30, small G 20.3 3.6E+02 0.0079 19.8 7.1 63 50-114 64-129 (213)
132 TIGR00389 glyS_dimeric glycyl- 20.2 3.7E+02 0.008 23.5 6.2 63 8-76 456-519 (551)
133 cd04113 Rab4 Rab4 subfamily. 20.2 2.8E+02 0.0061 18.6 7.3 26 54-79 62-87 (161)
134 KOG0462 Elongation factor-type 20.1 2.7E+02 0.0059 24.7 5.3 55 50-108 133-188 (650)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=5.1e-37 Score=226.02 Aligned_cols=109 Identities=38% Similarity=0.699 Sum_probs=102.9
Q ss_pred CCCCCCCcccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHh
Q 044631 2 ASSSSSCNYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKW 81 (136)
Q Consensus 2 ~~~~~~~~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~w 81 (136)
+||+|+.+|||||||+++|+|++|+.||+.+|++ .||++|+|..++.+|+.+.+.|.+||++|+++|+||||+|++|.|
T Consensus 19 ~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~-~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~W 97 (187)
T PLN03194 19 SSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSR-LNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYF 97 (187)
T ss_pred cCCCCCCCCcEEEeCCCccccccHHHHHHHHHHH-CCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchh
Confidence 3555666999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCCCEEEEEEeccCccccccc
Q 044631 82 CLNELVKILECKNTNGQIIIPVFYGVSPSDVRHQ 115 (136)
Q Consensus 82 c~~El~~~~~~~~~~~~~iiPVf~~v~p~~v~~~ 115 (136)
|++||..|+++. ..||||||+|+|++|++|
T Consensus 98 CLdEL~~I~e~~----~~ViPIFY~VdPsdVr~q 127 (187)
T PLN03194 98 CLHELALIMESK----KRVIPIFCDVKPSQLRVV 127 (187)
T ss_pred HHHHHHHHHHcC----CEEEEEEecCCHHHhhcc
Confidence 999999999863 479999999999999997
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=1.4e-35 Score=266.82 Aligned_cols=129 Identities=50% Similarity=0.867 Sum_probs=121.9
Q ss_pred CCCCCCCC---cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCC
Q 044631 1 MASSSSSC---NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYA 77 (136)
Q Consensus 1 ~~~~~~~~---~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~ 77 (136)
||+|||+. +|||||||+++|+|+.|+.||+.+|.+ +||++|.|. ++..|+.+.+++.+||++|+++|+|||++|+
T Consensus 1 ~~~~~~~~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~-~~i~~f~d~-~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya 78 (1153)
T PLN03210 1 MASSSSSSRNWVYDVFPSFSGEDVRITFLSHFLKELDR-KLIIAFKDN-EIERSQSLDPELKQAIRDSRIAVVVFSKNYA 78 (1153)
T ss_pred CCCCCCCCCCCCCcEEeeCCCcccccCHHHHHHHHHHH-CCCeEEccC-CccCCCcccHHHHHHHHhCeEEEEEecCCcc
Confidence 67766644 999999999999999999999999999 999999987 5999999999999999999999999999999
Q ss_pred CCHhHHHHHHHHHHhhcCCCCEEEEEEeccCccccccccCcHHHHHHHHHHHcc
Q 044631 78 SSKWCLNELVKILECKNTNGQIIIPVFYGVSPSDVRHQNGTFGDRFDELKKQFE 131 (136)
Q Consensus 78 ~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~p~~v~~~~~~~~~~f~~~~~~~~ 131 (136)
+|.||++||++|++|.++.+++|+||||+|+|++||+|+|.||++|.+++++..
T Consensus 79 ~s~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~~ 132 (1153)
T PLN03210 79 SSSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNKT 132 (1153)
T ss_pred cchHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhcccc
Confidence 999999999999999988999999999999999999999999999999987644
No 3
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.92 E-value=4e-25 Score=155.11 Aligned_cols=122 Identities=39% Similarity=0.705 Sum_probs=103.7
Q ss_pred cccEEEeccc-CcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHH
Q 044631 9 NYEVFLNFRG-EDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELV 87 (136)
Q Consensus 9 ~yDVFISys~-~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~ 87 (136)
.|||||||++ ++..+.|+.+|...|.. .|+.+|.|...+ .|..+ .+|.++|++|+++|+|+||+|+.|+||..|+.
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~-~~~~v~~d~~~~-~~~~~-~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~ 77 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRG-YGLCVFIDDFEP-GGGDL-EEIDEAIEKSRIAIVVLSPNYAESEWCLDELV 77 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhc-CCcEEEecCccc-ccchH-HHHHHHHHHCcEEEEEECcccccChhHHHHHH
Confidence 5999999999 34457899999999999 999999997643 33333 39999999999999999999999999999999
Q ss_pred HHHHhhcC-CCCEEEEEEeccCccccccccCcHHHHHHHHHHHcccC
Q 044631 88 KILECKNT-NGQIIIPVFYGVSPSDVRHQNGTFGDRFDELKKQFEDK 133 (136)
Q Consensus 88 ~~~~~~~~-~~~~iiPVf~~v~p~~v~~~~~~~~~~f~~~~~~~~~~ 133 (136)
.+++.... ...+||||+++..|+++..+.+.++.++..+...+..+
T Consensus 78 ~a~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~ 124 (140)
T smart00255 78 AALENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPED 124 (140)
T ss_pred HHHHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCc
Confidence 99987643 67899999999889889999999999998885555544
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=99.92 E-value=9.8e-27 Score=164.98 Aligned_cols=119 Identities=38% Similarity=0.631 Sum_probs=104.1
Q ss_pred EEEeccc-CcCchhHHHHHHHHHHcCC--CCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHH
Q 044631 12 VFLNFRG-EDTRKSFTCYLYDKLYEGK--KIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVK 88 (136)
Q Consensus 12 VFISys~-~D~~~~fv~~L~~~L~~~~--gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~ 88 (136)
|||||++ +| ++.|+.+|..+|++ . |+++|++.+|+.+|..+.++|.++|++|+++|+|+|++|+.|+||+.|+..
T Consensus 1 vfisy~~~~d-~~~~~~~L~~~Le~-~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~ 78 (141)
T PF01582_consen 1 VFISYSGKDD-REWFVSHLLPELEE-RPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQE 78 (141)
T ss_dssp EEEEE-GHHG-HHHHHHCHHHHHHC-TSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHH
T ss_pred cEEEeCCCCc-HHHHHHHHHHHHHh-CCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhh
Confidence 8999999 55 57899999999999 7 999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCC--CCEEEEEEeccCccccc-cccCcHHHHHHHHHHHccc
Q 044631 89 ILECKNTN--GQIIIPVFYGVSPSDVR-HQNGTFGDRFDELKKQFED 132 (136)
Q Consensus 89 ~~~~~~~~--~~~iiPVf~~v~p~~v~-~~~~~~~~~f~~~~~~~~~ 132 (136)
|+++.... ...|+|||+++.+++++ .+++.|+..|....+..+.
T Consensus 79 a~~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~ 125 (141)
T PF01582_consen 79 ALERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDD 125 (141)
T ss_dssp HHHHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSS
T ss_pred hhhhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCC
Confidence 99987543 58999999999999999 6888888887765554443
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.83 E-value=3.9e-21 Score=128.77 Aligned_cols=87 Identities=31% Similarity=0.582 Sum_probs=75.7
Q ss_pred EEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHH
Q 044631 12 VFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILE 91 (136)
Q Consensus 12 VFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~ 91 (136)
|||||+++| ..+|..|...|+. .|+++|+|. ++.+|+.+.+.|..+|++|+++|+++|++|..|+||..|+..+.+
T Consensus 1 VFIS~~~~D--~~~a~~l~~~L~~-~g~~v~~d~-~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~ 76 (102)
T PF13676_consen 1 VFISYSSED--REFAERLAERLES-AGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK 76 (102)
T ss_dssp EEEEEEGGG--CCCHHHHHHHHHH-TT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC
T ss_pred eEEEecCCc--HHHHHHHHHHHhh-cCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH
Confidence 899999999 4799999999999 999999997 899999999999999999999999999999999999999999844
Q ss_pred hhcCCCCEEEEEEec
Q 044631 92 CKNTNGQIIIPVFYG 106 (136)
Q Consensus 92 ~~~~~~~~iiPVf~~ 106 (136)
.+.+||||.++
T Consensus 77 ----~~~~iipv~~~ 87 (102)
T PF13676_consen 77 ----RGKPIIPVRLD 87 (102)
T ss_dssp ----TSESEEEEECS
T ss_pred ----CCCEEEEEEEC
Confidence 34489999975
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.19 E-value=5.7e-11 Score=98.65 Aligned_cols=91 Identities=24% Similarity=0.445 Sum_probs=79.1
Q ss_pred CcccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCC--------C
Q 044631 8 CNYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYAS--------S 79 (136)
Q Consensus 8 ~~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~--------S 79 (136)
-+.||||||++.- ....++-|.-.|+. +|++||+|.+.+..|. +.+.+.+.|..++.+|+|++|+.+. -
T Consensus 611 kq~DVFISYRRst-GnQLASLiKV~LQL-~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~nCe 687 (832)
T KOG3678|consen 611 KQIDVFISYRRST-GNQLASLIKVLLQL-RGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDDNCE 687 (832)
T ss_pred CCcceEEEeeccc-cHHHHHHHHHHHHh-cCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhccccHH
Confidence 3899999998875 47899999999999 9999999999888775 6678899999999999999999763 4
Q ss_pred HhHHHHHHHHHHhhcCCCCEEEEEEe
Q 044631 80 KWCLNELVKILECKNTNGQIIIPVFY 105 (136)
Q Consensus 80 ~wc~~El~~~~~~~~~~~~~iiPVf~ 105 (136)
.|..+||..++++.+ .|||||-
T Consensus 688 DWVHKEl~~Afe~~K----NIiPI~D 709 (832)
T KOG3678|consen 688 DWVHKELKCAFEHQK----NIIPIFD 709 (832)
T ss_pred HHHHHHHHHHHHhcC----Ceeeeec
Confidence 788889888888765 7999984
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=98.88 E-value=5.3e-09 Score=73.25 Aligned_cols=91 Identities=23% Similarity=0.373 Sum_probs=49.2
Q ss_pred ccEEEecccCcCchhHHHHHHHHHHcCCC-------CeE-E---------eeCCcccCCCcchHHHHhchhcCcEEEEEe
Q 044631 10 YEVFLNFRGEDTRKSFTCYLYDKLYEGKK-------IKT-F---------IDDEELRRGDEISPALLNAIQGSKISVVIF 72 (136)
Q Consensus 10 yDVFISys~~D~~~~fv~~L~~~L~~~~g-------i~v-f---------~d~~~i~~G~~~~~~i~~aI~~S~~~I~vl 72 (136)
|.|||||++.|. ...+..|...+.. .+ +.. + -+..+....+.|...|.++|..|+++||++
T Consensus 1 ~~vFIS~~~~d~-~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLi 78 (130)
T PF08937_consen 1 YKVFISYSHDDD-DWYYDQLKEWLEN-SYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLI 78 (130)
T ss_dssp ----------TH-H-HHHHHHHHHHH--------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE-
T ss_pred CCccccccccCc-HHHHHHHHHHhcc-ccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEe
Confidence 579999999994 2367777777766 31 211 1 122222234478889999999999999999
Q ss_pred ecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEec
Q 044631 73 SKDYASSKWCLNELVKILECKNTNGQIIIPVFYG 106 (136)
Q Consensus 73 S~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~ 106 (136)
+++...|.|+..|+..+++. +..||.|.+.
T Consensus 79 g~~T~~s~wV~~EI~~A~~~----~~~Ii~V~~~ 108 (130)
T PF08937_consen 79 GPNTAKSKWVNWEIEYALKK----GKPIIGVYLP 108 (130)
T ss_dssp -TT----HHHHHHHHHHTTT-------EEEEETT
T ss_pred CCCcccCcHHHHHHHHHHHC----CCCEEEEECC
Confidence 99999999999999998773 5588888764
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=98.44 E-value=1.7e-06 Score=61.46 Aligned_cols=65 Identities=18% Similarity=0.313 Sum_probs=53.6
Q ss_pred cEEEecccCcCc-hhHHHHHHHHHHcCC-CCeEEeeCCcccC--CCcchHHHHhchhcCcEEEEEeecCC
Q 044631 11 EVFLNFRGEDTR-KSFTCYLYDKLYEGK-KIKTFIDDEELRR--GDEISPALLNAIQGSKISVVIFSKDY 76 (136)
Q Consensus 11 DVFISys~~D~~-~~fv~~L~~~L~~~~-gi~vf~d~~~i~~--G~~~~~~i~~aI~~S~~~I~vlS~~y 76 (136)
-|||||++.... ...|..|...|+. . |+.|.+|..+... +..+..=+.+.+++++.+|+|+||.+
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 KVFISYSHDSEEHKEWVLALAEFLRQ-NCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY 70 (150)
T ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHh-ccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence 599999985532 3678999999999 8 9999999888743 66676677788999999999999654
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=97.51 E-value=0.00046 Score=48.35 Aligned_cols=98 Identities=20% Similarity=0.218 Sum_probs=71.3
Q ss_pred cEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCC-------------
Q 044631 11 EVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYA------------- 77 (136)
Q Consensus 11 DVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~------------- 77 (136)
.|||.|+ .| ...+..+..-|+. .|+.+.+-......|..+.+.+.+.+.+++.+|++++|+=.
T Consensus 1 kVFIvhg-~~--~~~~~~v~~~L~~-~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~ 76 (125)
T PF10137_consen 1 KVFIVHG-RD--LAAAEAVERFLEK-LGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPR 76 (125)
T ss_pred CEEEEeC-CC--HHHHHHHHHHHHh-CCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCccccccc
Confidence 4899998 55 3788899999998 88887655555689999999999999999999999999522
Q ss_pred CCHhHHHHHHHHHHhhcCCCCEEEEEEe-cc-Ccccccc
Q 044631 78 SSKWCLNELVKILECKNTNGQIIIPVFY-GV-SPSDVRH 114 (136)
Q Consensus 78 ~S~wc~~El~~~~~~~~~~~~~iiPVf~-~v-~p~~v~~ 114 (136)
....+..|+..++... +..+++-+.- ++ .|+|+..
T Consensus 77 aR~NVifE~G~f~g~L--Gr~rv~~l~~~~v~~PSDl~G 113 (125)
T PF10137_consen 77 ARQNVIFELGLFIGKL--GRERVFILVKGGVELPSDLSG 113 (125)
T ss_pred cccceeehhhHHHhhc--CcceEEEEEcCCccCCcccCC
Confidence 2234677888887753 2334544443 22 3777654
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=94.92 E-value=0.12 Score=33.24 Aligned_cols=68 Identities=15% Similarity=0.084 Sum_probs=49.0
Q ss_pred cEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCH
Q 044631 11 EVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSK 80 (136)
Q Consensus 11 DVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~ 80 (136)
.||||-.-.|- +.--..|.+.+.+ .|..+..-+.=-..+....+.+.+.|++|+++|.++...|-..+
T Consensus 1 rVFiSSt~~Dl-~~eR~~l~~~i~~-~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~~ 68 (83)
T PF13271_consen 1 RVFISSTFRDL-KEERDALIEAIRR-LGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSVP 68 (83)
T ss_pred CEEEecChhhH-HHHHHHHHHHHHH-CCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCCC
Confidence 38999887885 3445678888888 78776543221123556667889999999999999999987543
No 11
>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=92.66 E-value=1.4 Score=29.49 Aligned_cols=69 Identities=13% Similarity=0.027 Sum_probs=49.8
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCc-c---cCCCcc----hHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhh
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEE-L---RRGDEI----SPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECK 93 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~-i---~~G~~~----~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~ 93 (136)
..+...+.+.|++ .|+.++...+. . ..+..+ ...-.++|++|+++|+++.+.- .+.-+..|+..|....
T Consensus 13 ~~~~~~~~~~L~~-~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~alg 89 (113)
T PF05014_consen 13 KARVERLREALEK-NGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYALG 89 (113)
T ss_dssp HHHHHHHHHHHHT-TTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHh-CCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHCC
Confidence 5788999999999 99999866521 1 112333 3444578999999999988765 6677888999987754
No 12
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=92.34 E-value=0.2 Score=39.43 Aligned_cols=95 Identities=15% Similarity=0.071 Sum_probs=63.6
Q ss_pred CCCcccEEEecccCcCchhHHHHHHHHHHcC-CCCeEEeeCC---cccCCCcchHHHHhch-hcCcEEEEEeecCCCCCH
Q 044631 6 SSCNYEVFLNFRGEDTRKSFTCYLYDKLYEG-KKIKTFIDDE---ELRRGDEISPALLNAI-QGSKISVVIFSKDYASSK 80 (136)
Q Consensus 6 ~~~~yDVFISys~~D~~~~fv~~L~~~L~~~-~gi~vf~d~~---~i~~G~~~~~~i~~aI-~~S~~~I~vlS~~y~~S~ 80 (136)
+...||+=|||.++- ...|++...+++.- .-+..|+|-. -+.+| ++.+-+...- ..|++.++.+..+|....
T Consensus 174 ~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~-sL~~~L~~~Y~~rC~~~~VF~~~~Y~~K~ 250 (329)
T COG4916 174 SEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPG-SLVSTLDPGYDIRCVVTTVFNTGSYICKS 250 (329)
T ss_pred cccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCc-cHHHhcccccCceEEEEEEEeCCceEEee
Confidence 355899999999985 47999999999851 3345677642 12233 3333332222 368889999999999999
Q ss_pred hHHHHHHHHHHhhcCCCCEEEEEEe
Q 044631 81 WCLNELVKILECKNTNGQIIIPVFY 105 (136)
Q Consensus 81 wc~~El~~~~~~~~~~~~~iiPVf~ 105 (136)
||.-|...+-... .-+...||.|
T Consensus 251 ~c~~E~~~~r~~~--~~d~~~rI~~ 273 (329)
T COG4916 251 TCHIEGLEGRLNP--ILDTGFRIKY 273 (329)
T ss_pred eeccchhhccccc--cccccceEEE
Confidence 9999987653321 2345667766
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=88.47 E-value=1.5 Score=33.31 Aligned_cols=97 Identities=19% Similarity=0.226 Sum_probs=66.0
Q ss_pred cEEEecccCcCchhHHHHHHHHHHcCCCC-eEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCC--------C---
Q 044631 11 EVFLNFRGEDTRKSFTCYLYDKLYEGKKI-KTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYA--------S--- 78 (136)
Q Consensus 11 DVFISys~~D~~~~fv~~L~~~L~~~~gi-~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~--------~--- 78 (136)
.|||-|++. ..+.....+|.++.-. .+|.|. -...|..+.+.+++-|.+++.+|++.+|+=. +
T Consensus 84 kvFvv~ghd----~iArael~allrd~~l~~vi~d~-~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~ 158 (233)
T COG4271 84 KVFVVSGHD----AIARAELEALLRDWKLEPVILDG-LFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAF 158 (233)
T ss_pred eEEEEeccH----HHHHHHHHHHhhccccceEEecC-cccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhcc
Confidence 799999653 3677777777753443 467665 3678899999999999999999999999843 1
Q ss_pred ---CHhHHHHHHHHHHhhcCCCCEEEEEEec---c-Ccccccc
Q 044631 79 ---SKWCLNELVKILECKNTNGQIIIPVFYG---V-SPSDVRH 114 (136)
Q Consensus 79 ---S~wc~~El~~~~~~~~~~~~~iiPVf~~---v-~p~~v~~ 114 (136)
..-+..||...+.+. ++.+++-+.-+ + .|+|+..
T Consensus 159 praRqNVifELGm~mgrL--gRkrv~Il~k~~envelPSDi~G 199 (233)
T COG4271 159 PRARQNVIFELGMFMGRL--GRKRVMILMKRDENVELPSDIAG 199 (233)
T ss_pred ccccccchhhHhhHHhhc--ccceEEEEecccccccCccccCc
Confidence 123567888887753 23344433321 2 3777764
No 14
>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=83.70 E-value=5.6 Score=24.81 Aligned_cols=57 Identities=12% Similarity=0.107 Sum_probs=37.3
Q ss_pred ccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchh-cCcEEEEEe
Q 044631 10 YEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQ-GSKISVVIF 72 (136)
Q Consensus 10 yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~-~S~~~I~vl 72 (136)
++|+|...+.+. ...+..+...|++ .|+++-+|... ..+...+..|-. +.+.+|+|-
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~-~g~~v~~d~~~----~~~~~~~~~a~~~g~~~~iiig 59 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSD-AGIRVEVDLRN----EKLGKKIREAQLQKIPYILVVG 59 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHH-CCCEEEEECCC----CCHHHHHHHHHHcCCCEEEEEC
Confidence 677777655543 4678899999999 99999988643 345555555543 344444443
No 15
>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=82.07 E-value=2.6 Score=26.90 Aligned_cols=47 Identities=17% Similarity=0.211 Sum_probs=31.8
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
..++.+|.+.|+. .||++.+|..+ ..+...+..|-..=--+++|+.+
T Consensus 15 ~~~a~~l~~~L~~-~gi~v~~d~~~----~~~~k~~~~a~~~g~p~~iiiG~ 61 (94)
T PF03129_consen 15 IEYAQELANKLRK-AGIRVELDDSD----KSLGKQIKYADKLGIPFIIIIGE 61 (94)
T ss_dssp HHHHHHHHHHHHH-TTSEEEEESSS----STHHHHHHHHHHTTESEEEEEEH
T ss_pred HHHHHHHHHHHHH-CCCEEEEECCC----CchhHHHHHHhhcCCeEEEEECc
Confidence 4688999999999 99999999754 44445555555433334444444
No 16
>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=81.91 E-value=6.8 Score=24.53 Aligned_cols=60 Identities=17% Similarity=0.227 Sum_probs=39.2
Q ss_pred ccEEEecccC---cCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecC
Q 044631 10 YEVFLNFRGE---DTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKD 75 (136)
Q Consensus 10 yDVFISys~~---D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~ 75 (136)
++|+|-..+. .. ...+..+...|+. .|+.+.+|.. +..+...+..+-..--.+++++.++
T Consensus 2 ~~v~ii~~~~~~~~~-~~~a~~~~~~Lr~-~g~~v~~~~~----~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVEA-REYAQKLLNALLA-NGIRVLYDDR----ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHHH-HHHHHHHHHHHHH-CCCEEEecCC----CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 5676665443 22 4678889999999 9999998764 3455566655554433456666653
No 17
>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=77.00 E-value=11 Score=25.51 Aligned_cols=61 Identities=13% Similarity=-0.016 Sum_probs=40.4
Q ss_pred cccEEEeccc--CcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCC
Q 044631 9 NYEVFLNFRG--EDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDY 76 (136)
Q Consensus 9 ~yDVFISys~--~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y 76 (136)
.+||+|-..+ .+. ...+..|...|++ .|++|-+|.. ..+...+..|-+.--..++++.++-
T Consensus 26 p~~v~Ii~~~~~~~~-~~~a~~la~~LR~-~gi~v~~d~~-----~sl~kqlk~A~k~g~~~~iiiG~~e 88 (121)
T cd00858 26 PIKVAVLPLVKRDEL-VEIAKEISEELRE-LGFSVKYDDS-----GSIGRRYARQDEIGTPFCVTVDFDT 88 (121)
T ss_pred CcEEEEEecCCcHHH-HHHHHHHHHHHHH-CCCEEEEeCC-----CCHHHHHHHhHhcCCCEEEEECcCc
Confidence 6888887766 332 4577889999999 9999998753 3455566555443333555555543
No 18
>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=75.98 E-value=16 Score=23.37 Aligned_cols=65 Identities=11% Similarity=0.110 Sum_probs=41.2
Q ss_pred EEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCccc-------CCCcchHHHHhchhcCcEEEEEeecCCC
Q 044631 12 VFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELR-------RGDEISPALLNAIQGSKISVVIFSKDYA 77 (136)
Q Consensus 12 VFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~-------~G~~~~~~i~~aI~~S~~~I~vlS~~y~ 77 (136)
+|.|..+.-.+-.++.+|...|.+ .|.++.+-+-+.. -+..+......++..|+..|+++.++..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~-~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~ 74 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALAR-RGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL 74 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHh-CCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH
Confidence 356665554444667899999998 8988775433221 1112334455778888888888877643
No 19
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=70.58 E-value=5.9 Score=31.36 Aligned_cols=96 Identities=20% Similarity=0.345 Sum_probs=69.1
Q ss_pred CCcccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhc---h--hcCcEEEEEeecCCCCCHh
Q 044631 7 SCNYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNA---I--QGSKISVVIFSKDYASSKW 81 (136)
Q Consensus 7 ~~~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~a---I--~~S~~~I~vlS~~y~~S~w 81 (136)
+-++.+=+||.+.|. .+++...+-|.. .|+.+|+|..+ ...-|...|..- | ...-.++...|.+|-...|
T Consensus 4 ~~~~~~a~~f~~~d~--~~~~~~~n~~~~-~~v~~~y~~~~--~a~~~~~~~~~~~~e~~q~~~~~~~~f~~~~~~r~~~ 78 (329)
T COG4916 4 NVQFEIALSFAGEDR--EYVDRVANLLRE-AGVTVFYDIFE--EANLWGKNLYDYLSEIYQDKALFTIMFISEHYSRKMW 78 (329)
T ss_pred chheeeeeeecCchH--HHHHHHHHHHHh-hccEEEEeehh--hhhhhhhHHHHHHHHHHhhhhHHHhhhhhccccCcCC
Confidence 346778899999984 789998998999 99999998543 222233333322 2 2455678889999999999
Q ss_pred HHHHHHHHHHhhc-CCCCEEEEEEecc
Q 044631 82 CLNELVKILECKN-TNGQIIIPVFYGV 107 (136)
Q Consensus 82 c~~El~~~~~~~~-~~~~~iiPVf~~v 107 (136)
...|+...+...+ +....++|-.++.
T Consensus 79 ~~~~~~~~~a~~~~~~~~~~~~~~~~~ 105 (329)
T COG4916 79 TNHERQAMQARAFQEHQEYILPARFDE 105 (329)
T ss_pred CcHHHHHHHHHHhhhccEEehhhhhcc
Confidence 9999988776554 4456788887763
No 20
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=67.25 E-value=25 Score=21.19 Aligned_cols=61 Identities=18% Similarity=0.238 Sum_probs=36.5
Q ss_pred HHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEE
Q 044631 27 CYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIII 101 (136)
Q Consensus 27 ~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~ii 101 (136)
..+++-|++ .|++|-.... ..+++...+.++++++|.+.-+. ..++..+.+..++++..+|
T Consensus 8 ~a~~~~L~~-~g~~v~~~~~-----------~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~v~~G~~lvl 68 (70)
T PF14258_consen 8 YALYQLLEE-QGVKVERWRK-----------PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEWVEAGNTLVL 68 (70)
T ss_pred HHHHHHHHH-CCCeeEEecc-----------cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHHHHcCCEEEE
Confidence 457778888 8988843322 12344558889999999966654 2344444444444444443
No 21
>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=63.20 E-value=7.1 Score=27.06 Aligned_cols=48 Identities=13% Similarity=0.090 Sum_probs=32.4
Q ss_pred cccEEEeccc--CcCchhHHHHHHHHHHcCCCCeEEeeCCcc---cCCCcchHH
Q 044631 9 NYEVFLNFRG--EDTRKSFTCYLYDKLYEGKKIKTFIDDEEL---RRGDEISPA 57 (136)
Q Consensus 9 ~yDVFISys~--~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i---~~G~~~~~~ 57 (136)
-|+|-|---. .+.-...+..|++.|+. .|+.|++|.++- .+|..+.+.
T Consensus 27 P~qV~Iipi~~~~~~~~~~a~~l~~~L~~-~gi~v~~D~r~~~~~~~G~k~~~~ 79 (128)
T cd02426 27 PYKVAIDCGKGDTAELRDLCQGLKNELRE-AGLSVWPGYLETQHSSLEQLLDKY 79 (128)
T ss_pred CeEEEEEeccCChHHHHHHHHHHHHHHHH-cCCEEEeccCcccccCHHHHHHhh
Confidence 5666544321 12224678899999999 999999998653 566666443
No 22
>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=61.54 E-value=45 Score=25.64 Aligned_cols=69 Identities=17% Similarity=0.066 Sum_probs=49.9
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeC-CcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhc
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDD-EELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKN 94 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~-~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~ 94 (136)
..++.+|.+.|.. .|+.+-.+. ..+..|.-.. +.-...+.++-||.+|-+...+.....+|..++...+
T Consensus 80 ~eLa~~i~~~l~~-~gi~~~~~~~~~lDHG~~vP--L~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l~ 149 (253)
T cd07363 80 PELAERVAELLKA-AGIPARLDPERGLDHGAWVP--LKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPLR 149 (253)
T ss_pred HHHHHHHHHHHHh-cCCCccccCCcCCcccHHHH--HHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhhh
Confidence 4799999999999 999876543 3344554332 2222344678899999998888888889999998654
No 23
>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=60.98 E-value=32 Score=21.50 Aligned_cols=48 Identities=15% Similarity=0.160 Sum_probs=30.3
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecC
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKD 75 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~ 75 (136)
...+..|...|+. .|+++.+|...- .+...+..|-..---.++++.++
T Consensus 17 ~~~a~~la~~Lr~-~g~~v~~d~~~~----~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 17 QELAEKLYAELQA-AGVDVLLDDRNE----RPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHH-CCCEEEEECCCC----CcccchhHHHhcCCCEEEEECCc
Confidence 4678899999999 999999986533 33344444433322344445443
No 24
>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=58.92 E-value=38 Score=22.51 Aligned_cols=61 Identities=28% Similarity=0.329 Sum_probs=38.1
Q ss_pred EEEecccCcCchhHHHHHHHHHHcCCCCeEEee--------CCcc-----cCCCc-chHHHHhchhc-CcEEEEEeecC
Q 044631 12 VFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFID--------DEEL-----RRGDE-ISPALLNAIQG-SKISVVIFSKD 75 (136)
Q Consensus 12 VFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d--------~~~i-----~~G~~-~~~~i~~aI~~-S~~~I~vlS~~ 75 (136)
||||-+..|. .-...+...|.. .|+.++-- +.++ ..+.. -.+++.+.|.+ -.+-++|..|+
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 VFLSVSDHVK--AMLVDLAPKLSS-DGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEcccH--HHHHHHHHHHHH-CCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 7888877763 334477777777 88877522 1111 11111 12568888888 88888888775
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=58.43 E-value=18 Score=26.70 Aligned_cols=45 Identities=9% Similarity=0.161 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEE
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVV 70 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~ 70 (136)
..-...|..+... +|+-+|.|.+ .+|+.|...|.+.+.++..+-+
T Consensus 35 ~~~i~~i~~~~~~-rgVIIfTDpD--~~GekIRk~i~~~vp~~khafi 79 (174)
T TIGR00334 35 DETINLIKKAQKK-QGVIILTDPD--FPGEKIRKKIEQHLPGYENCFI 79 (174)
T ss_pred HHHHHHHHHHhhc-CCEEEEeCCC--CchHHHHHHHHHHCCCCeEEee
Confidence 4567788888888 9999999987 4999999999999988876533
No 26
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=57.05 E-value=22 Score=24.90 Aligned_cols=55 Identities=16% Similarity=0.149 Sum_probs=41.8
Q ss_pred ccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcE
Q 044631 10 YEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKI 67 (136)
Q Consensus 10 yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~ 67 (136)
.++|+-..+.=....++..|..++.. +|+-++.|.+ .+|+.+...|.+.+..+..
T Consensus 30 ~~~i~~~g~~i~~~~~ie~i~~~~~~-k~VIILTD~D--~~Ge~Irk~l~~~l~~~~~ 84 (127)
T COG1658 30 AGVIITNGSAINSLETIELIKKAQKY-KGVIILTDPD--RKGERIRKKLKEYLPGAKG 84 (127)
T ss_pred CceEEEcCCccchHHHHHHHHHhhcc-CCEEEEeCCC--cchHHHHHHHHHHhccccc
Confidence 46666665532224678899999999 9999999976 4899999999888887554
No 27
>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=56.30 E-value=37 Score=29.10 Aligned_cols=61 Identities=13% Similarity=0.161 Sum_probs=42.1
Q ss_pred CcccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 8 CNYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 8 ~~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
+..||+|-.-+++. ...+..|.+.|++ .|++|-+|.. +..+...+..|-..---.++|+.+
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~-~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~ 529 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKK-AGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGD 529 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHH-cCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEch
Confidence 46788887766543 5788999999999 9999999864 445666666665433334455544
No 28
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=54.99 E-value=26 Score=29.34 Aligned_cols=65 Identities=17% Similarity=0.171 Sum_probs=40.7
Q ss_pred CcccEEEeccc--CcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCC
Q 044631 8 CNYEVFLNFRG--EDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYA 77 (136)
Q Consensus 8 ~~yDVFISys~--~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~ 77 (136)
+.++|.|---. .+.....+..|...|++ .|++|.+|.++-..|..+.+.- ..+.. .++|+.++-+
T Consensus 344 aP~qV~Iipi~~~~~~~~~~a~~i~~~L~~-~Gi~v~~D~~~~~lg~ki~~a~---~~giP-~~iiVG~~e~ 410 (439)
T PRK12325 344 APFKVGIINLKQGDEACDAACEKLYAALSA-AGIDVLYDDTDERPGAKFATMD---LIGLP-WQIIVGPKGL 410 (439)
T ss_pred CCeEEEEEecCCCCHHHHHHHHHHHHHHHH-CCCEEEEECCCCCHhHHHHHHH---HcCCC-EEEEECCccc
Confidence 35788776542 22234678999999999 9999999987655554444322 22333 4455555443
No 29
>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=54.69 E-value=53 Score=21.57 Aligned_cols=62 Identities=19% Similarity=0.303 Sum_probs=36.6
Q ss_pred cEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeC--------Cccc-----CCCcchHHHHhchhcCcEEEEEeecC
Q 044631 11 EVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDD--------EELR-----RGDEISPALLNAIQGSKISVVIFSKD 75 (136)
Q Consensus 11 DVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~--------~~i~-----~G~~~~~~i~~aI~~S~~~I~vlS~~ 75 (136)
.|++|.+..|. .-...+.+.|.+ .|++++--. ..+. ....-.+++.+.|++-.+-++|-.|+
T Consensus 2 ~vl~s~~~~~k--~~~~~~~~~l~~-~G~~l~aT~gT~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn~~~ 76 (110)
T cd01424 2 TVFISVADRDK--PEAVEIAKRLAE-LGFKLVATEGTAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVINTPS 76 (110)
T ss_pred eEEEEEEcCcH--hHHHHHHHHHHH-CCCEEEEchHHHHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEECCC
Confidence 38899988773 345577788888 888886321 1110 00011245667777777766666554
No 30
>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=53.73 E-value=24 Score=26.24 Aligned_cols=49 Identities=16% Similarity=0.120 Sum_probs=34.9
Q ss_pred CcccEEEecccCcC-----chhHHHHHHHHHHcCCCCeEEeeCCcc-cCCCcchHH
Q 044631 8 CNYEVFLNFRGEDT-----RKSFTCYLYDKLYEGKKIKTFIDDEEL-RRGDEISPA 57 (136)
Q Consensus 8 ~~yDVFISys~~D~-----~~~fv~~L~~~L~~~~gi~vf~d~~~i-~~G~~~~~~ 57 (136)
+.++|+|---..+. ....+..|...|+. .||++.+|.++- .+|..+...
T Consensus 9 AP~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~-~Girv~~D~r~~~s~g~K~~~a 63 (202)
T cd00862 9 APIQVVIVPIGIKDEKREEVLEAADELAERLKA-AGIRVHVDDRDNYTPGWKFNDW 63 (202)
T ss_pred cCceEEEEEecCCccchHHHHHHHHHHHHHHHH-CCCEEEEECCCCCCHhHHHHHH
Confidence 35778776543220 23678999999999 999999998655 777766543
No 31
>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=53.07 E-value=1.1e+02 Score=23.85 Aligned_cols=79 Identities=14% Similarity=0.122 Sum_probs=52.9
Q ss_pred hhHHHHHHHHHHcCCCCeEE-eeCC--cccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHh-hcCCCC
Q 044631 23 KSFTCYLYDKLYEGKKIKTF-IDDE--ELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILEC-KNTNGQ 98 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf-~d~~--~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~-~~~~~~ 98 (136)
..++..|.+.+.+ .|+.+- .+.. .+..|.-..-... .-...++=|+.+|.+...+.....+|..++.. .++.+.
T Consensus 90 ~eLA~~i~~~~~~-~gi~~~~~~~~~~~lDHG~~vPL~~l-~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~~ 167 (271)
T cd07373 90 TALAEACVTACPE-HGVHARGVDYDGFPIDTGTITACTLM-GIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQNK 167 (271)
T ss_pred HHHHHHHHHHHHH-CCCcEEEecCCCCCCcchhHHHHHHH-cccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 4789999999999 999986 6663 3555543321111 01245666777888887788888899999885 344445
Q ss_pred EEEEE
Q 044631 99 IIIPV 103 (136)
Q Consensus 99 ~iiPV 103 (136)
+|.-|
T Consensus 168 rV~iI 172 (271)
T cd07373 168 RVAVV 172 (271)
T ss_pred eEEEE
Confidence 65533
No 32
>cd08584 PI-PLCc_GDPD_SF_unchar2 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=52.97 E-value=29 Score=26.05 Aligned_cols=59 Identities=12% Similarity=0.076 Sum_probs=38.9
Q ss_pred cEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCC
Q 044631 11 EVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYAS 78 (136)
Q Consensus 11 DVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~ 78 (136)
.+|++.|..+.. +++-.|+....- ||+|.- .+..+..++...+.+..+-|+++||.--.
T Consensus 103 ~i~tr~Se~E~~-~~~~~~~~~~~~-----VW~D~f---~~~~~~~~~~~~~~~~~~~~c~VSpELh~ 161 (192)
T cd08584 103 RTATRVSEYEPI-PTALSLYEKADW-----VWIDSF---TSLWLDNDLILKLLKAGKKICLVSPELHG 161 (192)
T ss_pred eeEEeecccccc-hHHHHhhccccE-----EEEecc---cccCCCHHHHHHHHHCCcEEEEECHHHcC
Confidence 477777655532 333333333222 899964 45677778888888889999999998554
No 33
>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=51.68 E-value=63 Score=20.83 Aligned_cols=59 Identities=14% Similarity=0.090 Sum_probs=38.3
Q ss_pred hHHHHHHHHHHcCCCCeEEeeCCcccCCC-cchHHHHhchhcCcEEEEEeecCCCCCHhHHHH
Q 044631 24 SFTCYLYDKLYEGKKIKTFIDDEELRRGD-EISPALLNAIQGSKISVVIFSKDYASSKWCLNE 85 (136)
Q Consensus 24 ~fv~~L~~~L~~~~gi~vf~d~~~i~~G~-~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~E 85 (136)
.....+.+.+++ .|...-+. .-..|. .-...|...|.+++++|++..--.-...|...+
T Consensus 10 ~~~~~~~~~~~~-~G~~~~~h--g~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~ 69 (97)
T PF10087_consen 10 DRERRYKRILEK-YGGKLIHH--GRDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKK 69 (97)
T ss_pred ccHHHHHHHHHH-cCCEEEEE--ecCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHH
Confidence 346788888999 99986555 111222 222358889999999888776555555554444
No 34
>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=50.74 E-value=54 Score=19.73 Aligned_cols=59 Identities=22% Similarity=0.187 Sum_probs=34.9
Q ss_pred ccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 10 YEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 10 yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
.||+|...+.+. ..-+-.+...|++ .|++|.++... ..+...+..+-...-..++++.+
T Consensus 2 ~~v~i~~~~~~~-~~~a~~i~~~Lr~-~g~~v~~~~~~----~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 2 VDVYVVPLGEGA-LSEALELAEQLRD-AGIKAEIDYGG----RKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred CcEEEEEcChHH-HHHHHHHHHHHHH-CCCEEEEecCC----CCHHHHHHHHHHcCCCEEEEEcH
Confidence 367776655432 3457789999999 99999887532 23444454444333234444444
No 35
>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=50.42 E-value=52 Score=21.22 Aligned_cols=68 Identities=15% Similarity=0.185 Sum_probs=44.6
Q ss_pred HHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEE
Q 044631 28 YLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPV 103 (136)
Q Consensus 28 ~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPV 103 (136)
.+..-|+. .|+..+... ...+...+.+.+.++.-++.|++++.++... -.+++...... .....|++|
T Consensus 8 ~~v~gFrL-aGv~~~~~~---~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~--~~~~l~~~~~~--~~~P~iv~I 75 (95)
T PF01990_consen 8 DTVLGFRL-AGVEGVYVN---TDPEEAEEALKELLKDEDVGIIIITEDLAEK--IRDELDEYREE--SSLPLIVEI 75 (95)
T ss_dssp HHHHHHHH-TTSEEEEES---HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT--HHHHHHHHHHT--SSSSEEEEE
T ss_pred HHHHHHHH-cCCCCccCC---CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH--HHHHHHHHHhc--cCCceEEEc
Confidence 35566777 999998875 1235566677777778999999999998884 33444443322 233455554
No 36
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=50.17 E-value=1.4e+02 Score=24.27 Aligned_cols=79 Identities=22% Similarity=0.304 Sum_probs=52.2
Q ss_pred HHHHHHHHHHcC---CCCeEEeeCCcccCCCcchHHHHhchhcC---cEEEEEeecCCCCCH--hHHHHHHHHHHhhcC-
Q 044631 25 FTCYLYDKLYEG---KKIKTFIDDEELRRGDEISPALLNAIQGS---KISVVIFSKDYASSK--WCLNELVKILECKNT- 95 (136)
Q Consensus 25 fv~~L~~~L~~~---~gi~vf~d~~~i~~G~~~~~~i~~aI~~S---~~~I~vlS~~y~~S~--wc~~El~~~~~~~~~- 95 (136)
+...+.++|+.. ..+.|++. +..|.+...+....+.+. +++++.+.|.|..|. -..+++..++...+.
T Consensus 74 ~T~~q~~~L~~~L~~~~~~V~~a---mry~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~~~~~ 150 (320)
T COG0276 74 ITRAQAAALEERLDLPDFKVYLA---MRYGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKELRGQ 150 (320)
T ss_pred HHHHHHHHHHHHhCCCCccEEEe---ecCCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHhcCCC
Confidence 344556666652 25778776 557887777777777643 458888899988654 356778787765432
Q ss_pred CCCEEEEEEec
Q 044631 96 NGQIIIPVFYG 106 (136)
Q Consensus 96 ~~~~iiPVf~~ 106 (136)
-....||-||+
T Consensus 151 ~~i~~I~~~~~ 161 (320)
T COG0276 151 PKISTIPDYYD 161 (320)
T ss_pred CceEEecCccC
Confidence 24577777776
No 37
>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=49.61 E-value=89 Score=21.93 Aligned_cols=62 Identities=15% Similarity=0.088 Sum_probs=35.1
Q ss_pred CCC-cchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEeccCccccc
Q 044631 50 RGD-EISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGVSPSDVR 113 (136)
Q Consensus 50 ~G~-~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~p~~v~ 113 (136)
+|. .+..-....+..++.+|++++.+-..|.-...++...+...... .-+|+++=....|+.
T Consensus 58 ~G~~~~~~l~~~~~~~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~~--~~~piilvgNK~Dl~ 120 (172)
T cd04141 58 AGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKKLITRVRLT--EDIPLVLVGNKVDLE 120 (172)
T ss_pred CCchhhHHHhHHHhhcCCEEEEEEECCchhHHHHHHHHHHHHHHhcCC--CCCCEEEEEEChhhh
Confidence 443 33333345678899999999988777655555554444433211 124666544455543
No 38
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=49.09 E-value=58 Score=27.13 Aligned_cols=57 Identities=18% Similarity=0.191 Sum_probs=39.2
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchh-cCcEEEEE
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQ-GSKISVVI 71 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~-~S~~~I~v 71 (136)
.++|+|-.-+++. ...+..|.+.|++ .|+++.+|.. +..+...+..|-+ +.+.+|+|
T Consensus 274 P~qV~IIpl~eel-~e~AlkLA~eLR~-aGIrVeiDl~----srSLgKQiK~AdK~GaPfvIII 331 (387)
T PRK14938 274 PIQVRILPVKKDF-LDFSIQVAERLRK-EGIRVNVDDL----DDSLGNKIRRAGTEWIPFVIII 331 (387)
T ss_pred cceEEEEEeChHH-HHHHHHHHHHHHH-CCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEE
Confidence 5788776665553 4678899999999 9999999864 3456666666554 34444444
No 39
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=48.98 E-value=28 Score=30.58 Aligned_cols=44 Identities=23% Similarity=0.208 Sum_probs=32.7
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcc
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEI 54 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~ 54 (136)
.++|+|.--+++ ....+..|.+.|+. .|++|.+|.++-..|..+
T Consensus 499 P~qV~IIpi~e~-~~~~A~eIa~~Lr~-~GirV~lDdr~~slgkKi 542 (613)
T PRK03991 499 PTQVRVIPVSER-HLDYAEEVADKLEA-AGIRVDVDDRDESLGKKI 542 (613)
T ss_pred CceEEEEEeCHH-HHHHHHHHHHHHHh-CCCEEEEECCCCCHHHHH
Confidence 578877665544 35789999999999 999999997654444433
No 40
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=48.97 E-value=31 Score=29.18 Aligned_cols=47 Identities=15% Similarity=0.140 Sum_probs=33.1
Q ss_pred cccEEEeccc-----CcCchhHHHHHHHHHHcCCCCeEEeeC-CcccCCCcchH
Q 044631 9 NYEVFLNFRG-----EDTRKSFTCYLYDKLYEGKKIKTFIDD-EELRRGDEISP 56 (136)
Q Consensus 9 ~yDVFISys~-----~D~~~~fv~~L~~~L~~~~gi~vf~d~-~~i~~G~~~~~ 56 (136)
.++|+|---. .+.....+..|.+.|+. .|++|-+|. .+-.+|..+..
T Consensus 287 P~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~-~GirV~lD~r~~~s~gkK~~~ 339 (477)
T PRK08661 287 PIQVVIVPIFKKEEKKEEVLEYAKELAEELKK-AGIRVKLDDRSDKTPGWKFNE 339 (477)
T ss_pred CCeEEEEEecCCCcCCHHHHHHHHHHHHHHHH-CCCEEEEECCCCCCHHHHHHH
Confidence 5788776541 12224678999999999 999999998 55566655543
No 41
>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=48.83 E-value=85 Score=21.46 Aligned_cols=80 Identities=15% Similarity=0.173 Sum_probs=48.9
Q ss_pred hhHHHHHHHHHHcCCCCeE-EeeCCcc-cC-----------CCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHH
Q 044631 23 KSFTCYLYDKLYEGKKIKT-FIDDEEL-RR-----------GDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKI 89 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~v-f~d~~~i-~~-----------G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~ 89 (136)
...+..+.+.|++ .|+.+ .++-.+. .| -.+..+++.+.+.+++ .|++.||.|..+.-- .+..+
T Consensus 17 ~~l~~~~~~~l~~-~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD-~iI~~sP~y~~~~s~--~lK~~ 92 (152)
T PF03358_consen 17 RKLAEAVAEQLEE-AGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEAD-GIIFASPVYNGSVSG--QLKNF 92 (152)
T ss_dssp HHHHHHHHHHHHH-TTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSS-EEEEEEEEBTTBE-H--HHHHH
T ss_pred HHHHHHHHHHHHH-cCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCC-eEEEeecEEcCcCCh--hhhHH
Confidence 4677888899988 88775 3454443 11 1223357778888999 678889999876332 23333
Q ss_pred HHhh------cCCCCEEEEEEec
Q 044631 90 LECK------NTNGQIIIPVFYG 106 (136)
Q Consensus 90 ~~~~------~~~~~~iiPVf~~ 106 (136)
+++. .-.+..+.+|-..
T Consensus 93 lD~~~~~~~~~~~~K~~~~i~~~ 115 (152)
T PF03358_consen 93 LDRLSCWFRRALRGKPVAIIAVG 115 (152)
T ss_dssp HHTHHHTHTTTTTTSEEEEEEEE
T ss_pred HHHhccccccccCCCEEEEEEEe
Confidence 3332 2245677776554
No 42
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=48.18 E-value=22 Score=30.72 Aligned_cols=66 Identities=18% Similarity=0.262 Sum_probs=43.0
Q ss_pred CCcccEEEeccc-C-cCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCC
Q 044631 7 SCNYEVFLNFRG-E-DTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYA 77 (136)
Q Consensus 7 ~~~yDVFISys~-~-D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~ 77 (136)
-+.++|+|---. + +.....+..|+..|+. .|+++.+|.++-.+|..+.+.- +.... .++++.++..
T Consensus 466 iaP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~-~gi~v~~Ddr~~~~g~k~~~ad---~~GiP-~~iiiG~~e~ 533 (565)
T PRK09194 466 IAPFDVHIVPVNMKDEEVKELAEKLYAELQA-AGIEVLLDDRKERPGVKFADAD---LIGIP-HRIVVGDRGL 533 (565)
T ss_pred cCCceEEEEECCCCcHHHHHHHHHHHHHHhc-cCCeEEEECCCCCHHHHHHHHH---hcCCC-EEEEEcCccc
Confidence 347899887654 2 2224678899999999 9999999987656666554332 22334 3444555533
No 43
>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=47.23 E-value=33 Score=22.85 Aligned_cols=29 Identities=10% Similarity=0.047 Sum_probs=22.4
Q ss_pred EEEecccCcCchhHHHHHHHHHHcCCCCeEEe
Q 044631 12 VFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFI 43 (136)
Q Consensus 12 VFISys~~D~~~~fv~~L~~~L~~~~gi~vf~ 43 (136)
||+|.+..|. .-...+.+.|.. .|++++-
T Consensus 3 vlisv~~~dk--~~~~~~a~~l~~-~G~~i~a 31 (116)
T cd01423 3 ILISIGSYSK--PELLPTAQKLSK-LGYKLYA 31 (116)
T ss_pred EEEecCcccc--hhHHHHHHHHHH-CCCEEEE
Confidence 7999988873 445588888888 8988863
No 44
>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=46.43 E-value=18 Score=23.85 Aligned_cols=57 Identities=25% Similarity=0.321 Sum_probs=33.8
Q ss_pred cCcCchhHHHHHHHHHHcCCCCeEEeeCCccc----------CCCcchHHHHhchhcCcEEEEEeecC
Q 044631 18 GEDTRKSFTCYLYDKLYEGKKIKTFIDDEELR----------RGDEISPALLNAIQGSKISVVIFSKD 75 (136)
Q Consensus 18 ~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~----------~G~~~~~~i~~aI~~S~~~I~vlS~~ 75 (136)
..|.|++=+..|.+.|.+ .|+.|.+.+--+. .|-...+.+.++++.++++|+...-.
T Consensus 11 ~~D~R~Sp~~~l~~~L~~-~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~h~ 77 (106)
T PF03720_consen 11 TDDIRESPALELIEELKE-RGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATDHD 77 (106)
T ss_dssp SS--TT-HHHHHHHHHHH-TT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS--G
T ss_pred CcccccCHHHHHHHHHHH-CCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEecCH
Confidence 356788889999999999 9999876542221 12223345678888888766654433
No 45
>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=45.59 E-value=83 Score=20.68 Aligned_cols=30 Identities=10% Similarity=0.248 Sum_probs=21.2
Q ss_pred CC-CcchHHHHhchhcCcEEEEEeecCCCCC
Q 044631 50 RG-DEISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 50 ~G-~~~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
|| ..+.......+++++.+|++++.+-..+
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~~~ 87 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNRES 87 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCHHH
Confidence 44 3444556677889999999999876443
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=45.58 E-value=34 Score=21.09 Aligned_cols=26 Identities=15% Similarity=0.243 Sum_probs=12.8
Q ss_pred CCCeEEeeCCcccCCCcchHHHHhchhc
Q 044631 37 KKIKTFIDDEELRRGDEISPALLNAIQG 64 (136)
Q Consensus 37 ~gi~vf~d~~~i~~G~~~~~~i~~aI~~ 64 (136)
+.+.+|+|.+ .+|......+.+.+..
T Consensus 44 ~~vii~~D~D--~aG~~a~~~~~~~l~~ 69 (79)
T cd03364 44 KEVILAFDGD--EAGQKAALRALELLLK 69 (79)
T ss_pred CeEEEEECCC--HHHHHHHHHHHHHHHH
Confidence 3555566654 3555444444444443
No 47
>COG0400 Predicted esterase [General function prediction only]
Probab=45.15 E-value=51 Score=24.82 Aligned_cols=52 Identities=21% Similarity=0.215 Sum_probs=39.1
Q ss_pred CcccEEEecccCcC--chhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhch
Q 044631 8 CNYEVFLNFRGEDT--RKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAI 62 (136)
Q Consensus 8 ~~yDVFISys~~D~--~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI 62 (136)
...-|||+|-..|. -.....+|.+.|+. .|..|+.... ..|-.+.++-.+++
T Consensus 145 ~~~pill~hG~~Dpvvp~~~~~~l~~~l~~-~g~~v~~~~~--~~GH~i~~e~~~~~ 198 (207)
T COG0400 145 AGTPILLSHGTEDPVVPLALAEALAEYLTA-SGADVEVRWH--EGGHEIPPEELEAA 198 (207)
T ss_pred CCCeEEEeccCcCCccCHHHHHHHHHHHHH-cCCCEEEEEe--cCCCcCCHHHHHHH
Confidence 37889999988885 24667899999999 9999988754 36666665544444
No 48
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=43.67 E-value=72 Score=26.53 Aligned_cols=58 Identities=26% Similarity=0.496 Sum_probs=37.7
Q ss_pred CcccCCCcchHHHHhchhcCcEEEEEeecCCC----CCHhHHH-HHHHHH-HhhcCCCCEEEEEEec
Q 044631 46 EELRRGDEISPALLNAIQGSKISVVIFSKDYA----SSKWCLN-ELVKIL-ECKNTNGQIIIPVFYG 106 (136)
Q Consensus 46 ~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~----~S~wc~~-El~~~~-~~~~~~~~~iiPVf~~ 106 (136)
.++.|...+.. ..|..+|--++|--..|. .|..|.+ |+.+++ +|-..++.++||||--
T Consensus 179 YnmTpDrHLGa---A~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvFAL 242 (501)
T KOG1136|consen 179 YNMTPDRHLGA---AWIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVFAL 242 (501)
T ss_pred ccCCcccccch---hhhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEeeec
Confidence 34444444432 345667777777666676 4778876 665554 4666789999999953
No 49
>PLN03194 putative disease resistance protein; Provisional
Probab=42.08 E-value=83 Score=23.56 Aligned_cols=64 Identities=13% Similarity=0.241 Sum_probs=44.7
Q ss_pred CCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEE
Q 044631 37 KKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVF 104 (136)
Q Consensus 37 ~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf 104 (136)
..+.||+.-+.-.....|..-+.+++++..+.+++-......+.--..+|..+++. ....|.||
T Consensus 25 ~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIee----Sri~IvVf 88 (187)
T PLN03194 25 KPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRN----CKVGVAVF 88 (187)
T ss_pred CCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHh----CeEEEEEE
Confidence 78899998764433446788899999998877777555555555555567666654 34778887
No 50
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=41.75 E-value=98 Score=20.15 Aligned_cols=63 Identities=11% Similarity=0.008 Sum_probs=42.6
Q ss_pred HHHHHHHHcCCCCeEEeeCC-cccCCCcchHHH---HhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHh
Q 044631 27 CYLYDKLYEGKKIKTFIDDE-ELRRGDEISPAL---LNAIQGSKISVVIFSKDYASSKWCLNELVKILEC 92 (136)
Q Consensus 27 ~~L~~~L~~~~gi~vf~d~~-~i~~G~~~~~~i---~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~ 92 (136)
......|+. .|..|.--.. ....|.++..-+ ...|..|+.+++ =|+.-.|.=|.-|...|...
T Consensus 19 ~~~a~~L~~-~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i~~--l~gWe~S~GA~~E~~~A~~l 85 (92)
T PF14359_consen 19 NAAAKRLRA-KGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAIYM--LPGWENSRGARLEHELAKKL 85 (92)
T ss_pred HHHHHHHHH-CCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEEEE--cCCcccCcchHHHHHHHHHC
Confidence 457888888 9977652222 135666555433 355667885444 49999999999999888654
No 51
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=41.05 E-value=1.1e+02 Score=20.76 Aligned_cols=82 Identities=17% Similarity=0.278 Sum_probs=40.6
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcC---cEEEEEeecCCCCCHhHHHH
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGS---KISVVIFSKDYASSKWCLNE 85 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S---~~~I~vlS~~y~~S~wc~~E 85 (136)
.+|++|+|+....+ .....+ ... .++.++. +.|.++...+.++++.. .-.++++..+.-. -+...
T Consensus 10 ~~~~~l~~~~~~~~-~~~~~~---~~~-~~~~~~~-----Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~--l~~~~ 77 (122)
T PF09837_consen 10 GADVVLAYTPDGDH-AAFRQL---WLP-SGFSFFP-----QQGGDLGERMANAFQQAARGYEPVVLIGSDCPD--LTPDD 77 (122)
T ss_dssp SSEEEEEE----TT-HHHHHH---HH--TTSEEEE-------SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT----HHH
T ss_pred CcCEEEEEcCCccH-HHHhcc---ccC-CCCEEee-----cCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCC--CCHHH
Confidence 79999999887743 333333 333 5666653 35677776666666654 2255555555443 24455
Q ss_pred HHHHHHhhcCCCCEEEE
Q 044631 86 LVKILECKNTNGQIIIP 102 (136)
Q Consensus 86 l~~~~~~~~~~~~~iiP 102 (136)
|..+.+..+....++-|
T Consensus 78 l~~A~~~L~~~d~VlgP 94 (122)
T PF09837_consen 78 LEQAFEALQRHDVVLGP 94 (122)
T ss_dssp HHHHHHHTTT-SEEEEE
T ss_pred HHHHHHHhccCCEEEee
Confidence 66666655444555555
No 52
>KOG1673 consensus Ras GTPases [General function prediction only]
Probab=40.94 E-value=1.2e+02 Score=22.44 Aligned_cols=66 Identities=17% Similarity=0.153 Sum_probs=33.8
Q ss_pred eEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEeccC
Q 044631 40 KTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGVS 108 (136)
Q Consensus 40 ~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~ 108 (136)
.+-+..+++...+...+.|--|-..|-..++.|.- .++-.+.-+..-.++.+.-++..|||+.+-.
T Consensus 68 ~IsfSIwdlgG~~~~~n~lPiac~dsvaIlFmFDL---t~r~TLnSi~~WY~QAr~~NktAiPilvGTK 133 (205)
T KOG1673|consen 68 DISFSIWDLGGQREFINMLPIACKDSVAILFMFDL---TRRSTLNSIKEWYRQARGLNKTAIPILVGTK 133 (205)
T ss_pred EEEEEEEecCCcHhhhccCceeecCcEEEEEEEec---CchHHHHHHHHHHHHHhccCCccceEEeccc
Confidence 33344445544444444444444556555555532 2222333333333445556789999998644
No 53
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=40.57 E-value=77 Score=26.36 Aligned_cols=60 Identities=13% Similarity=0.173 Sum_probs=40.2
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
..||+|.+-+.+. ...+-.+.+.|++ .|+++-+|.. +..+...+..|-+.--..++|+.+
T Consensus 325 ~~~v~v~~~~~~~-~~~a~~ia~~LR~-~Gi~veid~~----~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 325 SIDVYIATQGLKA-QKKGWEIIQFLEK-QNIKFELDLS----SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCEEEEEcCHHH-HHHHHHHHHHHHh-CCCeEEEeeC----CCCHHHHHHHHHHcCCCEEEEEec
Confidence 4689998755443 4567889999999 9999988643 344556666665543335555554
No 54
>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=39.91 E-value=59 Score=23.78 Aligned_cols=68 Identities=34% Similarity=0.348 Sum_probs=41.7
Q ss_pred HHHcCCCCeEE-eeCCc-c-cCC-CcchHHHHhchhcCcE-----EEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEE
Q 044631 32 KLYEGKKIKTF-IDDEE-L-RRG-DEISPALLNAIQGSKI-----SVVIFSKDYASSKWCLNELVKILECKNTNGQIIIP 102 (136)
Q Consensus 32 ~L~~~~gi~vf-~d~~~-i-~~G-~~~~~~i~~aI~~S~~-----~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiP 102 (136)
.|.+ .||+.. +|.++ + .|. ..+.+++.+.+++++. -|+|+|.+.-++.--..+-+..++..- + ||
T Consensus 35 ~Lk~-~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~~l--g---Ip 108 (168)
T PF09419_consen 35 HLKK-KGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEKAL--G---IP 108 (168)
T ss_pred hhhh-cCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHHhh--C---Cc
Confidence 3777 999954 66543 3 233 4667788888887763 389999987666533233334343321 2 78
Q ss_pred EEe
Q 044631 103 VFY 105 (136)
Q Consensus 103 Vf~ 105 (136)
|+.
T Consensus 109 vl~ 111 (168)
T PF09419_consen 109 VLR 111 (168)
T ss_pred EEE
Confidence 764
No 55
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=39.13 E-value=98 Score=26.63 Aligned_cols=61 Identities=11% Similarity=0.163 Sum_probs=40.5
Q ss_pred CcccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 8 CNYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 8 ~~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
+.+||+|---+++. ...+..|.+.|++ .||+|-+|.++ ..+...+..|-..---.++|+.+
T Consensus 475 ~p~~v~Ii~~~~~~-~~~a~~i~~~Lr~-~gi~v~~d~~~----~~l~kk~~~A~~~g~p~~iivG~ 535 (575)
T PRK12305 475 APVQVVIIPVADAH-NEYAEEVAKKLRA-AGIRVEVDTSN----ERLNKKIRNAQKQKIPYMLVVGD 535 (575)
T ss_pred CCccEEEEEeChHH-HHHHHHHHHHHHH-CCCEEEEECCC----CCHHHHHHHHHhcCCCEEEEEec
Confidence 35789887655432 4678999999999 99999998753 34555666655432234444444
No 56
>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=38.88 E-value=2e+02 Score=22.97 Aligned_cols=93 Identities=20% Similarity=0.306 Sum_probs=53.3
Q ss_pred hHHHHHHHHHHcCCC--CeEEeeCCcccCCCcchHHHHhchh---cCcEEEEEeecCCCCC--HhHHHHHHHHHHhh-cC
Q 044631 24 SFTCYLYDKLYEGKK--IKTFIDDEELRRGDEISPALLNAIQ---GSKISVVIFSKDYASS--KWCLNELVKILECK-NT 95 (136)
Q Consensus 24 ~fv~~L~~~L~~~~g--i~vf~d~~~i~~G~~~~~~i~~aI~---~S~~~I~vlS~~y~~S--~wc~~El~~~~~~~-~~ 95 (136)
..+..|.+.|.. .| +.|++. +..|.+...+..+.+. -.+++++.+.|.|..+ .-+.+++..++... ..
T Consensus 73 ~qa~~l~~~L~~-~~~~~~V~~a---mry~~P~i~~~l~~l~~~g~~~ivvlPLyPqyS~~ttgs~~~~~~~~~~~~~~~ 148 (316)
T PF00762_consen 73 RQAEALQQRLDE-RGVDVEVYYA---MRYGPPSIEDALEELKADGVDRIVVLPLYPQYSSSTTGSYLDEVERALKKSRPN 148 (316)
T ss_dssp HHHHHHHHHHHH-H-EEEEEEEE---ESSSSSBHHHHHHHHHHTT-SEEEEEESSSS--TTTHHHHHHHHHHHHHHTHSS
T ss_pred HHHHHHHHHHHh-cCCCeeEEEE---eccCCCCHHHHHHHHHHcCCCeEEEEeCCCchhHhhHHHHHHHHHHHHHhcCCC
Confidence 456677777776 53 445554 5677777766666666 3466888899999865 34677777777653 22
Q ss_pred CCCEEEEEEeccCccccccccCcHHHHHHHHHHH
Q 044631 96 NGQIIIPVFYGVSPSDVRHQNGTFGDRFDELKKQ 129 (136)
Q Consensus 96 ~~~~iiPVf~~v~p~~v~~~~~~~~~~f~~~~~~ 129 (136)
-..++|+=|++ ...|-+++.+..+.
T Consensus 149 ~~~~~i~~~~~---------~p~yi~a~~~~i~~ 173 (316)
T PF00762_consen 149 PKVRFIPSFYD---------HPAYIEALAERIRE 173 (316)
T ss_dssp SEEEEE---TT----------HHHHHHHHHHHHH
T ss_pred CeEEEeCCccC---------CHHHHHHHHHHHHH
Confidence 34456666654 34555555554443
No 57
>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=38.78 E-value=57 Score=22.41 Aligned_cols=45 Identities=13% Similarity=0.303 Sum_probs=28.9
Q ss_pred CcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEec
Q 044631 52 DEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYG 106 (136)
Q Consensus 52 ~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~ 106 (136)
+.+.+.+.+.+.+.+++|++++.++++ ++...++..+ .++|.++.
T Consensus 46 eei~~~~~~~l~~~digIIlIte~~a~------~i~~~I~~~~----~~~PaIie 90 (115)
T TIGR01101 46 SEIEDCFNRFLKRDDIAIILINQHIAE------MIRHAVDAHT----RSIPAVLE 90 (115)
T ss_pred HHHHHHHHHHhhcCCeEEEEEcHHHHH------HhHHHHHhcC----CcCCEEEE
Confidence 445566666688899999999988765 3444444332 45555554
No 58
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=38.46 E-value=94 Score=27.07 Aligned_cols=60 Identities=12% Similarity=0.083 Sum_probs=40.9
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
..||+|-.-+... ...+..|.+.|++ .|++|-+|.. +..+...+..|-..---.++|+.+
T Consensus 539 p~~v~Ii~~~~~~-~~~a~~i~~~Lr~-~gi~v~~d~~----~~~l~kki~~A~~~g~~~~iiiG~ 598 (638)
T PRK00413 539 PVQVVVLPITDKH-ADYAKEVAKKLKA-AGIRVEVDLR----NEKIGYKIREAQLQKVPYMLVVGD 598 (638)
T ss_pred cceEEEEEeChhH-HHHHHHHHHHHHh-CCCEEEEECC----CCCHhHHHHHhhccCCCEEEEEcc
Confidence 5688887655443 4678999999999 9999999864 344555666655433335555554
No 59
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=38.41 E-value=74 Score=25.95 Aligned_cols=61 Identities=18% Similarity=0.355 Sum_probs=41.0
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchh-cCcEEEEEeecCCCCC
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQ-GSKISVVIFSKDYASS 79 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~-~S~~~I~vlS~~y~~S 79 (136)
.||+-|.|+.+ .|...|.++--+ ||.++++. -|.++.++....+. .+|+.++=.=..|...
T Consensus 196 GfD~~idyk~~----d~~~~L~~a~P~--GIDvyfeN----VGg~v~DAv~~~ln~~aRi~~CG~IS~YN~~ 257 (340)
T COG2130 196 GFDAGIDYKAE----DFAQALKEACPK--GIDVYFEN----VGGEVLDAVLPLLNLFARIPVCGAISQYNAP 257 (340)
T ss_pred CCceeeecCcc----cHHHHHHHHCCC--CeEEEEEc----CCchHHHHHHHhhccccceeeeeehhhcCCC
Confidence 68999999765 366677666555 99999996 35566666666665 5666555554555543
No 60
>cd04127 Rab27A Rab27a subfamily. The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated
Probab=37.82 E-value=1.4e+02 Score=20.68 Aligned_cols=26 Identities=12% Similarity=0.051 Sum_probs=17.8
Q ss_pred chHHHHhchhcCcEEEEEeecCCCCC
Q 044631 54 ISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 54 ~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+..-....++.++.+|+|++.+-..|
T Consensus 76 ~~~~~~~~~~~~~~~i~v~d~~~~~s 101 (180)
T cd04127 76 FRSLTTAFFRDAMGFLLIFDLTNEQS 101 (180)
T ss_pred HHHHHHHHhCCCCEEEEEEECCCHHH
Confidence 33334556789999999999764443
No 61
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=37.64 E-value=90 Score=27.12 Aligned_cols=57 Identities=16% Similarity=0.307 Sum_probs=38.8
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchh-cCcEEEEE
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQ-GSKISVVI 71 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~-~S~~~I~v 71 (136)
..+|+|-.-+++. ...+..|.+.|++ .|++|-+|.. +..+...+..|-. +.+.+|+|
T Consensus 438 P~qV~Iipi~e~~-~~~A~~Ia~~LR~-~GirVelD~~----~~~lgkkir~A~k~gip~viII 495 (545)
T PRK14799 438 SVQVRVLPITDEV-NEYAEKVLNDMRK-RRIRAEIDYA----GETLSKRIKNAYDQGVPYILIV 495 (545)
T ss_pred CceEEEEEcCHHH-HHHHHHHHHHHHh-CCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEE
Confidence 5688877655443 4688999999999 9999999864 3455556655543 44444443
No 62
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. 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 dissociation inhi
Probab=37.10 E-value=1.4e+02 Score=20.51 Aligned_cols=27 Identities=4% Similarity=0.097 Sum_probs=18.1
Q ss_pred CcchHHHHhchhcCcEEEEEeecCCCC
Q 044631 52 DEISPALLNAIQGSKISVVIFSKDYAS 78 (136)
Q Consensus 52 ~~~~~~i~~aI~~S~~~I~vlS~~y~~ 78 (136)
+.+.......+++++.+|++++.+-..
T Consensus 63 ~~~~~~~~~~~~~ad~~i~v~d~~~~~ 89 (167)
T cd01867 63 ERFRTITTAYYRGAMGIILVYDITDEK 89 (167)
T ss_pred HHHHHHHHHHhCCCCEEEEEEECcCHH
Confidence 333434446678999999999865433
No 63
>cd01864 Rab19 Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. 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 dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=36.76 E-value=1.4e+02 Score=20.38 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=19.4
Q ss_pred CCCc-chHHHHhchhcCcEEEEEeecCCCCC
Q 044631 50 RGDE-ISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 50 ~G~~-~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
||.. +.......+..++.+|++++.+-..|
T Consensus 60 ~G~~~~~~~~~~~~~~~d~~llv~d~~~~~s 90 (165)
T cd01864 60 AGQERFRTITQSYYRSANGAIIAYDITRRSS 90 (165)
T ss_pred CChHHHHHHHHHHhccCCEEEEEEECcCHHH
Confidence 4533 33334456678999999998865443
No 64
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=36.26 E-value=1.3e+02 Score=19.84 Aligned_cols=65 Identities=9% Similarity=0.201 Sum_probs=37.9
Q ss_pred HHHHHcCCCCeEEe-eCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEE
Q 044631 30 YDKLYEGKKIKTFI-DDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPV 103 (136)
Q Consensus 30 ~~~L~~~~gi~vf~-d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPV 103 (136)
..-++. .|+..++ ... .+.....+.+.+.+-++.|++++.+.... +.+++...++. .....|+||
T Consensus 12 v~GFrL-aGi~~~~~~~~----~ee~~~~l~~l~~~~d~gII~Ite~~~~~--i~e~i~~~~~~--~~~P~ii~I 77 (100)
T PRK02228 12 TTGFRL-AGIRKVYEVPD----DEKLDEAVEEVLEDDDVGILVMHDDDLEK--LPRRLRRTLEE--SVEPTVVTL 77 (100)
T ss_pred HHHHHH-cCCceEEeeCC----HHHHHHHHHHHhhCCCEEEEEEehhHhHh--hHHHHHHHHhc--CCCCEEEEE
Confidence 345566 8887554 221 13455566666678889999999997764 33444443332 223445555
No 65
>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=35.93 E-value=1.2e+02 Score=19.65 Aligned_cols=57 Identities=18% Similarity=0.156 Sum_probs=34.8
Q ss_pred HHHHHHHHHcCCCCeEE-eeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHH
Q 044631 26 TCYLYDKLYEGKKIKTF-IDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKI 89 (136)
Q Consensus 26 v~~L~~~L~~~~gi~vf-~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~ 89 (136)
...|...|++ .|+.|- +|.. .. .+++.+.+.+.+.-++.+|-.+..+..-..++...
T Consensus 17 l~~la~~l~~-~G~~v~~~d~~-~~-----~~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~ 74 (121)
T PF02310_consen 17 LLYLAAYLRK-AGHEVDILDAN-VP-----PEELVEALRAERPDVVGISVSMTPNLPEAKRLARA 74 (121)
T ss_dssp HHHHHHHHHH-TTBEEEEEESS-B------HHHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHH
T ss_pred HHHHHHHHHH-CCCeEEEECCC-CC-----HHHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHH
Confidence 4678899999 999984 4432 21 15777777777766677776544433333343333
No 66
>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=35.74 E-value=1.1e+02 Score=22.17 Aligned_cols=53 Identities=9% Similarity=0.078 Sum_probs=29.4
Q ss_pred HHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcC---CCCEEEEEEeccCccccc
Q 044631 58 LLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNT---NGQIIIPVFYGVSPSDVR 113 (136)
Q Consensus 58 i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~---~~~~iiPVf~~v~p~~v~ 113 (136)
...+++.++++|+|++.+ +++..+.+....+.... ....-+|+++=....|+.
T Consensus 74 ~~~~~~~ad~iilv~D~~---~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~ 129 (198)
T cd04142 74 RFRGLRNSRAFILVYDIC---SPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQ 129 (198)
T ss_pred HHhhhccCCEEEEEEECC---CHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECcccc
Confidence 445688999999999986 34444444433332211 011235666644455553
No 67
>PLN02530 histidine-tRNA ligase
Probab=35.70 E-value=1.1e+02 Score=25.96 Aligned_cols=60 Identities=13% Similarity=0.023 Sum_probs=41.3
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
..||+|.+-.++. ...+-.+.+.|++ .|+++-+|... ..+...+..|-+.--..|+++.+
T Consensus 401 ~~dVlVi~~~~~~-~~~A~~ia~~LR~-~Gi~vevd~~~----~~l~k~ik~A~k~g~~~iviiG~ 460 (487)
T PLN02530 401 QVDDVVFALDEDL-QGAAAGVASRLRE-KGRSVDLVLEP----KKLKWVFKHAERIGAKRLVLVGA 460 (487)
T ss_pred CCcEEEEEcChHH-HHHHHHHHHHHHH-CCCeEEEecCC----CCHHHHHHHHHHCCCCEEEEEch
Confidence 4689998755543 4678899999999 99999887532 44566666666544445555554
No 68
>cd01868 Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP
Probab=35.10 E-value=1.4e+02 Score=20.17 Aligned_cols=54 Identities=11% Similarity=0.115 Sum_probs=27.2
Q ss_pred HHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEeccCccccc
Q 044631 57 ALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGVSPSDVR 113 (136)
Q Consensus 57 ~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~p~~v~ 113 (136)
.....++.++.+|++++..-. ....++...+.........-+||++=+...|+.
T Consensus 68 ~~~~~~~~~~~~i~v~d~~~~---~s~~~~~~~~~~~~~~~~~~~pi~vv~nK~Dl~ 121 (165)
T cd01868 68 ITSAYYRGAVGALLVYDITKK---QTFENVERWLKELRDHADSNIVIMLVGNKSDLR 121 (165)
T ss_pred HHHHHHCCCCEEEEEEECcCH---HHHHHHHHHHHHHHHhCCCCCeEEEEEECcccc
Confidence 344566788989999887633 334444433332211111124665544444443
No 69
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=34.79 E-value=55 Score=25.67 Aligned_cols=42 Identities=24% Similarity=0.258 Sum_probs=29.4
Q ss_pred HHHHHHHHHHcCCCCeEEeeCCcccCCC---cchHHHHhchhcCcEEEE
Q 044631 25 FTCYLYDKLYEGKKIKTFIDDEELRRGD---EISPALLNAIQGSKISVV 70 (136)
Q Consensus 25 fv~~L~~~L~~~~gi~vf~d~~~i~~G~---~~~~~i~~aI~~S~~~I~ 70 (136)
=+.+|.+.|.. .|+.+.... .-|| .|.+.+..++++++++|+
T Consensus 22 Na~~la~~L~~-~G~~v~~~~---~VgD~~~~I~~~l~~a~~r~D~vI~ 66 (255)
T COG1058 22 NAAFLADELTE-LGVDLARIT---TVGDNPDRIVEALREASERADVVIT 66 (255)
T ss_pred hHHHHHHHHHh-cCceEEEEE---ecCCCHHHHHHHHHHHHhCCCEEEE
Confidence 36689999999 999987653 2344 456677777778665544
No 70
>PRK12435 ferrochelatase; Provisional
Probab=34.59 E-value=2.4e+02 Score=22.54 Aligned_cols=52 Identities=13% Similarity=0.250 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHcCC----CCeEEeeCCcccCCCcchHHHHhchh--cC-cEEEEEeecCCCCC
Q 044631 24 SFTCYLYDKLYEGK----KIKTFIDDEELRRGDEISPALLNAIQ--GS-KISVVIFSKDYASS 79 (136)
Q Consensus 24 ~fv~~L~~~L~~~~----gi~vf~d~~~i~~G~~~~~~i~~aI~--~S-~~~I~vlS~~y~~S 79 (136)
..+..|.+.|.. . .+.|++. +..|.+...+..+.+. .+ +++++.+.|.|..+
T Consensus 61 ~qa~~L~~~L~~-~~~~~~~~V~~a---mry~~P~i~~~l~~l~~~g~~~iv~lpLyPqyS~~ 119 (311)
T PRK12435 61 EQAKALEKALNE-VQDEVEFKLYLG---LKHIEPFIEDAVEQMHNDGIEEAISIVLAPHYSTF 119 (311)
T ss_pred HHHHHHHHHHhh-ccCCCCceEEEE---ecCCCCCHHHHHHHHHHcCCCeEEEEECCCccccc
Confidence 345677777765 3 2667765 4567766666666664 33 44555579998865
No 71
>PLN02449 ferrochelatase
Probab=34.35 E-value=3e+02 Score=23.67 Aligned_cols=79 Identities=19% Similarity=0.282 Sum_probs=47.8
Q ss_pred hHHHHHHHHHHcCCC--CeEEeeCCcccCCCcchHHHHhchhc---CcEEEEEeecCCCCC--HhHHHHHHHHHHhhc--
Q 044631 24 SFTCYLYDKLYEGKK--IKTFIDDEELRRGDEISPALLNAIQG---SKISVVIFSKDYASS--KWCLNELVKILECKN-- 94 (136)
Q Consensus 24 ~fv~~L~~~L~~~~g--i~vf~d~~~i~~G~~~~~~i~~aI~~---S~~~I~vlS~~y~~S--~wc~~El~~~~~~~~-- 94 (136)
.-+..|.++|.+ .| +.|++. +..|.+...+..+.+.+ .+++++.+-|.|..+ .-+.+.+..+.....
T Consensus 164 ~Qa~~Lq~~L~~-~~~~~~V~~a---MRY~~P~iedal~~l~~~G~~~iVvLPLYPQyS~sTtgSs~~~l~~~~~~~~~~ 239 (485)
T PLN02449 164 EQAEALAKALEA-KNLPAKVYVG---MRYWHPFTEEAIDQIKADGITKLVVLPLYPQFSISTSGSSLRLLESIFREDEYL 239 (485)
T ss_pred HHHHHHHHHHhc-cCCCeEEEEh---hhcCCCCHHHHHHHHHhcCCCeEEEEECCcccccccHHHHHHHHHHHHhhcccc
Confidence 345677788876 65 567764 55777776666666653 456788888887654 345566655554321
Q ss_pred -CCCCEEEEEEec
Q 044631 95 -TNGQIIIPVFYG 106 (136)
Q Consensus 95 -~~~~~iiPVf~~ 106 (136)
.-..++||=+|+
T Consensus 240 ~~~~~~~I~~~~~ 252 (485)
T PLN02449 240 VNMQHTVIPSWYQ 252 (485)
T ss_pred cCCeeEEeccccC
Confidence 113356666654
No 72
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=33.62 E-value=1.7e+02 Score=23.11 Aligned_cols=73 Identities=14% Similarity=0.099 Sum_probs=47.9
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHH
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVK 88 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~ 88 (136)
.+||-|-|++.+ ....+|..+++. |+++-+-...+.+- -.+.|.++.++ +=+|++|||.-.-.-+..|..
T Consensus 69 ~~DV~IDFT~P~---~~~~~l~~~~~~--~~~lVIGTTGf~~e--~~~~l~~~a~~---v~vv~a~NfSiGvnll~~l~~ 138 (266)
T COG0289 69 DADVLIDFTTPE---ATLENLEFALEH--GKPLVIGTTGFTEE--QLEKLREAAEK---VPVVIAPNFSLGVNLLFKLAE 138 (266)
T ss_pred CCCEEEECCCch---hhHHHHHHHHHc--CCCeEEECCCCCHH--HHHHHHHHHhh---CCEEEeccchHHHHHHHHHHH
Confidence 679999999886 455666666665 78777665443211 12344444444 667899999988777777765
Q ss_pred HHH
Q 044631 89 ILE 91 (136)
Q Consensus 89 ~~~ 91 (136)
...
T Consensus 139 ~aa 141 (266)
T COG0289 139 QAA 141 (266)
T ss_pred HHH
Confidence 544
No 73
>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=33.33 E-value=1.5e+02 Score=20.33 Aligned_cols=46 Identities=4% Similarity=0.060 Sum_probs=27.8
Q ss_pred HHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEE
Q 044631 56 PALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVF 104 (136)
Q Consensus 56 ~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf 104 (136)
..+.+.+..++++|+|++.+-. |...+...+.+.......+.+-|+
T Consensus 120 ~~~~~~~~~~d~vi~V~~~~~~---~~~~~~~~l~~~~~~~~~~~i~V~ 165 (168)
T PF00350_consen 120 EITEEYLPKADVVIFVVDANQD---LTESDMEFLKQMLDPDKSRTIFVL 165 (168)
T ss_dssp HHHHHHHSTTEEEEEEEETTST---GGGHHHHHHHHHHTTTCSSEEEEE
T ss_pred HHHHHhhccCCEEEEEeccCcc---cchHHHHHHHHHhcCCCCeEEEEE
Confidence 4567888999999999977763 343344444443333333455443
No 74
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=33.22 E-value=98 Score=20.91 Aligned_cols=31 Identities=19% Similarity=0.224 Sum_probs=15.2
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEee
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFID 44 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d 44 (136)
..||-|-|+..+ ....++..+++. |+.+-+-
T Consensus 67 ~~DVvIDfT~p~---~~~~~~~~~~~~--g~~~ViG 97 (124)
T PF01113_consen 67 EADVVIDFTNPD---AVYDNLEYALKH--GVPLVIG 97 (124)
T ss_dssp H-SEEEEES-HH---HHHHHHHHHHHH--T-EEEEE
T ss_pred cCCEEEEcCChH---HhHHHHHHHHhC--CCCEEEE
Confidence 467777776543 334444444444 6665543
No 75
>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=33.17 E-value=77 Score=22.10 Aligned_cols=23 Identities=39% Similarity=0.271 Sum_probs=9.9
Q ss_pred CcchHHHHhchhcCcEEEEEeec
Q 044631 52 DEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 52 ~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
..+.+.+.++|.+++..|.+.++
T Consensus 20 ~~~~~~i~~~I~~A~~~I~i~~~ 42 (176)
T cd00138 20 RSDLDALLEAISNAKKSIYIASF 42 (176)
T ss_pred chHHHHHHHHHHhhheEEEEEEe
Confidence 33334444444444444444444
No 76
>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=33.14 E-value=1.5e+02 Score=20.04 Aligned_cols=17 Identities=29% Similarity=0.380 Sum_probs=7.9
Q ss_pred HHhchhcCcEEEEEeec
Q 044631 58 LLNAIQGSKISVVIFSK 74 (136)
Q Consensus 58 i~~aI~~S~~~I~vlS~ 74 (136)
+.++|++++++++|+..
T Consensus 5 ~~~~i~~aD~vl~ViD~ 21 (141)
T cd01857 5 LWRVVERSDIVVQIVDA 21 (141)
T ss_pred HHHHHhhCCEEEEEEEc
Confidence 34444445544444443
No 77
>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.
Probab=32.97 E-value=21 Score=23.14 Aligned_cols=21 Identities=5% Similarity=0.128 Sum_probs=15.6
Q ss_pred HhchhcCcEEEEEeecCCCCC
Q 044631 59 LNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 59 ~~aI~~S~~~I~vlS~~y~~S 79 (136)
...+..++.+|+|++..-..|
T Consensus 68 ~~~~~~~d~~ilv~D~s~~~s 88 (119)
T PF08477_consen 68 QFFLKKADAVILVYDLSDPES 88 (119)
T ss_dssp HHHHHHSCEEEEEEECCGHHH
T ss_pred cchhhcCcEEEEEEcCCChHH
Confidence 344899999999998664443
No 78
>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=32.96 E-value=38 Score=29.44 Aligned_cols=48 Identities=21% Similarity=0.419 Sum_probs=35.0
Q ss_pred cccEEEecc-cCc-CchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHH
Q 044631 9 NYEVFLNFR-GED-TRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPA 57 (136)
Q Consensus 9 ~yDVFISys-~~D-~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~ 57 (136)
.|+|-|--- .+| .....+..|++.|+. .|+.|.+|+++-.+|..+.+.
T Consensus 473 P~qV~Iip~~~~~~~~~~~a~~l~~~L~~-~gi~v~~DDr~~~~G~K~~da 522 (568)
T TIGR00409 473 PYDVVIVVMNMKDEEQQQLAEELYSELLA-QGVDVLLDDRNERAGVKFADS 522 (568)
T ss_pred CeEEEEEEcCCChHHHHHHHHHHHHHHHh-CCCEEEEECCCCCHHHHHHhh
Confidence 577765432 222 234688999999999 999999999877777766543
No 79
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=32.83 E-value=2e+02 Score=22.20 Aligned_cols=76 Identities=17% Similarity=0.144 Sum_probs=47.0
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCC--CCEE
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTN--GQII 100 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~--~~~i 100 (136)
+.+...|....+. +| ..|+|-+ +..+.....++...-.+-. +|+|-+...+.+..+|+..++...... +..-
T Consensus 78 ~~~i~ll~~la~~-~~-~d~iDiE-l~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~aDivK 151 (231)
T COG0710 78 EEYIELLKKLAEL-NG-PDYIDIE-LSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLGADIVK 151 (231)
T ss_pred HHHHHHHHHHHhh-cC-CCEEEEE-ccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhCCCeEE
Confidence 3566666666666 55 5677754 3333322233333333333 888999999999999999988876433 3445
Q ss_pred EEEE
Q 044631 101 IPVF 104 (136)
Q Consensus 101 iPVf 104 (136)
|+|.
T Consensus 152 iAvm 155 (231)
T COG0710 152 IAVM 155 (231)
T ss_pred EEec
Confidence 5554
No 80
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=32.55 E-value=1.4e+02 Score=26.21 Aligned_cols=62 Identities=13% Similarity=0.102 Sum_probs=41.3
Q ss_pred CcccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 8 CNYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 8 ~~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
+..+|+|-.-+++.....+..|.+.|++ .|++|-+|.. +..+...+..|-+.---.++++.+
T Consensus 540 ap~qV~Ii~~~~~~~~~~a~~la~~LR~-~Gi~veid~~----~~sl~kq~k~A~k~g~~~~iiiG~ 601 (639)
T PRK12444 540 APVQVKVIPVSNAVHVQYADEVADKLAQ-AGIRVERDER----DEKLGYKIREAQMQKIPYVLVIGD 601 (639)
T ss_pred CCceEEEEEcccHHHHHHHHHHHHHHHH-CCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEcc
Confidence 4678887775551124778999999999 9999999864 345556666654433334455544
No 81
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=31.65 E-value=2.1e+02 Score=20.99 Aligned_cols=82 Identities=10% Similarity=0.122 Sum_probs=47.7
Q ss_pred hHHHHHHHHHHcCCCCeE-EeeCCcccCC--------CcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhh-
Q 044631 24 SFTCYLYDKLYEGKKIKT-FIDDEELRRG--------DEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECK- 93 (136)
Q Consensus 24 ~fv~~L~~~L~~~~gi~v-f~d~~~i~~G--------~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~- 93 (136)
..+..+.+.|.. .|..+ .+|-.++.++ .+-...+.+.|.+++ .|++.||-|..|.--.- ..+++..
T Consensus 18 ~l~~~~~~~l~~-~g~ev~~idL~~l~~~~~~~~~~~~~~~~~~~~~i~~AD-~iIi~tP~Y~~s~pg~L--Kn~iD~l~ 93 (191)
T PRK10569 18 ALLEYAREWLNG-LGVEVYHWNLQNFAPEDLLYARFDSPALKTFTEQLAQAD-GLIVATPVYKASFSGAL--KTLLDLLP 93 (191)
T ss_pred HHHHHHHHHHHh-CCCEEEEEEccCCChHHHHhccCCCHHHHHHHHHHHHCC-EEEEECCccCCCCCHHH--HHHHHhCC
Confidence 456777778887 88876 4555555432 122346668888888 67888999987743221 1222211
Q ss_pred --cCCCCEEEEEEeccCc
Q 044631 94 --NTNGQIIIPVFYGVSP 109 (136)
Q Consensus 94 --~~~~~~iiPVf~~v~p 109 (136)
.-.+..++||--...+
T Consensus 94 ~~~l~~K~v~iiat~G~~ 111 (191)
T PRK10569 94 ERALEHKVVLPLATGGSV 111 (191)
T ss_pred hhhhCCCEEEEEEecCCc
Confidence 1134567777654343
No 82
>COG3613 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]
Probab=31.53 E-value=2.2e+02 Score=21.09 Aligned_cols=77 Identities=13% Similarity=-0.003 Sum_probs=50.5
Q ss_pred hHHHHHHHHHHcCCCCeEEee------CCcccC---CCcchHHHHhchhcCcEEEEEeecCC-CCCHhHHHHHHHHHHhh
Q 044631 24 SFTCYLYDKLYEGKKIKTFID------DEELRR---GDEISPALLNAIQGSKISVVIFSKDY-ASSKWCLNELVKILECK 93 (136)
Q Consensus 24 ~fv~~L~~~L~~~~gi~vf~d------~~~i~~---G~~~~~~i~~aI~~S~~~I~vlS~~y-~~S~wc~~El~~~~~~~ 93 (136)
...+.|...|.+ .|+.++.- ..+..| +..|...=.+.|.+|+++|+++.+-= ...+-+..|+..+....
T Consensus 20 ~~~d~lkall~~-~gf~~~~P~d~~~~~~~~~p~~~a~~i~e~d~~~i~~aD~vla~ld~fr~~~DsGTa~E~GYa~Alg 98 (172)
T COG3613 20 ELRDELKALLLE-AGFEVLSPFDEAEPIAETGPNETAEKIYEADIKLIDQADIVLANLDPFRPDPDSGTAFELGYAIALG 98 (172)
T ss_pred HHHHHHHHHHHH-cCCeeeCcchhccCccccCccHHHHHHHHHHHHHHhhcCEEEEecCCCCCCCCCcchHHHHHHHHcC
Confidence 456778888888 99998854 222223 22344444577899999999987755 11234667999887754
Q ss_pred cCCCCEEEEEEe
Q 044631 94 NTNGQIIIPVFY 105 (136)
Q Consensus 94 ~~~~~~iiPVf~ 105 (136)
..+++.+-
T Consensus 99 ----KPv~~~~~ 106 (172)
T COG3613 99 ----KPVYAYRK 106 (172)
T ss_pred ----CceEEEee
Confidence 36777653
No 83
>PF03481 SUA5: Putative GTP-binding controlling metal-binding; InterPro: IPR005145 The function of this domain is unknown, it is found in P32579 from SWISSPROT and its relatives. It is found C-terminal to the IPR006070 from INTERPRO.; PDB: 2EQA_A 3AJE_A 4E1B_A 2YV4_A.
Probab=30.39 E-value=55 Score=22.25 Aligned_cols=55 Identities=7% Similarity=0.167 Sum_probs=32.5
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHc--CCCCeEEeeCCcccCCCcchHHHHhchhcC
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYE--GKKIKTFIDDEELRRGDEISPALLNAIQGS 65 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~--~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S 65 (136)
.++.+++.+-.+.-+..+..|+..|+. +.|+.+-+-. ..+...+...|.+.|.++
T Consensus 67 ~~~~~~~l~~~~d~~~~A~~Lf~~LR~~D~~~~~~I~ie--~~~~~~~g~Ai~dRL~RA 123 (125)
T PF03481_consen 67 SFDIVYSLSLPGDPEEAARNLFAALRELDELGVDLILIE--GPPETGLGLAIMDRLRRA 123 (125)
T ss_dssp CGSEEEEEESTTSHHHHHHHHHHHHHHHHHTT-SEEEEE--EESGCCCHHHHHHHHHHH
T ss_pred ccceEEEecCCCCHHHHHHHHHHHHHHHhhcCCCEEEEe--eCCCcCcHHHHHHHHHHh
Confidence 345665544333336899999999998 3677643332 234455566777776653
No 84
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=29.68 E-value=49 Score=26.25 Aligned_cols=31 Identities=29% Similarity=0.477 Sum_probs=20.9
Q ss_pred hHHHHHHHHHH---hhc-CCCCEEEEEEeccCccc
Q 044631 81 WCLNELVKILE---CKN-TNGQIIIPVFYGVSPSD 111 (136)
Q Consensus 81 wc~~El~~~~~---~~~-~~~~~iiPVf~~v~p~~ 111 (136)
-|.+||.+... ..+ ..+..++|||.-++|+.
T Consensus 154 ICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPeR 188 (280)
T KOG2792|consen 154 ICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPER 188 (280)
T ss_pred cChHHHHHHHHHHHHHhccCCCCccceEEEeCccc
Confidence 47788866544 332 34667779999998843
No 85
>cd04175 Rap1 Rap1 subgroup. The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n
Probab=27.96 E-value=2e+02 Score=19.49 Aligned_cols=30 Identities=17% Similarity=0.159 Sum_probs=18.5
Q ss_pred CCCc-chHHHHhchhcCcEEEEEeecCCCCC
Q 044631 50 RGDE-ISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 50 ~G~~-~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+|.. +..-.....+.++.+|++++-+-..|
T Consensus 57 ~G~~~~~~~~~~~~~~~d~~ilv~d~~~~~s 87 (164)
T cd04175 57 AGTEQFTAMRDLYMKNGQGFVLVYSITAQST 87 (164)
T ss_pred CCcccchhHHHHHHhhCCEEEEEEECCCHHH
Confidence 5543 33333445678899999998654433
No 86
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=27.90 E-value=2.3e+02 Score=20.34 Aligned_cols=64 Identities=16% Similarity=0.215 Sum_probs=41.5
Q ss_pred HHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchh-cCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEE
Q 044631 26 TCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQ-GSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVF 104 (136)
Q Consensus 26 v~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~-~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf 104 (136)
+..|.+.-++ .|+++++- +|..+...+....+ ++=++|. |..+|...+......+..++-|+
T Consensus 75 Ig~l~~lae~-~g~~v~i~-----~Ggt~ar~~ik~~~p~~iigVA-----------C~~dL~~g~~~~~~~~ip~~gV~ 137 (158)
T PF01976_consen 75 IGDLKKLAEK-YGYKVYIA-----TGGTLARKIIKEYRPKAIIGVA-----------CERDLISGIQDLKPLGIPVQGVL 137 (158)
T ss_pred hhHHHHHHHH-cCCEEEEE-----cChHHHHHHHHHhCCCEEEEEe-----------chHHHHHHHHHHhhcCCCeeEEE
Confidence 5677777778 99999964 56555544433332 3222222 88899888876655567777777
Q ss_pred ec
Q 044631 105 YG 106 (136)
Q Consensus 105 ~~ 106 (136)
.+
T Consensus 138 l~ 139 (158)
T PF01976_consen 138 LD 139 (158)
T ss_pred eC
Confidence 65
No 87
>PLN03110 Rab GTPase; Provisional
Probab=27.23 E-value=2.5e+02 Score=20.52 Aligned_cols=26 Identities=4% Similarity=0.070 Sum_probs=17.6
Q ss_pred chHHHHhchhcCcEEEEEeecCCCCC
Q 044631 54 ISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 54 ~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+.......++.+..+|++++.+-..|
T Consensus 74 ~~~~~~~~~~~~~~~ilv~d~~~~~s 99 (216)
T PLN03110 74 YRAITSAYYRGAVGALLVYDITKRQT 99 (216)
T ss_pred HHHHHHHHhCCCCEEEEEEECCChHH
Confidence 33344456788999999998765443
No 88
>cd04140 ARHI_like ARHI subfamily. ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. 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. Due to
Probab=27.20 E-value=2.1e+02 Score=19.53 Aligned_cols=21 Identities=14% Similarity=0.162 Sum_probs=15.8
Q ss_pred HhchhcCcEEEEEeecCCCCC
Q 044631 59 LNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 59 ~~aI~~S~~~I~vlS~~y~~S 79 (136)
...+..++.+|+|++.+-..|
T Consensus 67 ~~~~~~~~~~ilv~d~~~~~s 87 (165)
T cd04140 67 RLSISKGHAFILVYSVTSKQS 87 (165)
T ss_pred HHHhhcCCEEEEEEECCCHHH
Confidence 356778999999999765554
No 89
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=27.06 E-value=50 Score=20.42 Aligned_cols=25 Identities=12% Similarity=0.363 Sum_probs=16.0
Q ss_pred CCCeEEeeCCcccCCCcchHHHHhchh
Q 044631 37 KKIKTFIDDEELRRGDEISPALLNAIQ 63 (136)
Q Consensus 37 ~gi~vf~d~~~i~~G~~~~~~i~~aI~ 63 (136)
..+-+|+|.+. +|+.....+.+.+.
T Consensus 47 ~~Vii~~D~D~--~G~~~a~~i~~~l~ 71 (81)
T PF13662_consen 47 KEVIIAFDNDK--AGEKAAQKIAKKLL 71 (81)
T ss_dssp SEEEEEEESSH--HHHHHHHHHHHHHG
T ss_pred ceEEEEeCcCH--HHHHHHHHHHHHHH
Confidence 45667777653 67766666666554
No 90
>KOG1014 consensus 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism]
Probab=26.94 E-value=1.2e+02 Score=24.47 Aligned_cols=60 Identities=20% Similarity=0.316 Sum_probs=41.4
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEe
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIF 72 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vl 72 (136)
.+.|+|-=|.++ =.+.+.++++++.++.|.+..-|+..|+...+.|.+.+.+-++.|+|=
T Consensus 73 G~nvvLIsRt~~----KL~~v~kEI~~~~~vev~~i~~Dft~~~~~ye~i~~~l~~~~VgILVN 132 (312)
T KOG1014|consen 73 GFNVVLISRTQE----KLEAVAKEIEEKYKVEVRIIAIDFTKGDEVYEKLLEKLAGLDVGILVN 132 (312)
T ss_pred CCEEEEEeCCHH----HHHHHHHHHHHHhCcEEEEEEEecCCCchhHHHHHHHhcCCceEEEEe
Confidence 345555444443 245667777766677777666677778777778888888888888874
No 91
>PF02900 LigB: Catalytic LigB subunit of aromatic ring-opening dioxygenase; InterPro: IPR004183 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A and B. Enzymes that belong to the extradiol class III family include Protocatechuate 4,5-dioxygenase (4,5-PCD; LigAB) (1.13.11.8 from EC) []; and 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarBaBb) []. The crystal structure of dioxygenase LigAB revealed that the molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit []. This entry represents the structural domain of subunit B.; GO: 0008198 ferrous iron binding, 0016491 oxidoreductase activity, 0006725 cellular aromatic compound metabolic process; PDB: 2PW6_A 1B4U_D 1BOU_B.
Probab=26.78 E-value=1.6e+02 Score=22.57 Aligned_cols=78 Identities=14% Similarity=0.108 Sum_probs=44.6
Q ss_pred hhHHHHHHHHHHcCCCCeE-EeeCCcccCCCcchHHHHhchhcCcEEEEEeecCC----CCCHhHHHHHHHHHHhhc-CC
Q 044631 23 KSFTCYLYDKLYEGKKIKT-FIDDEELRRGDEISPALLNAIQGSKISVVIFSKDY----ASSKWCLNELVKILECKN-TN 96 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~v-f~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y----~~S~wc~~El~~~~~~~~-~~ 96 (136)
..++.+|.+.|.+ .|+.+ ......+..|.-.. +.-.-.+.++=++-+|-+. ..+.--..+|..++.... +.
T Consensus 96 ~~la~~i~~~l~~-~g~~~~~~~~~~lDHG~~vP--L~~l~p~~~~Pvv~is~~~~~~p~~~~~~~~~lG~aL~~~~~~~ 172 (272)
T PF02900_consen 96 PELAERIAEHLRK-AGFDVAASPERGLDHGVWVP--LYFLFPDADIPVVPISINSFAPPSPSPERHYRLGRALRKARESS 172 (272)
T ss_dssp HHHHHHHHHHHHH-TTS-EEECSS--B-HHHHHH--HHHHCTT-SSEEEEEEEETSSS-TS-HHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHh-cCCCEEeccCcCCcccccee--eeecccccCcceeeeEeecccccCCCHHHHHHHHHHHHHHHHhc
Confidence 4799999999999 99986 43444444443222 1111224466666666666 667777778888888653 22
Q ss_pred CCEEEEE
Q 044631 97 GQIIIPV 103 (136)
Q Consensus 97 ~~~iiPV 103 (136)
+.+|.-|
T Consensus 173 ~~rv~vi 179 (272)
T PF02900_consen 173 DERVAVI 179 (272)
T ss_dssp GGCEEEE
T ss_pred CCCEEEE
Confidence 3444443
No 92
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=26.61 E-value=1.3e+02 Score=24.67 Aligned_cols=51 Identities=12% Similarity=0.194 Sum_probs=37.0
Q ss_pred CcCchhHHHHHHHHHHcCCCCeEEeeCCcccC----CCcchHHHHhchhcCcEEEE
Q 044631 19 EDTRKSFTCYLYDKLYEGKKIKTFIDDEELRR----GDEISPALLNAIQGSKISVV 70 (136)
Q Consensus 19 ~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~----G~~~~~~i~~aI~~S~~~I~ 70 (136)
.|.|++=+..|.+.|.. .|..|...+--+.. |-.+.++..++++.++.+|+
T Consensus 311 ~D~R~Sp~~~i~~~L~~-~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 311 DNFRASSIQGIMKRIKA-KGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred CccccChHHHHHHHHHh-CCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 46777888899999999 99987654322222 44566777888899997665
No 93
>cd04106 Rab23_lke Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G
Probab=26.38 E-value=2.1e+02 Score=19.20 Aligned_cols=28 Identities=18% Similarity=0.344 Sum_probs=18.4
Q ss_pred CCC-cchHHHHhchhcCcEEEEEeecCCC
Q 044631 50 RGD-EISPALLNAIQGSKISVVIFSKDYA 77 (136)
Q Consensus 50 ~G~-~~~~~i~~aI~~S~~~I~vlS~~y~ 77 (136)
||. .+..-....++.++.+|+|++..-.
T Consensus 59 ~G~~~~~~~~~~~~~~~~~~v~v~d~~~~ 87 (162)
T cd04106 59 AGQEEFDAITKAYYRGAQACILVFSTTDR 87 (162)
T ss_pred CchHHHHHhHHHHhcCCCEEEEEEECCCH
Confidence 453 3443445667889999999986533
No 94
>cd04114 Rab30 Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. 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 dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=26.38 E-value=2.1e+02 Score=19.34 Aligned_cols=30 Identities=7% Similarity=0.151 Sum_probs=20.5
Q ss_pred CCC-cchHHHHhchhcCcEEEEEeecCCCCC
Q 044631 50 RGD-EISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 50 ~G~-~~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+|. .+.......+..++.+|++++.....|
T Consensus 64 ~g~~~~~~~~~~~~~~~d~~i~v~d~~~~~s 94 (169)
T cd04114 64 AGQERFRSITQSYYRSANALILTYDITCEES 94 (169)
T ss_pred CCcHHHHHHHHHHhcCCCEEEEEEECcCHHH
Confidence 443 344444677889999999998765443
No 95
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=26.37 E-value=1.4e+02 Score=24.96 Aligned_cols=46 Identities=24% Similarity=0.283 Sum_probs=34.6
Q ss_pred HHHHhchhcCc-EEEEEeecCCC-CCHhHHHHHHHHHHhhcCCCCEEE
Q 044631 56 PALLNAIQGSK-ISVVIFSKDYA-SSKWCLNELVKILECKNTNGQIII 101 (136)
Q Consensus 56 ~~i~~aI~~S~-~~I~vlS~~y~-~S~wc~~El~~~~~~~~~~~~~ii 101 (136)
+.+++++...+ ...++++|+=- -.-|..+||.++.+...+.+-+||
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 57788888887 67777788755 467999999999886655555554
No 96
>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group
Probab=26.30 E-value=2.9e+02 Score=20.95 Aligned_cols=74 Identities=14% Similarity=0.157 Sum_probs=40.7
Q ss_pred CCC-cchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEeccCccccccccCcHHHHHHHHHH
Q 044631 50 RGD-EISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGVSPSDVRHQNGTFGDRFDELKK 128 (136)
Q Consensus 50 ~G~-~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~p~~v~~~~~~~~~~f~~~~~ 128 (136)
||. .+......++..++.+|+|++..-........-+ +.....+..++-++=+++. . ...+...+++..+
T Consensus 72 PG~~~f~~~~~~~l~~aD~~i~Vvd~~~g~~~~~~~~~----~~~~~~~~p~iivvNK~D~---~--~~~~~~~~~~l~~ 142 (268)
T cd04170 72 PGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLW----EFADEAGIPRIIFINKMDR---E--RADFDKTLAALQE 142 (268)
T ss_pred cCHHHHHHHHHHHHHHCCEEEEEEeCCCCCCHHHHHHH----HHHHHcCCCEEEEEECCcc---C--CCCHHHHHHHHHH
Confidence 553 4556778899999999999998865544333222 2212222222222223332 2 2356677777766
Q ss_pred Hccc
Q 044631 129 QFED 132 (136)
Q Consensus 129 ~~~~ 132 (136)
.++.
T Consensus 143 ~~~~ 146 (268)
T cd04170 143 AFGR 146 (268)
T ss_pred HhCC
Confidence 6653
No 97
>KOG1954 consensus Endocytosis/signaling protein EHD1 [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.25 E-value=2e+02 Score=24.51 Aligned_cols=77 Identities=13% Similarity=0.193 Sum_probs=49.0
Q ss_pred cccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEeccCccccccccCcHHHHHHHH
Q 044631 47 ELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGVSPSDVRHQNGTFGDRFDEL 126 (136)
Q Consensus 47 ~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~p~~v~~~~~~~~~~f~~~ 126 (136)
.+..|-++...+.--+++++..|+++.|+=+. .-+|+..++...+.....+=-|+=+-+.=+-.+....||.....+
T Consensus 164 risR~ydF~~v~~WFaeR~D~IiLlfD~hKLD---IsdEf~~vi~aLkG~EdkiRVVLNKADqVdtqqLmRVyGALmWsl 240 (532)
T KOG1954|consen 164 RISRGYDFTGVLEWFAERVDRIILLFDAHKLD---ISDEFKRVIDALKGHEDKIRVVLNKADQVDTQQLMRVYGALMWSL 240 (532)
T ss_pred cccccCChHHHHHHHHHhccEEEEEechhhcc---ccHHHHHHHHHhhCCcceeEEEeccccccCHHHHHHHHHHHHHhh
Confidence 36677788888999999999999999998775 446888887776655554444443322111122344455544433
No 98
>PRK08350 hypothetical protein; Provisional
Probab=26.09 E-value=66 Score=26.34 Aligned_cols=32 Identities=9% Similarity=-0.175 Sum_probs=28.1
Q ss_pred CcccEEEecccCcCchhHHHHHHHHHHcCCCCe
Q 044631 8 CNYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIK 40 (136)
Q Consensus 8 ~~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~ 40 (136)
+.|-+.+|||+-++.+.|+-+|.-+|.. .-|+
T Consensus 280 ~g~~~vvSHRSGETeD~~IAdLaVa~~a-gqIK 311 (341)
T PRK08350 280 ERITPILAEAKYESADEALPHLAVGLRC-PAML 311 (341)
T ss_pred cCCeEEeecCCCCCcchhHHHHHHHhCC-Cccc
Confidence 3689999999999989999999999999 5564
No 99
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=25.63 E-value=1.7e+02 Score=21.79 Aligned_cols=47 Identities=23% Similarity=0.318 Sum_probs=35.0
Q ss_pred HHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhc-------CcEEEEEeecCCCC
Q 044631 26 TCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQG-------SKISVVIFSKDYAS 78 (136)
Q Consensus 26 v~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~-------S~~~I~vlS~~y~~ 78 (136)
...|...|.+ .|+..+- . .|+.+.+.+-+|+.. ...++-|+.+.|.-
T Consensus 124 ~~~l~~~L~k-~Gv~~i~----~-~Ge~FDP~~HeAv~~~~~~~~~~~tVv~v~qkGY~l 177 (193)
T COG0576 124 LDQLLDALEK-LGVEEIG----P-EGEKFDPNLHEAVQRVESEDVEPNTVVEVLQKGYKL 177 (193)
T ss_pred HHHHHHHHHH-CCCEEeC----C-CCCCCCHHHhhheeeecCCCCCCCeEEEEeecCeee
Confidence 3678889999 9998742 1 599999999998863 33567777777754
No 100
>PLN02924 thymidylate kinase
Probab=25.39 E-value=2.4e+02 Score=21.21 Aligned_cols=41 Identities=17% Similarity=0.101 Sum_probs=31.5
Q ss_pred CCCCCCCCcccEEEecccCcCc--hhHHHHHHHHHHcCCCCeEE
Q 044631 1 MASSSSSCNYEVFLNFRGEDTR--KSFTCYLYDKLYEGKKIKTF 42 (136)
Q Consensus 1 ~~~~~~~~~yDVFISys~~D~~--~~fv~~L~~~L~~~~gi~vf 42 (136)
|.|.+.+.+--.||.+-|-|.. .+-+..|.+.|+. .|+.+-
T Consensus 6 ~~~~~~~~~~g~~IviEGiDGsGKsTq~~~L~~~l~~-~g~~v~ 48 (220)
T PLN02924 6 METESSVESRGALIVLEGLDRSGKSTQCAKLVSFLKG-LGVAAE 48 (220)
T ss_pred cCCCCCcCCCCeEEEEECCCCCCHHHHHHHHHHHHHh-cCCCce
Confidence 5666666666789999888842 4678899999999 999863
No 101
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase. This enzyme catalyzes the ring-opening step in the degradation of 4-hydroxyphenylacetate.
Probab=25.13 E-value=3.4e+02 Score=21.27 Aligned_cols=78 Identities=12% Similarity=0.076 Sum_probs=50.2
Q ss_pred hhHHHHHHHHHHcCCCCeEE---eeCCcccCCCcchHHHHhchhcCcEEEEEeecC-CCCCHhHHHHHHHHHHhh-cCCC
Q 044631 23 KSFTCYLYDKLYEGKKIKTF---IDDEELRRGDEISPALLNAIQGSKISVVIFSKD-YASSKWCLNELVKILECK-NTNG 97 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf---~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~-y~~S~wc~~El~~~~~~~-~~~~ 97 (136)
..++..|.+.+.. .|+.+- .....+..|.-+.-... -.+.++-||.+|.+ ...+..-..+|..++... ++.+
T Consensus 96 ~eLA~~i~~~~~~-~gi~~~~~~~~~~~lDHG~~vPL~~l--~p~~~ipvV~is~~~~~~~~~~~~~lG~al~~~i~~~~ 172 (282)
T TIGR02298 96 PALGQLIADEAQE-HGVKTLAHQVPSLGLEYGTLVPMRYM--NEDGHFKVVSIAAWCTVHDIEESRALGEAIRKAIEQSD 172 (282)
T ss_pred HHHHHHHHHHHHH-CCCceeeccCCCCCCCeehHhHHHHh--CCCCCCcEEEEeecCCCCCHHHHHHHHHHHHHHHHhcC
Confidence 4799999999999 999874 22334555543332221 13456778888887 555777778999888865 3344
Q ss_pred CEEEEE
Q 044631 98 QIIIPV 103 (136)
Q Consensus 98 ~~iiPV 103 (136)
.+|+-|
T Consensus 173 ~rV~iI 178 (282)
T TIGR02298 173 GRVAVL 178 (282)
T ss_pred CCEEEE
Confidence 555433
No 102
>cd04128 Spg1 Spg1p. Spg1p (septum-promoting GTPase) was first identified in the fission yeast S. pombe, where it regulates septum formation in the septation initiation network (SIN) through the cdc7 protein kinase. Spg1p is an essential gene that localizes to the spindle pole bodies. When GTP-bound, it binds cdc7 and causes it to translocate to spindle poles. Sid4p (septation initiation defective) is required for localization of Spg1p to the spindle pole body, and the ability of Spg1p to promote septum formation from any point in the cell cycle depends on Sid4p. Spg1p is negatively regulated by Byr4 and cdc16, which form a two-component GTPase activating protein (GAP) for Spg1p. The existence of a SIN-related pathway in plants has been proposed. 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
Probab=25.09 E-value=2.6e+02 Score=19.87 Aligned_cols=26 Identities=12% Similarity=0.056 Sum_probs=16.8
Q ss_pred chHHHHhchhcCcEEEEEeecCCCCC
Q 044631 54 ISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 54 ~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+..-....+.+++.+|+|++-.-..|
T Consensus 62 ~~~~~~~~~~~a~~iilv~D~t~~~s 87 (182)
T cd04128 62 FINMLPLVCNDAVAILFMFDLTRKST 87 (182)
T ss_pred HHHhhHHHCcCCCEEEEEEECcCHHH
Confidence 33333455788999999998544333
No 103
>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I. 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 families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.
Probab=24.97 E-value=1.1e+02 Score=25.80 Aligned_cols=46 Identities=15% Similarity=0.167 Sum_probs=32.0
Q ss_pred cccEEEecc--cC---cCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcch
Q 044631 9 NYEVFLNFR--GE---DTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEIS 55 (136)
Q Consensus 9 ~yDVFISys--~~---D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~ 55 (136)
.++|+|--- .+ +.....+..|.+.|++ .|++|-+|.++-.+|..+.
T Consensus 282 P~qV~Iipi~~~~~~~~~~~~~A~~l~~~Lr~-~girv~lD~r~~s~gkk~k 332 (472)
T TIGR00408 282 PIQVVIIPIIFKKKENEKVMEAAREVRSRLKK-AGFRVHIDDRDNRPGRKFY 332 (472)
T ss_pred cceEEEEEccCCCCCCHHHHHHHHHHHHHHHH-CCCEEEEECCCCCHHHHHH
Confidence 578887642 21 1224678999999999 9999999976545554443
No 104
>COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]
Probab=24.96 E-value=3.1e+02 Score=23.76 Aligned_cols=78 Identities=15% Similarity=0.117 Sum_probs=63.4
Q ss_pred HHHHHHHcCCCCeEEeeC--CcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEe
Q 044631 28 YLYDKLYEGKKIKTFIDD--EELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFY 105 (136)
Q Consensus 28 ~L~~~L~~~~gi~vf~d~--~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~ 105 (136)
.+..--++ +|+.+=.|. .++.-|+.-.-+|.+++-.-..++++--|..+-+|--.+||-.++...++.+..||-|-+
T Consensus 120 ~i~~l~~~-yGl~vdp~~~V~dLsVG~qQRVEIlKaLyr~a~iLILDEPTaVLTP~E~~~lf~~l~~l~~~G~tIi~ITH 198 (501)
T COG3845 120 RIKELSER-YGLPVDPDAKVADLSVGEQQRVEILKALYRGARLLILDEPTAVLTPQEADELFEILRRLAAEGKTIIFITH 198 (501)
T ss_pred HHHHHHHH-hCCCCCccceeecCCcchhHHHHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEec
Confidence 33333344 888765553 468889888889999999888889999999999999999999999988888999999887
Q ss_pred c
Q 044631 106 G 106 (136)
Q Consensus 106 ~ 106 (136)
+
T Consensus 199 K 199 (501)
T COG3845 199 K 199 (501)
T ss_pred c
Confidence 6
No 105
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=24.95 E-value=2.2e+02 Score=19.08 Aligned_cols=55 Identities=13% Similarity=0.002 Sum_probs=29.3
Q ss_pred cchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEecc
Q 044631 53 EISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGV 107 (136)
Q Consensus 53 ~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v 107 (136)
.+..-....+++++.+|++++.+-..|--....+...+.........++-|-.+.
T Consensus 60 ~~~~~~~~~~~~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivvg~K~ 114 (162)
T PF00071_consen 60 RFDSLRDIFYRNSDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVVGNKS 114 (162)
T ss_dssp GGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETT
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccceeeeccc
Confidence 3333334567899999999997766554444444333333332233444433333
No 106
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=24.62 E-value=3.1e+02 Score=20.67 Aligned_cols=75 Identities=11% Similarity=0.117 Sum_probs=44.8
Q ss_pred CCC-cchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEeccCccccccccCcHHHHHHHHHH
Q 044631 50 RGD-EISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGVSPSDVRHQNGTFGDRFDELKK 128 (136)
Q Consensus 50 ~G~-~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~p~~v~~~~~~~~~~f~~~~~ 128 (136)
||. .+......+++.++.+|+|++..-.-..+...-+. .+. ..+. |++.=+...|.. .-.|.+.+++...
T Consensus 72 PG~~~f~~~~~~~l~~aD~~IlVvd~~~g~~~~~~~~~~-~~~---~~~~---P~iivvNK~D~~--~a~~~~~~~~i~~ 142 (237)
T cd04168 72 PGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILWR-LLR---KLNI---PTIIFVNKIDRA--GADLEKVYQEIKE 142 (237)
T ss_pred CCccchHHHHHHHHHHhCeEEEEEeCCCCCCHHHHHHHH-HHH---HcCC---CEEEEEECcccc--CCCHHHHHHHHHH
Confidence 564 56677888999999999999877654444332222 222 1222 333222344433 2357888888888
Q ss_pred HcccC
Q 044631 129 QFEDK 133 (136)
Q Consensus 129 ~~~~~ 133 (136)
.++..
T Consensus 143 ~~~~~ 147 (237)
T cd04168 143 KLSSD 147 (237)
T ss_pred HHCCC
Confidence 87653
No 107
>smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking.
Probab=24.54 E-value=2.2e+02 Score=18.97 Aligned_cols=39 Identities=10% Similarity=0.227 Sum_probs=24.1
Q ss_pred CCC-cchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHH
Q 044631 50 RGD-EISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILE 91 (136)
Q Consensus 50 ~G~-~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~ 91 (136)
||. .+.......+..++.+|++++.+ .++..+++...+.
T Consensus 57 ~G~~~~~~~~~~~~~~~d~~ilv~d~~---~~~s~~~~~~~l~ 96 (164)
T smart00175 57 AGQERFRSITSSYYRGAVGALLVYDIT---NRESFENLKNWLK 96 (164)
T ss_pred CChHHHHHHHHHHhCCCCEEEEEEECC---CHHHHHHHHHHHH
Confidence 443 33444556778899999999874 3455555544433
No 108
>PF01915 Glyco_hydro_3_C: Glycosyl hydrolase family 3 C-terminal domain; InterPro: IPR002772 Glycoside hydrolase family 3 GH3 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-xylosidase (3.2.1.37 from EC); N-acetyl beta-glucosaminidase (3.2.1.52 from EC); glucan beta-1,3-glucosidase (3.2.1.58 from EC); cellodextrinase(3.2.1.74 from EC); exo-1,3-1,4-glucanase (3.2.1 from EC). These enzymes are two-domain globular proteins that are N-glycosylated at three sites []. This domain is often C-terminal to the glycoside hydrolase family 3, N-terminal domain IPR001764 from INTERPRO.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3LK6_D 3NVD_B 3BMX_B 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A 1J8V_A 1IEX_A ....
Probab=24.19 E-value=3e+02 Score=20.31 Aligned_cols=85 Identities=13% Similarity=0.103 Sum_probs=51.8
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCC----------------CCCHhHHHHH
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDY----------------ASSKWCLNEL 86 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y----------------~~S~wc~~El 86 (136)
..+...|.+.+.. .++.+.......... ....+..+...+++.+|+++.+.+ ..-+++..+|
T Consensus 46 ~t~~~~l~~~~~~-~~~~~~~~~~~~~~~-~~~~~~~~~~~~aD~vIv~~~~~~~e~~~~~~~~~~~~~~~~l~~~q~~l 123 (227)
T PF01915_consen 46 VTPLDALKQRFGN-AGVVVPEGGDAVDDD-EGIDEAVAAAKEADVVIVFVGRPSGEGNDNNTEGESDRSDLALPANQQEL 123 (227)
T ss_dssp BHHHHHHHHHHHT-TSEEEECCCCCCCCC-SCHHHHHHHHHCSSEEEEEEETTSBCCCSS-EETTGSCSSTBCCCHHHHH
T ss_pred ccHHhhhccccCC-CceEEeeeccccccc-cchHHHHHHhhcCCEEEEeccccccccccccccccCCcccccchhhHHHH
Confidence 3667778888888 777765433222222 334566788889999999988433 3335677787
Q ss_pred HHHHHhhcCCCCEEEEEEeccCcccc
Q 044631 87 VKILECKNTNGQIIIPVFYGVSPSDV 112 (136)
Q Consensus 87 ~~~~~~~~~~~~~iiPVf~~v~p~~v 112 (136)
...+.... ..+|-|+.-..|-++
T Consensus 124 i~~v~~~~---~~~Ivvv~~~~P~~l 146 (227)
T PF01915_consen 124 IKAVAAAG---KKVIVVVNSGNPYDL 146 (227)
T ss_dssp HHHHHHHH---SCEEEEEE-SSGGCG
T ss_pred HHHHHHhc---CCeEEEEecCCcccc
Confidence 77665432 345555554455555
No 109
>PLN02775 Probable dihydrodipicolinate reductase
Probab=24.14 E-value=3.7e+02 Score=21.42 Aligned_cols=72 Identities=4% Similarity=-0.054 Sum_probs=48.1
Q ss_pred ccc-EEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHH
Q 044631 9 NYE-VFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELV 87 (136)
Q Consensus 9 ~yD-VFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~ 87 (136)
..| |.|-|+..+ .....+..++. +|+.+-+-...+ .++-.+.+.++..+=+|++|||.-.---+..+.
T Consensus 79 ~~~~VvIDFT~P~---a~~~~~~~~~~--~g~~~VvGTTG~------~~e~l~~~~~~~~i~vv~apNfSiGv~ll~~l~ 147 (286)
T PLN02775 79 YPNLIVVDYTLPD---AVNDNAELYCK--NGLPFVMGTTGG------DRDRLLKDVEESGVYAVIAPQMGKQVVAFQAAM 147 (286)
T ss_pred CCCEEEEECCChH---HHHHHHHHHHH--CCCCEEEECCCC------CHHHHHHHHhcCCccEEEECcccHHHHHHHHHH
Confidence 488 999999886 34455555555 488887765432 222223455555677889999999888887776
Q ss_pred HHHH
Q 044631 88 KILE 91 (136)
Q Consensus 88 ~~~~ 91 (136)
....
T Consensus 148 ~~aA 151 (286)
T PLN02775 148 EIMA 151 (286)
T ss_pred HHHH
Confidence 6554
No 110
>PLN02908 threonyl-tRNA synthetase
Probab=24.09 E-value=2e+02 Score=25.61 Aligned_cols=60 Identities=8% Similarity=0.055 Sum_probs=40.9
Q ss_pred cccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeec
Q 044631 9 NYEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 9 ~yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
..+|+|-.-+.+. ...+..+.+.|+. .|++|-+|.. +..+...+..|-..---.++|+.+
T Consensus 589 p~qv~Vipv~~~~-~~~A~~va~~LR~-~Gi~vevd~~----~~~l~kkir~A~~~g~~~viivG~ 648 (686)
T PLN02908 589 PRQAIVVPISEKS-QDYAEEVRAQLHA-AGFYVDVDVT----DRKIQKKVREAQLAQYNYILVVGE 648 (686)
T ss_pred CceEEEEEECHHH-HHHHHHHHHHHHH-CCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECc
Confidence 4678777655443 4678999999999 9999998853 456666776665433334555543
No 111
>PF05636 HIGH_NTase1: HIGH Nucleotidyl Transferase; InterPro: IPR008513 This family consists of several bacterial proteins of unknown function.; PDB: 3GMI_A.
Probab=23.75 E-value=1e+02 Score=25.59 Aligned_cols=47 Identities=19% Similarity=0.541 Sum_probs=21.0
Q ss_pred hchhcCcEEEEEeecCCCC-------CHhHHHHHHHHHHhhcCCCCE--EEEEEeccCccc
Q 044631 60 NAIQGSKISVVIFSKDYAS-------SKWCLNELVKILECKNTNGQI--IIPVFYGVSPSD 111 (136)
Q Consensus 60 ~aI~~S~~~I~vlS~~y~~-------S~wc~~El~~~~~~~~~~~~~--iiPVf~~v~p~~ 111 (136)
+.+..++++|+|+|.||++ ++|.+-|++.. + +-+. =+|+.|-+.+.+
T Consensus 25 k~~~~ad~ii~vMSGnFvQRGEPAi~dKw~RA~~AL~--~---GaDLViELP~~~a~qsA~ 80 (388)
T PF05636_consen 25 KKITGADVIIAVMSGNFVQRGEPAIIDKWTRAEMALK--N---GADLVIELPVVYALQSAE 80 (388)
T ss_dssp H---TSSEEEEEE--TTSBTSSB-SS-HHHHHHHHHH--H---T-SEEEE---G-------
T ss_pred hccCCCCEEEEEECCCcccCCCeeeCCHHHHHHHHHH--c---CCCEEEECCCcccccccc
Confidence 3345788999999999996 67888776442 2 2223 368877665554
No 112
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=23.66 E-value=1.3e+02 Score=19.75 Aligned_cols=26 Identities=27% Similarity=0.105 Sum_probs=14.3
Q ss_pred EEecccCcCchhHHHHHHHHHHcCCCCeEE
Q 044631 13 FLNFRGEDTRKSFTCYLYDKLYEGKKIKTF 42 (136)
Q Consensus 13 FISys~~D~~~~fv~~L~~~L~~~~gi~vf 42 (136)
+||+++.. .-+....+.+++ +|.++.
T Consensus 52 ~iS~sG~t---~e~~~~~~~a~~-~g~~vi 77 (126)
T cd05008 52 AISQSGET---ADTLAALRLAKE-KGAKTV 77 (126)
T ss_pred EEeCCcCC---HHHHHHHHHHHH-cCCeEE
Confidence 55555553 234455566666 676654
No 113
>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566).
Probab=22.30 E-value=2.5e+02 Score=19.84 Aligned_cols=55 Identities=15% Similarity=0.190 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHcCCCCeE-EeeCCcccC-----C---CcchHHHHhchhcCcEEEEEeecCCCCCH
Q 044631 24 SFTCYLYDKLYEGKKIKT-FIDDEELRR-----G---DEISPALLNAIQGSKISVVIFSKDYASSK 80 (136)
Q Consensus 24 ~fv~~L~~~L~~~~gi~v-f~d~~~i~~-----G---~~~~~~i~~aI~~S~~~I~vlS~~y~~S~ 80 (136)
..+..+.+.|.. .|..+ .+|-.++.. + .+-...+.+.|.+++ .|++.||.|..|.
T Consensus 17 ~l~~~~~~~l~~-~~~~~~~idl~~l~~~~~~~~~~~~~~~~~l~~~i~~AD-~iI~~sP~Y~~si 80 (171)
T TIGR03567 17 ALLRHVREALQE-QGVEVDHLSVRDLPAEDLLFARFDSPAIKAATAQVAQAD-GVVVATPVYKASY 80 (171)
T ss_pred HHHHHHHHHHHH-CCCeEEEEEecCCChHHhhhcCCCCHHHHHHHHHHHHCC-EEEEECCcccCCC
Confidence 456677777777 77643 344333321 1 122346667778888 6777899998763
No 114
>cd07371 2A5CPDO_AB The alpha and beta subunits 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. This subfamily contains both alpha and beta subunits of 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, an intermediate during p-chloronitrobenzene degradation. 2A5CPDO 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. Alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication.
Probab=22.24 E-value=3.7e+02 Score=20.74 Aligned_cols=78 Identities=12% Similarity=0.038 Sum_probs=47.7
Q ss_pred hhHHHHHHHHHHcCCCCeEEe---eCCcccCCCcchHHHHhchhcCcEEEEEeecCC-CCCHhHHHHHHHHHHhh-cCCC
Q 044631 23 KSFTCYLYDKLYEGKKIKTFI---DDEELRRGDEISPALLNAIQGSKISVVIFSKDY-ASSKWCLNELVKILECK-NTNG 97 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~---d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y-~~S~wc~~El~~~~~~~-~~~~ 97 (136)
..++..|.+.|.. .|+.+-. ....+..|.-..-.. .-.+.++-++.+|=+. ..+..-..+|..++... ++.+
T Consensus 87 ~eLA~~i~~~~~~-~gi~~~~~~~~~~~lDHG~~vPL~~--l~p~~~ipvV~vs~~~~~~~~~~~~~lG~al~~~l~~~~ 163 (268)
T cd07371 87 VELAEACVEEGRK-AGLVTRMMRYPRFPIDTGTITALTL--MRPGTDIPPVVISANNLYLSGEETEGEMDLAGKATRDAG 163 (268)
T ss_pred HHHHHHHHHHHHH-CCCcEEEecCCCCCCCchhHHHHHH--hcCCCCCCeEEEEecCcCCCHHHHHHHHHHHHHHHHHcC
Confidence 5899999999999 9998764 222344554332122 1124566566666443 36777778999888633 4334
Q ss_pred CEEEEE
Q 044631 98 QIIIPV 103 (136)
Q Consensus 98 ~~iiPV 103 (136)
.+|.-|
T Consensus 164 ~rv~iI 169 (268)
T cd07371 164 KRVAVL 169 (268)
T ss_pred CcEEEE
Confidence 455433
No 115
>PLN03108 Rab family protein; Provisional
Probab=21.96 E-value=3.2e+02 Score=19.84 Aligned_cols=21 Identities=5% Similarity=0.172 Sum_probs=15.0
Q ss_pred HhchhcCcEEEEEeecCCCCC
Q 044631 59 LNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 59 ~~aI~~S~~~I~vlS~~y~~S 79 (136)
...+..++.+|+|++.+-..|
T Consensus 73 ~~~~~~ad~~vlv~D~~~~~s 93 (210)
T PLN03108 73 RSYYRGAAGALLVYDITRRET 93 (210)
T ss_pred HHHhccCCEEEEEEECCcHHH
Confidence 345667888999998865544
No 116
>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=21.82 E-value=3.9e+02 Score=20.80 Aligned_cols=61 Identities=8% Similarity=0.072 Sum_probs=33.1
Q ss_pred cEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCC-CcchHHHHhchhcCcEEEEEeec
Q 044631 11 EVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRG-DEISPALLNAIQGSKISVVIFSK 74 (136)
Q Consensus 11 DVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G-~~~~~~i~~aI~~S~~~I~vlS~ 74 (136)
.|.+-|...+-....+..+...+++ .|+.|-... .+.++ .++...+ ..|.+++.-++++.-
T Consensus 146 ~v~~l~~~~~~g~~~~~~~~~~~~~-~G~~vv~~~-~~~~~~~d~~~~i-~~l~~~~~d~v~~~~ 207 (347)
T cd06340 146 TVALVHEDTEFGTSVAEAIKKFAKE-RGFEIVEDI-SYPANARDLTSEV-LKLKAANPDAILPAS 207 (347)
T ss_pred eEEEEecCchHhHHHHHHHHHHHHH-cCCEEEEee-ccCCCCcchHHHH-HHHHhcCCCEEEEcc
Confidence 3555554333234567777788888 888876432 24444 3444444 445554444444433
No 117
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=21.77 E-value=1.4e+02 Score=20.62 Aligned_cols=46 Identities=17% Similarity=0.095 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCcccCC--CcchHHHHhchhcCcEEEEE
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEELRRG--DEISPALLNAIQGSKISVVI 71 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~i~~G--~~~~~~i~~aI~~S~~~I~v 71 (136)
+.....|...|++ .|+.+.... +.+. +.+...+.+++++++++|..
T Consensus 26 d~n~~~l~~~l~~-~G~~v~~~~--~v~Dd~~~i~~~l~~~~~~~DliItt 73 (144)
T TIGR00177 26 DSNGPLLAALLEE-AGFNVSRLG--IVPDDPEEIREILRKAVDEADVVLTT 73 (144)
T ss_pred eCcHHHHHHHHHH-CCCeEEEEe--ecCCCHHHHHHHHHHHHhCCCEEEEC
Confidence 3456678888999 999876432 1122 24455666666666655544
No 118
>PRK13762 tRNA-modifying enzyme; Provisional
Probab=21.69 E-value=2.8e+02 Score=22.16 Aligned_cols=38 Identities=18% Similarity=0.266 Sum_probs=30.0
Q ss_pred ccEEEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcc
Q 044631 10 YEVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEEL 48 (136)
Q Consensus 10 yDVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i 48 (136)
-+|-||..++-.-..++..|...+.+ .|++++++....
T Consensus 131 ~~v~iSl~GEPlL~p~l~eli~~~k~-~Gi~~~L~TNG~ 168 (322)
T PRK13762 131 KHVAISLSGEPTLYPYLPELIEEFHK-RGFTTFLVTNGT 168 (322)
T ss_pred CEEEEeCCccccchhhHHHHHHHHHH-cCCCEEEECCCC
Confidence 35778887776555678888999999 999999987653
No 119
>cd01865 Rab3 Rab3 subfamily. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. 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 promot
Probab=21.46 E-value=2.7e+02 Score=18.90 Aligned_cols=20 Identities=5% Similarity=0.097 Sum_probs=14.4
Q ss_pred HhchhcCcEEEEEeecCCCC
Q 044631 59 LNAIQGSKISVVIFSKDYAS 78 (136)
Q Consensus 59 ~~aI~~S~~~I~vlS~~y~~ 78 (136)
...++.++.++++++-+-..
T Consensus 68 ~~~~~~~~~~l~v~d~~~~~ 87 (165)
T cd01865 68 TAYYRGAMGFILMYDITNEE 87 (165)
T ss_pred HHHccCCcEEEEEEECCCHH
Confidence 34567899999999865433
No 120
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=21.28 E-value=1.6e+02 Score=17.67 Aligned_cols=31 Identities=19% Similarity=0.123 Sum_probs=23.1
Q ss_pred cEEEecccCcCchhHHHHHHHHHHcCCCCeEEee
Q 044631 11 EVFLNFRGEDTRKSFTCYLYDKLYEGKKIKTFID 44 (136)
Q Consensus 11 DVFISys~~D~~~~fv~~L~~~L~~~~gi~vf~d 44 (136)
.+.|+++..+ ..++..+...|.+ .||..-+.
T Consensus 21 ~~~i~~~~~s--~~ll~~v~~lL~~-lGi~~~i~ 51 (77)
T PF14528_consen 21 SVRISISSKS--KELLEDVQKLLLR-LGIKASIY 51 (77)
T ss_dssp EEEEEEEES---HHHHHHHHHHHHH-TT--EEEE
T ss_pred EEEEEEEECC--HHHHHHHHHHHHH-CCCeeEEE
Confidence 4578887776 5899999999999 99988665
No 121
>PRK14495 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/unknown domain fusion protein; Provisional
Probab=21.15 E-value=3.4e+02 Score=23.22 Aligned_cols=29 Identities=3% Similarity=0.154 Sum_probs=22.9
Q ss_pred EEecccCcCchhHHHHHHHHHHcCCCCeEEe
Q 044631 13 FLNFRGEDTRKSFTCYLYDKLYEGKKIKTFI 43 (136)
Q Consensus 13 FISys~~D~~~~fv~~L~~~L~~~~gi~vf~ 43 (136)
++.|++.. +.+++..|...|.. +|++|-.
T Consensus 6 IvG~sgSG-KTTLiekLI~~L~~-rG~rVav 34 (452)
T PRK14495 6 IIGWKDAG-KTGLVERLVAAIAA-RGFSVST 34 (452)
T ss_pred EEecCCCC-HHHHHHHHHHHHHh-CCCeEEE
Confidence 45565544 36899999999999 9999876
No 122
>COG2342 Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism]
Probab=21.04 E-value=1.5e+02 Score=23.89 Aligned_cols=44 Identities=25% Similarity=0.593 Sum_probs=34.5
Q ss_pred HHHHhchhcCcEEEEEeecCCC---CCHhHHHHHHHHHHhhcCCCCEEEEEEe
Q 044631 56 PALLNAIQGSKISVVIFSKDYA---SSKWCLNELVKILECKNTNGQIIIPVFY 105 (136)
Q Consensus 56 ~~i~~aI~~S~~~I~vlS~~y~---~S~wc~~El~~~~~~~~~~~~~iiPVf~ 105 (136)
+.=..+|.+++.-++|+-|++. .++|..+||.+..+ ++ ++||-|
T Consensus 33 d~~~~~i~~~~f~llVVDps~~g~~~~~~~~eelr~~~~----gg--~~pIAY 79 (300)
T COG2342 33 DAYINEILNSPFDLLVVDPSYCGPFNTPWTIEELRTKAD----GG--VKPIAY 79 (300)
T ss_pred cchHHHHhcCCCcEEEEeccccCCCCCcCcHHHHHHHhc----CC--eeEEEE
Confidence 5556889999999999999765 67999999987643 23 778876
No 123
>cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. 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 dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t
Probab=20.99 E-value=2.8e+02 Score=18.76 Aligned_cols=30 Identities=10% Similarity=0.223 Sum_probs=19.7
Q ss_pred CC-CcchHHHHhchhcCcEEEEEeecCCCCC
Q 044631 50 RG-DEISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 50 ~G-~~~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+| +.+.......++.++.+|++++.+-..|
T Consensus 59 ~G~~~~~~~~~~~~~~~~~ii~v~d~~~~~s 89 (166)
T cd01869 59 AGQERFRTITSSYYRGAHGIIIVYDVTDQES 89 (166)
T ss_pred CCcHhHHHHHHHHhCcCCEEEEEEECcCHHH
Confidence 55 3344344566778999999998765443
No 124
>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=20.97 E-value=1.9e+02 Score=23.71 Aligned_cols=53 Identities=23% Similarity=0.248 Sum_probs=34.7
Q ss_pred CcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCC----cchHHHHhchhcCcEEEEEe
Q 044631 19 EDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGD----EISPALLNAIQGSKISVVIF 72 (136)
Q Consensus 19 ~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~----~~~~~i~~aI~~S~~~I~vl 72 (136)
.|.|++=+..|.+.|.+ .|..|...+--..... ...+.+.++++.++.+|+.-
T Consensus 328 ~d~r~sp~~~~~~~L~~-~g~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~ad~~v~~t 384 (411)
T TIGR03026 328 DDVRESPALDIIELLKE-KGAKVKAYDPLVPEEEVKGLPLIDDLEEALKGADALVILT 384 (411)
T ss_pred CccccChHHHHHHHHHh-CCCEEEEECCCCChhhhhhcccCCCHHHHHhCCCEEEEec
Confidence 35677778899999999 9999876543222211 11245567888888766544
No 125
>PRK05569 flavodoxin; Provisional
Probab=20.90 E-value=2.7e+02 Score=18.66 Aligned_cols=47 Identities=11% Similarity=0.113 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCCCCC
Q 044631 23 KSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+..+..+.+.|++ .|+.+-+.. +..-. ...+.+++ .|++-||.|...
T Consensus 16 ~~iA~~i~~~~~~-~g~~v~~~~--~~~~~------~~~~~~~d-~iilgsPty~~~ 62 (141)
T PRK05569 16 EVLANTIADGAKE-AGAEVTIKH--VADAK------VEDVLEAD-AVAFGSPSMDNN 62 (141)
T ss_pred HHHHHHHHHHHHh-CCCeEEEEE--CCcCC------HHHHhhCC-EEEEECCCcCCC
Confidence 5788999999988 887653321 11110 02344555 577788888765
No 126
>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=20.88 E-value=3.4e+02 Score=21.74 Aligned_cols=39 Identities=18% Similarity=-0.028 Sum_probs=22.3
Q ss_pred HHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCc
Q 044631 26 TCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSK 66 (136)
Q Consensus 26 v~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~ 66 (136)
+..|.+.|+. .|+.+-.... ...++.-..++...|+++.
T Consensus 157 ~~~l~~~~~~-~gi~v~~~~~-~~~~~~d~~~~l~~ik~~~ 195 (387)
T cd06386 157 LEGVHHVFQE-EGYHMSIYPF-DETKDLDLDEIIRAIQASE 195 (387)
T ss_pred HHHHHHHHHh-cCceEEEEec-CCCCcccHHHHHHHHHhcC
Confidence 6788888888 8987765432 1233322334455555444
No 127
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=20.60 E-value=88 Score=20.56 Aligned_cols=19 Identities=26% Similarity=0.335 Sum_probs=13.9
Q ss_pred hhHHHHHHHHHHcCCCCeEE
Q 044631 23 KSFTCYLYDKLYEGKKIKTF 42 (136)
Q Consensus 23 ~~fv~~L~~~L~~~~gi~vf 42 (136)
+.|+..|...|.. +|+++-
T Consensus 8 ~~fv~~Lk~lLk~-rGi~v~ 26 (90)
T PF02337_consen 8 QPFVSILKHLLKE-RGIRVK 26 (90)
T ss_dssp HHHHHHHHHHHHC-CT----
T ss_pred hHHHHHHHHHHHH-cCeeec
Confidence 4899999999999 999874
No 128
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=20.36 E-value=1.7e+02 Score=19.27 Aligned_cols=26 Identities=15% Similarity=0.245 Sum_probs=12.9
Q ss_pred EEecccCcCchhHHHHHHHHHHcCCCCeEE
Q 044631 13 FLNFRGEDTRKSFTCYLYDKLYEGKKIKTF 42 (136)
Q Consensus 13 FISys~~D~~~~fv~~L~~~L~~~~gi~vf 42 (136)
++|++++. .. +....+.+++ +|+++.
T Consensus 49 ~iS~SG~t--~e-~i~~~~~a~~-~g~~iI 74 (119)
T cd05017 49 AVSYSGNT--EE-TLSAVEQAKE-RGAKIV 74 (119)
T ss_pred EEECCCCC--HH-HHHHHHHHHH-CCCEEE
Confidence 45555554 22 3344445555 676653
No 129
>PF09152 DUF1937: Domain of unknown function (DUF1937); InterPro: IPR015235 This entry is represented by Bacteriophage N15, Gp57. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a set of hypothetical bacterial and phage proteins whose exact function has not, as yet, been described. ; PDB: 1T1J_A.
Probab=20.28 E-value=2.2e+02 Score=19.62 Aligned_cols=64 Identities=14% Similarity=-0.048 Sum_probs=37.8
Q ss_pred HHHHHHcCCCCeEEee--------CCcc-----cCCCcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhh
Q 044631 29 LYDKLYEGKKIKTFID--------DEEL-----RRGDEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECK 93 (136)
Q Consensus 29 L~~~L~~~~gi~vf~d--------~~~i-----~~G~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~ 93 (136)
-...|-+ .|+.+|-- -.-+ ..+.-|.+--..-++.|+.+|++-.|.+..|.-...|+..+.+..
T Consensus 32 ~aa~l~~-~G~~~fSpv~~sH~~~~~~~~~~~~~~~~~W~~~d~~~L~~c~~lvV~~i~GW~~S~Gi~~Ei~~a~~~~ 108 (116)
T PF09152_consen 32 VAAELLK-AGHAAFSPVVMSHPINFELLGDDDPLIQKLWEDWDRPFLDACDELVVLDIPGWDDSEGIWAEIEAAEEMG 108 (116)
T ss_dssp HHHHHHH-TT-EEEEHHHHHHHHHCCGTTS-HHHHHHHHHHHHHHHHHH-SEEEE---TTGGG-HHHHHHHHHHHHTT
T ss_pred HHHHHHh-cCCeeEeccccccccchhcccccCcchhHHHHHHhHHHHHhcceeEEecCCCccccccHHHHHHHHHHcC
Confidence 3444555 89998833 0111 122334444445567899999999999999999999999887753
No 130
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=20.28 E-value=3.7e+02 Score=20.45 Aligned_cols=68 Identities=19% Similarity=0.257 Sum_probs=27.5
Q ss_pred ccE-EEecccCcCchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhch-hcCcE-EEEEeecCCCCCHh
Q 044631 10 YEV-FLNFRGEDTRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAI-QGSKI-SVVIFSKDYASSKW 81 (136)
Q Consensus 10 yDV-FISys~~D~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI-~~S~~-~I~vlS~~y~~S~w 81 (136)
++| |+-+...+...+|...|...|.. .|+....- ..||+....+-.+.+ .+..+ +-++=++.|+.+.-
T Consensus 63 ~~V~Y~~~~~~~~~~s~~~~L~~~~~~-~~~~~~~~---~~P~d~~l~~~l~~~~~~~~i~~~~~~~~~Fl~s~~ 133 (224)
T PF04244_consen 63 FRVHYIELDDPENTQSFEDALARALKQ-HGIDRLHV---MEPGDYRLEQRLESLAQQLGIPLEVLEDPHFLTSRE 133 (224)
T ss_dssp --EEEE-TT-TT--SSHHHHHHHHHHH-H----EEE---E--S-HHHHHHHHH----SSS-EEEE--TTSSS-HH
T ss_pred CEEEEEeCCCccccccHHHHHHHHHHH-cCCCEEEE---ECCCCHHHHHHHHhhhcccCCceEEeCCCCccCCHH
Confidence 444 44443333223678888888888 77765443 346765544333333 33343 44555777887643
No 131
>KOG0095 consensus GTPase Rab30, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.26 E-value=3.6e+02 Score=19.85 Aligned_cols=63 Identities=16% Similarity=0.296 Sum_probs=36.6
Q ss_pred CCCcchHHHHhchhc-CcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEec--cCcccccc
Q 044631 50 RGDEISPALLNAIQG-SKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYG--VSPSDVRH 114 (136)
Q Consensus 50 ~G~~~~~~i~~aI~~-S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~--v~p~~v~~ 114 (136)
.|..-..+|...--+ +...|++..-....|--|+-|...-++... +.+++.|+.+ ++..+-|.
T Consensus 64 agqerfrsitqsyyrsahalilvydiscqpsfdclpewlreie~ya--n~kvlkilvgnk~d~~drre 129 (213)
T KOG0095|consen 64 AGQERFRSITQSYYRSAHALILVYDISCQPSFDCLPEWLREIEQYA--NNKVLKILVGNKIDLADRRE 129 (213)
T ss_pred cchHHHHHHHHHHhhhcceEEEEEecccCcchhhhHHHHHHHHHHh--hcceEEEeeccccchhhhhh
Confidence 343333344443333 445677777777788888877655555432 3578888884 55554433
No 132
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase, dimeric type. This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases.
Probab=20.25 E-value=3.7e+02 Score=23.54 Aligned_cols=63 Identities=16% Similarity=0.068 Sum_probs=39.5
Q ss_pred CcccEEEecccCc-CchhHHHHHHHHHHcCCCCeEEeeCCcccCCCcchHHHHhchhcCcEEEEEeecCC
Q 044631 8 CNYEVFLNFRGED-TRKSFTCYLYDKLYEGKKIKTFIDDEELRRGDEISPALLNAIQGSKISVVIFSKDY 76 (136)
Q Consensus 8 ~~yDVFISys~~D-~~~~fv~~L~~~L~~~~gi~vf~d~~~i~~G~~~~~~i~~aI~~S~~~I~vlS~~y 76 (136)
+.++|+|-.-.++ .....+..|.+.|+. .|++|.+|.. |. +...+..+-+.---.++++..+-
T Consensus 456 AP~kV~VIpl~~~~el~~~A~eIa~~LR~-~GI~VeiD~s----~s-IGKq~rrADeiGiPf~IIIG~~E 519 (551)
T TIGR00389 456 APIKVAVLPLVNKEELKEIAKEIFQALRK-TGIRIKYDDS----GT-IGKRYRRADEIGTPFCVTIDFET 519 (551)
T ss_pred CCceEEEEEecCcHHHHHHHHHHHHHHHH-CCCEEEEECC----CC-HHHHHHHHHHcCCCEEEEECCch
Confidence 4678776654432 124678899999999 9999999863 32 65566555443333444444433
No 133
>cd04113 Rab4 Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. 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 p
Probab=20.23 E-value=2.8e+02 Score=18.56 Aligned_cols=26 Identities=8% Similarity=0.170 Sum_probs=17.8
Q ss_pred chHHHHhchhcCcEEEEEeecCCCCC
Q 044631 54 ISPALLNAIQGSKISVVIFSKDYASS 79 (136)
Q Consensus 54 ~~~~i~~aI~~S~~~I~vlS~~y~~S 79 (136)
+.......++.++.+|++++.+-..+
T Consensus 62 ~~~~~~~~~~~~~~~i~v~d~~~~~s 87 (161)
T cd04113 62 FRSVTRSYYRGAAGALLVYDITNRTS 87 (161)
T ss_pred HHHhHHHHhcCCCEEEEEEECCCHHH
Confidence 33334456778999999998876443
No 134
>KOG0462 consensus Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.07 E-value=2.7e+02 Score=24.71 Aligned_cols=55 Identities=15% Similarity=0.258 Sum_probs=39.7
Q ss_pred CC-CcchHHHHhchhcCcEEEEEeecCCCCCHhHHHHHHHHHHhhcCCCCEEEEEEeccC
Q 044631 50 RG-DEISPALLNAIQGSKISVVIFSKDYASSKWCLNELVKILECKNTNGQIIIPVFYGVS 108 (136)
Q Consensus 50 ~G-~~~~~~i~~aI~~S~~~I~vlS~~y~~S~wc~~El~~~~~~~~~~~~~iiPVf~~v~ 108 (136)
|| -++.-++...+..|.-+|+|+-.+----.....-+..|++ .+..||||+=+++
T Consensus 133 PGHvDFs~EVsRslaac~G~lLvVDA~qGvqAQT~anf~lAfe----~~L~iIpVlNKID 188 (650)
T KOG0462|consen 133 PGHVDFSGEVSRSLAACDGALLVVDASQGVQAQTVANFYLAFE----AGLAIIPVLNKID 188 (650)
T ss_pred CCcccccceehehhhhcCceEEEEEcCcCchHHHHHHHHHHHH----cCCeEEEeeeccC
Confidence 66 4777888899999999988887654444455555666655 4678999987654
Done!