Query 044205
Match_columns 192
No_of_seqs 252 out of 1430
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 12:27:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044205.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044205hhsearch_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 3.8E-52 8.2E-57 330.6 17.0 173 4-176 10-182 (187)
2 PLN03210 Resistant to P. syrin 100.0 1.5E-42 3.2E-47 340.4 14.0 178 11-191 3-199 (1153)
3 PF01582 TIR: TIR domain; Int 99.9 1.1E-23 2.5E-28 161.4 3.2 116 23-139 1-140 (141)
4 smart00255 TIR Toll - interleu 99.9 4.4E-22 9.5E-27 151.1 9.9 101 20-122 1-107 (140)
5 PF13676 TIR_2: TIR domain; PD 99.8 2E-20 4.4E-25 135.3 1.3 87 23-112 1-87 (102)
6 KOG3678 SARM protein (with ste 99.5 1.2E-13 2.5E-18 123.2 11.1 146 15-175 607-760 (832)
7 PF08937 DUF1863: MTH538 TIR-l 99.0 1.9E-09 4.2E-14 81.6 7.1 91 21-112 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 98.0 1.5E-05 3.2E-10 61.3 5.9 65 22-86 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.1 0.0024 5.2E-08 48.3 7.3 95 22-119 1-112 (125)
10 PF05014 Nuc_deoxyrib_tr: Nucl 94.6 0.35 7.6E-06 35.2 8.4 79 34-113 13-99 (113)
11 PF13271 DUF4062: Domain of un 93.9 0.36 7.9E-06 33.4 6.9 67 22-89 1-67 (83)
12 COG4916 Uncharacterized protei 93.3 0.14 2.9E-06 43.4 4.4 100 16-118 173-281 (329)
13 COG4271 Predicted nucleotide-b 90.6 2.8 6.1E-05 34.3 9.0 98 17-120 80-199 (233)
14 PF14359 DUF4406: Domain of un 88.0 4.2 9.2E-05 28.9 7.5 70 34-106 16-89 (92)
15 cd00860 ThrRS_anticodon ThrRS 83.7 7.7 0.00017 26.2 7.0 61 20-85 1-61 (91)
16 cd00738 HGTP_anticodon HGTP an 77.0 14 0.00031 24.9 6.5 60 21-85 2-64 (94)
17 PF03129 HGTP_anticodon: Antic 76.4 5.4 0.00012 27.5 4.2 47 34-84 15-61 (94)
18 cd02042 ParA ParA and ParB of 73.0 22 0.00047 24.7 6.8 64 23-86 3-73 (104)
19 cd00858 GlyRS_anticodon GlyRS 70.1 28 0.00061 25.4 7.0 63 17-85 23-87 (121)
20 COG3613 Nucleoside 2-deoxyribo 65.5 32 0.0007 27.4 6.8 78 35-112 20-107 (172)
21 PF02310 B12-binding: B12 bind 65.3 43 0.00094 23.8 7.2 70 37-112 17-87 (121)
22 COG0400 Predicted esterase [Ge 64.4 23 0.0005 28.9 6.0 58 15-74 141-200 (207)
23 COG1658 Small primase-like pro 62.9 17 0.00038 27.5 4.6 56 20-77 29-84 (127)
24 TIGR00418 thrS threonyl-tRNA s 56.0 50 0.0011 30.7 7.5 63 18-85 468-530 (563)
25 COG0125 Tmk Thymidylate kinase 55.7 1.1E+02 0.0024 24.9 12.9 145 23-170 4-204 (208)
26 cd00862 ProRS_anticodon_zinc P 52.9 46 0.001 26.8 5.9 50 17-66 7-62 (202)
27 PF14258 DUF4350: Domain of un 52.9 61 0.0013 21.0 6.3 59 37-106 7-66 (70)
28 PF10087 DUF2325: Uncharacteri 51.5 55 0.0012 22.9 5.5 59 36-96 11-70 (97)
29 TIGR00334 5S_RNA_mat_M5 ribonu 51.5 32 0.0007 27.4 4.6 51 33-87 34-84 (174)
30 PLN03194 putative disease resi 51.5 85 0.0018 25.4 7.1 67 46-112 24-90 (187)
31 cd00861 ProRS_anticodon_short 51.5 52 0.0011 22.2 5.3 48 34-85 17-64 (94)
32 cd02426 Pol_gamma_b_Cterm C-te 51.0 12 0.00026 28.1 2.0 49 16-64 23-76 (128)
33 PF03358 FMN_red: NADPH-depend 48.9 54 0.0012 24.4 5.5 56 34-90 17-85 (152)
34 PRK12325 prolyl-tRNA synthetas 48.0 40 0.00087 30.5 5.3 64 19-86 344-409 (439)
35 cd00859 HisRS_anticodon HisRS 47.4 77 0.0017 20.6 5.9 58 22-84 3-60 (91)
36 PF09837 DUF2064: Uncharacteri 46.9 1.2E+02 0.0025 22.5 8.7 79 17-104 7-89 (122)
37 PRK09194 prolyl-tRNA synthetas 46.0 22 0.00047 33.3 3.3 50 15-64 463-514 (565)
38 COG0276 HemH Protoheme ferro-l 45.3 2.1E+02 0.0046 25.1 9.3 64 36-102 74-146 (320)
39 PF01990 ATP-synt_F: ATP synth 44.7 56 0.0012 22.8 4.6 67 40-113 9-75 (95)
40 PRK08661 prolyl-tRNA synthetas 43.7 47 0.001 30.5 5.1 64 18-85 285-354 (477)
41 PF03437 BtpA: BtpA family; I 43.0 1.5E+02 0.0032 25.1 7.6 79 40-121 133-217 (254)
42 cd00138 PLDc Phospholipase D. 41.7 76 0.0016 24.0 5.4 38 36-73 22-64 (176)
43 PF11074 DUF2779: Domain of un 40.2 25 0.00053 26.6 2.3 34 64-99 60-93 (130)
44 CHL00201 syh histidine-tRNA sy 39.4 1.2E+02 0.0026 27.3 7.0 61 19-84 324-384 (430)
45 PRK14938 Ser-tRNA(Thr) hydrola 39.0 1.5E+02 0.0033 26.7 7.4 63 17-84 271-333 (387)
46 smart00391 MBD Methyl-CpG bind 38.8 49 0.0011 22.6 3.4 55 3-61 12-68 (77)
47 PF03720 UDPG_MGDP_dh_C: UDP-g 37.8 24 0.00053 25.2 1.9 54 30-83 12-75 (106)
48 PRK14799 thrS threonyl-tRNA sy 37.7 1.4E+02 0.0031 28.1 7.3 61 19-84 437-497 (545)
49 PRK02228 V-type ATP synthase s 37.2 96 0.0021 22.1 4.9 64 43-113 14-77 (100)
50 cd03364 TOPRIM_DnaG_primases T 37.0 47 0.001 22.1 3.1 32 47-80 44-75 (79)
51 PF01915 Glyco_hydro_3_C: Glyc 36.5 2.2E+02 0.0048 22.8 9.1 86 34-120 46-148 (227)
52 PRK10569 NAD(P)H-dependent FMN 36.4 1.6E+02 0.0034 23.4 6.6 82 35-117 18-113 (191)
53 PLN02530 histidine-tRNA ligase 36.1 1.6E+02 0.0034 27.1 7.3 62 18-84 399-460 (487)
54 COG0683 LivK ABC-type branched 36.0 2.4E+02 0.0053 24.4 8.3 74 22-96 150-223 (366)
55 PRK12305 thrS threonyl-tRNA sy 35.9 1.5E+02 0.0033 27.6 7.3 62 18-84 474-535 (575)
56 PF03709 OKR_DC_1_N: Orn/Lys/A 35.7 1.7E+02 0.0037 21.1 9.1 73 36-117 5-78 (115)
57 cd00532 MGS-like MGS-like doma 35.3 96 0.0021 22.2 4.8 61 23-85 2-77 (112)
58 COG3580 Uncharacterized protei 35.2 2.6E+02 0.0057 24.7 8.0 151 35-188 149-326 (351)
59 PRK00413 thrS threonyl-tRNA sy 34.4 1.6E+02 0.0034 27.9 7.2 62 19-85 538-599 (638)
60 TIGR01101 V_ATP_synt_F vacuola 34.1 1.2E+02 0.0026 22.5 5.1 47 62-114 46-92 (115)
61 PRK03991 threonyl-tRNA synthet 34.1 74 0.0016 30.3 4.9 64 17-85 496-559 (613)
62 PRK12444 threonyl-tRNA synthet 33.9 1.7E+02 0.0036 27.8 7.3 64 18-85 539-602 (639)
63 cd00984 DnaB_C DnaB helicase C 33.8 1.9E+02 0.0041 23.1 6.8 50 71-120 9-59 (242)
64 PF01269 Fibrillarin: Fibrilla 33.6 46 0.00099 27.8 3.0 48 60-113 84-131 (229)
65 PF01113 DapB_N: Dihydrodipico 33.0 1.8E+02 0.004 21.1 6.1 9 21-29 68-76 (124)
66 COG1180 PflA Pyruvate-formate 33.0 1.6E+02 0.0035 24.7 6.4 42 23-64 87-128 (260)
67 TIGR00640 acid_CoA_mut_C methy 30.6 2.3E+02 0.005 21.2 13.5 86 22-112 4-90 (132)
68 TIGR00409 proS_fam_II prolyl-t 30.1 46 0.001 31.4 2.8 50 16-65 469-520 (568)
69 cd02067 B12-binding B12 bindin 29.9 2.1E+02 0.0044 20.4 8.0 74 37-115 16-90 (119)
70 PLN02924 thymidylate kinase 29.5 3.1E+02 0.0067 22.3 14.3 149 20-174 14-208 (220)
71 COG2342 Predicted extracellula 29.1 92 0.002 26.9 4.2 44 66-111 33-79 (300)
72 KOG2903 Predicted glutathione 28.8 2E+02 0.0043 24.8 6.1 93 16-120 33-137 (319)
73 cd08584 PI-PLCc_GDPD_SF_unchar 28.7 1.4E+02 0.003 24.2 5.0 59 22-88 103-161 (192)
74 KOG2792 Putative cytochrome C 28.6 38 0.00082 28.9 1.8 26 91-116 154-187 (280)
75 cd01423 MGS_CPS_I_III Methylgl 28.6 83 0.0018 22.6 3.5 29 23-53 3-31 (116)
76 PRK15057 UDP-glucose 6-dehydro 28.6 1.1E+02 0.0023 27.4 4.8 56 25-80 304-365 (388)
77 TIGR03567 FMN_reduc_SsuE FMN r 27.9 2.3E+02 0.0049 21.8 6.1 55 35-90 17-80 (171)
78 PF06856 DUF1251: Protein of u 27.6 51 0.0011 24.8 2.1 63 15-91 55-119 (120)
79 PF13401 AAA_22: AAA domain; P 27.6 2.2E+02 0.0048 20.0 6.2 84 23-115 41-125 (131)
80 TIGR00408 proS_fam_I prolyl-tR 27.2 2.3E+02 0.005 26.0 6.8 65 17-85 279-348 (472)
81 KOG4132 Uroporphyrinogen III s 26.9 1.1E+02 0.0024 25.8 4.1 50 37-89 145-200 (260)
82 PRK13762 tRNA-modifying enzyme 26.7 2.2E+02 0.0047 24.7 6.3 60 20-86 130-189 (322)
83 PRK07933 thymidylate kinase; V 26.3 1.8E+02 0.0038 23.4 5.4 30 24-53 2-33 (213)
84 COG2130 Putative NADP-dependen 26.1 1.7E+02 0.0036 25.9 5.3 60 19-87 195-255 (340)
85 COG1058 CinA Predicted nucleot 26.1 1.1E+02 0.0023 26.0 4.1 42 37-83 23-67 (255)
86 cd07373 2A5CPDO_A The alpha su 25.3 3.4E+02 0.0073 22.8 7.1 84 34-118 90-181 (271)
87 cd01424 MGS_CPS_II Methylglyox 25.0 2.5E+02 0.0054 19.7 6.6 29 23-53 3-31 (110)
88 PF00762 Ferrochelatase: Ferro 24.1 3.3E+02 0.0072 23.5 6.9 66 35-103 73-145 (316)
89 PF09152 DUF1937: Domain of un 24.1 1.3E+02 0.0029 22.3 3.8 68 38-105 30-110 (116)
90 cd06340 PBP1_ABC_ligand_bindin 24.0 4.4E+02 0.0095 22.2 7.7 66 22-89 146-212 (347)
91 PF12146 Hydrolase_4: Putative 23.5 1.8E+02 0.0039 19.5 4.2 36 19-55 15-50 (79)
92 PF04244 DPRP: Deoxyribodipyri 23.5 1.8E+02 0.0039 24.0 4.9 68 20-90 62-132 (224)
93 cd01890 LepA LepA subfamily. 23.4 3.1E+02 0.0068 20.3 6.8 52 63-114 79-130 (179)
94 cd01857 HSR1_MMR1 HSR1/MMR1. 23.0 2.6E+02 0.0057 20.4 5.4 48 66-114 3-53 (141)
95 cd06342 PBP1_ABC_LIVBP_like Ty 22.9 4.3E+02 0.0094 21.7 8.2 59 22-82 137-196 (334)
96 COG0289 DapB Dihydrodipicolina 22.7 3.4E+02 0.0074 23.2 6.5 73 17-98 66-138 (266)
97 COG0431 Predicted flavoprotein 22.6 3.8E+02 0.0081 21.0 6.5 55 35-90 18-82 (184)
98 PHA02456 zinc metallopeptidase 22.1 99 0.0021 23.1 2.7 46 66-112 54-105 (141)
99 cd06335 PBP1_ABC_ligand_bindin 22.0 4E+02 0.0087 22.5 7.0 55 21-77 139-194 (347)
100 cd04167 Snu114p Snu114p subfam 21.6 4E+02 0.0088 20.9 8.9 88 60-147 79-167 (213)
101 TIGR03026 NDP-sugDHase nucleot 21.5 1.9E+02 0.0041 25.7 5.0 58 25-82 321-384 (411)
102 COG4916 Uncharacterized protei 21.5 1.3E+02 0.0028 25.8 3.7 94 18-113 4-105 (329)
103 smart00646 Ami_3 Ami_3. 21.4 1.1E+02 0.0024 21.6 3.0 48 18-74 6-55 (113)
104 KOG1610 Corticosteroid 11-beta 21.2 1.1E+02 0.0024 26.8 3.3 33 19-55 28-60 (322)
105 COG0124 HisS Histidyl-tRNA syn 21.2 4.8E+02 0.01 23.8 7.5 64 15-83 330-393 (429)
106 cd00881 GTP_translation_factor 21.2 3.5E+02 0.0076 20.0 6.8 53 60-112 70-123 (189)
107 COG0773 MurC UDP-N-acetylmuram 21.1 1.5E+02 0.0032 27.4 4.3 56 28-103 35-90 (459)
108 cd01864 Rab19 Rab19 subfamily. 21.1 3.4E+02 0.0074 19.9 5.9 30 60-89 60-90 (165)
109 PF13662 Toprim_4: Toprim doma 21.1 71 0.0015 21.4 1.8 34 42-77 40-75 (81)
110 COG0529 CysC Adenylylsulfate k 21.1 68 0.0015 26.1 1.8 34 27-61 31-65 (197)
111 PF13289 SIR2_2: SIR2-like dom 20.8 3.1E+02 0.0067 19.6 5.4 9 23-31 90-98 (143)
112 cd03028 GRX_PICOT_like Glutare 20.8 53 0.0011 22.6 1.1 31 71-103 4-36 (90)
113 PF00071 Ras: Ras family; Int 20.7 3.4E+02 0.0073 19.7 7.3 58 63-120 60-118 (162)
114 TIGR00665 DnaB replicative DNA 20.5 6.1E+02 0.013 22.5 9.9 87 58-144 178-278 (434)
115 TIGR02690 resist_ArsH arsenica 20.4 4.7E+02 0.01 21.5 6.8 55 35-90 44-105 (219)
116 PF09419 PGP_phosphatase: Mito 20.4 2.4E+02 0.0051 22.3 4.8 69 43-112 35-112 (168)
117 PF09673 TrbC_Ftype: Type-F co 20.3 3.5E+02 0.0075 19.6 5.6 38 23-66 2-39 (113)
118 PRK01021 lpxB lipid-A-disaccha 20.2 4.9E+02 0.011 25.0 7.6 94 16-117 222-347 (608)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=3.8e-52 Score=330.56 Aligned_cols=173 Identities=74% Similarity=1.280 Sum_probs=164.3
Q ss_pred cchhhhccccCCCCCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEec
Q 044205 4 QRQVFRQNRLRNQAIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFS 83 (192)
Q Consensus 4 ~~~~~~~~~~~~~~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S 83 (192)
.-|+|-+..++.+++++|||||||+|.|+|.+|+++|+.+|+++||+||+|+.++.+|+.+.+.|.+||++|+++|+|||
T Consensus 10 ~~~~~~~~~~~~~~~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS 89 (187)
T PLN03194 10 NNRLFLHYPSSSSSAKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFS 89 (187)
T ss_pred hhhhhcccccCCCCCCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEEC
Confidence 35778888888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCchhHHHHHHHHHhhcCceeeEEeecCCCcccccccCCCchhHhhhHHHHHHHHHHhcCccccCCCCCHHHHHHHH
Q 044205 84 PTYCQSYFCLHELALMMETKKKVIPIFCDIKPSQLLVIDDGKCSANELRRFSWALEEAKFTVGLTFDSLKGNWSDIVTSA 163 (192)
Q Consensus 84 ~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v~p~~vr~~~~g~~~~~~~~~W~~aL~~~~~~~G~~~~~~~~~~~~~v~~I 163 (192)
|+|++|.||++||++|+++++.||||||+|+|++||+|++|.+..+++++|+.||+++++++|++++..+++|+++|++|
T Consensus 90 ~~Ya~S~WCLdEL~~I~e~~~~ViPIFY~VdPsdVr~q~~~~~~~e~v~~Wr~AL~~va~l~G~~~~~~~~~e~e~i~~i 169 (187)
T PLN03194 90 PRYCESYFCLHELALIMESKKRVIPIFCDVKPSQLRVVDNGTCPDEEIRRFNWALEEAKYTVGLTFDSLKGNWSEVVTMA 169 (187)
T ss_pred CCcccchhHHHHHHHHHHcCCEEEEEEecCCHHHhhccccCCCCHHHHHHHHHHHHHHhccccccCCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999999998668888999999999999999999999876578999999999
Q ss_pred HHHHHHHhhhcCC
Q 044205 164 SDIIIRSLMEIDY 176 (192)
Q Consensus 164 v~~v~~~l~~~~~ 176 (192)
|++|.++|..+..
T Consensus 170 v~~v~k~l~~~~~ 182 (187)
T PLN03194 170 SDAVIKNLIELEE 182 (187)
T ss_pred HHHHHHHHHHHhh
Confidence 9999999977654
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=1.5e-42 Score=340.38 Aligned_cols=178 Identities=22% Similarity=0.309 Sum_probs=162.8
Q ss_pred cccCCCCCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCch
Q 044205 11 NRLRNQAIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSY 90 (192)
Q Consensus 11 ~~~~~~~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~ 90 (192)
++|+.+..++|||||||||+|+|++|++||+.+|.++||++|.|+ ++.+|+.+.+++.+||++|+++|||||++|++|.
T Consensus 3 ~~~~~~~~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~-~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~ 81 (1153)
T PLN03210 3 SSSSSSRNWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDN-EIERSQSLDPELKQAIRDSRIAVVVFSKNYASSS 81 (1153)
T ss_pred CCCCCCCCCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccC-CccCCCcccHHHHHHHHhCeEEEEEecCCcccch
Confidence 345566789999999999999999999999999999999999987 5999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhhc----CceeeEEeecCCCcccccccCCC-----------chhHhhhHHHHHHHHHHhcCccccCCCCC
Q 044205 91 FCLHELALMMETK----KKVIPIFCDIKPSQLLVIDDGKC-----------SANELRRFSWALEEAKFTVGLTFDSLKGN 155 (192)
Q Consensus 91 wc~~EL~~~~~~~----~~ViPVf~~v~p~~vr~~~~g~~-----------~~~~~~~W~~aL~~~~~~~G~~~~~~~~~ 155 (192)
||++||++|++|+ +.|+||||+|+|++||+|+ |.| .++++++|+.||++|++++||++.. +++
T Consensus 82 wcl~el~~i~~~~~~~~~~v~pvfy~v~p~~v~~~~-g~f~~~f~~~~~~~~~~~~~~w~~al~~~~~~~g~~~~~-~~~ 159 (1153)
T PLN03210 82 WCLNELLEIVRCKEELGQLVIPVFYGLDPSHVRKQT-GDFGEAFEKTCQNKTEDEKIQWKQALTDVANILGYHSQN-WPN 159 (1153)
T ss_pred HHHHHHHHHHHhhhhcCceEEEEEecccHHHHhhcc-chHHHHHHHHhcccchhHHHHHHHHHHHHhCcCceecCC-CCC
Confidence 9999999999985 4899999999999999998 876 3578999999999999999999864 688
Q ss_pred HHHHHHHHHHHHHHHhhhcC----CcchhhhhhhcccCcC
Q 044205 156 WSDIVTSASDIIIRSLMEID----YKEQRHWRRQNSTPML 191 (192)
Q Consensus 156 ~~~~v~~Iv~~v~~~l~~~~----~~~vg~~~rl~~~~~~ 191 (192)
|+++|++||++|.++|...+ .+.||++.++++|+.|
T Consensus 160 E~~~i~~Iv~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~l 199 (1153)
T PLN03210 160 EAKMIEEIANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSL 199 (1153)
T ss_pred HHHHHHHHHHHHHHhhccccCcccccccchHHHHHHHHHH
Confidence 99999999999999996554 3789999999988654
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=99.88 E-value=1.1e-23 Score=161.42 Aligned_cols=116 Identities=27% Similarity=0.444 Sum_probs=98.7
Q ss_pred EEEecccccCchhHHHHHHHHHhcC--CCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHH
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRL--NLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMM 100 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~--gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~ 100 (192)
|||||++.+.+..|+++|..+|++. |+++|++++|+.+|..+.+++.++|++|+++|+|+|++|+.|.||+.||..|+
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 8999999433678999999999999 99999999999999999999999999999999999999999999999999998
Q ss_pred hh----c--CceeeEEeecCCCccc-ccccCCC-----------c----hhHhhhHHHHHH
Q 044205 101 ET----K--KKVIPIFCDIKPSQLL-VIDDGKC-----------S----ANELRRFSWALE 139 (192)
Q Consensus 101 ~~----~--~~ViPVf~~v~p~~vr-~~~~g~~-----------~----~~~~~~W~~aL~ 139 (192)
++ + +.|+|||+++.+++++ .+. +++ . .+....|+.++.
T Consensus 81 ~~~~~~~~~~~Il~v~~~v~~~~~~~~~~-~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 81 ERLLEEGRDKLILPVFYDVSPSDVRPDQS-LRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHCSTCTTEEEEESSSS-CHHCHTHHH-HHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhccccccccceeeEeccCChhhcChhhh-HHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 74 3 5899999999999999 454 321 1 346778888765
No 4
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.87 E-value=4.4e-22 Score=151.06 Aligned_cols=101 Identities=32% Similarity=0.573 Sum_probs=86.6
Q ss_pred CccEEEeccc-ccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHH
Q 044205 20 PCDVFINHRG-IDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELAL 98 (192)
Q Consensus 20 ~ydVFISy~~-~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~ 98 (192)
.|||||||++ ++....|+.+|...|...|+.+|.|+... |.....+|.++|++|+++|+|+||+|..|+||..|+..
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~--~~~~~~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~ 78 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEP--GGGDLEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVA 78 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCccc--ccchHHHHHHHHHHCcEEEEEECcccccChhHHHHHHH
Confidence 5999999998 45567899999999999999999997643 33333399999999999999999999999999999999
Q ss_pred HHhh-----cCceeeEEeecCCCcccccc
Q 044205 99 MMET-----KKKVIPIFCDIKPSQLLVID 122 (192)
Q Consensus 99 ~~~~-----~~~ViPVf~~v~p~~vr~~~ 122 (192)
+.++ +++||||+++..|..+..+.
T Consensus 79 a~~~~~~~~~~~iIPI~~~~~~~~~~~~~ 107 (140)
T smart00255 79 ALENALEEGGLRVIPIFYEVIPSDVRKQP 107 (140)
T ss_pred HHHHHHHcCCCeEEEEEEecChHHHHhcc
Confidence 9873 46999999998887777665
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.79 E-value=2e-20 Score=135.34 Aligned_cols=87 Identities=32% Similarity=0.553 Sum_probs=78.1
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhh
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMET 102 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~ 102 (192)
|||||+++|. .+|..|...|++.|+++|+|. ++.+|+.+.+.|.++|++|+++|+++||+|..|+||..|+..+.+.
T Consensus 1 VFIS~~~~D~--~~a~~l~~~L~~~g~~v~~d~-~~~~g~~~~~~i~~~i~~s~~~i~~~S~~~~~s~~~~~E~~~a~~~ 77 (102)
T PF13676_consen 1 VFISYSSEDR--EFAERLAERLESAGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWKR 77 (102)
T ss_dssp EEEEEEGGGC--CCHHHHHHHHHHTT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHCT
T ss_pred eEEEecCCcH--HHHHHHHHHHhhcCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHHC
Confidence 8999999994 589999999999999999997 8999999999999999999999999999999999999999999988
Q ss_pred cCceeeEEee
Q 044205 103 KKKVIPIFCD 112 (192)
Q Consensus 103 ~~~ViPVf~~ 112 (192)
+++||||.++
T Consensus 78 ~~~iipv~~~ 87 (102)
T PF13676_consen 78 GKPIIPVRLD 87 (102)
T ss_dssp SESEEEEECS
T ss_pred CCEEEEEEEC
Confidence 8899999975
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.51 E-value=1.2e-13 Score=123.22 Aligned_cols=146 Identities=19% Similarity=0.240 Sum_probs=115.7
Q ss_pred CCCCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCC------
Q 044205 15 NQAIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQ------ 88 (192)
Q Consensus 15 ~~~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~------ 88 (192)
.+..++.||||||+... ...+++.|+-.|+-+|++||+|.+.+..|. +.+.+.+.|+.++.+|+|+||+...
T Consensus 607 a~~skq~DVFISYRRst-GnQLASLiKV~LQL~GyrVFIDVdKL~AGK-FdssLlkni~aAkhFiLVLtP~sLDr~lnD~ 684 (832)
T KOG3678|consen 607 AMLSKQIDVFISYRRST-GNQLASLIKVLLQLRGYRVFIDVDKLYAGK-FDSSLLKNIQAAKHFILVLTPNSLDRLLNDD 684 (832)
T ss_pred ccccCCcceEEEeeccc-cHHHHHHHHHHHHhcCceEEEehhhhhccc-ccHHHHHHHHhhheeEEEeCcchHHHHhccc
Confidence 34678999999999765 467899999999999999999999998887 5678899999999999999999763
Q ss_pred --chhHHHHHHHHHhhcCceeeEEeecCCCcccccccCCCchhHhhhHHHHHHHHHHhcCccccCCCCCHHHHHHHHHHH
Q 044205 89 --SYFCLHELALMMETKKKVIPIFCDIKPSQLLVIDDGKCSANELRRFSWALEEAKFTVGLTFDSLKGNWSDIVTSASDI 166 (192)
Q Consensus 89 --S~wc~~EL~~~~~~~~~ViPVf~~v~p~~vr~~~~g~~~~~~~~~W~~aL~~~~~~~G~~~~~~~~~~~~~v~~Iv~~ 166 (192)
-.|+.+||..+++|++.|||||-..- +. +++-..-.+-+.-+..+.|..+.. .+...++++||+-
T Consensus 685 nCeDWVHKEl~~Afe~~KNIiPI~D~aF--E~---------Pt~ed~iPnDirmi~kyNGvKWvH--dYQdA~maKvvRF 751 (832)
T KOG3678|consen 685 NCEDWVHKELKCAFEHQKNIIPIFDTAF--EF---------PTKEDQIPNDIRMITKYNGVKWVH--DYQDACMAKVVRF 751 (832)
T ss_pred cHHHHHHHHHHHHHHhcCCeeeeecccc--cC---------CCchhcCcHHHHHHHhccCeeeeh--hhHHHHHHHHHHH
Confidence 46999999999999999999995410 00 000111234455677788877653 5677899999999
Q ss_pred HHHHhhhcC
Q 044205 167 IIRSLMEID 175 (192)
Q Consensus 167 v~~~l~~~~ 175 (192)
+...|++..
T Consensus 752 itGe~nRtt 760 (832)
T KOG3678|consen 752 ITGELNRTT 760 (832)
T ss_pred HhccccCCC
Confidence 999987654
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=98.96 E-value=1.9e-09 Score=81.62 Aligned_cols=91 Identities=18% Similarity=0.249 Sum_probs=51.6
Q ss_pred ccEEEecccccCchhHHHHHHHHHhcC-------CCee----------EEeCCCCCCCCchHHHHHHHHHhcceeEEEec
Q 044205 21 CDVFINHRGIDTKRKVATLLYDHLSRL-------NLRP----------FLDNKNMKPGDKLFDNINRAIRNCKVGVAVFS 83 (192)
Q Consensus 21 ydVFISy~~~D~~~~fv~~L~~~L~~~-------gi~v----------f~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S 83 (192)
|.|||||++.|.. ..+..|...+... ++.. +-+..+....+.+...|.++|.+|+++||++|
T Consensus 1 ~~vFIS~~~~d~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~~I~~~i~~s~~~IVLig 79 (130)
T PF08937_consen 1 YKVFISYSHDDDD-WYYDQLKEWLENSYEIPRDKNFDFRFYDVSKWEPIRSRDDDSSSEYIKRKIRERIKNSSVTIVLIG 79 (130)
T ss_dssp ----------THH--HHHHHHHHHHH-------TTSS--BT---TTT---TTS---TTTTHHHHHHHHHHTEEEEEEE--
T ss_pred CCccccccccCcH-HHHHHHHHHhccccccccccccccCcccccccCcccCccccchHHHHHHHHHHHHhcCCEEEEEeC
Confidence 5799999998853 3577777777662 2221 11222233445789999999999999999999
Q ss_pred CCCCCchhHHHHHHHHHhhcCceeeEEee
Q 044205 84 PTYCQSYFCLHELALMMETKKKVIPIFCD 112 (192)
Q Consensus 84 ~~y~~S~wc~~EL~~~~~~~~~ViPVf~~ 112 (192)
++...|.|+..|+..+++.+++||.|.+.
T Consensus 80 ~~T~~s~wV~~EI~~A~~~~~~Ii~V~~~ 108 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALKKGKPIIGVYLP 108 (130)
T ss_dssp TT----HHHHHHHHHHTTT---EEEEETT
T ss_pred CCcccCcHHHHHHHHHHHCCCCEEEEECC
Confidence 99999999999999999999999999874
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=98.00 E-value=1.5e-05 Score=61.29 Aligned_cols=65 Identities=22% Similarity=0.254 Sum_probs=54.3
Q ss_pred cEEEecccccC-chhHHHHHHHHHhcC-CCeeEEeCCCCCC--CCchHHHHHHHHHhcceeEEEecCCC
Q 044205 22 DVFINHRGIDT-KRKVATLLYDHLSRL-NLRPFLDNKNMKP--GDKLFDNINRAIRNCKVGVAVFSPTY 86 (192)
Q Consensus 22 dVFISy~~~D~-~~~fv~~L~~~L~~~-gi~vf~D~~~l~~--G~~~~~~i~~aI~~S~~~Ivv~S~~y 86 (192)
.|||||++... ....|..|...|++. |+.|.+|..+... +..+..-+.+.+++++.+|+|+||.+
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 49999997443 235689999999999 9999999988744 66788889999999999999999544
No 9
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=97.13 E-value=0.0024 Score=48.29 Aligned_cols=95 Identities=22% Similarity=0.388 Sum_probs=70.5
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCC-------------C
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYC-------------Q 88 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~-------------~ 88 (192)
.|||.|+ .|. ..+..+...|+..|+.+.+=.+....|..+.+.+.+...+++.+|+++||+=. .
T Consensus 1 kVFIvhg-~~~--~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~a 77 (125)
T PF10137_consen 1 KVFIVHG-RDL--AAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRA 77 (125)
T ss_pred CEEEEeC-CCH--HHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCcccccccc
Confidence 3899998 553 56888999999889887765556689999999999999999999999998411 2
Q ss_pred chhHHHHHHHHHhh-c-CceeeEEee-c-CCCccc
Q 044205 89 SYFCLHELALMMET-K-KKVIPIFCD-I-KPSQLL 119 (192)
Q Consensus 89 S~wc~~EL~~~~~~-~-~~ViPVf~~-v-~p~~vr 119 (192)
...++.|+..++.. + ++++-+.-+ + .|||+.
T Consensus 78 R~NVifE~G~f~g~LGr~rv~~l~~~~v~~PSDl~ 112 (125)
T PF10137_consen 78 RQNVIFELGLFIGKLGRERVFILVKGGVELPSDLS 112 (125)
T ss_pred ccceeehhhHHHhhcCcceEEEEEcCCccCCcccC
Confidence 23567799888763 4 466655532 1 356653
No 10
>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=94.60 E-value=0.35 Score=35.21 Aligned_cols=79 Identities=18% Similarity=0.196 Sum_probs=57.0
Q ss_pred hhHHHHHHHHHhcCCCeeEEeCCC-CC---CCC----chHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCc
Q 044205 34 RKVATLLYDHLSRLNLRPFLDNKN-MK---PGD----KLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKK 105 (192)
Q Consensus 34 ~~fv~~L~~~L~~~gi~vf~D~~~-l~---~G~----~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ 105 (192)
..+...+.+.|+..|+.++...+. .. .+. .+.+.-.++|++|+++|+++.+.- .+.=+.-|+..|...+++
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~algkp 91 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYALGKP 91 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHCCCE
Confidence 467899999999999998875521 11 122 344445679999999999998755 566788899999999986
Q ss_pred eeeEEeec
Q 044205 106 VIPIFCDI 113 (192)
Q Consensus 106 ViPVf~~v 113 (192)
|+-+.-+.
T Consensus 92 v~~~~~d~ 99 (113)
T PF05014_consen 92 VILLTEDD 99 (113)
T ss_dssp EEEEECCC
T ss_pred EEEEEcCC
Confidence 66554443
No 11
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=93.92 E-value=0.36 Score=33.40 Aligned_cols=67 Identities=16% Similarity=0.218 Sum_probs=48.0
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCc
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQS 89 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S 89 (192)
.||||-.-.|.. .--..|.+.+.+.|..+..-+.--..+....+...+.|++|+++|.++-..|-..
T Consensus 1 rVFiSSt~~Dl~-~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~~ 67 (83)
T PF13271_consen 1 RVFISSTFRDLK-EERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGSV 67 (83)
T ss_pred CEEEecChhhHH-HHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCCC
Confidence 389998777764 3356678888877775543222112355667788899999999999999998754
No 12
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=93.26 E-value=0.14 Score=43.41 Aligned_cols=100 Identities=19% Similarity=0.182 Sum_probs=69.9
Q ss_pred CCCCCccEEEecccccCchhHHHHHHHHHh--cCCCeeEEeCC---CCCCCCchHHHHHHHH-HhcceeEEEecCCCCCc
Q 044205 16 QAIKPCDVFINHRGIDTKRKVATLLYDHLS--RLNLRPFLDNK---NMKPGDKLFDNINRAI-RNCKVGVAVFSPTYCQS 89 (192)
Q Consensus 16 ~~~~~ydVFISy~~~D~~~~fv~~L~~~L~--~~gi~vf~D~~---~l~~G~~~~~~i~~aI-~~S~~~Ivv~S~~y~~S 89 (192)
...+.||+=+||.|+. ++.|.....+++ ...+..|+|-. -+.+|+ +.+-+...- ..|++.+|+...+|...
T Consensus 173 ~~~~~~DiG~SFaGEA--R~LVEqV~~E~~~~~~p~~~FYD~~~~~~L~~~s-L~~~L~~~Y~~rC~~~~VF~~~~Y~~K 249 (329)
T COG4916 173 SSEKPVDSGISFAGEA--RNLVEQVQTEHSGLDIPTRRFYDLLVAHPLYPGS-LVSTLDPGYDIRCVVTTVFNTGSYICK 249 (329)
T ss_pred ccccccceeeEeehhh--hhHHHHHHHhhhcccCCceeeeechhhccccCcc-HHHhcccccCceEEEEEEEeCCceEEe
Confidence 3678999999999987 368999999998 44567788753 233443 333444443 34777888889999999
Q ss_pred hhHHHHHHHHHhhc--CceeeEEe-ecCCCcc
Q 044205 90 YFCLHELALMMETK--KKVIPIFC-DIKPSQL 118 (192)
Q Consensus 90 ~wc~~EL~~~~~~~--~~ViPVf~-~v~p~~v 118 (192)
.||.-|...+-+.. +...||.| .++-+.+
T Consensus 250 ~~c~~E~~~~r~~~~~d~~~rI~~~~~d~~a~ 281 (329)
T COG4916 250 STCHIEGLEGRLNPILDTGFRIKYLYADNIAI 281 (329)
T ss_pred eeeccchhhccccccccccceEEEEecCCccc
Confidence 99999977664432 36777776 3444433
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=90.64 E-value=2.8 Score=34.27 Aligned_cols=98 Identities=20% Similarity=0.323 Sum_probs=66.1
Q ss_pred CCCCccEEEecccccCchhHHHHHHHHHhcC-CC-eeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCC-----C-
Q 044205 17 AIKPCDVFINHRGIDTKRKVATLLYDHLSRL-NL-RPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYC-----Q- 88 (192)
Q Consensus 17 ~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~-gi-~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~-----~- 88 (192)
++.+ .|||-|+++. .+.....+|.+. -. .+|.|. -...|..+.+.+.+.|.+++.+|++.+|+=. .
T Consensus 80 p~~k-kvFvv~ghd~----iArael~allrd~~l~~vi~d~-~~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~ 153 (233)
T COG4271 80 PNLK-KVFVVSGHDA----IARAELEALLRDWKLEPVILDG-LFSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHS 153 (233)
T ss_pred CCce-eEEEEeccHH----HHHHHHHHHhhccccceEEecC-cccccHHHHHHHHHHhhhceEEEEEecCcccccccccc
Confidence 3444 8999997533 566766777643 33 456665 4678999999999999999999999999743 1
Q ss_pred --chh------HHHHHHHHHhh-c-CceeeEEee---c-CCCcccc
Q 044205 89 --SYF------CLHELALMMET-K-KKVIPIFCD---I-KPSQLLV 120 (192)
Q Consensus 89 --S~w------c~~EL~~~~~~-~-~~ViPVf~~---v-~p~~vr~ 120 (192)
..| +..||...+.. + ++|+-+.-+ + -|||+..
T Consensus 154 ~~k~~praRqNVifELGm~mgrLgRkrv~Il~k~~envelPSDi~G 199 (233)
T COG4271 154 REKAFPRARQNVIFELGMFMGRLGRKRVMILMKRDENVELPSDIAG 199 (233)
T ss_pred hhhccccccccchhhHhhHHhhcccceEEEEecccccccCccccCc
Confidence 123 56688887753 3 455544332 1 3677643
No 14
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=88.02 E-value=4.2 Score=28.87 Aligned_cols=70 Identities=11% Similarity=0.050 Sum_probs=47.3
Q ss_pred hhHHHHHHHHHhcCCCeeEEeCCC-CCCCCchHHHHH---HHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCce
Q 044205 34 RKVATLLYDHLSRLNLRPFLDNKN-MKPGDKLFDNIN---RAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKV 106 (192)
Q Consensus 34 ~~fv~~L~~~L~~~gi~vf~D~~~-l~~G~~~~~~i~---~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~V 106 (192)
..| ....+.|...|+.|.--... ...|.++.+-+. ..+..|+. +++=|++-+|.=|.-|...|.+.+..|
T Consensus 16 ~~f-~~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~--i~~l~gWe~S~GA~~E~~~A~~lGl~V 89 (92)
T PF14359_consen 16 PAF-NAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDA--IYMLPGWENSRGARLEHELAKKLGLPV 89 (92)
T ss_pred HHH-HHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCE--EEEcCCcccCcchHHHHHHHHHCCCeE
Confidence 344 35778889999766532221 356666555444 34566664 344599999999999999999888643
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=83.74 E-value=7.7 Score=26.18 Aligned_cols=61 Identities=21% Similarity=0.141 Sum_probs=39.6
Q ss_pred CccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 20 PCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 20 ~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
.++|+|...+.+. ...+..+...|.+.|++|-+|... ..+...+..|-..---.++++.++
T Consensus 1 p~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~~----~~~~~~~~~a~~~g~~~~iiig~~ 61 (91)
T cd00860 1 PVQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLRN----EKLGKKIREAQLQKIPYILVVGDK 61 (91)
T ss_pred CeEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHHcCCCEEEEECcc
Confidence 3677777655443 356888999999999999998643 355556666543333344555544
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=77.01 E-value=14 Score=24.93 Aligned_cols=60 Identities=20% Similarity=0.110 Sum_probs=39.8
Q ss_pred ccEEEecccc---cCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 21 CDVFINHRGI---DTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 21 ydVFISy~~~---D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
++|+|-.-+. . ....+..+...|.+.|+.+-+|.. +..+...+..|-..---+++++.++
T Consensus 2 ~~v~ii~~~~~~~~-~~~~a~~~~~~Lr~~g~~v~~~~~----~~~~~k~~~~a~~~g~~~~iiig~~ 64 (94)
T cd00738 2 IDVAIVPLTDPRVE-AREYAQKLLNALLANGIRVLYDDR----ERKIGKKFREADLRGVPFAVVVGED 64 (94)
T ss_pred eEEEEEECCCCcHH-HHHHHHHHHHHHHHCCCEEEecCC----CcCHhHHHHHHHhCCCCEEEEECCC
Confidence 5777765443 2 245688899999999999999764 3456666666544443566777654
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=76.41 E-value=5.4 Score=27.49 Aligned_cols=47 Identities=19% Similarity=0.127 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecC
Q 044205 34 RKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSP 84 (192)
Q Consensus 34 ~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~ 84 (192)
..++..|...|.+.||++.+|.. +..+...+..|-..=--+++++.+
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~----~~~~~k~~~~a~~~g~p~~iiiG~ 61 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDS----DKSLGKQIKYADKLGIPFIIIIGE 61 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESS----SSTHHHHHHHHHHTTESEEEEEEH
T ss_pred HHHHHHHHHHHHHCCCEEEEECC----CCchhHHHHHHhhcCCeEEEEECc
Confidence 45789999999999999999974 444556666665443334455443
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=73.01 E-value=22 Score=24.68 Aligned_cols=64 Identities=19% Similarity=0.105 Sum_probs=40.8
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCC-------CCCchHHHHHHHHHhcceeEEEecCCC
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMK-------PGDKLFDNINRAIRNCKVGVAVFSPTY 86 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~-------~G~~~~~~i~~aI~~S~~~Ivv~S~~y 86 (192)
+|.|..|.-.+-.++.+|...|.++|.++.+-+-+.. .+..+......++..|+..|+++.++.
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 4677776555667789999999989988876433322 111123344466777777777776654
No 19
>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=70.13 E-value=28 Score=25.36 Aligned_cols=63 Identities=13% Similarity=0.027 Sum_probs=42.5
Q ss_pred CCCCccEEEeccc--ccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 17 AIKPCDVFINHRG--IDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 17 ~~~~ydVFISy~~--~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
.-..+||||-.-+ .+ ....+..+...|...|++|-+|.. ..+...+..|-+.---.++++.++
T Consensus 23 ~lap~~v~Ii~~~~~~~-~~~~a~~la~~LR~~gi~v~~d~~-----~sl~kqlk~A~k~g~~~~iiiG~~ 87 (121)
T cd00858 23 ALAPIKVAVLPLVKRDE-LVEIAKEISEELRELGFSVKYDDS-----GSIGRRYARQDEIGTPFCVTVDFD 87 (121)
T ss_pred CcCCcEEEEEecCCcHH-HHHHHHHHHHHHHHCCCEEEEeCC-----CCHHHHHHHhHhcCCCEEEEECcC
Confidence 3457888888765 33 234678899999999999999863 355566666644444456666655
No 20
>COG3613 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]
Probab=65.47 E-value=32 Score=27.39 Aligned_cols=78 Identities=15% Similarity=0.124 Sum_probs=55.4
Q ss_pred hHHHHHHHHHhcCCCeeEEe------CCCCCC---CCchHHHHHHHHHhcceeEEEecCCCC-CchhHHHHHHHHHhhcC
Q 044205 35 KVATLLYDHLSRLNLRPFLD------NKNMKP---GDKLFDNINRAIRNCKVGVAVFSPTYC-QSYFCLHELALMMETKK 104 (192)
Q Consensus 35 ~fv~~L~~~L~~~gi~vf~D------~~~l~~---G~~~~~~i~~aI~~S~~~Ivv~S~~y~-~S~wc~~EL~~~~~~~~ 104 (192)
...+.|...|.+.|+.++.- ..+..+ +..+.+.=.+.|.+|+++|+.+.+-=. ..+=...|+..+...+|
T Consensus 20 ~~~d~lkall~~~gf~~~~P~d~~~~~~~~~p~~~a~~i~e~d~~~i~~aD~vla~ld~fr~~~DsGTa~E~GYa~AlgK 99 (172)
T COG3613 20 ELRDELKALLLEAGFEVLSPFDEAEPIAETGPNETAEKIYEADIKLIDQADIVLANLDPFRPDPDSGTAFELGYAIALGK 99 (172)
T ss_pred HHHHHHHHHHHHcCCeeeCcchhccCccccCccHHHHHHHHHHHHHHhhcCEEEEecCCCCCCCCCcchHHHHHHHHcCC
Confidence 35778899999999998874 222333 223445556789999999999986541 12235679999999999
Q ss_pred ceeeEEee
Q 044205 105 KVIPIFCD 112 (192)
Q Consensus 105 ~ViPVf~~ 112 (192)
+|++.+-+
T Consensus 100 Pv~~~~~d 107 (172)
T COG3613 100 PVYAYRKD 107 (172)
T ss_pred ceEEEeec
Confidence 99887753
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=65.33 E-value=43 Score=23.77 Aligned_cols=70 Identities=19% Similarity=0.159 Sum_probs=47.0
Q ss_pred HHHHHHHHhcCCCeeE-EeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEee
Q 044205 37 ATLLYDHLSRLNLRPF-LDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCD 112 (192)
Q Consensus 37 v~~L~~~L~~~gi~vf-~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~ 112 (192)
...|...|++.|+.|- +|.. .. .+++.+.+.+.+.-++.+|-.+..+..-..++....+...+=+||..+
T Consensus 17 l~~la~~l~~~G~~v~~~d~~-~~-----~~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~~iv~G 87 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDAN-VP-----PEELVEALRAERPDVVGISVSMTPNLPEAKRLARAIKERNPNIPIVVG 87 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESS-B------HHHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHHHHTTCTTSEEEEE
T ss_pred HHHHHHHHHHCCCeEEEECCC-CC-----HHHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHHHHhcCCCCEEEEE
Confidence 6678899999999984 5542 22 267888888888888888876554444445555555555555566664
No 22
>COG0400 Predicted esterase [General function prediction only]
Probab=64.35 E-value=23 Score=28.87 Aligned_cols=58 Identities=14% Similarity=0.096 Sum_probs=43.7
Q ss_pred CCCCCCccEEEecccccC--chhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHh
Q 044205 15 NQAIKPCDVFINHRGIDT--KRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRN 74 (192)
Q Consensus 15 ~~~~~~ydVFISy~~~D~--~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~ 74 (192)
.+......|||+|...|. -...+..|.+.|+..|..|..... ..|-.+.++-.+++++
T Consensus 141 ~~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~~--~~GH~i~~e~~~~~~~ 200 (207)
T COG0400 141 LPDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRWH--EGGHEIPPEELEAARS 200 (207)
T ss_pred ccccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEEe--cCCCcCCHHHHHHHHH
Confidence 345678889999998886 356789999999999999988754 3666666655555443
No 23
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=62.93 E-value=17 Score=27.47 Aligned_cols=56 Identities=11% Similarity=0.146 Sum_probs=44.4
Q ss_pred CccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcce
Q 044205 20 PCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKV 77 (192)
Q Consensus 20 ~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~ 77 (192)
-.++|+-..+.-....+...|..++..+|+-++.|.+ .+|+.+...|.+.+.++.-
T Consensus 29 ~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D--~~Ge~Irk~l~~~l~~~~~ 84 (127)
T COG1658 29 DAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD--RKGERIRKKLKEYLPGAKG 84 (127)
T ss_pred CCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC--cchHHHHHHHHHHhccccc
Confidence 4567777655432256799999999999999999986 7899999999998888544
No 24
>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=55.96 E-value=50 Score=30.66 Aligned_cols=63 Identities=16% Similarity=0.179 Sum_probs=44.8
Q ss_pred CCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 18 IKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 18 ~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
....||+|-.-+++. ...+..|...|++.|++|-+|.. +..+...+..|-..---.++|+.++
T Consensus 468 ~~p~~v~vi~~~~~~-~~~a~~ia~~LR~~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~~ 530 (563)
T TIGR00418 468 LAPVQVVVIPVNERH-LDYAKKVAQKLKKAGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGDK 530 (563)
T ss_pred CCCceEEEEEccchH-HHHHHHHHHHHHHcCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEchh
Confidence 457888888765443 46789999999999999999864 4566677777655444455666543
No 25
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=55.72 E-value=1.1e+02 Score=24.88 Aligned_cols=145 Identities=20% Similarity=0.283 Sum_probs=81.3
Q ss_pred EEEecccccC--chhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhc-------------------------
Q 044205 23 VFINHRGIDT--KRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNC------------------------- 75 (192)
Q Consensus 23 VFISy~~~D~--~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S------------------------- 75 (192)
.||.+-|-|. +.+.+..|++.|+.+|+.|.+=.+ +.|.++...|.+.+-+-
T Consensus 4 ~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~trE--P~~~~ige~iR~~ll~~~~~~~~~~e~lLfaadR~~h~~~~i 81 (208)
T COG0125 4 MFIVIEGIDGAGKTTQAELLKERLEERGIKVVLTRE--PGGTPIGEKIRELLLNGEEKLSPKAEALLFAADRAQHLEEVI 81 (208)
T ss_pred eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeC--CCCChHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5888877664 356788999999999998877542 33434444443333220
Q ss_pred ----ceeEEEecCCCCCchhHHHH--------HHHHHhh--c---CceeeEEeecCCCc-ccccc-c----CCCchh---
Q 044205 76 ----KVGVAVFSPTYCQSYFCLHE--------LALMMET--K---KKVIPIFCDIKPSQ-LLVID-D----GKCSAN--- 129 (192)
Q Consensus 76 ----~~~Ivv~S~~y~~S~wc~~E--------L~~~~~~--~---~~ViPVf~~v~p~~-vr~~~-~----g~~~~~--- 129 (192)
.-.-+|++..|..|.-+.+- ....+.. . ++-+-+|++++|.. ++... . .+|..+
T Consensus 82 ~pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~al~R~~~r~~~~~r~E~~~~~ 161 (208)
T COG0125 82 KPALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVALERIRKRGELRDRFEKEDDE 161 (208)
T ss_pred HHhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHHHHHHHhcCCccchhhhHHHH
Confidence 11248889999999887773 2222211 1 45666888999865 22111 1 122211
Q ss_pred HhhhHHHHHHHHHHhcC---ccccCCCCCHHHHHHHHHHHHHHH
Q 044205 130 ELRRFSWALEEAKFTVG---LTFDSLKGNWSDIVTSASDIIIRS 170 (192)
Q Consensus 130 ~~~~W~~aL~~~~~~~G---~~~~~~~~~~~~~v~~Iv~~v~~~ 170 (192)
..++=+....+++.... .+.+. +.+-.+..++|.+.+...
T Consensus 162 f~~kvr~~Y~~la~~~~~r~~vIda-~~~~e~v~~~i~~~l~~~ 204 (208)
T COG0125 162 FLEKVREGYLELAAKFPERIIVIDA-SRPLEEVHEEILKILKER 204 (208)
T ss_pred HHHHHHHHHHHHHhhCCCeEEEEEC-CCCHHHHHHHHHHHHHHh
Confidence 24455666666777665 33444 334444444444444433
No 26
>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=52.91 E-value=46 Score=26.78 Aligned_cols=50 Identities=28% Similarity=0.402 Sum_probs=35.2
Q ss_pred CCCCccEEEecccccC-----chhHHHHHHHHHhcCCCeeEEeCCCC-CCCCchHH
Q 044205 17 AIKPCDVFINHRGIDT-----KRKVATLLYDHLSRLNLRPFLDNKNM-KPGDKLFD 66 (192)
Q Consensus 17 ~~~~ydVFISy~~~D~-----~~~fv~~L~~~L~~~gi~vf~D~~~l-~~G~~~~~ 66 (192)
.-..++|+|---+.+. -...+..|...|...||++.+|.++- .+|..+..
T Consensus 7 ~iAP~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~~~ 62 (202)
T cd00862 7 RVAPIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFND 62 (202)
T ss_pred hhcCceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHHHH
Confidence 4457788877543220 23568899999999999999998654 66765543
No 27
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=52.86 E-value=61 Score=21.01 Aligned_cols=59 Identities=17% Similarity=0.051 Sum_probs=39.4
Q ss_pred HHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCch-hHHHHHHHHHhhcCce
Q 044205 37 ATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSY-FCLHELALMMETKKKV 106 (192)
Q Consensus 37 v~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~-wc~~EL~~~~~~~~~V 106 (192)
...+++.|++.|+.|-.... ...++....-++++++|.+.-+. --.++|...++.|..+
T Consensus 7 ~~a~~~~L~~~g~~v~~~~~-----------~~~~l~~~~~tll~i~~~~~~~~~~~~~~l~~~v~~G~~l 66 (70)
T PF14258_consen 7 TYALYQLLEEQGVKVERWRK-----------PYEALEADDGTLLVIGPDLRLSEPEEAEALLEWVEAGNTL 66 (70)
T ss_pred HHHHHHHHHHCCCeeEEecc-----------cHHHhCCCCCEEEEEeCCCCCCchHHHHHHHHHHHcCCEE
Confidence 45678888888998854332 12244558889999999966653 5556676666666543
No 28
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=51.54 E-value=55 Score=22.88 Aligned_cols=59 Identities=7% Similarity=0.052 Sum_probs=39.0
Q ss_pred HHHHHHHHHhcCCCeeEEeCCCCCCCCc-hHHHHHHHHHhcceeEEEecCCCCCchhHHHHH
Q 044205 36 VATLLYDHLSRLNLRPFLDNKNMKPGDK-LFDNINRAIRNCKVGVAVFSPTYCQSYFCLHEL 96 (192)
Q Consensus 36 fv~~L~~~L~~~gi~vf~D~~~l~~G~~-~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL 96 (192)
....+.+.+++.|...-.. .-..|.. -...|...|.+++++|++.+--.-+..|...+.
T Consensus 11 ~~~~~~~~~~~~G~~~~~h--g~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~~ 70 (97)
T PF10087_consen 11 RERRYKRILEKYGGKLIHH--GRDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKKA 70 (97)
T ss_pred cHHHHHHHHHHcCCEEEEE--ecCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHHH
Confidence 3678889999999986555 1112221 223488889999998888776555566655543
No 29
>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=51.53 E-value=32 Score=27.45 Aligned_cols=51 Identities=14% Similarity=0.219 Sum_probs=39.8
Q ss_pred chhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCC
Q 044205 33 KRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYC 87 (192)
Q Consensus 33 ~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~ 87 (192)
.......|..+.+.+|+-+|.|.+ .+|+.+...|.+.+-++..+ .++..++
T Consensus 34 ~~~~i~~i~~~~~~rgVIIfTDpD--~~GekIRk~i~~~vp~~kha--fi~~~~a 84 (174)
T TIGR00334 34 KDETINLIKKAQKKQGVIILTDPD--FPGEKIRKKIEQHLPGYENC--FIPKHLA 84 (174)
T ss_pred CHHHHHHHHHHhhcCCEEEEeCCC--CchHHHHHHHHHHCCCCeEE--eeeHHhc
Confidence 345578888889999999999987 78999999999888777754 4444443
No 30
>PLN03194 putative disease resistance protein; Provisional
Probab=51.48 E-value=85 Score=25.38 Aligned_cols=67 Identities=4% Similarity=0.054 Sum_probs=51.1
Q ss_pred cCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEee
Q 044205 46 RLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCD 112 (192)
Q Consensus 46 ~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~ 112 (192)
++.+.||+.-+.--....+...|.++++...+.+.+=......+.--..+|..+++..+..|.||=.
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~ 90 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSP 90 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECC
Confidence 4678999987644444568889999999999887775555555555667888999988888888843
No 31
>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=51.47 E-value=52 Score=22.22 Aligned_cols=48 Identities=19% Similarity=0.102 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 34 RKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 34 ~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
...+..|...|+..|++|.+|...- .+...+..|-..---.++++.++
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~~~----~l~k~i~~a~~~g~~~~iiiG~~ 64 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDRNE----RPGVKFADADLIGIPYRIVVGKK 64 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCC----CcccchhHHHhcCCCEEEEECCc
Confidence 3568889999999999999987533 34444544433333345555544
No 32
>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=50.98 E-value=12 Score=28.08 Aligned_cols=49 Identities=16% Similarity=0.161 Sum_probs=31.6
Q ss_pred CCCCCccEEEecc--cccCchhHHHHHHHHHhcCCCeeEEeCCCC---CCCCch
Q 044205 16 QAIKPCDVFINHR--GIDTKRKVATLLYDHLSRLNLRPFLDNKNM---KPGDKL 64 (192)
Q Consensus 16 ~~~~~ydVFISy~--~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l---~~G~~~ 64 (192)
+.-..|+|=|--- ..+.-...+..|++.|...|++|+.|+++- .+|..+
T Consensus 23 ~~iAP~qV~Iipi~~~~~~~~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~ 76 (128)
T cd02426 23 PCLAPYKVAIDCGKGDTAELRDLCQGLKNELREAGLSVWPGYLETQHSSLEQLL 76 (128)
T ss_pred CCCCCeEEEEEeccCChHHHHHHHHHHHHHHHHcCCEEEeccCcccccCHHHHH
Confidence 3445666654422 122234578899999999999999998653 345433
No 33
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=48.92 E-value=54 Score=24.36 Aligned_cols=56 Identities=20% Similarity=0.315 Sum_probs=38.3
Q ss_pred hhHHHHHHHHHhcCCCee-EEeCCCCC-C-----------CCchHHHHHHHHHhcceeEEEecCCCCCch
Q 044205 34 RKVATLLYDHLSRLNLRP-FLDNKNMK-P-----------GDKLFDNINRAIRNCKVGVAVFSPTYCQSY 90 (192)
Q Consensus 34 ~~fv~~L~~~L~~~gi~v-f~D~~~l~-~-----------G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~ 90 (192)
..+++.+.+.|++.|+.+ .+|-.+.. + -.+-.+++.+.+.+++ .|++.||.|..+.
T Consensus 17 ~~l~~~~~~~l~~~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD-~iI~~sP~y~~~~ 85 (152)
T PF03358_consen 17 RKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEAD-GIIFASPVYNGSV 85 (152)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSS-EEEEEEEEBTTBE
T ss_pred HHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCC-eEEEeecEEcCcC
Confidence 457888888998888766 34544431 1 1233457788899999 5677899888653
No 34
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=47.95 E-value=40 Score=30.51 Aligned_cols=64 Identities=17% Similarity=0.145 Sum_probs=40.1
Q ss_pred CCccEEEeccc--ccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCC
Q 044205 19 KPCDVFINHRG--IDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTY 86 (192)
Q Consensus 19 ~~ydVFISy~~--~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y 86 (192)
..++|+|---+ .+.....+..|...|.+.|++|.+|.++-..|. .+..|-..---.++|+.++-
T Consensus 344 aP~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~----ki~~a~~~giP~~iiVG~~e 409 (439)
T PRK12325 344 APFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGA----KFATMDLIGLPWQIIVGPKG 409 (439)
T ss_pred CCeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhH----HHHHHHHcCCCEEEEECCcc
Confidence 46899876542 222345788999999999999999987544443 44433322222555555543
No 35
>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=47.42 E-value=77 Score=20.59 Aligned_cols=58 Identities=19% Similarity=0.174 Sum_probs=34.6
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecC
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSP 84 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~ 84 (192)
||||...+.+. ..-+-.+...|...|++|.++... ..+...+..|-...-..++++.+
T Consensus 3 ~v~i~~~~~~~-~~~a~~i~~~Lr~~g~~v~~~~~~----~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 3 DVYVVPLGEGA-LSEALELAEQLRDAGIKAEIDYGG----RKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred cEEEEEcChHH-HHHHHHHHHHHHHCCCEEEEecCC----CCHHHHHHHHHHcCCCEEEEEcH
Confidence 67776544332 234778899999999999887542 23444555443333234455554
No 36
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=46.95 E-value=1.2e+02 Score=22.46 Aligned_cols=79 Identities=11% Similarity=0.042 Sum_probs=38.6
Q ss_pred CCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhc---ceeEEEecCCCC-CchhH
Q 044205 17 AIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNC---KVGVAVFSPTYC-QSYFC 92 (192)
Q Consensus 17 ~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S---~~~Ivv~S~~y~-~S~wc 92 (192)
....+|++|.|.+...+ .....+ ....++.++. +.|.++.+.+.++++.. .-.|+++.-+.. -...-
T Consensus 7 ~~~~~~~~l~~~~~~~~-~~~~~~---~~~~~~~~~~-----Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~l~~~~ 77 (122)
T PF09837_consen 7 QADGADVVLAYTPDGDH-AAFRQL---WLPSGFSFFP-----QQGGDLGERMANAFQQAARGYEPVVLIGSDCPDLTPDD 77 (122)
T ss_dssp -TSSSEEEEEE----TT-HHHHHH---HH-TTSEEEE-------SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT--HHH
T ss_pred cCCCcCEEEEEcCCccH-HHHhcc---ccCCCCEEee-----cCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCCCCHHH
Confidence 45689999999977643 223222 4455666655 46788888888888776 224555544433 23333
Q ss_pred HHHHHHHHhhcC
Q 044205 93 LHELALMMETKK 104 (192)
Q Consensus 93 ~~EL~~~~~~~~ 104 (192)
+.+....++...
T Consensus 78 l~~A~~~L~~~d 89 (122)
T PF09837_consen 78 LEQAFEALQRHD 89 (122)
T ss_dssp HHHHHHHTTT-S
T ss_pred HHHHHHHhccCC
Confidence 444444444443
No 37
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=46.00 E-value=22 Score=33.34 Aligned_cols=50 Identities=30% Similarity=0.489 Sum_probs=36.1
Q ss_pred CCCCCCccEEEeccc--ccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCch
Q 044205 15 NQAIKPCDVFINHRG--IDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKL 64 (192)
Q Consensus 15 ~~~~~~ydVFISy~~--~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~ 64 (192)
++.-..|+|+|---+ .+.....+..|++.|+..|+++.+|+++-.+|..+
T Consensus 463 P~~iaP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~ 514 (565)
T PRK09194 463 PKAIAPFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKF 514 (565)
T ss_pred CCccCCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHH
Confidence 345678999987654 12234578899999999999999998765555433
No 38
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=45.33 E-value=2.1e+02 Score=25.06 Aligned_cols=64 Identities=17% Similarity=0.288 Sum_probs=39.7
Q ss_pred HHHHHHHHHhcC----CCeeEEeCCCCCCCCchHHHHHHHHHhcc---eeEEEecCCCCCch--hHHHHHHHHHhh
Q 044205 36 VATLLYDHLSRL----NLRPFLDNKNMKPGDKLFDNINRAIRNCK---VGVAVFSPTYCQSY--FCLHELALMMET 102 (192)
Q Consensus 36 fv~~L~~~L~~~----gi~vf~D~~~l~~G~~~~~~i~~aI~~S~---~~Ivv~S~~y~~S~--wc~~EL~~~~~~ 102 (192)
....+.++|+.+ .+.|++. ++-|.+..++..+.+.... ++++.+.|.|..|. -..+++..+++.
T Consensus 74 ~T~~q~~~L~~~L~~~~~~V~~a---mry~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~ 146 (320)
T COG0276 74 ITRAQAAALEERLDLPDFKVYLA---MRYGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKE 146 (320)
T ss_pred HHHHHHHHHHHHhCCCCccEEEe---ecCCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHh
Confidence 444555555443 5777774 5677777777777776654 46667778777543 345566666653
No 39
>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=44.71 E-value=56 Score=22.81 Aligned_cols=67 Identities=12% Similarity=0.213 Sum_probs=45.5
Q ss_pred HHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEeec
Q 044205 40 LYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCDI 113 (192)
Q Consensus 40 L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v 113 (192)
+...++-.|+..+... ...+.....+.+.+++.++.|++++++++.. -.+++....+. ...|++..+
T Consensus 9 ~v~gFrLaGv~~~~~~---~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~--~~~~l~~~~~~--~~~P~iv~I 75 (95)
T PF01990_consen 9 TVLGFRLAGVEGVYVN---TDPEEAEEALKELLKDEDVGIIIITEDLAEK--IRDELDEYREE--SSLPLIVEI 75 (95)
T ss_dssp HHHHHHHTTSEEEEES---HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT--HHHHHHHHHHT--SSSSEEEEE
T ss_pred HHHHHHHcCCCCccCC---CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH--HHHHHHHHHhc--cCCceEEEc
Confidence 3456677899998875 1245667778888889999999999988764 34444444332 355666544
No 40
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=43.67 E-value=47 Score=30.46 Aligned_cols=64 Identities=22% Similarity=0.162 Sum_probs=39.3
Q ss_pred CCCccEEEeccc-----ccCchhHHHHHHHHHhcCCCeeEEeC-CCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 18 IKPCDVFINHRG-----IDTKRKVATLLYDHLSRLNLRPFLDN-KNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 18 ~~~ydVFISy~~-----~D~~~~fv~~L~~~L~~~gi~vf~D~-~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
...++|+|---. .+.....+..|.+.|+..|++|.+|. .+-.+|. .+.++-..---.++++.++
T Consensus 285 iAP~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~~GirV~lD~r~~~s~gk----K~~~ae~~GvP~~IiIG~~ 354 (477)
T PRK08661 285 IAPIQVVIVPIFKKEEKKEEVLEYAKELAEELKKAGIRVKLDDRSDKTPGW----KFNEWELKGVPLRIEIGPR 354 (477)
T ss_pred cCCCeEEEEEecCCCcCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHH----HHHHHHHCCCCEEEEECcc
Confidence 447889877541 12224568899999999999999998 4445554 4444322222244555544
No 41
>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=43.01 E-value=1.5e+02 Score=25.12 Aligned_cols=79 Identities=10% Similarity=0.095 Sum_probs=51.0
Q ss_pred HHHHHhcCCCeeEEeCCC----CCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEee--c
Q 044205 40 LYDHLSRLNLRPFLDNKN----MKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCD--I 113 (192)
Q Consensus 40 L~~~L~~~gi~vf~D~~~----l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~--v 113 (192)
.++.|... +++|.|-.. -..+.++.+....+++.+..=-+++|-.-...+=-+.++..+-+.-. +|||.+ +
T Consensus 133 ~R~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~~~~--~PVlvGSGv 209 (254)
T PF03437_consen 133 YRKRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVREAVP--VPVLVGSGV 209 (254)
T ss_pred HHHHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHhcCC--CCEEEecCC
Confidence 34444455 999988542 12345677777788888777777777665544444555555544333 999995 7
Q ss_pred CCCccccc
Q 044205 114 KPSQLLVI 121 (192)
Q Consensus 114 ~p~~vr~~ 121 (192)
.++++..+
T Consensus 210 t~~Ni~~~ 217 (254)
T PF03437_consen 210 TPENIAEY 217 (254)
T ss_pred CHHHHHHH
Confidence 77777654
No 42
>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=41.70 E-value=76 Score=24.00 Aligned_cols=38 Identities=18% Similarity=0.298 Sum_probs=18.1
Q ss_pred HHHHHHHHHhcCCCeeEEeCCCCCC-----CCchHHHHHHHHH
Q 044205 36 VATLLYDHLSRLNLRPFLDNKNMKP-----GDKLFDNINRAIR 73 (192)
Q Consensus 36 fv~~L~~~L~~~gi~vf~D~~~l~~-----G~~~~~~i~~aI~ 73 (192)
+...+.+.+.+..-.+++-...+.+ +..+.+.|.++.+
T Consensus 22 ~~~~i~~~I~~A~~~I~i~~~~~~~~~~~~~~~l~~~L~~a~~ 64 (176)
T cd00138 22 DLDALLEAISNAKKSIYIASFYLSPLITEYGPVILDALLAAAR 64 (176)
T ss_pred HHHHHHHHHHhhheEEEEEEeEecccccccchHHHHHHHHHHH
Confidence 4445555555444444443333333 4445555555554
No 43
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=40.19 E-value=25 Score=26.60 Aligned_cols=34 Identities=24% Similarity=0.406 Sum_probs=20.9
Q ss_pred hHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHH
Q 044205 64 LFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALM 99 (192)
Q Consensus 64 ~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~ 99 (192)
+...+.++|..-...|++.+..|-++ |+.||+.+
T Consensus 60 ~~~~L~~~i~~~~g~ivvyN~sfE~~--rL~ela~~ 93 (130)
T PF11074_consen 60 LIEALIKAIGSIYGSIVVYNKSFEKT--RLKELAEL 93 (130)
T ss_pred HHHHHHHHhhhhcCeEEEechHHHHH--HHHHHHHH
Confidence 44445555554435777777766554 78887766
No 44
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=39.45 E-value=1.2e+02 Score=27.34 Aligned_cols=61 Identities=18% Similarity=0.302 Sum_probs=42.0
Q ss_pred CCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecC
Q 044205 19 KPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSP 84 (192)
Q Consensus 19 ~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~ 84 (192)
...||+|.+-+.+. ...+-.+.+.|.++|++|-+|.. +..+...+..|-+.--..++|+.+
T Consensus 324 ~~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~----~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 324 QSIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS----SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC----CCCHHHHHHHHHHcCCCEEEEEec
Confidence 45789998755443 34577899999999999988753 345666776665554445666654
No 45
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=38.98 E-value=1.5e+02 Score=26.70 Aligned_cols=63 Identities=21% Similarity=0.156 Sum_probs=42.3
Q ss_pred CCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecC
Q 044205 17 AIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSP 84 (192)
Q Consensus 17 ~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~ 84 (192)
.-..++|+|-.-+++. ...+..+...|++.|++|.+|.. +..+...+..|-+.---.++++.+
T Consensus 271 wLAP~qV~IIpl~eel-~e~AlkLA~eLR~aGIrVeiDl~----srSLgKQiK~AdK~GaPfvIIIGe 333 (387)
T PRK14938 271 WLNPIQVRILPVKKDF-LDFSIQVAERLRKEGIRVNVDDL----DDSLGNKIRRAGTEWIPFVIIIGE 333 (387)
T ss_pred ccCcceEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECc
Confidence 3456788777655543 35688899999999999999864 446666776665444344555543
No 46
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=38.84 E-value=49 Score=22.62 Aligned_cols=55 Identities=16% Similarity=0.145 Sum_probs=34.9
Q ss_pred ccchhhhccccCCCCCCCccE-EEecccccCchhHHHHHHHHHhcCCC-eeEEeCCCCCCC
Q 044205 3 LQRQVFRQNRLRNQAIKPCDV-FINHRGIDTKRKVATLLYDHLSRLNL-RPFLDNKNMKPG 61 (192)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~ydV-FISy~~~D~~~~fv~~L~~~L~~~gi-~vf~D~~~l~~G 61 (192)
|+|++. .++.+....+.|| |+|=+|+-.|. ...+...|...|- .+.+|.-++.++
T Consensus 12 W~R~~~--~r~~g~~~~~~dV~Y~sP~GkklRs--~~ev~~YL~~~~~~~~~~~~F~F~~~ 68 (77)
T smart00391 12 WRRETK--QRKSGRSAGKFDVYYISPCGKKLRS--KSELARYLHKNGDLSLDLECFDFNAT 68 (77)
T ss_pred cEEEEE--EecCCCCCCcccEEEECCCCCeeeC--HHHHHHHHHhCCCcccccccccCcCC
Confidence 666665 3444556678888 77777776653 6788899987764 344444344443
No 47
>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=37.84 E-value=24 Score=25.17 Aligned_cols=54 Identities=15% Similarity=0.175 Sum_probs=32.5
Q ss_pred ccCchhHHHHHHHHHhcCCCeeEEeCCCCCC----------CCchHHHHHHHHHhcceeEEEec
Q 044205 30 IDTKRKVATLLYDHLSRLNLRPFLDNKNMKP----------GDKLFDNINRAIRNCKVGVAVFS 83 (192)
Q Consensus 30 ~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~----------G~~~~~~i~~aI~~S~~~Ivv~S 83 (192)
.|.|.+=+-.|.+.|.+.|+.|.+.+--+.. |-.+.+.+.++++.+++.|+...
T Consensus 12 ~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~ 75 (106)
T PF03720_consen 12 DDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATD 75 (106)
T ss_dssp S--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS-
T ss_pred cccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEec
Confidence 6788888999999999999998875432221 11222345778888887655444
No 48
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=37.71 E-value=1.4e+02 Score=28.05 Aligned_cols=61 Identities=13% Similarity=0.155 Sum_probs=40.5
Q ss_pred CCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecC
Q 044205 19 KPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSP 84 (192)
Q Consensus 19 ~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~ 84 (192)
...+|+|-.-+++. ...+..+.+.|+++|++|-+|.. +..+...+..|-..---.++|+.+
T Consensus 437 aP~qV~Iipi~e~~-~~~A~~Ia~~LR~~GirVelD~~----~~~lgkkir~A~k~gip~viIIG~ 497 (545)
T PRK14799 437 SSVQVRVLPITDEV-NEYAEKVLNDMRKRRIRAEIDYA----GETLSKRIKNAYDQGVPYILIVGK 497 (545)
T ss_pred CCceEEEEEcCHHH-HHHHHHHHHHHHhCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECh
Confidence 35688887655443 45788999999999999999864 445666666654333334444443
No 49
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=37.21 E-value=96 Score=22.10 Aligned_cols=64 Identities=16% Similarity=0.253 Sum_probs=37.7
Q ss_pred HHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEeec
Q 044205 43 HLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCDI 113 (192)
Q Consensus 43 ~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v 113 (192)
.++-.|+..+.-.. ..+...+.+.+.+.+-++.|+++|++++.. +.+++...++ +...|++.-+
T Consensus 14 GFrLaGi~~~~~~~---~~ee~~~~l~~l~~~~d~gII~Ite~~~~~--i~e~i~~~~~--~~~~P~ii~I 77 (100)
T PRK02228 14 GFRLAGIRKVYEVP---DDEKLDEAVEEVLEDDDVGILVMHDDDLEK--LPRRLRRTLE--ESVEPTVVTL 77 (100)
T ss_pred HHHHcCCceEEeeC---CHHHHHHHHHHHhhCCCEEEEEEehhHhHh--hHHHHHHHHh--cCCCCEEEEE
Confidence 45567887554211 113456667677788899999999997653 3344444333 3444555444
No 50
>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=36.99 E-value=47 Score=22.14 Aligned_cols=32 Identities=13% Similarity=0.059 Sum_probs=18.2
Q ss_pred CCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEE
Q 044205 47 LNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVA 80 (192)
Q Consensus 47 ~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Iv 80 (192)
+.+-+|+|.+ .+|......+.+.+......+-
T Consensus 44 ~~vii~~D~D--~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 44 KEVILAFDGD--EAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred CeEEEEECCC--HHHHHHHHHHHHHHHHCCCeEE
Confidence 4566666654 5666655566655555444433
No 51
>PF01915 Glyco_hydro_3_C: Glycosyl hydrolase family 3 C-terminal domain; InterPro: IPR002772 Glycoside hydrolase family 3 GH3 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-xylosidase (3.2.1.37 from EC); N-acetyl beta-glucosaminidase (3.2.1.52 from EC); glucan beta-1,3-glucosidase (3.2.1.58 from EC); cellodextrinase(3.2.1.74 from EC); exo-1,3-1,4-glucanase (3.2.1 from EC). These enzymes are two-domain globular proteins that are N-glycosylated at three sites []. This domain is often C-terminal to the glycoside hydrolase family 3, N-terminal domain IPR001764 from INTERPRO.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3LK6_D 3NVD_B 3BMX_B 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A 1J8V_A 1IEX_A ....
Probab=36.49 E-value=2.2e+02 Score=22.77 Aligned_cols=86 Identities=14% Similarity=0.034 Sum_probs=55.2
Q ss_pred hhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCC----------------CchhHHHHHH
Q 044205 34 RKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYC----------------QSYFCLHELA 97 (192)
Q Consensus 34 ~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~----------------~S~wc~~EL~ 97 (192)
..+.+.|.+.+...++.+..+....... ....+..+...+++++|+++.+.+. .-+++..||.
T Consensus 46 ~t~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~aD~vIv~~~~~~~e~~~~~~~~~~~~~~~~l~~~q~~li 124 (227)
T PF01915_consen 46 VTPLDALKQRFGNAGVVVPEGGDAVDDD-EGIDEAVAAAKEADVVIVFVGRPSGEGNDNNTEGESDRSDLALPANQQELI 124 (227)
T ss_dssp BHHHHHHHHHHHTTSEEEECCCCCCCCC-SCHHHHHHHHHCSSEEEEEEETTSBCCCSS-EETTGSCSSTBCCCHHHHHH
T ss_pred ccHHhhhccccCCCceEEeeeccccccc-cchHHHHHHhhcCCEEEEeccccccccccccccccCCcccccchhhHHHHH
Confidence 3567778888887777665433222223 3445778889999999999884332 3346777887
Q ss_pred HHHh-hcCceeeEEeecCCCcccc
Q 044205 98 LMME-TKKKVIPIFCDIKPSQLLV 120 (192)
Q Consensus 98 ~~~~-~~~~ViPVf~~v~p~~vr~ 120 (192)
..+. .++++|-|+....|-++..
T Consensus 125 ~~v~~~~~~~Ivvv~~~~P~~l~~ 148 (227)
T PF01915_consen 125 KAVAAAGKKVIVVVNSGNPYDLDP 148 (227)
T ss_dssp HHHHHHHSCEEEEEE-SSGGCGHC
T ss_pred HHHHHhcCCeEEEEecCCccccHH
Confidence 7654 3467777766666766643
No 52
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=36.42 E-value=1.6e+02 Score=23.44 Aligned_cols=82 Identities=18% Similarity=0.314 Sum_probs=47.4
Q ss_pred hHHHHHHHHHhcCCCee-EEeCCCCCCC--------CchHHHHHHHHHhcceeEEEecCCCCCchh-HHHHHH-HH---H
Q 044205 35 KVATLLYDHLSRLNLRP-FLDNKNMKPG--------DKLFDNINRAIRNCKVGVAVFSPTYCQSYF-CLHELA-LM---M 100 (192)
Q Consensus 35 ~fv~~L~~~L~~~gi~v-f~D~~~l~~G--------~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~w-c~~EL~-~~---~ 100 (192)
..+..+.+.|...|..+ .+|-.++..+ .+-...+.+.|++++ .|++.||-|..|-- .++-+- .+ .
T Consensus 18 ~l~~~~~~~l~~~g~ev~~idL~~l~~~~~~~~~~~~~~~~~~~~~i~~AD-~iIi~tP~Y~~s~pg~LKn~iD~l~~~~ 96 (191)
T PRK10569 18 ALLEYAREWLNGLGVEVYHWNLQNFAPEDLLYARFDSPALKTFTEQLAQAD-GLIVATPVYKASFSGALKTLLDLLPERA 96 (191)
T ss_pred HHHHHHHHHHHhCCCEEEEEEccCCChHHHHhccCCCHHHHHHHHHHHHCC-EEEEECCccCCCCCHHHHHHHHhCChhh
Confidence 35666777777788877 4565554432 223446778888988 56778999987632 111110 01 1
Q ss_pred hhcCceeeEEeecCCCc
Q 044205 101 ETKKKVIPIFCDIKPSQ 117 (192)
Q Consensus 101 ~~~~~ViPVf~~v~p~~ 117 (192)
=.++++.||-....+..
T Consensus 97 l~~K~v~iiat~G~~~~ 113 (191)
T PRK10569 97 LEHKVVLPLATGGSVAH 113 (191)
T ss_pred hCCCEEEEEEecCCchh
Confidence 12467777765544443
No 53
>PLN02530 histidine-tRNA ligase
Probab=36.12 E-value=1.6e+02 Score=27.08 Aligned_cols=62 Identities=15% Similarity=-0.052 Sum_probs=43.9
Q ss_pred CCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecC
Q 044205 18 IKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSP 84 (192)
Q Consensus 18 ~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~ 84 (192)
....||+|.+-+++. ...+-.+...|.++|++|-+|... ..+...+..|-+.---.++++.+
T Consensus 399 ~~~~dVlVi~~~~~~-~~~A~~ia~~LR~~Gi~vevd~~~----~~l~k~ik~A~k~g~~~iviiG~ 460 (487)
T PLN02530 399 PHQVDDVVFALDEDL-QGAAAGVASRLREKGRSVDLVLEP----KKLKWVFKHAERIGAKRLVLVGA 460 (487)
T ss_pred CCCCcEEEEEcChHH-HHHHHHHHHHHHHCCCeEEEecCC----CCHHHHHHHHHHCCCCEEEEEch
Confidence 355789998855543 356888999999999999887542 45666777776655556666664
No 54
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=36.02 E-value=2.4e+02 Score=24.36 Aligned_cols=74 Identities=15% Similarity=0.113 Sum_probs=48.3
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHH
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHEL 96 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL 96 (192)
.|+|-|+...-.+.++..+.+.|+..|..+-. .....+++.-...+...|..+..-+|++...+....-...++
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~-~~~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~~~~~~~r~~ 223 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVV-EEVYAPGDTDFSALVAKIKAAGPDAVLVGGYGPDAALFLRQA 223 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEE-EEeeCCCCCChHHHHHHHHhcCCCEEEECCCCccchHHHHHH
Confidence 57777766555677888899999999987333 234556554355666667777776777776666654444443
No 55
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=35.86 E-value=1.5e+02 Score=27.60 Aligned_cols=62 Identities=18% Similarity=0.163 Sum_probs=41.1
Q ss_pred CCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecC
Q 044205 18 IKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSP 84 (192)
Q Consensus 18 ~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~ 84 (192)
...+||+|---+++. ...+..+...|.+.||+|-+|.. +..+...+..|-..---.++|+.+
T Consensus 474 ~~p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~----~~~l~kk~~~A~~~g~p~~iivG~ 535 (575)
T PRK12305 474 LAPVQVVIIPVADAH-NEYAEEVAKKLRAAGIRVEVDTS----NERLNKKIRNAQKQKIPYMLVVGD 535 (575)
T ss_pred CCCccEEEEEeChHH-HHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEec
Confidence 346689887655442 35688999999999999999875 344556666655443334555544
No 56
>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=35.67 E-value=1.7e+02 Score=21.13 Aligned_cols=73 Identities=15% Similarity=0.080 Sum_probs=47.9
Q ss_pred HHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHh-cceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEeecC
Q 044205 36 VATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRN-CKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCDIK 114 (192)
Q Consensus 36 fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~-S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v~ 114 (192)
-+..|..+|++.|+.+..-.. .+.....+++ +++..+|+|=+ ....-...++...++....=+|||+-.+
T Consensus 5 ~~~~l~~~L~~~~~~vv~~~~--------~dd~~~~i~~~~~i~avvi~~d-~~~~~~~~~ll~~i~~~~~~iPVFl~~~ 75 (115)
T PF03709_consen 5 ASRELAEALEQRGREVVDADS--------TDDALAIIESFTDIAAVVISWD-GEEEDEAQELLDKIRERNFGIPVFLLAE 75 (115)
T ss_dssp HHHHHHHHHHHTTTEEEEESS--------HHHHHHHHHCTTTEEEEEEECH-HHHHHHHHHHHHHHHHHSTT-EEEEEES
T ss_pred HHHHHHHHHHHCCCEEEEeCC--------hHHHHHHHHhCCCeeEEEEEcc-cccchhHHHHHHHHHHhCCCCCEEEEec
Confidence 477899999999998866432 2344455554 99999999855 2222234455555666667889999766
Q ss_pred CCc
Q 044205 115 PSQ 117 (192)
Q Consensus 115 p~~ 117 (192)
+..
T Consensus 76 ~~~ 78 (115)
T PF03709_consen 76 RDT 78 (115)
T ss_dssp CCH
T ss_pred CCC
Confidence 443
No 57
>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=35.35 E-value=96 Score=22.25 Aligned_cols=61 Identities=16% Similarity=0.091 Sum_probs=33.3
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEEeC--------CCC-----CCCCc-hHHHHHHHHHh-cceeEEEecCC
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFLDN--------KNM-----KPGDK-LFDNINRAIRN-CKVGVAVFSPT 85 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~--------~~l-----~~G~~-~~~~i~~aI~~-S~~~Ivv~S~~ 85 (192)
||||-+..|. .. ...+...|...|++++--. .++ ..+.. -.+++.+.|.+ -++-+||..|+
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-AM-LVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEcccH-HH-HHHHHHHHHHCCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 7888776652 33 4467777777787775321 011 01000 11456666666 66666666654
No 58
>COG3580 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.20 E-value=2.6e+02 Score=24.65 Aligned_cols=151 Identities=17% Similarity=0.171 Sum_probs=79.8
Q ss_pred hHHHHHHHHHhcCCCeeEEeC----CCCCCCCchHH-------HHHHHHHhc-ceeEEEecCCCCCchhHHHHHHHHHhh
Q 044205 35 KVATLLYDHLSRLNLRPFLDN----KNMKPGDKLFD-------NINRAIRNC-KVGVAVFSPTYCQSYFCLHELALMMET 102 (192)
Q Consensus 35 ~fv~~L~~~L~~~gi~vf~D~----~~l~~G~~~~~-------~i~~aI~~S-~~~Ivv~S~~y~~S~wc~~EL~~~~~~ 102 (192)
.+..+++..++.-|+.---.. ..++.++.... ++..-+... ...||+++..|.-++-...++...+..
T Consensus 149 ~~~~~~~~~~~~~~~s~~E~~~Avqka~~~~~e~r~dir~k~~e~L~~l~~n~~~gVvLaGrPYh~DpeiNhgI~e~i~~ 228 (351)
T COG3580 149 LLKEQFYKVFKEIGLSKEENEEAVQKAWKEGEEYREDIRKKGEEVLKYLKENGEKGVVLAGRPYHFDPEINHGIPEKINS 228 (351)
T ss_pred HHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCceeEEEeCCccccCcccccchHHHHhh
Confidence 477788888877663210000 01223333322 233334444 789999999999999888887766654
Q ss_pred cCceeeEEeecCCCcccccccCCCchhHhhhHHHHHHHHHHhc-------CccccCCCCCHHHHHHHHHHHHHHHhhhc-
Q 044205 103 KKKVIPIFCDIKPSQLLVIDDGKCSANELRRFSWALEEAKFTV-------GLTFDSLKGNWSDIVTSASDIIIRSLMEI- 174 (192)
Q Consensus 103 ~~~ViPVf~~v~p~~vr~~~~g~~~~~~~~~W~~aL~~~~~~~-------G~~~~~~~~~~~~~v~~Iv~~v~~~l~~~- 174 (192)
. =+||+=..+-..+..+. |...-....+|..-+=.+|+.. |..+.+-.+--...+...+++|...-+.+
T Consensus 229 ~--g~~IlTedsI~~~~~~~-~~l~i~~~W~~hsr~y~AA~fvak~~nlegV~l~SFgCG~Davttd~i~eIl~~~nk~y 305 (351)
T COG3580 229 R--GIPILTEDSIPLLGEIE-GPLRIVNQWKYHSRLYAAAKFVAKHPNLEGVQLVSFGCGLDAVTTDLIEEILEGHNKIY 305 (351)
T ss_pred c--CCeeeecccchhhhccc-cceeehhhhHHHHHHHHHHHHHhcCCCeeeEEEeecccCcchhHHHHHHHHHHhCCCee
Confidence 3 35676654444454444 3222233444544444444443 44443322223345555556666554422
Q ss_pred -------CCcchhhhhhhccc
Q 044205 175 -------DYKEQRHWRRQNST 188 (192)
Q Consensus 175 -------~~~~vg~~~rl~~~ 188 (192)
-+++=|+.-|++.+
T Consensus 306 tvlkIDE~tn~gai~iRlesl 326 (351)
T COG3580 306 TVLKIDEGTNLGAIRIRLESL 326 (351)
T ss_pred EEEEecCCCCcchhhhhHHHH
Confidence 23556777776654
No 59
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=34.38 E-value=1.6e+02 Score=27.87 Aligned_cols=62 Identities=16% Similarity=0.069 Sum_probs=41.9
Q ss_pred CCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 19 KPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 19 ~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
...||+|-.-++.. ...+..|.+.|.+.|++|-+|.. +..+...+..|-..---.++|+.++
T Consensus 538 ~p~~v~Ii~~~~~~-~~~a~~i~~~Lr~~gi~v~~d~~----~~~l~kki~~A~~~g~~~~iiiG~~ 599 (638)
T PRK00413 538 APVQVVVLPITDKH-ADYAKEVAKKLKAAGIRVEVDLR----NEKIGYKIREAQLQKVPYMLVVGDK 599 (638)
T ss_pred CcceEEEEEeChhH-HHHHHHHHHHHHhCCCEEEEECC----CCCHhHHHHHhhccCCCEEEEEcch
Confidence 46688888755443 45688999999999999999864 3455566666544433355555543
No 60
>TIGR01101 V_ATP_synt_F vacuolar ATP synthase F subunit. This model describes the vacuolar ATP synthase F subunit (14 kDa subunit) in eukaryotes. In some archaeal species this protein subunit is referred as G subunit
Probab=34.11 E-value=1.2e+02 Score=22.48 Aligned_cols=47 Identities=13% Similarity=0.319 Sum_probs=32.8
Q ss_pred CchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEeecC
Q 044205 62 DKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCDIK 114 (192)
Q Consensus 62 ~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v~ 114 (192)
+.+.+.+.+.+.+.++.|+++++++++ ++...++..+.++|....+.
T Consensus 46 eei~~~~~~~l~~~digIIlIte~~a~------~i~~~I~~~~~~~PaIieIP 92 (115)
T TIGR01101 46 SEIEDCFNRFLKRDDIAIILINQHIAE------MIRHAVDAHTRSIPAVLEIP 92 (115)
T ss_pred HHHHHHHHHHhhcCCeEEEEEcHHHHH------HhHHHHHhcCCcCCEEEEEC
Confidence 456666777788899999999988654 34444444447888887654
No 61
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=34.08 E-value=74 Score=30.33 Aligned_cols=64 Identities=19% Similarity=0.129 Sum_probs=40.9
Q ss_pred CCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 17 AIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 17 ~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
.-..++|+|---+++ ....+..+.+.|...|++|.+|.++- .+...+.+|-..---.++|+.++
T Consensus 496 ~lAP~qV~IIpi~e~-~~~~A~eIa~~Lr~~GirV~lDdr~~----slgkKir~A~~~GiP~iIVIG~k 559 (613)
T PRK03991 496 WLSPTQVRVIPVSER-HLDYAEEVADKLEAAGIRVDVDDRDE----SLGKKIRDAGKEWIPYVVVIGDK 559 (613)
T ss_pred cccCceEEEEEeCHH-HHHHHHHHHHHHHhCCCEEEEECCCC----CHHHHHHHHHHcCCCEEEEECcc
Confidence 345678887765444 34679999999999999999997643 44445555433222244444433
No 62
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=33.92 E-value=1.7e+02 Score=27.84 Aligned_cols=64 Identities=20% Similarity=0.134 Sum_probs=43.8
Q ss_pred CCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 18 IKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 18 ~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
....+|+|-.-+++.....+..|...|.+.|++|-+|.. +..+...+..|-..---.++++.++
T Consensus 539 ~ap~qV~Ii~~~~~~~~~~a~~la~~LR~~Gi~veid~~----~~sl~kq~k~A~k~g~~~~iiiG~~ 602 (639)
T PRK12444 539 LAPVQVKVIPVSNAVHVQYADEVADKLAQAGIRVERDER----DEKLGYKIREAQMQKIPYVLVIGDK 602 (639)
T ss_pred cCCceEEEEEcccHHHHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEcch
Confidence 457788887765411245788999999999999999864 4556667766654444455666543
No 63
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=33.83 E-value=1.9e+02 Score=23.11 Aligned_cols=50 Identities=16% Similarity=0.208 Sum_probs=33.5
Q ss_pred HHHhcceeEEEecCCCCCchhHHHHHHHHHhh-cCceeeEEeecCCCcccc
Q 044205 71 AIRNCKVGVAVFSPTYCQSYFCLHELALMMET-KKKVIPIFCDIKPSQLLV 120 (192)
Q Consensus 71 aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~-~~~ViPVf~~v~p~~vr~ 120 (192)
++..-++.++.=.|..-.|.+|++-+..+... +.+++=+-++.+|.++..
T Consensus 9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~~~~~~~~ 59 (242)
T cd00984 9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQ 59 (242)
T ss_pred CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCCCHHHHHH
Confidence 45555566666677888888888887777665 666666666666655443
No 64
>PF01269 Fibrillarin: Fibrillarin; InterPro: IPR000692 Fibrillarin is a component of a nucleolar small nuclear ribonucleoprotein (SnRNP), functioning in vivo in ribosomal RNA processing [, ]. It is associated with U3, U8 and U13 small nuclear RNAs in mammals [] and is similar to the yeast NOP1 protein []. Fibrillarin has a well conserved sequence of around 320 amino acids, and contains 3 domains, an N-terminal Gly/Arg-rich region; a central domain resembling other RNA-binding proteins and containing an RNP-2-like consensus sequence; and a C-terminal alpha-helical domain. An evolutionarily related pre-rRNA processing protein, which lacks the Gly/Arg-rich domain, has been found in various archaebacteria.; GO: 0003723 RNA binding, 0008168 methyltransferase activity, 0006364 rRNA processing, 0008033 tRNA processing; PDB: 3PLA_E 3ID6_C 3ID5_B 1NT2_A 3NVK_J 2NNW_B 3NVM_B 3NMU_J 1PRY_A 1G8A_A ....
Probab=33.62 E-value=46 Score=27.78 Aligned_cols=48 Identities=21% Similarity=0.252 Sum_probs=32.0
Q ss_pred CCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEeec
Q 044205 60 PGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCDI 113 (192)
Q Consensus 60 ~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v 113 (192)
.|...+ -+..-+..+..+-.| --|+|+..+|...-+.+.+|+||+-+.
T Consensus 84 sGTTVS-HvSDIvg~~G~VYaV-----Efs~r~~rdL~~la~~R~NIiPIl~DA 131 (229)
T PF01269_consen 84 SGTTVS-HVSDIVGPDGVVYAV-----EFSPRSMRDLLNLAKKRPNIIPILEDA 131 (229)
T ss_dssp TSHHHH-HHHHHHTTTSEEEEE-----ESSHHHHHHHHHHHHHSTTEEEEES-T
T ss_pred CCCccc-hhhhccCCCCcEEEE-----EecchhHHHHHHHhccCCceeeeeccC
Confidence 444443 444545545544333 247899999999999999999999764
No 65
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=33.03 E-value=1.8e+02 Score=21.13 Aligned_cols=9 Identities=33% Similarity=0.556 Sum_probs=3.8
Q ss_pred ccEEEeccc
Q 044205 21 CDVFINHRG 29 (192)
Q Consensus 21 ydVFISy~~ 29 (192)
.||-|-|+.
T Consensus 68 ~DVvIDfT~ 76 (124)
T PF01113_consen 68 ADVVIDFTN 76 (124)
T ss_dssp -SEEEEES-
T ss_pred CCEEEEcCC
Confidence 555555553
No 66
>COG1180 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=33.01 E-value=1.6e+02 Score=24.70 Aligned_cols=42 Identities=19% Similarity=0.148 Sum_probs=31.5
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCch
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKL 64 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~ 64 (192)
|-+|+...-....|+..+..+.++.|+++.+|.....+....
T Consensus 87 vt~SGGEP~~q~e~~~~~~~~ake~Gl~~~l~TnG~~~~~~~ 128 (260)
T COG1180 87 VTFSGGEPTLQAEFALDLLRAAKERGLHVALDTNGFLPPEAL 128 (260)
T ss_pred EEEECCcchhhHHHHHHHHHHHHHCCCcEEEEcCCCCCHHHH
Confidence 556665444567889999999999999999998765554433
No 67
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=30.55 E-value=2.3e+02 Score=21.16 Aligned_cols=86 Identities=14% Similarity=0.120 Sum_probs=56.9
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHh
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMME 101 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~ 101 (192)
-|++.=-+.|.+.-=++.+...|+..|+.|..- .++.-.+++.++..+.+.-++++|--.....--..++...++
T Consensus 4 ~v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~l-----g~~~s~e~~v~aa~e~~adii~iSsl~~~~~~~~~~~~~~L~ 78 (132)
T TIGR00640 4 RILVAKMGQDGHDRGAKVIATAYADLGFDVDVG-----PLFQTPEEIARQAVEADVHVVGVSSLAGGHLTLVPALRKELD 78 (132)
T ss_pred EEEEEeeCCCccHHHHHHHHHHHHhCCcEEEEC-----CCCCCHHHHHHHHHHcCCCEEEEcCchhhhHHHHHHHHHHHH
Confidence 355555455554333556778889999998542 223344577788888899889998776665555667777665
Q ss_pred h-cCceeeEEee
Q 044205 102 T-KKKVIPIFCD 112 (192)
Q Consensus 102 ~-~~~ViPVf~~ 112 (192)
. +..-+||+.+
T Consensus 79 ~~g~~~i~vivG 90 (132)
T TIGR00640 79 KLGRPDILVVVG 90 (132)
T ss_pred hcCCCCCEEEEe
Confidence 5 3346788886
No 68
>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=30.13 E-value=46 Score=31.35 Aligned_cols=50 Identities=32% Similarity=0.462 Sum_probs=34.9
Q ss_pred CCCCCccEEEeccc-cc-CchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchH
Q 044205 16 QAIKPCDVFINHRG-ID-TKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLF 65 (192)
Q Consensus 16 ~~~~~ydVFISy~~-~D-~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~ 65 (192)
+.-..|+|=|---. .| .-...+..|++.|+..|++|.+|+++-.+|..+.
T Consensus 469 ~~iAP~qV~Iip~~~~~~~~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~ 520 (568)
T TIGR00409 469 KAIAPYDVVIVVMNMKDEEQQQLAEELYSELLAQGVDVLLDDRNERAGVKFA 520 (568)
T ss_pred hhhCCeEEEEEEcCCChHHHHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHH
Confidence 34456777655321 22 2345789999999999999999998766675554
No 69
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=29.94 E-value=2.1e+02 Score=20.36 Aligned_cols=74 Identities=9% Similarity=0.027 Sum_probs=44.7
Q ss_pred HHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCc-eeeEEeecCC
Q 044205 37 ATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKK-VIPIFCDIKP 115 (192)
Q Consensus 37 v~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~-ViPVf~~v~p 115 (192)
...+...|+..|+.|..-..+. -.+++.+++.+.+.-++.+|-......--..++...++...+ =++|+.+-.+
T Consensus 16 ~~~~~~~l~~~G~~V~~lg~~~-----~~~~l~~~~~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vGG~~ 90 (119)
T cd02067 16 KNIVARALRDAGFEVIDLGVDV-----PPEEIVEAAKEEDADAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVGGAI 90 (119)
T ss_pred HHHHHHHHHHCCCEEEECCCCC-----CHHHHHHHHHHcCCCEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEECCC
Confidence 3456777889999994422222 235778888888888888886633333233455555544333 4667776443
No 70
>PLN02924 thymidylate kinase
Probab=29.49 E-value=3.1e+02 Score=22.27 Aligned_cols=149 Identities=11% Similarity=0.160 Sum_probs=80.8
Q ss_pred CccEEEecccccC--chhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHH------------------------------
Q 044205 20 PCDVFINHRGIDT--KRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDN------------------------------ 67 (192)
Q Consensus 20 ~ydVFISy~~~D~--~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~------------------------------ 67 (192)
+--.||.+-|-|. +.+.+..|.+.|+.+|+.+-.=. +-..+..+...
T Consensus 14 ~~g~~IviEGiDGsGKsTq~~~L~~~l~~~g~~v~~~~-ep~~~~~~g~~ir~~l~~~~~~~~~~~~llf~adR~~~~~~ 92 (220)
T PLN02924 14 SRGALIVLEGLDRSGKSTQCAKLVSFLKGLGVAAELWR-FPDRTTSVGQMISAYLSNKSQLDDRAIHLLFSANRWEKRSL 92 (220)
T ss_pred CCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCCceeee-CCCCCChHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3347999988775 35678899999999999863311 10011111111
Q ss_pred HHHHHHhcceeEEEecCCCCCchhHHHH-------HHHHHhhc--CceeeEEeecCCCcccccc--c-CCC-chhHhhhH
Q 044205 68 INRAIRNCKVGVAVFSPTYCQSYFCLHE-------LALMMETK--KKVIPIFCDIKPSQLLVID--D-GKC-SANELRRF 134 (192)
Q Consensus 68 i~~aI~~S~~~Ivv~S~~y~~S~wc~~E-------L~~~~~~~--~~ViPVf~~v~p~~vr~~~--~-g~~-~~~~~~~W 134 (192)
|..+++. --+|++..|..|.....- ....++.+ ++=+-|+++++|+....-. . .++ ..+..++=
T Consensus 93 I~pal~~---g~vVI~DRy~~S~~ayq~~~g~~~~~~~~~~~~~~~PDlvi~Ld~~~~~a~~R~~~~~~~~E~~~~~~rv 169 (220)
T PLN02924 93 MERKLKS---GTTLVVDRYSYSGVAFSAAKGLDLEWCKAPEVGLPAPDLVLYLDISPEEAAERGGYGGERYEKLEFQKKV 169 (220)
T ss_pred HHHHHHC---CCEEEEccchhHHHHHHHhcCCCHHHHHHHHhCCCCCCEEEEEeCCHHHHHHHhccCccccccHHHHHHH
Confidence 1111211 225788889888766542 11112211 2334477888887543211 0 112 22344566
Q ss_pred HHHHHHHHHhcCccc-cCCCCCHHHHHHHHHHHHHHHhhhc
Q 044205 135 SWALEEAKFTVGLTF-DSLKGNWSDIVTSASDIIIRSLMEI 174 (192)
Q Consensus 135 ~~aL~~~~~~~G~~~-~~~~~~~~~~v~~Iv~~v~~~l~~~ 174 (192)
+.+..++++ ..+.. +. ..+-.+..++|.+.|.+.+..+
T Consensus 170 ~~~Y~~la~-~~~~vIDa-~~sieeV~~~I~~~I~~~l~~~ 208 (220)
T PLN02924 170 AKRFQTLRD-SSWKIIDA-SQSIEEVEKKIREVVLDTVQRC 208 (220)
T ss_pred HHHHHHHhh-cCEEEECC-CCCHHHHHHHHHHHHHHHHHhc
Confidence 677777765 34443 43 4556667777777776666543
No 71
>COG2342 Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism]
Probab=29.09 E-value=92 Score=26.94 Aligned_cols=44 Identities=27% Similarity=0.449 Sum_probs=36.6
Q ss_pred HHHHHHHHhcceeEEEecCCCC---CchhHHHHHHHHHhhcCceeeEEe
Q 044205 66 DNINRAIRNCKVGVAVFSPTYC---QSYFCLHELALMMETKKKVIPIFC 111 (192)
Q Consensus 66 ~~i~~aI~~S~~~Ivv~S~~y~---~S~wc~~EL~~~~~~~~~ViPVf~ 111 (192)
+.=..+|.+|+.-++|+-|+|. +++|..+||.++-+.+ ++||-|
T Consensus 33 d~~~~~i~~~~f~llVVDps~~g~~~~~~~~eelr~~~~gg--~~pIAY 79 (300)
T COG2342 33 DAYINEILNSPFDLLVVDPSYCGPFNTPWTIEELRTKADGG--VKPIAY 79 (300)
T ss_pred cchHHHHhcCCCcEEEEeccccCCCCCcCcHHHHHHHhcCC--eeEEEE
Confidence 4455789999999999999665 5789999999988777 788877
No 72
>KOG2903 consensus Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]
Probab=28.78 E-value=2e+02 Score=24.82 Aligned_cols=93 Identities=18% Similarity=0.244 Sum_probs=52.9
Q ss_pred CCCCCccEEEecccccCchhHHHH--HHHHHhcC----CCee--E-EeCCCCCCCCchHHHHHHHHHhcceeEEEecCCC
Q 044205 16 QAIKPCDVFINHRGIDTKRKVATL--LYDHLSRL----NLRP--F-LDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTY 86 (192)
Q Consensus 16 ~~~~~ydVFISy~~~D~~~~fv~~--L~~~L~~~----gi~v--f-~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y 86 (192)
|+...|..|+||... ||.. +..+|+.- |+.+ | .|+. |=.+.++- .-+.+|...++ +++.
T Consensus 33 pakgryhLYvslaCP-----WAhRtLi~r~LKGL~~~i~~s~v~~~~d~~----gW~F~~~~-~~~nDs~~l~~--~~d~ 100 (319)
T KOG2903|consen 33 PAKGRYHLYVSLACP-----WAHRTLIVRALKGLEPAIGVSVVHWHLDDK----GWRFLDEH-IIINDSERLGV--TPDP 100 (319)
T ss_pred CCCceEEEEEeccCc-----HHHHHHHHHHHcCccccceeEEeccccCCC----cccCCCcc-cCCCchhcccC--CCcc
Confidence 455889999999752 3333 33333311 3322 3 2222 22222200 12345555544 8888
Q ss_pred CCchhHHHHHHHHHhh---cCceeeEEeecCCCcccc
Q 044205 87 CQSYFCLHELALMMET---KKKVIPIFCDIKPSQLLV 120 (192)
Q Consensus 87 ~~S~wc~~EL~~~~~~---~~~ViPVf~~v~p~~vr~ 120 (192)
++..--+.||-.+-.- ++--+||+.+.....|-+
T Consensus 101 ~~g~k~l~elY~~~~p~Y~grfTVPVLWD~k~ktIVn 137 (319)
T KOG2903|consen 101 LNGAKRLRELYYIASPNYTGRFTVPVLWDLKTKTIVN 137 (319)
T ss_pred cccchhHHHHHhhcCCCCCceEEEEEEEccccceeec
Confidence 8877778888887653 578899999876655443
No 73
>cd08584 PI-PLCc_GDPD_SF_unchar2 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=28.69 E-value=1.4e+02 Score=24.19 Aligned_cols=59 Identities=12% Similarity=0.064 Sum_probs=38.1
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCC
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQ 88 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~ 88 (192)
.+|++.+..+.... +-.|++ +---||+|. -.+..+..++.+.+.++..-|+++||.--.
T Consensus 103 ~i~tr~Se~E~~~~-~~~~~~----~~~~VW~D~---f~~~~~~~~~~~~~~~~~~~~c~VSpELh~ 161 (192)
T cd08584 103 RTATRVSEYEPIPT-ALSLYE----KADWVWIDS---FTSLWLDNDLILKLLKAGKKICLVSPELHG 161 (192)
T ss_pred eeEEeecccccchH-HHHhhc----cccEEEEec---ccccCCCHHHHHHHHHCCcEEEEECHHHcC
Confidence 46776665443322 222222 222389986 345777888888888999999999997654
No 74
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=28.64 E-value=38 Score=28.93 Aligned_cols=26 Identities=27% Similarity=0.574 Sum_probs=19.4
Q ss_pred hHHHHHHHHHhh--------cCceeeEEeecCCC
Q 044205 91 FCLHELALMMET--------KKKVIPIFCDIKPS 116 (192)
Q Consensus 91 wc~~EL~~~~~~--------~~~ViPVf~~v~p~ 116 (192)
=|.+||.++... +-+++|||.-++|.
T Consensus 154 ICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 154 ICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred cChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 599999876532 23666999999995
No 75
>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=28.63 E-value=83 Score=22.59 Aligned_cols=29 Identities=14% Similarity=0.211 Sum_probs=22.3
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEE
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFL 53 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~ 53 (192)
||+|.+..|. .. ...+.+.|...|++++-
T Consensus 3 vlisv~~~dk-~~-~~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYSK-PE-LLPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCcccc-hh-HHHHHHHHHHCCCEEEE
Confidence 8999987763 34 45788888888998865
No 76
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=28.56 E-value=1.1e+02 Score=27.36 Aligned_cols=56 Identities=7% Similarity=0.089 Sum_probs=39.4
Q ss_pred Eeccc--ccCchhHHHHHHHHHhcCCCeeEEeCCCCCC----CCchHHHHHHHHHhcceeEE
Q 044205 25 INHRG--IDTKRKVATLLYDHLSRLNLRPFLDNKNMKP----GDKLFDNINRAIRNCKVGVA 80 (192)
Q Consensus 25 ISy~~--~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~----G~~~~~~i~~aI~~S~~~Iv 80 (192)
++|.. .|.|++=+-.|.+.|..+|..|-..+--+.. |-.+.+++..+++.++..|+
T Consensus 304 lafK~~t~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 304 LIMKSGSDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred ceeCCCCCccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 35643 5788888889999999999988765432222 34466677788888886644
No 77
>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566).
Probab=27.90 E-value=2.3e+02 Score=21.79 Aligned_cols=55 Identities=16% Similarity=0.309 Sum_probs=33.9
Q ss_pred hHHHHHHHHHhcCCCee-EEeCCCCCCC--------CchHHHHHHHHHhcceeEEEecCCCCCch
Q 044205 35 KVATLLYDHLSRLNLRP-FLDNKNMKPG--------DKLFDNINRAIRNCKVGVAVFSPTYCQSY 90 (192)
Q Consensus 35 ~fv~~L~~~L~~~gi~v-f~D~~~l~~G--------~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~ 90 (192)
..+..+.+.|...|..+ .+|-.++... .+-...+.+.|.+++ .|++.||-|..|-
T Consensus 17 ~l~~~~~~~l~~~~~~~~~idl~~l~~~~~~~~~~~~~~~~~l~~~i~~AD-~iI~~sP~Y~~si 80 (171)
T TIGR03567 17 ALLRHVREALQEQGVEVDHLSVRDLPAEDLLFARFDSPAIKAATAQVAQAD-GVVVATPVYKASY 80 (171)
T ss_pred HHHHHHHHHHHHCCCeEEEEEecCCChHHhhhcCCCCHHHHHHHHHHHHCC-EEEEECCcccCCC
Confidence 35666777777777643 3443333211 123356778888888 5677799998763
No 78
>PF06856 DUF1251: Protein of unknown function (DUF1251); InterPro: IPR009661 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17; it is a family of uncharacterised viral proteins.
Probab=27.61 E-value=51 Score=24.75 Aligned_cols=63 Identities=11% Similarity=0.042 Sum_probs=40.8
Q ss_pred CCCCCCccEEEecccccCchhH-HHHHHHHHhcC-CCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchh
Q 044205 15 NQAIKPCDVFINHRGIDTKRKV-ATLLYDHLSRL-NLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYF 91 (192)
Q Consensus 15 ~~~~~~ydVFISy~~~D~~~~f-v~~L~~~L~~~-gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~w 91 (192)
...+-.||-|+++-.+-.-..| +..|+....+. |.+| ..+.++|++..++=+.+-+.+..+.|
T Consensus 55 ~~~~i~FDGF~d~~DE~~T~PFvv~~L~~l~~~~~~l~V--------------r~ma~ame~~tvLkifINEAi~~~~~ 119 (120)
T PF06856_consen 55 KQRPIVFDGFPDEDDEGKTVPFVVGPLNSLRENHAGLKV--------------RDMAKAMESQTVLKIFINEAIIPRRW 119 (120)
T ss_pred CCCceEECCCCCccccccccccEeehhhhhhhhhcCccH--------------HHHHHHhcCCcEEEEEEeeeEccccC
Confidence 4456788999988332222345 44454444433 3332 36788999988888888888887766
No 79
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=27.61 E-value=2.2e+02 Score=19.98 Aligned_cols=84 Identities=18% Similarity=0.137 Sum_probs=48.9
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC-CCCchhHHHHHHHHHh
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT-YCQSYFCLHELALMME 101 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~-y~~S~wc~~EL~~~~~ 101 (192)
+++..........|...|..+|...... -...+.+.+.+.+.+++.+..++|+-+- +..+.-.++.|..+.+
T Consensus 41 ~~~~~~~~~~~~~~~~~i~~~l~~~~~~-------~~~~~~l~~~~~~~l~~~~~~~lviDe~~~l~~~~~l~~l~~l~~ 113 (131)
T PF13401_consen 41 IYVNCPSSRTPRDFAQEILEALGLPLKS-------RQTSDELRSLLIDALDRRRVVLLVIDEADHLFSDEFLEFLRSLLN 113 (131)
T ss_dssp EEEEHHHHSSHHHHHHHHHHHHT-SSSS-------TS-HHHHHHHHHHHHHHCTEEEEEEETTHHHHTHHHHHHHHHHTC
T ss_pred EEEEeCCCCCHHHHHHHHHHHhCccccc-------cCCHHHHHHHHHHHHHhcCCeEEEEeChHhcCCHHHHHHHHHHHh
Confidence 4666655555567888888888766544 1234456678889999988866666543 2213333444444433
Q ss_pred hcCceeeEEeecCC
Q 044205 102 TKKKVIPIFCDIKP 115 (192)
Q Consensus 102 ~~~~ViPVf~~v~p 115 (192)
..-++|.+-..|
T Consensus 114 --~~~~~vvl~G~~ 125 (131)
T PF13401_consen 114 --ESNIKVVLVGTP 125 (131)
T ss_dssp --SCBEEEEEEESS
T ss_pred --CCCCeEEEEECh
Confidence 444566654444
No 80
>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.
Probab=27.16 E-value=2.3e+02 Score=25.97 Aligned_cols=65 Identities=15% Similarity=0.213 Sum_probs=41.0
Q ss_pred CCCCccEEEec---ccc--cCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCC
Q 044205 17 AIKPCDVFINH---RGI--DTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPT 85 (192)
Q Consensus 17 ~~~~ydVFISy---~~~--D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~ 85 (192)
....++|+|-- ... +.....+..|...|++.|++|.+|.++-.+| ..+.++-..---.++++.++
T Consensus 279 ~iaP~qV~Iipi~~~~~~~~~~~~~A~~l~~~Lr~~girv~lD~r~~s~g----kk~k~Ae~~GvP~~IiIG~~ 348 (472)
T TIGR00408 279 RVAPIQVVIIPIIFKKKENEKVMEAAREVRSRLKKAGFRVHIDDRDNRPG----RKFYQWEIKGIPLRIEVGPN 348 (472)
T ss_pred hhCcceEEEEEccCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHH----HHHHHHHHCCCCEEEEECcc
Confidence 34568898874 221 1234578899999999999999998643444 44544433333355555554
No 81
>KOG4132 consensus Uroporphyrinogen III synthase UROS/HEM4 [Coenzyme transport and metabolism]
Probab=26.95 E-value=1.1e+02 Score=25.78 Aligned_cols=50 Identities=20% Similarity=0.312 Sum_probs=34.2
Q ss_pred HHHHHHHHhcCCCeeEE----eCCCCCCCCchHHHHHHHHHhcc--eeEEEecCCCCCc
Q 044205 37 ATLLYDHLSRLNLRPFL----DNKNMKPGDKLFDNINRAIRNCK--VGVAVFSPTYCQS 89 (192)
Q Consensus 37 v~~L~~~L~~~gi~vf~----D~~~l~~G~~~~~~i~~aI~~S~--~~Ivv~S~~y~~S 89 (192)
-+-|..+|..+||+|=- ..++. ..+..++..+++.+. -.|++|||.-..|
T Consensus 145 rdil~kkL~~~G~~Vds~~VY~T~~h---p~~~~~~~~alk~~~~~d~ivfFSPsgv~~ 200 (260)
T KOG4132|consen 145 RDILPKKLHDKGIRVDSCEVYETREH---PDGFKQFIHALKECGFIDWIVFFSPSGVKS 200 (260)
T ss_pred hHHHHHHHHhCCceeeEEEEEeeeec---ccHHHHHHHHHHhcCCcceEEEECcchHHH
Confidence 34688899999997621 11222 234567888888874 4899999987764
No 82
>PRK13762 tRNA-modifying enzyme; Provisional
Probab=26.72 E-value=2.2e+02 Score=24.70 Aligned_cols=60 Identities=15% Similarity=0.129 Sum_probs=41.6
Q ss_pred CccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCC
Q 044205 20 PCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTY 86 (192)
Q Consensus 20 ~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y 86 (192)
..+|-||..|+-+-+.+...|.+.+.+.|++++++..... ++..+.+ ......+.+|=+-
T Consensus 130 ~~~v~iSl~GEPlL~p~l~eli~~~k~~Gi~~~L~TNG~~------~e~l~~L-~~~~d~i~VSLda 189 (322)
T PRK13762 130 PKHVAISLSGEPTLYPYLPELIEEFHKRGFTTFLVTNGTR------PDVLEKL-EEEPTQLYVSLDA 189 (322)
T ss_pred CCEEEEeCCccccchhhHHHHHHHHHHcCCCEEEECCCCC------HHHHHHH-HhcCCEEEEEccC
Confidence 4578899888877666788888999999999999876532 2334445 3344455566443
No 83
>PRK07933 thymidylate kinase; Validated
Probab=26.26 E-value=1.8e+02 Score=23.43 Aligned_cols=30 Identities=23% Similarity=0.239 Sum_probs=23.0
Q ss_pred EEecccccC--chhHHHHHHHHHhcCCCeeEE
Q 044205 24 FINHRGIDT--KRKVATLLYDHLSRLNLRPFL 53 (192)
Q Consensus 24 FISy~~~D~--~~~fv~~L~~~L~~~gi~vf~ 53 (192)
||.+-|-|. +.+.+..|.+.|+.+|++|..
T Consensus 2 ~IviEG~dGsGKST~~~~L~~~L~~~g~~v~~ 33 (213)
T PRK07933 2 LIAIEGVDGAGKRTLTEALRAALEARGRSVAT 33 (213)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence 677766654 356788999999999988764
No 84
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=26.11 E-value=1.7e+02 Score=25.85 Aligned_cols=60 Identities=17% Similarity=0.228 Sum_probs=38.9
Q ss_pred CCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHH-hcceeEEEecCCCC
Q 044205 19 KPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIR-NCKVGVAVFSPTYC 87 (192)
Q Consensus 19 ~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~-~S~~~Ivv~S~~y~ 87 (192)
-.||+-|.|+.+| |...|.++-- +||.+++|. .|.++.+.....+. ..|+.++=.=..|.
T Consensus 195 lGfD~~idyk~~d----~~~~L~~a~P-~GIDvyfeN----VGg~v~DAv~~~ln~~aRi~~CG~IS~YN 255 (340)
T COG2130 195 LGFDAGIDYKAED----FAQALKEACP-KGIDVYFEN----VGGEVLDAVLPLLNLFARIPVCGAISQYN 255 (340)
T ss_pred cCCceeeecCccc----HHHHHHHHCC-CCeEEEEEc----CCchHHHHHHHhhccccceeeeeehhhcC
Confidence 4789999998654 6767766554 799999985 46666666555554 45555444333443
No 85
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=26.09 E-value=1.1e+02 Score=26.01 Aligned_cols=42 Identities=21% Similarity=0.327 Sum_probs=29.5
Q ss_pred HHHHHHHHhcCCCeeEEeCCCCCCCCc---hHHHHHHHHHhcceeEEEec
Q 044205 37 ATLLYDHLSRLNLRPFLDNKNMKPGDK---LFDNINRAIRNCKVGVAVFS 83 (192)
Q Consensus 37 v~~L~~~L~~~gi~vf~D~~~l~~G~~---~~~~i~~aI~~S~~~Ivv~S 83 (192)
+.+|.+.|...|+.+..-. -.||+ +.+.+..+.++++ +||+|
T Consensus 23 a~~la~~L~~~G~~v~~~~---~VgD~~~~I~~~l~~a~~r~D--~vI~t 67 (255)
T COG1058 23 AAFLADELTELGVDLARIT---TVGDNPDRIVEALREASERAD--VVITT 67 (255)
T ss_pred HHHHHHHHHhcCceEEEEE---ecCCCHHHHHHHHHHHHhCCC--EEEEC
Confidence 7899999999999998743 34554 5556666666644 44555
No 86
>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=25.32 E-value=3.4e+02 Score=22.77 Aligned_cols=84 Identities=13% Similarity=0.054 Sum_probs=53.0
Q ss_pred hhHHHHHHHHHhcCCCeeE-EeCCC--CCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhh-----cCc
Q 044205 34 RKVATLLYDHLSRLNLRPF-LDNKN--MKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMET-----KKK 105 (192)
Q Consensus 34 ~~fv~~L~~~L~~~gi~vf-~D~~~--l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~-----~~~ 105 (192)
..++..+.+.+.+.|+.+- .|... +--|.-..=... .-...++-||.+|.+...+.....+|.+++.. +++
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vPL~~l-~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~~r 168 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITACTLM-GIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQNKR 168 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHHHHHH-cccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcCCe
Confidence 5789999999999999996 66632 444543321111 01246777888998886677777788776652 256
Q ss_pred eeeEEeecCCCcc
Q 044205 106 VIPIFCDIKPSQL 118 (192)
Q Consensus 106 ViPVf~~v~p~~v 118 (192)
|+-|-=+.....+
T Consensus 169 V~iIgSG~lSH~L 181 (271)
T cd07373 169 VAVVGVGGLSGSL 181 (271)
T ss_pred EEEEEecccccCc
Confidence 6655444333334
No 87
>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=24.97 E-value=2.5e+02 Score=19.73 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=21.0
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEE
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFL 53 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~ 53 (192)
||+|.+..|. .. ...+.+.|.+.|++++-
T Consensus 3 vl~s~~~~~k-~~-~~~~~~~l~~~G~~l~a 31 (110)
T cd01424 3 VFISVADRDK-PE-AVEIAKRLAELGFKLVA 31 (110)
T ss_pred EEEEEEcCcH-hH-HHHHHHHHHHCCCEEEE
Confidence 8899887663 33 44777777778888865
No 88
>PF00762 Ferrochelatase: Ferrochelatase; InterPro: IPR001015 Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc. Ferrochelatase catalyses the last step in haem biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protohaem [, ]. In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane. The X-ray structure of Bacillus subtilis and human ferrochelatase have been solved [, ]. The human enzyme exists as a homodimer. Each subunit contains one [2Fe-2S] cluster. The monomer is folded into two similar domains, each with a four-stranded parallel beta-sheet flanked by an alpha-helix in a beta-alpha-beta motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the [2Fe-2S] cluster and in stabilisation of the homodimer. Ferrochelatase seems to have a structurally conserved core region that is common to the enzyme from bacteria, plants and mammals. Porphyrin binds in the identified cleft; this cleft also includes the metal-binding site of the enzyme. It is likely that the structure of the cleft region will have different conformations upon substrate binding and release [].; GO: 0004325 ferrochelatase activity, 0006783 heme biosynthetic process; PDB: 2QD3_B 2HRE_C 3HCN_B 2PNJ_A 2QD1_C 1HRK_A 2QD4_B 3AQI_B 2HRC_B 3HCO_B ....
Probab=24.14 E-value=3.3e+02 Score=23.52 Aligned_cols=66 Identities=17% Similarity=0.277 Sum_probs=44.1
Q ss_pred hHHHHHHHHHhcC--CCeeEEeCCCCCCCCchHHHHHHHHHh---cceeEEEecCCCCCch--hHHHHHHHHHhhc
Q 044205 35 KVATLLYDHLSRL--NLRPFLDNKNMKPGDKLFDNINRAIRN---CKVGVAVFSPTYCQSY--FCLHELALMMETK 103 (192)
Q Consensus 35 ~fv~~L~~~L~~~--gi~vf~D~~~l~~G~~~~~~i~~aI~~---S~~~Ivv~S~~y~~S~--wc~~EL~~~~~~~ 103 (192)
..+..|.+.|... .+.|++ .+.-|.+..++..+.+.+ .++.++.+.|.|..+. -+.+++..+++..
T Consensus 73 ~qa~~l~~~L~~~~~~~~V~~---amry~~P~i~~~l~~l~~~g~~~ivvlPLyPqyS~~ttgs~~~~~~~~~~~~ 145 (316)
T PF00762_consen 73 RQAEALQQRLDERGVDVEVYY---AMRYGPPSIEDALEELKADGVDRIVVLPLYPQYSSSTTGSYLDEVERALKKS 145 (316)
T ss_dssp HHHHHHHHHHHHH-EEEEEEE---EESSSSSBHHHHHHHHHHTT-SEEEEEESSSS--TTTHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhcCCCeeEEE---EeccCCCCHHHHHHHHHHcCCCeEEEEeCCCchhHhhHHHHHHHHHHHHHhc
Confidence 4577777777766 455555 367787777777666663 4667888899998654 4778888887653
No 89
>PF09152 DUF1937: Domain of unknown function (DUF1937); InterPro: IPR015235 This entry is represented by Bacteriophage N15, Gp57. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a set of hypothetical bacterial and phage proteins whose exact function has not, as yet, been described. ; PDB: 1T1J_A.
Probab=24.12 E-value=1.3e+02 Score=22.34 Aligned_cols=68 Identities=13% Similarity=-0.005 Sum_probs=40.5
Q ss_pred HHHHHHHhcCCCeeEEeC--------CCCCCC-----CchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcC
Q 044205 38 TLLYDHLSRLNLRPFLDN--------KNMKPG-----DKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKK 104 (192)
Q Consensus 38 ~~L~~~L~~~gi~vf~D~--------~~l~~G-----~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~ 104 (192)
.+-...|-+.|+.+|--. .-+... .-|.+--..-++.|+.+||.-.|.+..|.=-..|+..+.+.+.
T Consensus 30 ~r~aa~l~~~G~~~fSpv~~sH~~~~~~~~~~~~~~~~~W~~~d~~~L~~c~~lvV~~i~GW~~S~Gi~~Ei~~a~~~~~ 109 (116)
T PF09152_consen 30 NRVAAELLKAGHAAFSPVVMSHPINFELLGDDDPLIQKLWEDWDRPFLDACDELVVLDIPGWDDSEGIWAEIEAAEEMGM 109 (116)
T ss_dssp HHHHHHHHHTT-EEEEHHHHHHHHHCCGTTS-HHHHHHHHHHHHHHHHHH-SEEEE---TTGGG-HHHHHHHHHHHHTT-
T ss_pred HHHHHHHHhcCCeeEeccccccccchhcccccCcchhHHHHHHhHHHHHhcceeEEecCCCccccccHHHHHHHHHHcCC
Confidence 334455667899988641 112122 2233333445678999999999999999999999999999887
Q ss_pred c
Q 044205 105 K 105 (192)
Q Consensus 105 ~ 105 (192)
+
T Consensus 110 ~ 110 (116)
T PF09152_consen 110 P 110 (116)
T ss_dssp E
T ss_pred e
Confidence 3
No 90
>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=24.03 E-value=4.4e+02 Score=22.23 Aligned_cols=66 Identities=9% Similarity=0.027 Sum_probs=39.5
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCC-chHHHHHHHHHhcceeEEEecCCCCCc
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGD-KLFDNINRAIRNCKVGVAVFSPTYCQS 89 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~-~~~~~i~~aI~~S~~~Ivv~S~~y~~S 89 (192)
.|.+-|...+-....+..+...+++.|+.+-... .+.+++ ++.. +...|..++.-+|++.-.....
T Consensus 146 ~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~-~~~~~~~d~~~-~i~~l~~~~~d~v~~~~~~~~~ 212 (347)
T cd06340 146 TVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDI-SYPANARDLTS-EVLKLKAANPDAILPASYTNDA 212 (347)
T ss_pred eEEEEecCchHhHHHHHHHHHHHHHcCCEEEEee-ccCCCCcchHH-HHHHHHhcCCCEEEEcccchhH
Confidence 4666665433334567778888888998876432 355554 4444 4455677666666666554443
No 91
>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=23.52 E-value=1.8e+02 Score=19.54 Aligned_cols=36 Identities=17% Similarity=0.043 Sum_probs=27.7
Q ss_pred CCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeC
Q 044205 19 KPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDN 55 (192)
Q Consensus 19 ~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~ 55 (192)
.+--|+|+|.-.+-. ..-.++.+.|.++|+.|+.-+
T Consensus 15 ~k~~v~i~HG~~eh~-~ry~~~a~~L~~~G~~V~~~D 50 (79)
T PF12146_consen 15 PKAVVVIVHGFGEHS-GRYAHLAEFLAEQGYAVFAYD 50 (79)
T ss_pred CCEEEEEeCCcHHHH-HHHHHHHHHHHhCCCEEEEEC
Confidence 577799999665533 346789999999999998754
No 92
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=23.47 E-value=1.8e+02 Score=23.99 Aligned_cols=68 Identities=15% Similarity=0.217 Sum_probs=26.6
Q ss_pred CccE-EEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHH-Hhcce-eEEEecCCCCCch
Q 044205 20 PCDV-FINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAI-RNCKV-GVAVFSPTYCQSY 90 (192)
Q Consensus 20 ~ydV-FISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI-~~S~~-~Ivv~S~~y~~S~ 90 (192)
.|+| |+-+...+...+|...|...|.+.|+..+.- ..||+.....-.+.+ ++..+ +-++=|+.|.+|.
T Consensus 62 G~~V~Y~~~~~~~~~~s~~~~L~~~~~~~~~~~~~~---~~P~d~~l~~~l~~~~~~~~i~~~~~~~~~Fl~s~ 132 (224)
T PF04244_consen 62 GFRVHYIELDDPENTQSFEDALARALKQHGIDRLHV---MEPGDYRLEQRLESLAQQLGIPLEVLEDPHFLTSR 132 (224)
T ss_dssp T--EEEE-TT-TT--SSHHHHHHHHHHHH----EEE---E--S-HHHHHHHHH----SSS-EEEE--TTSSS-H
T ss_pred CCEEEEEeCCCccccccHHHHHHHHHHHcCCCEEEE---ECCCCHHHHHHHHhhhcccCCceEEeCCCCccCCH
Confidence 5555 4444433333367777777777777665543 346665433333332 22333 4455567777654
No 93
>cd01890 LepA LepA subfamily. LepA belongs to the GTPase family of and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype.
Probab=23.37 E-value=3.1e+02 Score=20.30 Aligned_cols=52 Identities=17% Similarity=0.328 Sum_probs=30.5
Q ss_pred chHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEeecC
Q 044205 63 KLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCDIK 114 (192)
Q Consensus 63 ~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v~ 114 (192)
.+......++..++++|+|++..-..+..-...+..+...+.+++.|.=+.+
T Consensus 79 ~~~~~~~~~~~~ad~~i~v~D~~~~~~~~~~~~~~~~~~~~~~iiiv~NK~D 130 (179)
T cd01890 79 DFSYEVSRSLAACEGALLLVDATQGVEAQTLANFYLALENNLEIIPVINKID 130 (179)
T ss_pred hhHHHHHHHHHhcCeEEEEEECCCCccHhhHHHHHHHHHcCCCEEEEEECCC
Confidence 4566777889999999999986543332222333333334445555544444
No 94
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.
Probab=23.01 E-value=2.6e+02 Score=20.44 Aligned_cols=48 Identities=13% Similarity=0.168 Sum_probs=29.2
Q ss_pred HHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhh---cCceeeEEeecC
Q 044205 66 DNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMET---KKKVIPIFCDIK 114 (192)
Q Consensus 66 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~---~~~ViPVf~~v~ 114 (192)
.++.++|++++++++|++..-..+.+. .++...+.. +++++.|+=+.+
T Consensus 3 ~~~~~~i~~aD~vl~ViD~~~p~~~~~-~~l~~~l~~~~~~k~~iivlNK~D 53 (141)
T cd01857 3 RQLWRVVERSDIVVQIVDARNPLLFRP-PDLERYVKEVDPRKKNILLLNKAD 53 (141)
T ss_pred HHHHHHHhhCCEEEEEEEccCCcccCC-HHHHHHHHhccCCCcEEEEEechh
Confidence 367788999999999988765555442 244444432 455555554433
No 95
>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=22.89 E-value=4.3e+02 Score=21.73 Aligned_cols=59 Identities=12% Similarity=0.059 Sum_probs=34.5
Q ss_pred cEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCC-CchHHHHHHHHHhcceeEEEe
Q 044205 22 DVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPG-DKLFDNINRAIRNCKVGVAVF 82 (192)
Q Consensus 22 dVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G-~~~~~~i~~aI~~S~~~Ivv~ 82 (192)
.|.+-|...+-....+..+.+.|+..|+++-... .+.+| .++... ...|.++..-+|++
T Consensus 137 ~v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~-~~~~~~~d~~~~-l~~i~~~~~~~vi~ 196 (334)
T cd06342 137 KVAIIDDKTAYGQGLADEFKKALKAAGGKVVARE-GTTDGATDFSAI-LTKIKAANPDAVFF 196 (334)
T ss_pred EEEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEe-cCCCCCccHHHH-HHHHHhcCCCEEEE
Confidence 3555555444345567888888888898775433 34555 345444 44566655444444
No 96
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=22.69 E-value=3.4e+02 Score=23.19 Aligned_cols=73 Identities=14% Similarity=0.177 Sum_probs=45.4
Q ss_pred CCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHH
Q 044205 17 AIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHEL 96 (192)
Q Consensus 17 ~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL 96 (192)
....+||-|-|+..+. ...++ +...+.|++.-+-...+..-+ .+.|.++.+. .=+|+||||.-.-..+..|
T Consensus 66 ~~~~~DV~IDFT~P~~---~~~~l-~~~~~~~~~lVIGTTGf~~e~--~~~l~~~a~~---v~vv~a~NfSiGvnll~~l 136 (266)
T COG0289 66 VKADADVLIDFTTPEA---TLENL-EFALEHGKPLVIGTTGFTEEQ--LEKLREAAEK---VPVVIAPNFSLGVNLLFKL 136 (266)
T ss_pred cccCCCEEEECCCchh---hHHHH-HHHHHcCCCeEEECCCCCHHH--HHHHHHHHhh---CCEEEeccchHHHHHHHHH
Confidence 4567899999998763 34444 444456677777654433211 2344444444 6678999998877666655
Q ss_pred HH
Q 044205 97 AL 98 (192)
Q Consensus 97 ~~ 98 (192)
.+
T Consensus 137 ~~ 138 (266)
T COG0289 137 AE 138 (266)
T ss_pred HH
Confidence 43
No 97
>COG0431 Predicted flavoprotein [General function prediction only]
Probab=22.55 E-value=3.8e+02 Score=20.98 Aligned_cols=55 Identities=18% Similarity=0.252 Sum_probs=34.2
Q ss_pred hHHHHHHHHHhcCC-CeeEEeCCC-------CCC-CCc-hHHHHHHHHHhcceeEEEecCCCCCch
Q 044205 35 KVATLLYDHLSRLN-LRPFLDNKN-------MKP-GDK-LFDNINRAIRNCKVGVAVFSPTYCQSY 90 (192)
Q Consensus 35 ~fv~~L~~~L~~~g-i~vf~D~~~-------l~~-G~~-~~~~i~~aI~~S~~~Ivv~S~~y~~S~ 90 (192)
.++..+.+.|...+ +.+..+..+ ... +.+ -...+.++|..++. +++.||.|..|-
T Consensus 18 ~la~~~~~~l~~~~~~~~~~~~~~lP~~~~d~~~~~~p~~v~~~~~~i~~aD~-li~~tPeYn~s~ 82 (184)
T COG0431 18 ALAEAAAKLLPAGGEVEVEFDDLDLPLYNEDLEADGLPPAVQALREAIAAADG-LIIATPEYNGSY 82 (184)
T ss_pred HHHHHHHHhhcccCceEEEecccccCCCCcchhhccCCHHHHHHHHHHHhCCE-EEEECCccCCCC
Confidence 56777888887777 444442212 111 111 14567788888884 567799998873
No 98
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=22.13 E-value=99 Score=23.11 Aligned_cols=46 Identities=22% Similarity=0.286 Sum_probs=34.7
Q ss_pred HHHHHHHHhcceeEEEecCCCCCchhHHH----HHHHHHhhcC--ceeeEEee
Q 044205 66 DNINRAIRNCKVGVAVFSPTYCQSYFCLH----ELALMMETKK--KVIPIFCD 112 (192)
Q Consensus 66 ~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~----EL~~~~~~~~--~ViPVf~~ 112 (192)
..+...+.+|-..-+++.|+|.+. -|.+ ||..+.+.+. .|.||-|-
T Consensus 54 ~~L~~~LCG~~~~~i~IDP~~~~K-GC~~TL~HEL~H~WQ~RsYG~i~PITY~ 105 (141)
T PHA02456 54 RALPQDLCGQFVGWIEIDPDYANK-GCRDTLAHELNHAWQFRTYGLVQPITYA 105 (141)
T ss_pred hhcCcchhhcceeEEEECCccccc-chHHHHHHHHHHHHhhhccceeeeeehh
Confidence 345556778889999999999985 4655 6777776654 89999884
No 99
>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=21.98 E-value=4e+02 Score=22.49 Aligned_cols=55 Identities=13% Similarity=0.047 Sum_probs=28.2
Q ss_pred ccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCC-CchHHHHHHHHHhcce
Q 044205 21 CDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPG-DKLFDNINRAIRNCKV 77 (192)
Q Consensus 21 ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G-~~~~~~i~~aI~~S~~ 77 (192)
..|.|-|...+-....+..+.+.|++.|+.+-... .+.++ .++...+. .|.++..
T Consensus 139 ~~v~ii~~~~~~g~~~~~~~~~~~~~~G~~v~~~~-~~~~~~~d~s~~i~-~i~~~~~ 194 (347)
T cd06335 139 KKVALLLDNTGWGRSNRKDLTAALAARGLKPVAVE-WFNWGDKDMTAQLL-RAKAAGA 194 (347)
T ss_pred CeEEEEeccCchhhhHHHHHHHHHHHcCCeeEEEe-eecCCCccHHHHHH-HHHhCCC
Confidence 34555554433344567777777777777764322 23333 23444443 3444444
No 100
>cd04167 Snu114p Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.
Probab=21.64 E-value=4e+02 Score=20.91 Aligned_cols=88 Identities=13% Similarity=0.041 Sum_probs=45.2
Q ss_pred CCC-chHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEeecCCCcccccccCCCchhHhhhHHHHH
Q 044205 60 PGD-KLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCDIKPSQLLVIDDGKCSANELRRFSWAL 138 (192)
Q Consensus 60 ~G~-~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~v~p~~vr~~~~g~~~~~~~~~W~~aL 138 (192)
||. .+......++..++.+|+|++..-..+.+...-+..+...+.+++.|.=+.+--..+.........+++.+....+
T Consensus 79 pG~~~f~~~~~~~~~~aD~~llVvD~~~~~~~~~~~~~~~~~~~~~p~iiviNK~D~~~~~~~l~~~~~~~~l~~~i~~~ 158 (213)
T cd04167 79 PGHVNFMDEVAAALRLSDGVVLVVDVVEGVTSNTERLIRHAILEGLPIVLVINKIDRLILELKLPPNDAYFKLRHIIDEV 158 (213)
T ss_pred CCCcchHHHHHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECcccCcccccCCHHHHHHHHHHHHHHH
Confidence 443 4566778899999999999986544444432222223333444554444444221111000011124566666666
Q ss_pred HHHHHhcCc
Q 044205 139 EEAKFTVGL 147 (192)
Q Consensus 139 ~~~~~~~G~ 147 (192)
...+...++
T Consensus 159 n~~~~~~~~ 167 (213)
T cd04167 159 NNIIASFST 167 (213)
T ss_pred HHHHHHhcC
Confidence 666655554
No 101
>TIGR03026 NDP-sugDHase nucleotide sugar dehydrogenase. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively.
Probab=21.51 E-value=1.9e+02 Score=25.70 Aligned_cols=58 Identities=12% Similarity=0.137 Sum_probs=37.7
Q ss_pred Eeccc--ccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCc----hHHHHHHHHHhcceeEEEe
Q 044205 25 INHRG--IDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDK----LFDNINRAIRNCKVGVAVF 82 (192)
Q Consensus 25 ISy~~--~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~----~~~~i~~aI~~S~~~Ivv~ 82 (192)
++|.. .|.|++=+-.|.+.|.++|..|...+--...... ..+.+.++++++++.|+.-
T Consensus 321 lafK~~t~d~r~sp~~~~~~~L~~~g~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~ad~~v~~t 384 (411)
T TIGR03026 321 LAFKPNTDDVRESPALDIIELLKEKGAKVKAYDPLVPEEEVKGLPLIDDLEEALKGADALVILT 384 (411)
T ss_pred eEecCCCCccccChHHHHHHHHHhCCCEEEEECCCCChhhhhhcccCCCHHHHHhCCCEEEEec
Confidence 35644 5778888889999999999998775532222110 1135567788888765554
No 102
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=21.47 E-value=1.3e+02 Score=25.84 Aligned_cols=94 Identities=16% Similarity=0.227 Sum_probs=63.9
Q ss_pred CCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCC--CCCCchHHHHHHHH-HhcceeEEEecCCCCCchhHHH
Q 044205 18 IKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNM--KPGDKLFDNINRAI-RNCKVGVAVFSPTYCQSYFCLH 94 (192)
Q Consensus 18 ~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l--~~G~~~~~~i~~aI-~~S~~~Ivv~S~~y~~S~wc~~ 94 (192)
+-++.+=+||.++|. .+|+....-|..+|+.+|+|-.+- .-|.++.+-+.+-- +..-+++.+.|.+|-...|-..
T Consensus 4 ~~~~~~a~~f~~~d~--~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~~~~e~~q~~~~~~~~f~~~~~~r~~~~~~ 81 (329)
T COG4916 4 NVQFEIALSFAGEDR--EYVDRVANLLREAGVTVFYDIFEEANLWGKNLYDYLSEIYQDKALFTIMFISEHYSRKMWTNH 81 (329)
T ss_pred chheeeeeeecCchH--HHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHHHHHHHHhhhhHHHhhhhhccccCcCCCcH
Confidence 445667799999994 579999999999999999975421 12444443222222 2355678889999999999988
Q ss_pred HHHHHHhh-----cCceeeEEeec
Q 044205 95 ELALMMET-----KKKVIPIFCDI 113 (192)
Q Consensus 95 EL~~~~~~-----~~~ViPVf~~v 113 (192)
|+..++.. ...++|-.++.
T Consensus 82 ~~~~~~a~~~~~~~~~~~~~~~~~ 105 (329)
T COG4916 82 ERQAMQARAFQEHQEYILPARFDE 105 (329)
T ss_pred HHHHHHHHHhhhccEEehhhhhcc
Confidence 88766542 23666766653
No 103
>smart00646 Ami_3 Ami_3.
Probab=21.36 E-value=1.1e+02 Score=21.60 Aligned_cols=48 Identities=8% Similarity=0.148 Sum_probs=27.3
Q ss_pred CCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCC--CCCCchHHHHHHHHHh
Q 044205 18 IKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNM--KPGDKLFDNINRAIRN 74 (192)
Q Consensus 18 ~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l--~~G~~~~~~i~~aI~~ 74 (192)
....|+|||......... ...|+.+|+....- ..+..+...|...+..
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 357899999864322111 24699999976532 2344555555544443
No 104
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=21.23 E-value=1.1e+02 Score=26.81 Aligned_cols=33 Identities=27% Similarity=0.391 Sum_probs=26.6
Q ss_pred CCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeC
Q 044205 19 KPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDN 55 (192)
Q Consensus 19 ~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~ 55 (192)
...=|||. |.|+ +|-..|...|-++|++||-.-
T Consensus 28 ~~k~VlIT--GCDS--GfG~~LA~~L~~~Gf~V~Agc 60 (322)
T KOG1610|consen 28 SDKAVLIT--GCDS--GFGRLLAKKLDKKGFRVFAGC 60 (322)
T ss_pred CCcEEEEe--cCCc--HHHHHHHHHHHhcCCEEEEEe
Confidence 34449995 6785 799999999999999998753
No 105
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.23 E-value=4.8e+02 Score=23.84 Aligned_cols=64 Identities=19% Similarity=0.154 Sum_probs=44.8
Q ss_pred CCCCCCccEEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEec
Q 044205 15 NQAIKPCDVFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFS 83 (192)
Q Consensus 15 ~~~~~~ydVFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S 83 (192)
.+.+...||||..-+++. ...+-.+...|+..|+++=+|-. +..+..++..|-+.--.+++++-
T Consensus 330 ~~~~~~~~v~v~~~~~~~-~~~a~~la~~LR~~g~~~~~~~~----~r~~k~q~k~A~~~g~~~~viiG 393 (429)
T COG0124 330 DPVETRVDVYVVPLGEDA-EPEALKLAQKLRAAGISVEVDYS----GRKLKKQFKYADKLGARFAVILG 393 (429)
T ss_pred CCcCCCCCEEEEEcCchh-HHHHHHHHHHHHHcCCcEEEEec----cccHHHHHHHHHHCCCCEEEEEc
Confidence 445778999999988775 35688999999999999988754 22266666666554333444444
No 106
>cd00881 GTP_translation_factor GTP translation factor family. This family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
Probab=21.17 E-value=3.5e+02 Score=20.00 Aligned_cols=53 Identities=13% Similarity=0.123 Sum_probs=32.6
Q ss_pred CCC-chHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcCceeeEEee
Q 044205 60 PGD-KLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCD 112 (192)
Q Consensus 60 ~G~-~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~ 112 (192)
||. .+......++..++.+++|++.....+.+....+..+.+.+.+++.|+=+
T Consensus 70 pG~~~~~~~~~~~~~~~d~~i~v~d~~~~~~~~~~~~~~~~~~~~~~i~iv~nK 123 (189)
T cd00881 70 PGHEDFSSEVIRGLSVSDGAILVVDANEGVQPQTREHLRIAREGGLPIIVAINK 123 (189)
T ss_pred CCcHHHHHHHHHHHHhcCEEEEEEECCCCCcHHHHHHHHHHHHCCCCeEEEEEC
Confidence 553 34556677889999999999987666665544443333334444444433
No 107
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=21.14 E-value=1.5e+02 Score=27.36 Aligned_cols=56 Identities=20% Similarity=0.290 Sum_probs=33.5
Q ss_pred ccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhc
Q 044205 28 RGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETK 103 (192)
Q Consensus 28 ~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~ 103 (192)
+|.|...++ .-+.|++.|+.++...+. +.+.+.. +||.|..+.... .|+..+.+.+
T Consensus 35 sGSD~~~~~---~t~~L~~~G~~i~~gh~~------------~ni~~~~--~VV~s~Ai~~~N---pEi~~A~e~~ 90 (459)
T COG0773 35 SGSDLAESP---MTQRLEALGIEIFIGHDA------------ENILDAD--VVVVSNAIKEDN---PEIVAALERG 90 (459)
T ss_pred ECccccccH---HHHHHHHCCCeEeCCCCH------------HHcCCCc--eEEEecccCCCC---HHHHHHHHcC
Confidence 466665433 567788889988875431 0122222 278888887664 4566666554
No 108
>cd01864 Rab19 Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
Probab=21.14 E-value=3.4e+02 Score=19.87 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=19.6
Q ss_pred CCCc-hHHHHHHHHHhcceeEEEecCCCCCc
Q 044205 60 PGDK-LFDNINRAIRNCKVGVAVFSPTYCQS 89 (192)
Q Consensus 60 ~G~~-~~~~i~~aI~~S~~~Ivv~S~~y~~S 89 (192)
+|.. +.......+..++.++++++..-..|
T Consensus 60 ~G~~~~~~~~~~~~~~~d~~llv~d~~~~~s 90 (165)
T cd01864 60 AGQERFRTITQSYYRSANGAIIAYDITRRSS 90 (165)
T ss_pred CChHHHHHHHHHHhccCCEEEEEEECcCHHH
Confidence 4433 33334556788999999998765443
No 109
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=21.11 E-value=71 Score=21.36 Aligned_cols=34 Identities=21% Similarity=0.344 Sum_probs=19.9
Q ss_pred HHHhc--CCCeeEEeCCCCCCCCchHHHHHHHHHhcce
Q 044205 42 DHLSR--LNLRPFLDNKNMKPGDKLFDNINRAIRNCKV 77 (192)
Q Consensus 42 ~~L~~--~gi~vf~D~~~l~~G~~~~~~i~~aI~~S~~ 77 (192)
..+.. +.+-+++|.+ .+|+.....+.+.+....+
T Consensus 40 ~~~~~~~~~Vii~~D~D--~~G~~~a~~i~~~l~~~gi 75 (81)
T PF13662_consen 40 EKLEKKVKEVIIAFDND--KAGEKAAQKIAKKLLPLGI 75 (81)
T ss_dssp HHHH---SEEEEEEESS--HHHHHHHHHHHHHHG----
T ss_pred HhhhccCceEEEEeCcC--HHHHHHHHHHHHHHHhhcc
Confidence 44444 6677788875 5787777777776654433
No 110
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=21.07 E-value=68 Score=26.06 Aligned_cols=34 Identities=26% Similarity=0.406 Sum_probs=24.3
Q ss_pred cccccCchhHHHHHHHHHhcCCCeeEE-eCCCCCCC
Q 044205 27 HRGIDTKRKVATLLYDHLSRLNLRPFL-DNKNMKPG 61 (192)
Q Consensus 27 y~~~D~~~~fv~~L~~~L~~~gi~vf~-D~~~l~~G 61 (192)
-+|.. +.+.+..|.+.|..+|+++++ |.++++.|
T Consensus 31 LSGsG-KSTiA~ale~~L~~~G~~~y~LDGDnvR~g 65 (197)
T COG0529 31 LSGSG-KSTIANALEEKLFAKGYHVYLLDGDNVRHG 65 (197)
T ss_pred CCCCC-HHHHHHHHHHHHHHcCCeEEEecChhHhhc
Confidence 34433 346899999999999999976 65554433
No 111
>PF13289 SIR2_2: SIR2-like domain
Probab=20.83 E-value=3.1e+02 Score=19.62 Aligned_cols=9 Identities=33% Similarity=0.279 Sum_probs=3.9
Q ss_pred EEEeccccc
Q 044205 23 VFINHRGID 31 (192)
Q Consensus 23 VFISy~~~D 31 (192)
+||.|+..|
T Consensus 90 lfiGys~~D 98 (143)
T PF13289_consen 90 LFIGYSFND 98 (143)
T ss_pred EEEEECCCC
Confidence 344444444
No 112
>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=20.80 E-value=53 Score=22.58 Aligned_cols=31 Identities=13% Similarity=0.167 Sum_probs=18.2
Q ss_pred HHHhcceeEEEecCCCCCchhHHH--HHHHHHhhc
Q 044205 71 AIRNCKVGVAVFSPTYCQSYFCLH--ELALMMETK 103 (192)
Q Consensus 71 aI~~S~~~Ivv~S~~y~~S~wc~~--EL~~~~~~~ 103 (192)
.|++. -|+|||..+.+.+||.. .+..+++..
T Consensus 4 ~i~~~--~vvvf~k~~~~~~~Cp~C~~ak~~L~~~ 36 (90)
T cd03028 4 LIKEN--PVVLFMKGTPEEPRCGFSRKVVQILNQL 36 (90)
T ss_pred hhccC--CEEEEEcCCCCCCCCcHHHHHHHHHHHc
Confidence 34444 45677887777777653 455555543
No 113
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=20.71 E-value=3.4e+02 Score=19.67 Aligned_cols=58 Identities=22% Similarity=0.131 Sum_probs=32.2
Q ss_pred chHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHHhhcC-ceeeEEeecCCCcccc
Q 044205 63 KLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMMETKK-KVIPIFCDIKPSQLLV 120 (192)
Q Consensus 63 ~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~-~ViPVf~~v~p~~vr~ 120 (192)
.+.......+++++.+|+++|.+-.+|---+..+...+.... .-+|+++-....|+..
T Consensus 60 ~~~~~~~~~~~~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivvg~K~D~~~ 118 (162)
T PF00071_consen 60 RFDSLRDIFYRNSDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVVGNKSDLSD 118 (162)
T ss_dssp GGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccceeeeccccccc
Confidence 344334456899999999999776555333333333333222 2356665444455443
No 114
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=20.55 E-value=6.1e+02 Score=22.53 Aligned_cols=87 Identities=15% Similarity=0.195 Sum_probs=54.4
Q ss_pred CCCCCchHHHHHHHHHhcceeEEEecCCCCCchhHHHHHHHHH-hhcCceeeEEeecCCCcccc-------------ccc
Q 044205 58 MKPGDKLFDNINRAIRNCKVGVAVFSPTYCQSYFCLHELALMM-ETKKKVIPIFCDIKPSQLLV-------------IDD 123 (192)
Q Consensus 58 l~~G~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~wc~~EL~~~~-~~~~~ViPVf~~v~p~~vr~-------------~~~ 123 (192)
+..|=.-.+.+..++......|+--.|.--.+.++++-...+. +.+.+|+-+-++.++.++.. ...
T Consensus 178 i~tG~~~LD~~~~G~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~SlEm~~~~i~~R~~~~~~~v~~~~~~~ 257 (434)
T TIGR00665 178 VPTGFTDLDKLTSGLQPSDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFSLEMSAEQLAMRMLSSESRVDSQKLRT 257 (434)
T ss_pred ccCCchhhHhhcCCCCCCeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEeCcCCHHHHHHHHHHHhcCCCHHHhcc
Confidence 4555444455556778888888888899999999998877654 35666655545655554421 112
Q ss_pred CCCchhHhhhHHHHHHHHHHh
Q 044205 124 GKCSANELRRFSWALEEAKFT 144 (192)
Q Consensus 124 g~~~~~~~~~W~~aL~~~~~~ 144 (192)
|.+..+..++...|...+.+.
T Consensus 258 g~l~~~~~~~~~~a~~~l~~~ 278 (434)
T TIGR00665 258 GKLSDEDWEKLTSAAGKLSEA 278 (434)
T ss_pred CCCCHHHHHHHHHHHHHHhcC
Confidence 444555555556666666554
No 115
>TIGR02690 resist_ArsH arsenical resistance protein ArsH. Members of this protein family occur in arsenate resistance operons that include at least two different types of arsenate reductase. ArsH is not required for arsenate resistance in some systems. This family belongs to the larger family of NADPH-dependent FMN reductases (Pfam model pfam03358). The function of ArsH is not known.
Probab=20.40 E-value=4.7e+02 Score=21.46 Aligned_cols=55 Identities=11% Similarity=0.040 Sum_probs=32.7
Q ss_pred hHHHHHHHHHhcCCCee-EEeCCCCC--CC----CchHHHHHHHHHhcceeEEEecCCCCCch
Q 044205 35 KVATLLYDHLSRLNLRP-FLDNKNMK--PG----DKLFDNINRAIRNCKVGVAVFSPTYCQSY 90 (192)
Q Consensus 35 ~fv~~L~~~L~~~gi~v-f~D~~~l~--~G----~~~~~~i~~aI~~S~~~Ivv~S~~y~~S~ 90 (192)
..+..+.+.+...|..+ .+|-.++. .. .+-...+.+.++.++ .+++.||.|..|-
T Consensus 44 ~la~~~~~~~~~~g~~v~~idl~~lPl~~~d~~~~p~v~~l~~~v~~AD-gvii~TPEYn~si 105 (219)
T TIGR02690 44 LLAEEAARLLGCEGRETRIFDPPGLPLPDAAHADHPKVRELRQLSEWSE-GQVWCSPERHGAI 105 (219)
T ss_pred HHHHHHHHHHhhcCCEEEEeCcccCCCCCcCcccCHHHHHHHHHHHhCC-EEEEeCCccccCc
Confidence 35566666666667766 33432222 11 112245667788886 6778899999873
No 116
>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=20.37 E-value=2.4e+02 Score=22.25 Aligned_cols=69 Identities=22% Similarity=0.243 Sum_probs=41.7
Q ss_pred HHhcCCCeeEE-eCCC-C-CCC-CchHHHHHHHHHhcce-----eEEEecCCCCCchhHHHHHHHHHhhcCceeeEEee
Q 044205 43 HLSRLNLRPFL-DNKN-M-KPG-DKLFDNINRAIRNCKV-----GVAVFSPTYCQSYFCLHELALMMETKKKVIPIFCD 112 (192)
Q Consensus 43 ~L~~~gi~vf~-D~~~-l-~~G-~~~~~~i~~aI~~S~~-----~Ivv~S~~y~~S~wc~~EL~~~~~~~~~ViPVf~~ 112 (192)
.|.+.||+..+ |.++ + .+. +.+.+++.+.+++++. -|+|+|-+.-++.--..+-+..++..-. ||||..
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~~lg-Ipvl~h 112 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEKALG-IPVLRH 112 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHHhhC-CcEEEe
Confidence 48999999765 5443 3 233 4577788888877763 3899998865554222233333332212 787743
No 117
>PF09673 TrbC_Ftype: Type-F conjugative transfer system pilin assembly protein; InterPro: IPR019106 This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system (aka type 4 secretion system) for the transfer of plasmid DNA [, ]. The N-terminal portion of these proteins is heterogeneous.
Probab=20.28 E-value=3.5e+02 Score=19.60 Aligned_cols=38 Identities=13% Similarity=0.199 Sum_probs=23.6
Q ss_pred EEEecccccCchhHHHHHHHHHhcCCCeeEEeCCCCCCCCchHH
Q 044205 23 VFINHRGIDTKRKVATLLYDHLSRLNLRPFLDNKNMKPGDKLFD 66 (192)
Q Consensus 23 VFISy~~~D~~~~fv~~L~~~L~~~gi~vf~D~~~l~~G~~~~~ 66 (192)
||+|++-.+. . ...|....++.|+.+-+- .+.+| .+.+
T Consensus 2 iFvS~SMP~~--~-L~~l~~~a~~~~~~~V~R--G~~~g-~~~~ 39 (113)
T PF09673_consen 2 IFVSFSMPDA--S-LRNLLKQAERAGVVVVFR--GFPDG-SFKP 39 (113)
T ss_pred EEEECCCCHH--H-HHHHHHHHHhCCcEEEEE--CCCCC-CHHH
Confidence 7999998773 4 444555555557666553 56766 5544
No 118
>PRK01021 lpxB lipid-A-disaccharide synthase; Reviewed
Probab=20.17 E-value=4.9e+02 Score=24.98 Aligned_cols=94 Identities=14% Similarity=0.241 Sum_probs=55.6
Q ss_pred CCCCCccEEEecccccCchhHHHHHHHHHhc-----------------CCCeeEEeCCCCCC-C--C---------chHH
Q 044205 16 QAIKPCDVFINHRGIDTKRKVATLLYDHLSR-----------------LNLRPFLDNKNMKP-G--D---------KLFD 66 (192)
Q Consensus 16 ~~~~~ydVFISy~~~D~~~~fv~~L~~~L~~-----------------~gi~vf~D~~~l~~-G--~---------~~~~ 66 (192)
..--...+|||= |+.+..-....|.++|++ .|....+|-+++.. | + ....
T Consensus 222 ~~~~~~kIfI~A-GE~SGDlhgA~Li~aLk~~~P~i~~~GvGG~~M~aaG~e~l~d~~eLsVmG~~EVL~~l~~l~~~~~ 300 (608)
T PRK01021 222 KPFSNTSCFISA-GEHSGDTLGGNLLKEIKALYPDIHCFGVGGPQMRAEGFHPLFNMEEFQVSGFWEVLLALFKLWYRYR 300 (608)
T ss_pred ccccCCeEEEEe-ccccHHHHHHHHHHHHHhcCCCcEEEEEccHHHHhCcCcccCChHHhhhhhHHHHHHHHHHHHHHHH
Confidence 344456799994 555554567777777764 35555565554332 1 0 1224
Q ss_pred HHHHHHH--hcceeEEEecCCCCCchhHHHHHHHHHhhcCce-eeEEeecCCCc
Q 044205 67 NINRAIR--NCKVGVAVFSPTYCQSYFCLHELALMMETKKKV-IPIFCDIKPSQ 117 (192)
Q Consensus 67 ~i~~aI~--~S~~~Ivv~S~~y~~S~wc~~EL~~~~~~~~~V-iPVf~~v~p~~ 117 (192)
.+.+.+. +-+++|.|=+|+|.- -+.+.++.. .+ +||+|-+.|+-
T Consensus 301 ~l~~~i~~~kPD~vIlID~PgFNl------rLAK~lkk~-Gi~ipviyYVsPqV 347 (608)
T PRK01021 301 KLYKTILKTNPRTVICIDFPDFHF------LLIKKLRKR-GYKGKIVHYVCPSI 347 (608)
T ss_pred HHHHHHHhcCCCEEEEeCCCCCCH------HHHHHHHhc-CCCCCEEEEECccc
Confidence 4555555 466788887888742 144444333 34 79999999874
Done!