Query 029589
Match_columns 191
No_of_seqs 219 out of 814
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 15:20:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029589.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029589hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00365 60S ribosomal protein 100.0 8.8E-81 1.9E-85 540.6 15.9 179 12-190 16-194 (266)
2 PTZ00222 60S ribosomal protein 100.0 7.6E-78 1.6E-82 521.2 16.4 171 20-190 22-194 (263)
3 KOG3166 60S ribosomal protein 100.0 6.4E-59 1.4E-63 392.8 6.3 150 18-170 1-151 (209)
4 COG1358 RPL8A Ribosomal protei 99.9 1.3E-21 2.9E-26 153.1 8.6 87 94-191 4-90 (116)
5 PRK13600 putative ribosomal pr 99.8 6.3E-19 1.4E-23 131.2 7.0 64 127-191 12-75 (84)
6 TIGR03677 rpl7ae 50S ribosomal 99.7 6.8E-17 1.5E-21 125.9 9.4 79 101-190 10-88 (117)
7 PRK04175 rpl7ae 50S ribosomal 99.7 7.3E-17 1.6E-21 126.8 9.2 82 98-190 11-92 (122)
8 PRK13602 putative ribosomal pr 99.7 7.5E-17 1.6E-21 118.8 7.1 64 127-191 10-73 (82)
9 PRK13601 putative L7Ae-like ri 99.7 1.3E-16 2.8E-21 118.1 7.4 65 126-191 6-70 (82)
10 PRK06683 hypothetical protein; 99.6 4.6E-16 1E-20 114.9 7.4 64 127-191 10-73 (82)
11 PF01248 Ribosomal_L7Ae: Ribos 99.6 2.2E-15 4.7E-20 111.3 9.0 64 127-190 14-77 (95)
12 PRK01018 50S ribosomal protein 99.5 1.8E-14 3.9E-19 109.3 7.2 63 127-190 15-78 (99)
13 KOG3387 60S ribosomal protein 99.5 1.6E-14 3.4E-19 114.8 5.3 62 127-188 33-94 (131)
14 KOG3167 Box H/ACA snoRNP compo 99.5 1.9E-14 4.1E-19 116.2 5.8 63 128-190 59-121 (153)
15 PRK07714 hypothetical protein; 99.4 9.2E-13 2E-17 99.7 9.7 63 127-190 17-79 (100)
16 PTZ00106 60S ribosomal protein 99.4 1.1E-12 2.3E-17 101.5 9.3 63 127-190 24-87 (108)
17 PRK07283 hypothetical protein; 99.4 3E-12 6.5E-17 96.9 9.1 63 127-190 17-79 (98)
18 PRK05583 ribosomal protein L7A 99.2 1E-10 2.3E-15 89.7 9.2 63 127-190 16-78 (104)
19 PRK09190 hypothetical protein; 99.1 6.8E-10 1.5E-14 95.4 12.5 127 37-190 23-178 (220)
20 KOG3406 40S ribosomal protein 99.1 1.8E-10 4E-15 91.8 5.1 63 128-190 34-96 (134)
21 COG1911 RPL30 Ribosomal protei 97.8 3.8E-05 8.3E-10 59.1 5.6 62 127-189 18-80 (100)
22 KOG2988 60S ribosomal protein 94.2 0.096 2.1E-06 41.3 4.8 59 128-188 26-86 (112)
23 PF08228 RNase_P_pop3: RNase P 94.2 0.16 3.4E-06 42.1 6.3 66 125-190 52-123 (158)
24 PF08032 SpoU_sub_bind: RNA 2' 94.0 0.25 5.5E-06 34.2 6.3 58 129-188 1-59 (76)
25 PF03465 eRF1_3: eRF1 domain 3 93.9 0.1 2.2E-06 40.3 4.5 63 125-187 18-98 (113)
26 PF15608 PELOTA_1: PELOTA RNA 93.0 0.29 6.3E-06 37.9 5.7 54 125-180 36-89 (100)
27 PRK04011 peptide chain release 91.0 1.4 3E-05 41.2 8.7 61 125-185 293-394 (411)
28 TIGR00108 eRF peptide chain re 90.2 1.9 4.1E-05 40.3 8.8 60 126-185 290-390 (409)
29 PF10087 DUF2325: Uncharacteri 89.9 0.88 1.9E-05 33.6 5.3 49 132-180 34-84 (97)
30 TIGR03676 aRF1/eRF1 peptide ch 88.1 3.2 6.9E-05 38.8 8.7 59 126-184 286-385 (403)
31 TIGR00111 pelota probable tran 85.6 4.5 9.8E-05 36.9 8.2 62 124-185 273-335 (351)
32 PF13727 CoA_binding_3: CoA-bi 85.0 1.7 3.6E-05 33.5 4.5 51 128-178 125-175 (175)
33 PF07997 DUF1694: Protein of u 80.7 3.8 8.3E-05 32.3 4.9 49 133-182 51-99 (120)
34 cd01422 MGS Methylglyoxal synt 77.4 6.1 0.00013 30.4 5.1 48 130-177 56-107 (115)
35 PRK05234 mgsA methylglyoxal sy 72.0 8.8 0.00019 30.9 4.9 46 132-177 63-112 (142)
36 smart00851 MGS MGS-like domain 71.0 6.8 0.00015 28.2 3.8 47 129-175 40-89 (90)
37 cd00532 MGS-like MGS-like doma 68.9 12 0.00025 28.3 4.8 45 132-176 55-104 (112)
38 PF02142 MGS: MGS-like domain 68.6 6.6 0.00014 28.7 3.3 41 135-175 51-94 (95)
39 PF00391 PEP-utilizers: PEP-ut 64.5 17 0.00036 26.0 4.7 19 161-179 43-61 (80)
40 PF13611 Peptidase_S76: Serine 63.6 8 0.00017 30.9 3.1 41 139-181 20-60 (121)
41 TIGR03023 WcaJ_sugtrans Undeca 62.4 17 0.00037 33.5 5.5 54 131-184 178-231 (451)
42 TIGR03025 EPS_sugtrans exopoly 61.9 19 0.00042 33.1 5.7 52 132-183 176-227 (445)
43 PRK11181 23S rRNA (guanosine-2 59.2 39 0.00084 29.2 6.8 59 129-189 4-64 (244)
44 cd01879 FeoB Ferrous iron tran 57.9 24 0.00052 26.2 4.7 41 143-183 73-113 (158)
45 cd01424 MGS_CPS_II Methylglyox 57.0 25 0.00055 26.0 4.7 46 131-176 54-100 (110)
46 PRK10124 putative UDP-glucose 56.9 25 0.00055 33.1 5.7 53 131-183 190-242 (463)
47 PF01601 Corona_S2: Coronaviru 56.3 3.5 7.5E-05 40.8 -0.2 13 45-57 540-552 (610)
48 PF00009 GTP_EFTU: Elongation 54.9 17 0.00037 29.0 3.7 51 133-183 84-134 (188)
49 COG0796 MurI Glutamate racemas 54.5 24 0.00053 31.7 4.8 41 133-177 57-97 (269)
50 cd01483 E1_enzyme_family Super 54.1 22 0.00047 27.3 4.0 37 143-181 88-124 (143)
51 KOG2486 Predicted GTPase [Gene 52.6 16 0.00034 33.6 3.4 46 137-182 212-259 (320)
52 PF02603 Hpr_kinase_N: HPr Ser 51.2 21 0.00045 27.8 3.5 38 139-179 76-113 (127)
53 TIGR03729 acc_ester putative p 49.9 46 0.00099 27.9 5.6 49 134-182 22-72 (239)
54 PRK10864 putative methyltransf 49.6 67 0.0014 29.7 7.0 60 127-189 108-169 (346)
55 PF02421 FeoB_N: Ferrous iron 49.3 31 0.00067 28.2 4.4 53 137-189 71-123 (156)
56 PF07905 PucR: Purine cataboli 48.2 50 0.0011 25.3 5.2 50 135-185 64-113 (123)
57 TIGR00186 rRNA_methyl_3 rRNA m 48.1 72 0.0016 27.3 6.6 56 129-189 3-59 (237)
58 cd04165 GTPBP1_like GTPBP1-lik 46.6 32 0.0007 29.1 4.2 50 134-183 99-150 (224)
59 PF13241 NAD_binding_7: Putati 45.7 23 0.00049 26.2 2.8 34 144-179 60-93 (103)
60 cd03420 SirA_RHOD_Pry_redox Si 44.7 71 0.0015 22.1 5.1 40 136-178 16-57 (69)
61 COG0352 ThiE Thiamine monophos 44.3 66 0.0014 27.7 5.8 56 133-189 24-82 (211)
62 COG1419 FlhF Flagellar GTP-bin 42.3 42 0.00091 31.9 4.6 48 141-188 230-277 (407)
63 PF00899 ThiF: ThiF family; I 40.0 41 0.00089 25.7 3.6 43 134-180 84-126 (135)
64 COG1537 PelA Predicted RNA-bin 39.9 64 0.0014 30.2 5.3 62 124-185 268-335 (352)
65 cd01491 Ube1_repeat1 Ubiquitin 39.0 24 0.00053 31.6 2.4 39 144-184 105-143 (286)
66 cd01485 E1-1_like Ubiquitin ac 38.9 22 0.00048 29.5 2.1 39 144-184 113-151 (198)
67 cd01857 HSR1_MMR1 HSR1/MMR1. 37.8 75 0.0016 24.2 4.8 13 171-183 42-54 (141)
68 PF14639 YqgF: Holliday-juncti 37.4 49 0.0011 26.8 3.8 46 134-179 53-106 (150)
69 cd01861 Rab6 Rab6 subfamily. 37.2 34 0.00073 25.7 2.7 39 145-183 73-117 (161)
70 cd01821 Rhamnogalacturan_acety 37.1 76 0.0016 25.2 4.8 23 158-180 133-155 (198)
71 cd00757 ThiF_MoeB_HesA_family 37.0 45 0.00097 28.1 3.6 36 144-181 111-146 (228)
72 TIGR03022 WbaP_sugtrans Undeca 36.6 69 0.0015 29.6 5.1 53 132-184 176-229 (456)
73 COG0566 SpoU rRNA methylases [ 36.0 1E+02 0.0022 27.0 5.7 59 127-188 21-80 (260)
74 TIGR00619 sbcd exonuclease Sbc 35.7 93 0.002 26.7 5.4 19 136-154 31-49 (253)
75 PRK00098 GTPase RsgA; Reviewed 35.5 47 0.001 29.3 3.7 17 167-183 107-123 (298)
76 PRK15116 sulfur acceptor prote 35.4 56 0.0012 29.0 4.1 36 142-179 119-154 (268)
77 TIGR00035 asp_race aspartate r 35.2 55 0.0012 27.5 3.9 43 132-178 63-105 (229)
78 cd01020 TroA_b Metal binding p 34.9 1E+02 0.0022 26.5 5.6 45 133-178 195-239 (264)
79 PRK05562 precorrin-2 dehydroge 34.3 47 0.001 28.8 3.4 35 144-180 85-119 (223)
80 TIGR01544 HAD-SF-IE haloacid d 34.1 73 0.0016 28.6 4.6 33 79-111 55-93 (277)
81 cd07388 MPP_Tt1561 Thermus the 34.1 88 0.0019 26.9 5.0 46 136-182 23-73 (224)
82 cd01493 APPBP1_RUB Ubiquitin a 34.0 30 0.00065 32.7 2.3 40 144-185 112-151 (425)
83 cd01492 Aos1_SUMO Ubiquitin ac 33.8 31 0.00068 28.7 2.2 37 143-181 109-145 (197)
84 cd04104 p47_IIGP_like p47 (47- 33.8 74 0.0016 25.8 4.4 39 145-183 81-119 (197)
85 cd04164 trmE TrmE (MnmE, ThdF, 33.6 90 0.0019 22.8 4.4 42 144-185 80-121 (157)
86 PRK09590 celB cellobiose phosp 33.6 52 0.0011 25.1 3.2 49 130-180 36-84 (104)
87 PF00462 Glutaredoxin: Glutare 33.3 1.1E+02 0.0024 19.8 4.4 46 134-180 13-58 (60)
88 PF03618 Kinase-PPPase: Kinase 32.9 1.2E+02 0.0027 26.9 5.9 41 148-189 55-97 (255)
89 PF11823 DUF3343: Protein of u 32.8 33 0.00072 24.0 1.9 29 162-190 16-44 (73)
90 cd00755 YgdL_like Family of ac 32.3 93 0.002 26.8 4.9 36 142-179 100-135 (231)
91 PF07085 DRTGG: DRTGG domain; 31.7 52 0.0011 24.2 2.8 41 135-179 53-93 (105)
92 cd01423 MGS_CPS_I_III Methylgl 31.2 50 0.0011 24.7 2.7 42 134-175 61-105 (116)
93 KOG1615 Phosphoserine phosphat 30.8 58 0.0013 28.6 3.3 47 123-174 83-129 (227)
94 COG0420 SbcD DNA repair exonuc 30.7 92 0.002 28.1 4.8 48 133-181 29-85 (390)
95 PF13545 HTH_Crp_2: Crp-like h 30.4 54 0.0012 22.2 2.6 32 159-190 3-41 (76)
96 COG0252 AnsB L-asparaginase/ar 30.3 93 0.002 28.8 4.8 47 135-181 91-137 (351)
97 PF01297 TroA: Periplasmic sol 29.7 1.1E+02 0.0023 25.9 4.8 44 133-180 188-231 (256)
98 TIGR03603 cyclo_dehy_ocin bact 29.3 67 0.0015 29.0 3.6 40 136-177 145-184 (318)
99 TIGR03013 EpsB_2 sugar transfe 29.3 1.2E+02 0.0027 28.0 5.5 52 132-183 174-225 (442)
100 PTZ00408 NAD-dependent deacety 29.2 1.7E+02 0.0038 25.3 6.1 54 124-179 149-207 (242)
101 PRK01889 GTPase RsgA; Reviewed 28.6 69 0.0015 29.1 3.6 26 159-184 130-155 (356)
102 PRK00865 glutamate racemase; P 28.3 1E+02 0.0022 26.6 4.5 42 133-177 56-97 (261)
103 cd01822 Lysophospholipase_L1_l 28.1 1.6E+02 0.0035 22.4 5.2 46 132-177 89-141 (177)
104 TIGR02356 adenyl_thiF thiazole 28.1 79 0.0017 26.2 3.6 36 143-180 110-145 (202)
105 cd01859 MJ1464 MJ1464. This f 27.7 84 0.0018 24.1 3.5 16 166-181 65-80 (156)
106 cd01018 ZntC Metal binding pro 27.6 1.5E+02 0.0032 25.5 5.3 42 134-179 207-248 (266)
107 cd07396 MPP_Nbla03831 Homo sap 27.2 1.5E+02 0.0032 25.3 5.3 51 134-184 30-86 (267)
108 PRK11018 hypothetical protein; 27.0 1.8E+02 0.0039 20.7 4.9 41 135-178 24-66 (78)
109 PRK05690 molybdopterin biosynt 26.9 50 0.0011 28.4 2.3 35 143-179 121-155 (245)
110 PF12850 Metallophos_2: Calcin 26.9 1.1E+02 0.0024 22.8 4.0 40 135-182 18-58 (156)
111 cd01866 Rab2 Rab2 subfamily. 26.8 66 0.0014 24.7 2.8 18 163-180 132-149 (168)
112 PRK10200 putative racemase; Pr 26.8 90 0.002 26.6 3.9 42 133-178 64-105 (230)
113 cd03770 SR_TndX_transposase Se 26.8 1.5E+02 0.0033 22.9 4.9 48 131-179 55-107 (140)
114 PF00205 TPP_enzyme_M: Thiamin 26.6 56 0.0012 24.8 2.3 46 133-178 1-46 (137)
115 TIGR02355 moeB molybdopterin s 26.6 80 0.0017 27.2 3.5 35 143-179 113-147 (240)
116 TIGR00157 ribosome small subun 26.4 65 0.0014 27.6 2.9 18 166-183 62-79 (245)
117 PRK10966 exonuclease subunit S 26.4 1.5E+02 0.0033 27.6 5.5 46 134-180 29-83 (407)
118 PHA02546 47 endonuclease subun 26.4 1.7E+02 0.0036 26.3 5.6 50 133-182 28-87 (340)
119 cd07392 MPP_PAE1087 Pyrobaculu 26.3 1.3E+02 0.0028 23.2 4.4 43 139-182 18-63 (188)
120 COG1135 AbcC ABC-type metal io 26.0 73 0.0016 29.7 3.3 38 58-95 146-186 (339)
121 PF14367 DUF4411: Domain of un 25.9 51 0.0011 26.7 2.0 33 148-180 119-154 (162)
122 cd01422 MGS Methylglyoxal synt 25.8 1.2E+02 0.0026 23.1 4.1 33 146-179 1-35 (115)
123 TIGR02342 chap_CCT_delta T-com 25.7 1.7E+02 0.0037 27.9 5.9 51 135-185 264-314 (517)
124 cd03423 SirA SirA (also known 25.7 2.2E+02 0.0048 19.5 5.1 40 136-178 16-57 (69)
125 PF13344 Hydrolase_6: Haloacid 25.6 2E+02 0.0044 21.2 5.2 44 129-174 15-58 (101)
126 PF08534 Redoxin: Redoxin; In 25.5 1.6E+02 0.0034 22.1 4.6 46 139-189 57-103 (146)
127 cd00877 Ran Ran (Ras-related n 25.5 81 0.0017 24.5 3.1 13 171-183 104-116 (166)
128 cd07400 MPP_YydB Bacillus subt 25.4 1.6E+02 0.0035 22.0 4.7 47 133-180 24-77 (144)
129 cd01894 EngA1 EngA1 subfamily. 25.2 1.6E+02 0.0035 21.5 4.6 39 145-183 77-117 (157)
130 PRK03980 flap endonuclease-1; 25.2 83 0.0018 28.2 3.4 35 152-187 78-114 (292)
131 PF13932 GIDA_assoc_3: GidA as 25.1 60 0.0013 23.2 2.1 50 49-101 1-53 (72)
132 PF00875 DNA_photolyase: DNA p 24.9 1.2E+02 0.0026 23.8 4.0 53 127-179 69-125 (165)
133 PF00072 Response_reg: Respons 24.8 2.4E+02 0.0052 19.4 6.2 53 129-181 28-81 (112)
134 cd03422 YedF YedF is a bacteri 24.5 2.1E+02 0.0046 19.7 4.8 41 135-178 15-57 (69)
135 PRK15016 isochorismate synthas 24.4 62 0.0013 30.4 2.6 61 130-190 130-195 (391)
136 cd03338 TCP1_delta TCP-1 (CTT 24.2 2E+02 0.0043 27.3 5.9 50 135-184 263-312 (515)
137 TIGR00693 thiE thiamine-phosph 24.1 2.5E+02 0.0055 22.4 5.9 54 133-188 16-73 (196)
138 COG1136 SalX ABC-type antimicr 24.1 85 0.0019 27.4 3.2 40 56-95 145-187 (226)
139 cd01017 AdcA Metal binding pro 24.0 2E+02 0.0043 24.9 5.5 44 133-180 209-252 (282)
140 COG1648 CysG Siroheme synthase 23.9 1.5E+02 0.0033 25.3 4.6 35 145-181 73-107 (210)
141 COG1363 FrvX Cellulase M and r 23.7 71 0.0015 29.7 2.8 32 146-177 255-289 (355)
142 PF15632 ATPgrasp_Ter: ATP-gra 23.6 1.5E+02 0.0033 27.1 4.9 45 131-176 9-71 (329)
143 TIGR02339 thermosome_arch ther 23.6 1.8E+02 0.004 27.6 5.6 48 135-187 273-320 (519)
144 PF13407 Peripla_BP_4: Peripla 23.5 2.3E+02 0.005 22.8 5.6 43 135-180 47-89 (257)
145 cd01854 YjeQ_engC YjeQ/EngC. 23.4 1E+02 0.0022 27.0 3.6 20 164-183 102-121 (287)
146 PRK00766 hypothetical protein; 23.4 1.7E+02 0.0037 24.9 4.9 50 137-187 60-118 (194)
147 cd04501 SGNH_hydrolase_like_4 23.4 2.1E+02 0.0046 22.1 5.1 51 129-179 81-146 (183)
148 cd05017 SIS_PGI_PMI_1 The memb 23.4 1.5E+02 0.0033 22.1 4.1 34 139-179 65-98 (119)
149 cd01892 Miro2 Miro2 subfamily. 23.3 90 0.0019 24.3 3.0 13 171-183 108-120 (169)
150 PF02571 CbiJ: Precorrin-6x re 23.0 1.3E+02 0.0028 26.3 4.2 46 132-177 54-99 (249)
151 cd03339 TCP1_epsilon TCP-1 (CT 23.0 2.1E+02 0.0046 27.2 5.9 45 137-186 280-324 (526)
152 PRK09453 phosphodiesterase; Pr 22.8 1.6E+02 0.0035 23.4 4.5 21 134-154 17-37 (182)
153 cd04146 RERG_RasL11_like RERG/ 22.7 93 0.002 23.6 2.9 16 164-179 130-145 (165)
154 cd03017 PRX_BCP Peroxiredoxin 22.5 2.3E+02 0.0051 20.8 5.0 50 136-190 49-99 (140)
155 TIGR02181 GRX_bact Glutaredoxi 22.5 2.1E+02 0.0046 19.3 4.5 47 134-181 13-59 (79)
156 PF08085 Entericidin: Enterici 22.5 16 0.00035 20.8 -1.1 8 34-41 5-12 (21)
157 cd07383 MPP_Dcr2 Saccharomyces 22.4 2.3E+02 0.005 22.8 5.3 47 135-181 32-86 (199)
158 PRK09331 Sep-tRNA:Cys-tRNA syn 22.2 1.8E+02 0.004 26.0 5.1 50 133-184 141-200 (387)
159 PRK06512 thiamine-phosphate py 22.2 2.3E+02 0.0049 24.2 5.4 55 134-189 30-88 (221)
160 TIGR00853 pts-lac PTS system, 22.1 1.3E+02 0.0029 22.2 3.5 47 130-180 38-84 (95)
161 PRK08057 cobalt-precorrin-6x r 22.0 1.6E+02 0.0035 25.7 4.6 47 132-178 53-99 (248)
162 TIGR00715 precor6x_red precorr 22.0 1.2E+02 0.0026 26.6 3.8 45 133-177 54-98 (256)
163 PRK13011 formyltetrahydrofolat 21.9 2E+02 0.0042 25.7 5.2 48 125-178 91-144 (286)
164 PRK12475 thiamine/molybdopteri 21.8 1.2E+02 0.0026 27.5 3.8 40 143-184 115-154 (338)
165 cd04106 Rab23_lke Rab23-like s 21.7 1.1E+02 0.0025 22.8 3.2 38 144-181 106-147 (162)
166 PF01206 TusA: Sulfurtransfera 21.7 2.2E+02 0.0049 19.1 4.4 42 134-178 15-58 (70)
167 cd06379 PBP1_iGluR_NMDA_NR1 N- 21.7 1.6E+02 0.0036 25.8 4.6 45 132-177 69-115 (377)
168 TIGR00040 yfcE phosphoesterase 21.6 1.9E+02 0.0042 22.3 4.6 45 134-182 17-62 (158)
169 cd02971 PRX_family Peroxiredox 21.6 2E+02 0.0043 21.1 4.5 48 137-189 49-98 (140)
170 cd04163 Era Era subfamily. Er 21.6 1.2E+02 0.0027 22.0 3.3 17 167-183 107-123 (168)
171 TIGR00067 glut_race glutamate 21.6 1.8E+02 0.004 25.1 4.8 41 135-178 51-92 (251)
172 cd07402 MPP_GpdQ Enterobacter 21.5 2.6E+02 0.0057 22.7 5.5 50 133-183 27-82 (240)
173 KOG2016 NEDD8-activating compl 21.5 82 0.0018 30.8 2.8 113 63-184 38-157 (523)
174 PF13361 UvrD_C: UvrD-like hel 21.1 1.5E+02 0.0032 24.9 4.0 33 144-179 77-109 (351)
175 PF00425 Chorismate_bind: chor 21.1 1.9E+02 0.0041 25.0 4.8 48 132-179 8-60 (257)
176 TIGR02765 crypto_DASH cryptoch 20.9 2.6E+02 0.0057 25.6 5.9 54 126-179 76-133 (429)
177 PF02593 dTMP_synthase: Thymid 20.9 1.4E+02 0.003 26.0 3.9 30 149-179 55-84 (217)
178 cd00378 SHMT Serine-glycine hy 20.8 2E+02 0.0044 25.4 5.1 47 132-179 149-196 (402)
179 cd01489 Uba2_SUMO Ubiquitin ac 20.7 87 0.0019 28.4 2.7 39 144-184 90-128 (312)
180 cd04127 Rab27A Rab27a subfamil 20.6 1.1E+02 0.0024 23.4 3.0 40 144-183 120-163 (180)
181 cd02970 PRX_like2 Peroxiredoxi 20.5 2.2E+02 0.0048 21.0 4.6 44 141-189 54-98 (149)
182 PF00578 AhpC-TSA: AhpC/TSA fa 20.4 1.5E+02 0.0032 21.3 3.5 51 134-189 49-100 (124)
183 PRK12723 flagellar biosynthesi 20.4 1.7E+02 0.0037 27.3 4.7 43 144-186 206-248 (388)
184 PRK09437 bcp thioredoxin-depen 20.3 2.6E+02 0.0057 21.3 5.1 45 140-189 60-105 (154)
185 cd01887 IF2_eIF5B IF2/eIF5B (i 20.3 1.1E+02 0.0024 22.9 2.9 18 166-183 97-114 (168)
186 cd01832 SGNH_hydrolase_like_1 20.2 2.3E+02 0.0049 21.9 4.7 49 132-180 93-154 (185)
187 COG1503 eRF1 Peptide chain rel 20.2 2.6E+02 0.0056 26.8 5.8 60 127-186 294-393 (411)
188 cd03418 GRX_GRXb_1_3_like Glut 20.2 2.7E+02 0.0059 18.3 4.8 47 134-181 14-61 (75)
No 1
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=100.00 E-value=8.8e-81 Score=540.58 Aligned_cols=179 Identities=65% Similarity=1.035 Sum_probs=173.2
Q ss_pred cccccCCccccCCccccCCCccccCCCCCCCCccccccccchhhHhHHHHHHHHhhhcCCCccccccccCChhhHHHHHh
Q 029589 12 APAKKKPEKVVNPLFEKRPKQFGIGGALPPKKDLHRYVKWPKAIRIQRQRRILRQRLKVPPALNQFTKTLDKNLASSLFK 91 (191)
Q Consensus 12 ~~~~~~~kk~~nplfekrpknfgig~~iqpkrdltrfvkwP~yirlQrq~~il~~rlKvppainqf~~~l~~~~a~~l~k 91 (191)
..++.+.++++|||||+|||||||||||||+|||||||+||+||||||||+||++||||||+||||+++||+|+|+|||+
T Consensus 16 ~~~~~~~~k~~~plfe~rpknf~iG~~iqpkrdlsrfvkwP~yirlQRqk~iL~~RlKvPp~inqF~~~ldk~~a~~lfk 95 (266)
T PTZ00365 16 PLKKSKKKKQKHPLFEKTPRNFRIGGDIRPKVDLSRYVRWPRYILLQRQRRVLLQRLKVPPALNQFTYTLDKNQASQLLR 95 (266)
T ss_pred cccccccccccCcccccCccccCcCCCCCCCccchhhcccchhhhHHHHHHHHHHhcCCCccHhhhhhhhcHhhHHHHHH
Confidence 33455667889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCcccHHHHHHHHHHHHHHHHcCCCcccCCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcC
Q 029589 92 LLLKYRPEDRAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKME 171 (191)
Q Consensus 92 l~~kyrPEt~~ekk~rl~~~a~~~a~gk~~~~k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~ 171 (191)
|++||||||++||++||++.||++|+|++.++++|..|.+|+|+|+++|++++|+|||||+||||++++.|||+||++|+
T Consensus 96 ll~KYrPEtk~~kk~RL~~~A~~~a~g~~~~~kkp~~vk~Gin~VtklIekkKAkLVIIA~DVsP~t~kk~LP~LC~k~~ 175 (266)
T PTZ00365 96 LLSKYKPETRAEKKARLLKEAEKAAAGEEVESKKPFMLKYGLNHVTDLVEYKKAKLVVIAHDVDPIELVCFLPALCRKKE 175 (266)
T ss_pred HHHhcCCccHHHHHHHHHHHHHHHhcCCCCCCCCchHHHhhhHHHHHHHHhCCccEEEEeCCCCHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999779999999999999999999999999999999999999999999999999
Q ss_pred CCEEEECCHhHHhhhhCCC
Q 029589 172 IPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 172 VPy~iV~sK~~LG~a~Gi~ 190 (191)
||||+++|+++||+++|.+
T Consensus 176 VPY~iv~sK~eLG~AIGkk 194 (266)
T PTZ00365 176 VPYCIIKGKSRLGKLVHQK 194 (266)
T ss_pred CCEEEECCHHHHHHHhCCC
Confidence 9999999999999999964
No 2
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=100.00 E-value=7.6e-78 Score=521.16 Aligned_cols=171 Identities=47% Similarity=0.836 Sum_probs=166.1
Q ss_pred cccCCccccCCCccccCCCCCCCCccccccccchhhHhHHHHHHHHhhhcCCCccccccccCChhhHHHHHhhhhcCCcc
Q 029589 20 KVVNPLFEKRPKQFGIGGALPPKKDLHRYVKWPKAIRIQRQRRILRQRLKVPPALNQFTKTLDKNLASSLFKLLLKYRPE 99 (191)
Q Consensus 20 k~~nplfekrpknfgig~~iqpkrdltrfvkwP~yirlQrq~~il~~rlKvppainqf~~~l~~~~a~~l~kl~~kyrPE 99 (191)
-...||||+|||||||||||||+|||||||+||+||||||||+||++||||||+||||+++||+|+|+|||+|++|||||
T Consensus 22 ~~~~~lfe~rpknf~ig~di~pkrdlsrfvkwP~yirlQrqk~iL~~rlKvPp~inqF~~~ldk~~a~~lfkll~KYrPE 101 (263)
T PTZ00222 22 PAAASHFVARPKNFGIGQDVPYARDLSRFMRWPTFVTMQRKKRVLQRRLKVPPALNQFTKVLDRSSRNELLKLIKKYAPE 101 (263)
T ss_pred CCcchhhhcCccccCCCCCCCCCccchhhhcchhhhhHHHHHHHHHHhcCCCchHhhhhhhhhHhhHHHHHHHHHHcCCc
Confidence 34678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHcCCC-ccc-CCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE
Q 029589 100 DRAAKKERLLKRAQAEAEGKT-VEA-KKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 100 t~~ekk~rl~~~a~~~a~gk~-~~~-k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV 177 (191)
|++||++||++.||++++|+. .++ ++|..|++|+++|+++|++|+|+|||||+||||+++++|||+||++|+||||++
T Consensus 102 tk~~kk~Rl~~~A~~~~~g~~~~~~~kkp~~LvsG~n~VtkaIekkKAkLVIIA~DVsPie~vk~LpaLCrk~~VPY~iV 181 (263)
T PTZ00222 102 TRKARRDRLHKVAEEKKKDPKKTVSTKAPLAVVTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIV 181 (263)
T ss_pred cHHHHHHHHHHHHHHHhcCCCCCCCCCCCCeeccCHHHHHHHHHcCCceEEEEeCCCCHHHHHHHHHHHHHhcCCCEEEE
Confidence 999999999999999999999 454 999999999999999999999999999999999999999999999999999999
Q ss_pred CCHhHHhhhhCCC
Q 029589 178 KGKSRLGSVNILN 190 (191)
Q Consensus 178 ~sK~~LG~a~Gi~ 190 (191)
+|+++||++||.+
T Consensus 182 ktKaeLG~AIGkK 194 (263)
T PTZ00222 182 KDMARLGDAIGRK 194 (263)
T ss_pred CCHHHHHHHHCCC
Confidence 9999999999964
No 3
>KOG3166 consensus 60S ribosomal protein L7A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.4e-59 Score=392.79 Aligned_cols=150 Identities=65% Similarity=1.032 Sum_probs=143.7
Q ss_pred CccccCCccccCCCccccCCCCCCCCccccccccchhhHhHHHHHHHHhhhcCCCccccccccCChhhHHHHHhhhhcCC
Q 029589 18 PEKVVNPLFEKRPKQFGIGGALPPKKDLHRYVKWPKAIRIQRQRRILRQRLKVPPALNQFTKTLDKNLASSLFKLLLKYR 97 (191)
Q Consensus 18 ~kk~~nplfekrpknfgig~~iqpkrdltrfvkwP~yirlQrq~~il~~rlKvppainqf~~~l~~~~a~~l~kl~~kyr 97 (191)
+++++|||||+||+||||||||||+|||||||+||+||++|||++||+ ||||||+||||+++||.++|+++++|+|+||
T Consensus 1 ~~k~~~~l~~~rp~nfg~gq~iqpk~dlt~~~k~p~~i~lq~q~~~l~-~lkvpp~i~qf~~~l~~~~a~~~~kl~hkyr 79 (209)
T KOG3166|consen 1 AKKVVNPLFEKRPKNFGIGQDIQPKRDLTCFVKWPRYIRLQRQKAILY-RLKVPPAINQFTQALDLQTATKLLKLAHKYR 79 (209)
T ss_pred CCcccchhHHhcccccCcccccccccccccceeccHHHHhhhchhhhe-eeccCcchhhhhcccchHHHHHHHHHHhhcC
Confidence 468999999999999999999999999999999999999999999999 9999999999999999999999999999999
Q ss_pred cccHHHHHHHHHHHHHHHHcCCC-cccCCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhc
Q 029589 98 PEDRAAKKERLLKRAQAEAEGKT-VEAKKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKM 170 (191)
Q Consensus 98 PEt~~ekk~rl~~~a~~~a~gk~-~~~k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~ 170 (191)
||+++++++|+++ ++++++++ +++++|+.+..|+|+||++||+++|||||||||+||||+|+|||+||++|
T Consensus 80 P~~~~~~~~r~~a--~~~~~~kg~v~tkrp~~~~~gvnTVttLVenKKAQLVV~ahDvDPIELVvFLPaLC~km 151 (209)
T KOG3166|consen 80 PETKKKKKQRLLA--EAKAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVTAHDVDPIELVVFLPALCRKM 151 (209)
T ss_pred chhhhhhhhhHHH--HHHHHhccCCCcCCCcccccCcceEeehhhccccceeEEecccCchhheeecHHhhhhh
Confidence 9998888888774 56677777 99999999999999999999999999999999999999999999999999
No 4
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=1.3e-21 Score=153.11 Aligned_cols=87 Identities=43% Similarity=0.521 Sum_probs=78.8
Q ss_pred hcCCcccHHHHHHHHHHHHHHHHcCCCcccCCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCC
Q 029589 94 LKYRPEDRAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIP 173 (191)
Q Consensus 94 ~kyrPEt~~ekk~rl~~~a~~~a~gk~~~~k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VP 173 (191)
.-+.|++..++.-+++..|.. ...|++|+|+|+++|++|+|+|||||+|+||.+++.|||.||++++||
T Consensus 4 ~~~~~~~~~~k~l~~l~~a~~-----------~~ki~~G~~e~~Kai~~g~a~LVviA~Dv~P~~~~~~l~~lc~~~~vp 72 (116)
T COG1358 4 KPLAPEMLEQKALSLLGKASR-----------AGKLKKGTNEVTKAIERGKAKLVVIAEDVSPEELVKHLPALCEEKNVP 72 (116)
T ss_pred cccCcHHHHHHHHHHHHHHHh-----------cCCchhhHHHHHHHHHcCCCcEEEEecCCCHHHHHHHHHHHHHhcCCC
Confidence 346788888888888877642 357899999999999999999999999999999999999999999999
Q ss_pred EEEECCHhHHhhhhCCCC
Q 029589 174 YCIVKGKSRLGSVNILNS 191 (191)
Q Consensus 174 y~iV~sK~~LG~a~Gi~~ 191 (191)
|++|+|+.+||++||+++
T Consensus 73 yv~V~sk~~LG~a~g~~~ 90 (116)
T COG1358 73 YVYVGSKKELGKAVGKEV 90 (116)
T ss_pred EEEeCCHHHHHHHhCCCc
Confidence 999999999999999973
No 5
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=99.77 E-value=6.3e-19 Score=131.20 Aligned_cols=64 Identities=22% Similarity=0.284 Sum_probs=60.8
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILNS 191 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~~ 191 (191)
..++.|+++++++|++|++++||||.|+|| .++.+||.+|++++|||++|+||.+||++|||++
T Consensus 12 ~~~vvG~kqt~Kai~kg~~~~v~iA~Da~~-~vv~~l~~lceek~Ip~v~V~s~~~LGkAcgi~V 75 (84)
T PRK13600 12 QHFVVGLKETLKALKKDQVTSLIIAEDVEV-YLMTRVLSQINQKNIPVSFFKSKHALGKHVGINV 75 (84)
T ss_pred cCceeeHHHHHHHHhcCCceEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEECCHHHHHHHhCCCc
Confidence 467899999999999999999999999999 5889999999999999999999999999999985
No 6
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=99.70 E-value=6.8e-17 Score=125.94 Aligned_cols=79 Identities=43% Similarity=0.591 Sum_probs=68.7
Q ss_pred HHHHHHHHHHHHHHHHcCCCcccCCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 101 RAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 101 ~~ekk~rl~~~a~~~a~gk~~~~k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
..+|-..|+..|.+ -..|.+|.++|+++|++|+++|||||.|++|.++..+++.+|++++|||+++.|+
T Consensus 10 l~~ki~~lL~la~r-----------agkl~~G~~~v~kaikkgka~LVilA~D~s~~~~~~~i~~lc~~~~Ip~~~~~sk 78 (117)
T TIGR03677 10 LANKALEAVEKARE-----------TGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYVYVKKK 78 (117)
T ss_pred HHHHHHHHHHHHHH-----------cCCEeEcHHHHHHHHHcCCccEEEEeCCCCcHHHHHHHHHHHHHcCCCEEEeCCH
Confidence 44555566665542 2468899999999999999999999999999888889999999999999999999
Q ss_pred hHHhhhhCCC
Q 029589 181 SRLGSVNILN 190 (191)
Q Consensus 181 ~~LG~a~Gi~ 190 (191)
.+||++||.+
T Consensus 79 ~eLG~a~Gk~ 88 (117)
T TIGR03677 79 EDLGAAAGLE 88 (117)
T ss_pred HHHHHHhCCC
Confidence 9999999984
No 7
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=99.70 E-value=7.3e-17 Score=126.80 Aligned_cols=82 Identities=41% Similarity=0.599 Sum_probs=70.4
Q ss_pred cccHHHHHHHHHHHHHHHHcCCCcccCCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE
Q 029589 98 PEDRAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 98 PEt~~ekk~rl~~~a~~~a~gk~~~~k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV 177 (191)
|+...++-..|+..|.+ -..|.+|.++|+++|++|+++|||||.|++|.+++.+++.+|++++|||+++
T Consensus 11 ~~~l~~ki~~lL~la~r-----------agklv~G~~~v~kaikkgkakLVilA~D~s~~~i~~~~~~lc~~~~Vp~~~~ 79 (122)
T PRK04175 11 PEELAEKALEAVEKARD-----------TGKIKKGTNETTKAVERGIAKLVVIAEDVDPEEIVAHLPLLCEEKKIPYVYV 79 (122)
T ss_pred CHHHHHHHHHHHHHHHH-----------cCCEeEcHHHHHHHHHcCCccEEEEeCCCChHHHHHHHHHHHHHcCCCEEEE
Confidence 34444555566665542 2468999999999999999999999999999998889999999999999999
Q ss_pred CCHhHHhhhhCCC
Q 029589 178 KGKSRLGSVNILN 190 (191)
Q Consensus 178 ~sK~~LG~a~Gi~ 190 (191)
.++.+||++||.+
T Consensus 80 ~tk~eLG~a~Gk~ 92 (122)
T PRK04175 80 PSKKDLGKAAGLE 92 (122)
T ss_pred CCHHHHHHHhCCC
Confidence 9999999999986
No 8
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=99.68 E-value=7.5e-17 Score=118.78 Aligned_cols=64 Identities=22% Similarity=0.331 Sum_probs=60.6
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILNS 191 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~~ 191 (191)
..+..|.++|+++|++|+++|||||.|++| .++..++.+|++++|||++++|+.+||++||+++
T Consensus 10 gkl~~G~~~v~kai~~gkaklViiA~D~~~-~~~~~i~~~c~~~~Vp~~~~~s~~eLG~a~G~~~ 73 (82)
T PRK13602 10 KSIVIGTKQTVKALKRGSVKEVVVAEDADP-RLTEKVEALANEKGVPVSKVDSMKKLGKACGIEV 73 (82)
T ss_pred CCEEEcHHHHHHHHHcCCeeEEEEECCCCH-HHHHHHHHHHHHcCCCEEEECCHHHHHHHHCCCc
Confidence 467899999999999999999999999999 5778899999999999999999999999999974
No 9
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=99.67 E-value=1.3e-16 Score=118.12 Aligned_cols=65 Identities=18% Similarity=0.240 Sum_probs=61.4
Q ss_pred CceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCCC
Q 029589 126 PIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILNS 191 (191)
Q Consensus 126 p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~~ 191 (191)
+..+..|.++|+++|++|+++|||||.|+++ +++..++.+|++++|||+++.|+.+||++||+++
T Consensus 6 ~GKlv~G~~~vlkaIk~gkakLViiA~Da~~-~~~k~i~~~c~~~~Vpv~~~~t~~eLG~A~G~~v 70 (82)
T PRK13601 6 PSKRVVGAKQTLKAITNCNVLQVYIAKDAEE-HVTKKIKELCEEKSIKIVYIDTMKELGVMCGIDV 70 (82)
T ss_pred CccEEEchHHHHHHHHcCCeeEEEEeCCCCH-HHHHHHHHHHHhCCCCEEEeCCHHHHHHHHCCcc
Confidence 4578999999999999999999999999998 7778899999999999999999999999999985
No 10
>PRK06683 hypothetical protein; Provisional
Probab=99.64 E-value=4.6e-16 Score=114.85 Aligned_cols=64 Identities=25% Similarity=0.215 Sum_probs=59.5
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILNS 191 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~~ 191 (191)
..+..|.++|+++|++|+++|||||.|+++. +...+..+|++++|||+++.|+.+||++||+++
T Consensus 10 gk~v~G~~~v~kaik~gkaklViiA~Da~~~-~~~~i~~~~~~~~Vpv~~~~t~~eLG~A~G~~~ 73 (82)
T PRK06683 10 ENVVVGHKRTLEAIKNGIVKEVVIAEDADMR-LTHVIIRTALQHNIPITKVESVRKLGKVAGIQV 73 (82)
T ss_pred CCEEEcHHHHHHHHHcCCeeEEEEECCCCHH-HHHHHHHHHHhcCCCEEEECCHHHHHHHhCCcc
Confidence 4678999999999999999999999999995 556689999999999999999999999999975
No 11
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=99.62 E-value=2.2e-15 Score=111.26 Aligned_cols=64 Identities=33% Similarity=0.515 Sum_probs=61.8
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
..|..|+++|+++|+++++++||||.|++|.....+++.+|++++|||+++.|+.+||++||++
T Consensus 14 ~~lv~G~~~v~k~l~~~~~~lvilA~d~~~~~~~~~l~~~c~~~~Ip~~~~~s~~eLG~~~g~~ 77 (95)
T PF01248_consen 14 GRLVKGIKEVLKALKKGKAKLVILAEDCSPDSIKKHLPALCEEKNIPYVFVPSKEELGRACGKK 77 (95)
T ss_dssp SEEEESHHHHHHHHHTTCESEEEEETTSSSGHHHHHHHHHHHHTTEEEEEESHHHHHHHHTTSS
T ss_pred CCEEEchHHHHHHHHcCCCcEEEEcCCCChhhhcccchhheeccceeEEEECCHHHHHHHHCCC
Confidence 4689999999999999999999999999999999889999999999999999999999999987
No 12
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=99.54 E-value=1.8e-14 Score=109.32 Aligned_cols=63 Identities=19% Similarity=0.162 Sum_probs=58.0
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE-CCHhHHhhhhCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV-KGKSRLGSVNILN 190 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV-~sK~~LG~a~Gi~ 190 (191)
..+.+|.++|+++|++|+|+|||||.|+++ +....++.+|++++|||+.+ .|+.+||++||.+
T Consensus 15 gkl~~G~~~v~kai~~gkaklViiA~D~~~-~~~~~i~~~c~~~~Ip~~~~~~tk~eLG~a~Gk~ 78 (99)
T PRK01018 15 GKVILGSKRTIKAIKLGKAKLVIVASNCPK-DIKEDIEYYAKLSGIPVYEYEGSSVELGTLCGKP 78 (99)
T ss_pred CCEEEcHHHHHHHHHcCCceEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEECCCHHHHHHHhCCC
Confidence 478899999999999999999999999988 77788999999999998665 8999999999976
No 13
>KOG3387 consensus 60S ribosomal protein 15.5kD/SNU13, NHP2/L7A family (includes ribonuclease P subunit p38), involved in splicing [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=99.51 E-value=1.6e-14 Score=114.84 Aligned_cols=62 Identities=34% Similarity=0.580 Sum_probs=60.7
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNI 188 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~G 188 (191)
.+++.|.|++|+.+++|...+||+|.||.|.++..|||.||++.|||||+|.++..||.+||
T Consensus 33 kql~kg~NEaTk~Lnrgi~~~Vv~aaD~kP~eIt~HLp~LcedknVp~v~Vpsk~alG~~cg 94 (131)
T KOG3387|consen 33 KQLKKGANEATKTLNRGISEFVVMAADVKPLEITLHLPLLCEDKNVPYVFVPSKQALGLACG 94 (131)
T ss_pred HHHhcccchHhhhhccCceeEEEEEccCCHHHHHHHhHHHhhccCCceEEeeccHHhhhhhh
Confidence 57888999999999999999999999999999999999999999999999999999999999
No 14
>KOG3167 consensus Box H/ACA snoRNP component, involved in ribosomal RNA pseudouridinylation [RNA processing and modification]
Probab=99.51 E-value=1.9e-14 Score=116.18 Aligned_cols=63 Identities=29% Similarity=0.550 Sum_probs=60.5
Q ss_pred eeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 128 VVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 128 ~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
.|..|+++|.+.|++|.-.|+|||.|++|+++..|||+||++.||||+++.|++.||.+.|..
T Consensus 59 ~lrrGvKevqK~vrkGeKGl~VlAgd~sPiDvi~HlP~lCEd~~vPYvy~psk~dlg~A~~~k 121 (153)
T KOG3167|consen 59 GLRRGVKEVQKRVRKGEKGLCVLAGDTSPIDVITHLPALCEDRGVPYVYTPSKEDLGAAGGTK 121 (153)
T ss_pred hHHHHHHHHHHHHhcCCcceEEEecCCccHHHHhccchhhhccCCCccccccHHHHHHhcCCC
Confidence 478899999999999999999999999999999999999999999999999999999998863
No 15
>PRK07714 hypothetical protein; Provisional
Probab=99.43 E-value=9.2e-13 Score=99.68 Aligned_cols=63 Identities=21% Similarity=0.232 Sum_probs=58.9
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
..+.+|.++|.++|++|++++||+|.|+++. ....+..+|+.++|||+++.++.+||.+||.+
T Consensus 17 Gk~v~G~~~v~~al~~g~~~lViiA~D~s~~-~~~ki~~~~~~~~vp~~~~~sk~eLG~a~Gk~ 79 (100)
T PRK07714 17 RKVISGEELVLKEVRSGKAKLVLLSEDASVN-TTKKITDKCTYYNVPMRKVENRQQLGHAIGKD 79 (100)
T ss_pred CCeeecHHHHHHHHHhCCceEEEEeCCCCHH-HHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCC
Confidence 4678999999999999999999999999995 66779999999999999999999999999976
No 16
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=99.42 E-value=1.1e-12 Score=101.47 Aligned_cols=63 Identities=16% Similarity=0.128 Sum_probs=57.5
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEE-ECCHhHHhhhhCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCI-VKGKSRLGSVNILN 190 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~i-V~sK~~LG~a~Gi~ 190 (191)
..+..|.++|.++|++|+++|||||.|+++... ..+..+|+.++||++. ..++.+||++||++
T Consensus 24 GKlv~G~~~vlkalk~gkaklViiA~D~~~~~k-kki~~~~~~~~Vpv~~~~~t~~eLG~A~Gk~ 87 (108)
T PTZ00106 24 GKYTLGTKSTLKALRNGKAKLVIISNNCPPIRR-SEIEYYAMLSKTGVHHYAGNNNDLGTACGRH 87 (108)
T ss_pred CCeeecHHHHHHHHHcCCeeEEEEeCCCCHHHH-HHHHHHHhhcCCCEEEeCCCHHHHHHHhCCc
Confidence 468899999999999999999999999999555 5589999999999985 69999999999986
No 17
>PRK07283 hypothetical protein; Provisional
Probab=99.38 E-value=3e-12 Score=96.88 Aligned_cols=63 Identities=19% Similarity=0.152 Sum_probs=57.9
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
..|.+|.++|.++|++|++++||+|.|+++ +....+..+|+.++|||+.+.++.+||++||.+
T Consensus 17 Gklv~G~~~v~~aik~gk~~lVi~A~Das~-~~~kk~~~~~~~~~Vp~~~~~t~~eLG~a~Gk~ 79 (98)
T PRK07283 17 GRIISGEELVVKAIQSGQAKLVFLANDAGP-NLTKKVTDKSNYYQVEVSTVFSTLELSAAVGKP 79 (98)
T ss_pred CCeeEcHHHHHHHHHcCCccEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEeCCHHHHHHHhCCC
Confidence 468899999999999999999999999999 455568999999999999999999999999964
No 18
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=99.20 E-value=1e-10 Score=89.73 Aligned_cols=63 Identities=24% Similarity=0.299 Sum_probs=58.2
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
..+++|.++|.++|++++++|||+|.|+++.... -+-.+|+.++||++...++.+||.+||-+
T Consensus 16 Gklv~G~~~v~~aik~gk~~lVI~A~D~s~~~kk-ki~~~~~~~~vp~~~~~t~~eLg~a~Gk~ 78 (104)
T PRK05583 16 GKLLEGYNKCEEAIKKKKVYLIIISNDISENSKN-KFKNYCNKYNIPYIEGYSKEELGNAIGRD 78 (104)
T ss_pred CCeeecHHHHHHHHHcCCceEEEEeCCCCHhHHH-HHHHHHHHcCCCEEEecCHHHHHHHhCCC
Confidence 4788999999999999999999999999996665 48999999999999999999999999965
No 19
>PRK09190 hypothetical protein; Provisional
Probab=99.14 E-value=6.8e-10 Score=95.45 Aligned_cols=127 Identities=21% Similarity=0.179 Sum_probs=93.2
Q ss_pred CCCCCCCccccccccch----------------h-------hHhHHHHHHHHhhhcCCCccccccccCChhhHHHHHhhh
Q 029589 37 GALPPKKDLHRYVKWPK----------------A-------IRIQRQRRILRQRLKVPPALNQFTKTLDKNLASSLFKLL 93 (191)
Q Consensus 37 ~~iqpkrdltrfvkwP~----------------y-------irlQrq~~il~~rlKvppainqf~~~l~~~~a~~l~kl~ 93 (191)
+-..|+.+|-|||+=|. | +..=.++..|.+.||.+-.+ ..+...+|-.++
T Consensus 23 r~~~~k~~LiR~v~~~dg~v~~D~~~k~pGRGaYvc~~~~c~~~A~kkk~l~Ralk~~v~v-------~~~l~~~l~~~l 95 (220)
T PRK09190 23 REVGPPDELIRFVVGPDGQVVPDLKRKLPGRGCWVSADRAAVEKAVAKKLFARAAKADVKV-------PPDLADLVEALL 95 (220)
T ss_pred CCccCHHHcEEEEEcCCCcEEECCCCCCCCCEEEEcCCHHHHHHHHHhChhHHHhCCCCCC-------CHHHHHHHHHHH
Confidence 45677888888886442 2 22234567777778854211 233344444444
Q ss_pred hcCCcccHHHHHHHHHHHHHHHHcCCCcccCCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHh----
Q 029589 94 LKYRPEDRAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRK---- 169 (191)
Q Consensus 94 ~kyrPEt~~ekk~rl~~~a~~~a~gk~~~~k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k---- 169 (191)
.++--.+|..|. |-..|++|.+.|..+|.++++.|||+|.|+++.+..+ |-.+|+.
T Consensus 96 --------~~ril~lLGLAr-----------RAGklVsG~~~V~~alk~gk~~Lvi~A~DaS~~t~kK-l~~~~~~~~~~ 155 (220)
T PRK09190 96 --------ARRALDALGLAR-----------KAGQVVSGFEKVDAALRSGEAAALIHASDGAADGKRK-LDQARRALVHE 155 (220)
T ss_pred --------HHHHHHHHHHHh-----------hhCCEeecHHHHHHHHHcCCceEEEEeccCChhHHHH-HHHHHHhhccc
Confidence 345555666554 2357899999999999999999999999999977766 7889999
Q ss_pred --cCCCEEEECCHhHHhhhhCCC
Q 029589 170 --MEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 170 --~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
++|||+...++++||.++|.+
T Consensus 156 ~~~~Vp~v~~~tk~eLg~AlGr~ 178 (220)
T PRK09190 156 TGREIPVIGLFTAAELGLAFGRE 178 (220)
T ss_pred ccCCccEEEecCHHHHHHHhCCC
Confidence 999999999999999999975
No 20
>KOG3406 consensus 40S ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=99.06 E-value=1.8e-10 Score=91.79 Aligned_cols=63 Identities=25% Similarity=0.370 Sum_probs=60.3
Q ss_pred eeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 128 VVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 128 ~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
.|..|+.+.++++++.+|+|||+|+|+|.-.+++.+.+||.+++||++.|.+...||+|+|+.
T Consensus 34 GlarGi~Ea~KaldkrqA~lcvLaencdep~yvKLVeALcaeh~iplikV~d~k~LGew~Glc 96 (134)
T KOG3406|consen 34 GLARGIHEAAKALDKRQAHLCVLAENCDEPMYVKLVEALCAEHQIPLIKVGDAKELGEWAGLC 96 (134)
T ss_pred hHHhHHHHHHHHHhhCceeEEEEeccCCchHHHHHHHHHHhhcCCCeEEeccchhhhhhhcee
Confidence 567899999999999999999999999999999999999999999999999999999999974
No 21
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=97.84 E-value=3.8e-05 Score=59.06 Aligned_cols=62 Identities=23% Similarity=0.223 Sum_probs=51.1
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE-CCHhHHhhhhCC
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV-KGKSRLGSVNIL 189 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV-~sK~~LG~a~Gi 189 (191)
.....|.+.+.+++..|++++||||.|+-+ ++..-|.-.+.=-+||+... .+..+||.+||-
T Consensus 18 GkvilG~k~tiK~lk~gkaKliiiAsN~P~-~~k~~ieyYAkLs~ipV~~y~Gt~~eLG~~cgk 80 (100)
T COG1911 18 GKVILGSKRTIKSLKLGKAKLIIIASNCPK-ELKEDIEYYAKLSDIPVYVYEGTSVELGTVCGK 80 (100)
T ss_pred CCEEEehHHHHHHHHcCCCcEEEEecCCCH-HHHHHHHHHHHHcCCcEEEecCCceeHHhhhCC
Confidence 356779999999999999999999999966 77666666666669998755 556789999994
No 22
>KOG2988 consensus 60S ribosomal protein L30 [Translation, ribosomal structure and biogenesis]
Probab=94.21 E-value=0.096 Score=41.25 Aligned_cols=59 Identities=17% Similarity=0.290 Sum_probs=44.0
Q ss_pred eeeechhHHHHHHHhcCcceEEEecCCCccch--hhhHHHHHHhcCCCEEEECCHhHHhhhhC
Q 029589 128 VVKYGLNHVTYLIEQNKAQLVVIAHDVDPIEL--VVWLPALCRKMEIPYCIVKGKSRLGSVNI 188 (191)
Q Consensus 128 ~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~el--v~~LpaLC~k~~VPy~iV~sK~~LG~a~G 188 (191)
.-.-|.+++.++++.++|+|++||.+|-+... ..++.-|+. .+|-. +-.+..+||++||
T Consensus 26 kY~lgyK~T~k~~r~gkakL~~is~n~p~lrks~ieyyamlak-~~v~~-~sg~n~~lgt~~g 86 (112)
T KOG2988|consen 26 KYILGYKQTLKSLRQGKAKLIIISSNCPPLRKSEIEYYAMLAK-TGVHH-YSGNNVELGTACG 86 (112)
T ss_pred ceeechHHHHHHHHhccceEEEeecCCCCcchhHHHHHHHHhc-Cceee-ecCCcEeHHHHhc
Confidence 34568999999999999999999999987543 234555555 33333 4456778999998
No 23
>PF08228 RNase_P_pop3: RNase P subunit Pop3; InterPro: IPR013241 This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs. The structure of Pop3 has been assigned the L7Ae/L30e fold []. This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologues.
Probab=94.15 E-value=0.16 Score=42.08 Aligned_cols=66 Identities=18% Similarity=0.255 Sum_probs=50.7
Q ss_pred CCceeeechhHHHHHHHhcCc--ceEEEecCCCccchhhhHHHHHHhcC--CCEEEE--CCHhHHhhhhCCC
Q 029589 125 KPIVVKYGLNHVTYLIEQNKA--QLVVIAHDVDPIELVVWLPALCRKME--IPYCIV--KGKSRLGSVNILN 190 (191)
Q Consensus 125 ~p~~L~~G~~~Vtk~IekkKA--kLVVIA~DvdP~elv~~LpaLC~k~~--VPy~iV--~sK~~LG~a~Gi~ 190 (191)
.+..+..|.|.|++.+|...+ -+||++..=+|.-+..|+|.||.--+ |.++-. ++.++|+.++|++
T Consensus 52 ~~~~v~~GfNsi~~~Le~~~~~~~~vFVcr~D~ps~L~~h~P~Lva~as~~vrLV~Lpkgs~~rLs~aLgi~ 123 (158)
T PF08228_consen 52 WPWGVTVGFNSIVRYLECQASDNVYVFVCRSDQPSILTSHFPQLVATASKSVRLVQLPKGSEARLSEALGIP 123 (158)
T ss_pred CCccEEEehHHHHHHHhcccCCCeEEEEECCCCcHHHHHHHHHHHHhccCcceEEeCChhHHHHHHHHhCCC
Confidence 446788999999999994333 26666654478889999999999777 666654 4677899999985
No 24
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=94.02 E-value=0.25 Score=34.17 Aligned_cols=58 Identities=14% Similarity=0.141 Sum_probs=43.1
Q ss_pred eeechhHHHHHHHhcC-cceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhC
Q 029589 129 VKYGLNHVTYLIEQNK-AQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNI 188 (191)
Q Consensus 129 L~~G~~~Vtk~IekkK-AkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~G 188 (191)
++.|.+.|..+++++. ..-|++..+.....+ ..+..+|.+.|||+..+.. ..|.++++
T Consensus 1 lieG~~~V~eaL~~~~~i~~l~~~~~~~~~~~-~~i~~~~~~~~i~v~~v~~-~~l~~ls~ 59 (76)
T PF08032_consen 1 LIEGRHAVEEALKSGPRIKKLFVTEEKADKRI-KEILKLAKKKGIPVYEVSK-KVLDKLSD 59 (76)
T ss_dssp EEESHHHHHHHHHCTGGEEEEEEETT---CCT-HHHHHHHHHCT-EEEEE-H-HHHHHCTT
T ss_pred CEEEHHHHHHHHcCCCCccEEEEEcCccchhH-HHHHHHHHHcCCeEEEeCH-HHHHHHcC
Confidence 4689999999999975 888899988333243 4589999999999988754 56888775
No 25
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination but this awaits experimental verification.; PDB: 3OBY_A 3E1Y_D 1DT9_A 2KTU_A 2KTV_A 3IR9_A 3E20_H 3OBW_A 3AGJ_F 3MCA_B ....
Probab=93.94 E-value=0.1 Score=40.31 Aligned_cols=63 Identities=19% Similarity=0.249 Sum_probs=52.2
Q ss_pred CCceeeechhHHHHHHHhcCcceEEEecCCCccc------------------hhhhHHHHHHhcCCCEEEECCHhHHhhh
Q 029589 125 KPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIE------------------LVVWLPALCRKMEIPYCIVKGKSRLGSV 186 (191)
Q Consensus 125 ~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~e------------------lv~~LpaLC~k~~VPy~iV~sK~~LG~a 186 (191)
.+.....|.++|.++++.|-+..++|..|..-.. ++..|..+++++|.-+.+|.+..+-|.-
T Consensus 18 ~~~~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~~~r~~~~~~~~~~~~~~~i~~l~~~a~~~g~~v~iis~~~e~G~~ 97 (113)
T PF03465_consen 18 DPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRDVERCKCPECGGELEVVELIEELIELAEQSGAKVEIISSEHEEGEQ 97 (113)
T ss_dssp TCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESCHHHHHSTTTHSEEEEEEHHHHHHHHHHHTTSEEEEE-TTSHHHHH
T ss_pred CCCcEEECHHHHHHHHHhCCCcEEEEecccccccceeccccccccchhhhHHHHHHHHHHHHHcCCEEEEEcCCCccHHH
Confidence 3467789999999999999999999999986654 3678999999999999999999877764
Q ss_pred h
Q 029589 187 N 187 (191)
Q Consensus 187 ~ 187 (191)
+
T Consensus 98 L 98 (113)
T PF03465_consen 98 L 98 (113)
T ss_dssp H
T ss_pred H
Confidence 4
No 26
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=93.05 E-value=0.29 Score=37.88 Aligned_cols=54 Identities=19% Similarity=0.259 Sum_probs=46.8
Q ss_pred CCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 125 KPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 125 ~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
..+.++=|+-++|+.+-+.-.-.|++-..-+| ++ .||-.||++.|||+..+.++
T Consensus 36 diN~IKPGIgEaTRvLLRRvP~~vLVr~~~~p-d~-~Hl~~LA~ekgVpVe~~~d~ 89 (100)
T PF15608_consen 36 DINLIKPGIGEATRVLLRRVPWKVLVRDPDDP-DL-AHLLLLAEEKGVPVEVYPDL 89 (100)
T ss_pred CcccccCChhHHHHHHHhcCCCEEEECCCCCc-cH-HHHHHHHHHcCCcEEEeCCC
Confidence 34677779999999999999999988876666 65 68999999999999998876
No 27
>PRK04011 peptide chain release factor 1; Provisional
Probab=90.98 E-value=1.4 Score=41.22 Aligned_cols=61 Identities=15% Similarity=0.231 Sum_probs=50.9
Q ss_pred CCceeeechhHHHHHHHhcCcceEEEecCCC-----------------------------------------ccchhhhH
Q 029589 125 KPIVVKYGLNHVTYLIEQNKAQLVVIAHDVD-----------------------------------------PIELVVWL 163 (191)
Q Consensus 125 ~p~~L~~G~~~Vtk~IekkKAkLVVIA~Dvd-----------------------------------------P~elv~~L 163 (191)
.+.....|..+|.++++.|.+..++|..|.. ..+++.+|
T Consensus 293 d~g~avyG~~~V~~Ale~GAVetLLV~d~l~~~r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~v~~l 372 (411)
T PRK04011 293 DGGLAVYGEEEVRKALEMGAVDTLLISEDLRKDRVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSELEIVEEEDIIEEL 372 (411)
T ss_pred CCCcEEEcHHHHHHHHHcCCceEEEEeccccceeEEEEcCCCCcceeeecccccccccccCcccCcccccchhhhHHHHH
Confidence 3456789999999999999999999987641 22467889
Q ss_pred HHHHHhcCCCEEEECCHhHHhh
Q 029589 164 PALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 164 paLC~k~~VPy~iV~sK~~LG~ 185 (191)
..+++++|.-+.+|.+..+-|.
T Consensus 373 ~e~a~~~g~~v~iis~~~e~G~ 394 (411)
T PRK04011 373 SELAEQSGTKVEVISTDTEEGE 394 (411)
T ss_pred HHHHHHcCCEEEEECCCChhHH
Confidence 9999999999999999877664
No 28
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=90.15 E-value=1.9 Score=40.32 Aligned_cols=60 Identities=17% Similarity=0.362 Sum_probs=50.8
Q ss_pred CceeeechhHHHHHHHhcCcceEEEecCCCc-----------------------------------------cchhhhHH
Q 029589 126 PIVVKYGLNHVTYLIEQNKAQLVVIAHDVDP-----------------------------------------IELVVWLP 164 (191)
Q Consensus 126 p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP-----------------------------------------~elv~~Lp 164 (191)
+....+|..+|.++++.|.+..++|..|..- ..++.+|.
T Consensus 290 ~G~avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~ve~L~ 369 (409)
T TIGR00108 290 DGLACYGEDEVLKALDLGAVETLIVSEDLEYIRVTYKCAECGEVIEKTVRELKDKKFAICPACGQEMDVVEERDLIEWLS 369 (409)
T ss_pred CCcEEeCHHHHHHHHHhCCCcEEEEeccccceeEEEEcCCCCceeecccccccccccccCcccCccccchhhhhHHHHHH
Confidence 3566799999999999999999999998731 13567899
Q ss_pred HHHHhcCCCEEEECCHhHHhh
Q 029589 165 ALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 165 aLC~k~~VPy~iV~sK~~LG~ 185 (191)
.+|+++|.-+.+|.+..+-|.
T Consensus 370 e~a~~~Ga~V~iiS~~~eeG~ 390 (409)
T TIGR00108 370 ELAENFGAKLEFISTESEEGA 390 (409)
T ss_pred HHHHHcCCEEEEECCCChhHH
Confidence 999999999999999987663
No 29
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=89.94 E-value=0.88 Score=33.62 Aligned_cols=49 Identities=18% Similarity=0.224 Sum_probs=39.0
Q ss_pred chhHHHHHHHh--cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 132 GLNHVTYLIEQ--NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 132 G~~~Vtk~Iek--kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
|.+.-...|++ ++|.+||+--|.-.-.....+-..|+++++|++++.+.
T Consensus 34 ~~~~~~~~l~~~i~~aD~VIv~t~~vsH~~~~~vk~~akk~~ip~~~~~~~ 84 (97)
T PF10087_consen 34 GDEKKASRLPSKIKKADLVIVFTDYVSHNAMWKVKKAAKKYGIPIIYSRSR 84 (97)
T ss_pred CCccchhHHHHhcCCCCEEEEEeCCcChHHHHHHHHHHHHcCCcEEEECCC
Confidence 44444445655 67899999988877788888999999999999999843
No 30
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=88.08 E-value=3.2 Score=38.81 Aligned_cols=59 Identities=17% Similarity=0.244 Sum_probs=50.7
Q ss_pred CceeeechhHHHHHHHhcCcceEEEecCCC-----------------------------------------ccchhhhHH
Q 029589 126 PIVVKYGLNHVTYLIEQNKAQLVVIAHDVD-----------------------------------------PIELVVWLP 164 (191)
Q Consensus 126 p~~L~~G~~~Vtk~IekkKAkLVVIA~Dvd-----------------------------------------P~elv~~Lp 164 (191)
+.....|..+|.++++.|.+..++|..|.. ..+++.+|.
T Consensus 286 ~g~avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ve~L~ 365 (403)
T TIGR03676 286 GGLAAYGEEEVRKALEMGAVDTLLISEDLRKIRVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSELEIVEEEDIIEELS 365 (403)
T ss_pred CCcEEEcHHHHHHHHHhCCCcEEEEEccccceeEEEEcCCCCcceeeecccccccccccCcccCcccccchhhhHHHHHH
Confidence 456779999999999999999999988772 124677899
Q ss_pred HHHHhcCCCEEEECCHhHHh
Q 029589 165 ALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 165 aLC~k~~VPy~iV~sK~~LG 184 (191)
.+++++|.-+.+|.+..+-|
T Consensus 366 e~a~~~Ga~V~~iS~~~eeG 385 (403)
T TIGR03676 366 ELAEESGAKVEIISTDTEEG 385 (403)
T ss_pred HHHHHcCCEEEEECCCChhH
Confidence 99999999999999998777
No 31
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=85.63 E-value=4.5 Score=36.92 Aligned_cols=62 Identities=19% Similarity=0.163 Sum_probs=51.8
Q ss_pred CCCceeeechhHHHHHHHhcCcceEEEecCC-CccchhhhHHHHHHhcCCCEEEECCHhHHhh
Q 029589 124 KKPIVVKYGLNHVTYLIEQNKAQLVVIAHDV-DPIELVVWLPALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 124 k~p~~L~~G~~~Vtk~IekkKAkLVVIA~Dv-dP~elv~~LpaLC~k~~VPy~iV~sK~~LG~ 185 (191)
+.+....+|.++|.++++.|-+.-++|..+. ...+-+..|...++++|.-+.++++..+-|.
T Consensus 273 kd~~~~~YG~~eV~~Ale~GAVetLLIsD~l~~~r~~~~~l~~~v~~~gg~V~i~Ss~~e~G~ 335 (351)
T TIGR00111 273 KDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVLVQREEIEKLLDSVESMGGKVVILSTEHELGK 335 (351)
T ss_pred cCCCeEEECHHHHHHHHHcCCceEEEEecchhhhHHHHHHHHHHHHHcCCEEEEEcCCCccHH
Confidence 3456788999999999999999999999998 3222244588899999999999999988885
No 32
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=85.04 E-value=1.7 Score=33.49 Aligned_cols=51 Identities=16% Similarity=0.108 Sum_probs=37.1
Q ss_pred eeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 128 VVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 128 ~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
.+....+++...+++..+..|+||-+-++.+.+..+-..|++++|.+.+++
T Consensus 125 ~~lg~~~~l~~~~~~~~id~v~ial~~~~~~~i~~ii~~~~~~~v~v~~vP 175 (175)
T PF13727_consen 125 PVLGDLDDLPELVREHDIDEVIIALPWSEEEQIKRIIEELENHGVRVRVVP 175 (175)
T ss_dssp EEE--GGGHHHHHHHHT--EEEE--TTS-HHHHHHHHHHHHTTT-EEEE--
T ss_pred eeEcCHHHHHHHHHhCCCCEEEEEcCccCHHHHHHHHHHHHhCCCEEEEeC
Confidence 344567999999999999999999998888888899999999999998763
No 33
>PF07997 DUF1694: Protein of unknown function (DUF1694); InterPro: IPR012543 This family contains many hypothetical proteins.; PDB: 2OHW_A.
Probab=80.74 E-value=3.8 Score=32.30 Aligned_cols=49 Identities=16% Similarity=0.171 Sum_probs=36.6
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhH
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~ 182 (191)
..++.+.+.+...-.++|..+++. +....+..+|.++|+||.+|.+...
T Consensus 51 ~~~~~~~l~~~~~~~l~ing~l~~-~~~~~YiklA~~~~~~fTiv~~~~~ 99 (120)
T PF07997_consen 51 YPEFEQALKDYPNYKLKINGNLDY-SFQSKYIKLANKHGIPFTIVNDPEY 99 (120)
T ss_dssp -HHHHHHHHC-SSEEEEEETTS-H-HHHHHHHHHHHHTT--EEEE---SS
T ss_pred HHHHHHHHhhCCCeEEEEcCCCCH-HHHHHHHHHHHHcCCCEEEeCCCCc
Confidence 468888999999999999999999 5667799999999999999988653
No 34
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=77.41 E-value=6.1 Score=30.36 Aligned_cols=48 Identities=25% Similarity=0.287 Sum_probs=37.7
Q ss_pred eechhHHHHHHHhcCcceEEEecCC---Cc-cchhhhHHHHHHhcCCCEEEE
Q 029589 130 KYGLNHVTYLIEQNKAQLVVIAHDV---DP-IELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 130 ~~G~~~Vtk~IekkKAkLVVIA~Dv---dP-~elv~~LpaLC~k~~VPy~iV 177 (191)
.-|..++..+|.+|+..+||-.-|- ++ ..--..|...|-+++|||+.-
T Consensus 56 ~~g~~~i~~~i~~g~i~~VInt~~~~~~~~~~~dg~~iRr~a~~~~Ip~~Tt 107 (115)
T cd01422 56 LGGDQQIGALIAEGEIDAVIFFRDPLTAQPHEPDVKALLRLCDVYNIPLATN 107 (115)
T ss_pred CCchhHHHHHHHcCceeEEEEcCCCCCCCcccccHHHHHHHHHHcCCCEEEc
Confidence 3577889999999999999888762 33 333456899999999999863
No 35
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=71.98 E-value=8.8 Score=30.85 Aligned_cols=46 Identities=22% Similarity=0.241 Sum_probs=35.6
Q ss_pred chhHHHHHHHhcCcceEEEecC-CCc---cchhhhHHHHHHhcCCCEEEE
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHD-VDP---IELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~D-vdP---~elv~~LpaLC~k~~VPy~iV 177 (191)
|..++..+|.+|+..+||--.| .++ ..-...|...|-.++|||+.-
T Consensus 63 g~~~i~~~I~~g~i~lVInt~dp~~~~~~~~D~~~IRR~Av~~~IP~~T~ 112 (142)
T PRK05234 63 GDQQIGALIAEGKIDMLIFFRDPLTAQPHDPDVKALLRLADVWNIPVATN 112 (142)
T ss_pred CchhHHHHHHcCceeEEEEecCCCCCCcccchHHHHHHHHHHcCCCEEcC
Confidence 6788999999999999988764 232 222335899999999999853
No 36
>smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357.
Probab=71.03 E-value=6.8 Score=28.22 Aligned_cols=47 Identities=23% Similarity=0.239 Sum_probs=35.7
Q ss_pred eeechhHHHHHHHhcCcceEEEecC---CCccchhhhHHHHHHhcCCCEE
Q 029589 129 VKYGLNHVTYLIEQNKAQLVVIAHD---VDPIELVVWLPALCRKMEIPYC 175 (191)
Q Consensus 129 L~~G~~~Vtk~IekkKAkLVVIA~D---vdP~elv~~LpaLC~k~~VPy~ 175 (191)
+-.|...+..++++++..+||-.-+ -++.+-...+..+|.+++||+.
T Consensus 40 i~~~~~~i~~~i~~g~id~VIn~~~~~~~~~~~d~~~iRr~A~~~~Ip~~ 89 (90)
T smart00851 40 VHGGILAILDLIKNGEIDLVINTLYPLGAQPHEDGKALRRAAENIDIPGA 89 (90)
T ss_pred CCCCCHHHHHHhcCCCeEEEEECCCcCcceeccCcHHHHHHHHHcCCCee
Confidence 3346667999999999999998654 2233334568999999999985
No 37
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=68.90 E-value=12 Score=28.26 Aligned_cols=45 Identities=27% Similarity=0.192 Sum_probs=34.6
Q ss_pred chhHHHHHHHh-cCcceEEEecCCC----ccchhhhHHHHHHhcCCCEEE
Q 029589 132 GLNHVTYLIEQ-NKAQLVVIAHDVD----PIELVVWLPALCRKMEIPYCI 176 (191)
Q Consensus 132 G~~~Vtk~Iek-kKAkLVVIA~Dvd----P~elv~~LpaLC~k~~VPy~i 176 (191)
|..++..+|++ ++..+||-.-|-. ...--..+...|-+++|||+.
T Consensus 55 g~~~i~~~i~~~g~idlVIn~~~~~~~~~~~~dg~~iRR~A~~~~Ip~~T 104 (112)
T cd00532 55 GEPTVDAAIAEKGKFDVVINLRDPRRDRCTDEDGTALLRLARLYKIPVTT 104 (112)
T ss_pred CCcHHHHHHhCCCCEEEEEEcCCCCcccccCCChHHHHHHHHHcCCCEEE
Confidence 66789999999 9999998865511 122234588999999999986
No 38
>PF02142 MGS: MGS-like domain This is a subfamily of this family; InterPro: IPR011607 This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. The known structures in this domain show a common phosphate binding site []. ; PDB: 4A1O_A 3ZZM_A 1ZCZ_A 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A ....
Probab=68.58 E-value=6.6 Score=28.70 Aligned_cols=41 Identities=17% Similarity=0.096 Sum_probs=31.7
Q ss_pred HHHHHHHhcCcceEEEecCCCccch---hhhHHHHHHhcCCCEE
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIEL---VVWLPALCRKMEIPYC 175 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~el---v~~LpaLC~k~~VPy~ 175 (191)
++..+|++++..|||..-+-..... -..+..+|.+++||+.
T Consensus 51 ~i~~~i~~~~IdlVIn~~~~~~~~~~~dg~~irr~a~~~~Ip~~ 94 (95)
T PF02142_consen 51 QIMDLIKNGKIDLVINTPYPFSDQEHTDGYKIRRAAVEYNIPLF 94 (95)
T ss_dssp HHHHHHHTTSEEEEEEE--THHHHHTHHHHHHHHHHHHTTSHEE
T ss_pred HHHHHHHcCCeEEEEEeCCCCcccccCCcHHHHHHHHHcCCCCc
Confidence 5999999999999998877654333 3457899999999986
No 39
>PF00391 PEP-utilizers: PEP-utilising enzyme, mobile domain; InterPro: IPR008279 A number of enzymes that catalyze the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) via a phospho-histidine intermediate have been shown to be structurally related [, , , ]. All these enzymes share the same catalytic mechanism: they bind PEP and transfer the phosphoryl group from it to a histidine residue. This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it []. It is often found associated with the pyruvate phosphate dikinase, PEP/pyruvate-binding domain (IPR002192 from INTERPRO) at its N terminus.; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0016310 phosphorylation; PDB: 2X0S_A 2OLS_A 2HRO_A 2E28_A 2WQD_A 3T05_D 3T0T_D 3T07_B 2DIK_A 2FM4_A ....
Probab=64.47 E-value=17 Score=25.97 Aligned_cols=19 Identities=26% Similarity=0.386 Sum_probs=14.4
Q ss_pred hhHHHHHHhcCCCEEEECC
Q 029589 161 VWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 161 ~~LpaLC~k~~VPy~iV~s 179 (191)
.|.--+|+++|||+++--+
T Consensus 43 SH~aIlAr~~giP~ivg~~ 61 (80)
T PF00391_consen 43 SHAAILARELGIPAIVGVG 61 (80)
T ss_dssp SHHHHHHHHTT-EEEESTT
T ss_pred chHHHHHHHcCCCEEEeec
Confidence 5778899999999987443
No 40
>PF13611 Peptidase_S76: Serine peptidase of plant viral polyprotein, P1
Probab=63.60 E-value=8 Score=30.95 Aligned_cols=41 Identities=27% Similarity=0.421 Sum_probs=29.8
Q ss_pred HHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHh
Q 029589 139 LIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 139 ~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
.+...++.=| +|. ++-.+++.-+..+|.+.|+|+.+|++..
T Consensus 20 ~~~~~~~~~v-v~~-~~i~dL~~~~~~ic~ergiPIe~I~~~k 60 (121)
T PF13611_consen 20 LVKRRKEKQV-VAN-NEIDDLVREVTEICCERGIPIEIIDKKK 60 (121)
T ss_pred hhhhhhhcce-Eec-CcHHHHHHHHHHHHHHcCCCEEEecCcc
Confidence 3333344444 775 4555788889999999999999998764
No 41
>TIGR03023 WcaJ_sugtrans Undecaprenyl-phosphate glucose phosphotransferase. Colanic acid biosynthesis utilizes a glucose-undecaprenyl carrier, knockout of EpsB abolishes incorporation of UDP-glucose into the lipid phase and the C-terminal portion of GumD has been shown to be responsible for the glucosyl-1-transferase activity.
Probab=62.39 E-value=17 Score=33.47 Aligned_cols=54 Identities=15% Similarity=0.132 Sum_probs=45.4
Q ss_pred echhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 131 YGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 131 ~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
.+.++....+++..+..|+||.+....+....+-..|+++||++.++.+-.++.
T Consensus 178 g~~~dl~~~i~~~~vd~ViIA~p~~~~~~~~~ll~~~~~~gv~V~vvP~~~e~~ 231 (451)
T TIGR03023 178 GKLDDLEELIREGEVDEVYIALPLAAEDRILELLDALEDLTVDVRLVPDLFDFA 231 (451)
T ss_pred CCHHHHHHHHHhcCCCEEEEeeCcccHHHHHHHHHHHHhcCCEEEEeCchhhhc
Confidence 346789999999999999999887665666778999999999999999876653
No 42
>TIGR03025 EPS_sugtrans exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase. Certain closely related transferase enzymes such as Sinorhizobium ExoY and Lactococcus EpsD lack the N-terminal domain and are not found by this model.
Probab=61.91 E-value=19 Score=33.09 Aligned_cols=52 Identities=15% Similarity=0.186 Sum_probs=44.8
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
+.+++...+++..+.-|+||.+-...+....+-..|+++||.+.++.+-.++
T Consensus 176 ~~~~l~~~i~~~~id~ViIa~p~~~~~~~~~ll~~~~~~gv~V~~vP~~~e~ 227 (445)
T TIGR03025 176 KLDDLVELVRAHRVDEVIIALPLSEEARILELLLQLRDLGVDVRLVPDLFEF 227 (445)
T ss_pred CHHHHHHHHHhCCCCEEEEecCcccHHHHHHHHHHHHhcCCEEEEeCchhhh
Confidence 4577889999999999999988776666677899999999999999987765
No 43
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=59.20 E-value=39 Score=29.17 Aligned_cols=59 Identities=17% Similarity=0.158 Sum_probs=43.5
Q ss_pred eeechhHHHHHHHhc--CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCC
Q 029589 129 VKYGLNHVTYLIEQN--KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNIL 189 (191)
Q Consensus 129 L~~G~~~Vtk~Iekk--KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi 189 (191)
+..|.+.|..+++++ ...-+++..+.+...+ .-+-.+|.+.+|++..+ +.+.|-++++-
T Consensus 4 ~i~G~~~v~eal~~~~~~~~~l~~~~~~~~~~~-~~~~~~~~~~~i~~~~v-~~~~l~~ls~~ 64 (244)
T PRK11181 4 IIYGIHAVQALLERAPERFIEVFVLKGREDKRL-LPLINELEAQGIVIQLA-NRQTLDEKAEG 64 (244)
T ss_pred EEEehHHHHHHHhCCCCceeEEEEECCCcchHH-HHHHHHHHHcCCcEEEe-CHHHHhhhhcC
Confidence 468999999999863 5667888877655333 34667899999998776 46778777653
No 44
>cd01879 FeoB Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
Probab=57.89 E-value=24 Score=26.24 Aligned_cols=41 Identities=17% Similarity=0.231 Sum_probs=24.2
Q ss_pred cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 143 NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 143 kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
..+.+|++..|++..+-...+...+.+.++|++++-+|.+|
T Consensus 73 ~~~d~vi~v~d~~~~~~~~~~~~~~~~~~~~~iiv~NK~Dl 113 (158)
T cd01879 73 EKPDLIVNVVDATNLERNLYLTLQLLELGLPVVVALNMIDE 113 (158)
T ss_pred CCCcEEEEEeeCCcchhHHHHHHHHHHcCCCEEEEEehhhh
Confidence 45666666666665443223333445567777777777766
No 45
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=57.04 E-value=25 Score=26.05 Aligned_cols=46 Identities=20% Similarity=0.231 Sum_probs=34.9
Q ss_pred echhHHHHHHHhcCcceEEEecCC-CccchhhhHHHHHHhcCCCEEE
Q 029589 131 YGLNHVTYLIEQNKAQLVVIAHDV-DPIELVVWLPALCRKMEIPYCI 176 (191)
Q Consensus 131 ~G~~~Vtk~IekkKAkLVVIA~Dv-dP~elv~~LpaLC~k~~VPy~i 176 (191)
.|..++..+|++++..+||-.-+- +...--..+..+|-++||||..
T Consensus 54 ~~~~~i~~~i~~~~id~vIn~~~~~~~~~~~~~iRR~Av~~~ipl~T 100 (110)
T cd01424 54 EGRPNIVDLIKNGEIQLVINTPSGKRAIRDGFSIRRAALEYKVPYFT 100 (110)
T ss_pred CCchhHHHHHHcCCeEEEEECCCCCccCccHHHHHHHHHHhCCCEEe
Confidence 467889999999999999885442 1122234689999999999974
No 46
>PRK10124 putative UDP-glucose lipid carrier transferase; Provisional
Probab=56.87 E-value=25 Score=33.07 Aligned_cols=53 Identities=13% Similarity=-0.043 Sum_probs=44.9
Q ss_pred echhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 131 YGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 131 ~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
.+.+++...+++..+..|+||.+....+....+-..|++++|.+.++.+..++
T Consensus 190 G~~~dL~~~v~~~~IdeViIAip~~~~~~l~ell~~~~~~~v~V~ivP~l~~~ 242 (463)
T PRK10124 190 GNLQQLVEDAKAGKIHNVYIAMSMCDGARVKKLVRQLADTTCSVLLIPDVFTF 242 (463)
T ss_pred CCHHHHHHHHHhCCCCEEEEeCCCcchHHHHHHHHHHHHcCCeEEEecchhhc
Confidence 34577889999999999999998777666677889999999999999987644
No 47
>PF01601 Corona_S2: Coronavirus S2 glycoprotein; InterPro: IPR002552 The type I glycoprotein S of Coronavirus, trimers of which constitute the typical viral spikes, is assembled into virions through noncovalent interactions with the M protein. The spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 IPR002551 from INTERPRO and S2 []. Both chimeric S proteins appeared to cause cell fusion when expressed individually, suggesting that they were biologically fully active []. The spike is a type I membrane glycoprotein that possesses a conserved transmembrane anchor and an unusual cysteine-rich (cys) domain that bridges the putative junction of the anchor and the cytoplasmic tail [].; GO: 0006944 cellular membrane fusion, 0046813 virion attachment, binding of host cell surface receptor, 0016021 integral to membrane, 0019031 viral envelope; PDB: 2BEQ_B 2FXP_A 1ZVB_A 1WNC_D 1ZV8_H 1ZV7_B 1WYY_B 1ZVA_A 2BEZ_F 1WDG_A ....
Probab=56.29 E-value=3.5 Score=40.82 Aligned_cols=13 Identities=31% Similarity=0.889 Sum_probs=3.6
Q ss_pred cccccccchhhHh
Q 029589 45 LHRYVKWPKAIRI 57 (191)
Q Consensus 45 ltrfvkwP~yirl 57 (191)
...|+|||-||||
T Consensus 540 ~e~YiKWPWyVWL 552 (610)
T PF01601_consen 540 YETYIKWPWYVWL 552 (610)
T ss_dssp CCCHH--------
T ss_pred eeEEeehHHHHHH
Confidence 4579999999996
No 48
>PF00009 GTP_EFTU: Elongation factor Tu GTP binding domain; InterPro: IPR000795 Elongation factors belong to a family of proteins that promote the GTP-dependent binding of aminoacyl tRNA to the A site of ribosomes during protein biosynthesis, and catalyse the translocation of the synthesised protein chain from the A to the P site. The proteins are all relatively similar in the vicinity of their C-termini, and are also highly similar to a range of proteins that includes the nodulation Q protein from Rhizobium meliloti (Sinorhizobium meliloti), bacterial tetracycline resistance proteins [] and the omnipotent suppressor protein 2 from yeast. In both prokaryotes and eukaryotes, there are three distinct types of elongation factors, EF-1alpha (EF-Tu), which binds GTP and an aminoacyl-tRNAand delivers the latter to the A site of ribosomes; EF-1beta (EF-Ts), which interacts with EF-1a/EF-Tu to displace GDP and thus allows the regeneration of GTP-EF-1a; and EF-2 (EF-G), which binds GTP and peptidyl-tRNA and translocates the latter from the A site to the P site. In EF-1-alpha, a specific region has been shown [] to be involved in a conformational change mediated by the hydrolysis of GTP to GDP. This region is conserved in both EF-1alpha/EF-Tu as well as EF-2/EF-G and thus seems typical for GTP-dependent proteins which bind non-initiator tRNAs to the ribosome. The GTP-binding protein synthesis factor family also includes the eukaryotic peptide chain release factor GTP-binding subunits [] and prokaryotic peptide chain release factor 3 (RF-3) []; the prokaryotic GTP-binding protein lepA and its homologue in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1 []; rat statin S1 []; and the prokaryotic selenocysteine-specific elongation factor selB [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3IZW_C 1DG1_G 2BVN_B 3IZV_C 3MMP_C 1OB2_A 1EFU_A 3FIH_Z 3TR5_A 1TUI_C ....
Probab=54.85 E-value=17 Score=29.05 Aligned_cols=51 Identities=16% Similarity=0.167 Sum_probs=33.7
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
..++.+++..=.+-++||..+-.+......+..+|..+++|++++-+|-++
T Consensus 84 ~~~~~~~~~~~D~ailvVda~~g~~~~~~~~l~~~~~~~~p~ivvlNK~D~ 134 (188)
T PF00009_consen 84 IKEMIRGLRQADIAILVVDANDGIQPQTEEHLKILRELGIPIIVVLNKMDL 134 (188)
T ss_dssp HHHHHHHHTTSSEEEEEEETTTBSTHHHHHHHHHHHHTT-SEEEEEETCTS
T ss_pred eecccceecccccceeeeecccccccccccccccccccccceEEeeeeccc
Confidence 345555655555555666555445555666788999999999998877654
No 49
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=54.47 E-value=24 Score=31.65 Aligned_cols=41 Identities=34% Similarity=0.460 Sum_probs=32.8
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV 177 (191)
..-+..+++++ +++||||+|... - .-|+.|=++.+||++-|
T Consensus 57 ~~i~~~l~~~~-ik~lVIACNTAS--a-~al~~LR~~~~iPVvGv 97 (269)
T COG0796 57 LEIVDFLLERG-IKALVIACNTAS--A-VALEDLREKFDIPVVGV 97 (269)
T ss_pred HHHHHHHHHcC-CCEEEEecchHH--H-HHHHHHHHhCCCCEEEe
Confidence 44566777888 999999999754 3 34899999999999865
No 50
>cd01483 E1_enzyme_family Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.
Probab=54.11 E-value=22 Score=27.32 Aligned_cols=37 Identities=27% Similarity=0.343 Sum_probs=29.9
Q ss_pred cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHh
Q 029589 143 NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 143 kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
....+||.+.|- .+....+-.+|++.++||+...+..
T Consensus 88 ~~~diVi~~~d~--~~~~~~l~~~~~~~~i~~i~~~~~g 124 (143)
T cd01483 88 DGVDLVIDAIDN--IAVRRALNRACKELGIPVIDAGGLG 124 (143)
T ss_pred cCCCEEEECCCC--HHHHHHHHHHHHHcCCCEEEEcCCC
Confidence 478899999886 3455678999999999999987643
No 51
>KOG2486 consensus Predicted GTPase [General function prediction only]
Probab=52.63 E-value=16 Score=33.62 Aligned_cols=46 Identities=20% Similarity=0.103 Sum_probs=31.5
Q ss_pred HHHHHhcCcceEEEecCCC--ccchhhhHHHHHHhcCCCEEEECCHhH
Q 029589 137 TYLIEQNKAQLVVIAHDVD--PIELVVWLPALCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 137 tk~IekkKAkLVVIA~Dvd--P~elv~~LpaLC~k~~VPy~iV~sK~~ 182 (191)
..++|+..-.-|+++.|++ +...-....++|.+++||+.+|.++-+
T Consensus 212 ~Y~leR~nLv~~FLLvd~sv~i~~~D~~~i~~~ge~~VP~t~vfTK~D 259 (320)
T KOG2486|consen 212 SYLLERENLVRVFLLVDASVPIQPTDNPEIAWLGENNVPMTSVFTKCD 259 (320)
T ss_pred HHHHhhhhhheeeeeeeccCCCCCCChHHHHHHhhcCCCeEEeeehhh
Confidence 3456666555566655553 333444568999999999999998753
No 52
>PF02603 Hpr_kinase_N: HPr Serine kinase N terminus; InterPro: IPR011126 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria []. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes []. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains []. ; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1KNX_B 1KO7_A.
Probab=51.22 E-value=21 Score=27.81 Aligned_cols=38 Identities=16% Similarity=0.194 Sum_probs=23.4
Q ss_pred HHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 139 LIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 139 ~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
.+-....=.+|+++|..|. ..+..+|++++||+....-
T Consensus 76 ~l~~~~~P~iIvt~~~~~p---~~l~e~a~~~~ipll~t~~ 113 (127)
T PF02603_consen 76 KLFSYNPPCIIVTRGLEPP---PELIELAEKYNIPLLRTPL 113 (127)
T ss_dssp HHCTTT-S-EEEETTT------HHHHHHHHHCT--EEEESS
T ss_pred HHhCCCCCEEEEECcCCCC---HHHHHHHHHhCCcEEEcCC
Confidence 3334566678999998763 3478899999999987654
No 53
>TIGR03729 acc_ester putative phosphoesterase. Members of this protein family belong to the larger family pfam00149 (calcineurin-like phosphoesterase), a family largely defined by small motifs of metal-chelating residues. The subfamily in this model shows a good but imperfect co-occurrence in species with domain TIGR03715 that defines a novel class of signal peptide typical of the accessory secretory system.
Probab=49.93 E-value=46 Score=27.89 Aligned_cols=49 Identities=14% Similarity=0.191 Sum_probs=32.6
Q ss_pred hHHHHHHHhcCcceEEEecCCCc--cchhhhHHHHHHhcCCCEEEECCHhH
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDP--IELVVWLPALCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP--~elv~~LpaLC~k~~VPy~iV~sK~~ 182 (191)
..+...+.+.++.+||++.|... .+...++-.+.+..++|+.+|.|--+
T Consensus 22 ~~~~~~~~~~~~d~vv~~GDl~~~~~~~~~~~~~l~~~~~~pv~~v~GNHD 72 (239)
T TIGR03729 22 ETLAQYLKKQKIDHLHIAGDISNDFQRSLPFIEKLQELKGIKVTFNAGNHD 72 (239)
T ss_pred HHHHHHHHhcCCCEEEECCccccchhhHHHHHHHHHHhcCCcEEEECCCCC
Confidence 34556666677999999999764 12233455566556789988877555
No 54
>PRK10864 putative methyltransferase; Provisional
Probab=49.62 E-value=67 Score=29.73 Aligned_cols=60 Identities=15% Similarity=0.107 Sum_probs=43.8
Q ss_pred ceeeechhHHHHHHHhc--CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCC
Q 029589 127 IVVKYGLNHVTYLIEQN--KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNIL 189 (191)
Q Consensus 127 ~~L~~G~~~Vtk~Iekk--KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi 189 (191)
..++.|.+.|..+++++ ...-+++....++ .. .-+..++...+++|..| +.+.|-+++|-
T Consensus 108 ~~~I~G~~aV~ealk~~~~~i~~l~~~~~~~~-~~-~~il~~~~~~~~~v~~V-~~~~l~kls~~ 169 (346)
T PRK10864 108 ETRVYGENACQALFQSRPEAIVRAWFIQSVTP-RF-KEALRWMAANRKAYHVV-DEAELTKASGT 169 (346)
T ss_pred CcEEEEHHHHHHHHhCCCCceeEEEEecCccH-HH-HHHHHHHHHcCCcEEEe-CHHHHHHHhCC
Confidence 36779999999999873 4556677777765 33 33566777889998776 66778888764
No 55
>PF02421 FeoB_N: Ferrous iron transport protein B; InterPro: IPR011619 Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system and may play a role in the transport of ferrous iron. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent [].; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0016021 integral to membrane; PDB: 3TAH_B 3B1X_A 3SS8_A 3B1W_C 3B1V_A 3LX5_A 3B1Y_A 3LX8_A 3B1Z_A 3K53_B ....
Probab=49.32 E-value=31 Score=28.16 Aligned_cols=53 Identities=17% Similarity=0.243 Sum_probs=37.2
Q ss_pred HHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCC
Q 029589 137 TYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNIL 189 (191)
Q Consensus 137 tk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi 189 (191)
...+...+..+|+.-.|+...+--..|-.--.++|+|++.+-+|.++-.--|+
T Consensus 71 ~~~l~~~~~D~ii~VvDa~~l~r~l~l~~ql~e~g~P~vvvlN~~D~a~~~g~ 123 (156)
T PF02421_consen 71 RDYLLSEKPDLIIVVVDATNLERNLYLTLQLLELGIPVVVVLNKMDEAERKGI 123 (156)
T ss_dssp HHHHHHTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTE
T ss_pred HHHHhhcCCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEEeCHHHHHHcCC
Confidence 44555677888888888877766666656666788888888888766554443
No 56
>PF07905 PucR: Purine catabolism regulatory protein-like family; InterPro: IPR012914 This domain is found in the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138 from SWISSPROT). PucR is thought to be a transcriptional regulator of genes involved in the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression []. The other members of this family are also putative regulatory proteins.
Probab=48.23 E-value=50 Score=25.28 Aligned_cols=50 Identities=14% Similarity=0.121 Sum_probs=36.3
Q ss_pred HHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhh
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~ 185 (191)
-+..+.+.|-+.|+|=..+--+ ++-..+.++|+++++|++.+.....+..
T Consensus 64 ~i~~L~~~~~agL~i~~~~~~~-~iP~~~i~~A~~~~lPli~ip~~~~f~~ 113 (123)
T PF07905_consen 64 FIRELAEKGAAGLGIKTGRYLD-EIPEEIIELADELGLPLIEIPWEVPFSD 113 (123)
T ss_pred HHHHHHHCCCeEEEEeccCccc-cCCHHHHHHHHHcCCCEEEeCCCCCHHH
Confidence 3555667788888875543333 6667789999999999999987655543
No 57
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=48.05 E-value=72 Score=27.28 Aligned_cols=56 Identities=21% Similarity=0.249 Sum_probs=39.1
Q ss_pred eeechhHHHHHHHhcCcceEEEecCC-CccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCC
Q 029589 129 VKYGLNHVTYLIEQNKAQLVVIAHDV-DPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNIL 189 (191)
Q Consensus 129 L~~G~~~Vtk~IekkKAkLVVIA~Dv-dP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi 189 (191)
++.|.+.|..+++++ -.+. +.... ++ +.. .+-.+|.+.+||+..+. ++.|-+++|-
T Consensus 3 ~i~G~~~v~eal~~~-~~~~-~~~~~~~~-~~~-~~~~~~~~~~~~~~~v~-~~~l~~l~~~ 59 (237)
T TIGR00186 3 YLYGKNAVLEALLNQ-QRVF-ILKGLESK-RLK-KLIQLAKKQGINIQLVD-RQKLDQLTKG 59 (237)
T ss_pred EEEehHHHHHHHhCC-CEEE-EEecCcch-HHH-HHHHHHHHcCCcEEEeC-HHHHHHHhCC
Confidence 468999999999988 3333 33332 22 333 36788899999998884 6778887763
No 58
>cd04165 GTPBP1_like GTPBP1-like. Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and
Probab=46.61 E-value=32 Score=29.07 Aligned_cols=50 Identities=14% Similarity=0.144 Sum_probs=32.3
Q ss_pred hHHHHHHHhcCcceEEEecCC--CccchhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 134 NHVTYLIEQNKAQLVVIAHDV--DPIELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~Dv--dP~elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
+++...+....+.++++..|+ .+......+-.+|..+++|++++-+|.++
T Consensus 99 ~~~~~~~~~~~~D~~llVvda~~g~~~~d~~~l~~l~~~~ip~ivvvNK~D~ 150 (224)
T cd04165 99 KTTLFGLTGYAPDYAMLVVAANAGIIGMTKEHLGLALALNIPVFVVVTKIDL 150 (224)
T ss_pred HHHHHhhcccCCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEECccc
Confidence 344555543334444444443 44555556778899999999999988876
No 59
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=45.66 E-value=23 Score=26.23 Aligned_cols=34 Identities=35% Similarity=0.262 Sum_probs=25.4
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
.+.||++|.|- + ++-..+-..|+.+++|+..++.
T Consensus 60 ~~~lV~~at~d-~-~~n~~i~~~a~~~~i~vn~~D~ 93 (103)
T PF13241_consen 60 GADLVFAATDD-P-ELNEAIYADARARGILVNVVDD 93 (103)
T ss_dssp TESEEEE-SS--H-HHHHHHHHHHHHTTSEEEETT-
T ss_pred hheEEEecCCC-H-HHHHHHHHHHhhCCEEEEECCC
Confidence 37799988863 3 5666789999999999988765
No 60
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=44.66 E-value=71 Score=22.08 Aligned_cols=40 Identities=23% Similarity=0.150 Sum_probs=26.7
Q ss_pred HHHHHHhcCc--ceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 136 VTYLIEQNKA--QLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 136 Vtk~IekkKA--kLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
+-+++++-+. .|.|++.| |... ..+|.+|+.+|-.+..+.
T Consensus 16 ~kkal~~l~~G~~l~V~~d~--~~a~-~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 16 LKKEIDKLQDGEQLEVKASD--PGFA-RDAQAWCKSTGNTLISLE 57 (69)
T ss_pred HHHHHHcCCCCCEEEEEECC--ccHH-HHHHHHHHHcCCEEEEEE
Confidence 4455655332 47777776 4334 569999999999987544
No 61
>COG0352 ThiE Thiamine monophosphate synthase [Coenzyme metabolism]
Probab=44.33 E-value=66 Score=27.66 Aligned_cols=56 Identities=20% Similarity=0.255 Sum_probs=43.7
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccch---hhhHHHHHHhcCCCEEEECCHhHHhhhhCC
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIEL---VVWLPALCRKMEIPYCIVKGKSRLGSVNIL 189 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~el---v~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi 189 (191)
.+.+..+++.|-.-+.+-..|.+..+. ..-+..+|+++++|++ |.+.-+|-..+|-
T Consensus 24 ~~~ve~al~~Gv~~vQlR~K~~~~~~~~~~a~~~~~lc~~~~v~li-INd~~dlA~~~~A 82 (211)
T COG0352 24 LEWVEAALKGGVTAVQLREKDLSDEEYLALAEKLRALCQKYGVPLI-INDRVDLALAVGA 82 (211)
T ss_pred HHHHHHHHhCCCeEEEEecCCCChHHHHHHHHHHHHHHHHhCCeEE-ecCcHHHHHhCCC
Confidence 689999999997777788888887553 3458999999999994 5777777665543
No 62
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=42.32 E-value=42 Score=31.90 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=43.1
Q ss_pred HhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhC
Q 029589 141 EQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNI 188 (191)
Q Consensus 141 ekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~G 188 (191)
..++-++-+|.-|.--|-=+.-|-..|+-||||++.+.+..+|-.++.
T Consensus 230 ~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~ 277 (407)
T COG1419 230 LKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIE 277 (407)
T ss_pred hccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHH
Confidence 567888889999998888888899999999999999999999987753
No 63
>PF00899 ThiF: ThiF family; InterPro: IPR000594 Ubiquitin-activating enzyme (E1 enzyme) [, ] activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin- conjugating enzymes (E2). The family of ubiquitin-activating enzymes shares in its catalytic domain significant similarity with a large family of NAD/FAD-binding proteins. This domain is based on the common NAD/FAD-binding fold and finds members of several families, including UBA ubiquitin activating enzymes; the hesA/moeB/thiF family; NADH peroxidases; the LDH family; sarcosin oxidase; phytoene dehydrogenases; alanine dehydrogenases; hydroxyacyl-CoA dehydrogenases and many other NAD/FAD dependent dehydrogenases and oxidases.; GO: 0003824 catalytic activity; PDB: 1ZKM_D 1ZUD_3 1ZFN_D 1R4M_G 2NVU_A 1R4N_C 3DBR_A 3DBH_C 3DBL_G 1YOV_A ....
Probab=39.97 E-value=41 Score=25.66 Aligned_cols=43 Identities=19% Similarity=0.375 Sum_probs=30.9
Q ss_pred hHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
.....++ ....+||.+.|- .+...++-.+|+++++|++....-
T Consensus 84 ~~~~~~~--~~~d~vi~~~d~--~~~~~~l~~~~~~~~~p~i~~~~~ 126 (135)
T PF00899_consen 84 ENIEELL--KDYDIVIDCVDS--LAARLLLNEICREYGIPFIDAGVN 126 (135)
T ss_dssp HHHHHHH--HTSSEEEEESSS--HHHHHHHHHHHHHTT-EEEEEEEE
T ss_pred ccccccc--cCCCEEEEecCC--HHHHHHHHHHHHHcCCCEEEEEee
Confidence 4455555 467899888775 455567899999999999987653
No 64
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=39.85 E-value=64 Score=30.17 Aligned_cols=62 Identities=23% Similarity=0.180 Sum_probs=50.9
Q ss_pred CCCceeeechhHHHHHHHhcCcceEEEecCCCcc------chhhhHHHHHHhcCCCEEEECCHhHHhh
Q 029589 124 KKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPI------ELVVWLPALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 124 k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~------elv~~LpaLC~k~~VPy~iV~sK~~LG~ 185 (191)
+.+....+|.++|.++++=|-+.-++|+...=-. +-+.-+-...+.+|-+++++.+-.+.|.
T Consensus 268 k~~~~v~YG~~eV~~A~e~GAve~LLv~De~lr~~~~~~re~~~~ll~~ve~~ggkV~Ivs~~he~Ge 335 (352)
T COG1537 268 KDDDKVAYGLEEVEKAAEYGAVETLLVTDELLRSDDVEEREDVEELLEEVESMGGKVVIVSTEHEPGE 335 (352)
T ss_pred cCCCceeEcHHHHHHHHhcCcceeEEeehhhhcccchhhHHHHHHHHHHHHHcCCeEEEEecCCcchH
Confidence 3356778999999999999999999998765333 4445578888999999999999888775
No 65
>cd01491 Ube1_repeat1 Ubiquitin activating enzyme (E1), repeat 1. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Ubiquitin-E1 is a single-chain protein with a weakly conserved two-fold repeat. This CD represents the first repeat of Ub-E1.
Probab=39.00 E-value=24 Score=31.58 Aligned_cols=39 Identities=21% Similarity=0.368 Sum_probs=29.0
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
+..+||++.| + .+....+-.+|++.+||++...+..-.|
T Consensus 105 ~fdvVV~~~~-~-~~~~~~in~~c~~~~ipfI~a~~~G~~G 143 (286)
T cd01491 105 KFQVVVLTDA-S-LEDQLKINEFCHSPGIKFISADTRGLFG 143 (286)
T ss_pred cCCEEEEecC-C-HHHHHHHHHHHHHcCCEEEEEeccccEE
Confidence 4667777765 4 4565679999999999999887754444
No 66
>cd01485 E1-1_like Ubiquitin activating enzyme (E1), repeat 1-like. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. A set of novel molecules with a structural similarity to Ub, called Ub-like proteins (Ubls), have similar conjugation cascades. In contrast to ubiquitin-E1, which is a single-chain protein with a weakly conserved two-fold repeat, many of the Ubls-E1are a heterodimer where each subunit corresponds to one half of a single-chain E1. This CD represents the family homol
Probab=38.86 E-value=22 Score=29.53 Aligned_cols=39 Identities=26% Similarity=0.423 Sum_probs=29.0
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
...+||.+.| +.+...++-.+|++++||++...+..-.|
T Consensus 113 ~~dvVi~~~d--~~~~~~~ln~~c~~~~ip~i~~~~~G~~G 151 (198)
T cd01485 113 KFTLVIATEE--NYERTAKVNDVCRKHHIPFISCATYGLIG 151 (198)
T ss_pred CCCEEEECCC--CHHHHHHHHHHHHHcCCCEEEEEeecCEE
Confidence 5678877755 34566679999999999999876644433
No 67
>cd01857 HSR1_MMR1 HSR1/MMR1. Human HSR1, is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N terminus.
Probab=37.80 E-value=75 Score=24.22 Aligned_cols=13 Identities=15% Similarity=0.158 Sum_probs=6.2
Q ss_pred CCCEEEECCHhHH
Q 029589 171 EIPYCIVKGKSRL 183 (191)
Q Consensus 171 ~VPy~iV~sK~~L 183 (191)
+.|++++-+|.+|
T Consensus 42 ~k~~iivlNK~DL 54 (141)
T cd01857 42 RKKNILLLNKADL 54 (141)
T ss_pred CCcEEEEEechhc
Confidence 4455555444443
No 68
>PF14639 YqgF: Holliday-junction resolvase-like of SPT6 ; PDB: 3PSI_A 3PSF_A.
Probab=37.35 E-value=49 Score=26.82 Aligned_cols=46 Identities=17% Similarity=0.355 Sum_probs=26.7
Q ss_pred hHHHHHHHhcCcceEEE-ecCCCccchhhhHHHHHHhc-------CCCEEEECC
Q 029589 134 NHVTYLIEQNKAQLVVI-AHDVDPIELVVWLPALCRKM-------EIPYCIVKG 179 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVI-A~DvdP~elv~~LpaLC~k~-------~VPy~iV~s 179 (191)
..+.++|++.+..+|+| +.+.+-.++...+-.+-++. .||++++.+
T Consensus 53 ~~l~~~i~~~kP~vI~v~g~~~~s~~l~~~v~~~v~~~~~~~~~~~i~V~~v~~ 106 (150)
T PF14639_consen 53 ERLKKFIEKHKPDVIAVGGNSRESRKLYDDVRDIVEELDEDEQMPPIPVVIVDD 106 (150)
T ss_dssp HHHHHHHHHH--SEEEE--SSTHHHHHHHHHHHHHHHTTB-TTS-B--EEE---
T ss_pred HHHHHHHHHcCCeEEEEcCCChhHHHHHHHHHHHHHHhhhcccCCCceEEEECc
Confidence 45667888888888888 65565666666666666665 488888765
No 69
>cd01861 Rab6 Rab6 subfamily. Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate
Probab=37.23 E-value=34 Score=25.67 Aligned_cols=39 Identities=15% Similarity=0.287 Sum_probs=20.8
Q ss_pred cceEEEecCCCc----cchhhhHHHHHHhcC--CCEEEECCHhHH
Q 029589 145 AQLVVIAHDVDP----IELVVWLPALCRKME--IPYCIVKGKSRL 183 (191)
Q Consensus 145 AkLVVIA~DvdP----~elv~~LpaLC~k~~--VPy~iV~sK~~L 183 (191)
+..+++.-|.+. .++..++..+....+ +|++++.+|.++
T Consensus 73 ~~~ii~v~d~~~~~s~~~~~~~~~~~~~~~~~~~~iilv~nK~D~ 117 (161)
T cd01861 73 SSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDL 117 (161)
T ss_pred CCEEEEEEECcCHHHHHHHHHHHHHHHHhCCCCCEEEEEEEChhc
Confidence 445555555542 333445555554444 666666666665
No 70
>cd01821 Rhamnogalacturan_acetylesterase_like Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are highly branched regions in pectic polysaccharides, consisting of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide units, with many rhamnose residues substituted by neutral oligosaccharides such as arabinans, galactans and arabinogalactans. Extracellular enzymes participating in the degradation of plant cell wall polymers, such as Rhamnogalacturonan acetylesterase, would typically be found in saprophytic and plant pathogenic fungi and bacteria.
Probab=37.15 E-value=76 Score=25.23 Aligned_cols=23 Identities=9% Similarity=0.148 Sum_probs=18.8
Q ss_pred chhhhHHHHHHhcCCCEEEECCH
Q 029589 158 ELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 158 elv~~LpaLC~k~~VPy~iV~sK 180 (191)
.+...+..+|+++||||+.+.+.
T Consensus 133 ~~~~~~~~~a~~~~~~~vD~~~~ 155 (198)
T cd01821 133 DYPAAMRELAAEEGVPLIDLNAA 155 (198)
T ss_pred hHHHHHHHHHHHhCCCEEecHHH
Confidence 45667899999999999987653
No 71
>cd00757 ThiF_MoeB_HesA_family ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1).
Probab=36.97 E-value=45 Score=28.07 Aligned_cols=36 Identities=17% Similarity=0.066 Sum_probs=28.4
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHh
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
.+.+||.|.|- + +...++-.+|.++++|++......
T Consensus 111 ~~DvVi~~~d~-~-~~r~~l~~~~~~~~ip~i~~g~~g 146 (228)
T cd00757 111 GYDLVLDCTDN-F-ATRYLINDACVKLGKPLVSGAVLG 146 (228)
T ss_pred CCCEEEEcCCC-H-HHHHHHHHHHHHcCCCEEEEEecc
Confidence 48899999884 4 445679999999999999876543
No 72
>TIGR03022 WbaP_sugtrans Undecaprenyl-phosphate galactose phosphotransferase, WbaP. This model includes the enterobacterial enzymes, where the function is presumed to be identical to the S. typhimurium enzyme as well as a somewhat broader group which are likely to catalyze the same or highly similar reactions based on a phylogenetic tree-building analysis of the broader sugar transferase family. Most of these genes are found within large operons dedicated to the production of complex exopolysaccharides such as the enterobacterial O-antigen. The most likely heterogeneity would be in the precise nature of the sugar molecule transferred.
Probab=36.65 E-value=69 Score=29.57 Aligned_cols=53 Identities=17% Similarity=0.109 Sum_probs=42.3
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCC-CEEEECCHhHHh
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEI-PYCIVKGKSRLG 184 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~V-Py~iV~sK~~LG 184 (191)
|..+....+++..+..|+||.+....+....+-..|++.++ .+..+.+..++.
T Consensus 176 g~~~l~~~i~~~~id~ViIAip~~~~~~~~~ll~~l~~~~v~~V~~vP~~~e~~ 229 (456)
T TIGR03022 176 GADDALRLYARTRYAYVIVAMPGTQAEDMARLVRKLGALHFRNVLIVPSLFGLP 229 (456)
T ss_pred ChhHHHHHHHhCCCCEEEEecCCccHHHHHHHHHHHHhCCCeEEEEeCcccccc
Confidence 33677788898999999999876555666668889999999 999988877654
No 73
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=35.98 E-value=1e+02 Score=27.03 Aligned_cols=59 Identities=17% Similarity=0.103 Sum_probs=46.5
Q ss_pred ceeeechhHHHHHHHhc-CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhhC
Q 029589 127 IVVKYGLNHVTYLIEQN-KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVNI 188 (191)
Q Consensus 127 ~~L~~G~~~Vtk~Iekk-KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~G 188 (191)
..+..|.+.|..+++++ .+.-+++..+.. .+.. .+.......+++|..+.. ..|-.+.+
T Consensus 21 ~~~~~G~~~v~~al~~~~~i~~i~~~~~~~-~~~~-~~~~~~~~~~~~~~~v~~-~~l~~~~~ 80 (260)
T COG0566 21 EFLIEGEHAVLEALASGPKIVRILVTEGRL-PRFE-ELLALAAAKGIPVYVVSE-AILDKLSG 80 (260)
T ss_pred cEEEeeHHHHHHHHhcCCCceEEEEecccc-hhHH-HHHHHHHhcCCeEEEECH-HHHHHHhC
Confidence 48899999999999999 888888999887 2443 478888899999988765 44655443
No 74
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.71 E-value=93 Score=26.74 Aligned_cols=19 Identities=16% Similarity=0.302 Sum_probs=8.7
Q ss_pred HHHHHHhcCcceEEEecCC
Q 029589 136 VTYLIEQNKAQLVVIAHDV 154 (191)
Q Consensus 136 Vtk~IekkKAkLVVIA~Dv 154 (191)
+...+.+.++.+|+|+.|+
T Consensus 31 l~~~~~~~~~D~lli~GDi 49 (253)
T TIGR00619 31 LLEFAKAEQIDALLVAGDV 49 (253)
T ss_pred HHHHHHHcCCCEEEECCcc
Confidence 3334444445555555444
No 75
>PRK00098 GTPase RsgA; Reviewed
Probab=35.50 E-value=47 Score=29.28 Aligned_cols=17 Identities=29% Similarity=0.149 Sum_probs=9.5
Q ss_pred HHhcCCCEEEECCHhHH
Q 029589 167 CRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 167 C~k~~VPy~iV~sK~~L 183 (191)
++..++|+++|-+|.+|
T Consensus 107 ~~~~~ip~iIVlNK~DL 123 (298)
T PRK00098 107 AEANGIKPIIVLNKIDL 123 (298)
T ss_pred HHHCCCCEEEEEEhHHc
Confidence 44555555555555555
No 76
>PRK15116 sulfur acceptor protein CsdL; Provisional
Probab=35.43 E-value=56 Score=28.98 Aligned_cols=36 Identities=28% Similarity=0.349 Sum_probs=28.4
Q ss_pred hcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 142 QNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 142 kkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
.....+||.|.|- ..-...|-..|++++||++.+.+
T Consensus 119 ~~~~D~VIdaiD~--~~~k~~L~~~c~~~~ip~I~~gG 154 (268)
T PRK15116 119 SAGFSYVIDAIDS--VRPKAALIAYCRRNKIPLVTTGG 154 (268)
T ss_pred cCCCCEEEEcCCC--HHHHHHHHHHHHHcCCCEEEECC
Confidence 3468899999884 23455689999999999998865
No 77
>TIGR00035 asp_race aspartate racemase.
Probab=35.22 E-value=55 Score=27.54 Aligned_cols=43 Identities=12% Similarity=0.231 Sum_probs=33.1
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
.+.+..+.+++..+.+++||++... .++..+-+..+||++.+-
T Consensus 63 ~l~~~~~~L~~~g~d~iviaCNTah----~~~~~l~~~~~iPii~i~ 105 (229)
T TIGR00035 63 ILIDIAVKLENAGADFIIMPCNTAH----KFAEDIQKAIGIPLISMI 105 (229)
T ss_pred HHHHHHHHHHHcCCCEEEECCccHH----HHHHHHHHhCCCCEechH
Confidence 3556666778889999999999755 346788888899998753
No 78
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=34.88 E-value=1e+02 Score=26.53 Aligned_cols=45 Identities=9% Similarity=0.215 Sum_probs=35.1
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
+..+.+.|+..++..||...-.++ .....|..++++.|+|++.+.
T Consensus 195 l~~l~~~ik~~~v~~if~e~~~~~-k~~~~l~~la~~~~~~v~~l~ 239 (264)
T cd01020 195 IAAFQNAIKNRQIDALIVNPQQAS-SATTNITGLAKRSGVPVVEVT 239 (264)
T ss_pred HHHHHHHHHhCCCCEEEeCCCCCc-HHHHHHHHHHHHcCCCEEeec
Confidence 356777788889998888777765 665667788999999998763
No 79
>PRK05562 precorrin-2 dehydrogenase; Provisional
Probab=34.32 E-value=47 Score=28.77 Aligned_cols=35 Identities=26% Similarity=0.328 Sum_probs=28.8
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
.+.|||+|-| |+ ++-..+-..|+.+++++..+++.
T Consensus 85 g~~LViaATd-D~-~vN~~I~~~a~~~~~lvn~vd~p 119 (223)
T PRK05562 85 DKHLIVIATD-DE-KLNNKIRKHCDRLYKLYIDCSDY 119 (223)
T ss_pred CCcEEEECCC-CH-HHHHHHHHHHHHcCCeEEEcCCc
Confidence 5789999976 44 77777899999999999988774
No 80
>TIGR01544 HAD-SF-IE haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.
Probab=34.12 E-value=73 Score=28.55 Aligned_cols=33 Identities=24% Similarity=0.303 Sum_probs=23.0
Q ss_pred ccCChhhHHHHHhhhhcCCccc------HHHHHHHHHHH
Q 029589 79 KTLDKNLASSLFKLLLKYRPED------RAAKKERLLKR 111 (191)
Q Consensus 79 ~~l~~~~a~~l~kl~~kyrPEt------~~ekk~rl~~~ 111 (191)
..+..+-...+.+|.+||.|=+ .+||-.-..++
T Consensus 55 ~~~~~~~~~~~~~l~~~Y~PiE~d~~~~~~eK~~~m~eW 93 (277)
T TIGR01544 55 KLLTDECRKKLLQLKEKYYPIEVDPVLTVEEKYPYMVEW 93 (277)
T ss_pred CCCCHHHHHHHHHHHhhccceecCCCCChHHhhhHHHHH
Confidence 4456677788999999999954 45675444444
No 81
>cd07388 MPP_Tt1561 Thermus thermophilus Tt1561 and related proteins, metallophosphatase domain. This family includes bacterial proteins related to Tt1561 (also known as Aq1956 in Aquifex aeolicus), an uncharacterized Thermus thermophilus protein. The conserved domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets,
Probab=34.10 E-value=88 Score=26.87 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=27.6
Q ss_pred HHHHHHhcCcceEEEecCCCc-----cchhhhHHHHHHhcCCCEEEECCHhH
Q 029589 136 VTYLIEQNKAQLVVIAHDVDP-----IELVVWLPALCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 136 Vtk~IekkKAkLVVIA~DvdP-----~elv~~LpaLC~k~~VPy~iV~sK~~ 182 (191)
+...++...+.+||++.|... .++..++..+ ...++|+..|.+..+
T Consensus 23 l~~~~~~~~~D~vv~~GDl~~~g~~~~~~~~~l~~l-~~l~~pv~~V~GNhD 73 (224)
T cd07388 23 LVGLAPETGADAIVLIGNLLPKAAKSEDYAAFFRIL-GEAHLPTFYVPGPQD 73 (224)
T ss_pred HHHHHhhcCCCEEEECCCCCCCCCCHHHHHHHHHHH-HhcCCceEEEcCCCC
Confidence 333444467888888888843 2334433333 355678888877554
No 82
>cd01493 APPBP1_RUB Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain.
Probab=34.04 E-value=30 Score=32.65 Aligned_cols=40 Identities=15% Similarity=0.250 Sum_probs=28.2
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhh
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~ 185 (191)
...+||. .+.+. .....|-.+|++++||++.+.+..-.|.
T Consensus 112 ~fdiVI~-t~~~~-~~~~~L~~~c~~~~iPlI~~~s~G~~G~ 151 (425)
T cd01493 112 QFTVVIA-TNLPE-STLLRLADVLWSANIPLLYVRSYGLYGY 151 (425)
T ss_pred CCCEEEE-CCCCH-HHHHHHHHHHHHcCCCEEEEecccCEEE
Confidence 4456654 44444 3445589999999999999988776664
No 83
>cd01492 Aos1_SUMO Ubiquitin activating enzyme (E1) subunit Aos1. Aos1 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. Aos1 contains part of the adenylation domain.
Probab=33.85 E-value=31 Score=28.67 Aligned_cols=37 Identities=19% Similarity=0.298 Sum_probs=28.0
Q ss_pred cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHh
Q 029589 143 NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 143 kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
....+||.+.| +.+....+-.+|++++||++......
T Consensus 109 ~~~dvVi~~~~--~~~~~~~ln~~c~~~~ip~i~~~~~G 145 (197)
T cd01492 109 SQFDVVVATEL--SRAELVKINELCRKLGVKFYATGVHG 145 (197)
T ss_pred hCCCEEEECCC--CHHHHHHHHHHHHHcCCCEEEEEecC
Confidence 35678888866 34566679999999999998766543
No 84
>cd04104 p47_IIGP_like p47 (47-kDa) family. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protei
Probab=33.82 E-value=74 Score=25.77 Aligned_cols=39 Identities=15% Similarity=0.063 Sum_probs=26.0
Q ss_pred cceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 145 AQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 145 AkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
+.++++-.|.+..+....+-..+++++.|+++|.+|.++
T Consensus 81 ~d~~l~v~~~~~~~~d~~~~~~l~~~~~~~ilV~nK~D~ 119 (197)
T cd04104 81 YDFFIIISSTRFSSNDVKLAKAIQCMGKKFYFVRTKVDR 119 (197)
T ss_pred cCEEEEEeCCCCCHHHHHHHHHHHHhCCCEEEEEecccc
Confidence 344444334444444445666777789999999999987
No 85
>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
Probab=33.58 E-value=90 Score=22.83 Aligned_cols=42 Identities=26% Similarity=0.107 Sum_probs=28.7
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhh
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~ 185 (191)
.+.++++..|++..+-......+....++|++++-+|.++..
T Consensus 80 ~~~~~v~v~d~~~~~~~~~~~~~~~~~~~~vi~v~nK~D~~~ 121 (157)
T cd04164 80 EADLVLFVIDASRGLDEEDLEILELPADKPIIVVLNKSDLLP 121 (157)
T ss_pred hCCEEEEEEECCCCCCHHHHHHHHhhcCCCEEEEEEchhcCC
Confidence 567777777877433333344444467899999999988753
No 86
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=33.56 E-value=52 Score=25.15 Aligned_cols=49 Identities=8% Similarity=0.025 Sum_probs=38.0
Q ss_pred eechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 130 KYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 130 ~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
..++.++...++...+.+|+++-++.- ....+..+|..+|||+..++..
T Consensus 36 a~~~~e~~~~~~~~~~DvIll~PQi~~--~~~~i~~~~~~~~ipv~~I~~~ 84 (104)
T PRK09590 36 AITATEGEKAIAAAEYDLYLVSPQTKM--YFKQFEEAGAKVGKPVVQIPPQ 84 (104)
T ss_pred EecHHHHHHhhccCCCCEEEEChHHHH--HHHHHHHHhhhcCCCEEEeCHH
Confidence 456777777777778999999988754 3345789999999999988753
No 87
>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=33.29 E-value=1.1e+02 Score=19.79 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=33.8
Q ss_pred hHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
..+...+++..+..-++=-|.++ +....|..+-....+|.++++|+
T Consensus 13 ~~~~~~L~~~~i~y~~~dv~~~~-~~~~~l~~~~g~~~~P~v~i~g~ 58 (60)
T PF00462_consen 13 KKAKEFLDEKGIPYEEVDVDEDE-EAREELKELSGVRTVPQVFIDGK 58 (60)
T ss_dssp HHHHHHHHHTTBEEEEEEGGGSH-HHHHHHHHHHSSSSSSEEEETTE
T ss_pred HHHHHHHHHcCCeeeEcccccch-hHHHHHHHHcCCCccCEEEECCE
Confidence 45667778888887777666665 55556677777789999999874
No 88
>PF03618 Kinase-PPPase: Kinase/pyrophosphorylase; InterPro: IPR005177 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.; GO: 0005524 ATP binding, 0016772 transferase activity, transferring phosphorus-containing groups
Probab=32.95 E-value=1.2e+02 Score=26.86 Aligned_cols=41 Identities=32% Similarity=0.408 Sum_probs=31.1
Q ss_pred EEEecCCCccchhhhHHHHHHhcCCCEEEECCHh--HHhhhhCC
Q 029589 148 VVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS--RLGSVNIL 189 (191)
Q Consensus 148 VVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~--~LG~a~Gi 189 (191)
+|+.-=||+ ++...+-..|+++|||++.+-+-- .|....|.
T Consensus 55 iV~~Tlv~~-~lr~~l~~~~~~~~i~~~Dll~~~l~~l~~~lg~ 97 (255)
T PF03618_consen 55 IVFYTLVDP-ELREYLEEFCREHGIPCVDLLGPLLSALEEFLGQ 97 (255)
T ss_pred EEEEeCCCH-HHHHHHHHHHHhcCCCEEeccHHHHHHHHHHHCc
Confidence 455555778 899999999999999999987743 45555554
No 89
>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=32.84 E-value=33 Score=23.97 Aligned_cols=29 Identities=17% Similarity=0.121 Sum_probs=26.6
Q ss_pred hHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 162 WLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 162 ~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
..-.++++.|+++..+..-.+++.-||+.
T Consensus 16 ~~ek~lk~~gi~~~liP~P~~i~~~CG~a 44 (73)
T PF11823_consen 16 KAEKLLKKNGIPVRLIPTPREISAGCGLA 44 (73)
T ss_pred HHHHHHHHCCCcEEEeCCChhccCCCCEE
Confidence 46889999999999999999999999975
No 90
>cd00755 YgdL_like Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown.
Probab=32.28 E-value=93 Score=26.81 Aligned_cols=36 Identities=36% Similarity=0.353 Sum_probs=28.6
Q ss_pred hcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 142 QNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 142 kkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
.....+||.|.|-- +....|-.+|.+++||++...+
T Consensus 100 ~~~~D~VvdaiD~~--~~k~~L~~~c~~~~ip~I~s~g 135 (231)
T cd00755 100 GGDPDFVVDAIDSI--RAKVALIAYCRKRKIPVISSMG 135 (231)
T ss_pred cCCCCEEEEcCCCH--HHHHHHHHHHHHhCCCEEEEeC
Confidence 44588999998854 3445689999999999998765
No 91
>PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A.
Probab=31.72 E-value=52 Score=24.19 Aligned_cols=41 Identities=17% Similarity=0.239 Sum_probs=25.7
Q ss_pred HHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
....+++.+ +..+||..+..|.+- +-.+|++.+||++..+.
T Consensus 53 i~~~a~~~~-i~~iIltg~~~~~~~---v~~la~~~~i~vi~t~~ 93 (105)
T PF07085_consen 53 IQLAAIEAG-IACIILTGGLEPSEE---VLELAKELGIPVISTPY 93 (105)
T ss_dssp HHHHHCCTT-ECEEEEETT----HH---HHHHHHHHT-EEEE-SS
T ss_pred HHHHHHHhC-CCEEEEeCCCCCCHH---HHHHHHHCCCEEEEECC
Confidence 344555555 788888888777443 57899999999988764
No 92
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=31.17 E-value=50 Score=24.72 Aligned_cols=42 Identities=12% Similarity=0.162 Sum_probs=31.0
Q ss_pred hHHHHHHHhcCcceEEEecC--CCc-cchhhhHHHHHHhcCCCEE
Q 029589 134 NHVTYLIEQNKAQLVVIAHD--VDP-IELVVWLPALCRKMEIPYC 175 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~D--vdP-~elv~~LpaLC~k~~VPy~ 175 (191)
..+..+|++++..+||-.-+ -+. .+--..+...|-+++|||+
T Consensus 61 ~~i~~~i~~~~idlVIn~~~~~~~~~~~~~~~iRr~Av~~~ip~i 105 (116)
T cd01423 61 PSLRELLAEGKIDLVINLPSNRGKRVLDNDYVMRRAADDFAVPLI 105 (116)
T ss_pred hhHHHHHHcCCceEEEECCCCCCCccccCcEeeehhhHhhCCccc
Confidence 67999999999999988543 222 1112357889999999996
No 93
>KOG1615 consensus Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=30.81 E-value=58 Score=28.62 Aligned_cols=47 Identities=13% Similarity=0.259 Sum_probs=39.9
Q ss_pred cCCCceeeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCE
Q 029589 123 AKKPIVVKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPY 174 (191)
Q Consensus 123 ~k~p~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy 174 (191)
.++|+.|..|+.+..+.+...-+++++|..--.+ ++--.....|||+
T Consensus 83 ~~~k~~lT~Gi~eLv~~L~~~~~~v~liSGGF~~-----~i~~Va~~Lgi~~ 129 (227)
T KOG1615|consen 83 IKQKPTLTPGIRELVSRLHARGTQVYLISGGFRQ-----LIEPVAEQLGIPK 129 (227)
T ss_pred hcCCCccCCCHHHHHHHHHHcCCeEEEEcCChHH-----HHHHHHHHhCCcH
Confidence 4567889999999999999999999999987655 4555678899999
No 94
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=30.74 E-value=92 Score=28.12 Aligned_cols=48 Identities=21% Similarity=0.322 Sum_probs=34.2
Q ss_pred hhHHHHHHHhcCcceEEEecCCCcc---------chhhhHHHHHHhcCCCEEEECCHh
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPI---------ELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~---------elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
..++...+...++.+||||.|+=.. ....+|-.||. -|||++.+.|--
T Consensus 29 f~~~l~~a~~~~vD~vliAGDlFd~~~Ps~~a~~~~~~~l~~l~~-~~Ipv~~I~GNH 85 (390)
T COG0420 29 FDELLEIAKEEKVDFVLIAGDLFDTNNPSPRALKLFLEALRRLKD-AGIPVVVIAGNH 85 (390)
T ss_pred HHHHHHHHHHccCCEEEEccccccCCCCCHHHHHHHHHHHHHhcc-CCCcEEEecCCC
Confidence 5678888888899999999998442 12334455555 679999887754
No 95
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=30.42 E-value=54 Score=22.19 Aligned_cols=32 Identities=9% Similarity=0.098 Sum_probs=26.0
Q ss_pred hhhhHHHHHHhcCCC-------EEEECCHhHHhhhhCCC
Q 029589 159 LVVWLPALCRKMEIP-------YCIVKGKSRLGSVNILN 190 (191)
Q Consensus 159 lv~~LpaLC~k~~VP-------y~iV~sK~~LG~a~Gi~ 190 (191)
+..+|-.+|+..|.+ +.+--+.++|+..+|++
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~s 41 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVS 41 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSC
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCC
Confidence 456788888888764 66778999999999986
No 96
>COG0252 AnsB L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D [Amino acid transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=30.34 E-value=93 Score=28.81 Aligned_cols=47 Identities=17% Similarity=0.277 Sum_probs=39.9
Q ss_pred HHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHh
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
.|.+.+..+.+.=|||.|-.|-.+...++-+|+-+.+.|++++.++-
T Consensus 91 ~I~~~~~~~~~dGvVItHGTDTmeeTA~~L~l~l~~~kPVVlTGamr 137 (351)
T COG0252 91 AINEALDDGDVDGVVITHGTDTMEETAFFLSLTLNTPKPVVLTGAMR 137 (351)
T ss_pred HHHHHhccCCCCeEEEeCCCchHHHHHHHHHHHhcCCCCEEEeCCCC
Confidence 45556666666678999999999999999999999999999998763
No 97
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=29.73 E-value=1.1e+02 Score=25.85 Aligned_cols=44 Identities=16% Similarity=0.223 Sum_probs=30.7
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
+.++.+.+++++++.||.-...++ ..+-.|+++.|+|++.+...
T Consensus 188 l~~l~~~ik~~~v~~i~~e~~~~~----~~~~~la~~~g~~vv~ld~l 231 (256)
T PF01297_consen 188 LAELIKLIKENKVKCIFTEPQFSS----KLAEALAKETGVKVVYLDPL 231 (256)
T ss_dssp HHHHHHHHHHTT-SEEEEETTS-T----HHHHHHHHCCT-EEEESSTT
T ss_pred HHHHHHHhhhcCCcEEEecCCCCh----HHHHHHHHHcCCcEEEeCCC
Confidence 456777788889888888766655 23566799999999887765
No 98
>TIGR03603 cyclo_dehy_ocin bacteriocin biosynthesis cyclodehydratase, SagC family. Members of this protein family include enzymes related to SagC, a cyclodehydratase involved in the biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. Note that this model does not find all possible examples of bacteriocin biosynthesis cyclodehydratases, an in particular misses the E. coli plasmid protein McbB of microcin B17 biosynthesis.
Probab=29.31 E-value=67 Score=28.99 Aligned_cols=40 Identities=20% Similarity=0.330 Sum_probs=31.5
Q ss_pred HHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE
Q 029589 136 VTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 136 Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV 177 (191)
+..++ +...+||.+.|-....+..++-..|.++++|+++.
T Consensus 145 ~~~li--~~~DlVid~tDn~~~r~L~~iN~ac~~~~~PlV~g 184 (318)
T TIGR03603 145 LKDLL--KDYNYIIICTEHSNISLLRGLNKLSKETKKPNTIA 184 (318)
T ss_pred HHHHh--CCCCEEEECCCCccHhHHHHHHHHHHHHCCCEEEE
Confidence 34444 44899999999877667667899999999999853
No 99
>TIGR03013 EpsB_2 sugar transferase, PEP-CTERM system associated. Members of this protein family belong to the family of bacterial sugar transferases (pfam02397). Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria (notable exceptions appear to include Magnetococcus sp. MC-1 and Myxococcus xanthus DK 1622 ). These genes are generally found near one or more of the PrsK, PrsR or PrsT genes that have been related to the PEP-CTERM system by phylogenetic profiling methods. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species. These proteins are homologs of the EpsB protien found in Methylobacillus sp. strain 12S, which is also associated with a PEP-CTERM system, but of a distinct type. A name which appears attached to a number of genes (by transitive annotation) in this family is "undecapre
Probab=29.30 E-value=1.2e+02 Score=28.04 Aligned_cols=52 Identities=15% Similarity=-0.004 Sum_probs=39.2
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
+..+....+++..+.-|+||.+....+.....-..|+.++|.+.++.+-.++
T Consensus 174 ~~~dl~~~v~~~~Id~ViIAlp~~~~~~~~~~l~~~~~~gv~V~ivP~~~e~ 225 (442)
T TIGR03013 174 NGDGLVEYVLRHRIDEIVIALDERRGSLPVDELLECKLSGIEVVDAPSFFER 225 (442)
T ss_pred CHHHHHHHHHhCCCCEEEEECchhhcchHHHHHHHHHhCCCEEEEcchHHHH
Confidence 3567888999999999999987544332112346799999999999887764
No 100
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=29.19 E-value=1.7e+02 Score=25.32 Aligned_cols=54 Identities=11% Similarity=0.103 Sum_probs=37.5
Q ss_pred CCCceeeech-----hHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 124 KKPIVVKYGL-----NHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 124 k~p~~L~~G~-----~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
-||.++..|. +.+.++++ ++.|+++-.=.--..-...|+..+...|.++++|.-
T Consensus 149 lrP~vV~FGE~~~~~~~~~~~~~--~~DlllviGTSl~V~pa~~l~~~a~~~g~~vi~IN~ 207 (242)
T PTZ00408 149 LRPHIVWFGEMPLYMDEIESVMS--KTDLFVAVGTSGNVYPAAGFVGRAQFYGATTLELNL 207 (242)
T ss_pred CCCCEEEcCCCCCcHHHHHHHHH--hCCEEEEEccCCccccHHHHHHHHHHcCCeEEEECC
Confidence 5889999999 35555644 467766544332334456688899999999988764
No 101
>PRK01889 GTPase RsgA; Reviewed
Probab=28.60 E-value=69 Score=29.14 Aligned_cols=26 Identities=23% Similarity=0.069 Sum_probs=19.9
Q ss_pred hhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 159 LVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 159 lv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
....+-.+|+..|+|.++|-+|.+|.
T Consensus 130 ~ldr~L~~a~~~~i~piIVLNK~DL~ 155 (356)
T PRK01889 130 RIERYLALAWESGAEPVIVLTKADLC 155 (356)
T ss_pred HHHHHHHHHHHcCCCEEEEEEChhcC
Confidence 34456677888889999998888884
No 102
>PRK00865 glutamate racemase; Provisional
Probab=28.35 E-value=1e+02 Score=26.64 Aligned_cols=42 Identities=21% Similarity=0.331 Sum_probs=31.3
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV 177 (191)
+.+....+++..+..+|||++.++. .++..|-+..+||++-+
T Consensus 56 ~~~~~~~L~~~g~d~iVIaCNTa~~---~~l~~lr~~~~iPvigi 97 (261)
T PRK00865 56 TLEIVEFLLEYGVKMLVIACNTASA---VALPDLRERYDIPVVGI 97 (261)
T ss_pred HHHHHHHHHhCCCCEEEEeCchHHH---HHHHHHHHhCCCCEEee
Confidence 3455566777889999999997652 24677878889998874
No 103
>cd01822 Lysophospholipase_L1_like Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity.
Probab=28.15 E-value=1.6e+02 Score=22.38 Aligned_cols=46 Identities=13% Similarity=0.291 Sum_probs=29.7
Q ss_pred chhHHHHHHHhcCcceEEEecCCCc-------cchhhhHHHHHHhcCCCEEEE
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDP-------IELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP-------~elv~~LpaLC~k~~VPy~iV 177 (191)
++.++...++...+.++++.--..+ ..+...+..+|++++++|+..
T Consensus 89 ~l~~li~~~~~~~~~vil~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~d~ 141 (177)
T cd01822 89 NLRQMIETAQARGAPVLLVGMQAPPNYGPRYTRRFAAIYPELAEEYGVPLVPF 141 (177)
T ss_pred HHHHHHHHHHHCCCeEEEEecCCCCccchHHHHHHHHHHHHHHHHcCCcEech
Confidence 3445666666667777777532222 134456788999999998864
No 104
>TIGR02356 adenyl_thiF thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the more widely distributed clade of ThiF proteins such found in E. coli.
Probab=28.13 E-value=79 Score=26.23 Aligned_cols=36 Identities=17% Similarity=0.135 Sum_probs=28.0
Q ss_pred cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 143 NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 143 kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
..+.+||.|.|-- +...++-.+|+++++|++....-
T Consensus 110 ~~~D~Vi~~~d~~--~~r~~l~~~~~~~~ip~i~~~~~ 145 (202)
T TIGR02356 110 NNVDLVLDCTDNF--ATRYLINDACVALGTPLISAAVV 145 (202)
T ss_pred hCCCEEEECCCCH--HHHHHHHHHHHHcCCCEEEEEec
Confidence 3678999888753 45556899999999999987643
No 105
>cd01859 MJ1464 MJ1464. This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.
Probab=27.73 E-value=84 Score=24.09 Aligned_cols=16 Identities=25% Similarity=0.312 Sum_probs=8.4
Q ss_pred HHHhcCCCEEEECCHh
Q 029589 166 LCRKMEIPYCIVKGKS 181 (191)
Q Consensus 166 LC~k~~VPy~iV~sK~ 181 (191)
+++..+.|++.+..+.
T Consensus 65 ~~~~~~~~~~~iSa~~ 80 (156)
T cd01859 65 IKESEGIPVVYVSAKE 80 (156)
T ss_pred HHHhCCCcEEEEEccc
Confidence 3444556666555444
No 106
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=27.65 E-value=1.5e+02 Score=25.51 Aligned_cols=42 Identities=10% Similarity=0.195 Sum_probs=27.9
Q ss_pred hHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
..+.+.|++.++.+||.....++ . .+..++++.|+|++.+..
T Consensus 207 ~~l~~~ik~~~v~~if~e~~~~~-~---~~~~la~~~g~~v~~ld~ 248 (266)
T cd01018 207 KRLIDLAKEKGVRVVFVQPQFST-K---SAEAIAREIGAKVVTIDP 248 (266)
T ss_pred HHHHHHHHHcCCCEEEEcCCCCc-H---HHHHHHHHcCCeEEEeCC
Confidence 45666677777777776665555 2 245777788888777654
No 107
>cd07396 MPP_Nbla03831 Homo sapiens Nbla03831 and related proteins, metallophosphatase domain. Nbla03831 (also known as LOC56985) is an uncharacterized Homo sapiens protein with a domain that belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.
Probab=27.24 E-value=1.5e+02 Score=25.31 Aligned_cols=51 Identities=16% Similarity=0.078 Sum_probs=35.6
Q ss_pred hHHHHHHHhcCcceEEEecCCCccch------hhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIEL------VVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~el------v~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
..++..|.+.++.+||++.|.-.... ...+-..+...++|+..+.|--+..
T Consensus 30 ~~~i~~i~~~~~d~vv~~GDlv~~~~~~~~~~~~~~~~~l~~l~~p~~~v~GNHD~~ 86 (267)
T cd07396 30 EEAVEEWNRESLDFVVQLGDIIDGDNARAEEALDAVLAILDRLKGPVHHVLGNHDLY 86 (267)
T ss_pred HHHHHHHHcCCCCEEEECCCeecCCCchHHHHHHHHHHHHHhcCCCEEEecCccccc
Confidence 44566666677999999999853222 2223556678899999999877654
No 108
>PRK11018 hypothetical protein; Provisional
Probab=27.03 E-value=1.8e+02 Score=20.67 Aligned_cols=41 Identities=17% Similarity=0.118 Sum_probs=26.2
Q ss_pred HHHHHHHhcCcc--eEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 135 HVTYLIEQNKAQ--LVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 135 ~Vtk~IekkKAk--LVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
.+.+++++-+.. |.|++.| |... ..+|.+|+++|-.+..+.
T Consensus 24 ~~kk~l~~l~~G~~L~V~~d~--~~a~-~di~~~~~~~G~~v~~~~ 66 (78)
T PRK11018 24 ATLEALPQLKKGEILEVVSDC--PQSI-NNIPLDARNHGYTVLDIQ 66 (78)
T ss_pred HHHHHHHhCCCCCEEEEEeCC--ccHH-HHHHHHHHHcCCEEEEEE
Confidence 345566554422 5566665 3334 458999999999887543
No 109
>PRK05690 molybdopterin biosynthesis protein MoeB; Provisional
Probab=26.94 E-value=50 Score=28.43 Aligned_cols=35 Identities=17% Similarity=0.069 Sum_probs=27.5
Q ss_pred cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 143 NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 143 kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
....+||.|.|- + +...++-.+|.++++|++....
T Consensus 121 ~~~DiVi~~~D~-~-~~r~~ln~~~~~~~ip~v~~~~ 155 (245)
T PRK05690 121 AGHDLVLDCTDN-V-ATRNQLNRACFAAKKPLVSGAA 155 (245)
T ss_pred hcCCEEEecCCC-H-HHHHHHHHHHHHhCCEEEEeee
Confidence 357899999884 3 5556789999999999987543
No 110
>PF12850 Metallophos_2: Calcineurin-like phosphoesterase superfamily domain; InterPro: IPR024654 Domains in this entry are members of the calcineurin-like phosphoesterase domain superfamily [].; PDB: 2GJU_A 1Z2W_A 1Z2X_B 3PSO_B 3PSN_B 1W24_A 2R17_B 3QFN_B 3QFO_A 3QFM_A ....
Probab=26.89 E-value=1.1e+02 Score=22.79 Aligned_cols=40 Identities=33% Similarity=0.571 Sum_probs=22.5
Q ss_pred HHHHHHHhcCcceEEEecCC-CccchhhhHHHHHHhcCCCEEEECCHhH
Q 029589 135 HVTYLIEQNKAQLVVIAHDV-DPIELVVWLPALCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~Dv-dP~elv~~LpaLC~k~~VPy~iV~sK~~ 182 (191)
.+...+ .++.+||++.|. ++.++...+..+ |+..|.|--+
T Consensus 18 ~~~~~~--~~~d~vi~~GDi~~~~~~~~~~~~~------~~~~v~GNHD 58 (156)
T PF12850_consen 18 AVLEYI--NEPDFVIILGDIFDPEEVLELLRDI------PVYVVRGNHD 58 (156)
T ss_dssp HHHHHH--TTESEEEEES-SCSHHHHHHHHHHH------EEEEE--CCH
T ss_pred HHHHHh--cCCCEEEECCCchhHHHHHHHHhcC------CEEEEeCCcc
Confidence 344444 569999999998 654444433222 7777766443
No 111
>cd01866 Rab2 Rab2 subfamily. Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur
Probab=26.83 E-value=66 Score=24.72 Aligned_cols=18 Identities=11% Similarity=0.137 Sum_probs=9.8
Q ss_pred HHHHHHhcCCCEEEECCH
Q 029589 163 LPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 163 LpaLC~k~~VPy~iV~sK 180 (191)
...+|..++++|..+..+
T Consensus 132 ~~~~~~~~~~~~~e~Sa~ 149 (168)
T cd01866 132 GEAFAKEHGLIFMETSAK 149 (168)
T ss_pred HHHHHHHcCCEEEEEeCC
Confidence 345556666666555443
No 112
>PRK10200 putative racemase; Provisional
Probab=26.82 E-value=90 Score=26.61 Aligned_cols=42 Identities=12% Similarity=0.197 Sum_probs=32.8
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
+-+..+.+++..+.+++||+|... .++..+-...+||++.+-
T Consensus 64 l~~~~~~L~~~g~~~iviaCNTah----~~~~~l~~~~~iPii~ii 105 (230)
T PRK10200 64 LAEAALGLQRAGAEGIVLCTNTMH----KVADAIESRCSLPFLHIA 105 (230)
T ss_pred HHHHHHHHHHcCCCEEEECCchHH----HHHHHHHHhCCCCEeehH
Confidence 445667888888999999999755 456888888899988743
No 113
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=26.79 E-value=1.5e+02 Score=22.92 Aligned_cols=48 Identities=19% Similarity=0.389 Sum_probs=34.4
Q ss_pred echhHHHHHHHhcCcceEEEecCCCc-----cchhhhHHHHHHhcCCCEEEECC
Q 029589 131 YGLNHVTYLIEQNKAQLVVIAHDVDP-----IELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 131 ~G~~~Vtk~IekkKAkLVVIA~DvdP-----~elv~~LpaLC~k~~VPy~iV~s 179 (191)
-|.+.....++.|++..||+. +.|= .+...++-.||+.+||.++++..
T Consensus 55 p~l~~ll~~~~~g~vd~vvv~-~ldRl~R~~~d~~~~~~~l~~~~gv~l~~~~~ 107 (140)
T cd03770 55 PGFNRMIEDIEAGKIDIVIVK-DMSRLGRNYLKVGLYMEILFPKKGVRFIAIND 107 (140)
T ss_pred HHHHHHHHHHHcCCCCEEEEe-ccchhccCHHHHHHHHHHHHhhcCcEEEEecC
Confidence 389999999999998877664 3432 23344566666667999998875
No 114
>PF00205 TPP_enzyme_M: Thiamine pyrophosphate enzyme, central domain; InterPro: IPR012000 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This central domain of TPP enzymes contains a 2-fold Rossman fold. ; GO: 0000287 magnesium ion binding, 0030976 thiamine pyrophosphate binding; PDB: 1OZH_C 1OZF_B 1OZG_B 2Q29_B 2Q28_A 2Q27_B 1OVM_B 1PVD_A 1PYD_B 2VK1_C ....
Probab=26.64 E-value=56 Score=24.84 Aligned_cols=46 Identities=15% Similarity=0.232 Sum_probs=31.5
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
++++..+|.+-+-=++++...+.-.....-+-.|++..|+|++...
T Consensus 1 i~~~~~~L~~A~rP~il~G~g~~~~~a~~~l~~lae~~~~Pv~~t~ 46 (137)
T PF00205_consen 1 IDEAADLLSSAKRPVILAGRGARRSGAAEELRELAEKLGIPVATTP 46 (137)
T ss_dssp HHHHHHHHHH-SSEEEEE-HHHHHTTCHHHHHHHHHHHTSEEEEEG
T ss_pred CHHHHHHHHhCCCEEEEEcCCcChhhHHHHHHHHHHHHCCCEEecC
Confidence 3566777777776677777666533455668999999999997643
No 115
>TIGR02355 moeB molybdopterin synthase sulfurylase MoeB. This model describes the molybdopterin biosynthesis protein MoeB in E. coli and related species. The enzyme covalently modifies the molybdopterin synthase MoaD by sulfurylation. This enzyme is closely related to ThiF, a thiamine biosynthesis enzyme that modifies ThiS by an analogous adenylation. Both MoeB and ThiF belong to the HesA/MoeB/ThiF family (pfam00899).
Probab=26.62 E-value=80 Score=27.16 Aligned_cols=35 Identities=20% Similarity=0.193 Sum_probs=27.6
Q ss_pred cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 143 NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 143 kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
..+.+||.|.|-- +...+|-.+|.+++||++....
T Consensus 113 ~~~DlVvd~~D~~--~~r~~ln~~~~~~~ip~v~~~~ 147 (240)
T TIGR02355 113 AEHDIVVDCTDNV--EVRNQLNRQCFAAKVPLVSGAA 147 (240)
T ss_pred hcCCEEEEcCCCH--HHHHHHHHHHHHcCCCEEEEEe
Confidence 3578999898863 4556789999999999997543
No 116
>TIGR00157 ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).
Probab=26.44 E-value=65 Score=27.59 Aligned_cols=18 Identities=28% Similarity=0.229 Sum_probs=9.0
Q ss_pred HHHhcCCCEEEECCHhHH
Q 029589 166 LCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 166 LC~k~~VPy~iV~sK~~L 183 (191)
+++..++|.++|.+|.+|
T Consensus 62 ~~~~~~i~~vIV~NK~DL 79 (245)
T TIGR00157 62 VAEAQNIEPIIVLNKIDL 79 (245)
T ss_pred HHHHCCCCEEEEEECccc
Confidence 344445555555555554
No 117
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=26.41 E-value=1.5e+02 Score=27.60 Aligned_cols=46 Identities=9% Similarity=0.200 Sum_probs=24.7
Q ss_pred hHHHHHHHhcCcceEEEecCCCccch---------hhhHHHHHHhcCCCEEEECCH
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIEL---------VVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~el---------v~~LpaLC~k~~VPy~iV~sK 180 (191)
+.+...+..-++.+||||.|+-.... ..++..|. +.++|+++|.|-
T Consensus 29 ~~l~~~i~~~~~D~viIaGDifD~~~p~~~a~~~~~~~l~~L~-~~~~~v~~I~GN 83 (407)
T PRK10966 29 DWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQ-QTGCQLVVLAGN 83 (407)
T ss_pred HHHHHHHHhcCCCEEEECCccccCCCCcHHHHHHHHHHHHHHH-hcCCcEEEEcCC
Confidence 34555566667777777777654211 12223333 346777766554
No 118
>PHA02546 47 endonuclease subunit; Provisional
Probab=26.36 E-value=1.7e+02 Score=26.34 Aligned_cols=50 Identities=8% Similarity=0.123 Sum_probs=34.3
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccc------hhhhHHH----HHHhcCCCEEEECCHhH
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIE------LVVWLPA----LCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~e------lv~~Lpa----LC~k~~VPy~iV~sK~~ 182 (191)
++++...++..++.+||||.|+=... ...++.. +-.+.|||++++.|--+
T Consensus 28 l~~ii~~a~~~~vD~VliaGDlfD~~~~~~~~~~~~~~~~l~~~L~~~gi~v~~I~GNHD 87 (340)
T PHA02546 28 IKQAIEYSKAHGITTWIQLGDTFDVRKAITQNTMNFVREKIFDLLKEAGITLHVLVGNHD 87 (340)
T ss_pred HHHHHHHHHHcCCCEEEECCcccCCCCCCCHHHHHHHHHHHHHHHHHCCCeEEEEccCCC
Confidence 56777788888999999999986532 1123333 23456899999877654
No 119
>cd07392 MPP_PAE1087 Pyrobaculum aerophilum PAE1087 and related proteins, metallophosphatase domain. PAE1087 is an uncharacterized Pyrobaculum aerophilum protein with a metallophosphatase domain. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordina
Probab=26.26 E-value=1.3e+02 Score=23.16 Aligned_cols=43 Identities=21% Similarity=0.373 Sum_probs=28.1
Q ss_pred HHHhcCcceEEEecCCCccc---hhhhHHHHHHhcCCCEEEECCHhH
Q 029589 139 LIEQNKAQLVVIAHDVDPIE---LVVWLPALCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 139 ~IekkKAkLVVIA~DvdP~e---lv~~LpaLC~k~~VPy~iV~sK~~ 182 (191)
.++..++.+||++.|..... ....+ ......++|+++|.|--+
T Consensus 18 ~~~~~~~D~vv~~GDl~~~~~~~~~~~~-~~l~~~~~p~~~v~GNHD 63 (188)
T cd07392 18 ILKAEEADAVIVAGDITNFGGKEAAVEI-NLLLAIGVPVLAVPGNCD 63 (188)
T ss_pred HhhccCCCEEEECCCccCcCCHHHHHHH-HHHHhcCCCEEEEcCCCC
Confidence 45567788999999974422 12223 555667888888877544
No 120
>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=25.99 E-value=73 Score=29.68 Aligned_cols=38 Identities=29% Similarity=0.453 Sum_probs=33.2
Q ss_pred HHHHHHHHhhhcCCCcc---ccccccCChhhHHHHHhhhhc
Q 029589 58 QRQRRILRQRLKVPPAL---NQFTKTLDKNLASSLFKLLLK 95 (191)
Q Consensus 58 Qrq~~il~~rlKvppai---nqf~~~l~~~~a~~l~kl~~k 95 (191)
|+||--..+.|=.-|.| +-=|.+||.+|+.+++.|+..
T Consensus 146 QKQRVaIARALa~~P~iLL~DEaTSALDP~TT~sIL~LL~~ 186 (339)
T COG1135 146 QKQRVAIARALANNPKILLCDEATSALDPETTQSILELLKD 186 (339)
T ss_pred hhhHHHHHHHHhcCCCEEEecCccccCChHHHHHHHHHHHH
Confidence 88998888888888877 666999999999999999954
No 121
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=25.88 E-value=51 Score=26.67 Aligned_cols=33 Identities=18% Similarity=0.394 Sum_probs=22.4
Q ss_pred EEEecCCCc-c--chhhhHHHHHHhcCCCEEEECCH
Q 029589 148 VVIAHDVDP-I--ELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 148 VVIA~DvdP-~--elv~~LpaLC~k~~VPy~iV~sK 180 (191)
.|+.+.... . .....+|+.|+.+||||+....+
T Consensus 119 ~VVT~E~~~~~~~~~~~KIPdvC~~~gV~ci~~~~~ 154 (162)
T PF14367_consen 119 TVVTHEVSNPNKKKKKIKIPDVCEHFGVPCINLFEF 154 (162)
T ss_pred EEEccCCCCCCCCccCCCCChhHHhCCCcCCCHHHH
Confidence 666766662 2 11245899999999999865443
No 122
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=25.79 E-value=1.2e+02 Score=23.10 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.2
Q ss_pred ceEEEecCCCccchhhhHHHHHHhc--CCCEEEECC
Q 029589 146 QLVVIAHDVDPIELVVWLPALCRKM--EIPYCIVKG 179 (191)
Q Consensus 146 kLVVIA~DvdP~elv~~LpaLC~k~--~VPy~iV~s 179 (191)
.+++||+|-|..+++. +-..+.+. |..++--.+
T Consensus 1 ~~~l~a~d~dK~~~~~-~a~~~~~ll~Gf~i~AT~g 35 (115)
T cd01422 1 RIALIAHDNKKEDLVE-FVKQHQELLSRHRLVATGT 35 (115)
T ss_pred CEeEEecccchHHHHH-HHHHHHHHhcCCEEEEech
Confidence 3789999999988876 45555555 665544433
No 123
>TIGR02342 chap_CCT_delta T-complex protein 1, delta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=25.71 E-value=1.7e+02 Score=27.86 Aligned_cols=51 Identities=10% Similarity=0.045 Sum_probs=33.8
Q ss_pred HHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhh
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGS 185 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~ 185 (191)
.....|.+..+.+|+++.+++..-+-...-.+|.++||-.+..-++.+|-+
T Consensus 264 ~~v~~i~~~g~~lvi~~~~I~~~~l~~l~~~~l~~~~I~av~~v~~~~Ler 314 (517)
T TIGR02342 264 NIVKKIKKTGCNVLLIQKSILRDAVNDLALHFLAKMKIMVVKDIEREEVEF 314 (517)
T ss_pred HHHHHHHhcCCCEEEECCCcccccccHHHHHHHhhCCceEEecCCHHHHHH
Confidence 344455555678899988886544444567788888888887766544433
No 124
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of 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 thought 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=25.71 E-value=2.2e+02 Score=19.49 Aligned_cols=40 Identities=20% Similarity=0.304 Sum_probs=25.9
Q ss_pred HHHHHHhcCc--ceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 136 VTYLIEQNKA--QLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 136 Vtk~IekkKA--kLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
+-+++++-.. .|.|++.| |... .-+|.+|+++|-.+..+.
T Consensus 16 ~k~~l~~l~~G~~l~V~~dd--~~s~-~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 16 LHKKVRKMKPGDTLLVLATD--PSTT-RDIPKFCTFLGHELLAQE 57 (69)
T ss_pred HHHHHHcCCCCCEEEEEeCC--CchH-HHHHHHHHHcCCEEEEEE
Confidence 4455555442 36666665 4333 458999999999887644
No 125
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=25.64 E-value=2e+02 Score=21.16 Aligned_cols=44 Identities=14% Similarity=0.184 Sum_probs=31.5
Q ss_pred eeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCE
Q 029589 129 VKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPY 174 (191)
Q Consensus 129 L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy 174 (191)
..-|..+....++.....++++.++.+. +...+...| +.+|++.
T Consensus 15 ~ipga~e~l~~L~~~g~~~~~lTNns~~-s~~~~~~~L-~~~Gi~~ 58 (101)
T PF13344_consen 15 PIPGAVEALDALRERGKPVVFLTNNSSR-SREEYAKKL-KKLGIPV 58 (101)
T ss_dssp E-TTHHHHHHHHHHTTSEEEEEES-SSS--HHHHHHHH-HHTTTT-
T ss_pred cCcCHHHHHHHHHHcCCCEEEEeCCCCC-CHHHHHHHH-HhcCcCC
Confidence 4568899999999999999999999766 333333444 8899985
No 126
>PF08534 Redoxin: Redoxin; InterPro: IPR013740 This redoxin domain is found in peroxiredoxin, thioredoxin and glutaredoxin proteins. Peroxiredoxins (Prxs) constitute a family of thiol peroxidases that reduce hydrogen peroxide, peroxinitrite, and hydroperoxides using a strictly conserved cysteine []. Chloroplast thioredoxin systems in plants regulate the enzymes involved in photosynthetic carbon assimilation []. It is thought that redoxins have a large role to play in anti-oxidant defence. Cadmium-sensitive proteins are also regulated via thioredoxin and glutaredoxin thiol redox systems [].; GO: 0016491 oxidoreductase activity; PDB: 2H30_A 1TP9_A 1Y25_A 1XVQ_A 2B1K_A 2G0F_A 2B1L_B 3K8N_A 1Z5Y_E 3OR5_A ....
Probab=25.50 E-value=1.6e+02 Score=22.15 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=31.2
Q ss_pred HHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC-CHhHHhhhhCC
Q 029589 139 LIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK-GKSRLGSVNIL 189 (191)
Q Consensus 139 ~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~-sK~~LG~a~Gi 189 (191)
....+...+|.|+.|-++. +..++++++++|.++. ...++....|+
T Consensus 57 ~~~~~~v~~v~v~~~~~~~-----~~~~~~~~~~~~~~~~D~~~~~~~~~~~ 103 (146)
T PF08534_consen 57 KYKDKGVDVVGVSSDDDPP-----VREFLKKYGINFPVLSDPDGALAKALGV 103 (146)
T ss_dssp HHHTTTCEEEEEEESSSHH-----HHHHHHHTTTTSEEEEETTSHHHHHTTC
T ss_pred hhccCceEEEEecccCCHH-----HHHHHHhhCCCceEEechHHHHHHHhCC
Confidence 3445668888888887773 5666777777776665 44567777774
No 127
>cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is
Probab=25.49 E-value=81 Score=24.45 Aligned_cols=13 Identities=23% Similarity=0.478 Sum_probs=7.2
Q ss_pred CCCEEEECCHhHH
Q 029589 171 EIPYCIVKGKSRL 183 (191)
Q Consensus 171 ~VPy~iV~sK~~L 183 (191)
++|+++|.+|.+|
T Consensus 104 ~~piiiv~nK~Dl 116 (166)
T cd00877 104 NIPIVLCGNKVDI 116 (166)
T ss_pred CCcEEEEEEchhc
Confidence 4555555555554
No 128
>cd07400 MPP_YydB Bacillus subtilis YydB and related proteins, metallophosphatase domain. YydB (BSU40220) is an uncharacterized Bacillus subtilis protein that belongs to the following Bacillus subtilis gene cluster yydB-yydC-yydD-yydG-yydH-yydI-yydJ. YydB belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productiv
Probab=25.39 E-value=1.6e+02 Score=22.01 Aligned_cols=47 Identities=28% Similarity=0.323 Sum_probs=30.6
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccc-------hhhhHHHHHHhcCCCEEEECCH
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIE-------LVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~e-------lv~~LpaLC~k~~VPy~iV~sK 180 (191)
++.+...++..++.+|+++.|+-... ...++-.++... +|+.++.|-
T Consensus 24 l~~~~~~~~~~~~d~vi~~GDl~~~~~~~~~~~~~~~~~~l~~~~-~~~~~v~GN 77 (144)
T cd07400 24 LDRLLAEIKALDPDLVVITGDLTQRGLPEEFEEAREFLDALPAPL-EPVLVVPGN 77 (144)
T ss_pred HHHHHHHHhccCCCEEEECCCCCCCCCHHHHHHHHHHHHHccccC-CcEEEeCCC
Confidence 44566778888899999999986532 223344444332 588887664
No 129
>cd01894 EngA1 EngA1 subfamily. This CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
Probab=25.21 E-value=1.6e+02 Score=21.50 Aligned_cols=39 Identities=18% Similarity=0.091 Sum_probs=20.6
Q ss_pred cceEEEecCCCcc--chhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 145 AQLVVIAHDVDPI--ELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 145 AkLVVIA~DvdP~--elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
+.++++..|++.. .....+..++...++|++++-+|.++
T Consensus 77 ~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~ 117 (157)
T cd01894 77 ADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKVDN 117 (157)
T ss_pred CCEEEEEEeccccCCccHHHHHHHHHhcCCCEEEEEECccc
Confidence 4455555554321 11223344555567787777777654
No 130
>PRK03980 flap endonuclease-1; Provisional
Probab=25.20 E-value=83 Score=28.17 Aligned_cols=35 Identities=20% Similarity=0.221 Sum_probs=25.9
Q ss_pred cCCCccchhhhHHHHHHhcCCCEEEECCHh--HHhhhh
Q 029589 152 HDVDPIELVVWLPALCRKMEIPYCIVKGKS--RLGSVN 187 (191)
Q Consensus 152 ~DvdP~elv~~LpaLC~k~~VPy~iV~sK~--~LG~a~ 187 (191)
.++++ +.+..+..+++.+||||+...+-+ .++.++
T Consensus 78 ~~vt~-~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~ 114 (292)
T PRK03980 78 SRLTD-EIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMA 114 (292)
T ss_pred ccCCH-HHHHHHHHHHHHCCCCEEecCchHHHHHHHHH
Confidence 35555 566778999999999999999873 455443
No 131
>PF13932 GIDA_assoc_3: GidA associated domain 3; PDB: 3CES_C 3CP2_A 3G05_A 3CP8_A 2ZXI_B 2ZXH_A.
Probab=25.14 E-value=60 Score=23.23 Aligned_cols=50 Identities=24% Similarity=0.274 Sum_probs=27.6
Q ss_pred cccchhhHhHHHHHH---HHhhhcCCCccccccccCChhhHHHHHhhhhcCCcccH
Q 029589 49 VKWPKAIRIQRQRRI---LRQRLKVPPALNQFTKTLDKNLASSLFKLLLKYRPEDR 101 (191)
Q Consensus 49 vkwP~yirlQrq~~i---l~~rlKvppainqf~~~l~~~~a~~l~kl~~kyrPEt~ 101 (191)
||.=.|+.-|.+..- -...+.+|+.||-.. . .+.+.....-|.+.||+|-
T Consensus 1 iKY~~Yi~rq~~~i~~~~~~e~~~iP~~~dy~~-i--~~LS~E~~ekL~~~rP~Ti 53 (72)
T PF13932_consen 1 IKYEGYIERQQQEIERLRKDESLKIPEDFDYSK-I--PGLSNEAREKLEKIRPRTI 53 (72)
T ss_dssp HHTHHHHHHHHHHCHHHHHHHTSB--TTS-CCC-S--TT--CHHHHHHHHH--SCH
T ss_pred CCcHHHHHHHHHHHHHHHHHhCCCCcCCCChhh-c--cccHHHHHHHHHhcCCCCH
Confidence 355567776665442 234578999987643 2 2566777788889999994
No 132
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=24.93 E-value=1.2e+02 Score=23.80 Aligned_cols=53 Identities=17% Similarity=0.129 Sum_probs=30.6
Q ss_pred ceeeech--hHHHHHHHhcCcceEEEecCCCccchh--hhHHHHHHhcCCCEEEECC
Q 029589 127 IVVKYGL--NHVTYLIEQNKAQLVVIAHDVDPIELV--VWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 127 ~~L~~G~--~~Vtk~IekkKAkLVVIA~DvdP~elv--~~LpaLC~k~~VPy~iV~s 179 (191)
..+..|- ..+..+++.-.+.-|+...|.++.+.. ..+...|.+.||.+..+.+
T Consensus 69 L~v~~g~~~~~l~~l~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~~ 125 (165)
T PF00875_consen 69 LLVLRGDPEEVLPELAKEYGATAVYFNEEYTPYERRRDERVRKALKKHGIKVHTFDD 125 (165)
T ss_dssp EEEEESSHHHHHHHHHHHHTESEEEEE---SHHHHHHHHHHHHHHHHTTSEEEEE--
T ss_pred eEEEecchHHHHHHHHHhcCcCeeEeccccCHHHHHHHHHHHHHHHhcceEEEEECC
Confidence 4455553 444456666678888888888775543 3355677777888877665
No 133
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=24.82 E-value=2.4e+02 Score=19.42 Aligned_cols=53 Identities=13% Similarity=0.191 Sum_probs=40.4
Q ss_pred eeechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhc-CCCEEEECCHh
Q 029589 129 VKYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKM-EIPYCIVKGKS 181 (191)
Q Consensus 129 L~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~-~VPy~iV~sK~ 181 (191)
...-.++....+++....+++|-.+.+..+-..++..+.... ++|++.+.+..
T Consensus 28 ~~~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t~~~ 81 (112)
T PF00072_consen 28 TASSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVTDED 81 (112)
T ss_dssp EESSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEESST
T ss_pred EECCHHHHHHHhcccCceEEEEEeeeccccccccccccccccccccEEEecCCC
Confidence 344567888889999999999998777777777677776655 78988887554
No 134
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. 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=24.47 E-value=2.1e+02 Score=19.65 Aligned_cols=41 Identities=17% Similarity=0.130 Sum_probs=26.3
Q ss_pred HHHHHHHhcCcc--eEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 135 HVTYLIEQNKAQ--LVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 135 ~Vtk~IekkKAk--LVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
.+-+++++-... |.|++.| |... .-+|.+|+.+|--+..+.
T Consensus 15 ~~kkal~~l~~G~~l~V~~d~--~~s~-~ni~~~~~~~g~~v~~~~ 57 (69)
T cd03422 15 ATLEALPSLKPGEILEVISDC--PQSI-NNIPIDARNHGYKVLAIE 57 (69)
T ss_pred HHHHHHHcCCCCCEEEEEecC--chHH-HHHHHHHHHcCCEEEEEE
Confidence 355566654422 5566665 4334 458999999998887543
No 135
>PRK15016 isochorismate synthase EntC; Provisional
Probab=24.44 E-value=62 Score=30.43 Aligned_cols=61 Identities=15% Similarity=0.102 Sum_probs=43.2
Q ss_pred eechhHHHHHHHhcCcceEEEecCCC-----ccchhhhHHHHHHhcCCCEEEECCHhHHhhhhCCC
Q 029589 130 KYGLNHVTYLIEQNKAQLVVIAHDVD-----PIELVVWLPALCRKMEIPYCIVKGKSRLGSVNILN 190 (191)
Q Consensus 130 ~~G~~~Vtk~IekkKAkLVVIA~Dvd-----P~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi~ 190 (191)
...+......|++|...-||+|..++ +++....+-.|+..+.-||.+.-.-..-+.++|-|
T Consensus 130 ~~~V~~a~~~i~~G~l~KVVLsR~~~l~~~~~~d~~~l~~~L~~~nP~~y~f~~~~~~~~~lvGaS 195 (391)
T PRK15016 130 EAMVARAAALTATPQVDKVVLSRLIDITTDAAIDSGALLERLIAQNPVSYNFHVPLADGGVLLGAS 195 (391)
T ss_pred HHHHHHHHHHHHcCCccEEEcCcEEeecCCCCCCHHHHHHHHHHhCCCCeEEEEEcCCCCEEEEeC
Confidence 34577888899999999999997543 44555668899999999999875322222355543
No 136
>cd03338 TCP1_delta TCP-1 (CTT or eukaryotic type II) chaperonin family, delta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=24.18 E-value=2e+02 Score=27.30 Aligned_cols=50 Identities=8% Similarity=0.058 Sum_probs=32.7
Q ss_pred HHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
.....|.+..+.+|+++.|++..-+-..+-.++.++||-.+.--++.+|-
T Consensus 263 ~~v~~i~~~g~~lvi~~~~i~~~~v~~l~~~~l~~~~I~av~~~~~~~Le 312 (515)
T cd03338 263 NMCKKIKKSGCNVLLIQKSILRDAVSDLALHFLAKLKIMVVKDIEREEIE 312 (515)
T ss_pred HHHHHHHhcCCCEEEECCCcccccccHHHHHHHHHCCceEEecCCHHHHH
Confidence 33444445567899999888654444456777788888887766644443
No 137
>TIGR00693 thiE thiamine-phosphate pyrophosphorylase. This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI.
Probab=24.10 E-value=2.5e+02 Score=22.42 Aligned_cols=54 Identities=24% Similarity=0.386 Sum_probs=32.3
Q ss_pred hhHHHHHHHhcCcceEEEec-CCCccc---hhhhHHHHHHhcCCCEEEECCHhHHhhhhC
Q 029589 133 LNHVTYLIEQNKAQLVVIAH-DVDPIE---LVVWLPALCRKMEIPYCIVKGKSRLGSVNI 188 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~-DvdP~e---lv~~LpaLC~k~~VPy~iV~sK~~LG~a~G 188 (191)
.+.+..+++.| +.+|.+-. |.+..+ +..-+-.+|+++++|+++ .+..+|-...|
T Consensus 16 ~~~~~~~~~~g-~~~v~lR~~~~~~~~~~~~~~~l~~~~~~~~~~l~i-~~~~~la~~~g 73 (196)
T TIGR00693 16 LNRVEAALKGG-VTLVQLRDKGSNTRERLALAEKLQELCRRYGVPFIV-NDRVDLALALG 73 (196)
T ss_pred HHHHHHHHhcC-CCEEEEecCCCCHHHHHHHHHHHHHHHHHhCCeEEE-ECHHHHHHHcC
Confidence 34566677777 56666643 344433 445567888888888766 44444444444
No 138
>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=24.08 E-value=85 Score=27.35 Aligned_cols=40 Identities=28% Similarity=0.336 Sum_probs=32.8
Q ss_pred HhHHHHHHHHhhhcCCCcc---ccccccCChhhHHHHHhhhhc
Q 029589 56 RIQRQRRILRQRLKVPPAL---NQFTKTLDKNLASSLFKLLLK 95 (191)
Q Consensus 56 rlQrq~~il~~rlKvppai---nqf~~~l~~~~a~~l~kl~~k 95 (191)
-=||||..+.+.|=-.|.| .-=|-.||..++..++.|+..
T Consensus 145 GGqqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~ 187 (226)
T COG1136 145 GGQQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRE 187 (226)
T ss_pred HHHHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHH
Confidence 4589999988888876666 555889999999999999944
No 139
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=23.99 E-value=2e+02 Score=24.88 Aligned_cols=44 Identities=5% Similarity=0.178 Sum_probs=33.3
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
+.++.+.|+.+.+..||+-...++ ..+-.++++.|++++.+...
T Consensus 209 l~~l~~~ik~~~v~~if~e~~~~~----~~~~~la~~~g~~v~~ld~l 252 (282)
T cd01017 209 LAELVEFVKKSDVKYIFFEENASS----KIAETLAKETGAKLLVLNPL 252 (282)
T ss_pred HHHHHHHHHHcCCCEEEEeCCCCh----HHHHHHHHHcCCcEEEeccc
Confidence 456777888889998888887766 23456888999998877643
No 140
>COG1648 CysG Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]
Probab=23.90 E-value=1.5e+02 Score=25.28 Aligned_cols=35 Identities=29% Similarity=0.237 Sum_probs=28.1
Q ss_pred cceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHh
Q 029589 145 AQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 145 AkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
+-|||+|.|= .++-.-+-.+|+++++|+..++...
T Consensus 73 ~~lviaAt~d--~~ln~~i~~~a~~~~i~vNv~D~p~ 107 (210)
T COG1648 73 AFLVIAATDD--EELNERIAKAARERRILVNVVDDPE 107 (210)
T ss_pred ceEEEEeCCC--HHHHHHHHHHHHHhCCceeccCCcc
Confidence 9999999873 3666678999999999997776643
No 141
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=23.71 E-value=71 Score=29.70 Aligned_cols=32 Identities=28% Similarity=0.354 Sum_probs=24.7
Q ss_pred ceEEEecCCC---ccchhhhHHHHHHhcCCCEEEE
Q 029589 146 QLVVIAHDVD---PIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 146 kLVVIA~Dvd---P~elv~~LpaLC~k~~VPy~iV 177 (191)
..++.+.|.+ +-.+..+|..+|+++||||-.-
T Consensus 255 Gp~i~~~D~~~~~~~~l~~~L~~~A~~~~Ip~Q~~ 289 (355)
T COG1363 255 GPVIRVKDASGIYHPKLRKFLLELAEKNNIPYQVD 289 (355)
T ss_pred CCEEEEEcCCCCCCHHHHHHHHHHHHHcCCCeEEE
Confidence 3456677774 2379999999999999999753
No 142
>PF15632 ATPgrasp_Ter: ATP-grasp in the biosynthetic pathway with Ter operon
Probab=23.59 E-value=1.5e+02 Score=27.09 Aligned_cols=45 Identities=22% Similarity=0.422 Sum_probs=35.8
Q ss_pred echhHHHHHHHhcCcceEEEecCCCcc------------------chhhhHHHHHHhcCCCEEE
Q 029589 131 YGLNHVTYLIEQNKAQLVVIAHDVDPI------------------ELVVWLPALCRKMEIPYCI 176 (191)
Q Consensus 131 ~G~~~Vtk~IekkKAkLVVIA~DvdP~------------------elv~~LpaLC~k~~VPy~i 176 (191)
++...+..+|+++ ..+-|+|.|.+|. +.+.|+-..|++++|-+++
T Consensus 9 s~~~~~i~~lr~~-~~~~i~~sh~~~~~~~~~~aD~~~~eP~~~~~yv~~~l~~C~~~~Idv~~ 71 (329)
T PF15632_consen 9 SSQRDIIRSLRAN-RDFTIIASHRDPRAPILYAADEAYLEPADGEEYVDWCLDFCKEHGIDVFV 71 (329)
T ss_pred ccHHHHHHHHHcC-CCeEEEEEeCCCCchHHhcCceeeecCCCHHHHHHHHHHHHHHhCCeEEE
Confidence 4566788888888 7788888777653 6788999999999999865
No 143
>TIGR02339 thermosome_arch thermosome, various subunits, archaeal. Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacterial), a torroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.
Probab=23.56 E-value=1.8e+02 Score=27.57 Aligned_cols=48 Identities=17% Similarity=0.118 Sum_probs=32.7
Q ss_pred HHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhhh
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSVN 187 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a~ 187 (191)
.....|.+-.+.+|+++.++|+. .-.+|.++||-.+..-++.+|.+++
T Consensus 273 ~~v~~i~~~g~~lvi~~~~I~~~-----al~~L~~~gI~~v~~v~~~~L~rIa 320 (519)
T TIGR02339 273 EMVDKIADAGANVVFCQKGIDDL-----AQHYLAKAGILAVRRVKKSDIEKLA 320 (519)
T ss_pred HHHHHHHhcCCcEEEECCCccHH-----HHHHHHHCCCEEEecCCHHHHHHHH
Confidence 44455556678899999999882 2334568888877766766665543
No 144
>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A ....
Probab=23.45 E-value=2.3e+02 Score=22.84 Aligned_cols=43 Identities=21% Similarity=0.331 Sum_probs=26.3
Q ss_pred HHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
.+..++..+ +.-+++.. +++..... +-..|.+.|||++.+.+-
T Consensus 47 ~i~~~i~~~-~d~Iiv~~-~~~~~~~~-~l~~~~~~gIpvv~~d~~ 89 (257)
T PF13407_consen 47 QIEQAISQG-VDGIIVSP-VDPDSLAP-FLEKAKAAGIPVVTVDSD 89 (257)
T ss_dssp HHHHHHHTT-ESEEEEES-SSTTTTHH-HHHHHHHTTSEEEEESST
T ss_pred HHHHHHHhc-CCEEEecC-CCHHHHHH-HHHHHhhcCceEEEEecc
Confidence 344455445 66555443 33434444 456688889999998876
No 145
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=23.43 E-value=1e+02 Score=27.05 Aligned_cols=20 Identities=25% Similarity=0.139 Sum_probs=12.9
Q ss_pred HHHHHhcCCCEEEECCHhHH
Q 029589 164 PALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 164 paLC~k~~VPy~iV~sK~~L 183 (191)
..+++..++|.++|-+|.+|
T Consensus 102 L~~~~~~~ip~iIVlNK~DL 121 (287)
T cd01854 102 LVAAEAAGIEPVIVLTKADL 121 (287)
T ss_pred HHHHHHcCCCEEEEEEHHHC
Confidence 33455666777777777766
No 146
>PRK00766 hypothetical protein; Provisional
Probab=23.42 E-value=1.7e+02 Score=24.95 Aligned_cols=50 Identities=12% Similarity=0.212 Sum_probs=33.1
Q ss_pred HHHHHh----cCcceEEEecCCC-ccchhhhHHHHHHhcCCCEEEE----CCHhHHhhhh
Q 029589 137 TYLIEQ----NKAQLVVIAHDVD-PIELVVWLPALCRKMEIPYCIV----KGKSRLGSVN 187 (191)
Q Consensus 137 tk~Iek----kKAkLVVIA~Dvd-P~elv~~LpaLC~k~~VPy~iV----~sK~~LG~a~ 187 (191)
..++++ .+.++|++..=+- -..++. +..|+++.|+|++.| .+.+.+-.|+
T Consensus 60 ~~mv~~~~~r~~i~~V~L~Git~agFNvvD-~~~l~~~tg~PVI~V~r~~p~~~~ie~AL 118 (194)
T PRK00766 60 IEMVNSSRHKGQLRVIMLDGITYGGFNVVD-IEELYRETGLPVIVVMRKKPDFEAIESAL 118 (194)
T ss_pred HHHHHhcccccceEEEEECCEeeeeeEEec-HHHHHHHHCCCEEEEEecCCCHHHHHHHH
Confidence 345554 4677777765332 123443 799999999999999 6666666554
No 147
>cd04501 SGNH_hydrolase_like_4 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid.
Probab=23.41 E-value=2.1e+02 Score=22.15 Aligned_cols=51 Identities=16% Similarity=0.225 Sum_probs=32.7
Q ss_pred eeechhHHHHHHHhcCcceEEEec------C---------CCccchhhhHHHHHHhcCCCEEEECC
Q 029589 129 VKYGLNHVTYLIEQNKAQLVVIAH------D---------VDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 129 L~~G~~~Vtk~IekkKAkLVVIA~------D---------vdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
+..++....+.+.+.-+.+|++.- . .+-..+...+..+|++++|+|+.+.+
T Consensus 81 ~~~~~~~li~~~~~~~~~~il~~~~p~~~~~~~~~~~~~~~~~~~~n~~~~~~a~~~~v~~vd~~~ 146 (183)
T cd04501 81 IKDNIRSMVELAEANGIKVILASPLPVDDYPWKPQWLRPANKLKSLNRWLKDYARENGLLFLDFYS 146 (183)
T ss_pred HHHHHHHHHHHHHHCCCcEEEEeCCCcCccccchhhcchHHHHHHHHHHHHHHHHHcCCCEEechh
Confidence 344555566666666677776641 1 11124455678999999999998765
No 148
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=23.40 E-value=1.5e+02 Score=22.05 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=22.9
Q ss_pred HHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 139 LIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 139 ~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
..+...+..|.|..|- .+..+|.+.|.+.+.+.+
T Consensus 65 ~a~~~g~~iI~IT~~~-------~l~~~~~~~~~~~~~~p~ 98 (119)
T cd05017 65 QAKERGAKIVAITSGG-------KLLEMAREHGVPVIIIPK 98 (119)
T ss_pred HHHHCCCEEEEEeCCc-------hHHHHHHHcCCcEEECCC
Confidence 3344567788887653 266788888888877655
No 149
>cd01892 Miro2 Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
Probab=23.32 E-value=90 Score=24.33 Aligned_cols=13 Identities=46% Similarity=0.659 Sum_probs=9.0
Q ss_pred CCCEEEECCHhHH
Q 029589 171 EIPYCIVKGKSRL 183 (191)
Q Consensus 171 ~VPy~iV~sK~~L 183 (191)
++|+++|.+|.+|
T Consensus 108 ~~p~iiv~NK~Dl 120 (169)
T cd01892 108 EIPCLFVAAKADL 120 (169)
T ss_pred CCeEEEEEEcccc
Confidence 5777777777666
No 150
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=23.04 E-value=1.3e+02 Score=26.26 Aligned_cols=46 Identities=20% Similarity=0.246 Sum_probs=36.2
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV 177 (191)
|.......+......+||=|--=-..++....-..|++.||||.-+
T Consensus 54 ~~~~l~~~l~~~~i~~vIDATHPfA~~is~na~~a~~~~~ipylR~ 99 (249)
T PF02571_consen 54 DEEGLAEFLRENGIDAVIDATHPFAAEISQNAIEACRELGIPYLRF 99 (249)
T ss_pred CHHHHHHHHHhCCCcEEEECCCchHHHHHHHHHHHHhhcCcceEEE
Confidence 5678889999999999985544334466777889999999999754
No 151
>cd03339 TCP1_epsilon TCP-1 (CTT or eukaryotic type II) chaperonin family, epsilon subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=22.96 E-value=2.1e+02 Score=27.24 Aligned_cols=45 Identities=16% Similarity=0.122 Sum_probs=32.5
Q ss_pred HHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhh
Q 029589 137 TYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSV 186 (191)
Q Consensus 137 tk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a 186 (191)
...|.+-.+.+|+++.++|+ ..-.+|.++||..+..-++.+|-++
T Consensus 280 v~~i~~~g~~lvi~~~~I~~-----~al~~L~~~~I~av~~v~~~~LerI 324 (526)
T cd03339 280 VEQVKDAGANLVICQWGFDD-----EANHLLLQNGLPAVRWVGGVEIELI 324 (526)
T ss_pred HHHHHHCCCCEEEeCCCCCH-----HHHHHHHHCCCEEEEeCCHHHHHHH
Confidence 44445556799999999998 2456778999998877676665543
No 152
>PRK09453 phosphodiesterase; Provisional
Probab=22.79 E-value=1.6e+02 Score=23.42 Aligned_cols=21 Identities=29% Similarity=0.259 Sum_probs=12.3
Q ss_pred hHHHHHHHhcCcceEEEecCC
Q 029589 134 NHVTYLIEQNKAQLVVIAHDV 154 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~Dv 154 (191)
+.+...++...+..||++.|+
T Consensus 17 ~~~l~~~~~~~~d~ii~lGDi 37 (182)
T PRK09453 17 EKALELFAQSGADWLVHLGDV 37 (182)
T ss_pred HHHHHHHHhcCCCEEEEcccc
Confidence 345555555566666666665
No 153
>cd04146 RERG_RasL11_like RERG/RasL11-like subfamily. RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tu
Probab=22.72 E-value=93 Score=23.61 Aligned_cols=16 Identities=13% Similarity=0.185 Sum_probs=7.1
Q ss_pred HHHHHhcCCCEEEECC
Q 029589 164 PALCRKMEIPYCIVKG 179 (191)
Q Consensus 164 paLC~k~~VPy~iV~s 179 (191)
..+|+..+.||..+..
T Consensus 130 ~~~~~~~~~~~~e~Sa 145 (165)
T cd04146 130 EKLASELGCLFFEVSA 145 (165)
T ss_pred HHHHHHcCCEEEEeCC
Confidence 3444444444444443
No 154
>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=22.49 E-value=2.3e+02 Score=20.81 Aligned_cols=50 Identities=12% Similarity=0.142 Sum_probs=29.6
Q ss_pred HHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC-HhHHhhhhCCC
Q 029589 136 VTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG-KSRLGSVNILN 190 (191)
Q Consensus 136 Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s-K~~LG~a~Gi~ 190 (191)
....+..+.+.+|.|+.|- + + -+-+++++++++|-++.+ ...+++..|+.
T Consensus 49 ~~~~~~~~~~~vv~is~d~-~-~---~~~~~~~~~~~~~~~l~D~~~~~~~~~gv~ 99 (140)
T cd03017 49 LYEEFKALGAVVIGVSPDS-V-E---SHAKFAEKYGLPFPLLSDPDGKLAKAYGVW 99 (140)
T ss_pred HHHHHHHCCCEEEEEcCCC-H-H---HHHHHHHHhCCCceEEECCccHHHHHhCCc
Confidence 3334444567777777662 2 2 245677777777765554 34677777653
No 155
>TIGR02181 GRX_bact Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides.
Probab=22.47 E-value=2.1e+02 Score=19.31 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=30.2
Q ss_pred hHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHh
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~ 181 (191)
..+...++......-.+-.|-++ +...-+-.+-..+.||.+++.++.
T Consensus 13 ~~a~~~L~~~~i~~~~~di~~~~-~~~~~~~~~~g~~~vP~i~i~g~~ 59 (79)
T TIGR02181 13 TRAKALLSSKGVTFTEIRVDGDP-ALRDEMMQRSGRRTVPQIFIGDVH 59 (79)
T ss_pred HHHHHHHHHcCCCcEEEEecCCH-HHHHHHHHHhCCCCcCEEEECCEE
Confidence 44556666777777777666565 232334444556789999999863
No 156
>PF08085 Entericidin: Entericidin EcnA/B family; InterPro: IPR012556 This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing [].; GO: 0009636 response to toxin, 0016020 membrane
Probab=22.46 E-value=16 Score=20.80 Aligned_cols=8 Identities=25% Similarity=0.746 Sum_probs=5.8
Q ss_pred ccCCCCCC
Q 029589 34 GIGGALPP 41 (191)
Q Consensus 34 gig~~iqp 41 (191)
|+|+|||.
T Consensus 5 G~G~Di~~ 12 (21)
T PF08085_consen 5 GVGKDIQS 12 (21)
T ss_pred hhhHhHHH
Confidence 77888763
No 157
>cd07383 MPP_Dcr2 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain. DCR2 phosphatase (Dosage-dependent Cell Cycle Regulator 2) functions together with DCR1 (Gid8) in a common pathway to accelerate initiation of DNA replication in Saccharomyces cerevisiae. Genetic analysis suggests that DCR1 functions upstream of DCR2. DCR2 interacts with and dephosphorylates Sic1, an inhibitor of mitotic cyclin/cyclin-dependent kinase complexes, which may serve to trigger the initiation of cell division. DCR2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAP
Probab=22.43 E-value=2.3e+02 Score=22.80 Aligned_cols=47 Identities=21% Similarity=0.295 Sum_probs=29.2
Q ss_pred HHHHHHHhcCcceEEEecCCCccch-----hhhHHHHHH---hcCCCEEEECCHh
Q 029589 135 HVTYLIEQNKAQLVVIAHDVDPIEL-----VVWLPALCR---KMEIPYCIVKGKS 181 (191)
Q Consensus 135 ~Vtk~IekkKAkLVVIA~DvdP~el-----v~~LpaLC~---k~~VPy~iV~sK~ 181 (191)
.+.+.++..+..+||++.|.-...- ...+..+.+ ..++|+..+.+--
T Consensus 32 ~~~~~~~~~~~d~vv~~GDl~~~~~~~~~~~~~~~~~~~~l~~~~~p~~~~~GNH 86 (199)
T cd07383 32 FIERVLDAEKPDLVVLTGDLITGENTNDNSTSALDKAVSPMIDRKIPWAATFGNH 86 (199)
T ss_pred HHHHHHhhcCCCEEEECCccccCCCCchHHHHHHHHHHHHHHHcCCCEEEECccC
Confidence 3445566778899999999833111 122344433 3489999887643
No 158
>PRK09331 Sep-tRNA:Cys-tRNA synthetase; Provisional
Probab=22.24 E-value=1.8e+02 Score=25.98 Aligned_cols=50 Identities=16% Similarity=0.288 Sum_probs=33.5
Q ss_pred hhHHHHHHHhc------CcceEEEecC----CCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 133 LNHVTYLIEQN------KAQLVVIAHD----VDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 133 ~~~Vtk~Iekk------KAkLVVIA~D----vdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
...+..+++.. ++++|+|.+= -+...+ .-+-.+|+++|+++ +++.-..+|
T Consensus 141 ~~~l~~~l~~~~~~~~~~~~lV~l~~~~~~tG~~~~l-~~I~~la~~~g~~l-ivD~a~~~g 200 (387)
T PRK09331 141 PEAYAEKIEEVKEETGKPPALALLTHVDGNYGNLADA-KKVAKVAHEYGIPF-LLNGAYTVG 200 (387)
T ss_pred HHHHHHHHHHhhhccCCCCEEEEEECCCCCCcccccH-HHHHHHHHHcCCEE-EEECCcccC
Confidence 56777777653 7889998762 222233 34788999999976 556655555
No 159
>PRK06512 thiamine-phosphate pyrophosphorylase; Provisional
Probab=22.19 E-value=2.3e+02 Score=24.17 Aligned_cols=55 Identities=11% Similarity=0.109 Sum_probs=37.0
Q ss_pred hHHHHHHHhcCcceEEE-ecCCCccc---hhhhHHHHHHhcCCCEEEECCHhHHhhhhCC
Q 029589 134 NHVTYLIEQNKAQLVVI-AHDVDPIE---LVVWLPALCRKMEIPYCIVKGKSRLGSVNIL 189 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVI-A~DvdP~e---lv~~LpaLC~k~~VPy~iV~sK~~LG~a~Gi 189 (191)
..+..+++.|.+.+|.+ ..|.+..+ +...+-.+|+.+|+|++ |.+..+|...+|-
T Consensus 30 ~~l~~al~~G~v~~vQlR~K~l~~~~~~~~a~~l~~l~~~~gv~li-INd~~dlA~~~~a 88 (221)
T PRK06512 30 KLLRAALQGGDVASVILPQYGLDEATFQKQAEKLVPVIQEAGAAAL-IAGDSRIAGRVKA 88 (221)
T ss_pred HHHHHHHcCCCccEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCEEE-EeCHHHHHHHhCC
Confidence 35556666675555555 45666544 35568889999999975 5777888776653
No 160
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=22.06 E-value=1.3e+02 Score=22.24 Aligned_cols=47 Identities=21% Similarity=0.191 Sum_probs=35.1
Q ss_pred eechhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCH
Q 029589 130 KYGLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 130 ~~G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
..++.++...+ ..+.+|+++-.+.. .. ..+...|.++|||+..++..
T Consensus 38 a~~~~~~~~~~--~~~Dvill~pqi~~-~~-~~i~~~~~~~~ipv~~I~~~ 84 (95)
T TIGR00853 38 AGSYGAAGEKL--DDADVVLLAPQVAY-ML-PDLKKETDKKGIPVEVINGA 84 (95)
T ss_pred EecHHHHHhhc--CCCCEEEECchHHH-HH-HHHHHHhhhcCCCEEEeChh
Confidence 44566665544 46899999988865 34 44789999999999998764
No 161
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=21.99 E-value=1.6e+02 Score=25.70 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=37.1
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
|......++......+||=|--=-..++....-..|++.||||+-+.
T Consensus 53 ~~~~l~~~l~~~~i~~VIDATHPfA~~is~~a~~ac~~~~ipyiR~e 99 (248)
T PRK08057 53 GAEGLAAYLREEGIDLVIDATHPYAAQISANAAAACRALGIPYLRLE 99 (248)
T ss_pred CHHHHHHHHHHCCCCEEEECCCccHHHHHHHHHHHHHHhCCcEEEEe
Confidence 44788999999999999855444445677788999999999997543
No 162
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=21.96 E-value=1.2e+02 Score=26.57 Aligned_cols=45 Identities=16% Similarity=0.335 Sum_probs=35.3
Q ss_pred hhHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEE
Q 029589 133 LNHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 133 ~~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV 177 (191)
......++....+.+||=|.---..++....-..|++.||||+-+
T Consensus 54 ~~~l~~~l~~~~i~~VIDAtHPfA~~is~~a~~a~~~~~ipylR~ 98 (256)
T TIGR00715 54 PQELREFLKRHSIDILVDATHPFAAQITTNATAVCKELGIPYVRF 98 (256)
T ss_pred HHHHHHHHHhcCCCEEEEcCCHHHHHHHHHHHHHHHHhCCcEEEE
Confidence 345668888889998887755444577778899999999999765
No 163
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=21.93 E-value=2e+02 Score=25.68 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=31.6
Q ss_pred CCceeeech----hHHHHHHHhcC--cceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 125 KPIVVKYGL----NHVTYLIEQNK--AQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 125 ~p~~L~~G~----~~Vtk~IekkK--AkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
|-..+.+|- ..+..++++|. +.++++..|-.. +.++|+++|||++.+.
T Consensus 91 ri~vl~Sg~g~nl~al~~~~~~~~~~~~i~~visn~~~------~~~lA~~~gIp~~~~~ 144 (286)
T PRK13011 91 KVLIMVSKFDHCLNDLLYRWRIGELPMDIVGVVSNHPD------LEPLAAWHGIPFHHFP 144 (286)
T ss_pred eEEEEEcCCcccHHHHHHHHHcCCCCcEEEEEEECCcc------HHHHHHHhCCCEEEeC
Confidence 334556665 44455555664 678777666321 5677999999998763
No 164
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=21.84 E-value=1.2e+02 Score=27.53 Aligned_cols=40 Identities=20% Similarity=0.282 Sum_probs=29.7
Q ss_pred cCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 143 NKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 143 kKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
..+.+||.|.|-. +...++-.+|.++++|+++...-..-|
T Consensus 115 ~~~DlVid~~D~~--~~r~~in~~~~~~~ip~i~~~~~g~~G 154 (338)
T PRK12475 115 KEVDLIIDATDNF--DTRLLINDLSQKYNIPWIYGGCVGSYG 154 (338)
T ss_pred cCCCEEEEcCCCH--HHHHHHHHHHHHcCCCEEEEEecccEE
Confidence 3588999998854 444568999999999999875543333
No 165
>cd04106 Rab23_lke Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signalling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with G
Probab=21.75 E-value=1.1e+02 Score=22.77 Aligned_cols=38 Identities=16% Similarity=0.379 Sum_probs=20.8
Q ss_pred CcceEEEecCCCccc--hh--hhHHHHHHhcCCCEEEECCHh
Q 029589 144 KAQLVVIAHDVDPIE--LV--VWLPALCRKMEIPYCIVKGKS 181 (191)
Q Consensus 144 KAkLVVIA~DvdP~e--lv--~~LpaLC~k~~VPy~iV~sK~ 181 (191)
..-++++++=+|-.. .+ .-.-.+++.+++||+.+..+.
T Consensus 106 ~~p~iiv~nK~Dl~~~~~v~~~~~~~~~~~~~~~~~~~Sa~~ 147 (162)
T cd04106 106 DIPMVLVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKD 147 (162)
T ss_pred CCCEEEEEEChhcccccCCCHHHHHHHHHHcCCeEEEEECCC
Confidence 455666666555211 11 123456777777877666544
No 166
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=21.74 E-value=2.2e+02 Score=19.09 Aligned_cols=42 Identities=14% Similarity=0.157 Sum_probs=27.3
Q ss_pred hHHHHHHHhc--CcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 134 NHVTYLIEQN--KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 134 ~~Vtk~Iekk--KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
-.+.+++++= -..|.|++.|-+ .. .-++.+|+.+|.-+..+.
T Consensus 15 l~~~~~l~~l~~G~~l~v~~d~~~--~~-~di~~~~~~~g~~~~~~~ 58 (70)
T PF01206_consen 15 LKAKKALKELPPGEVLEVLVDDPA--AV-EDIPRWCEENGYEVVEVE 58 (70)
T ss_dssp HHHHHHHHTSGTT-EEEEEESSTT--HH-HHHHHHHHHHTEEEEEEE
T ss_pred HHHHHHHHhcCCCCEEEEEECCcc--HH-HHHHHHHHHCCCEEEEEE
Confidence 3456666662 235667777743 33 458999999998876653
No 167
>cd06379 PBP1_iGluR_NMDA_NR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore
Probab=21.70 E-value=1.6e+02 Score=25.84 Aligned_cols=45 Identities=16% Similarity=0.161 Sum_probs=29.8
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccc--hhhhHHHHHHhcCCCEEEE
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIE--LVVWLPALCRKMEIPYCIV 177 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~e--lv~~LpaLC~k~~VPy~iV 177 (191)
+.+.+.++++. .+.-||+.+..++.. ....+-.+|..++||++..
T Consensus 69 a~~~~~~Li~~-~V~aii~~~~~ss~~~~~~~~v~~~~~~~~iP~Is~ 115 (377)
T cd06379 69 ALSVCEQLISN-QVYAVIVSHPPTSNDHLTPTSVSYTAGFYRIPVVGI 115 (377)
T ss_pred HHHHHHHHhhc-ceEEEEEeCCCCCcccccHHHHHHHhhCCCCcEEec
Confidence 45556677764 555555566555544 4455677999999999864
No 168
>TIGR00040 yfcE phosphoesterase, MJ0936 family. Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown (PubMed:15128743) to act on model phosphodiesterase substrates; a divalent cation was required.
Probab=21.60 E-value=1.9e+02 Score=22.32 Aligned_cols=45 Identities=16% Similarity=0.172 Sum_probs=29.0
Q ss_pred hHHHHHHHhc-CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhH
Q 029589 134 NHVTYLIEQN-KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSR 182 (191)
Q Consensus 134 ~~Vtk~Iekk-KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~ 182 (191)
..+...++.. .+.+|+++.|+-+.+... ..++.+.|+..|.|--+
T Consensus 17 ~~~~~~~~~~~~~d~ii~~GD~~~~~~~~----~l~~~~~~~~~V~GN~D 62 (158)
T TIGR00040 17 ELPVELFNLESNVDLVIHAGDLTSPFVLK----EFEDLAAKVIAVRGNND 62 (158)
T ss_pred HhHHHHHhhccCCCEEEEcCCCCCHHHHH----HHHHhCCceEEEccCCC
Confidence 3455666665 789999999986534433 33455677877776544
No 169
>cd02971 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They 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 TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a
Probab=21.59 E-value=2e+02 Score=21.14 Aligned_cols=48 Identities=10% Similarity=0.175 Sum_probs=27.1
Q ss_pred HHHHHhcCcceEEEecCCCccchhhhHHHHHHhc-CCCEEEEC-CHhHHhhhhCC
Q 029589 137 TYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKM-EIPYCIVK-GKSRLGSVNIL 189 (191)
Q Consensus 137 tk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~-~VPy~iV~-sK~~LG~a~Gi 189 (191)
...+..+.+.+|.|..| ++.. +-.+++++ +.++.++. ....++...|+
T Consensus 49 ~~~~~~~~~~~i~is~d-~~~~----~~~~~~~~~~~~~~~l~D~~~~~~~~~g~ 98 (140)
T cd02971 49 AEEFAKGGAEVLGVSVD-SPFS----HKAWAEKEGGLNFPLLSDPDGEFAKAYGV 98 (140)
T ss_pred HHHHHHCCCEEEEEeCC-CHHH----HHHHHhcccCCCceEEECCChHHHHHcCC
Confidence 33334466777777776 2322 34555655 56555554 34567777765
No 170
>cd04163 Era Era subfamily. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
Probab=21.58 E-value=1.2e+02 Score=21.97 Aligned_cols=17 Identities=29% Similarity=0.366 Sum_probs=8.9
Q ss_pred HHhcCCCEEEECCHhHH
Q 029589 167 CRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 167 C~k~~VPy~iV~sK~~L 183 (191)
+..+++|++++-+|.+|
T Consensus 107 ~~~~~~~~iiv~nK~Dl 123 (168)
T cd04163 107 LKKSKTPVILVLNKIDL 123 (168)
T ss_pred HHHhCCCEEEEEEchhc
Confidence 33445566665555544
No 171
>TIGR00067 glut_race glutamate racemase. The most closely related proteins differing in function are aspartate racemases.
Probab=21.58 E-value=1.8e+02 Score=25.10 Aligned_cols=41 Identities=20% Similarity=0.344 Sum_probs=30.7
Q ss_pred HHHHHHH-hcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEEC
Q 029589 135 HVTYLIE-QNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVK 178 (191)
Q Consensus 135 ~Vtk~Ie-kkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~ 178 (191)
+....++ +..+.++|||+|... ..+++.|-...+||++.+-
T Consensus 51 ~~~~~L~~~~g~d~ivIaCNTA~---a~~~~~l~~~~~iPii~ii 92 (251)
T TIGR00067 51 ELLTFLKERHNIKLLVVACNTAS---ALALEDLQRNFDFPVVGVI 92 (251)
T ss_pred HHHHHHHHhCCCCEEEEeCchHH---HHHHHHHHHHCCCCEEeec
Confidence 4445565 888999999999643 2347888888899998743
No 172
>cd07402 MPP_GpdQ Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain. GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. The GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide phosphodiesterase activity. GpdQ and Rv0805 belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosa
Probab=21.48 E-value=2.6e+02 Score=22.72 Aligned_cols=50 Identities=22% Similarity=0.277 Sum_probs=31.8
Q ss_pred hhHHHHHHHhc--CcceEEEecCCCcc----chhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 133 LNHVTYLIEQN--KAQLVVIAHDVDPI----ELVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 133 ~~~Vtk~Iekk--KAkLVVIA~DvdP~----elv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
+..+...+++. ++.+||++.|.-.. +... +-.+-+..++|+.+|.|--+.
T Consensus 27 l~~~~~~i~~~~~~~d~vi~~GDl~~~~~~~~~~~-~~~~l~~~~~p~~~v~GNHD~ 82 (240)
T cd07402 27 LEAVLAHINALHPRPDLVLVTGDLTDDGSPESYER-LRELLAALPIPVYLLPGNHDD 82 (240)
T ss_pred HHHHHHHHHhcCCCCCEEEECccCCCCCCHHHHHH-HHHHHhhcCCCEEEeCCCCCC
Confidence 34556666665 88999999996542 2222 223334568999998875543
No 173
>KOG2016 consensus NEDD8-activating complex, APP-BP1/UBA5 component [Posttranslational modification, protein turnover, chaperones]
Probab=21.48 E-value=82 Score=30.80 Aligned_cols=113 Identities=22% Similarity=0.255 Sum_probs=65.1
Q ss_pred HHHhhhc--CCCccccccccCChhhH-----HHHHhhhhcCCcccHHHHHHHHHHHHHHHHcCCCcccCCCceeeechhH
Q 029589 63 ILRQRLK--VPPALNQFTKTLDKNLA-----SSLFKLLLKYRPEDRAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNH 135 (191)
Q Consensus 63 il~~rlK--vppainqf~~~l~~~~a-----~~l~kl~~kyrPEt~~ekk~rl~~~a~~~a~gk~~~~k~p~~L~~G~~~ 135 (191)
+...-|| |-|-|.-||- +|.... -+.|=+=.++-=+++++....++..--....|.-+ ...| ..-
T Consensus 38 ~g~e~lKnLvl~Gigs~tv-vd~~~v~~~d~g~nF~~~~~~~GksrA~a~~e~LqeLN~~V~~~~v-ee~p------~~L 109 (523)
T KOG2016|consen 38 LGSEALKNLVLPGIGSFTV-VDGSKVEQGDLGNNFFLDAKSIGKSRAEATLEFLQELNPSVSGSFV-EESP------DFL 109 (523)
T ss_pred hHHHHHHhhcccccccEEE-EecceeeecchhhHHHHHHHhhchhHHHHHHHHHHHhChhhhcCcc-ccCh------hhh
Confidence 4455566 7778888863 333222 23344444555555555555544433222233221 1122 223
Q ss_pred HHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 136 VTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 136 Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
+....+-..--=||||.+....++.. |+..|++.+||+++..+---.|
T Consensus 110 i~~~p~ff~qFtvViatnl~E~~~~k-l~~~l~~~~vpll~~rs~Gl~G 157 (523)
T KOG2016|consen 110 IDNDPSFFSQFTVVIATNLNEQTLLK-LAEILREANVPLLLTRSYGLAG 157 (523)
T ss_pred hhcCchhhheeeeeeccccchhhhhh-hHHHHHhcCCceEEEeeecceE
Confidence 44444555566688999998877766 8999999999999887744333
No 174
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A ....
Probab=21.08 E-value=1.5e+02 Score=24.88 Aligned_cols=33 Identities=15% Similarity=0.257 Sum_probs=24.7
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
-..++||..| ......+-..|.++||||.+..+
T Consensus 77 ~~diAVL~R~---~~~~~~i~~~L~~~gIp~~~~~~ 109 (351)
T PF13361_consen 77 PSDIAVLVRT---NSQIKEIEDALKEAGIPYRISGS 109 (351)
T ss_dssp GGGEEEEESS---GGHHHHHHHHHHHTTS-EEESSS
T ss_pred cccEEEEEEC---chhHHHHHHHHhhhcceeEeccc
Confidence 3568999999 34455689999999999966555
No 175
>PF00425 Chorismate_bind: chorismate binding enzyme; InterPro: IPR015890 This entry represents the catalytic regions of the chorismate binding enzymes anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase and para-aminobenzoate synthase. Anthranilate synthase catalyses the reaction: chorismate + l-glutamine = anthranilate + pyruvate + l-glutamate. The enzyme is a tetramer comprising 2 I and 2 II components: this entry is restricted to component I that catalyses the formation of anthranilate using ammonia rather than glutamine, while component II provides glutamine amidotransferase activity IPR006220 from INTERPRO.; PDB: 3GSE_A 3OS6_C 2FN0_B 2FN1_B 1I7S_C 1I7Q_C 3LOG_D 3RV8_D 2G5F_D 3RV9_C ....
Probab=21.06 E-value=1.9e+02 Score=25.01 Aligned_cols=48 Identities=17% Similarity=0.243 Sum_probs=37.9
Q ss_pred chhHHHHHHHhcCcceEEEecCCC-----ccchhhhHHHHHHhcCCCEEEECC
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVD-----PIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~Dvd-----P~elv~~LpaLC~k~~VPy~iV~s 179 (191)
.+.++...|++|...-||+|.... +.+...++..||+.+.-+|++.-.
T Consensus 8 ~v~~~~~~I~~G~~~KvVLar~~~~~~~~~~~~~~l~~~L~~~~p~~y~f~~~ 60 (257)
T PF00425_consen 8 AVRKAQEHIRAGELYKVVLARRFELPFPSPIDPLALFRRLRKRNPSAYVFYFQ 60 (257)
T ss_dssp HHHHHHHHHHTTS-SEEEEEEEEEEEESSECHHHHHHHHHHHHSTTSEEEEEE
T ss_pred HHHHHHHHHHcCCcEEEEEeeEEEEecCCCCCHHHHHHHHHHhCCCceEEEEe
Confidence 477888999999999999997653 334566789999999999998764
No 176
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=20.90 E-value=2.6e+02 Score=25.64 Aligned_cols=54 Identities=19% Similarity=0.180 Sum_probs=41.6
Q ss_pred Cceeeec--hhHHHHHHHhcCcceEEEecCCCccch--hhhHHHHHHhcCCCEEEECC
Q 029589 126 PIVVKYG--LNHVTYLIEQNKAQLVVIAHDVDPIEL--VVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 126 p~~L~~G--~~~Vtk~IekkKAkLVVIA~DvdP~el--v~~LpaLC~k~~VPy~iV~s 179 (191)
+..+..| .+.+..+++.-.|.-|+...|.+|.+. ...+-..|.+.||++..+.+
T Consensus 76 ~L~v~~G~~~~vl~~L~~~~~~~~V~~~~~~~~~~~~rd~~v~~~l~~~~i~~~~~~~ 133 (429)
T TIGR02765 76 DLLVRSGKPEDVLPELIKELGVRTVFLHQEVGSEEKSVERLLQQALARLGIHVEQHWG 133 (429)
T ss_pred CeEEEeCCHHHHHHHHHHHhCCCEEEEeccCCHHHHHHHHHHHHHHHhcCceEEEecC
Confidence 3455566 455666778889999999999999877 66677789999999865544
No 177
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=20.88 E-value=1.4e+02 Score=25.96 Aligned_cols=30 Identities=27% Similarity=0.468 Sum_probs=19.1
Q ss_pred EEecCCCccchhhhHHHHHHhcCCCEEEECC
Q 029589 149 VIAHDVDPIELVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 149 VIA~DvdP~elv~~LpaLC~k~~VPy~iV~s 179 (191)
+|+-.+.| ++..-|+..|.+.|+..+||.+
T Consensus 55 ~I~y~lHP-Dl~~~l~~~~~e~g~kavIvp~ 84 (217)
T PF02593_consen 55 LIAYGLHP-DLTYELPEIAKEAGVKAVIVPS 84 (217)
T ss_pred EEEeccCc-hhHHHHHHHHHHcCCCEEEEec
Confidence 45556666 5555566666667777776654
No 178
>cd00378 SHMT Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl group of N5, N10-methylene tetrahydrofolate to glycine resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers; the mammalian enzyme forms a homotetramer comprising four pyridoxal phosphate-bound active sites.
Probab=20.77 E-value=2e+02 Score=25.38 Aligned_cols=47 Identities=9% Similarity=0.069 Sum_probs=32.2
Q ss_pred chhHHHHHHHhcCcceEEEecCCCccc-hhhhHHHHHHhcCCCEEEECC
Q 029589 132 GLNHVTYLIEQNKAQLVVIAHDVDPIE-LVVWLPALCRKMEIPYCIVKG 179 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~DvdP~e-lv~~LpaLC~k~~VPy~iV~s 179 (191)
-...+.+++...+.++|++.+...|.. -+.-|-.+|+++|+.++. +.
T Consensus 149 d~~~l~~~i~~~~~~~v~~~~~~~~~~~~~~~I~~l~~~~~~~li~-D~ 196 (402)
T cd00378 149 DYDALEKMALEFKPKLIVAGASAYPRPIDFKRFREIADEVGAYLLV-DM 196 (402)
T ss_pred CHHHHHHHHHhCCCCEEEecCcccCCCcCHHHHHHHHHhcCCEEEE-Ec
Confidence 356677778766788998877655532 223478899999987654 44
No 179
>cd01489 Uba2_SUMO Ubiquitin activating enzyme (E1) subunit UBA2. UBA2 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. UBA2 contains both the nucleotide-binding motif involved in adenylation and the catalytic cysteine involved in the thioester intermediate and Ublp transfer to E2.
Probab=20.71 E-value=87 Score=28.41 Aligned_cols=39 Identities=21% Similarity=0.261 Sum_probs=30.1
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHh
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLG 184 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG 184 (191)
...+||.|.|- .+...++-.+|+.++||++...+..-.|
T Consensus 90 ~~DvVv~a~Dn--~~ar~~in~~c~~~~ip~I~~gt~G~~G 128 (312)
T cd01489 90 QFDLVFNALDN--LAARRHVNKMCLAADVPLIESGTTGFLG 128 (312)
T ss_pred cCCEEEECCCC--HHHHHHHHHHHHHCCCCEEEEecCccee
Confidence 57788888874 3556679999999999999987654444
No 180
>cd04127 Rab27A Rab27a subfamily. The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated
Probab=20.60 E-value=1.1e+02 Score=23.44 Aligned_cols=40 Identities=20% Similarity=0.229 Sum_probs=23.8
Q ss_pred CcceEEEecCCCccc----hhhhHHHHHHhcCCCEEEECCHhHH
Q 029589 144 KAQLVVIAHDVDPIE----LVVWLPALCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 144 KAkLVVIA~DvdP~e----lv~~LpaLC~k~~VPy~iV~sK~~L 183 (191)
..-+++++.-+|-.+ -...+-.+|++.++||+.+..+...
T Consensus 120 ~~piiiv~nK~Dl~~~~~v~~~~~~~~~~~~~~~~~e~Sak~~~ 163 (180)
T cd04127 120 NPDIVLCGNKADLEDQRQVSEEQAKALADKYGIPYFETSAATGT 163 (180)
T ss_pred CCcEEEEEeCccchhcCccCHHHHHHHHHHcCCeEEEEeCCCCC
Confidence 455677776655321 1123567777788887777665543
No 181
>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=20.49 E-value=2.2e+02 Score=21.00 Aligned_cols=44 Identities=18% Similarity=0.208 Sum_probs=27.5
Q ss_pred HhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC-HhHHhhhhCC
Q 029589 141 EQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG-KSRLGSVNIL 189 (191)
Q Consensus 141 ekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s-K~~LG~a~Gi 189 (191)
....+.+|.|..|.. +. .-+++++++++|-++.+ ..++.++.|+
T Consensus 54 ~~~~v~vv~V~~~~~--~~---~~~~~~~~~~~~p~~~D~~~~~~~~~g~ 98 (149)
T cd02970 54 DALGVELVAVGPESP--EK---LEAFDKGKFLPFPVYADPDRKLYRALGL 98 (149)
T ss_pred HhcCeEEEEEeCCCH--HH---HHHHHHhcCCCCeEEECCchhHHHHcCc
Confidence 334566666666632 22 23678888888876554 4567777775
No 182
>PF00578 AhpC-TSA: AhpC/TSA family; InterPro: IPR000866 Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels which mediate signal transduction in mammalian cells. Prxs can be regulated by changes to phosphorylation, redox and possibly oligomerisation states. Prxs are divided into three classes: typical 2-Cys Prxs; atypical 2-Cys Prxs; and 1-Cys Prxs. All Prxs share the same basic catalytic mechanism, in which an active-site cysteine (the peroxidatic cysteine) is oxidised to a sulphenic acid by the peroxide substrate. The recycling of the sulphenic acid back to a thiol is what distinguishes the three enzyme classes. Using crystal structures, a detailed catalytic cycle has been derived for typical 2-Cys Prxs, including a model for the redox-regulated oligomeric state proposed to control enzyme activity []. Alkyl hydroperoxide reductase (AhpC) is responsible for directly reducing organic hyperoxides in its reduced dithiol form. Thiol specific antioxidant (TSA) is a physiologically important antioxidant which constitutes an enzymatic defence against sulphur-containing radicals. This family contains AhpC and TSA, as well as related proteins.; GO: 0016209 antioxidant activity, 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1QMV_A 1PRX_B 3HJP_C 3HA9_A 2V41_G 2V32_C 2V2G_C 3LWA_A 3IA1_B 1ZYE_G ....
Probab=20.43 E-value=1.5e+02 Score=21.31 Aligned_cols=51 Identities=14% Similarity=0.216 Sum_probs=31.8
Q ss_pred hHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC-HhHHhhhhCC
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG-KSRLGSVNIL 189 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s-K~~LG~a~Gi 189 (191)
++....++...++++.|..| +.+ -+-.+++++++++-++.+ ..++....|+
T Consensus 49 ~~~~~~~~~~~~~vi~is~d--~~~---~~~~~~~~~~~~~~~~~D~~~~~~~~~~~ 100 (124)
T PF00578_consen 49 NELYKKYKDKGVQVIGISTD--DPE---EIKQFLEEYGLPFPVLSDPDGELAKAFGI 100 (124)
T ss_dssp HHHHHHHHTTTEEEEEEESS--SHH---HHHHHHHHHTCSSEEEEETTSHHHHHTTC
T ss_pred HHHhhhhccceEEeeecccc--ccc---chhhhhhhhccccccccCcchHHHHHcCC
Confidence 34444455556777777765 333 256778888777766664 4567777665
No 183
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=20.40 E-value=1.7e+02 Score=27.29 Aligned_cols=43 Identities=16% Similarity=0.099 Sum_probs=35.2
Q ss_pred CcceEEEecCCCccchhhhHHHHHHhcCCCEEEECCHhHHhhh
Q 029589 144 KAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKGKSRLGSV 186 (191)
Q Consensus 144 KAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~sK~~LG~a 186 (191)
.....+|+.|+.-+.-...|..+|+.+|||+..+.+-.+|..+
T Consensus 206 g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~ 248 (388)
T PRK12723 206 SLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEE 248 (388)
T ss_pred CCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHH
Confidence 3578889999876666677999999999999998887777654
No 184
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=20.31 E-value=2.6e+02 Score=21.27 Aligned_cols=45 Identities=9% Similarity=0.130 Sum_probs=26.2
Q ss_pred HHhcCcceEEEecCCCccchhhhHHHHHHhcCCCEEEECC-HhHHhhhhCC
Q 029589 140 IEQNKAQLVVIAHDVDPIELVVWLPALCRKMEIPYCIVKG-KSRLGSVNIL 189 (191)
Q Consensus 140 IekkKAkLVVIA~DvdP~elv~~LpaLC~k~~VPy~iV~s-K~~LG~a~Gi 189 (191)
+....+.+|-|..| +. .-+-+.+++++++|-++.+ ...+++..|+
T Consensus 60 ~~~~~v~vi~Is~d--~~---~~~~~~~~~~~~~~~~l~D~~~~~~~~~gv 105 (154)
T PRK09437 60 LKKAGVVVLGISTD--KP---EKLSRFAEKELLNFTLLSDEDHQVAEQFGV 105 (154)
T ss_pred HHHCCCEEEEEcCC--CH---HHHHHHHHHhCCCCeEEECCCchHHHHhCC
Confidence 33444555555544 32 2245778888888776654 3456666664
No 185
>cd01887 IF2_eIF5B IF2/eIF5B (initiation factors 2/ eukaryotic initiation factor 5B) subfamily. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s.
Probab=20.29 E-value=1.1e+02 Score=22.90 Aligned_cols=18 Identities=17% Similarity=0.412 Sum_probs=9.9
Q ss_pred HHHhcCCCEEEECCHhHH
Q 029589 166 LCRKMEIPYCIVKGKSRL 183 (191)
Q Consensus 166 LC~k~~VPy~iV~sK~~L 183 (191)
+++..++|+++|-+|.+|
T Consensus 97 ~~~~~~~p~ivv~NK~Dl 114 (168)
T cd01887 97 LAKAANVPFIVALNKIDK 114 (168)
T ss_pred HHHHcCCCEEEEEEceec
Confidence 344556666666555544
No 186
>cd01832 SGNH_hydrolase_like_1 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. Myxobacterial members of this subfamily have been reported to be involved in adventurous gliding motility.
Probab=20.22 E-value=2.3e+02 Score=21.86 Aligned_cols=49 Identities=14% Similarity=0.138 Sum_probs=30.9
Q ss_pred chhHHHHHHHhcCcceEEEec-CC---Cc---------cchhhhHHHHHHhcCCCEEEECCH
Q 029589 132 GLNHVTYLIEQNKAQLVVIAH-DV---DP---------IELVVWLPALCRKMEIPYCIVKGK 180 (191)
Q Consensus 132 G~~~Vtk~IekkKAkLVVIA~-Dv---dP---------~elv~~LpaLC~k~~VPy~iV~sK 180 (191)
++....+.+....+.++++.. +. ++ .++...+..+|++++|+|+.+.+.
T Consensus 93 ~~~~~i~~i~~~~~~vil~~~~~~~~~~~~~~~~~~~~~~~n~~l~~~a~~~~v~~vd~~~~ 154 (185)
T cd01832 93 DLEEAVRRLRAAGARVVVFTIPDPAVLEPFRRRVRARLAAYNAVIRAVAARYGAVHVDLWEH 154 (185)
T ss_pred HHHHHHHHHHhCCCEEEEecCCCccccchhHHHHHHHHHHHHHHHHHHHHHcCCEEEecccC
Confidence 344455556555666666642 11 11 224556889999999999988764
No 187
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=20.21 E-value=2.6e+02 Score=26.76 Aligned_cols=60 Identities=18% Similarity=0.252 Sum_probs=51.0
Q ss_pred ceeeechhHHHHHHHhcCcceEEEecCCCcc----------------------------------------chhhhHHHH
Q 029589 127 IVVKYGLNHVTYLIEQNKAQLVVIAHDVDPI----------------------------------------ELVVWLPAL 166 (191)
Q Consensus 127 ~~L~~G~~~Vtk~IekkKAkLVVIA~DvdP~----------------------------------------elv~~LpaL 166 (191)
....+|..+|..+++-|-+...+|..|.+-. .++.++-.+
T Consensus 294 Gla~yG~~~vr~aL~~gaVd~llv~Edl~~~r~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~~~v~~~d~vd~l~e~ 373 (411)
T COG1503 294 GLAVYGEEEVREALEMGAVDTLLVSEDLEKERVTYKCPTCGYENLKSKREFEQKRFRCPECGSEMEEVEVSDLVDELAEL 373 (411)
T ss_pred ceeecchHHHHHHHHhcccceEEeeccccccceeecCCCcchhhhhcccccccccccCccccccccchhhhhHHHHHHHH
Confidence 4556999999999999999999999999842 347788999
Q ss_pred HHhcCCCEEEECCHhHHhhh
Q 029589 167 CRKMEIPYCIVKGKSRLGSV 186 (191)
Q Consensus 167 C~k~~VPy~iV~sK~~LG~a 186 (191)
|+..|.-+.+|.+..+=|..
T Consensus 374 a~~~Ga~ve~is~~~~eg~q 393 (411)
T COG1503 374 AEESGAKVEIISDDTDEGAQ 393 (411)
T ss_pred HHhcCCeEEEecCchHHHHH
Confidence 99999999999997776653
No 188
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=20.17 E-value=2.7e+02 Score=18.32 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=28.3
Q ss_pred hHHHHHHHhcCcceEEEecCCCccchhhhHHHHHHhc-CCCEEEECCHh
Q 029589 134 NHVTYLIEQNKAQLVVIAHDVDPIELVVWLPALCRKM-EIPYCIVKGKS 181 (191)
Q Consensus 134 ~~Vtk~IekkKAkLVVIA~DvdP~elv~~LpaLC~k~-~VPy~iV~sK~ 181 (191)
..+..++++.....-.+-.|-++ +....+...-... .||.+++.++.
T Consensus 14 ~~ak~~L~~~~i~~~~i~i~~~~-~~~~~~~~~~~~~~~vP~v~i~g~~ 61 (75)
T cd03418 14 VRAKALLDKKGVDYEEIDVDGDP-ALREEMINRSGGRRTVPQIFIGDVH 61 (75)
T ss_pred HHHHHHHHHCCCcEEEEECCCCH-HHHHHHHHHhCCCCccCEEEECCEE
Confidence 45566677777776666555554 3323333333334 89999999853
Done!