Query 043195
Match_columns 162
No_of_seqs 156 out of 1201
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 02:26:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043195.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043195hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03210 Resistant to P. syrin 100.0 1E-45 2.3E-50 348.3 14.9 155 1-160 1-155 (1153)
2 PLN03194 putative disease resi 100.0 1.9E-45 4.1E-50 282.3 13.3 131 13-160 24-156 (187)
3 PF01582 TIR: TIR domain; Int 99.9 1.3E-28 2.9E-33 182.1 1.7 133 18-150 1-141 (141)
4 smart00255 TIR Toll - interleu 99.9 1.7E-26 3.6E-31 169.2 12.8 137 15-153 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.8 8.5E-20 1.8E-24 127.5 4.4 87 18-110 1-87 (102)
6 KOG3678 SARM protein (with ste 99.1 3.9E-10 8.4E-15 97.7 8.1 103 13-121 610-730 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.7 3.9E-08 8.5E-13 71.8 5.7 90 16-110 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 98.0 3.1E-05 6.7E-10 57.3 8.0 64 17-80 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.0 0.0022 4.8E-08 46.8 5.7 96 17-117 1-112 (125)
10 PF13271 DUF4062: Domain of un 94.9 0.084 1.8E-06 35.4 5.3 67 17-84 1-68 (83)
11 PF05014 Nuc_deoxyrib_tr: Nucl 91.2 1.1 2.4E-05 31.3 6.6 67 29-96 13-88 (113)
12 COG4271 Predicted nucleotide-b 90.1 1.1 2.3E-05 35.4 6.0 95 17-118 84-199 (233)
13 COG4916 Uncharacterized protei 89.3 0.39 8.5E-06 39.3 3.2 99 12-115 174-280 (329)
14 PF14258 DUF4350: Domain of un 81.8 10 0.00022 24.0 6.5 61 33-105 8-68 (70)
15 cd00860 ThrRS_anticodon ThrRS 70.7 18 0.00038 23.4 5.5 61 16-80 2-62 (91)
16 PF09441 Abp2: ARS binding pro 68.4 2.3 4.9E-05 32.4 0.7 57 83-149 54-111 (175)
17 cd00738 HGTP_anticodon HGTP an 64.7 27 0.00059 22.6 5.5 60 16-79 2-64 (94)
18 PF03129 HGTP_anticodon: Antic 63.7 17 0.00037 24.0 4.4 48 29-79 15-62 (94)
19 PF14359 DUF4406: Domain of un 59.7 44 0.00095 22.8 5.8 62 33-96 19-85 (92)
20 cd00858 GlyRS_anticodon GlyRS 57.7 33 0.00071 24.1 5.2 62 15-81 26-89 (121)
21 KOG2792 Putative cytochrome C 51.9 20 0.00042 29.6 3.5 30 85-114 154-187 (280)
22 cd07363 45_DOPA_Dioxygenase Th 51.6 79 0.0017 25.4 7.0 68 29-98 80-149 (253)
23 PF02310 B12-binding: B12 bind 50.6 78 0.0017 21.6 6.5 69 32-108 17-86 (121)
24 KOG1136 Predicted cleavage and 50.3 24 0.00053 30.4 3.9 45 65-109 191-241 (501)
25 cd02426 Pol_gamma_b_Cterm C-te 48.1 15 0.00032 26.6 2.1 32 29-60 43-78 (128)
26 PF03720 UDPG_MGDP_dh_C: UDP-g 47.3 15 0.00033 25.3 2.0 57 25-81 12-79 (106)
27 cd01424 MGS_CPS_II Methylglyox 46.1 79 0.0017 21.6 5.5 61 17-79 2-76 (110)
28 cd00532 MGS-like MGS-like doma 44.4 67 0.0015 22.2 5.0 60 18-79 2-77 (112)
29 cd07373 2A5CPDO_A The alpha su 42.9 1.8E+02 0.0039 23.5 8.2 76 29-107 90-172 (271)
30 COG0710 AroD 3-dehydroquinate 41.7 91 0.002 25.1 5.8 68 30-101 79-146 (231)
31 cd02042 ParA ParA and ParB of 41.6 1E+02 0.0022 20.3 6.0 74 18-95 3-84 (104)
32 cd00861 ProRS_anticodon_short 41.3 65 0.0014 20.9 4.4 50 29-81 17-66 (94)
33 PF09419 PGP_phosphatase: Mito 40.3 71 0.0015 24.3 4.8 68 38-110 35-112 (168)
34 cd04142 RRP22 RRP22 subfamily. 39.9 1.5E+02 0.0033 22.5 6.8 54 62-118 74-130 (198)
35 COG1658 Small primase-like pro 36.3 58 0.0013 23.8 3.6 55 16-71 30-84 (127)
36 PF10087 DUF2325: Uncharacteri 35.3 1.4E+02 0.003 20.0 6.5 59 30-89 10-69 (97)
37 PF01990 ATP-synt_F: ATP synth 34.3 71 0.0015 21.5 3.7 47 35-83 9-55 (95)
38 TIGR00418 thrS threonyl-tRNA s 33.3 93 0.002 27.8 5.2 61 15-79 470-530 (563)
39 PF11074 DUF2779: Domain of un 33.3 30 0.00066 25.2 1.8 32 60-93 62-93 (130)
40 cd06342 PBP1_ABC_LIVBP_like Ty 33.0 2.1E+02 0.0045 22.8 6.9 58 18-76 138-196 (334)
41 cd06340 PBP1_ABC_ligand_bindin 31.8 1.8E+02 0.0039 23.8 6.4 64 17-81 146-210 (347)
42 PF00875 DNA_photolyase: DNA p 31.5 2E+02 0.0043 21.0 6.0 93 33-132 56-150 (165)
43 PF09837 DUF2064: Uncharacteri 30.9 2E+02 0.0043 20.4 7.4 84 14-107 9-95 (122)
44 cd01423 MGS_CPS_I_III Methylgl 30.8 64 0.0014 22.4 3.1 29 18-48 3-31 (116)
45 KOG3043 Predicted hydrolase re 30.3 1.2E+02 0.0026 24.6 4.8 77 68-146 37-114 (242)
46 cd06386 PBP1_NPR_C_like Ligand 29.7 3.3E+02 0.0072 22.8 7.8 39 32-70 157-195 (387)
47 PF10579 Rapsyn_N: Rapsyn N-te 29.5 34 0.00074 23.0 1.4 21 136-156 21-41 (80)
48 COG0415 PhrB Deoxyribodipyrimi 29.3 2.2E+02 0.0047 25.4 6.7 89 33-130 58-150 (461)
49 COG0576 GrpE Molecular chapero 29.2 1.1E+02 0.0024 23.7 4.4 48 31-82 123-177 (193)
50 PRK09194 prolyl-tRNA synthetas 28.8 61 0.0013 29.3 3.3 63 15-81 468-533 (565)
51 cd00138 PLDc Phospholipase D. 28.7 92 0.002 22.6 3.8 12 56-67 53-64 (176)
52 COG0683 LivK ABC-type branched 28.5 3E+02 0.0065 22.9 7.3 74 17-90 150-223 (366)
53 COG1168 MalY Bifunctional PLP- 28.3 1.5E+02 0.0033 25.8 5.4 46 60-105 148-195 (388)
54 PHA02110 hypothetical protein 28.2 2E+02 0.0042 19.5 4.8 37 46-82 41-78 (98)
55 cd06371 PBP1_sensory_GC_DEF_li 28.0 2.6E+02 0.0055 23.5 6.8 52 30-81 147-201 (382)
56 cd00859 HisRS_anticodon HisRS 27.9 1.6E+02 0.0034 18.3 4.8 58 17-78 3-60 (91)
57 cd06352 PBP1_NPR_GC_like Ligan 27.4 3E+02 0.0065 22.7 7.1 41 29-70 152-195 (389)
58 PF08477 Miro: Miro-like prote 27.4 1.3E+02 0.0029 20.0 4.2 43 63-109 68-113 (119)
59 cd08584 PI-PLCc_GDPD_SF_unchar 27.4 1.4E+02 0.0031 23.3 4.7 35 46-82 127-161 (192)
60 PF13289 SIR2_2: SIR2-like dom 26.9 1.4E+02 0.003 20.8 4.3 12 31-42 76-87 (143)
61 cd02951 SoxW SoxW family; SoxW 26.8 2.1E+02 0.0046 19.5 5.7 29 60-90 4-33 (125)
62 cd01241 PH_Akt Akt pleckstrin 26.5 57 0.0012 22.3 2.1 17 136-152 86-102 (102)
63 PRK13364 protocatechuate 4,5-d 26.3 3.7E+02 0.008 22.1 8.9 79 29-107 98-185 (278)
64 TIGR00334 5S_RNA_mat_M5 ribonu 26.1 93 0.002 24.0 3.4 50 29-81 35-84 (174)
65 PF00350 Dynamin_N: Dynamin fa 25.3 2.5E+02 0.0054 20.0 5.6 46 60-108 120-165 (168)
66 CHL00201 syh histidine-tRNA sy 25.2 1.6E+02 0.0034 25.6 5.1 60 15-78 325-384 (430)
67 cd04904 ACT_AAAH ACT domain of 25.1 1.2E+02 0.0026 19.3 3.4 29 11-42 38-66 (74)
68 COG0400 Predicted esterase [Ge 24.9 1.5E+02 0.0032 23.3 4.5 55 12-67 143-199 (207)
69 PRK14938 Ser-tRNA(Thr) hydrola 24.7 1.7E+02 0.0038 25.4 5.1 59 16-78 275-333 (387)
70 COG2130 Putative NADP-dependen 24.3 1.6E+02 0.0034 25.1 4.6 60 15-82 196-256 (340)
71 PF01915 Glyco_hydro_3_C: Glyc 24.1 3.4E+02 0.0073 20.9 9.7 86 29-117 46-147 (227)
72 PRK02228 V-type ATP synthase s 23.8 1.2E+02 0.0026 20.9 3.3 42 38-82 14-56 (100)
73 cd06366 PBP1_GABAb_receptor Li 23.6 3.2E+02 0.007 22.1 6.5 52 18-70 138-192 (350)
74 TIGR01101 V_ATP_synt_F vacuola 23.4 74 0.0016 22.8 2.3 47 57-114 47-93 (115)
75 cd07371 2A5CPDO_AB The alpha a 23.3 4E+02 0.0087 21.5 7.1 77 29-107 87-169 (268)
76 cd01266 PH_Gab Gab (Grb2-assoc 23.2 72 0.0016 21.9 2.2 17 136-152 92-108 (108)
77 cd01857 HSR1_MMR1 HSR1/MMR1. 23.1 2.8E+02 0.006 19.6 5.5 20 61-80 4-23 (141)
78 cd06335 PBP1_ABC_ligand_bindin 23.1 3.1E+02 0.0068 22.3 6.4 27 29-55 152-178 (347)
79 cd06379 PBP1_iGluR_NMDA_NR1 N- 23.1 2.3E+02 0.0049 23.5 5.5 46 30-75 169-218 (377)
80 PRK12325 prolyl-tRNA synthetas 23.0 2.4E+02 0.0053 24.5 5.8 64 15-82 345-411 (439)
81 cd02986 DLP Dim1 family, Dim1- 22.9 1.7E+02 0.0037 20.9 4.0 52 62-120 5-61 (114)
82 cd03364 TOPRIM_DnaG_primases T 22.7 99 0.0022 19.8 2.7 30 42-72 44-73 (79)
83 COG1058 CinA Predicted nucleot 22.7 88 0.0019 25.6 2.8 42 31-74 22-66 (255)
84 PF01113 DapB_N: Dihydrodipico 22.5 1.4E+02 0.003 21.1 3.6 10 16-25 68-77 (124)
85 cd03411 Ferrochelatase_N Ferro 22.4 3.2E+02 0.007 20.1 6.2 64 30-95 72-142 (159)
86 PRK08350 hypothetical protein; 22.3 89 0.0019 26.7 2.9 32 14-45 280-311 (341)
87 cd03028 GRX_PICOT_like Glutare 22.2 51 0.0011 21.8 1.2 24 72-95 9-34 (90)
88 PF00762 Ferrochelatase: Ferro 22.2 3.1E+02 0.0068 22.8 6.2 67 30-96 73-144 (316)
89 COG0512 PabA Anthranilate/para 21.9 1.3E+02 0.0029 23.5 3.6 48 26-82 8-57 (191)
90 PRK14158 heat shock protein Gr 21.8 2E+02 0.0044 22.4 4.6 47 33-82 127-180 (194)
91 PLN02449 ferrochelatase 21.5 5.6E+02 0.012 23.0 7.8 78 31-110 165-252 (485)
92 TIGR00295 conserved hypothetic 21.4 1.7E+02 0.0036 21.9 4.0 32 123-154 132-163 (164)
93 TIGR00640 acid_CoA_mut_C methy 21.1 3.3E+02 0.007 19.6 8.6 86 17-110 4-90 (132)
94 PF01269 Fibrillarin: Fibrilla 20.9 1E+02 0.0023 24.8 2.9 71 30-110 53-130 (229)
95 PRK08155 acetolactate synthase 20.8 2.6E+02 0.0057 25.0 5.8 36 30-69 14-49 (564)
96 cd06361 PBP1_GPC6A_like Ligand 20.8 2.3E+02 0.0049 24.1 5.2 27 29-55 186-212 (403)
97 PRK14799 thrS threonyl-tRNA sy 20.7 2.1E+02 0.0046 25.9 5.1 60 15-78 438-497 (545)
98 cd06367 PBP1_iGluR_NMDA N-term 20.6 4.7E+02 0.01 21.3 7.0 24 22-45 143-166 (362)
99 cd06328 PBP1_SBP_like_2 Peripl 20.5 3.3E+02 0.0072 22.0 6.0 54 17-71 138-192 (333)
100 PRK15057 UDP-glucose 6-dehydro 20.4 1.9E+02 0.0042 24.8 4.6 50 25-74 311-365 (388)
101 cd04141 Rit_Rin_Ric Rit/Rin/Ri 20.1 3.5E+02 0.0076 19.6 7.1 54 63-118 68-121 (172)
102 PRK14161 heat shock protein Gr 20.1 2.1E+02 0.0045 22.0 4.3 48 32-82 108-162 (178)
No 1
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=1e-45 Score=348.26 Aligned_cols=155 Identities=48% Similarity=0.786 Sum_probs=146.0
Q ss_pred CCCCCCCCCCCCCceeeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCC
Q 043195 1 MASSSSSINMNPQIKYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGY 80 (162)
Q Consensus 1 m~~~~~~~~~~~~~~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 80 (162)
||+||||++ .++|||||||||+|+|++|++||+.+|.++||.+|.|+++++|+.|.+++.+||++|+++|||||++|
T Consensus 1 ~~~~~~~~~---~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~y 77 (1153)
T PLN03210 1 MASSSSSSR---NWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNY 77 (1153)
T ss_pred CCCCCCCCC---CCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCc
Confidence 677665443 58999999999999999999999999999999999998899999999999999999999999999999
Q ss_pred CCChhHHHHHHHHHHHhhhcCCeeEeEEEeeCCcccccccCchHHHHHHHHHHhhhChHHHHHHHHHHHHhhcccccccC
Q 043195 81 ASSRWCLNELVKILESKNKYGQIVVPVFYLVDPSDVRNQTGTIGDSFLKLEERFKEKIDMLQTWRIAMREAANLSGFDSH 160 (162)
Q Consensus 81 ~~S~wc~~El~~~~~~~~~~~~~viPVfy~v~p~dv~~q~~~f~~~f~~~~~~~~~~~e~~~~W~~aL~~v~~~~G~~~~ 160 (162)
++|.||++||++|++|.++.+++|+||||+|+|+|||+|+|.||++|.+++++. +.+++++||.||++||+++||+++
T Consensus 78 a~s~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~ 155 (1153)
T PLN03210 78 ASSSWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQ 155 (1153)
T ss_pred ccchHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecC
Confidence 999999999999999999999999999999999999999999999999988764 478999999999999999999875
No 2
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=1.9e-45 Score=282.28 Aligned_cols=131 Identities=32% Similarity=0.562 Sum_probs=121.6
Q ss_pred CceeeEEEeccccccccchHHHHHHHHccCCceeeecCC-cCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHH
Q 043195 13 QIKYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDK-LNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELV 91 (162)
Q Consensus 13 ~~~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~ 91 (162)
..+|||||||+++|+|++|++||+.+|+++||++|+|+. +.+|+.|.+.|.+||++|+++|+||||+|++|.||++||+
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~ 103 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELA 103 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHH
Confidence 357999999999999999999999999999999999997 9999999999999999999999999999999999999999
Q ss_pred HHHHHhhhcCCeeEeEEEeeCCcccccc-cCchHHHHHHHHHHhhhChHHHHHHHHHHHHhhcccccccC
Q 043195 92 KILESKNKYGQIVVPVFYLVDPSDVRNQ-TGTIGDSFLKLEERFKEKIDMLQTWRIAMREAANLSGFDSH 160 (162)
Q Consensus 92 ~~~~~~~~~~~~viPVfy~v~p~dv~~q-~~~f~~~f~~~~~~~~~~~e~~~~W~~aL~~v~~~~G~~~~ 160 (162)
+|+++. ..||||||+|+|+|||+| .+. .+.+++++||.||++|++++|++++
T Consensus 104 ~I~e~~----~~ViPIFY~VdPsdVr~q~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~ 156 (187)
T PLN03194 104 LIMESK----KRVIPIFCDVKPSQLRVVDNGT-------------CPDEEIRRFNWALEEAKYTVGLTFD 156 (187)
T ss_pred HHHHcC----CEEEEEEecCCHHHhhccccCC-------------CCHHHHHHHHHHHHHHhccccccCC
Confidence 999863 489999999999999997 332 2368999999999999999999775
No 3
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=99.94 E-value=1.3e-28 Score=182.14 Aligned_cols=133 Identities=35% Similarity=0.544 Sum_probs=115.6
Q ss_pred EEEeccccccccchHHHHHHHHccC--CceeeecCC-cCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHH
Q 043195 18 VFLSFRGRDVRHNFISHLNAALCRK--KIETFIDDK-LNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKIL 94 (162)
Q Consensus 18 VFISys~~D~~~~f~~~L~~~L~~~--gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~ 94 (162)
|||||++.+.+..|+.+|..+|+++ |+++|++++ +.+|..+.++|.++|++|+++|+|+|++|+.|+||+.||..|+
T Consensus 1 vfisy~~~~d~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a~ 80 (141)
T PF01582_consen 1 VFISYSGKDDREWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEAL 80 (141)
T ss_dssp EEEEE-GHHGHHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHHH
T ss_pred cEEEeCCCCcHHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhhh
Confidence 8999999333578999999999999 999999886 9999999999999999999999999999999999999999999
Q ss_pred HHhhhc--CCeeEeEEEeeCCcccc-cccCchHHHHHHHHHHhhhC--hHHHHHHHHHHHH
Q 043195 95 ESKNKY--GQIVVPVFYLVDPSDVR-NQTGTIGDSFLKLEERFKEK--IDMLQTWRIAMRE 150 (162)
Q Consensus 95 ~~~~~~--~~~viPVfy~v~p~dv~-~q~~~f~~~f~~~~~~~~~~--~e~~~~W~~aL~~ 150 (162)
++..+. ..+|+||||++.+++++ .+.+.|+..|..+.+....+ ..+...|++++.+
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~~ 141 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRYH 141 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhcC
Confidence 987654 48999999999999999 79999999998877765433 5789999998763
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.94 E-value=1.7e-26 Score=169.17 Aligned_cols=137 Identities=40% Similarity=0.661 Sum_probs=115.7
Q ss_pred eeeEEEeccc-cccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHH
Q 043195 15 KYDVFLSFRG-RDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKI 93 (162)
Q Consensus 15 ~ydVFISys~-~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~ 93 (162)
+|||||||++ .+....|+.+|...|...|+.+|.|+....|... .+|.++|++|+++|+|+||+|+.|+||..|+..+
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~-~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a 79 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDL-EEIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA 79 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccchH-HHHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence 4899999999 3445689999999999999999998764333333 3999999999999999999999999999999999
Q ss_pred HHHhhh-cCCeeEeEEEeeCCcccccccCchHHHHHHHHHHhhhChHHHHHHHHHHHHhhc
Q 043195 94 LESKNK-YGQIVVPVFYLVDPSDVRNQTGTIGDSFLKLEERFKEKIDMLQTWRIAMREAAN 153 (162)
Q Consensus 94 ~~~~~~-~~~~viPVfy~v~p~dv~~q~~~f~~~f~~~~~~~~~~~e~~~~W~~aL~~v~~ 153 (162)
+++..+ ...+||||+++..|+++.++.+.++..+......+..+..+ +.|+.++..+++
T Consensus 80 ~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 80 LENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 987654 67899999999889999999999999998876666543333 799999988764
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.79 E-value=8.5e-20 Score=127.46 Aligned_cols=87 Identities=31% Similarity=0.509 Sum_probs=75.3
Q ss_pred EEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHh
Q 043195 18 VFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESK 97 (162)
Q Consensus 18 VFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~ 97 (162)
|||||+++|. .++..|...|++.|+++|+|+++.+|+.+.+.|.++|++|+.+|+++|++|..|+||..|+..+.+
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 VFISYSSEDR--EFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK-- 76 (102)
T ss_dssp EEEEEEGGGC--CCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC--
T ss_pred eEEEecCCcH--HHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH--
Confidence 8999999994 799999999999999999997799999999999999999999999999999999999999999843
Q ss_pred hhcCCeeEeEEEe
Q 043195 98 NKYGQIVVPVFYL 110 (162)
Q Consensus 98 ~~~~~~viPVfy~ 110 (162)
.+..||||.++
T Consensus 77 --~~~~iipv~~~ 87 (102)
T PF13676_consen 77 --RGKPIIPVRLD 87 (102)
T ss_dssp --TSESEEEEECS
T ss_pred --CCCEEEEEEEC
Confidence 45689999864
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.08 E-value=3.9e-10 Score=97.68 Aligned_cols=103 Identities=26% Similarity=0.418 Sum_probs=81.3
Q ss_pred CceeeEEEeccccccccchHHHHHHHHccCCceeeecCC-cCCCCCcchHHHHhhhhCceEEEEeecCCC----CC----
Q 043195 13 QIKYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDK-LNRGNQISPSLSSAIEGSKISIVIFSKGYA----SS---- 83 (162)
Q Consensus 13 ~~~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~----~S---- 83 (162)
+.+.|||||||+.. ....++-|...|+-+|++||+|-+ +..|. +.+.+.+.|...+.+|+|++|+.+ +.
T Consensus 610 skq~DVFISYRRst-GnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~nCe 687 (832)
T KOG3678|consen 610 SKQIDVFISYRRST-GNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDDNCE 687 (832)
T ss_pred cCCcceEEEeeccc-cHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhccccHH
Confidence 46799999998764 467999999999999999999988 88887 667899999999999999999976 33
Q ss_pred hhHHHHHHHHHHHhhhcCCeeEeEEEe---------eCCcccccccC
Q 043195 84 RWCLNELVKILESKNKYGQIVVPVFYL---------VDPSDVRNQTG 121 (162)
Q Consensus 84 ~wc~~El~~~~~~~~~~~~~viPVfy~---------v~p~dv~~q~~ 121 (162)
.|.-.||.-+++| +..|||||-. +.|.|++-.+.
T Consensus 688 DWVHKEl~~Afe~----~KNIiPI~D~aFE~Pt~ed~iPnDirmi~k 730 (832)
T KOG3678|consen 688 DWVHKELKCAFEH----QKNIIPIFDTAFEFPTKEDQIPNDIRMITK 730 (832)
T ss_pred HHHHHHHHHHHHh----cCCeeeeecccccCCCchhcCcHHHHHHHh
Confidence 4555566666655 5599999843 55666665443
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=98.68 E-value=3.9e-08 Score=71.79 Aligned_cols=90 Identities=22% Similarity=0.381 Sum_probs=47.8
Q ss_pred eeEEEeccccccccchHHHHHHHHccC-------Ccee-ee---------cCC-cCCCCCcchHHHHhhhhCceEEEEee
Q 043195 16 YDVFLSFRGRDVRHNFISHLNAALCRK-------KIET-FI---------DDK-LNRGNQISPSLSSAIEGSKISIVIFS 77 (162)
Q Consensus 16 ydVFISys~~D~~~~f~~~L~~~L~~~-------gi~~-f~---------d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S 77 (162)
|+|||||++.|.. ..+..|...+... .+.. |. +.. ......|...|.++|..|.++||+++
T Consensus 1 ~~vFIS~~~~d~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig 79 (130)
T PF08937_consen 1 YKVFISYSHDDDD-WYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG 79 (130)
T ss_dssp ----------THH--HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred CCccccccccCcH-HHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence 5799999999852 3677777777652 2211 11 111 22334678899999999999999999
Q ss_pred cCCCCChhHHHHHHHHHHHhhhcCCeeEeEEEe
Q 043195 78 KGYASSRWCLNELVKILESKNKYGQIVVPVFYL 110 (162)
Q Consensus 78 ~~y~~S~wc~~El~~~~~~~~~~~~~viPVfy~ 110 (162)
++...|.|+..|+..+++ .+..||-|-+.
T Consensus 80 ~~T~~s~wV~~EI~~A~~----~~~~Ii~V~~~ 108 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALK----KGKPIIGVYLP 108 (130)
T ss_dssp TT----HHHHHHHHHHTT----T---EEEEETT
T ss_pred CCcccCcHHHHHHHHHHH----CCCCEEEEECC
Confidence 999999999999998876 45678887653
No 8
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=98.03 E-value=3.1e-05 Score=57.34 Aligned_cols=64 Identities=20% Similarity=0.360 Sum_probs=52.0
Q ss_pred eEEEeccccccc-cchHHHHHHHHccC-CceeeecCC-cC--CCCCcchHHHHhhhhCceEEEEeecCC
Q 043195 17 DVFLSFRGRDVR-HNFISHLNAALCRK-KIETFIDDK-LN--RGNQISPSLSSAIEGSKISIVIFSKGY 80 (162)
Q Consensus 17 dVFISys~~D~~-~~f~~~L~~~L~~~-gi~~f~d~~-~~--~G~~i~~~i~~aI~~S~~~Ivv~S~~y 80 (162)
.|||||++.... ...|..|...|++. |+.|.+|.. .. ++..+..=+.+.+++++.+|+|+||.+
T Consensus 2 kVfI~Ys~d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~~~~~~~ad~Vliv~S~~~ 70 (150)
T PF08357_consen 2 KVFISYSHDSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWMERQIREADKVLIVCSPGY 70 (150)
T ss_pred eEEEEeCCCCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHHHHHHhcCCEEEEEeccch
Confidence 599999985432 36789999999999 999999986 52 366666677788999999999999654
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=96.98 E-value=0.0022 Score=46.80 Aligned_cols=96 Identities=23% Similarity=0.240 Sum_probs=67.6
Q ss_pred eEEEeccccccccchHHHHHHHHccCCceeeecCC-cCCCCCcchHHHHhhhhCceEEEEeecCCC-------------C
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDK-LNRGNQISPSLSSAIEGSKISIVIFSKGYA-------------S 82 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~-------------~ 82 (162)
.|||.|+ .|. ..+..+..-|+..|+.+..-.+ ...|..+.+.+.+.+.+++..|++++|+=. .
T Consensus 1 kVFIvhg-~~~--~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~a 77 (125)
T PF10137_consen 1 KVFIVHG-RDL--AAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRA 77 (125)
T ss_pred CEEEEeC-CCH--HHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCcccccccc
Confidence 4899998 553 6888898889878887765433 789999999999999999999999999522 2
Q ss_pred ChhHHHHHHHHHHHhhhcCCeeEeEEEe-e-CCcccc
Q 043195 83 SRWCLNELVKILESKNKYGQIVVPVFYL-V-DPSDVR 117 (162)
Q Consensus 83 S~wc~~El~~~~~~~~~~~~~viPVfy~-v-~p~dv~ 117 (162)
-...+.|+..++... +..+++-+.-+ + -|||+.
T Consensus 78 R~NVifE~G~f~g~L--Gr~rv~~l~~~~v~~PSDl~ 112 (125)
T PF10137_consen 78 RQNVIFELGLFIGKL--GRERVFILVKGGVELPSDLS 112 (125)
T ss_pred ccceeehhhHHHhhc--CcceEEEEEcCCccCCcccC
Confidence 234567888877542 22344444321 2 466654
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=94.93 E-value=0.084 Score=35.39 Aligned_cols=67 Identities=21% Similarity=0.175 Sum_probs=48.5
Q ss_pred eEEEeccccccccchHHHHHHHHccCCceeeecCCc-CCCCCcchHHHHhhhhCceEEEEeecCCCCCh
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKL-NRGNQISPSLSSAIEGSKISIVIFSKGYASSR 84 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~-~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~ 84 (162)
.||||-.-.|.. .--..|...|.+.|..+..-+.+ ..+....+.+.+.|++|+++|.++-..|-..+
T Consensus 1 rVFiSSt~~Dl~-~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~~ 68 (83)
T PF13271_consen 1 RVFISSTFRDLK-EERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSVP 68 (83)
T ss_pred CEEEecChhhHH-HHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCCC
Confidence 389998777752 44567777787777765443333 23556667889999999999999999997643
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=91.23 E-value=1.1 Score=31.31 Aligned_cols=67 Identities=16% Similarity=0.064 Sum_probs=48.9
Q ss_pred cchHHHHHHHHccCCceeeecCC--cC---CCC----CcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHH
Q 043195 29 HNFISHLNAALCRKKIETFIDDK--LN---RGN----QISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILES 96 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~--~~---~G~----~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~ 96 (162)
..+...+.+.|++.|+.+|...+ .. .+. .|.+.-.++|++|+++|+++...- .+.-+.-|+..+...
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~al 88 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYAL 88 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHC
Confidence 47889999999999999987553 21 122 333444679999999999998766 566788899988653
No 12
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=90.12 E-value=1.1 Score=35.44 Aligned_cols=95 Identities=22% Similarity=0.211 Sum_probs=66.6
Q ss_pred eEEEeccccccccchHHHHHHHHccC--CceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCC--------CChh-
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRK--KIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYA--------SSRW- 85 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~--gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~--------~S~w- 85 (162)
.|||-|+++ ..+.....+|.+. -..+|.|.-+..|..+.+.+.+-|.+++..|++.+|+=. +-.|
T Consensus 84 kvFvv~ghd----~iArael~allrd~~l~~vi~d~~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~p 159 (233)
T COG4271 84 KVFVVSGHD----AIARAELEALLRDWKLEPVILDGLFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAFP 159 (233)
T ss_pred eEEEEeccH----HHHHHHHHHHhhccccceEEecCcccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhccc
Confidence 999999764 3676767777643 356777777899999999999999999999999999854 1222
Q ss_pred -----HHHHHHHHHHHhhhcCCeeEeEEEe----e-CCccccc
Q 043195 86 -----CLNELVKILESKNKYGQIVVPVFYL----V-DPSDVRN 118 (162)
Q Consensus 86 -----c~~El~~~~~~~~~~~~~viPVfy~----v-~p~dv~~ 118 (162)
...||..++.+. +..+|+- ++. | -|||+..
T Consensus 160 raRqNVifELGm~mgrL--gRkrv~I-l~k~~envelPSDi~G 199 (233)
T COG4271 160 RARQNVIFELGMFMGRL--GRKRVMI-LMKRDENVELPSDIAG 199 (233)
T ss_pred cccccchhhHhhHHhhc--ccceEEE-EecccccccCccccCc
Confidence 566777777643 2234433 332 2 4777654
No 13
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=89.35 E-value=0.39 Score=39.34 Aligned_cols=99 Identities=16% Similarity=0.171 Sum_probs=65.9
Q ss_pred CCceeeEEEeccccccccchHHHHHHHHcc--CCceeeecCC----cCCCCCcchHHHHhh-hhCceEEEEeecCCCCCh
Q 043195 12 PQIKYDVFLSFRGRDVRHNFISHLNAALCR--KKIETFIDDK----LNRGNQISPSLSSAI-EGSKISIVIFSKGYASSR 84 (162)
Q Consensus 12 ~~~~ydVFISys~~D~~~~f~~~L~~~L~~--~gi~~f~d~~----~~~G~~i~~~i~~aI-~~S~~~Ivv~S~~y~~S~ 84 (162)
..+.||+=|||.|+- .+.|+....+++. .-+..|+|.. +-+|+ +.+-+...- ..|+..+|.+..+|....
T Consensus 174 ~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~~~L~~~Y~~rC~~~~VF~~~~Y~~K~ 250 (329)
T COG4916 174 SEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LVSTLDPGYDIRCVVTTVFNTGSYICKS 250 (329)
T ss_pred cccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCcc-HHHhcccccCceEEEEEEEeCCceEEee
Confidence 456799999999986 3799999999983 3455677754 33433 222222222 268889999999999999
Q ss_pred hHHHHHHHHHHHhhhcCCeeEeEEE-eeCCcc
Q 043195 85 WCLNELVKILESKNKYGQIVVPVFY-LVDPSD 115 (162)
Q Consensus 85 wc~~El~~~~~~~~~~~~~viPVfy-~v~p~d 115 (162)
||.-|...+-+- ..-..+.||.| +++-+-
T Consensus 251 ~c~~E~~~~r~~--~~~d~~~rI~~~~~d~~a 280 (329)
T COG4916 251 TCHIEGLEGRLN--PILDTGFRIKYLYADNIA 280 (329)
T ss_pred eeccchhhcccc--ccccccceEEEEecCCcc
Confidence 999988765332 12245677766 344443
No 14
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=81.79 E-value=10 Score=23.97 Aligned_cols=61 Identities=16% Similarity=0.094 Sum_probs=36.7
Q ss_pred HHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeE
Q 043195 33 SHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYGQIVV 105 (162)
Q Consensus 33 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~vi 105 (162)
.-|+.-|++.|+++-..+. ..+++...+-++++++|++.-+. -.++..+.+..+.++..||
T Consensus 8 ~a~~~~L~~~g~~v~~~~~----------~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~v~~G~~lvl 68 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWRK----------PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEWVEAGNTLVL 68 (70)
T ss_pred HHHHHHHHHCCCeeEEecc----------cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHHHHcCCEEEE
Confidence 4567778888988743221 12345557889999999966553 3444444444444555544
No 15
>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=70.68 E-value=18 Score=23.43 Aligned_cols=61 Identities=10% Similarity=0.092 Sum_probs=38.2
Q ss_pred eeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCC
Q 043195 16 YDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGY 80 (162)
Q Consensus 16 ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 80 (162)
++|+|...+.+. ...+-.+...|++.|+.+-+|.. +..+...+..|-+.---.++++.++-
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~---~~~~~~~~~~a~~~g~~~~iiig~~e 62 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLR---NEKLGKKIREAQLQKIPYILVVGDKE 62 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEECcch
Confidence 677776655443 35678899999999999988653 34555555555443333445555443
No 16
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=68.36 E-value=2.3 Score=32.40 Aligned_cols=57 Identities=28% Similarity=0.362 Sum_probs=35.1
Q ss_pred ChhHHHHHHHHHHHhhhcCCeeEeEEEeeCCccccc-ccCchHHHHHHHHHHhhhChHHHHHHHHHHH
Q 043195 83 SRWCLNELVKILESKNKYGQIVVPVFYLVDPSDVRN-QTGTIGDSFLKLEERFKEKIDMLQTWRIAMR 149 (162)
Q Consensus 83 S~wc~~El~~~~~~~~~~~~~viPVfy~v~p~dv~~-q~~~f~~~f~~~~~~~~~~~e~~~~W~~aL~ 149 (162)
|.|-+.||..-++..+-+.=.=+-+.+.|+|-++.+ |+ .++...+.-+++||+.|++
T Consensus 54 s~~~Lf~LI~k~~~keikTW~~La~~LGVepp~~ek~qS----------tQKvqQYaVRLKRWM~aMH 111 (175)
T PF09441_consen 54 STFTLFELIRKLESKEIKTWAQLALELGVEPPDPEKGQS----------TQKVQQYAVRLKRWMRAMH 111 (175)
T ss_pred hHHHHHHHHHHHhhhhHhHHHHHHHHhCCCCCCcccccc----------hHHHHHHHHHHHHHHHHhh
Confidence 467888887766543322222334456788888764 33 2223344789999999986
No 17
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=64.75 E-value=27 Score=22.61 Aligned_cols=60 Identities=18% Similarity=0.190 Sum_probs=38.3
Q ss_pred eeEEEecccc---ccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecC
Q 043195 16 YDVFLSFRGR---DVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKG 79 (162)
Q Consensus 16 ydVFISys~~---D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 79 (162)
++|+|-..+. .. ...+..+...|++.|+.+-+|.. +..+...+..|-..---.++++.++
T Consensus 2 ~~v~ii~~~~~~~~~-~~~a~~~~~~Lr~~g~~v~~~~~---~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVEA-REYAQKLLNALLANGIRVLYDDR---ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHHH-HHHHHHHHHHHHHCCCEEEecCC---CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 5666665433 22 35778899999999999988653 3455555555544444566777763
No 18
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=63.73 E-value=17 Score=23.97 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=33.0
Q ss_pred cchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecC
Q 043195 29 HNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKG 79 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 79 (162)
..++.+|...|.+.|+.+.+|.. +..+...+..|-..=--.++|+.++
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~---~~~~~k~~~~a~~~g~p~~iiiG~~ 62 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDS---DKSLGKQIKYADKLGIPFIIIIGEK 62 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESS---SSTHHHHHHHHHHTTESEEEEEEHH
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCchhHHHHHHhhcCCeEEEEECch
Confidence 46789999999999999988863 4455556666555433455555543
No 19
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=59.70 E-value=44 Score=22.78 Aligned_cols=62 Identities=13% Similarity=0.043 Sum_probs=41.2
Q ss_pred HHHHHHHccCCceeeecCC--cCCCCCcchHH---HHhhhhCceEEEEeecCCCCChhHHHHHHHHHHH
Q 043195 33 SHLNAALCRKKIETFIDDK--LNRGNQISPSL---SSAIEGSKISIVIFSKGYASSRWCLNELVKILES 96 (162)
Q Consensus 33 ~~L~~~L~~~gi~~f~d~~--~~~G~~i~~~i---~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~ 96 (162)
......|+..|..|.---. ...|.++.+-+ ...|..|+.. ++=|++-.|.-|.-|...+...
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 NAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAI--YMLPGWENSRGARLEHELAKKL 85 (92)
T ss_pred HHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEE--EEcCCcccCcchHHHHHHHHHC
Confidence 4577888889977653222 24555544433 3456677744 3459999999999999887653
No 20
>cd00858 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=57.69 E-value=33 Score=24.10 Aligned_cols=62 Identities=11% Similarity=-0.025 Sum_probs=41.0
Q ss_pred eeeEEEeccc--cccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCC
Q 043195 15 KYDVFLSFRG--RDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYA 81 (162)
Q Consensus 15 ~ydVFISys~--~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 81 (162)
.+||||-.-+ .+. ...+..|...|++.|+.+-+|.. ..+...+..|-+.---.++++.++-.
T Consensus 26 p~~v~Ii~~~~~~~~-~~~a~~la~~LR~~gi~v~~d~~----~sl~kqlk~A~k~g~~~~iiiG~~e~ 89 (121)
T cd00858 26 PIKVAVLPLVKRDEL-VEIAKEISEELRELGFSVKYDDS----GSIGRRYARQDEIGTPFCVTVDFDTL 89 (121)
T ss_pred CcEEEEEecCCcHHH-HHHHHHHHHHHHHCCCEEEEeCC----CCHHHHHHHhHhcCCCEEEEECcCch
Confidence 4788887755 322 35678899999999999988652 45655666665544446666665543
No 21
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=51.94 E-value=20 Score=29.59 Aligned_cols=30 Identities=40% Similarity=0.559 Sum_probs=21.8
Q ss_pred hHHHHHHHHHHH---hh-hcCCeeEeEEEeeCCc
Q 043195 85 WCLNELVKILES---KN-KYGQIVVPVFYLVDPS 114 (162)
Q Consensus 85 wc~~El~~~~~~---~~-~~~~~viPVfy~v~p~ 114 (162)
-|-+||.++..- .+ ..+..++|||.-|+|.
T Consensus 154 ICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 154 ICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred cChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 489999886543 32 3466777999999994
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=51.56 E-value=79 Score=25.35 Aligned_cols=68 Identities=16% Similarity=0.134 Sum_probs=47.7
Q ss_pred cchHHHHHHHHccCCceeeecCC--cCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhh
Q 043195 29 HNFISHLNAALCRKKIETFIDDK--LNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKN 98 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~--~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~ 98 (162)
..++.+|.+.|.+.|+.+-.+.+ +--|--+. +.-...+.++-||.+|-+...+..-..+|.+++....
T Consensus 80 ~eLa~~i~~~l~~~gi~~~~~~~~~lDHG~~vP--L~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l~ 149 (253)
T cd07363 80 PELAERVAELLKAAGIPARLDPERGLDHGAWVP--LKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPLR 149 (253)
T ss_pred HHHHHHHHHHHHhcCCCccccCCcCCcccHHHH--HHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhhh
Confidence 47999999999999998765432 33333222 1112234578899999998878887789999987654
No 23
>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=50.60 E-value=78 Score=21.56 Aligned_cols=69 Identities=17% Similarity=0.122 Sum_probs=43.1
Q ss_pred HHHHHHHHccCCceee-ecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeEeEE
Q 043195 32 ISHLNAALCRKKIETF-IDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYGQIVVPVF 108 (162)
Q Consensus 32 ~~~L~~~L~~~gi~~f-~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPVf 108 (162)
...|...|++.|..+- +|-.... +++.+.+.+.+--+|.+|-.+. |...++..+.+..++....+.-|+
T Consensus 17 l~~la~~l~~~G~~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~---~~~~~~~~l~~~~k~~~p~~~iv~ 86 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDANVPP-----EELVEALRAERPDVVGISVSMT---PNLPEAKRLARAIKERNPNIPIVV 86 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSS---THHHHHHHHHHHHHTTCTTSEEEE
T ss_pred HHHHHHHHHHCCCeEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCc---CcHHHHHHHHHHHHhcCCCCEEEE
Confidence 4678888999999884 4443211 6788888888888888876543 344555555554444444433333
No 24
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=50.26 E-value=24 Score=30.39 Aligned_cols=45 Identities=27% Similarity=0.519 Sum_probs=33.9
Q ss_pred hhhhCceEEEEeecCCC----CChhHHH-HHHHH-HHHhhhcCCeeEeEEE
Q 043195 65 AIEGSKISIVIFSKGYA----SSRWCLN-ELVKI-LESKNKYGQIVVPVFY 109 (162)
Q Consensus 65 aI~~S~~~Ivv~S~~y~----~S~wc~~-El~~~-~~~~~~~~~~viPVfy 109 (162)
-|..++--++|--..|+ .|..|.+ |+.+. .+|-..++.++||||-
T Consensus 191 ~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvFA 241 (501)
T KOG1136|consen 191 WIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVFA 241 (501)
T ss_pred hhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEeee
Confidence 45667777776666677 4889977 66665 5788888999999995
No 25
>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=48.09 E-value=15 Score=26.57 Aligned_cols=32 Identities=6% Similarity=0.042 Sum_probs=24.7
Q ss_pred cchHHHHHHHHccCCceeeecCCc----CCCCCcch
Q 043195 29 HNFISHLNAALCRKKIETFIDDKL----NRGNQISP 60 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~----~~G~~i~~ 60 (162)
...+..|+..|...|+.++.|.+. .+|..+.+
T Consensus 43 ~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~~~ 78 (128)
T cd02426 43 RDLCQGLKNELREAGLSVWPGYLETQHSSLEQLLDK 78 (128)
T ss_pred HHHHHHHHHHHHHcCCEEEeccCcccccCHHHHHHh
Confidence 467899999999999999988763 45655543
No 26
>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=47.26 E-value=15 Score=25.31 Aligned_cols=57 Identities=18% Similarity=0.264 Sum_probs=35.3
Q ss_pred cccccchHHHHHHHHccCCceeeecCC-cC----------CCCCcchHHHHhhhhCceEEEEeecCCC
Q 043195 25 RDVRHNFISHLNAALCRKKIETFIDDK-LN----------RGNQISPSLSSAIEGSKISIVIFSKGYA 81 (162)
Q Consensus 25 ~D~~~~f~~~L~~~L~~~gi~~f~d~~-~~----------~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 81 (162)
.|.|.+=+-.|.+.|.+.|+.|...+- +. .|-...+.+.++++.++..|+....+-.
T Consensus 12 ~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~h~~f 79 (106)
T PF03720_consen 12 DDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATDHDEF 79 (106)
T ss_dssp S--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS--GGG
T ss_pred cccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEecCHHH
Confidence 478888899999999999999876543 21 1233345677888999887775554433
No 27
>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=46.12 E-value=79 Score=21.61 Aligned_cols=61 Identities=21% Similarity=0.308 Sum_probs=36.3
Q ss_pred eEEEeccccccccchHHHHHHHHccCCceeeecCC----c-CCCC---------CcchHHHHhhhhCceEEEEeecC
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDK----L-NRGN---------QISPSLSSAIEGSKISIVIFSKG 79 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~----~-~~G~---------~i~~~i~~aI~~S~~~Ivv~S~~ 79 (162)
.||+|.+..|. .-...+.+.|.+.|+++|--.. + ..|- .=.++|.+.|++-++.+||-.|+
T Consensus 2 ~vl~s~~~~~k--~~~~~~~~~l~~~G~~l~aT~gT~~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn~~~ 76 (110)
T cd01424 2 TVFISVADRDK--PEAVEIAKRLAELGFKLVATEGTAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVINTPS 76 (110)
T ss_pred eEEEEEEcCcH--hHHHHHHHHHHHCCCEEEEchHHHHHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEECCC
Confidence 38899987763 3445677777778888864211 0 0111 11246677777777766666554
No 28
>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=44.40 E-value=67 Score=22.23 Aligned_cols=60 Identities=22% Similarity=0.350 Sum_probs=37.5
Q ss_pred EEEeccccccccchHHHHHHHHccCCceeeecCC---------c-----CCCCC-cchHHHHhhhh-CceEEEEeecC
Q 043195 18 VFLSFRGRDVRHNFISHLNAALCRKKIETFIDDK---------L-----NRGNQ-ISPSLSSAIEG-SKISIVIFSKG 79 (162)
Q Consensus 18 VFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~---------~-----~~G~~-i~~~i~~aI~~-S~~~Ivv~S~~ 79 (162)
||||-+..|. .-...+...|.+.|++++--.. + ..+.. -.+++.+.|.+ -++.+||..|+
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--AMLVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEcccH--HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 6888876663 3344666777777887763211 1 11111 12678888888 88888888775
No 29
>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=42.91 E-value=1.8e+02 Score=23.55 Aligned_cols=76 Identities=13% Similarity=0.123 Sum_probs=52.0
Q ss_pred cchHHHHHHHHccCCceee-ecCC---cCCCCCcchHHHHhh--hhCceEEEEeecCCCCChhHHHHHHHHHHH-hhhcC
Q 043195 29 HNFISHLNAALCRKKIETF-IDDK---LNRGNQISPSLSSAI--EGSKISIVIFSKGYASSRWCLNELVKILES-KNKYG 101 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f-~d~~---~~~G~~i~~~i~~aI--~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~-~~~~~ 101 (162)
..++..+.+.|.+.|+.+- .|.. +--|--+. +.-+ ...++-||.+|.+...+.....+|.+++.. .++.+
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA---CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH---HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 4789999999999999885 5542 22333222 2223 146777888999887788888899999884 45545
Q ss_pred CeeEeE
Q 043195 102 QIVVPV 107 (162)
Q Consensus 102 ~~viPV 107 (162)
.+|+-|
T Consensus 167 ~rV~iI 172 (271)
T cd07373 167 KRVAVV 172 (271)
T ss_pred CeEEEE
Confidence 666655
No 30
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=41.69 E-value=91 Score=25.09 Aligned_cols=68 Identities=18% Similarity=0.155 Sum_probs=42.5
Q ss_pred chHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcC
Q 043195 30 NFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYG 101 (162)
Q Consensus 30 ~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~ 101 (162)
.....|.+.++.+| .-|+|=++..++....++.+.-.+-. +|+|-|...+.+.++|+..++..+...+
T Consensus 79 ~~i~ll~~la~~~~-~d~iDiEl~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~ 146 (231)
T COG0710 79 EYIELLKKLAELNG-PDYIDIELSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLG 146 (231)
T ss_pred HHHHHHHHHHhhcC-CCEEEEEccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhC
Confidence 45555666566555 46777663333222223333222333 8899999999999999999988765544
No 31
>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=41.57 E-value=1e+02 Score=20.35 Aligned_cols=74 Identities=18% Similarity=0.204 Sum_probs=44.3
Q ss_pred EEEeccccccccchHHHHHHHHccCCceeee-cCCc-------CCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHH
Q 043195 18 VFLSFRGRDVRHNFISHLNAALCRKKIETFI-DDKL-------NRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNE 89 (162)
Q Consensus 18 VFISys~~D~~~~f~~~L~~~L~~~gi~~f~-d~~~-------~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~E 89 (162)
+|.|..+--.+..++.+|...|.++|.++.. |-+. --+-.+.+....++..|+..|+++.++.. .+..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~----s~~~ 78 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL----DLDG 78 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH----HHHH
Confidence 3556554433446789999999888887764 3221 11122344455788888888888877643 3444
Q ss_pred HHHHHH
Q 043195 90 LVKILE 95 (162)
Q Consensus 90 l~~~~~ 95 (162)
+..+++
T Consensus 79 ~~~~~~ 84 (104)
T cd02042 79 LEKLLE 84 (104)
T ss_pred HHHHHH
Confidence 444433
No 32
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=41.32 E-value=65 Score=20.90 Aligned_cols=50 Identities=16% Similarity=0.174 Sum_probs=32.0
Q ss_pred cchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCC
Q 043195 29 HNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYA 81 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 81 (162)
...+..|...|++.|+++.+|.. +..+...+..|-..---.++++.++-+
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~---~~~l~k~i~~a~~~g~~~~iiiG~~e~ 66 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDR---NERPGVKFADADLIGIPYRIVVGKKSA 66 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCCcccchhHHHhcCCCEEEEECCchh
Confidence 35788899999999999998764 234444555554443345566655443
No 33
>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=40.31 E-value=71 Score=24.34 Aligned_cols=68 Identities=28% Similarity=0.332 Sum_probs=43.3
Q ss_pred HHccCCceeee-cCC--c-CCC-CCcchHHHHhhhhCce-----EEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeEeE
Q 043195 38 ALCRKKIETFI-DDK--L-NRG-NQISPSLSSAIEGSKI-----SIVIFSKGYASSRWCLNELVKILESKNKYGQIVVPV 107 (162)
Q Consensus 38 ~L~~~gi~~f~-d~~--~-~~G-~~i~~~i~~aI~~S~~-----~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPV 107 (162)
.|.+.||+..+ |.+ + .++ +.+.+++.+.+++++. .|+|+|-+--++.---.+-+..++. ..+ |||
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~--~lg---Ipv 109 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEK--ALG---IPV 109 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHH--hhC---CcE
Confidence 38889998764 554 4 455 5677888888887763 4899999876665322333343332 223 888
Q ss_pred EEe
Q 043195 108 FYL 110 (162)
Q Consensus 108 fy~ 110 (162)
|..
T Consensus 110 l~h 112 (168)
T PF09419_consen 110 LRH 112 (168)
T ss_pred EEe
Confidence 743
No 34
>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=39.90 E-value=1.5e+02 Score=22.45 Aligned_cols=54 Identities=11% Similarity=0.114 Sum_probs=33.6
Q ss_pred HHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhc---CCeeEeEEEeeCCccccc
Q 043195 62 LSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKY---GQIVVPVFYLVDPSDVRN 118 (162)
Q Consensus 62 i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~---~~~viPVfy~v~p~dv~~ 118 (162)
...+++.++.+|+|++.+ ++.-++++..+++..... ...=+||+.-....|+..
T Consensus 74 ~~~~~~~ad~iilv~D~~---~~~S~~~~~~~~~~i~~~~~~~~~~~piiivgNK~Dl~~ 130 (198)
T cd04142 74 RFRGLRNSRAFILVYDIC---SPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQR 130 (198)
T ss_pred HHhhhccCCEEEEEEECC---CHHHHHHHHHHHHHHHHhcccCCCCCCEEEEEECccccc
Confidence 445788999999999975 455555555444432211 123368877667777754
No 35
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=36.34 E-value=58 Score=23.76 Aligned_cols=55 Identities=18% Similarity=0.175 Sum_probs=35.8
Q ss_pred eeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCce
Q 043195 16 YDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKI 71 (162)
Q Consensus 16 ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~ 71 (162)
.++|+-..+.=....+++.|..++..+|+-++.|-+ .+|+.|...|.+.+.++..
T Consensus 30 ~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D-~~Ge~Irk~l~~~l~~~~~ 84 (127)
T COG1658 30 AGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD-RKGERIRKKLKEYLPGAKG 84 (127)
T ss_pred CceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC-cchHHHHHHHHHHhccccc
Confidence 455665544311145777788888888888877765 4677777777777766443
No 36
>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=35.28 E-value=1.4e+02 Score=20.02 Aligned_cols=59 Identities=14% Similarity=0.151 Sum_probs=35.7
Q ss_pred chHHHHHHHHccCCceeeecCCcCCCC-CcchHHHHhhhhCceEEEEeecCCCCChhHHHH
Q 043195 30 NFISHLNAALCRKKIETFIDDKLNRGN-QISPSLSSAIEGSKISIVIFSKGYASSRWCLNE 89 (162)
Q Consensus 30 ~f~~~L~~~L~~~gi~~f~d~~~~~G~-~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~E 89 (162)
.-...+...+++.|...-.. .-..|. .-...|...|.+++++|++..----...|...+
T Consensus 10 ~~~~~~~~~~~~~G~~~~~h-g~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~ 69 (97)
T PF10087_consen 10 DRERRYKRILEKYGGKLIHH-GRDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKK 69 (97)
T ss_pred ccHHHHHHHHHHcCCEEEEE-ecCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHH
Confidence 34667888888889876554 111122 122247788999999888765544444454433
No 37
>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=34.33 E-value=71 Score=21.46 Aligned_cols=47 Identities=11% Similarity=0.189 Sum_probs=32.7
Q ss_pred HHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCC
Q 043195 35 LNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASS 83 (162)
Q Consensus 35 L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S 83 (162)
+..-++-.|+..+... ...+.....+.+.+++.++.|++++++++..
T Consensus 9 ~v~gFrLaGv~~~~~~--~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~ 55 (95)
T PF01990_consen 9 TVLGFRLAGVEGVYVN--TDPEEAEEALKELLKDEDVGIIIITEDLAEK 55 (95)
T ss_dssp HHHHHHHTTSEEEEES--HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT
T ss_pred HHHHHHHcCCCCccCC--CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH
Confidence 3445566799887754 0123455566677778999999999998873
No 38
>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=33.35 E-value=93 Score=27.85 Aligned_cols=61 Identities=10% Similarity=0.160 Sum_probs=41.6
Q ss_pred eeeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecC
Q 043195 15 KYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKG 79 (162)
Q Consensus 15 ~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 79 (162)
..+|+|-.-+++. ...+..|...|++.|+.|-+|.. +..+...+..|-+.---.++|+.++
T Consensus 470 p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~---~~sl~~q~k~A~~~g~~~~iiiG~~ 530 (563)
T TIGR00418 470 PVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR---NERLGKKIREAQKQKIPYMLVVGDK 530 (563)
T ss_pred CceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC---CCCHHHHHHHHHhcCCCEEEEEchh
Confidence 4778877655443 46788999999999999988753 4556666666655444456666553
No 39
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=33.25 E-value=30 Score=25.18 Aligned_cols=32 Identities=31% Similarity=0.457 Sum_probs=17.8
Q ss_pred hHHHHhhhhCceEEEEeecCCCCChhHHHHHHHH
Q 043195 60 PSLSSAIEGSKISIVIFSKGYASSRWCLNELVKI 93 (162)
Q Consensus 60 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~ 93 (162)
..+.++|..-...|++.+..|-++ |+.||..+
T Consensus 62 ~~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~ 93 (130)
T PF11074_consen 62 EALIKAIGSIYGSIVVYNKSFEKT--RLKELAEL 93 (130)
T ss_pred HHHHHHhhhhcCeEEEechHHHHH--HHHHHHHH
Confidence 344444444435666666665543 77777665
No 40
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=33.03 E-value=2.1e+02 Score=22.82 Aligned_cols=58 Identities=14% Similarity=0.156 Sum_probs=31.9
Q ss_pred EEEeccccccccchHHHHHHHHccCCceeeecCCcCCCC-CcchHHHHhhhhCceEEEEe
Q 043195 18 VFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGN-QISPSLSSAIEGSKISIVIF 76 (162)
Q Consensus 18 VFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~-~i~~~i~~aI~~S~~~Ivv~ 76 (162)
|.+-|...+.....+..|...|+..|+++-....+.+|. .+. .+...|+++..-+|++
T Consensus 138 v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~d~~-~~l~~i~~~~~~~vi~ 196 (334)
T cd06342 138 VAIIDDKTAYGQGLADEFKKALKAAGGKVVAREGTTDGATDFS-AILTKIKAANPDAVFF 196 (334)
T ss_pred EEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEecCCCCCccHH-HHHHHHHhcCCCEEEE
Confidence 444443333334566778888888888775444455553 344 4445566654444443
No 41
>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=31.78 E-value=1.8e+02 Score=23.76 Aligned_cols=64 Identities=8% Similarity=0.039 Sum_probs=36.0
Q ss_pred eEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCC-CcchHHHHhhhhCceEEEEeecCCC
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGN-QISPSLSSAIEGSKISIVIFSKGYA 81 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~-~i~~~i~~aI~~S~~~Ivv~S~~y~ 81 (162)
.|.+-|...+-....+..+...+++.|+.+-....+.+++ ++. .+...|.+++.-+|++.-...
T Consensus 146 ~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~-~~i~~l~~~~~d~v~~~~~~~ 210 (347)
T cd06340 146 TVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPANARDLT-SEVLKLKAANPDAILPASYTN 210 (347)
T ss_pred eEEEEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCCCcchH-HHHHHHHhcCCCEEEEcccch
Confidence 3555453222224566777778888888775444455554 444 444556666655555554443
No 42
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=31.49 E-value=2e+02 Score=20.99 Aligned_cols=93 Identities=19% Similarity=0.241 Sum_probs=47.6
Q ss_pred HHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeEeEEE--e
Q 043195 33 SHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYGQIVVPVFY--L 110 (162)
Q Consensus 33 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPVfy--~ 110 (162)
..|..+|.+.|+...+- .|+ ..+.+.+-+++..+.-|++..+|..-. ...-..+.+...+.+-.+.-+-- =
T Consensus 56 ~~L~~~L~~~g~~L~v~----~g~-~~~~l~~l~~~~~~~~V~~~~~~~~~~--~~rd~~v~~~l~~~~i~~~~~~~~~L 128 (165)
T PF00875_consen 56 ADLQESLRKLGIPLLVL----RGD-PEEVLPELAKEYGATAVYFNEEYTPYE--RRRDERVRKALKKHGIKVHTFDDHTL 128 (165)
T ss_dssp HHHHHHHHHTTS-EEEE----ESS-HHHHHHHHHHHHTESEEEEE---SHHH--HHHHHHHHHHHHHTTSEEEEE--SSS
T ss_pred HHHHHHHHhcCcceEEE----ecc-hHHHHHHHHHhcCcCeeEeccccCHHH--HHHHHHHHHHHHhcceEEEEECCcEE
Confidence 55788888889887652 344 233555666777899999999987622 12111222222222323321111 1
Q ss_pred eCCcccccccCchHHHHHHHHH
Q 043195 111 VDPSDVRNQTGTIGDSFLKLEE 132 (162)
Q Consensus 111 v~p~dv~~q~~~f~~~f~~~~~ 132 (162)
+.|.++....|..-+.|....+
T Consensus 129 ~~~~~i~~~~~~~~~vFtpf~k 150 (165)
T PF00875_consen 129 VPPDDIPKKDGEPYKVFTPFRK 150 (165)
T ss_dssp S-HHHCHSTTSSSHSSHHHHHH
T ss_pred EeccccccCCCCCcccHHHHHH
Confidence 5688887777766666654433
No 43
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=30.91 E-value=2e+02 Score=20.44 Aligned_cols=84 Identities=13% Similarity=0.228 Sum_probs=43.0
Q ss_pred ceeeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhC---ceEEEEeecCCCCChhHHHHH
Q 043195 14 IKYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGS---KISIVIFSKGYASSRWCLNEL 90 (162)
Q Consensus 14 ~~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~~S~wc~~El 90 (162)
..+|++|.|.+...+ .....+ ....++.++. +.|..+.+.+.+|++.. .-.|+++.-+-.. -+...|
T Consensus 9 ~~~~~~l~~~~~~~~-~~~~~~---~~~~~~~~~~----Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~--l~~~~l 78 (122)
T PF09837_consen 9 DGADVVLAYTPDGDH-AAFRQL---WLPSGFSFFP----QQGGDLGERMANAFQQAARGYEPVVLIGSDCPD--LTPDDL 78 (122)
T ss_dssp SSSEEEEEE----TT-HHHHHH---HH-TTSEEEE------SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT----HHHH
T ss_pred CCcCEEEEEcCCccH-HHHhcc---ccCCCCEEee----cCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCC--CCHHHH
Confidence 468999999877643 333333 3333554443 46777777777776655 3366666666554 345566
Q ss_pred HHHHHHhhhcCCeeEeE
Q 043195 91 VKILESKNKYGQIVVPV 107 (162)
Q Consensus 91 ~~~~~~~~~~~~~viPV 107 (162)
..+.+..+....++-|-
T Consensus 79 ~~A~~~L~~~d~VlgPa 95 (122)
T PF09837_consen 79 EQAFEALQRHDVVLGPA 95 (122)
T ss_dssp HHHHHHTTT-SEEEEEB
T ss_pred HHHHHHhccCCEEEeec
Confidence 66766665555555553
No 44
>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=30.79 E-value=64 Score=22.35 Aligned_cols=29 Identities=7% Similarity=0.085 Sum_probs=21.8
Q ss_pred EEEeccccccccchHHHHHHHHccCCceeee
Q 043195 18 VFLSFRGRDVRHNFISHLNAALCRKKIETFI 48 (162)
Q Consensus 18 VFISys~~D~~~~f~~~L~~~L~~~gi~~f~ 48 (162)
||||.+..|. .-...+.+.|...|++++-
T Consensus 3 vlisv~~~dk--~~~~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYSK--PELLPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCcccc--hhHHHHHHHHHHCCCEEEE
Confidence 7999987764 3455777888888988864
No 45
>KOG3043 consensus Predicted hydrolase related to dienelactone hydrolase [General function prediction only]
Probab=30.27 E-value=1.2e+02 Score=24.64 Aligned_cols=77 Identities=14% Similarity=0.117 Sum_probs=50.6
Q ss_pred hCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeEeEEEeeCCcccccccCchHHHHHHHHH-HhhhChHHHHHHHH
Q 043195 68 GSKISIVIFSKGYASSRWCLNELVKILESKNKYGQIVVPVFYLVDPSDVRNQTGTIGDSFLKLEE-RFKEKIDMLQTWRI 146 (162)
Q Consensus 68 ~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPVfy~v~p~dv~~q~~~f~~~f~~~~~-~~~~~~e~~~~W~~ 146 (162)
.+...|++|+.=|--+.--..|....+.+ .+=.+++|=||..+|-....|...+.+-+..+.- ....+-..+.+|.+
T Consensus 37 ~~~~~li~i~DvfG~~~~n~r~~Adk~A~--~Gy~v~vPD~~~Gdp~~~~~~~~~~~~w~~~~~~~~~~~~i~~v~k~lk 114 (242)
T KOG3043|consen 37 SSKKVLIVIQDVFGFQFPNTREGADKVAL--NGYTVLVPDFFRGDPWSPSLQKSERPEWMKGHSPPKIWKDITAVVKWLK 114 (242)
T ss_pred CCCeEEEEEEeeeccccHHHHHHHHHHhc--CCcEEEcchhhcCCCCCCCCChhhhHHHHhcCCcccchhHHHHHHHHHH
Confidence 34479999999998776666666665543 2447899999999999988887666554443311 11123445666655
No 46
>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=29.69 E-value=3.3e+02 Score=22.78 Aligned_cols=39 Identities=10% Similarity=0.003 Sum_probs=22.9
Q ss_pred HHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCc
Q 043195 32 ISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSK 70 (162)
Q Consensus 32 ~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~ 70 (162)
+..|.+.|+..|+.+-.......++.-..++.+.|+++.
T Consensus 157 ~~~l~~~~~~~gi~v~~~~~~~~~~~d~~~~l~~ik~~~ 195 (387)
T cd06386 157 LEGVHHVFQEEGYHMSIYPFDETKDLDLDEIIRAIQASE 195 (387)
T ss_pred HHHHHHHHHhcCceEEEEecCCCCcccHHHHHHHHHhcC
Confidence 677888888888776543323344433345555565544
No 47
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=29.50 E-value=34 Score=23.00 Aligned_cols=21 Identities=29% Similarity=0.517 Sum_probs=17.1
Q ss_pred hChHHHHHHHHHHHHhhcccc
Q 043195 136 EKIDMLQTWRIAMREAANLSG 156 (162)
Q Consensus 136 ~~~e~~~~W~~aL~~v~~~~G 156 (162)
++.+-+.+|+.||.++.+-.+
T Consensus 21 ~~~~Al~~W~~aL~k~~~~~~ 41 (80)
T PF10579_consen 21 ETQQALQKWRKALEKITDRED 41 (80)
T ss_pred hHHHHHHHHHHHHhhcCChHH
Confidence 346789999999999988654
No 48
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=29.34 E-value=2.2e+02 Score=25.42 Aligned_cols=89 Identities=19% Similarity=0.343 Sum_probs=53.1
Q ss_pred HHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHH-hhhcCCeeEeEEEe-
Q 043195 33 SHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILES-KNKYGQIVVPVFYL- 110 (162)
Q Consensus 33 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~-~~~~~~~viPVfy~- 110 (162)
..|..+|...|+++++-. |+.. ..+.+-+++..+..|+...+| ..| ..+-..++.. ..+.+..+.- |.+
T Consensus 58 ~~L~~~L~~~gi~L~v~~----~~~~-~~l~~~~~~~~~~~v~~n~~~--~~~-~~~rD~al~~~l~~~gi~~~~-~~d~ 128 (461)
T COG0415 58 QALQQSLAELGIPLLVRE----GDPE-QVLPELAKQLAATTVFWNRDY--EEW-ERQRDAALAQPLTEVGIAVHS-FWDA 128 (461)
T ss_pred HHHHHHHHHcCCceEEEe----CCHH-HHHHHHHHHhCcceEEeeeee--chh-HHHHHHHHHHHHHhcCceEEE-eccc
Confidence 448888889999988743 4433 245566666668888888888 333 3333333332 2233333333 433
Q ss_pred --eCCcccccccCchHHHHHHH
Q 043195 111 --VDPSDVRNQTGTIGDSFLKL 130 (162)
Q Consensus 111 --v~p~dv~~q~~~f~~~f~~~ 130 (162)
..|.+|+.+.|..-+.|...
T Consensus 129 ~l~~p~~~~t~~~~~y~vfT~F 150 (461)
T COG0415 129 LLHEPGEVRTGSGEPYKVFTPF 150 (461)
T ss_pred cccCHhhccCCCCCCccccchH
Confidence 68999999888554444433
No 49
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=29.17 E-value=1.1e+02 Score=23.71 Aligned_cols=48 Identities=23% Similarity=0.400 Sum_probs=35.7
Q ss_pred hHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhC-------ceEEEEeecCCCC
Q 043195 31 FISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGS-------KISIVIFSKGYAS 82 (162)
Q Consensus 31 f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S-------~~~Ivv~S~~y~~ 82 (162)
....|...|.+.|+..+- ..|+.+.|++-+|+... ..++-|+.+.|.-
T Consensus 123 ~~~~l~~~L~k~Gv~~i~----~~Ge~FDP~~HeAv~~~~~~~~~~~tVv~v~qkGY~l 177 (193)
T COG0576 123 TLDQLLDALEKLGVEEIG----PEGEKFDPNLHEAVQRVESEDVEPNTVVEVLQKGYKL 177 (193)
T ss_pred HHHHHHHHHHHCCCEEeC----CCCCCCCHHHhhheeeecCCCCCCCeEEEEeecCeee
Confidence 346788888899997643 25999999999998743 3577788888753
No 50
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=28.83 E-value=61 Score=29.25 Aligned_cols=63 Identities=16% Similarity=0.183 Sum_probs=39.2
Q ss_pred eeeEEEeccc-c-ccccchHHHHHHHHccCCceeeecCC-cCCCCCcchHHHHhhhhCceEEEEeecCCC
Q 043195 15 KYDVFLSFRG-R-DVRHNFISHLNAALCRKKIETFIDDK-LNRGNQISPSLSSAIEGSKISIVIFSKGYA 81 (162)
Q Consensus 15 ~ydVFISys~-~-D~~~~f~~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 81 (162)
.++|+|---. . +.-...+..|+..|++.|+.+.+|++ -.+|..+.+.-..+ --.++++.++..
T Consensus 468 P~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~~~ad~~G----iP~~iiiG~~e~ 533 (565)
T PRK09194 468 PFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKFADADLIG----IPHRIVVGDRGL 533 (565)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHHHHHHhcC----CCEEEEEcCccc
Confidence 4888886543 1 22246788999999999999999875 44554443322211 125566666543
No 51
>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=28.66 E-value=92 Score=22.64 Aligned_cols=12 Identities=25% Similarity=0.138 Sum_probs=5.2
Q ss_pred CCcchHHHHhhh
Q 043195 56 NQISPSLSSAIE 67 (162)
Q Consensus 56 ~~i~~~i~~aI~ 67 (162)
..+.+.|.++.+
T Consensus 53 ~~l~~~L~~a~~ 64 (176)
T cd00138 53 PVILDALLAAAR 64 (176)
T ss_pred hHHHHHHHHHHH
Confidence 334444444444
No 52
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=28.46 E-value=3e+02 Score=22.93 Aligned_cols=74 Identities=14% Similarity=0.075 Sum_probs=45.3
Q ss_pred eEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHH
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNEL 90 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El 90 (162)
.|+|-++...-.+.+...+.+.|+..|.++-.+....+++.-...+...|..+..-+|++...+....-...++
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~ 223 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVVEEVYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQA 223 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCCCChHHHHHHHHhcCCCEEEECCCCccchHHHHHH
Confidence 45565655444567888888889888887433334555543344566666666666666666665554444444
No 53
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=28.34 E-value=1.5e+02 Score=25.76 Aligned_cols=46 Identities=22% Similarity=0.267 Sum_probs=34.7
Q ss_pred hHHHHhhhhCc-eEEEEeecCCC-CChhHHHHHHHHHHHhhhcCCeeE
Q 043195 60 PSLSSAIEGSK-ISIVIFSKGYA-SSRWCLNELVKILESKNKYGQIVV 105 (162)
Q Consensus 60 ~~i~~aI~~S~-~~Ivv~S~~y~-~S~wc~~El~~~~~~~~~~~~~vi 105 (162)
+.+.+++.+.+ ...++.+|+=- -.-|-.+||.++.+...+.+-+||
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 47778888887 67777888754 578999999999886555555554
No 54
>PHA02110 hypothetical protein
Probab=28.15 E-value=2e+02 Score=19.53 Aligned_cols=37 Identities=22% Similarity=0.200 Sum_probs=23.6
Q ss_pred eeecCC-cCCCCCcchHHHHhhhhCceEEEEeecCCCC
Q 043195 46 TFIDDK-LNRGNQISPSLSSAIEGSKISIVIFSKGYAS 82 (162)
Q Consensus 46 ~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 82 (162)
+|+.+. +.+.-..--++.+-+..|+-.-+++-.+|++
T Consensus 41 vf~~d~~~~~d~~~~~e~~r~~h~s~ei~~~mvddyvs 78 (98)
T PHA02110 41 VFIGDPPIDPDLCVVFEKVRYIHKSNEIHAIMVDDYVS 78 (98)
T ss_pred EEeCCCCCCCceeehHHHHHHhhccCcEEEEEEehhhc
Confidence 455444 4444444456677777777777777777776
No 55
>cd06371 PBP1_sensory_GC_DEF_like Ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phyloge
Probab=27.99 E-value=2.6e+02 Score=23.46 Aligned_cols=52 Identities=8% Similarity=0.082 Sum_probs=29.0
Q ss_pred chHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhC---ceEEEEeecCCC
Q 043195 30 NFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGS---KISIVIFSKGYA 81 (162)
Q Consensus 30 ~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~ 81 (162)
.....|.+.|++.|+.+-....+.+++.-...+.+.|+.. +++|+.....+.
T Consensus 147 ~~~~~l~~~l~~~gi~v~~~~~~~~~~~d~~~~L~~lk~~~~~~viv~~~~~~~~ 201 (382)
T cd06371 147 ETAQKLASALRAHGLPVGLVTSMGPDEKGAREALKKVRSADRVRVVIMCMHSVLI 201 (382)
T ss_pred HHHHHHHHHHHHCCCcEEEEEEecCCHHHHHHHHHHHhcCCCcEEEEEEeecccc
Confidence 4567788888888886644333554543233555556643 344444444444
No 56
>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=27.95 E-value=1.6e+02 Score=18.33 Aligned_cols=58 Identities=21% Similarity=0.194 Sum_probs=33.0
Q ss_pred eEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeec
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSK 78 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 78 (162)
||+|-..+.+. ..-+-.+...|++.|+.+.++.. +..+...+..|-..--..++++.+
T Consensus 3 ~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~---~~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 3 DVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYG---GRKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred cEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecC---CCCHHHHHHHHHHcCCCEEEEEcH
Confidence 67666544432 23467788999999999877542 123444444443333234555554
No 57
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=27.44 E-value=3e+02 Score=22.68 Aligned_cols=41 Identities=15% Similarity=0.058 Sum_probs=23.8
Q ss_pred cchHHHHHHHHccCCceeeecCCcCCC---CCcchHHHHhhhhCc
Q 043195 29 HNFISHLNAALCRKKIETFIDDKLNRG---NQISPSLSSAIEGSK 70 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~~~G---~~i~~~i~~aI~~S~ 70 (162)
...+..+.++|++.|+.+-....+.++ ..+.+.+ +.|..+.
T Consensus 152 ~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l-~~i~~~~ 195 (389)
T cd06352 152 FFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEIL-QDIKRRS 195 (389)
T ss_pred HHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHH-HHhhhcc
Confidence 356677888888888776443334554 3444444 4455544
No 58
>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=27.42 E-value=1.3e+02 Score=19.97 Aligned_cols=43 Identities=14% Similarity=0.246 Sum_probs=25.7
Q ss_pred HHhhhhCceEEEEeecCCCCChhHHHHHHHH---HHHhhhcCCeeEeEEE
Q 043195 63 SSAIEGSKISIVIFSKGYASSRWCLNELVKI---LESKNKYGQIVVPVFY 109 (162)
Q Consensus 63 ~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~---~~~~~~~~~~viPVfy 109 (162)
...+..++.+|+|++..- +..++++..+ +...+..... +||.+
T Consensus 68 ~~~~~~~d~~ilv~D~s~---~~s~~~~~~~~~~l~~~~~~~~~-~piil 113 (119)
T PF08477_consen 68 QFFLKKADAVILVYDLSD---PESLEYLSQLLKWLKNIRKRDKN-IPIIL 113 (119)
T ss_dssp HHHHHHSCEEEEEEECCG---HHHHHHHHHHHHHHHHHHHHSSC-SEEEE
T ss_pred cchhhcCcEEEEEEcCCC---hHHHHHHHHHHHHHHHHHccCCC-CCEEE
Confidence 345899999999998654 4445554333 3333332333 77665
No 59
>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=27.38 E-value=1.4e+02 Score=23.28 Aligned_cols=35 Identities=14% Similarity=0.107 Sum_probs=27.0
Q ss_pred eeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCC
Q 043195 46 TFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYAS 82 (162)
Q Consensus 46 ~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 82 (162)
||+|. .-+..+..++.....+..+-|+++||.--.
T Consensus 127 VW~D~--f~~~~~~~~~~~~~~~~~~~~c~VSpELh~ 161 (192)
T cd08584 127 VWIDS--FTSLWLDNDLILKLLKAGKKICLVSPELHG 161 (192)
T ss_pred EEEec--ccccCCCHHHHHHHHHCCcEEEEECHHHcC
Confidence 78876 234667778888888889999999998554
No 60
>PF13289 SIR2_2: SIR2-like domain
Probab=26.95 E-value=1.4e+02 Score=20.78 Aligned_cols=12 Identities=33% Similarity=0.395 Sum_probs=5.5
Q ss_pred hHHHHHHHHccC
Q 043195 31 FISHLNAALCRK 42 (162)
Q Consensus 31 f~~~L~~~L~~~ 42 (162)
+-..|...|..+
T Consensus 76 ~~~~l~~~l~~~ 87 (143)
T PF13289_consen 76 FPNFLRSLLRSK 87 (143)
T ss_pred HHHHHHHHHcCC
Confidence 444455555433
No 61
>cd02951 SoxW SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to sulfate. SoxW is specifically kept in the reduced state by SoxV, which is essential in thiosulfate oxidation.
Probab=26.79 E-value=2.1e+02 Score=19.54 Aligned_cols=29 Identities=21% Similarity=0.295 Sum_probs=19.7
Q ss_pred hHHHHhhhhC-ceEEEEeecCCCCChhHHHHH
Q 043195 60 PSLSSAIEGS-KISIVIFSKGYASSRWCLNEL 90 (162)
Q Consensus 60 ~~i~~aI~~S-~~~Ivv~S~~y~~S~wc~~El 90 (162)
+++.+|+++- +.++|.|..... ++|....
T Consensus 4 ~~~~~a~~~~~k~vlv~f~a~wC--~~C~~~~ 33 (125)
T cd02951 4 EDLAEAAADGKKPLLLLFSQPGC--PYCDKLK 33 (125)
T ss_pred HHHHHHHHcCCCcEEEEEeCCCC--HHHHHHH
Confidence 5677888888 777777765553 5676543
No 62
>cd01241 PH_Akt Akt pleckstrin homology (PH) domain. Akt pleckstrin homology (PH) domain. Akt (Protein Kinase B (PKB)) is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase. The PH domain recruits Akt to the plasma membrane by binding to phosphoinositides (PtdIns-3,4-P2) and is required for activation. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=26.46 E-value=57 Score=22.26 Aligned_cols=17 Identities=24% Similarity=0.386 Sum_probs=14.0
Q ss_pred hChHHHHHHHHHHHHhh
Q 043195 136 EKIDMLQTWRIAMREAA 152 (162)
Q Consensus 136 ~~~e~~~~W~~aL~~v~ 152 (162)
++.+..+.|..||..|+
T Consensus 86 ~s~ee~~eWi~ai~~v~ 102 (102)
T cd01241 86 ESPEEREEWIHAIQTVA 102 (102)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 35788999999998874
No 63
>PRK13364 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=26.26 E-value=3.7e+02 Score=22.08 Aligned_cols=79 Identities=10% Similarity=0.060 Sum_probs=46.3
Q ss_pred cchHHHHHHHHccCCceeeecCC--cCCCCCcchHHHHhhhhCceEEEEeecCCCC----ChhHHHHHHHHHHHh-hh--
Q 043195 29 HNFISHLNAALCRKKIETFIDDK--LNRGNQISPSLSSAIEGSKISIVIFSKGYAS----SRWCLNELVKILESK-NK-- 99 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~--~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~----S~wc~~El~~~~~~~-~~-- 99 (162)
..++.+|.+.|.+.|+.+-...+ +--|--+.-.....=.+..+-||-+|-|... +..-..+|.+++... +.
T Consensus 98 ~~lA~~i~~~l~~~gid~~~~~~~~lDHG~~vPL~~l~~~~d~~~pvVpv~ln~~~~p~~~~~r~~~lG~al~~~i~~~~ 177 (278)
T PRK13364 98 TELSWHIIESLVEEEFDITTCQEMLVDHAFTLPLELFWPGRDYPVKVVPVCINTVQHPLPSARRCYKLGQAIGRAIASWP 177 (278)
T ss_pred HHHHHHHHHHHHHcCCCeecccCCCCCcchhhhHHHhCcccCCCCCEEEEEeeccCCCCCCHHHHHHHHHHHHHHHHhcC
Confidence 47899999999999998765433 4444433322221101122445555555554 677778999988764 22
Q ss_pred cCCeeEeE
Q 043195 100 YGQIVVPV 107 (162)
Q Consensus 100 ~~~~viPV 107 (162)
.+++|+-|
T Consensus 178 ~d~rV~iI 185 (278)
T PRK13364 178 SDERVVVI 185 (278)
T ss_pred CCCCEEEE
Confidence 34566644
No 64
>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=26.12 E-value=93 Score=23.98 Aligned_cols=50 Identities=16% Similarity=0.234 Sum_probs=36.6
Q ss_pred cchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCC
Q 043195 29 HNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYA 81 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 81 (162)
..-...|..+...+|+-+|.|-+ .+|+.|...|.+.+-++...- +++.++
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD-~~GekIRk~i~~~vp~~khaf--i~~~~a 84 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPD-FPGEKIRKKIEQHLPGYENCF--IPKHLA 84 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCC-CchHHHHHHHHHHCCCCeEEe--eeHHhc
Confidence 35567777888889999999876 578888888888887776543 344444
No 65
>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=25.27 E-value=2.5e+02 Score=19.98 Aligned_cols=46 Identities=4% Similarity=0.014 Sum_probs=29.7
Q ss_pred hHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeEeEE
Q 043195 60 PSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYGQIVVPVF 108 (162)
Q Consensus 60 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPVf 108 (162)
.-+.+.+..+++.|+|++.+- .|...+...+.+..+....+.+-|+
T Consensus 120 ~~~~~~~~~~d~vi~V~~~~~---~~~~~~~~~l~~~~~~~~~~~i~V~ 165 (168)
T PF00350_consen 120 EITEEYLPKADVVIFVVDANQ---DLTESDMEFLKQMLDPDKSRTIFVL 165 (168)
T ss_dssp HHHHHHHSTTEEEEEEEETTS---TGGGHHHHHHHHHHTTTCSSEEEEE
T ss_pred HHHHHhhccCCEEEEEeccCc---ccchHHHHHHHHHhcCCCCeEEEEE
Confidence 456778899999999997766 4444455555555444455555553
No 66
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=25.18 E-value=1.6e+02 Score=25.59 Aligned_cols=60 Identities=13% Similarity=0.164 Sum_probs=39.3
Q ss_pred eeeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeec
Q 043195 15 KYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSK 78 (162)
Q Consensus 15 ~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 78 (162)
..||+|.+-+.+. ...+-.+.+.|+++|+++-+|-. +..+...+..|-+.--..++|+.+
T Consensus 325 ~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~---~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 325 SIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS---SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC---CCCHHHHHHHHHHcCCCEEEEEec
Confidence 4689988754432 35677899999999999876532 344555666665544455666665
No 67
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=25.13 E-value=1.2e+02 Score=19.27 Aligned_cols=29 Identities=17% Similarity=0.289 Sum_probs=20.6
Q ss_pred CCCceeeEEEeccccccccchHHHHHHHHccC
Q 043195 11 NPQIKYDVFLSFRGRDVRHNFISHLNAALCRK 42 (162)
Q Consensus 11 ~~~~~ydVFISys~~D~~~~f~~~L~~~L~~~ 42 (162)
...++|.+||-+.+.|. . +.++...|++.
T Consensus 38 ~~~~~y~Ffvd~~~~~~--~-~~~~l~~L~~~ 66 (74)
T cd04904 38 RNGSEYEFFVDCEVDRG--D-LDQLISSLRRV 66 (74)
T ss_pred CCCceEEEEEEEEcChH--H-HHHHHHHHHHh
Confidence 36689999999988553 3 56666777654
No 68
>COG0400 Predicted esterase [General function prediction only]
Probab=24.90 E-value=1.5e+02 Score=23.27 Aligned_cols=55 Identities=16% Similarity=0.118 Sum_probs=39.4
Q ss_pred CCceeeEEEecccccc--ccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhh
Q 043195 12 PQIKYDVFLSFRGRDV--RHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIE 67 (162)
Q Consensus 12 ~~~~ydVFISys~~D~--~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~ 67 (162)
.....-|||+|-..|. ......+|.+.|+..|..|.... ++.|=.+.++-.+++.
T Consensus 143 ~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~-~~~GH~i~~e~~~~~~ 199 (207)
T COG0400 143 DLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRW-HEGGHEIPPEELEAAR 199 (207)
T ss_pred ccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEE-ecCCCcCCHHHHHHHH
Confidence 4567889999987785 34667899999999999887643 3456666655444443
No 69
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=24.69 E-value=1.7e+02 Score=25.40 Aligned_cols=59 Identities=15% Similarity=0.172 Sum_probs=38.5
Q ss_pred eeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeec
Q 043195 16 YDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSK 78 (162)
Q Consensus 16 ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 78 (162)
++|+|-.-+++. ...+..|...|++.|+.+.+|.. +..+..++..|-+.---.++++.+
T Consensus 275 ~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl~---srSLgKQiK~AdK~GaPfvIIIGe 333 (387)
T PRK14938 275 IQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDDL---DDSLGNKIRRAGTEWIPFVIIIGE 333 (387)
T ss_pred ceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEECc
Confidence 677666555443 35778899999999999988753 445666666665543344444443
No 70
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=24.26 E-value=1.6e+02 Score=25.13 Aligned_cols=60 Identities=15% Similarity=0.344 Sum_probs=40.5
Q ss_pred eeeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhh-hCceEEEEeecCCCC
Q 043195 15 KYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIE-GSKISIVIFSKGYAS 82 (162)
Q Consensus 15 ~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~-~S~~~Ivv~S~~y~~ 82 (162)
.+|+-|.|+.+ +|...|.++-- +||.+|+|. .|..+.+.....+. ..|+.++=.=..|.+
T Consensus 196 GfD~~idyk~~----d~~~~L~~a~P-~GIDvyfeN---VGg~v~DAv~~~ln~~aRi~~CG~IS~YN~ 256 (340)
T COG2130 196 GFDAGIDYKAE----DFAQALKEACP-KGIDVYFEN---VGGEVLDAVLPLLNLFARIPVCGAISQYNA 256 (340)
T ss_pred CCceeeecCcc----cHHHHHHHHCC-CCeEEEEEc---CCchHHHHHHHhhccccceeeeeehhhcCC
Confidence 48999999755 47777766555 699999986 46667777776665 455555544444444
No 71
>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=24.12 E-value=3.4e+02 Score=20.90 Aligned_cols=86 Identities=13% Similarity=0.075 Sum_probs=51.9
Q ss_pred cchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCC----------------CCChhHHHHHHH
Q 043195 29 HNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGY----------------ASSRWCLNELVK 92 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y----------------~~S~wc~~El~~ 92 (162)
..+.+.|...+...++.+.....-..-+.-..+..+..++++.+|+++.+.+ ..-+++..||..
T Consensus 46 ~t~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aD~vIv~~~~~~~e~~~~~~~~~~~~~~~~l~~~q~~li~ 125 (227)
T PF01915_consen 46 VTPLDALKQRFGNAGVVVPEGGDAVDDDEGIDEAVAAAKEADVVIVFVGRPSGEGNDNNTEGESDRSDLALPANQQELIK 125 (227)
T ss_dssp BHHHHHHHHHHHTTSEEEECCCCCCCCCSCHHHHHHHHHCSSEEEEEEETTSBCCCSS-EETTGSCSSTBCCCHHHHHHH
T ss_pred ccHHhhhccccCCCceEEeeeccccccccchHHHHHHhhcCCEEEEeccccccccccccccccCCcccccchhhHHHHHH
Confidence 3677778888887777654422211122333567788889999999988433 334567777777
Q ss_pred HHHHhhhcCCeeEeEEEeeCCcccc
Q 043195 93 ILESKNKYGQIVVPVFYLVDPSDVR 117 (162)
Q Consensus 93 ~~~~~~~~~~~viPVfy~v~p~dv~ 117 (162)
.+... . ..+|-|+.-..|-++.
T Consensus 126 ~v~~~--~-~~~Ivvv~~~~P~~l~ 147 (227)
T PF01915_consen 126 AVAAA--G-KKVIVVVNSGNPYDLD 147 (227)
T ss_dssp HHHHH--H-SCEEEEEE-SSGGCGH
T ss_pred HHHHh--c-CCeEEEEecCCccccH
Confidence 66432 2 3445555555666653
No 72
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=23.85 E-value=1.2e+02 Score=20.85 Aligned_cols=42 Identities=7% Similarity=0.188 Sum_probs=26.0
Q ss_pred HHccCCceeee-cCCcCCCCCcchHHHHhhhhCceEEEEeecCCCC
Q 043195 38 ALCRKKIETFI-DDKLNRGNQISPSLSSAIEGSKISIVIFSKGYAS 82 (162)
Q Consensus 38 ~L~~~gi~~f~-d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 82 (162)
-++-.|+..+. .. ..+.+...+.+.+.+-++.|++++++++.
T Consensus 14 GFrLaGi~~~~~~~---~~ee~~~~l~~l~~~~d~gII~Ite~~~~ 56 (100)
T PRK02228 14 GFRLAGIRKVYEVP---DDEKLDEAVEEVLEDDDVGILVMHDDDLE 56 (100)
T ss_pred HHHHcCCceEEeeC---CHHHHHHHHHHHhhCCCEEEEEEehhHhH
Confidence 34445886443 21 11334455555667778999999999776
No 73
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=23.55 E-value=3.2e+02 Score=22.08 Aligned_cols=52 Identities=15% Similarity=0.146 Sum_probs=28.7
Q ss_pred EEEeccccccccchHHHHHHHHccCCceeeecCCcCCC---CCcchHHHHhhhhCc
Q 043195 18 VFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRG---NQISPSLSSAIEGSK 70 (162)
Q Consensus 18 VFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G---~~i~~~i~~aI~~S~ 70 (162)
|.+-|...+........+...|++.|+.+-....+.+| ..+.+. ...|+.++
T Consensus 138 v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~~-l~~i~~~~ 192 (350)
T cd06366 138 VATIYEDDDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITDA-LKKLKEKD 192 (350)
T ss_pred EEEEEEcCcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHHH-HHHHhcCC
Confidence 44444333323456777888888888877544445665 234433 44455433
No 74
>TIGR01101 V_ATP_synt_F vacuolar ATP synthase F subunit. This model describes the vacuolar ATP synthase F subunit (14 kDa subunit) in eukaryotes. In some archaeal species this protein subunit is referred as G subunit
Probab=23.44 E-value=74 Score=22.77 Aligned_cols=47 Identities=15% Similarity=0.367 Sum_probs=28.7
Q ss_pred CcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeEeEEEeeCCc
Q 043195 57 QISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYGQIVVPVFYLVDPS 114 (162)
Q Consensus 57 ~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPVfy~v~p~ 114 (162)
.+...+.+.+.+.++.|++++.++++ ++...++..+ .++|....+ |+
T Consensus 47 ei~~~~~~~l~~~digIIlIte~~a~------~i~~~I~~~~----~~~PaIieI-P~ 93 (115)
T TIGR01101 47 EIEDCFNRFLKRDDIAIILINQHIAE------MIRHAVDAHT----RSIPAVLEI-PS 93 (115)
T ss_pred HHHHHHHHHhhcCCeEEEEEcHHHHH------HhHHHHHhcC----CcCCEEEEE-CC
Confidence 44445555577899999999988765 3344443322 455655543 44
No 75
>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=23.32 E-value=4e+02 Score=21.47 Aligned_cols=77 Identities=13% Similarity=0.089 Sum_probs=48.2
Q ss_pred cchHHHHHHHHccCCceeee--cCC--cCCCCCcchHHHHhhhhCceEEEEeecCC-CCChhHHHHHHHHHH-HhhhcCC
Q 043195 29 HNFISHLNAALCRKKIETFI--DDK--LNRGNQISPSLSSAIEGSKISIVIFSKGY-ASSRWCLNELVKILE-SKNKYGQ 102 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~--d~~--~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y-~~S~wc~~El~~~~~-~~~~~~~ 102 (162)
..++..|.+.|.+.|+.+-. +.. +--|--+.-..+. .+.++-+|.+|=+. ..+..-..+|.+++. ..++.++
T Consensus 87 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vPL~~l~--p~~~ipvV~vs~~~~~~~~~~~~~lG~al~~~l~~~~~ 164 (268)
T cd07371 87 VELAEACVEEGRKAGLVTRMMRYPRFPIDTGTITALTLMR--PGTDIPPVVISANNLYLSGEETEGEMDLAGKATRDAGK 164 (268)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCCchhHHHHHHhc--CCCCCCeEEEEecCcCCCHHHHHHHHHHHHHHHHHcCC
Confidence 47999999999999998764 222 3344333222211 23566677777444 356777778999885 3355456
Q ss_pred eeEeE
Q 043195 103 IVVPV 107 (162)
Q Consensus 103 ~viPV 107 (162)
+|+-|
T Consensus 165 rv~iI 169 (268)
T cd07371 165 RVAVL 169 (268)
T ss_pred cEEEE
Confidence 66655
No 76
>cd01266 PH_Gab Gab (Grb2-associated binder) pleckstrin homology (PH) domain. Gab (Grb2-associated binder) pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display str
Probab=23.24 E-value=72 Score=21.89 Aligned_cols=17 Identities=6% Similarity=0.241 Sum_probs=14.3
Q ss_pred hChHHHHHHHHHHHHhh
Q 043195 136 EKIDMLQTWRIAMREAA 152 (162)
Q Consensus 136 ~~~e~~~~W~~aL~~v~ 152 (162)
++.+.++.|..|+.+|+
T Consensus 92 ~s~ee~~~Wi~~I~~~~ 108 (108)
T cd01266 92 KNEEEMTLWVNCICKLC 108 (108)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 45789999999999875
No 77
>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=23.14 E-value=2.8e+02 Score=19.55 Aligned_cols=20 Identities=25% Similarity=0.262 Sum_probs=10.5
Q ss_pred HHHHhhhhCceEEEEeecCC
Q 043195 61 SLSSAIEGSKISIVIFSKGY 80 (162)
Q Consensus 61 ~i~~aI~~S~~~Ivv~S~~y 80 (162)
++.++|+++++.++|+.-.-
T Consensus 4 ~~~~~i~~aD~vl~ViD~~~ 23 (141)
T cd01857 4 QLWRVVERSDIVVQIVDARN 23 (141)
T ss_pred HHHHHHhhCCEEEEEEEccC
Confidence 34455555555555555433
No 78
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=23.11 E-value=3.1e+02 Score=22.28 Aligned_cols=27 Identities=22% Similarity=0.271 Sum_probs=14.3
Q ss_pred cchHHHHHHHHccCCceeeecCCcCCC
Q 043195 29 HNFISHLNAALCRKKIETFIDDKLNRG 55 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~~~G 55 (162)
...+..+.+.|++.|+.+-....+.++
T Consensus 152 ~~~~~~~~~~~~~~G~~v~~~~~~~~~ 178 (347)
T cd06335 152 RSNRKDLTAALAARGLKPVAVEWFNWG 178 (347)
T ss_pred hhHHHHHHHHHHHcCCeeEEEeeecCC
Confidence 345566666666667665332224444
No 79
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=23.10 E-value=2.3e+02 Score=23.51 Aligned_cols=46 Identities=11% Similarity=0.108 Sum_probs=21.6
Q ss_pred chHHHHHHHHccCCc----eeeecCCcCCCCCcchHHHHhhhhCceEEEE
Q 043195 30 NFISHLNAALCRKKI----ETFIDDKLNRGNQISPSLSSAIEGSKISIVI 75 (162)
Q Consensus 30 ~f~~~L~~~L~~~gi----~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv 75 (162)
..+..|.+.|++.|+ .+-....+.+|+.-...+.+.|+.++.-+||
T Consensus 169 ~~~~~~~~~~~~~g~~~~~~v~~~~~~~~~~~d~~~~l~~ik~~~~~vIv 218 (377)
T cd06379 169 AAQKRFETLLEEREIEFKIKVEKVVEFEPGEKNVTSLLQEAKELTSRVIL 218 (377)
T ss_pred HHHHHHHHHHHhcCCccceeeeEEEecCCchhhHHHHHHHHhhcCCeEEE
Confidence 355666677777776 3322222444432222334445544433333
No 80
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=22.95 E-value=2.4e+02 Score=24.55 Aligned_cols=64 Identities=16% Similarity=0.058 Sum_probs=39.4
Q ss_pred eeeEEEeccc--cccccchHHHHHHHHccCCceeeecCC-cCCCCCcchHHHHhhhhCceEEEEeecCCCC
Q 043195 15 KYDVFLSFRG--RDVRHNFISHLNAALCRKKIETFIDDK-LNRGNQISPSLSSAIEGSKISIVIFSKGYAS 82 (162)
Q Consensus 15 ~ydVFISys~--~D~~~~f~~~L~~~L~~~gi~~f~d~~-~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 82 (162)
.++|.|---. .+.....+..|...|.+.|+.|.+|.+ -..|. .+.+|-..---.++|+.++-+.
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~----ki~~a~~~giP~~iiVG~~e~~ 411 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGA----KFATMDLIGLPWQIIVGPKGLA 411 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhH----HHHHHHHcCCCEEEEECCcccc
Confidence 3788775432 122346788999999999999999875 33343 4434333333466666665443
No 81
>cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif.
Probab=22.87 E-value=1.7e+02 Score=20.89 Aligned_cols=52 Identities=25% Similarity=0.350 Sum_probs=27.7
Q ss_pred HHHhhh--hCceEEEEeecCCCCChhHHH--HHHHHHHHhh-hcCCeeEeEEEeeCCccccccc
Q 043195 62 LSSAIE--GSKISIVIFSKGYASSRWCLN--ELVKILESKN-KYGQIVVPVFYLVDPSDVRNQT 120 (162)
Q Consensus 62 i~~aI~--~S~~~Ivv~S~~y~~S~wc~~--El~~~~~~~~-~~~~~viPVfy~v~p~dv~~q~ 120 (162)
..++|. +.+.+|+-|.. .||.- .+..+++... +-... -+||.|+.+++.+..
T Consensus 5 ~d~~i~~~~~klVVVdF~a-----~WC~pCk~mdp~l~ela~~~~~~--~~f~kVDVDev~dva 61 (114)
T cd02986 5 VDQAIKSTAEKVLVLRFGR-----DEDAVCLQLDDILSKTSHDLSKM--ASIYLVDVDKVPVYT 61 (114)
T ss_pred HHHHHHhcCCCEEEEEEeC-----CCChhHHHHHHHHHHHHHHccCc--eEEEEEeccccHHHH
Confidence 344444 45566666665 56633 4444554332 22222 567888877776543
No 82
>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=22.71 E-value=99 Score=19.76 Aligned_cols=30 Identities=10% Similarity=0.108 Sum_probs=16.2
Q ss_pred CCceeeecCCcCCCCCcchHHHHhhhhCceE
Q 043195 42 KKIETFIDDKLNRGNQISPSLSSAIEGSKIS 72 (162)
Q Consensus 42 ~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~ 72 (162)
+.+-+|+|.+ .+|..-...+.+.+..-...
T Consensus 44 ~~vii~~D~D-~aG~~a~~~~~~~l~~~g~~ 73 (79)
T cd03364 44 KEVILAFDGD-EAGQKAALRALELLLKLGLN 73 (79)
T ss_pred CeEEEEECCC-HHHHHHHHHHHHHHHHCCCe
Confidence 4566666665 45655555555555444333
No 83
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=22.70 E-value=88 Score=25.58 Aligned_cols=42 Identities=19% Similarity=0.190 Sum_probs=27.4
Q ss_pred hHHHHHHHHccCCceeeecCCcCCCCC---cchHHHHhhhhCceEEE
Q 043195 31 FISHLNAALCRKKIETFIDDKLNRGNQ---ISPSLSSAIEGSKISIV 74 (162)
Q Consensus 31 f~~~L~~~L~~~gi~~f~d~~~~~G~~---i~~~i~~aI~~S~~~Iv 74 (162)
=+.+|.+.|...|+.+..-. -.||+ |.+.+..++++++++|+
T Consensus 22 Na~~la~~L~~~G~~v~~~~--~VgD~~~~I~~~l~~a~~r~D~vI~ 66 (255)
T COG1058 22 NAAFLADELTELGVDLARIT--TVGDNPDRIVEALREASERADVVIT 66 (255)
T ss_pred hHHHHHHHHHhcCceEEEEE--ecCCCHHHHHHHHHHHHhCCCEEEE
Confidence 36788999999999886532 23443 45566667777555443
No 84
>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=22.53 E-value=1.4e+02 Score=21.06 Aligned_cols=10 Identities=30% Similarity=0.521 Sum_probs=4.2
Q ss_pred eeEEEecccc
Q 043195 16 YDVFLSFRGR 25 (162)
Q Consensus 16 ydVFISys~~ 25 (162)
.||-|-|+..
T Consensus 68 ~DVvIDfT~p 77 (124)
T PF01113_consen 68 ADVVIDFTNP 77 (124)
T ss_dssp -SEEEEES-H
T ss_pred CCEEEEcCCh
Confidence 4555555533
No 85
>cd03411 Ferrochelatase_N Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=22.44 E-value=3.2e+02 Score=20.05 Aligned_cols=64 Identities=16% Similarity=0.277 Sum_probs=36.8
Q ss_pred chHHHHHHHHccCC--ceeeecCCcCCCCCcchHHHHhhhh---CceEEEEeecCCCCC--hhHHHHHHHHHH
Q 043195 30 NFISHLNAALCRKK--IETFIDDKLNRGNQISPSLSSAIEG---SKISIVIFSKGYASS--RWCLNELVKILE 95 (162)
Q Consensus 30 ~f~~~L~~~L~~~g--i~~f~d~~~~~G~~i~~~i~~aI~~---S~~~Ivv~S~~y~~S--~wc~~El~~~~~ 95 (162)
..+..|.+.|.+.+ +.++.- +.-|.+..++..+.+.+ .++.++.+.|.|..+ .-+.+++..++.
T Consensus 72 ~q~~~l~~~L~~~~~~~~v~~a--mry~~P~i~~~l~~l~~~g~~~iivlPl~P~~S~~Tt~s~~~~~~~~~~ 142 (159)
T cd03411 72 AQAEALEKALDERGIDVKVYLA--MRYGPPSIEEALEELKADGVDRIVVLPLYPQYSASTTGSYLDEVERALK 142 (159)
T ss_pred HHHHHHHHHHhccCCCcEEEeh--HhcCCCCHHHHHHHHHHcCCCEEEEEECCcccccccHHHHHHHHHHHHH
Confidence 45566777776643 333332 44555555444444433 557888888888754 346667666554
No 86
>PRK08350 hypothetical protein; Provisional
Probab=22.28 E-value=89 Score=26.69 Aligned_cols=32 Identities=13% Similarity=0.087 Sum_probs=27.1
Q ss_pred ceeeEEEeccccccccchHHHHHHHHccCCce
Q 043195 14 IKYDVFLSFRGRDVRHNFISHLNAALCRKKIE 45 (162)
Q Consensus 14 ~~ydVFISys~~D~~~~f~~~L~~~L~~~gi~ 45 (162)
..|.+.+|||+-++..+|+.+|..+|...-|+
T Consensus 280 ~g~~~vvSHRSGETeD~~IAdLaVa~~agqIK 311 (341)
T PRK08350 280 ERITPILAEAKYESADEALPHLAVGLRCPAML 311 (341)
T ss_pred cCCeEEeecCCCCCcchhHHHHHHHhCCCccc
Confidence 45889999998888889999999999875554
No 87
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=22.21 E-value=51 Score=21.82 Aligned_cols=24 Identities=33% Similarity=0.587 Sum_probs=15.1
Q ss_pred EEEEeecCCCCChhHHH--HHHHHHH
Q 043195 72 SIVIFSKGYASSRWCLN--ELVKILE 95 (162)
Q Consensus 72 ~Ivv~S~~y~~S~wc~~--El~~~~~ 95 (162)
-|+|||+.+.+.+||-. .+..+++
T Consensus 9 ~vvvf~k~~~~~~~Cp~C~~ak~~L~ 34 (90)
T cd03028 9 PVVLFMKGTPEEPRCGFSRKVVQILN 34 (90)
T ss_pred CEEEEEcCCCCCCCCcHHHHHHHHHH
Confidence 46677888877777754 4444444
No 88
>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=22.16 E-value=3.1e+02 Score=22.81 Aligned_cols=67 Identities=15% Similarity=0.200 Sum_probs=39.5
Q ss_pred chHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhh---CceEEEEeecCCCCCh--hHHHHHHHHHHH
Q 043195 30 NFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEG---SKISIVIFSKGYASSR--WCLNELVKILES 96 (162)
Q Consensus 30 ~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~---S~~~Ivv~S~~y~~S~--wc~~El~~~~~~ 96 (162)
..+..|.+.|...|..+-..--+.-|.+..++..+.+.+ .++.++.+.|.|..+. -+++++..++..
T Consensus 73 ~qa~~l~~~L~~~~~~~~V~~amry~~P~i~~~l~~l~~~g~~~ivvlPLyPqyS~~ttgs~~~~~~~~~~~ 144 (316)
T PF00762_consen 73 RQAEALQQRLDERGVDVEVYYAMRYGPPSIEDALEELKADGVDRIVVLPLYPQYSSSTTGSYLDEVERALKK 144 (316)
T ss_dssp HHHHHHHHHHHHH-EEEEEEEEESSSSSBHHHHHHHHHHTT-SEEEEEESSSS--TTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCeeEEEEeccCCCCHHHHHHHHHHcCCCeEEEEeCCCchhHhhHHHHHHHHHHHHHh
Confidence 456667777776543222222255666666666666653 4578888999998543 467777776654
No 89
>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=21.89 E-value=1.3e+02 Score=23.49 Aligned_cols=48 Identities=25% Similarity=0.263 Sum_probs=32.1
Q ss_pred ccccchHHHHHHHHccCC--ceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCC
Q 043195 26 DVRHNFISHLNAALCRKK--IETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYAS 82 (162)
Q Consensus 26 D~~~~f~~~L~~~L~~~g--i~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~ 82 (162)
|...+|+-.|++.|.+-| +.|+..+. +.. ..++..+--.+|+||.=-.
T Consensus 8 DNyDSFtyNLv~yl~~lg~~v~V~rnd~------~~~---~~~~~~~pd~iviSPGPG~ 57 (191)
T COG0512 8 DNYDSFTYNLVQYLRELGAEVTVVRNDD------ISL---ELIEALKPDAIVISPGPGT 57 (191)
T ss_pred ECccchHHHHHHHHHHcCCceEEEECCc------cCH---HHHhhcCCCEEEEcCCCCC
Confidence 445689999999999877 55555432 221 1556666678889987443
No 90
>PRK14158 heat shock protein GrpE; Provisional
Probab=21.83 E-value=2e+02 Score=22.43 Aligned_cols=47 Identities=21% Similarity=0.404 Sum_probs=34.1
Q ss_pred HHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhh-------CceEEEEeecCCCC
Q 043195 33 SHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEG-------SKISIVIFSKGYAS 82 (162)
Q Consensus 33 ~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~-------S~~~Ivv~S~~y~~ 82 (162)
..|...|++.|+... + -..|+.+.|++-+||.. ...++-|+.+.|.-
T Consensus 127 k~l~~vLek~Gv~~I-~--~~~G~~FDP~~HEAv~~~~~~~~~~gtVv~v~qkGY~l 180 (194)
T PRK14158 127 SMLLSTLKKFGVTPV-E--AEKGTPFDPAYHQAMCQVESAEQEPNTVVAVFQKGYLL 180 (194)
T ss_pred HHHHHHHHHCCCEEe-c--CCCCCCCChHHhhhheeecCCCCCcCEEEEEeeCCcEe
Confidence 457778888898762 1 12499999999999853 34677888888854
No 91
>PLN02449 ferrochelatase
Probab=21.50 E-value=5.6e+02 Score=23.01 Aligned_cols=78 Identities=17% Similarity=0.258 Sum_probs=45.0
Q ss_pred hHHHHHHHHccCC--ceeeecCCcCCCCCcchHHHHhhhh---CceEEEEeecCCCCC--hhHHHHHHHHHHHhhh---c
Q 043195 31 FISHLNAALCRKK--IETFIDDKLNRGNQISPSLSSAIEG---SKISIVIFSKGYASS--RWCLNELVKILESKNK---Y 100 (162)
Q Consensus 31 f~~~L~~~L~~~g--i~~f~d~~~~~G~~i~~~i~~aI~~---S~~~Ivv~S~~y~~S--~wc~~El~~~~~~~~~---~ 100 (162)
-+..|.++|.+.| ++|++- |.-|.+..++..+.+.+ .+++++.+-|.|-.+ .-+.+.+..++..... -
T Consensus 165 Qa~~Lq~~L~~~~~~~~V~~a--MRY~~P~iedal~~l~~~G~~~iVvLPLYPQyS~sTtgSs~~~l~~~~~~~~~~~~~ 242 (485)
T PLN02449 165 QAEALAKALEAKNLPAKVYVG--MRYWHPFTEEAIDQIKADGITKLVVLPLYPQFSISTSGSSLRLLESIFREDEYLVNM 242 (485)
T ss_pred HHHHHHHHHhccCCCeEEEEh--hhcCCCCHHHHHHHHHhcCCCeEEEEECCcccccccHHHHHHHHHHHHhhcccccCC
Confidence 4556777776665 455542 44556666666666653 457888888887643 4466676666543211 1
Q ss_pred CCeeEeEEEe
Q 043195 101 GQIVVPVFYL 110 (162)
Q Consensus 101 ~~~viPVfy~ 110 (162)
...+||=||+
T Consensus 243 ~~~~I~~~~~ 252 (485)
T PLN02449 243 QHTVIPSWYQ 252 (485)
T ss_pred eeEEeccccC
Confidence 2355665554
No 92
>TIGR00295 conserved hypothetical protein TIGR00295. This set of orthologs is narrowly defined, comprising proteins found in three Archaea but not in Pyrococcus horikoshii. The closest homologs are other archaeal proteins that appear to be represent distinct orthologous clusters.
Probab=21.42 E-value=1.7e+02 Score=21.86 Aligned_cols=32 Identities=28% Similarity=0.316 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHhhhChHHHHHHHHHHHHhhcc
Q 043195 123 IGDSFLKLEERFKEKIDMLQTWRIAMREAANL 154 (162)
Q Consensus 123 f~~~f~~~~~~~~~~~e~~~~W~~aL~~v~~~ 154 (162)
..+.+.+..+++..++....+|+.+..+|.++
T Consensus 132 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (164)
T TIGR00295 132 IDEVIKKLEERLGKNHPSIERARKLKEELERL 163 (164)
T ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHHhh
Confidence 45667777788888888999999999998775
No 93
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=21.09 E-value=3.3e+02 Score=19.61 Aligned_cols=86 Identities=13% Similarity=0.033 Sum_probs=48.9
Q ss_pred eEEEeccccccccchH-HHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHH
Q 043195 17 DVFLSFRGRDVRHNFI-SHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILE 95 (162)
Q Consensus 17 dVFISys~~D~~~~f~-~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~ 95 (162)
.|++.=-+.|.. ..- .-+...|+..|+.|..- .++.-.+++.++..+.+.-++++|--.....--+.++...
T Consensus 4 ~v~~a~~g~D~H-d~g~~iv~~~l~~~GfeVi~l----g~~~s~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~-- 76 (132)
T TIGR00640 4 RILVAKMGQDGH-DRGAKVIATAYADLGFDVDVG----PLFQTPEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKE-- 76 (132)
T ss_pred EEEEEeeCCCcc-HHHHHHHHHHHHhCCcEEEEC----CCCCCHHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHH--
Confidence 345544444542 222 22334467789998531 2233445777888888988888887765543334444443
Q ss_pred HhhhcCCeeEeEEEe
Q 043195 96 SKNKYGQIVVPVFYL 110 (162)
Q Consensus 96 ~~~~~~~~viPVfy~ 110 (162)
.++.+..-+||+..
T Consensus 77 -L~~~g~~~i~vivG 90 (132)
T TIGR00640 77 -LDKLGRPDILVVVG 90 (132)
T ss_pred -HHhcCCCCCEEEEe
Confidence 33444445778876
No 94
>PF01269 Fibrillarin: Fibrillarin; InterPro: IPR000692 Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [, ]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [] and is similar to the yeast NOP1 protein []. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.; GO: 0003723 RNA binding, 0008168 methyltransferase activity, 0006364 rRNA processing, 0008033 tRNA processing; PDB: 3PLA_E 3ID6_C 3ID5_B 1NT2_A 3NVK_J 2NNW_B 3NVM_B 3NMU_J 1PRY_A 1G8A_A ....
Probab=20.91 E-value=1e+02 Score=24.80 Aligned_cols=71 Identities=20% Similarity=0.294 Sum_probs=35.3
Q ss_pred chHHHHHHHHccCCce-eeec--CC-cCCCCCcc---hHHHHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCC
Q 043195 30 NFISHLNAALCRKKIE-TFID--DK-LNRGNQIS---PSLSSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYGQ 102 (162)
Q Consensus 30 ~f~~~L~~~L~~~gi~-~f~d--~~-~~~G~~i~---~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~ 102 (162)
.|-++|.+++-. |+. +++. .+ +-.|..-. .-+.+-+..+..+-.| --|+|++.+|....+. ..
T Consensus 53 P~RSKLaAai~~-Gl~~~~ik~gskVLYLGAasGTTVSHvSDIvg~~G~VYaV-----Efs~r~~rdL~~la~~----R~ 122 (229)
T PF01269_consen 53 PFRSKLAAAILK-GLENIPIKPGSKVLYLGAASGTTVSHVSDIVGPDGVVYAV-----EFSPRSMRDLLNLAKK----RP 122 (229)
T ss_dssp TTT-HHHHHHHT-T-S--S--TT-EEEEETTTTSHHHHHHHHHHTTTSEEEEE-----ESSHHHHHHHHHHHHH----ST
T ss_pred chhhHHHHHHHc-CccccCCCCCCEEEEecccCCCccchhhhccCCCCcEEEE-----EecchhHHHHHHHhcc----CC
Confidence 456778777754 543 2221 12 33333221 1233334333332221 1378999999876554 45
Q ss_pred eeEeEEEe
Q 043195 103 IVVPVFYL 110 (162)
Q Consensus 103 ~viPVfy~ 110 (162)
.|+||+=+
T Consensus 123 NIiPIl~D 130 (229)
T PF01269_consen 123 NIIPILED 130 (229)
T ss_dssp TEEEEES-
T ss_pred ceeeeecc
Confidence 89999865
No 95
>PRK08155 acetolactate synthase catalytic subunit; Validated
Probab=20.81 E-value=2.6e+02 Score=24.95 Aligned_cols=36 Identities=22% Similarity=0.106 Sum_probs=23.4
Q ss_pred chHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhC
Q 043195 30 NFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGS 69 (162)
Q Consensus 30 ~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S 69 (162)
+-.+.|...|.+.|++..+ -.||..+. .+.+++.++
T Consensus 14 ~~~~~l~~~L~~~GV~~vF---gvpG~~~~-~l~dal~~~ 49 (564)
T PRK08155 14 TGAELIVRLLERQGIRIVT---GIPGGAIL-PLYDALSQS 49 (564)
T ss_pred cHHHHHHHHHHHcCCCEEE---eCCCcccH-HHHHHHhcc
Confidence 3567788888888886544 34676665 356666554
No 96
>cd06361 PBP1_GPC6A_like Ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor. This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses.
Probab=20.78 E-value=2.3e+02 Score=24.14 Aligned_cols=27 Identities=4% Similarity=-0.032 Sum_probs=16.6
Q ss_pred cchHHHHHHHHccCCceeeecCCcCCC
Q 043195 29 HNFISHLNAALCRKKIETFIDDKLNRG 55 (162)
Q Consensus 29 ~~f~~~L~~~L~~~gi~~f~d~~~~~G 55 (162)
...+..|.++|+++|+.+-....+.++
T Consensus 186 ~~~~~~f~~~~~~~GicIa~~e~~~~~ 212 (403)
T cd06361 186 RSALETFIIQAEANGVCIAFKEILPAS 212 (403)
T ss_pred HHHHHHHHHHHHHCCeEEEEEEEecCc
Confidence 456777778888888765433334443
No 97
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=20.74 E-value=2.1e+02 Score=25.91 Aligned_cols=60 Identities=18% Similarity=0.255 Sum_probs=38.3
Q ss_pred eeeEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhhCceEEEEeec
Q 043195 15 KYDVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEGSKISIVIFSK 78 (162)
Q Consensus 15 ~ydVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 78 (162)
..+|+|-.-+++. ...+..+...|++.|++|-+|.. +..+...+..|-..---.++|+.+
T Consensus 438 P~qV~Iipi~e~~-~~~A~~Ia~~LR~~GirVelD~~---~~~lgkkir~A~k~gip~viIIG~ 497 (545)
T PRK14799 438 SVQVRVLPITDEV-NEYAEKVLNDMRKRRIRAEIDYA---GETLSKRIKNAYDQGVPYILIVGK 497 (545)
T ss_pred CceEEEEEcCHHH-HHHHHHHHHHHHhCCCEEEEECC---CCCHHHHHHHHHHcCCCEEEEECh
Confidence 3578776644432 46788899999999999988763 445555665554433334555554
No 98
>cd06367 PBP1_iGluR_NMDA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits
Probab=20.63 E-value=4.7e+02 Score=21.32 Aligned_cols=24 Identities=8% Similarity=0.122 Sum_probs=15.1
Q ss_pred ccccccccchHHHHHHHHccCCce
Q 043195 22 FRGRDVRHNFISHLNAALCRKKIE 45 (162)
Q Consensus 22 ys~~D~~~~f~~~L~~~L~~~gi~ 45 (162)
|...|....++..|.+.|++.|+.
T Consensus 143 ~~~~~~g~~~~~~l~~~l~~~g~~ 166 (362)
T cd06367 143 TSRDPGYRDFLDRVETTLEESFVG 166 (362)
T ss_pred EEcCcccHHHHHHHHHHHHhcccc
Confidence 443333345677788888877765
No 99
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=20.54 E-value=3.3e+02 Score=22.03 Aligned_cols=54 Identities=7% Similarity=0.049 Sum_probs=32.5
Q ss_pred eEEEeccccccccchHHHHHHHHccCCceeeecCCcCCCC-CcchHHHHhhhhCce
Q 043195 17 DVFLSFRGRDVRHNFISHLNAALCRKKIETFIDDKLNRGN-QISPSLSSAIEGSKI 71 (162)
Q Consensus 17 dVFISys~~D~~~~f~~~L~~~L~~~gi~~f~d~~~~~G~-~i~~~i~~aI~~S~~ 71 (162)
.|.+-|...+..+.+...+.+.|++.|+++-.+..+.+|. .+...+ ..|..+..
T Consensus 138 ~v~~i~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~~~v-~~l~~~~p 192 (333)
T cd06328 138 KIATLAQDYAFGRDGVAAFKAALEKLGAAIVTEEYAPTDTTDFTPYA-QRLLDALK 192 (333)
T ss_pred eEEEEecCccccHHHHHHHHHHHHhCCCEEeeeeeCCCCCcchHHHH-HHHHhcCC
Confidence 3444454333335677788888988999886544466775 355444 45555543
No 100
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=20.43 E-value=1.9e+02 Score=24.80 Aligned_cols=50 Identities=14% Similarity=0.249 Sum_probs=36.2
Q ss_pred cccccchHHHHHHHHccCCceeeecCC-cCC----CCCcchHHHHhhhhCceEEE
Q 043195 25 RDVRHNFISHLNAALCRKKIETFIDDK-LNR----GNQISPSLSSAIEGSKISIV 74 (162)
Q Consensus 25 ~D~~~~f~~~L~~~L~~~gi~~f~d~~-~~~----G~~i~~~i~~aI~~S~~~Iv 74 (162)
.|.|++=+-.|.+.|..+|..|-..+- +.. |-.+.++..++++.++..|+
T Consensus 311 ~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 311 DNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred CccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 477888888999999999988765443 221 34456677788888887665
No 101
>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=20.11 E-value=3.5e+02 Score=19.61 Aligned_cols=54 Identities=13% Similarity=0.103 Sum_probs=34.5
Q ss_pred HHhhhhCceEEEEeecCCCCChhHHHHHHHHHHHhhhcCCeeEeEEEeeCCccccc
Q 043195 63 SSAIEGSKISIVIFSKGYASSRWCLNELVKILESKNKYGQIVVPVFYLVDPSDVRN 118 (162)
Q Consensus 63 ~~aI~~S~~~Ivv~S~~y~~S~wc~~El~~~~~~~~~~~~~viPVfy~v~p~dv~~ 118 (162)
...+..++..|++++.+-..|---+.++...+..... ..=+|+++=....|+.+
T Consensus 68 ~~~~~~~d~~ilv~d~~~~~Sf~~~~~~~~~i~~~~~--~~~~piilvgNK~Dl~~ 121 (172)
T cd04141 68 DQYMRCGEGFIICYSVTDRHSFQEASEFKKLITRVRL--TEDIPLVLVGNKVDLES 121 (172)
T ss_pred HHHhhcCCEEEEEEECCchhHHHHHHHHHHHHHHhcC--CCCCCEEEEEEChhhhh
Confidence 3567889999999998877665555555444433221 12267777667777654
No 102
>PRK14161 heat shock protein GrpE; Provisional
Probab=20.05 E-value=2.1e+02 Score=22.04 Aligned_cols=48 Identities=21% Similarity=0.324 Sum_probs=34.3
Q ss_pred HHHHHHHHccCCceeeecCCcCCCCCcchHHHHhhhh-------CceEEEEeecCCCC
Q 043195 32 ISHLNAALCRKKIETFIDDKLNRGNQISPSLSSAIEG-------SKISIVIFSKGYAS 82 (162)
Q Consensus 32 ~~~L~~~L~~~gi~~f~d~~~~~G~~i~~~i~~aI~~-------S~~~Ivv~S~~y~~ 82 (162)
...|...|++.|+...- -..|+.+.|++-+|+.. ...++-|+.+.|.-
T Consensus 108 ~k~l~~vL~~~Gv~~I~---~~~G~~FDP~~HEAv~~~~~~~~~~gtVi~v~q~GY~l 162 (178)
T PRK14161 108 KDELDKVFHKHHIEEIK---PEIGSMFDYNLHNAISQIEHPDHAPNSIITLMQSGYKI 162 (178)
T ss_pred HHHHHHHHHHCCCEEec---CCCCCCCChHHhhhheeeCCCCCCcCEEEEEeeCCcEe
Confidence 35677888889997631 12499999999998874 23577777877753
Done!