Query 041427
Match_columns 158
No_of_seqs 147 out of 1107
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 06:54:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041427.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041427hhsearch_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 1.1E-42 2.4E-47 261.4 13.3 132 18-157 25-156 (187)
2 PLN03210 Resistant to P. syrin 100.0 8.6E-37 1.9E-41 282.8 14.7 137 17-157 10-155 (1153)
3 smart00255 TIR Toll - interleu 99.9 9E-25 2E-29 157.5 12.5 129 19-150 1-139 (140)
4 PF01582 TIR: TIR domain; Int 99.9 5.9E-26 1.3E-30 165.1 3.1 124 22-146 1-140 (141)
5 PF13676 TIR_2: TIR domain; PD 99.8 1.5E-21 3.3E-26 134.1 3.6 87 22-116 1-87 (102)
6 KOG3678 SARM protein (with ste 99.4 1.4E-12 3.1E-17 110.2 8.0 95 15-116 608-710 (832)
7 PF08937 DUF1863: MTH538 TIR-l 99.1 1.8E-10 4E-15 82.7 6.1 91 20-116 1-108 (130)
8 PF08357 SEFIR: SEFIR domain; 98.3 4.3E-06 9.4E-11 60.9 8.4 65 21-85 2-70 (150)
9 PF10137 TIR-like: Predicted n 97.8 0.00023 5E-09 50.9 8.7 96 21-122 1-111 (125)
10 PF13271 DUF4062: Domain of un 95.6 0.052 1.1E-06 35.7 5.9 66 21-87 1-66 (83)
11 PF05014 Nuc_deoxyrib_tr: Nucl 95.5 0.17 3.8E-06 34.9 8.6 78 33-116 13-98 (113)
12 COG4916 Uncharacterized protei 94.5 0.076 1.6E-06 42.5 4.8 84 15-101 173-262 (329)
13 COG4271 Predicted nucleotide-b 91.8 1.5 3.2E-05 34.0 7.9 94 21-122 84-197 (233)
14 PF14359 DUF4406: Domain of un 89.6 3.9 8.4E-05 27.5 7.8 64 36-101 18-85 (92)
15 cd00860 ThrRS_anticodon ThrRS 87.4 3.1 6.8E-05 26.7 6.1 61 20-85 2-62 (91)
16 PF14258 DUF4350: Domain of un 83.6 8.3 0.00018 23.9 6.6 61 37-111 8-68 (70)
17 cd00738 HGTP_anticodon HGTP an 82.8 6.2 0.00013 25.4 5.9 60 20-84 2-64 (94)
18 PF03129 HGTP_anticodon: Antic 81.4 4.8 0.0001 26.3 5.0 48 33-84 15-62 (94)
19 cd00858 GlyRS_anticodon GlyRS 74.5 12 0.00027 25.8 5.7 64 18-86 25-89 (121)
20 COG4916 Uncharacterized protei 73.1 4.5 9.7E-05 32.6 3.3 98 18-118 5-106 (329)
21 cd00861 ProRS_anticodon_short 71.5 12 0.00027 24.1 4.8 50 33-86 17-66 (94)
22 COG0400 Predicted esterase [Ge 70.6 14 0.00031 28.5 5.6 56 15-72 142-199 (207)
23 cd02426 Pol_gamma_b_Cterm C-te 69.4 6.2 0.00013 28.0 3.2 50 33-86 43-95 (128)
24 COG3613 Nucleoside 2-deoxyribo 68.5 31 0.00066 26.1 6.8 78 34-116 20-107 (172)
25 TIGR00418 thrS threonyl-tRNA s 65.7 22 0.00047 31.4 6.5 62 18-84 469-530 (563)
26 COG0125 Tmk Thymidylate kinase 64.3 51 0.0011 25.5 7.6 99 22-122 4-141 (208)
27 PF05636 HIGH_NTase1: HIGH Nuc 61.8 7.2 0.00016 33.1 2.6 61 57-122 13-81 (388)
28 PRK12325 prolyl-tRNA synthetas 61.2 29 0.00062 29.8 6.3 65 19-87 345-411 (439)
29 cd07373 2A5CPDO_A The alpha su 59.7 64 0.0014 25.7 7.7 78 33-113 90-172 (271)
30 cd00859 HisRS_anticodon HisRS 59.1 41 0.00088 20.9 5.5 58 21-83 3-60 (91)
31 COG0710 AroD 3-dehydroquinate 58.4 45 0.00097 26.3 6.4 84 33-122 78-162 (231)
32 PRK08661 prolyl-tRNA synthetas 55.9 29 0.00063 30.1 5.4 65 18-86 286-356 (477)
33 cd00862 ProRS_anticodon_zinc P 54.1 20 0.00044 27.3 3.8 64 18-85 9-78 (202)
34 PF01990 ATP-synt_F: ATP synth 53.7 42 0.0009 22.2 4.9 58 38-100 8-65 (95)
35 PRK14938 Ser-tRNA(Thr) hydrola 52.9 48 0.001 28.3 6.0 62 18-84 273-334 (387)
36 cd03364 TOPRIM_DnaG_primases T 52.8 22 0.00048 22.5 3.3 26 46-73 44-69 (79)
37 PRK09194 prolyl-tRNA synthetas 52.5 17 0.00036 32.3 3.4 65 18-86 467-533 (565)
38 cd02042 ParA ParA and ParB of 50.2 69 0.0015 20.9 8.9 65 22-86 3-74 (104)
39 PLN03194 putative disease resi 50.0 88 0.0019 23.9 6.6 67 45-116 24-90 (187)
40 cd01423 MGS_CPS_I_III Methylgl 49.9 26 0.00057 23.9 3.5 29 22-52 3-31 (116)
41 PF10087 DUF2325: Uncharacteri 49.7 74 0.0016 21.0 5.8 58 35-94 11-69 (97)
42 PRK14799 thrS threonyl-tRNA sy 49.0 55 0.0012 29.1 6.1 61 19-84 438-498 (545)
43 KOG1136 Predicted cleavage and 48.7 51 0.0011 27.9 5.4 57 56-116 180-242 (501)
44 PLN02530 histidine-tRNA ligase 47.5 59 0.0013 28.3 6.0 61 18-83 400-460 (487)
45 PRK05339 PEP synthetase regula 47.2 53 0.0011 26.6 5.2 70 38-111 158-244 (269)
46 PRK12305 thrS threonyl-tRNA sy 47.0 59 0.0013 28.7 6.1 61 19-84 476-536 (575)
47 PRK00413 thrS threonyl-tRNA sy 45.4 68 0.0015 28.7 6.2 61 19-84 539-599 (638)
48 CHL00201 syh histidine-tRNA sy 44.9 68 0.0015 27.4 5.9 60 19-83 325-384 (430)
49 PF09152 DUF1937: Domain of un 44.1 59 0.0013 22.9 4.5 64 38-101 31-107 (116)
50 cd00138 PLDc Phospholipase D. 44.1 83 0.0018 22.5 5.7 23 61-83 20-42 (176)
51 PRK12444 threonyl-tRNA synthet 43.8 75 0.0016 28.6 6.3 63 18-84 540-602 (639)
52 PF09837 DUF2064: Uncharacteri 43.7 1.1E+02 0.0024 21.3 8.1 85 16-112 7-94 (122)
53 KOG2792 Putative cytochrome C 43.5 25 0.00054 28.4 2.8 33 88-120 152-187 (280)
54 PF03618 Kinase-PPPase: Kinase 43.1 70 0.0015 25.7 5.3 70 38-111 152-240 (255)
55 PRK03991 threonyl-tRNA synthet 42.7 55 0.0012 29.6 5.2 62 19-85 499-560 (613)
56 TIGR02298 HpaD_Fe 3,4-dihydrox 42.7 1.4E+02 0.003 24.1 7.1 79 33-113 96-178 (282)
57 TIGR00408 proS_fam_I prolyl-tR 42.3 63 0.0014 28.1 5.4 65 18-86 281-350 (472)
58 PF09441 Abp2: ARS binding pro 42.2 7.9 0.00017 28.9 -0.1 59 88-147 54-112 (175)
59 PF03437 BtpA: BtpA family; I 41.8 94 0.002 24.9 5.9 100 39-146 133-253 (254)
60 cd07363 45_DOPA_Dioxygenase Th 41.7 1.2E+02 0.0025 24.0 6.4 68 33-102 80-148 (253)
61 TIGR00409 proS_fam_II prolyl-t 41.3 20 0.00044 31.9 2.3 65 19-87 473-539 (568)
62 PF03720 UDPG_MGDP_dh_C: UDP-g 41.2 27 0.00058 23.6 2.4 58 28-85 11-78 (106)
63 cd01424 MGS_CPS_II Methylglyox 40.6 45 0.00096 22.5 3.5 29 22-52 3-31 (110)
64 PF07894 DUF1669: Protein of u 40.0 1.9E+02 0.0042 23.6 7.5 77 47-132 120-197 (284)
65 KOG0117 Heterogeneous nuclear 39.1 31 0.00067 30.0 2.9 60 22-101 128-187 (506)
66 PF03709 OKR_DC_1_N: Orn/Lys/A 38.2 1.2E+02 0.0026 20.7 5.4 71 35-119 5-76 (115)
67 cd00154 Rab Rab family. Rab G 38.1 99 0.0022 20.9 5.1 60 59-119 57-117 (159)
68 COG1658 Small primase-like pro 37.8 80 0.0017 22.6 4.5 55 20-76 30-84 (127)
69 PF02310 B12-binding: B12 bind 36.9 1.3E+02 0.0028 20.1 6.6 57 36-98 17-74 (121)
70 COG2130 Putative NADP-dependen 36.0 85 0.0018 26.2 4.9 52 19-79 196-248 (340)
71 PF08902 DUF1848: Domain of un 35.8 2.4E+02 0.0051 22.8 10.6 134 18-156 46-198 (266)
72 cd01857 HSR1_MMR1 HSR1/MMR1. 35.5 1.5E+02 0.0033 20.6 5.9 34 66-100 4-37 (141)
73 COG1168 MalY Bifunctional PLP- 35.4 73 0.0016 27.2 4.5 46 65-111 148-195 (388)
74 KOG4132 Uroporphyrinogen III s 34.4 54 0.0012 26.1 3.3 50 36-88 145-200 (260)
75 TIGR00334 5S_RNA_mat_M5 ribonu 34.2 79 0.0017 23.9 4.1 65 33-101 35-107 (174)
76 COG2342 Predicted extracellula 34.1 74 0.0016 26.1 4.2 43 66-115 34-79 (300)
77 PF13662 Toprim_4: Toprim doma 33.1 34 0.00074 21.7 1.8 25 46-72 47-71 (81)
78 COG1058 CinA Predicted nucleot 32.9 60 0.0013 26.1 3.5 41 36-79 23-66 (255)
79 PF01915 Glyco_hydro_3_C: Glyc 32.3 2.2E+02 0.0049 21.6 9.3 85 33-122 46-146 (227)
80 PF00350 Dynamin_N: Dynamin fa 31.3 1.8E+02 0.0038 20.5 5.6 46 65-114 120-165 (168)
81 TIGR01101 V_ATP_synt_F vacuola 31.3 63 0.0014 22.7 3.0 48 61-119 46-93 (115)
82 COG1806 Uncharacterized protei 30.8 71 0.0015 25.9 3.6 70 38-111 159-248 (273)
83 PF13289 SIR2_2: SIR2-like dom 30.4 1.4E+02 0.003 20.4 4.8 7 23-29 91-97 (143)
84 PRK07933 thymidylate kinase; V 29.8 1.5E+02 0.0032 22.6 5.2 30 23-52 2-33 (213)
85 PF03358 FMN_red: NADPH-depend 29.8 2E+02 0.0043 20.1 10.0 83 33-118 17-117 (152)
86 cd00532 MGS-like MGS-like doma 29.6 1.5E+02 0.0032 20.1 4.7 61 22-84 2-77 (112)
87 PRK10569 NAD(P)H-dependent FMN 28.9 2.1E+02 0.0045 21.5 5.8 85 33-120 17-112 (191)
88 COG0683 LivK ABC-type branched 28.7 3E+02 0.0065 22.5 7.2 65 21-86 150-214 (366)
89 COG4088 Predicted nucleotide k 27.7 1.4E+02 0.0031 23.7 4.7 73 23-100 6-97 (261)
90 PLN02734 glycyl-tRNA synthetas 27.2 80 0.0017 29.0 3.7 62 16-82 569-630 (684)
91 cd07371 2A5CPDO_AB The alpha a 27.0 3.2E+02 0.007 21.7 8.4 87 24-113 79-169 (268)
92 PF01976 DUF116: Protein of un 27.0 2.3E+02 0.005 20.8 5.6 83 16-117 58-140 (158)
93 PF01269 Fibrillarin: Fibrilla 27.0 77 0.0017 25.0 3.1 25 87-116 106-130 (229)
94 PLN02908 threonyl-tRNA synthet 26.5 1.6E+02 0.0034 27.0 5.4 61 19-84 589-649 (686)
95 COG2077 Tpx Peroxiredoxin [Pos 26.3 48 0.001 24.6 1.7 23 72-94 73-97 (158)
96 cd06340 PBP1_ABC_ligand_bindin 26.3 3E+02 0.0064 22.1 6.7 63 21-84 146-208 (347)
97 PF09413 DUF2007: Domain of un 26.2 73 0.0016 19.3 2.4 23 35-57 11-33 (67)
98 COG0276 HemH Protoheme ferro-l 26.1 3.1E+02 0.0066 22.8 6.6 79 35-116 74-161 (320)
99 COG3340 PepE Peptidase E [Amin 25.7 2.4E+02 0.0051 22.3 5.6 55 21-79 35-90 (224)
100 PF11071 DUF2872: Protein of u 25.4 1.4E+02 0.003 21.7 3.9 40 67-113 66-106 (141)
101 COG4567 Response regulator con 25.1 2.5E+02 0.0054 21.2 5.3 23 32-54 18-40 (182)
102 cd06342 PBP1_ABC_LIVBP_like Ty 24.8 3.4E+02 0.0074 21.2 7.1 52 21-74 137-189 (334)
103 cd01867 Rab8_Rab10_Rab13_like 24.7 2.5E+02 0.0055 19.7 6.1 22 66-87 68-89 (167)
104 KOG2903 Predicted glutathione 23.8 2.2E+02 0.0048 23.3 5.2 97 15-122 33-135 (319)
105 PF02900 LigB: Catalytic LigB 23.6 1.7E+02 0.0036 23.0 4.6 80 33-114 96-180 (272)
106 TIGR02742 TrbC_Ftype type-F co 23.6 2.5E+02 0.0055 20.0 5.1 35 22-61 3-37 (130)
107 KOG1559 Gamma-glutamyl hydrola 23.5 65 0.0014 26.0 2.2 23 103-126 86-108 (340)
108 TIGR00389 glyS_dimeric glycyl- 23.4 3E+02 0.0064 24.7 6.4 64 18-86 456-520 (551)
109 PF05985 EutC: Ethanolamine am 23.4 1.2E+02 0.0025 24.2 3.6 47 33-84 123-173 (237)
110 PRK07283 hypothetical protein; 23.2 2.3E+02 0.005 18.9 4.6 49 30-86 43-91 (98)
111 TIGR03646 YtoQ_fam YtoQ family 23.2 1.6E+02 0.0034 21.4 3.9 40 67-113 69-109 (144)
112 KOG2534 DNA polymerase IV (fam 23.0 3.5E+02 0.0077 22.7 6.3 66 18-83 188-255 (353)
113 PRK02228 V-type ATP synthase s 23.0 1.2E+02 0.0026 20.4 3.2 53 42-99 14-66 (100)
114 PF14528 LAGLIDADG_3: LAGLIDAD 23.0 1.4E+02 0.003 18.5 3.3 31 21-53 21-51 (77)
115 PF02337 Gag_p10: Retroviral G 22.5 77 0.0017 21.3 2.1 21 33-53 8-28 (90)
116 cd07370 HPCD The Class III ext 22.2 4.1E+02 0.0088 21.2 7.9 78 33-113 94-175 (280)
117 COG0773 MurC UDP-N-acetylmuram 22.1 2.4E+02 0.0051 24.7 5.4 55 27-101 35-89 (459)
118 cd02951 SoxW SoxW family; SoxW 22.1 2.2E+02 0.0047 19.2 4.5 31 64-96 3-34 (125)
119 PF03446 NAD_binding_2: NAD bi 22.0 85 0.0018 22.7 2.5 50 35-84 12-68 (163)
120 KOG4598 Putative ubiquitin-spe 21.8 55 0.0012 30.4 1.6 65 87-152 1032-1098(1203)
121 PF01380 SIS: SIS domain SIS d 21.7 1.4E+02 0.0031 20.0 3.4 54 20-86 56-110 (131)
122 cd08584 PI-PLCc_GDPD_SF_unchar 21.5 2.4E+02 0.0052 21.6 4.8 35 50-87 127-161 (192)
123 cd05402 NT_PAP_TUTase Nucleoti 21.3 2.2E+02 0.0048 18.9 4.3 38 11-48 30-68 (114)
124 PRK01189 V-type ATP synthase s 21.2 1.6E+02 0.0034 20.1 3.5 41 42-87 16-57 (104)
125 PRK15057 UDP-glucose 6-dehydro 21.1 2.2E+02 0.0047 24.1 5.0 52 28-79 310-365 (388)
126 PF04244 DPRP: Deoxyribodipyri 20.9 2E+02 0.0044 22.4 4.5 16 34-49 78-93 (224)
127 PF13155 Toprim_2: Toprim-like 20.9 1.6E+02 0.0035 18.9 3.4 39 35-75 34-75 (96)
128 COG0434 SgcQ Predicted TIM-bar 20.7 4.6E+02 0.0099 21.1 6.6 74 40-122 139-219 (263)
129 PF09673 TrbC_Ftype: Type-F co 20.6 2.9E+02 0.0063 18.9 4.9 38 22-65 2-39 (113)
130 TIGR00177 molyb_syn molybdenum 20.6 1.5E+02 0.0031 21.1 3.4 45 34-80 27-73 (144)
131 COG3286 Uncharacterized protei 20.6 3.5E+02 0.0077 20.9 5.5 45 108-152 146-197 (204)
132 PRK15018 1-acyl-sn-glycerol-3- 20.6 92 0.002 24.5 2.5 48 69-116 133-180 (245)
133 cd07362 HPCD_like Class III ex 20.5 4.4E+02 0.0096 21.0 7.5 79 33-113 92-174 (272)
134 cd03411 Ferrochelatase_N Ferro 20.5 3.4E+02 0.0073 19.6 7.1 65 34-101 72-143 (159)
135 PF09419 PGP_phosphatase: Mito 20.4 3.7E+02 0.008 20.0 6.4 69 42-116 35-112 (168)
136 COG0124 HisS Histidyl-tRNA syn 20.4 3.2E+02 0.007 23.6 5.9 63 17-84 333-395 (429)
137 cd06335 PBP1_ABC_ligand_bindin 20.3 4.6E+02 0.0099 21.0 6.7 31 21-51 140-170 (347)
138 cd06386 PBP1_NPR_C_like Ligand 20.2 3.1E+02 0.0068 22.6 5.8 18 36-53 157-174 (387)
139 PF02878 PGM_PMM_I: Phosphoglu 20.1 2.2E+02 0.0048 19.8 4.3 32 20-51 41-72 (137)
140 COG1323 Predicted nucleotidylt 20.1 2.7E+02 0.0059 23.5 5.3 40 57-96 13-59 (358)
141 PF07454 SpoIIP: Stage II spor 20.0 1.4E+02 0.003 24.1 3.5 40 16-55 70-132 (268)
No 1
>PLN03194 putative disease resistance protein; Provisional
Probab=100.00 E-value=1.1e-42 Score=261.40 Aligned_cols=132 Identities=26% Similarity=0.453 Sum_probs=120.4
Q ss_pred CceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHH
Q 041427 18 TKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAK 97 (158)
Q Consensus 18 ~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~ 97 (158)
+.|||||||+++|+++.|+++|+.+|+++||++|+|+.++.+|+.+.+.|.+||++|+++|+||||+|+.|.||++||..
T Consensus 25 ~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCLdEL~~ 104 (187)
T PLN03194 25 KPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCLHELAL 104 (187)
T ss_pred CCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhccCCCceeEEEEEecCCchhhHHhhHHHhhhCHHHHHHHHHHHHHhhccccceec
Q 041427 98 IVECGNKRNDRKVFAVFYGVDPTDRVFAKYEEEFKENHEKVLKWRAALTRVASLAGWHLQ 157 (158)
Q Consensus 98 ~~~~~~~~~~~~iiPV~~~v~p~~v~f~~~~~~~~~~~~~~~~W~~al~~i~~~~G~~~~ 157 (158)
|+++ +..||||||+|+|++|+-... .....+++++||+||++||++.|++++
T Consensus 105 I~e~-----~~~ViPIFY~VdPsdVr~q~~---~~~~~e~v~~Wr~AL~~va~l~G~~~~ 156 (187)
T PLN03194 105 IMES-----KKRVIPIFCDVKPSQLRVVDN---GTCPDEEIRRFNWALEEAKYTVGLTFD 156 (187)
T ss_pred HHHc-----CCEEEEEEecCCHHHhhcccc---CCCCHHHHHHHHHHHHHHhccccccCC
Confidence 9987 568999999999999932111 122478999999999999999999764
No 2
>PLN03210 Resistant to P. syringae 6; Provisional
Probab=100.00 E-value=8.6e-37 Score=282.76 Aligned_cols=137 Identities=42% Similarity=0.786 Sum_probs=126.2
Q ss_pred CCceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHH
Q 041427 17 QTKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELA 96 (158)
Q Consensus 17 ~~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~ 96 (158)
.+.|||||||+++|+|+.|++||+.+|.++||.+|.|+ ++.+|+.+..++.+||++|++.|+|||++|+.|.||++||+
T Consensus 10 ~~~~~vf~sfrg~d~r~~f~~hl~~~l~~~~i~~f~d~-~~~~g~~~~~~l~~~i~~s~~~ivv~s~~ya~s~wcl~el~ 88 (1153)
T PLN03210 10 NWVYDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDN-EIERSQSLDPELKQAIRDSRIAVVVFSKNYASSSWCLNELL 88 (1153)
T ss_pred CCCCcEEeeCCCcccccCHHHHHHHHHHHCCCeEEccC-CccCCCcccHHHHHHHHhCeEEEEEecCCcccchHHHHHHH
Confidence 46899999999999999999999999999999999987 59999999999999999999999999999999999999999
Q ss_pred HHHHhhccCCCceeEEEEEecCCchh---------hHHhhHHHhhhCHHHHHHHHHHHHHhhccccceec
Q 041427 97 KIVECGNKRNDRKVFAVFYGVDPTDR---------VFAKYEEEFKENHEKVLKWRAALTRVASLAGWHLQ 157 (158)
Q Consensus 97 ~~~~~~~~~~~~~iiPV~~~v~p~~v---------~f~~~~~~~~~~~~~~~~W~~al~~i~~~~G~~~~ 157 (158)
.++++ .+.+++.||||||+|+|++| +|.++++. ...+++++||+||++||+++|+++.
T Consensus 89 ~i~~~-~~~~~~~v~pvfy~v~p~~v~~~~g~f~~~f~~~~~~--~~~~~~~~w~~al~~~~~~~g~~~~ 155 (1153)
T PLN03210 89 EIVRC-KEELGQLVIPVFYGLDPSHVRKQTGDFGEAFEKTCQN--KTEDEKIQWKQALTDVANILGYHSQ 155 (1153)
T ss_pred HHHHh-hhhcCceEEEEEecccHHHHhhccchHHHHHHHHhcc--cchhHHHHHHHHHHHHhCcCceecC
Confidence 99999 78889999999999999999 45444433 2468899999999999999999874
No 3
>smart00255 TIR Toll - interleukin 1 - resistance.
Probab=99.92 E-value=9e-25 Score=157.49 Aligned_cols=129 Identities=41% Similarity=0.680 Sum_probs=100.8
Q ss_pred ceeEEEeccc-CcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHH
Q 041427 19 KYDVFLSFRG-EDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAK 97 (158)
Q Consensus 19 ~ydVFISys~-~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~ 97 (158)
.|||||||++ ++....|+.+|...|...|+.+|.|+.....|. ..+|.++|++|+++|+|+||+|+.|+||..|+..
T Consensus 1 ~~dvFISys~~~~~~~~~v~~L~~~l~~~~~~v~~d~~~~~~~~--~~~i~~~i~~s~~~i~vlS~~~~~S~w~~~E~~~ 78 (140)
T smart00255 1 EYDVFISYSGKEDVRNEFLSHLLEKLRGYGLCVFIDDFEPGGGD--LEEIDEAIEKSRIAIVVLSPNYAESEWCLDELVA 78 (140)
T ss_pred CCeEEEECCCCHHHHHHHHHHHHHHhhcCCcEEEecCcccccch--HHHHHHHHHHCcEEEEEECcccccChhHHHHHHH
Confidence 4899999999 344578999999999999999999975433333 3399999999999999999999999999999999
Q ss_pred HHHhhccCCCceeEEEEEecCCchh---------hHHhhHHHhhhCHHHHHHHHHHHHHhhc
Q 041427 98 IVECGNKRNDRKVFAVFYGVDPTDR---------VFAKYEEEFKENHEKVLKWRAALTRVAS 150 (158)
Q Consensus 98 ~~~~~~~~~~~~iiPV~~~v~p~~v---------~f~~~~~~~~~~~~~~~~W~~al~~i~~ 150 (158)
+.++....++.+||||+++..|.++ .+..+...+.+...+ ..|+.++..+.+
T Consensus 79 a~~~~~~~~~~~iIPI~~~~~~~~~~~~~~~l~~~~~~~~~~w~~~~~~-~fW~~~~~~l~~ 139 (140)
T smart00255 79 ALENALEEGGLRVIPIFYEVIPSDVRKQPGKFRKVLKKNYLKWPEDEKE-RFWKKALYAVPS 139 (140)
T ss_pred HHHHHHHcCCCeEEEEEEecChHHHHhcccHHHHHHHHHHhhcCCchhH-HHHHHHHHHhcc
Confidence 9988444477899999999777655 222222333322222 789999888754
No 4
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=99.92 E-value=5.9e-26 Score=165.15 Aligned_cols=124 Identities=33% Similarity=0.568 Sum_probs=101.9
Q ss_pred EEEeccc-CcCchhHHHHHHHHHhcC--CeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHH
Q 041427 22 VFLSFRG-EDTRNNFTDHLHVALIRN--GFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKI 98 (158)
Q Consensus 22 VFISys~-~D~~~~fv~~L~~~L~~~--gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~ 98 (158)
|||||++ +| ++.|+.+|..+|++. |+++|++++|+.+|..+.++|.++|++|+++|+|+|++|+.|.||+.||..|
T Consensus 1 vfisy~~~~d-~~~~~~~L~~~Le~~~~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~~y~~s~wc~~el~~a 79 (141)
T PF01582_consen 1 VFISYSGKDD-REWFVSHLLPELEERPYGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSRNYLSSEWCLFELQEA 79 (141)
T ss_dssp EEEEE-GHHG-HHHHHHCHHHHHHCTSSTS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESHHHHHHTHHHHHHHHH
T ss_pred cEEEeCCCCc-HHHHHHHHHHHHHhCCCCeEEEEechhhcccccccchhhHhhhhceeeEEEeecccccccchhhhhhhh
Confidence 7999999 55 578999999999999 9999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccCC-CceeEEEEEecCCchhh-HHhh--HHHh------hhC---HHHHHHHHHHHH
Q 041427 99 VECGNKRN-DRKVFAVFYGVDPTDRV-FAKY--EEEF------KEN---HEKVLKWRAALT 146 (158)
Q Consensus 99 ~~~~~~~~-~~~iiPV~~~v~p~~v~-f~~~--~~~~------~~~---~~~~~~W~~al~ 146 (158)
++++...+ ..+|+|||+++.++++. .... ...+ ... .+....|++++.
T Consensus 80 ~~~~~~~~~~~~Il~v~~~v~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~fW~~l~~ 140 (141)
T PF01582_consen 80 LERLLEEGRDKLILPVFYDVSPSDVRPDQSLRFLLRFLTYLRWPDDDSREDRSWFWKKLRY 140 (141)
T ss_dssp HHHHHCSTCTTEEEEESSSS-CHHCHTHHHHHHHHHCTHCEETSSSGGGGGHHHHHHHHHH
T ss_pred hhhccccccccceeeEeccCChhhcChhhhHHHHHHhhhheeCCCCCCccHHHHHHHHHhc
Confidence 99965544 68999999999999983 2221 1111 111 457889998875
No 5
>PF13676 TIR_2: TIR domain; PDB: 3H16_B 3UB4_A 2Y92_A 3UB3_A 3UB2_A.
Probab=99.83 E-value=1.5e-21 Score=134.09 Aligned_cols=87 Identities=34% Similarity=0.597 Sum_probs=76.7
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHh
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~ 101 (158)
|||||+++| ..+|..|...|++.|+++|+|. ++.+|+.+.+.|.++|++|+.+|+++||+|..|+||..|+..+.+.
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 VFISYSSED--REFAERLAERLESAGIRVFLDR-DIPPGEDWREEIERAIERSDCVIVLLSPNYLKSPWCRFELGAAWKR 77 (102)
T ss_dssp EEEEEEGGG--CCCHHHHHHHHHHTT--EE-GG-EE-TTS-HHCCCHHCCTTEEEEEEEEEHHHHCTHHHHHHHHHHHCT
T ss_pred eEEEecCCc--HHHHHHHHHHHhhcCCEEEEEE-eCCCCCCHHHHHHHHHHhCCEEEEEECcccccChHHHHHHHHHHHC
Confidence 899999999 4599999999999999999997 8999999999999999999999999999999999999999999654
Q ss_pred hccCCCceeEEEEEe
Q 041427 102 GNKRNDRKVFAVFYG 116 (158)
Q Consensus 102 ~~~~~~~~iiPV~~~ 116 (158)
+++||||.++
T Consensus 78 -----~~~iipv~~~ 87 (102)
T PF13676_consen 78 -----GKPIIPVRLD 87 (102)
T ss_dssp -----SESEEEEECS
T ss_pred -----CCEEEEEEEC
Confidence 6799999975
No 6
>KOG3678 consensus SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures]
Probab=99.37 E-value=1.4e-12 Score=110.19 Aligned_cols=95 Identities=27% Similarity=0.454 Sum_probs=84.0
Q ss_pred CCCCceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC--------
Q 041427 15 ILQTKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA-------- 86 (158)
Q Consensus 15 ~~~~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~-------- 86 (158)
+.+++.||||||++.. ...+++.|.-.|+.+|++||+|-+.+..|.. .+.+.+.|...+.+|+|++|+..
T Consensus 608 ~~skq~DVFISYRRst-GnQLASLiKV~LQL~GyrVFIDVdKL~AGKF-dssLlkni~aAkhFiLVLtP~sLDr~lnD~n 685 (832)
T KOG3678|consen 608 MLSKQIDVFISYRRST-GNQLASLIKVLLQLRGYRVFIDVDKLYAGKF-DSSLLKNIQAAKHFILVLTPNSLDRLLNDDN 685 (832)
T ss_pred cccCCcceEEEeeccc-cHHHHHHHHHHHHhcCceEEEehhhhhcccc-cHHHHHHHHhhheeEEEeCcchHHHHhcccc
Confidence 5568899999998775 4679999999999999999999988999874 56888999999999999999976
Q ss_pred CChhhHHHHHHHHHhhccCCCceeEEEEEe
Q 041427 87 SSPWCLDELAKIVECGNKRNDRKVFAVFYG 116 (158)
Q Consensus 87 ~S~wc~~El~~~~~~~~~~~~~~iiPV~~~ 116 (158)
.-+|+.+||..++++ ++.|||||-.
T Consensus 686 CeDWVHKEl~~Afe~-----~KNIiPI~D~ 710 (832)
T KOG3678|consen 686 CEDWVHKELKCAFEH-----QKNIIPIFDT 710 (832)
T ss_pred HHHHHHHHHHHHHHh-----cCCeeeeecc
Confidence 468999999999999 8899999853
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=99.10 E-value=1.8e-10 Score=82.67 Aligned_cols=91 Identities=24% Similarity=0.425 Sum_probs=50.8
Q ss_pred eeEEEecccCcCchhHHHHHHHHHhcC-------CeEE-E---------ecCCCCCCCccccHHHHHhhhhcceEEEEEe
Q 041427 20 YDVFLSFRGEDTRNNFTDHLHVALIRN-------GFVA-F---------KDDETLDRGNEISSELSKAIEESNVSIVILS 82 (158)
Q Consensus 20 ydVFISys~~D~~~~fv~~L~~~L~~~-------gi~v-f---------~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS 82 (158)
|+|||||++.|.. ..+..|...+... .+.. | -+..+....+.|...|.+.|.+|+++||+++
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 5799999999842 3677777777663 2211 1 2222233445788999999999999999999
Q ss_pred cCCCCChhhHHHHHHHHHhhccCCCceeEEEEEe
Q 041427 83 KNYASSPWCLDELAKIVECGNKRNDRKVFAVFYG 116 (158)
Q Consensus 83 ~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~~~ 116 (158)
++...|.|+.+|+..+++. +.+||.|.+.
T Consensus 80 ~~T~~s~wV~~EI~~A~~~-----~~~Ii~V~~~ 108 (130)
T PF08937_consen 80 PNTAKSKWVNWEIEYALKK-----GKPIIGVYLP 108 (130)
T ss_dssp TT----HHHHHHHHHHTTT--------EEEEETT
T ss_pred CCcccCcHHHHHHHHHHHC-----CCCEEEEECC
Confidence 9999999999999999886 8899999764
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=98.31 E-value=4.3e-06 Score=60.90 Aligned_cols=65 Identities=20% Similarity=0.332 Sum_probs=53.2
Q ss_pred eEEEecccCcCc-hhHHHHHHHHHhcC-CeEEEecCCCCCC--CccccHHHHHhhhhcceEEEEEecCC
Q 041427 21 DVFLSFRGEDTR-NNFTDHLHVALIRN-GFVAFKDDETLDR--GNEISSELSKAIEESNVSIVILSKNY 85 (158)
Q Consensus 21 dVFISys~~D~~-~~fv~~L~~~L~~~-gi~vf~d~~~l~~--G~~i~~~i~~~i~~s~~~IvvlS~~~ 85 (158)
.|||||++.... ...|..|...|++. |+.|.+|..+... +..+..=+.+.+++++.+|+|+||.+
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 499999986544 36789999999999 9999999877743 65666667788999999999999544
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=97.79 E-value=0.00023 Score=50.95 Aligned_cols=96 Identities=20% Similarity=0.252 Sum_probs=72.2
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC-------------CCC
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN-------------YAS 87 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~-------------~~~ 87 (158)
.|||.|+ +| ...+..+...|+..|+.+.+-.+....|..+.+.+.+.+.+++..|++++|+ ...
T Consensus 1 kVFIvhg-~~--~~~~~~v~~~L~~~~~ep~i~~~~~~~g~tiie~le~~~~~~~faIvl~TpDD~~~~~~~~~~~~~~a 77 (125)
T PF10137_consen 1 KVFIVHG-RD--LAAAEAVERFLEKLGLEPIIWHEQPNLGQTIIEKLEEAADSVDFAIVLFTPDDIGYSRGEEEDLQPRA 77 (125)
T ss_pred CEEEEeC-CC--HHHHHHHHHHHHhCCCceEEeecCCCCCCchHHHHHHHhccCCEEEEEEcccccccccCCcccccccc
Confidence 3899998 55 3578899999998888777766667999999999999999999999999995 223
Q ss_pred ChhhHHHHHHHHHhhccCCCceeEEEEEe--cCCchh
Q 041427 88 SPWCLDELAKIVECGNKRNDRKVFAVFYG--VDPTDR 122 (158)
Q Consensus 88 S~wc~~El~~~~~~~~~~~~~~iiPV~~~--v~p~~v 122 (158)
...+..|+..++.++ +..+++-+.-+ --|+|+
T Consensus 78 R~NVifE~G~f~g~L---Gr~rv~~l~~~~v~~PSDl 111 (125)
T PF10137_consen 78 RQNVIFELGLFIGKL---GRERVFILVKGGVELPSDL 111 (125)
T ss_pred ccceeehhhHHHhhc---CcceEEEEEcCCccCCccc
Confidence 456788999988652 33455544432 235555
No 10
>PF13271 DUF4062: Domain of unknown function (DUF4062)
Probab=95.61 E-value=0.052 Score=35.72 Aligned_cols=66 Identities=24% Similarity=0.222 Sum_probs=46.7
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCC
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS 87 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~ 87 (158)
.||||-.-.|.. .--..|.+.+.+.|.....-+.--..+....+.+.+.|++|+++|.++..+|-.
T Consensus 1 rVFiSSt~~Dl~-~eR~~l~~~i~~~~~~~~~~e~~~a~~~~~~~~cl~~v~~cDifI~ilG~rYG~ 66 (83)
T PF13271_consen 1 RVFISSTFRDLK-EERDALIEAIRRLGCEPVGMEFFPASDQSPLEICLKEVDECDIFILILGNRYGS 66 (83)
T ss_pred CEEEecChhhHH-HHHHHHHHHHHHCCCeeeeeeeecCCCCCHHHHHHHHHhhCCEEEEeeccccCC
Confidence 389998888863 445778888877776543322111234555567789999999999999999864
No 11
>PF05014 Nuc_deoxyrib_tr: Nucleoside 2-deoxyribosyltransferase; InterPro: IPR007710 Nucleoside 2-deoxyribosyltransferase (2.4.2.6 from EC) catalyses the cleavage of the glycosidic bonds of 2-deoxyribonucleosides. Nucleoside 2-deoxyribosyltransferases can be divided into two groups based on their substrate specificity: class I enzymes are specific for the transfer of deoxyribose between two purines, while class II enzymes will transfer the deoxyribose between either purines or pyrimidines. The structure of the class I [] and class II [] enzymes are very similar. In class I enzymes, the purine base shields the active site from solvent, which the smaller pyrimidine base cannot do, while in class II enzymes the active site is shielded by a loop (residues 48-62). Both classes of enzymes are found in various Lactobacillus species and participate in nucleoside recycling in these microorganisms. This entry represents both classes of enzymes.; GO: 0050144 nucleoside deoxyribosyltransferase activity, 0070694 deoxyribonucleoside 5'-monophosphate N-glycosidase activity, 0009159 deoxyribonucleoside monophosphate catabolic process; PDB: 1S2L_A 1S2D_C 1S2I_A 1S3F_B 1S2G_C 2A0K_A 2F67_A 2F64_B 2F62_A 2F2T_A ....
Probab=95.53 E-value=0.17 Score=34.89 Aligned_cols=78 Identities=18% Similarity=0.161 Sum_probs=56.3
Q ss_pred hhHHHHHHHHHhcCCeEEEecCC-CCC---CCccc----cHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhcc
Q 041427 33 NNFTDHLHVALIRNGFVAFKDDE-TLD---RGNEI----SSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNK 104 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~~-~l~---~G~~i----~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~ 104 (158)
..+...+.+.|+++|+.++...+ +.. .+..+ .+.-.++|++|+++|+++.+.- .+.-+..|+..|...
T Consensus 13 ~~~~~~~~~~L~~~g~~v~~P~~~~~~~~~~~~~~~~~i~~~d~~~i~~~D~via~l~~~~-~d~Gt~~ElG~A~al--- 88 (113)
T PF05014_consen 13 KARVERLREALEKNGFEVYSPQDNDENDEEDSQEWAREIFERDLEGIRECDIVIANLDGFR-PDSGTAFELGYAYAL--- 88 (113)
T ss_dssp HHHHHHHHHHHHTTTTEEEGGCTCSSS--TTSHHCHHHHHHHHHHHHHHSSEEEEEECSSS---HHHHHHHHHHHHT---
T ss_pred HHHHHHHHHHHHhCCCEEEeccccccccccccchHHHHHHHHHHHHHHHCCEEEEECCCCC-CCCcHHHHHHHHHHC---
Confidence 56889999999999999998652 121 23333 3334568999999999998755 667788999999887
Q ss_pred CCCceeEEEEEe
Q 041427 105 RNDRKVFAVFYG 116 (158)
Q Consensus 105 ~~~~~iiPV~~~ 116 (158)
+++|+-+.-+
T Consensus 89 --gkpv~~~~~d 98 (113)
T PF05014_consen 89 --GKPVILLTED 98 (113)
T ss_dssp --TSEEEEEECC
T ss_pred --CCEEEEEEcC
Confidence 7666655443
No 12
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=94.51 E-value=0.076 Score=42.52 Aligned_cols=84 Identities=20% Similarity=0.137 Sum_probs=60.9
Q ss_pred CCCCceeEEEecccCcCchhHHHHHHHHHhc--CCeEEEecCC---CCCCCccccHHHHHhh-hhcceEEEEEecCCCCC
Q 041427 15 ILQTKYDVFLSFRGEDTRNNFTDHLHVALIR--NGFVAFKDDE---TLDRGNEISSELSKAI-EESNVSIVILSKNYASS 88 (158)
Q Consensus 15 ~~~~~ydVFISys~~D~~~~fv~~L~~~L~~--~gi~vf~d~~---~l~~G~~i~~~i~~~i-~~s~~~IvvlS~~~~~S 88 (158)
+..+.||+=+||.++- +.+|+....+++. .-+..|+|-. -+.+|+ +.+-+...- ..|++.+|++..+|...
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 4567899999999886 5799999999983 4567788743 234443 222222221 47888999999999999
Q ss_pred hhhHHHHHHHHHh
Q 041427 89 PWCLDELAKIVEC 101 (158)
Q Consensus 89 ~wc~~El~~~~~~ 101 (158)
.||.-|...+-..
T Consensus 250 ~~c~~E~~~~r~~ 262 (329)
T COG4916 250 STCHIEGLEGRLN 262 (329)
T ss_pred eeeccchhhcccc
Confidence 9999998776543
No 13
>COG4271 Predicted nucleotide-binding protein containing TIR -like domain [Transcription]
Probab=91.80 E-value=1.5 Score=33.99 Aligned_cols=94 Identities=20% Similarity=0.214 Sum_probs=67.7
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcC--CeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC------------
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRN--GFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA------------ 86 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~--gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~------------ 86 (158)
.|||-|+++. .+.....+|.+. =..+|.|.- +..|..+.+.+.+-|.+++..|++.+|+=.
T Consensus 84 kvFvv~ghd~----iArael~allrd~~l~~vi~d~~-~~~g~~ile~lek~i~~v~FAi~latPDDkgy~~~~~~~k~~ 158 (233)
T COG4271 84 KVFVVSGHDA----IARAELEALLRDWKLEPVILDGL-FSEGQTILESLEKYIAEVKFAIVLATPDDKGYRAVHSREKAF 158 (233)
T ss_pred eEEEEeccHH----HHHHHHHHHhhccccceEEecCc-ccccHHHHHHHHHHhhhceEEEEEecCcccccccccchhhcc
Confidence 8999997653 676677777643 346777764 889999999999999999999999999843
Q ss_pred --CChhhHHHHHHHHHhhccCCCceeEEEEEe----cCCchh
Q 041427 87 --SSPWCLDELAKIVECGNKRNDRKVFAVFYG----VDPTDR 122 (158)
Q Consensus 87 --~S~wc~~El~~~~~~~~~~~~~~iiPV~~~----v~p~~v 122 (158)
....+..||..++.+ -+.++|+-+..+ --|+|+
T Consensus 159 praRqNVifELGm~mgr---LgRkrv~Il~k~~envelPSDi 197 (233)
T COG4271 159 PRARQNVIFELGMFMGR---LGRKRVMILMKRDENVELPSDI 197 (233)
T ss_pred ccccccchhhHhhHHhh---cccceEEEEecccccccCcccc
Confidence 234477899998876 334455444332 236666
No 14
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=89.62 E-value=3.9 Score=27.51 Aligned_cols=64 Identities=9% Similarity=0.049 Sum_probs=44.5
Q ss_pred HHHHHHHHhcCCeEEEecCCC-CCCCccccHHH---HHhhhhcceEEEEEecCCCCChhhHHHHHHHHHh
Q 041427 36 TDHLHVALIRNGFVAFKDDET-LDRGNEISSEL---SKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (158)
Q Consensus 36 v~~L~~~L~~~gi~vf~d~~~-l~~G~~i~~~i---~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~ 101 (158)
.....+.|...|+.|.---.. ...|..+.+-+ ...|.+|+.+++ =|+.-+|+-|+.|+..|.+.
T Consensus 18 f~~~a~~L~~~G~~vvnPa~~~~~~~~~~~~ym~~~l~~L~~cD~i~~--l~gWe~S~GA~~E~~~A~~l 85 (92)
T PF14359_consen 18 FNAAAKRLRAKGYEVVNPAELGIPEGLSWEEYMRICLAMLSDCDAIYM--LPGWENSRGARLEHELAKKL 85 (92)
T ss_pred HHHHHHHHHHCCCEEeCchhhCCCCCCCHHHHHHHHHHHHHhCCEEEE--cCCcccCcchHHHHHHHHHC
Confidence 455788888999766543221 24555554433 345678886555 49999999999999999877
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=87.35 E-value=3.1 Score=26.72 Aligned_cols=61 Identities=10% Similarity=0.126 Sum_probs=40.0
Q ss_pred eeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCC
Q 041427 20 YDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNY 85 (158)
Q Consensus 20 ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~ 85 (158)
++|+|...+++. ...+..+...|.+.|+++-+|.+. ..+...+..|-+.---.++++.++-
T Consensus 2 ~~v~ii~~~~~~-~~~a~~~~~~Lr~~g~~v~~d~~~----~~~~~~~~~a~~~g~~~~iiig~~e 62 (91)
T cd00860 2 VQVVVIPVTDEH-LDYAKEVAKKLSDAGIRVEVDLRN----EKLGKKIREAQLQKIPYILVVGDKE 62 (91)
T ss_pred eEEEEEeeCchH-HHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHHcCCCEEEEECcch
Confidence 677776654432 457889999999999999998753 3444455555444444555555544
No 16
>PF14258 DUF4350: Domain of unknown function (DUF4350)
Probab=83.58 E-value=8.3 Score=23.93 Aligned_cols=61 Identities=15% Similarity=0.163 Sum_probs=38.0
Q ss_pred HHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeE
Q 041427 37 DHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVF 111 (158)
Q Consensus 37 ~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~ii 111 (158)
..|++.|++.|+.+-.... ..+++...+.++++++|.+.-+. -.|+..+.+. .+.|+..||
T Consensus 8 ~a~~~~L~~~g~~v~~~~~-----------~~~~l~~~~~tll~i~~~~~~~~--~~~~~~l~~~-v~~G~~lvl 68 (70)
T PF14258_consen 8 YALYQLLEEQGVKVERWRK-----------PYEALEADDGTLLVIGPDLRLSE--PEEAEALLEW-VEAGNTLVL 68 (70)
T ss_pred HHHHHHHHHCCCeeEEecc-----------cHHHhCCCCCEEEEEeCCCCCCc--hHHHHHHHHH-HHcCCEEEE
Confidence 4577788888988854332 12344558889999999966554 3455555555 334555443
No 17
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=82.79 E-value=6.2 Score=25.38 Aligned_cols=60 Identities=20% Similarity=0.286 Sum_probs=39.7
Q ss_pred eeEEEecccC---cCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 20 YDVFLSFRGE---DTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 20 ydVFISys~~---D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
++|+|-.-+. . ....+..+...|++.|+++-+|.. +..+...+..+-...-.+++++.++
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 5666665433 2 245788899999999999999874 3455555555544444567777764
No 18
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=81.38 E-value=4.8 Score=26.29 Aligned_cols=48 Identities=19% Similarity=0.215 Sum_probs=34.0
Q ss_pred hhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 33 NNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
..++..|...|.+.|+++.+|..+...| ..+.+|-..---+++|+.++
T Consensus 15 ~~~a~~l~~~L~~~gi~v~~d~~~~~~~----k~~~~a~~~g~p~~iiiG~~ 62 (94)
T PF03129_consen 15 IEYAQELANKLRKAGIRVELDDSDKSLG----KQIKYADKLGIPFIIIIGEK 62 (94)
T ss_dssp HHHHHHHHHHHHHTTSEEEEESSSSTHH----HHHHHHHHTTESEEEEEEHH
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCCchh----HHHHHHhhcCCeEEEEECch
Confidence 4688999999999999999997654444 45555554444456666654
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=74.51 E-value=12 Score=25.83 Aligned_cols=64 Identities=16% Similarity=0.079 Sum_probs=42.8
Q ss_pred CceeEEEecccC-cCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 18 TKYDVFLSFRGE-DTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 18 ~~ydVFISys~~-D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
..+||||-.-++ +.....+..|...|.+.|++|-+|.+ ..+...+..|-+.--.+++++.++-.
T Consensus 25 ap~~v~Ii~~~~~~~~~~~a~~la~~LR~~gi~v~~d~~-----~sl~kqlk~A~k~g~~~~iiiG~~e~ 89 (121)
T cd00858 25 APIKVAVLPLVKRDELVEIAKEISEELRELGFSVKYDDS-----GSIGRRYARQDEIGTPFCVTVDFDTL 89 (121)
T ss_pred CCcEEEEEecCCcHHHHHHHHHHHHHHHHCCCEEEEeCC-----CCHHHHHHHhHhcCCCEEEEECcCch
Confidence 457888877652 12245778899999999999999864 24444555665544556777776643
No 20
>COG4916 Uncharacterized protein containing a TIR (Toll-Interleukin 1-resistance) domain [Function unknown]
Probab=73.08 E-value=4.5 Score=32.65 Aligned_cols=98 Identities=20% Similarity=0.343 Sum_probs=70.2
Q ss_pred CceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCC--CCCCccccHHHHHhhh--hcceEEEEEecCCCCChhhHH
Q 041427 18 TKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDET--LDRGNEISSELSKAIE--ESNVSIVILSKNYASSPWCLD 93 (158)
Q Consensus 18 ~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~--l~~G~~i~~~i~~~i~--~s~~~IvvlS~~~~~S~wc~~ 93 (158)
.++.+=+||.++| ..+++....-|...|+.+|+|-.+ =..|.++.+-+. .|. ..-..+.++|.+|-...|...
T Consensus 5 ~~~~~a~~f~~~d--~~~~~~~~n~~~~~~v~~~y~~~~~a~~~~~~~~~~~~-e~~q~~~~~~~~f~~~~~~r~~~~~~ 81 (329)
T COG4916 5 VQFEIALSFAGED--REYVDRVANLLREAGVTVFYDIFEEANLWGKNLYDYLS-EIYQDKALFTIMFISEHYSRKMWTNH 81 (329)
T ss_pred hheeeeeeecCch--HHHHHHHHHHHHhhccEEEEeehhhhhhhhhHHHHHHH-HHHhhhhHHHhhhhhccccCcCCCcH
Confidence 4566779999888 468999999999999999998532 124444443222 232 344568889999999999999
Q ss_pred HHHHHHHhhccCCCceeEEEEEecC
Q 041427 94 ELAKIVECGNKRNDRKVFAVFYGVD 118 (158)
Q Consensus 94 El~~~~~~~~~~~~~~iiPV~~~v~ 118 (158)
|++.++.+........++|-.++.-
T Consensus 82 ~~~~~~a~~~~~~~~~~~~~~~~~~ 106 (329)
T COG4916 82 ERQAMQARAFQEHQEYILPARFDET 106 (329)
T ss_pred HHHHHHHHHhhhccEEehhhhhccC
Confidence 9998887744555567777777533
No 21
>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=71.52 E-value=12 Score=24.12 Aligned_cols=50 Identities=16% Similarity=0.140 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 33 NNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
...+..|...|++.|+++.+|.+.-. +...+..+-..---+++++.++-.
T Consensus 17 ~~~a~~la~~Lr~~g~~v~~d~~~~~----l~k~i~~a~~~g~~~~iiiG~~e~ 66 (94)
T cd00861 17 QELAEKLYAELQAAGVDVLLDDRNER----PGVKFADADLIGIPYRIVVGKKSA 66 (94)
T ss_pred HHHHHHHHHHHHHCCCEEEEECCCCC----cccchhHHHhcCCCEEEEECCchh
Confidence 45788999999999999999876433 444455554444445666665543
No 22
>COG0400 Predicted esterase [General function prediction only]
Probab=70.55 E-value=14 Score=28.54 Aligned_cols=56 Identities=21% Similarity=0.107 Sum_probs=43.3
Q ss_pred CCCCceeEEEecccCcC--chhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhh
Q 041427 15 ILQTKYDVFLSFRGEDT--RNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIE 72 (158)
Q Consensus 15 ~~~~~ydVFISys~~D~--~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~ 72 (158)
...+..-|||+|-..|. -.....+|.+.|+..|..|.... ...|..+..+-.++++
T Consensus 142 ~~~~~~pill~hG~~Dpvvp~~~~~~l~~~l~~~g~~v~~~~--~~~GH~i~~e~~~~~~ 199 (207)
T COG0400 142 PDLAGTPILLSHGTEDPVVPLALAEALAEYLTASGADVEVRW--HEGGHEIPPEELEAAR 199 (207)
T ss_pred cccCCCeEEEeccCcCCccCHHHHHHHHHHHHHcCCCEEEEE--ecCCCcCCHHHHHHHH
Confidence 34567889999998886 35678999999999999999876 4478888765554443
No 23
>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=69.44 E-value=6.2 Score=28.02 Aligned_cols=50 Identities=8% Similarity=0.087 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHhcCCeEEEecCCCC---CCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 33 NNFTDHLHVALIRNGFVAFKDDETL---DRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~~~l---~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
...+..|+..|+..|+++++|+++- .+|..+.+.-.-++ =+.+++.++.+
T Consensus 43 ~~~a~~l~~~L~~~gi~v~~D~r~~~~~~~G~k~~~~dliGi----P~~I~IG~~~l 95 (128)
T cd02426 43 RDLCQGLKNELREAGLSVWPGYLETQHSSLEQLLDKYDEMGV----LFTLLISEQTL 95 (128)
T ss_pred HHHHHHHHHHHHHcCCEEEeccCcccccCHHHHHHhhhhcCC----CEEEEECCCcc
Confidence 5678999999999999999998764 45555433222121 24555566554
No 24
>COG3613 Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]
Probab=68.55 E-value=31 Score=26.06 Aligned_cols=78 Identities=17% Similarity=0.189 Sum_probs=55.3
Q ss_pred hHHHHHHHHHhcCCeEEEec------CCCCCC---CccccHHHHHhhhhcceEEEEEecCC-CCChhhHHHHHHHHHhhc
Q 041427 34 NFTDHLHVALIRNGFVAFKD------DETLDR---GNEISSELSKAIEESNVSIVILSKNY-ASSPWCLDELAKIVECGN 103 (158)
Q Consensus 34 ~fv~~L~~~L~~~gi~vf~d------~~~l~~---G~~i~~~i~~~i~~s~~~IvvlS~~~-~~S~wc~~El~~~~~~~~ 103 (158)
...+.|.+.|.+.|+.++.- ..+..+ +..|.+.-.+.|.+|+++|.++.+-= ....-...|+..+...
T Consensus 20 ~~~d~lkall~~~gf~~~~P~d~~~~~~~~~p~~~a~~i~e~d~~~i~~aD~vla~ld~fr~~~DsGTa~E~GYa~Al-- 97 (172)
T COG3613 20 ELRDELKALLLEAGFEVLSPFDEAEPIAETGPNETAEKIYEADIKLIDQADIVLANLDPFRPDPDSGTAFELGYAIAL-- 97 (172)
T ss_pred HHHHHHHHHHHHcCCeeeCcchhccCccccCccHHHHHHHHHHHHHHhhcCEEEEecCCCCCCCCCcchHHHHHHHHc--
Confidence 46788899999999998875 222333 22344444567999999999998765 1223456799999887
Q ss_pred cCCCceeEEEEEe
Q 041427 104 KRNDRKVFAVFYG 116 (158)
Q Consensus 104 ~~~~~~iiPV~~~ 116 (158)
++++++.+-+
T Consensus 98 ---gKPv~~~~~d 107 (172)
T COG3613 98 ---GKPVYAYRKD 107 (172)
T ss_pred ---CCceEEEeec
Confidence 8899987754
No 25
>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=65.68 E-value=22 Score=31.37 Aligned_cols=62 Identities=11% Similarity=0.208 Sum_probs=44.1
Q ss_pred CceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 18 TKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 18 ~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
...||+|-.-+++ ....+..|...|++.|++|-+|.+ +..+...+..|-+.---.++|+.++
T Consensus 469 ~p~~v~vi~~~~~-~~~~a~~ia~~LR~~Gi~v~~d~~----~~sl~~q~k~A~~~g~~~~iiiG~~ 530 (563)
T TIGR00418 469 APVQVVVIPVNER-HLDYAKKVAQKLKKAGIRVDVDDR----NERLGKKIREAQKQKIPYMLVVGDK 530 (563)
T ss_pred CCceEEEEEccch-HHHHHHHHHHHHHHcCCEEEEECC----CCCHHHHHHHHHhcCCCEEEEEchh
Confidence 4578888765543 356889999999999999999875 4456666666655544566666654
No 26
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=64.29 E-value=51 Score=25.46 Aligned_cols=99 Identities=14% Similarity=0.220 Sum_probs=60.2
Q ss_pred EEEecccCcCc--hhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhh--------------------------
Q 041427 22 VFLSFRGEDTR--NNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEE-------------------------- 73 (158)
Q Consensus 22 VFISys~~D~~--~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~-------------------------- 73 (158)
.||.+-+-|.. .+.+..|.+.|+.+|+.|.+-.+ ..|.++.+.|.+.+.+
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 58888666642 56889999999999998877542 2222333333332221
Q ss_pred ---cceEEEEEecCCCCChhhHH--------HHHHHHHhhccCCCceeEEEEEecCCchh
Q 041427 74 ---SNVSIVILSKNYASSPWCLD--------ELAKIVECGNKRNDRKVFAVFYGVDPTDR 122 (158)
Q Consensus 74 ---s~~~IvvlS~~~~~S~wc~~--------El~~~~~~~~~~~~~~iiPV~~~v~p~~v 122 (158)
-.-.-+|++..|.-|.-+.. +....+......+-.+=+.++++++|..-
T Consensus 82 ~pal~~g~vVI~DRy~~Ss~AYQg~~~~~~~~~~~~l~~~~~~~~~PD~ti~Ldv~~e~a 141 (208)
T COG0125 82 KPALKEGKVVICDRYVDSSLAYQGGGRGLDLDWVLALNEFAPGGLKPDLTLYLDVPPEVA 141 (208)
T ss_pred HHhhcCCCEEEECCcccHHHHhhhhccCCCHHHHHHHHHhccCCCCCCEEEEEeCCHHHH
Confidence 01124788999987777665 33333333233233567788889988775
No 27
>PF05636 HIGH_NTase1: HIGH Nucleotidyl Transferase; InterPro: IPR008513 This family consists of several bacterial proteins of unknown function.; PDB: 3GMI_A.
Probab=61.78 E-value=7.2 Score=33.10 Aligned_cols=61 Identities=23% Similarity=0.413 Sum_probs=26.9
Q ss_pred CCCCccccHHHHHhhhhcceEEEEEecCCCC-------ChhhHHHHHHHHHhhccCCCcee-EEEEEecCCchh
Q 041427 57 LDRGNEISSELSKAIEESNVSIVILSKNYAS-------SPWCLDELAKIVECGNKRNDRKV-FAVFYGVDPTDR 122 (158)
Q Consensus 57 l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~-------S~wc~~El~~~~~~~~~~~~~~i-iPV~~~v~p~~v 122 (158)
+.-|...+-+-.+.+-.++++|+|+|-||++ ++|.+-|+...... +.+| +|+.|-+.+.+.
T Consensus 13 FHnGH~y~i~~~k~~~~ad~ii~vMSGnFvQRGEPAi~dKw~RA~~AL~~Ga-----DLViELP~~~a~qsA~~ 81 (388)
T PF05636_consen 13 FHNGHLYQIEQAKKITGADVIIAVMSGNFVQRGEPAIIDKWTRAEMALKNGA-----DLVIELPVVYALQSAEY 81 (388)
T ss_dssp --HHHHHHHHHHH---TSSEEEEEE--TTSBTSSB-SS-HHHHHHHHHHHT------SEEEE---G--------
T ss_pred ccHHHHHHHHHHhccCCCCEEEEEECCCcccCCCeeeCCHHHHHHHHHHcCC-----CEEEECCCccccccccc
Confidence 4445544322234456889999999999985 78888876654332 4444 798888777775
No 28
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=61.23 E-value=29 Score=29.80 Aligned_cols=65 Identities=14% Similarity=0.085 Sum_probs=42.7
Q ss_pred ceeEEEeccc--CcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCC
Q 041427 19 KYDVFLSFRG--EDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS 87 (158)
Q Consensus 19 ~ydVFISys~--~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~ 87 (158)
.++|+|---. .+.....+..|...|.+.|++|.+|+++-..|. .+..+-..---+++|+.++-..
T Consensus 345 P~qV~Iipi~~~~~~~~~~a~~i~~~L~~~Gi~v~~D~~~~~lg~----ki~~a~~~giP~~iiVG~~e~~ 411 (439)
T PRK12325 345 PFKVGIINLKQGDEACDAACEKLYAALSAAGIDVLYDDTDERPGA----KFATMDLIGLPWQIIVGPKGLA 411 (439)
T ss_pred CeEEEEEecCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHhH----HHHHHHHcCCCEEEEECCcccc
Confidence 4788876542 222356789999999999999999987655554 4444433333466677766543
No 29
>cd07373 2A5CPDO_A The alpha subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO) catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the alpha subunit, which does not contain a potential metal binding site and may not possess catalytic activity.
Probab=59.73 E-value=64 Score=25.74 Aligned_cols=78 Identities=19% Similarity=0.220 Sum_probs=52.3
Q ss_pred hhHHHHHHHHHhcCCeEEE-ecCCC--CCCCccccHHHHHhh-h-hcceEEEEEecCCCCChhhHHHHHHHHHhhccCCC
Q 041427 33 NNFTDHLHVALIRNGFVAF-KDDET--LDRGNEISSELSKAI-E-ESNVSIVILSKNYASSPWCLDELAKIVECGNKRND 107 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf-~d~~~--l~~G~~i~~~i~~~i-~-~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~ 107 (158)
.+++..|.+.|.+.|+.+- +|... +--|--+. ..-+ . ..++-||.+|.+...+.....+|..++....+..+
T Consensus 90 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP---L~~l~~~~~~iPvV~~s~~~~~~~~~~~~lG~al~~~l~~~~ 166 (271)
T cd07373 90 TALAEACVTACPEHGVHARGVDYDGFPIDTGTITA---CTLMGIGTEALPLVVASNNLYHSGEITEKLGAIAADAAKDQN 166 (271)
T ss_pred HHHHHHHHHHHHHCCCcEEEecCCCCCCcchhHHH---HHHHcccCCCCCEEEEEeCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 6799999999999999986 66633 33343222 2223 2 45676788998887788888899998884223334
Q ss_pred ceeEEE
Q 041427 108 RKVFAV 113 (158)
Q Consensus 108 ~~iiPV 113 (158)
++|+-|
T Consensus 167 ~rV~iI 172 (271)
T cd07373 167 KRVAVV 172 (271)
T ss_pred CeEEEE
Confidence 566544
No 30
>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=59.07 E-value=41 Score=20.85 Aligned_cols=58 Identities=22% Similarity=0.151 Sum_probs=35.1
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEec
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSK 83 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~ 83 (158)
||||...++. ...-+-.+...|.+.|++|.++... ..+...+..+-...-..++++.+
T Consensus 3 ~v~i~~~~~~-~~~~a~~i~~~Lr~~g~~v~~~~~~----~~~~~~~~~a~~~~~~~~i~i~~ 60 (91)
T cd00859 3 DVYVVPLGEG-ALSEALELAEQLRDAGIKAEIDYGG----RKLKKQFKYADRSGARFAVILGE 60 (91)
T ss_pred cEEEEEcChH-HHHHHHHHHHHHHHCCCEEEEecCC----CCHHHHHHHHHHcCCCEEEEEcH
Confidence 6777654443 2345778899999999999987643 12344444443333345566655
No 31
>COG0710 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]
Probab=58.37 E-value=45 Score=26.35 Aligned_cols=84 Identities=18% Similarity=0.158 Sum_probs=50.8
Q ss_pred hhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCc-eeE
Q 041427 33 NNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDR-KVF 111 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~-~ii 111 (158)
+.....|.+..+.+| ..|+|-+-..+++.+ .++...-.+-. +|+|-|.+.+.+..+|+...+..|...+.. .-|
T Consensus 78 ~~~i~ll~~la~~~~-~d~iDiEl~~~~~~~-~~~~~~~~~~~---vI~SyH~F~~TP~~~~i~~~l~km~~~~aDivKi 152 (231)
T COG0710 78 EEYIELLKKLAELNG-PDYIDIELSSPEDDV-KEIIKFAKKHG---VIVSYHDFEKTPPLEEIIERLDKMESLGADIVKI 152 (231)
T ss_pred HHHHHHHHHHHhhcC-CCEEEEEccCcchhH-HHHHhccccCC---EEEEeccCCCCCcHHHHHHHHHHHHhhCCCeEEE
Confidence 445666666666666 667776423333322 23333223333 888999999999999999999987666533 334
Q ss_pred EEEEecCCchh
Q 041427 112 AVFYGVDPTDR 122 (158)
Q Consensus 112 PV~~~v~p~~v 122 (158)
+|- -.+..|+
T Consensus 153 Avm-~~~~~Dv 162 (231)
T COG0710 153 AVM-PQSKEDV 162 (231)
T ss_pred Eec-CCCHHHH
Confidence 433 3345555
No 32
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=55.86 E-value=29 Score=30.15 Aligned_cols=65 Identities=11% Similarity=0.026 Sum_probs=41.6
Q ss_pred CceeEEEeccc-----CcCchhHHHHHHHHHhcCCeEEEecC-CCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 18 TKYDVFLSFRG-----EDTRNNFTDHLHVALIRNGFVAFKDD-ETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 18 ~~ydVFISys~-----~D~~~~fv~~L~~~L~~~gi~vf~d~-~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
..++|+|---. .+.....+..|...|++.|++|-+|+ ++-.+|.. +.++-..---+++++.++-.
T Consensus 286 AP~qV~Iipi~~~~~~~~~~~~~a~~l~~~Lr~~GirV~lD~r~~~s~gkK----~~~ae~~GvP~~IiIG~~el 356 (477)
T PRK08661 286 APIQVVIVPIFKKEEKKEEVLEYAKELAEELKKAGIRVKLDDRSDKTPGWK----FNEWELKGVPLRIEIGPRDL 356 (477)
T ss_pred CCCeEEEEEecCCCcCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHH----HHHHHHCCCCEEEEECcchh
Confidence 35888876531 11124578999999999999999998 44555554 44443333345666676643
No 33
>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=54.14 E-value=20 Score=27.33 Aligned_cols=64 Identities=14% Similarity=0.032 Sum_probs=41.3
Q ss_pred CceeEEEecccCcC-----chhHHHHHHHHHhcCCeEEEecCCCC-CCCccccHHHHHhhhhcceEEEEEecCC
Q 041427 18 TKYDVFLSFRGEDT-----RNNFTDHLHVALIRNGFVAFKDDETL-DRGNEISSELSKAIEESNVSIVILSKNY 85 (158)
Q Consensus 18 ~~ydVFISys~~D~-----~~~fv~~L~~~L~~~gi~vf~d~~~l-~~G~~i~~~i~~~i~~s~~~IvvlS~~~ 85 (158)
..++|+|---..+. -...+..|...|...|+++.+|.++- .+|..+.+ +-..---+++++.|+-
T Consensus 9 AP~qVvIipi~~~~~~~~~~~~~a~~i~~~Lr~~Girv~~D~r~~~s~g~K~~~----ae~~GvP~~I~IG~~E 78 (202)
T cd00862 9 APIQVVIVPIGIKDEKREEVLEAADELAERLKAAGIRVHVDDRDNYTPGWKFND----WELKGVPLRIEIGPRD 78 (202)
T ss_pred cCceEEEEEecCCccchHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHhHHHHH----HHhCCCCEEEEECcch
Confidence 34677776433220 24578999999999999999998765 77775543 3233333566666663
No 34
>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=53.67 E-value=42 Score=22.21 Aligned_cols=58 Identities=19% Similarity=0.292 Sum_probs=40.7
Q ss_pred HHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHH
Q 041427 38 HLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVE 100 (158)
Q Consensus 38 ~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~ 100 (158)
.+...++..|+..+... ...+...+.+.+.+++-++.|++++++.... -..++....+
T Consensus 8 ~~v~gFrLaGv~~~~~~---~~~ee~~~~l~~l~~~~~~gIIii~e~~~~~--~~~~l~~~~~ 65 (95)
T PF01990_consen 8 DTVLGFRLAGVEGVYVN---TDPEEAEEALKELLKDEDVGIIIITEDLAEK--IRDELDEYRE 65 (95)
T ss_dssp HHHHHHHHTTSEEEEES---HSHHHHHHHHHHHHHHTTEEEEEEEHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHcCCCCccCC---CCHHHHHHHHHHHhcCCCccEEEeeHHHHHH--HHHHHHHHHh
Confidence 34556677899988875 1244556677777889999999999999884 4445555443
No 35
>PRK14938 Ser-tRNA(Thr) hydrolase; Provisional
Probab=52.88 E-value=48 Score=28.28 Aligned_cols=62 Identities=16% Similarity=0.173 Sum_probs=42.2
Q ss_pred CceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 18 TKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 18 ~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
..++|+|-.-+++ ....+..|...|++.|+++.+|.. +..+...+..|-+.---.++++.++
T Consensus 273 AP~qV~IIpl~ee-l~e~AlkLA~eLR~aGIrVeiDl~----srSLgKQiK~AdK~GaPfvIIIGed 334 (387)
T PRK14938 273 NPIQVRILPVKKD-FLDFSIQVAERLRKEGIRVNVDDL----DDSLGNKIRRAGTEWIPFVIIIGER 334 (387)
T ss_pred CcceEEEEEeChH-HHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECch
Confidence 3577777665554 345788999999999999999874 3455556666655444455666544
No 36
>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=52.83 E-value=22 Score=22.51 Aligned_cols=26 Identities=8% Similarity=0.143 Sum_probs=11.2
Q ss_pred CCeEEEecCCCCCCCccccHHHHHhhhh
Q 041427 46 NGFVAFKDDETLDRGNEISSELSKAIEE 73 (158)
Q Consensus 46 ~gi~vf~d~~~l~~G~~i~~~i~~~i~~ 73 (158)
+.+.+|+|.. .+|.....++.+.+..
T Consensus 44 ~~vii~~D~D--~aG~~a~~~~~~~l~~ 69 (79)
T cd03364 44 KEVILAFDGD--EAGQKAALRALELLLK 69 (79)
T ss_pred CeEEEEECCC--HHHHHHHHHHHHHHHH
Confidence 3455555542 3444444444444333
No 37
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=52.45 E-value=17 Score=32.32 Aligned_cols=65 Identities=14% Similarity=0.167 Sum_probs=42.5
Q ss_pred CceeEEEeccc-C-cCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 18 TKYDVFLSFRG-E-DTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 18 ~~ydVFISys~-~-D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
..++|+|---. + +.....+..|+..|++.|+++.+|+++-.+|..+. .+=..---+++++.++..
T Consensus 467 aP~~v~Iv~~~~~~~~~~~~a~~i~~~L~~~gi~v~~Ddr~~~~g~k~~----~ad~~GiP~~iiiG~~e~ 533 (565)
T PRK09194 467 APFDVHIVPVNMKDEEVKELAEKLYAELQAAGIEVLLDDRKERPGVKFA----DADLIGIPHRIVVGDRGL 533 (565)
T ss_pred CCceEEEEECCCCcHHHHHHHHHHHHHHhccCCeEEEECCCCCHHHHHH----HHHhcCCCEEEEEcCccc
Confidence 45889887543 2 22246789999999999999999998655565443 332222235666676644
No 38
>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=50.21 E-value=69 Score=20.85 Aligned_cols=65 Identities=12% Similarity=0.104 Sum_probs=40.3
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCC-------CCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLD-------RGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~-------~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
+|.+..+.-.+..++.+|...|.++|.++.+-+-|.. -+..+......++..|+.+|+++.++..
T Consensus 3 ~~~~~kgG~Gkst~~~~la~~~~~~~~~vl~~d~d~~~d~viiD~p~~~~~~~~~~l~~ad~viv~~~~~~~ 74 (104)
T cd02042 3 AVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPL 74 (104)
T ss_pred EEEeCCCCcCHHHHHHHHHHHHHhCCCcEEEEeCCCCCCEEEEeCcCCCCHHHHHHHHHCCEEEEeccCCHH
Confidence 3566654444456779999999989988877543322 1111233344677778888777777543
No 39
>PLN03194 putative disease resistance protein; Provisional
Probab=50.01 E-value=88 Score=23.93 Aligned_cols=67 Identities=16% Similarity=0.174 Sum_probs=48.7
Q ss_pred cCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEEEe
Q 041427 45 RNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVFYG 116 (158)
Q Consensus 45 ~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~~~ 116 (158)
+..+.||+..+.--....+..-+.+++++..+-+.+-......+.--..+|..+++. .+..|.||=.
T Consensus 24 ~~~yDVFISFrG~DtR~~FvshL~~aL~~~GI~vF~D~~el~~G~~i~~~L~~AIee-----Sri~IvVfS~ 90 (187)
T PLN03194 24 AKPCDVFINHRGIDTKRTIATLLYDHLSRLNLRPFLDNKNMKPGDKLFDKINSAIRN-----CKVGVAVFSP 90 (187)
T ss_pred CCCCcEEEeCCCccccccHHHHHHHHHHHCCCEEEEcCccccCCCcHHHHHHHHHHh-----CeEEEEEECC
Confidence 357899998764444446777888999998877777555566666666688888777 7788888843
No 40
>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=49.88 E-value=26 Score=23.94 Aligned_cols=29 Identities=10% Similarity=0.101 Sum_probs=22.2
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEe
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFK 52 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~ 52 (158)
||||.+..|. .-...+.+.|...|++++-
T Consensus 3 vlisv~~~dk--~~~~~~a~~l~~~G~~i~a 31 (116)
T cd01423 3 ILISIGSYSK--PELLPTAQKLSKLGYKLYA 31 (116)
T ss_pred EEEecCcccc--hhHHHHHHHHHHCCCEEEE
Confidence 7999988763 3455778888888998864
No 41
>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=49.68 E-value=74 Score=21.01 Aligned_cols=58 Identities=19% Similarity=0.250 Sum_probs=37.1
Q ss_pred HHHHHHHHHhcCCeEEEecCCCCCCCccc-cHHHHHhhhhcceEEEEEecCCCCChhhHHH
Q 041427 35 FTDHLHVALIRNGFVAFKDDETLDRGNEI-SSELSKAIEESNVSIVILSKNYASSPWCLDE 94 (158)
Q Consensus 35 fv~~L~~~L~~~gi~vf~d~~~l~~G~~i-~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~E 94 (158)
....+...+++.|...-+.. -..|..- ...|...|.+++.+|++.+--.-...|...+
T Consensus 11 ~~~~~~~~~~~~G~~~~~hg--~~~~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~ 69 (97)
T PF10087_consen 11 RERRYKRILEKYGGKLIHHG--RDGGDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKK 69 (97)
T ss_pred cHHHHHHHHHHcCCEEEEEe--cCCCCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHH
Confidence 46688888999998765551 1222222 2247889999999988776555555454433
No 42
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=48.96 E-value=55 Score=29.12 Aligned_cols=61 Identities=16% Similarity=0.220 Sum_probs=41.1
Q ss_pred ceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 19 KYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 19 ~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
..+|+|-.-+++ ....+..|...|++.|++|-+|.+ +..+...+..|-..---.++|+.++
T Consensus 438 P~qV~Iipi~e~-~~~~A~~Ia~~LR~~GirVelD~~----~~~lgkkir~A~k~gip~viIIG~~ 498 (545)
T PRK14799 438 SVQVRVLPITDE-VNEYAEKVLNDMRKRRIRAEIDYA----GETLSKRIKNAYDQGVPYILIVGKK 498 (545)
T ss_pred CceEEEEEcCHH-HHHHHHHHHHHHHhCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEChh
Confidence 468887765443 346789999999999999999875 3445556666544333456666643
No 43
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=48.67 E-value=51 Score=27.95 Aligned_cols=57 Identities=21% Similarity=0.403 Sum_probs=36.7
Q ss_pred CCCCCccccHHHHHhhhhcceEEEEEecCCC----CChhhHH-HHHHH-HHhhccCCCceeEEEEEe
Q 041427 56 TLDRGNEISSELSKAIEESNVSIVILSKNYA----SSPWCLD-ELAKI-VECGNKRNDRKVFAVFYG 116 (158)
Q Consensus 56 ~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~----~S~wc~~-El~~~-~~~~~~~~~~~iiPV~~~ 116 (158)
.+.|...+.. ..|..++--++|--..|+ .|+.|++ |+... .+| -..+++.+||||--
T Consensus 180 nmTpDrHLGa---A~id~~rpdlLIsESTYattiRdskr~rERdFLk~Vhec-Va~GGkvlIPvFAL 242 (501)
T KOG1136|consen 180 NMTPDRHLGA---AWIDKCRPDLLISESTYATTIRDSKRCRERDFLKKVHEC-VARGGKVLIPVFAL 242 (501)
T ss_pred cCCcccccch---hhhccccCceEEeeccceeeeccccchhHHHHHHHHHHH-HhcCCeEEEEeeec
Confidence 3444444432 236667666666555565 6888887 55554 455 77889999999963
No 44
>PLN02530 histidine-tRNA ligase
Probab=47.49 E-value=59 Score=28.31 Aligned_cols=61 Identities=13% Similarity=0.030 Sum_probs=43.0
Q ss_pred CceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEec
Q 041427 18 TKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSK 83 (158)
Q Consensus 18 ~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~ 83 (158)
...||+|.+-.++. ...+-.+...|.+.|+++-+|... ..+...+..|-+.--..++++.+
T Consensus 400 ~~~dVlVi~~~~~~-~~~A~~ia~~LR~~Gi~vevd~~~----~~l~k~ik~A~k~g~~~iviiG~ 460 (487)
T PLN02530 400 HQVDDVVFALDEDL-QGAAAGVASRLREKGRSVDLVLEP----KKLKWVFKHAERIGAKRLVLVGA 460 (487)
T ss_pred CCCcEEEEEcChHH-HHHHHHHHHHHHHCCCeEEEecCC----CCHHHHHHHHHHCCCCEEEEEch
Confidence 34689998755442 457888999999999999887543 34555666666655556777765
No 45
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=47.16 E-value=53 Score=26.59 Aligned_cols=70 Identities=21% Similarity=0.205 Sum_probs=47.7
Q ss_pred HHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEec-----------------CCCCChhhHHHHHHHHH
Q 041427 38 HLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSK-----------------NYASSPWCLDELAKIVE 100 (158)
Q Consensus 38 ~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~-----------------~~~~S~wc~~El~~~~~ 100 (158)
.|.-.|..+|+++---. +.|+.+++.++.+ +...+++=+.++| +|++-.-|..||..+.+
T Consensus 158 PlS~YLA~~G~KvAN~P--Lvpe~~lP~~L~~-~~~~kivGLtIdp~rL~~IR~~Rl~~lg~s~Ya~~~~i~~El~~A~~ 234 (269)
T PRK05339 158 PTSLYLANKGIKAANYP--LVPEVPLPEELFP-IDPKKIFGLTIDPERLIEIRKERLPNLGLSRYASLEQCREELAEAER 234 (269)
T ss_pred HHHHHHHccCCceEeeC--CCCCCCCCHHHHh-CCCCcEEEEeCCHHHHHHHHHHHhcccCcCcCCCHHHHHHHHHHHHH
Confidence 56677777999887554 6677776666554 4444565555554 48888999999999988
Q ss_pred hhccCCCceeE
Q 041427 101 CGNKRNDRKVF 111 (158)
Q Consensus 101 ~~~~~~~~~ii 111 (158)
.+.+ .+-++|
T Consensus 235 l~~k-~~~pvI 244 (269)
T PRK05339 235 LFRR-EGIPVI 244 (269)
T ss_pred HHHH-cCCCEE
Confidence 7433 444443
No 46
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=47.02 E-value=59 Score=28.73 Aligned_cols=61 Identities=10% Similarity=0.207 Sum_probs=41.8
Q ss_pred ceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 19 KYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 19 ~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
.+||+|---+++ ....+..|...|.+.|++|-+|.++ ..+...+..|-..---.++|+.++
T Consensus 476 p~~v~Ii~~~~~-~~~~a~~i~~~Lr~~gi~v~~d~~~----~~l~kk~~~A~~~g~p~~iivG~~ 536 (575)
T PRK12305 476 PVQVVIIPVADA-HNEYAEEVAKKLRAAGIRVEVDTSN----ERLNKKIRNAQKQKIPYMLVVGDK 536 (575)
T ss_pred CccEEEEEeChH-HHHHHHHHHHHHHHCCCEEEEECCC----CCHHHHHHHHHhcCCCEEEEEech
Confidence 468888764443 2457899999999999999998763 345556666655444456666664
No 47
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=45.39 E-value=68 Score=28.72 Aligned_cols=61 Identities=10% Similarity=0.128 Sum_probs=42.5
Q ss_pred ceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 19 KYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 19 ~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
..||+|-.-++. ....+..|...|.+.|++|-+|.+ +..+...+..|-..---.++|+.++
T Consensus 539 p~~v~Ii~~~~~-~~~~a~~i~~~Lr~~gi~v~~d~~----~~~l~kki~~A~~~g~~~~iiiG~~ 599 (638)
T PRK00413 539 PVQVVVLPITDK-HADYAKEVAKKLKAAGIRVEVDLR----NEKIGYKIREAQLQKVPYMLVVGDK 599 (638)
T ss_pred cceEEEEEeChh-HHHHHHHHHHHHHhCCCEEEEECC----CCCHhHHHHHhhccCCCEEEEEcch
Confidence 468888765443 246789999999999999999875 3445556666655444467777764
No 48
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=44.87 E-value=68 Score=27.40 Aligned_cols=60 Identities=13% Similarity=0.147 Sum_probs=41.4
Q ss_pred ceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEec
Q 041427 19 KYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSK 83 (158)
Q Consensus 19 ~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~ 83 (158)
..||+|.+-+.+. ...+-.+.+.|.+.|+++-+|.. +..+...+..|-+..-..++|+.+
T Consensus 325 ~~~v~v~~~~~~~-~~~a~~ia~~LR~~Gi~veid~~----~~~l~k~~k~A~~~~~~~viiiG~ 384 (430)
T CHL00201 325 SIDVYIATQGLKA-QKKGWEIIQFLEKQNIKFELDLS----SSNFHKQIKQAGKKRAKACIILGD 384 (430)
T ss_pred CCCEEEEEcCHHH-HHHHHHHHHHHHhCCCeEEEeeC----CCCHHHHHHHHHHcCCCEEEEEec
Confidence 4689998754432 45678899999999999988753 244555666665554456666766
No 49
>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=44.09 E-value=59 Score=22.94 Aligned_cols=64 Identities=13% Similarity=0.080 Sum_probs=39.7
Q ss_pred HHHHHHhcCCeEEEec---------CC----CCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHh
Q 041427 38 HLHVALIRNGFVAFKD---------DE----TLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (158)
Q Consensus 38 ~L~~~L~~~gi~vf~d---------~~----~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~ 101 (158)
+-...|-+.|+.+|.- .. +-..+..|.+--..-++.|+-+|+.-.|.+..|.-...|+..+.++
T Consensus 31 r~aa~l~~~G~~~fSpv~~sH~~~~~~~~~~~~~~~~~W~~~d~~~L~~c~~lvV~~i~GW~~S~Gi~~Ei~~a~~~ 107 (116)
T PF09152_consen 31 RVAAELLKAGHAAFSPVVMSHPINFELLGDDDPLIQKLWEDWDRPFLDACDELVVLDIPGWDDSEGIWAEIEAAEEM 107 (116)
T ss_dssp HHHHHHHHTT-EEEEHHHHHHHHHCCGTTS-HHHHHHHHHHHHHHHHHH-SEEEE---TTGGG-HHHHHHHHHHHHT
T ss_pred HHHHHHHhcCCeeEeccccccccchhcccccCcchhHHHHHHhHHHHHhcceeEEecCCCccccccHHHHHHHHHHc
Confidence 3344556689998875 10 1112233443334457899999999999999999999999999887
No 50
>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=44.06 E-value=83 Score=22.51 Aligned_cols=23 Identities=30% Similarity=0.186 Sum_probs=9.8
Q ss_pred ccccHHHHHhhhhcceEEEEEec
Q 041427 61 NEISSELSKAIEESNVSIVILSK 83 (158)
Q Consensus 61 ~~i~~~i~~~i~~s~~~IvvlS~ 83 (158)
+.+.+.+.+.|.+++..|.+.++
T Consensus 20 ~~~~~~i~~~I~~A~~~I~i~~~ 42 (176)
T cd00138 20 RSDLDALLEAISNAKKSIYIASF 42 (176)
T ss_pred chHHHHHHHHHHhhheEEEEEEe
Confidence 33333444444444444444444
No 51
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=43.83 E-value=75 Score=28.59 Aligned_cols=63 Identities=10% Similarity=0.183 Sum_probs=43.4
Q ss_pred CceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 18 TKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 18 ~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
...+|+|-.-+++.....+..|...|++.|++|-+|.+ +..+...+..|-+.---.++|+.++
T Consensus 540 ap~qV~Ii~~~~~~~~~~a~~la~~LR~~Gi~veid~~----~~sl~kq~k~A~k~g~~~~iiiG~~ 602 (639)
T PRK12444 540 APVQVKVIPVSNAVHVQYADEVADKLAQAGIRVERDER----DEKLGYKIREAQMQKIPYVLVIGDK 602 (639)
T ss_pred CCceEEEEEcccHHHHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEEcch
Confidence 35788777655411246789999999999999999875 3455556666655554566666654
No 52
>PF09837 DUF2064: Uncharacterized protein conserved in bacteria (DUF2064); InterPro: IPR018641 This entry contains proteins that have no known function. ; PDB: 3CGX_A.
Probab=43.75 E-value=1.1e+02 Score=21.34 Aligned_cols=85 Identities=18% Similarity=0.346 Sum_probs=44.0
Q ss_pred CCCceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhc---ceEEEEEecCCCCChhhH
Q 041427 16 LQTKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEES---NVSIVILSKNYASSPWCL 92 (158)
Q Consensus 16 ~~~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s---~~~IvvlS~~~~~S~wc~ 92 (158)
....+|++|.|+..... .....+ ....++.++ .+.|..+.+.+.++++.. .-.|+++.-+... -+.
T Consensus 7 ~~~~~~~~l~~~~~~~~-~~~~~~---~~~~~~~~~-----~Q~g~dLG~Rm~~a~~~~~~g~~~vvliGsD~P~--l~~ 75 (122)
T PF09837_consen 7 QADGADVVLAYTPDGDH-AAFRQL---WLPSGFSFF-----PQQGGDLGERMANAFQQAARGYEPVVLIGSDCPD--LTP 75 (122)
T ss_dssp -TSSSEEEEEE----TT-HHHHHH---HH-TTSEEE-----E--SSSHHHHHHHHHHHHHTT-SEEEEE-SS-TT----H
T ss_pred cCCCcCEEEEEcCCccH-HHHhcc---ccCCCCEEe-----ecCCCCHHHHHHHHHHHHHcCCCcEEEEcCCCCC--CCH
Confidence 34578999999877643 222222 455667776 346777777777777665 3366666666554 345
Q ss_pred HHHHHHHHhhccCCCceeEE
Q 041427 93 DELAKIVECGNKRNDRKVFA 112 (158)
Q Consensus 93 ~El~~~~~~~~~~~~~~iiP 112 (158)
..|..+.+. -+....++-|
T Consensus 76 ~~l~~A~~~-L~~~d~VlgP 94 (122)
T PF09837_consen 76 DDLEQAFEA-LQRHDVVLGP 94 (122)
T ss_dssp HHHHHHHHH-TTT-SEEEEE
T ss_pred HHHHHHHHH-hccCCEEEee
Confidence 566777666 3333445444
No 53
>KOG2792 consensus Putative cytochrome C oxidase assembly protein [Energy production and conversion]
Probab=43.51 E-value=25 Score=28.42 Aligned_cols=33 Identities=27% Similarity=0.424 Sum_probs=23.9
Q ss_pred ChhhHHHHHHHHHh---hccCCCceeEEEEEecCCc
Q 041427 88 SPWCLDELAKIVEC---GNKRNDRKVFAVFYGVDPT 120 (158)
Q Consensus 88 S~wc~~El~~~~~~---~~~~~~~~iiPV~~~v~p~ 120 (158)
-.=|-+||..+... +....+..++|||+-++|.
T Consensus 152 PDICPdELeKm~~~Vd~i~~~~~~~~~PlFIsvDPe 187 (280)
T KOG2792|consen 152 PDICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPE 187 (280)
T ss_pred CCcChHHHHHHHHHHHHHhccCCCCccceEEEeCcc
Confidence 35688898776554 3455667777999999993
No 54
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=43.09 E-value=70 Score=25.66 Aligned_cols=70 Identities=16% Similarity=0.146 Sum_probs=48.6
Q ss_pred HHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEec-------------------CCCCChhhHHHHHHH
Q 041427 38 HLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSK-------------------NYASSPWCLDELAKI 98 (158)
Q Consensus 38 ~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~-------------------~~~~S~wc~~El~~~ 98 (158)
.|.-.|..+|+++---. +.|+-.+++++.+ +...+++=+.++| +|+.-.-|.+||..+
T Consensus 152 PlS~YLA~~G~KvAN~P--Lvpe~~lP~~L~~-~~~~ki~GLtidp~~L~~IR~~Rl~~lg~~~s~Ya~~~~i~~El~~A 228 (255)
T PF03618_consen 152 PLSMYLANKGYKVANVP--LVPEVPLPEELFE-VDPKKIFGLTIDPERLIEIRRERLKSLGLDDSSYADLERIEEELEYA 228 (255)
T ss_pred chhHHHHhcCcceeecC--cCCCCCCCHHHHh-CCCCcEEEEECCHHHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHH
Confidence 46667777899887544 7777777777664 3555666666554 588888999999999
Q ss_pred HHhhccCCCceeE
Q 041427 99 VECGNKRNDRKVF 111 (158)
Q Consensus 99 ~~~~~~~~~~~ii 111 (158)
.+.+ +..+-++|
T Consensus 229 ~~l~-~~~~~pvI 240 (255)
T PF03618_consen 229 ERLF-RKLGCPVI 240 (255)
T ss_pred HHHH-HHcCCCEE
Confidence 8874 33354444
No 55
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=42.74 E-value=55 Score=29.56 Aligned_cols=62 Identities=16% Similarity=0.131 Sum_probs=40.7
Q ss_pred ceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCC
Q 041427 19 KYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNY 85 (158)
Q Consensus 19 ~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~ 85 (158)
.++|+|---+++ ....+..|.+.|++.|++|.+|+++-..|. .+.+|-..---.++|+.++-
T Consensus 499 P~qV~IIpi~e~-~~~~A~eIa~~Lr~~GirV~lDdr~~slgk----Kir~A~~~GiP~iIVIG~kE 560 (613)
T PRK03991 499 PTQVRVIPVSER-HLDYAEEVADKLEAAGIRVDVDDRDESLGK----KIRDAGKEWIPYVVVIGDKE 560 (613)
T ss_pred CceEEEEEeCHH-HHHHHHHHHHHHHhCCCEEEEECCCCCHHH----HHHHHHHcCCCEEEEECcch
Confidence 478877654433 356899999999999999999987544444 44444333333556665543
No 56
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase. This enzyme catalyzes the ring-opening step in the degradation of 4-hydroxyphenylacetate.
Probab=42.72 E-value=1.4e+02 Score=24.06 Aligned_cols=79 Identities=10% Similarity=0.105 Sum_probs=51.3
Q ss_pred hhHHHHHHHHHhcCCeEEEe---cCCCCCCCccccHHHHHhhhhcceEEEEEecC-CCCChhhHHHHHHHHHhhccCCCc
Q 041427 33 NNFTDHLHVALIRNGFVAFK---DDETLDRGNEISSELSKAIEESNVSIVILSKN-YASSPWCLDELAKIVECGNKRNDR 108 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~---d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~-~~~S~wc~~El~~~~~~~~~~~~~ 108 (158)
..++..|.+.+.+.|+.+-. ....+--|.-+. +.-.-.+.++-||.+|.+ ...+..-..+|..++....+..++
T Consensus 96 ~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vP--L~~l~p~~~ipvV~is~~~~~~~~~~~~~lG~al~~~i~~~~~ 173 (282)
T TIGR02298 96 PALGQLIADEAQEHGVKTLAHQVPSLGLEYGTLVP--MRYMNEDGHFKVVSIAAWCTVHDIEESRALGEAIRKAIEQSDG 173 (282)
T ss_pred HHHHHHHHHHHHHCCCceeeccCCCCCCCeehHhH--HHHhCCCCCCcEEEEeecCCCCCHHHHHHHHHHHHHHHHhcCC
Confidence 57999999999999998752 222343444333 111223466778888887 545677778999988875444456
Q ss_pred eeEEE
Q 041427 109 KVFAV 113 (158)
Q Consensus 109 ~iiPV 113 (158)
+|+-|
T Consensus 174 rV~iI 178 (282)
T TIGR02298 174 RVAVL 178 (282)
T ss_pred CEEEE
Confidence 66544
No 57
>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=42.26 E-value=63 Score=28.09 Aligned_cols=65 Identities=12% Similarity=0.090 Sum_probs=42.4
Q ss_pred CceeEEEec---ccC--cCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 18 TKYDVFLSF---RGE--DTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 18 ~~ydVFISy---s~~--D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
..++|+|-- ... +.....+..|...|++.|+++-+|.++-.+|. .+..+-..---+++++.++-.
T Consensus 281 aP~qV~Iipi~~~~~~~~~~~~~A~~l~~~Lr~~girv~lD~r~~s~gk----k~k~Ae~~GvP~~IiIG~~El 350 (472)
T TIGR00408 281 APIQVVIIPIIFKKKENEKVMEAAREVRSRLKKAGFRVHIDDRDNRPGR----KFYQWEIKGIPLRIEVGPNDI 350 (472)
T ss_pred CcceEEEEEccCCCCCCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHH----HHHHHHHCCCCEEEEECcchh
Confidence 457888764 221 12256789999999999999999987544454 444444444446677776643
No 58
>PF09441 Abp2: ARS binding protein 2; InterPro: IPR018562 This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals [].
Probab=42.19 E-value=7.9 Score=28.89 Aligned_cols=59 Identities=20% Similarity=0.329 Sum_probs=34.0
Q ss_pred ChhhHHHHHHHHHhhccCCCceeEEEEEecCCchhhHHhhHHHhhhCHHHHHHHHHHHHH
Q 041427 88 SPWCLDELAKIVECGNKRNDRKVFAVFYGVDPTDRVFAKYEEEFKENHEKVLKWRAALTR 147 (158)
Q Consensus 88 S~wc~~El~~~~~~~~~~~~~~iiPV~~~v~p~~v~f~~~~~~~~~~~~~~~~W~~al~~ 147 (158)
|.|.+.||..-++. .+.+.=.=+.+.++|+|-++.=...-.+..|+.-+++||+.++.-
T Consensus 54 s~~~Lf~LI~k~~~-keikTW~~La~~LGVepp~~ek~qStQKvqQYaVRLKRWM~aMHV 112 (175)
T PF09441_consen 54 STFTLFELIRKLES-KEIKTWAQLALELGVEPPDPEKGQSTQKVQQYAVRLKRWMRAMHV 112 (175)
T ss_pred hHHHHHHHHHHHhh-hhHhHHHHHHHHhCCCCCCcccccchHHHHHHHHHHHHHHHHhhH
Confidence 46777777766554 222222234456778888761111222334567889999988753
No 59
>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=41.81 E-value=94 Score=24.88 Aligned_cols=100 Identities=16% Similarity=0.192 Sum_probs=60.0
Q ss_pred HHHHHhcCCeEEEecCC----CCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEE
Q 041427 39 LHVALIRNGFVAFKDDE----TLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVF 114 (158)
Q Consensus 39 L~~~L~~~gi~vf~d~~----~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~ 114 (158)
.++.|... +++|.|-. .-..+.++.+....+++.+..=-+++|-.-...+=-+.++..+.+. - . +|||
T Consensus 133 ~R~~l~a~-v~ilaDV~~kh~~~l~~~~~~~~~~~a~~~~~aDaviVtG~~TG~~~~~~~l~~vr~~-----~-~-~PVl 204 (254)
T PF03437_consen 133 YRKRLGAD-VKILADVHVKHSSPLATRDLEEAAKDAVERGGADAVIVTGKATGEPPDPEKLKRVREA-----V-P-VPVL 204 (254)
T ss_pred HHHHcCCC-eEEEeeechhhcccCCCCCHHHHHHHHHHhcCCCEEEECCcccCCCCCHHHHHHHHhc-----C-C-CCEE
Confidence 34444445 99999843 1223445665666677776665666677766655566777776554 2 2 9999
Q ss_pred Ee--cCCchh-hHHh-------------hHHHh-hhCHHHHHHHHHHHH
Q 041427 115 YG--VDPTDR-VFAK-------------YEEEF-KENHEKVLKWRAALT 146 (158)
Q Consensus 115 ~~--v~p~~v-~f~~-------------~~~~~-~~~~~~~~~W~~al~ 146 (158)
.+ +.+.++ .+.+ .+.-. +.+.+++.++.+++.
T Consensus 205 vGSGvt~~Ni~~~l~~ADG~IVGS~~K~~G~~~n~VD~~Rv~~fm~~v~ 253 (254)
T PF03437_consen 205 VGSGVTPENIAEYLSYADGAIVGSYFKKDGKWENPVDPERVRRFMEAVK 253 (254)
T ss_pred EecCCCHHHHHHHHHhCCEEEEeeeeeeCCEeCCcCCHHHHHHHHHHhh
Confidence 95 888888 2221 11100 135777888777654
No 60
>cd07363 45_DOPA_Dioxygenase The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine. This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine (4,5-DOPA). The reaction results in the opening of the cyclic ring between carbons 4 and 5 and producing an unstable seco-DOPA that rearranges to betalamic acid. 4,5-DOPA Dioxygenase is a key enzyme in the biosynthetic pathway of the plant pigment betalain. Homologs of DODA are present not only in betalain-producing plants but also in bacteria and archaea. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated ca
Probab=41.71 E-value=1.2e+02 Score=23.98 Aligned_cols=68 Identities=19% Similarity=0.186 Sum_probs=48.5
Q ss_pred hhHHHHHHHHHhcCCeEEEecC-CCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhh
Q 041427 33 NNFTDHLHVALIRNGFVAFKDD-ETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECG 102 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~-~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~ 102 (158)
.+++.+|.+.|.+.|+.+-.+. ..+--|--+. +.-...+.++-||.+|.+...+..-..+|..++...
T Consensus 80 ~eLa~~i~~~l~~~gi~~~~~~~~~lDHG~~vP--L~~~~p~~~iPvV~isi~~~~~~~~~~~lG~aL~~l 148 (253)
T cd07363 80 PELAERVAELLKAAGIPARLDPERGLDHGAWVP--LKLMYPDADIPVVQLSLPASLDPAEHYALGRALAPL 148 (253)
T ss_pred HHHHHHHHHHHHhcCCCccccCCcCCcccHHHH--HHHHcCCCCCcEEEEEecCCCCHHHHHHHHHHHHhh
Confidence 5799999999999999887643 2233333222 222233467889999998887888888999999873
No 61
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=41.30 E-value=20 Score=31.91 Aligned_cols=65 Identities=20% Similarity=0.287 Sum_probs=40.8
Q ss_pred ceeEEEecc-cCc-CchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCC
Q 041427 19 KYDVFLSFR-GED-TRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS 87 (158)
Q Consensus 19 ~ydVFISys-~~D-~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~ 87 (158)
.|+|-|--- .+| ....++..|++.|+..|++|.+|+++-.+|..+.+.-.-+| - +.+++.++...
T Consensus 473 P~qV~Iip~~~~~~~~~~~a~~l~~~L~~~gi~v~~DDr~~~~G~K~~dadliGi---P-~~i~vG~~~l~ 539 (568)
T TIGR00409 473 PYDVVIVVMNMKDEEQQQLAEELYSELLAQGVDVLLDDRNERAGVKFADSELIGI---P-LRVVVGKKNLD 539 (568)
T ss_pred CeEEEEEEcCCChHHHHHHHHHHHHHHHhCCCEEEEECCCCCHHHHHHhhhhcCC---C-EEEEECCCccc
Confidence 466655432 222 23568899999999999999999987667765543211111 1 35566666543
No 62
>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=41.24 E-value=27 Score=23.62 Aligned_cols=58 Identities=19% Similarity=0.252 Sum_probs=35.0
Q ss_pred cCcCchhHHHHHHHHHhcCCeEEEecCCCCC----------CCccccHHHHHhhhhcceEEEEEecCC
Q 041427 28 GEDTRNNFTDHLHVALIRNGFVAFKDDETLD----------RGNEISSELSKAIEESNVSIVILSKNY 85 (158)
Q Consensus 28 ~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~----------~G~~i~~~i~~~i~~s~~~IvvlS~~~ 85 (158)
..|.|++=+-.|.+.|.+.|+.|.+.+--+. .|-.+.+.+.++++.++++|+.-...-
T Consensus 11 ~~D~R~Sp~~~l~~~L~~~g~~V~~~DP~v~~~~~~~~~~~~~~~~~~~~~~~~~~~D~vvl~t~h~~ 78 (106)
T PF03720_consen 11 TDDIRESPALELIEELKERGAEVSVYDPYVDEEEIKELGKLEGVEVCDDLEEALKGADAVVLATDHDE 78 (106)
T ss_dssp SS--TT-HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHCHHHCEEEESSHHHHHTTESEEEESS--GG
T ss_pred CcccccCHHHHHHHHHHHCCCEEEEECCccChHHHHhhCCccceEEecCHHHHhcCCCEEEEEecCHH
Confidence 4577888899999999999999877543221 123333456788888888777554443
No 63
>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=40.55 E-value=45 Score=22.48 Aligned_cols=29 Identities=24% Similarity=0.280 Sum_probs=21.1
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEe
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFK 52 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~ 52 (158)
||+|.+..|. .-...+.+.|.+.|++++-
T Consensus 3 vl~s~~~~~k--~~~~~~~~~l~~~G~~l~a 31 (110)
T cd01424 3 VFISVADRDK--PEAVEIAKRLAELGFKLVA 31 (110)
T ss_pred EEEEEEcCcH--hHHHHHHHHHHHCCCEEEE
Confidence 7899987763 3445777777778888864
No 64
>PF07894 DUF1669: Protein of unknown function (DUF1669); InterPro: IPR012461 This family is composed of sequences derived from hypothetical eukaryotic proteins of unknown function. Some members of this family are annotated as being potential phospholipases but no literature was found to support this.
Probab=40.04 E-value=1.9e+02 Score=23.61 Aligned_cols=77 Identities=13% Similarity=0.202 Sum_probs=52.9
Q ss_pred CeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEEEecCCchh-hHH
Q 041427 47 GFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVFYGVDPTDR-VFA 125 (158)
Q Consensus 47 gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~~~v~p~~v-~f~ 125 (158)
.+.+++..- ....-+|.+.+.+.|++++.+|.|+-.-|-.-. -..+|..|.. ++=+||++=++...+ .|.
T Consensus 120 r~~vy~qPp-~~~~p~IKE~vR~~I~~A~kVIAIVMD~FTD~d-If~DLleAa~-------kR~VpVYiLLD~~~~~~Fl 190 (284)
T PF07894_consen 120 RATVYFQPP-KDGQPHIKEVVRRMIQQAQKVIAIVMDVFTDVD-IFCDLLEAAN-------KRGVPVYILLDEQNLPHFL 190 (284)
T ss_pred eEEEEeCCC-CCCCCCHHHHHHHHHHHhcceeEEEeeccccHH-HHHHHHHHHH-------hcCCcEEEEechhcChHHH
Confidence 356776552 244567888899999999999999888776633 3334554442 244588777777788 888
Q ss_pred hhHHHhh
Q 041427 126 KYEEEFK 132 (158)
Q Consensus 126 ~~~~~~~ 132 (158)
++.+++.
T Consensus 191 ~Mc~~~~ 197 (284)
T PF07894_consen 191 EMCEKLG 197 (284)
T ss_pred HHHHHCC
Confidence 8877654
No 65
>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]
Probab=39.12 E-value=31 Score=29.99 Aligned_cols=60 Identities=10% Similarity=0.118 Sum_probs=32.3
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHh
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~ 101 (158)
+|+-||++|... .-.+.|++. +|.+|..|.-. -.+.+||.+|-=+ -..|-.+|+...++.
T Consensus 128 AFVtf~~Ke~Aq----~Aik~lnn~---------Eir~GK~igvc--~Svan~RLFiG~I-----PK~k~keeIlee~~k 187 (506)
T KOG0117|consen 128 AFVTFCTKEEAQ----EAIKELNNY---------EIRPGKLLGVC--VSVANCRLFIGNI-----PKTKKKEEILEEMKK 187 (506)
T ss_pred EEEEeecHHHHH----HHHHHhhCc---------cccCCCEeEEE--EeeecceeEeccC-----CccccHHHHHHHHHh
Confidence 799999998543 333444433 34456655422 2345566655422 234666666555543
No 66
>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=38.25 E-value=1.2e+02 Score=20.75 Aligned_cols=71 Identities=18% Similarity=0.161 Sum_probs=41.5
Q ss_pred HHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhh-hcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEE
Q 041427 35 FTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIE-ESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAV 113 (158)
Q Consensus 35 fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~-~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV 113 (158)
....|..+|++.|+.+-.-.. .+.....++ ..++.-+|++=+ .+..-...++...++. ...=|||
T Consensus 5 ~~~~l~~~L~~~~~~vv~~~~--------~dd~~~~i~~~~~i~avvi~~d-~~~~~~~~~ll~~i~~-----~~~~iPV 70 (115)
T PF03709_consen 5 ASRELAEALEQRGREVVDADS--------TDDALAIIESFTDIAAVVISWD-GEEEDEAQELLDKIRE-----RNFGIPV 70 (115)
T ss_dssp HHHHHHHHHHHTTTEEEEESS--------HHHHHHHHHCTTTEEEEEEECH-HHHHHHHHHHHHHHHH-----HSTT-EE
T ss_pred HHHHHHHHHHHCCCEEEEeCC--------hHHHHHHHHhCCCeeEEEEEcc-cccchhHHHHHHHHHH-----hCCCCCE
Confidence 467899999999998876432 123444444 588888888866 1111122233333333 3345888
Q ss_pred EEecCC
Q 041427 114 FYGVDP 119 (158)
Q Consensus 114 ~~~v~p 119 (158)
|+-.+.
T Consensus 71 Fl~~~~ 76 (115)
T PF03709_consen 71 FLLAER 76 (115)
T ss_dssp EEEESC
T ss_pred EEEecC
Confidence 886553
No 67
>cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di
Probab=38.13 E-value=99 Score=20.87 Aligned_cols=60 Identities=17% Similarity=0.085 Sum_probs=31.6
Q ss_pred CCcc-ccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEEEecCC
Q 041427 59 RGNE-ISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVFYGVDP 119 (158)
Q Consensus 59 ~G~~-i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~~~v~p 119 (158)
||.. +.......+++++.+|++++..-..+.....++...+.. ....+.+++.|.-+.|.
T Consensus 57 ~g~~~~~~~~~~~~~~~d~ii~v~d~~~~~~~~~~~~~~~~~~~-~~~~~~p~ivv~nK~D~ 117 (159)
T cd00154 57 AGQERFRSITPSYYRGAHGAILVYDITNRESFENLDKWLKELKE-YAPENIPIILVGNKIDL 117 (159)
T ss_pred CChHHHHHHHHHHhcCCCEEEEEEECCCHHHHHHHHHHHHHHHH-hCCCCCcEEEEEEcccc
Confidence 4543 333455678899999999998764433333333222222 11134555555544433
No 68
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=37.83 E-value=80 Score=22.59 Aligned_cols=55 Identities=13% Similarity=0.190 Sum_probs=41.1
Q ss_pred eeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcce
Q 041427 20 YDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNV 76 (158)
Q Consensus 20 ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~ 76 (158)
.++|+-..+.=....+.+.|..++..+|+-++.|.. .+|+.|...|.+.+..+..
T Consensus 30 ~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D--~~Ge~Irk~l~~~l~~~~~ 84 (127)
T COG1658 30 AGVIITNGSAINSLETIELIKKAQKYKGVIILTDPD--RKGERIRKKLKEYLPGAKG 84 (127)
T ss_pred CceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCC--cchHHHHHHHHHHhccccc
Confidence 456666654322245889999999999999999973 6899998888888877443
No 69
>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=36.93 E-value=1.3e+02 Score=20.10 Aligned_cols=57 Identities=19% Similarity=0.117 Sum_probs=35.9
Q ss_pred HHHHHHHHhcCCeEEE-ecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHH
Q 041427 36 TDHLHVALIRNGFVAF-KDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKI 98 (158)
Q Consensus 36 v~~L~~~L~~~gi~vf-~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~ 98 (158)
...|...|++.|+.+- +|.. ... +++.+.+.+.+.-++.+|-.+.....-..++...
T Consensus 17 l~~la~~l~~~G~~v~~~d~~-~~~-----~~l~~~~~~~~pd~V~iS~~~~~~~~~~~~l~~~ 74 (121)
T PF02310_consen 17 LLYLAAYLRKAGHEVDILDAN-VPP-----EELVEALRAERPDVVGISVSMTPNLPEAKRLARA 74 (121)
T ss_dssp HHHHHHHHHHTTBEEEEEESS-B-H-----HHHHHHHHHTTCSEEEEEESSSTHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCeEEEECCC-CCH-----HHHHHHHhcCCCcEEEEEccCcCcHHHHHHHHHH
Confidence 3678889999999885 4432 211 5777788877777777776544433333344443
No 70
>COG2130 Putative NADP-dependent oxidoreductases [General function prediction only]
Probab=35.95 E-value=85 Score=26.17 Aligned_cols=52 Identities=17% Similarity=0.388 Sum_probs=35.1
Q ss_pred ceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhh-hcceEEE
Q 041427 19 KYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIE-ESNVSIV 79 (158)
Q Consensus 19 ~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~-~s~~~Iv 79 (158)
-+|+-|.|..+| |...|.++-- +||.+|+|. .|..+.+.....+. ..|+.++
T Consensus 196 GfD~~idyk~~d----~~~~L~~a~P-~GIDvyfeN----VGg~v~DAv~~~ln~~aRi~~C 248 (340)
T COG2130 196 GFDAGIDYKAED----FAQALKEACP-KGIDVYFEN----VGGEVLDAVLPLLNLFARIPVC 248 (340)
T ss_pred CCceeeecCccc----HHHHHHHHCC-CCeEEEEEc----CCchHHHHHHHhhccccceeee
Confidence 589999997665 6666665544 899999986 36666666665555 4444433
No 71
>PF08902 DUF1848: Domain of unknown function (DUF1848); InterPro: IPR014998 This group of proteins are functionally uncharacterised. The C terminus contains a cluster of cysteines that are similar to the iron-sulphur cluster found at the N terminus of IPR007197 from INTERPRO.
Probab=35.78 E-value=2.4e+02 Score=22.84 Aligned_cols=134 Identities=17% Similarity=0.244 Sum_probs=76.2
Q ss_pred CceeEEEecccCcCchhHHHHHHHHHhcCCeEEEec------CCCCCCCccccHHHHH-------hhhhcceEE----EE
Q 041427 18 TKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKD------DETLDRGNEISSELSK-------AIEESNVSI----VI 80 (158)
Q Consensus 18 ~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d------~~~l~~G~~i~~~i~~-------~i~~s~~~I----vv 80 (158)
...|.++ |-.++. ..|..+| ..|.+.|++.++. .++++|+-+-.+++.+ .|..-++.. ++
T Consensus 46 ~~Vd~iV-FWTKnp-~P~l~~L-~~l~~~gy~~yfq~Tit~Y~~~lEp~vP~~~~~i~~f~~Ls~~iG~~rViWRYDPIi 122 (266)
T PF08902_consen 46 EDVDCIV-FWTKNP-APFLPYL-DELDERGYPYYFQFTITGYGKDLEPNVPPKDERIETFRELSERIGPERVIWRYDPII 122 (266)
T ss_pred hcceEEE-EecCCc-HHHHhhH-HHHHhCCCceEEEEEeCCCCccccCCCCCHHHHHHHHHHHHHHHCCCcEEEecCCEe
Confidence 3445444 656765 4677666 5677789988876 5568888644333322 233333321 45
Q ss_pred EecCCCCChhhHHHHHHHHHhhccCCCceeEEEEEecCCchh-hHHhhHHHh-hhCHHHHHHHHHHHHHhhcccccee
Q 041427 81 LSKNYASSPWCLDELAKIVECGNKRNDRKVFAVFYGVDPTDR-VFAKYEEEF-KENHEKVLKWRAALTRVASLAGWHL 156 (158)
Q Consensus 81 lS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~~~v~p~~v-~f~~~~~~~-~~~~~~~~~W~~al~~i~~~~G~~~ 156 (158)
++..|-- .|-++.+..+.+. ......+++-=|++..+.-- .+....-.+ .-..+....--..|.+||.--|..+
T Consensus 123 l~~~~~~-~~h~~~F~~la~~-L~g~t~~~viSF~D~Y~k~~~~l~~~~~~~~~~~~~~~~~l~~~l~~ia~~~g~~l 198 (266)
T PF08902_consen 123 LTDKYTV-DYHLEAFERLAEA-LAGYTDRCVISFLDLYRKVRRNLARLGFRIREPSEEEKRELAKRLAEIAKKYGMTL 198 (266)
T ss_pred ECCCCCH-HHHHHHHHHHHHH-HhccCCEEEEEeeeccHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHcCCEE
Confidence 6666544 6777777777777 44555666666766432221 222222011 1135666666778888887777654
No 72
>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=35.45 E-value=1.5e+02 Score=20.57 Aligned_cols=34 Identities=18% Similarity=0.251 Sum_probs=19.1
Q ss_pred HHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHH
Q 041427 66 ELSKAIEESNVSIVILSKNYASSPWCLDELAKIVE 100 (158)
Q Consensus 66 ~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~ 100 (158)
++.++|++++.+++|++-.-..+.+. .++...+.
T Consensus 4 ~~~~~i~~aD~vl~ViD~~~p~~~~~-~~l~~~l~ 37 (141)
T cd01857 4 QLWRVVERSDIVVQIVDARNPLLFRP-PDLERYVK 37 (141)
T ss_pred HHHHHHhhCCEEEEEEEccCCcccCC-HHHHHHHH
Confidence 45667777777777776654444332 24444443
No 73
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=35.42 E-value=73 Score=27.15 Aligned_cols=46 Identities=24% Similarity=0.370 Sum_probs=35.2
Q ss_pred HHHHHhhhhcc-eEEEEEecCCC-CChhhHHHHHHHHHhhccCCCceeE
Q 041427 65 SELSKAIEESN-VSIVILSKNYA-SSPWCLDELAKIVECGNKRNDRKVF 111 (158)
Q Consensus 65 ~~i~~~i~~s~-~~IvvlS~~~~-~S~wc~~El~~~~~~~~~~~~~~ii 111 (158)
+.+.+++.+.+ .+.++++|+=. ..-|..+||..+.+. ....+.+||
T Consensus 148 ~~LE~~~~~~~vkl~iLCnPHNP~Grvwt~eeL~~i~el-c~kh~v~VI 195 (388)
T COG1168 148 DALEKAFVDERVKLFILCNPHNPTGRVWTKEELRKIAEL-CLRHGVRVI 195 (388)
T ss_pred HHHHHHHhcCCccEEEEeCCCCCCCccccHHHHHHHHHH-HHHcCCEEE
Confidence 57788888887 67888888865 788999999999987 454454543
No 74
>KOG4132 consensus Uroporphyrinogen III synthase UROS/HEM4 [Coenzyme transport and metabolism]
Probab=34.42 E-value=54 Score=26.11 Aligned_cols=50 Identities=20% Similarity=0.145 Sum_probs=34.2
Q ss_pred HHHHHHHHhcCCeEEE----ecCCCCCCCccccHHHHHhhhhcce--EEEEEecCCCCC
Q 041427 36 TDHLHVALIRNGFVAF----KDDETLDRGNEISSELSKAIEESNV--SIVILSKNYASS 88 (158)
Q Consensus 36 v~~L~~~L~~~gi~vf----~d~~~l~~G~~i~~~i~~~i~~s~~--~IvvlS~~~~~S 88 (158)
-+.|...|..+||+|= +..++.. .+..++..+++.+.. +|++|||.-+++
T Consensus 145 rdil~kkL~~~G~~Vds~~VY~T~~hp---~~~~~~~~alk~~~~~d~ivfFSPsgv~~ 200 (260)
T KOG4132|consen 145 RDILPKKLHDKGIRVDSCEVYETREHP---DGFKQFIHALKECGFIDWIVFFSPSGVKS 200 (260)
T ss_pred hHHHHHHHHhCCceeeEEEEEeeeecc---cHHHHHHHHHHhcCCcceEEEECcchHHH
Confidence 3578899999999762 2222222 233477888888854 799999998764
No 75
>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=34.18 E-value=79 Score=23.90 Aligned_cols=65 Identities=12% Similarity=0.253 Sum_probs=46.0
Q ss_pred hhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCC--h------hhHHHHHHHHHh
Q 041427 33 NNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASS--P------WCLDELAKIVEC 101 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S--~------wc~~El~~~~~~ 101 (158)
..-...|..+.+.+|+-+|.|.+ .+|+.|...|.+.+-++... .++..+... . =..+.+..+++.
T Consensus 35 ~~~i~~i~~~~~~rgVIIfTDpD--~~GekIRk~i~~~vp~~kha--fi~~~~a~~~~~~iGVE~As~e~I~~AL~~ 107 (174)
T TIGR00334 35 DETINLIKKAQKKQGVIILTDPD--FPGEKIRKKIEQHLPGYENC--FIPKHLAKPNKKKIGVEEASVEAIIAALEN 107 (174)
T ss_pred HHHHHHHHHHhhcCCEEEEeCCC--CchHHHHHHHHHHCCCCeEE--eeeHHhcCcCCCCcccCCCCHHHHHHHHHH
Confidence 45678888889999999999984 68999999998888777754 335444421 0 114456666665
No 76
>COG2342 Predicted extracellular endo alpha-1,4 polygalactosaminidase or related polysaccharide hydrolase [Carbohydrate transport and metabolism]
Probab=34.13 E-value=74 Score=26.06 Aligned_cols=43 Identities=21% Similarity=0.510 Sum_probs=34.4
Q ss_pred HHHHhhhhcceEEEEEecCCC---CChhhHHHHHHHHHhhccCCCceeEEEEE
Q 041427 66 ELSKAIEESNVSIVILSKNYA---SSPWCLDELAKIVECGNKRNDRKVFAVFY 115 (158)
Q Consensus 66 ~i~~~i~~s~~~IvvlS~~~~---~S~wc~~El~~~~~~~~~~~~~~iiPV~~ 115 (158)
.-..+|.+++.-++|+-|.+. +++|..+||.+..+. + ++||-|
T Consensus 34 ~~~~~i~~~~f~llVVDps~~g~~~~~~~~eelr~~~~g-----g--~~pIAY 79 (300)
T COG2342 34 AYINEILNSPFDLLVVDPSYCGPFNTPWTIEELRTKADG-----G--VKPIAY 79 (300)
T ss_pred chHHHHhcCCCcEEEEeccccCCCCCcCcHHHHHHHhcC-----C--eeEEEE
Confidence 445689999999999999665 789999999987554 4 777766
No 77
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=33.07 E-value=34 Score=21.74 Aligned_cols=25 Identities=12% Similarity=0.314 Sum_probs=16.1
Q ss_pred CCeEEEecCCCCCCCccccHHHHHhhh
Q 041427 46 NGFVAFKDDETLDRGNEISSELSKAIE 72 (158)
Q Consensus 46 ~gi~vf~d~~~l~~G~~i~~~i~~~i~ 72 (158)
+.+-+++|.. .+|+.....+.+.+.
T Consensus 47 ~~Vii~~D~D--~~G~~~a~~i~~~l~ 71 (81)
T PF13662_consen 47 KEVIIAFDND--KAGEKAAQKIAKKLL 71 (81)
T ss_dssp SEEEEEEESS--HHHHHHHHHHHHHHG
T ss_pred ceEEEEeCcC--HHHHHHHHHHHHHHH
Confidence 6677777764 467766666666554
No 78
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=32.86 E-value=60 Score=26.06 Aligned_cols=41 Identities=24% Similarity=0.241 Sum_probs=28.0
Q ss_pred HHHHHHHHhcCCeEEEecCCCCCCCcc---ccHHHHHhhhhcceEEE
Q 041427 36 TDHLHVALIRNGFVAFKDDETLDRGNE---ISSELSKAIEESNVSIV 79 (158)
Q Consensus 36 v~~L~~~L~~~gi~vf~d~~~l~~G~~---i~~~i~~~i~~s~~~Iv 79 (158)
+.+|.+.|...|+.+..- ...||+ |.+.+..++++++++|+
T Consensus 23 a~~la~~L~~~G~~v~~~---~~VgD~~~~I~~~l~~a~~r~D~vI~ 66 (255)
T COG1058 23 AAFLADELTELGVDLARI---TTVGDNPDRIVEALREASERADVVIT 66 (255)
T ss_pred HHHHHHHHHhcCceEEEE---EecCCCHHHHHHHHHHHHhCCCEEEE
Confidence 678999999999998864 344554 34456666667555444
No 79
>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=32.32 E-value=2.2e+02 Score=21.55 Aligned_cols=85 Identities=25% Similarity=0.257 Sum_probs=53.5
Q ss_pred hhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCC----------------CCChhhHHHHH
Q 041427 33 NNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNY----------------ASSPWCLDELA 96 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~----------------~~S~wc~~El~ 96 (158)
..+.+.|.+.+...++.+........... -.++..+...+++.+|+++.+.+ ..-.++..||.
T Consensus 46 ~t~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~aD~vIv~~~~~~~e~~~~~~~~~~~~~~~~l~~~q~~li 124 (227)
T PF01915_consen 46 VTPLDALKQRFGNAGVVVPEGGDAVDDDE-GIDEAVAAAKEADVVIVFVGRPSGEGNDNNTEGESDRSDLALPANQQELI 124 (227)
T ss_dssp BHHHHHHHHHHHTTSEEEECCCCCCCCCS-CHHHHHHHHHCSSEEEEEEETTSBCCCSS-EETTGSCSSTBCCCHHHHHH
T ss_pred ccHHhhhccccCCCceEEeeecccccccc-chHHHHHHhhcCCEEEEeccccccccccccccccCCcccccchhhHHHHH
Confidence 46778888888888887765332222222 23466778889999999998433 33346777776
Q ss_pred HHHHhhccCCCceeEEEEEecCCchh
Q 041427 97 KIVECGNKRNDRKVFAVFYGVDPTDR 122 (158)
Q Consensus 97 ~~~~~~~~~~~~~iiPV~~~v~p~~v 122 (158)
..+.. . +.++|-|+.-..|.++
T Consensus 125 ~~v~~---~-~~~~Ivvv~~~~P~~l 146 (227)
T PF01915_consen 125 KAVAA---A-GKKVIVVVNSGNPYDL 146 (227)
T ss_dssp HHHHH---H-HSCEEEEEE-SSGGCG
T ss_pred HHHHH---h-cCCeEEEEecCCcccc
Confidence 66544 1 2455666655567666
No 80
>PF00350 Dynamin_N: Dynamin family; InterPro: IPR001401 Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another. Dynamins are large GTPases that belong to a protein superfamily [] that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins [, , , ], and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance. The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity. This entry represents the GTPase domain, containing the GTP-binding motifs that are needed for guanine-nucleotide binding and hydrolysis. The conservation of these motifs is absolute except for the the final motif in guanylate-binding proteins. The GTPase catalytic activity can be stimulated by oligomerisation of the protein, which is mediated by interactions between the GTPase domain, the middle domain and the GED.; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1JWY_B 1JX2_B 3ZVR_A 2AKA_B 3L43_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D ....
Probab=31.32 E-value=1.8e+02 Score=20.49 Aligned_cols=46 Identities=9% Similarity=0.159 Sum_probs=29.1
Q ss_pred HHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEE
Q 041427 65 SELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVF 114 (158)
Q Consensus 65 ~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~ 114 (158)
+-+.+.+.+++++|+|++.+- .|...+...+.+. .+....+++-|+
T Consensus 120 ~~~~~~~~~~d~vi~V~~~~~---~~~~~~~~~l~~~-~~~~~~~~i~V~ 165 (168)
T PF00350_consen 120 EITEEYLPKADVVIFVVDANQ---DLTESDMEFLKQM-LDPDKSRTIFVL 165 (168)
T ss_dssp HHHHHHHSTTEEEEEEEETTS---TGGGHHHHHHHHH-HTTTCSSEEEEE
T ss_pred HHHHHhhccCCEEEEEeccCc---ccchHHHHHHHHH-hcCCCCeEEEEE
Confidence 446677899999999997766 4454455555555 343444555554
No 81
>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=31.26 E-value=63 Score=22.68 Aligned_cols=48 Identities=10% Similarity=0.355 Sum_probs=31.8
Q ss_pred ccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEEEecCC
Q 041427 61 NEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVFYGVDP 119 (158)
Q Consensus 61 ~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~~~v~p 119 (158)
+.+.+.+.+.+.+.++.|++++++.++ ++...++. -..++|.++.+.-
T Consensus 46 eei~~~~~~~l~~~digIIlIte~~a~------~i~~~I~~-----~~~~~PaIieIP~ 93 (115)
T TIGR01101 46 SEIEDCFNRFLKRDDIAIILINQHIAE------MIRHAVDA-----HTRSIPAVLEIPS 93 (115)
T ss_pred HHHHHHHHHHhhcCCeEEEEEcHHHHH------HhHHHHHh-----cCCcCCEEEEECC
Confidence 445556666688899999999998765 44444444 2267777776544
No 82
>COG1806 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.85 E-value=71 Score=25.90 Aligned_cols=70 Identities=26% Similarity=0.220 Sum_probs=43.9
Q ss_pred HHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC--------------------CCCChhhHHHHHH
Q 041427 38 HLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN--------------------YASSPWCLDELAK 97 (158)
Q Consensus 38 ~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~--------------------~~~S~wc~~El~~ 97 (158)
.+.-.|..+|+++---. +.|++...+++..+++.- ++=+++||. |++-.-|.+|+..
T Consensus 159 PtS~YLA~q~ikaAN~P--lVpe~~~p~~L~~~~~~~-i~GLti~peRL~~IR~eRL~~~~~~~~s~Ya~~~~~~eEl~~ 235 (273)
T COG1806 159 PTSLYLALQGIKAANYP--LVPEDPEPDELPAALKPL-LFGLTISPERLSAIREERLKSLGLRENSRYASLDQCREELAY 235 (273)
T ss_pred chHHHHHHhcchhccCC--cCCCCCChhhhhhcccce-EEEEecCHHHHHHHHHHHhhccCCCCccccccHHHHHHHHHH
Confidence 34555666666654332 666776666666655544 555555543 7788889999999
Q ss_pred HHHhhccCCCceeE
Q 041427 98 IVECGNKRNDRKVF 111 (158)
Q Consensus 98 ~~~~~~~~~~~~ii 111 (158)
+-.. .+..+-++|
T Consensus 236 ae~l-~~r~~~pvi 248 (273)
T COG1806 236 AEAL-FRRNGIPVI 248 (273)
T ss_pred HHHH-HHHhCCCEE
Confidence 8876 444454444
No 83
>PF13289 SIR2_2: SIR2-like domain
Probab=30.40 E-value=1.4e+02 Score=20.40 Aligned_cols=7 Identities=14% Similarity=0.515 Sum_probs=2.7
Q ss_pred EEecccC
Q 041427 23 FLSFRGE 29 (158)
Q Consensus 23 FISys~~ 29 (158)
||.|+..
T Consensus 91 fiGys~~ 97 (143)
T PF13289_consen 91 FIGYSFN 97 (143)
T ss_pred EEEECCC
Confidence 3333333
No 84
>PRK07933 thymidylate kinase; Validated
Probab=29.85 E-value=1.5e+02 Score=22.63 Aligned_cols=30 Identities=23% Similarity=0.341 Sum_probs=22.7
Q ss_pred EEecccCcCc--hhHHHHHHHHHhcCCeEEEe
Q 041427 23 FLSFRGEDTR--NNFTDHLHVALIRNGFVAFK 52 (158)
Q Consensus 23 FISys~~D~~--~~fv~~L~~~L~~~gi~vf~ 52 (158)
||.+-+-|.. .+.+..|.+.|+..|++|..
T Consensus 2 ~IviEG~dGsGKST~~~~L~~~L~~~g~~v~~ 33 (213)
T PRK07933 2 LIAIEGVDGAGKRTLTEALRAALEARGRSVAT 33 (213)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence 6777665542 56889999999999988764
No 85
>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=29.77 E-value=2e+02 Score=20.09 Aligned_cols=83 Identities=16% Similarity=0.118 Sum_probs=51.8
Q ss_pred hhHHHHHHHHHhcCCeEE-EecCCCC-CC-----------CccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHH
Q 041427 33 NNFTDHLHVALIRNGFVA-FKDDETL-DR-----------GNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIV 99 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~v-f~d~~~l-~~-----------G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~ 99 (158)
..+++.+.+.|+..|+.+ .+|-.+. .| -..-.+++.+.+.+++. |++.||.|..+.- -.+..++
T Consensus 17 ~~l~~~~~~~l~~~g~e~~~i~l~~~~~p~~~~~~~~~~~~~d~~~~~~~~l~~aD~-iI~~sP~y~~~~s--~~lK~~l 93 (152)
T PF03358_consen 17 RKLAEAVAEQLEEAGAEVEVIDLADYPLPCCDGDFECPCYIPDDVQELYDKLKEADG-IIFASPVYNGSVS--GQLKNFL 93 (152)
T ss_dssp HHHHHHHHHHHHHTTEEEEEEECTTSHCHHHHHHHHHTGCTSHHHHHHHHHHHHSSE-EEEEEEEBTTBE---HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCEEEEEeccccchhhcccccccccCCcHHHHHHHhceecCCe-EEEeecEEcCcCC--hhhhHHH
Confidence 567889999998888765 3354443 11 11222466777888885 5668999987532 3566666
Q ss_pred Hhhc-----cCCCceeEEEEEecC
Q 041427 100 ECGN-----KRNDRKVFAVFYGVD 118 (158)
Q Consensus 100 ~~~~-----~~~~~~iiPV~~~v~ 118 (158)
+++. .-.++.+.+|-....
T Consensus 94 D~~~~~~~~~~~~K~~~~i~~~g~ 117 (152)
T PF03358_consen 94 DRLSCWFRRALRGKPVAIIAVGGG 117 (152)
T ss_dssp HTHHHTHTTTTTTSEEEEEEEESS
T ss_pred HHhccccccccCCCEEEEEEEecC
Confidence 6642 445677777766533
No 86
>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=29.65 E-value=1.5e+02 Score=20.10 Aligned_cols=61 Identities=25% Similarity=0.341 Sum_probs=35.2
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEecCC--------CC-----CCCcc-ccHHHHHhhhh-cceEEEEEecC
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDE--------TL-----DRGNE-ISSELSKAIEE-SNVSIVILSKN 84 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~--------~l-----~~G~~-i~~~i~~~i~~-s~~~IvvlS~~ 84 (158)
||||-+..|. .-...+...|.+.|+.++--.- .+ ..+.. -.+++.+.|.+ -++-+||..|+
T Consensus 2 i~isv~d~~K--~~~~~~a~~l~~~G~~i~AT~gTa~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn~~~ 77 (112)
T cd00532 2 VFLSVSDHVK--AMLVDLAPKLSSDGFPLFATGGTSRVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVINLRD 77 (112)
T ss_pred EEEEEEcccH--HHHHHHHHHHHHCCCEEEECcHHHHHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEEcCC
Confidence 6888876663 3344666777777877753210 11 11100 12457777777 77777777665
No 87
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=28.89 E-value=2.1e+02 Score=21.55 Aligned_cols=85 Identities=8% Similarity=0.082 Sum_probs=49.0
Q ss_pred hhHHHHHHHHHhcCCeEE-EecCCCCCCCc--------cccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhh-
Q 041427 33 NNFTDHLHVALIRNGFVA-FKDDETLDRGN--------EISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECG- 102 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~v-f~d~~~l~~G~--------~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~- 102 (158)
...+..+.+.|.+.|..+ .+|-.++.+++ +-...+.+.|++++. |++.||-|..|---. |..+++++
T Consensus 17 ~~l~~~~~~~l~~~g~ev~~idL~~l~~~~~~~~~~~~~~~~~~~~~i~~AD~-iIi~tP~Y~~s~pg~--LKn~iD~l~ 93 (191)
T PRK10569 17 SALLEYAREWLNGLGVEVYHWNLQNFAPEDLLYARFDSPALKTFTEQLAQADG-LIVATPVYKASFSGA--LKTLLDLLP 93 (191)
T ss_pred HHHHHHHHHHHHhCCCEEEEEEccCCChHHHHhccCCCHHHHHHHHHHHHCCE-EEEECCccCCCCCHH--HHHHHHhCC
Confidence 346677777788788766 44655554321 122355677888885 566899987663322 33333332
Q ss_pred -ccCCCceeEEEEEecCCc
Q 041427 103 -NKRNDRKVFAVFYGVDPT 120 (158)
Q Consensus 103 -~~~~~~~iiPV~~~v~p~ 120 (158)
..-.++++++|-....+.
T Consensus 94 ~~~l~~K~v~iiat~G~~~ 112 (191)
T PRK10569 94 ERALEHKVVLPLATGGSVA 112 (191)
T ss_pred hhhhCCCEEEEEEecCCch
Confidence 123456777776654443
No 88
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=28.68 E-value=3e+02 Score=22.55 Aligned_cols=65 Identities=17% Similarity=0.095 Sum_probs=31.5
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
.|+|-|....-.+.+...+.+.|+..|..+-. .....+++.-...+...|..+..-++++.....
T Consensus 150 ~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~-~~~~~~~~~~~~~~v~~i~~~~~d~v~~~~~~~ 214 (366)
T COG0683 150 RVAIIGDDYAYGEGLADAFKAALKALGGEVVV-EEVYAPGDTDFSALVAKIKAAGPDAVLVGGYGP 214 (366)
T ss_pred EEEEEeCCCCcchhHHHHHHHHHHhCCCeEEE-EEeeCCCCCChHHHHHHHHhcCCCEEEECCCCc
Confidence 34444444333455666666666667665222 223444443233444445544444444444443
No 89
>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=27.65 E-value=1.4e+02 Score=23.70 Aligned_cols=73 Identities=22% Similarity=0.300 Sum_probs=40.9
Q ss_pred EEecccCcCchhHHHHHHHHHhcCCeEEEec----------CCCCCCCccc---------cHHHHHhhhhcceEEEEEec
Q 041427 23 FLSFRGEDTRNNFTDHLHVALIRNGFVAFKD----------DETLDRGNEI---------SSELSKAIEESNVSIVILSK 83 (158)
Q Consensus 23 FISys~~D~~~~fv~~L~~~L~~~gi~vf~d----------~~~l~~G~~i---------~~~i~~~i~~s~~~IvvlS~ 83 (158)
|-.|-+.. ...|+.+|.++|++++..+--- ++.+..-... ...|..|++ ..+|++=+-
T Consensus 6 lTGyPgsG-KTtfakeLak~L~~~i~~vi~l~kdy~~~i~~DEslpi~ke~yres~~ks~~rlldSalk--n~~VIvDdt 82 (261)
T COG4088 6 LTGYPGSG-KTTFAKELAKELRQEIWRVIHLEKDYLRGILWDESLPILKEVYRESFLKSVERLLDSALK--NYLVIVDDT 82 (261)
T ss_pred EecCCCCC-chHHHHHHHHHHHHhhhhccccchhhhhheecccccchHHHHHHHHHHHHHHHHHHHHhc--ceEEEEecc
Confidence 44454444 2579999999999887644322 2222111111 112333343 558888999
Q ss_pred CCCCChhhHHHHHHHHH
Q 041427 84 NYASSPWCLDELAKIVE 100 (158)
Q Consensus 84 ~~~~S~wc~~El~~~~~ 100 (158)
||.+| -+.+|.-...
T Consensus 83 NYyks--mRrqL~ceak 97 (261)
T COG4088 83 NYYKS--MRRQLACEAK 97 (261)
T ss_pred cHHHH--HHHHHHHHHH
Confidence 99987 3455554443
No 90
>PLN02734 glycyl-tRNA synthetase
Probab=27.17 E-value=80 Score=29.01 Aligned_cols=62 Identities=16% Similarity=0.096 Sum_probs=39.0
Q ss_pred CCCceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEe
Q 041427 16 LQTKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILS 82 (158)
Q Consensus 16 ~~~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS 82 (158)
-+.+..|+.--.. +.....+..|...|.+.|+++.+|.++-..|. .+..+-+.---+++++.
T Consensus 569 AP~qVaIlPL~~~-ee~~~~A~eLa~~LR~~GIrVelDd~~~SIGK----RyrrADeiGIPf~ItIG 630 (684)
T PLN02734 569 APIKCTVFPLVQN-QQLNAVAKVISKELTAAGISHKIDITGTSIGK----RYARTDELGVPFAVTVD 630 (684)
T ss_pred CCcEEEEEEecCC-hHHHHHHHHHHHHHHhCCCEEEEECCCCCHhH----HHHHHHHcCCCEEEEEC
Confidence 3456777755333 22356889999999999999999976444444 44444333333455555
No 91
>cd07371 2A5CPDO_AB The alpha and beta subunits of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. This subfamily contains both alpha and beta subunits of 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, an intermediate during p-chloronitrobenzene degradation. 2A5CPDO is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. Alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication.
Probab=27.05 E-value=3.2e+02 Score=21.66 Aligned_cols=87 Identities=13% Similarity=0.101 Sum_probs=50.4
Q ss_pred EecccCcCchhHHHHHHHHHhcCCeEEEe-cCC--CCCCCccccHHHHHhhhhcceEEEEEecCC-CCChhhHHHHHHHH
Q 041427 24 LSFRGEDTRNNFTDHLHVALIRNGFVAFK-DDE--TLDRGNEISSELSKAIEESNVSIVILSKNY-ASSPWCLDELAKIV 99 (158)
Q Consensus 24 ISys~~D~~~~fv~~L~~~L~~~gi~vf~-d~~--~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~-~~S~wc~~El~~~~ 99 (158)
+.|.-.. ..+++..|.+.|...|+.+-. +.. .+--|.-+.=.+ .-.+.++-++.+|=+. .-+..-..+|..++
T Consensus 79 ~~y~~~g-~~eLA~~i~~~~~~~gi~~~~~~~~~~~lDHG~~vPL~~--l~p~~~ipvV~vs~~~~~~~~~~~~~lG~al 155 (268)
T cd07371 79 LDYSINV-DVELAEACVEEGRKAGLVTRMMRYPRFPIDTGTITALTL--MRPGTDIPPVVISANNLYLSGEETEGEMDLA 155 (268)
T ss_pred eeecCCC-CHHHHHHHHHHHHHCCCcEEEecCCCCCCCchhHHHHHH--hcCCCCCCeEEEEecCcCCCHHHHHHHHHHH
Confidence 4453332 257999999999999998875 222 233343332111 1124566677777443 35677778899888
Q ss_pred HhhccCCCceeEEE
Q 041427 100 ECGNKRNDRKVFAV 113 (158)
Q Consensus 100 ~~~~~~~~~~iiPV 113 (158)
....+..+++|.-|
T Consensus 156 ~~~l~~~~~rv~iI 169 (268)
T cd07371 156 GKATRDAGKRVAVL 169 (268)
T ss_pred HHHHHHcCCcEEEE
Confidence 63223334555544
No 92
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=27.04 E-value=2.3e+02 Score=20.84 Aligned_cols=83 Identities=14% Similarity=0.132 Sum_probs=50.3
Q ss_pred CCCceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHH
Q 041427 16 LQTKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDEL 95 (158)
Q Consensus 16 ~~~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El 95 (158)
...+.|...+.+-..- =+..|.+..++.|+++++ .+|..+...+.+..+ -+..|.| =|..+|
T Consensus 58 ~k~t~~g~~C~~Cg~C---~Ig~l~~lae~~g~~v~i-----~~Ggt~ar~~ik~~~-p~~iigV---------AC~~dL 119 (158)
T PF01976_consen 58 AKITSDGYNCKRCGKC---DIGDLKKLAEKYGYKVYI-----ATGGTLARKIIKEYR-PKAIIGV---------ACERDL 119 (158)
T ss_pred CccCCCCCcCCCCCCC---chhHHHHHHHHcCCEEEE-----EcChHHHHHHHHHhC-CCEEEEE---------echHHH
Confidence 3344566665532222 367888888999999995 456555443333222 1122222 299999
Q ss_pred HHHHHhhccCCCceeEEEEEec
Q 041427 96 AKIVECGNKRNDRKVFAVFYGV 117 (158)
Q Consensus 96 ~~~~~~~~~~~~~~iiPV~~~v 117 (158)
...++. ....+.+++.|+.+.
T Consensus 120 ~~g~~~-~~~~~ip~~gV~l~~ 140 (158)
T PF01976_consen 120 ISGIQD-LKPLGIPVQGVLLDR 140 (158)
T ss_pred HHHHHH-HhhcCCCeeEEEeCC
Confidence 998877 454567888888753
No 93
>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=27.02 E-value=77 Score=25.04 Aligned_cols=25 Identities=12% Similarity=0.296 Sum_probs=20.9
Q ss_pred CChhhHHHHHHHHHhhccCCCceeEEEEEe
Q 041427 87 SSPWCLDELAKIVECGNKRNDRKVFAVFYG 116 (158)
Q Consensus 87 ~S~wc~~El~~~~~~~~~~~~~~iiPV~~~ 116 (158)
-|+|++.+|....+. ...|+||+-+
T Consensus 106 fs~r~~rdL~~la~~-----R~NIiPIl~D 130 (229)
T PF01269_consen 106 FSPRSMRDLLNLAKK-----RPNIIPILED 130 (229)
T ss_dssp SSHHHHHHHHHHHHH-----STTEEEEES-
T ss_pred ecchhHHHHHHHhcc-----CCceeeeecc
Confidence 478999999988887 7799999865
No 94
>PLN02908 threonyl-tRNA synthetase
Probab=26.46 E-value=1.6e+02 Score=26.99 Aligned_cols=61 Identities=13% Similarity=0.198 Sum_probs=41.8
Q ss_pred ceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 19 KYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 19 ~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
..+|+|-.-+.+ ....+..+.+.|.+.|++|-+|.. +..+...+..|-..--.+++|+.++
T Consensus 589 p~qv~Vipv~~~-~~~~A~~va~~LR~~Gi~vevd~~----~~~l~kkir~A~~~g~~~viivG~~ 649 (686)
T PLN02908 589 PRQAIVVPISEK-SQDYAEEVRAQLHAAGFYVDVDVT----DRKIQKKVREAQLAQYNYILVVGEA 649 (686)
T ss_pred CceEEEEEECHH-HHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHcCCCEEEEECch
Confidence 357777664443 246789999999999999999864 4556666666655444466666653
No 95
>COG2077 Tpx Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=26.30 E-value=48 Score=24.64 Aligned_cols=23 Identities=22% Similarity=0.466 Sum_probs=17.7
Q ss_pred hhcceEEEEEecC--CCCChhhHHH
Q 041427 72 EESNVSIVILSKN--YASSPWCLDE 94 (158)
Q Consensus 72 ~~s~~~IvvlS~~--~~~S~wc~~E 94 (158)
+-....++++|-+ |+++.||-.|
T Consensus 73 ~~~~~~Vl~IS~DLPFAq~RfC~ae 97 (158)
T COG2077 73 KLGNTVVLCISMDLPFAQKRFCGAE 97 (158)
T ss_pred ccCCcEEEEEeCCChhHHhhhhhhc
Confidence 3444778888988 7899999765
No 96
>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=26.25 E-value=3e+02 Score=22.10 Aligned_cols=63 Identities=10% Similarity=0.099 Sum_probs=32.3
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
.|.+-|...+-.+..+..+...+++.|+.+-... .+.+++.=.......|.+++.=++++.-.
T Consensus 146 ~v~~l~~~~~~g~~~~~~~~~~~~~~G~~vv~~~-~~~~~~~d~~~~i~~l~~~~~d~v~~~~~ 208 (347)
T cd06340 146 TVALVHEDTEFGTSVAEAIKKFAKERGFEIVEDI-SYPANARDLTSEVLKLKAANPDAILPASY 208 (347)
T ss_pred eEEEEecCchHhHHHHHHHHHHHHHcCCEEEEee-ccCCCCcchHHHHHHHHhcCCCEEEEccc
Confidence 4555554333234566777777778887776432 24444322233344455544444444433
No 97
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=26.17 E-value=73 Score=19.31 Aligned_cols=23 Identities=26% Similarity=0.352 Sum_probs=14.1
Q ss_pred HHHHHHHHHhcCCeEEEecCCCC
Q 041427 35 FTDHLHVALIRNGFVAFKDDETL 57 (158)
Q Consensus 35 fv~~L~~~L~~~gi~vf~d~~~l 57 (158)
-+..+...|+..||.+++.+...
T Consensus 11 ea~~i~~~L~~~gI~~~v~~~~~ 33 (67)
T PF09413_consen 11 EAELIKGLLEENGIPAFVKNEHM 33 (67)
T ss_dssp HHHHHHHHHHHTT--EE--S---
T ss_pred HHHHHHHHHHhCCCcEEEECCcc
Confidence 46889999999999999976543
No 98
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=26.13 E-value=3.1e+02 Score=22.82 Aligned_cols=79 Identities=19% Similarity=0.274 Sum_probs=49.5
Q ss_pred HHHHHHHHHhcC----CeEEEecCCCCCCCccccHHHHHhhhhcc---eEEEEEecCCCCC--hhhHHHHHHHHHhhccC
Q 041427 35 FTDHLHVALIRN----GFVAFKDDETLDRGNEISSELSKAIEESN---VSIVILSKNYASS--PWCLDELAKIVECGNKR 105 (158)
Q Consensus 35 fv~~L~~~L~~~----gi~vf~d~~~l~~G~~i~~~i~~~i~~s~---~~IvvlS~~~~~S--~wc~~El~~~~~~~~~~ 105 (158)
+.+.+.++|+++ .+.|++. +.-|.+..++..+.+.... ++++.+.|.|-.+ .-..+++..+++.....
T Consensus 74 ~T~~q~~~L~~~L~~~~~~V~~a---mry~~P~i~~~v~~l~~~gv~~iv~~pLyPqyS~sTt~s~~~~~~~al~~~~~~ 150 (320)
T COG0276 74 ITRAQAAALEERLDLPDFKVYLA---MRYGPPFIEEAVEELKKDGVERIVVLPLYPQYSSSTTGSYVDELARALKELRGQ 150 (320)
T ss_pred HHHHHHHHHHHHhCCCCccEEEe---ecCCCCcHHHHHHHHHHcCCCeEEEEECCcccccccHHHHHHHHHHHHHhcCCC
Confidence 344555555443 5777765 5567777666666666444 4788888888643 34567888888763322
Q ss_pred CCceeEEEEEe
Q 041427 106 NDRKVFAVFYG 116 (158)
Q Consensus 106 ~~~~iiPV~~~ 116 (158)
-....||-||+
T Consensus 151 ~~i~~I~~~~~ 161 (320)
T COG0276 151 PKISTIPDYYD 161 (320)
T ss_pred CceEEecCccC
Confidence 34567777765
No 99
>COG3340 PepE Peptidase E [Amino acid transport and metabolism]
Probab=25.66 E-value=2.4e+02 Score=22.25 Aligned_cols=55 Identities=13% Similarity=0.230 Sum_probs=39.0
Q ss_pred eEEEecccCcCc-hhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEE
Q 041427 21 DVFLSFRGEDTR-NNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIV 79 (158)
Q Consensus 21 dVFISys~~D~~-~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~Iv 79 (158)
=+||=+++.|.. ..++...+++|+..|..+- ++.....-.+.|.+-+.+.+++.|
T Consensus 35 i~FIPtAs~~~~~~~Yv~k~~~~l~~lg~~v~----~L~l~~~~~~~Ie~~l~~~d~IyV 90 (224)
T COG3340 35 IAFIPTASVDSEDDFYVEKVRNALAKLGLEVS----ELHLSKPPLAAIENKLMKADIIYV 90 (224)
T ss_pred EEEEecCccccchHHHHHHHHHHHHHcCCeee----eeeccCCCHHHHHHhhhhccEEEE
Confidence 359999888754 3488999999999997654 355555555667776777777544
No 100
>PF11071 DUF2872: Protein of unknown function (DUF2872); InterPro: IPR019884 This entry represents a family of uncharacterised proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=25.35 E-value=1.4e+02 Score=21.72 Aligned_cols=40 Identities=15% Similarity=0.333 Sum_probs=26.6
Q ss_pred HHHhhhhcceEEEEEecCCCCChhh-HHHHHHHHHhhccCCCceeEEE
Q 041427 67 LSKAIEESNVSIVILSKNYASSPWC-LDELAKIVECGNKRNDRKVFAV 113 (158)
Q Consensus 67 i~~~i~~s~~~IvvlS~~~~~S~wc-~~El~~~~~~~~~~~~~~iiPV 113 (158)
....|++|+++|+.|.++|-+ |- -..-..+... ++++|.+
T Consensus 66 T~~li~~aDvVVvrFGekYKQ--WNaAfDAg~a~Al-----gKplI~l 106 (141)
T PF11071_consen 66 TRTLIEKADVVVVRFGEKYKQ--WNAAFDAGYAAAL-----GKPLITL 106 (141)
T ss_pred HHHHHhhCCEEEEEechHHHH--HHHHhhHHHHHHc-----CCCeEEe
Confidence 345799999999999999986 32 1223333333 6677665
No 101
>COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain [Signal transduction mechanisms / Transcription]
Probab=25.06 E-value=2.5e+02 Score=21.15 Aligned_cols=23 Identities=26% Similarity=0.429 Sum_probs=19.9
Q ss_pred chhHHHHHHHHHhcCCeEEEecC
Q 041427 32 RNNFTDHLHVALIRNGFVAFKDD 54 (158)
Q Consensus 32 ~~~fv~~L~~~L~~~gi~vf~d~ 54 (158)
...|...|..+++++|+.|-...
T Consensus 18 D~~f~~~LaRa~e~RGf~v~~a~ 40 (182)
T COG4567 18 DTPFLRTLARAMERRGFAVVTAE 40 (182)
T ss_pred ChHHHHHHHHHHhccCceeEeec
Confidence 36899999999999999887654
No 102
>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=24.77 E-value=3.4e+02 Score=21.21 Aligned_cols=52 Identities=15% Similarity=0.160 Sum_probs=27.9
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCc-cccHHHHHhhhhc
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGN-EISSELSKAIEES 74 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~-~i~~~i~~~i~~s 74 (158)
.|.+-|...+-....+..+.+.|+..|+++-... .+.+|. .+. .+...|+++
T Consensus 137 ~v~~v~~~~~~g~~~~~~~~~~~~~~g~~v~~~~-~~~~~~~d~~-~~l~~i~~~ 189 (334)
T cd06342 137 KVAIIDDKTAYGQGLADEFKKALKAAGGKVVARE-GTTDGATDFS-AILTKIKAA 189 (334)
T ss_pred EEEEEeCCcchhhHHHHHHHHHHHHcCCEEEEEe-cCCCCCccHH-HHHHHHHhc
Confidence 3544454444335567777788887887765433 244443 333 333445543
No 103
>cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi
Probab=24.66 E-value=2.5e+02 Score=19.66 Aligned_cols=22 Identities=5% Similarity=-0.108 Sum_probs=15.8
Q ss_pred HHHHhhhhcceEEEEEecCCCC
Q 041427 66 ELSKAIEESNVSIVILSKNYAS 87 (158)
Q Consensus 66 ~i~~~i~~s~~~IvvlS~~~~~ 87 (158)
.....+++++.+|++++-+-..
T Consensus 68 ~~~~~~~~ad~~i~v~d~~~~~ 89 (167)
T cd01867 68 ITTAYYRGAMGIILVYDITDEK 89 (167)
T ss_pred HHHHHhCCCCEEEEEEECcCHH
Confidence 3345678999999999865443
No 104
>KOG2903 consensus Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]
Probab=23.83 E-value=2.2e+02 Score=23.27 Aligned_cols=97 Identities=19% Similarity=0.181 Sum_probs=56.9
Q ss_pred CCCCceeEEEecccCcCchhHHHHHHHHHh---c-CCeEE--EecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCC
Q 041427 15 ILQTKYDVFLSFRGEDTRNNFTDHLHVALI---R-NGFVA--FKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASS 88 (158)
Q Consensus 15 ~~~~~ydVFISys~~D~~~~fv~~L~~~L~---~-~gi~v--f~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S 88 (158)
+....|..|+||..--..+ ..+..+|. . -|+.+ |+++ ..|-.+.++ ...+.++.++++ +++.++.
T Consensus 33 pakgryhLYvslaCPWAhR---tLi~r~LKGL~~~i~~s~v~~~~d---~~gW~F~~~-~~~~nDs~~l~~--~~d~~~g 103 (319)
T KOG2903|consen 33 PAKGRYHLYVSLACPWAHR---TLIVRALKGLEPAIGVSVVHWHLD---DKGWRFLDE-HIIINDSERLGV--TPDPLNG 103 (319)
T ss_pred CCCceEEEEEeccCcHHHH---HHHHHHHcCccccceeEEeccccC---CCcccCCCc-ccCCCchhcccC--CCccccc
Confidence 5557899999996543222 23333332 2 23333 4221 124333321 012355655555 8888888
Q ss_pred hhhHHHHHHHHHhhccCCCceeEEEEEecCCchh
Q 041427 89 PWCLDELAKIVECGNKRNDRKVFAVFYGVDPTDR 122 (158)
Q Consensus 89 ~wc~~El~~~~~~~~~~~~~~iiPV~~~v~p~~v 122 (158)
.--+.||..+..- .-.++--+||+.+.....|
T Consensus 104 ~k~l~elY~~~~p--~Y~grfTVPVLWD~k~ktI 135 (319)
T KOG2903|consen 104 AKRLRELYYIASP--NYTGRFTVPVLWDLKTKTI 135 (319)
T ss_pred chhHHHHHhhcCC--CCCceEEEEEEEcccccee
Confidence 8888899887654 3345889999998776665
No 105
>PF02900 LigB: Catalytic LigB subunit of aromatic ring-opening dioxygenase; InterPro: IPR004183 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A and B. Enzymes that belong to the extradiol class III family include Protocatechuate 4,5-dioxygenase (4,5-PCD; LigAB) (1.13.11.8 from EC) []; and 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarBaBb) []. The crystal structure of dioxygenase LigAB revealed that the molecule is an alpha2beta2 tetramer. The active site contains a non-heme iron coordinated by His12, His61, Glu242, and a water molecule located in a deep cleft of the beta subunit, which is covered by the alpha subunit []. This entry represents the structural domain of subunit B.; GO: 0008198 ferrous iron binding, 0016491 oxidoreductase activity, 0006725 cellular aromatic compound metabolic process; PDB: 2PW6_A 1B4U_D 1BOU_B.
Probab=23.60 E-value=1.7e+02 Score=23.03 Aligned_cols=80 Identities=19% Similarity=0.279 Sum_probs=47.8
Q ss_pred hhHHHHHHHHHhcCCeEEEe-cCCCCCCCccccHHHHHhhhhcceEEEEEecCC----CCChhhHHHHHHHHHhhccCCC
Q 041427 33 NNFTDHLHVALIRNGFVAFK-DDETLDRGNEISSELSKAIEESNVSIVILSKNY----ASSPWCLDELAKIVECGNKRND 107 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~-d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~----~~S~wc~~El~~~~~~~~~~~~ 107 (158)
..++.+|.+.|.+.|+.+-. ....+--|--+. +.-.-.+.++-|+-+|-+. ..+.--..+|..++....+..+
T Consensus 96 ~~la~~i~~~l~~~g~~~~~~~~~~lDHG~~vP--L~~l~p~~~~Pvv~is~~~~~~p~~~~~~~~~lG~aL~~~~~~~~ 173 (272)
T PF02900_consen 96 PELAERIAEHLRKAGFDVAASPERGLDHGVWVP--LYFLFPDADIPVVPISINSFAPPSPSPERHYRLGRALRKARESSD 173 (272)
T ss_dssp HHHHHHHHHHHHHTTS-EEECSS--B-HHHHHH--HHHHCTT-SSEEEEEEEETSSS-TS-HHHHHHHHHHHHHHHHTSG
T ss_pred HHHHHHHHHHHHhcCCCEEeccCcCCcccccee--eeecccccCcceeeeEeecccccCCCHHHHHHHHHHHHHHHHhcC
Confidence 57999999999999998643 333333333221 1122234567777777776 5666667789888887555456
Q ss_pred ceeEEEE
Q 041427 108 RKVFAVF 114 (158)
Q Consensus 108 ~~iiPV~ 114 (158)
++|.-|-
T Consensus 174 ~rv~vi~ 180 (272)
T PF02900_consen 174 ERVAVIA 180 (272)
T ss_dssp GCEEEEE
T ss_pred CCEEEEE
Confidence 6666554
No 106
>TIGR02742 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC. This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins are heterogeneous and are not covered by this model.
Probab=23.58 E-value=2.5e+02 Score=19.99 Aligned_cols=35 Identities=20% Similarity=0.131 Sum_probs=22.9
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCc
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGN 61 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~ 61 (158)
||+|+|--+. -...|....++.|+.+.+-. +..|+
T Consensus 3 vFvS~SMP~~---~Lk~l~~~a~~~g~~~VlRG--~~~~~ 37 (130)
T TIGR02742 3 VFVSFSMPEP---LLKQLLDQAEALGAPLVIRG--LLDNG 37 (130)
T ss_pred EEEEcCCCHH---HHHHHHHHHHHhCCeEEEeC--CCCCC
Confidence 7999998762 35556666667777666543 55554
No 107
>KOG1559 consensus Gamma-glutamyl hydrolase [Coenzyme transport and metabolism]
Probab=23.47 E-value=65 Score=26.02 Aligned_cols=23 Identities=22% Similarity=0.599 Sum_probs=16.5
Q ss_pred ccCCCceeEEEEEecCCchhhHHh
Q 041427 103 NKRNDRKVFAVFYGVDPTDRVFAK 126 (158)
Q Consensus 103 ~~~~~~~iiPV~~~v~p~~v~f~~ 126 (158)
.+.++.+|||+.|+ .|+++.|.+
T Consensus 86 aEsgGARViPli~n-epEe~lfqk 108 (340)
T KOG1559|consen 86 AESGGARVIPLIYN-EPEEILFQK 108 (340)
T ss_pred HHcCCceEEEEecC-CcHHHHHHH
Confidence 56789999999997 455553433
No 108
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase, dimeric type. This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases.
Probab=23.43 E-value=3e+02 Score=24.72 Aligned_cols=64 Identities=17% Similarity=0.116 Sum_probs=42.2
Q ss_pred CceeEEEecccCc-CchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 18 TKYDVFLSFRGED-TRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 18 ~~ydVFISys~~D-~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
..++|+|-.-..+ .....+..|...|++.|+++.+|.. |. +...+..+-+.---+++++.++-.
T Consensus 456 AP~kV~VIpl~~~~el~~~A~eIa~~LR~~GI~VeiD~s----~s-IGKq~rrADeiGiPf~IIIG~~El 520 (551)
T TIGR00389 456 APIKVAVLPLVNKEELKEIAKEIFQALRKTGIRIKYDDS----GT-IGKRYRRADEIGTPFCVTIDFETL 520 (551)
T ss_pred CCceEEEEEecCcHHHHHHHHHHHHHHHHCCCEEEEECC----CC-HHHHHHHHHHcCCCEEEEECCchh
Confidence 3577776554432 2245788999999999999999874 32 655666665544446666666544
No 109
>PF05985 EutC: Ethanolamine ammonia-lyase light chain (EutC); InterPro: IPR009246 This family consists of several bacterial ethanolamine ammonia-lyase light chain (EutC) sequences. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia [].; GO: 0008851 ethanolamine ammonia-lyase activity, 0006520 cellular amino acid metabolic process; PDB: 3ABO_B 3ABR_B 3ABS_B 3ANY_B 3AO0_D 3ABQ_B.
Probab=23.36 E-value=1.2e+02 Score=24.16 Aligned_cols=47 Identities=19% Similarity=0.348 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHhcCCeE----EEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 33 NNFTDHLHVALIRNGFV----AFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~----vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
..|...|...|...|++ ++...-.+..||.|. +.+ +.+++|+++.+.
T Consensus 123 ~~~l~~L~~~L~~~g~~~ap~~~v~~gRVa~gD~Ig----e~L-~a~~vv~LIGER 173 (237)
T PF05985_consen 123 APLLPALLPGLKSAGWSVAPPVLVRQGRVALGDEIG----EAL-GARVVVVLIGER 173 (237)
T ss_dssp HHHHHHHHHHHHTTTS-B---EEEET--TTHHHHHH----HHH-T-SEEEEEEE--
T ss_pred HHHHHHHHHHHHhcCCCcCCeEEEeeceeehhHHHH----HHh-CCCEEEEEEeCC
Confidence 56889999999998874 344554566666555 333 888899988776
No 110
>PRK07283 hypothetical protein; Provisional
Probab=23.15 E-value=2.3e+02 Score=18.89 Aligned_cols=49 Identities=14% Similarity=0.100 Sum_probs=23.3
Q ss_pred cCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 30 DTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 30 D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
|....-...+...-+..++.+..... .+++..++.+.+.+|.|..+.|.
T Consensus 43 Das~~~~kk~~~~~~~~~Vp~~~~~t--------~~eLG~a~Gk~~~vvai~d~g~a 91 (98)
T PRK07283 43 DAGPNLTKKVTDKSNYYQVEVSTVFS--------TLELSAAVGKPRKVLAVTDAGFS 91 (98)
T ss_pred CCCHHHHHHHHHHHHHcCCCEEEeCC--------HHHHHHHhCCCceEEEEeChhHH
Confidence 33334445555544455555532211 13555566655555555555443
No 111
>TIGR03646 YtoQ_fam YtoQ family protein. Members of this family are uncharacterized proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship.
Probab=23.15 E-value=1.6e+02 Score=21.45 Aligned_cols=40 Identities=18% Similarity=0.370 Sum_probs=26.6
Q ss_pred HHHhhhhcceEEEEEecCCCCChhh-HHHHHHHHHhhccCCCceeEEE
Q 041427 67 LSKAIEESNVSIVILSKNYASSPWC-LDELAKIVECGNKRNDRKVFAV 113 (158)
Q Consensus 67 i~~~i~~s~~~IvvlS~~~~~S~wc-~~El~~~~~~~~~~~~~~iiPV 113 (158)
....|++|+++|+-|.++|-+ |- -..-..+... ++.+|.+
T Consensus 69 T~~li~~aDvvVvrFGekYKQ--WNaAfDAg~aaAl-----gKplI~l 109 (144)
T TIGR03646 69 TRKLIEKADVVIALFGEKYKQ--WNAAFDAGYAAAL-----GKPLIIL 109 (144)
T ss_pred HHHHHhhCCEEEEEechHHHH--HHHHhhHHHHHHc-----CCCeEEe
Confidence 356799999999999999986 32 1223333333 6677655
No 112
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=23.01 E-value=3.5e+02 Score=22.68 Aligned_cols=66 Identities=12% Similarity=0.150 Sum_probs=42.2
Q ss_pred CceeEEEecccCcC-chhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhh-cceEEEEEec
Q 041427 18 TKYDVFLSFRGEDT-RNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEE-SNVSIVILSK 83 (158)
Q Consensus 18 ~~ydVFISys~~D~-~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~-s~~~IvvlS~ 83 (158)
...|+-|.+.+... .......|...|++.|+..|+|+.....+......+..++.. -+.+.++..|
T Consensus 188 gDvD~LithP~~~s~~~~~~~~l~~~le~~g~il~~~~~~S~~Ek~~l~~~~s~~~~~~~~mgv~~LP 255 (353)
T KOG2534|consen 188 GDVDFLITHPGSTSTEAKLLQLLMILLEKKGLLLYYDQLHSCGEKLRLPSRKSALDHFKKFMGVFRLP 255 (353)
T ss_pred CCeeEEEeCCCCCchhhhHHHHHHHHHHhcCeEEEEeeeccccccccccchhhhHhhhhhEEEEEEcC
Confidence 45788888854432 355678899999999999999875433333333334444443 3456666677
No 113
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=22.99 E-value=1.2e+02 Score=20.41 Aligned_cols=53 Identities=9% Similarity=0.244 Sum_probs=31.7
Q ss_pred HHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHH
Q 041427 42 ALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIV 99 (158)
Q Consensus 42 ~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~ 99 (158)
.+...|+..++-.. ..+...+.+.+.+.+-++.|++++++.+.. +.+++...+
T Consensus 14 GFrLaGi~~~~~~~---~~ee~~~~l~~l~~~~d~gII~Ite~~~~~--i~e~i~~~~ 66 (100)
T PRK02228 14 GFRLAGIRKVYEVP---DDEKLDEAVEEVLEDDDVGILVMHDDDLEK--LPRRLRRTL 66 (100)
T ss_pred HHHHcCCceEEeeC---CHHHHHHHHHHHhhCCCEEEEEEehhHhHh--hHHHHHHHH
Confidence 45566886544211 113455556666677889999999998763 334444433
No 114
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=22.98 E-value=1.4e+02 Score=18.46 Aligned_cols=31 Identities=19% Similarity=0.252 Sum_probs=23.0
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEEec
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKD 53 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d 53 (158)
.+.|+++..+ +.+++.+...|.+.||..-+.
T Consensus 21 ~~~i~~~~~s--~~ll~~v~~lL~~lGi~~~i~ 51 (77)
T PF14528_consen 21 SVRISISSKS--KELLEDVQKLLLRLGIKASIY 51 (77)
T ss_dssp EEEEEEEES---HHHHHHHHHHHHHTT--EEEE
T ss_pred EEEEEEEECC--HHHHHHHHHHHHHCCCeeEEE
Confidence 5678887776 579999999999999987665
No 115
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=22.54 E-value=77 Score=21.29 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHhcCCeEEEec
Q 041427 33 NNFTDHLHVALIRNGFVAFKD 53 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~d 53 (158)
..|+..|...|..+|+++-..
T Consensus 8 ~~fv~~Lk~lLk~rGi~v~~~ 28 (90)
T PF02337_consen 8 QPFVSILKHLLKERGIRVKKK 28 (90)
T ss_dssp HHHHHHHHHHHHCCT----HH
T ss_pred hHHHHHHHHHHHHcCeeecHH
Confidence 369999999999999988654
No 116
>cd07370 HPCD The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. HPCD 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.
Probab=22.19 E-value=4.1e+02 Score=21.16 Aligned_cols=78 Identities=12% Similarity=0.181 Sum_probs=48.9
Q ss_pred hhHHHHHHHHHhcCCeEEEe--cC-CCCCCCccccHHHHHhhh-hcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCc
Q 041427 33 NNFTDHLHVALIRNGFVAFK--DD-ETLDRGNEISSELSKAIE-ESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDR 108 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~--d~-~~l~~G~~i~~~i~~~i~-~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~ 108 (158)
..++..|.+.+...|+.+-. +. ..+.-|--+. + ..+. +.++-||.+|-+...+.--..+|..++....+..++
T Consensus 94 ~ela~~i~~~~~~~g~~~~~~~~~~~~lDhg~~vP--L-~~l~p~~~~pvV~is~~~~~~~~~~~~lG~al~~~~~~~~~ 170 (280)
T cd07370 94 PELAHLIAEEATEHGVKTLAHEDPSLPLEYGTLVP--M-RFMNEDDHFKVVSVAVWCTHDIEESRRLGEAIRRAIAASDR 170 (280)
T ss_pred HHHHHHHHHHHHHCCCCeeeecCCCCCCCeeHhhH--H-HHhCCCCCceEEEEeecCCCCHHHHHHHHHHHHHHHHhcCC
Confidence 56999999999999987653 22 1122222111 1 2222 346778888887767777778999988775444455
Q ss_pred eeEEE
Q 041427 109 KVFAV 113 (158)
Q Consensus 109 ~iiPV 113 (158)
+|+-|
T Consensus 171 ~v~iI 175 (280)
T cd07370 171 RVALL 175 (280)
T ss_pred CEEEE
Confidence 55544
No 117
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=22.12 E-value=2.4e+02 Score=24.74 Aligned_cols=55 Identities=20% Similarity=0.297 Sum_probs=34.4
Q ss_pred ccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHh
Q 041427 27 RGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVEC 101 (158)
Q Consensus 27 s~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~ 101 (158)
++.|.... ...+.|++.|+.+++.... +.+.+... ||.|..+... .-|+..++++
T Consensus 35 sGSD~~~~---~~t~~L~~~G~~i~~gh~~------------~ni~~~~~--VV~s~Ai~~~---NpEi~~A~e~ 89 (459)
T COG0773 35 SGSDLAES---PMTQRLEALGIEIFIGHDA------------ENILDADV--VVVSNAIKED---NPEIVAALER 89 (459)
T ss_pred ECcccccc---HHHHHHHHCCCeEeCCCCH------------HHcCCCce--EEEecccCCC---CHHHHHHHHc
Confidence 35555433 3566778889888886531 12333333 7778888864 3478888776
No 118
>cd02951 SoxW SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to sulfate. SoxW is specifically kept in the reduced state by SoxV, which is essential in thiosulfate oxidation.
Probab=22.10 E-value=2.2e+02 Score=19.17 Aligned_cols=31 Identities=16% Similarity=0.343 Sum_probs=20.8
Q ss_pred cHHHHHhhhhc-ceEEEEEecCCCCChhhHHHHH
Q 041427 64 SSELSKAIEES-NVSIVILSKNYASSPWCLDELA 96 (158)
Q Consensus 64 ~~~i~~~i~~s-~~~IvvlS~~~~~S~wc~~El~ 96 (158)
.+++.+++++- +.+++.|..... .+|.....
T Consensus 3 ~~~~~~a~~~~~k~vlv~f~a~wC--~~C~~~~~ 34 (125)
T cd02951 3 YEDLAEAAADGKKPLLLLFSQPGC--PYCDKLKR 34 (125)
T ss_pred HHHHHHHHHcCCCcEEEEEeCCCC--HHHHHHHH
Confidence 35677888888 777777765554 46766443
No 119
>PF03446 NAD_binding_2: NAD binding domain of 6-phosphogluconate dehydrogenase; InterPro: IPR006115 6-Phosphogluconate dehydrogenase (1.1.1.44 from EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) [, ]. Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequence are highly conserved []. The protein is a homodimer in which the monomers act independently []: each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet []. NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket []. This family represents the NADP binding domain of 6-phosphogluconate dehydrogenase which adopts a Rossman fold. The C-terminal domain is described in IPR006114 from INTERPRO.; GO: 0004616 phosphogluconate dehydrogenase (decarboxylating) activity, 0006098 pentose-phosphate shunt, 0055114 oxidation-reduction process; PDB: 3AX6_D 3PDU_G 3Q3C_A 3OBB_A 4DLL_B 1PGP_A 1PGN_A 2PGD_A 1PGQ_A 1PGO_A ....
Probab=22.00 E-value=85 Score=22.67 Aligned_cols=50 Identities=18% Similarity=0.349 Sum_probs=32.4
Q ss_pred HHHHHHHHHhcCCeEEEecCCCC-------CCCccccHHHHHhhhhcceEEEEEecC
Q 041427 35 FTDHLHVALIRNGFVAFKDDETL-------DRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 35 fv~~L~~~L~~~gi~vf~d~~~l-------~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
.-..+...|.+.|+.++.-++.- ..|-...+...+.++++++++..+...
T Consensus 12 mG~~~a~~L~~~g~~v~~~d~~~~~~~~~~~~g~~~~~s~~e~~~~~dvvi~~v~~~ 68 (163)
T PF03446_consen 12 MGSAMARNLAKAGYEVTVYDRSPEKAEALAEAGAEVADSPAEAAEQADVVILCVPDD 68 (163)
T ss_dssp HHHHHHHHHHHTTTEEEEEESSHHHHHHHHHTTEEEESSHHHHHHHBSEEEE-SSSH
T ss_pred HHHHHHHHHHhcCCeEEeeccchhhhhhhHHhhhhhhhhhhhHhhcccceEeecccc
Confidence 34556666677788876644321 245556667788899998888876653
No 120
>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=21.76 E-value=55 Score=30.44 Aligned_cols=65 Identities=14% Similarity=0.308 Sum_probs=42.6
Q ss_pred CChhhHHHHHH-HHHhhccCCCceeEEEEEe-cCCchhhHHhhHHHhhhCHHHHHHHHHHHHHhhccc
Q 041427 87 SSPWCLDELAK-IVECGNKRNDRKVFAVFYG-VDPTDRVFAKYEEEFKENHEKVLKWRAALTRVASLA 152 (158)
Q Consensus 87 ~S~wc~~El~~-~~~~~~~~~~~~iiPV~~~-v~p~~v~f~~~~~~~~~~~~~~~~W~~al~~i~~~~ 152 (158)
++.||.+++.. +.+........-=+|||.+ =.|+.+.|.++.+-.. +.+.+...|++|++|++|+
T Consensus 1032 ~~~~~~~~~~qE~~deV~~~k~~~sL~i~vRRW~Ps~~e~~pFQEV~L-d~~~~~E~Re~LS~ISgIP 1098 (1203)
T KOG4598|consen 1032 SYNWCSHLYLQEITDEVMIGKPGESLPIMVRRWRPSTVEVNPFQEVLL-DANAEVEFREALSKISGIP 1098 (1203)
T ss_pred hhhhHHHHHHHHHHhhcccCCCCccchhhheeccccceecCCceeEEe-cCcchHHHHHHHHHhcCCc
Confidence 56899887644 4443344455566888874 6788885544433221 3455678899999999987
No 121
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=21.68 E-value=1.4e+02 Score=19.97 Aligned_cols=54 Identities=11% Similarity=0.191 Sum_probs=30.2
Q ss_pred eeEEEecccCcCchhHHHHHHHHHhcCCeEEEe-cCCCCCCCccccHHHHHhhhhcceEEEEEecCCC
Q 041427 20 YDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFK-DDETLDRGNEISSELSKAIEESNVSIVILSKNYA 86 (158)
Q Consensus 20 ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~-d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~ 86 (158)
.=++||+++.. ...+..+. .++++|.++-. -.. ++. ...+.++..+.+-+.+..
T Consensus 56 ~vi~is~sg~~--~~~~~~~~-~ak~~g~~vi~iT~~---~~~-------~l~~~ad~~l~~~~~~~~ 110 (131)
T PF01380_consen 56 LVIIISYSGET--RELIELLR-FAKERGAPVILITSN---SES-------PLARLADIVLYIPTGEES 110 (131)
T ss_dssp EEEEEESSSTT--HHHHHHHH-HHHHTTSEEEEEESS---TTS-------HHHHHSSEEEEEESSCGS
T ss_pred eeEeeeccccc--hhhhhhhH-HHHhcCCeEEEEeCC---CCC-------chhhhCCEEEEecCCCcc
Confidence 34577777665 44555555 88888876632 211 111 223566777776665544
No 122
>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=21.47 E-value=2.4e+02 Score=21.63 Aligned_cols=35 Identities=11% Similarity=0.137 Sum_probs=26.5
Q ss_pred EEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCC
Q 041427 50 AFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS 87 (158)
Q Consensus 50 vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~ 87 (158)
||+|.- -+..+..++...+.+..+-|+++||.--.
T Consensus 127 VW~D~f---~~~~~~~~~~~~~~~~~~~~c~VSpELh~ 161 (192)
T cd08584 127 VWIDSF---TSLWLDNDLILKLLKAGKKICLVSPELHG 161 (192)
T ss_pred EEEecc---cccCCCHHHHHHHHHCCcEEEEECHHHcC
Confidence 888862 24667777777778888889999998654
No 123
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=21.28 E-value=2.2e+02 Score=18.89 Aligned_cols=38 Identities=21% Similarity=0.183 Sum_probs=27.2
Q ss_pred ccCCCCCCceeEEEecccC-cCchhHHHHHHHHHhcCCe
Q 041427 11 THHQILQTKYDVFLSFRGE-DTRNNFTDHLHVALIRNGF 48 (158)
Q Consensus 11 ~~~~~~~~~ydVFISys~~-D~~~~fv~~L~~~L~~~gi 48 (158)
+....+.-..|++|.+... .....+...|.+.|++.+.
T Consensus 30 ~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~ 68 (114)
T cd05402 30 TGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGE 68 (114)
T ss_pred cCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCC
Confidence 3444556689999999764 2346788999999987773
No 124
>PRK01189 V-type ATP synthase subunit F; Provisional
Probab=21.16 E-value=1.6e+02 Score=20.13 Aligned_cols=41 Identities=5% Similarity=0.177 Sum_probs=29.2
Q ss_pred HHhcCCeE-EEecCCCCCCCccccHHHHHhhhhcceEEEEEecCCCC
Q 041427 42 ALIRNGFV-AFKDDETLDRGNEISSELSKAIEESNVSIVILSKNYAS 87 (158)
Q Consensus 42 ~L~~~gi~-vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~ 87 (158)
.++..|+. +|-..++ + -..++.+.+.+-++.|++++++.+.
T Consensus 16 GFrlaGi~~v~~~~~~----e-~~~~~~~~l~~~~~gII~iTE~~a~ 57 (104)
T PRK01189 16 GFRLLGIGDTIEAEGK----D-LVKKFLEIFNNPKCKYIFVSESTKN 57 (104)
T ss_pred HHHHcCCceEEEcCCH----H-HHHHHHHHHhcCCeEEEEEEHHHHh
Confidence 45667885 7754332 2 2357777888999999999999876
No 125
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=21.06 E-value=2.2e+02 Score=24.07 Aligned_cols=52 Identities=10% Similarity=0.199 Sum_probs=37.1
Q ss_pred cCcCchhHHHHHHHHHhcCCeEEEecCCCCCC----CccccHHHHHhhhhcceEEE
Q 041427 28 GEDTRNNFTDHLHVALIRNGFVAFKDDETLDR----GNEISSELSKAIEESNVSIV 79 (158)
Q Consensus 28 ~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~----G~~i~~~i~~~i~~s~~~Iv 79 (158)
..|.|++=+-.|.+.|..+|..|-..+--+.. |-.+.++...+++.++.+|+
T Consensus 310 t~D~R~Sp~~~i~~~L~~~G~~v~~~DP~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 365 (388)
T PRK15057 310 SDNFRASSIQGIMKRIKAKGVEVIIYEPVMKEDSFFNSRLERDLATFKQQADVIIS 365 (388)
T ss_pred CCccccChHHHHHHHHHhCCCEEEEECCCCCchhhcCCeeeCCHHHHHHhCCEEEE
Confidence 35777888889999999999877664322222 34456677788888888766
No 126
>PF04244 DPRP: Deoxyribodipyrimidine photo-lyase-related protein; InterPro: IPR007357 This family appears to be related to DNA photolyases.; PDB: 3ZXS_A.
Probab=20.88 E-value=2e+02 Score=22.40 Aligned_cols=16 Identities=38% Similarity=0.513 Sum_probs=7.1
Q ss_pred hHHHHHHHHHhcCCeE
Q 041427 34 NFTDHLHVALIRNGFV 49 (158)
Q Consensus 34 ~fv~~L~~~L~~~gi~ 49 (158)
+|...|...|+..|+.
T Consensus 78 s~~~~L~~~~~~~~~~ 93 (224)
T PF04244_consen 78 SFEDALARALKQHGID 93 (224)
T ss_dssp SHHHHHHHHHHHH---
T ss_pred cHHHHHHHHHHHcCCC
Confidence 4555555555555543
No 127
>PF13155 Toprim_2: Toprim-like
Probab=20.86 E-value=1.6e+02 Score=18.87 Aligned_cols=39 Identities=18% Similarity=0.239 Sum_probs=25.9
Q ss_pred HHHHHHHHHhc---CCeEEEecCCCCCCCccccHHHHHhhhhcc
Q 041427 35 FTDHLHVALIR---NGFVAFKDDETLDRGNEISSELSKAIEESN 75 (158)
Q Consensus 35 fv~~L~~~L~~---~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~ 75 (158)
....+...|++ +.|.+++|.. ..|......+.+.+....
T Consensus 34 ~~~~~~~~l~~~~~~~i~l~~DnD--~aG~~~~~~~~~~l~~~~ 75 (96)
T PF13155_consen 34 SEKQQIKFLKENPYKKIVLAFDND--EAGRKAAEKLQKELKEEG 75 (96)
T ss_pred HHHHHHHHHHhCCCCcEEEEeCCC--HHHHHHHHHHHHHHHhhC
Confidence 34456666633 3577777763 678888888877777654
No 128
>COG0434 SgcQ Predicted TIM-barrel enzyme [General function prediction only]
Probab=20.66 E-value=4.6e+02 Score=21.14 Aligned_cols=74 Identities=20% Similarity=0.260 Sum_probs=53.7
Q ss_pred HHHHhcCCeEEEecCCCCCCCccc-----cHHHHHhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEE
Q 041427 40 HVALIRNGFVAFKDDETLDRGNEI-----SSELSKAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVF 114 (158)
Q Consensus 40 ~~~L~~~gi~vf~d~~~l~~G~~i-----~~~i~~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~ 114 (158)
+..|. .+++++-|-. .+-|.++ .+...+.++....=-+|+|-.-..++=-.+||..+.+. .. .|||
T Consensus 139 r~~L~-~~v~vlADv~-VKHa~~l~~~~~~~~v~dtver~~aDaVI~tG~~TG~~~d~~el~~a~~~-----~~--~pvl 209 (263)
T COG0434 139 RARLG-SRVKVLADVH-VKHAVHLGNRSLEEAVKDTVERGLADAVIVTGSRTGSPPDLEELKLAKEA-----VD--TPVL 209 (263)
T ss_pred HHhcc-CCcEEEeecc-hhcccccCCcCHHHHHHHHHHccCCCEEEEecccCCCCCCHHHHHHHHhc-----cC--CCEE
Confidence 33444 6899999864 5555444 34555567777777788899999999999999998776 22 8999
Q ss_pred Ee--cCCchh
Q 041427 115 YG--VDPTDR 122 (158)
Q Consensus 115 ~~--v~p~~v 122 (158)
.+ +.+.++
T Consensus 210 vGSGv~~eN~ 219 (263)
T COG0434 210 VGSGVNPENI 219 (263)
T ss_pred EecCCCHHHH
Confidence 85 777776
No 129
>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=20.64 E-value=2.9e+02 Score=18.90 Aligned_cols=38 Identities=24% Similarity=0.329 Sum_probs=23.0
Q ss_pred EEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccH
Q 041427 22 VFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISS 65 (158)
Q Consensus 22 VFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~ 65 (158)
||+|+|--+ .. ...|....++.|+.+-+- .+..| .+.+
T Consensus 2 iFvS~SMP~--~~-L~~l~~~a~~~~~~~V~R--G~~~g-~~~~ 39 (113)
T PF09673_consen 2 IFVSFSMPD--AS-LRNLLKQAERAGVVVVFR--GFPDG-SFKP 39 (113)
T ss_pred EEEECCCCH--HH-HHHHHHHHHhCCcEEEEE--CCCCC-CHHH
Confidence 799999887 33 444445555556666553 36666 4443
No 130
>TIGR00177 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis.
Probab=20.59 E-value=1.5e+02 Score=21.13 Aligned_cols=45 Identities=24% Similarity=0.274 Sum_probs=26.0
Q ss_pred hHHHHHHHHHhcCCeEEEecCCCCCCC--ccccHHHHHhhhhcceEEEE
Q 041427 34 NFTDHLHVALIRNGFVAFKDDETLDRG--NEISSELSKAIEESNVSIVI 80 (158)
Q Consensus 34 ~fv~~L~~~L~~~gi~vf~d~~~l~~G--~~i~~~i~~~i~~s~~~Ivv 80 (158)
.....|.+.|++.|+.+..-. ..+- +.+.+.+.+++++++++|..
T Consensus 27 ~n~~~l~~~l~~~G~~v~~~~--~v~Dd~~~i~~~l~~~~~~~DliItt 73 (144)
T TIGR00177 27 SNGPLLAALLEEAGFNVSRLG--IVPDDPEEIREILRKAVDEADVVLTT 73 (144)
T ss_pred CcHHHHHHHHHHCCCeEEEEe--ecCCCHHHHHHHHHHHHhCCCEEEEC
Confidence 345678888899998766421 1111 23445555566666665554
No 131
>COG3286 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.59 E-value=3.5e+02 Score=20.92 Aligned_cols=45 Identities=29% Similarity=0.341 Sum_probs=26.3
Q ss_pred ceeEEE--EEecCCchhhHHhhHHHhh-hC----HHHHHHHHHHHHHhhccc
Q 041427 108 RKVFAV--FYGVDPTDRVFAKYEEEFK-EN----HEKVLKWRAALTRVASLA 152 (158)
Q Consensus 108 ~~iiPV--~~~v~p~~v~f~~~~~~~~-~~----~~~~~~W~~al~~i~~~~ 152 (158)
+.|.|+ .|+.+|.|+.-.-....+- +. ...+..|+.+|..+++.-
T Consensus 146 klVv~~S~~~~~~~dd~~eeave~Gll~e~E~~~~~~~~~~e~~L~~l~~~l 197 (204)
T COG3286 146 KLVVAVSIVYGLDPDDAAEEAVELGLLEEGEDGLRELIKNKERALETLLKAL 197 (204)
T ss_pred hhhhhhhhHhCCCHHHHHHHHHHhhhhhccchhHHHhhhhHHHHHHHHHHHh
Confidence 344554 4689999982222222221 11 245778999999887654
No 132
>PRK15018 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional
Probab=20.57 E-value=92 Score=24.49 Aligned_cols=48 Identities=10% Similarity=0.027 Sum_probs=29.6
Q ss_pred HhhhhcceEEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEEEEEe
Q 041427 69 KAIEESNVSIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFAVFYG 116 (158)
Q Consensus 69 ~~i~~s~~~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiPV~~~ 116 (158)
+.+.+-...|+|+=+..-+..-.+.++..-.-.+....+.+|+||.+.
T Consensus 133 ~~l~~~g~sv~IFPEGTRs~~g~l~~Fk~Ga~~lA~~~~~PIvPv~i~ 180 (245)
T PRK15018 133 NHFKKRRISIWMFPEGTRSRGRGLLPFKTGAFHAAIAAGVPIIPVCVS 180 (245)
T ss_pred HHHHhCCCEEEEECCccCCCCCCCCCccHHHHHHHHHcCCCEEEEEEE
Confidence 344445667888888776655555555543333344457889998775
No 133
>cd07362 HPCD_like Class III extradiol dioxygenases with similarity to homoprotocatechuate 2,3-dioxygenase, which catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. This subfamily of class III extradiol dioxygenases consists of two types of proteins with known enzymatic activities; 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) and 2-amino-5-chlorophenol 1,6-dioxygenase. HPCD catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield the product alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. 2-amino-5-chlorophenol 1,6-dioxygenase catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. The enzyme is probably a heterotetrame
Probab=20.55 E-value=4.4e+02 Score=20.95 Aligned_cols=79 Identities=14% Similarity=0.109 Sum_probs=48.4
Q ss_pred hhHHHHHHHHHhcCCeEEEe-c--CCCCCCCccccHHHHHhhhhcceEEEEEecCC-CCChhhHHHHHHHHHhhccCCCc
Q 041427 33 NNFTDHLHVALIRNGFVAFK-D--DETLDRGNEISSELSKAIEESNVSIVILSKNY-ASSPWCLDELAKIVECGNKRNDR 108 (158)
Q Consensus 33 ~~fv~~L~~~L~~~gi~vf~-d--~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~~-~~S~wc~~El~~~~~~~~~~~~~ 108 (158)
..++..|.+.|.+.|+.+-. . ...+--|.-+. +.-.-.+.++-||-+|-+. ..+..-..+|..++.+..+..++
T Consensus 92 ~~LA~~i~~~l~~~Gi~~~~~~~~~~~lDHG~~vP--L~~l~p~~~iPVV~vs~~~~~~~~~~~~~lG~ai~~al~~~~~ 169 (272)
T cd07362 92 PELGRLLVEEGQEAGLRVKAVNDPTYIWDYGTVVP--LRYLNPNKDIPVVSISACWTAASLEESYTWGEVIGKALLESDK 169 (272)
T ss_pred HHHHHHHHHHHHHcCCceeeccCCCCCCCcchHHH--HHHhCCCCCCcEEEEeccCCCCCHHHHHHHHHHHHHHHHhhCC
Confidence 67999999999999998853 2 22333444332 1112234678889999887 56677777888555332222245
Q ss_pred eeEEE
Q 041427 109 KVFAV 113 (158)
Q Consensus 109 ~iiPV 113 (158)
+|+-|
T Consensus 170 rv~ii 174 (272)
T cd07362 170 RVVFL 174 (272)
T ss_pred CEEEE
Confidence 55544
No 134
>cd03411 Ferrochelatase_N Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=20.49 E-value=3.4e+02 Score=19.57 Aligned_cols=65 Identities=17% Similarity=0.242 Sum_probs=37.7
Q ss_pred hHHHHHHHHHhcCC--eEEEecCCCCCCCccccHHHH-Hhhhh--cceEEEEEecCCC--CChhhHHHHHHHHHh
Q 041427 34 NFTDHLHVALIRNG--FVAFKDDETLDRGNEISSELS-KAIEE--SNVSIVILSKNYA--SSPWCLDELAKIVEC 101 (158)
Q Consensus 34 ~fv~~L~~~L~~~g--i~vf~d~~~l~~G~~i~~~i~-~~i~~--s~~~IvvlS~~~~--~S~wc~~El~~~~~~ 101 (158)
..+..|.+.|.+.+ +.+++- +.-|.+..++.. +..++ -+++++-+.|.|. +..-+.+++..++..
T Consensus 72 ~q~~~l~~~L~~~~~~~~v~~a---mry~~P~i~~~l~~l~~~g~~~iivlPl~P~~S~~Tt~s~~~~~~~~~~~ 143 (159)
T cd03411 72 AQAEALEKALDERGIDVKVYLA---MRYGPPSIEEALEELKADGVDRIVVLPLYPQYSASTTGSYLDEVERALKK 143 (159)
T ss_pred HHHHHHHHHHhccCCCcEEEeh---HhcCCCCHHHHHHHHHHcCCCEEEEEECCcccccccHHHHHHHHHHHHHh
Confidence 45667777776643 445443 445555444433 33333 4557777888776 445567777776654
No 135
>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=20.44 E-value=3.7e+02 Score=20.02 Aligned_cols=69 Identities=26% Similarity=0.246 Sum_probs=42.1
Q ss_pred HHhcCCeEEEe-cCC-CCC-CC-ccccHHHHHhhhhcce-----EEEEEecCCCCChhhHHHHHHHHHhhccCCCceeEE
Q 041427 42 ALIRNGFVAFK-DDE-TLD-RG-NEISSELSKAIEESNV-----SIVILSKNYASSPWCLDELAKIVECGNKRNDRKVFA 112 (158)
Q Consensus 42 ~L~~~gi~vf~-d~~-~l~-~G-~~i~~~i~~~i~~s~~-----~IvvlS~~~~~S~wc~~El~~~~~~~~~~~~~~iiP 112 (158)
.|.+.||+..+ |.. .+. ++ +.+.+++.+.+++++. -|+|+|.+.-.+.--..+-...++. ..+ ||
T Consensus 35 ~Lk~~Gik~li~DkDNTL~~~~~~~i~~~~~~~~~~l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~---~lg---Ip 108 (168)
T PF09419_consen 35 HLKKKGIKALIFDKDNTLTPPYEDEIPPEYAEWLNELKKQFGKDRVLIVSNSAGSSDDPDGERAEALEK---ALG---IP 108 (168)
T ss_pred hhhhcCceEEEEcCCCCCCCCCcCcCCHHHHHHHHHHHHHCCCCeEEEEECCCCcccCccHHHHHHHHH---hhC---Cc
Confidence 48899998876 422 353 33 4667788888887774 3899999876555322333333332 122 88
Q ss_pred EEEe
Q 041427 113 VFYG 116 (158)
Q Consensus 113 V~~~ 116 (158)
|+..
T Consensus 109 vl~h 112 (168)
T PF09419_consen 109 VLRH 112 (168)
T ss_pred EEEe
Confidence 7743
No 136
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.43 E-value=3.2e+02 Score=23.65 Aligned_cols=63 Identities=22% Similarity=0.211 Sum_probs=43.6
Q ss_pred CCceeEEEecccCcCchhHHHHHHHHHhcCCeEEEecCCCCCCCccccHHHHHhhhhcceEEEEEecC
Q 041427 17 QTKYDVFLSFRGEDTRNNFTDHLHVALIRNGFVAFKDDETLDRGNEISSELSKAIEESNVSIVILSKN 84 (158)
Q Consensus 17 ~~~ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf~d~~~l~~G~~i~~~i~~~i~~s~~~IvvlS~~ 84 (158)
....||||..-+++. ...+-.|...|++.|+++-+|... ..+..++..|-+.--.+++|+.++
T Consensus 333 ~~~~~v~v~~~~~~~-~~~a~~la~~LR~~g~~~~~~~~~----r~~k~q~k~A~~~g~~~~viiGe~ 395 (429)
T COG0124 333 ETRVDVYVVPLGEDA-EPEALKLAQKLRAAGISVEVDYSG----RKLKKQFKYADKLGARFAVILGED 395 (429)
T ss_pred CCCCCEEEEEcCchh-HHHHHHHHHHHHHcCCcEEEEecc----ccHHHHHHHHHHCCCCEEEEEcch
Confidence 346789999877775 467889999999999999887542 125556666655444455555543
No 137
>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=20.27 E-value=4.6e+02 Score=20.99 Aligned_cols=31 Identities=19% Similarity=0.177 Sum_probs=16.1
Q ss_pred eEEEecccCcCchhHHHHHHHHHhcCCeEEE
Q 041427 21 DVFLSFRGEDTRNNFTDHLHVALIRNGFVAF 51 (158)
Q Consensus 21 dVFISys~~D~~~~fv~~L~~~L~~~gi~vf 51 (158)
.|.|-|...+-.+..+..+.+.|++.|+.+-
T Consensus 140 ~v~ii~~~~~~g~~~~~~~~~~~~~~G~~v~ 170 (347)
T cd06335 140 KVALLLDNTGWGRSNRKDLTAALAARGLKPV 170 (347)
T ss_pred eEEEEeccCchhhhHHHHHHHHHHHcCCeeE
Confidence 3444443332234456666666666666654
No 138
>cd06386 PBP1_NPR_C_like Ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANPCNPBNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation.
Probab=20.22 E-value=3.1e+02 Score=22.58 Aligned_cols=18 Identities=11% Similarity=0.161 Sum_probs=12.0
Q ss_pred HHHHHHHHhcCCeEEEec
Q 041427 36 TDHLHVALIRNGFVAFKD 53 (158)
Q Consensus 36 v~~L~~~L~~~gi~vf~d 53 (158)
+..|.+.|+..|+.+-..
T Consensus 157 ~~~l~~~~~~~gi~v~~~ 174 (387)
T cd06386 157 LEGVHHVFQEEGYHMSIY 174 (387)
T ss_pred HHHHHHHHHhcCceEEEE
Confidence 566777777777766543
No 139
>PF02878 PGM_PMM_I: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I; InterPro: IPR005844 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents domain I found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 3I3W_B 1WQA_C 1KFQ_B 1KFI_A 2Z0F_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=20.11 E-value=2.2e+02 Score=19.82 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=18.7
Q ss_pred eeEEEecccCcCchhHHHHHHHHHhcCCeEEE
Q 041427 20 YDVFLSFRGEDTRNNFTDHLHVALIRNGFVAF 51 (158)
Q Consensus 20 ydVFISys~~D~~~~fv~~L~~~L~~~gi~vf 51 (158)
..|.|+|-.......++..+.+.|...|+.|+
T Consensus 41 ~~VvVg~D~R~~s~~~~~~~~~~l~~~G~~V~ 72 (137)
T PF02878_consen 41 SRVVVGRDTRPSSPMLAKALAAGLRANGVDVI 72 (137)
T ss_dssp SEEEEEE-SSTTHHHHHHHHHHHHHHTTEEEE
T ss_pred CeEEEEEcccCCHHHHHHHHHHHHhhcccccc
Confidence 44666664444445566666666666666666
No 140
>COG1323 Predicted nucleotidyltransferase [General function prediction only]
Probab=20.06 E-value=2.7e+02 Score=23.51 Aligned_cols=40 Identities=13% Similarity=0.334 Sum_probs=25.5
Q ss_pred CCCCccccHHHHHhhhhcceEEEEEecCCCC-------ChhhHHHHH
Q 041427 57 LDRGNEISSELSKAIEESNVSIVILSKNYAS-------SPWCLDELA 96 (158)
Q Consensus 57 l~~G~~i~~~i~~~i~~s~~~IvvlS~~~~~-------S~wc~~El~ 96 (158)
+..|....-+-.+..-.++..|+++|-+|.+ ..|-+.++.
T Consensus 13 fHnGH~y~i~~Ar~~~~~d~~i~~msgdf~qRgepai~~k~~r~~~a 59 (358)
T COG1323 13 FHNGHQYHINKAREEFKGDEIIAVMSGDFTQRGEPAIGHKWERKKMA 59 (358)
T ss_pred ccccHHHHHHHHHHhccCCceEEeeecchhhcCCCccccHHHHHhhh
Confidence 4455544433334456888999999999974 567554443
No 141
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=20.04 E-value=1.4e+02 Score=24.09 Aligned_cols=40 Identities=18% Similarity=0.189 Sum_probs=29.2
Q ss_pred CCCceeEEEecccCcCch-----------------------hHHHHHHHHHhcCCeEEEecCC
Q 041427 16 LQTKYDVFLSFRGEDTRN-----------------------NFTDHLHVALIRNGFVAFKDDE 55 (158)
Q Consensus 16 ~~~~ydVFISys~~D~~~-----------------------~fv~~L~~~L~~~gi~vf~d~~ 55 (158)
.+.+..|+|=|.|.++.. .....|.+.|+++||.|..|..
T Consensus 70 ~~~~~~V~IYhTH~~EsY~p~~~~~~~~~~~~~~~~~~nV~~VG~~L~~~Le~~Gi~v~h~~t 132 (268)
T PF07454_consen 70 TSGKPQVLIYHTHSTESYLPSDGLKSVPGPGGATDEEVNVVKVGDRLAQELEKYGIGVIHDKT 132 (268)
T ss_pred CCCCCEEEEEeCCCccccccccccccCCCCCccccccchHHHHHHHHHHHHHHCCCcEEEeCC
Confidence 456788999877665420 1236789999999999988865
Done!