Query 043542
Match_columns 99
No_of_seqs 101 out of 356
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 06:03:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043542hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04800 ETC_C1_NDUFA4: ETC co 100.0 1.4E-53 3.1E-58 293.3 5.8 93 1-96 4-97 (101)
2 KOG3389 NADH:ubiquinone oxidor 100.0 1.6E-47 3.5E-52 280.4 6.6 97 1-98 79-175 (178)
3 PF09954 DUF2188: Uncharacteri 88.6 0.36 7.8E-06 29.5 2.0 27 51-77 22-53 (62)
4 PHA02552 4 head completion pro 85.7 0.75 1.6E-05 33.8 2.6 21 57-77 120-140 (151)
5 PRK05370 argininosuccinate syn 83.3 0.79 1.7E-05 39.0 2.0 23 52-74 164-186 (447)
6 PF08727 P3A: Poliovirus 3A pr 81.7 1.1 2.3E-05 28.4 1.7 16 58-73 30-45 (57)
7 PF05573 NosL: NosL; InterPro 80.0 2.2 4.8E-05 30.4 3.1 51 17-68 76-135 (149)
8 PF08722 Tn7_Tnp_TnsA_N: TnsA 76.7 3 6.5E-05 26.7 2.7 19 57-75 69-87 (88)
9 PF03462 PCRF: PCRF domain; I 69.5 4.2 9E-05 27.9 2.2 17 61-77 73-89 (115)
10 PF11360 DUF3110: Protein of u 68.8 6.5 0.00014 26.2 3.0 20 58-77 58-77 (86)
11 PF07045 DUF1330: Protein of u 66.2 5.9 0.00013 24.3 2.2 14 51-64 43-56 (65)
12 KOG2854 Possible pfkB family c 66.0 5.1 0.00011 33.2 2.4 22 51-72 216-237 (343)
13 PF11360 DUF3110: Protein of u 65.6 5.3 0.00012 26.6 2.0 17 51-67 26-42 (86)
14 PRK04527 argininosuccinate syn 64.1 4.8 0.0001 33.7 1.9 20 53-72 150-169 (400)
15 PF06194 Phage_Orf51: Phage Co 64.1 6.2 0.00013 26.4 2.1 24 50-73 50-73 (80)
16 PF03108 DBD_Tnp_Mut: MuDR fam 61.7 9.4 0.0002 23.2 2.5 32 51-82 7-42 (67)
17 PF12518 DUF3721: Protein of u 61.7 8 0.00017 22.0 2.0 16 54-69 1-16 (34)
18 KOG4748 Subunit of Golgi manno 60.2 6.2 0.00013 32.9 1.9 23 56-78 127-149 (364)
19 PF01071 GARS_A: Phosphoribosy 58.1 14 0.0003 28.0 3.4 27 51-77 20-46 (194)
20 PF02844 GARS_N: Phosphoribosy 57.6 12 0.00027 25.5 2.8 28 51-78 45-72 (100)
21 PF08803 ydhR: Putative mono-o 56.6 7.2 0.00016 26.9 1.5 29 37-67 38-66 (97)
22 PF01693 Cauli_VI: Caulimoviru 56.3 11 0.00023 21.7 1.9 13 51-63 32-44 (44)
23 PF10075 PCI_Csn8: COP9 signal 54.7 8.3 0.00018 26.7 1.6 20 52-72 107-126 (143)
24 PRK05773 3,4-dihydroxy-2-butan 54.1 12 0.00026 29.0 2.5 18 55-72 191-208 (219)
25 COG0137 ArgG Argininosuccinate 53.7 14 0.0003 31.3 3.0 21 53-74 151-171 (403)
26 PF13031 DUF3892: Protein of u 52.7 13 0.00028 23.9 2.2 22 53-74 29-50 (85)
27 PRK00823 phhB pterin-4-alpha-c 52.7 16 0.00034 24.3 2.6 35 32-68 16-50 (97)
28 COG0108 RibB 3,4-dihydroxy-2-b 52.1 13 0.00028 28.7 2.4 20 55-74 172-191 (203)
29 PF07862 Nif11: Nitrogen fixat 51.9 7.3 0.00016 22.6 0.8 21 54-74 26-46 (49)
30 PLN00139 hypothetical protein; 50.6 15 0.00032 29.5 2.6 26 52-77 195-220 (320)
31 PRK13820 argininosuccinate syn 50.1 24 0.00051 29.4 3.8 18 56-73 148-165 (394)
32 PLN00200 argininosuccinate syn 49.1 26 0.00055 29.4 3.8 19 53-71 152-170 (404)
33 cd00913 PCD_DCoH_subfamily_a P 49.1 26 0.00057 22.1 3.1 30 36-67 1-30 (76)
34 PF03793 PASTA: PASTA domain; 48.5 24 0.00053 20.7 2.8 22 55-76 9-30 (63)
35 cd00914 PCD_DCoH_subfamily_b P 47.1 22 0.00047 22.6 2.5 29 36-66 1-29 (76)
36 PF09383 NIL: NIL domain; Int 46.0 22 0.00047 22.0 2.3 18 57-74 59-76 (76)
37 PF01329 Pterin_4a: Pterin 4 a 45.8 20 0.00043 23.6 2.3 30 33-66 16-46 (95)
38 PF05637 Glyco_transf_34: gala 44.8 16 0.00034 28.0 1.8 18 58-75 31-48 (239)
39 PF03682 UPF0158: Uncharacteri 44.6 17 0.00037 26.6 1.9 20 57-76 127-146 (163)
40 PRK11118 putative monooxygenas 44.5 29 0.00063 24.1 3.0 29 37-67 41-69 (100)
41 COG5470 Uncharacterized conser 44.2 23 0.0005 24.5 2.4 26 32-63 44-69 (96)
42 KOG1706 Argininosuccinate synt 44.2 13 0.00029 31.1 1.5 23 53-75 154-176 (412)
43 PF05406 WGR: WGR domain; Int 43.8 24 0.00051 22.3 2.3 47 15-66 17-64 (81)
44 smart00461 WH1 WASP homology r 43.6 21 0.00046 24.0 2.2 17 51-67 86-102 (106)
45 COG3341 Predicted double-stran 43.6 14 0.0003 29.1 1.4 14 53-66 39-52 (225)
46 PF00568 WH1: WH1 domain; Int 43.1 23 0.0005 23.8 2.3 16 51-66 91-106 (111)
47 PF07014 Hs1pro-1_C: Hs1pro-1 42.4 11 0.00025 29.9 0.7 27 38-64 228-254 (261)
48 PRK09437 bcp thioredoxin-depen 41.5 34 0.00074 23.2 3.0 28 50-77 68-95 (154)
49 cd00837 EVH1 EVH1 (Enabled, Va 40.9 26 0.00056 23.4 2.2 16 51-66 84-99 (104)
50 PF02786 CPSase_L_D2: Carbamoy 40.3 31 0.00068 25.8 2.9 23 55-77 25-47 (211)
51 TIGR00506 ribB 3,4-dihydroxy-2 40.3 27 0.00059 26.6 2.5 19 54-72 172-190 (199)
52 PF10566 Glyco_hydro_97: Glyco 40.2 30 0.00065 27.5 2.9 26 51-76 28-53 (273)
53 smart00156 PP2Ac Protein phosp 40.1 53 0.0012 25.5 4.2 42 29-77 176-220 (271)
54 PF12745 HGTP_anticodon2: Anti 40.1 33 0.00072 27.1 3.1 24 54-77 43-66 (273)
55 PRK01792 ribB 3,4-dihydroxy-2- 39.9 27 0.0006 27.0 2.5 19 54-72 182-200 (214)
56 PF02177 APP_N: Amyloid A4 N-t 39.6 32 0.0007 23.9 2.6 24 51-74 31-54 (102)
57 cd01207 Ena-Vasp Enabled-VASP- 39.3 26 0.00056 24.5 2.1 17 51-67 87-103 (111)
58 PF05198 IF3_N: Translation in 39.1 42 0.00092 21.7 3.0 28 51-78 24-51 (76)
59 PRK08179 prfH peptide chain re 39.1 26 0.00056 26.8 2.2 18 61-78 27-44 (200)
60 COG0290 InfC Translation initi 38.8 44 0.00095 25.4 3.4 37 51-87 30-68 (176)
61 COG4314 NosL Predicted lipopro 38.8 23 0.00051 26.8 1.9 22 51-72 130-151 (176)
62 PF14791 DNA_pol_B_thumb: DNA 38.1 3 6.4E-05 26.2 -2.6 25 34-71 2-26 (64)
63 PF14259 RRM_6: RNA recognitio 37.9 37 0.00081 19.8 2.4 19 50-68 42-60 (70)
64 PRK13864 type IV secretion sys 37.9 49 0.0011 26.2 3.7 28 50-77 68-98 (245)
65 PF14542 Acetyltransf_CG: GCN5 37.0 32 0.0007 21.8 2.1 20 57-76 44-63 (78)
66 PF14657 Integrase_AP2: AP2-li 36.3 32 0.00069 19.7 1.9 13 54-66 24-36 (46)
67 smart00757 CRA CT11-RanBPM. pr 35.8 30 0.00066 21.8 1.9 17 56-72 2-18 (99)
68 PF00076 RRM_1: RNA recognitio 35.7 42 0.00092 19.0 2.4 19 50-68 42-61 (70)
69 PRK00910 ribB 3,4-dihydroxy-2- 35.7 35 0.00076 26.5 2.5 19 54-72 183-201 (218)
70 PF03795 YCII: YCII-related do 35.6 22 0.00047 22.4 1.2 17 50-66 61-77 (95)
71 PRK00509 argininosuccinate syn 35.6 59 0.0013 27.2 4.0 19 53-71 148-166 (399)
72 PF00926 DHBP_synthase: 3,4-di 35.5 35 0.00077 25.8 2.5 19 54-72 167-185 (194)
73 COG5453 Uncharacterized conser 35.2 27 0.00057 24.1 1.6 18 53-70 68-85 (96)
74 TIGR01465 cobM_cbiF precorrin- 35.2 53 0.0012 24.0 3.4 32 37-76 76-107 (229)
75 COG2154 Pterin-4a-carbinolamin 35.0 45 0.00098 23.0 2.7 35 31-67 15-49 (101)
76 KOG1468 Predicted translation 34.2 43 0.00093 27.8 2.9 34 38-79 245-278 (354)
77 PRK00014 ribB 3,4-dihydroxy-2- 34.1 38 0.00083 26.5 2.5 19 54-72 187-205 (230)
78 TIGR03072 release_prfH putativ 34.1 34 0.00074 26.1 2.2 18 61-78 26-43 (200)
79 KOG0237 Glycinamide ribonucleo 33.8 40 0.00086 30.6 2.8 73 19-94 18-92 (788)
80 PF03960 ArsC: ArsC family; I 33.8 43 0.00093 22.1 2.4 23 56-78 8-30 (110)
81 PF00764 Arginosuc_synth: Argi 33.4 30 0.00064 29.0 1.9 18 57-74 147-164 (388)
82 KOG0081 GTPase Rab27, small G 33.4 34 0.00074 26.4 2.1 23 53-75 140-162 (219)
83 PF07611 DUF1574: Protein of u 33.3 28 0.00061 28.7 1.7 28 51-78 248-275 (345)
84 cd06576 PASTA_Pbp2x-like_1 PAS 33.2 68 0.0015 17.5 2.9 22 55-76 8-29 (55)
85 cd03017 PRX_BCP Peroxiredoxin 33.2 58 0.0013 21.3 3.0 29 50-78 61-89 (140)
86 smart00481 POLIIIAc DNA polyme 33.0 74 0.0016 18.8 3.2 24 55-78 15-38 (67)
87 COG5079 SAC3 Nuclear protein e 32.7 24 0.00052 31.4 1.3 25 51-75 356-380 (646)
88 COG1225 Bcp Peroxiredoxin [Pos 32.6 34 0.00074 25.2 1.9 30 50-79 68-97 (157)
89 PF00331 Glyco_hydro_10: Glyco 32.4 28 0.00062 27.5 1.6 22 51-72 55-76 (320)
90 cd00488 PCD_DCoH PCD_DCoH: The 32.3 65 0.0014 20.1 3.0 17 51-67 13-29 (75)
91 PTZ00056 glutathione peroxidas 32.3 46 0.00099 24.5 2.6 21 55-75 89-109 (199)
92 PF10009 DUF2252: Uncharacteri 32.2 30 0.00066 28.4 1.8 42 28-69 287-335 (385)
93 PF13911 AhpC-TSA_2: AhpC/TSA 31.7 40 0.00086 22.0 2.0 29 51-79 18-46 (115)
94 KOG1769 Ubiquitin-like protein 31.7 26 0.00055 24.3 1.1 14 61-74 48-61 (99)
95 KOG0369 Pyruvate carboxylase [ 31.6 42 0.0009 31.2 2.6 25 53-77 169-193 (1176)
96 PF09691 PulS_OutS: Bacterial 31.1 33 0.00071 23.9 1.6 15 58-72 53-67 (109)
97 KOG0098 GTPase Rab2, small G p 30.9 39 0.00085 26.4 2.1 18 55-72 129-146 (216)
98 PRK12354 carbamate kinase; Rev 30.6 42 0.0009 27.2 2.3 22 53-74 125-146 (307)
99 COG0216 PrfA Protein chain rel 30.5 38 0.00082 28.4 2.1 18 62-79 140-157 (363)
100 cd00860 ThrRS_anticodon ThrRS 30.3 76 0.0016 19.2 3.0 23 54-76 37-59 (91)
101 COG0007 CysG Uroporphyrinogen- 30.2 68 0.0015 25.3 3.3 25 53-77 94-118 (244)
102 TIGR03798 ocin_TIGR03798 bacte 30.1 24 0.00052 21.6 0.7 23 53-75 23-45 (64)
103 PF12123 Amidase02_C: N-acetyl 30.0 69 0.0015 19.1 2.6 18 56-73 28-45 (45)
104 PF04895 DUF651: Archaeal prot 29.9 41 0.00089 23.5 1.9 17 51-67 67-83 (110)
105 cd07202 cPLA2_Grp-IVC Group IV 29.9 27 0.00058 29.8 1.1 24 53-76 320-343 (430)
106 cd04438 DEP_dishevelled DEP (D 29.4 61 0.0013 21.2 2.6 24 54-77 46-72 (84)
107 cd03421 SirA_like_N SirA_like_ 28.9 68 0.0015 19.2 2.6 21 56-76 37-57 (67)
108 TIGR00385 dsbE periplasmic pro 28.9 54 0.0012 23.1 2.4 22 51-72 97-119 (173)
109 cd07996 WGR_MMR_like WGR domai 28.8 1.4E+02 0.003 18.2 4.0 50 15-67 12-62 (74)
110 KOG0097 GTPase Rab14, small G 28.2 44 0.00096 25.4 1.9 18 56-73 135-152 (215)
111 PF02811 PHP: PHP domain; Int 28.1 65 0.0014 21.7 2.6 24 55-78 16-39 (175)
112 TIGR02432 lysidine_TilS_N tRNA 28.1 73 0.0016 22.4 3.0 22 56-77 46-67 (189)
113 PRK00923 sirohydrochlorin coba 28.0 96 0.0021 20.7 3.4 25 52-76 43-67 (126)
114 PF01910 DUF77: Domain of unkn 28.0 53 0.0012 21.7 2.1 19 57-75 19-37 (92)
115 PLN02923 xylose isomerase 27.7 62 0.0013 28.1 2.9 30 57-86 255-285 (478)
116 PF05159 Capsule_synth: Capsul 27.5 65 0.0014 24.2 2.8 23 55-77 11-33 (269)
117 cd03012 TlpA_like_DipZ_like Tl 27.4 55 0.0012 21.5 2.1 23 55-77 71-93 (126)
118 PF11216 DUF3012: Protein of u 27.3 45 0.00098 18.7 1.4 10 56-65 19-28 (32)
119 cd01999 Argininosuccinate_Synt 27.2 96 0.0021 25.7 3.9 21 54-74 146-166 (385)
120 KOG2741 Dimeric dihydrodiol de 27.0 45 0.00098 27.8 1.9 20 51-70 37-56 (351)
121 PF00462 Glutaredoxin: Glutare 26.9 89 0.0019 17.9 2.8 20 58-77 13-32 (60)
122 TIGR00746 arcC carbamate kinas 26.6 67 0.0015 25.8 2.8 21 53-73 131-151 (310)
123 COG1979 Uncharacterized oxidor 26.5 41 0.00088 28.4 1.6 22 53-74 70-91 (384)
124 PRK13010 purU formyltetrahydro 26.5 87 0.0019 24.8 3.4 27 51-77 124-150 (289)
125 PF07476 MAAL_C: Methylasparta 26.4 55 0.0012 26.1 2.2 19 56-74 177-195 (248)
126 PF00059 Lectin_C: Lectin C-ty 26.1 48 0.001 20.0 1.5 19 56-74 4-22 (105)
127 cd04448 DEP_PIKfyve DEP (Dishe 25.9 57 0.0012 21.1 1.9 25 53-77 43-70 (81)
128 PF10686 DUF2493: Protein of u 25.9 75 0.0016 20.1 2.4 19 59-77 48-66 (71)
129 cd06575 PASTA_Pbp2x-like_2 PAS 25.9 1.1E+02 0.0024 16.4 2.9 21 55-75 8-28 (54)
130 cd03593 CLECT_NK_receptors_lik 25.9 55 0.0012 20.8 1.8 37 36-75 4-40 (116)
131 smart00034 CLECT C-type lectin 25.7 59 0.0013 20.1 1.9 19 55-73 20-38 (126)
132 cd00859 HisRS_anticodon HisRS 25.5 1E+02 0.0022 18.1 2.9 21 56-76 39-59 (91)
133 cd01206 Homer Homer type EVH1 25.4 65 0.0014 22.8 2.2 33 33-67 63-103 (111)
134 cd04449 DEP_DEPDC5-like DEP (D 25.4 59 0.0013 20.9 1.9 22 54-75 46-70 (83)
135 cd03027 GRX_DEP Glutaredoxin ( 25.0 95 0.0021 18.5 2.7 24 55-78 12-35 (73)
136 PRK06746 peptide chain release 24.9 58 0.0013 26.7 2.2 17 61-77 113-129 (326)
137 cd04442 DEP_1_DEP6 DEP (Dishev 24.9 61 0.0013 21.3 1.9 21 55-75 45-68 (82)
138 KOG0855 Alkyl hydroperoxide re 24.9 52 0.0011 25.4 1.8 30 51-80 129-158 (211)
139 PLN03181 glycosyltransferase; 24.8 52 0.0011 28.3 1.9 22 55-76 152-173 (453)
140 TIGR01004 PulS_OutS lipoprotei 24.8 58 0.0013 23.5 1.9 14 59-72 70-83 (128)
141 cd07415 MPP_PP2A_PP4_PP6 PP2A, 24.4 1.5E+02 0.0033 23.3 4.4 26 51-77 209-234 (285)
142 cd07238 Glo_EDI_BRP_like_5 Thi 24.3 1.5E+02 0.0032 18.4 3.7 23 51-73 62-84 (112)
143 PF11387 DUF2795: Protein of u 24.3 78 0.0017 18.3 2.1 24 52-75 4-28 (44)
144 TIGR02540 gpx7 putative glutat 24.1 59 0.0013 22.2 1.9 21 55-75 72-93 (153)
145 cd03592 CLECT_selectins_like C 24.1 62 0.0014 20.8 1.9 19 55-73 10-28 (115)
146 cd02977 ArsC_family Arsenate R 24.0 80 0.0017 20.4 2.4 21 57-77 12-32 (105)
147 smart00633 Glyco_10 Glycosyl h 24.0 76 0.0017 23.9 2.6 22 51-72 12-33 (254)
148 PF06243 PaaB: Phenylacetic ac 23.9 81 0.0018 21.4 2.4 26 39-66 13-38 (94)
149 TIGR00032 argG argininosuccina 23.6 90 0.002 25.9 3.1 20 56-75 147-166 (394)
150 cd04440 DEP_2_P-Rex DEP (Dishe 23.6 65 0.0014 21.8 1.9 22 54-75 53-77 (93)
151 cd04441 DEP_2_DEP6 DEP (Dishev 23.6 66 0.0014 21.3 1.9 23 53-75 47-72 (85)
152 COG1453 Predicted oxidoreducta 23.5 72 0.0016 27.0 2.5 20 59-78 187-206 (391)
153 PRK03353 ribB 3,4-dihydroxy-2- 23.4 76 0.0017 24.3 2.5 18 55-72 183-200 (217)
154 PRK10696 tRNA 2-thiocytidine b 23.0 1E+02 0.0022 23.4 3.1 22 56-77 75-96 (258)
155 TIGR03748 conj_PilL conjugativ 22.9 77 0.0017 22.1 2.2 28 41-70 18-51 (105)
156 cd03412 CbiK_N Anaerobic cobal 22.9 1.2E+02 0.0025 20.9 3.1 26 52-77 53-78 (127)
157 PRK09958 DNA-binding transcrip 22.9 69 0.0015 21.7 2.0 20 51-70 185-204 (204)
158 cd04908 ACT_Bt0572_1 N-termina 22.9 1.2E+02 0.0025 17.9 2.8 22 51-72 44-65 (66)
159 PF05389 MecA: Negative regula 22.9 53 0.0012 24.5 1.5 19 51-69 133-151 (220)
160 PF03129 HGTP_anticodon: Antic 22.7 1.1E+02 0.0025 18.9 2.9 21 55-75 39-59 (94)
161 PRK00578 prfB peptide chain re 22.7 67 0.0015 26.7 2.2 18 61-78 151-168 (367)
162 COG0656 ARA1 Aldo/keto reducta 22.7 86 0.0019 25.1 2.7 26 54-79 169-194 (280)
163 PRK12454 carbamate kinase-like 22.6 79 0.0017 25.7 2.5 20 53-72 134-153 (313)
164 PF02407 Viral_Rep: Putative v 22.3 10 0.00022 25.1 -2.2 12 55-66 74-85 (86)
165 PF14370 Topo_C_assoc: C-termi 22.3 33 0.00071 22.4 0.2 17 56-72 32-48 (71)
166 PRK05589 peptide chain release 22.3 70 0.0015 26.2 2.2 18 61-78 112-129 (325)
167 PRK06027 purU formyltetrahydro 22.2 1.1E+02 0.0024 24.1 3.2 27 51-77 120-146 (286)
168 TIGR00552 nadE NAD+ synthetase 22.1 73 0.0016 24.1 2.1 22 55-76 64-85 (250)
169 PRK10638 glutaredoxin 3; Provi 21.9 97 0.0021 19.1 2.4 21 57-77 15-35 (83)
170 cd00037 CLECT C-type lectin (C 21.8 78 0.0017 18.9 1.9 19 54-73 9-27 (116)
171 PF11823 DUF3343: Protein of u 21.7 1.1E+02 0.0023 18.9 2.5 23 51-73 46-68 (73)
172 KOG1380 Heme A farnesyltransfe 21.7 32 0.00069 29.0 0.1 11 31-41 234-244 (409)
173 PF13669 Glyoxalase_4: Glyoxal 21.7 91 0.002 19.9 2.3 35 40-77 65-99 (109)
174 cd07420 MPP_RdgC Drosophila me 21.5 1.8E+02 0.004 23.5 4.4 26 51-77 248-273 (321)
175 PF14555 UBA_4: UBA-like domai 21.5 97 0.0021 17.4 2.1 17 56-72 14-30 (43)
176 PRK12865 YciI-like protein; Re 21.3 81 0.0018 20.6 2.0 25 51-75 56-87 (97)
177 PTZ00175 diphthine synthase; P 21.3 1.4E+02 0.003 23.4 3.6 29 39-75 83-111 (270)
178 PF12671 Amidase_6: Putative a 21.3 70 0.0015 22.6 1.8 16 56-71 3-18 (157)
179 PF06356 DUF1064: Protein of u 21.2 79 0.0017 22.2 2.0 15 51-65 13-27 (118)
180 PF11247 DUF2675: Protein of u 21.2 47 0.001 23.0 0.8 18 57-74 58-75 (98)
181 cd03018 PRX_AhpE_like Peroxire 21.1 1.2E+02 0.0027 20.0 2.9 27 51-77 67-93 (149)
182 PRK12465 xylose isomerase; Pro 21.1 1.1E+02 0.0024 26.3 3.2 30 57-86 221-251 (445)
183 PRK07342 peptide chain release 21.1 76 0.0017 26.2 2.2 18 61-78 115-132 (339)
184 PF02540 NAD_synthase: NAD syn 21.0 88 0.0019 23.9 2.4 20 56-75 61-80 (242)
185 KOG3048 Molecular chaperone Pr 20.9 66 0.0014 23.9 1.6 13 55-67 97-109 (153)
186 KOG0091 GTPase Rab39, small G 20.9 88 0.0019 24.2 2.3 20 56-75 135-154 (213)
187 cd07249 MMCE Methylmalonyl-CoA 20.8 1.3E+02 0.0028 18.7 2.8 22 51-72 77-98 (128)
188 cd00248 Mth938-like Mth938-lik 20.8 1.1E+02 0.0025 20.5 2.7 25 51-76 63-87 (109)
189 PF02244 Propep_M14: Carboxype 20.7 1.5E+02 0.0033 17.8 3.1 27 51-77 39-65 (74)
190 cd00738 HGTP_anticodon HGTP an 20.7 1.4E+02 0.003 18.1 2.9 22 55-76 41-62 (94)
191 cd02970 PRX_like2 Peroxiredoxi 20.7 1.5E+02 0.0033 19.3 3.3 28 51-78 62-89 (149)
192 cd07416 MPP_PP2B PP2B, metallo 20.6 1.6E+02 0.0034 23.4 3.8 26 51-77 217-242 (305)
193 PRK08787 peptide chain release 20.5 81 0.0018 25.8 2.2 18 61-78 92-109 (313)
194 KOG0092 GTPase Rab5/YPT51 and 20.3 82 0.0018 24.4 2.1 53 18-77 97-150 (200)
195 PF08901 DUF1847: Protein of u 20.3 75 0.0016 23.7 1.8 16 55-70 41-56 (157)
196 cd07417 MPP_PP5_C PP5, C-termi 20.2 2.2E+02 0.0048 22.8 4.6 26 51-77 228-253 (316)
197 TIGR03645 glyox_marine lactoyl 20.2 1.3E+02 0.0029 20.8 3.1 24 51-74 96-121 (162)
198 TIGR00020 prfB peptide chain r 20.0 82 0.0018 26.1 2.2 18 61-78 151-168 (364)
199 PRK09732 hypothetical protein; 20.0 1.1E+02 0.0023 21.8 2.5 18 57-74 16-33 (134)
No 1
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=100.00 E-value=1.4e-53 Score=293.33 Aligned_cols=93 Identities=44% Similarity=0.896 Sum_probs=58.8
Q ss_pred CCccCCCCCCCCCCCCCCCcEEEecCCCCCCCCCcCcCCCCCcccc-cCCceeecCCHHHHHHHHHHhCCcEEEeecCCC
Q 043542 1 SSFTHARTASQQGSGKVGKWFINFLSTQKWENPLMGWTSTGDPYAN-VGEAGLCFDSEAAARAFAEKHGWEYTVRKFHAP 79 (99)
Q Consensus 1 rIy~p~k~a~QSG~~~~~~W~lefe~~~~~~dPLMGWtss~D~~sq-v~~~~l~F~ske~Ai~yaek~G~~y~V~~p~~~ 79 (99)
|||+|+|+|||||+++++.|+|||+..++|+|||||||||+||++| | +|+|+|+|+||+||++|||+|+|++|+.+
T Consensus 4 rIy~pak~amQSG~~~t~~W~lefe~~~~~~~PLMGWtss~D~~~q~v---~l~F~skE~Ai~yaer~G~~Y~V~~p~~r 80 (101)
T PF04800_consen 4 RIYQPAKNAMQSGTANTKKWVLEFETRARWENPLMGWTSSGDPLSQSV---RLKFDSKEDAIAYAERNGWDYEVEEPKKR 80 (101)
T ss_dssp EEE--SS--STTTT-SS--EEEEEEESSS---TTT-SSSS--SEEE-C---EEEESSHHHHHHHHHHCT-EEEEE-STT-
T ss_pred EEeCCCCCCCCCCCCCCCCEEEeecCcCCcCCCccCCCCCCChhhCee---EeeeCCHHHHHHHHHHcCCeEEEeCCCCC
Confidence 7999999999999999999999999889999999999999999998 8 99999999999999999999999999999
Q ss_pred CCCCccccccCCCCCCC
Q 043542 80 LLKPKSYGDNFKWKGPP 96 (99)
Q Consensus 80 ~~~~ksYadNF~~~~~~ 96 (99)
++++|||||||+|++..
T Consensus 81 ~~~~ksY~dNF~~~r~~ 97 (101)
T PF04800_consen 81 KRRPKSYADNFSWNRRT 97 (101)
T ss_dssp -----------------
T ss_pred cCCcccHHHhCCcCCCC
Confidence 99999999999999865
No 2
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=100.00 E-value=1.6e-47 Score=280.43 Aligned_cols=97 Identities=56% Similarity=1.032 Sum_probs=94.3
Q ss_pred CCccCCCCCCCCCCCCCCCcEEEecCCCCCCCCCcCcCCCCCcccccCCceeecCCHHHHHHHHHHhCCcEEEeecCCCC
Q 043542 1 SSFTHARTASQQGSGKVGKWFINFLSTQKWENPLMGWTSTGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRKFHAPL 80 (99)
Q Consensus 1 rIy~p~k~a~QSG~~~~~~W~lefe~~~~~~dPLMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~p~~~~ 80 (99)
|||.|+|++||||.+|+++|.|||+.+.+|+||||||+|++||+++|+ +.|.|+|+|+|++|||||||+|.|++|+.++
T Consensus 79 rIf~PAR~~tQSg~gntkkWkiefd~r~rWENPLMGWtsTaDPlsNvg-m~L~F~tkEdA~sFaEkngW~ydveep~~pk 157 (178)
T KOG3389|consen 79 RIFSPARTATQSGSGNTKKWKIEFDSRLRWENPLMGWTSTADPLSNVG-MALAFDTKEDAKSFAEKNGWDYDVEEPNTPK 157 (178)
T ss_pred EEecchhhhhhcccCCccceEEEecchhhccCccccccccCCcccccc-eeeeeccHHHHHHHHHHcCCcccccCCCCCc
Confidence 799999999999999999999999999999999999999999999996 5899999999999999999999999999999
Q ss_pred CCCccccccCCCCCCCCC
Q 043542 81 LKPKSYGDNFKWKGPPKD 98 (99)
Q Consensus 81 ~~~ksYadNF~~~~~~~~ 98 (99)
+++||||+||+|||++..
T Consensus 158 ~K~KsYg~NFsWn~rtr~ 175 (178)
T KOG3389|consen 158 LKVKSYGDNFSWNGRTRP 175 (178)
T ss_pred cccccccccccccCCCCC
Confidence 999999999999999854
No 3
>PF09954 DUF2188: Uncharacterized protein conserved in bacteria (DUF2188); InterPro: IPR018691 This family has no known function.
Probab=88.64 E-value=0.36 Score=29.53 Aligned_cols=27 Identities=26% Similarity=0.284 Sum_probs=19.7
Q ss_pred eeecCCHHHHHHHHHH----h-CCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEK----H-GWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek----~-G~~y~V~~p~ 77 (99)
...|+|+++||++|++ + +-+..|....
T Consensus 22 ~~~~~Tk~eAi~~Ar~~a~~~~~~el~Ih~~d 53 (62)
T PF09954_consen 22 SKTFDTKAEAIEAARELAKNQGGGELIIHGRD 53 (62)
T ss_pred ccccCcHHHHHHHHHHHHHhCCCcEEEEECCC
Confidence 5789999999998764 3 5666666544
No 4
>PHA02552 4 head completion protein; Provisional
Probab=85.73 E-value=0.75 Score=33.80 Aligned_cols=21 Identities=38% Similarity=0.661 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhCCcEEEeecC
Q 043542 57 EAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~~p~ 77 (99)
-++|.+||+++||.|.|....
T Consensus 120 ~~Aa~~~a~~~Gw~F~iiTE~ 140 (151)
T PHA02552 120 WKAARALCEKKGWKFKIITED 140 (151)
T ss_pred HHHHHHHHHHcCCEEEEEEHH
Confidence 478999999999999988754
No 5
>PRK05370 argininosuccinate synthase; Validated
Probab=83.29 E-value=0.79 Score=38.99 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=19.9
Q ss_pred eecCCHHHHHHHHHHhCCcEEEe
Q 043542 52 LCFDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 52 l~F~ske~Ai~yaek~G~~y~V~ 74 (99)
-.|+|+++.|+||++|||+..+.
T Consensus 164 ~~f~sR~e~i~Ya~~hGIpv~~~ 186 (447)
T PRK05370 164 DELGGRAEMSEFLIAHGFDYKMS 186 (447)
T ss_pred cccCCHHHHHHHHHHcCCCCCcc
Confidence 36899999999999999998543
No 6
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=81.69 E-value=1.1 Score=28.37 Aligned_cols=16 Identities=25% Similarity=0.715 Sum_probs=11.1
Q ss_pred HHHHHHHHHhCCcEEE
Q 043542 58 AAARAFAEKHGWEYTV 73 (99)
Q Consensus 58 e~Ai~yaek~G~~y~V 73 (99)
++-+.||+++||-..+
T Consensus 30 ~eV~~YC~~~GWIip~ 45 (57)
T PF08727_consen 30 PEVREYCEEQGWIIPA 45 (57)
T ss_dssp HHHHHHHHHHT--TT-
T ss_pred HHHHHHHHHCCccccC
Confidence 5689999999996544
No 7
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=80.02 E-value=2.2 Score=30.39 Aligned_cols=51 Identities=25% Similarity=0.574 Sum_probs=28.2
Q ss_pred CCCcEEEecCCCCCCCCCc-CcCCC--------CCcccccCCceeecCCHHHHHHHHHHhC
Q 043542 17 VGKWFINFLSTQKWENPLM-GWTST--------GDPYANVGEAGLCFDSEAAARAFAEKHG 68 (99)
Q Consensus 17 ~~~W~lefe~~~~~~dPLM-GWtss--------~D~~sqv~~~~l~F~ske~Ai~yaek~G 68 (99)
...|+-+|.. ..|.+|-- -|... +|-.+-++..-+-|.++++|.+|+++||
T Consensus 76 ~~~~V~D~~~-~~~~~p~~~~~Ida~~A~yV~gs~~~~pMg~~~~aF~~~~~A~~F~~~~G 135 (149)
T PF05573_consen 76 AAIYVTDYST-TDWDQPGDGEWIDAKKAYYVVGSDVRGPMGPDLIAFASKEDAEAFAKEHG 135 (149)
T ss_dssp EEEEEEES-T-S-TT-S---EEEEGGGSEEEEESSSS-TTS--EEEES-HHHHHHHHHHTE
T ss_pred cEEEEEeccc-ccccCCCCCceEEcceEEEEECCCcCCCCCCcccccCCHHHHHHHHHHcC
Confidence 3568888877 44555442 33332 2222222334688999999999999998
No 8
>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.
Probab=76.65 E-value=3 Score=26.73 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=13.7
Q ss_pred HHHHHHHHHHhCCcEEEee
Q 043542 57 EAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~~ 75 (99)
.+.|-.||+++||+|.|..
T Consensus 69 ~~~~~~y~~~~g~~f~ivT 87 (88)
T PF08722_consen 69 LEIEREYWEEQGIPFRIVT 87 (88)
T ss_dssp HHHHHHHHHHCT--EEEE-
T ss_pred HHHHHHHHHHcCCeEEEEc
Confidence 4568899999999999864
No 9
>PF03462 PCRF: PCRF domain; InterPro: IPR005139 This domain is found in peptide chain release factors. Peptide chain release factors are important for protein synthesis since they direct the termination of translation in response to the peptide chain termination codons UAG and UAA. These are structurally distinct but both contain the PCRF domain [].; GO: 0016149 translation release factor activity, codon specific, 0006415 translational termination, 0005737 cytoplasm; PDB: 3D5A_X 3D5C_X 3MR8_V 3MS0_V 3F1G_X 3F1E_X 1ZBT_A 2IHR_1 2X9R_Y 2X9T_Y ....
Probab=69.50 E-value=4.2 Score=27.90 Aligned_cols=17 Identities=29% Similarity=0.837 Sum_probs=13.5
Q ss_pred HHHHHHhCCcEEEeecC
Q 043542 61 RAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~ 77 (99)
..||+++||+++|..-.
T Consensus 73 ~~~a~~~gw~~~~l~~~ 89 (115)
T PF03462_consen 73 QRYAERRGWKVEVLDYS 89 (115)
T ss_dssp HHHHHHTT-EEEEEEEE
T ss_pred HHHHHHcCCEEEEEecC
Confidence 48999999999998743
No 10
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=68.79 E-value=6.5 Score=26.20 Aligned_cols=20 Identities=20% Similarity=0.403 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCCcEEEeecC
Q 043542 58 AAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 58 e~Ai~yaek~G~~y~V~~p~ 77 (99)
++-+.||+.+|+.|.|..+.
T Consensus 58 ~~i~~fC~~~gy~~~iv~~g 77 (86)
T PF11360_consen 58 EEIEEFCRSAGYEYEIVPPG 77 (86)
T ss_pred HHHHHHHHHCCceEEEECCC
Confidence 44455678889999988776
No 11
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=66.16 E-value=5.9 Score=24.27 Aligned_cols=14 Identities=36% Similarity=0.313 Sum_probs=12.7
Q ss_pred eeecCCHHHHHHHH
Q 043542 51 GLCFDSEAAARAFA 64 (99)
Q Consensus 51 ~l~F~ske~Ai~ya 64 (99)
-|.|+|.++|++|-
T Consensus 43 iieFPs~~aa~~~~ 56 (65)
T PF07045_consen 43 IIEFPSMEAAKAWY 56 (65)
T ss_dssp EEEESSHHHHHHHH
T ss_pred EEECCCHHHHHHHH
Confidence 79999999999874
No 12
>KOG2854 consensus Possible pfkB family carbohydrate kinase [Carbohydrate transport and metabolism]
Probab=66.04 E-value=5.1 Score=33.19 Aligned_cols=22 Identities=45% Similarity=0.838 Sum_probs=20.0
Q ss_pred eeecCCHHHHHHHHHHhCCcEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~ 72 (99)
-+-|.+.+||.+||+.+||+-.
T Consensus 216 DiifgNe~EA~af~~~~~~~t~ 237 (343)
T KOG2854|consen 216 DIIFGNEDEAAAFARAHGWETK 237 (343)
T ss_pred eEEEcCHHHHHHHHHhhCCccc
Confidence 5789999999999999999865
No 13
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=65.61 E-value=5.3 Score=26.62 Aligned_cols=17 Identities=29% Similarity=0.352 Sum_probs=15.1
Q ss_pred eeecCCHHHHHHHHHHh
Q 043542 51 GLCFDSEAAARAFAEKH 67 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~ 67 (99)
.|-|.+.+||..||.--
T Consensus 26 Vl~FE~edDA~RYa~lL 42 (86)
T PF11360_consen 26 VLMFEDEDDAERYAGLL 42 (86)
T ss_pred EEEEccHHHHHHHHHHH
Confidence 89999999999999653
No 14
>PRK04527 argininosuccinate synthase; Provisional
Probab=64.09 E-value=4.8 Score=33.68 Aligned_cols=20 Identities=15% Similarity=0.302 Sum_probs=17.5
Q ss_pred ecCCHHHHHHHHHHhCCcEE
Q 043542 53 CFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~ 72 (99)
+++++++.|+||++|||+..
T Consensus 150 k~~~R~~~i~ya~~~gipv~ 169 (400)
T PRK04527 150 HTQTRAYEQKYLEERGFGVR 169 (400)
T ss_pred ccccHHHHHHHHHHcCCCCC
Confidence 45799999999999999873
No 15
>PF06194 Phage_Orf51: Phage Conserved Open Reading Frame 51; InterPro: IPR009338 This entry is represented by the Staphylococcus phage PVL (bacteriophage phi-PVL), Orf51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=64.06 E-value=6.2 Score=26.38 Aligned_cols=24 Identities=8% Similarity=0.243 Sum_probs=21.6
Q ss_pred ceeecCCHHHHHHHHHHhCCcEEE
Q 043542 50 AGLCFDSEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 50 ~~l~F~ske~Ai~yaek~G~~y~V 73 (99)
.+..|+|+++-..|-+.+|+.|+=
T Consensus 50 vKktFn~~~Ef~~Yi~~~~L~~ee 73 (80)
T PF06194_consen 50 VKKTFNNKEEFENYIKQHELYFEE 73 (80)
T ss_pred hhhhcCcHHHHHHHHHHcCCceeh
Confidence 388999999999999999998873
No 16
>PF03108 DBD_Tnp_Mut: MuDR family transposase; InterPro: IPR004332 The plant MuDR transposase domain is present in plant proteins that are presumed to be the transposases for Mutator transposable elements [, ]. The function of these proteins is unknown. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=61.69 E-value=9.4 Score=23.19 Aligned_cols=32 Identities=31% Similarity=0.534 Sum_probs=25.2
Q ss_pred eeecCCHHHH----HHHHHHhCCcEEEeecCCCCCC
Q 043542 51 GLCFDSEAAA----RAFAEKHGWEYTVRKFHAPLLK 82 (99)
Q Consensus 51 ~l~F~ske~A----i~yaek~G~~y~V~~p~~~~~~ 82 (99)
.+.|+|+++. ..||-+++.+|.|..-.+.+.+
T Consensus 7 G~~F~~~~e~k~av~~yai~~~~~~~v~ksd~~r~~ 42 (67)
T PF03108_consen 7 GQTFPSKEEFKEAVREYAIKNGFEFKVKKSDKKRYR 42 (67)
T ss_pred CCEECCHHHHHHHHHHHHHhcCcEEEEeccCCEEEE
Confidence 7899999876 4699999999999876654443
No 17
>PF12518 DUF3721: Protein of unknown function; InterPro: IPR022196 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.
Probab=61.66 E-value=8 Score=21.99 Aligned_cols=16 Identities=25% Similarity=0.360 Sum_probs=14.2
Q ss_pred cCCHHHHHHHHHHhCC
Q 043542 54 FDSEAAARAFAEKHGW 69 (99)
Q Consensus 54 F~ske~Ai~yaek~G~ 69 (99)
|+|+++|.+=|.+.|-
T Consensus 1 y~tk~eAe~~A~~~GC 16 (34)
T PF12518_consen 1 YPTKAEAEKRAKELGC 16 (34)
T ss_pred CCcHHHHHHHHHHcCC
Confidence 7999999999998773
No 18
>KOG4748 consensus Subunit of Golgi mannosyltransferase complex [Carbohydrate transport and metabolism; Cell wall/membrane/envelope biogenesis]
Probab=60.23 E-value=6.2 Score=32.89 Aligned_cols=23 Identities=22% Similarity=0.436 Sum_probs=19.1
Q ss_pred CHHHHHHHHHHhCCcEEEeecCC
Q 043542 56 SEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
+-+-=|+||++||+++++..-..
T Consensus 127 ~ikNridYA~rHgy~~~~~~~~~ 149 (364)
T KOG4748|consen 127 SIKNRIDYARRHGYEFEYKNATL 149 (364)
T ss_pred HHHhHHHHHHHhCCeEEEEeccc
Confidence 66777999999999999876543
No 19
>PF01071 GARS_A: Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; InterPro: IPR020561 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the A-domain of the enzyme, and is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase.; PDB: 1GSO_A 3LP8_A 2IP4_A 1VKZ_A 2QK4_A 2XD4_A 2XCL_A 3MJF_A 2YRW_A 2YS6_A ....
Probab=58.12 E-value=14 Score=27.96 Aligned_cols=27 Identities=26% Similarity=0.361 Sum_probs=22.9
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
--.|.+.++|++|.++++..+.|..+.
T Consensus 20 ~~~f~~~~~A~~~l~~~~~p~~ViKad 46 (194)
T PF01071_consen 20 YKVFTDYEEALEYLEEQGYPYVVIKAD 46 (194)
T ss_dssp EEEESSHHHHHHHHHHHSSSEEEEEES
T ss_pred eeEECCHHHHHHHHHhcCCCceEEccC
Confidence 357999999999999999999666654
No 20
>PF02844 GARS_N: Phosphoribosylglycinamide synthetase, N domain; InterPro: IPR020562 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) [] catalyses the second step in the de novo biosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide: ATP + 5-phosphoribosylamine + glycine = ADP + Pi + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART. This entry represents the N-domain, which is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (IPR005481 from INTERPRO).; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 3MJF_A 2XD4_A 2XCL_A 2IP4_A 2YW2_B 2YYA_A 3LP8_A 1VKZ_A 2YS6_A 2YRX_A ....
Probab=57.57 E-value=12 Score=25.53 Aligned_cols=28 Identities=14% Similarity=0.109 Sum_probs=22.8
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecCC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
.+...+.++-++||+++++++.|.-|..
T Consensus 45 ~~~~~d~~~l~~~a~~~~idlvvvGPE~ 72 (100)
T PF02844_consen 45 PIDITDPEELADFAKENKIDLVVVGPEA 72 (100)
T ss_dssp -S-TT-HHHHHHHHHHTTESEEEESSHH
T ss_pred CCCCCCHHHHHHHHHHcCCCEEEECChH
Confidence 4578899999999999999999998864
No 21
>PF08803 ydhR: Putative mono-oxygenase ydhR; InterPro: IPR014910 YdhR is a homodimeric protein that comprises of a central four-stranded beta sheet and four surrounding alpha helices []. It shows structural homology to the ActVA-Orf6 and YgiN proteins which indicates it could be a mono-oxygenase. ; PDB: 1WD6_B 2HIQ_B 2ASY_B.
Probab=56.65 E-value=7.2 Score=26.86 Aligned_cols=29 Identities=34% Similarity=0.570 Sum_probs=22.4
Q ss_pred cCCCCCcccccCCceeecCCHHHHHHHHHHh
Q 043542 37 WTSTGDPYANVGEAGLCFDSEAAARAFAEKH 67 (99)
Q Consensus 37 Wtss~D~~sqv~~~~l~F~ske~Ai~yaek~ 67 (99)
||.+.++..- ++ -.-|+|+++|.+|+++|
T Consensus 38 Wten~~t~ea-GG-iYLFe~e~~A~aY~~~h 66 (97)
T PF08803_consen 38 WTENEETGEA-GG-IYLFEDEASAEAYLEMH 66 (97)
T ss_dssp EEEETTTTEE-EE-EEEESSHHHHHHHHHHH
T ss_pred EEecCCCCcc-ce-EEEECCHHHHHHHHHHH
Confidence 7777776422 33 56799999999999987
No 22
>PF01693 Cauli_VI: Caulimovirus viroplasmin; InterPro: IPR011320 This entry represents the N-terminal domain of RNase HI, which has a 3-layer alpha/beta/alpha structure []. This domain is lacking in retroviral and prokaryotic enzymes, but shows a striking structural similarity to the ribosomal protein L9 N-terminal domain, and may function as a regulatory RNA-binding module. However, the topology of this domain differs from structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD), the hnRNP K homology (KH) domain and the RNP motif. Eukaryotic RNases HI possess either one or two copies of this small N-terminal domain, in addition to the well-conserved catalytic RNase H domain. RNase HI belongs to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. ; PDB: 1QHK_A 3BSU_C.
Probab=56.25 E-value=11 Score=21.69 Aligned_cols=13 Identities=23% Similarity=0.340 Sum_probs=11.6
Q ss_pred eeecCCHHHHHHH
Q 043542 51 GLCFDSEAAARAF 63 (99)
Q Consensus 51 ~l~F~ske~Ai~y 63 (99)
..+|.|+++|.+|
T Consensus 32 ~k~F~t~~eA~~~ 44 (44)
T PF01693_consen 32 YKSFKTREEAEEF 44 (44)
T ss_dssp EEEESSHHHHHHH
T ss_pred ECCcCCHHHHhhC
Confidence 6789999999986
No 23
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=54.69 E-value=8.3 Score=26.71 Aligned_cols=20 Identities=25% Similarity=0.577 Sum_probs=15.2
Q ss_pred eecCCHHHHHHHHHHhCCcEE
Q 043542 52 LCFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 52 l~F~ske~Ai~yaek~G~~y~ 72 (99)
|-|. -+++++||+++||.++
T Consensus 107 Lg~~-~~el~~~~~~~gW~~d 126 (143)
T PF10075_consen 107 LGLS-EEELEKFIKSRGWTVD 126 (143)
T ss_dssp TTS--HHHHHHHHHHHT-EE-
T ss_pred hCCC-HHHHHHHHHHcCCEEC
Confidence 4566 8999999999999986
No 24
>PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated
Probab=54.06 E-value=12 Score=28.99 Aligned_cols=18 Identities=22% Similarity=0.314 Sum_probs=16.1
Q ss_pred CCHHHHHHHHHHhCCcEE
Q 043542 55 DSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~ 72 (99)
-++++|++||++||+.+.
T Consensus 191 ~~~~~~~~fA~~~~l~~i 208 (219)
T PRK05773 191 LSKEKAKKIAKNLGFPLV 208 (219)
T ss_pred cCHHHHHHHHHHcCCcEE
Confidence 379999999999999983
No 25
>COG0137 ArgG Argininosuccinate synthase [Amino acid transport and metabolism]
Probab=53.69 E-value=14 Score=31.26 Aligned_cols=21 Identities=19% Similarity=0.314 Sum_probs=18.8
Q ss_pred ecCCHHHHHHHHHHhCCcEEEe
Q 043542 53 CFDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~ 74 (99)
.|. +|+.|+||+++||++.+.
T Consensus 151 ~~~-R~~~i~Ya~~~gipv~~~ 171 (403)
T COG0137 151 NLT-REEEIEYAEEHGIPVKAT 171 (403)
T ss_pred ccC-hHHHHHHHHHcCCCcccc
Confidence 456 999999999999999877
No 26
>PF13031 DUF3892: Protein of unknown function (DUF3892)
Probab=52.70 E-value=13 Score=23.87 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=19.2
Q ss_pred ecCCHHHHHHHHHHhCCcEEEe
Q 043542 53 CFDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~ 74 (99)
-.-|+++||+++++..+.|.|.
T Consensus 29 ~~~s~~~~i~~ie~g~~~~yv~ 50 (85)
T PF13031_consen 29 WKYSREEAIAWIENGKWSFYVE 50 (85)
T ss_pred ccccHHHHHHHHHcCCceEEeC
Confidence 4459999999999988999888
No 27
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=52.69 E-value=16 Score=24.30 Aligned_cols=35 Identities=29% Similarity=0.411 Sum_probs=25.0
Q ss_pred CCCcCcCCCCCcccccCCceeecCCHHHHHHHHHHhC
Q 043542 32 NPLMGWTSTGDPYANVGEAGLCFDSEAAARAFAEKHG 68 (99)
Q Consensus 32 dPLMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek~G 68 (99)
..|-||.-..++. .+. .+..|++-.+|++|+.+-+
T Consensus 16 ~~l~gW~~~~~~~-~l~-r~f~f~~f~~a~~f~~~Va 50 (97)
T PRK00823 16 PQLPGWTLVGDRD-AIE-RTFKFKNFNEAFAFMNRVA 50 (97)
T ss_pred hcCCCCeEeCCcC-eEE-EEEEeCCHHHHHHHHHHHH
Confidence 4567999887743 222 2788999999998876643
No 28
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=52.12 E-value=13 Score=28.73 Aligned_cols=20 Identities=20% Similarity=0.257 Sum_probs=16.9
Q ss_pred CCHHHHHHHHHHhCCcEEEe
Q 043542 55 DSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~ 74 (99)
..++++++||++||+.+.-.
T Consensus 172 ar~~~~~~fa~~h~l~~iti 191 (203)
T COG0108 172 ARLPELEEFAKEHGLPVITI 191 (203)
T ss_pred cChHHHHHHHHHcCCcEEEH
Confidence 46899999999999998643
No 29
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=51.88 E-value=7.3 Score=22.56 Aligned_cols=21 Identities=19% Similarity=0.409 Sum_probs=17.9
Q ss_pred cCCHHHHHHHHHHhCCcEEEe
Q 043542 54 FDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~V~ 74 (99)
..+.++-|++|+.+|+.+...
T Consensus 26 ~~~~~e~~~lA~~~Gy~ft~~ 46 (49)
T PF07862_consen 26 CQNPEEVVALAREAGYDFTEE 46 (49)
T ss_pred cCCHHHHHHHHHHcCCCCCHH
Confidence 459999999999999988643
No 30
>PLN00139 hypothetical protein; Provisional
Probab=50.62 E-value=15 Score=29.51 Aligned_cols=26 Identities=15% Similarity=0.013 Sum_probs=21.7
Q ss_pred eecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 52 LCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 52 l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
..-++++++.+||.++|++|+-.+..
T Consensus 195 F~t~d~~eve~~~~~~g~~~eW~~dg 220 (320)
T PLN00139 195 FGTSDKAEAERRAKALGMDMEWLPNG 220 (320)
T ss_pred hCCCCHHHHHHHHHHcCCeEEEcCCC
Confidence 44578999999999999999876554
No 31
>PRK13820 argininosuccinate synthase; Provisional
Probab=50.11 E-value=24 Score=29.43 Aligned_cols=18 Identities=17% Similarity=0.244 Sum_probs=16.4
Q ss_pred CHHHHHHHHHHhCCcEEE
Q 043542 56 SEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V 73 (99)
||++-++||+++|+++..
T Consensus 148 tK~ei~~ya~~~gip~~~ 165 (394)
T PRK13820 148 TREWEIEYAKEKGIPVPV 165 (394)
T ss_pred CHHHHHHHHHHcCCCCCc
Confidence 999999999999998843
No 32
>PLN00200 argininosuccinate synthase; Provisional
Probab=49.13 E-value=26 Score=29.37 Aligned_cols=19 Identities=16% Similarity=0.179 Sum_probs=16.5
Q ss_pred ecCCHHHHHHHHHHhCCcE
Q 043542 53 CFDSEAAARAFAEKHGWEY 71 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y 71 (99)
.|.||++.++||+++|++.
T Consensus 152 ~~~~r~e~~~~A~~~Gipv 170 (404)
T PLN00200 152 DIKGREDLIEYAKKHNIPV 170 (404)
T ss_pred CCCCHHHHHHHHHHcCCCC
Confidence 3559999999999999965
No 33
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=49.06 E-value=26 Score=22.10 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=21.3
Q ss_pred CcCCCCCcccccCCceeecCCHHHHHHHHHHh
Q 043542 36 GWTSTGDPYANVGEAGLCFDSEAAARAFAEKH 67 (99)
Q Consensus 36 GWtss~D~~sqv~~~~l~F~ske~Ai~yaek~ 67 (99)
||.-..|+.. +. .+..|++-.+|++|+.+-
T Consensus 1 gW~~~~~~~~-l~-r~f~f~~f~~a~~f~~~v 30 (76)
T cd00913 1 GWELADDGLK-LE-RTFRFKNFVEALEFVNAV 30 (76)
T ss_pred CCcCcCCCCe-EE-EEEEcCCHHHHHHHHHHH
Confidence 7887776521 21 278899999999997653
No 34
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=48.55 E-value=24 Score=20.70 Aligned_cols=22 Identities=18% Similarity=0.120 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHhCCcEEEeec
Q 043542 55 DSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p 76 (99)
-|.++|.+..+.+||.+.+...
T Consensus 9 ~~~~~a~~~l~~~g~~~~~~~~ 30 (63)
T PF03793_consen 9 MTYDEAKSILEAAGLTVNVVEE 30 (63)
T ss_dssp SBHHHHHHHHHHTT-EEEEEEE
T ss_pred CcHHHHHHHHHHCCCEEEEEEE
Confidence 4789999999999998887764
No 35
>cd00914 PCD_DCoH_subfamily_b PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon
Probab=47.07 E-value=22 Score=22.55 Aligned_cols=29 Identities=24% Similarity=0.385 Sum_probs=20.9
Q ss_pred CcCCCCCcccccCCceeecCCHHHHHHHHHH
Q 043542 36 GWTSTGDPYANVGEAGLCFDSEAAARAFAEK 66 (99)
Q Consensus 36 GWtss~D~~sqv~~~~l~F~ske~Ai~yaek 66 (99)
||.-..++.. +. .+..|+|-.+|++|+.+
T Consensus 1 gW~~~~~~~~-l~-r~f~f~~f~~a~~f~~~ 29 (76)
T cd00914 1 GWTLVDGRDA-IH-KSFKFKDFNEAFGFMTR 29 (76)
T ss_pred CCeEeCCCCe-EE-EEEEeCCHHHHHHHHHH
Confidence 6777666531 21 27899999999999765
No 36
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=45.98 E-value=22 Score=21.98 Aligned_cols=18 Identities=28% Similarity=0.254 Sum_probs=15.7
Q ss_pred HHHHHHHHHHhCCcEEEe
Q 043542 57 EAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~ 74 (99)
.++|++|.+.+|+.++|.
T Consensus 59 ~~~a~~~L~~~~v~vEvl 76 (76)
T PF09383_consen 59 IEKAIAYLREQGVEVEVL 76 (76)
T ss_dssp HHHHHHHHHHTTEEEEEE
T ss_pred HHHHHHHHHHCCCeEEEC
Confidence 478999999999998874
No 37
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=45.84 E-value=20 Score=23.63 Aligned_cols=30 Identities=27% Similarity=0.464 Sum_probs=21.8
Q ss_pred CCcCcCCCC-CcccccCCceeecCCHHHHHHHHHH
Q 043542 33 PLMGWTSTG-DPYANVGEAGLCFDSEAAARAFAEK 66 (99)
Q Consensus 33 PLMGWtss~-D~~sqv~~~~l~F~ske~Ai~yaek 66 (99)
.|-||.-.+ ..+.. ...|++-.+|++|..+
T Consensus 16 ~l~~W~~~~~~~l~r----~f~f~~f~~a~~f~~~ 46 (95)
T PF01329_consen 16 ELPGWKLDGGGRLER----TFKFKDFAEAVEFVNR 46 (95)
T ss_dssp TSTTSEEETSSEEEE----EEE-SSHHHHHHHHHH
T ss_pred cCcCCEECCCCcEEE----EEEeCCHHHHHHHHHH
Confidence 577999888 33322 7899999999998654
No 38
>PF05637 Glyco_transf_34: galactosyl transferase GMA12/MNN10 family; InterPro: IPR008630 This family contains a number of glycosyltransferase enzymes that contain a DXD motif. This family includes a number of Caenorhabditis elegans homologues where the DXD is replaced by DXH. Some members of this family are included in glycosyltransferase family 34.; GO: 0016758 transferase activity, transferring hexosyl groups, 0016021 integral to membrane; PDB: 2P72_B 2P73_A 2P6W_A.
Probab=44.80 E-value=16 Score=27.98 Aligned_cols=18 Identities=22% Similarity=0.540 Sum_probs=12.2
Q ss_pred HHHHHHHHHhCCcEEEee
Q 043542 58 AAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 58 e~Ai~yaek~G~~y~V~~ 75 (99)
+-=+.||++||++|.+..
T Consensus 31 ~Nr~~Ya~~HgY~~~~~~ 48 (239)
T PF05637_consen 31 QNRVDYARRHGYDLYYRN 48 (239)
T ss_dssp --HHHHHHHHT-EEEEE-
T ss_pred HHHHHHHHhcCCEEEEEC
Confidence 334689999999999843
No 39
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=44.56 E-value=17 Score=26.57 Aligned_cols=20 Identities=20% Similarity=0.180 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhCCcEEEeec
Q 043542 57 EAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~~p 76 (99)
++.|+..|+.|||.+...++
T Consensus 127 r~~a~eWleen~I~~~~~~~ 146 (163)
T PF03682_consen 127 RERAIEWLEENGIEPVFEED 146 (163)
T ss_pred HHHHHHHHHHcCCCcccccc
Confidence 67899999999999998875
No 40
>PRK11118 putative monooxygenase; Provisional
Probab=44.54 E-value=29 Score=24.12 Aligned_cols=29 Identities=34% Similarity=0.586 Sum_probs=22.4
Q ss_pred cCCCCCcccccCCceeecCCHHHHHHHHHHh
Q 043542 37 WTSTGDPYANVGEAGLCFDSEAAARAFAEKH 67 (99)
Q Consensus 37 Wtss~D~~sqv~~~~l~F~ske~Ai~yaek~ 67 (99)
||.+.++..- + --.-|++.++|-+|.++|
T Consensus 41 WTen~~t~ea-G-GiYlF~~e~~a~aYl~mH 69 (100)
T PRK11118 41 WTENEKTQEA-G-GIYLFEDEASAEAYLEMH 69 (100)
T ss_pred eecCCCCccc-c-eEEEECCHHHHHHHHHHH
Confidence 7877776432 3 367799999999999876
No 41
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=44.24 E-value=23 Score=24.46 Aligned_cols=26 Identities=38% Similarity=0.362 Sum_probs=18.9
Q ss_pred CCCcCcCCCCCcccccCCceeecCCHHHHHHH
Q 043542 32 NPLMGWTSTGDPYANVGEAGLCFDSEAAARAF 63 (99)
Q Consensus 32 dPLMGWtss~D~~sqv~~~~l~F~ske~Ai~y 63 (99)
++|=| ..+|-..| .|.|+|++.|.++
T Consensus 44 ~~lEG---~w~ptr~v---viEFps~~~ar~~ 69 (96)
T COG5470 44 ETLEG---EWRPTRNV---VIEFPSLEAARDC 69 (96)
T ss_pred eeccC---CCCcccEE---EEEcCCHHHHHHH
Confidence 44544 34666666 8999999999875
No 42
>KOG1706 consensus Argininosuccinate synthase [Amino acid transport and metabolism]
Probab=44.20 E-value=13 Score=31.11 Aligned_cols=23 Identities=22% Similarity=0.351 Sum_probs=20.5
Q ss_pred ecCCHHHHHHHHHHhCCcEEEee
Q 043542 53 CFDSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~~ 75 (99)
+|.-++|+++||+++||+.-|..
T Consensus 154 rf~Gr~Dl~eYakq~giPvpvT~ 176 (412)
T KOG1706|consen 154 RFKGRKDLLEYAKQHGIPVPVTP 176 (412)
T ss_pred hhcCchHHHHHHHhcCCCccccC
Confidence 58899999999999999987764
No 43
>PF05406 WGR: WGR domain; InterPro: IPR008893 This domain is named after the most conserved central motif of the domain. It is found in a variety of polyA polymerases as well as the Escherichia coli molybdate metabolism regulator P33345 from SWISSPROT and other proteins of unknown function.The domain is found in isolation in proteins such as Q9JN21 from SWISSPROT and is between 70 and 80 residues in length. ; PDB: 2EOC_A 2RA8_A 4DQY_C 2CR9_A.
Probab=43.78 E-value=24 Score=22.35 Aligned_cols=47 Identities=23% Similarity=0.154 Sum_probs=26.5
Q ss_pred CCCCCcEEEecCCCCCC-CCCcCcCCCCCcccccCCceeecCCHHHHHHHHHH
Q 043542 15 GKVGKWFINFLSTQKWE-NPLMGWTSTGDPYANVGEAGLCFDSEAAARAFAEK 66 (99)
Q Consensus 15 ~~~~~W~lefe~~~~~~-dPLMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek 66 (99)
+..+.|.|+..+..-|. --==|-.++. ...+ .-.|+|.++|++.+++
T Consensus 17 n~~kfY~iql~~~~~~~v~~~wGRiG~~-gq~~----~~~f~s~~eA~~~f~~ 64 (81)
T PF05406_consen 17 NSNKFYRIQLLPDLEWVVFRRWGRIGSK-GQTR----IKPFDSEEEAIKEFEK 64 (81)
T ss_dssp TEEEEEEEEEEEETTEEEEEEEEETTSS-EEEE----EEEESSHHHHHHHHHH
T ss_pred CcEEEEEEEEEeCCCeEEEEEECCCCCc-CcEE----EEeCCCHHHHHHHHHH
Confidence 33466777776432000 0011334444 3433 4589999999998876
No 44
>smart00461 WH1 WASP homology region 1. Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain.
Probab=43.65 E-value=21 Score=24.01 Aligned_cols=17 Identities=47% Similarity=0.683 Sum_probs=15.4
Q ss_pred eeecCCHHHHHHHHHHh
Q 043542 51 GLCFDSEAAARAFAEKH 67 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~ 67 (99)
-|.|.|.+||-.|.++.
T Consensus 86 GLnF~se~EA~~F~~~v 102 (106)
T smart00461 86 GLNFASEEEAKKFRKKV 102 (106)
T ss_pred EeecCCHHHHHHHHHHH
Confidence 79999999999998863
No 45
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=43.59 E-value=14 Score=29.07 Aligned_cols=14 Identities=36% Similarity=0.487 Sum_probs=12.9
Q ss_pred ecCCHHHHHHHHHH
Q 043542 53 CFDSEAAARAFAEK 66 (99)
Q Consensus 53 ~F~ske~Ai~yaek 66 (99)
.|+|+|+|.+||+-
T Consensus 39 sf~s~EeA~a~~~g 52 (225)
T COG3341 39 SFKSYEEAEAYCEG 52 (225)
T ss_pred ccccHHHHHHHhcc
Confidence 59999999999994
No 46
>PF00568 WH1: WH1 domain; InterPro: IPR000697 The EVH1 (WH1, RanBP1-WASP) domain is found in multi-domain proteins implicated in a diverse range of signalling, nuclear transport and cytoskeletal events. This domain of around 115 amino acids is present in species ranging from yeast to mammals. Many EVH1-containing proteins associate with actin-based structures and play a role in cytoskeletal organisation. EVH1 domains recognise and bind the proline-rich motif FPPPP with low-affinity, further interactions then form between flanking residues [][]. WASP family proteins contain a EVH1 (WH1) in their N-terminals which bind proline-rich sequences in the WASP interacting protein. Proteins of the RanBP1 family contain a WH1 domain in their N-terminal region, which seems to bind a different sequence motif present in the C-terminal part of RanGTP protein [,]. Tertiary structure of the WH1 domain of the Mena protein revealed structure similarities with the pleckstrin homology (PH) domain. The overall fold consists of a compact parallel beta-sandwich, closed along one edge by a long alpha-helix. A highly conserved cluster of three surface-exposed aromatic side-chains forms the recognition site for the molecules target ligands. [].; GO: 0005515 protein binding; PDB: 1I2H_A 1DDV_A 1DDW_A 1EGX_A 3SYX_A 1TJ6_B 1XOD_B 1EVH_A 1I7A_B 2JP2_A ....
Probab=43.12 E-value=23 Score=23.79 Aligned_cols=16 Identities=50% Similarity=0.675 Sum_probs=15.0
Q ss_pred eeecCCHHHHHHHHHH
Q 043542 51 GLCFDSEAAARAFAEK 66 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek 66 (99)
-|.|.|.+||-.|+++
T Consensus 91 GLnF~se~eA~~F~~~ 106 (111)
T PF00568_consen 91 GLNFASEEEADQFYKK 106 (111)
T ss_dssp EEEESSHHHHHHHHHH
T ss_pred EEecCCHHHHHHHHHH
Confidence 8999999999999975
No 47
>PF07014 Hs1pro-1_C: Hs1pro-1 protein C-terminus; InterPro: IPR009743 This entry represents the C terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance [].
Probab=42.38 E-value=11 Score=29.95 Aligned_cols=27 Identities=22% Similarity=0.242 Sum_probs=21.9
Q ss_pred CCCCCcccccCCceeecCCHHHHHHHH
Q 043542 38 TSTGDPYANVGEAGLCFDSEAAARAFA 64 (99)
Q Consensus 38 tss~D~~sqv~~~~l~F~ske~Ai~ya 64 (99)
++++|+++|+.-.--.|+|+++|-.|-
T Consensus 228 ~~~~D~Lsq~flEPtYfPSLDaAKTFL 254 (261)
T PF07014_consen 228 IESADSLSQIFLEPTYFPSLDAAKTFL 254 (261)
T ss_pred ccccchHHHHhcCCCCCCchhHHHHHH
Confidence 578999999854455799999998874
No 48
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=41.47 E-value=34 Score=23.22 Aligned_cols=28 Identities=25% Similarity=0.282 Sum_probs=24.2
Q ss_pred ceeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 50 AGLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 50 ~~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
..+..++.+++.+|++++|+.|.+....
T Consensus 68 i~Is~d~~~~~~~~~~~~~~~~~~l~D~ 95 (154)
T PRK09437 68 LGISTDKPEKLSRFAEKELLNFTLLSDE 95 (154)
T ss_pred EEEcCCCHHHHHHHHHHhCCCCeEEECC
Confidence 3778899999999999999999987643
No 49
>cd00837 EVH1 EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. EVH1 (Enabled, Vasp-Homology) or WASP Homology (WH1) domain. The EVH1 domain binds to other proteins at proline rich sequences in either FPPPP or PPXXF motifs. It is found in the cytoskeletal reorganization proteins Enabled VASP, and WASP, and in the synaptic scaffolding protein Homer. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=40.91 E-value=26 Score=23.42 Aligned_cols=16 Identities=50% Similarity=0.702 Sum_probs=14.9
Q ss_pred eeecCCHHHHHHHHHH
Q 043542 51 GLCFDSEAAARAFAEK 66 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek 66 (99)
-|.|.|.+||-.|.++
T Consensus 84 GL~F~se~eA~~F~~~ 99 (104)
T cd00837 84 GLNFASEEEAAQFRKK 99 (104)
T ss_pred EEeeCCHHHHHHHHHH
Confidence 8999999999999876
No 50
>PF02786 CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain; InterPro: IPR005479 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the ATP-binding domain found in the large subunit of carbamoyl phosphate synthase, as well as in related proteins.; GO: 0003824 catalytic activity, 0005524 ATP binding, 0008152 metabolic process; PDB: 3U9S_A 3U9T_A 2C00_B 2VQD_A 1W96_B 1W93_A 1M6V_C 1CS0_C 1C30_E 1C3O_G ....
Probab=40.31 E-value=31 Score=25.85 Aligned_cols=23 Identities=26% Similarity=0.329 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHhCCcEEEeecC
Q 043542 55 DSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
.|.|+|+.+|++.|++..|..-.
T Consensus 25 ~~~eea~~~a~~iGyPVliKas~ 47 (211)
T PF02786_consen 25 SSVEEALEFAEEIGYPVLIKASA 47 (211)
T ss_dssp SSHHHHHHHHHHH-SSEEEEETT
T ss_pred CCHHHHHHHHHhcCCceEEeecc
Confidence 78999999999999998876543
No 51
>TIGR00506 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase. Several members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal.
Probab=40.28 E-value=27 Score=26.62 Aligned_cols=19 Identities=16% Similarity=0.316 Sum_probs=16.6
Q ss_pred cCCHHHHHHHHHHhCCcEE
Q 043542 54 FDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~ 72 (99)
-.+++++.+||++||+.+.
T Consensus 172 m~~~~~~~~fA~~~~l~~i 190 (199)
T TIGR00506 172 MARKPELMEYAKKHNLKLI 190 (199)
T ss_pred ccCHHHHHHHHHHcCCcEE
Confidence 4678999999999999884
No 52
>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro: IPR019563 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands []. ; PDB: 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A 3A24_A.
Probab=40.21 E-value=30 Score=27.52 Aligned_cols=26 Identities=23% Similarity=0.337 Sum_probs=21.3
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeec
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p 76 (99)
.+.+++-..=|+||.++||+|.+...
T Consensus 28 g~~t~~~k~yIDfAa~~G~eYvlvD~ 53 (273)
T PF10566_consen 28 GATTETQKRYIDFAAEMGIEYVLVDA 53 (273)
T ss_dssp SSSHHHHHHHHHHHHHTT-SEEEEBT
T ss_pred CCCHHHHHHHHHHHHHcCCCEEEecc
Confidence 35788888999999999999999843
No 53
>smart00156 PP2Ac Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members.
Probab=40.15 E-value=53 Score=25.51 Aligned_cols=42 Identities=21% Similarity=0.472 Sum_probs=28.3
Q ss_pred CCCCC---CcCcCCCCCcccccCCceeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 29 KWENP---LMGWTSTGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 29 ~~~dP---LMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
-|.|| ..||..|. .. ....|. .+++.+|++++|+++.|..=+
T Consensus 176 lWsDP~~~~~~~~~~~---Rg---~g~~fg-~~~~~~Fl~~n~l~~iiR~He 220 (271)
T smart00156 176 LWSDPDQPVDGFQPSI---RG---ASYYFG-PDAVDEFLKKNNLKLIIRAHQ 220 (271)
T ss_pred eecCCCcccCCCccCC---CC---CccccC-HHHHHHHHHHCCCeEEEecCc
Confidence 46677 34555441 11 245675 688889999999999987543
No 54
>PF12745 HGTP_anticodon2: Anticodon binding domain of tRNAs; InterPro: IPR024435 This is an anticodon binding domain, found largely on Gcn2 proteins which bind tRNA to down regulate translation in certain stress situations [].; GO: 0000049 tRNA binding
Probab=40.10 E-value=33 Score=27.06 Aligned_cols=24 Identities=13% Similarity=0.206 Sum_probs=20.9
Q ss_pred cCCHHHHHHHHHHhCCcEEEeecC
Q 043542 54 FDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
..|.||.+.+|..+|+.|.|.--+
T Consensus 43 ~~S~Eel~~~~~~~gi~wiViikq 66 (273)
T PF12745_consen 43 SPSQEELQSYCREDGISWIVIIKQ 66 (273)
T ss_pred CCCHHHHHHHHHHCCCCEEEEEec
Confidence 359999999999999999987654
No 55
>PRK01792 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=39.92 E-value=27 Score=26.98 Aligned_cols=19 Identities=21% Similarity=0.384 Sum_probs=16.8
Q ss_pred cCCHHHHHHHHHHhCCcEE
Q 043542 54 FDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~ 72 (99)
..+++++++||++||+.+.
T Consensus 182 ma~~~~~~~fA~~~~l~~i 200 (214)
T PRK01792 182 MARTPEIVEFAKKFGYAVV 200 (214)
T ss_pred ccCHHHHHHHHHHcCCcEE
Confidence 4679999999999999984
No 56
>PF02177 APP_N: Amyloid A4 N-terminal heparin-binding; InterPro: IPR015849 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. This entry represents a heparin-binding domain found at the N-terminal of the extracellular domain, which is itself found at the N-terminal of amyloidogenic glycoproteins such as amyloid-beta precursor protein (APP, or A4). The core of the heparin-binding domain has an unusual disulphide-rich fold, consisting of a beta-x-alpha-beta-loop-beta topology []. More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein [].; GO: 0005488 binding, 0016021 integral to membrane; PDB: 3KTM_E 1MWP_A 2FKL_A 1OWT_A.
Probab=39.57 E-value=32 Score=23.88 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=16.1
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEe
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~ 74 (99)
.-.|.++++.++||++.--+..|.
T Consensus 31 ~~C~~~k~eIL~YCrkvYP~l~It 54 (102)
T PF02177_consen 31 ASCLKDKEEILKYCRKVYPELQIT 54 (102)
T ss_dssp -B---SHHHHHHHHHHHSTTS-EE
T ss_pred ccccCChHHHHHHHHHhCCCCcee
Confidence 568999999999999987666543
No 57
>cd01207 Ena-Vasp Enabled-VASP-type homology (EVH1) domain. Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=39.26 E-value=26 Score=24.51 Aligned_cols=17 Identities=41% Similarity=0.557 Sum_probs=15.3
Q ss_pred eeecCCHHHHHHHHHHh
Q 043542 51 GLCFDSEAAARAFAEKH 67 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~ 67 (99)
-|.|.|++||-+|.+..
T Consensus 87 GLnF~Se~eA~~F~~~v 103 (111)
T cd01207 87 GLNFGSKEDATMFASAM 103 (111)
T ss_pred eeccCCHHHHHHHHHHH
Confidence 89999999999998754
No 58
>PF05198 IF3_N: Translation initiation factor IF-3, N-terminal domain; InterPro: IPR019814 Initiation factor 3 (IF-3) (gene infC) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-3 is thought to function as a fidelity factor during the assembly of the ternary initiation complex which consist of the 30S ribosomal subunit, the initiator tRNA and the messenger RNA. IF-3 is a basic protein that binds to the 30S ribosomal subunit []. The chloroplast initiation factor IF-3(chl) is a protein that enhances the poly(A,U,G)-dependent binding of the initiator tRNA to chloroplast ribosomal 30s subunits in which the central section is evolutionary related to the sequence of bacterial IF-3 []. ; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1TIF_A.
Probab=39.15 E-value=42 Score=21.65 Aligned_cols=28 Identities=21% Similarity=0.103 Sum_probs=22.0
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecCC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
.|-.=+.++|+.-|++.|++.....|..
T Consensus 24 ~lGv~~~~eAl~~A~~~~lDLV~v~~~~ 51 (76)
T PF05198_consen 24 QLGVMSLREALRLAKEKGLDLVEVSPNA 51 (76)
T ss_dssp EEEEEEHHHHHHHHHHTT-EEEEEETTS
T ss_pred EeceEEHHHHHHHHHHcCCcEEEEcCCC
Confidence 3445578999999999999999888654
No 59
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=39.11 E-value=26 Score=26.79 Aligned_cols=18 Identities=22% Similarity=0.128 Sum_probs=15.4
Q ss_pred HHHHHHhCCcEEEeecCC
Q 043542 61 RAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~~ 78 (99)
+.||+++||+++|.+-..
T Consensus 27 ~~~a~~~g~~~~ii~~~~ 44 (200)
T PRK08179 27 LKEAARQGVRVTVLETET 44 (200)
T ss_pred HHHHHHcCCeEEEEeCCC
Confidence 579999999999988654
No 60
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=38.79 E-value=44 Score=25.38 Aligned_cols=37 Identities=27% Similarity=0.225 Sum_probs=28.4
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecCCC--CCCCcccc
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFHAP--LLKPKSYG 87 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~~~--~~~~ksYa 87 (99)
.|---|.++|+..|+..|++..+..|+.. .-+.--||
T Consensus 30 qlGiv~~~eAL~lA~e~~LDLV~Ispna~PPVcKImDYG 68 (176)
T COG0290 30 QLGIVSIEEALKLAEEAGLDLVEISPNAKPPVCKIMDYG 68 (176)
T ss_pred EEcceeHHHHHHHHHHcCCCEEEECCCCCCCeeEeeecc
Confidence 34456899999999999999999998753 33444665
No 61
>COG4314 NosL Predicted lipoprotein involved in nitrous oxide reduction [Energy production and conversion]
Probab=38.75 E-value=23 Score=26.76 Aligned_cols=22 Identities=32% Similarity=0.353 Sum_probs=18.5
Q ss_pred eeecCCHHHHHHHHHHhCCcEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~ 72 (99)
-+-|.++|+|.+||.++|=...
T Consensus 130 A~pF~~e~aA~~faa~~GGrvl 151 (176)
T COG4314 130 ASPFSDEEAAERFAADNGGRVL 151 (176)
T ss_pred cccccCHHHHHHHHHhcCCeEE
Confidence 4469999999999999996554
No 62
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=38.10 E-value=3 Score=26.25 Aligned_cols=25 Identities=24% Similarity=0.460 Sum_probs=15.0
Q ss_pred CcCcCCCCCcccccCCceeecCCHHHHHHHHHHhCCcE
Q 043542 34 LMGWTSTGDPYANVGEAGLCFDSEAAARAFAEKHGWEY 71 (99)
Q Consensus 34 LMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y 71 (99)
|.+||||.+-...+ -.+|+++|+..
T Consensus 2 ll~~TGs~~fnr~l-------------R~~A~~~g~~L 26 (64)
T PF14791_consen 2 LLYFTGSKEFNRDL-------------RQYAKKKGMKL 26 (64)
T ss_dssp HHHHHS-HHHHHHH-------------HHHHHHTTEEE
T ss_pred cccccCCHHHHHHH-------------HHHHHHcCCee
Confidence 56788887765444 24667776654
No 63
>PF14259 RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....
Probab=37.94 E-value=37 Score=19.76 Aligned_cols=19 Identities=32% Similarity=0.177 Sum_probs=16.8
Q ss_pred ceeecCCHHHHHHHHHHhC
Q 043542 50 AGLCFDSEAAARAFAEKHG 68 (99)
Q Consensus 50 ~~l~F~ske~Ai~yaek~G 68 (99)
.-+.|.|.++|...++.++
T Consensus 42 a~v~f~~~~~a~~al~~~~ 60 (70)
T PF14259_consen 42 AFVEFSSEEDAKRALELLN 60 (70)
T ss_dssp EEEEESSHHHHHHHHHHHT
T ss_pred EEEEeCCHHHHHHHHHHCC
Confidence 3689999999999999886
No 64
>PRK13864 type IV secretion system lytic transglycosylase VirB1; Provisional
Probab=37.91 E-value=49 Score=26.16 Aligned_cols=28 Identities=14% Similarity=0.128 Sum_probs=21.1
Q ss_pred ceeecCCHHHHHHHHHH---hCCcEEEeecC
Q 043542 50 AGLCFDSEAAARAFAEK---HGWEYTVRKFH 77 (99)
Q Consensus 50 ~~l~F~ske~Ai~yaek---~G~~y~V~~p~ 77 (99)
..|.+.++++||+.+++ .|..|.|---+
T Consensus 68 ~~l~~qs~~EAi~~a~~l~~~g~s~DvGLmQ 98 (245)
T PRK13864 68 ETLHWQNHAQATQSVRHRLEARHSLDVGLMQ 98 (245)
T ss_pred CccCCCCHHHHHHHHHHHHhcCCceeeechh
Confidence 46889999999998864 57777765433
No 65
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=36.99 E-value=32 Score=21.80 Aligned_cols=20 Identities=20% Similarity=0.154 Sum_probs=15.2
Q ss_pred HHHHHHHHHHhCCcEEEeec
Q 043542 57 EAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~~p 76 (99)
.++|++||+++|+.....=|
T Consensus 44 ~~~~l~~a~~~~~kv~p~C~ 63 (78)
T PF14542_consen 44 VEAALDYARENGLKVVPTCS 63 (78)
T ss_dssp HHHHHHHHHHTT-EEEETSH
T ss_pred HHHHHHHHHHCCCEEEEECH
Confidence 47899999999998775443
No 66
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=36.29 E-value=32 Score=19.67 Aligned_cols=13 Identities=23% Similarity=0.307 Sum_probs=12.0
Q ss_pred cCCHHHHHHHHHH
Q 043542 54 FDSEAAARAFAEK 66 (99)
Q Consensus 54 F~ske~Ai~yaek 66 (99)
|.|+.||..++.+
T Consensus 24 F~TkkeA~~~~~~ 36 (46)
T PF14657_consen 24 FKTKKEAEKALAK 36 (46)
T ss_pred CCcHHHHHHHHHH
Confidence 9999999999876
No 67
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=35.81 E-value=30 Score=21.79 Aligned_cols=17 Identities=18% Similarity=0.089 Sum_probs=13.1
Q ss_pred CHHHHHHHHHHhCCcEE
Q 043542 56 SEAAARAFAEKHGWEYT 72 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~ 72 (99)
+.++||.||+++=-+|.
T Consensus 2 ~~~eAi~yar~~l~~~~ 18 (99)
T smart00757 2 KIEEALAYARELLAPFA 18 (99)
T ss_pred cHHHHHHHHHHHHhhhc
Confidence 46899999998765554
No 68
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=35.72 E-value=42 Score=18.97 Aligned_cols=19 Identities=37% Similarity=0.342 Sum_probs=15.9
Q ss_pred ceeecCCHHHHHHHHH-HhC
Q 043542 50 AGLCFDSEAAARAFAE-KHG 68 (99)
Q Consensus 50 ~~l~F~ske~Ai~yae-k~G 68 (99)
.-+.|.+.++|....+ -+|
T Consensus 42 a~V~F~~~~~a~~a~~~l~g 61 (70)
T PF00076_consen 42 AFVEFESEEDAEKALEELNG 61 (70)
T ss_dssp EEEEESSHHHHHHHHHHHTT
T ss_pred EEEEEcCHHHHHHHHHHcCC
Confidence 3689999999999888 555
No 69
>PRK00910 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=35.69 E-value=35 Score=26.47 Aligned_cols=19 Identities=16% Similarity=0.176 Sum_probs=17.0
Q ss_pred cCCHHHHHHHHHHhCCcEE
Q 043542 54 FDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~ 72 (99)
..+++++++||++||+.+.
T Consensus 183 ma~~~~l~~fA~~h~l~~i 201 (218)
T PRK00910 183 MAKTPEIIAFGKLHNMPVL 201 (218)
T ss_pred cCCHHHHHHHHHHcCCcEE
Confidence 5689999999999999984
No 70
>PF03795 YCII: YCII-related domain; InterPro: IPR005545 The majority of proteins in this group contain a single copy of this domain, though it is also found as a repeat (e.g. in Q9AJZ7 from SWISSPROT). A strongly conserved histidine and a aspartate suggest that the domain has an enzymatic function. This entry also covers what was previously known as the DGPF domain (COG3795). Although its function is unknown it is found fused to a sigma-70 factor family domain in Q9A8M4 from SWISSPROT, suggesting that this domain may plays a role in transcription initiation. This domain is named after the most conserved motif in the alignment.; PDB: 1S7I_A 1MWQ_A.
Probab=35.63 E-value=22 Score=22.43 Aligned_cols=17 Identities=18% Similarity=0.102 Sum_probs=14.6
Q ss_pred ceeecCCHHHHHHHHHH
Q 043542 50 AGLCFDSEAAARAFAEK 66 (99)
Q Consensus 50 ~~l~F~ske~Ai~yaek 66 (99)
..+..+|+|+|+++|++
T Consensus 61 ~i~~a~s~e~A~~~~~~ 77 (95)
T PF03795_consen 61 IIVEAESREEAEEIAKE 77 (95)
T ss_dssp EEEEESSHHHHHHHHCT
T ss_pred EEEEeCCHHHHHHHHHh
Confidence 36789999999999975
No 71
>PRK00509 argininosuccinate synthase; Provisional
Probab=35.58 E-value=59 Score=27.19 Aligned_cols=19 Identities=32% Similarity=0.398 Sum_probs=16.7
Q ss_pred ecCCHHHHHHHHHHhCCcE
Q 043542 53 CFDSEAAARAFAEKHGWEY 71 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y 71 (99)
.|.||++-++||+++|++.
T Consensus 148 ~~~tK~eir~~A~~~Gipv 166 (399)
T PRK00509 148 DLKSREELIAYAEEHGIPI 166 (399)
T ss_pred CCCCHHHHHHHHHHcCCCC
Confidence 3559999999999999975
No 72
>PF00926 DHBP_synthase: 3,4-dihydroxy-2-butanone 4-phosphate synthase; InterPro: IPR000422 3,4-dihydroxy-2-butanone 4-phosphate synthase (4.1.99.12 from EC) (DHBP synthase) (RibB) catalyses the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate, the latter serving as the biosynthetic precursor for the xylene ring of riboflavin []. In Photobacterium leiognathi, the riboflavin synthesis genes ribB (DHBP synthase), ribE (riboflavin synthase), ribH (lumazone synthase) and ribA (GTP cyclohydrolase II) all reside in the lux operon []. RibB is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin (IPR000926 from INTERPRO). No sequences with significant homology to DHBP synthase are found in the metazoa.; GO: 0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity, 0009231 riboflavin biosynthetic process; PDB: 1K4O_A 1K4L_A 1K4P_A 1K49_A 1K4I_A 1TKU_A 1TKS_B 2RIS_A 2RIU_A 3MIO_A ....
Probab=35.48 E-value=35 Score=25.82 Aligned_cols=19 Identities=26% Similarity=0.438 Sum_probs=15.5
Q ss_pred cCCHHHHHHHHHHhCCcEE
Q 043542 54 FDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~ 72 (99)
-.+++++.+||++||+.+.
T Consensus 167 ~~~~~~~~~fA~~~~l~~v 185 (194)
T PF00926_consen 167 MARRDELEEFAKKHGLPIV 185 (194)
T ss_dssp BHCHHHHHHHHHHTT-EEE
T ss_pred cCCHHHHHHHHHHcCCcEE
Confidence 4578999999999999875
No 73
>COG5453 Uncharacterized conserved protein [Function unknown]
Probab=35.25 E-value=27 Score=24.13 Aligned_cols=18 Identities=33% Similarity=0.294 Sum_probs=15.8
Q ss_pred ecCCHHHHHHHHHHhCCc
Q 043542 53 CFDSEAAARAFAEKHGWE 70 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~ 70 (99)
.|.++++||+++-|.|..
T Consensus 68 ~ft~~~DAve~~lkKg~q 85 (96)
T COG5453 68 LFTSLDDAVEIALKKGRQ 85 (96)
T ss_pred hccchhHHHHHHHHHHHH
Confidence 399999999999998854
No 74
>TIGR01465 cobM_cbiF precorrin-4 C11-methyltransferase. This model represents precorrin-4 C11-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-3B C17-methyltransferase, EC 2.1.1.131). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products.
Probab=35.19 E-value=53 Score=23.96 Aligned_cols=32 Identities=28% Similarity=0.303 Sum_probs=24.5
Q ss_pred cCCCCCcccccCCceeecCCHHHHHHHHHHhCCcEEEeec
Q 043542 37 WTSTGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 37 Wtss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~p 76 (99)
.-.+|||+ .|.+--.-+..++++|++++|..-
T Consensus 76 ~L~~GDP~--------~~~~~~~l~~~~~~~g~~veviPG 107 (229)
T TIGR01465 76 RLHTGDPS--------IYGAIAEQMQLLEALGIPYEVVPG 107 (229)
T ss_pred EEeCcCcc--------ccccHHHHHHHHHHCCCCEEEECC
Confidence 34578874 577777888889999999998753
No 75
>COG2154 Pterin-4a-carbinolamine dehydratase [Coenzyme metabolism]
Probab=34.96 E-value=45 Score=23.04 Aligned_cols=35 Identities=26% Similarity=0.365 Sum_probs=26.0
Q ss_pred CCCCcCcCCCCCcccccCCceeecCCHHHHHHHHHHh
Q 043542 31 ENPLMGWTSTGDPYANVGEAGLCFDSEAAARAFAEKH 67 (99)
Q Consensus 31 ~dPLMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek~ 67 (99)
...|-||.-..|= ..+. ...+|++-.+|++|..+-
T Consensus 15 l~~l~gW~l~~~~-~~l~-r~f~FknF~~a~~F~~~v 49 (101)
T COG2154 15 LRALPGWELADDG-AKLT-RTFKFKNFKQAIAFVNRV 49 (101)
T ss_pred hcCCCCCEEecCc-ceEE-EEEEcCCHHHHHHHHHHH
Confidence 3679999999881 1222 278999999999997653
No 76
>KOG1468 consensus Predicted translation initiation factor related to eIF-2B alpha/beta/delta subunits (CIG2/IDI2) [Translation, ribosomal structure and biogenesis]
Probab=34.23 E-value=43 Score=27.75 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=25.7
Q ss_pred CCCCCcccccCCceeecCCHHHHHHHHHHhCCcEEEeecCCC
Q 043542 38 TSTGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRKFHAP 79 (99)
Q Consensus 38 tss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~p~~~ 79 (99)
++.|||-..| .|-.=|| .||.||++|.|..|...
T Consensus 245 arNGDTANKI-------GTy~LAv-~aKhhgipFyvaaP~ts 278 (354)
T KOG1468|consen 245 ARNGDTANKI-------GTYQLAV-LAKHHGIPFYVAAPFTS 278 (354)
T ss_pred eccCcchhhh-------hhhHHHH-HHHhcCCceEEeccccc
Confidence 4568886554 5666666 69999999999999764
No 77
>PRK00014 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=34.14 E-value=38 Score=26.55 Aligned_cols=19 Identities=21% Similarity=0.200 Sum_probs=16.9
Q ss_pred cCCHHHHHHHHHHhCCcEE
Q 043542 54 FDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~ 72 (99)
..+++++++||++||+.+.
T Consensus 187 ma~~~~l~~fA~~~~l~ii 205 (230)
T PRK00014 187 MMRGASLERYAAKEGLVAL 205 (230)
T ss_pred ccCHHHHHHHHHHcCCcEE
Confidence 4678999999999999984
No 78
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=34.07 E-value=34 Score=26.10 Aligned_cols=18 Identities=17% Similarity=0.032 Sum_probs=15.4
Q ss_pred HHHHHHhCCcEEEeecCC
Q 043542 61 RAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~~ 78 (99)
+.||+++||+++|.+-..
T Consensus 26 ~~~a~~~g~~~eii~~~~ 43 (200)
T TIGR03072 26 TREAAARGVRVEVLEQEP 43 (200)
T ss_pred HHHHHHcCCeEEEEeCCC
Confidence 579999999999988654
No 79
>KOG0237 consensus Glycinamide ribonucleotide synthetase (GARS)/Aminoimidazole ribonucleotide synthetase (AIRS) [Nucleotide transport and metabolism]
Probab=33.84 E-value=40 Score=30.60 Aligned_cols=73 Identities=19% Similarity=0.270 Sum_probs=47.7
Q ss_pred CcEEEecCC--CCCCCCCcCcCCCCCcccccCCceeecCCHHHHHHHHHHhCCcEEEeecCCCCCCCccccccCCCCC
Q 043542 19 KWFINFLST--QKWENPLMGWTSTGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRKFHAPLLKPKSYGDNFKWKG 94 (99)
Q Consensus 19 ~W~lefe~~--~~~~dPLMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~p~~~~~~~ksYadNF~~~~ 94 (99)
.|+|--.|. .-..-|=-|=|+++|+- .|.+..+.-.+.|+-+.||+++.|...|.-|..+ -...-+++|..-|
T Consensus 18 ~wkL~qSp~v~~v~vaPGn~G~a~~~~~-~~~~~dI~~~d~~ala~f~~e~~I~lVvvGPE~P--L~~Gl~~~l~~~g 92 (788)
T KOG0237|consen 18 AWKLKQSPKVKKVYVAPGNGGTASGDAS-KVPNLDISVADFEALASFCKEHNINLVVVGPELP--LVAGLADVLRSAG 92 (788)
T ss_pred HHHhhcCCccceEEEccCCCCcccCccc-cCcccccChhhHHHHHHHHHHcceeEEEECCchh--hhhhhhhhhhccC
Confidence 466665554 22335656667777762 3433467777999999999999999999998754 2223344444443
No 80
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=33.80 E-value=43 Score=22.10 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=16.8
Q ss_pred CHHHHHHHHHHhCCcEEEeecCC
Q 043542 56 SEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
|-..|+++.+.+|++|++..-..
T Consensus 8 t~rka~~~L~~~gi~~~~~d~~k 30 (110)
T PF03960_consen 8 TCRKALKWLEENGIEYEFIDYKK 30 (110)
T ss_dssp HHHHHHHHHHHTT--EEEEETTT
T ss_pred HHHHHHHHHHHcCCCeEeehhhh
Confidence 34579999999999999887543
No 81
>PF00764 Arginosuc_synth: Arginosuccinate synthase; InterPro: IPR001518 Argininosuccinate synthase (6.3.4.5 from EC) (AS) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate [, ]. In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterised by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity.; GO: 0004055 argininosuccinate synthase activity, 0005524 ATP binding, 0006526 arginine biosynthetic process; PDB: 1K97_A 1KP2_A 1K92_A 1KP3_A 2NZ2_A 1VL2_A 1J1Z_D 1KOR_C 1J20_D 1KH2_C ....
Probab=33.38 E-value=30 Score=28.96 Aligned_cols=18 Identities=28% Similarity=0.416 Sum_probs=12.9
Q ss_pred HHHHHHHHHHhCCcEEEe
Q 043542 57 EAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~ 74 (99)
+|+.|+||+++||+..+.
T Consensus 147 R~~~i~ya~~~gIpv~~~ 164 (388)
T PF00764_consen 147 REEEIEYAKKHGIPVPVT 164 (388)
T ss_dssp HHHHHHHHHHTT----SS
T ss_pred HHHHHHHHHHcCCCCCCC
Confidence 999999999999987654
No 82
>KOG0081 consensus GTPase Rab27, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.36 E-value=34 Score=26.39 Aligned_cols=23 Identities=35% Similarity=0.314 Sum_probs=19.1
Q ss_pred ecCCHHHHHHHHHHhCCcEEEee
Q 043542 53 CFDSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~~ 75 (99)
+--|.++|++.|++.|++|.-..
T Consensus 140 R~Vs~~qa~~La~kyglPYfETS 162 (219)
T KOG0081|consen 140 RVVSEDQAAALADKYGLPYFETS 162 (219)
T ss_pred hhhhHHHHHHHHHHhCCCeeeec
Confidence 45588999999999999997543
No 83
>PF07611 DUF1574: Protein of unknown function (DUF1574); InterPro: IPR011468 This is a family of hypothetical proteins found in Leptospira interrogans and other bacteria.
Probab=33.35 E-value=28 Score=28.67 Aligned_cols=28 Identities=11% Similarity=-0.093 Sum_probs=24.9
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecCC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
.+.|.-.|++++.||++||++.|.-|+.
T Consensus 248 ~~q~~F~e~~L~~ake~~I~~vl~~P~V 275 (345)
T PF07611_consen 248 ETQFFFLEKFLKLAKENGIPVVLWWPKV 275 (345)
T ss_pred hhHHHHHHHHHHHHHHcCCcEEEEEecc
Confidence 3467789999999999999999999976
No 84
>cd06576 PASTA_Pbp2x-like_1 PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are connected to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=33.21 E-value=68 Score=17.51 Aligned_cols=22 Identities=18% Similarity=0.052 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHhCCcEEEeec
Q 043542 55 DSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p 76 (99)
.+.++|.+.+++.|+.+++..+
T Consensus 8 ~~~~~a~~~l~~~g~~~~~~~~ 29 (55)
T cd06576 8 KSVEEAKKELKEAGLQPVVIGN 29 (55)
T ss_pred CCHHHHHHHHHHCCCEEEEeCC
Confidence 5789999999999999987654
No 85
>cd03017 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), w
Probab=33.21 E-value=58 Score=21.31 Aligned_cols=29 Identities=28% Similarity=0.307 Sum_probs=24.3
Q ss_pred ceeecCCHHHHHHHHHHhCCcEEEeecCC
Q 043542 50 AGLCFDSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 50 ~~l~F~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
..+.-++.+++.+|++++|+.|.+.....
T Consensus 61 v~is~d~~~~~~~~~~~~~~~~~~l~D~~ 89 (140)
T cd03017 61 IGVSPDSVESHAKFAEKYGLPFPLLSDPD 89 (140)
T ss_pred EEEcCCCHHHHHHHHHHhCCCceEEECCc
Confidence 36778899999999999999999876543
No 86
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=32.96 E-value=74 Score=18.84 Aligned_cols=24 Identities=17% Similarity=-0.026 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHhCCcEEEeecCC
Q 043542 55 DSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
.+.++.++.|+++|++....-.+.
T Consensus 15 ~~~~~~~~~a~~~g~~~v~iTDh~ 38 (67)
T smart00481 15 LSPEELVKRAKELGLKAIAITDHG 38 (67)
T ss_pred CCHHHHHHHHHHcCCCEEEEeeCC
Confidence 368999999999999999877764
No 87
>COG5079 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]
Probab=32.73 E-value=24 Score=31.36 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=22.5
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEee
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~ 75 (99)
.|.|+++++++.||+-+|++..++.
T Consensus 356 il~f~~~~e~~efckyy~lei~~ed 380 (646)
T COG5079 356 ILDFEEKGEGEEFCKYYGLEIRIED 380 (646)
T ss_pred hccccccchhHHHhhhcceeeeccc
Confidence 5899999999999999999987655
No 88
>COG1225 Bcp Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=32.63 E-value=34 Score=25.16 Aligned_cols=30 Identities=30% Similarity=0.445 Sum_probs=26.3
Q ss_pred ceeecCCHHHHHHHHHHhCCcEEEeecCCC
Q 043542 50 AGLCFDSEAAARAFAEKHGWEYTVRKFHAP 79 (99)
Q Consensus 50 ~~l~F~ske~Ai~yaek~G~~y~V~~p~~~ 79 (99)
.-++-+|.++=-+||+++|+.|.+.....+
T Consensus 68 ~GIS~Ds~~~~~~F~~k~~L~f~LLSD~~~ 97 (157)
T COG1225 68 LGISPDSPKSHKKFAEKHGLTFPLLSDEDG 97 (157)
T ss_pred EEEeCCCHHHHHHHHHHhCCCceeeECCcH
Confidence 368999999999999999999998877654
No 89
>PF00331 Glyco_hydro_10: Glycosyl hydrolase family 10; InterPro: IPR001000 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 10 GH10 from CAZY comprises enzymes with a number of known activities; xylanase (3.2.1.8 from EC); endo-1,3-beta-xylanase (3.2.1.32 from EC); cellobiohydrolase (3.2.1.91 from EC). These enzymes were formerly known as cellulase family F. The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (3.2.1.4 from EC), cellobiohydrolases (3.2.1.91 from EC) (exoglucanases), or xylanases (3.2.1.8 from EC) [, ]. Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family F [] or as the glycosyl hydrolases family 10 []. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1UQZ_A 1UQY_A 1UR2_A 1UR1_A 2CNC_A 1OD8_A 1E0W_A 1E0V_A 1V0M_A 1E0X_B ....
Probab=32.44 E-value=28 Score=27.49 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=18.7
Q ss_pred eeecCCHHHHHHHHHHhCCcEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~ 72 (99)
++.|.+.++.++||+++|+...
T Consensus 55 ~~~~~~~D~~~~~a~~~g~~vr 76 (320)
T PF00331_consen 55 RFNFESADAILDWARENGIKVR 76 (320)
T ss_dssp BEE-HHHHHHHHHHHHTT-EEE
T ss_pred ccCccchhHHHHHHHhcCccee
Confidence 6799999999999999999987
No 90
>cd00488 PCD_DCoH PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carc
Probab=32.34 E-value=65 Score=20.13 Aligned_cols=17 Identities=24% Similarity=0.255 Sum_probs=14.5
Q ss_pred eeecCCHHHHHHHHHHh
Q 043542 51 GLCFDSEAAARAFAEKH 67 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~ 67 (99)
+..|++-.+|++|+.+-
T Consensus 13 ~f~f~~f~~a~~f~~~v 29 (75)
T cd00488 13 TFKFKDFKEAIAFVNRV 29 (75)
T ss_pred EEEcCCHHHHHHHHHHH
Confidence 78899999999987653
No 91
>PTZ00056 glutathione peroxidase; Provisional
Probab=32.33 E-value=46 Score=24.50 Aligned_cols=21 Identities=19% Similarity=0.341 Sum_probs=18.9
Q ss_pred CCHHHHHHHHHHhCCcEEEee
Q 043542 55 DSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~ 75 (99)
++.|++.+|++++|+.|.|..
T Consensus 89 d~~e~~~~f~~~~~~~fpvl~ 109 (199)
T PTZ00056 89 PNTKDIRKFNDKNKIKYNFFE 109 (199)
T ss_pred CCHHHHHHHHHHcCCCceeee
Confidence 688999999999999999864
No 92
>PF10009 DUF2252: Uncharacterized protein conserved in bacteria (DUF2252); InterPro: IPR018721 This domain has no known function.
Probab=32.22 E-value=30 Score=28.44 Aligned_cols=42 Identities=17% Similarity=0.335 Sum_probs=25.7
Q ss_pred CCCCCCCcCcCCCCCc---ccccCCceeecC----CHHHHHHHHHHhCC
Q 043542 28 QKWENPLMGWTSTGDP---YANVGEAGLCFD----SEAAARAFAEKHGW 69 (99)
Q Consensus 28 ~~~~dPLMGWtss~D~---~sqv~~~~l~F~----ske~Ai~yaek~G~ 69 (99)
..-.||++||++.++- ..|++..+.+++ +.++...||+-.|+
T Consensus 287 q~~sD~~LG~~~~~g~~f~VRql~p~k~~~d~~~l~~~~~~~~a~~~g~ 335 (385)
T PF10009_consen 287 QAASDPFLGWVTIDGRDFYVRQLRPMKGSVDLEDLDPEELQDYARLCGR 335 (385)
T ss_pred hhcCCcccCceeeCCceEEEEECCCcCCCcChhhCCHHHHHHHHHHHHH
Confidence 3456999999998662 111111122222 67888888887764
No 93
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=31.74 E-value=40 Score=22.02 Aligned_cols=29 Identities=14% Similarity=0.158 Sum_probs=24.5
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecCCC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFHAP 79 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~~~ 79 (99)
-+...+.+.+-+||+..++++.|.-...+
T Consensus 18 ~I~~g~~~~~~~f~~~~~~p~~ly~D~~~ 46 (115)
T PF13911_consen 18 VIGCGSPEGIEKFCELTGFPFPLYVDPER 46 (115)
T ss_pred EEEcCCHHHHHHHHhccCCCCcEEEeCcH
Confidence 56789998899999999999998766553
No 94
>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]
Probab=31.71 E-value=26 Score=24.33 Aligned_cols=14 Identities=21% Similarity=0.510 Sum_probs=11.6
Q ss_pred HHHHHHhCCcEEEe
Q 043542 61 RAFAEKHGWEYTVR 74 (99)
Q Consensus 61 i~yaek~G~~y~V~ 74 (99)
-+||+++|+++.-.
T Consensus 48 ~aYc~r~Gl~~~s~ 61 (99)
T KOG1769|consen 48 KAYCERQGLSMNSL 61 (99)
T ss_pred HHHHHHcCCccceE
Confidence 58999999988644
No 95
>KOG0369 consensus Pyruvate carboxylase [Energy production and conversion]
Probab=31.63 E-value=42 Score=31.24 Aligned_cols=25 Identities=12% Similarity=0.130 Sum_probs=21.0
Q ss_pred ecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 53 CFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
-..|.|+|++||+++|++..+....
T Consensus 169 Pitt~~EA~eF~k~yG~PvI~KAAy 193 (1176)
T KOG0369|consen 169 PITTVEEALEFVKEYGLPVIIKAAY 193 (1176)
T ss_pred CcccHHHHHHHHHhcCCcEEEeecc
Confidence 3568999999999999999887653
No 96
>PF09691 PulS_OutS: Bacterial chaperone lipoprotein (PulS_OutS); InterPro: IPR019114 This family comprises lipoproteins from gamma proteobacterial species: pullulanase secretion protein PulS protein of Klebsiella pneumoniae (P20440 from SWISSPROT), the lipoprotein OutS protein of Erwinia chrysanthemi (Q01567 from SWISSPROT) and the functionally uncharacterised type II secretion protein EtpO (Q7BSV3 from SWISSPROT) from Escherichia coli O157:H7. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. In addition to the PulS/OutS proteins this entry also includes other functionally uncharacterised proteins, such as YacC from Escherischia coli (P0AA95 from SWISSPROT).; PDB: 3SOL_A 3UYM_A 3UTK_A 4A56_A.
Probab=31.10 E-value=33 Score=23.92 Aligned_cols=15 Identities=40% Similarity=0.838 Sum_probs=11.0
Q ss_pred HHHHHHHHHhCCcEE
Q 043542 58 AAARAFAEKHGWEYT 72 (99)
Q Consensus 58 e~Ai~yaek~G~~y~ 72 (99)
-.||.||+++||+..
T Consensus 53 ~~a~~~A~~~gWd~~ 67 (109)
T PF09691_consen 53 RAAVIFAQQRGWDTS 67 (109)
T ss_dssp HHHHHHHHHTT--CG
T ss_pred HHHHHHHHHcCCCcc
Confidence 479999999999854
No 97
>KOG0098 consensus GTPase Rab2, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.89 E-value=39 Score=26.39 Aligned_cols=18 Identities=33% Similarity=0.529 Sum_probs=16.2
Q ss_pred CCHHHHHHHHHHhCCcEE
Q 043542 55 DSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~ 72 (99)
=++||-.+||++||+-|-
T Consensus 129 Vs~EEGeaFA~ehgLifm 146 (216)
T KOG0098|consen 129 VSKEEGEAFAREHGLIFM 146 (216)
T ss_pred ccHHHHHHHHHHcCceee
Confidence 478999999999999886
No 98
>PRK12354 carbamate kinase; Reviewed
Probab=30.58 E-value=42 Score=27.21 Aligned_cols=22 Identities=27% Similarity=0.412 Sum_probs=19.1
Q ss_pred ecCCHHHHHHHHHHhCCcEEEe
Q 043542 53 CFDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~ 74 (99)
.|-|+|+|.+.++++||.+...
T Consensus 125 ~~y~~~~a~~~~~e~g~~~~~d 146 (307)
T PRK12354 125 PVYDEAEAERLAAEKGWTIKPD 146 (307)
T ss_pred cccCHHHHHHHHHhcCCEEeec
Confidence 5999999999999999965554
No 99
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=30.55 E-value=38 Score=28.37 Aligned_cols=18 Identities=22% Similarity=0.573 Sum_probs=15.9
Q ss_pred HHHHHhCCcEEEeecCCC
Q 043542 62 AFAEKHGWEYTVRKFHAP 79 (99)
Q Consensus 62 ~yaek~G~~y~V~~p~~~ 79 (99)
.||+.+||.++|..-...
T Consensus 140 rYAe~kgWk~ei~s~se~ 157 (363)
T COG0216 140 RYAESKGWKVEILSASES 157 (363)
T ss_pred HHHHhCCCEEEEeecCcc
Confidence 799999999999987654
No 100
>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=30.28 E-value=76 Score=19.21 Aligned_cols=23 Identities=9% Similarity=-0.148 Sum_probs=19.4
Q ss_pred cCCHHHHHHHHHHhCCcEEEeec
Q 043542 54 FDSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~V~~p 76 (99)
=.+....+.||++.|+.+.|.-.
T Consensus 37 ~~~~~~~~~~a~~~g~~~~iiig 59 (91)
T cd00860 37 NEKLGKKIREAQLQKIPYILVVG 59 (91)
T ss_pred CCCHHHHHHHHHHcCCCEEEEEC
Confidence 35788999999999999987765
No 101
>COG0007 CysG Uroporphyrinogen-III methylase [Coenzyme metabolism]
Probab=30.18 E-value=68 Score=25.31 Aligned_cols=25 Identities=16% Similarity=0.093 Sum_probs=20.9
Q ss_pred ecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 53 CFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
-|.=--|=+.++.++|++|+|..--
T Consensus 94 iFGRggEE~~~l~~~gI~~eVVPGi 118 (244)
T COG0007 94 IFGRGGEEIEALAEAGIEFEVVPGI 118 (244)
T ss_pred eecCcHHHHHHHHHcCCceEEeCcc
Confidence 5777778889999999999998653
No 102
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=30.05 E-value=24 Score=21.61 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=19.7
Q ss_pred ecCCHHHHHHHHHHhCCcEEEee
Q 043542 53 CFDSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~~ 75 (99)
...+.++-|++|+.+|+++...+
T Consensus 23 ~~~~~e~~~~lA~~~Gf~ft~~e 45 (64)
T TIGR03798 23 AAEDPEDRVAIAKEAGFEFTGED 45 (64)
T ss_pred HcCCHHHHHHHHHHcCCCCCHHH
Confidence 46789999999999999987654
No 103
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=29.97 E-value=69 Score=19.06 Aligned_cols=18 Identities=28% Similarity=0.577 Sum_probs=13.9
Q ss_pred CHHHHHHHHHHhCCcEEE
Q 043542 56 SEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V 73 (99)
.++.+-+|-.++||-|+|
T Consensus 28 ~L~k~~~wld~rgWwYe~ 45 (45)
T PF12123_consen 28 ELDKFTAWLDERGWWYEV 45 (45)
T ss_dssp HHHHHHHHHHHTT--EEE
T ss_pred HHHHHHHHHHhcCcEEeC
Confidence 467889999999999986
No 104
>PF04895 DUF651: Archaeal protein of unknown function (DUF651); InterPro: IPR006979 This conserved region is found in the C-terminal region of a number of conserved archaeal proteins of unknown function.
Probab=29.89 E-value=41 Score=23.49 Aligned_cols=17 Identities=12% Similarity=0.149 Sum_probs=15.1
Q ss_pred eeecCCHHHHHHHHHHh
Q 043542 51 GLCFDSEAAARAFAEKH 67 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~ 67 (99)
-..|+|.++|+.|+...
T Consensus 67 p~~f~~l~eAl~~~~~~ 83 (110)
T PF04895_consen 67 PEKFETLEEALEYVSSR 83 (110)
T ss_pred CcccCCHHHHHHHHHHH
Confidence 57999999999999865
No 105
>cd07202 cPLA2_Grp-IVC Group IVC cytoplasmic phospholipase A2; catalytic domain; Ca-independent. Group IVC cPLA2, a small 61 kDa protein, is a single domain alpha/beta hydrolase. It lacks a C2 domain; therefore, it has no Ca-dependence. Group IVC cPLA2 is also referred to as cPLA2-gamma. The cPLA2-gamma enzyme is predominantly found in cardiac and skeletal muscles, and to a lesser extent in the brain. Human cPLA2-gamma is approximately 30% identical to cPLA2-alpha. The catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both "closed lid" and "open lid" forms. Movement of the cPLA2 lid possibly exposes a greater hydrophobic surface and the active site. cPLA2 be
Probab=29.86 E-value=27 Score=29.82 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=19.5
Q ss_pred ecCCHHHHHHHHHHhCCcEEEeec
Q 043542 53 CFDSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~~p 76 (99)
-|.+...|-+||++|||+|-=.+|
T Consensus 320 pf~~l~~~~~~c~~~~ipfp~i~~ 343 (430)
T cd07202 320 PFETIKDTAEYCRKHNIPFPQVDE 343 (430)
T ss_pred hhHHHHHHHHHHHHcCCCCCCcCc
Confidence 366788999999999999965554
No 106
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=29.37 E-value=61 Score=21.21 Aligned_cols=24 Identities=21% Similarity=0.241 Sum_probs=19.3
Q ss_pred cCCHHHHHHHHH---HhCCcEEEeecC
Q 043542 54 FDSEAAARAFAE---KHGWEYTVRKFH 77 (99)
Q Consensus 54 F~ske~Ai~yae---k~G~~y~V~~p~ 77 (99)
..|+++|+.||. ++|+-+-|..-+
T Consensus 46 ~~~R~eAv~~g~~Ll~~G~i~HV~~~h 72 (84)
T cd04438 46 LTDRREARKYASSLLKLGYIRHTVNKI 72 (84)
T ss_pred CCCHHHHHHHHHHHHHCCcEEecCCCc
Confidence 579999999998 678887776543
No 107
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=28.92 E-value=68 Score=19.24 Aligned_cols=21 Identities=29% Similarity=0.499 Sum_probs=17.0
Q ss_pred CHHHHHHHHHHhCCcEEEeec
Q 043542 56 SEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~p 76 (99)
+.++-.+||+++|..+.+.+.
T Consensus 37 s~~~i~~~~~~~G~~~~~~~~ 57 (67)
T cd03421 37 AKENVSRFAESRGYEVSVEEK 57 (67)
T ss_pred HHHHHHHHHHHcCCEEEEEec
Confidence 346788999999999977654
No 108
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily. Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins.
Probab=28.86 E-value=54 Score=23.07 Aligned_cols=22 Identities=27% Similarity=0.475 Sum_probs=17.0
Q ss_pred eeec-CCHHHHHHHHHHhCCcEE
Q 043542 51 GLCF-DSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 51 ~l~F-~ske~Ai~yaek~G~~y~ 72 (99)
.+.. ++.+++.+|++++|++|.
T Consensus 97 ~V~~~~~~~~~~~~~~~~~~~f~ 119 (173)
T TIGR00385 97 GVDYKDQSQNALKFLKELGNPYQ 119 (173)
T ss_pred EEECCCChHHHHHHHHHcCCCCc
Confidence 3444 356778899999999986
No 109
>cd07996 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.
Probab=28.77 E-value=1.4e+02 Score=18.20 Aligned_cols=50 Identities=22% Similarity=0.139 Sum_probs=29.7
Q ss_pred CCCCCcEEEecCCCCC-CCCCcCcCCCCCcccccCCceeecCCHHHHHHHHHHh
Q 043542 15 GKVGKWFINFLSTQKW-ENPLMGWTSTGDPYANVGEAGLCFDSEAAARAFAEKH 67 (99)
Q Consensus 15 ~~~~~W~lefe~~~~~-~dPLMGWtss~D~~sqv~~~~l~F~ske~Ai~yaek~ 67 (99)
+..+.|.|+....-.- ..-+.=|---| +..|. ....|+|.++|++.+++.
T Consensus 12 n~~kfy~i~l~~~lfg~~~v~~~wGRiG-~~Gq~--~~~~~~s~~~A~~~~~k~ 62 (74)
T cd07996 12 NSARFYEIELEGDLFGEWSLVRRWGRIG-TKGQS--RTKTFDSEEEALKAAEKL 62 (74)
T ss_pred CCCcEEEEEEcccCCCCEEEEEEECCCC-CCCce--EEEECCCHHHHHHHHHHH
Confidence 3346789888863111 12233344444 23333 256799999999998864
No 110
>KOG0097 consensus GTPase Rab14, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.17 E-value=44 Score=25.36 Aligned_cols=18 Identities=28% Similarity=0.466 Sum_probs=15.5
Q ss_pred CHHHHHHHHHHhCCcEEE
Q 043542 56 SEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V 73 (99)
+-|+|-+|||.+|+-|.-
T Consensus 135 ~yeeak~faeengl~fle 152 (215)
T KOG0097|consen 135 TYEEAKEFAEENGLMFLE 152 (215)
T ss_pred cHHHHHHHHhhcCeEEEE
Confidence 568999999999998753
No 111
>PF02811 PHP: PHP domain; InterPro: IPR004013 The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. This family is often associated with an N-terminal region IPR003141 from INTERPRO.; GO: 0003824 catalytic activity; PDB: 2WJE_A 3QY8_A 2WJD_A 2WJF_A 1PB0_B 1M68_A 1M65_A 3E38_B 2W9M_A 3E0F_A ....
Probab=28.08 E-value=65 Score=21.66 Aligned_cols=24 Identities=21% Similarity=0.138 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHhCCcEEEeecCC
Q 043542 55 DSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
.+.|+.|..|+++|++......+.
T Consensus 16 ~~~~e~v~~A~~~Gl~~i~iTDH~ 39 (175)
T PF02811_consen 16 DSPEEYVEQAKEKGLDAIAITDHN 39 (175)
T ss_dssp SSHHHHHHHHHHTTESEEEEEEET
T ss_pred CCHHHHHHHHHHcCCCEEEEcCCc
Confidence 489999999999999999888773
No 112
>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).
Probab=28.06 E-value=73 Score=22.39 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=18.4
Q ss_pred CHHHHHHHHHHhCCcEEEeecC
Q 043542 56 SEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~p~ 77 (99)
..+.|..+|+..|+++.+..-.
T Consensus 46 ~~~~~~~~~~~~gi~~~~~~~~ 67 (189)
T TIGR02432 46 EAEFVQQFCKKLNIPLEIKKVD 67 (189)
T ss_pred HHHHHHHHHHHcCCCEEEEEec
Confidence 3688999999999999987653
No 113
>PRK00923 sirohydrochlorin cobaltochelatase; Reviewed
Probab=28.04 E-value=96 Score=20.73 Aligned_cols=25 Identities=8% Similarity=-0.203 Sum_probs=21.9
Q ss_pred eecCCHHHHHHHHHHhCCcEEEeec
Q 043542 52 LCFDSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 52 l~F~ske~Ai~yaek~G~~y~V~~p 76 (99)
+..+|.+++++-|.++|..-.|.-|
T Consensus 43 ~~~P~l~~~l~~l~~~g~~~v~vvP 67 (126)
T PRK00923 43 FNEPTIPEALKKLIGTGADKIIVVP 67 (126)
T ss_pred cCCCCHHHHHHHHHHcCCCEEEEEc
Confidence 3468999999999999999888877
No 114
>PF01910 DUF77: Domain of unknown function DUF77; InterPro: IPR002767 This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined []. These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. ; PDB: 1LXJ_A 1YQH_A 2EKY_G 2EPI_A 1VK8_D 2IBO_C 1LXN_B.
Probab=27.98 E-value=53 Score=21.73 Aligned_cols=19 Identities=26% Similarity=0.328 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhCCcEEEee
Q 043542 57 EAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~~ 75 (99)
-.+||++.++.|++|+|..
T Consensus 19 V~~~i~~i~~sgl~y~v~p 37 (92)
T PF01910_consen 19 VAEAIEVIKESGLKYEVGP 37 (92)
T ss_dssp HHHHHHHHHTSSSEEEEET
T ss_pred HHHHHHHHHHcCCceEEcC
Confidence 3689999999999999864
No 115
>PLN02923 xylose isomerase
Probab=27.71 E-value=62 Score=28.07 Aligned_cols=30 Identities=23% Similarity=0.217 Sum_probs=22.4
Q ss_pred HHHHHHHHHHhCCcEE-EeecCCCCCCCccc
Q 043542 57 EAAARAFAEKHGWEYT-VRKFHAPLLKPKSY 86 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~-V~~p~~~~~~~ksY 86 (99)
..-|++|+++.|.+.. .+||++...+.-.|
T Consensus 255 l~ma~dY~~~iGf~g~flIEPKP~EPtkHqY 285 (478)
T PLN02923 255 LEAAVAYKKKIGFNGTLLIEPKPQEPTKHQY 285 (478)
T ss_pred HHHHHHHHHhcCCCceEEecCCCCCCCCCcc
Confidence 3468999999999987 56777766655555
No 116
>PF05159 Capsule_synth: Capsule polysaccharide biosynthesis protein; InterPro: IPR007833 This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS P42218 from SWISSPROT and LipB P57038 from SWISSPROT. Capsule polysaccharide modification protein lipB/A is involved in the phospholipid modification of the capsular polysaccharide and is a strong requirement for its translocation to the cell surface. The capsule of Neisseria meningitidis serogroup B and of other meningococcal serogroups and other Gram-negative bacterial pathogens, are anchored in the outer membrane through a 1,2-diacylglycerol moiety. The lipA and lipB genes are located on the 3' end of the ctr operon. lipA and lipB do not encode proteins responsible for diacylglycerophosphatidic acid substitution of the meningococcal capsule polymer, but they are required for proper translocation and surface expression of the lipidated polymer []. KpsS is an unusual sulphate-modified form of the capsular polysaccharide in Rhizobium loti (Mesorhizobium loti). Many plants, including R. loti, enter into symbiotic relationships with bacteria that allow survival in nutrient-limiting environments. KpsS functions as a fucosyl sulphotransferase in vitro. The kpsS gene product shares no significant amino acid similarity with previously identified sulphotransferases []. Sulphated cell surface polysaccharides are required for optimum nodule formation but limit growth rate and nodule colonisation in M. loti [].; GO: 0000271 polysaccharide biosynthetic process, 0015774 polysaccharide transport
Probab=27.48 E-value=65 Score=24.17 Aligned_cols=23 Identities=17% Similarity=-0.035 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHHhCCcEEEeecC
Q 043542 55 DSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
.....|+..|+++|+++.+.|.-
T Consensus 11 ~~~~~~~~~a~~~~i~~~~~E~G 33 (269)
T PF05159_consen 11 PYHRAAIEVAKELGIPVIFFEDG 33 (269)
T ss_pred cHHHHHHHHHHHhCCCEEEEecC
Confidence 34567889999999999999964
No 117
>cd03012 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3.
Probab=27.38 E-value=55 Score=21.53 Aligned_cols=23 Identities=17% Similarity=0.173 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHhCCcEEEeecC
Q 043542 55 DSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
++.++..+|++++|+.|.+....
T Consensus 71 ~~~~~~~~~~~~~~~~~p~~~D~ 93 (126)
T cd03012 71 RDLANVKSAVLRYGITYPVANDN 93 (126)
T ss_pred cCHHHHHHHHHHcCCCCCEEECC
Confidence 56899999999999999877644
No 118
>PF11216 DUF3012: Protein of unknown function (DUF3012); InterPro: IPR021379 This family of proteins with unknown function is restricted to Gammaproteobacteria.
Probab=27.31 E-value=45 Score=18.73 Aligned_cols=10 Identities=30% Similarity=0.444 Sum_probs=8.4
Q ss_pred CHHHHHHHHH
Q 043542 56 SEAAARAFAE 65 (99)
Q Consensus 56 ske~Ai~yae 65 (99)
|.++|.+||+
T Consensus 19 tanea~~fAK 28 (32)
T PF11216_consen 19 TANEAADFAK 28 (32)
T ss_pred cHhHHHHHHH
Confidence 6788999987
No 119
>cd01999 Argininosuccinate_Synthase Argininosuccinate synthase. The Argininosuccinate synthase is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate . In humans, a defect in the AS gene causes citrullinemia, a genetic disease characterized by severe vomiting spells and mental retardation. AS is a homotetrameric enzyme of chains of about 400 amino-acid residues. An arginine seems to be important for the enzyme's catalytic mechanism. The sequences of AS from various prokaryotes, archaebacteria and eukaryotes show significant similarity
Probab=27.24 E-value=96 Score=25.70 Aligned_cols=21 Identities=33% Similarity=0.445 Sum_probs=17.9
Q ss_pred cCCHHHHHHHHHHhCCcEEEe
Q 043542 54 FDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~V~ 74 (99)
+-||++-++||+++|+++...
T Consensus 146 ~~sr~ev~~~A~~~Gip~~~~ 166 (385)
T cd01999 146 FLSREEEIEYAEEHGIPVPVT 166 (385)
T ss_pred cCCHHHHHHHHHHcCCCCccc
Confidence 449999999999999987543
No 120
>KOG2741 consensus Dimeric dihydrodiol dehydrogenase [Carbohydrate transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=26.98 E-value=45 Score=27.77 Aligned_cols=20 Identities=25% Similarity=0.325 Sum_probs=17.2
Q ss_pred eeecCCHHHHHHHHHHhCCc
Q 043542 51 GLCFDSEAAARAFAEKHGWE 70 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~ 70 (99)
-+-=.|.|-|++||++|+|.
T Consensus 37 ava~~s~~~A~~fAq~~~~~ 56 (351)
T KOG2741|consen 37 AVADPSLERAKEFAQRHNIP 56 (351)
T ss_pred EEecccHHHHHHHHHhcCCC
Confidence 55567999999999999994
No 121
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=26.85 E-value=89 Score=17.88 Aligned_cols=20 Identities=20% Similarity=0.396 Sum_probs=16.6
Q ss_pred HHHHHHHHHhCCcEEEeecC
Q 043542 58 AAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 58 e~Ai~yaek~G~~y~V~~p~ 77 (99)
..|.++-+++|++|++.+=.
T Consensus 13 ~~~~~~L~~~~i~y~~~dv~ 32 (60)
T PF00462_consen 13 KKAKEFLDEKGIPYEEVDVD 32 (60)
T ss_dssp HHHHHHHHHTTBEEEEEEGG
T ss_pred HHHHHHHHHcCCeeeEcccc
Confidence 46889999999999987643
No 122
>TIGR00746 arcC carbamate kinase. The seed alignment for this model includes experimentally confirmed examples from a set of phylogenetically distinct species. In a neighbor-joining tree constructed from an alignment of candidate carbamate kinases and several acetylglutamate kinases, the latter group forms a clear outgroup which roots the tree of carbamate kinase-like proteins. This analysis suggests that in E. coli, the ArcC paralog YqeA may be a second isozyme, while the paralog YahI branches as an outlier and is less likely to be an authentic carbamate kinase. The homolog from Mycoplasma pneumoniae likewise branches outside the set containing known carbamate kinases and also scores below the trusted cutoff.
Probab=26.62 E-value=67 Score=25.81 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=18.2
Q ss_pred ecCCHHHHHHHHHHhCCcEEE
Q 043542 53 CFDSEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V 73 (99)
.|-|+|+|.+.++++||.|.-
T Consensus 131 ~~y~~~~a~~~~~~~~~~~~~ 151 (310)
T TIGR00746 131 PFYTEEEAKRLAAEKGWIVKE 151 (310)
T ss_pred CCcCHHHHHHHHHHcCCeEee
Confidence 589999999999999996544
No 123
>COG1979 Uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family [Energy production and conversion]
Probab=26.46 E-value=41 Score=28.36 Aligned_cols=22 Identities=5% Similarity=0.170 Sum_probs=19.5
Q ss_pred ecCCHHHHHHHHHHhCCcEEEe
Q 043542 53 CFDSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~V~ 74 (99)
++.|...||..|+++|++|.+-
T Consensus 70 ~~~Tv~kaV~i~kee~idflLA 91 (384)
T COG1979 70 RLETLMKAVEICKEENIDFLLA 91 (384)
T ss_pred hHHHHHHHHHHHHHcCceEEEE
Confidence 5678999999999999999864
No 124
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=26.45 E-value=87 Score=24.84 Aligned_cols=27 Identities=7% Similarity=0.030 Sum_probs=23.5
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
.+-..++.+|..+|+++|+++.+...+
T Consensus 124 ~~visn~~~~~~~A~~~gIp~~~~~~~ 150 (289)
T PRK13010 124 VGIISNHPDLQPLAVQHDIPFHHLPVT 150 (289)
T ss_pred EEEEECChhHHHHHHHcCCCEEEeCCC
Confidence 677889999999999999999987544
No 125
>PF07476 MAAL_C: Methylaspartate ammonia-lyase C-terminus; InterPro: IPR022662 Methylaspartate ammonia-lyase 4.3.1.2 from EC catalyses the second step of fermentation of glutamate. It is a homodimer. This domain represents the C-terminal region of methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the PF01188 from PFAM. This domain represents the catalytic domain and contains a metal binding site []. ; PDB: 1KKO_B 1KKR_A 3ZVI_A 1KD0_B 1KCZ_B 3ZVH_A.
Probab=26.36 E-value=55 Score=26.10 Aligned_cols=19 Identities=16% Similarity=0.232 Sum_probs=13.9
Q ss_pred CHHHHHHHHHHhCCcEEEe
Q 043542 56 SEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~ 74 (99)
+--+||-||+++|+.-.+-
T Consensus 177 ntieAvlyCk~~gvgaY~G 195 (248)
T PF07476_consen 177 NTIEAVLYCKEHGVGAYLG 195 (248)
T ss_dssp HHHHHHHHHHHTT-EEEE-
T ss_pred hHHHHHHHHHhcCCceeec
Confidence 3468999999999887653
No 126
>PF00059 Lectin_C: Lectin C-type domain; InterPro: IPR001304 Lectins occur in plants, animals, bacteria and viruses. Initially described for their carbohydrate-binding activity [], they are now recognised as a more diverse group of proteins, some of which are involved in protein-protein, protein-lipid or protein-nucleic acid interactions []. There are at least twelve structural families of lectins: C-type lectins, which are Ca+-dependent. S-type (galectins), a widespread family of glycan-binding proteins []. I-type, which have an immunoglobulin-like fold and can recognise sialic acids, other sugars and glycosaminoglycans []. P-type, which bind phosphomannosyl receptors []. Pentraxins []. (Trout) egg lectins. Calreticulin and calnexin, which act as molecular chaperones of the endoplasmic reticulum []. ERGIC-53 and VIP-36 []. Discoidins []. Eel aggutinins (fucolectins) []. Annexin lectins []. Fibrinogen-type lectins, which includes ficolins, tachylectins 5A and 5B, and Limax flavus (Spotted garden slug) agglutinin (these proteins have clear distinctions from one another, but they share a homologous fibrinogen-like domain used for carbohydrate binding). Also unclassified orphan lectins, including amphoterin, Cel-II, complement factor H, thrombospondin, sailic acid-binding lectins, adherence lectin, and cytokins (such as tumour necrosis factor and several interleukins). C-type lectins can be further divided into seven subgroups based on additional non-lectin domains and gene structure: (I) hyalectans, (II) asialoglycoprotein receptors, (III) collectins, (IV) selectins, (V) NK group transmembrane receptors, (VI) macrophage mannose receptors, and (VII) simple (single domain) lectins []. Therefore, lectins are a diverse group of proteins, both in terms of structure and activity. Carbohydrate binding ability may have evolved independently and sporadically in numerous unrelated families, where each evolved a structure that was conserved to fulfil some other activity and function. In general, animal lectins act as recognition molecules within the immune system, their functions involving defence against pathogens, cell trafficking, immune regulation and the prevention of autoimmunity [].; GO: 0005488 binding; PDB: 1T8D_A 2H2T_B 1T8C_A 2H2R_A 1TN3_A 1RJH_A 1HTN_A 3G8K_B 2E3X_B 1UMR_D ....
Probab=26.11 E-value=48 Score=19.95 Aligned_cols=19 Identities=11% Similarity=0.136 Sum_probs=13.1
Q ss_pred CHHHHHHHHHHhCCcEEEe
Q 043542 56 SEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~ 74 (99)
|-++|..+|+++|=..-+.
T Consensus 4 ~~~~A~~~C~~~~~~L~~i 22 (105)
T PF00059_consen 4 TWEEAQQYCQSMGAHLASI 22 (105)
T ss_dssp EHHHHHHHHHHTTSEEB-G
T ss_pred CHHHHHHHHhcCCCEEeEe
Confidence 3478999999987554443
No 127
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=25.92 E-value=57 Score=21.09 Aligned_cols=25 Identities=20% Similarity=0.218 Sum_probs=18.8
Q ss_pred ecCCHHHHHHHHH---HhCCcEEEeecC
Q 043542 53 CFDSEAAARAFAE---KHGWEYTVRKFH 77 (99)
Q Consensus 53 ~F~ske~Ai~yae---k~G~~y~V~~p~ 77 (99)
...|+++||++|. .+|+-.-|...+
T Consensus 43 ~~~~R~eAv~~gq~Ll~~g~i~hV~~~~ 70 (81)
T cd04448 43 KAATRVQAIAIGQALLDAGWIECVSDDD 70 (81)
T ss_pred CCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 4689999999998 467766665543
No 128
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=25.91 E-value=75 Score=20.11 Aligned_cols=19 Identities=16% Similarity=0.050 Sum_probs=15.7
Q ss_pred HHHHHHHHhCCcEEEeecC
Q 043542 59 AARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 59 ~Ai~yaek~G~~y~V~~p~ 77 (99)
-|..+|+++|+..++..|.
T Consensus 48 iA~~wA~~~gv~~~~~~ad 66 (71)
T PF10686_consen 48 IAARWARERGVPVIRFPAD 66 (71)
T ss_pred HHHHHHHHCCCeeEEeCcC
Confidence 4778999999999887664
No 129
>cd06575 PASTA_Pbp2x-like_2 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are attached to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine
Probab=25.89 E-value=1.1e+02 Score=16.36 Aligned_cols=21 Identities=19% Similarity=0.041 Sum_probs=18.0
Q ss_pred CCHHHHHHHHHHhCCcEEEee
Q 043542 55 DSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~ 75 (99)
.+.++|.+..++.|+.+.+..
T Consensus 8 ~~~~~a~~~l~~~g~~~~~~~ 28 (54)
T cd06575 8 WSKRDALKLLELLGLKVKFSG 28 (54)
T ss_pred CCHHHHHHHHHHCCCeEEEee
Confidence 578999999999999987664
No 130
>cd03593 CLECT_NK_receptors_like C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs). CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis up
Probab=25.85 E-value=55 Score=20.77 Aligned_cols=37 Identities=5% Similarity=0.054 Sum_probs=22.0
Q ss_pred CcCCCCCcccccCCceeecCCHHHHHHHHHHhCCcEEEee
Q 043542 36 GWTSTGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 36 GWtss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~ 75 (99)
||+.-++-==.+. ..-.|=.+|..+|+.+|=...+..
T Consensus 4 gw~~~~~~Cy~~~---~~~~~w~~A~~~C~~~g~~La~i~ 40 (116)
T cd03593 4 DWICYGNKCYYFS---MEKKTWNESKEACSSKNSSLLKID 40 (116)
T ss_pred cCEEeCCEEEEEE---cCCCCHHHHHHHHHhCCCcEEEEC
Confidence 5666555322221 112567889999999996655443
No 131
>smart00034 CLECT C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules.
Probab=25.66 E-value=59 Score=20.11 Aligned_cols=19 Identities=26% Similarity=0.291 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHhCCcEEE
Q 043542 55 DSEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V 73 (99)
.+-++|.++|+++|=....
T Consensus 20 ~~~~~A~~~C~~~~~~La~ 38 (126)
T smart00034 20 KTWADAQAFCQSLGAHLAS 38 (126)
T ss_pred cCHHHHHHHHHhcCCEEcc
Confidence 6788999999999844433
No 132
>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=25.49 E-value=1e+02 Score=18.09 Aligned_cols=21 Identities=14% Similarity=0.132 Sum_probs=17.6
Q ss_pred CHHHHHHHHHHhCCcEEEeec
Q 043542 56 SEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~p 76 (99)
+....+.||++.|+.+.|.--
T Consensus 39 ~~~~~~~~a~~~~~~~~i~i~ 59 (91)
T cd00859 39 KLKKQFKYADRSGARFAVILG 59 (91)
T ss_pred CHHHHHHHHHHcCCCEEEEEc
Confidence 678999999999999876553
No 133
>cd01206 Homer Homer type EVH1 domain. Homer type EVH1 domain. Homer is a synaptic scaffolding protein, involved in neuronal signaling. It contains an EVH1 domain, which binds to both neurotransmitter receptors, such as the metabotropic glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=25.40 E-value=65 Score=22.77 Aligned_cols=33 Identities=48% Similarity=0.608 Sum_probs=23.3
Q ss_pred CCcCcCCCC-------Cccc-ccCCceeecCCHHHHHHHHHHh
Q 043542 33 PLMGWTSTG-------DPYA-NVGEAGLCFDSEAAARAFAEKH 67 (99)
Q Consensus 33 PLMGWtss~-------D~~s-qv~~~~l~F~ske~Ai~yaek~ 67 (99)
|=|+.+.+. |+.+ +| --|.|.|+++|-.|+++.
T Consensus 63 ~~~~y~kas~~FhQWrD~R~~tV--yGLnF~Sk~ea~~F~~~f 103 (111)
T cd01206 63 PNMTFTKTSQKFGQWADSRANTV--YGLGFSSEQQLTKFAEKF 103 (111)
T ss_pred CCcceeeccccccccccccccee--eecccCCHHHHHHHHHHH
Confidence 445665553 6552 55 369999999999999763
No 134
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=25.36 E-value=59 Score=20.88 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=16.7
Q ss_pred cCCHHHHHHHHHH---hCCcEEEee
Q 043542 54 FDSEAAARAFAEK---HGWEYTVRK 75 (99)
Q Consensus 54 F~ske~Ai~yaek---~G~~y~V~~ 75 (99)
..|+++||++|++ +|+-.-|..
T Consensus 46 ~~~r~eAv~lgq~Ll~~g~I~hv~~ 70 (83)
T cd04449 46 VDTREEAVELGQELMNEGLIEHVSG 70 (83)
T ss_pred CCCHHHHHHHHHHHHHCCCEEecCC
Confidence 5799999999994 566555543
No 135
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=24.98 E-value=95 Score=18.51 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHhCCcEEEeecCC
Q 043542 55 DSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
+.=..|..+.+++|++|++..-..
T Consensus 12 ~~C~ka~~~L~~~gi~~~~~di~~ 35 (73)
T cd03027 12 EDCTAVRLFLREKGLPYVEINIDI 35 (73)
T ss_pred hhHHHHHHHHHHCCCceEEEECCC
Confidence 455789999999999999887653
No 136
>PRK06746 peptide chain release factor 2; Provisional
Probab=24.89 E-value=58 Score=26.75 Aligned_cols=17 Identities=24% Similarity=0.481 Sum_probs=14.4
Q ss_pred HHHHHHhCCcEEEeecC
Q 043542 61 RAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~ 77 (99)
..||+++||+++|.+-.
T Consensus 113 ~r~a~~~g~~~evi~~~ 129 (326)
T PRK06746 113 TRWAEKRGFKVETVDYL 129 (326)
T ss_pred HHHHHHcCCEEEEEecC
Confidence 46999999999998754
No 137
>cd04442 DEP_1_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=24.89 E-value=61 Score=21.28 Aligned_cols=21 Identities=14% Similarity=0.085 Sum_probs=15.7
Q ss_pred CCHHHHHHHHH---HhCCcEEEee
Q 043542 55 DSEAAARAFAE---KHGWEYTVRK 75 (99)
Q Consensus 55 ~ske~Ai~yae---k~G~~y~V~~ 75 (99)
.|+++||.+|. ..|+---|..
T Consensus 45 ~sR~eAv~lgq~Ll~~gvi~HV~~ 68 (82)
T cd04442 45 SDRETAIKIMQKLLDHSIIHHVCD 68 (82)
T ss_pred CCHHHHHHHHHHHHHCCCEEeccC
Confidence 79999999998 4566555543
No 138
>KOG0855 consensus Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=24.88 E-value=52 Score=25.44 Aligned_cols=30 Identities=30% Similarity=0.335 Sum_probs=26.3
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecCCCC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFHAPL 80 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~~~~ 80 (99)
-|+|++-.+--+|+-+++++|.+.....+.
T Consensus 129 GlS~D~s~sqKaF~sKqnlPYhLLSDpk~e 158 (211)
T KOG0855|consen 129 GLSGDDSASQKAFASKQNLPYHLLSDPKNE 158 (211)
T ss_pred eeccCchHHHHHhhhhccCCeeeecCcchh
Confidence 689999999999999999999988766543
No 139
>PLN03181 glycosyltransferase; Provisional
Probab=24.84 E-value=52 Score=28.34 Aligned_cols=22 Identities=9% Similarity=0.119 Sum_probs=16.7
Q ss_pred CCHHHHHHHHHHhCCcEEEeec
Q 043542 55 DSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p 76 (99)
...+-=++||++||+++.+...
T Consensus 152 riikNR~dYArrHGY~lf~~~a 173 (453)
T PLN03181 152 RFFKNKVDYCRIHGYDIFYNNA 173 (453)
T ss_pred HHHHHHHHHHHHhCCcEEEecc
Confidence 3455567999999999986654
No 140
>TIGR01004 PulS_OutS lipoprotein, PulS/OutS family. This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae, the OutS protein of Erwinia chrysanthemi and Pectobacterium chrysanthemi, and the functionally uncharacterized E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family.
Probab=24.77 E-value=58 Score=23.53 Aligned_cols=14 Identities=29% Similarity=0.544 Sum_probs=12.1
Q ss_pred HHHHHHHHhCCcEE
Q 043542 59 AARAFAEKHGWEYT 72 (99)
Q Consensus 59 ~Ai~yaek~G~~y~ 72 (99)
.||.||+.+||+-.
T Consensus 70 aai~~A~~~gWd~~ 83 (128)
T TIGR01004 70 TANNVAIGKGWDSG 83 (128)
T ss_pred HHHHHHHHcCCchh
Confidence 79999999999643
No 141
>cd07415 MPP_PP2A_PP4_PP6 PP2A, PP4, and PP6 phosphoprotein phosphatases, metallophosphatase domain. PP2A-like family of phosphoprotein phosphatases (PPP's) including PP4 and PP6. PP2A (Protein phosphatase 2A) is a critical regulator of many cellular activities. PP2A comprises about 1% of total cellular proteins. PP2A, together with protein phosphatase 1 (PP1), accounts for more than 90% of all serine/threonine phosphatase activities in most cells and tissues. The PP2A subunit in addition to having a catalytic domain homologous to PP1, has a unique C-terminal tail, containing a motif that is conserved in the catalytic subunits of all PP2A-like phosphatases including PP4 and PP6, and has an important role in PP2A regulation. The PP2A-like family of phosphatases all share a similar heterotrimeric architecture, that includes: a 65kDa scaffolding subunit (A), a 36kDa catalytic subunit (C), and one of 18 regulatory subunits (B). The PPP (phosphoprotein phosphatase) family, to which PP2
Probab=24.39 E-value=1.5e+02 Score=23.34 Aligned_cols=26 Identities=19% Similarity=0.436 Sum_probs=21.2
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
...|. .+++.+|++++|+++.|..=+
T Consensus 209 g~~fg-~~~~~~Fl~~n~l~~iiR~He 234 (285)
T cd07415 209 GYLFG-QDVVEEFNHNNGLTLICRAHQ 234 (285)
T ss_pred ccccC-HHHHHHHHHHCCCeEEEEcCc
Confidence 45665 789999999999999987543
No 142
>cd07238 Glo_EDI_BRP_like_5 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structure of this family is a that of a strand-swapped dimer.
Probab=24.33 E-value=1.5e+02 Score=18.37 Aligned_cols=23 Identities=26% Similarity=0.187 Sum_probs=20.1
Q ss_pred eeecCCHHHHHHHHHHhCCcEEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V 73 (99)
.+.-++.+++++.++++|+.+..
T Consensus 62 ~~~v~d~~~~~~~l~~~G~~~~~ 84 (112)
T cd07238 62 SIEVDDVDAALARAVAAGFAIVY 84 (112)
T ss_pred EEEeCCHHHHHHHHHhcCCeEec
Confidence 67789999999999999998753
No 143
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=24.32 E-value=78 Score=18.29 Aligned_cols=24 Identities=13% Similarity=0.122 Sum_probs=18.2
Q ss_pred eecC-CHHHHHHHHHHhCCcEEEee
Q 043542 52 LCFD-SEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 52 l~F~-ske~Ai~yaek~G~~y~V~~ 75 (99)
+.|+ ||++=|.+|+++|.+=.|.+
T Consensus 4 ~dyPa~k~~Lv~~A~~~gA~~~vl~ 28 (44)
T PF11387_consen 4 VDYPADKDELVRHARRNGAPDDVLD 28 (44)
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 3453 79999999999998755543
No 144
>TIGR02540 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7.
Probab=24.12 E-value=59 Score=22.23 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=18.1
Q ss_pred CCHHHHHHHHHH-hCCcEEEee
Q 043542 55 DSEAAARAFAEK-HGWEYTVRK 75 (99)
Q Consensus 55 ~ske~Ai~yaek-~G~~y~V~~ 75 (99)
++.+++.+|+++ +|+.|-|..
T Consensus 72 d~~~~~~~f~~~~~~~~fp~~~ 93 (153)
T TIGR02540 72 DSSKEIESFARRNYGVTFPMFS 93 (153)
T ss_pred CCHHHHHHHHHHhcCCCCCccc
Confidence 778999999986 899998853
No 145
>cd03592 CLECT_selectins_like C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels). CLECT_selectins_like: C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. P- E- and L-sels are cell adhesion receptors that mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. L- sel is expressed constitutively on most leukocytes. P-sel is stored in the Weibel-Palade bodies of endothelial cells and in the alpha granules of platlets. E- sels are present on endothelial cells. Following platelet and/or endothelial cell activation P- sel is rapidly translocated to the cell surface and E-sel exp
Probab=24.07 E-value=62 Score=20.77 Aligned_cols=19 Identities=11% Similarity=0.137 Sum_probs=14.2
Q ss_pred CCHHHHHHHHHHhCCcEEE
Q 043542 55 DSEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V 73 (99)
.|=++|.+||+++|-....
T Consensus 10 ~~w~~A~~~C~~~g~~La~ 28 (115)
T cd03592 10 MTFNEAVKYCKSRGTDLVA 28 (115)
T ss_pred cCHHHHHHHHHHcCCeEee
Confidence 3557899999999954443
No 146
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=24.05 E-value=80 Score=20.41 Aligned_cols=21 Identities=33% Similarity=0.517 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCCcEEEeecC
Q 043542 57 EAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~~p~ 77 (99)
=..|.+|.+++|++|++..-.
T Consensus 12 c~ka~~~L~~~~i~~~~idi~ 32 (105)
T cd02977 12 SRKALAWLEEHGIEYEFIDYL 32 (105)
T ss_pred HHHHHHHHHHcCCCcEEEeec
Confidence 457899999999999988754
No 147
>smart00633 Glyco_10 Glycosyl hydrolase family 10.
Probab=23.98 E-value=76 Score=23.91 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=19.6
Q ss_pred eeecCCHHHHHHHHHHhCCcEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~ 72 (99)
+..|...+++|++|+++|+.+.
T Consensus 12 ~~n~~~~D~~~~~a~~~gi~v~ 33 (254)
T smart00633 12 QFNFSGADAIVNFAKENGIKVR 33 (254)
T ss_pred ccChHHHHHHHHHHHHCCCEEE
Confidence 5689999999999999999964
No 148
>PF06243 PaaB: Phenylacetic acid degradation B; InterPro: IPR009359 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation [, ]. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA [].; PDB: 3EGR_A.
Probab=23.94 E-value=81 Score=21.39 Aligned_cols=26 Identities=23% Similarity=0.221 Sum_probs=20.0
Q ss_pred CCCCcccccCCceeecCCHHHHHHHHHH
Q 043542 39 STGDPYANVGEAGLCFDSEAAARAFAEK 66 (99)
Q Consensus 39 ss~D~~sqv~~~~l~F~ske~Ai~yaek 66 (99)
+.++++..|+ .|.=++.|.|+.+|..
T Consensus 13 ~~g~~~~HvG--sV~A~d~e~Al~~Ar~ 38 (94)
T PF06243_consen 13 KPGLPHQHVG--SVHAPDPEMALQQARD 38 (94)
T ss_dssp TT-SS-EEEE--EEE-SSHHHHHHHHHH
T ss_pred CCCCCceEEe--eeeCCCHHHHHHHHHH
Confidence 4578888885 8999999999999987
No 149
>TIGR00032 argG argininosuccinate synthase. argG in bacteria, ARG1 in Saccharomyces cerevisiae. There is a very unusual clustering in the alignment, with a deep split between one cohort of E. coli, H. influenzae, and Streptomyces, and the other cohort of eukaryotes, archaea, and the rest of the eubacteria.
Probab=23.59 E-value=90 Score=25.94 Aligned_cols=20 Identities=20% Similarity=0.356 Sum_probs=18.2
Q ss_pred CHHHHHHHHHHhCCcEEEee
Q 043542 56 SEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~ 75 (99)
++++-+.||+++|+++.+..
T Consensus 147 ~r~ei~~ya~~~Gip~~~~~ 166 (394)
T TIGR00032 147 TREEEIEYAIQCGIPYPMSK 166 (394)
T ss_pred CHHHHHHHHHHcCCCeeEec
Confidence 79999999999999998764
No 150
>cd04440 DEP_2_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=23.58 E-value=65 Score=21.81 Aligned_cols=22 Identities=14% Similarity=0.170 Sum_probs=17.1
Q ss_pred cCCHHHHHHHHH---HhCCcEEEee
Q 043542 54 FDSEAAARAFAE---KHGWEYTVRK 75 (99)
Q Consensus 54 F~ske~Ai~yae---k~G~~y~V~~ 75 (99)
-.|+|+||.|++ .+||---|..
T Consensus 53 ~~tR~eAv~~gq~Ll~~gii~HV~~ 77 (93)
T cd04440 53 CRTREEAVILGVGLCNNGFMHHVLE 77 (93)
T ss_pred CCCHHHHHHHHHHHHhCCCEEecCC
Confidence 469999999998 4677666664
No 151
>cd04441 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=23.56 E-value=66 Score=21.30 Aligned_cols=23 Identities=22% Similarity=0.202 Sum_probs=17.0
Q ss_pred ecCCHHHHHHHHH---HhCCcEEEee
Q 043542 53 CFDSEAAARAFAE---KHGWEYTVRK 75 (99)
Q Consensus 53 ~F~ske~Ai~yae---k~G~~y~V~~ 75 (99)
...|+++||.+|+ .+|+---|..
T Consensus 47 ~~~sR~eAv~lgq~Ll~~gii~HV~~ 72 (85)
T cd04441 47 EAESRREAVQLCRRLLEHGIIQHVSN 72 (85)
T ss_pred CCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 3689999999998 4566555543
No 152
>COG1453 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]
Probab=23.48 E-value=72 Score=27.01 Aligned_cols=20 Identities=10% Similarity=0.084 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCcEEEeecCC
Q 043542 59 AARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 59 ~Ai~yaek~G~~y~V~~p~~ 78 (99)
+|++||.++|....|-+|-.
T Consensus 187 ~~l~~A~~~~~gI~IMeP~~ 206 (391)
T COG1453 187 EGLKYAASKGLGIFIMEPLD 206 (391)
T ss_pred HHHHHHHhCCCcEEEEeeCC
Confidence 68999999999999999964
No 153
>PRK03353 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=23.39 E-value=76 Score=24.35 Aligned_cols=18 Identities=22% Similarity=0.278 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHHhCCcEE
Q 043542 55 DSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~ 72 (99)
..++++++||++||+...
T Consensus 183 ~~~~~~~~fA~~~~l~~v 200 (217)
T PRK03353 183 ARAPECIAFAKQHNMPVL 200 (217)
T ss_pred ccHHHHHHHHHHcCCcEE
Confidence 468999999999999883
No 154
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=22.96 E-value=1e+02 Score=23.38 Aligned_cols=22 Identities=18% Similarity=0.311 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHhCCcEEEeecC
Q 043542 56 SEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~p~ 77 (99)
+.+.+.++|++.|+++.|....
T Consensus 75 ~~~~~~~~~~~lgI~~~v~~~~ 96 (258)
T PRK10696 75 PEHVLPEYLESLGVPYHIEEQD 96 (258)
T ss_pred CHHHHHHHHHHhCCCEEEEEec
Confidence 3456789999999999987643
No 155
>TIGR03748 conj_PilL conjugative transfer region protein, TIGR03748 family. This model describes the conserved N-terminal region of a variable length protein family associated with laterally transfered regions flanked by markers of conjugative plasmid integration and/or transposition. Most members of the family have the lipoprotein signal peptide motif. A member of the family from a pathogenicity island in Salmonella enterica serovar Dublin strain was designated PilL for nomenclature consistency with a neighboring gene for the pilin structural protein PilS. However, the species distribution of this protein family tracks much better with markers of conjugal transfer than with markers of PilS-like pilin structure.
Probab=22.93 E-value=77 Score=22.09 Aligned_cols=28 Identities=14% Similarity=0.252 Sum_probs=21.7
Q ss_pred CCcccccCCceeecC-----CHHHHHHHHHH-hCCc
Q 043542 41 GDPYANVGEAGLCFD-----SEAAARAFAEK-HGWE 70 (99)
Q Consensus 41 ~D~~sqv~~~~l~F~-----ske~Ai~yaek-~G~~ 70 (99)
-||+.|| ..+.|+ |-.+|+.|.-+ -|+.
T Consensus 18 ~dpL~qv--v~v~~P~~~~~TVGdAl~~~L~~SGY~ 51 (105)
T TIGR03748 18 RDLLNQV--IDITIPPSLVATVGDALRYLLRRSGYS 51 (105)
T ss_pred hChHhhe--eEEECCccccCCHHHHHHHHHHccCcC
Confidence 4788888 589999 99999999854 3443
No 156
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=22.90 E-value=1.2e+02 Score=20.86 Aligned_cols=26 Identities=15% Similarity=0.124 Sum_probs=23.0
Q ss_pred eecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 52 LCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 52 l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
+.++|.++|++-+.++|+.=.|..|-
T Consensus 53 ~~~p~~~eaL~~l~~~G~~~V~V~Pl 78 (127)
T cd03412 53 IEVDTPEEALAKLAADGYTEVIVQSL 78 (127)
T ss_pred CCCCCHHHHHHHHHHCCCCEEEEEeC
Confidence 46899999999999999998888774
No 157
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=22.89 E-value=69 Score=21.72 Aligned_cols=20 Identities=20% Similarity=0.117 Sum_probs=17.1
Q ss_pred eeecCCHHHHHHHHHHhCCc
Q 043542 51 GLCFDSEAAARAFAEKHGWE 70 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~ 70 (99)
+|...++.+++.+|.+.|+.
T Consensus 185 Kl~~~~~~~l~~~~~~~~~~ 204 (204)
T PRK09958 185 KLECKSLMDLYTFAQRNKIG 204 (204)
T ss_pred HcCCCCHHHHHHHHHHhCCC
Confidence 67789999999999998863
No 158
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=22.86 E-value=1.2e+02 Score=17.89 Aligned_cols=22 Identities=14% Similarity=0.217 Sum_probs=19.0
Q ss_pred eeecCCHHHHHHHHHHhCCcEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~ 72 (99)
+|.+++.|.|++--+++|+...
T Consensus 44 rl~~~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 44 RLIVSDPDKAKEALKEAGFAVK 65 (66)
T ss_pred EEEECCHHHHHHHHHHCCCEEE
Confidence 8899999999999999997653
No 159
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=22.86 E-value=53 Score=24.48 Aligned_cols=19 Identities=16% Similarity=0.027 Sum_probs=16.9
Q ss_pred eeecCCHHHHHHHHHHhCC
Q 043542 51 GLCFDSEAAARAFAEKHGW 69 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~ 69 (99)
.+.|++.|++|.+|+...-
T Consensus 133 v~~F~dfedvI~la~~l~~ 151 (220)
T PF05389_consen 133 VFEFDDFEDVIQLAKRLQD 151 (220)
T ss_dssp EEEESSHHHHHHHHCHCCH
T ss_pred EEEcCCHHHHHHHHhhccc
Confidence 6899999999999998753
No 160
>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=22.73 E-value=1.1e+02 Score=18.86 Aligned_cols=21 Identities=19% Similarity=0.254 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHhCCcEEEee
Q 043542 55 DSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~ 75 (99)
.+.-..+.+|++.|++|.|.-
T Consensus 39 ~~~~k~~~~a~~~g~p~~iii 59 (94)
T PF03129_consen 39 KSLGKQIKYADKLGIPFIIII 59 (94)
T ss_dssp STHHHHHHHHHHTTESEEEEE
T ss_pred CchhHHHHHHhhcCCeEEEEE
Confidence 467789999999999999764
No 161
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=22.72 E-value=67 Score=26.66 Aligned_cols=18 Identities=28% Similarity=0.599 Sum_probs=14.9
Q ss_pred HHHHHHhCCcEEEeecCC
Q 043542 61 RAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~~ 78 (99)
..||+++||+++|.+-..
T Consensus 151 ~~~a~~~g~~~evi~~~~ 168 (367)
T PRK00578 151 LRWAERHGFKVEVLDYSE 168 (367)
T ss_pred HHHHHHcCCEEEEEecCC
Confidence 469999999999987543
No 162
>COG0656 ARA1 Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]
Probab=22.71 E-value=86 Score=25.08 Aligned_cols=26 Identities=15% Similarity=0.204 Sum_probs=20.4
Q ss_pred cCCHHHHHHHHHHhCCcEEEeecCCC
Q 043542 54 FDSEAAARAFAEKHGWEYTVRKFHAP 79 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~V~~p~~~ 79 (99)
+....+-+.||++||+..+.-.|-.+
T Consensus 169 ~~~q~el~~~~~~~gI~v~AysPL~~ 194 (280)
T COG0656 169 YLRQPELLPFCQRHGIAVEAYSPLAK 194 (280)
T ss_pred CCCcHHHHHHHHHcCCEEEEECCccc
Confidence 34444499999999999998888654
No 163
>PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed
Probab=22.56 E-value=79 Score=25.68 Aligned_cols=20 Identities=30% Similarity=0.574 Sum_probs=17.5
Q ss_pred ecCCHHHHHHHHHHhCCcEE
Q 043542 53 CFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 53 ~F~ske~Ai~yaek~G~~y~ 72 (99)
.|-|+|+|.+.++++||.|.
T Consensus 134 ~~y~~~~a~~~~~~~g~~~~ 153 (313)
T PRK12454 134 PFYDEEEAKKLAKEKGWIVK 153 (313)
T ss_pred CCcCHHHHHHHHHHcCCEEE
Confidence 49999999999999999543
No 164
>PF02407 Viral_Rep: Putative viral replication protein; InterPro: IPR003365 Proteins in this entry are essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication introducing an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3'. This initiates rolling circle replication (RCR). Following cleavage, the protein binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication.; GO: 0016779 nucleotidyltransferase activity, 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters, 0042624 ATPase activity, uncoupled, 0006260 DNA replication, 0018142 protein-DNA covalent cross-linking; PDB: 2HW0_A 2HWT_A.
Probab=22.35 E-value=10 Score=25.12 Aligned_cols=12 Identities=33% Similarity=0.581 Sum_probs=10.3
Q ss_pred CCHHHHHHHHHH
Q 043542 55 DSEAAARAFAEK 66 (99)
Q Consensus 55 ~ske~Ai~yaek 66 (99)
.|.++|++||.|
T Consensus 74 Gs~~qa~~YC~K 85 (86)
T PF02407_consen 74 GSDEQAREYCSK 85 (86)
T ss_dssp TTCCHHHCCHCT
T ss_pred CCHHHHHHHccC
Confidence 578999999976
No 165
>PF14370 Topo_C_assoc: C-terminal topoisomerase domain; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=22.30 E-value=33 Score=22.45 Aligned_cols=17 Identities=12% Similarity=0.176 Sum_probs=10.8
Q ss_pred CHHHHHHHHHHhCCcEE
Q 043542 56 SEAAARAFAEKHGWEYT 72 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~ 72 (99)
+.-=.|++|+++|++.+
T Consensus 32 DPRItvAWck~~~VPie 48 (71)
T PF14370_consen 32 DPRITVAWCKRHEVPIE 48 (71)
T ss_dssp -HHHHHHHHHHTT--GG
T ss_pred CcHHHHHHHHHhCCcHH
Confidence 33446899999998765
No 166
>PRK05589 peptide chain release factor 2; Provisional
Probab=22.29 E-value=70 Score=26.20 Aligned_cols=18 Identities=22% Similarity=0.457 Sum_probs=15.1
Q ss_pred HHHHHHhCCcEEEeecCC
Q 043542 61 RAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~~ 78 (99)
..||+++||+++|.+-..
T Consensus 112 ~~~a~~~g~~~~vi~~~~ 129 (325)
T PRK05589 112 TRWAEKKGYKVEIIDLLE 129 (325)
T ss_pred HHHHHHcCCEEEEEecCC
Confidence 469999999999987644
No 167
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=22.17 E-value=1.1e+02 Score=24.11 Aligned_cols=27 Identities=11% Similarity=0.233 Sum_probs=23.5
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
.+-+.++++|-++|+++|+++.+..++
T Consensus 120 ~~visn~~~~~~lA~~~gIp~~~~~~~ 146 (286)
T PRK06027 120 AAVISNHDDLRSLVERFGIPFHHVPVT 146 (286)
T ss_pred EEEEEcChhHHHHHHHhCCCEEEeccC
Confidence 677889999999999999999987654
No 168
>TIGR00552 nadE NAD+ synthetase. NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of the family, such as from Mycobacterium tuberculosis, are considerably longer, contain an apparent amidotransferase domain, and show glutamine-dependent as well as NH(3)-dependent activity.
Probab=22.08 E-value=73 Score=24.06 Aligned_cols=22 Identities=27% Similarity=0.268 Sum_probs=18.9
Q ss_pred CCHHHHHHHHHHhCCcEEEeec
Q 043542 55 DSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p 76 (99)
.+.+.|.++|++.|+++.+..-
T Consensus 64 ~e~~~a~~~a~~lgi~~~~i~i 85 (250)
T TIGR00552 64 QDVQDALALAEPLGINYKNIDI 85 (250)
T ss_pred HHHHHHHHHHHHhCCeEEEEcc
Confidence 4678999999999999998754
No 169
>PRK10638 glutaredoxin 3; Provisional
Probab=21.87 E-value=97 Score=19.06 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCCcEEEeecC
Q 043542 57 EAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~~p~ 77 (99)
-..|..+.+++|++|++.+-.
T Consensus 15 C~~a~~~L~~~gi~y~~~dv~ 35 (83)
T PRK10638 15 CHRAKALLNSKGVSFQEIPID 35 (83)
T ss_pred HHHHHHHHHHcCCCcEEEECC
Confidence 357899999999999988654
No 170
>cd00037 CLECT C-type lectin (CTL)/C-type lectin-like (CTLD) domain. CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initia
Probab=21.76 E-value=78 Score=18.86 Aligned_cols=19 Identities=11% Similarity=0.010 Sum_probs=14.9
Q ss_pred cCCHHHHHHHHHHhCCcEEE
Q 043542 54 FDSEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 54 F~ske~Ai~yaek~G~~y~V 73 (99)
..+-++|.++|+++| ...+
T Consensus 9 ~~~~~~A~~~C~~~~-~~L~ 27 (116)
T cd00037 9 KLTWEEAQEYCRSLG-GHLA 27 (116)
T ss_pred ccCHHHHHHHHHHcC-CEEc
Confidence 467899999999999 4433
No 171
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=21.71 E-value=1.1e+02 Score=18.90 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=18.8
Q ss_pred eeecCCHHHHHHHHHHhCCcEEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTV 73 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V 73 (99)
++....+|.++...+++|+.|+=
T Consensus 46 ~~~~~d~~~i~~~l~~~~i~~~~ 68 (73)
T PF11823_consen 46 RFEPEDLEKIKEILEENGIEYEG 68 (73)
T ss_pred EEChhhHHHHHHHHHHCCCCeeE
Confidence 34447899999999999999873
No 172
>KOG1380 consensus Heme A farnesyltransferase [Coenzyme transport and metabolism]
Probab=21.69 E-value=32 Score=29.04 Aligned_cols=11 Identities=45% Similarity=1.084 Sum_probs=8.7
Q ss_pred CCCCcCcCCCC
Q 043542 31 ENPLMGWTSTG 41 (99)
Q Consensus 31 ~dPLMGWtss~ 41 (99)
+-|||||...+
T Consensus 234 IPPLMGwAAas 244 (409)
T KOG1380|consen 234 IPPLMGWAAAS 244 (409)
T ss_pred CCccchhhhhc
Confidence 57999998664
No 173
>PF13669 Glyoxalase_4: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily; PDB: 3RMU_B 3ISQ_A 1JC5_D 1JC4_D 3HDP_A 2QH0_A 3GM5_A 3OA4_A 3CT8_A.
Probab=21.65 E-value=91 Score=19.89 Aligned_cols=35 Identities=20% Similarity=0.142 Sum_probs=27.4
Q ss_pred CCCcccccCCceeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 40 TGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 40 s~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
.+.-+..| -+.-++.++|++.++.+|+...-..+.
T Consensus 65 ~~~gi~Hi---a~~v~D~d~~~~~l~~~G~~~~~~~~~ 99 (109)
T PF13669_consen 65 GGGGIHHI---AFEVDDLDAAIARLEAQGFRVLDEGPR 99 (109)
T ss_dssp TSSEEEEE---EEEESHHHHHHHHHHHTTECEEECEEE
T ss_pred CCCCEEEE---EEEeCCHHHHHHHHHHCCCEEcccCcc
Confidence 34446666 677899999999999999998866543
No 174
>cd07420 MPP_RdgC Drosophila melanogaster RdgC and related proteins, metallophosphatase domain. RdgC (retinal degeneration C) is a vertebrate serine-threonine protein phosphatase that is required to prevent light-induced retinal degeneration. In addition to its catalytic domain, RdgC has two C-terminal EF hands. Homologs of RdgC include the human phosphatases protein phosphatase with EF hands 1 and -2 (PPEF-1 and -2). PPEF-1 transcripts are present at low levels in the retina, PPEF-2 transcripts and PPEF-2 protein are present at high levels in photoreceptors. The PPP (phosphoprotein phosphatase) family, to which RdgC belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all
Probab=21.53 E-value=1.8e+02 Score=23.47 Aligned_cols=26 Identities=23% Similarity=0.434 Sum_probs=20.4
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
...|. .++..+||+++|+++.|..=+
T Consensus 248 g~~FG-~~~~~~Fl~~n~l~~IIR~He 273 (321)
T cd07420 248 GCYFG-PDVTSKVLQKHGLSLLIRSHE 273 (321)
T ss_pred ccccC-HHHHHHHHHHCCCcEEEEcCh
Confidence 45566 777789999999999987543
No 175
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=21.50 E-value=97 Score=17.36 Aligned_cols=17 Identities=24% Similarity=0.573 Sum_probs=14.0
Q ss_pred CHHHHHHHHHHhCCcEE
Q 043542 56 SEAAARAFAEKHGWEYT 72 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~ 72 (99)
+.+.|+.|-++++|+.+
T Consensus 14 ~~~~A~~~L~~~~wdle 30 (43)
T PF14555_consen 14 DEDVAIQYLEANNWDLE 30 (43)
T ss_dssp SHHHHHHHHHHTTT-HH
T ss_pred CHHHHHHHHHHcCCCHH
Confidence 77999999999999753
No 176
>PRK12865 YciI-like protein; Reviewed
Probab=21.33 E-value=81 Score=20.60 Aligned_cols=25 Identities=24% Similarity=0.322 Sum_probs=18.5
Q ss_pred eeecCCHHHHHHHHHH-----hCC--cEEEee
Q 043542 51 GLCFDSEAAARAFAEK-----HGW--EYTVRK 75 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek-----~G~--~y~V~~ 75 (99)
-+.++|+|+|.++++. +|+ .++|.+
T Consensus 56 i~~a~s~e~a~~~~~~DP~~~~g~~~~v~I~~ 87 (97)
T PRK12865 56 IVKAETKEAAKALADADPYAKAGLFESVEVKA 87 (97)
T ss_pred EEEcCCHHHHHHHHHcCCchhcCCeeEEEEEE
Confidence 4689999999999974 564 355543
No 177
>PTZ00175 diphthine synthase; Provisional
Probab=21.31 E-value=1.4e+02 Score=23.44 Aligned_cols=29 Identities=31% Similarity=0.497 Sum_probs=24.0
Q ss_pred CCCCcccccCCceeecCCHHHHHHHHHHhCCcEEEee
Q 043542 39 STGDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 39 ss~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~ 75 (99)
.+|||+ .|.+--+=+..|+++|++++|..
T Consensus 83 ~~GDP~--------i~~t~~~l~~~~~~~gi~vevIP 111 (270)
T PTZ00175 83 VVGDPF--------CATTHTDLYLRAKKKGIEVEVIH 111 (270)
T ss_pred ECCCCC--------ccCCHHHHHHHHHHCCCcEEEEC
Confidence 467874 57788888889999999999987
No 178
>PF12671 Amidase_6: Putative amidase domain
Probab=21.30 E-value=70 Score=22.62 Aligned_cols=16 Identities=31% Similarity=0.245 Sum_probs=13.6
Q ss_pred CHHHHHHHHHHhCCcE
Q 043542 56 SEAAARAFAEKHGWEY 71 (99)
Q Consensus 56 ske~Ai~yaek~G~~y 71 (99)
+++.||+||++.-..+
T Consensus 3 nr~~Av~YA~k~~~~~ 18 (157)
T PF12671_consen 3 NRSAAVAYANKYANNP 18 (157)
T ss_pred CHHHHHHHHHHHhcCC
Confidence 5789999999987766
No 179
>PF06356 DUF1064: Protein of unknown function (DUF1064); InterPro: IPR009414 This entry is represented by Bacteriophage 92, Orf34. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins whose functions have not been experimentally determined. Computational analysis involving sequence, predicted strucutre and genomic context suggests that these proteins may be endonucleases which function in phage genome segregation, or the repair of double-stranded breaks introduced during either this process or DNA replication [].
Probab=21.22 E-value=79 Score=22.18 Aligned_cols=15 Identities=40% Similarity=0.676 Sum_probs=12.9
Q ss_pred eeecCCHHHHHHHHH
Q 043542 51 GLCFDSEAAARAFAE 65 (99)
Q Consensus 51 ~l~F~ske~Ai~yae 65 (99)
.+.|+|+-||-.|++
T Consensus 13 Gi~FDSk~Ea~~Y~~ 27 (118)
T PF06356_consen 13 GIKFDSKKEAEYYQE 27 (118)
T ss_pred CeEEccHHHHHHHHH
Confidence 468999999999884
No 180
>PF11247 DUF2675: Protein of unknown function (DUF2675) ; InterPro: IPR022611 Members in this family of proteins include Bacteriophage T7 gene 5.5; they have no known function.
Probab=21.20 E-value=47 Score=23.00 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=14.3
Q ss_pred HHHHHHHHHHhCCcEEEe
Q 043542 57 EAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~ 74 (99)
.|.||+||-|+|+.=.|.
T Consensus 58 ~egav~f~~k~g~R~~IK 75 (98)
T PF11247_consen 58 PEGAVAFVVKQGIREAIK 75 (98)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 699999999999754443
No 181
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=21.15 E-value=1.2e+02 Score=19.97 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=22.7
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
.+..++.+++.+|++++++.|.+....
T Consensus 67 ~vs~d~~~~~~~~~~~~~~~~~~~~D~ 93 (149)
T cd03018 67 GISVDSPFSLRAWAEENGLTFPLLSDF 93 (149)
T ss_pred EecCCCHHHHHHHHHhcCCCceEecCC
Confidence 567789999999999999999987643
No 182
>PRK12465 xylose isomerase; Provisional
Probab=21.12 E-value=1.1e+02 Score=26.30 Aligned_cols=30 Identities=13% Similarity=0.135 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhCCcEE-EeecCCCCCCCccc
Q 043542 57 EAAARAFAEKHGWEYT-VRKFHAPLLKPKSY 86 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~-V~~p~~~~~~~ksY 86 (99)
.+-|++|+.+.|++.. .+||++...+.-+|
T Consensus 221 l~ma~dY~~~iGf~g~f~IEPKP~EPr~hqy 251 (445)
T PRK12465 221 LTLARDYGRSIGFKGNFLIEPKPMEPMKHQY 251 (445)
T ss_pred HHHHHHHhHhcCCCceEEeccCCCCCCcccc
Confidence 4567789999999766 45677666666555
No 183
>PRK07342 peptide chain release factor 2; Provisional
Probab=21.05 E-value=76 Score=26.19 Aligned_cols=18 Identities=28% Similarity=0.481 Sum_probs=15.1
Q ss_pred HHHHHHhCCcEEEeecCC
Q 043542 61 RAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~~ 78 (99)
..||+++||+++|.+-..
T Consensus 115 ~~~a~~~g~~~~vi~~~~ 132 (339)
T PRK07342 115 TRWAERQGRKVEVLEVHD 132 (339)
T ss_pred HHHHHHcCCEEEEEecCC
Confidence 469999999999987654
No 184
>PF02540 NAD_synthase: NAD synthase; InterPro: IPR022310 NAD+ synthase (6.3.5.1 from EC) catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide and is induced by stress factors such as heat shock and glucose limitation. The three-dimensional structure of NH3-dependent NAD+ synthetase from Bacillus subtilis, in its free form and in complex with ATP shows that the enzyme consists of a tight homodimer with alpha/beta subunit topology []. Catalyzes the synthesis of GMP from XMP. The protein is a homodimer, but in the archaea it is a heterodimer composed of a glutamine amidotransferase subunit (A) and a GMP-binding subunit (B). This entry contains the GMP-binding subunit (B). ; PDB: 2VXO_A 3UOW_B 3N05_A 2DPL_B 3A4I_A 3SEQ_D 3SZG_A 3SYT_A 3SDB_A 3SEZ_C ....
Probab=20.99 E-value=88 Score=23.92 Aligned_cols=20 Identities=40% Similarity=0.484 Sum_probs=17.7
Q ss_pred CHHHHHHHHHHhCCcEEEee
Q 043542 56 SEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~ 75 (99)
+.++|...|++.|+++.+..
T Consensus 61 ~~~~A~~la~~lgi~~~~i~ 80 (242)
T PF02540_consen 61 DIEDAKELAEKLGIEYIVID 80 (242)
T ss_dssp HHHHHHHHHHHHTSEEEEEE
T ss_pred HHHHHHHHHHHhCCCeeccc
Confidence 46799999999999999875
No 185
>KOG3048 consensus Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones]
Probab=20.94 E-value=66 Score=23.93 Aligned_cols=13 Identities=8% Similarity=0.330 Sum_probs=11.5
Q ss_pred CCHHHHHHHHHHh
Q 043542 55 DSEAAARAFAEKH 67 (99)
Q Consensus 55 ~ske~Ai~yaek~ 67 (99)
.|.|+|.+||+|.
T Consensus 97 K~~e~akdyfkRK 109 (153)
T KOG3048|consen 97 KDAEDAKDYFKRK 109 (153)
T ss_pred echHHHHHHHHHH
Confidence 5899999999984
No 186
>KOG0091 consensus GTPase Rab39, small G protein superfamily [General function prediction only]
Probab=20.86 E-value=88 Score=24.24 Aligned_cols=20 Identities=20% Similarity=0.386 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHhCCcEEEee
Q 043542 56 SEAAARAFAEKHGWEYTVRK 75 (99)
Q Consensus 56 ske~Ai~yaek~G~~y~V~~ 75 (99)
|.|+|..||+.+|..|.=..
T Consensus 135 t~EEaEklAa~hgM~FVETS 154 (213)
T KOG0091|consen 135 TAEEAEKLAASHGMAFVETS 154 (213)
T ss_pred cHHHHHHHHHhcCceEEEec
Confidence 89999999999999986443
No 187
>cd07249 MMCE Methylmalonyl-CoA epimerase (MMCE). MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) interconverts (2R)-methylmalonyl-CoA and (2S)-methylmalonyl-CoA. MMCE has been found in bacteria, archaea, and in animals. In eukaryotes, MMCE is an essential enzyme in a pathway that converts propionyl-CoA to succinyl-CoA, and is important in the breakdown of odd-chain length fatty acids, branched-chain amino acids, and other metabolites. In bacteria, MMCE participates in the reverse pathway for propionate fermentation, glyoxylate regeneration, and the biosynthesis of polyketide antibiotics. MMCE is closely related to glyoxalase I and type I extradiol dioxygenases.
Probab=20.76 E-value=1.3e+02 Score=18.69 Aligned_cols=22 Identities=23% Similarity=0.116 Sum_probs=19.5
Q ss_pred eeecCCHHHHHHHHHHhCCcEE
Q 043542 51 GLCFDSEAAARAFAEKHGWEYT 72 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~ 72 (99)
.+..++.+++++.+.+.|+.+.
T Consensus 77 ~f~v~d~~~~~~~l~~~G~~~~ 98 (128)
T cd07249 77 AFEVDDIDAALARLKAQGVRLL 98 (128)
T ss_pred EEEeCCHHHHHHHHHHCCCeee
Confidence 6778999999999999999753
No 188
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=20.75 E-value=1.1e+02 Score=20.50 Aligned_cols=25 Identities=24% Similarity=0.171 Sum_probs=19.3
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeec
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p 76 (99)
+..|.+.+ ..++++++|+..+|..-
T Consensus 63 ~~~~~~~~-~~~~l~~~gI~vE~m~T 87 (109)
T cd00248 63 EIAFLPRA-LRAALRAAGIGVEVMST 87 (109)
T ss_pred CCCcCCHH-HHHHHHHcCCeEEEeCc
Confidence 34677755 67899999999998764
No 189
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=20.75 E-value=1.5e+02 Score=17.79 Aligned_cols=27 Identities=19% Similarity=0.130 Sum_probs=21.8
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
.+.=...+....+.+++|+.|+|.-..
T Consensus 39 ~V~p~~~~~f~~~L~~~~i~~~v~i~d 65 (74)
T PF02244_consen 39 MVPPEKLEEFEELLKEHGIEYEVLIED 65 (74)
T ss_dssp EEEGGGHHHHHHHHHHTT-EEEEEES-
T ss_pred EECHHHHHHHHHHHHHCCCcEEEEeHH
Confidence 677788899999999999999997543
No 190
>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=20.73 E-value=1.4e+02 Score=18.08 Aligned_cols=22 Identities=14% Similarity=-0.052 Sum_probs=18.4
Q ss_pred CCHHHHHHHHHHhCCcEEEeec
Q 043542 55 DSEAAARAFAEKHGWEYTVRKF 76 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~y~V~~p 76 (99)
.+....+.+|++.|+.|.+.--
T Consensus 41 ~~~~k~~~~a~~~g~~~~iiig 62 (94)
T cd00738 41 RKIGKKFREADLRGVPFAVVVG 62 (94)
T ss_pred cCHhHHHHHHHhCCCCEEEEEC
Confidence 4678899999999999887654
No 191
>cd02970 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins.
Probab=20.66 E-value=1.5e+02 Score=19.30 Aligned_cols=28 Identities=14% Similarity=0.045 Sum_probs=23.5
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecCC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~~ 78 (99)
.+..++.+++.+|++++++.|.+.....
T Consensus 62 ~V~~~~~~~~~~~~~~~~~~~p~~~D~~ 89 (149)
T cd02970 62 AVGPESPEKLEAFDKGKFLPFPVYADPD 89 (149)
T ss_pred EEeCCCHHHHHHHHHhcCCCCeEEECCc
Confidence 6678888889999999999999877543
No 192
>cd07416 MPP_PP2B PP2B, metallophosphatase domain. PP2B (calcineurin) is a unique serine/threonine protein phosphatase in its regulation by a second messenger (calcium and calmodulin). PP2B is involved in many biological processes including immune responses, the second messenger cAMP pathway, sodium/potassium ion transport in the nephron, cell cycle progression in lower eukaryotes, cardiac hypertrophy, and memory formation. PP2B is highly conserved from yeast to humans, but is absent from plants. PP2B is a heterodimer consisting of a catalytic subunit (CnA) and a regulatory subunit (CnB); CnB contains four Ca2+ binding motifs referred to as EF hands. The PPP (phosphoprotein phosphatase) family, to which PP2B belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -G
Probab=20.56 E-value=1.6e+02 Score=23.41 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=20.4
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
...|.. +++.+||+++|+++.|..=+
T Consensus 217 g~~fG~-~~~~~Fl~~n~l~~iiR~He 242 (305)
T cd07416 217 SYFYSY-RAVCEFLQKNNLLSIIRAHE 242 (305)
T ss_pred ceecCH-HHHHHHHHHcCCeEEEEecc
Confidence 456654 78889999999999887644
No 193
>PRK08787 peptide chain release factor 2; Provisional
Probab=20.53 E-value=81 Score=25.80 Aligned_cols=18 Identities=22% Similarity=0.542 Sum_probs=14.9
Q ss_pred HHHHHHhCCcEEEeecCC
Q 043542 61 RAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~~ 78 (99)
..||+++||+++|.+-..
T Consensus 92 ~r~A~~~g~~~evi~~~~ 109 (313)
T PRK08787 92 LRWAESRGWKTELMEVSG 109 (313)
T ss_pred HHHHHHcCCeEEEEecCC
Confidence 469999999999987543
No 194
>KOG0092 consensus GTPase Rab5/YPT51 and related small G protein superfamily GTPases [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.28 E-value=82 Score=24.37 Aligned_cols=53 Identities=15% Similarity=0.212 Sum_probs=34.2
Q ss_pred CCcEEEecCCCCCCCCCcCcCCC-CCcccccCCceeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 18 GKWFINFLSTQKWENPLMGWTST-GDPYANVGEAGLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 18 ~~W~lefe~~~~~~dPLMGWtss-~D~~sqv~~~~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
+.|+.|...... .|-+|-=.|+ .|-...- . =+.+||.+||+.+|+-|--...+
T Consensus 97 K~WvkeL~~~~~-~~~vialvGNK~DL~~~R---~---V~~~ea~~yAe~~gll~~ETSAK 150 (200)
T KOG0092|consen 97 KNWVKELQRQAS-PNIVIALVGNKADLLERR---E---VEFEEAQAYAESQGLLFFETSAK 150 (200)
T ss_pred HHHHHHHHhhCC-CCeEEEEecchhhhhhcc---c---ccHHHHHHHHHhcCCEEEEEecc
Confidence 567777665544 5555555555 3544311 2 25789999999999998766544
No 195
>PF08901 DUF1847: Protein of unknown function (DUF1847); InterPro: IPR014997 This group of proteins are functionally uncharacterised. They contain 4 N-terminal cysteines that may form a zinc-binding domain.
Probab=20.27 E-value=75 Score=23.68 Aligned_cols=16 Identities=19% Similarity=0.389 Sum_probs=13.4
Q ss_pred CCHHHHHHHHHHhCCc
Q 043542 55 DSEAAARAFAEKHGWE 70 (99)
Q Consensus 55 ~ske~Ai~yaek~G~~ 70 (99)
.-.|+-|+||+++|+.
T Consensus 41 tRveEiieFak~mgyk 56 (157)
T PF08901_consen 41 TRVEEIIEFAKRMGYK 56 (157)
T ss_pred chHHHHHHHHHHcCCC
Confidence 3468999999999975
No 196
>cd07417 MPP_PP5_C PP5, C-terminal metallophosphatase domain. Serine/threonine protein phosphatase-5 (PP5) is a member of the PPP gene family of protein phosphatases that is highly conserved among eukaryotes and widely expressed in mammalian tissues. PP5 has a C-terminal phosphatase domain and an extended N-terminal TPR (tetratricopeptide repeat) domain containing three TPR motifs. The PPP (phosphoprotein phosphatase) family, to which PP5 belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cel
Probab=20.21 E-value=2.2e+02 Score=22.81 Aligned_cols=26 Identities=27% Similarity=0.547 Sum_probs=20.7
Q ss_pred eeecCCHHHHHHHHHHhCCcEEEeecC
Q 043542 51 GLCFDSEAAARAFAEKHGWEYTVRKFH 77 (99)
Q Consensus 51 ~l~F~ske~Ai~yaek~G~~y~V~~p~ 77 (99)
...| ..+++.+||+++|+++.|..=+
T Consensus 228 g~~f-g~~~~~~Fl~~n~l~~iiR~He 253 (316)
T cd07417 228 GCQF-GPDVTKRFLEENNLEYIIRSHE 253 (316)
T ss_pred ceEe-CHHHHHHHHHHcCCcEEEECCc
Confidence 4566 6777789999999999887543
No 197
>TIGR03645 glyox_marine lactoylglutathione lyase family protein. Members of this protein family share homology with lactoylglutathione lyase (glyoxalase I) and are found mainly in marine members of the gammaproteobacteria, including CPS_0532 from Colwellia psychrerythraea 34H. This family excludes a well-separated, more narrowly distributed paralogous family, exemplified by CPS_3492 from C. psychrerythraea. The function is of this protein family is unknown.
Probab=20.18 E-value=1.3e+02 Score=20.79 Aligned_cols=24 Identities=8% Similarity=0.056 Sum_probs=19.6
Q ss_pred eeec--CCHHHHHHHHHHhCCcEEEe
Q 043542 51 GLCF--DSEAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 51 ~l~F--~ske~Ai~yaek~G~~y~V~ 74 (99)
+|.| ++.+++++-++++|+.....
T Consensus 96 Hla~~v~dida~~~~l~~~G~~~~~~ 121 (162)
T TIGR03645 96 HFCVQDPDVEGLAERIVAAGGKKRMP 121 (162)
T ss_pred EEEEEcCCHHHHHHHHHHcCCcccCC
Confidence 5666 78999999999999885543
No 198
>TIGR00020 prfB peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.
Probab=20.04 E-value=82 Score=26.15 Aligned_cols=18 Identities=17% Similarity=0.490 Sum_probs=14.8
Q ss_pred HHHHHHhCCcEEEeecCC
Q 043542 61 RAFAEKHGWEYTVRKFHA 78 (99)
Q Consensus 61 i~yaek~G~~y~V~~p~~ 78 (99)
..||+++||+++|.+-..
T Consensus 151 ~~~a~~~g~~~evi~~~~ 168 (364)
T TIGR00020 151 LRWAERRGFKVEIIDYSE 168 (364)
T ss_pred HHHHHHcCCEEEEEecCC
Confidence 469999999999987543
No 199
>PRK09732 hypothetical protein; Provisional
Probab=20.02 E-value=1.1e+02 Score=21.81 Aligned_cols=18 Identities=28% Similarity=0.490 Sum_probs=14.3
Q ss_pred HHHHHHHHHHhCCcEEEe
Q 043542 57 EAAARAFAEKHGWEYTVR 74 (99)
Q Consensus 57 ke~Ai~yaek~G~~y~V~ 74 (99)
.++|++.|+++||..-|-
T Consensus 16 ~~aA~~~A~~~g~~v~ia 33 (134)
T PRK09732 16 IAAGQEEAQKNNWSVSIA 33 (134)
T ss_pred HHHHHHHHHHhCCCEEEE
Confidence 367899999999887643
Done!