Query 042466
Match_columns 178
No_of_seqs 179 out of 1396
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 06:27:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042466.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042466hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03194 putative disease resi 100.0 1E-49 2.2E-54 312.1 16.0 155 3-174 19-177 (187)
2 PLN03210 Resistant to P. syrin 100.0 7E-49 1.5E-53 378.4 17.6 174 1-176 1-177 (1153)
3 PF01582 TIR: TIR domain; Int 99.9 2.9E-28 6.3E-33 184.1 3.0 132 13-144 1-140 (141)
4 smart00255 TIR Toll - interleu 99.9 1.2E-25 2.6E-30 168.0 12.7 137 10-148 1-139 (140)
5 PF13676 TIR_2: TIR domain; PD 99.8 3.2E-19 6.9E-24 127.1 3.1 87 13-105 1-87 (102)
6 KOG3678 SARM protein (with ste 99.4 4.1E-13 9E-18 118.1 9.3 143 6-177 608-759 (832)
7 PF08937 DUF1863: MTH538 TIR-l 98.6 9.8E-08 2.1E-12 71.1 5.7 90 11-105 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 98.0 3.5E-05 7.5E-10 58.3 8.3 64 12-75 2-70 (150)
9 PF10137 TIR-like: Predicted n 96.9 0.0032 7E-08 46.9 6.1 77 12-91 1-91 (125)
10 PF13271 DUF4062: Domain of un 93.9 0.25 5.3E-06 33.8 6.0 67 12-79 1-68 (83)
11 COG4916 Uncharacterized protei 91.6 0.24 5.1E-06 41.4 3.7 102 6-112 173-282 (329)
12 PF05014 Nuc_deoxyrib_tr: Nucl 91.5 1.9 4.1E-05 30.8 8.1 67 24-91 13-88 (113)
13 COG4271 Predicted nucleotide-b 82.5 5.1 0.00011 32.4 6.2 76 12-91 84-175 (233)
14 PF14258 DUF4350: Domain of un 80.3 10 0.00022 24.5 6.2 61 28-100 8-68 (70)
15 cd00860 ThrRS_anticodon ThrRS 74.9 13 0.00027 24.7 5.7 60 11-74 2-61 (91)
16 cd00738 HGTP_anticodon HGTP an 68.0 20 0.00043 23.8 5.4 59 11-73 2-63 (94)
17 PF03129 HGTP_anticodon: Antic 63.9 11 0.00024 25.4 3.6 36 24-62 15-50 (94)
18 cd02042 ParA ParA and ParB of 62.2 35 0.00075 23.2 5.9 63 13-75 3-73 (104)
19 COG0400 Predicted esterase [Ge 59.5 22 0.00047 28.6 5.0 56 6-62 142-199 (207)
20 cd00858 GlyRS_anticodon GlyRS 58.9 30 0.00065 24.8 5.2 61 10-75 26-88 (121)
21 PF02310 B12-binding: B12 bind 52.8 76 0.0017 22.1 6.6 61 27-95 17-78 (121)
22 cd01424 MGS_CPS_II Methylglyox 50.3 35 0.00075 24.0 4.3 30 12-43 2-31 (110)
23 COG1658 Small primase-like pro 50.0 36 0.00077 25.4 4.4 55 11-66 30-84 (127)
24 PF14359 DUF4406: Domain of un 49.1 88 0.0019 21.7 7.2 61 28-90 19-84 (92)
25 PF03720 UDPG_MGDP_dh_C: UDP-g 49.0 24 0.00051 24.8 3.3 54 19-72 11-75 (106)
26 cd01867 Rab8_Rab10_Rab13_like 44.2 1.2E+02 0.0025 22.3 6.6 57 53-112 65-121 (167)
27 KOG2792 Putative cytochrome C 44.1 22 0.00047 29.9 2.7 30 80-109 154-187 (280)
28 TIGR00334 5S_RNA_mat_M5 ribonu 43.9 37 0.00081 26.7 3.8 50 24-76 35-84 (174)
29 COG0710 AroD 3-dehydroquinate 43.3 69 0.0015 26.3 5.5 69 24-96 78-146 (231)
30 cd02426 Pol_gamma_b_Cterm C-te 42.4 16 0.00035 26.9 1.6 32 24-55 43-78 (128)
31 PF09441 Abp2: ARS binding pro 39.1 18 0.00038 28.2 1.3 58 78-144 54-111 (175)
32 cd04142 RRP22 RRP22 subfamily. 38.8 1E+02 0.0022 24.0 5.7 54 57-113 74-130 (198)
33 cd00861 ProRS_anticodon_short 38.6 84 0.0018 20.8 4.7 48 24-74 17-64 (94)
34 PRK09194 prolyl-tRNA synthetas 38.4 35 0.00076 31.4 3.4 63 9-75 467-532 (565)
35 cd07363 45_DOPA_Dioxygenase Th 37.5 1.1E+02 0.0025 24.9 6.0 68 24-93 80-149 (253)
36 PF10087 DUF2325: Uncharacteri 37.4 98 0.0021 21.2 4.9 59 25-84 10-69 (97)
37 PF00875 DNA_photolyase: DNA p 37.4 1.7E+02 0.0038 21.8 7.6 92 28-126 56-149 (165)
38 COG4916 Uncharacterized protei 37.3 54 0.0012 27.7 4.0 98 8-108 4-107 (329)
39 cd00532 MGS-like MGS-like doma 35.4 1.1E+02 0.0023 21.6 5.0 60 13-74 2-77 (112)
40 PF03709 OKR_DC_1_N: Orn/Lys/A 34.9 1.6E+02 0.0035 20.9 5.8 72 26-109 5-77 (115)
41 TIGR00418 thrS threonyl-tRNA s 34.9 1.1E+02 0.0023 28.0 6.0 61 9-73 469-529 (563)
42 cd06342 PBP1_ABC_LIVBP_like Ty 34.4 1.9E+02 0.0041 23.5 7.0 58 13-71 138-196 (334)
43 cd01423 MGS_CPS_I_III Methylgl 33.7 57 0.0012 23.1 3.3 29 13-43 3-31 (116)
44 PF03437 BtpA: BtpA family; I 33.1 82 0.0018 26.2 4.5 107 31-144 134-253 (254)
45 cd07373 2A5CPDO_A The alpha su 32.9 2.8E+02 0.0061 22.9 7.8 76 24-102 90-172 (271)
46 COG1168 MalY Bifunctional PLP- 32.7 2.8E+02 0.006 24.7 7.8 46 55-100 148-195 (388)
47 COG0125 Tmk Thymidylate kinase 32.3 2.6E+02 0.0057 22.3 11.0 157 13-175 4-206 (208)
48 PRK12325 prolyl-tRNA synthetas 32.3 52 0.0011 29.4 3.4 63 10-76 345-410 (439)
49 PF09419 PGP_phosphatase: Mito 31.9 1.2E+02 0.0025 23.7 4.9 68 33-105 35-112 (168)
50 PF01113 DapB_N: Dihydrodipico 31.8 1.3E+02 0.0028 21.7 4.9 8 11-18 68-75 (124)
51 PF01990 ATP-synt_F: ATP synth 31.6 1E+02 0.0022 21.1 4.2 47 30-78 9-55 (95)
52 cd00859 HisRS_anticodon HisRS 30.5 1.5E+02 0.0032 18.9 5.1 34 11-45 2-35 (91)
53 cd06340 PBP1_ABC_ligand_bindin 28.8 2.3E+02 0.005 23.6 6.7 63 12-75 146-209 (347)
54 PF03358 FMN_red: NADPH-depend 28.8 2.1E+02 0.0045 20.7 5.8 78 24-104 17-114 (152)
55 cd06371 PBP1_sensory_GC_DEF_li 28.1 2.7E+02 0.0058 23.8 7.1 53 24-76 146-201 (382)
56 COG0683 LivK ABC-type branched 28.0 3.4E+02 0.0074 23.1 7.7 73 12-84 150-222 (366)
57 CHL00201 syh histidine-tRNA sy 27.7 1.5E+02 0.0033 26.2 5.6 61 9-73 324-384 (430)
58 cd00862 ProRS_anticodon_zinc P 27.5 88 0.0019 24.7 3.7 48 9-56 9-63 (202)
59 cd01241 PH_Akt Akt pleckstrin 27.3 50 0.0011 23.0 2.0 17 131-147 86-102 (102)
60 TIGR03556 photolyase_8HDF deox 26.8 3.8E+02 0.0083 24.0 8.1 82 28-117 58-142 (471)
61 TIGR00409 proS_fam_II prolyl-t 26.7 67 0.0014 29.8 3.2 49 24-76 489-538 (568)
62 COG0512 PabA Anthranilate/para 26.7 1.1E+02 0.0024 24.4 4.0 47 21-76 8-56 (191)
63 COG0415 PhrB Deoxyribodipyrimi 26.5 2.9E+02 0.0063 25.1 7.1 87 28-123 58-148 (461)
64 PF07429 Glyco_transf_56: 4-al 26.5 70 0.0015 28.1 3.1 46 30-77 300-347 (360)
65 cd00154 Rab Rab family. Rab G 26.3 1.8E+02 0.004 20.2 5.0 26 52-77 61-86 (159)
66 PF09837 DUF2064: Uncharacteri 25.9 2.6E+02 0.0056 20.2 8.3 86 7-102 7-95 (122)
67 KOG1136 Predicted cleavage and 25.6 1.6E+02 0.0034 26.1 5.0 56 46-104 180-241 (501)
68 COG0276 HemH Protoheme ferro-l 25.6 2.9E+02 0.0064 23.8 6.7 79 25-105 73-161 (320)
69 PRK08350 hypothetical protein; 25.4 66 0.0014 28.0 2.7 33 8-40 279-311 (341)
70 cd01251 PH_centaurin_alpha Cen 25.4 63 0.0014 22.6 2.2 19 131-149 84-102 (103)
71 PF13289 SIR2_2: SIR2-like dom 25.3 1.7E+02 0.0036 20.8 4.6 9 26-34 76-84 (143)
72 PF00762 Ferrochelatase: Ferro 25.3 2.5E+02 0.0055 23.9 6.3 64 26-91 74-144 (316)
73 cd06352 PBP1_NPR_GC_like Ligan 25.2 3.4E+02 0.0075 22.8 7.2 64 24-96 152-218 (389)
74 PRK14938 Ser-tRNA(Thr) hydrola 24.8 1.8E+02 0.0039 25.8 5.4 59 10-72 274-332 (387)
75 cd03364 TOPRIM_DnaG_primases T 24.7 82 0.0018 20.6 2.6 39 30-69 35-75 (79)
76 cd03411 Ferrochelatase_N Ferro 24.6 3.1E+02 0.0066 20.6 6.5 64 25-90 72-142 (159)
77 cd00138 PLDc Phospholipase D. 24.1 1.4E+02 0.0031 22.0 4.2 23 51-73 20-42 (176)
78 cd03028 GRX_PICOT_like Glutare 24.0 44 0.00095 22.6 1.2 25 67-91 9-35 (90)
79 PLN02924 thymidylate kinase 23.9 3.8E+02 0.0082 21.4 11.5 31 12-42 16-48 (220)
80 cd07371 2A5CPDO_AB The alpha a 23.5 3.8E+02 0.0082 22.1 6.9 77 24-102 87-169 (268)
81 PF00155 Aminotran_1_2: Aminot 23.1 3.9E+02 0.0085 22.1 7.1 43 54-96 132-181 (363)
82 cd06335 PBP1_ABC_ligand_bindin 22.9 3.3E+02 0.0073 22.6 6.6 54 12-66 140-194 (347)
83 PRK03991 threonyl-tRNA synthet 22.9 77 0.0017 29.7 2.9 42 11-53 500-542 (613)
84 PRK12435 ferrochelatase; Provi 22.6 3.9E+02 0.0085 22.7 6.9 52 26-79 62-120 (311)
85 PF12146 Hydrolase_4: Putative 22.2 1.5E+02 0.0032 19.7 3.5 36 9-45 15-50 (79)
86 cd06386 PBP1_NPR_C_like Ligand 22.2 5E+02 0.011 22.2 7.8 39 27-65 157-195 (387)
87 TIGR01093 aroD 3-dehydroquinat 22.2 3.7E+02 0.008 21.4 6.5 56 43-99 96-151 (228)
88 COG1058 CinA Predicted nucleot 22.1 1.4E+02 0.003 24.9 4.0 43 25-69 21-66 (255)
89 COG2130 Putative NADP-dependen 22.0 2.1E+02 0.0045 24.9 5.0 60 10-77 196-256 (340)
90 smart00646 Ami_3 Ami_3. 21.7 1.1E+02 0.0024 21.3 3.0 47 8-63 6-55 (113)
91 PRK14799 thrS threonyl-tRNA sy 21.3 2.1E+02 0.0045 26.5 5.3 47 10-60 438-484 (545)
92 PF00350 Dynamin_N: Dynamin fa 20.9 3E+02 0.0065 20.0 5.4 46 55-103 120-165 (168)
93 cd06366 PBP1_GABAb_receptor Li 20.9 3.9E+02 0.0085 22.0 6.6 53 13-66 138-193 (350)
94 PRK06893 DNA replication initi 20.7 2E+02 0.0042 23.0 4.5 13 28-40 57-69 (229)
95 COG4802 FtrB Ferredoxin-thiore 20.5 2.8E+02 0.0061 20.0 4.7 24 134-157 4-27 (110)
96 PRK13762 tRNA-modifying enzyme 20.5 2.7E+02 0.0059 23.7 5.6 60 11-76 131-190 (322)
97 PF14479 HeLo: Prion-inhibitio 20.5 2.2E+02 0.0047 22.1 4.7 60 115-174 26-88 (212)
98 PF01976 DUF116: Protein of un 20.2 3.5E+02 0.0076 20.7 5.6 65 27-105 75-139 (158)
99 PF13519 VWA_2: von Willebrand 20.1 3.2E+02 0.007 19.5 5.3 37 64-105 99-135 (172)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=1e-49 Score=312.05 Aligned_cols=155 Identities=30% Similarity=0.513 Sum_probs=143.1
Q ss_pred CCCCCCCcccEEEecccccCcccHHHHHHHHhhcCCcEEEecC-CCCCcccchHHHHHHHHhcceeeEEecCCCCCChhh
Q 042466 3 SSYRNNKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISVIIFSESYPSSRWC 81 (178)
Q Consensus 3 ~~~~~~~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc 81 (178)
|||+...+|||||||+|+|+|++|++||+.+|+++||++|+|+ ++++|+.|.++|.+||++|+++|+|||++|++|+||
T Consensus 19 ~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WC 98 (187)
T PLN03194 19 SSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFC 98 (187)
T ss_pred cCCCCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhH
Confidence 4577888899999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhccceeeeEEeecCccccccc-cCchHHHHHHHHHhhhhchhHHHHHHHHHHHhhhhcCcccC--CCc
Q 042466 82 LDELVKILECKKEYAQILIPVFYRVDPSDVRNQ-TGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQ--SIR 158 (178)
Q Consensus 82 ~~EL~~i~~~~~~~~~~viPVfy~v~psdV~~~-~g~f~~~f~~~~~~~~~~~~~v~~W~~AL~~v~~~~G~~~~--~~~ 158 (178)
++||++|+++. ..||||||+|+|+|||+| .|. .+.+++++||.||++|++++|++++ ++.
T Consensus 99 LdEL~~I~e~~----~~ViPIFY~VdPsdVr~q~~~~-------------~~~e~v~~Wr~AL~~va~l~G~~~~~~~~~ 161 (187)
T PLN03194 99 LHELALIMESK----KRVIPIFCDVKPSQLRVVDNGT-------------CPDEEIRRFNWALEEAKYTVGLTFDSLKGN 161 (187)
T ss_pred HHHHHHHHHcC----CEEEEEEecCCHHHhhccccCC-------------CCHHHHHHHHHHHHHHhccccccCCCCCCC
Confidence 99999999874 379999999999999997 432 1368999999999999999999886 456
Q ss_pred hHHHHHHHHHHHHHhh
Q 042466 159 INNKSKRILQYISNKI 174 (178)
Q Consensus 159 ~~~~i~~Iv~~i~~~l 174 (178)
+.++|++||++|.++|
T Consensus 162 e~e~i~~iv~~v~k~l 177 (187)
T PLN03194 162 WSEVVTMASDAVIKNL 177 (187)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8999999999999987
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=7e-49 Score=378.39 Aligned_cols=174 Identities=41% Similarity=0.704 Sum_probs=164.8
Q ss_pred CCCC--CCCCCcccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCC
Q 042466 1 MASS--YRNNKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSS 78 (178)
Q Consensus 1 m~~~--~~~~~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S 78 (178)
|||| +++.++|||||||||+|+|++|++||+.+|.++||.+|.|+++++|+.|.+++.+||++|+++|||||++|++|
T Consensus 1 ~~~~~~~~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s 80 (1153)
T PLN03210 1 MASSSSSSRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNEIERSQSLDPELKQAIRDSRIAVVVFSKNYASS 80 (1153)
T ss_pred CCCCCCCCCCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccCCccCCCcccHHHHHHHHhCeEEEEEecCCcccc
Confidence 6776 67899999999999999999999999999999999999988999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHhhhhccceeeeEEeecCccccccccCchHHHHHHHHHhhhhchhHHHHHHHHHHHhhhhcCcccCCC-
Q 042466 79 RWCLDELVKILECKKEYAQILIPVFYRVDPSDVRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQSI- 157 (178)
Q Consensus 79 ~wc~~EL~~i~~~~~~~~~~viPVfy~v~psdV~~~~g~f~~~f~~~~~~~~~~~~~v~~W~~AL~~v~~~~G~~~~~~- 157 (178)
.||++||++|++|+++.+++|+||||+|+|+|||+|+|.||++|.++++.. +++++++||+||++||+++||++.+.
T Consensus 81 ~wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~~--~~~~~~~w~~al~~~~~~~g~~~~~~~ 158 (1153)
T PLN03210 81 SWCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQNK--TEDEKIQWKQALTDVANILGYHSQNWP 158 (1153)
T ss_pred hHHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhccchHHHHHHHHhccc--chhHHHHHHHHHHHHhCcCceecCCCC
Confidence 999999999999999999999999999999999999999999999988753 47899999999999999999999764
Q ss_pred chHHHHHHHHHHHHHhhcC
Q 042466 158 RINNKSKRILQYISNKISG 176 (178)
Q Consensus 158 ~~~~~i~~Iv~~i~~~l~~ 176 (178)
.+.+.|++||++|+++|+.
T Consensus 159 ~E~~~i~~Iv~~v~~~l~~ 177 (1153)
T PLN03210 159 NEAKMIEEIANDVLGKLNL 177 (1153)
T ss_pred CHHHHHHHHHHHHHHhhcc
Confidence 5889999999999999964
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=2.9e-28 Score=184.08 Aligned_cols=132 Identities=34% Similarity=0.590 Sum_probs=116.1
Q ss_pred EEEecccccCcccHHHHHHHHhhcC--CcEEEecC-CCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHH
Q 042466 13 VFVSFRGEDTRDNFTSHLYSALSRQ--NIQTFIDD-QLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKIL 89 (178)
Q Consensus 13 VFIS~~~~D~~~~fv~~L~~aL~~~--gi~vf~d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~ 89 (178)
|||||++.+.+..|+++|..+|+++ |+++|+++ ++.+|..+.++|.++|++|+++|+|+|++|++|+||+.||..++
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 8999999433578999999999999 99999999 99999999999999999999999999999999999999999999
Q ss_pred Hhhhhcc--ceeeeEEeecCccccc-cccCchHHHHHHHHHhhhhc--hhHHHHHHHHHH
Q 042466 90 ECKKEYA--QILIPVFYRVDPSDVR-NQTGSFGDSFSKLEERFKEN--SKKLQTWRKALK 144 (178)
Q Consensus 90 ~~~~~~~--~~viPVfy~v~psdV~-~~~g~f~~~f~~~~~~~~~~--~~~v~~W~~AL~ 144 (178)
++..+.+ ..|+||||++.+++++ .+.+.|+..|.........+ .++...|++++.
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 9986644 8999999999999999 79999999998877655443 578899999875
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.93 E-value=1.2e-25 Score=168.04 Aligned_cols=137 Identities=42% Similarity=0.722 Sum_probs=115.3
Q ss_pred cccEEEeccc-ccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHH
Q 042466 10 KYDVFVSFRG-EDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKI 88 (178)
Q Consensus 10 ~ydVFIS~~~-~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i 88 (178)
+|||||||++ ++....|+.+|..+|...|+.+|.|+....|.... +|.++|++|+++|+|+||+|..|+||..|+..+
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~~~-~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~a 79 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGDLE-EIDEAIEKSRIAIVVLSPNYAESEWCLDELVAA 79 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccchHH-HHHHHHHHCcEEEEEECcccccChhHHHHHHHH
Confidence 5999999998 45557899999999999999999998433333333 999999999999999999999999999999999
Q ss_pred HHhhhh-ccceeeeEEeecCccccccccCchHHHHHHHHHhhhhchhHHHHHHHHHHHhhh
Q 042466 89 LECKKE-YAQILIPVFYRVDPSDVRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAAS 148 (178)
Q Consensus 89 ~~~~~~-~~~~viPVfy~v~psdV~~~~g~f~~~f~~~~~~~~~~~~~v~~W~~AL~~v~~ 148 (178)
+++..+ ...+||||+++..|+++..+.+.++..+......+.++..+ +.|+.++..+.+
T Consensus 80 ~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 80 LENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 987654 66899999999999999999999999998775555443333 789999987754
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.76 E-value=3.2e-19 Score=127.10 Aligned_cols=87 Identities=31% Similarity=0.555 Sum_probs=75.5
Q ss_pred EEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhh
Q 042466 13 VFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECK 92 (178)
Q Consensus 13 VFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~ 92 (178)
|||||+++| ..++..|...|++.|+++|+|.++.+|+.+.+.|.++|++|+..|+++|++|..|+||..|+..+.+
T Consensus 1 VFIS~~~~D--~~~a~~l~~~L~~~g~~v~~d~~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~-- 76 (102)
T PF13676_consen 1 VFISYSSED--REFAERLAERLESAGIRVFLDRDIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWK-- 76 (102)
T ss_dssp EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GGEE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHC--
T ss_pred eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEEeCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHH--
Confidence 899999999 4799999999999999999999889999999999999999999999999999999999999999843
Q ss_pred hhccceeeeEEee
Q 042466 93 KEYAQILIPVFYR 105 (178)
Q Consensus 93 ~~~~~~viPVfy~ 105 (178)
.+..|+||.++
T Consensus 77 --~~~~iipv~~~ 87 (102)
T PF13676_consen 77 --RGKPIIPVRLD 87 (102)
T ss_dssp --TSESEEEEECS
T ss_pred --CCCEEEEEEEC
Confidence 45589999954
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.44 E-value=4.1e-13 Score=118.08 Aligned_cols=143 Identities=21% Similarity=0.382 Sum_probs=108.0
Q ss_pred CCCCcccEEEecccccCcccHHHHHHHHhhcCCcEEEecC-CCCCcccchHHHHHHHHhcceeeEEecCCCC----CCh-
Q 042466 6 RNNKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISVIIFSESYP----SSR- 79 (178)
Q Consensus 6 ~~~~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~----~S~- 79 (178)
+.+.+.||||||+.. +.+..++-|...|+-+|++||+|- .+..|+. ...+.+.|...+.+|+|+|||.. +..
T Consensus 608 ~~skq~DVFISYRRs-tGnQLASLiKV~LQL~GyrVFIDVdKL~AGKF-dssLlkni~aAkhFiLVLtP~sLDr~lnD~n 685 (832)
T KOG3678|consen 608 MLSKQIDVFISYRRS-TGNQLASLIKVLLQLRGYRVFIDVDKLYAGKF-DSSLLKNIQAAKHFILVLTPNSLDRLLNDDN 685 (832)
T ss_pred cccCCcceEEEeecc-ccHHHHHHHHHHHHhcCceEEEehhhhhcccc-cHHHHHHHHhhheeEEEeCcchHHHHhcccc
Confidence 557789999999876 457899999999999999999998 8888865 45889999999999999999964 444
Q ss_pred ---hhHHHHHHHHHhhhhccceeeeEEeecCccccccccCchHHHHHHHHHhhhhchhHHHHHHHHHHHhhhhcCcccCC
Q 042466 80 ---WCLDELVKILECKKEYAQILIPVFYRVDPSDVRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQS 156 (178)
Q Consensus 80 ---wc~~EL~~i~~~~~~~~~~viPVfy~v~psdV~~~~g~f~~~f~~~~~~~~~~~~~v~~W~~AL~~v~~~~G~~~~~ 156 (178)
|.-.||..+++|. ..|||||-. .|. |..-+..+++|... |..+.|....+
T Consensus 686 CeDWVHKEl~~Afe~~----KNIiPI~D~-----------aFE--~Pt~ed~iPnDirm----------i~kyNGvKWvH 738 (832)
T KOG3678|consen 686 CEDWVHKELKCAFEHQ----KNIIPIFDT-----------AFE--FPTKEDQIPNDIRM----------ITKYNGVKWVH 738 (832)
T ss_pred HHHHHHHHHHHHHHhc----CCeeeeecc-----------ccc--CCCchhcCcHHHHH----------HHhccCeeeeh
Confidence 5555666666554 489999821 111 11112222223333 44558999988
Q ss_pred CchHHHHHHHHHHHHHhhcCC
Q 042466 157 IRINNKSKRILQYISNKISGA 177 (178)
Q Consensus 157 ~~~~~~i~~Iv~~i~~~l~~~ 177 (178)
.+++.++++||+.|.+.+|++
T Consensus 739 dYQdA~maKvvRFitGe~nRt 759 (832)
T KOG3678|consen 739 DYQDACMAKVVRFITGELNRT 759 (832)
T ss_pred hhHHHHHHHHHHHHhccccCC
Confidence 899999999999999999874
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=98.59 E-value=9.8e-08 Score=71.14 Aligned_cols=90 Identities=21% Similarity=0.400 Sum_probs=48.5
Q ss_pred ccEEEecccccCcccHHHHHHHHhhcC-------CcEE-Ee---------cC-CCCCcccchHHHHHHHHhcceeeEEec
Q 042466 11 YDVFVSFRGEDTRDNFTSHLYSALSRQ-------NIQT-FI---------DD-QLNRGDEISESLVNAIEASAISVIIFS 72 (178)
Q Consensus 11 ydVFIS~~~~D~~~~fv~~L~~aL~~~-------gi~v-f~---------d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S 72 (178)
|.|||||++.|. ...+..|...+... ++.. |. +. +....+.|...|.++|..|.++||+++
T Consensus 1 ~~vFIS~~~~d~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig 79 (130)
T PF08937_consen 1 YKVFISYSHDDD-DWYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG 79 (130)
T ss_dssp ----------TH-H-HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred CCccccccccCc-HHHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence 689999999984 23777777777663 2221 11 11 222344788899999999999999999
Q ss_pred CCCCCChhhHHHHHHHHHhhhhccceeeeEEee
Q 042466 73 ESYPSSRWCLDELVKILECKKEYAQILIPVFYR 105 (178)
Q Consensus 73 ~~y~~S~wc~~EL~~i~~~~~~~~~~viPVfy~ 105 (178)
++-..|.|+..|+..+++ .+..||.|.+.
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 45578877653
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=98.02 E-value=3.5e-05 Score=58.26 Aligned_cols=64 Identities=20% Similarity=0.370 Sum_probs=52.2
Q ss_pred cEEEecccccCc-ccHHHHHHHHhhcC-CcEEEecC-CCCC--cccchHHHHHHHHhcceeeEEecCCC
Q 042466 12 DVFVSFRGEDTR-DNFTSHLYSALSRQ-NIQTFIDD-QLNR--GDEISESLVNAIEASAISVIIFSESY 75 (178)
Q Consensus 12 dVFIS~~~~D~~-~~fv~~L~~aL~~~-gi~vf~d~-~~~~--G~~i~~~i~~aI~~S~~~Ivv~S~~y 75 (178)
.|||||+..... ...|..|...|++. |+.|.+|. +... +.....=+.+.+++++..|+|+||.+
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 499999875432 36799999999999 99999999 6633 65666677788999999999999543
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=96.89 E-value=0.0032 Score=46.89 Aligned_cols=77 Identities=19% Similarity=0.241 Sum_probs=60.1
Q ss_pred cEEEecccccCcccHHHHHHHHhhcCCcEEEecC-CCCCcccchHHHHHHHHhcceeeEEecCCC-------------CC
Q 042466 12 DVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISVIIFSESY-------------PS 77 (178)
Q Consensus 12 dVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y-------------~~ 77 (178)
.|||.|+ .| ...+..+...|+..|+.+..-. ....|..+.+.+.+.+.+|+.+|++++|+= ..
T Consensus 1 kVFIvhg-~~--~~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~a 77 (125)
T PF10137_consen 1 KVFIVHG-RD--LAAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRA 77 (125)
T ss_pred CEEEEeC-CC--HHHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCcccccccc
Confidence 4899998 55 3788899999998888765433 568899999999999999999999999952 12
Q ss_pred ChhhHHHHHHHHHh
Q 042466 78 SRWCLDELVKILEC 91 (178)
Q Consensus 78 S~wc~~EL~~i~~~ 91 (178)
....+.|+..++..
T Consensus 78 R~NVifE~G~f~g~ 91 (125)
T PF10137_consen 78 RQNVIFELGLFIGK 91 (125)
T ss_pred ccceeehhhHHHhh
Confidence 33466788777654
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=93.93 E-value=0.25 Score=33.75 Aligned_cols=67 Identities=18% Similarity=0.204 Sum_probs=48.2
Q ss_pred cEEEecccccCcccHHHHHHHHhhcCCcEEEecCCC-CCcccchHHHHHHHHhcceeeEEecCCCCCCh
Q 042466 12 DVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQL-NRGDEISESLVNAIEASAISVIIFSESYPSSR 79 (178)
Q Consensus 12 dVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~-~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~ 79 (178)
.||||-.-.|. ..--..|.+.|.+.|.....-+.+ ..+....+.+++.|++|+++|.++-..|-..+
T Consensus 1 rVFiSSt~~Dl-~~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~~ 68 (83)
T PF13271_consen 1 RVFISSTFRDL-KEERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSVP 68 (83)
T ss_pred CEEEecChhhH-HHHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCCC
Confidence 48999877775 344567888888777665432212 22556667889999999999999999996543
No 11
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=91.58 E-value=0.24 Score=41.41 Aligned_cols=102 Identities=19% Similarity=0.181 Sum_probs=69.2
Q ss_pred CCCCcccEEEecccccCcccHHHHHHHHhh--cCCcEEEecCC----CCCcccchHHHHHHH-HhcceeeEEecCCCCCC
Q 042466 6 RNNKKYDVFVSFRGEDTRDNFTSHLYSALS--RQNIQTFIDDQ----LNRGDEISESLVNAI-EASAISVIIFSESYPSS 78 (178)
Q Consensus 6 ~~~~~ydVFIS~~~~D~~~~fv~~L~~aL~--~~gi~vf~d~~----~~~G~~i~~~i~~aI-~~S~~~Ivv~S~~y~~S 78 (178)
...+.||+=|||.|+- +..|+.....++ ...+..|+|-+ +-+| ++..-+...- ..|+..+|....+|...
T Consensus 173 ~~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~-sL~~~L~~~Y~~rC~~~~VF~~~~Y~~K 249 (329)
T COG4916 173 SSEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPG-SLVSTLDPGYDIRCVVTTVFNTGSYICK 249 (329)
T ss_pred ccccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCc-cHHHhcccccCceEEEEEEEeCCceEEe
Confidence 4667899999999986 479999999999 44567788862 2233 3332232322 35888999999999999
Q ss_pred hhhHHHHHHHHHhhhhccceeeeEEe-ecCccccc
Q 042466 79 RWCLDELVKILECKKEYAQILIPVFY-RVDPSDVR 112 (178)
Q Consensus 79 ~wc~~EL~~i~~~~~~~~~~viPVfy-~v~psdV~ 112 (178)
.||.-|...+-+.. .-....||-| +++.+-+.
T Consensus 250 ~~c~~E~~~~r~~~--~~d~~~rI~~~~~d~~a~d 282 (329)
T COG4916 250 STCHIEGLEGRLNP--ILDTGFRIKYLYADNIAID 282 (329)
T ss_pred eeeccchhhccccc--cccccceEEEEecCCcccc
Confidence 99999877764321 1235566665 45555443
No 12
>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=91.51 E-value=1.9 Score=30.79 Aligned_cols=67 Identities=16% Similarity=0.102 Sum_probs=49.3
Q ss_pred ccHHHHHHHHhhcCCcEEEecC--CCC---Cc----ccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHh
Q 042466 24 DNFTSHLYSALSRQNIQTFIDD--QLN---RG----DEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILEC 91 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~--~~~---~G----~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~ 91 (178)
..+...+.++|++.|+.++... +.. .+ ..+.+.-.++|++|++.|+++...- .++-+.-|+..+...
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 5788999999999999998765 221 12 3344455668999999999997755 567788899888653
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=82.47 E-value=5.1 Score=32.37 Aligned_cols=76 Identities=20% Similarity=0.229 Sum_probs=57.0
Q ss_pred cEEEecccccCcccHHHHHHHHhhcC-C-cEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCC--------C----
Q 042466 12 DVFVSFRGEDTRDNFTSHLYSALSRQ-N-IQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYP--------S---- 77 (178)
Q Consensus 12 dVFIS~~~~D~~~~fv~~L~~aL~~~-g-i~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~--------~---- 77 (178)
.|||-|+++ ..+.....+|.+. - ..+|.|.-...|..+.+.+.+-|.+++.+|++.+|+=. +
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 899998653 3777777777743 3 45677777788999999999999999999999999843 1
Q ss_pred --ChhhHHHHHHHHHh
Q 042466 78 --SRWCLDELVKILEC 91 (178)
Q Consensus 78 --S~wc~~EL~~i~~~ 91 (178)
.....-||..++..
T Consensus 160 raRqNVifELGm~mgr 175 (233)
T COG4271 160 RARQNVIFELGMFMGR 175 (233)
T ss_pred cccccchhhHhhHHhh
Confidence 22255677776654
No 14
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=80.26 E-value=10 Score=24.48 Aligned_cols=61 Identities=18% Similarity=0.205 Sum_probs=37.6
Q ss_pred HHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceee
Q 042466 28 SHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILI 100 (178)
Q Consensus 28 ~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~vi 100 (178)
.-|+.-|++.|+++-.... ..++++..+-.+++++|.+.-+. -.++..+.+..+.++..||
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 4577788888988754321 12344557889999999966553 3455555555555555543
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=74.88 E-value=13 Score=24.68 Aligned_cols=60 Identities=13% Similarity=0.214 Sum_probs=37.0
Q ss_pred ccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCC
Q 042466 11 YDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSES 74 (178)
Q Consensus 11 ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 74 (178)
++|+|...+++. ...+-.+...|++.|+++-+|. .+.++...+..|-..---.++++.++
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~---~~~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDL---RNEKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEEC---CCCCHHHHHHHHHHcCCCEEEEECcc
Confidence 677776655443 4578889999999999998875 13455555555533222234444433
No 16
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=67.96 E-value=20 Score=23.79 Aligned_cols=59 Identities=20% Similarity=0.284 Sum_probs=37.2
Q ss_pred ccEEEecccc---cCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecC
Q 042466 11 YDVFVSFRGE---DTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSE 73 (178)
Q Consensus 11 ydVFIS~~~~---D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 73 (178)
++|+|-..+. . ....+..+...|++.|+.+-+|. .+..+...+..|-..---+++++.+
T Consensus 2 ~~v~ii~~~~~~~~-~~~~a~~~~~~Lr~~g~~v~~~~---~~~~~~k~~~~a~~~g~~~~iiig~ 63 (94)
T cd00738 2 IDVAIVPLTDPRVE-AREYAQKLLNALLANGIRVLYDD---RERKIGKKFREADLRGVPFAVVVGE 63 (94)
T ss_pred eEEEEEECCCCcHH-HHHHHHHHHHHHHHCCCEEEecC---CCcCHhHHHHHHHhCCCCEEEEECC
Confidence 5666654333 2 24677889999999999998875 2345555555554333346666665
No 17
>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=63.93 E-value=11 Score=25.40 Aligned_cols=36 Identities=17% Similarity=0.288 Sum_probs=26.3
Q ss_pred ccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHH
Q 042466 24 DNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIE 62 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~ 62 (178)
..++.+|...|.+.||.+.+|. .+..+...+..|-.
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~---~~~~~~k~~~~a~~ 50 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDD---SDKSLGKQIKYADK 50 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEES---SSSTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCEEEEEC---CCCchhHHHHHHhh
Confidence 4688999999999999999987 33444445555543
No 18
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=62.20 E-value=35 Score=23.24 Aligned_cols=63 Identities=17% Similarity=0.188 Sum_probs=39.4
Q ss_pred EEEecccccCcccHHHHHHHHhhcCCcEEEecC-CCC-------CcccchHHHHHHHHhcceeeEEecCCC
Q 042466 13 VFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-QLN-------RGDEISESLVNAIEASAISVIIFSESY 75 (178)
Q Consensus 13 VFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~-------~G~~i~~~i~~aI~~S~~~Ivv~S~~y 75 (178)
+|.|..|--.+..++.+|...|.++|.++..-+ +.. -+-.+.+....++..|+..|+++.+..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~ 73 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSP 73 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCH
Confidence 356665443345678999999998998876544 322 111223344467777888777776654
No 19
>COG0400 Predicted esterase [General function prediction only]
Probab=59.47 E-value=22 Score=28.58 Aligned_cols=56 Identities=16% Similarity=0.121 Sum_probs=42.7
Q ss_pred CCCCcccEEEecccccC--cccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHH
Q 042466 6 RNNKKYDVFVSFRGEDT--RDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIE 62 (178)
Q Consensus 6 ~~~~~ydVFIS~~~~D~--~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~ 62 (178)
+.....-|||+|-..|. ......+|.+.|+..|..|.... ...|-++.++-.+++.
T Consensus 142 ~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~-~~~GH~i~~e~~~~~~ 199 (207)
T COG0400 142 PDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRW-HEGGHEIPPEELEAAR 199 (207)
T ss_pred cccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEE-ecCCCcCCHHHHHHHH
Confidence 34567889999988886 35678999999999999998875 2367777766555554
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=58.93 E-value=30 Score=24.82 Aligned_cols=61 Identities=11% Similarity=0.024 Sum_probs=39.9
Q ss_pred cccEEEeccc--ccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCC
Q 042466 10 KYDVFVSFRG--EDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESY 75 (178)
Q Consensus 10 ~ydVFIS~~~--~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 75 (178)
.+||||-.-+ ++ ....+..|...|+++|++|-+|.. ..+...+..|-+.---.++++.++-
T Consensus 26 p~~v~Ii~~~~~~~-~~~~a~~la~~LR~~gi~v~~d~~----~sl~kqlk~A~k~g~~~~iiiG~~e 88 (121)
T cd00858 26 PIKVAVLPLVKRDE-LVEIAKEISEELRELGFSVKYDDS----GSIGRRYARQDEIGTPFCVTVDFDT 88 (121)
T ss_pred CcEEEEEecCCcHH-HHHHHHHHHHHHHHCCCEEEEeCC----CCHHHHHHHhHhcCCCEEEEECcCc
Confidence 4788877755 32 245778899999999999998752 4666566565443333555555543
No 21
>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=52.83 E-value=76 Score=22.09 Aligned_cols=61 Identities=25% Similarity=0.182 Sum_probs=40.3
Q ss_pred HHHHHHHhhcCCcEEE-ecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhc
Q 042466 27 TSHLYSALSRQNIQTF-IDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEY 95 (178)
Q Consensus 27 v~~L~~aL~~~gi~vf-~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~ 95 (178)
...|...|+++|+.+- +|-.... +++.+.+.+.+--+|.+|-.+. |...++..+.+..++.
T Consensus 17 l~~la~~l~~~G~~v~~~d~~~~~-----~~l~~~~~~~~pd~V~iS~~~~---~~~~~~~~l~~~~k~~ 78 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDANVPP-----EELVEALRAERPDVVGISVSMT---PNLPEAKRLARAIKER 78 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESSB-H-----HHHHHHHHHTTCSEEEEEESSS---THHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHCCCeEEEECCCCCH-----HHHHHHHhcCCCcEEEEEccCc---CcHHHHHHHHHHHHhc
Confidence 4678899999999984 4433322 6777888888888888876544 3445555555544433
No 22
>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=50.26 E-value=35 Score=23.96 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=21.6
Q ss_pred cEEEecccccCcccHHHHHHHHhhcCCcEEEe
Q 042466 12 DVFVSFRGEDTRDNFTSHLYSALSRQNIQTFI 43 (178)
Q Consensus 12 dVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~ 43 (178)
.||+|.+..|. .-...+...|.+.|++++-
T Consensus 2 ~vl~s~~~~~k--~~~~~~~~~l~~~G~~l~a 31 (110)
T cd01424 2 TVFISVADRDK--PEAVEIAKRLAELGFKLVA 31 (110)
T ss_pred eEEEEEEcCcH--hHHHHHHHHHHHCCCEEEE
Confidence 38899987763 3444777778888888865
No 23
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=50.05 E-value=36 Score=25.40 Aligned_cols=55 Identities=11% Similarity=0.115 Sum_probs=40.8
Q ss_pred ccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcce
Q 042466 11 YDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAI 66 (178)
Q Consensus 11 ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~ 66 (178)
.++|+-..+.-....++..|..++..+|+-++.|.| .+|+.|...|.+.+..+..
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 466666644322256889999999999999999874 5789998888888877444
No 24
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=49.11 E-value=88 Score=21.71 Aligned_cols=61 Identities=11% Similarity=0.038 Sum_probs=40.5
Q ss_pred HHHHHHhhcCCcEEEecCCC--CCcccchHHH---HHHHHhcceeeEEecCCCCCChhhHHHHHHHHH
Q 042466 28 SHLYSALSRQNIQTFIDDQL--NRGDEISESL---VNAIEASAISVIIFSESYPSSRWCLDELVKILE 90 (178)
Q Consensus 28 ~~L~~aL~~~gi~vf~d~~~--~~G~~i~~~i---~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~ 90 (178)
......|+.+|..|.---.+ ..|.++..-+ ...+..|+.. ++=|+.-.|.=|.-|+..+.+
T Consensus 19 ~~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i--~~l~gWe~S~GA~~E~~~A~~ 84 (92)
T PF14359_consen 19 NAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAI--YMLPGWENSRGARLEHELAKK 84 (92)
T ss_pred HHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEE--EEcCCcccCcchHHHHHHHHH
Confidence 35778889999766532233 5555544322 3346677753 334999999999999988754
No 25
>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=49.04 E-value=24 Score=24.84 Aligned_cols=54 Identities=19% Similarity=0.317 Sum_probs=33.5
Q ss_pred cccCcccHHHHHHHHhhcCCcEEEecC-CCCC----------cccchHHHHHHHHhcceeeEEec
Q 042466 19 GEDTRDNFTSHLYSALSRQNIQTFIDD-QLNR----------GDEISESLVNAIEASAISVIIFS 72 (178)
Q Consensus 19 ~~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~~----------G~~i~~~i~~aI~~S~~~Ivv~S 72 (178)
..|+|.+=+-.|.+.|.+.|+.|...+ -+.. |-.+.+.+.++++.+++.|+.-.
T Consensus 11 ~~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~ 75 (106)
T PF03720_consen 11 TDDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATD 75 (106)
T ss_dssp SS--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS-
T ss_pred CcccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEec
Confidence 457899999999999999999987655 3221 22223356778888887666443
No 26
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi
Probab=44.23 E-value=1.2e+02 Score=22.30 Aligned_cols=57 Identities=5% Similarity=0.035 Sum_probs=29.5
Q ss_pred chHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeEEeecCccccc
Q 042466 53 ISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVFYRVDPSDVR 112 (178)
Q Consensus 53 i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPVfy~v~psdV~ 112 (178)
........++.++.+|++++-+- ..-+.++...+.........=+|++.=....|+.
T Consensus 65 ~~~~~~~~~~~ad~~i~v~d~~~---~~s~~~~~~~~~~i~~~~~~~~p~iiv~nK~Dl~ 121 (167)
T cd01867 65 FRTITTAYYRGAMGIILVYDITD---EKSFENIRNWMRNIEEHASEDVERMLVGNKCDME 121 (167)
T ss_pred HHHHHHHHhCCCCEEEEEEECcC---HHHHHhHHHHHHHHHHhCCCCCcEEEEEECcccc
Confidence 33333456789999999998643 4445555444433222111223444433455554
No 27
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=44.07 E-value=22 Score=29.94 Aligned_cols=30 Identities=33% Similarity=0.528 Sum_probs=21.8
Q ss_pred hhHHHHHHHHHhh---h-hccceeeeEEeecCcc
Q 042466 80 WCLDELVKILECK---K-EYAQILIPVFYRVDPS 109 (178)
Q Consensus 80 wc~~EL~~i~~~~---~-~~~~~viPVfy~v~ps 109 (178)
=|-+||.++.... + +.+..++|||.-++|.
T Consensus 154 ICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 154 ICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred cChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 4889988765532 2 3456777999999994
No 28
>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=43.92 E-value=37 Score=26.71 Aligned_cols=50 Identities=12% Similarity=0.199 Sum_probs=38.6
Q ss_pred ccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCC
Q 042466 24 DNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYP 76 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 76 (178)
..-...|..+.+.+|+-+|.|.| .+|+.|...|.+.+.++..+- +++.++
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 45677888888999999999974 579999999988888877643 344443
No 29
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=43.35 E-value=69 Score=26.32 Aligned_cols=69 Identities=13% Similarity=0.184 Sum_probs=44.3
Q ss_pred ccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhcc
Q 042466 24 DNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYA 96 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~ 96 (178)
......|...++.+| .-|+|=++..++....++.+.-.+-+ +|+|-|...+.+.++|+..++..+...+
T Consensus 78 ~~~i~ll~~la~~~~-~d~iDiEl~~~~~~~~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~ 146 (231)
T COG0710 78 EEYIELLKKLAELNG-PDYIDIELSSPEDDVKEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLG 146 (231)
T ss_pred HHHHHHHHHHHhhcC-CCEEEEEccCcchhHHHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhC
Confidence 346666666666666 44565544444333233333322223 8889999999999999999998886554
No 30
>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=42.35 E-value=16 Score=26.88 Aligned_cols=32 Identities=6% Similarity=0.123 Sum_probs=25.2
Q ss_pred ccHHHHHHHHhhcCCcEEEecC-CC---CCcccchH
Q 042466 24 DNFTSHLYSALSRQNIQTFIDD-QL---NRGDEISE 55 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~-~~---~~G~~i~~ 55 (178)
...+..|+..|+..|+.++.|+ +- .+|..+.+
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 5678999999999999999988 42 46666543
No 31
>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=39.09 E-value=18 Score=28.20 Aligned_cols=58 Identities=22% Similarity=0.409 Sum_probs=34.0
Q ss_pred ChhhHHHHHHHHHhhhhccceeeeEEeecCccccccccCchHHHHHHHHHhhhhchhHHHHHHHHHH
Q 042466 78 SRWCLDELVKILECKKEYAQILIPVFYRVDPSDVRNQTGSFGDSFSKLEERFKENSKKLQTWRKALK 144 (178)
Q Consensus 78 S~wc~~EL~~i~~~~~~~~~~viPVfy~v~psdV~~~~g~f~~~f~~~~~~~~~~~~~v~~W~~AL~ 144 (178)
|.|.+-||..-++..+-+.=.=+-+.++|+|-++..... .++.....-++++|+.|+.
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 567788877766544322223344567888888654211 1112223567899999986
No 32
>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=38.83 E-value=1e+02 Score=23.98 Aligned_cols=54 Identities=9% Similarity=0.048 Sum_probs=33.3
Q ss_pred HHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhc---cceeeeEEeecCcccccc
Q 042466 57 LVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEY---AQILIPVFYRVDPSDVRN 113 (178)
Q Consensus 57 i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~---~~~viPVfy~v~psdV~~ 113 (178)
...+++.++++|+|++.+ +++-++++....+..... ...-+|++.=....|+..
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 445688999999999975 455556555544432211 123367777666777643
No 33
>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=38.63 E-value=84 Score=20.79 Aligned_cols=48 Identities=15% Similarity=0.296 Sum_probs=29.3
Q ss_pred ccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCC
Q 042466 24 DNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSES 74 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~ 74 (178)
...+..|...|++.|+++.+|.. +..+...+..|-..---.++++.++
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~---~~~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDR---NERPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECC---CCCcccchhHHHhcCCCEEEEECCc
Confidence 35788899999999999999861 2234334444433323345555443
No 34
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=38.36 E-value=35 Score=31.44 Aligned_cols=63 Identities=16% Similarity=0.321 Sum_probs=40.0
Q ss_pred CcccEEEeccc--ccCcccHHHHHHHHhhcCCcEEEecC-CCCCcccchHHHHHHHHhcceeeEEecCCC
Q 042466 9 KKYDVFVSFRG--EDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISVIIFSESY 75 (178)
Q Consensus 9 ~~ydVFIS~~~--~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y 75 (178)
..++|+|---+ .+.-...+..|+..|++.||.+.+|+ +-.+|..+...-.. ... .++++.++.
T Consensus 467 aP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~~~ad~~---GiP-~~iiiG~~e 532 (565)
T PRK09194 467 APFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKFADADLI---GIP-HRIVVGDRG 532 (565)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHHHHHHhc---CCC-EEEEEcCcc
Confidence 45888886543 12235688899999999999999998 54555555432222 222 455566553
No 35
>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=37.47 E-value=1.1e+02 Score=24.94 Aligned_cols=68 Identities=16% Similarity=0.112 Sum_probs=49.1
Q ss_pred ccHHHHHHHHhhcCCcEEEecC--CCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhh
Q 042466 24 DNFTSHLYSALSRQNIQTFIDD--QLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKK 93 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~--~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~ 93 (178)
..++.+|.+.|.++|+.+-.+. .+.-|--+. +.-...+.++-||.+|-+...+..-..+|.+++...+
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 4799999999999999886544 444554443 1222334688899999988877777778999887654
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=37.42 E-value=98 Score=21.22 Aligned_cols=59 Identities=12% Similarity=0.193 Sum_probs=35.2
Q ss_pred cHHHHHHHHhhcCCcEEEecCCCCCccc-chHHHHHHHHhcceeeEEecCCCCCChhhHHH
Q 042466 25 NFTSHLYSALSRQNIQTFIDDQLNRGDE-ISESLVNAIEASAISVIIFSESYPSSRWCLDE 84 (178)
Q Consensus 25 ~fv~~L~~aL~~~gi~vf~d~~~~~G~~-i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~E 84 (178)
.....+...+++.|...-... -..|.. -...+...|.++++.|++.+----...|...+
T Consensus 10 ~~~~~~~~~~~~~G~~~~~hg-~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~ 69 (97)
T PF10087_consen 10 DRERRYKRILEKYGGKLIHHG-RDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKK 69 (97)
T ss_pred ccHHHHHHHHHHcCCEEEEEe-cCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHH
Confidence 456788888999998865541 111211 12247778899999888764444444444333
No 37
>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=37.39 E-value=1.7e+02 Score=21.76 Aligned_cols=92 Identities=17% Similarity=0.229 Sum_probs=49.5
Q ss_pred HHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeE--Eee
Q 042466 28 SHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPV--FYR 105 (178)
Q Consensus 28 ~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPV--fy~ 105 (178)
..|...|.+.|+...+-. |+ ..+.+.+-+++..+.-|++...|... -...-..+.+...+.+..+.-+ -+=
T Consensus 56 ~~L~~~L~~~g~~L~v~~----g~-~~~~l~~l~~~~~~~~V~~~~~~~~~--~~~rd~~v~~~l~~~~i~~~~~~~~~L 128 (165)
T PF00875_consen 56 ADLQESLRKLGIPLLVLR----GD-PEEVLPELAKEYGATAVYFNEEYTPY--ERRRDERVRKALKKHGIKVHTFDDHTL 128 (165)
T ss_dssp HHHHHHHHHTTS-EEEEE----SS-HHHHHHHHHHHHTESEEEEE---SHH--HHHHHHHHHHHHHHTTSEEEEE--SSS
T ss_pred HHHHHHHHhcCcceEEEe----cc-hHHHHHHHHHhcCcCeeEeccccCHH--HHHHHHHHHHHHHhcceEEEEECCcEE
Confidence 567788889999877533 43 23455666788889999999988762 2222222222222222222111 112
Q ss_pred cCccccccccCchHHHHHHHH
Q 042466 106 VDPSDVRNQTGSFGDSFSKLE 126 (178)
Q Consensus 106 v~psdV~~~~g~f~~~f~~~~ 126 (178)
+.|.++....|.....|....
T Consensus 129 ~~~~~i~~~~~~~~~vFtpf~ 149 (165)
T PF00875_consen 129 VPPDDIPKKDGEPYKVFTPFR 149 (165)
T ss_dssp S-HHHCHSTTSSSHSSHHHHH
T ss_pred EeccccccCCCCCcccHHHHH
Confidence 678888877777666665443
No 38
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=37.28 E-value=54 Score=27.71 Aligned_cols=98 Identities=19% Similarity=0.419 Sum_probs=70.6
Q ss_pred CCcccEEEecccccCcccHHHHHHHHhhcCCcEEEecC-C--CCCcccchHHHHHHHH--hcceeeEEecCCCCCChhhH
Q 042466 8 NKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-Q--LNRGDEISESLVNAIE--ASAISVIIFSESYPSSRWCL 82 (178)
Q Consensus 8 ~~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~-~--~~~G~~i~~~i~~aI~--~S~~~Ivv~S~~y~~S~wc~ 82 (178)
.-++.+=+||.++|. .+++....-|..+|+.+|+|- + -..|.++.. ++..|- ..-+++...|.+|-.-.|..
T Consensus 4 ~~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~-~~~e~~q~~~~~~~~f~~~~~~r~~~~~ 80 (329)
T COG4916 4 NVQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFEEANLWGKNLYD-YLSEIYQDKALFTIMFISEHYSRKMWTN 80 (329)
T ss_pred chheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHH-HHHHHHhhhhHHHhhhhhccccCcCCCc
Confidence 345667789999994 789999999999999999875 2 124555553 233333 34557788999999999999
Q ss_pred HHHHHHHHhh-hhccceeeeEEeecCc
Q 042466 83 DELVKILECK-KEYAQILIPVFYRVDP 108 (178)
Q Consensus 83 ~EL~~i~~~~-~~~~~~viPVfy~v~p 108 (178)
.|+..+.... .+....++|-.++..|
T Consensus 81 ~~~~~~~a~~~~~~~~~~~~~~~~~~~ 107 (329)
T COG4916 81 HERQAMQARAFQEHQEYILPARFDETP 107 (329)
T ss_pred HHHHHHHHHHhhhccEEehhhhhccCC
Confidence 9998876543 4556688888886544
No 39
>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=35.44 E-value=1.1e+02 Score=21.61 Aligned_cols=60 Identities=20% Similarity=0.247 Sum_probs=36.0
Q ss_pred EEEecccccCcccHHHHHHHHhhcCCcEEEecC---------CC-----CCccc-chHHHHHHHHh-cceeeEEecCC
Q 042466 13 VFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD---------QL-----NRGDE-ISESLVNAIEA-SAISVIIFSES 74 (178)
Q Consensus 13 VFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~---------~~-----~~G~~-i~~~i~~aI~~-S~~~Ivv~S~~ 74 (178)
||||-+..|. .-...+...|...|+.++--. .+ ..+.. -.+++.+.|.+ -++.+||..|+
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 7888877663 334467777778888775431 11 01100 12567777777 77777777665
No 40
>PF03709 OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal domain; InterPro: IPR005308 This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC, P43099 from SWISSPROT) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 106 Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation [].; GO: 0016831 carboxy-lyase activity; PDB: 3Q16_C 3N75_A 1C4K_A 1ORD_A 2VYC_D.
Probab=34.90 E-value=1.6e+02 Score=20.92 Aligned_cols=72 Identities=21% Similarity=0.244 Sum_probs=42.9
Q ss_pred HHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHH-hcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeEEe
Q 042466 26 FTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIE-ASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVFY 104 (178)
Q Consensus 26 fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~-~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPVfy 104 (178)
-+..|..+|++.|+.+..-.+ .+.....++ .++++-||+|-+ .--.++...+++..+ ....=+|||.
T Consensus 5 ~~~~l~~~L~~~~~~vv~~~~-------~dd~~~~i~~~~~i~avvi~~d----~~~~~~~~~ll~~i~-~~~~~iPVFl 72 (115)
T PF03709_consen 5 ASRELAEALEQRGREVVDADS-------TDDALAIIESFTDIAAVVISWD----GEEEDEAQELLDKIR-ERNFGIPVFL 72 (115)
T ss_dssp HHHHHHHHHHHTTTEEEEESS-------HHHHHHHHHCTTTEEEEEEECH----HHHHHHHHHHHHHHH-HHSTT-EEEE
T ss_pred HHHHHHHHHHHCCCEEEEeCC-------hHHHHHHHHhCCCeeEEEEEcc----cccchhHHHHHHHHH-HhCCCCCEEE
Confidence 467899999999998865331 224445555 489999999866 111223333333332 2345689998
Q ss_pred ecCcc
Q 042466 105 RVDPS 109 (178)
Q Consensus 105 ~v~ps 109 (178)
-.++.
T Consensus 73 ~~~~~ 77 (115)
T PF03709_consen 73 LAERD 77 (115)
T ss_dssp EESCC
T ss_pred EecCC
Confidence 66643
No 41
>TIGR00418 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..
Probab=34.85 E-value=1.1e+02 Score=28.01 Aligned_cols=61 Identities=15% Similarity=0.261 Sum_probs=40.7
Q ss_pred CcccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecC
Q 042466 9 KKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSE 73 (178)
Q Consensus 9 ~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 73 (178)
...||+|-.-+++. ...+..|...|+++|++|-+|. .+.++...+..|-+.---.++|+.+
T Consensus 469 ~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~---~~~sl~~q~k~A~~~g~~~~iiiG~ 529 (563)
T TIGR00418 469 APVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDD---RNERLGKKIREAQKQKIPYMLVVGD 529 (563)
T ss_pred CCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEEC---CCCCHHHHHHHHHhcCCCEEEEEch
Confidence 45788877655443 5678899999999999999986 2455666666664433334555543
No 42
>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=34.45 E-value=1.9e+02 Score=23.54 Aligned_cols=58 Identities=14% Similarity=0.212 Sum_probs=33.8
Q ss_pred EEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCc-ccchHHHHHHHHhcceeeEEe
Q 042466 13 VFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRG-DEISESLVNAIEASAISVIIF 71 (178)
Q Consensus 13 VFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G-~~i~~~i~~aI~~S~~~Ivv~ 71 (178)
|.+-+...+-....+..|..+|++.|+++-....+.+| ..+. .+...|.++..-+|++
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 44445433333456778888888889877654444444 3444 4455566655545544
No 43
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=33.71 E-value=57 Score=23.08 Aligned_cols=29 Identities=10% Similarity=0.085 Sum_probs=22.4
Q ss_pred EEEecccccCcccHHHHHHHHhhcCCcEEEe
Q 042466 13 VFVSFRGEDTRDNFTSHLYSALSRQNIQTFI 43 (178)
Q Consensus 13 VFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~ 43 (178)
||||.+..|. .-...+...|...|++++-
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 7999987763 3445788888889998875
No 44
>PF03437 BtpA: BtpA family; InterPro: IPR005137 Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. It consists of 11 subunits, ~100 chlorophyll a molecules, 2 phylloquinones, and 3 Fe4S4-clusters. The three dimensional structure of the PSI complex has been resolved at 2.5 A [], which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA [], Ycf3 [, ], and Ycf4 (IPR003359 from INTERPRO) []. Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. These gene products are therefore involved either in the stabilisation or in the assembly of the PSI complex. However, their exact roles remain unknown. The BtpA protein appears to act at the level of PSI stabilisation []. It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane [, ]. Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain []. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids []. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners []. Ycf3 contains a number of tetratrico peptide repeats (TPR, IPR001440 from INTERPRO); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions.
Probab=33.13 E-value=82 Score=26.22 Aligned_cols=107 Identities=16% Similarity=0.269 Sum_probs=61.7
Q ss_pred HHHhhcCCcEEEecCCC-----CCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeEEe-
Q 042466 31 YSALSRQNIQTFIDDQL-----NRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVFY- 104 (178)
Q Consensus 31 ~~aL~~~gi~vf~d~~~-----~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPVfy- 104 (178)
.+.|... +++|.|=.. ..+.++.+....+++.+..=-+++|-.-...+=-++++..+-+. . . +|||.
T Consensus 134 R~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~~---~--~-~PVlvG 206 (254)
T PF03437_consen 134 RKRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVREA---V--P-VPVLVG 206 (254)
T ss_pred HHHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHhc---C--C-CCEEEe
Confidence 3444445 899887422 23566777777788887776667777665444344555444221 1 2 99999
Q ss_pred -ecCccccccccC----ch-HHHHHHHHHhh-hhchhHHHHHHHHHH
Q 042466 105 -RVDPSDVRNQTG----SF-GDSFSKLEERF-KENSKKLQTWRKALK 144 (178)
Q Consensus 105 -~v~psdV~~~~g----~f-~~~f~~~~~~~-~~~~~~v~~W~~AL~ 144 (178)
++.+.++..+.. -. |-.|.+..... +.|++++++..+++.
T Consensus 207 SGvt~~Ni~~~l~~ADG~IVGS~~K~~G~~~n~VD~~Rv~~fm~~v~ 253 (254)
T PF03437_consen 207 SGVTPENIAEYLSYADGAIVGSYFKKDGKWENPVDPERVRRFMEAVK 253 (254)
T ss_pred cCCCHHHHHHHHHhCCEEEEeeeeeeCCEeCCcCCHHHHHHHHHHhh
Confidence 588888876532 11 33333222211 236777777776654
No 45
>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=32.94 E-value=2.8e+02 Score=22.88 Aligned_cols=76 Identities=13% Similarity=0.152 Sum_probs=52.6
Q ss_pred ccHHHHHHHHhhcCCcEEE-ecC-C--CCCcccchHHHHHHH-H-hcceeeEEecCCCCCChhhHHHHHHHHHh-hhhcc
Q 042466 24 DNFTSHLYSALSRQNIQTF-IDD-Q--LNRGDEISESLVNAI-E-ASAISVIIFSESYPSSRWCLDELVKILEC-KKEYA 96 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf-~d~-~--~~~G~~i~~~i~~aI-~-~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~-~~~~~ 96 (178)
..++..|.+.|.+.||.+- .|. . +.-|--+. +.-+ . ..++-||.+|.+...+.....+|.+++.. .++.+
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 4789999999999999985 555 2 44454333 2223 2 46777888999886677777899998874 45445
Q ss_pred ceeeeE
Q 042466 97 QILIPV 102 (178)
Q Consensus 97 ~~viPV 102 (178)
.+|+=|
T Consensus 167 ~rV~iI 172 (271)
T cd07373 167 KRVAVV 172 (271)
T ss_pred CeEEEE
Confidence 666644
No 46
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=32.68 E-value=2.8e+02 Score=24.67 Aligned_cols=46 Identities=22% Similarity=0.221 Sum_probs=35.3
Q ss_pred HHHHHHHHhcc-eeeEEecCCC-CCChhhHHHHHHHHHhhhhccceee
Q 042466 55 ESLVNAIEASA-ISVIIFSESY-PSSRWCLDELVKILECKKEYAQILI 100 (178)
Q Consensus 55 ~~i~~aI~~S~-~~Ivv~S~~y-~~S~wc~~EL~~i~~~~~~~~~~vi 100 (178)
+.+.+++.+.+ ...++.+|+= ...-|..+||.++.+...+.+-+||
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 47777888887 5667777775 4788999999999997766665554
No 47
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=32.33 E-value=2.6e+02 Score=22.34 Aligned_cols=157 Identities=17% Similarity=0.239 Sum_probs=80.7
Q ss_pred EEEecccccC--cccHHHHHHHHhhcCCcEEEecC---CCCCcccchHHHHH------------------------HHHh
Q 042466 13 VFVSFRGEDT--RDNFTSHLYSALSRQNIQTFIDD---QLNRGDEISESLVN------------------------AIEA 63 (178)
Q Consensus 13 VFIS~~~~D~--~~~fv~~L~~aL~~~gi~vf~d~---~~~~G~~i~~~i~~------------------------aI~~ 63 (178)
.||.+-|-|. ..+.+..|.+.|+.+|++|.+-. .-..|+.+...+.+ -|.-
T Consensus 4 ~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~trEP~~~~ige~iR~~ll~~~~~~~~~~e~lLfaadR~~h~~~~i~p 83 (208)
T COG0125 4 MFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTREPGGTPIGEKIRELLLNGEEKLSPKAEALLFAADRAQHLEEVIKP 83 (208)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCCCChHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4888866663 24688999999999999886654 21112222221111 1110
Q ss_pred -cceeeEEecCCCCCChhhHHH--------HHHHHHhh-hhccceeeeEEeecCccccccccCch---HHHHHHHHHhhh
Q 042466 64 -SAISVIIFSESYPSSRWCLDE--------LVKILECK-KEYAQILIPVFYRVDPSDVRNQTGSF---GDSFSKLEERFK 130 (178)
Q Consensus 64 -S~~~Ivv~S~~y~~S~wc~~E--------L~~i~~~~-~~~~~~viPVfy~v~psdV~~~~g~f---~~~f~~~~~~~~ 130 (178)
..-.-+|++..|.-|.-+.+- ....++.. ...-.+-+-+|++++|..--...+.- .+.|.+...
T Consensus 84 al~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~al~R~~~r~~~~~r~E~~~~--- 160 (208)
T COG0125 84 ALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVALERIRKRGELRDRFEKEDD--- 160 (208)
T ss_pred hhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHHHHHHHhcCCccchhhhHHH---
Confidence 111347888999988887662 22222211 11113455577899987643222111 123322211
Q ss_pred hchhHHHHHHHHHHHhhhhcC--cc-cCCC-chHHHHHHHHHHHHHhhc
Q 042466 131 ENSKKLQTWRKALKEAASLSG--FP-SQSI-RINNKSKRILQYISNKIS 175 (178)
Q Consensus 131 ~~~~~v~~W~~AL~~v~~~~G--~~-~~~~-~~~~~i~~Iv~~i~~~l~ 175 (178)
+-.++=+....+++.... +. .+.+ ...+..++|.+.+...+.
T Consensus 161 ---~f~~kvr~~Y~~la~~~~~r~~vIda~~~~e~v~~~i~~~l~~~l~ 206 (208)
T COG0125 161 ---EFLEKVREGYLELAAKFPERIIVIDASRPLEEVHEEILKILKERLG 206 (208)
T ss_pred ---HHHHHHHHHHHHHHhhCCCeEEEEECCCCHHHHHHHHHHHHHHhhc
Confidence 124445555555665554 32 3332 345666666666666553
No 48
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=32.32 E-value=52 Score=29.35 Aligned_cols=63 Identities=21% Similarity=0.182 Sum_probs=38.5
Q ss_pred cccEEEeccc--ccCcccHHHHHHHHhhcCCcEEEecC-CCCCcccchHHHHHHHHhcceeeEEecCCCC
Q 042466 10 KYDVFVSFRG--EDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISVIIFSESYP 76 (178)
Q Consensus 10 ~ydVFIS~~~--~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 76 (178)
.++|+|---+ .+.....+..|...|++.||.|.+|+ +-..|..+. .|-..---.++|+.++-.
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~ki~----~a~~~giP~~iiVG~~e~ 410 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGAKFA----TMDLIGLPWQIIVGPKGL 410 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhHHHH----HHHHcCCCEEEEECCccc
Confidence 3788765432 22234678999999999999999987 444454443 332222225556655543
No 49
>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=31.93 E-value=1.2e+02 Score=23.68 Aligned_cols=68 Identities=29% Similarity=0.312 Sum_probs=42.4
Q ss_pred HhhcCCcEEEe-cC--CCC-C-cccchHHHHHHHHhcce-----eeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeE
Q 042466 33 ALSRQNIQTFI-DD--QLN-R-GDEISESLVNAIEASAI-----SVIIFSESYPSSRWCLDELVKILECKKEYAQILIPV 102 (178)
Q Consensus 33 aL~~~gi~vf~-d~--~~~-~-G~~i~~~i~~aI~~S~~-----~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPV 102 (178)
.|.+.||+..+ |. -+. + -+.+.+++.+.+++++. .|+|+|.+--++.---.+-+..++. ..+ +||
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 38999999754 54 332 3 36778888888888763 3889998876655322333333332 222 888
Q ss_pred Eee
Q 042466 103 FYR 105 (178)
Q Consensus 103 fy~ 105 (178)
|..
T Consensus 110 l~h 112 (168)
T PF09419_consen 110 LRH 112 (168)
T ss_pred EEe
Confidence 743
No 50
>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=31.80 E-value=1.3e+02 Score=21.66 Aligned_cols=8 Identities=38% Similarity=0.683 Sum_probs=3.4
Q ss_pred ccEEEecc
Q 042466 11 YDVFVSFR 18 (178)
Q Consensus 11 ydVFIS~~ 18 (178)
.||-|-|+
T Consensus 68 ~DVvIDfT 75 (124)
T PF01113_consen 68 ADVVIDFT 75 (124)
T ss_dssp -SEEEEES
T ss_pred CCEEEEcC
Confidence 44444444
No 51
>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=31.62 E-value=1e+02 Score=21.11 Aligned_cols=47 Identities=13% Similarity=0.247 Sum_probs=34.3
Q ss_pred HHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCC
Q 042466 30 LYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSS 78 (178)
Q Consensus 30 L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S 78 (178)
+..-|+-.|+..+... ...+++...+.+.+++.++.|++++.+++..
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 4455677899988763 1235566677777888999999999988763
No 52
>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=30.47 E-value=1.5e+02 Score=18.85 Aligned_cols=34 Identities=29% Similarity=0.246 Sum_probs=23.6
Q ss_pred ccEEEecccccCcccHHHHHHHHhhcCCcEEEecC
Q 042466 11 YDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD 45 (178)
Q Consensus 11 ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~ 45 (178)
.||+|-..+++. ..-+-.+...|++.|+.+.++.
T Consensus 2 ~~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~ 35 (91)
T cd00859 2 VDVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDY 35 (91)
T ss_pred CcEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEec
Confidence 367666544432 3446788999999999998765
No 53
>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=28.77 E-value=2.3e+02 Score=23.58 Aligned_cols=63 Identities=10% Similarity=0.075 Sum_probs=36.9
Q ss_pred cEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcc-cchHHHHHHHHhcceeeEEecCCC
Q 042466 12 DVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGD-EISESLVNAIEASAISVIIFSESY 75 (178)
Q Consensus 12 dVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~-~i~~~i~~aI~~S~~~Ivv~S~~y 75 (178)
.|.+-+...+-....+..+..+|++.|+.+-....+.+++ ++. .+...|..++.-+|++.-..
T Consensus 146 ~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~d~~-~~i~~l~~~~~d~v~~~~~~ 209 (347)
T cd06340 146 TVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDISYPANARDLT-SEVLKLKAANPDAILPASYT 209 (347)
T ss_pred eEEEEecCchHhHHHHHHHHHHHHHcCCEEEEeeccCCCCcchH-HHHHHHHhcCCCEEEEcccc
Confidence 3555453332234567777888888998876544454443 444 44556676666666665443
No 54
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=28.77 E-value=2.1e+02 Score=20.75 Aligned_cols=78 Identities=12% Similarity=0.072 Sum_probs=44.6
Q ss_pred ccHHHHHHHHhhcCCcEEEe-cC-CC-CC-----------cccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHH
Q 042466 24 DNFTSHLYSALSRQNIQTFI-DD-QL-NR-----------GDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKIL 89 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~-d~-~~-~~-----------G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~ 89 (178)
...++.+.+.|++.|+.+-+ |= +. .+ -.+-..++.+.+.+++. ||+.||.|..+.- -.|..++
T Consensus 17 ~~l~~~~~~~l~~~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD~-iI~~sP~y~~~~s--~~lK~~l 93 (152)
T PF03358_consen 17 RKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEADG-IIFASPVYNGSVS--GQLKNFL 93 (152)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSSE-EEEEEEEBTTBE---HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCCe-EEEeecEEcCcCC--hhhhHHH
Confidence 45778888888888877633 32 33 11 11223477788888885 5667899876532 2344444
Q ss_pred Hhhh------hccceeeeEEe
Q 042466 90 ECKK------EYAQILIPVFY 104 (178)
Q Consensus 90 ~~~~------~~~~~viPVfy 104 (178)
+... -.+..+.+|-+
T Consensus 94 D~~~~~~~~~~~~K~~~~i~~ 114 (152)
T PF03358_consen 94 DRLSCWFRRALRGKPVAIIAV 114 (152)
T ss_dssp HTHHHTHTTTTTTSEEEEEEE
T ss_pred HHhccccccccCCCEEEEEEE
Confidence 4331 13445665543
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=28.06 E-value=2.7e+02 Score=23.85 Aligned_cols=53 Identities=8% Similarity=0.129 Sum_probs=29.4
Q ss_pred ccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhc---ceeeEEecCCCC
Q 042466 24 DNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEAS---AISVIIFSESYP 76 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~ 76 (178)
......|.++|++.|+.+-....+..++.-...+.+.|+.. ++.|+.....+.
T Consensus 146 ~~~~~~l~~~l~~~gi~v~~~~~~~~~~~d~~~~L~~lk~~~~~~viv~~~~~~~~ 201 (382)
T cd06371 146 VETAQKLASALRAHGLPVGLVTSMGPDEKGAREALKKVRSADRVRVVIMCMHSVLI 201 (382)
T ss_pred HHHHHHHHHHHHHCCCcEEEEEEecCCHHHHHHHHHHHhcCCCcEEEEEEeecccc
Confidence 34677888889889987654333444433223455556643 444444444444
No 56
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=27.97 E-value=3.4e+02 Score=23.07 Aligned_cols=73 Identities=15% Similarity=0.171 Sum_probs=47.0
Q ss_pred cEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHH
Q 042466 12 DVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDE 84 (178)
Q Consensus 12 dVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~E 84 (178)
.|+|-++...-.+.+...+.++|+.+|..+-.+....+++.-...+...|..++.-+|++...+....-.+.+
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~ 222 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVVEEVYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQ 222 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEEEEeeCCCCCChHHHHHHHHhcCCCEEEECCCCccchHHHHH
Confidence 5666665555457889999999999999743333455554324566677777777666666666554444433
No 57
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=27.73 E-value=1.5e+02 Score=26.22 Aligned_cols=61 Identities=20% Similarity=0.285 Sum_probs=39.6
Q ss_pred CcccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecC
Q 042466 9 KKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSE 73 (178)
Q Consensus 9 ~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~ 73 (178)
...||+|-+-+.+. ...+-.+...|+++|++|-+|. .+..+...+..|-+..-..++|+.+
T Consensus 324 ~~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~---~~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 324 QSIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDL---SSSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEee---CCCCHHHHHHHHHHcCCCEEEEEec
Confidence 34789998754432 4567789999999999988764 2345555666665443345555554
No 58
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=27.52 E-value=88 Score=24.73 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=33.0
Q ss_pred CcccEEEeccccc-----CcccHHHHHHHHhhcCCcEEEecC-CC-CCcccchHH
Q 042466 9 KKYDVFVSFRGED-----TRDNFTSHLYSALSRQNIQTFIDD-QL-NRGDEISES 56 (178)
Q Consensus 9 ~~ydVFIS~~~~D-----~~~~fv~~L~~aL~~~gi~vf~d~-~~-~~G~~i~~~ 56 (178)
..++|+|---+.+ .-...+..|...|+..||++.+|. +- .+|..+...
T Consensus 9 AP~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~~~a 63 (202)
T cd00862 9 APIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFNDW 63 (202)
T ss_pred cCceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHHHHH
Confidence 3467776543322 024578999999999999999988 44 677776543
No 59
>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=27.34 E-value=50 Score=23.04 Aligned_cols=17 Identities=24% Similarity=0.554 Sum_probs=13.9
Q ss_pred hchhHHHHHHHHHHHhh
Q 042466 131 ENSKKLQTWRKALKEAA 147 (178)
Q Consensus 131 ~~~~~v~~W~~AL~~v~ 147 (178)
++++..++|.+||..|+
T Consensus 86 ~s~ee~~eWi~ai~~v~ 102 (102)
T cd01241 86 ESPEEREEWIHAIQTVA 102 (102)
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 45788999999998874
No 60
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=26.82 E-value=3.8e+02 Score=24.02 Aligned_cols=82 Identities=12% Similarity=0.174 Sum_probs=47.2
Q ss_pred HHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeEE---e
Q 042466 28 SHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVF---Y 104 (178)
Q Consensus 28 ~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPVf---y 104 (178)
..|...|++.|+..++- .|+.. +.+.+.+++..+.-|++...|..-.--.+ ..+.+..+..+..+.- | +
T Consensus 58 ~~L~~~L~~~G~~L~v~----~G~p~-~vl~~l~~~~~~~~V~~~~~~~~~~~~rd--~~v~~~l~~~~i~~~~-~~~~~ 129 (471)
T TIGR03556 58 QELQQRYQQAGSQLLIL----QGDPV-QLIPQLAQQLGAKAVYWNLDVEPYGRKRD--RAVAAALKEAGIAVVT-LWDQL 129 (471)
T ss_pred HHHHHHHHHCCCCeEEE----ECCHH-HHHHHHHHHcCCCEEEEecccCHHHHHHH--HHHHHHHHHCCCEEEE-eCCcE
Confidence 55778888899988764 34433 34555567788999999999876332222 2222222222222221 1 1
Q ss_pred ecCccccccccCc
Q 042466 105 RVDPSDVRNQTGS 117 (178)
Q Consensus 105 ~v~psdV~~~~g~ 117 (178)
-+.|.+|....|.
T Consensus 130 l~~p~~i~~~~~~ 142 (471)
T TIGR03556 130 LHSPDEILTGSGN 142 (471)
T ss_pred EECccccccCCCC
Confidence 2578888766553
No 61
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=26.73 E-value=67 Score=29.81 Aligned_cols=49 Identities=20% Similarity=0.350 Sum_probs=33.4
Q ss_pred ccHHHHHHHHhhcCCcEEEecC-CCCCcccchHHHHHHHHhcceeeEEecCCCC
Q 042466 24 DNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISVIIFSESYP 76 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~-~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 76 (178)
...+..|+..|+..|+.|.+|+ +-.+|..+.+.-.-+|- ..+++.++..
T Consensus 489 ~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~dadliGiP----~~i~vG~~~l 538 (568)
T TIGR00409 489 QQLAEELYSELLAQGVDVLLDDRNERAGVKFADSELIGIP----LRVVVGKKNL 538 (568)
T ss_pred HHHHHHHHHHHHhCCCEEEEECCCCCHHHHHHhhhhcCCC----EEEEECCCcc
Confidence 4688999999999999999998 65677666543222222 3455555543
No 62
>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=26.68 E-value=1.1e+02 Score=24.44 Aligned_cols=47 Identities=30% Similarity=0.329 Sum_probs=31.7
Q ss_pred cCcccHHHHHHHHhhcCC--cEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCC
Q 042466 21 DTRDNFTSHLYSALSRQN--IQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYP 76 (178)
Q Consensus 21 D~~~~fv~~L~~aL~~~g--i~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 76 (178)
|...+|+-.|++.|.+.| +.|+..+ .+.. ..++..+--.+|+||.=-
T Consensus 8 DNyDSFtyNLv~yl~~lg~~v~V~rnd------~~~~---~~~~~~~pd~iviSPGPG 56 (191)
T COG0512 8 DNYDSFTYNLVQYLRELGAEVTVVRND------DISL---ELIEALKPDAIVISPGPG 56 (191)
T ss_pred ECccchHHHHHHHHHHcCCceEEEECC------ccCH---HHHhhcCCCEEEEcCCCC
Confidence 334589999999999987 5556543 1221 146666667888998743
No 63
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=26.49 E-value=2.9e+02 Score=25.13 Aligned_cols=87 Identities=20% Similarity=0.340 Sum_probs=52.2
Q ss_pred HHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHh-hhhccceeeeEEe--
Q 042466 28 SHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILEC-KKEYAQILIPVFY-- 104 (178)
Q Consensus 28 ~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~-~~~~~~~viPVfy-- 104 (178)
..|.++|.+.|+.+++-. |+.. +.+.+.+++..+..|+....| +.| ..+-..++.. ..+.+..+. .|.
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-ERQRDAALAQPLTEVGIAVH-SFWDA 128 (461)
T ss_pred HHHHHHHHHcCCceEEEe----CCHH-HHHHHHHHHhCcceEEeeeee--chh-HHHHHHHHHHHHHhcCceEE-Eeccc
Confidence 458888999999998754 4433 255566666667777887888 333 2333333332 223333332 343
Q ss_pred -ecCccccccccCchHHHHH
Q 042466 105 -RVDPSDVRNQTGSFGDSFS 123 (178)
Q Consensus 105 -~v~psdV~~~~g~f~~~f~ 123 (178)
-..|.+|+.+.|..-+.|.
T Consensus 129 ~l~~p~~~~t~~~~~y~vfT 148 (461)
T COG0415 129 LLHEPGEVRTGSGEPYKVFT 148 (461)
T ss_pred cccCHhhccCCCCCCccccc
Confidence 3689999998886544443
No 64
>PF07429 Glyco_transf_56: 4-alpha-L-fucosyltransferase glycosyl transferase group 56; InterPro: IPR009993 This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc [].; GO: 0008417 fucosyltransferase activity, 0009246 enterobacterial common antigen biosynthetic process, 0009276 Gram-negative-bacterium-type cell wall
Probab=26.48 E-value=70 Score=28.07 Aligned_cols=46 Identities=13% Similarity=0.285 Sum_probs=24.1
Q ss_pred HHHHhhcCCcEEEecC-CCCCcccchHHHHHHHHhc-ceeeEEecCCCCC
Q 042466 30 LYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEAS-AISVIIFSESYPS 77 (178)
Q Consensus 30 L~~aL~~~gi~vf~d~-~~~~G~~i~~~i~~aI~~S-~~~Ivv~S~~y~~ 77 (178)
+++.|.++|+.|+++. ++. ++.+. +..+.+... +..|..|+|||..
T Consensus 300 ~~~~l~~~~ipVlf~~d~L~-~~~v~-ea~rql~~~dk~~iaFf~pny~~ 347 (360)
T PF07429_consen 300 FWQDLKEQGIPVLFYGDELD-EALVR-EAQRQLANVDKQQIAFFAPNYLQ 347 (360)
T ss_pred HHHHHHhCCCeEEeccccCC-HHHHH-HHHHHHhhCcccceeeeCCchHH
Confidence 4566677777776654 322 22222 222223333 2355678888876
No 65
>cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di
Probab=26.35 E-value=1.8e+02 Score=20.21 Aligned_cols=26 Identities=0% Similarity=0.049 Sum_probs=18.6
Q ss_pred cchHHHHHHHHhcceeeEEecCCCCC
Q 042466 52 EISESLVNAIEASAISVIIFSESYPS 77 (178)
Q Consensus 52 ~i~~~i~~aI~~S~~~Ivv~S~~y~~ 77 (178)
.+.......+++++..|++++..-..
T Consensus 61 ~~~~~~~~~~~~~d~ii~v~d~~~~~ 86 (159)
T cd00154 61 RFRSITPSYYRGAHGAILVYDITNRE 86 (159)
T ss_pred HHHHHHHHHhcCCCEEEEEEECCCHH
Confidence 34445556788999999999986533
No 66
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=25.91 E-value=2.6e+02 Score=20.22 Aligned_cols=86 Identities=17% Similarity=0.312 Sum_probs=44.2
Q ss_pred CCCcccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhc---ceeeEEecCCCCCChhhHH
Q 042466 7 NNKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEAS---AISVIIFSESYPSSRWCLD 83 (178)
Q Consensus 7 ~~~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~~S~wc~~ 83 (178)
....+|++|.|.+... ......+ ....++.++. +.|..+.+.+..|++.. .-.|+++-.+... -+..
T Consensus 7 ~~~~~~~~l~~~~~~~-~~~~~~~---~~~~~~~~~~----Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~--l~~~ 76 (122)
T PF09837_consen 7 QADGADVVLAYTPDGD-HAAFRQL---WLPSGFSFFP----QQGGDLGERMANAFQQAARGYEPVVLIGSDCPD--LTPD 76 (122)
T ss_dssp -TSSSEEEEEE----T-THHHHHH---HH-TTSEEEE------SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT----HH
T ss_pred cCCCcCEEEEEcCCcc-HHHHhcc---ccCCCCEEee----cCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCC--CCHH
Confidence 4556899999988764 3333332 4445566654 45667766666666655 3366667666554 2455
Q ss_pred HHHHHHHhhhhccceeeeE
Q 042466 84 ELVKILECKKEYAQILIPV 102 (178)
Q Consensus 84 EL~~i~~~~~~~~~~viPV 102 (178)
.|..+.+..+....++-|-
T Consensus 77 ~l~~A~~~L~~~d~VlgPa 95 (122)
T PF09837_consen 77 DLEQAFEALQRHDVVLGPA 95 (122)
T ss_dssp HHHHHHHHTTT-SEEEEEB
T ss_pred HHHHHHHHhccCCEEEeec
Confidence 6666766665555566663
No 67
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=25.64 E-value=1.6e+02 Score=26.09 Aligned_cols=56 Identities=23% Similarity=0.498 Sum_probs=40.0
Q ss_pred CCCCcccchHHHHHHHHhcceeeEEecCCCC----CChhhHH-HH-HHHHHhhhhccceeeeEEe
Q 042466 46 QLNRGDEISESLVNAIEASAISVIIFSESYP----SSRWCLD-EL-VKILECKKEYAQILIPVFY 104 (178)
Q Consensus 46 ~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~----~S~wc~~-EL-~~i~~~~~~~~~~viPVfy 104 (178)
++.|...+.. ..|..++--++|--..|+ .|..|.+ |+ .+..+|...++.++||||-
T Consensus 180 nmTpDrHLGa---A~id~~rpdlLIsESTYattiRdskr~rERdFLk~VhecVa~GGkvlIPvFA 241 (501)
T KOG1136|consen 180 NMTPDRHLGA---AWIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHECVARGGKVLIPVFA 241 (501)
T ss_pred cCCcccccch---hhhccccCceEEeeccceeeeccccchhHHHHHHHHHHHHhcCCeEEEEeee
Confidence 6666666553 236778877777667776 4888866 44 4556788889999999994
No 68
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=25.63 E-value=2.9e+02 Score=23.84 Aligned_cols=79 Identities=23% Similarity=0.342 Sum_probs=49.6
Q ss_pred cHHHHHHHHhhcC----CcEEEecCCCCCcccchHHHHHHHHhc---ceeeEEecCCCCCCh--hhHHHHHHHHHhhhh-
Q 042466 25 NFTSHLYSALSRQ----NIQTFIDDQLNRGDEISESLVNAIEAS---AISVIIFSESYPSSR--WCLDELVKILECKKE- 94 (178)
Q Consensus 25 ~fv~~L~~aL~~~----gi~vf~d~~~~~G~~i~~~i~~aI~~S---~~~Ivv~S~~y~~S~--wc~~EL~~i~~~~~~- 94 (178)
.+...+..+|+++ .+.|++ -+.-|.+..++....+.+. ++.++.+.|.|..|. -..+++..+++..+.
T Consensus 73 ~~T~~q~~~L~~~L~~~~~~V~~--amry~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~~~~~ 150 (320)
T COG0276 73 VITRAQAAALEERLDLPDFKVYL--AMRYGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKELRGQ 150 (320)
T ss_pred HHHHHHHHHHHHHhCCCCccEEE--eecCCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHhcCCC
Confidence 3455556666544 466666 3566777777777777654 457778888887544 346677777665432
Q ss_pred ccceeeeEEee
Q 042466 95 YAQILIPVFYR 105 (178)
Q Consensus 95 ~~~~viPVfy~ 105 (178)
.....||-||+
T Consensus 151 ~~i~~I~~~~~ 161 (320)
T COG0276 151 PKISTIPDYYD 161 (320)
T ss_pred CceEEecCccC
Confidence 24467777765
No 69
>PRK08350 hypothetical protein; Provisional
Probab=25.38 E-value=66 Score=28.01 Aligned_cols=33 Identities=12% Similarity=0.135 Sum_probs=28.8
Q ss_pred CCcccEEEecccccCcccHHHHHHHHhhcCCcE
Q 042466 8 NKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQ 40 (178)
Q Consensus 8 ~~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~ 40 (178)
...|.+.+|||+-+|..+|+.+|..+|....|+
T Consensus 279 ~~g~~~vvSHRSGETeD~~IAdLaVa~~agqIK 311 (341)
T PRK08350 279 SERITPILAEAKYESADEALPHLAVGLRCPAML 311 (341)
T ss_pred HcCCeEEeecCCCCCcchhHHHHHHHhCCCccc
Confidence 346889999998888899999999999988887
No 70
>cd01251 PH_centaurin_alpha Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha Pleckstrin homology (PH) domain. Centaurin alpha is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specifici
Probab=25.36 E-value=63 Score=22.60 Aligned_cols=19 Identities=21% Similarity=0.398 Sum_probs=15.6
Q ss_pred hchhHHHHHHHHHHHhhhh
Q 042466 131 ENSKKLQTWRKALKEAASL 149 (178)
Q Consensus 131 ~~~~~v~~W~~AL~~v~~~ 149 (178)
++++..+.|.+||..|-+.
T Consensus 84 ~s~~e~~~Wi~ai~~v~~~ 102 (103)
T cd01251 84 ETEQDRREWIAAFQNVLSR 102 (103)
T ss_pred CCHHHHHHHHHHHHHHhcC
Confidence 4578889999999988654
No 71
>PF13289 SIR2_2: SIR2-like domain
Probab=25.34 E-value=1.7e+02 Score=20.77 Aligned_cols=9 Identities=44% Similarity=0.560 Sum_probs=4.0
Q ss_pred HHHHHHHHh
Q 042466 26 FTSHLYSAL 34 (178)
Q Consensus 26 fv~~L~~aL 34 (178)
+-..|...|
T Consensus 76 ~~~~l~~~l 84 (143)
T PF13289_consen 76 FPNFLRSLL 84 (143)
T ss_pred HHHHHHHHH
Confidence 334444444
No 72
>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=25.25 E-value=2.5e+02 Score=23.88 Aligned_cols=64 Identities=22% Similarity=0.322 Sum_probs=34.3
Q ss_pred HHHHHHHHhhcCC--cEEEecCCCCCcccchHHHHHHHHh---cceeeEEecCCCCCCh--hhHHHHHHHHHh
Q 042466 26 FTSHLYSALSRQN--IQTFIDDQLNRGDEISESLVNAIEA---SAISVIIFSESYPSSR--WCLDELVKILEC 91 (178)
Q Consensus 26 fv~~L~~aL~~~g--i~vf~d~~~~~G~~i~~~i~~aI~~---S~~~Ivv~S~~y~~S~--wc~~EL~~i~~~ 91 (178)
.+..|.+.|...| +.|+. -+.-|.+..++..+.+.+ .++.++.+.|.|..+. -+++++..++..
T Consensus 74 qa~~l~~~L~~~~~~~~V~~--amry~~P~i~~~l~~l~~~g~~~ivvlPLyPqyS~~ttgs~~~~~~~~~~~ 144 (316)
T PF00762_consen 74 QAEALQQRLDERGVDVEVYY--AMRYGPPSIEDALEELKADGVDRIVVLPLYPQYSSSTTGSYLDEVERALKK 144 (316)
T ss_dssp HHHHHHHHHHHH-EEEEEEE--EESSSSSBHHHHHHHHHHTT-SEEEEEESSSS--TTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCeeEEE--EeccCCCCHHHHHHHHHHcCCCeEEEEeCCCchhHhhHHHHHHHHHHHHHh
Confidence 4555666666554 33333 455666665555555553 3556777788877443 355666655543
No 73
>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=25.20 E-value=3.4e+02 Score=22.79 Aligned_cols=64 Identities=17% Similarity=0.177 Sum_probs=34.5
Q ss_pred ccHHHHHHHHhhcCCcEEEecCCCCCc---ccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhcc
Q 042466 24 DNFTSHLYSALSRQNIQTFIDDQLNRG---DEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYA 96 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~d~~~~~G---~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~ 96 (178)
...+..+.++|++.|+.+-....+.++ ..+...+ +.|..+.- ++++.... .+...++++.++.+
T Consensus 152 ~~~~~~~~~~~~~~G~~v~~~~~~~~~~~~~d~~~~l-~~i~~~~~-vii~~~~~-------~~~~~~l~q~~~~g 218 (389)
T cd06352 152 FFTLEALEAALREFNLTVSHVVFMEDNSGAEDLLEIL-QDIKRRSR-IIIMCGSS-------EDVRELLLAAHDLG 218 (389)
T ss_pred HHHHHHHHHHHHhcCCeEEEEEEecCCccchhHHHHH-HHhhhcce-EEEEECCH-------HHHHHHHHHHHHcC
Confidence 456778888888888876544334443 4455444 44555542 33332111 45566666544433
No 74
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=24.84 E-value=1.8e+02 Score=25.81 Aligned_cols=59 Identities=20% Similarity=0.203 Sum_probs=37.2
Q ss_pred cccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEec
Q 042466 10 KYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFS 72 (178)
Q Consensus 10 ~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S 72 (178)
.++|+|-.-+++. ...+..|...|+++|+++.+|. .+..+...+..|-+.---.++++-
T Consensus 274 P~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl---~srSLgKQiK~AdK~GaPfvIIIG 332 (387)
T PRK14938 274 PIQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDD---LDDSLGNKIRRAGTEWIPFVIIIG 332 (387)
T ss_pred cceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEEC---CCCCHHHHHHHHHHcCCCEEEEEC
Confidence 3677665545442 4577889999999999999976 234555566565443333344443
No 75
>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=24.67 E-value=82 Score=20.59 Aligned_cols=39 Identities=13% Similarity=0.173 Sum_probs=23.5
Q ss_pred HHHHhhc--CCcEEEecCCCCCcccchHHHHHHHHhcceeeE
Q 042466 30 LYSALSR--QNIQTFIDDQLNRGDEISESLVNAIEASAISVI 69 (178)
Q Consensus 30 L~~aL~~--~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Iv 69 (178)
....|.+ +.+-+|+|.| .+|.....++.+....-...+-
T Consensus 35 ~~~~L~~~~~~vii~~D~D-~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 35 QAELLKRLAKEVILAFDGD-EAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred HHHHHHhcCCeEEEEECCC-HHHHHHHHHHHHHHHHCCCeEE
Confidence 3444554 5677888874 5677666666666655444433
No 76
>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=24.58 E-value=3.1e+02 Score=20.59 Aligned_cols=64 Identities=22% Similarity=0.351 Sum_probs=36.5
Q ss_pred cHHHHHHHHhhcCC--cEEEecCCCCCcccchHHHHHHHHh---cceeeEEecCCCCCC--hhhHHHHHHHHH
Q 042466 25 NFTSHLYSALSRQN--IQTFIDDQLNRGDEISESLVNAIEA---SAISVIIFSESYPSS--RWCLDELVKILE 90 (178)
Q Consensus 25 ~fv~~L~~aL~~~g--i~vf~d~~~~~G~~i~~~i~~aI~~---S~~~Ivv~S~~y~~S--~wc~~EL~~i~~ 90 (178)
..+..|.+.|.+.+ +.++. -++-|.+..++..+.+.+ .++.++-+.|.|..+ .-+.+++...+.
T Consensus 72 ~q~~~l~~~L~~~~~~~~v~~--amry~~P~i~~~l~~l~~~g~~~iivlPl~P~~S~~Tt~s~~~~~~~~~~ 142 (159)
T cd03411 72 AQAEALEKALDERGIDVKVYL--AMRYGPPSIEEALEELKADGVDRIVVLPLYPQYSASTTGSYLDEVERALK 142 (159)
T ss_pred HHHHHHHHHHhccCCCcEEEe--hHhcCCCCHHHHHHHHHHcCCCEEEEEECCcccccccHHHHHHHHHHHHH
Confidence 34556666666543 44444 255566555554444433 566777788888644 345666666554
No 77
>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=24.15 E-value=1.4e+02 Score=22.04 Aligned_cols=23 Identities=26% Similarity=0.205 Sum_probs=10.8
Q ss_pred ccchHHHHHHHHhcceeeEEecC
Q 042466 51 DEISESLVNAIEASAISVIIFSE 73 (178)
Q Consensus 51 ~~i~~~i~~aI~~S~~~Ivv~S~ 73 (178)
+.+.+.+.++|.+++..|.+.++
T Consensus 20 ~~~~~~i~~~I~~A~~~I~i~~~ 42 (176)
T cd00138 20 RSDLDALLEAISNAKKSIYIASF 42 (176)
T ss_pred chHHHHHHHHHHhhheEEEEEEe
Confidence 34444444444444444444444
No 78
>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=23.98 E-value=44 Score=22.64 Aligned_cols=25 Identities=28% Similarity=0.501 Sum_probs=15.9
Q ss_pred eeEEecCCCCCChhhHH--HHHHHHHh
Q 042466 67 SVIIFSESYPSSRWCLD--ELVKILEC 91 (178)
Q Consensus 67 ~Ivv~S~~y~~S~wc~~--EL~~i~~~ 91 (178)
-|+|||+.+.+.+||.. .+..+++.
T Consensus 9 ~vvvf~k~~~~~~~Cp~C~~ak~~L~~ 35 (90)
T cd03028 9 PVVLFMKGTPEEPRCGFSRKVVQILNQ 35 (90)
T ss_pred CEEEEEcCCCCCCCCcHHHHHHHHHHH
Confidence 45777888877777753 44455543
No 79
>PLN02924 thymidylate kinase
Probab=23.89 E-value=3.8e+02 Score=21.41 Aligned_cols=31 Identities=16% Similarity=0.203 Sum_probs=24.7
Q ss_pred cEEEecccccCc--ccHHHHHHHHhhcCCcEEE
Q 042466 12 DVFVSFRGEDTR--DNFTSHLYSALSRQNIQTF 42 (178)
Q Consensus 12 dVFIS~~~~D~~--~~fv~~L~~aL~~~gi~vf 42 (178)
-.||.+-|-|.. .+-+..|.+.|+.+|+.+-
T Consensus 16 g~~IviEGiDGsGKsTq~~~L~~~l~~~g~~v~ 48 (220)
T PLN02924 16 GALIVLEGLDRSGKSTQCAKLVSFLKGLGVAAE 48 (220)
T ss_pred CeEEEEECCCCCCHHHHHHHHHHHHHhcCCCce
Confidence 469999887742 5678999999999998863
No 80
>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=23.52 E-value=3.8e+02 Score=22.09 Aligned_cols=77 Identities=8% Similarity=0.073 Sum_probs=49.5
Q ss_pred ccHHHHHHHHhhcCCcEEEe--cC--CCCCcccchHHHHHHHHhcceeeEEecCCCC-CChhhHHHHHHHHH-hhhhccc
Q 042466 24 DNFTSHLYSALSRQNIQTFI--DD--QLNRGDEISESLVNAIEASAISVIIFSESYP-SSRWCLDELVKILE-CKKEYAQ 97 (178)
Q Consensus 24 ~~fv~~L~~aL~~~gi~vf~--d~--~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~-~S~wc~~EL~~i~~-~~~~~~~ 97 (178)
..++..|.+.|.+.|+.+-. +. .+.-|--+.-..+. .+.++-+|.+|-+.. .+..-..+|.+++. ..++.+.
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 47999999999999998865 22 44556554422221 245676777775543 56666778888885 3355455
Q ss_pred eeeeE
Q 042466 98 ILIPV 102 (178)
Q Consensus 98 ~viPV 102 (178)
+|+=|
T Consensus 165 rv~iI 169 (268)
T cd07371 165 RVAVL 169 (268)
T ss_pred cEEEE
Confidence 66544
No 81
>PF00155 Aminotran_1_2: Aminotransferase class I and II 1-aminocyclopropane-1-carboxylate synthase signature aspartate aminotransferase signature; InterPro: IPR004839 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into class I and class II. This entry includes proteins from both subfamilies.; GO: 0016769 transferase activity, transferring nitrogenous groups, 0030170 pyridoxal phosphate binding, 0009058 biosynthetic process; PDB: 3NRA_B 3P6K_B 3OP7_A 3ASB_A 3ASA_A 1W7M_A 3FVX_A 1W7N_A 3FVU_B 3FVS_A ....
Probab=23.08 E-value=3.9e+02 Score=22.14 Aligned_cols=43 Identities=30% Similarity=0.486 Sum_probs=28.1
Q ss_pred hHHHHHHHHh------cceeeEEecCCCC-CChhhHHHHHHHHHhhhhcc
Q 042466 54 SESLVNAIEA------SAISVIIFSESYP-SSRWCLDELVKILECKKEYA 96 (178)
Q Consensus 54 ~~~i~~aI~~------S~~~Ivv~S~~y~-~S~wc~~EL~~i~~~~~~~~ 96 (178)
.+.+.+.+++ ...+|++-+|+.. ...+..+|+.++++..++.+
T Consensus 132 ~~~l~~~l~~~~~~~~~~~~v~~~~p~nPtG~~~~~~~l~~l~~~~~~~~ 181 (363)
T PF00155_consen 132 PEALEEALDELPSKGPRPKAVLICNPNNPTGSVLSLEELRELAELAREYN 181 (363)
T ss_dssp HHHHHHHHHTSHTTTETEEEEEEESSBTTTTBB--HHHHHHHHHHHHHTT
T ss_pred ccccccccccccccccccceeeecccccccccccccccccchhhhhcccc
Confidence 3567777777 3457777777764 45677889999887665443
No 82
>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=22.92 E-value=3.3e+02 Score=22.60 Aligned_cols=54 Identities=13% Similarity=0.173 Sum_probs=27.4
Q ss_pred cEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCc-ccchHHHHHHHHhcce
Q 042466 12 DVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRG-DEISESLVNAIEASAI 66 (178)
Q Consensus 12 dVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G-~~i~~~i~~aI~~S~~ 66 (178)
.|.|-|...+-....+..+.++|++.|+.+-....+.++ ..+.+ ....|.++..
T Consensus 140 ~v~ii~~~~~~g~~~~~~~~~~~~~~G~~v~~~~~~~~~~~d~s~-~i~~i~~~~~ 194 (347)
T cd06335 140 KVALLLDNTGWGRSNRKDLTAALAARGLKPVAVEWFNWGDKDMTA-QLLRAKAAGA 194 (347)
T ss_pred eEEEEeccCchhhhHHHHHHHHHHHcCCeeEEEeeecCCCccHHH-HHHHHHhCCC
Confidence 444444333333456777777777777776433233333 33443 3344444444
No 83
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=22.86 E-value=77 Score=29.74 Aligned_cols=42 Identities=21% Similarity=0.239 Sum_probs=29.9
Q ss_pred ccEEEecccccCcccHHHHHHHHhhcCCcEEEecC-CCCCcccc
Q 042466 11 YDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEI 53 (178)
Q Consensus 11 ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~-~~~~G~~i 53 (178)
++|+|---+++ ....+..|...|++.|++|.+|+ +-..|..+
T Consensus 500 ~qV~IIpi~e~-~~~~A~eIa~~Lr~~GirV~lDdr~~slgkKi 542 (613)
T PRK03991 500 TQVRVIPVSER-HLDYAEEVADKLEAAGIRVDVDDRDESLGKKI 542 (613)
T ss_pred ceEEEEEeCHH-HHHHHHHHHHHHHhCCCEEEEECCCCCHHHHH
Confidence 67766554433 35789999999999999999987 43334333
No 84
>PRK12435 ferrochelatase; Provisional
Probab=22.58 E-value=3.9e+02 Score=22.70 Aligned_cols=52 Identities=15% Similarity=0.236 Sum_probs=30.9
Q ss_pred HHHHHHHHhhcC--C--cEEEecCCCCCcccchHHHHHHHHh--c-ceeeEEecCCCCCCh
Q 042466 26 FTSHLYSALSRQ--N--IQTFIDDQLNRGDEISESLVNAIEA--S-AISVIIFSESYPSSR 79 (178)
Q Consensus 26 fv~~L~~aL~~~--g--i~vf~d~~~~~G~~i~~~i~~aI~~--S-~~~Ivv~S~~y~~S~ 79 (178)
.+..|.+.|.+. | +.|++ -+.-|.+..++..+.+.+ + ++.++.+.|.|..++
T Consensus 62 qa~~L~~~L~~~~~~~~~~V~~--amry~~P~i~~~l~~l~~~g~~~iv~lpLyPqyS~~T 120 (311)
T PRK12435 62 QAKALEKALNEVQDEVEFKLYL--GLKHIEPFIEDAVEQMHNDGIEEAISIVLAPHYSTFS 120 (311)
T ss_pred HHHHHHHHHhhccCCCCceEEE--EecCCCCCHHHHHHHHHHcCCCeEEEEECCCcccccc
Confidence 455666666543 2 55655 356666666666666653 3 445555788887653
No 85
>PF12146 Hydrolase_4: Putative lysophospholipase; InterPro: IPR022742 This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. Many members are annotated as being lysophospholipases, and others as alpha-beta hydrolase fold-containing proteins.
Probab=22.24 E-value=1.5e+02 Score=19.67 Aligned_cols=36 Identities=22% Similarity=0.166 Sum_probs=27.1
Q ss_pred CcccEEEecccccCcccHHHHHHHHhhcCCcEEEecC
Q 042466 9 KKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD 45 (178)
Q Consensus 9 ~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~ 45 (178)
.+--|+|+|.-.+ ....-.+|.+.|.++|+.|+.-+
T Consensus 15 ~k~~v~i~HG~~e-h~~ry~~~a~~L~~~G~~V~~~D 50 (79)
T PF12146_consen 15 PKAVVVIVHGFGE-HSGRYAHLAEFLAEQGYAVFAYD 50 (79)
T ss_pred CCEEEEEeCCcHH-HHHHHHHHHHHHHhCCCEEEEEC
Confidence 3778899996443 23456789999999999998654
No 86
>cd06386 PBP1_NPR_C_like Ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANPCNPBNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation.
Probab=22.21 E-value=5e+02 Score=22.17 Aligned_cols=39 Identities=15% Similarity=0.089 Sum_probs=23.9
Q ss_pred HHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcc
Q 042466 27 TSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASA 65 (178)
Q Consensus 27 v~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~ 65 (178)
...|.++|+..|+.+-.......++.-..++.+.|+.+.
T Consensus 157 ~~~l~~~~~~~gi~v~~~~~~~~~~~d~~~~l~~ik~~~ 195 (387)
T cd06386 157 LEGVHHVFQEEGYHMSIYPFDETKDLDLDEIIRAIQASE 195 (387)
T ss_pred HHHHHHHHHhcCceEEEEecCCCCcccHHHHHHHHHhcC
Confidence 778888999999887654422233333335556665554
No 87
>TIGR01093 aroD 3-dehydroquinate dehydratase, type I. Type II 3-dehydroquinate dehydratase, designated AroQ, is described by TIGR01088.
Probab=22.18 E-value=3.7e+02 Score=21.41 Aligned_cols=56 Identities=23% Similarity=0.230 Sum_probs=34.6
Q ss_pred ecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhcccee
Q 042466 43 IDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQIL 99 (178)
Q Consensus 43 ~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~v 99 (178)
+|=++..++....++.+.+...+ .-+|.|-+....+|-.+|+..+++.+...+--|
T Consensus 96 vDiEl~~~~~~~~~l~~~~~~~~-~kvI~S~H~f~~tp~~~~l~~~~~~~~~~gaDi 151 (228)
T TIGR01093 96 VDIELFLPDDAVKELINIAKKGG-TKIIMSYHDFQKTPSWEEIVERLEKALSYGADI 151 (228)
T ss_pred EEEEccCCHHHHHHHHHHHHHCC-CEEEEeccCCCCCCCHHHHHHHHHHHHHhCCCE
Confidence 33344444444445555444444 346668887788888899988888776654333
No 88
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=22.12 E-value=1.4e+02 Score=24.94 Aligned_cols=43 Identities=21% Similarity=0.238 Sum_probs=27.6
Q ss_pred cHHHHHHHHhhcCCcEEEecCCCCCccc---chHHHHHHHHhcceeeE
Q 042466 25 NFTSHLYSALSRQNIQTFIDDQLNRGDE---ISESLVNAIEASAISVI 69 (178)
Q Consensus 25 ~fv~~L~~aL~~~gi~vf~d~~~~~G~~---i~~~i~~aI~~S~~~Iv 69 (178)
+=+.+|.+.|...|+.+..-. -.||+ |.+.+..+++++++.|+
T Consensus 21 tNa~~la~~L~~~G~~v~~~~--~VgD~~~~I~~~l~~a~~r~D~vI~ 66 (255)
T COG1058 21 TNAAFLADELTELGVDLARIT--TVGDNPDRIVEALREASERADVVIT 66 (255)
T ss_pred chHHHHHHHHHhcCceEEEEE--ecCCCHHHHHHHHHHHHhCCCEEEE
Confidence 346789999999999987643 33444 44455556666555443
No 89
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=21.95 E-value=2.1e+02 Score=24.88 Aligned_cols=60 Identities=18% Similarity=0.404 Sum_probs=39.2
Q ss_pred cccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHH-hcceeeEEecCCCCC
Q 042466 10 KYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIE-ASAISVIIFSESYPS 77 (178)
Q Consensus 10 ~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~-~S~~~Ivv~S~~y~~ 77 (178)
.+|+-|.|+.+ +|...|.++-- +||.+++|. .|-++.+..+..+. ..|+.++=.=..|..
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 48899999765 47777766554 899999986 45556666666555 456655533344443
No 90
>smart00646 Ami_3 Ami_3.
Probab=21.69 E-value=1.1e+02 Score=21.26 Aligned_cols=47 Identities=11% Similarity=0.239 Sum_probs=27.6
Q ss_pred CCcccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCC---CCcccchHHHHHHHHh
Q 042466 8 NKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQL---NRGDEISESLVNAIEA 63 (178)
Q Consensus 8 ~~~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~---~~G~~i~~~i~~aI~~ 63 (178)
....|+|||....-.... ...|+.+|+...- ..+..+...|...+..
T Consensus 6 ~~~ad~~iSiH~Ns~~~~---------~~~G~~v~~~~~~~~~~~~~~la~~i~~~l~~ 55 (113)
T smart00646 6 AAKADLFVSIHANAGGAS---------AARGFEVYYYSDKGAIRESRALASIIQKSLVK 55 (113)
T ss_pred hcCCCEEEEEeeCCCCCC---------CCCEEEEEEECCCCCchHHHHHHHHHHHHHHH
Confidence 456899999853322111 3469999997622 3455565555555443
No 91
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=21.31 E-value=2.1e+02 Score=26.51 Aligned_cols=47 Identities=19% Similarity=0.346 Sum_probs=32.8
Q ss_pred cccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHH
Q 042466 10 KYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNA 60 (178)
Q Consensus 10 ~ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~a 60 (178)
..+|+|-.-+++. ...+..+...|+++|++|-+|. .+..+...+..|
T Consensus 438 P~qV~Iipi~e~~-~~~A~~Ia~~LR~~GirVelD~---~~~~lgkkir~A 484 (545)
T PRK14799 438 SVQVRVLPITDEV-NEYAEKVLNDMRKRRIRAEIDY---AGETLSKRIKNA 484 (545)
T ss_pred CceEEEEEcCHHH-HHHHHHHHHHHHhCCCEEEEEC---CCCCHHHHHHHH
Confidence 4578776544432 4678899999999999999986 234555555555
No 92
>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=20.89 E-value=3e+02 Score=19.97 Aligned_cols=46 Identities=7% Similarity=0.031 Sum_probs=29.2
Q ss_pred HHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeEE
Q 042466 55 ESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVF 103 (178)
Q Consensus 55 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPVf 103 (178)
.-+.+.+..+++.|+|++.+- .|...+...+.+..+....+.+-|+
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 456677899999999996665 4554555555555444444444443
No 93
>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=20.87 E-value=3.9e+02 Score=22.05 Aligned_cols=53 Identities=15% Similarity=0.223 Sum_probs=28.2
Q ss_pred EEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCc---ccchHHHHHHHHhcce
Q 042466 13 VFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRG---DEISESLVNAIEASAI 66 (178)
Q Consensus 13 VFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G---~~i~~~i~~aI~~S~~ 66 (178)
|.+-|...+-.......+..+|++.|+.+-....+.+| ..+.+ +...|..++-
T Consensus 138 v~ii~~~~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~~~~d~~~-~l~~i~~~~~ 193 (350)
T cd06366 138 VATIYEDDDYGSGGLPDLVDALQEAGIEISYRAAFPPSANDDDITD-ALKKLKEKDS 193 (350)
T ss_pred EEEEEEcCcccchhHHHHHHHHHHcCCEEEEEeccCCCCChhHHHH-HHHHHhcCCC
Confidence 44444333323456777778888888776544444444 24443 3344544333
No 94
>PRK06893 DNA replication initiation factor; Validated
Probab=20.70 E-value=2e+02 Score=22.96 Aligned_cols=13 Identities=0% Similarity=-0.151 Sum_probs=5.1
Q ss_pred HHHHHHhhcCCcE
Q 042466 28 SHLYSALSRQNIQ 40 (178)
Q Consensus 28 ~~L~~aL~~~gi~ 40 (178)
..+..++.++|.+
T Consensus 57 ~ai~~~~~~~~~~ 69 (229)
T PRK06893 57 KAVSNHYLLNQRT 69 (229)
T ss_pred HHHHHHHHHcCCC
Confidence 3333344334433
No 95
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=20.54 E-value=2.8e+02 Score=19.99 Aligned_cols=24 Identities=17% Similarity=0.181 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHhhhhcCcccCCC
Q 042466 134 KKLQTWRKALKEAASLSGFPSQSI 157 (178)
Q Consensus 134 ~~v~~W~~AL~~v~~~~G~~~~~~ 157 (178)
+.+++-.+-+.+-|+.+||+++..
T Consensus 4 e~l~~my~~~eq~AeksG~~lnpD 27 (110)
T COG4802 4 EELNKMYRFTEQYAEKSGYRLNPD 27 (110)
T ss_pred HHHHHHHHHHHHHHHhcCceeCCC
Confidence 344455555677889999999874
No 96
>PRK13762 tRNA-modifying enzyme; Provisional
Probab=20.49 E-value=2.7e+02 Score=23.74 Aligned_cols=60 Identities=18% Similarity=0.304 Sum_probs=40.1
Q ss_pred ccEEEecccccCcccHHHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCC
Q 042466 11 YDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYP 76 (178)
Q Consensus 11 ydVFIS~~~~D~~~~fv~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~ 76 (178)
-+|-||..|+-+-+.++..|...+.++|+.++++-+ |. . ++..+.+ ......+.+|=+-.
T Consensus 131 ~~v~iSl~GEPlL~p~l~eli~~~k~~Gi~~~L~TN---G~-~-~e~l~~L-~~~~d~i~VSLda~ 190 (322)
T PRK13762 131 KHVAISLSGEPTLYPYLPELIEEFHKRGFTTFLVTN---GT-R-PDVLEKL-EEEPTQLYVSLDAP 190 (322)
T ss_pred CEEEEeCCccccchhhHHHHHHHHHHcCCCEEEECC---CC-C-HHHHHHH-HhcCCEEEEEccCC
Confidence 367889888877667888899999999999998762 21 1 2344455 33444555665543
No 97
>PF14479 HeLo: Prion-inhibition and propagation; PDB: 2WVQ_A 2WVN_A 2WVO_A.
Probab=20.47 E-value=2.2e+02 Score=22.13 Aligned_cols=60 Identities=18% Similarity=0.298 Sum_probs=35.6
Q ss_pred cCchHHHHHHHHHhhhhchhHHHHHHHHHHHhhhhcCcc-cCCCch--HHHHHHHHHHHHHhh
Q 042466 115 TGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFP-SQSIRI--NNKSKRILQYISNKI 174 (178)
Q Consensus 115 ~g~f~~~f~~~~~~~~~~~~~v~~W~~AL~~v~~~~G~~-~~~~~~--~~~i~~Iv~~i~~~l 174 (178)
...|+..|..+.-++..-.-++.+|-.++--...-.+-. +.+... ...|.+|+..|...+
T Consensus 26 ~r~~~~d~~~l~~kL~ie~~RL~~Wg~~vGL~~~~~~~~~l~~~~~~~~~~v~~~L~~I~~ll 88 (212)
T PF14479_consen 26 ARNFGKDFEVLQLKLDIEKLRLLRWGEAVGLLDDPDSDSRLDDPDTQNRQTVERILSQIQDLL 88 (212)
T ss_dssp BGGGGGGHHHHHHHHHHHHHHHHHHHHHCTTTT-GGGGS--SS--SHHHHHHHHHHHHHHHHH
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHcCCCCCccccccCCccchhHHHHHHHHHHHHHHHH
Confidence 357888888888777655667999988742111111111 122223 577888888877665
No 98
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=20.17 E-value=3.5e+02 Score=20.67 Aligned_cols=65 Identities=11% Similarity=0.201 Sum_probs=41.9
Q ss_pred HHHHHHHhhcCCcEEEecCCCCCcccchHHHHHHHHhcceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeEEee
Q 042466 27 TSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVFYR 105 (178)
Q Consensus 27 v~~L~~aL~~~gi~vf~d~~~~~G~~i~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPVfy~ 105 (178)
+..|.+..++.|+++++- +|..+.-.+.+..+ -+..|-| -|..+|...++-....+..+.-|+.+
T Consensus 75 Ig~l~~lae~~g~~v~i~----~Ggt~ar~~ik~~~-p~~iigV---------AC~~dL~~g~~~~~~~~ip~~gV~l~ 139 (158)
T PF01976_consen 75 IGDLKKLAEKYGYKVYIA----TGGTLARKIIKEYR-PKAIIGV---------ACERDLISGIQDLKPLGIPVQGVLLD 139 (158)
T ss_pred hhHHHHHHHHcCCEEEEE----cChHHHHHHHHHhC-CCEEEEE---------echHHHHHHHHHHhhcCCCeeEEEeC
Confidence 677888889999999974 34444333333222 2223333 39999999888766566777777764
No 99
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=20.07 E-value=3.2e+02 Score=19.46 Aligned_cols=37 Identities=8% Similarity=0.056 Sum_probs=19.1
Q ss_pred cceeeEEecCCCCCChhhHHHHHHHHHhhhhccceeeeEEee
Q 042466 64 SAISVIIFSESYPSSRWCLDELVKILECKKEYAQILIPVFYR 105 (178)
Q Consensus 64 S~~~Ivv~S~~y~~S~wc~~EL~~i~~~~~~~~~~viPVfy~ 105 (178)
.+..||++|....+..-+ + .++..+..+..|..|.+.
T Consensus 99 ~~~~iv~iTDG~~~~~~~-~----~~~~~~~~~i~i~~v~~~ 135 (172)
T PF13519_consen 99 RRRAIVLITDGEDNSSDI-E----AAKALKQQGITIYTVGIG 135 (172)
T ss_dssp EEEEEEEEES-TTHCHHH-H----HHHHHHCTTEEEEEEEES
T ss_pred CceEEEEecCCCCCcchh-H----HHHHHHHcCCeEEEEEEC
Confidence 456888888876553333 2 222223445556666554
Done!