Query 033552
Match_columns 117
No_of_seqs 112 out of 750
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 03:36:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033552hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13600 putative ribosomal pr 99.9 3E-25 6.5E-30 151.1 6.1 69 13-82 15-83 (84)
2 KOG3167 Box H/ACA snoRNP compo 99.9 1.8E-24 4E-29 159.0 6.8 92 14-116 62-153 (153)
3 TIGR03677 rpl7ae 50S ribosomal 99.9 7.8E-24 1.7E-28 150.9 7.6 91 11-112 26-116 (117)
4 PRK04175 rpl7ae 50S ribosomal 99.9 2.1E-23 4.5E-28 149.8 7.2 91 11-112 30-120 (122)
5 PRK13601 putative L7Ae-like ri 99.9 5.6E-23 1.2E-27 139.1 6.9 78 6-84 3-80 (82)
6 PRK06683 hypothetical protein; 99.9 6.1E-23 1.3E-27 138.7 5.8 71 11-82 11-81 (82)
7 PRK13602 putative ribosomal pr 99.9 2.3E-22 4.9E-27 135.6 6.4 71 11-82 11-81 (82)
8 COG1358 RPL8A Ribosomal protei 99.8 3.1E-21 6.8E-26 138.1 6.0 76 10-86 26-101 (116)
9 PRK01018 50S ribosomal protein 99.8 1E-20 2.3E-25 131.3 6.6 77 10-87 15-92 (99)
10 PTZ00106 60S ribosomal protein 99.8 8.5E-20 1.8E-24 129.0 6.1 77 11-88 25-102 (108)
11 PTZ00222 60S ribosomal protein 99.8 1.4E-19 2.9E-24 144.2 7.4 73 13-86 134-206 (263)
12 PF01248 Ribosomal_L7Ae: Ribos 99.8 1.2E-19 2.5E-24 122.9 5.3 76 11-86 15-90 (95)
13 PRK07714 hypothetical protein; 99.8 3E-19 6.6E-24 123.7 5.9 75 11-87 18-92 (100)
14 PTZ00365 60S ribosomal protein 99.8 7.3E-19 1.6E-23 140.3 7.5 69 14-83 135-203 (266)
15 PRK07283 hypothetical protein; 99.8 1.1E-18 2.3E-23 120.9 5.6 74 11-87 18-91 (98)
16 PRK05583 ribosomal protein L7A 99.7 3.1E-17 6.7E-22 115.1 7.0 73 12-86 18-90 (104)
17 KOG3387 60S ribosomal protein 99.6 7.8E-15 1.7E-19 106.5 6.5 78 11-88 34-114 (131)
18 PRK09190 hypothetical protein; 99.6 4.2E-15 9E-20 116.4 5.3 90 11-103 111-206 (220)
19 COG1911 RPL30 Ribosomal protei 99.3 6.2E-12 1.3E-16 87.8 5.6 76 11-87 19-95 (100)
20 KOG3406 40S ribosomal protein 99.0 4.7E-10 1E-14 81.7 6.1 76 9-84 32-118 (134)
21 KOG2988 60S ribosomal protein 98.1 4.9E-06 1.1E-10 59.3 5.1 76 10-86 25-101 (112)
22 KOG3166 60S ribosomal protein 97.7 1.9E-05 4.1E-10 61.8 2.5 81 14-107 112-195 (209)
23 PF08228 RNase_P_pop3: RNase P 96.4 0.0059 1.3E-07 46.0 4.4 74 10-84 54-133 (158)
24 PF08032 SpoU_sub_bind: RNA 2' 95.3 0.045 9.8E-07 34.7 4.6 69 13-83 2-71 (76)
25 PF15608 PELOTA_1: PELOTA RNA 94.1 0.07 1.5E-06 37.6 3.5 47 15-63 43-89 (100)
26 PF03465 eRF1_3: eRF1 domain 3 94.0 0.04 8.8E-07 38.7 2.1 60 11-70 21-98 (113)
27 PF10087 DUF2325: Uncharacteri 89.5 0.83 1.8E-05 30.7 4.5 36 27-62 48-83 (97)
28 PRK05562 precorrin-2 dehydroge 89.0 0.95 2.1E-05 35.7 5.1 62 28-92 86-150 (223)
29 PRK04011 peptide chain release 88.3 0.79 1.7E-05 38.9 4.5 59 12-70 297-396 (411)
30 TIGR03676 aRF1/eRF1 peptide ch 86.1 1.4 3E-05 37.5 4.7 59 12-70 289-388 (403)
31 TIGR00111 pelota probable tran 86.0 0.97 2.1E-05 37.5 3.7 61 11-71 277-338 (351)
32 TIGR00108 eRF peptide chain re 85.6 1.4 3.1E-05 37.3 4.6 59 12-70 293-392 (409)
33 PLN02821 1-hydroxy-2-methyl-2- 82.6 3.5 7.5E-05 36.0 5.7 48 20-68 355-402 (460)
34 PF13727 CoA_binding_3: CoA-bi 81.8 0.94 2E-05 31.8 1.7 52 10-61 123-175 (175)
35 PRK05234 mgsA methylglyoxal sy 81.2 2.1 4.6E-05 31.3 3.4 47 15-61 63-113 (142)
36 PRK13371 4-hydroxy-3-methylbut 81.0 5.2 0.00011 34.2 6.1 81 20-103 281-380 (387)
37 TIGR01470 cysG_Nterm siroheme 80.8 2.6 5.7E-05 32.2 4.0 59 28-89 70-131 (205)
38 TIGR00186 rRNA_methyl_3 rRNA m 80.7 8.2 0.00018 30.1 6.8 68 12-84 3-71 (237)
39 PF07997 DUF1694: Protein of u 80.0 3.7 8E-05 29.4 4.3 49 18-67 53-101 (120)
40 PRK11181 23S rRNA (guanosine-2 78.8 11 0.00023 29.7 6.9 70 12-83 4-75 (244)
41 PF00009 GTP_EFTU: Elongation 78.3 1.3 2.7E-05 32.5 1.4 51 16-66 84-134 (188)
42 PF02603 Hpr_kinase_N: HPr Ser 78.1 3.3 7.1E-05 29.4 3.5 42 17-61 71-112 (127)
43 cd03420 SirA_RHOD_Pry_redox Si 77.9 2.1 4.6E-05 27.1 2.3 41 17-61 17-57 (69)
44 cd01422 MGS Methylglyoxal synt 77.4 3.3 7.2E-05 28.9 3.3 47 15-61 58-108 (115)
45 PRK10864 putative methyltransf 76.4 12 0.00027 31.3 7.0 73 9-84 107-181 (346)
46 PF02142 MGS: MGS-like domain 74.9 1.3 2.8E-05 29.6 0.6 41 18-58 51-94 (95)
47 PF13611 Peptidase_S76: Serine 74.5 2.7 5.8E-05 30.6 2.2 30 33-64 30-60 (121)
48 TIGR00216 ispH_lytB (E)-4-hydr 74.2 14 0.0003 30.2 6.5 65 20-88 202-266 (280)
49 PF02401 LYTB: LytB protein; 74.0 18 0.00038 29.5 7.1 64 20-88 203-267 (281)
50 COG1419 FlhF Flagellar GTP-bin 73.8 13 0.00028 32.1 6.5 81 23-104 229-309 (407)
51 PRK01045 ispH 4-hydroxy-3-meth 73.2 19 0.00042 29.6 7.2 65 20-88 204-268 (298)
52 cd04165 GTPBP1_like GTPBP1-lik 73.1 2.8 6.1E-05 32.3 2.2 49 18-66 100-150 (224)
53 TIGR03025 EPS_sugtrans exopoly 72.7 4.9 0.00011 33.6 3.7 49 19-67 180-228 (445)
54 cd00532 MGS-like MGS-like doma 72.1 6.3 0.00014 27.0 3.6 46 15-60 55-105 (112)
55 KOG2486 Predicted GTPase [Gene 72.0 3.8 8.1E-05 34.2 2.8 42 28-69 220-263 (320)
56 cd01483 E1_enzyme_family Super 71.9 4.5 9.8E-05 28.4 2.9 36 27-64 89-124 (143)
57 PF07085 DRTGG: DRTGG domain; 71.4 4.3 9.4E-05 27.3 2.6 31 28-61 62-92 (105)
58 PRK12723 flagellar biosynthesi 71.2 17 0.00037 30.8 6.6 57 27-83 206-262 (388)
59 COG1363 FrvX Cellulase M and r 70.8 21 0.00046 30.1 7.1 56 28-83 254-317 (355)
60 PRK11018 hypothetical protein; 68.5 4.8 0.0001 26.3 2.3 41 17-61 26-66 (78)
61 smart00851 MGS MGS-like domain 68.0 5.9 0.00013 26.0 2.6 41 18-58 46-89 (90)
62 COG1445 FrwB Phosphotransferas 67.9 6.5 0.00014 28.6 3.0 49 13-69 42-91 (122)
63 cd07984 LPLAT_LABLAT-like Lyso 67.2 38 0.00082 24.3 7.0 47 15-63 79-139 (192)
64 COG1648 CysG Siroheme synthase 67.2 6.6 0.00014 30.5 3.2 60 28-91 73-136 (210)
65 PF11823 DUF3343: Protein of u 66.3 14 0.0003 23.5 4.1 30 43-72 14-43 (73)
66 PRK12360 4-hydroxy-3-methylbut 66.3 27 0.00058 28.5 6.6 64 20-88 203-267 (281)
67 cd02983 P5_C P5 family, C-term 65.5 34 0.00073 24.2 6.4 54 56-112 3-56 (130)
68 TIGR03023 WcaJ_sugtrans Undeca 65.3 7.7 0.00017 32.5 3.4 55 13-67 176-231 (451)
69 PRK00087 4-hydroxy-3-methylbut 64.3 37 0.00079 30.4 7.6 78 20-101 200-278 (647)
70 PRK10637 cysG siroheme synthas 63.9 11 0.00023 32.2 4.1 61 28-91 73-136 (457)
71 cd03422 YedF YedF is a bacteri 62.9 12 0.00026 23.6 3.3 41 17-61 17-57 (69)
72 cd03423 SirA SirA (also known 62.1 16 0.00034 23.0 3.7 41 17-61 17-57 (69)
73 cd01485 E1-1_like Ubiquitin ac 60.0 8 0.00017 29.3 2.4 38 27-66 113-150 (198)
74 PF00391 PEP-utilizers: PEP-ut 59.9 16 0.00034 23.7 3.5 20 43-62 42-61 (80)
75 cd01424 MGS_CPS_II Methylglyox 59.6 13 0.00028 25.1 3.2 45 15-59 55-100 (110)
76 PF07905 PucR: Purine cataboli 59.5 13 0.00029 25.9 3.3 48 17-65 62-110 (123)
77 COG0796 MurI Glutamate racemas 57.0 43 0.00093 27.3 6.2 48 21-73 61-108 (269)
78 COG0761 lytB 4-Hydroxy-3-methy 57.0 35 0.00077 28.3 5.8 79 20-102 206-285 (294)
79 PRK10124 putative UDP-glucose 56.9 15 0.00033 31.4 3.8 48 20-67 196-243 (463)
80 PF03279 Lip_A_acyltrans: Bact 56.0 34 0.00073 26.8 5.4 46 16-63 181-240 (295)
81 cd01879 FeoB Ferrous iron tran 55.0 22 0.00048 24.0 3.8 42 26-67 73-114 (158)
82 PRK05703 flhF flagellar biosyn 54.5 45 0.00097 28.4 6.2 59 25-83 249-307 (424)
83 PF00899 ThiF: ThiF family; I 54.3 8.1 0.00017 26.9 1.5 35 27-63 92-126 (135)
84 TIGR01295 PedC_BrcD bacterioci 54.1 17 0.00036 25.4 3.1 58 6-63 3-62 (122)
85 TIGR03022 WbaP_sugtrans Undeca 54.0 17 0.00036 30.5 3.6 56 12-67 173-229 (456)
86 PRK06719 precorrin-2 dehydroge 53.4 37 0.00081 24.8 5.0 78 28-109 71-151 (157)
87 cd01857 HSR1_MMR1 HSR1/MMR1. 53.2 18 0.00039 25.2 3.1 50 17-66 3-54 (141)
88 TIGR01917 gly_red_sel_B glycin 52.7 70 0.0015 27.9 7.1 94 20-115 329-423 (431)
89 TIGR01626 ytfJ_HI0045 conserve 52.7 86 0.0019 23.9 7.0 51 31-81 98-153 (184)
90 PRK14723 flhF flagellar biosyn 52.4 42 0.00091 31.2 6.0 62 24-85 212-273 (767)
91 cd00755 YgdL_like Family of ac 52.2 17 0.00036 28.5 3.1 39 22-62 97-135 (231)
92 PRK01889 GTPase RsgA; Reviewed 51.4 15 0.00033 30.3 2.9 38 30-67 117-155 (356)
93 TIGR03107 glu_aminopep glutamy 51.3 67 0.0015 26.7 6.7 52 30-81 252-310 (350)
94 PRK00299 sulfur transfer prote 51.2 12 0.00027 24.5 1.9 42 16-61 26-67 (81)
95 PF04705 TSNR_N: Thiostrepton- 50.7 20 0.00043 25.7 3.0 41 20-62 41-81 (115)
96 cd00757 ThiF_MoeB_HesA_family 50.7 15 0.00033 28.1 2.6 35 27-63 111-145 (228)
97 COG5258 GTPBP1 GTPase [General 50.0 62 0.0014 28.6 6.4 67 18-110 217-285 (527)
98 PRK11889 flhF flagellar biosyn 49.9 93 0.002 27.2 7.4 47 25-71 267-313 (436)
99 cd01491 Ube1_repeat1 Ubiquitin 49.8 13 0.00029 30.1 2.3 40 28-69 106-145 (286)
100 cd01492 Aos1_SUMO Ubiquitin ac 49.8 17 0.00036 27.5 2.7 39 27-67 110-148 (197)
101 PRK00124 hypothetical protein; 49.6 17 0.00037 27.2 2.6 30 31-62 3-32 (151)
102 TIGR03729 acc_ester putative p 49.4 19 0.00042 27.4 3.0 45 17-61 22-68 (239)
103 PF04430 DUF498: Protein of un 49.1 47 0.001 22.7 4.6 52 17-68 41-94 (110)
104 PRK06718 precorrin-2 dehydroge 48.9 31 0.00067 26.2 4.0 59 27-89 70-131 (202)
105 cd00248 Mth938-like Mth938-lik 48.9 73 0.0016 21.9 5.6 49 20-68 44-93 (109)
106 PRK14722 flhF flagellar biosyn 48.9 59 0.0013 27.5 6.0 59 25-83 165-223 (374)
107 PF15632 ATPgrasp_Ter: ATP-gra 48.6 20 0.00043 29.8 3.1 51 15-66 10-78 (329)
108 cd07396 MPP_Nbla03831 Homo sap 48.5 21 0.00045 27.8 3.1 51 17-67 30-86 (267)
109 cd00291 SirA_YedF_YeeD SirA, Y 48.5 33 0.00071 20.9 3.5 42 18-62 15-58 (69)
110 PF13344 Hydrolase_6: Haloacid 48.2 16 0.00034 24.7 2.1 44 12-57 15-58 (101)
111 KOG4201 Anthranilate synthase 47.8 18 0.00039 29.4 2.6 62 18-82 151-213 (289)
112 PRK06731 flhF flagellar biosyn 46.8 1.2E+02 0.0026 24.3 7.3 48 24-71 100-147 (270)
113 TIGR01918 various_sel_PB selen 46.8 1E+02 0.0022 27.0 7.1 92 21-115 330-423 (431)
114 TIGR02342 chap_CCT_delta T-com 46.0 28 0.00061 30.0 3.8 49 19-67 265-313 (517)
115 PRK00865 glutamate racemase; P 45.6 54 0.0012 25.7 5.1 48 18-70 58-105 (261)
116 TIGR03106 trio_M42_hydro hydro 45.4 84 0.0018 26.0 6.4 51 31-81 254-312 (343)
117 COG0425 SirA Predicted redox p 45.1 23 0.00049 23.3 2.4 43 14-60 20-63 (78)
118 PF00448 SRP54: SRP54-type pro 45.0 36 0.00078 25.7 3.9 76 27-103 29-110 (196)
119 cd03421 SirA_like_N SirA_like_ 44.6 15 0.00032 22.8 1.4 38 16-58 16-53 (67)
120 TIGR02356 adenyl_thiF thiazole 44.3 21 0.00046 26.9 2.5 35 27-63 111-145 (202)
121 COG1537 PelA Predicted RNA-bin 43.7 29 0.00063 29.4 3.4 68 11-78 272-345 (352)
122 cd01020 TroA_b Metal binding p 43.6 28 0.0006 27.2 3.2 19 43-61 195-213 (264)
123 COG1671 Uncharacterized protei 43.5 25 0.00054 26.5 2.7 34 31-66 4-37 (150)
124 smart00187 INB Integrin beta s 43.2 40 0.00087 29.2 4.3 77 24-109 226-342 (423)
125 cd01493 APPBP1_RUB Ubiquitin a 43.2 13 0.00029 31.8 1.3 39 29-69 114-152 (425)
126 cd01894 EngA1 EngA1 subfamily. 42.9 26 0.00056 23.5 2.5 40 28-67 77-118 (157)
127 PF13848 Thioredoxin_6: Thiore 42.6 77 0.0017 22.2 5.1 60 43-108 64-123 (184)
128 cd01143 YvrC Periplasmic bindi 41.5 1.3E+02 0.0027 21.4 7.8 57 12-73 43-111 (195)
129 cd05565 PTS_IIB_lactose PTS_II 41.3 1.2E+02 0.0025 20.9 5.6 40 32-71 6-46 (99)
130 TIGR00853 pts-lac PTS system, 40.8 22 0.00049 24.0 2.0 36 26-63 49-84 (95)
131 PF01206 TusA: Sulfurtransfera 40.6 16 0.00035 22.6 1.2 39 20-62 21-59 (70)
132 PRK12726 flagellar biosynthesi 40.6 1.2E+02 0.0025 26.4 6.6 45 27-71 234-278 (407)
133 TIGR02208 lipid_A_msbB lipid A 40.5 66 0.0014 25.6 4.9 23 15-39 181-203 (305)
134 PRK15116 sulfur acceptor prote 40.4 35 0.00077 27.5 3.3 36 23-60 117-152 (268)
135 PRK00098 GTPase RsgA; Reviewed 40.3 27 0.00058 28.0 2.6 40 28-67 81-124 (298)
136 cd03372 TPP_ComE Thiamine pyro 39.8 1.2E+02 0.0025 22.4 5.8 39 45-83 114-155 (179)
137 COG2229 Predicted GTPase [Gene 39.8 34 0.00074 26.6 3.0 53 19-71 84-138 (187)
138 PF13241 NAD_binding_7: Putati 39.0 14 0.0003 24.8 0.7 33 28-62 61-93 (103)
139 TIGR00679 hpr-ser Hpr(Ser) kin 39.0 41 0.00088 27.9 3.5 49 18-69 73-122 (304)
140 PF13407 Peripla_BP_4: Peripla 38.9 46 0.00099 24.6 3.6 39 22-63 51-89 (257)
141 TIGR03013 EpsB_2 sugar transfe 38.9 63 0.0014 27.2 4.7 47 20-66 179-225 (442)
142 COG0566 SpoU rRNA methylases [ 38.8 1.4E+02 0.003 23.7 6.5 75 9-86 20-95 (260)
143 PF08534 Redoxin: Redoxin; In 38.6 85 0.0018 21.4 4.7 45 24-73 59-104 (146)
144 KOG0368 Acetyl-CoA carboxylase 38.0 34 0.00074 34.7 3.3 77 6-83 1523-1611(2196)
145 PRK10474 putative PTS system f 37.9 48 0.001 22.1 3.2 48 14-68 25-72 (88)
146 COG0420 SbcD DNA repair exonuc 37.9 27 0.00058 28.7 2.3 45 16-61 29-82 (390)
147 PRK08419 lipid A biosynthesis 37.5 98 0.0021 24.4 5.4 47 15-63 172-232 (298)
148 cd03338 TCP1_delta TCP-1 (CTT 37.1 48 0.0011 28.5 3.9 47 20-66 265-311 (515)
149 COG2129 Predicted phosphoester 37.1 35 0.00077 27.2 2.8 47 16-62 19-72 (226)
150 cd07402 MPP_GpdQ Enterobacter 36.6 38 0.00083 25.2 2.8 47 16-62 27-78 (240)
151 cd05564 PTS_IIB_chitobiose_lic 36.5 1.1E+02 0.0023 20.5 4.8 36 32-67 5-41 (96)
152 COG1086 Predicted nucleoside-d 36.0 54 0.0012 29.7 4.0 64 5-68 155-218 (588)
153 TIGR03659 IsdE heme ABC transp 35.3 2.1E+02 0.0046 22.2 7.1 60 9-73 71-141 (289)
154 PRK07377 hypothetical protein; 35.3 1.3E+02 0.0028 23.4 5.5 47 27-73 76-128 (184)
155 PF00578 AhpC-TSA: AhpC/TSA fa 35.3 36 0.00079 22.3 2.3 51 18-73 50-101 (124)
156 PF01497 Peripla_BP_2: Peripla 35.0 1.4E+02 0.003 21.8 5.6 75 19-112 52-136 (238)
157 PRK10200 putative racemase; Pr 34.9 86 0.0019 24.2 4.6 42 17-62 65-106 (230)
158 cd07392 MPP_PAE1087 Pyrobaculu 34.8 59 0.0013 22.8 3.5 41 21-62 17-60 (188)
159 PRK09545 znuA high-affinity zi 34.4 99 0.0021 25.0 5.1 65 38-110 237-307 (311)
160 TIGR03603 cyclo_dehy_ocin bact 34.0 41 0.0009 27.5 2.8 33 28-60 152-184 (318)
161 PF03618 Kinase-PPPase: Kinase 33.8 48 0.001 26.7 3.1 52 19-73 45-98 (255)
162 cd01489 Uba2_SUMO Ubiquitin ac 33.6 35 0.00076 28.1 2.4 40 28-69 91-130 (312)
163 cd01884 EF_Tu EF-Tu subfamily. 33.5 33 0.00072 25.7 2.1 49 17-65 80-129 (195)
164 PF14367 DUF4411: Domain of un 33.5 8.8 0.00019 28.2 -1.1 33 30-62 118-153 (162)
165 cd04104 p47_IIGP_like p47 (47- 33.4 56 0.0012 24.0 3.3 32 36-67 89-120 (197)
166 PF01751 Toprim: Toprim domain 33.3 13 0.00028 24.7 -0.2 37 18-54 48-88 (100)
167 cd01423 MGS_CPS_I_III Methylgl 33.3 53 0.0012 22.3 2.9 42 17-58 61-105 (116)
168 PRK05690 molybdopterin biosynt 33.2 32 0.0007 26.9 2.0 39 27-67 122-160 (245)
169 TIGR00315 cdhB CO dehydrogenas 33.2 51 0.0011 24.7 3.0 50 13-62 14-63 (162)
170 PF13545 HTH_Crp_2: Crp-like h 32.9 22 0.00047 22.0 0.8 33 44-76 5-44 (76)
171 PRK14721 flhF flagellar biosyn 32.9 1.5E+02 0.0032 25.5 6.1 61 26-86 220-280 (420)
172 PRK00945 acetyl-CoA decarbonyl 32.8 52 0.0011 25.0 3.0 46 17-62 25-71 (171)
173 PF00205 TPP_enzyme_M: Thiamin 32.6 10 0.00022 26.4 -0.9 45 17-61 2-46 (137)
174 PF00071 Ras: Ras family; Int 32.2 79 0.0017 21.5 3.7 42 27-68 71-118 (162)
175 PRK06153 hypothetical protein; 31.9 42 0.00091 28.8 2.6 39 27-67 266-304 (393)
176 COG1535 EntB Isochorismate hyd 31.9 31 0.00068 27.2 1.7 19 43-61 60-78 (218)
177 cd01895 EngA2 EngA2 subfamily. 31.8 59 0.0013 21.9 3.0 40 28-67 85-126 (174)
178 PRK07920 lipid A biosynthesis 31.5 2.2E+02 0.0048 22.5 6.6 46 15-62 171-229 (298)
179 cd05560 Xcc1710_like Xcc1710_l 31.5 1.8E+02 0.0038 20.1 5.8 48 21-68 46-93 (109)
180 TIGR00789 flhB_rel flhB C-term 31.5 43 0.00094 22.4 2.1 35 32-71 20-54 (82)
181 TIGR02355 moeB molybdopterin s 31.4 39 0.00084 26.4 2.2 35 27-63 114-148 (240)
182 PRK06995 flhF flagellar biosyn 31.3 92 0.002 27.3 4.7 60 24-83 283-342 (484)
183 TIGR03594 GTPase_EngA ribosome 31.3 45 0.00097 27.4 2.6 49 18-66 247-295 (429)
184 PF01297 TroA: Periplasmic sol 31.3 35 0.00075 26.2 1.9 68 38-110 184-253 (256)
185 TIGR00715 precor6x_red precorr 31.2 38 0.00083 26.9 2.1 40 21-60 59-98 (256)
186 cd04168 TetM_like Tet(M)-like 31.0 48 0.001 25.6 2.6 50 18-67 80-129 (237)
187 PRK05645 lipid A biosynthesis 30.8 1.2E+02 0.0025 24.0 4.9 23 15-39 171-193 (295)
188 TIGR02339 thermosome_arch ther 30.8 51 0.0011 28.4 3.0 43 21-68 276-318 (519)
189 PRK13957 indole-3-glycerol-pho 30.7 1E+02 0.0022 24.7 4.5 64 16-82 114-178 (247)
190 PF01976 DUF116: Protein of un 30.5 1.5E+02 0.0033 21.9 5.2 41 43-83 75-115 (158)
191 PRK09437 bcp thioredoxin-depen 30.0 1.3E+02 0.0028 20.8 4.6 51 18-73 55-106 (154)
192 COG1493 HprK Serine kinase of 30.0 73 0.0016 26.6 3.6 42 17-61 71-112 (308)
193 PF05343 Peptidase_M42: M42 gl 30.0 86 0.0019 25.3 4.0 55 29-83 209-271 (292)
194 KOG2016 NEDD8-activating compl 29.9 44 0.00096 29.6 2.4 37 30-67 121-157 (523)
195 cd01018 ZntC Metal binding pro 29.9 53 0.0012 25.6 2.7 58 37-109 201-264 (266)
196 cd01891 TypA_BipA TypA (tyrosi 29.8 50 0.0011 23.9 2.4 48 20-67 83-130 (194)
197 PRK08057 cobalt-precorrin-6x r 29.7 41 0.0009 26.7 2.1 47 15-61 53-99 (248)
198 PF06684 AA_synth: Amino acid 29.6 55 0.0012 25.2 2.7 45 62-107 11-56 (175)
199 cd07395 MPP_CSTP1 Homo sapiens 29.4 77 0.0017 24.2 3.5 46 16-61 36-93 (262)
200 COG1503 eRF1 Peptide chain rel 29.3 69 0.0015 27.7 3.5 60 11-70 295-394 (411)
201 PRK05428 HPr kinase/phosphoryl 29.2 82 0.0018 26.1 3.8 42 18-62 73-114 (308)
202 PF07498 Rho_N: Rho terminatio 29.1 17 0.00038 21.2 -0.1 27 43-69 7-33 (43)
203 cd04169 RF3 RF3 subfamily. Pe 28.8 44 0.00096 26.4 2.1 48 19-66 88-135 (267)
204 PF04716 ETC_C1_NDUFA5: ETC co 28.4 70 0.0015 20.0 2.6 21 95-115 4-24 (57)
205 cd07393 MPP_DR1119 Deinococcus 28.4 59 0.0013 24.8 2.7 49 13-61 19-78 (232)
206 PRK06036 translation initiatio 28.2 60 0.0013 27.2 2.9 40 22-61 221-266 (339)
207 PLN02828 formyltetrahydrofolat 28.2 1.1E+02 0.0024 24.7 4.4 44 18-62 86-131 (268)
208 PRK09864 putative peptidase; P 28.2 1.6E+02 0.0035 24.7 5.4 20 40-59 264-283 (356)
209 cd01019 ZnuA Zinc binding prot 28.2 2.2E+02 0.0047 22.6 6.0 26 37-63 212-237 (286)
210 PRK08328 hypothetical protein; 28.1 60 0.0013 25.0 2.7 34 28-63 119-152 (231)
211 cd03339 TCP1_epsilon TCP-1 (CT 27.9 69 0.0015 27.7 3.3 44 19-67 279-322 (526)
212 PHA02546 47 endonuclease subun 27.9 69 0.0015 26.1 3.2 46 16-61 28-83 (340)
213 PRK03147 thiol-disulfide oxido 27.8 1.5E+02 0.0033 20.6 4.7 57 22-82 89-146 (173)
214 TIGR00829 FRU PTS system, fruc 27.7 79 0.0017 21.0 2.9 44 14-64 39-82 (85)
215 TIGR03499 FlhF flagellar biosy 27.6 1.4E+02 0.003 23.7 4.8 48 26-73 223-270 (282)
216 PF02571 CbiJ: Precorrin-6x re 27.6 43 0.00093 26.5 1.9 49 12-60 51-99 (249)
217 cd01028 TOPRIM_TopoIA TOPRIM_T 27.4 72 0.0016 22.6 2.9 31 27-57 90-122 (142)
218 PRK06628 lipid A biosynthesis 27.3 1.2E+02 0.0027 23.9 4.4 46 15-62 174-231 (290)
219 cd04164 trmE TrmE (MnmE, ThdF, 27.3 72 0.0016 21.2 2.7 44 27-70 80-123 (157)
220 COG0218 Predicted GTPase [Gene 27.2 69 0.0015 25.1 2.9 38 28-65 107-146 (200)
221 cd01822 Lysophospholipase_L1_l 27.2 62 0.0014 22.5 2.5 46 16-61 90-142 (177)
222 TIGR01766 tspaseT_teng_C trans 27.2 47 0.001 21.1 1.7 23 40-62 56-78 (82)
223 KOG2869 Meiotic cell division 27.1 33 0.00071 29.3 1.1 72 10-86 290-370 (379)
224 PRK08943 lipid A biosynthesis 27.1 1.6E+02 0.0036 23.5 5.2 23 15-39 190-212 (314)
225 PRK00771 signal recognition pa 26.7 2.2E+02 0.0048 24.5 6.1 40 22-61 118-157 (437)
226 TIGR00619 sbcd exonuclease Sbc 26.6 74 0.0016 24.8 3.0 45 17-61 29-82 (253)
227 TIGR03598 GTPase_YsxC ribosome 26.5 59 0.0013 23.2 2.3 21 46-66 121-141 (179)
228 COG1168 MalY Bifunctional PLP- 26.5 73 0.0016 27.5 3.1 44 15-58 146-195 (388)
229 PF00218 IGPS: Indole-3-glycer 26.5 80 0.0017 25.3 3.2 66 15-83 120-186 (254)
230 PRK14725 pyruvate kinase; Prov 26.4 1.6E+02 0.0035 26.8 5.4 45 41-86 522-578 (608)
231 cd05017 SIS_PGI_PMI_1 The memb 26.4 1.2E+02 0.0026 20.5 3.8 45 29-73 45-89 (119)
232 cd01484 E1-2_like Ubiquitin ac 26.3 57 0.0012 25.6 2.4 39 27-67 91-129 (234)
233 PRK09590 celB cellobiose phosp 26.3 2.1E+02 0.0045 19.7 4.9 39 31-69 6-45 (104)
234 COG1879 RbsB ABC-type sugar tr 26.3 77 0.0017 24.7 3.1 42 19-63 84-125 (322)
235 cd04170 EF-G_bact Elongation f 26.3 67 0.0015 24.8 2.7 51 17-67 79-129 (268)
236 cd02001 TPP_ComE_PpyrDC Thiami 26.2 82 0.0018 22.8 3.0 28 44-71 112-139 (157)
237 cd03018 PRX_AhpE_like Peroxire 26.1 1.9E+02 0.0041 19.6 4.8 49 20-73 55-106 (149)
238 COG0182 Predicted translation 26.0 88 0.0019 26.6 3.5 40 23-62 224-270 (346)
239 cd01821 Rhamnogalacturan_acety 25.8 45 0.00098 24.1 1.6 47 17-63 97-155 (198)
240 PRK10427 putative PTS system f 25.8 1.1E+02 0.0024 21.5 3.6 49 14-69 44-92 (114)
241 TIGR02740 TraF-like TraF-like 25.7 1.6E+02 0.0035 23.4 4.9 59 18-76 159-232 (271)
242 cd03361 TOPRIM_TopoIA_RevGyr T 25.6 61 0.0013 24.1 2.3 42 15-56 104-149 (170)
243 PF03494 Beta-APP: Beta-amyloi 25.5 19 0.00042 21.1 -0.3 13 28-40 12-24 (39)
244 PRK08734 lipid A biosynthesis 25.5 2.7E+02 0.0058 22.2 6.1 23 15-39 172-194 (305)
245 COG2401 ABC-type ATPase fused 25.5 49 0.0011 29.6 1.9 34 40-73 544-577 (593)
246 PRK08706 lipid A biosynthesis 25.4 2.6E+02 0.0056 21.9 6.0 24 15-39 165-188 (289)
247 PF10281 Ish1: Putative stress 25.3 44 0.00095 18.8 1.2 25 44-68 7-32 (38)
248 PRK15174 Vi polysaccharide exp 25.1 2.6E+02 0.0056 24.9 6.5 47 15-63 534-593 (656)
249 PRK12475 thiamine/molybdopteri 24.9 66 0.0014 26.5 2.6 39 27-67 116-154 (338)
250 COG1029 FwdB Formylmethanofura 24.8 1.7E+02 0.0036 25.5 5.0 82 21-107 328-427 (429)
251 cd03017 PRX_BCP Peroxiredoxin 24.8 2.2E+02 0.0048 19.0 5.3 48 22-74 52-100 (140)
252 PF01297 TroA: Periplasmic sol 24.7 92 0.002 23.8 3.2 42 18-63 190-231 (256)
253 PF02347 GDC-P: Glycine cleava 24.6 1.4E+02 0.0031 25.8 4.6 62 24-89 150-211 (429)
254 KOG3123 Diphthine synthase [Tr 24.6 2.7E+02 0.0058 22.6 5.8 75 24-110 74-155 (272)
255 PF02421 FeoB_N: Ferrous iron 24.5 68 0.0015 23.7 2.4 54 19-72 70-123 (156)
256 cd04117 Rab15 Rab15 subfamily. 24.4 49 0.0011 23.1 1.5 41 28-68 73-119 (161)
257 COG1707 ACT domain-containing 24.4 75 0.0016 24.9 2.6 35 26-60 140-174 (218)
258 cd01854 YjeQ_engC YjeQ/EngC. 24.3 69 0.0015 25.4 2.5 24 43-66 98-121 (287)
259 cd01537 PBP1_Repressors_Sugar_ 24.3 1.5E+02 0.0034 21.1 4.2 42 18-62 46-87 (264)
260 cd07388 MPP_Tt1561 Thermus the 24.2 97 0.0021 24.1 3.3 47 16-62 20-70 (224)
261 cd06278 PBP1_LacI_like_2 Ligan 24.2 1.4E+02 0.0031 21.7 4.0 40 18-62 45-85 (266)
262 PF10996 Beta-Casp: Beta-Casp 24.1 1.2E+02 0.0026 20.3 3.4 54 8-61 60-115 (126)
263 TIGR00157 ribosome small subun 24.0 61 0.0013 25.2 2.1 24 43-66 56-79 (245)
264 cd03343 cpn60 cpn60 chaperonin 24.0 79 0.0017 27.1 3.0 44 20-68 272-315 (517)
265 cd00568 TPP_enzymes Thiamine p 24.0 1E+02 0.0022 21.4 3.1 27 45-71 127-153 (168)
266 PF02472 ExbD: Biopolymer tran 24.0 72 0.0016 21.6 2.3 51 15-65 77-130 (130)
267 TIGR03846 sulfopy_beta sulfopy 23.9 3E+02 0.0066 20.3 7.2 27 45-71 114-141 (181)
268 PF08862 DUF1829: Domain of un 23.9 1.2E+02 0.0026 20.3 3.2 39 21-60 47-85 (88)
269 cd01017 AdcA Metal binding pro 23.7 93 0.002 24.4 3.1 68 36-110 203-278 (282)
270 cd01859 MJ1464 MJ1464. This f 23.7 1.2E+02 0.0027 21.0 3.5 47 20-67 6-54 (156)
271 COG0541 Ffh Signal recognition 23.6 83 0.0018 27.6 3.0 41 21-61 122-162 (451)
272 cd01017 AdcA Metal binding pro 23.6 1.2E+02 0.0027 23.7 3.8 43 17-63 210-252 (282)
273 PRK11509 hydrogenase-1 operon 23.5 2.9E+02 0.0063 20.0 5.8 64 21-85 29-102 (132)
274 PRK12721 secretion system appa 23.5 64 0.0014 27.0 2.2 36 31-71 281-316 (349)
275 PRK08733 lipid A biosynthesis 23.4 2.2E+02 0.0048 22.6 5.3 46 15-62 183-242 (306)
276 PRK00093 GTP-binding protein D 23.3 75 0.0016 26.2 2.6 48 19-66 74-121 (435)
277 PRK05646 lipid A biosynthesis 23.3 2.4E+02 0.0053 22.4 5.5 23 15-39 182-204 (310)
278 COG0352 ThiE Thiamine monophos 23.3 69 0.0015 25.0 2.3 56 16-72 24-82 (211)
279 PRK12736 elongation factor Tu; 23.3 63 0.0014 26.8 2.2 50 17-66 90-140 (394)
280 cd00861 ProRS_anticodon_short 23.2 1.2E+02 0.0026 19.1 3.1 45 20-68 24-68 (94)
281 PF10686 DUF2493: Protein of u 23.1 75 0.0016 20.5 2.1 45 16-61 20-64 (71)
282 PRK03980 flap endonuclease-1; 23.1 1.2E+02 0.0027 24.5 3.8 36 35-71 78-115 (292)
283 TIGR00461 gcvP glycine dehydro 23.1 3.3E+02 0.0071 26.1 6.9 59 24-88 149-207 (939)
284 PRK08762 molybdopterin biosynt 23.1 68 0.0015 26.5 2.3 36 27-64 225-260 (376)
285 cd03010 TlpA_like_DsbE TlpA-li 23.1 1.7E+02 0.0036 19.5 4.0 28 46-73 70-99 (127)
286 cd00636 TroA-like Helical back 23.1 2.1E+02 0.0047 18.3 8.6 41 18-63 52-92 (148)
287 TIGR02343 chap_CCT_epsi T-comp 23.0 76 0.0016 27.6 2.7 43 19-66 283-325 (532)
288 PF13519 VWA_2: von Willebrand 22.9 1.1E+02 0.0023 20.7 3.0 34 28-61 100-133 (172)
289 smart00857 Resolvase Resolvase 22.6 62 0.0013 22.2 1.7 19 49-67 60-78 (148)
290 cd01886 EF-G Elongation factor 22.5 70 0.0015 25.3 2.2 51 17-67 79-129 (270)
291 TIGR01404 FlhB_rel_III type II 22.4 69 0.0015 26.7 2.2 37 31-72 280-316 (342)
292 cd06267 PBP1_LacI_sugar_bindin 22.3 1.7E+02 0.0036 21.0 4.0 41 19-63 47-87 (264)
293 COG2099 CobK Precorrin-6x redu 22.0 60 0.0013 26.4 1.7 67 15-83 54-135 (257)
294 PRK06298 type III secretion sy 22.0 68 0.0015 27.0 2.1 37 31-72 282-318 (356)
295 cd01885 EF2 EF2 (for archaea a 21.9 90 0.002 24.0 2.7 49 18-66 89-137 (222)
296 cd06312 PBP1_ABC_sugar_binding 21.9 1.1E+02 0.0024 22.7 3.1 44 17-62 47-90 (271)
297 cd06318 PBP1_ABC_sugar_binding 21.8 1.4E+02 0.003 22.1 3.6 41 19-62 47-88 (282)
298 cd04102 RabL3 RabL3 (Rab-like3 21.7 56 0.0012 24.7 1.5 42 27-68 77-143 (202)
299 COG4359 Uncharacterized conser 21.7 76 0.0017 25.2 2.2 41 42-83 77-123 (220)
300 COG2257 Uncharacterized homolo 21.6 57 0.0012 22.7 1.3 40 26-71 20-59 (92)
301 PLN02331 phosphoribosylglycina 21.6 1.7E+02 0.0037 22.5 4.2 43 17-63 14-58 (207)
302 PF00362 Integrin_beta: Integr 21.5 58 0.0013 28.0 1.7 15 24-38 229-243 (426)
303 PLN03126 Elongation factor Tu; 21.5 82 0.0018 27.3 2.6 50 17-66 159-209 (478)
304 cd03362 TOPRIM_TopoIA_TopoIII 21.5 1.2E+02 0.0027 21.7 3.2 33 19-52 91-125 (151)
305 cd02004 TPP_BZL_OCoD_HPCL Thia 21.5 1.2E+02 0.0027 21.7 3.2 25 46-70 131-155 (172)
306 cd05125 Mth938_2P1-like Mth938 21.4 3E+02 0.0064 19.3 5.9 55 27-81 54-111 (114)
307 PF12850 Metallophos_2: Calcin 21.3 58 0.0013 22.1 1.4 40 18-65 18-58 (156)
308 PRK13109 flhB flagellar biosyn 21.2 71 0.0015 26.9 2.1 37 31-72 290-326 (358)
309 PRK10966 exonuclease subunit S 21.2 1E+02 0.0022 26.1 3.0 45 17-61 29-81 (407)
310 cd01887 IF2_eIF5B IF2/eIF5B (i 21.1 1.1E+02 0.0025 20.7 2.9 40 28-67 74-115 (168)
311 PRK06553 lipid A biosynthesis 21.1 3.9E+02 0.0085 21.2 6.3 51 15-72 193-243 (308)
312 PRK10444 UMP phosphatase; Prov 21.0 78 0.0017 24.7 2.2 41 13-55 19-59 (248)
313 cd01832 SGNH_hydrolase_like_1 21.0 73 0.0016 22.4 1.9 50 15-64 93-155 (185)
314 cd02009 TPP_SHCHC_synthase Thi 20.9 1.1E+02 0.0023 22.3 2.8 24 46-69 134-157 (175)
315 COG0552 FtsY Signal recognitio 20.9 72 0.0016 27.0 2.0 53 8-60 139-200 (340)
316 COG1105 FruK Fructose-1-phosph 20.8 3.7E+02 0.0081 22.3 6.2 47 27-73 129-178 (310)
317 PRK09108 type III secretion sy 20.7 78 0.0017 26.5 2.2 36 31-71 283-318 (353)
318 TIGR00639 PurN phosphoribosylg 20.6 1.4E+02 0.0031 22.5 3.5 41 17-61 15-57 (190)
319 PF07282 OrfB_Zn_ribbon: Putat 20.6 73 0.0016 19.6 1.6 23 42-64 4-26 (69)
320 PRK06552 keto-hydroxyglutarate 20.6 1E+02 0.0022 23.8 2.7 46 18-70 80-126 (213)
321 cd06423 CESA_like CESA_like is 20.5 83 0.0018 20.5 2.0 52 16-68 12-66 (180)
322 PRK14869 putative manganese-de 20.3 1.7E+02 0.0036 25.3 4.2 52 21-76 196-248 (546)
323 COG0050 TufB GTPases - transla 20.3 1E+02 0.0022 26.4 2.8 47 13-61 82-134 (394)
324 TIGR00035 asp_race aspartate r 20.2 88 0.0019 23.8 2.3 47 16-66 64-112 (229)
325 PRK10867 signal recognition pa 20.2 3.3E+02 0.0071 23.5 5.9 39 23-61 124-163 (433)
326 PRK06027 purU formyltetrahydro 20.2 1.7E+02 0.0038 23.5 4.1 38 18-61 105-144 (286)
327 cd06299 PBP1_LacI_like_13 Liga 20.1 1.8E+02 0.004 21.2 3.9 39 20-62 48-86 (265)
328 CHL00071 tufA elongation facto 20.1 85 0.0018 26.2 2.3 50 17-66 90-140 (409)
329 PRK09331 Sep-tRNA:Cys-tRNA syn 20.0 1.2E+02 0.0025 24.7 3.1 39 27-67 158-200 (387)
No 1
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=99.92 E-value=3e-25 Score=151.06 Aligned_cols=69 Identities=19% Similarity=0.235 Sum_probs=66.9
Q ss_pred eeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEe
Q 033552 13 CVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVL 82 (117)
Q Consensus 13 ~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~ 82 (117)
++|+|||+++|++|++++||||.|++|. ++.|++.+|+++||||+|++||++||+|||+++++++++|.
T Consensus 15 vvG~kqt~Kai~kg~~~~v~iA~Da~~~-vv~~l~~lceek~Ip~v~V~s~~~LGkAcgi~V~aa~aai~ 83 (84)
T PRK13600 15 VVGLKETLKALKKDQVTSLIIAEDVEVY-LMTRVLSQINQKNIPVSFFKSKHALGKHVGINVNATIVALI 83 (84)
T ss_pred eeeHHHHHHHHhcCCceEEEEeCCCCHH-HHHHHHHHHHHcCCCEEEECCHHHHHHHhCCCcCeEEEEEe
Confidence 9999999999999999999999999995 89999999999999999999999999999999999999885
No 2
>KOG3167 consensus Box H/ACA snoRNP component, involved in ribosomal RNA pseudouridinylation [RNA processing and modification]
Probab=99.91 E-value=1.8e-24 Score=159.00 Aligned_cols=92 Identities=49% Similarity=0.820 Sum_probs=87.3
Q ss_pred eeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCccchH
Q 033552 14 VGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQE 93 (117)
Q Consensus 14 vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~~~~ 93 (117)
-|+|.+.+.+++|+.+|+|||+|++|+++++|||.+||++||||++++|+++||+|.|.+||++|++|..+
T Consensus 62 rGvKevqK~vrkGeKGl~VlAgd~sPiDvi~HlP~lCEd~~vPYvy~psk~dlg~A~~~krpt~~v~v~p~--------- 132 (153)
T KOG3167|consen 62 RGVKEVQKRVRKGEKGLCVLAGDTSPIDVITHLPALCEDRGVPYVYTPSKEDLGAAGGTKRPTCCVFVKPG--------- 132 (153)
T ss_pred HHHHHHHHHHhcCCcceEEEecCCccHHHHhccchhhhccCCCccccccHHHHHHhcCCCCCceEEEEeeC---------
Confidence 38999999999999999999999999999999999999999999999999999999999999999999873
Q ss_pred HHHhhHHHHHHHHHHHHhhhccC
Q 033552 94 EQDKLKADYTLVVEDVKELASSL 116 (117)
Q Consensus 94 e~~~~~~~~~e~~~~~~~l~~~~ 116 (117)
.+|++.|+|+.++++.|+.+.
T Consensus 133 --~eyke~ydev~eel~~l~~~~ 153 (153)
T KOG3167|consen 133 --GEYKELYDEVLEELEALAVEV 153 (153)
T ss_pred --hhHHHHHHHHHHHHHhhccCC
Confidence 389999999999999998764
No 3
>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=99.90 E-value=7.8e-24 Score=150.90 Aligned_cols=91 Identities=27% Similarity=0.445 Sum_probs=80.8
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCcc
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGEL 90 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~ 90 (117)
+-+.|.+|++++|++|+++|||||+|++|.++.++++.+|++++|||++++||++||+|||+++++++++|++.++
T Consensus 26 kl~~G~~~v~kaikkgka~LVilA~D~s~~~~~~~i~~lc~~~~Ip~~~~~sk~eLG~a~Gk~~~~svvaI~d~g~---- 101 (117)
T TIGR03677 26 KIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYVYVKKKEDLGAAAGLEVGAASAAIVDEGK---- 101 (117)
T ss_pred CEeEcHHHHHHHHHcCCccEEEEeCCCCcHHHHHHHHHHHHHcCCCEEEeCCHHHHHHHhCCCCCeEEEEEEchhh----
Confidence 4578999999999999999999999999977899999999999999999999999999999988999999997444
Q ss_pred chHHHHhhHHHHHHHHHHHHhh
Q 033552 91 GQEEQDKLKADYTLVVEDVKEL 112 (117)
Q Consensus 91 ~~~e~~~~~~~~~e~~~~~~~l 112 (117)
.+..++++.++++.|
T Consensus 102 -------a~~~~~~~~~~i~~~ 116 (117)
T TIGR03677 102 -------AEELLKEIIEKVEAL 116 (117)
T ss_pred -------hHHHHHHHHHHHHhc
Confidence 344677777777665
No 4
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=99.89 E-value=2.1e-23 Score=149.84 Aligned_cols=91 Identities=31% Similarity=0.483 Sum_probs=79.1
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCcc
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGEL 90 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~ 90 (117)
+=+.|.+|++++|++|+++|||||+|++|.+++++++.+|++++|||++++||++||+|||+++++++++|++.++
T Consensus 30 klv~G~~~v~kaikkgkakLVilA~D~s~~~i~~~~~~lc~~~~Vp~~~~~tk~eLG~a~Gk~~~~svvaI~d~g~---- 105 (122)
T PRK04175 30 KIKKGTNETTKAVERGIAKLVVIAEDVDPEEIVAHLPLLCEEKKIPYVYVPSKKDLGKAAGLEVGAAAAAIVDAGK---- 105 (122)
T ss_pred CEeEcHHHHHHHHHcCCccEEEEeCCCChHHHHHHHHHHHHHcCCCEEEECCHHHHHHHhCCCCCeEEEEEechhh----
Confidence 3468999999999999999999999999987889999999999999999999999999999998899999997444
Q ss_pred chHHHHhhHHHHHHHHHHHHhh
Q 033552 91 GQEEQDKLKADYTLVVEDVKEL 112 (117)
Q Consensus 91 ~~~e~~~~~~~~~e~~~~~~~l 112 (117)
.+..++++.+.++.|
T Consensus 106 -------a~~~~~~~~~~i~~~ 120 (122)
T PRK04175 106 -------AKELVEDIVEKVNEL 120 (122)
T ss_pred -------hHHHHHHHHHHHHHh
Confidence 334566666666554
No 5
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=99.88 E-value=5.6e-23 Score=139.12 Aligned_cols=78 Identities=17% Similarity=0.201 Sum_probs=73.3
Q ss_pred CCCCccceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeec
Q 033552 6 DNLHSFNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 84 (117)
Q Consensus 6 ~~~~~~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~ 84 (117)
+.+..+-++|.+||+++|++|+++|||||+|++| +++++|+++|++++|||++++||+|||+|||+++++++++|+-+
T Consensus 3 ~~~~GKlv~G~~~vlkaIk~gkakLViiA~Da~~-~~~k~i~~~c~~~~Vpv~~~~t~~eLG~A~G~~v~aa~~~~~~~ 80 (82)
T PRK13601 3 QDCPSKRVVGAKQTLKAITNCNVLQVYIAKDAEE-HVTKKIKELCEEKSIKIVYIDTMKELGVMCGIDVGAAAAADIIG 80 (82)
T ss_pred cccCccEEEchHHHHHHHHcCCeeEEEEeCCCCH-HHHHHHHHHHHhCCCCEEEeCCHHHHHHHHCCccCeeeEEEeec
Confidence 5567788999999999999999999999999998 68999999999999999999999999999999999999998753
No 6
>PRK06683 hypothetical protein; Provisional
Probab=99.88 E-value=6.1e-23 Score=138.69 Aligned_cols=71 Identities=14% Similarity=0.085 Sum_probs=68.0
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEe
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVL 82 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~ 82 (117)
+.++|.+||+++|++|++++||||+|++| ++.++|.++|++++|||++++||+|||+|||+++++++++|.
T Consensus 11 k~v~G~~~v~kaik~gkaklViiA~Da~~-~~~~~i~~~~~~~~Vpv~~~~t~~eLG~A~G~~~~~a~~ai~ 81 (82)
T PRK06683 11 NVVVGHKRTLEAIKNGIVKEVVIAEDADM-RLTHVIIRTALQHNIPITKVESVRKLGKVAGIQVGASAIGII 81 (82)
T ss_pred CEEEcHHHHHHHHHcCCeeEEEEECCCCH-HHHHHHHHHHHhcCCCEEEECCHHHHHHHhCCcccEEEEEEe
Confidence 45999999999999999999999999999 479999999999999999999999999999999999999986
No 7
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=99.87 E-value=2.3e-22 Score=135.64 Aligned_cols=71 Identities=20% Similarity=0.243 Sum_probs=67.8
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEe
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVL 82 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~ 82 (117)
+-++|.+||+++|++|++++||||+|++| .+.++|+.+|++++|||++++|++|||+|||+++++++++|+
T Consensus 11 kl~~G~~~v~kai~~gkaklViiA~D~~~-~~~~~i~~~c~~~~Vp~~~~~s~~eLG~a~G~~~~~a~~ai~ 81 (82)
T PRK13602 11 SIVIGTKQTVKALKRGSVKEVVVAEDADP-RLTEKVEALANEKGVPVSKVDSMKKLGKACGIEVGAAAVAII 81 (82)
T ss_pred CEEEcHHHHHHHHHcCCeeEEEEECCCCH-HHHHHHHHHHHHcCCCEEEECCHHHHHHHHCCCcCEEEEEEe
Confidence 34899999999999999999999999999 589999999999999999999999999999999999999985
No 8
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=3.1e-21 Score=138.06 Aligned_cols=76 Identities=30% Similarity=0.497 Sum_probs=67.9
Q ss_pred ccceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 10 SFNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 10 ~~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
.+=..|+++++++|++|+++|||||+|++|.+++.|+|.+|+++||||++++||++||+|||++. +.++++.+.++
T Consensus 26 ~ki~~G~~e~~Kai~~g~a~LVviA~Dv~P~~~~~~l~~lc~~~~vpyv~V~sk~~LG~a~g~~~-~~vv~i~~~~~ 101 (116)
T COG1358 26 GKLKKGTNEVTKAIERGKAKLVVIAEDVSPEELVKHLPALCEEKNVPYVYVGSKKELGKAVGKEV-RKVVAIVDKGF 101 (116)
T ss_pred CCchhhHHHHHHHHHcCCCcEEEEecCCCHHHHHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCCc-ceeEEEeehhh
Confidence 34568999999999999999999999999989999999999999999999999999999999984 45566666444
No 9
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=99.83 E-value=1e-20 Score=131.26 Aligned_cols=77 Identities=13% Similarity=0.166 Sum_probs=69.9
Q ss_pred ccceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE-CCHhHHHhhcCCCcceEEEEEeecCCC
Q 033552 10 SFNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYV-ASKEDLANAGATKRPTCCVLVLTKPTK 87 (117)
Q Consensus 10 ~~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v-~tK~eLG~A~G~~~~~svv~I~~~~~~ 87 (117)
.+-++|.+||+++|++|+++|||||+|+++ ++.++++.+|++++||++.+ +||+|||+|||+++++++++|++.++.
T Consensus 15 gkl~~G~~~v~kai~~gkaklViiA~D~~~-~~~~~i~~~c~~~~Ip~~~~~~tk~eLG~a~Gk~~~~~~vaI~D~G~a 92 (99)
T PRK01018 15 GKVILGSKRTIKAIKLGKAKLVIVASNCPK-DIKEDIEYYAKLSGIPVYEYEGSSVELGTLCGKPFTVSALAIVDPGES 92 (99)
T ss_pred CCEEEcHHHHHHHHHcCCceEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEECCCHHHHHHHhCCCCCEEEEEEecCCHH
Confidence 356899999999999999999999999987 68999999999999998665 899999999999977899999986653
No 10
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=99.80 E-value=8.5e-20 Score=128.95 Aligned_cols=77 Identities=13% Similarity=0.086 Sum_probs=70.0
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEE-ECCHhHHHhhcCCCcceEEEEEeecCCCC
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIY-VASKEDLANAGATKRPTCCVLVLTKPTKG 88 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~-v~tK~eLG~A~G~~~~~svv~I~~~~~~~ 88 (117)
+-++|.+||+++|++|++++||||+|+++ ++.++|..+|++++||++. .+|++|||+|||++.++++++|++.++..
T Consensus 25 Klv~G~~~vlkalk~gkaklViiA~D~~~-~~kkki~~~~~~~~Vpv~~~~~t~~eLG~A~Gk~~r~svvaI~D~G~a~ 102 (108)
T PTZ00106 25 KYTLGTKSTLKALRNGKAKLVIISNNCPP-IRRSEIEYYAMLSKTGVHHYAGNNNDLGTACGRHFRVSVMSITDAGDSD 102 (108)
T ss_pred CeeecHHHHHHHHHcCCeeEEEEeCCCCH-HHHHHHHHHHhhcCCCEEEeCCCHHHHHHHhCCccCeEEEEEeCcchHH
Confidence 45899999999999999999999999998 4799999999999999985 69999999999999778899999866643
No 11
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=99.79 E-value=1.4e-19 Score=144.25 Aligned_cols=73 Identities=26% Similarity=0.499 Sum_probs=66.9
Q ss_pred eeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 13 CVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 13 ~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
+-|...++++|++|+++|||||+|+||++++.||+.+|++++|||++++||++||+|+|++ .+++++|++.+.
T Consensus 134 vsG~n~VtkaIekkKAkLVIIA~DVsPie~vk~LpaLCrk~~VPY~iVktKaeLG~AIGkK-travVAItD~g~ 206 (263)
T PTZ00222 134 VTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIGRK-TATCVAITDVNA 206 (263)
T ss_pred ccCHHHHHHHHHcCCceEEEEeCCCCHHHHHHHHHHHHHhcCCCEEEECCHHHHHHHHCCC-CCeEEEEeeCCc
Confidence 5699999999999999999999999999988999999999999999999999999999997 466788887443
No 12
>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=99.79 E-value=1.2e-19 Score=122.94 Aligned_cols=76 Identities=32% Similarity=0.527 Sum_probs=70.0
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
.=++|++++.++|++|++++||+|+|++|.....|++.+|++++|||++++||++||++||+++++++++|++.++
T Consensus 15 ~lv~G~~~v~k~l~~~~~~lvilA~d~~~~~~~~~l~~~c~~~~Ip~~~~~s~~eLG~~~g~~~~~~~~~i~d~~~ 90 (95)
T PF01248_consen 15 RLVKGIKEVLKALKKGKAKLVILAEDCSPDSIKKHLPALCEEKNIPYVFVPSKEELGRACGKKRPVSALAIKDAGD 90 (95)
T ss_dssp EEEESHHHHHHHHHTTCESEEEEETTSSSGHHHHHHHHHHHHTTEEEEEESHHHHHHHHTTSSSTSSEEEEEESTT
T ss_pred CEEEchHHHHHHHHcCCCcEEEEcCCCChhhhcccchhheeccceeEEEECCHHHHHHHHCCCCcEEEEEEECccc
Confidence 3578999999999999999999999999987667799999999999999999999999999998899999988554
No 13
>PRK07714 hypothetical protein; Provisional
Probab=99.78 E-value=3e-19 Score=123.69 Aligned_cols=75 Identities=15% Similarity=0.112 Sum_probs=68.7
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCC
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTK 87 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~ 87 (117)
+-++|.++++++|++|++++||+|+|++|. ..+++..+|+.++|||++++|++|||+|||++ ++++++|+++++.
T Consensus 18 k~v~G~~~v~~al~~g~~~lViiA~D~s~~-~~~ki~~~~~~~~vp~~~~~sk~eLG~a~Gk~-~~~~vai~d~g~a 92 (100)
T PRK07714 18 KVISGEELVLKEVRSGKAKLVLLSEDASVN-TTKKITDKCTYYNVPMRKVENRQQLGHAIGKD-ERVVVAVLDEGFA 92 (100)
T ss_pred CeeecHHHHHHHHHhCCceEEEEeCCCCHH-HHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCC-cceEEEEeCchhH
Confidence 458899999999999999999999999994 79999999999999999999999999999998 5668999886663
No 14
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=99.77 E-value=7.3e-19 Score=140.33 Aligned_cols=69 Identities=23% Similarity=0.487 Sum_probs=65.3
Q ss_pred eeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 14 VGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 14 vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
-|++.++++|++|+++|||||+|+||++++.++|++|++++|||++++||++||+|+|++ ++++++|++
T Consensus 135 ~Gin~VtklIekkKAkLVIIA~DVsP~t~kk~LP~LC~k~~VPY~iv~sK~eLG~AIGkk-traVVAItd 203 (266)
T PTZ00365 135 YGLNHVTDLVEYKKAKLVVIAHDVDPIELVCFLPALCRKKEVPYCIIKGKSRLGKLVHQK-TAAVVAIDN 203 (266)
T ss_pred hhhHHHHHHHHhCCccEEEEeCCCCHHHHHHHHHHHHhccCCCEEEECCHHHHHHHhCCC-CceEEEecc
Confidence 599999999999999999999999999999999999999999999999999999999996 677888876
No 15
>PRK07283 hypothetical protein; Provisional
Probab=99.76 E-value=1.1e-18 Score=120.90 Aligned_cols=74 Identities=14% Similarity=0.029 Sum_probs=67.2
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCC
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTK 87 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~ 87 (117)
+=++|.+||+++|++|++++||+|+|++| +..+++.++|++++||++.++|++|||+|||++ +++++|++.+++
T Consensus 18 klv~G~~~v~~aik~gk~~lVi~A~Das~-~~~kk~~~~~~~~~Vp~~~~~t~~eLG~a~Gk~--~~vvai~d~g~a 91 (98)
T PRK07283 18 RIISGEELVVKAIQSGQAKLVFLANDAGP-NLTKKVTDKSNYYQVEVSTVFSTLELSAAVGKP--RKVLAVTDAGFS 91 (98)
T ss_pred CeeEcHHHHHHHHHcCCccEEEEeCCCCH-HHHHHHHHHHHHcCCCEEEeCCHHHHHHHhCCC--ceEEEEeChhHH
Confidence 34789999999999999999999999999 579999999999999999999999999999985 567899886653
No 16
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=99.70 E-value=3.1e-17 Score=115.07 Aligned_cols=73 Identities=25% Similarity=0.223 Sum_probs=67.7
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
=+.|..+++++|++|+++|||+|+|++| +..++|..+|+.++||++..+|++|||.|||++ .+++++|+++++
T Consensus 18 lv~G~~~v~~aik~gk~~lVI~A~D~s~-~~kkki~~~~~~~~vp~~~~~t~~eLg~a~Gk~-~~~~iai~d~g~ 90 (104)
T PRK05583 18 LLEGYNKCEEAIKKKKVYLIIISNDISE-NSKNKFKNYCNKYNIPYIEGYSKEELGNAIGRD-EIKILGVKDKNM 90 (104)
T ss_pred eeecHHHHHHHHHcCCceEEEEeCCCCH-hHHHHHHHHHHHcCCCEEEecCHHHHHHHhCCC-CeEEEEEeChHH
Confidence 3679999999999999999999999999 569999999999999999999999999999997 489999998655
No 17
>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=99.56 E-value=7.8e-15 Score=106.50 Aligned_cols=78 Identities=26% Similarity=0.462 Sum_probs=71.4
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC---CCcceEEEEEeecCCC
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA---TKRPTCCVLVLTKPTK 87 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G---~~~~~svv~I~~~~~~ 87 (117)
+...|.+-+.+++.+|...+|++|.|+.|..+..|+|.+|+.+||||+||+++..||.+|| ..+++.++.|+....+
T Consensus 34 ql~kg~NEaTk~Lnrgi~~~Vv~aaD~kP~eIt~HLp~LcedknVp~v~Vpsk~alG~~cg~~~~~r~~~a~~i~~~~~~ 113 (131)
T KOG3387|consen 34 QLKKGANEATKTLNRGISEFVVMAADVKPLEITLHLPLLCEDKNVPYVFVPSKQALGLACGELVVLRPVIACSITTNEAS 113 (131)
T ss_pred HHhcccchHhhhhccCceeEEEEEccCCHHHHHHHhHHHhhccCCceEEeeccHHhhhhhhhHhhcCcceeEEEEecccc
Confidence 4457888899999999999999999999999999999999999999999999999999999 8899988999875554
Q ss_pred C
Q 033552 88 G 88 (117)
Q Consensus 88 ~ 88 (117)
.
T Consensus 114 ~ 114 (131)
T KOG3387|consen 114 I 114 (131)
T ss_pred c
Confidence 3
No 18
>PRK09190 hypothetical protein; Provisional
Probab=99.56 E-value=4.2e-15 Score=116.35 Aligned_cols=90 Identities=12% Similarity=-0.004 Sum_probs=78.8
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhh------CCCCEEEECCHhHHHhhcCCCcceEEEEEeec
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEE------SDIPYIYVASKEDLANAGATKRPTCCVLVLTK 84 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~------~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~ 84 (117)
+=+.|.-++.++|++|++.|||+|+|+|+. ..++|..+|+. ++|||+..+|++|||.|+|++ ++++++|+++
T Consensus 111 klVsG~~~V~~alk~gk~~Lvi~A~DaS~~-t~kKl~~~~~~~~~~~~~~Vp~v~~~tk~eLg~AlGr~-~~~~vav~d~ 188 (220)
T PRK09190 111 QVVSGFEKVDAALRSGEAAALIHASDGAAD-GKRKLDQARRALVHETGREIPVIGLFTAAELGLAFGRE-NVIHAALLAG 188 (220)
T ss_pred CEeecHHHHHHHHHcCCceEEEEeccCChh-HHHHHHHHHHhhcccccCCccEEEecCHHHHHHHhCCC-ceeEEEEcCh
Confidence 346799999999999999999999999995 69999999999 999999999999999999997 6888999998
Q ss_pred CCCCccchHHHHhhHHHHH
Q 033552 85 PTKGELGQEEQDKLKADYT 103 (117)
Q Consensus 85 ~~~~~~~~~e~~~~~~~~~ 103 (117)
++... ..++.++|..+-+
T Consensus 189 gfA~~-l~~~~~rl~~~~~ 206 (220)
T PRK09190 189 GAAER-VVKRAQRLAGYRG 206 (220)
T ss_pred HHHHH-HHHHHHHHHhhhc
Confidence 87664 5677788877543
No 19
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=99.28 E-value=6.2e-12 Score=87.81 Aligned_cols=76 Identities=14% Similarity=0.194 Sum_probs=67.4
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhhcCCCcceEEEEEeecCCC
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANAGATKRPTCCVLVLTKPTK 87 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A~G~~~~~svv~I~~~~~~ 87 (117)
+-++|.|+|+++++.|++++||||+++-+ ++.+.|.-.++=.+||+.+.. |..|||.+||+.-.+++++|++.+.+
T Consensus 19 kvilG~k~tiK~lk~gkaKliiiAsN~P~-~~k~~ieyYAkLs~ipV~~y~Gt~~eLG~~cgkpf~v~~laIiD~G~S 95 (100)
T COG1911 19 KVILGSKRTIKSLKLGKAKLIIIASNCPK-ELKEDIEYYAKLSDIPVYVYEGTSVELGTVCGKPFRVAALAIIDEGDS 95 (100)
T ss_pred CEEEehHHHHHHHHcCCCcEEEEecCCCH-HHHHHHHHHHHHcCCcEEEecCCceeHHhhhCCCceEEEEEEecCchh
Confidence 45789999999999999999999999987 689999888888899987665 99999999999988999999985553
No 20
>KOG3406 consensus 40S ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=99.04 E-value=4.7e-10 Score=81.73 Aligned_cols=76 Identities=26% Similarity=0.344 Sum_probs=66.3
Q ss_pred CccceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCC-----------cceE
Q 033552 9 HSFNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATK-----------RPTC 77 (117)
Q Consensus 9 ~~~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~-----------~~~s 77 (117)
|..-.=|++.+-|+|.+.++.||++|+|+++..+++-+..||.+++||++.+++..+||.++|.. .+.|
T Consensus 32 ~dGlarGi~Ea~KaldkrqA~lcvLaencdep~yvKLVeALcaeh~iplikV~d~k~LGew~Glckid~eGnarKvvGcs 111 (134)
T KOG3406|consen 32 HDGLARGIHEAAKALDKRQAHLCVLAENCDEPMYVKLVEALCAEHQIPLIKVGDAKELGEWAGLCKIDSEGNARKVVGCS 111 (134)
T ss_pred hchHHhHHHHHHHHHhhCceeEEEEeccCCchHHHHHHHHHHhhcCCCeEEeccchhhhhhhceeeecCCCCeeEeecce
Confidence 34445689999999999999999999998876899999999999999999999999999998853 2677
Q ss_pred EEEEeec
Q 033552 78 CVLVLTK 84 (117)
Q Consensus 78 vv~I~~~ 84 (117)
++++++-
T Consensus 112 ~vvVkd~ 118 (134)
T KOG3406|consen 112 CVVVKDY 118 (134)
T ss_pred EEEEeec
Confidence 8888863
No 21
>KOG2988 consensus 60S ribosomal protein L30 [Translation, ribosomal structure and biogenesis]
Probab=98.13 E-value=4.9e-06 Score=59.35 Aligned_cols=76 Identities=11% Similarity=0.090 Sum_probs=60.1
Q ss_pred ccceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEE-ECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 10 SFNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIY-VASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 10 ~~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~-v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
++-+.|-|||++.+|.|+++|+++|+++-|-. .+.|.-.+--.+.+|.+ -++-.+||.+||+--..+|..|++-+.
T Consensus 25 gkY~lgyK~T~k~~r~gkakL~~is~n~p~lr-ks~ieyyamlak~~v~~~sg~n~~lgt~~g~~fRv~v~~ivd~gd 101 (112)
T KOG2988|consen 25 GKYILGYKQTLKSLRQGKAKLIIISSNCPPLR-KSEIEYYAMLAKTGVHHYSGNNVELGTACGKTFRVSVLSIVDLGD 101 (112)
T ss_pred cceeechHHHHHHHHhccceEEEeecCCCCcc-hhHHHHHHHHhcCceeeecCCcEeHHHHhcCeeEeeEEEEEeccc
Confidence 46789999999999999999999999999843 55555554444455554 458889999999987788889887444
No 22
>KOG3166 consensus 60S ribosomal protein L7A [Translation, ribosomal structure and biogenesis]
Probab=97.73 E-value=1.9e-05 Score=61.83 Aligned_cols=81 Identities=22% Similarity=0.377 Sum_probs=56.6
Q ss_pred eeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCC---cc
Q 033552 14 VGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKG---EL 90 (117)
Q Consensus 14 vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~---~~ 90 (117)
.|+.-+...+++.++.||++|.|++|++++.++|.+|..+ ++..+ ..+ .++++++....+.+ .+
T Consensus 112 ~gvnTVttLVenKKAQLVV~ahDvDPIELVvFLPaLC~km-----ivk~~-------~~k-T~t~~a~v~~edk~~l~kl 178 (209)
T KOG3166|consen 112 AGVNTVTTLVENKKAQLVVTAHDVDPIELVVFLPALCRKM-----IVKGK-------HRK-TCTTVAFVNSEDKGALAKL 178 (209)
T ss_pred cCcceEeehhhccccceeEEecccCchhheeecHHhhhhh-----ccccc-------ccc-eeeeeeeechhhHHHHHHH
Confidence 4777788889999999999999999999999999999988 33333 333 34445553322233 22
Q ss_pred chHHHHhhHHHHHHHHH
Q 033552 91 GQEEQDKLKADYTLVVE 107 (117)
Q Consensus 91 ~~~e~~~~~~~~~e~~~ 107 (117)
...-...|.+-|||+.+
T Consensus 179 ~e~i~tn~ndrydei~~ 195 (209)
T KOG3166|consen 179 VEAIRTNYNDRYDEICR 195 (209)
T ss_pred HHHHhcccccchhhhhh
Confidence 23335578888888754
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=96.35 E-value=0.0059 Score=45.99 Aligned_cols=74 Identities=15% Similarity=0.090 Sum_probs=58.7
Q ss_pred ccceeeeecchhhhhcCCc--cEEEEeCCCCCcchheeHHHHhhhCC--CCEEEEC--CHhHHHhhcCCCcceEEEEEee
Q 033552 10 SFNCVGVVNDPLPLLFHEC--RLCVIAGNISPIDVITHVPILCEESD--IPYIYVA--SKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 10 ~~~~vG~kqt~kaL~kg~~--~LViLA~Dasp~~i~~~i~~lce~~~--IP~i~v~--tK~eLG~A~G~~~~~svv~I~~ 83 (117)
..=.+|+..+.+.|..... .+||++..-.|.-+..|||.+|.-.+ |..+..+ +.+.|+.++|.. .+++++|..
T Consensus 54 ~~v~~GfNsi~~~Le~~~~~~~~vFVcr~D~ps~L~~h~P~Lva~as~~vrLV~Lpkgs~~rLs~aLgi~-r~g~l~v~~ 132 (158)
T PF08228_consen 54 WGVTVGFNSIVRYLECQASDNVYVFVCRSDQPSILTSHFPQLVATASKSVRLVQLPKGSEARLSEALGIP-RVGILAVRA 132 (158)
T ss_pred ccEEEehHHHHHHHhcccCCCeEEEEECCCCcHHHHHHHHHHHHhccCcceEEeCChhHHHHHHHHhCCC-CccEEEEec
Confidence 4458999999999994332 36677655477678999999999988 8888876 788999999997 577888876
Q ss_pred c
Q 033552 84 K 84 (117)
Q Consensus 84 ~ 84 (117)
+
T Consensus 133 ~ 133 (158)
T PF08228_consen 133 D 133 (158)
T ss_pred C
Confidence 3
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=95.29 E-value=0.045 Score=34.66 Aligned_cols=69 Identities=19% Similarity=0.121 Sum_probs=50.5
Q ss_pred eeeeecchhhhhcCC-ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 13 CVGVVNDPLPLLFHE-CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 13 ~vG~kqt~kaL~kg~-~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
+-|.+-+..+|+.+. ..-|++..+..... ...+..+|...++|+..+ +++.|.+.++...+-.++++..
T Consensus 2 ieG~~~V~eaL~~~~~i~~l~~~~~~~~~~-~~~i~~~~~~~~i~v~~v-~~~~l~~ls~~~~hQGv~a~v~ 71 (76)
T PF08032_consen 2 IEGRHAVEEALKSGPRIKKLFVTEEKADKR-IKEILKLAKKKGIPVYEV-SKKVLDKLSDTENHQGVVAVVK 71 (76)
T ss_dssp EESHHHHHHHHHCTGGEEEEEEETT---CC-THHHHHHHHHCT-EEEEE--HHHHHHCTTTSS-TTEEEEEE
T ss_pred EEEHHHHHHHHcCCCCccEEEEEcCccchh-HHHHHHHHHHcCCeEEEe-CHHHHHHHcCCCCCCeEEEEEe
Confidence 347788889999986 88889998833222 678899999999999888 5667999998776666666655
No 25
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=94.08 E-value=0.07 Score=37.56 Aligned_cols=47 Identities=21% Similarity=0.280 Sum_probs=41.6
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
|+--|.+.|-+...-.|++-...+| + ..||..||+++|||+..++++
T Consensus 43 GIgEaTRvLLRRvP~~vLVr~~~~p-d-~~Hl~~LA~ekgVpVe~~~d~ 89 (100)
T PF15608_consen 43 GIGEATRVLLRRVPWKVLVRDPDDP-D-LAHLLLLAEEKGVPVEVYPDL 89 (100)
T ss_pred ChhHHHHHHHhcCCCEEEECCCCCc-c-HHHHHHHHHHcCCcEEEeCCC
Confidence 6777888898888889999877777 5 899999999999999999886
No 26
>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=93.97 E-value=0.04 Score=38.73 Aligned_cols=60 Identities=13% Similarity=0.128 Sum_probs=50.6
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCcc------------------hheeHHHHhhhCCCCEEEECCHhHHHhhc
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPID------------------VITHVPILCEESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~------------------i~~~i~~lce~~~IP~i~v~tK~eLG~A~ 70 (117)
.-+.|.++|.+|++.|.+..++|..|..-.. ++..+...+++.|.-+.++++..+-|.-+
T Consensus 21 ~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~~~r~~~~~~~~~~~~~~~i~~l~~~a~~~g~~v~iis~~~e~G~~L 98 (113)
T PF03465_consen 21 LAVYGIEEVKKALEMGAVETLLISDDLFRSRDVERCKCPECGGELEVVELIEELIELAEQSGAKVEIISSEHEEGEQL 98 (113)
T ss_dssp SEEESHHHHHHHHHTT-EEEEEEEHHHHTESCHHHHHSTTTHSEEEEEEHHHHHHHHHHHTTSEEEEE-TTSHHHHHH
T ss_pred cEEECHHHHHHHHHhCCCcEEEEecccccccceeccccccccchhhhHHHHHHHHHHHHHcCCEEEEEcCCCccHHHH
Confidence 4588999999999999999999999877432 36788899999999999999999888766
No 27
>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=89.51 E-value=0.83 Score=30.70 Aligned_cols=36 Identities=19% Similarity=0.304 Sum_probs=31.8
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
++-+||+-.|.-.-+....+...|+.+++|+++..+
T Consensus 48 ~aD~VIv~t~~vsH~~~~~vk~~akk~~ip~~~~~~ 83 (97)
T PF10087_consen 48 KADLVIVFTDYVSHNAMWKVKKAAKKYGIPIIYSRS 83 (97)
T ss_pred CCCEEEEEeCCcChHHHHHHHHHHHHcCCcEEEECC
Confidence 368999999988777899999999999999999983
No 28
>PRK05562 precorrin-2 dehydrogenase; Provisional
Probab=88.98 E-value=0.95 Score=35.65 Aligned_cols=62 Identities=15% Similarity=0.048 Sum_probs=43.5
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC---CCcceEEEEEeecCCCCccch
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA---TKRPTCCVLVLTKPTKGELGQ 92 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G---~~~~~svv~I~~~~~~~~~~~ 92 (117)
+.|||.|.|-. ++-..+-..|+++++++..+.+. +++...- .+++-..++|.+++.+..+..
T Consensus 86 ~~LViaATdD~--~vN~~I~~~a~~~~~lvn~vd~p-~~~dFi~PAiv~rg~l~IaIST~G~sP~lar 150 (223)
T PRK05562 86 KHLIVIATDDE--KLNNKIRKHCDRLYKLYIDCSDY-KKGLCIIPYQRSTKNFVFALNTKGGSPKTSV 150 (223)
T ss_pred CcEEEECCCCH--HHHHHHHHHHHHcCCeEEEcCCc-ccCeEEeeeEEecCCEEEEEECCCcCcHHHH
Confidence 67899998733 57889999999999999988775 4464321 123445688888776664443
No 29
>PRK04011 peptide chain release factor 1; Provisional
Probab=88.34 E-value=0.79 Score=38.93 Aligned_cols=59 Identities=14% Similarity=0.133 Sum_probs=48.7
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCCC-----------------------------------------CcchheeHHHHh
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNIS-----------------------------------------PIDVITHVPILC 50 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Das-----------------------------------------p~~i~~~i~~lc 50 (117)
-+-|..+|.+|++.|.+..++|..|.. ..+.+..+...+
T Consensus 297 avyG~~~V~~Ale~GAVetLLV~d~l~~~r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~v~~l~e~a 376 (411)
T PRK04011 297 AVYGEEEVRKALEMGAVDTLLISEDLRKDRVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSELEIVEEEDIIEELSELA 376 (411)
T ss_pred EEEcHHHHHHHHHcCCceEEEEeccccceeEEEEcCCCCcceeeecccccccccccCcccCcccccchhhhHHHHHHHHH
Confidence 456999999999999999999986541 123577788999
Q ss_pred hhCCCCEEEECCHhHHHhhc
Q 033552 51 EESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 51 e~~~IP~i~v~tK~eLG~A~ 70 (117)
+++|..+.++.+..+-|.-+
T Consensus 377 ~~~g~~v~iis~~~e~G~qL 396 (411)
T PRK04011 377 EQSGTKVEVISTDTEEGEQL 396 (411)
T ss_pred HHcCCEEEEECCCChhHHHH
Confidence 99999999999999888655
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=86.14 E-value=1.4 Score=37.47 Aligned_cols=59 Identities=15% Similarity=0.147 Sum_probs=48.9
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCCC-----------------------------------------CcchheeHHHHh
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNIS-----------------------------------------PIDVITHVPILC 50 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Das-----------------------------------------p~~i~~~i~~lc 50 (117)
-+-|..+|.+|++.|.+..++|..|.. ..+++..+...+
T Consensus 289 avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ve~L~e~a 368 (403)
T TIGR03676 289 AAYGEEEVRKALEMGAVDTLLISEDLRKIRVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSELEIVEEEDIIEELSELA 368 (403)
T ss_pred EEEcHHHHHHHHHhCCCcEEEEEccccceeEEEEcCCCCcceeeecccccccccccCcccCcccccchhhhHHHHHHHHH
Confidence 355999999999999999999988762 123567788899
Q ss_pred hhCCCCEEEECCHhHHHhhc
Q 033552 51 EESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 51 e~~~IP~i~v~tK~eLG~A~ 70 (117)
+++|.-+.++.++.+-|.-+
T Consensus 369 ~~~Ga~V~~iS~~~eeG~ql 388 (403)
T TIGR03676 369 EESGAKVEIISTDTEEGEQL 388 (403)
T ss_pred HHcCCEEEEECCCChhHHHH
Confidence 99999999999998888554
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=86.03 E-value=0.97 Score=37.49 Aligned_cols=61 Identities=7% Similarity=0.011 Sum_probs=51.3
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCC-CCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNI-SPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Da-sp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
.-+.|.+++.+|++.|.+.-++|..+. ....-+..+.+.+++.|..+.++++..+-|.-+.
T Consensus 277 ~~~YG~~eV~~Ale~GAVetLLIsD~l~~~r~~~~~l~~~v~~~gg~V~i~Ss~~e~G~qL~ 338 (351)
T TIGR00111 277 KAVYGEDEVVKAAEYGAIEYLLVTDKVLVQREEIEKLLDSVESMGGKVVILSTEHELGKQLD 338 (351)
T ss_pred eEEECHHHHHHHHHcCCceEEEEecchhhhHHHHHHHHHHHHHcCCEEEEEcCCCccHHHHh
Confidence 568899999999999999999999988 3212256678888999999999999999997663
No 32
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=85.63 E-value=1.4 Score=37.32 Aligned_cols=59 Identities=12% Similarity=0.167 Sum_probs=48.6
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCCCC-----------------------------------------cchheeHHHHh
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNISP-----------------------------------------IDVITHVPILC 50 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Dasp-----------------------------------------~~i~~~i~~lc 50 (117)
-+-|..+|.+|++.|.+..++|..|..- .+++..+.+.|
T Consensus 293 avyG~~eV~~ALe~GAVetLLV~d~l~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~ve~L~e~a 372 (409)
T TIGR00108 293 ACYGEDEVLKALDLGAVETLIVSEDLEYIRVTYKCAECGEVIEKTVRELKDKKFAICPACGQEMDVVEERDLIEWLSELA 372 (409)
T ss_pred EEeCHHHHHHHHHhCCCcEEEEeccccceeEEEEcCCCCceeecccccccccccccCcccCccccchhhhhHHHHHHHHH
Confidence 3569999999999999999999998620 13456788889
Q ss_pred hhCCCCEEEECCHhHHHhhc
Q 033552 51 EESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 51 e~~~IP~i~v~tK~eLG~A~ 70 (117)
+++|..+.++.++.+=|.-+
T Consensus 373 ~~~Ga~V~iiS~~~eeG~ql 392 (409)
T TIGR00108 373 ENFGAKLEFISTESEEGAQL 392 (409)
T ss_pred HHcCCEEEEECCCChhHHHH
Confidence 99999999999999888544
No 33
>PLN02821 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
Probab=82.59 E-value=3.5 Score=36.02 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=35.9
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
+..|-..++-++|+-++-...+ ..||..+|+++++|-.++.+.++|+.
T Consensus 355 ~~~L~~~~vDlmiVVGG~NSSN-T~~L~eIa~~~g~~sy~Ie~~~eI~~ 402 (460)
T PLN02821 355 MYKLVEEKLDLMLVVGGWNSSN-TSHLQEIAEHKGIPSYWIDSEERIGP 402 (460)
T ss_pred HHHHhhcCCCEEEEECCCCCcc-HHHHHHHHHHhCCCEEEECCHHHcCc
Confidence 4455334466555555554335 79999999999999999999999985
No 34
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=81.81 E-value=0.94 Score=31.81 Aligned_cols=52 Identities=17% Similarity=0.094 Sum_probs=36.9
Q ss_pred ccceee-eecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 10 SFNCVG-VVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 10 ~~~~vG-~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
...+.| ..+..+.++++.+.-|++|-+-++.+...++.+.|+++++.+..+|
T Consensus 123 ~~~~lg~~~~l~~~~~~~~id~v~ial~~~~~~~i~~ii~~~~~~~v~v~~vP 175 (175)
T PF13727_consen 123 GVPVLGDLDDLPELVREHDIDEVIIALPWSEEEQIKRIIEELENHGVRVRVVP 175 (175)
T ss_dssp TEEEE--GGGHHHHHHHHT--EEEE--TTS-HHHHHHHHHHHHTTT-EEEE--
T ss_pred CceeEcCHHHHHHHHHhCCCCEEEEEcCccCHHHHHHHHHHHHhCCCEEEEeC
Confidence 456777 4777788899999999999888877789999999999999998765
No 35
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=81.21 E-value=2.1 Score=31.29 Aligned_cols=47 Identities=9% Similarity=0.005 Sum_probs=35.5
Q ss_pred eeecchhhhhcCCccEEEEeCC-CCC---cchheeHHHHhhhCCCCEEEEC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGN-ISP---IDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~D-asp---~~i~~~i~~lce~~~IP~i~v~ 61 (117)
|--|....|++|++.+||--.| .++ ..-...|...|-++||||+.-.
T Consensus 63 g~~~i~~~I~~g~i~lVInt~dp~~~~~~~~D~~~IRR~Av~~~IP~~T~l 113 (142)
T PRK05234 63 GDQQIGALIAEGKIDMLIFFRDPLTAQPHDPDVKALLRLADVWNIPVATNR 113 (142)
T ss_pred CchhHHHHHHcCceeEEEEecCCCCCCcccchHHHHHHHHHHcCCCEEcCH
Confidence 6678899999999999988664 222 1125588999999999997543
No 36
>PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=81.04 E-value=5.2 Score=34.17 Aligned_cols=81 Identities=17% Similarity=0.160 Sum_probs=51.1
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh------------------hcCCCcceEEEEE
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN------------------AGATKRPTCCVLV 81 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~------------------A~G~~~~~svv~I 81 (117)
++.|...++-++|+-++-...+ ..+|-.+|++.+.|..++.+.++|-. ++-. ....|+|
T Consensus 281 ~~~La~~~vD~miVVGG~nSSN-T~rL~eia~~~g~~ty~Ie~~~eL~~~~~i~h~~~~~~~~~t~~wl~~--~~~~VGI 357 (387)
T PRK13371 281 MFSLVEEPLDLMVVIGGYNSSN-TTHLQEIAIERGIPSYHIDSPERILSGNSIEHKPLGKELVVTENWLPE--GPVTVGI 357 (387)
T ss_pred HHHHhhcCCCEEEEECCCCCcc-HHHHHHHHHhcCCCEEEECCHHHcCCccccccccccchhhhhhhhhcc--CCCEEEE
Confidence 4555443455555544444334 79999999999999999999999965 3321 1335788
Q ss_pred eecCCCC-ccchHHHHhhHHHHH
Q 033552 82 LTKPTKG-ELGQEEQDKLKADYT 103 (117)
Q Consensus 82 ~~~~~~~-~~~~~e~~~~~~~~~ 103 (117)
+.|-+-. .+.++-.++++.+|+
T Consensus 358 TAGASTP~~lI~eVi~~l~~l~~ 380 (387)
T PRK13371 358 TSGASTPDKVVEDVIEKIFALKE 380 (387)
T ss_pred ecCCCCCHHHHHHHHHHHHHhhc
Confidence 8766533 223344555555544
No 37
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=80.75 E-value=2.6 Score=32.22 Aligned_cols=59 Identities=14% Similarity=0.090 Sum_probs=40.0
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC---CCcceEEEEEeecCCCCc
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA---TKRPTCCVLVLTKPTKGE 89 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G---~~~~~svv~I~~~~~~~~ 89 (117)
+.+||+|.|-.. +-.++-..|+..+||+..++.. +++...= ..++-..++|.+++....
T Consensus 70 ~~lVi~at~d~~--ln~~i~~~a~~~~ilvn~~d~~-e~~~f~~pa~~~~g~l~iaisT~G~sP~ 131 (205)
T TIGR01470 70 AFLVIAATDDEE--LNRRVAHAARARGVPVNVVDDP-ELCSFIFPSIVDRSPVVVAISSGGAAPV 131 (205)
T ss_pred cEEEEECCCCHH--HHHHHHHHHHHcCCEEEECCCc-ccCeEEEeeEEEcCCEEEEEECCCCCcH
Confidence 678899988753 5678999999999999766554 3443211 123455688887776553
No 38
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=80.70 E-value=8.2 Score=30.06 Aligned_cols=68 Identities=13% Similarity=0.104 Sum_probs=49.1
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCC-CCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeec
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNI-SPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 84 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Da-sp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~ 84 (117)
.+-|.+-+..+++++ .++.+. ... .+ + ...+..+|++.+||+..+ ++++|-+.++...+-.++++...
T Consensus 3 ~i~G~~~v~eal~~~-~~~~~~-~~~~~~-~-~~~~~~~~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~~~~ 71 (237)
T TIGR00186 3 YLYGKNAVLEALLNQ-QRVFIL-KGLESK-R-LKKLIQLAKKQGINIQLV-DRQKLDQLTKGGNHQGIAAKVKP 71 (237)
T ss_pred EEEehHHHHHHHhCC-CEEEEE-ecCcch-H-HHHHHHHHHHcCCcEEEe-CHHHHHHHhCCCCCCeEEEEEec
Confidence 456888999999988 333332 222 23 2 455778899999999988 58899999998767777777653
No 39
>PF07997 DUF1694: Protein of unknown function (DUF1694); InterPro: IPR012543 This family contains many hypothetical proteins.; PDB: 2OHW_A.
Probab=80.00 E-value=3.7 Score=29.41 Aligned_cols=49 Identities=18% Similarity=0.101 Sum_probs=35.0
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
...+.|++.....++|.++.+. +...++..+|+++|+|+..|.+...=|
T Consensus 53 ~~~~~l~~~~~~~l~ing~l~~-~~~~~YiklA~~~~~~fTiv~~~~~~~ 101 (120)
T PF07997_consen 53 EFEQALKDYPNYKLKINGNLDY-SFQSKYIKLANKHGIPFTIVNDPEYHS 101 (120)
T ss_dssp HHHHHHHC-SSEEEEEETTS-H-HHHHHHHHHHHHTT--EEEE---SS--
T ss_pred HHHHHHhhCCCeEEEEcCCCCH-HHHHHHHHHHHHcCCCEEEeCCCCccC
Confidence 3456788888999999999997 579999999999999999999876544
No 40
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=78.81 E-value=11 Score=29.67 Aligned_cols=70 Identities=7% Similarity=-0.083 Sum_probs=52.2
Q ss_pred ceeeeecchhhhhcC--CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 12 NCVGVVNDPLPLLFH--ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg--~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
-+-|.+-+..+|+.+ ...-+++..+.... -...+..+|+..+|++..+ ++++|-+.++...+-.++++..
T Consensus 4 ~i~G~~~v~eal~~~~~~~~~l~~~~~~~~~-~~~~~~~~~~~~~i~~~~v-~~~~l~~ls~~~~~qGv~a~~~ 75 (244)
T PRK11181 4 IIYGIHAVQALLERAPERFIEVFVLKGREDK-RLLPLINELEAQGIVIQLA-NRQTLDEKAEGAVHQGIIARVK 75 (244)
T ss_pred EEEehHHHHHHHhCCCCceeEEEEECCCcch-HHHHHHHHHHHcCCcEEEe-CHHHHhhhhcCCCCceEEEEEe
Confidence 356889999999753 46677887776542 2456677888899998776 6899999998876766677665
No 41
>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=78.27 E-value=1.3 Score=32.47 Aligned_cols=51 Identities=22% Similarity=0.116 Sum_probs=37.5
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
++++.++++.-.+-++++..+..+..-......+|...++|++.+-+|-++
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 345677777777778888877666555677778899999999998887554
No 42
>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=78.06 E-value=3.3 Score=29.42 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=29.7
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
++.++.|-+.+.-++|++.+..| -..+.+.|++++||+....
T Consensus 71 ~~~l~~l~~~~~P~iIvt~~~~~---p~~l~e~a~~~~ipll~t~ 112 (127)
T PF02603_consen 71 KERLEKLFSYNPPCIIVTRGLEP---PPELIELAEKYNIPLLRTP 112 (127)
T ss_dssp CCHHHHHCTTT-S-EEEETTT------HHHHHHHHHCT--EEEES
T ss_pred HHHHHHHhCCCCCEEEEECcCCC---CHHHHHHHHHhCCcEEEcC
Confidence 46778888888999999999986 3567889999999998765
No 43
>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=77.87 E-value=2.1 Score=27.15 Aligned_cols=41 Identities=17% Similarity=0.092 Sum_probs=28.9
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
|.-++.+..|+ .|.|++.|... ...|+.+|++.|-.+....
T Consensus 17 kkal~~l~~G~-~l~V~~d~~~a---~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 17 KKEIDKLQDGE-QLEVKASDPGF---ARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred HHHHHcCCCCC-EEEEEECCccH---HHHHHHHHHHcCCEEEEEE
Confidence 34444444554 58888887553 7789999999999987544
No 44
>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=77.45 E-value=3.3 Score=28.93 Aligned_cols=47 Identities=15% Similarity=0.111 Sum_probs=35.7
Q ss_pred eeecchhhhhcCCccEEEEeCCC---CC-cchheeHHHHhhhCCCCEEEEC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNI---SP-IDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Da---sp-~~i~~~i~~lce~~~IP~i~v~ 61 (117)
|-.+....|++|++.+||--.|- .+ ..-...|...|-+++|||+.--
T Consensus 58 g~~~i~~~i~~g~i~~VInt~~~~~~~~~~~dg~~iRr~a~~~~Ip~~Ttl 108 (115)
T cd01422 58 GDQQIGALIAEGEIDAVIFFRDPLTAQPHEPDVKALLRLCDVYNIPLATNR 108 (115)
T ss_pred chhHHHHHHHcCceeEEEEcCCCCCCCcccccHHHHHHHHHHcCCCEEEcH
Confidence 33568899999999999888763 22 2236688999999999997643
No 45
>PRK10864 putative methyltransferase; Provisional
Probab=76.38 E-value=12 Score=31.31 Aligned_cols=73 Identities=11% Similarity=0.097 Sum_probs=54.4
Q ss_pred CccceeeeecchhhhhcC--CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeec
Q 033552 9 HSFNCVGVVNDPLPLLFH--ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 84 (117)
Q Consensus 9 ~~~~~vG~kqt~kaL~kg--~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~ 84 (117)
....+-|..-+..+|+++ .+.-+++.....+ . ...+..++..++++|..+ +.++|-+.++...+-.++++...
T Consensus 107 ~~~~I~G~~aV~ealk~~~~~i~~l~~~~~~~~-~-~~~il~~~~~~~~~v~~V-~~~~l~kls~~~~hqGV~A~v~~ 181 (346)
T PRK10864 107 EETRVYGENACQALFQSRPEAIVRAWFIQSVTP-R-FKEALRWMAANRKAYHVV-DEAELTKASGTEHHGGVCFLIKK 181 (346)
T ss_pred CCcEEEEHHHHHHHHhCCCCceeEEEEecCccH-H-HHHHHHHHHHcCCcEEEe-CHHHHHHHhCCCCCCeEEEEEeC
Confidence 356778999999999863 3556677777665 2 566677888889997665 88899999998766666666653
No 46
>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=74.92 E-value=1.3 Score=29.61 Aligned_cols=41 Identities=10% Similarity=-0.134 Sum_probs=31.9
Q ss_pred cchhhhhcCCccEEEEeCCCCCcc---hheeHHHHhhhCCCCEE
Q 033552 18 NDPLPLLFHECRLCVIAGNISPID---VITHVPILCEESDIPYI 58 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~---i~~~i~~lce~~~IP~i 58 (117)
|.++.|++|++.+||.--+-.... --..+..+|.+++||++
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 588999999999999888766422 15678999999999986
No 47
>PF13611 Peptidase_S76: Serine peptidase of plant viral polyprotein, P1
Probab=74.52 E-value=2.7 Score=30.58 Aligned_cols=30 Identities=30% Similarity=0.573 Sum_probs=25.3
Q ss_pred EeC-CCCCcchheeHHHHhhhCCCCEEEECCHh
Q 033552 33 IAG-NISPIDVITHVPILCEESDIPYIYVASKE 64 (117)
Q Consensus 33 LA~-Dasp~~i~~~i~~lce~~~IP~i~v~tK~ 64 (117)
+|+ +++ +++..+.++|-+.|||+.+++++.
T Consensus 30 v~~~~i~--dL~~~~~~ic~ergiPIe~I~~~k 60 (121)
T PF13611_consen 30 VANNEID--DLVREVTEICCERGIPIEIIDKKK 60 (121)
T ss_pred EecCcHH--HHHHHHHHHHHHcCCCEEEecCcc
Confidence 664 555 689999999999999999999764
No 48
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=74.19 E-value=14 Score=30.18 Aligned_cols=65 Identities=18% Similarity=0.132 Sum_probs=43.3
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKG 88 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~ 88 (117)
.+.|.+.-=-++|+++--|+ + ..+|-++|++++.|..++.+.+||....=.. ...++|+.|-+-.
T Consensus 202 ~~~la~~vD~miVVGg~nSs-N-T~rL~ei~~~~~~~t~~Ie~~~el~~~~l~~--~~~VGiTAGASTP 266 (280)
T TIGR00216 202 VKELAPEVDLMIVIGGKNSS-N-TTRLYEIAEEHGPPSYLIETAEELPEEWLKG--VKVVGITAGASTP 266 (280)
T ss_pred HHHHHhhCCEEEEECCCCCc-h-HHHHHHHHHHhCCCEEEECChHHCCHHHhCC--CCEEEEEecCCCC
Confidence 34444432234555555555 4 7999999999999999999999998442222 2347888766633
No 49
>PF02401 LYTB: LytB protein; InterPro: IPR003451 Terpenes are among the largest groups of natural products and include compounds such as vitamins, cholesterol and carotenoids. The biosynthesis of all terpenoids begins with one or both of the two C5 precursors of the pathway: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In animals, fungi, and certain bacteria, the synthesis of IPP and DMAPP occurs via the well-known mevalonate pathway, however, a second, nonmevalonate terpenoid pathway has been identified in many eubacteria, algae and the chloroplasts of higher plants []. LytB(IspH) catalyses the conversion of 1-hydroy-2-methyl-2-(E)-butenyl 4-diphosphate into IPP and DMAPP in this second pathway The enzyme appears to be responsible for a branch-step in the nonmevalonate pathway, in that IPP and DMAPP are produced in parallel from a single precursor although the exact mechanism of this is not currently fully understood []. Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response [].; GO: 0019288 isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, 0055114 oxidation-reduction process; PDB: 3DNF_B 3SZL_B 3KE8_B 3KEF_B 3SZU_A 3KEL_A 3F7T_B 3KE9_B 3KEM_B 3T0G_A ....
Probab=74.01 E-value=18 Score=29.48 Aligned_cols=64 Identities=9% Similarity=0.070 Sum_probs=39.9
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH-hhcCCCcceEEEEEeecCCCC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA-NAGATKRPTCCVLVLTKPTKG 88 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG-~A~G~~~~~svv~I~~~~~~~ 88 (117)
++.|.+. +-++|+-++-...+ ..+|-++|++++.|..++.+-+||= .++... -.++|+.|-+-.
T Consensus 203 ~~~La~~-vD~miVIGg~~SsN-T~kL~eia~~~~~~t~~Ie~~~el~~~~l~~~---~~VGItaGASTP 267 (281)
T PF02401_consen 203 ARELAKE-VDAMIVIGGKNSSN-TRKLAEIAKEHGKPTYHIETADELDPEWLKGV---KKVGITAGASTP 267 (281)
T ss_dssp HHHHHCC-SSEEEEES-TT-HH-HHHHHHHHHHCTTCEEEESSGGG--HHHHTT----SEEEEEE-TTS-
T ss_pred HHHHHhh-CCEEEEecCCCCcc-HHHHHHHHHHhCCCEEEeCCccccCHhHhCCC---CEEEEEccCCCC
Confidence 3445443 55554444444435 8999999999999999999999996 343322 257888866633
No 50
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=73.75 E-value=13 Score=32.05 Aligned_cols=81 Identities=20% Similarity=0.226 Sum_probs=59.3
Q ss_pred hhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCccchHHHHhhHHHH
Q 033552 23 LLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADY 102 (117)
Q Consensus 23 L~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~ 102 (117)
+..++.++-||..|..-+-=++.+...|+-.|+|+..+.+.++|-.|+.--+..=+|+|-.-|-.+. +..-.+.++.++
T Consensus 229 ~~~~~~kVaiITtDtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l~~~d~ILVDTaGrs~~-D~~~i~el~~~~ 307 (407)
T COG1419 229 MLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEALRDCDVILVDTAGRSQY-DKEKIEELKELI 307 (407)
T ss_pred hhccCcceEEEEeccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHhhcCCEEEEeCCCCCcc-CHHHHHHHHHHH
Confidence 3678889999999999766689999999999999999999999999988654444566654333332 333444555444
Q ss_pred HH
Q 033552 103 TL 104 (117)
Q Consensus 103 ~e 104 (117)
..
T Consensus 308 ~~ 309 (407)
T COG1419 308 DV 309 (407)
T ss_pred hc
Confidence 43
No 51
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=73.17 E-value=19 Score=29.58 Aligned_cols=65 Identities=12% Similarity=0.054 Sum_probs=44.6
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKG 88 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~ 88 (117)
++.|.+.-=-++|+++--|. + ..+|-++|++++.|..++.+.+||-...=. +...++|+.|-+-.
T Consensus 204 ~~~La~~vD~miVVGg~~Ss-N-T~kL~~i~~~~~~~t~~Ie~~~el~~~~l~--~~~~VGitaGASTP 268 (298)
T PRK01045 204 VKELAPQADLVIVVGSKNSS-N-SNRLREVAEEAGAPAYLIDDASEIDPEWFK--GVKTVGVTAGASAP 268 (298)
T ss_pred HHHHHhhCCEEEEECCCCCc-c-HHHHHHHHHHHCCCEEEECChHHCcHHHhc--CCCEEEEEecCCCC
Confidence 34454433345555555565 4 799999999999999999999999843222 23457888766533
No 52
>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=73.07 E-value=2.8 Score=32.28 Aligned_cols=49 Identities=24% Similarity=0.215 Sum_probs=33.7
Q ss_pred cchhhhhc--CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 18 NDPLPLLF--HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 18 qt~kaL~k--g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
.+++++.. -..-++++..|..+......+..++.+.++|++.+-||.++
T Consensus 100 ~~~~~~~~~~~D~~llVvda~~g~~~~d~~~l~~l~~~~ip~ivvvNK~D~ 150 (224)
T cd04165 100 TTLFGLTGYAPDYAMLVVAANAGIIGMTKEHLGLALALNIPVFVVVTKIDL 150 (224)
T ss_pred HHHHhhcccCCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEECccc
Confidence 44555542 23456666665555455667777899999999999998876
No 53
>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=72.68 E-value=4.9 Score=33.61 Aligned_cols=49 Identities=12% Similarity=-0.015 Sum_probs=40.7
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
..+.+++..+.-|++|....+.+...++...|+++++++..+++..++-
T Consensus 180 l~~~i~~~~id~ViIa~p~~~~~~~~~ll~~~~~~gv~V~~vP~~~e~~ 228 (445)
T TIGR03025 180 LVELVRAHRVDEVIIALPLSEEARILELLLQLRDLGVDVRLVPDLFEFL 228 (445)
T ss_pred HHHHHHhCCCCEEEEecCcccHHHHHHHHHHHHhcCCEEEEeCchhhhc
Confidence 3455677889999999877665567889999999999999999998874
No 54
>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=72.09 E-value=6.3 Score=27.04 Aligned_cols=46 Identities=11% Similarity=-0.056 Sum_probs=34.8
Q ss_pred eeecchhhhhc-CCccEEEEeCCCC----CcchheeHHHHhhhCCCCEEEE
Q 033552 15 GVVNDPLPLLF-HECRLCVIAGNIS----PIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 15 G~kqt~kaL~k-g~~~LViLA~Das----p~~i~~~i~~lce~~~IP~i~v 60 (117)
|-.|....|++ |++.+||---|-. ...--..+...|-+++|||+.-
T Consensus 55 g~~~i~~~i~~~g~idlVIn~~~~~~~~~~~~dg~~iRR~A~~~~Ip~~T~ 105 (112)
T cd00532 55 GEPTVDAAIAEKGKFDVVINLRDPRRDRCTDEDGTALLRLARLYKIPVTTP 105 (112)
T ss_pred CCcHHHHHHhCCCCEEEEEEcCCCCcccccCCChHHHHHHHHHcCCCEEEC
Confidence 56778999999 9999998865521 1122567888999999999754
No 55
>KOG2486 consensus Predicted GTPase [General function prediction only]
Probab=72.03 E-value=3.8 Score=34.20 Aligned_cols=42 Identities=14% Similarity=-0.008 Sum_probs=28.9
Q ss_pred ccEEEEeCCCC--CcchheeHHHHhhhCCCCEEEECCHhHHHhh
Q 033552 28 CRLCVIAGNIS--PIDVITHVPILCEESDIPYIYVASKEDLANA 69 (117)
Q Consensus 28 ~~LViLA~Das--p~~i~~~i~~lce~~~IP~i~v~tK~eLG~A 69 (117)
..-||++-|++ +..+=-....+|.++|||+..|+||-+=-..
T Consensus 220 Lv~~FLLvd~sv~i~~~D~~~i~~~ge~~VP~t~vfTK~DK~k~ 263 (320)
T KOG2486|consen 220 LVRVFLLVDASVPIQPTDNPEIAWLGENNVPMTSVFTKCDKQKK 263 (320)
T ss_pred hheeeeeeeccCCCCCCChHHHHHHhhcCCCeEEeeehhhhhhh
Confidence 44556666665 3333345678999999999999998665443
No 56
>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=71.87 E-value=4.5 Score=28.37 Aligned_cols=36 Identities=22% Similarity=0.176 Sum_probs=30.4
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHh
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKE 64 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~ 64 (117)
...+||.+.|.. .....+.++|.++++|++...+.-
T Consensus 89 ~~diVi~~~d~~--~~~~~l~~~~~~~~i~~i~~~~~g 124 (143)
T cd01483 89 GVDLVIDAIDNI--AVRRALNRACKELGIPVIDAGGLG 124 (143)
T ss_pred CCCEEEECCCCH--HHHHHHHHHHHHcCCCEEEEcCCC
Confidence 477999999974 358899999999999999998754
No 57
>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=71.44 E-value=4.3 Score=27.32 Aligned_cols=31 Identities=26% Similarity=0.398 Sum_probs=20.9
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+..+||.++..|. ..+.++|++++||++.++
T Consensus 62 i~~iIltg~~~~~---~~v~~la~~~~i~vi~t~ 92 (105)
T PF07085_consen 62 IACIILTGGLEPS---EEVLELAKELGIPVISTP 92 (105)
T ss_dssp ECEEEEETT-------HHHHHHHHHHT-EEEE-S
T ss_pred CCEEEEeCCCCCC---HHHHHHHHHCCCEEEEEC
Confidence 7888888887773 467779999999998876
No 58
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=71.22 E-value=17 Score=30.80 Aligned_cols=57 Identities=19% Similarity=0.121 Sum_probs=43.7
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
..++.+++.|+.-..-...+..+|+..|+|+..+.+.+++..++......-.++|-.
T Consensus 206 g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~~~~DlVLIDT 262 (388)
T PRK12723 206 SLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQSKDFDLVLVDT 262 (388)
T ss_pred CCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHhCCCCEEEEcC
Confidence 468999999987544567799999999999999999999988776544444455533
No 59
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=70.81 E-value=21 Score=30.07 Aligned_cols=56 Identities=21% Similarity=0.181 Sum_probs=38.2
Q ss_pred ccEEEEeCCCC---CcchheeHHHHhhhCCCCEEEECCH---hHHHhh--cCCCcceEEEEEee
Q 033552 28 CRLCVIAGNIS---PIDVITHVPILCEESDIPYIYVASK---EDLANA--GATKRPTCCVLVLT 83 (117)
Q Consensus 28 ~~LViLA~Das---p~~i~~~i~~lce~~~IP~i~v~tK---~eLG~A--~G~~~~~svv~I~~ 83 (117)
-+-+|.+.|.+ +..+.++|.++|+++||||-+--.. .+-|.+ .|-..|++++.|..
T Consensus 254 ~Gp~i~~~D~~~~~~~~l~~~L~~~A~~~~Ip~Q~~v~~~ggTDA~a~~~~g~gvpta~Igip~ 317 (355)
T COG1363 254 KGPVIRVKDASGIYHPKLRKFLLELAEKNNIPYQVDVSPGGGTDAGAAHLTGGGVPTALIGIPT 317 (355)
T ss_pred CCCEEEEEcCCCCCCHHHHHHHHHHHHHcCCCeEEEecCCCCccHHHHHHcCCCCceEEEeccc
Confidence 45677788886 2368999999999999999765433 333433 34446777776644
No 60
>PRK11018 hypothetical protein; Provisional
Probab=68.51 E-value=4.8 Score=26.31 Aligned_cols=41 Identities=15% Similarity=0.167 Sum_probs=28.2
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
|.-++.+..|+. |.|++.|..+ ...|+.+|++.|-.++...
T Consensus 26 kk~l~~l~~G~~-L~V~~d~~~a---~~di~~~~~~~G~~v~~~~ 66 (78)
T PRK11018 26 LEALPQLKKGEI-LEVVSDCPQS---INNIPLDARNHGYTVLDIQ 66 (78)
T ss_pred HHHHHhCCCCCE-EEEEeCCccH---HHHHHHHHHHcCCEEEEEE
Confidence 334444455543 6778887553 6789999999999887543
No 61
>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=68.00 E-value=5.9 Score=25.96 Aligned_cols=41 Identities=17% Similarity=-0.041 Sum_probs=31.3
Q ss_pred cchhhhhcCCccEEEEeCCC-C--CcchheeHHHHhhhCCCCEE
Q 033552 18 NDPLPLLFHECRLCVIAGNI-S--PIDVITHVPILCEESDIPYI 58 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Da-s--p~~i~~~i~~lce~~~IP~i 58 (117)
..++.++.|++.+||--.+- . +.+-...+...|.+++||++
T Consensus 46 ~i~~~i~~g~id~VIn~~~~~~~~~~~d~~~iRr~A~~~~Ip~~ 89 (90)
T smart00851 46 AILDLIKNGEIDLVINTLYPLGAQPHEDGKALRRAAENIDIPGA 89 (90)
T ss_pred HHHHHhcCCCeEEEEECCCcCcceeccCcHHHHHHHHHcCCCee
Confidence 37889999999999986542 2 22225578999999999986
No 62
>COG1445 FrwB Phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism]
Probab=67.87 E-value=6.5 Score=28.63 Aligned_cols=49 Identities=24% Similarity=0.322 Sum_probs=38.0
Q ss_pred eeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhC-CCCEEEECCHhHHHhh
Q 033552 13 CVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEES-DIPYIYVASKEDLANA 69 (117)
Q Consensus 13 ~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~-~IP~i~v~tK~eLG~A 69 (117)
-+|++..+.+=.=..+..||||.|... + ..+.. |-|++.+++++-|-.+
T Consensus 42 s~G~eN~LT~edI~~Ad~VI~AaD~~i-~-------~~~ff~gk~vi~~~~~~aik~~ 91 (122)
T COG1445 42 AVGIENRLTAEDIAAADVVILAADIEV-D-------LSRFFAGKPVIEVSTKDAIKNP 91 (122)
T ss_pred cccccCcCCHHHHHhCCEEEEEecccc-c-------HhHhhcCCeEEEecHHHHHhCH
Confidence 467777777666677999999999985 4 34555 9999999998877644
No 63
>cd07984 LPLAT_LABLAT-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as lipid A biosynthesis lauroyl/myristoyl (LABLAT, HtrB) acyltransferases and similar proteins.
Probab=67.24 E-value=38 Score=24.26 Aligned_cols=47 Identities=17% Similarity=0.041 Sum_probs=31.4
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcc--------------hheeHHHHhhhCCCCEEEECCH
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPID--------------VITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~--------------i~~~i~~lce~~~IP~i~v~tK 63 (117)
++++.+++|++|+ .|.|..|-.... ...-...++...|+|++.+...
T Consensus 79 ~~~~~~~~l~~g~--~v~i~pD~~~~~~~~~~~~F~G~~~~~~~G~~~lA~~~~~pivp~~~~ 139 (192)
T cd07984 79 GLRELIRALKKGE--IVGILPDQDPGRKGGVFVPFFGRPAATPTGPARLALKTGAPVVPAFAY 139 (192)
T ss_pred hHHHHHHHHhCCC--EEEEEeCCCCCCCCCEEeccCCCCccchHHHHHHHHHHCCcEEEEEEE
Confidence 5778888888886 455555555311 1333456888999999888753
No 64
>COG1648 CysG Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]
Probab=67.16 E-value=6.6 Score=30.46 Aligned_cols=60 Identities=15% Similarity=0.057 Sum_probs=43.5
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhH----HHhhcCCCcceEEEEEeecCCCCccc
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKED----LANAGATKRPTCCVLVLTKPTKGELG 91 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~e----LG~A~G~~~~~svv~I~~~~~~~~~~ 91 (117)
+-|||+|.|-.+ +-..+-..|+++++|+-.++..+. +.....+. + ..++|.+++....+.
T Consensus 73 ~~lviaAt~d~~--ln~~i~~~a~~~~i~vNv~D~p~~~~f~~Pa~~~r~-~-l~iaIsT~G~sP~la 136 (210)
T COG1648 73 AFLVIAATDDEE--LNERIAKAARERRILVNVVDDPELCDFIFPAIVDRG-P-LQIAISTGGKSPVLA 136 (210)
T ss_pred ceEEEEeCCCHH--HHHHHHHHHHHhCCceeccCCcccCceecceeeccC-C-eEEEEECCCCChHHH
Confidence 789999999664 678999999999999987776653 33444443 4 468888877655433
No 65
>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=66.27 E-value=14 Score=23.55 Aligned_cols=30 Identities=10% Similarity=0.217 Sum_probs=26.9
Q ss_pred heeHHHHhhhCCCCEEEECCHhHHHhhcCC
Q 033552 43 ITHVPILCEESDIPYIYVASKEDLANAGAT 72 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~tK~eLG~A~G~ 72 (117)
..+...+++++|+++..+++-.+++..||.
T Consensus 14 a~~~ek~lk~~gi~~~liP~P~~i~~~CG~ 43 (73)
T PF11823_consen 14 AMKAEKLLKKNGIPVRLIPTPREISAGCGL 43 (73)
T ss_pred HHHHHHHHHHCCCcEEEeCCChhccCCCCE
Confidence 456678999999999999999999999996
No 66
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=66.26 E-value=27 Score=28.51 Aligned_cols=64 Identities=13% Similarity=0.085 Sum_probs=43.3
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh-hcCCCcceEEEEEeecCCCC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN-AGATKRPTCCVLVLTKPTKG 88 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~-A~G~~~~~svv~I~~~~~~~ 88 (117)
.+.|.+.-=-++|+++--|+ + ..+|-++|++.+.|-.++.+.+||-. ++- +...++|+.|-+-.
T Consensus 203 ~~~La~~vD~miVVGg~~Ss-N-T~rL~eia~~~~~~t~~Ie~~~el~~~~~~---~~~~VGitaGASTP 267 (281)
T PRK12360 203 AKELSKEVDVMIVIGGKHSS-N-TQKLVKICEKNCPNTFHIETADELDLEMLK---DYKIIGITAGASTP 267 (281)
T ss_pred HHHHHHhCCEEEEecCCCCc-c-HHHHHHHHHHHCCCEEEECChHHCCHHHhC---CCCEEEEEccCCCC
Confidence 34454332234555555565 4 79999999999999999999999964 332 23457888766533
No 67
>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.
Probab=65.54 E-value=34 Score=24.24 Aligned_cols=54 Identities=17% Similarity=0.163 Sum_probs=37.7
Q ss_pred CEEEECCHhHHHhhcCCCcceEEEEEeecCCCCccchHHHHhhHHHHHHHHHHHHhh
Q 033552 56 PYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVEDVKEL 112 (117)
Q Consensus 56 P~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e~~~~~~~l 112 (117)
.++.+-+.+.|...|+.+ +.|++++.+.-.+ ...++.+.|.+.|.++.+..+.-
T Consensus 3 ~~~~l~~~~~~~~~C~~~-~~C~i~~l~~~~d--~~~e~~~~~~~~l~~vAk~~kgk 56 (130)
T cd02983 3 EIIELTSEDVFEETCEEK-QLCIIAFLPHILD--CQASCRNKYLEILKSVAEKFKKK 56 (130)
T ss_pred ceEEecCHHHHHhhccCC-CeEEEEEcCcccc--CCHHHHHHHHHHHHHHHHHhcCC
Confidence 467778899999999875 7888888643221 13455677888888877766543
No 68
>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=65.32 E-value=7.7 Score=32.50 Aligned_cols=55 Identities=18% Similarity=0.048 Sum_probs=43.1
Q ss_pred eeeeec-chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 13 CVGVVN-DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 13 ~vG~kq-t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
++|..+ ..+.+++..+.-|++|......+-...+...|+..++++..+++-.++.
T Consensus 176 Vlg~~~dl~~~i~~~~vd~ViIA~p~~~~~~~~~ll~~~~~~gv~V~vvP~~~e~~ 231 (451)
T TIGR03023 176 VLGKLDDLEELIREGEVDEVYIALPLAAEDRILELLDALEDLTVDVRLVPDLFDFA 231 (451)
T ss_pred ccCCHHHHHHHHHhcCCCEEEEeeCcccHHHHHHHHHHHHhcCCEEEEeCchhhhc
Confidence 444333 3455677889999999877665567889999999999999999988876
No 69
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=64.26 E-value=37 Score=30.39 Aligned_cols=78 Identities=14% Similarity=0.100 Sum_probs=49.2
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCc-cchHHHHhh
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGE-LGQEEQDKL 98 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~-~~~~e~~~~ 98 (117)
++.|.+.-=-++|+++--|+ + ..+|-.+|+..+.|..++.+.+||-...=. +...++|+.|-+-.. +.++-.+++
T Consensus 200 ~~~la~~~d~~~vvGg~~Ss-N-t~~L~~i~~~~~~~~~~ie~~~el~~~~~~--~~~~vgitagaStP~~~i~~v~~~l 275 (647)
T PRK00087 200 AEKLAKKVDVMIVVGGKNSS-N-TTKLYEICKSNCTNTIHIENAGELPEEWFK--GVKIIGVTAGASTPDWIIEEVIKKM 275 (647)
T ss_pred HHHHHhhCCEEEEECCCCCc-c-HHHHHHHHHHHCCCEEEECChHHCCHHHhC--CCCEEEEEeccCCCHHHHHHHHHHH
Confidence 34555432334555555555 4 799999999999999999999999753222 223478888666442 233444454
Q ss_pred HHH
Q 033552 99 KAD 101 (117)
Q Consensus 99 ~~~ 101 (117)
.++
T Consensus 276 ~~~ 278 (647)
T PRK00087 276 SEL 278 (647)
T ss_pred HHh
Confidence 443
No 70
>PRK10637 cysG siroheme synthase; Provisional
Probab=63.93 E-value=11 Score=32.19 Aligned_cols=61 Identities=23% Similarity=0.141 Sum_probs=41.1
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhc-C--CCcceEEEEEeecCCCCccc
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG-A--TKRPTCCVLVLTKPTKGELG 91 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~-G--~~~~~svv~I~~~~~~~~~~ 91 (117)
+.|||.|.|-. ++-..|-..|++.++++..+++. +++... . .+++-..++|.+++....+.
T Consensus 73 ~~lv~~at~d~--~~n~~i~~~a~~~~~lvN~~d~~-~~~~f~~pa~~~~g~l~iaisT~G~sP~~a 136 (457)
T PRK10637 73 CWLAIAATDDD--AVNQRVSEAAEARRIFCNVVDAP-KAASFIMPSIIDRSPLMVAVSSGGTSPVLA 136 (457)
T ss_pred CEEEEECCCCH--HHhHHHHHHHHHcCcEEEECCCc-ccCeEEEeeEEecCCEEEEEECCCCCcHHH
Confidence 67888888755 46788999999999998766665 444321 1 12344568888877666433
No 71
>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=62.87 E-value=12 Score=23.65 Aligned_cols=41 Identities=20% Similarity=0.186 Sum_probs=27.4
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
|+-++.+..|+. |.|++.|-.+ ...|+.+|++.|-.+....
T Consensus 17 kkal~~l~~G~~-l~V~~d~~~s---~~ni~~~~~~~g~~v~~~~ 57 (69)
T cd03422 17 LEALPSLKPGEI-LEVISDCPQS---INNIPIDARNHGYKVLAIE 57 (69)
T ss_pred HHHHHcCCCCCE-EEEEecCchH---HHHHHHHHHHcCCEEEEEE
Confidence 333444444432 6677777553 6789999999999887554
No 72
>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=62.06 E-value=16 Score=23.03 Aligned_cols=41 Identities=15% Similarity=0.138 Sum_probs=27.8
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
|..++.+..|+ .|.|++.|... ...++.+|+..|-.++...
T Consensus 17 k~~l~~l~~G~-~l~V~~dd~~s---~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 17 HKKVRKMKPGD-TLLVLATDPST---TRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred HHHHHcCCCCC-EEEEEeCCCch---HHHHHHHHHHcCCEEEEEE
Confidence 34444444443 36777777553 6789999999999887554
No 73
>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=60.01 E-value=8 Score=29.26 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=28.5
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
...+||.+.|. + +...++.++|.+++||++...+.--.
T Consensus 113 ~~dvVi~~~d~-~-~~~~~ln~~c~~~~ip~i~~~~~G~~ 150 (198)
T cd01485 113 KFTLVIATEEN-Y-ERTAKVNDVCRKHHIPFISCATYGLI 150 (198)
T ss_pred CCCEEEECCCC-H-HHHHHHHHHHHHcCCCEEEEEeecCE
Confidence 35677777664 3 46788999999999999998764333
No 74
>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=59.94 E-value=16 Score=23.68 Aligned_cols=20 Identities=35% Similarity=0.456 Sum_probs=15.6
Q ss_pred heeHHHHhhhCCCCEEEECC
Q 033552 43 ITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~t 62 (117)
.+|.--+|++.|||++.--.
T Consensus 42 ~SH~aIlAr~~giP~ivg~~ 61 (80)
T PF00391_consen 42 TSHAAILARELGIPAIVGVG 61 (80)
T ss_dssp TSHHHHHHHHTT-EEEESTT
T ss_pred cchHHHHHHHcCCCEEEeec
Confidence 37888999999999987664
No 75
>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=59.64 E-value=13 Score=25.07 Aligned_cols=45 Identities=18% Similarity=0.039 Sum_probs=32.6
Q ss_pred eeecchhhhhcCCccEEEEeCCCC-CcchheeHHHHhhhCCCCEEE
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNIS-PIDVITHVPILCEESDIPYIY 59 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Das-p~~i~~~i~~lce~~~IP~i~ 59 (117)
|..+....|++|+..+||---+-. +..--..+...|-++|||++.
T Consensus 55 ~~~~i~~~i~~~~id~vIn~~~~~~~~~~~~~iRR~Av~~~ipl~T 100 (110)
T cd01424 55 GRPNIVDLIKNGEIQLVINTPSGKRAIRDGFSIRRAALEYKVPYFT 100 (110)
T ss_pred CchhHHHHHHcCCeEEEEECCCCCccCccHHHHHHHHHHhCCCEEe
Confidence 456678888999999998754421 111245788999999999973
No 76
>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=59.46 E-value=13 Score=25.89 Aligned_cols=48 Identities=15% Similarity=0.097 Sum_probs=34.3
Q ss_pred ecchhhhhc-CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhH
Q 033552 17 VNDPLPLLF-HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKED 65 (117)
Q Consensus 17 kqt~kaL~k-g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~e 65 (117)
++.++.|.+ |-++|+|--.+--+ ++-..+.+.|+++++|++.++..-.
T Consensus 62 ~~~i~~L~~~~~agL~i~~~~~~~-~iP~~~i~~A~~~~lPli~ip~~~~ 110 (123)
T PF07905_consen 62 REFIRELAEKGAAGLGIKTGRYLD-EIPEEIIELADELGLPLIEIPWEVP 110 (123)
T ss_pred HHHHHHHHHCCCeEEEEeccCccc-cCCHHHHHHHHHcCCCEEEeCCCCC
Confidence 445666655 55777775554444 5778899999999999999986433
No 77
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=56.96 E-value=43 Score=27.33 Aligned_cols=48 Identities=29% Similarity=0.176 Sum_probs=33.8
Q ss_pred hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCC
Q 033552 21 LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATK 73 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~ 73 (117)
..|.+..++++|||.++.. .--++++=+..++|++-+- -..-.|....
T Consensus 61 ~~l~~~~ik~lVIACNTAS---a~al~~LR~~~~iPVvGvi--Paik~A~~~t 108 (269)
T COG0796 61 DFLLERGIKALVIACNTAS---AVALEDLREKFDIPVVGVI--PAIKPAVALT 108 (269)
T ss_pred HHHHHcCCCEEEEecchHH---HHHHHHHHHhCCCCEEEec--cchHHHHHhc
Confidence 3444555999999999885 3456677788899999887 4444454443
No 78
>COG0761 lytB 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]
Probab=56.96 E-value=35 Score=28.28 Aligned_cols=79 Identities=15% Similarity=0.120 Sum_probs=54.3
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCc-cchHHHHhh
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGE-LGQEEQDKL 98 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~-~~~~e~~~~ 98 (117)
++.|.++ +-++|+=++....+ ..+|..+|++.+.|-..+.+-++|....=.. ...++|+.|-+... +.++-.+++
T Consensus 206 vk~la~~-~Dl~iVVG~~nSSN-s~rL~eiA~~~g~~aylId~~~ei~~~w~~~--~~~VGvTAGAStPd~lV~~Vi~~l 281 (294)
T COG0761 206 VKELAPE-VDLVIVVGSKNSSN-SNRLAEIAKRHGKPAYLIDDAEEIDPEWLKG--VKTVGVTAGASTPDWLVQEVIAKL 281 (294)
T ss_pred HHHHhhc-CCEEEEECCCCCcc-HHHHHHHHHHhCCCeEEeCChHhCCHHHhcC--ccEEEEecCCCCCHHHHHHHHHHH
Confidence 3445554 67777777666545 7899999999999999999999999554332 44678888766443 233445555
Q ss_pred HHHH
Q 033552 99 KADY 102 (117)
Q Consensus 99 ~~~~ 102 (117)
++++
T Consensus 282 ~~~~ 285 (294)
T COG0761 282 RELG 285 (294)
T ss_pred HHhc
Confidence 5543
No 79
>PRK10124 putative UDP-glucose lipid carrier transferase; Provisional
Probab=56.92 E-value=15 Score=31.41 Aligned_cols=48 Identities=4% Similarity=-0.090 Sum_probs=40.5
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
.+.+++..+.-|+||-+..+.+-...+.+.|+..++++..+++..++.
T Consensus 196 ~~~v~~~~IdeViIAip~~~~~~l~ell~~~~~~~v~V~ivP~l~~~~ 243 (463)
T PRK10124 196 VEDAKAGKIHNVYIAMSMCDGARVKKLVRQLADTTCSVLLIPDVFTFN 243 (463)
T ss_pred HHHHHhCCCCEEEEeCCCcchHHHHHHHHHHHHcCCeEEEecchhhcc
Confidence 345678889999999987765668889999999999999999987664
No 80
>PF03279 Lip_A_acyltrans: Bacterial lipid A biosynthesis acyltransferase; InterPro: IPR004960 Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS moleculesare variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A []. The polysaccharide component consists of a variable repeat-structure polysaccharide known as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS []. The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids []. These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units. The bacterial lipid A biosynthesis protein, or lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase 2.3.1 from EC, transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA during lipopolysaccharide core biosynthesis.; GO: 0016746 transferase activity, transferring acyl groups, 0009244 lipopolysaccharide core region biosynthetic process, 0016021 integral to membrane
Probab=55.98 E-value=34 Score=26.79 Aligned_cols=46 Identities=15% Similarity=0.071 Sum_probs=30.2
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcc--------------hheeHHHHhhhCCCCEEEECCH
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPID--------------VITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~--------------i~~~i~~lce~~~IP~i~v~tK 63 (117)
+++.+++|++|+ +|.+..|-++.. ...-...++...|.|++.+...
T Consensus 181 ~~~~~~~Lk~g~--~v~~l~Dq~~~~~~~~~v~FfG~~a~~~~g~a~lA~~~~apvvp~~~~ 240 (295)
T PF03279_consen 181 IRELIRALKEGG--IVGLLGDQDPGKKDGVFVPFFGRPASTPTGPARLARKTGAPVVPVFAY 240 (295)
T ss_pred HHHHHHHhccCC--EEEEEECCCCCCCCceEEeECCeecccccHHHHHHHHhCCcEEEEEEE
Confidence 778899999987 888899976422 1112334566666666666643
No 81
>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=55.04 E-value=22 Score=24.03 Aligned_cols=42 Identities=14% Similarity=0.077 Sum_probs=28.5
Q ss_pred CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 26 g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
..+..+++--|++..+-...+...+.+.++|++.+.+|.+|-
T Consensus 73 ~~~d~vi~v~d~~~~~~~~~~~~~~~~~~~~~iiv~NK~Dl~ 114 (158)
T cd01879 73 EKPDLIVNVVDATNLERNLYLTLQLLELGLPVVVALNMIDEA 114 (158)
T ss_pred CCCcEEEEEeeCCcchhHHHHHHHHHHcCCCEEEEEehhhhc
Confidence 456677777777643222334445667899999999999883
No 82
>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=54.51 E-value=45 Score=28.39 Aligned_cols=59 Identities=19% Similarity=0.219 Sum_probs=42.1
Q ss_pred cCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 25 FHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 25 kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
++..+..++..|..-..-...+..+++..++|+..+.+..+|..++..-...-.++|-.
T Consensus 249 ~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~~~DlVlIDt 307 (424)
T PRK05703 249 YGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLRDCDVILIDT 307 (424)
T ss_pred cCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhCCCCEEEEeC
Confidence 55578888988865322356778889999999999999999888776443343455543
No 83
>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=54.26 E-value=8.1 Score=26.91 Aligned_cols=35 Identities=14% Similarity=0.256 Sum_probs=27.5
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
...+||.+.|-- +....+...|.++++|+++...-
T Consensus 92 ~~d~vi~~~d~~--~~~~~l~~~~~~~~~p~i~~~~~ 126 (135)
T PF00899_consen 92 DYDIVIDCVDSL--AARLLLNEICREYGIPFIDAGVN 126 (135)
T ss_dssp TSSEEEEESSSH--HHHHHHHHHHHHTT-EEEEEEEE
T ss_pred CCCEEEEecCCH--HHHHHHHHHHHHcCCCEEEEEee
Confidence 467999998864 35778999999999999988653
No 84
>TIGR01295 PedC_BrcD bacteriocin transport accessory protein, putative. This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris.
Probab=54.10 E-value=17 Score=25.40 Aligned_cols=58 Identities=19% Similarity=0.248 Sum_probs=44.7
Q ss_pred CCCCccceeeeecchhhhhcCCccEEEEeCCCCC--cchheeHHHHhhhCCCCEEEECCH
Q 033552 6 DNLHSFNCVGVVNDPLPLLFHECRLCVIAGNISP--IDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 6 ~~~~~~~~vG~kqt~kaL~kg~~~LViLA~Dasp--~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
.|...+..+...+-.+.+.+|+..+|++...-=| ..+.-.+..+.++.++++.++.+-
T Consensus 3 ~~i~~~~~it~~~~~~~i~~~~~~iv~f~~~~Cp~C~~~~P~l~~~~~~~~~~~y~vdvd 62 (122)
T TIGR01295 3 DNIKGLEVTTVVRALEALDKKETATFFIGRKTCPYCRKFSGTLSGVVAQTKAPIYYIDSE 62 (122)
T ss_pred hhhccceecCHHHHHHHHHcCCcEEEEEECCCChhHHHHhHHHHHHHHhcCCcEEEEECC
Confidence 4677788888889899999999888877655444 344556778888888999888865
No 85
>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=54.02 E-value=17 Score=30.54 Aligned_cols=56 Identities=11% Similarity=-0.018 Sum_probs=42.2
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCC-CEEEECCHhHHH
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDI-PYIYVASKEDLA 67 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~I-P~i~v~tK~eLG 67 (117)
.+.|..+..+.+++..+.-|++|-+....+....+...|++.++ ++..+++..++.
T Consensus 173 pVlg~~~l~~~i~~~~id~ViIAip~~~~~~~~~ll~~l~~~~v~~V~~vP~~~e~~ 229 (456)
T TIGR03022 173 PVVGADDALRLYARTRYAYVIVAMPGTQAEDMARLVRKLGALHFRNVLIVPSLFGLP 229 (456)
T ss_pred cccChhHHHHHHHhCCCCEEEEecCCccHHHHHHHHHHHHhCCCeEEEEeCcccccc
Confidence 34444333445677788889999876554567888899999999 999999998877
No 86
>PRK06719 precorrin-2 dehydrogenase; Validated
Probab=53.36 E-value=37 Score=24.76 Aligned_cols=78 Identities=12% Similarity=0.038 Sum_probs=48.7
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC---CCcceEEEEEeecCCCCccchHHHHhhHHHHHH
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA---TKRPTCCVLVLTKPTKGELGQEEQDKLKADYTL 104 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G---~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e 104 (117)
+.+||.|.|-+. +=..+-..|+. ++|+..+++ .++|...= .+++-..++|.+++....+...-.++..+.|.+
T Consensus 71 a~lViaaT~d~e--~N~~i~~~a~~-~~~vn~~d~-~~~~~f~~pa~v~~~~l~iaisT~G~sP~la~~lr~~ie~~l~~ 146 (157)
T PRK06719 71 AHLIYAATNQHA--VNMMVKQAAHD-FQWVNVVSD-GTESSFHTPGVIRNDEYVVTISTSGKDPSFTKRLKQELTSILPK 146 (157)
T ss_pred ceEEEECCCCHH--HHHHHHHHHHH-CCcEEECCC-CCcCcEEeeeEEEECCeEEEEECCCcChHHHHHHHHHHHHHhhH
Confidence 678888887664 34566677877 567765544 44565421 123445688888887776666666666666666
Q ss_pred HHHHH
Q 033552 105 VVEDV 109 (117)
Q Consensus 105 ~~~~~ 109 (117)
..+.+
T Consensus 147 ~~~~~ 151 (157)
T PRK06719 147 LIKKI 151 (157)
T ss_pred HHHHH
Confidence 54444
No 87
>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=53.17 E-value=18 Score=25.17 Aligned_cols=50 Identities=10% Similarity=-0.049 Sum_probs=27.9
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhC--CCCEEEECCHhHH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEES--DIPYIYVASKEDL 66 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~--~IP~i~v~tK~eL 66 (117)
++..++|+.-.+-++++.....+.+.-..+..+..+. +.|++.+.+|.+|
T Consensus 3 ~~~~~~i~~aD~vl~ViD~~~p~~~~~~~l~~~l~~~~~~k~~iivlNK~DL 54 (141)
T cd01857 3 RQLWRVVERSDIVVQIVDARNPLLFRPPDLERYVKEVDPRKKNILLLNKADL 54 (141)
T ss_pred HHHHHHHhhCCEEEEEEEccCCcccCCHHHHHHHHhccCCCcEEEEEechhc
Confidence 4556677766655555533221111122444555444 7888888888876
No 88
>TIGR01917 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon.
Probab=52.73 E-value=70 Score=27.90 Aligned_cols=94 Identities=12% Similarity=0.124 Sum_probs=57.9
Q ss_pred hhhhhcCCccEEEEeCCCCC-cchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCccchHHHHhh
Q 033552 20 PLPLLFHECRLCVIAGNISP-IDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKL 98 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp-~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~ 98 (117)
.+.|+.-.+.-|||-+-|.- ..-..-+..--|..|||++++.+--.+....|-.|-+-.++|. -|.-+... ..++.+
T Consensus 329 a~~Lk~dgVDAvILtstCgtCtrcga~m~keiE~~GIPvV~i~~~~pI~~~vGanRiv~~~~i~-~PlGnp~l-~~~~e~ 406 (431)
T TIGR01917 329 SKELLAAGVDAVILTSTUGTCTRCGATMVKEIERAGIPVVHICTVTPIALTVGANRIIPAIAIP-HPLGDPAL-DAAEEK 406 (431)
T ss_pred HHHHHHcCCCEEEEcCCCCcchhHHHHHHHHHHHcCCCEEEEeechhHHHhcCCCceecCCCCC-CCCCCCCC-ChhHHH
Confidence 45567777899999988763 1112333344577999999999999999999987644445553 24422212 223333
Q ss_pred HHHHHHHHHHHHhhhcc
Q 033552 99 KADYTLVVEDVKELASS 115 (117)
Q Consensus 99 ~~~~~e~~~~~~~l~~~ 115 (117)
+-...-+.++++.|.++
T Consensus 407 ~~rr~~v~~AL~aL~t~ 423 (431)
T TIGR01917 407 ALRRKIVEKALKALETE 423 (431)
T ss_pred HHHHHHHHHHHHHhcCC
Confidence 33345556666666544
No 89
>TIGR01626 ytfJ_HI0045 conserved hypothetical protein YtfJ-family, TIGR01626. This model represents sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ.
Probab=52.67 E-value=86 Score=23.90 Aligned_cols=51 Identities=10% Similarity=0.111 Sum_probs=23.9
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCE----EEECCHhHHHhhcCCC-cceEEEEE
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPY----IYVASKEDLANAGATK-RPTCCVLV 81 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~----i~v~tK~eLG~A~G~~-~~~svv~I 81 (117)
.+|.-|-++......+....++.+.++ +..+....++.+-|.. .|.+..+|
T Consensus 98 ~~IN~dd~~~~~~~fVk~fie~~~~~~P~~~vllD~~g~v~~~~gv~~~P~T~fVI 153 (184)
T TIGR01626 98 TIINADDAIVGTGMFVKSSAKKGKKENPWSQVVLDDKGAVKNAWQLNSEDSAIIVL 153 (184)
T ss_pred EEEECccchhhHHHHHHHHHHHhcccCCcceEEECCcchHHHhcCCCCCCceEEEE
Confidence 455544433233344444444444333 4455555666666664 23443344
No 90
>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=52.43 E-value=42 Score=31.21 Aligned_cols=62 Identities=19% Similarity=0.090 Sum_probs=47.2
Q ss_pred hcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecC
Q 033552 24 LFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKP 85 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~ 85 (117)
++|..++.+++.|..-..-...+..+++..+||+..+.+.+++-.++..-...-.|+|-..|
T Consensus 212 ~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~~~~~D~VLIDTAG 273 (767)
T PRK14723 212 REGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAALGDKHLVLIDTVG 273 (767)
T ss_pred HcCCCeEEEecCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHHhcCCCEEEEeCCC
Confidence 45556888999998865568899999999999999999999988877644444455654433
No 91
>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=52.17 E-value=17 Score=28.54 Aligned_cols=39 Identities=21% Similarity=0.152 Sum_probs=30.6
Q ss_pred hhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 22 PLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 22 aL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
.+-.....+||.|.|..+ ....+..+|.+++||++...+
T Consensus 97 ~l~~~~~D~VvdaiD~~~--~k~~L~~~c~~~~ip~I~s~g 135 (231)
T cd00755 97 DLLGGDPDFVVDAIDSIR--AKVALIAYCRKRKIPVISSMG 135 (231)
T ss_pred HHhcCCCCEEEEcCCCHH--HHHHHHHHHHHhCCCEEEEeC
Confidence 344445789999999765 367899999999999999743
No 92
>PRK01889 GTPase RsgA; Reviewed
Probab=51.43 E-value=15 Score=30.33 Aligned_cols=38 Identities=26% Similarity=0.121 Sum_probs=28.4
Q ss_pred EEEEeCCCCCc-chheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 30 LCVIAGNISPI-DVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 30 LViLA~Dasp~-~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
+++++.|-.+. ....++..+|+..|+|.+.+.||.+|-
T Consensus 117 liV~s~~p~~~~~~ldr~L~~a~~~~i~piIVLNK~DL~ 155 (356)
T PRK01889 117 FIVCSLNHDFNLRRIERYLALAWESGAEPVIVLTKADLC 155 (356)
T ss_pred EEEEecCCCCChhHHHHHHHHHHHcCCCEEEEEEChhcC
Confidence 44555442222 267788889999999999999999994
No 93
>TIGR03107 glu_aminopep glutamyl aminopeptidase. This model represents the M42.001 clade within MEROPS family M42. M42 includes glutamyl aminopeptidase as in the present model, deblocking aminopeptidases as from Pyrococcus horikoshii and related species, and endo-1,4-beta-glucanase (cellulase M) as from Clostridium thermocellum. The current family includes
Probab=51.34 E-value=67 Score=26.73 Aligned_cols=52 Identities=17% Similarity=0.146 Sum_probs=32.8
Q ss_pred EEEEeCCCCC---cchheeHHHHhhhCCCCEEEECCH--hHHH--hhcCCCcceEEEEE
Q 033552 30 LCVIAGNISP---IDVITHVPILCEESDIPYIYVASK--EDLA--NAGATKRPTCCVLV 81 (117)
Q Consensus 30 LViLA~Dasp---~~i~~~i~~lce~~~IP~i~v~tK--~eLG--~A~G~~~~~svv~I 81 (117)
-++...|.++ ..+.+.+..+|+++||||-+..+. .+-+ +..+.-.+++++.|
T Consensus 252 p~i~~~D~~~i~~~~l~~~l~~~A~~~~I~~Q~~~~~gGtDa~~~~~~~~Gvpt~~i~i 310 (350)
T TIGR03107 252 TLLRFFDPGHIMLPRMKDFLLTTAEEAGIKYQYYVAKGGTDAGAAHLKNSGVPSTTIGV 310 (350)
T ss_pred ceEEEecCCCCCCHHHHHHHHHHHHHcCCCcEEecCCCCchHHHHHHhCCCCcEEEEcc
Confidence 3344446553 468889999999999999986542 2222 33444455655555
No 94
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=51.17 E-value=12 Score=24.51 Aligned_cols=42 Identities=19% Similarity=0.222 Sum_probs=29.9
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+|..++.+..|+ .+.+++.|-. -...|+.||++.|-+++...
T Consensus 26 ~kk~l~~l~~G~-~l~V~~dd~~---~~~di~~~~~~~G~~~~~~~ 67 (81)
T PRK00299 26 VRKTVRNMQPGE-TLLIIADDPA---TTRDIPSFCRFMDHELLAQE 67 (81)
T ss_pred HHHHHHcCCCCC-EEEEEeCCcc---HHHHHHHHHHHcCCEEEEEE
Confidence 455666666665 3666777744 37789999999999997643
No 95
>PF04705 TSNR_N: Thiostrepton-resistance methylase, N terminus; InterPro: IPR006795 This region is found in some members of the SpoU-type rRNA methylase family (IPR001537 from INTERPRO).; GO: 0008649 rRNA methyltransferase activity, 0046677 response to antibiotic; PDB: 3GYQ_B 3NK6_A 3NK7_A.
Probab=50.75 E-value=20 Score=25.72 Aligned_cols=41 Identities=22% Similarity=0.197 Sum_probs=27.2
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
+.+|+-|---+=+-+.|.+| +--.+.++|+..+||+..+..
T Consensus 41 ~~~i~AGvefieVYg~~~~p--~~~~ll~~c~~r~Ipvrlv~~ 81 (115)
T PF04705_consen 41 THSIRAGVEFIEVYGSDGSP--VPPELLAACRQRGIPVRLVDS 81 (115)
T ss_dssp HHHHCTT-EEEEEEEETTS-----CCCCHHHHCTT--EEEE-H
T ss_pred HHHHhcCcEEEEEeeecCCC--CChHHHHHHHhcCCceEEecH
Confidence 45667676666677899998 457889999999999988864
No 96
>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=50.72 E-value=15 Score=28.11 Aligned_cols=35 Identities=11% Similarity=-0.011 Sum_probs=29.0
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
...+||.|.|.- .....+.++|.++++|+++....
T Consensus 111 ~~DvVi~~~d~~--~~r~~l~~~~~~~~ip~i~~g~~ 145 (228)
T cd00757 111 GYDLVLDCTDNF--ATRYLINDACVKLGKPLVSGAVL 145 (228)
T ss_pred CCCEEEEcCCCH--HHHHHHHHHHHHcCCCEEEEEec
Confidence 378999999944 34788999999999999998764
No 97
>COG5258 GTPBP1 GTPase [General function prediction only]
Probab=50.05 E-value=62 Score=28.56 Aligned_cols=67 Identities=21% Similarity=0.148 Sum_probs=41.5
Q ss_pred cchhhhhcCC--ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCccchHHH
Q 033552 18 NDPLPLLFHE--CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQ 95 (117)
Q Consensus 18 qt~kaL~kg~--~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~ 95 (117)
-|++-|-.++ -.|+++|+|-.|.. -||+.||-++-.+-|+.++.... +--+.
T Consensus 217 TtirGL~gqk~dYglLvVaAddG~~~-------------------~tkEHLgi~~a~~lPviVvvTK~-------D~~~d 270 (527)
T COG5258 217 TTIRGLLGQKVDYGLLVVAADDGVTK-------------------MTKEHLGIALAMELPVIVVVTKI-------DMVPD 270 (527)
T ss_pred HHHHHHhccccceEEEEEEccCCcch-------------------hhhHhhhhhhhhcCCEEEEEEec-------ccCcH
Confidence 3555555555 56888888877732 47899998888887776555433 11234
Q ss_pred HhhHHHHHHHHHHHH
Q 033552 96 DKLKADYTLVVEDVK 110 (117)
Q Consensus 96 ~~~~~~~~e~~~~~~ 110 (117)
++++..-+|+...++
T Consensus 271 dr~~~v~~ei~~~Lk 285 (527)
T COG5258 271 DRFQGVVEEISALLK 285 (527)
T ss_pred HHHHHHHHHHHHHHH
Confidence 566666655544443
No 98
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=49.86 E-value=93 Score=27.20 Aligned_cols=47 Identities=13% Similarity=0.085 Sum_probs=38.4
Q ss_pred cCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 25 FHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 25 kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
+...+..+++.|.....-...+..+++..|+|++...+-++|..++.
T Consensus 267 ~~GkkVglI~aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~ 313 (436)
T PRK11889 267 GKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALT 313 (436)
T ss_pred HcCCcEEEEecCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHH
Confidence 33457889999987544578888899999999999999999988874
No 99
>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=49.82 E-value=13 Score=30.15 Aligned_cols=40 Identities=13% Similarity=0.274 Sum_probs=31.4
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhh
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANA 69 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A 69 (117)
..+||.+.| +. +...++.++|..++||++...+.--.|..
T Consensus 106 fdvVV~~~~-~~-~~~~~in~~c~~~~ipfI~a~~~G~~G~v 145 (286)
T cd01491 106 FQVVVLTDA-SL-EDQLKINEFCHSPGIKFISADTRGLFGSI 145 (286)
T ss_pred CCEEEEecC-CH-HHHHHHHHHHHHcCCEEEEEeccccEEEE
Confidence 457777765 54 56889999999999999999887766654
No 100
>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=49.75 E-value=17 Score=27.52 Aligned_cols=39 Identities=8% Similarity=0.138 Sum_probs=29.8
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
...+||.+.|- .+....+.++|.+++||++...+..-.|
T Consensus 110 ~~dvVi~~~~~--~~~~~~ln~~c~~~~ip~i~~~~~G~~G 148 (197)
T cd01492 110 QFDVVVATELS--RAELVKINELCRKLGVKFYATGVHGLFG 148 (197)
T ss_pred CCCEEEECCCC--HHHHHHHHHHHHHcCCCEEEEEecCCEE
Confidence 35688888773 3468889999999999999888744333
No 101
>PRK00124 hypothetical protein; Validated
Probab=49.58 E-value=17 Score=27.16 Aligned_cols=30 Identities=27% Similarity=0.351 Sum_probs=27.2
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
++|=+|+-| ++.-+...|+.+++|+++|.|
T Consensus 3 I~VDADACP--Vk~~i~r~a~r~~i~v~~Vas 32 (151)
T PRK00124 3 IYVDADACP--VKDIIIRVAERHGIPVTLVAS 32 (151)
T ss_pred EEEECCCCc--HHHHHHHHHHHHCCeEEEEEe
Confidence 788899999 789999999999999999884
No 102
>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=49.43 E-value=19 Score=27.36 Aligned_cols=45 Identities=22% Similarity=0.096 Sum_probs=30.1
Q ss_pred ecchhhhhcCCccEEEEeCCCCCc--chheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPI--DVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~--~i~~~i~~lce~~~IP~i~v~ 61 (117)
+..++.+++.++.+|++++|.... .....+..+.+..++|+.++.
T Consensus 22 ~~~~~~~~~~~~d~vv~~GDl~~~~~~~~~~~~~l~~~~~~pv~~v~ 68 (239)
T TIGR03729 22 ETLAQYLKKQKIDHLHIAGDISNDFQRSLPFIEKLQELKGIKVTFNA 68 (239)
T ss_pred HHHHHHHHhcCCCEEEECCccccchhhHHHHHHHHHHhcCCcEEEEC
Confidence 345666777789999999998751 122334445554678998774
No 103
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This is entry represents an essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) []. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology [].; PDB: 2K2E_A 2Q4Q_B 2AB1_A 2FVT_A 2CYJ_A 1IHN_B 2GM2_A 3CPK_A 2FI9_A.
Probab=49.11 E-value=47 Score=22.74 Aligned_cols=52 Identities=10% Similarity=-0.011 Sum_probs=37.7
Q ss_pred ecchhhhhcC--CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 17 VNDPLPLLFH--ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 17 kqt~kaL~kg--~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
..+++.+..- +..+|||..-....-+-..+....+++||.+....|.+....
T Consensus 41 ~~~l~~l~~~~p~pe~liiGtG~~~~~~~~~~~~~l~~~GI~ve~m~T~~Ac~t 94 (110)
T PF04430_consen 41 PEDLEELLELEPKPEVLIIGTGKRQLFLPPELREYLRKKGIGVEVMDTPAACRT 94 (110)
T ss_dssp THHHHHHHCTCCS-SEEEEEETTS-SECTHHHHHHHHTTT-EEEEE-HHHHHHH
T ss_pred HHHHHHHHhccCCCcEEEEccCCccccCCHHHHHHHHHcCCeEEEECHHHHHHH
Confidence 3455666666 789999999877655667788889999999999999987773
No 104
>PRK06718 precorrin-2 dehydrogenase; Reviewed
Probab=48.95 E-value=31 Score=26.22 Aligned_cols=59 Identities=15% Similarity=0.067 Sum_probs=37.1
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC---CCcceEEEEEeecCCCCc
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA---TKRPTCCVLVLTKPTKGE 89 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G---~~~~~svv~I~~~~~~~~ 89 (117)
.+.+||.|.|-.. +-..+...| ..++++..+++ .++|...= .+++-..++|.+++....
T Consensus 70 ~adlViaaT~d~e--lN~~i~~~a-~~~~lvn~~d~-~~~~~f~~Pa~~~~g~l~iaIsT~G~sP~ 131 (202)
T PRK06718 70 DAFLVIAATNDPR--VNEQVKEDL-PENALFNVITD-AESGNVVFPSALHRGKLTISVSTDGASPK 131 (202)
T ss_pred CceEEEEcCCCHH--HHHHHHHHH-HhCCcEEECCC-CccCeEEEeeEEEcCCeEEEEECCCCChH
Confidence 3567888877664 567788899 45788765554 44564321 123456688888776553
No 105
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=48.93 E-value=73 Score=21.94 Aligned_cols=49 Identities=12% Similarity=0.063 Sum_probs=37.2
Q ss_pred hhhhhcCC-ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 20 PLPLLFHE-CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 20 ~kaL~kg~-~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
++.+...+ ..+|+|..-....-+-..+...++++||.+...+|.+....
T Consensus 44 l~~~~~~~~peiliiGTG~~~~~~~~~~~~~l~~~gI~vE~m~T~aAcrT 93 (109)
T cd00248 44 LLPLLAEDRPDILLIGTGAEIAFLPRALRAALRAAGIGVEVMSTGAACRT 93 (109)
T ss_pred HHHHHhhCCCCEEEEcCCCCCCcCCHHHHHHHHHcCCeEEEeCcHHHHHH
Confidence 44444444 88999998887644556677888999999999999987763
No 106
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=48.92 E-value=59 Score=27.52 Aligned_cols=59 Identities=22% Similarity=0.198 Sum_probs=43.7
Q ss_pred cCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 25 FHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 25 kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
.|..++.++..|..-..-...+..+|+..|+|+..+.+..+|..++..-...-.++|-.
T Consensus 165 ~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~~DlVLIDT 223 (374)
T PRK14722 165 FGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELRNKHMVLIDT 223 (374)
T ss_pred cCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhcCCCEEEEcC
Confidence 45567889999987444578899999999999999999888877765333334455544
No 107
>PF15632 ATPgrasp_Ter: ATP-grasp in the biosynthetic pathway with Ter operon
Probab=48.56 E-value=20 Score=29.82 Aligned_cols=51 Identities=16% Similarity=0.195 Sum_probs=40.6
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCc------------------chheeHHHHhhhCCCCEEEECCHhHH
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPI------------------DVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~------------------~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
+..+.+++||++ ..+-|+|+|.+|. +.+.++.+.|++++|.+++-.--.++
T Consensus 10 ~~~~~i~~lr~~-~~~~i~~sh~~~~~~~~~~aD~~~~eP~~~~~yv~~~l~~C~~~~Idv~~P~~~~~~ 78 (329)
T PF15632_consen 10 SQRDIIRSLRAN-RDFTIIASHRDPRAPILYAADEAYLEPADGEEYVDWCLDFCKEHGIDVFVPGRNREL 78 (329)
T ss_pred cHHHHHHHHHcC-CCeEEEEEeCCCCchHHhcCceeeecCCCHHHHHHHHHHHHHHhCCeEEEcCccHHH
Confidence 456788999998 8899999988752 45677889999999999988854444
No 108
>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=48.51 E-value=21 Score=27.80 Aligned_cols=51 Identities=18% Similarity=0.077 Sum_probs=37.2
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcc------hheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPID------VITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~------i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
++.++.|++.++.+||+++|..... -...+....+..++|+..++.=.+..
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 5677888878899999999997422 13344556667889999998665544
No 109
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial 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=48.50 E-value=33 Score=20.89 Aligned_cols=42 Identities=14% Similarity=0.132 Sum_probs=28.6
Q ss_pred cchhhhhcCC--ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 18 NDPLPLLFHE--CRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 18 qt~kaL~kg~--~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
.+.++|++-. -.+.+++.|..+ ...++.+|++.|-.+.....
T Consensus 15 ~~~~~l~~l~~g~~l~v~~d~~~~---~~~i~~~~~~~g~~~~~~~~ 58 (69)
T cd00291 15 KTKKALEKLKSGEVLEVLLDDPGA---VEDIPAWAKETGHEVLEVEE 58 (69)
T ss_pred HHHHHHhcCCCCCEEEEEecCCcH---HHHHHHHHHHcCCEEEEEEE
Confidence 3455565533 347777777553 67899999999998876553
No 110
>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=48.16 E-value=16 Score=24.69 Aligned_cols=44 Identities=16% Similarity=0.053 Sum_probs=32.0
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCE
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPY 57 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~ 57 (117)
-+=|....++.|++...+++|+.++.+. + ...+...-+..|+|+
T Consensus 15 ~ipga~e~l~~L~~~g~~~~~lTNns~~-s-~~~~~~~L~~~Gi~~ 58 (101)
T PF13344_consen 15 PIPGAVEALDALRERGKPVVFLTNNSSR-S-REEYAKKLKKLGIPV 58 (101)
T ss_dssp E-TTHHHHHHHHHHTTSEEEEEES-SSS---HHHHHHHHHHTTTT-
T ss_pred cCcCHHHHHHHHHHcCCCEEEEeCCCCC-C-HHHHHHHHHhcCcCC
Confidence 3558889999999999999999999885 2 344444558889985
No 111
>KOG4201 consensus Anthranilate synthase component II [Amino acid transport and metabolism]
Probab=47.79 E-value=18 Score=29.42 Aligned_cols=62 Identities=15% Similarity=0.111 Sum_probs=44.7
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCC-CEEEECCHhHHHhhcCCCcceEEEEEe
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDI-PYIYVASKEDLANAGATKRPTCCVLVL 82 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~I-P~i~v~tK~eLG~A~G~~~~~svv~I~ 82 (117)
|...+--+|.-..++|++=.+.. ..+.+-..|+.-|. |.+.|.+.+|+++++++ ++-++.|-
T Consensus 151 QI~~aR~~GADaVLLIvamLs~~-~lk~l~k~~K~L~me~LVEVn~~eEm~ralei--GakvvGvN 213 (289)
T KOG4201|consen 151 QIYEARLKGADAVLLIVAMLSDL-LLKELYKISKDLGMEPLVEVNDEEEMQRALEI--GAKVVGVN 213 (289)
T ss_pred HHHHHHhcCCceeehHHHHcChH-HHHHHHHHHHHcCCcceeeeccHHHHHHHHHh--CcEEEeec
Confidence 44445556655555666555543 47788889999885 99999999999999988 45556653
No 112
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=46.85 E-value=1.2e+02 Score=24.31 Aligned_cols=48 Identities=13% Similarity=0.070 Sum_probs=37.2
Q ss_pred hcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 24 LFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
.+......+++.|.........+...++..++|+....+.++|..++.
T Consensus 100 ~~~~~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l~ 147 (270)
T PRK06731 100 HGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALT 147 (270)
T ss_pred HHcCCeEEEEecCCCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHHH
Confidence 333456788888877655677888899999999999889888887653
No 113
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.
Probab=46.85 E-value=1e+02 Score=26.99 Aligned_cols=92 Identities=15% Similarity=0.161 Sum_probs=57.7
Q ss_pred hhhhcCCccEEEEeCCCCC-cchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCC-ccchHHHHhh
Q 033552 21 LPLLFHECRLCVIAGNISP-IDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKG-ELGQEEQDKL 98 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp-~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~-~~~~~e~~~~ 98 (117)
+.|+...+.-|||-+-|.- ..-..-+..--|..|||++.+.+--.+...+|-.|-+-.++|. -|.-+ .+..+|+-.+
T Consensus 330 ~~Lk~dgVDAVILTstCgtC~r~~a~m~keiE~~GiPvv~~~~~~pis~tvGanrivp~~~ip-~PlGnp~l~~~~e~~~ 408 (431)
T TIGR01918 330 VELKQGGVDAVILTSTUGTCTRCGATMVKEIERAGIPVVHMCTVIPIALTVGANRIVPTIAIP-HPLGDPALSKAEEKKL 408 (431)
T ss_pred HHHHHcCCCEEEEcCCCCcchhHHHHHHHHHHHcCCCEEEEeecccHhhhcCccceecccCcC-CCCCCCCCCHHHHHHH
Confidence 4566677889999988763 1112333334567999999999999999999988755556664 35433 2223333333
Q ss_pred HHHHHHHHHHHHhhhcc
Q 033552 99 KADYTLVVEDVKELASS 115 (117)
Q Consensus 99 ~~~~~e~~~~~~~l~~~ 115 (117)
...-+.++++.|.++
T Consensus 409 --Rr~~v~~AL~aL~t~ 423 (431)
T TIGR01918 409 --RRKRVEKALKALETE 423 (431)
T ss_pred --HHHHHHHHHHHhcCC
Confidence 344455666655543
No 114
>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=46.00 E-value=28 Score=30.05 Aligned_cols=49 Identities=12% Similarity=0.045 Sum_probs=34.3
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
-++.|.+..+.+||++.++++..+-.-...++.++||-++.-.++.+|-
T Consensus 265 ~v~~i~~~g~~lvi~~~~I~~~~l~~l~~~~l~~~~I~av~~v~~~~Le 313 (517)
T TIGR02342 265 IVKKIKKTGCNVLLIQKSILRDAVNDLALHFLAKMKIMVVKDIEREEVE 313 (517)
T ss_pred HHHHHHhcCCCEEEECCCcccccccHHHHHHHhhCCceEEecCCHHHHH
Confidence 3566777778999999998653333344557777888888877655543
No 115
>PRK00865 glutamate racemase; Provisional
Probab=45.59 E-value=54 Score=25.74 Aligned_cols=48 Identities=27% Similarity=0.227 Sum_probs=32.7
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhc
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~ 70 (117)
+.++.|.+..+.+++||.+..+.. -+..+-+..++|++-+. .-+..|+
T Consensus 58 ~~~~~L~~~g~d~iVIaCNTa~~~---~l~~lr~~~~iPvigi~--~a~~~a~ 105 (261)
T PRK00865 58 EIVEFLLEYGVKMLVIACNTASAV---ALPDLRERYDIPVVGIV--PAIKPAA 105 (261)
T ss_pred HHHHHHHhCCCCEEEEeCchHHHH---HHHHHHHhCCCCEEeeH--HHHHHHH
Confidence 456777888899999999987521 23445567799998833 3444443
No 116
>TIGR03106 trio_M42_hydro hydrolase, peptidase M42 family. This model describes a subfamily of MEROPS peptidase family M42, a glutamyl aminopeptidase family that also includes the cellulase CelM from Clostridium thermocellum and deblocking aminopeptidases that can remove acylated amino acids. Members of this family occur in a three gene cassette with an amidotransferase (TIGR03104)in the asparagine synthase (glutamine-hydrolyzing) family, and a probable acetyltransferase (TIGR03103) in the GNAT family.
Probab=45.38 E-value=84 Score=25.97 Aligned_cols=51 Identities=18% Similarity=0.175 Sum_probs=31.6
Q ss_pred EEEeCCCCC---cchheeHHHHhhhCCCCEEE-ECC----HhHHHhhcCCCcceEEEEE
Q 033552 31 CVIAGNISP---IDVITHVPILCEESDIPYIY-VAS----KEDLANAGATKRPTCCVLV 81 (117)
Q Consensus 31 ViLA~Dasp---~~i~~~i~~lce~~~IP~i~-v~t----K~eLG~A~G~~~~~svv~I 81 (117)
+|...|.++ ..+...+.++|++++|||-+ +.+ =..--+..|...+++++.|
T Consensus 254 ~i~~~d~~~~~~~~l~~~l~~~A~~~~Ip~Q~~~~~~~gtDa~~~~~~~~Gi~t~~i~i 312 (343)
T TIGR03106 254 TIAMADSSGPFDYHLTRKLIRLCQDHGIPHRRDVFRYYRSDAASAVEAGHDIRTALVTF 312 (343)
T ss_pred eEEEecCCCCCCHHHHHHHHHHHHHcCCCcEEEecCCCCChHHHHHHcCCCCCEEEeec
Confidence 444556652 46889999999999999988 433 1222233444455655554
No 117
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=45.05 E-value=23 Score=23.32 Aligned_cols=43 Identities=21% Similarity=0.145 Sum_probs=29.3
Q ss_pred eeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCC-CCEEEE
Q 033552 14 VGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESD-IPYIYV 60 (117)
Q Consensus 14 vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~-IP~i~v 60 (117)
+=++..++.|+.|+ .|-|++.|-.. +..|+.+|+..+ ..++.+
T Consensus 20 ~~~kk~l~~m~~Ge-~LeV~~ddp~~---~~dIp~~~~~~~~~~ll~~ 63 (78)
T COG0425 20 VETKKALAKLKPGE-ILEVIADDPAA---KEDIPAWAKKEGGHELLEV 63 (78)
T ss_pred HHHHHHHHcCCCCC-EEEEEecCcch---HHHHHHHHHHcCCcEEEEE
Confidence 33566677777774 47788888553 588999999655 555443
No 118
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=44.96 E-value=36 Score=25.71 Aligned_cols=76 Identities=14% Similarity=0.135 Sum_probs=45.6
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHh----HHHhhcCCC--cceEEEEEeecCCCCccchHHHHhhHH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKE----DLANAGATK--RPTCCVLVLTKPTKGELGQEEQDKLKA 100 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~----eLG~A~G~~--~~~svv~I~~~~~~~~~~~~e~~~~~~ 100 (117)
..+..+++.|..-..-...+..+|+..|||+....+.+ .+-+++..- ...=.++|-..+-... +.+..+++++
T Consensus 29 ~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~~~~~~D~vlIDT~Gr~~~-d~~~~~el~~ 107 (196)
T PF00448_consen 29 GKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKFRKKGYDLVLIDTAGRSPR-DEELLEELKK 107 (196)
T ss_dssp T--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE-SSSST-HHHHHHHHHH
T ss_pred cccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHHhhcCCCEEEEecCCcchh-hHHHHHHHHH
Confidence 68899999999976678999999999999999887543 233333321 1223466655333222 3333445555
Q ss_pred HHH
Q 033552 101 DYT 103 (117)
Q Consensus 101 ~~~ 103 (117)
+++
T Consensus 108 ~~~ 110 (196)
T PF00448_consen 108 LLE 110 (196)
T ss_dssp HHH
T ss_pred Hhh
Confidence 443
No 119
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=44.61 E-value=15 Score=22.76 Aligned_cols=38 Identities=13% Similarity=0.022 Sum_probs=25.7
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEE
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYI 58 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i 58 (117)
+|.-+ .+..|+ .+.|++.|-.. ...|+.+|+++|-.+.
T Consensus 16 ~k~al-~~~~g~-~l~v~~d~~~s---~~~i~~~~~~~G~~~~ 53 (67)
T cd03421 16 TKKAL-ELEAGG-EIEVLVDNEVA---KENVSRFAESRGYEVS 53 (67)
T ss_pred HHHHH-hcCCCC-EEEEEEcChhH---HHHHHHHHHHcCCEEE
Confidence 34444 445554 46777777443 6789999999998873
No 120
>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=44.28 E-value=21 Score=26.90 Aligned_cols=35 Identities=14% Similarity=0.063 Sum_probs=28.8
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
...+||.|.|.-+ ....+.+.|..+++|+++...-
T Consensus 111 ~~D~Vi~~~d~~~--~r~~l~~~~~~~~ip~i~~~~~ 145 (202)
T TIGR02356 111 NVDLVLDCTDNFA--TRYLINDACVALGTPLISAAVV 145 (202)
T ss_pred CCCEEEECCCCHH--HHHHHHHHHHHcCCCEEEEEec
Confidence 4679999988654 4778999999999999997753
No 121
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=43.67 E-value=29 Score=29.44 Aligned_cols=68 Identities=4% Similarity=-0.026 Sum_probs=52.8
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCc------chheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEE
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPI------DVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCC 78 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~------~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~sv 78 (117)
.-+.|+.++.+|++=|.+.-++|+...--. .-+..+....++.|-+++.+++-.+.|.-+-.-.+.++
T Consensus 272 ~v~YG~~eV~~A~e~GAve~LLv~De~lr~~~~~~re~~~~ll~~ve~~ggkV~Ivs~~he~Ge~Lk~lGGiaa 345 (352)
T COG1537 272 KVAYGLEEVEKAAEYGAVETLLVTDELLRSDDVEEREDVEELLEEVESMGGKVVIVSTEHEPGERLKALGGIAA 345 (352)
T ss_pred ceeEcHHHHHHHHhcCcceeEEeehhhhcccchhhHHHHHHHHHHHHHcCCeEEEEecCCcchHHHHhccCeEE
Confidence 347899999999999999988887654322 33667778889999999999999999976554434543
No 122
>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=43.59 E-value=28 Score=27.23 Aligned_cols=19 Identities=16% Similarity=0.137 Sum_probs=11.8
Q ss_pred heeHHHHhhhCCCCEEEEC
Q 033552 43 ITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~ 61 (117)
...+....++.+|++++..
T Consensus 195 l~~l~~~ik~~~v~~if~e 213 (264)
T cd01020 195 IAAFQNAIKNRQIDALIVN 213 (264)
T ss_pred HHHHHHHHHhCCCCEEEeC
Confidence 4555666666677766654
No 123
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.52 E-value=25 Score=26.47 Aligned_cols=34 Identities=15% Similarity=0.195 Sum_probs=29.3
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
+++=+|+=| ++..|...++++++|+++|.+...-
T Consensus 4 I~VDADACP--Vk~~i~r~A~r~~~~v~~Van~~~~ 37 (150)
T COG1671 4 IWVDADACP--VKDEIYRVAERMGLKVTFVANFPHR 37 (150)
T ss_pred EEEeCCCCc--hHHHHHHHHHHhCCeEEEEeCCCcc
Confidence 567788888 7999999999999999999987653
No 124
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=43.24 E-value=40 Score=29.24 Aligned_cols=77 Identities=21% Similarity=0.207 Sum_probs=45.9
Q ss_pred hcCCccEEEEeCCCCC--------------cch--------------------heeHHHHhhhCCCCEEEECCH------
Q 033552 24 LFHECRLCVIAGNISP--------------IDV--------------------ITHVPILCEESDIPYIYVASK------ 63 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp--------------~~i--------------------~~~i~~lce~~~IP~i~v~tK------ 63 (117)
|++.-+|||++.|+.. ++- +.+|..+-.+++|-.||.=|+
T Consensus 226 R~~a~rllv~~TDa~fH~AGDGkLaGIv~PNDg~CHL~~~g~Yt~s~~~DYPSi~ql~~kL~e~nI~~IFAVT~~~~~~Y 305 (423)
T smart00187 226 REDARRLLVFSTDAGFHFAGDGKLAGIVQPNDGQCHLDNNGEYTMSTTQDYPSIGQLNQKLAENNINPIFAVTKKQVSLY 305 (423)
T ss_pred CCCceEEEEEEcCCCccccCCcceeeEecCCCCcceeCCCCCcCccCcCCCCCHHHHHHHHHhcCceEEEEEcccchhHH
Confidence 5666789999999873 222 344556667778877775444
Q ss_pred hHHHhhcCCCcceEEEEEeecCCCCccchHHHHhhHHHHHHHHHHH
Q 033552 64 EDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVEDV 109 (117)
Q Consensus 64 ~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e~~~~~ 109 (117)
++|...+. -+.+++++..+.+. .+-.++.|+++.+.|
T Consensus 306 ~~Ls~lip----gs~vg~Ls~DSsNI-----v~LI~~aY~~i~S~V 342 (423)
T smart00187 306 KELSALIP----GSSVGVLSEDSSNV-----VELIKDAYNKISSRV 342 (423)
T ss_pred HHHHHhcC----cceeeecccCcchH-----HHHHHHHHHhhceEE
Confidence 44556654 23456665444442 455555666655443
No 125
>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=43.19 E-value=13 Score=31.81 Aligned_cols=39 Identities=18% Similarity=0.271 Sum_probs=29.9
Q ss_pred cEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhh
Q 033552 29 RLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANA 69 (117)
Q Consensus 29 ~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A 69 (117)
.+|| +++.++ ....++.++|.+++||++.+.+.--.|..
T Consensus 114 diVI-~t~~~~-~~~~~L~~~c~~~~iPlI~~~s~G~~G~v 152 (425)
T cd01493 114 TVVI-ATNLPE-STLLRLADVLWSANIPLLYVRSYGLYGYI 152 (425)
T ss_pred CEEE-ECCCCH-HHHHHHHHHHHHcCCCEEEEecccCEEEE
Confidence 4554 555454 34667999999999999999998888855
No 126
>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=42.93 E-value=26 Score=23.54 Aligned_cols=40 Identities=15% Similarity=0.101 Sum_probs=24.2
Q ss_pred ccEEEEeCCCCC--cchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 28 CRLCVIAGNISP--IDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 28 ~~LViLA~Dasp--~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
+.++++--|+.. ......+..+....++|++.+.+|.++=
T Consensus 77 ~d~ii~v~d~~~~~~~~~~~~~~~~~~~~~piiiv~nK~D~~ 118 (157)
T cd01894 77 ADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKVDNI 118 (157)
T ss_pred CCEEEEEEeccccCCccHHHHHHHHHhcCCCEEEEEECcccC
Confidence 444444445442 1122345566777889999999997753
No 127
>PF13848 Thioredoxin_6: Thioredoxin-like domain; PDB: 3EC3_B 3BOA_A 2B5E_A 1BJX_A 2K18_A 3UEM_A 3BJ5_A 2BJX_A 2R2J_A 2L4C_A ....
Probab=42.55 E-value=77 Score=22.20 Aligned_cols=60 Identities=10% Similarity=0.212 Sum_probs=43.4
Q ss_pred heeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCccchHHHHhhHHHHHHHHHH
Q 033552 43 ITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVED 108 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e~~~~ 108 (117)
...|..|-+.+..|.+...|.+.+....+...+..++++.. ...+..+.+.+.+.++.+.
T Consensus 64 ~~~l~~fI~~~~~P~v~~~t~~n~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~l~~~a~~ 123 (184)
T PF13848_consen 64 PEELKKFIKKNSFPLVPELTPENFEKLFSSPKPPVLILFDN------KDNESTEAFKKELQDIAKK 123 (184)
T ss_dssp HHHHHHHHHHHSSTSCEEESTTHHHHHHSTSSEEEEEEEET------TTHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHhccccccccchhhHHHHhcCCCceEEEEEEc------CCchhHHHHHHHHHHHHHh
Confidence 67788899999999999999999999999886655555532 1234456666666555543
No 128
>cd01143 YvrC Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding 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.
Probab=41.52 E-value=1.3e+02 Score=21.36 Aligned_cols=57 Identities=11% Similarity=0.152 Sum_probs=38.1
Q ss_pred ceeeee--cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH----------hHHHhhcCCC
Q 033552 12 NCVGVV--NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK----------EDLANAGATK 73 (117)
Q Consensus 12 ~~vG~k--qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK----------~eLG~A~G~~ 73 (117)
..+|.. -.+..|.+-+.-+||......+ .+.+..++.++|++.+... ..||+++|+.
T Consensus 43 ~~~g~~~~~n~E~l~~l~PDlii~~~~~~~-----~~~~~l~~~gi~v~~~~~~~~~~~~~~~~~~lg~~~g~~ 111 (195)
T cd01143 43 PKVGSYSNPNVEKIVALKPDLVIVSSSSLA-----ELLEKLKDAGIPVVVLPAASSLDEIYDQIELIGKITGAE 111 (195)
T ss_pred CcccCCCCCCHHHHhccCCCEEEEcCCcCH-----HHHHHHHHcCCcEEEeCCCCCHHHHHHHHHHHHHHhCCh
Confidence 455543 3678888888999887543222 2455668899998887643 2678888865
No 129
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=41.29 E-value=1.2e+02 Score=20.88 Aligned_cols=40 Identities=13% Similarity=-0.002 Sum_probs=26.6
Q ss_pred EEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhhcC
Q 033552 32 VIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANAGA 71 (117)
Q Consensus 32 iLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A~G 71 (117)
+.++=+|..-+.+++.+.|+++|+++.+.. +-.++-....
T Consensus 6 ~C~~GaSSs~la~km~~~a~~~gi~~~i~a~~~~e~~~~~~ 46 (99)
T cd05565 6 LCAGGGTSGLLANALNKGAKERGVPLEAAAGAYGSHYDMIP 46 (99)
T ss_pred ECCCCCCHHHHHHHHHHHHHHCCCcEEEEEeeHHHHHHhcc
Confidence 333334443468899999999999995544 5566655443
No 130
>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=40.81 E-value=22 Score=23.98 Aligned_cols=36 Identities=8% Similarity=0.248 Sum_probs=29.5
Q ss_pred CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 26 g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
.+.-+|+++-.+.. ....+...++.+|+|+..++..
T Consensus 49 ~~~Dvill~pqi~~--~~~~i~~~~~~~~ipv~~I~~~ 84 (95)
T TIGR00853 49 DDADVVLLAPQVAY--MLPDLKKETDKKGIPVEVINGA 84 (95)
T ss_pred CCCCEEEECchHHH--HHHHHHHHhhhcCCCEEEeChh
Confidence 45679999988875 4888999999999999987643
No 131
>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=40.58 E-value=16 Score=22.58 Aligned_cols=39 Identities=21% Similarity=0.236 Sum_probs=26.6
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
++.+..| -.|.|++.|-.. ...|+.+|+++|-.++.+..
T Consensus 21 l~~l~~G-~~l~v~~d~~~~---~~di~~~~~~~g~~~~~~~~ 59 (70)
T PF01206_consen 21 LKELPPG-EVLEVLVDDPAA---VEDIPRWCEENGYEVVEVEE 59 (70)
T ss_dssp HHTSGTT--EEEEEESSTTH---HHHHHHHHHHHTEEEEEEEE
T ss_pred HHhcCCC-CEEEEEECCccH---HHHHHHHHHHCCCEEEEEEE
Confidence 3344444 447788888552 67899999999988776643
No 132
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=40.56 E-value=1.2e+02 Score=26.37 Aligned_cols=45 Identities=13% Similarity=0.144 Sum_probs=36.6
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
..+..+++.|..-..-...+..+++..++|+....+.++|..++.
T Consensus 234 g~~V~lItaDtyR~gAveQLk~yae~lgvpv~~~~dp~dL~~al~ 278 (407)
T PRK12726 234 NRTVGFITTDTFRSGAVEQFQGYADKLDVELIVATSPAELEEAVQ 278 (407)
T ss_pred CCeEEEEeCCccCccHHHHHHHHhhcCCCCEEecCCHHHHHHHHH
Confidence 357888999976433377899999999999998889999987654
No 133
>TIGR02208 lipid_A_msbB lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase. This family consists of MsbB in E. coli and closely related proteins in other species. MsbB is homologous to HtrB (TIGR02207) and acts immediately after it in the biosynthesis of KDO-2 lipid A (also called Re LPS and Re endotoxin). These two enzymes act after creation of KDO-2 lipid IV-A by addition of the KDO sugars.
Probab=40.55 E-value=66 Score=25.60 Aligned_cols=23 Identities=13% Similarity=-0.117 Sum_probs=19.2
Q ss_pred eeecchhhhhcCCccEEEEeCCCCC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISP 39 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp 39 (117)
|+++.+++|++|+ .|.+..|-++
T Consensus 181 ~~r~i~~aLk~g~--~v~il~Dq~~ 203 (305)
T TIGR02208 181 GIKALLASLKRGE--SGYYLPDEDH 203 (305)
T ss_pred hHHHHHHHHhCCC--eEEEeCCCCC
Confidence 7888999999886 7888888874
No 134
>PRK15116 sulfur acceptor protein CsdL; Provisional
Probab=40.40 E-value=35 Score=27.46 Aligned_cols=36 Identities=11% Similarity=0.131 Sum_probs=28.5
Q ss_pred hhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE
Q 033552 23 LLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 23 L~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v 60 (117)
+-.+..-+||.|.|.-. ....+.++|.+++||++.+
T Consensus 117 ll~~~~D~VIdaiD~~~--~k~~L~~~c~~~~ip~I~~ 152 (268)
T PRK15116 117 YMSAGFSYVIDAIDSVR--PKAALIAYCRRNKIPLVTT 152 (268)
T ss_pred HhcCCCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEE
Confidence 33345789999999543 3678999999999999988
No 135
>PRK00098 GTPase RsgA; Reviewed
Probab=40.26 E-value=27 Score=27.96 Aligned_cols=40 Identities=28% Similarity=0.311 Sum_probs=26.4
Q ss_pred ccEEEEeCCC-CCc---chheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 28 CRLCVIAGNI-SPI---DVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 28 ~~LViLA~Da-sp~---~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
+..+++--|+ +|. ....++...++..++|++.+.+|.+|-
T Consensus 81 iD~vllV~d~~~p~~~~~~idr~L~~~~~~~ip~iIVlNK~DL~ 124 (298)
T PRK00098 81 VDQAVLVFAAKEPDFSTDLLDRFLVLAEANGIKPIIVLNKIDLL 124 (298)
T ss_pred CCEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCEEEEEEhHHcC
Confidence 3344444455 241 233455566888999999999999994
No 136
>cd03372 TPP_ComE Thiamine pyrophosphate (TPP) family, ComE subfamily, TPP-binding module; composed of proteins similar to Methanococcus jannaschii sulfopyruvate decarboxylase beta subunit (ComE). M. jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits, which catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. ComDE requires TPP and divalent metal cation cofactors.
Probab=39.82 E-value=1.2e+02 Score=22.42 Aligned_cols=39 Identities=10% Similarity=0.195 Sum_probs=29.3
Q ss_pred eHHHHhhhCCCCEEEEC-CHhHHHhhcCC--CcceEEEEEee
Q 033552 45 HVPILCEESDIPYIYVA-SKEDLANAGAT--KRPTCCVLVLT 83 (117)
Q Consensus 45 ~i~~lce~~~IP~i~v~-tK~eLG~A~G~--~~~~svv~I~~ 83 (117)
.+..+++.+|+++..+. +.++|..|+.. +.|+.+-+.++
T Consensus 114 d~~~lA~a~G~~~~~v~~~~~el~~al~~a~~gp~lIev~~~ 155 (179)
T cd03372 114 DLEAVAKACGLDNVATVASEEAFEKAVEQALDGPSFIHVKIK 155 (179)
T ss_pred CHHHHHHHcCCCeEEecCCHHHHHHHHHHhcCCCEEEEEEEc
Confidence 57789999999999999 99999877654 34555444443
No 137
>COG2229 Predicted GTPase [General function prediction only]
Probab=39.81 E-value=34 Score=26.59 Aligned_cols=53 Identities=19% Similarity=0.134 Sum_probs=39.2
Q ss_pred chhhhhcCCccEEEEeCCCCCcch-heeHHHHhhhCC-CCEEEECCHhHHHhhcC
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDV-ITHVPILCEESD-IPYIYVASKEDLANAGA 71 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i-~~~i~~lce~~~-IP~i~v~tK~eLG~A~G 71 (117)
.+.-+-+|..++||+=-...|.+. -.++.+.-+..+ ||++..-+|.+|..|..
T Consensus 84 m~~~l~~ga~gaivlVDss~~~~~~a~~ii~f~~~~~~ip~vVa~NK~DL~~a~p 138 (187)
T COG2229 84 MWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAINKQDLFDALP 138 (187)
T ss_pred HHHHHhCCcceEEEEEecCCCcchHHHHHHHHHhhccCCCEEEEeeccccCCCCC
Confidence 355667888888887766666541 156666777777 99999999999998743
No 138
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=39.04 E-value=14 Score=24.84 Aligned_cols=33 Identities=12% Similarity=0.010 Sum_probs=24.6
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
..|||+|.|-. .+-..+-..|+.+++|+..++.
T Consensus 61 ~~lV~~at~d~--~~n~~i~~~a~~~~i~vn~~D~ 93 (103)
T PF13241_consen 61 ADLVFAATDDP--ELNEAIYADARARGILVNVVDD 93 (103)
T ss_dssp ESEEEE-SS-H--HHHHHHHHHHHHTTSEEEETT-
T ss_pred heEEEecCCCH--HHHHHHHHHHhhCCEEEEECCC
Confidence 67899888754 3678889999999999987664
No 139
>TIGR00679 hpr-ser Hpr(Ser) kinase/phosphatase. The hprK gene of Enterococcus faecalis encodes a bifunctional enzyme: the HPr kinase/phosphatase
Probab=39.00 E-value=41 Score=27.89 Aligned_cols=49 Identities=12% Similarity=0.059 Sum_probs=37.4
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhh
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANA 69 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A 69 (117)
+.++.+-+.+.-++|++.+..|. ..+...|++++||.+..+ .-.+++..
T Consensus 73 ~~~~~~~~~~~P~iIvt~~~~~p---~~l~~~a~~~~ip~l~t~~~~~~~~~~ 122 (304)
T TIGR00679 73 QIIHNLLTLNPPAIILSKSFTDP---TVLLQVNETYQVPILKTDLFSTELSFR 122 (304)
T ss_pred HHHHHHhCCCCCEEEEECcCCCC---HHHHHHHHHhCCcEEEeCCcHHHHHHH
Confidence 35566677788899999998874 467779999999999877 44555544
No 140
>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=38.86 E-value=46 Score=24.56 Aligned_cols=39 Identities=13% Similarity=0.066 Sum_probs=25.1
Q ss_pred hhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 22 PLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 22 aL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
.+.+|--.+++...|.+. ...+.+.|.++|||++.+.+-
T Consensus 51 ~i~~~~d~Iiv~~~~~~~---~~~~l~~~~~~gIpvv~~d~~ 89 (257)
T PF13407_consen 51 AISQGVDGIIVSPVDPDS---LAPFLEKAKAAGIPVVTVDSD 89 (257)
T ss_dssp HHHTTESEEEEESSSTTT---THHHHHHHHHTTSEEEEESST
T ss_pred HHHhcCCEEEecCCCHHH---HHHHHHHHhhcCceEEEEecc
Confidence 344443334444455442 335666799999999999887
No 141
>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=38.85 E-value=63 Score=27.21 Aligned_cols=47 Identities=19% Similarity=0.017 Sum_probs=33.8
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
.+.+++..+.-|++|-+....+........|+..++++..+++..++
T Consensus 179 ~~~v~~~~Id~ViIAlp~~~~~~~~~~l~~~~~~gv~V~ivP~~~e~ 225 (442)
T TIGR03013 179 VEYVLRHRIDEIVIALDERRGSLPVDELLECKLSGIEVVDAPSFFER 225 (442)
T ss_pred HHHHHhCCCCEEEEECchhhcchHHHHHHHHHhCCCEEEEcchHHHH
Confidence 34567788999999986443221122356899999999999998876
No 142
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=38.85 E-value=1.4e+02 Score=23.67 Aligned_cols=75 Identities=19% Similarity=0.109 Sum_probs=58.1
Q ss_pred CccceeeeecchhhhhcC-CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 9 HSFNCVGVVNDPLPLLFH-ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 9 ~~~~~vG~kqt~kaL~kg-~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
.++.+-|..-+..+++.+ .+.-+++.....+ -...+..+....++|+..+ +++.|-...+...+..++++...+.
T Consensus 20 ~~~~~~G~~~v~~al~~~~~i~~i~~~~~~~~--~~~~~~~~~~~~~~~~~~v-~~~~l~~~~~~~~hqGi~a~~~~~~ 95 (260)
T COG0566 20 GEFLIEGEHAVLEALASGPKIVRILVTEGRLP--RFEELLALAAAKGIPVYVV-SEAILDKLSGTENHQGIVAVVKKRR 95 (260)
T ss_pred CcEEEeeHHHHHHHHhcCCCceEEEEecccch--hHHHHHHHHHhcCCeEEEE-CHHHHHHHhCCCCCCeEEEEEeccc
Confidence 357788999999999999 6778888888773 3777888888999999776 5677888877666666677665443
No 143
>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=38.64 E-value=85 Score=21.43 Aligned_cols=45 Identities=13% Similarity=0.104 Sum_probs=33.5
Q ss_pred hcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhhcCCC
Q 033552 24 LFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANAGATK 73 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A~G~~ 73 (117)
+.+.+.++.++.|-++. +..+++++++++.+.. ...++.++.|..
T Consensus 59 ~~~~v~~v~v~~~~~~~-----~~~~~~~~~~~~~~~~D~~~~~~~~~~~~ 104 (146)
T PF08534_consen 59 KDKGVDVVGVSSDDDPP-----VREFLKKYGINFPVLSDPDGALAKALGVT 104 (146)
T ss_dssp HTTTCEEEEEEESSSHH-----HHHHHHHTTTTSEEEEETTSHHHHHTTCE
T ss_pred ccCceEEEEecccCCHH-----HHHHHHhhCCCceEEechHHHHHHHhCCc
Confidence 45558888888887763 6667777887777766 557899999964
No 144
>KOG0368 consensus Acetyl-CoA carboxylase [Lipid transport and metabolism]
Probab=37.97 E-value=34 Score=34.73 Aligned_cols=77 Identities=25% Similarity=0.221 Sum_probs=52.7
Q ss_pred CCCCccceeeeecchhhhhcCC-ccEEEEeCCCC---------CcchheeHHHHhhhCCCCEEEEC--CHhHHHhhcCCC
Q 033552 6 DNLHSFNCVGVVNDPLPLLFHE-CRLCVIAGNIS---------PIDVITHVPILCEESDIPYIYVA--SKEDLANAGATK 73 (117)
Q Consensus 6 ~~~~~~~~vG~kqt~kaL~kg~-~~LViLA~Das---------p~~i~~~i~~lce~~~IP~i~v~--tK~eLG~A~G~~ 73 (117)
..+.+.-.|-.+-+++.=+.-+ -.+++||+|+. +..+......++++++||-|++. |-+.+|-|--+.
T Consensus 1523 pG~N~~GMVAw~~~~~TpEyP~Gr~~iVIgNDiTfqiGSFGp~ED~lF~~aselAR~~~iPrIylaaNSGARIGlAeei~ 1602 (2196)
T KOG0368|consen 1523 PGLNSCGMVAWKLTVKTPEYPEGRDLIVIGNDVTFQIGSFGPREDLLFLAASELAREKGIPRIYLAANSGARIGLAEEIK 1602 (2196)
T ss_pred CCCCcceeEEEEEEecCCCCCCCceEEEEeccceEeccCCCChHHHHHHHHHHHHHhcCCCeEEEeccCccccccHHHHH
Confidence 3445555666666766665333 57999999997 24567788899999999988876 778888775553
Q ss_pred cceEEEEEee
Q 033552 74 RPTCCVLVLT 83 (117)
Q Consensus 74 ~~~svv~I~~ 83 (117)
+.--|+..+
T Consensus 1603 -~lfkVaw~d 1611 (2196)
T KOG0368|consen 1603 -PLFKVAWVD 1611 (2196)
T ss_pred -HHheeeccC
Confidence 333344433
No 145
>PRK10474 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=37.93 E-value=48 Score=22.06 Aligned_cols=48 Identities=8% Similarity=0.053 Sum_probs=33.0
Q ss_pred eeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 14 VGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 14 vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
.|+.+.+..-.-..+.+||+|+|....+ ..+..|.|++.+...+-|-.
T Consensus 25 ~g~~~~lt~~~i~~Ad~VIia~d~~i~~-------~~rf~gk~v~~~s~~~ai~~ 72 (88)
T PRK10474 25 IGLENELTAEDVASADMVILTKDIGIKF-------EERFAGKTIVRVNISDAVKR 72 (88)
T ss_pred cCcCCCCCHHHHHhCCEEEEEecCCCcc-------hhccCCCceEEecHHHHHHC
Confidence 5666666555566789999999987312 23556778888877766643
No 146
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=37.90 E-value=27 Score=28.67 Aligned_cols=45 Identities=16% Similarity=0.123 Sum_probs=31.1
Q ss_pred eecchhhhhcCCccEEEEeCCCCC---------cchheeHHHHhhhCCCCEEEEC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISP---------IDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp---------~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+.+.++.++..++-+|++|+|.-. ......+..+| ..+||++.+.
T Consensus 29 f~~~l~~a~~~~vD~vliAGDlFd~~~Ps~~a~~~~~~~l~~l~-~~~Ipv~~I~ 82 (390)
T COG0420 29 FDELLEIAKEEKVDFVLIAGDLFDTNNPSPRALKLFLEALRRLK-DAGIPVVVIA 82 (390)
T ss_pred HHHHHHHHHHccCCEEEEccccccCCCCCHHHHHHHHHHHHHhc-cCCCcEEEec
Confidence 356788888999999999999873 11222333333 3689998876
No 147
>PRK08419 lipid A biosynthesis lauroyl acyltransferase; Reviewed
Probab=37.49 E-value=98 Score=24.40 Aligned_cols=47 Identities=17% Similarity=-0.022 Sum_probs=31.0
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCc--c-h-----------heeHHHHhhhCCCCEEEECCH
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPI--D-V-----------ITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~--~-i-----------~~~i~~lce~~~IP~i~v~tK 63 (117)
|+++.+++|++|+ .|.+..|-++. + + ..-...+|...|.|++.+...
T Consensus 172 ~~r~~l~~Lk~g~--~v~il~Dq~~~~~~gv~v~FfG~~a~~~~g~a~LA~k~~apvvpv~~~ 232 (298)
T PRK08419 172 AMKELLKALKQGR--ALGILVDQNVVPKEGVEVKFFNKRVTHTTIASILARRYNALIIPVFIF 232 (298)
T ss_pred HHHHHHHHHHcCC--eEEEEecCCCCCCCCeEEecCCCCcccchhHHHHHHHHCCCEEEEEEE
Confidence 6788899999886 56666665531 1 1 122335888888888887763
No 148
>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=37.13 E-value=48 Score=28.47 Aligned_cols=47 Identities=13% Similarity=0.075 Sum_probs=31.4
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
++.|.+..+.+||++.|+++..+-.....++.++||-++.--.+.+|
T Consensus 265 v~~i~~~g~~lvi~~~~i~~~~v~~l~~~~l~~~~I~av~~~~~~~L 311 (515)
T cd03338 265 CKKIKKSGCNVLLIQKSILRDAVSDLALHFLAKLKIMVVKDIEREEI 311 (515)
T ss_pred HHHHHhcCCCEEEECCCcccccccHHHHHHHHHCCceEEecCCHHHH
Confidence 55567777899999999865333333455666788877776654443
No 149
>COG2129 Predicted phosphoesterases, related to the Icc protein [General function prediction only]
Probab=37.05 E-value=35 Score=27.23 Aligned_cols=47 Identities=23% Similarity=0.229 Sum_probs=32.7
Q ss_pred eecchhhhhcCCccEEEEeCCCC-----CcchheeH--HHHhhhCCCCEEEECC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNIS-----PIDVITHV--PILCEESDIPYIYVAS 62 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Das-----p~~i~~~i--~~lce~~~IP~i~v~t 62 (117)
++|.+.+...-++-++|+|+|.+ |....... ...-.+.++|++.++.
T Consensus 19 ~~k~~~~~~~~~~D~lviaGDlt~~~~~~~~~~~~~~~~e~l~~~~~~v~avpG 72 (226)
T COG2129 19 LKKLLNAAADIRADLLVIAGDLTYFHFGPKEVAEELNKLEALKELGIPVLAVPG 72 (226)
T ss_pred HHHHHHHHhhccCCEEEEecceehhhcCchHHHHhhhHHHHHHhcCCeEEEEcC
Confidence 35666777777899999999998 32223332 2344567999999974
No 150
>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=36.56 E-value=38 Score=25.16 Aligned_cols=47 Identities=11% Similarity=0.087 Sum_probs=33.1
Q ss_pred eecchhhhhcC--CccEEEEeCCCCCcc---hheeHHHHhhhCCCCEEEECC
Q 033552 16 VVNDPLPLLFH--ECRLCVIAGNISPID---VITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 16 ~kqt~kaL~kg--~~~LViLA~Dasp~~---i~~~i~~lce~~~IP~i~v~t 62 (117)
+.+.++.+++. ++.+||+++|..... -...+...-+..++|+.++..
T Consensus 27 l~~~~~~i~~~~~~~d~vi~~GDl~~~~~~~~~~~~~~~l~~~~~p~~~v~G 78 (240)
T cd07402 27 LEAVLAHINALHPRPDLVLVTGDLTDDGSPESYERLRELLAALPIPVYLLPG 78 (240)
T ss_pred HHHHHHHHHhcCCCCCEEEECccCCCCCCHHHHHHHHHHHhhcCCCEEEeCC
Confidence 45677888776 899999999987421 123444455566999999864
No 151
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=36.55 E-value=1.1e+02 Score=20.46 Aligned_cols=36 Identities=17% Similarity=0.175 Sum_probs=23.5
Q ss_pred EEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHH
Q 033552 32 VIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLA 67 (117)
Q Consensus 32 iLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG 67 (117)
+.++=.+..-+.+++.+.++++|+|+.... +-.++.
T Consensus 5 ~Cg~G~sTS~~~~ki~~~~~~~~~~~~v~~~~~~~~~ 41 (96)
T cd05564 5 VCSAGMSTSILVKKMKKAAEKRGIDAEIEAVPESELE 41 (96)
T ss_pred EcCCCchHHHHHHHHHHHHHHCCCceEEEEecHHHHH
Confidence 333333433467899999999999985554 444444
No 152
>COG1086 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]
Probab=35.98 E-value=54 Score=29.68 Aligned_cols=64 Identities=11% Similarity=0.060 Sum_probs=51.5
Q ss_pred CCCCCccceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 5 NDNLHSFNCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 5 ~~~~~~~~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
+..++..+|.|.+....-+++-.+..++||.-.-..+-.+.+...|...++.+-..+..++|..
T Consensus 155 g~~i~Gv~V~g~~~i~~~v~~~~~~~iiiAips~~~~~~~~i~~~l~~~~~~v~~lP~~~~l~~ 218 (588)
T COG1086 155 GMKIRGVPVLGRIEIERVVEELGIQLILIAIPSASQEERRRILLRLARTGIAVRILPQLTDLKD 218 (588)
T ss_pred CCEEeceeeechhHHHHHHHHcCCceEEEecCCCCHHHHHHHHHHHHhcCCcEEecCcHHHHHH
Confidence 4556677889999977777888888888876554445688999999999999999999999776
No 153
>TIGR03659 IsdE heme ABC transporter, heme-binding protein isdE. This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localized to the cell wall and bearing the NEAT (NEAr Transporter, pfam05031) heme-binding domain. IsdE has been shown to bind heme and is involved in the process of scavenging heme for the purpose of obtaining iron.
Probab=35.35 E-value=2.1e+02 Score=22.17 Aligned_cols=60 Identities=8% Similarity=0.057 Sum_probs=38.3
Q ss_pred Cccceeee--ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC---------HhHHHhhcCCC
Q 033552 9 HSFNCVGV--VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS---------KEDLANAGATK 73 (117)
Q Consensus 9 ~~~~~vG~--kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t---------K~eLG~A~G~~ 73 (117)
.+...+|. .-.+..|..=+.-|||.....++ +...+ =++.+||++++.. -+.||+++|++
T Consensus 71 ~~i~~vg~~~~~n~E~I~al~PDlIi~~~~~~~-~~~~~----l~~~gi~v~~~~~~~~~~~~~~i~~lg~~~G~~ 141 (289)
T TIGR03659 71 KDVPEVGNPMSPDMEKIKSLKPTVVLSVTTLEE-DLGPK----FKQLGVEATFLNLTSVDGMKKSITELGEKYGRE 141 (289)
T ss_pred hCCCccCCCCCCCHHHHhccCCcEEEEcCcccH-HHHHH----HHHcCCcEEEEcCCCHHHHHHHHHHHHHHhCCH
Confidence 34455663 24577788888889987655443 33333 3556899987743 45678888865
No 154
>PRK07377 hypothetical protein; Provisional
Probab=35.28 E-value=1.3e+02 Score=23.41 Aligned_cols=47 Identities=15% Similarity=0.120 Sum_probs=35.0
Q ss_pred CccEEEEeC--C--CCCcchheeHHHHhhhCC--CCEEEECCHhHHHhhcCCC
Q 033552 27 ECRLCVIAG--N--ISPIDVITHVPILCEESD--IPYIYVASKEDLANAGATK 73 (117)
Q Consensus 27 ~~~LViLA~--D--asp~~i~~~i~~lce~~~--IP~i~v~tK~eLG~A~G~~ 73 (117)
..++-|+.. + -....+..++..+++.++ +.++...+.++|++|+-.+
T Consensus 76 ~~Rlgv~~~~~~~~~~~~~l~~~l~~~~~~y~~rlElv~y~~~~~l~~aL~~~ 128 (184)
T PRK07377 76 VMRLGVLEIETETSSVFDQLIDQLRTILDKYHLRLELVVYPDLQALEQALRDK 128 (184)
T ss_pred EEEEEEEeccccccccHHHHHHHHHHHHHHhCceeeEEecCCHHHHHHHHhcC
Confidence 356666663 1 122456788888999988 8888899999999998765
No 155
>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=35.27 E-value=36 Score=22.32 Aligned_cols=51 Identities=14% Similarity=0.103 Sum_probs=34.8
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC-HhHHHhhcCCC
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS-KEDLANAGATK 73 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t-K~eLG~A~G~~ 73 (117)
+-.+.++...+.++.|..|-.. .+..+++++++|+-++.+ ..++.++.|..
T Consensus 50 ~~~~~~~~~~~~vi~is~d~~~-----~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~ 101 (124)
T PF00578_consen 50 ELYKKYKDKGVQVIGISTDDPE-----EIKQFLEEYGLPFPVLSDPDGELAKAFGIE 101 (124)
T ss_dssp HHHHHHHTTTEEEEEEESSSHH-----HHHHHHHHHTCSSEEEEETTSHHHHHTTCE
T ss_pred HHhhhhccceEEeeeccccccc-----chhhhhhhhccccccccCcchHHHHHcCCc
Confidence 3344556666778888776442 456678888887776664 66888888876
No 156
>PF01497 Peripla_BP_2: Periplasmic binding protein; InterPro: IPR002491 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Most bacterial importers employ a periplasmic substrate-binding protein (PBP) that delivers the ligand to the extracellular gate of the TM domains. These proteins bind their substrates selectively and with high affinity, which is thought to ensure the specificity of the transport reaction. Binding proteins in Gram-negative bacteria are present within the periplasm, whereas those in Gram-positive bacteria are tethered to the cell membrane via the acylation of a cysteine residue that is an integral component of a lipoprotein signal sequence. In planta expression of a high-affinity iron-uptake system involving the siderophore chrysobactin in Erwinia chrysanthemi 3937 contributes greatly to invasive growth of this pathogen on its natural host, African violets []. The cobalamin (vitamin B12) and the iron transport systems share many common attributes and probably evolved from the same origin [, ]. The periplasmic-binding domain is composed of two subdomains, each consisting of a central beta-sheet and surrounding alpha-helices, linked by a rigid alpha-helix. The substrate binding site is located in a cleft between the two alpha/beta subdomains [].; GO: 0005488 binding; PDB: 2X4L_A 1N4A_B 1N2Z_B 1N4D_B 4DBL_J 2QI9_F 3EIW_A 3EIX_A 3MWG_A 3MWF_A ....
Probab=35.05 E-value=1.4e+02 Score=21.79 Aligned_cols=75 Identities=12% Similarity=0.071 Sum_probs=47.6
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHh----------HHHhhcCCCcceEEEEEeecCCCC
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKE----------DLANAGATKRPTCCVLVLTKPTKG 88 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~----------eLG~A~G~~~~~svv~I~~~~~~~ 88 (117)
.+..|..-+.-|||......+.+ ....-.+.+||++.+.+.. .||+++|++. .
T Consensus 52 ~~E~i~~l~PDlIi~~~~~~~~~----~~~~~~~~~ip~~~~~~~~~~~~~~~~i~~lg~~~g~~~-~------------ 114 (238)
T PF01497_consen 52 NLEAILALKPDLIIGSSFYGQSE----EIEKLLEAGIPVVVFDSSSPFDDWKEQIRQLGKALGKED-Q------------ 114 (238)
T ss_dssp -HHHHHHT--SEEEEETTSSCHH----HHHHHHHTTSEEEEESSTTCSHHHHHHHHHHHHHHTSHH-H------------
T ss_pred cHHHHHhCCCCEEEEeccccchH----HHHHHhcccceEEEeecccchHHHHHHHHHHHHhcccHH-H------------
Confidence 45777888889999888872211 2223467799999999874 6888888752 1
Q ss_pred ccchHHHHhhHHHHHHHHHHHHhh
Q 033552 89 ELGQEEQDKLKADYTLVVEDVKEL 112 (117)
Q Consensus 89 ~~~~~e~~~~~~~~~e~~~~~~~l 112 (117)
.++-.+.|+..++++.+.+.+.
T Consensus 115 --a~~~~~~~~~~~~~~~~~~~~~ 136 (238)
T PF01497_consen 115 --AEALIAEYDARLDEIRKRLAKI 136 (238)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHH
T ss_pred --HHHHHHHHHHHHHHHHHhhhcc
Confidence 1223456666666666666665
No 157
>PRK10200 putative racemase; Provisional
Probab=34.88 E-value=86 Score=24.24 Aligned_cols=42 Identities=17% Similarity=0.226 Sum_probs=31.8
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
.+..+.|++..+.+++||.++.. .. +..+-+..+||++.+-.
T Consensus 65 ~~~~~~L~~~g~~~iviaCNTah-~~---~~~l~~~~~iPii~ii~ 106 (230)
T PRK10200 65 AEAALGLQRAGAEGIVLCTNTMH-KV---ADAIESRCSLPFLHIAD 106 (230)
T ss_pred HHHHHHHHHcCCCEEEECCchHH-HH---HHHHHHhCCCCEeehHH
Confidence 45677788888999999999885 33 45566777999988543
No 158
>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=34.78 E-value=59 Score=22.84 Aligned_cols=41 Identities=20% Similarity=0.312 Sum_probs=28.0
Q ss_pred hhhhcCCccEEEEeCCCCCcc---hheeHHHHhhhCCCCEEEECC
Q 033552 21 LPLLFHECRLCVIAGNISPID---VITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~---i~~~i~~lce~~~IP~i~v~t 62 (117)
..+++.++.+||+++|..... -...+ .+-...++|+.+++.
T Consensus 17 ~~~~~~~~D~vv~~GDl~~~~~~~~~~~~-~~l~~~~~p~~~v~G 60 (188)
T cd07392 17 IILKAEEADAVIVAGDITNFGGKEAAVEI-NLLLAIGVPVLAVPG 60 (188)
T ss_pred HHhhccCCCEEEECCCccCcCCHHHHHHH-HHHHhcCCCEEEEcC
Confidence 346677899999999986421 12233 455667899988874
No 159
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=34.41 E-value=99 Score=24.99 Aligned_cols=65 Identities=8% Similarity=0.117 Sum_probs=37.4
Q ss_pred CCcchheeHHHHhhhCCCCEEEECCH------hHHHhhcCCCcceEEEEEeecCCCCccchHHHHhhHHHHHHHHHHHH
Q 033552 38 SPIDVITHVPILCEESDIPYIYVASK------EDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVEDVK 110 (117)
Q Consensus 38 sp~~i~~~i~~lce~~~IP~i~v~tK------~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e~~~~~~ 110 (117)
||.+ ...+.+..++++|+++++... +.|.+-+|.+ ++.+ + |.... ...+.+.|-+++....+.+.
T Consensus 237 s~~~-l~~l~~~ik~~~v~~If~e~~~~~~~~~~la~e~g~~----v~~l-d-pl~~~-~~~~~~~Y~~~m~~n~~~l~ 307 (311)
T PRK09545 237 GAQR-LHEIRTQLVEQKATCVFAEPQFRPAVIESVAKGTSVR----MGTL-D-PLGTN-IKLGKDSYSEFLSQLANQYA 307 (311)
T ss_pred CHHH-HHHHHHHHHHcCCCEEEecCCCChHHHHHHHHhcCCe----EEEe-c-ccccc-ccCCHhHHHHHHHHHHHHHH
Confidence 3444 667888899999999998753 3444545532 2232 2 33221 11123577777766666554
No 160
>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=34.00 E-value=41 Score=27.52 Aligned_cols=33 Identities=18% Similarity=0.257 Sum_probs=27.4
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v 60 (117)
..+|+.+.|--+......+.+.|..+++|+++.
T Consensus 152 ~DlVid~tDn~~~r~L~~iN~ac~~~~~PlV~g 184 (318)
T TIGR03603 152 YNYIIICTEHSNISLLRGLNKLSKETKKPNTIA 184 (318)
T ss_pred CCEEEECCCCccHhHHHHHHHHHHHHCCCEEEE
Confidence 689999999876445567999999999999863
No 161
>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=33.81 E-value=48 Score=26.73 Aligned_cols=52 Identities=15% Similarity=0.164 Sum_probs=40.6
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC--HhHHHhhcCCC
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS--KEDLANAGATK 73 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t--K~eLG~A~G~~ 73 (117)
++..++...+ +|+..=++| ++...+...|++++||++.+.+ ...|...+|.+
T Consensus 45 il~~i~~~~~--iV~~Tlv~~-~lr~~l~~~~~~~~i~~~Dll~~~l~~l~~~lg~~ 98 (255)
T PF03618_consen 45 ILEEIKEENA--IVFYTLVDP-ELREYLEEFCREHGIPCVDLLGPLLSALEEFLGQK 98 (255)
T ss_pred HHHHHhccCC--EEEEeCCCH-HHHHHHHHHHHhcCCCEEeccHHHHHHHHHHHCcC
Confidence 3444555333 777777887 6899999999999999999985 57888999986
No 162
>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=33.55 E-value=35 Score=28.07 Aligned_cols=40 Identities=23% Similarity=0.252 Sum_probs=31.9
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhh
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANA 69 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A 69 (117)
..+||.|.|..+ ...++..+|..++||++..++.--.|+.
T Consensus 91 ~DvVv~a~Dn~~--ar~~in~~c~~~~ip~I~~gt~G~~G~v 130 (312)
T cd01489 91 FDLVFNALDNLA--ARRHVNKMCLAADVPLIESGTTGFLGQV 130 (312)
T ss_pred CCEEEECCCCHH--HHHHHHHHHHHCCCCEEEEecCcceeEE
Confidence 568888888543 5889999999999999999876555543
No 163
>cd01884 EF_Tu EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=33.51 E-value=33 Score=25.70 Aligned_cols=49 Identities=14% Similarity=0.174 Sum_probs=29.8
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCC-EEEECCHhH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIP-YIYVASKED 65 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP-~i~v~tK~e 65 (117)
+++..++..-.+-++++..+-.+..-...+..++.+.++| .+.+-+|-+
T Consensus 80 ~~~~~~~~~~D~~ilVvda~~g~~~~~~~~~~~~~~~~~~~iIvviNK~D 129 (195)
T cd01884 80 KNMITGAAQMDGAILVVSATDGPMPQTREHLLLARQVGVPYIVVFLNKAD 129 (195)
T ss_pred HHHHHHhhhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCcEEEEEeCCC
Confidence 4556667666666777766554333344556678888998 445544443
No 164
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=33.48 E-value=8.8 Score=28.25 Aligned_cols=33 Identities=24% Similarity=0.463 Sum_probs=22.9
Q ss_pred EEEEeCCCC-Ccc--hheeHHHHhhhCCCCEEEECC
Q 033552 30 LCVIAGNIS-PID--VITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 30 LViLA~Das-p~~--i~~~i~~lce~~~IP~i~v~t 62 (117)
..|+..-.. |.. -..+||+.|+..||||+..+.
T Consensus 118 ~~VVT~E~~~~~~~~~~~KIPdvC~~~gV~ci~~~~ 153 (162)
T PF14367_consen 118 ATVVTHEVSNPNKKKKKIKIPDVCEHFGVPCINLFE 153 (162)
T ss_pred CEEEccCCCCCCCCccCCCCChhHHhCCCcCCCHHH
Confidence 366666655 221 146899999999999976554
No 165
>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=33.43 E-value=56 Score=24.03 Aligned_cols=32 Identities=9% Similarity=-0.005 Sum_probs=22.9
Q ss_pred CCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 36 NISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 36 Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
|.+..+.-.++...+.+.+.|++.|.||.++-
T Consensus 89 ~~~~~~~d~~~~~~l~~~~~~~ilV~nK~D~~ 120 (197)
T cd04104 89 STRFSSNDVKLAKAIQCMGKKFYFVRTKVDRD 120 (197)
T ss_pred CCCCCHHHHHHHHHHHHhCCCEEEEEecccch
Confidence 43433344556667777899999999999983
No 166
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=33.30 E-value=13 Score=24.72 Aligned_cols=37 Identities=11% Similarity=-0.027 Sum_probs=24.7
Q ss_pred cchhhhhc--CCccEEEEeCCCCC--cchheeHHHHhhhCC
Q 033552 18 NDPLPLLF--HECRLCVIAGNISP--IDVITHVPILCEESD 54 (117)
Q Consensus 18 qt~kaL~k--g~~~LViLA~Dasp--~~i~~~i~~lce~~~ 54 (117)
..++.|++ .++.-||+|.|.+. ..+..++..++..++
T Consensus 48 ~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i~~~~~~~~ 88 (100)
T PF01751_consen 48 KQIKNLKKLLKKADEIIIATDPDREGELIAWEIIELLGKNN 88 (100)
T ss_dssp HHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHHHHHHHHHS
T ss_pred ccchhhHHHhhhccEeeecCCCChHHHHHHHHHHHHHhHhC
Confidence 34566665 46899999999995 446666666666554
No 167
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=33.25 E-value=53 Score=22.27 Aligned_cols=42 Identities=12% Similarity=-0.026 Sum_probs=26.3
Q ss_pred ecchhhhhcCCccEEEEeCCCCC---cchheeHHHHhhhCCCCEE
Q 033552 17 VNDPLPLLFHECRLCVIAGNISP---IDVITHVPILCEESDIPYI 58 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp---~~i~~~i~~lce~~~IP~i 58 (117)
...+..|++|+..+||-.-+-+. ..--..+...|-+++|||+
T Consensus 61 ~~i~~~i~~~~idlVIn~~~~~~~~~~~~~~~iRr~Av~~~ip~i 105 (116)
T cd01423 61 PSLRELLAEGKIDLVINLPSNRGKRVLDNDYVMRRAADDFAVPLI 105 (116)
T ss_pred hhHHHHHHcCCceEEEECCCCCCCccccCcEeeehhhHhhCCccc
Confidence 34566777888888877433211 1113567778888888885
No 168
>PRK05690 molybdopterin biosynthesis protein MoeB; Provisional
Probab=33.24 E-value=32 Score=26.86 Aligned_cols=39 Identities=10% Similarity=0.026 Sum_probs=29.9
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
...+||.|.|.. +....+.++|.++++|++......--|
T Consensus 122 ~~DiVi~~~D~~--~~r~~ln~~~~~~~ip~v~~~~~g~~G 160 (245)
T PRK05690 122 GHDLVLDCTDNV--ATRNQLNRACFAAKKPLVSGAAIRMEG 160 (245)
T ss_pred cCCEEEecCCCH--HHHHHHHHHHHHhCCEEEEeeeccCCc
Confidence 467999999854 357889999999999999865543333
No 169
>TIGR00315 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis.
Probab=33.17 E-value=51 Score=24.72 Aligned_cols=50 Identities=12% Similarity=0.031 Sum_probs=37.3
Q ss_pred eeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 13 CVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 13 ~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
+|=-+...+.|++.+--++++..-+........+..+++..|+|++....
T Consensus 14 ~~~p~~aa~lLk~AKRPvIivG~ga~~~~a~e~l~~laEklgiPVvtT~~ 63 (162)
T TIGR00315 14 LVSPKLVAMMIKRAKRPLLIVGPENLEDEEKELIVKFIEKFDLPVVATAD 63 (162)
T ss_pred ccCHHHHHHHHHcCCCcEEEECCCcCcccHHHHHHHHHHHHCCCEEEcCc
Confidence 33334466777877777777777775334688999999999999998874
No 170
>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=32.89 E-value=22 Score=21.96 Aligned_cols=33 Identities=18% Similarity=0.119 Sum_probs=23.9
Q ss_pred eeHHHHhhhCCC-------CEEEECCHhHHHhhcCCCcce
Q 033552 44 THVPILCEESDI-------PYIYVASKEDLANAGATKRPT 76 (117)
Q Consensus 44 ~~i~~lce~~~I-------P~i~v~tK~eLG~A~G~~~~~ 76 (117)
..+..+|+..+. .+..-.|+++|+..+|.++.+
T Consensus 5 ~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~t 44 (76)
T PF13545_consen 5 RFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRET 44 (76)
T ss_dssp HHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHH
T ss_pred HHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHH
Confidence 345556666554 467778999999999998643
No 171
>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=32.88 E-value=1.5e+02 Score=25.53 Aligned_cols=61 Identities=13% Similarity=0.023 Sum_probs=44.8
Q ss_pred CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 26 g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
+..+.-++..|..-......+..+|+-.|+|+..+.+..++-.+...-...-.+.|-..+.
T Consensus 220 ~~~~v~~i~~d~~rigalEQL~~~a~ilGvp~~~v~~~~dl~~al~~l~~~d~VLIDTaGr 280 (420)
T PRK14721 220 GADKVALLTTDSYRIGGHEQLRIYGKLLGVSVRSIKDIADLQLMLHELRGKHMVLIDTVGM 280 (420)
T ss_pred CCCeEEEEecCCcchhHHHHHHHHHHHcCCceecCCCHHHHHHHHHHhcCCCEEEecCCCC
Confidence 4355667888887667788899999999999999999999887655433444456554333
No 172
>PRK00945 acetyl-CoA decarbonylase/synthase complex subunit epsilon; Provisional
Probab=32.77 E-value=52 Score=24.96 Aligned_cols=46 Identities=9% Similarity=0.120 Sum_probs=35.7
Q ss_pred ecchhhhhcCCccEEEEeCCCCC-cchheeHHHHhhhCCCCEEEECC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISP-IDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp-~~i~~~i~~lce~~~IP~i~v~t 62 (117)
++..+.|++.+--++++..-+.. .+....+.++++..++|++....
T Consensus 25 ~~aa~lI~~AKrPlIivG~ga~~~~ea~e~l~elaEkl~iPVvtT~~ 71 (171)
T PRK00945 25 KIAAMMIKKAKRPLLVVGSLLLDDEELLDRAVKIAKKANIPVAATGG 71 (171)
T ss_pred HHHHHHHHhCCCcEEEECcCccccchHHHHHHHHHHHHCCCEEEccc
Confidence 34567778777778887777754 34678899999999999998776
No 173
>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=32.63 E-value=10 Score=26.38 Aligned_cols=45 Identities=11% Similarity=-0.003 Sum_probs=32.5
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
++..+.|++-+--++++...+.-......+..+++..|+|++..+
T Consensus 2 ~~~~~~L~~A~rP~il~G~g~~~~~a~~~l~~lae~~~~Pv~~t~ 46 (137)
T PF00205_consen 2 DEAADLLSSAKRPVILAGRGARRSGAAEELRELAEKLGIPVATTP 46 (137)
T ss_dssp HHHHHHHHH-SSEEEEE-HHHHHTTCHHHHHHHHHHHTSEEEEEG
T ss_pred HHHHHHHHhCCCEEEEEcCCcChhhHHHHHHHHHHHHCCCEEecC
Confidence 345667777777777777766622458889999999999997766
No 174
>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_A ....
Probab=32.18 E-value=79 Score=21.50 Aligned_cols=42 Identities=24% Similarity=0.352 Sum_probs=24.2
Q ss_pred CccEEEEeCCCCCcchheeHHHHhh----hC--CCCEEEECCHhHHHh
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCE----ES--DIPYIYVASKEDLAN 68 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce----~~--~IP~i~v~tK~eLG~ 68 (117)
.+..+|+.-|.+-.+-...+..|.+ .. ++|++.+++|.+|..
T Consensus 71 ~~~~~ii~fd~~~~~S~~~~~~~~~~i~~~~~~~~~iivvg~K~D~~~ 118 (162)
T PF00071_consen 71 NSDAIIIVFDVTDEESFENLKKWLEEIQKYKPEDIPIIVVGNKSDLSD 118 (162)
T ss_dssp TESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG
T ss_pred ccccccccccccccccccccccccccccccccccccceeeeccccccc
Confidence 3555556656553233444444433 22 488888888887775
No 175
>PRK06153 hypothetical protein; Provisional
Probab=31.94 E-value=42 Score=28.84 Aligned_cols=39 Identities=15% Similarity=0.158 Sum_probs=33.0
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
..-+||.|.|..+ ...-+-.+|.+++||++.++-.-++.
T Consensus 266 ~~DiV~dcvDn~~--aR~~ln~~a~~~gIP~Id~G~~l~~~ 304 (393)
T PRK06153 266 GFTFVFVCVDKGS--SRKLIVDYLEALGIPFIDVGMGLELS 304 (393)
T ss_pred CCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEeeecceec
Confidence 4789999999775 37778899999999999998777764
No 176
>COG1535 EntB Isochorismate hydrolase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.90 E-value=31 Score=27.23 Aligned_cols=19 Identities=37% Similarity=0.856 Sum_probs=16.4
Q ss_pred heeHHHHhhhCCCCEEEEC
Q 033552 43 ITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~ 61 (117)
+.++..+|++.|||+++.-
T Consensus 60 i~~Lr~~~~~~giPVvyTa 78 (218)
T COG1535 60 IAKLRIWCKQAGIPVVYTA 78 (218)
T ss_pred HHHHHHHHHHcCCcEEEEe
Confidence 5678889999999999874
No 177
>cd01895 EngA2 EngA2 subfamily. This CD represents the second 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=31.81 E-value=59 Score=21.91 Aligned_cols=40 Identities=15% Similarity=0.106 Sum_probs=25.2
Q ss_pred ccEEEEeCCCCCc--chheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 28 CRLCVIAGNISPI--DVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 28 ~~LViLA~Dasp~--~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
+.++++--|++.. ....++...+...+.|++.+.+|.+|.
T Consensus 85 ~d~vi~v~d~~~~~~~~~~~~~~~~~~~~~~~iiv~nK~Dl~ 126 (174)
T cd01895 85 ADVVLLVIDATEGITEQDLRIAGLILEEGKALVIVVNKWDLV 126 (174)
T ss_pred cCeEEEEEeCCCCcchhHHHHHHHHHhcCCCEEEEEeccccC
Confidence 4566666566421 122344556666789999999987764
No 178
>PRK07920 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=31.51 E-value=2.2e+02 Score=22.51 Aligned_cols=46 Identities=9% Similarity=-0.086 Sum_probs=28.8
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcc-------------hheeHHHHhhhCCCCEEEECC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPID-------------VITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~-------------i~~~i~~lce~~~IP~i~v~t 62 (117)
|+++.+++|++|+ .|.+..|-++.. ...-...++...|.|++.+..
T Consensus 171 ~~r~ii~~Lk~g~--~v~il~Dq~~~~~g~~v~FFG~~a~t~~g~a~LA~~~~apVvp~~~ 229 (298)
T PRK07920 171 PFEVLAERLRAGG--VVCLLADRDLTRSGVEVDFFGERTRMPAGPAALALETGAALLPVHL 229 (298)
T ss_pred HHHHHHHHHHcCC--eEEEEeccCccCCCCEEeeCCCCCCCCCCHHHHHHHHCCcEEEEEE
Confidence 6778889999986 677777766421 111223466666666666554
No 179
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=31.47 E-value=1.8e+02 Score=20.07 Aligned_cols=48 Identities=6% Similarity=-0.121 Sum_probs=34.8
Q ss_pred hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 21 LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
+.+-.-+..+|+|..-....-.-..+...++++||.+....|.+....
T Consensus 46 ~~l~~~~peiliiGTG~~~~~~~~~~~~~l~~~gi~vE~m~T~~AcrT 93 (109)
T cd05560 46 EALLALQPEVILLGTGERQRFPPPALLAPLLARGIGVEVMDTQAACRT 93 (109)
T ss_pred HHHHhcCCCEEEEecCCCCCcCCHHHHHHHHHcCCeEEEECHHHHHHH
Confidence 334444578999998877533345566788999999999999877663
No 180
>TIGR00789 flhB_rel flhB C-terminus-related protein. This model describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set.
Probab=31.45 E-value=43 Score=22.38 Aligned_cols=35 Identities=20% Similarity=0.342 Sum_probs=24.3
Q ss_pred EEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 32 VIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 32 iLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
|+|.=.+ .+-.+|...++++|||++.- ..|.+++-
T Consensus 20 VvAKG~g--~~A~~I~~~A~e~~VPi~~~---~~LAr~L~ 54 (82)
T TIGR00789 20 VVASGVG--EVAERIIEIAKKHGIPIVED---PDLVDVLL 54 (82)
T ss_pred EEEEeCC--HHHHHHHHHHHHcCCCEEeC---HHHHHHHH
Confidence 4444444 36889999999999999654 45555553
No 181
>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=31.42 E-value=39 Score=26.41 Aligned_cols=35 Identities=17% Similarity=0.197 Sum_probs=28.3
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
...+||-|.|.-. ....+.+.|.++++|+++....
T Consensus 114 ~~DlVvd~~D~~~--~r~~ln~~~~~~~ip~v~~~~~ 148 (240)
T TIGR02355 114 EHDIVVDCTDNVE--VRNQLNRQCFAAKVPLVSGAAI 148 (240)
T ss_pred cCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEEEec
Confidence 3678999998753 5888999999999999985543
No 182
>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=31.31 E-value=92 Score=27.32 Aligned_cols=60 Identities=18% Similarity=0.130 Sum_probs=42.6
Q ss_pred hcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 24 LFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
++|..++.+++.|..-....+.+..+|+.+|+|+..+.+..++-.....-...-.+.|-.
T Consensus 283 ~~G~~kV~LI~~Dt~RigA~EQLr~~AeilGVpv~~~~~~~Dl~~aL~~L~d~d~VLIDT 342 (484)
T PRK06995 283 RHGASKVALLTTDSYRIGGHEQLRIYGKILGVPVHAVKDAADLRLALSELRNKHIVLIDT 342 (484)
T ss_pred hcCCCeEEEEeCCccchhHHHHHHHHHHHhCCCeeccCCchhHHHHHHhccCCCeEEeCC
Confidence 455567889999987556678899999999999998888877665543222333455544
No 183
>TIGR03594 GTPase_EngA ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
Probab=31.25 E-value=45 Score=27.40 Aligned_cols=49 Identities=16% Similarity=0.070 Sum_probs=32.4
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
+++++++.-.+-++++...-.....-.++...+.+.++|++.+.+|-+|
T Consensus 247 ~~~~~~~~ad~~ilV~D~~~~~~~~~~~~~~~~~~~~~~iiiv~NK~Dl 295 (429)
T TIGR03594 247 RTLKAIERADVVLLVLDATEGITEQDLRIAGLILEAGKALVIVVNKWDL 295 (429)
T ss_pred HHHHHHHhCCEEEEEEECCCCccHHHHHHHHHHHHcCCcEEEEEECccc
Confidence 3456777776666666444222222345667788889999999999776
No 184
>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=31.25 E-value=35 Score=26.20 Aligned_cols=68 Identities=22% Similarity=0.299 Sum_probs=31.7
Q ss_pred CCcchheeHHHHhhhCCCCEEEECC--HhHHHhhcCCCcceEEEEEeecCCCCccchHHHHhhHHHHHHHHHHHH
Q 033552 38 SPIDVITHVPILCEESDIPYIYVAS--KEDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVEDVK 110 (117)
Q Consensus 38 sp~~i~~~i~~lce~~~IP~i~v~t--K~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e~~~~~~ 110 (117)
+|.+ ...+...+++++|++++..+ ...+.+.+.+..++-++- -.|..+ ...+.+.|-+.+......+.
T Consensus 184 s~~~-l~~l~~~ik~~~v~~i~~e~~~~~~~~~~la~~~g~~vv~--ld~l~~--~~~~~~~y~~~~~~n~~~l~ 253 (256)
T PF01297_consen 184 SPKD-LAELIKLIKENKVKCIFTEPQFSSKLAEALAKETGVKVVY--LDPLGG--GIPDGDSYLDMMEQNLDTLA 253 (256)
T ss_dssp -HHH-HHHHHHHHHHTT-SEEEEETTS-THHHHHHHHCCT-EEEE--SSTTCS--TTSSTTSHHHHHHHHHHHHH
T ss_pred CHHH-HHHHHHHhhhcCCcEEEecCCCChHHHHHHHHHcCCcEEE--eCCCcC--CCCCcCCHHHHHHHHHHHHH
Confidence 3443 66677778888888888752 233333332222222222 223311 11123467766666555543
No 185
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=31.21 E-value=38 Score=26.95 Aligned_cols=40 Identities=25% Similarity=0.316 Sum_probs=32.3
Q ss_pred hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE
Q 033552 21 LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v 60 (117)
+.|+...+.+||=|.=-....+.......|++.||||+-+
T Consensus 59 ~~l~~~~i~~VIDAtHPfA~~is~~a~~a~~~~~ipylR~ 98 (256)
T TIGR00715 59 EFLKRHSIDILVDATHPFAAQITTNATAVCKELGIPYVRF 98 (256)
T ss_pred HHHHhcCCCEEEEcCCHHHHHHHHHHHHHHHHhCCcEEEE
Confidence 5667778999987766555677888999999999999765
No 186
>cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB.
Probab=30.96 E-value=48 Score=25.63 Aligned_cols=50 Identities=20% Similarity=0.078 Sum_probs=33.1
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
++..+++...+-++++...-....-...+-..+...++|++.+.+|-++-
T Consensus 80 ~~~~~l~~aD~~IlVvd~~~g~~~~~~~~~~~~~~~~~P~iivvNK~D~~ 129 (237)
T cd04168 80 EVERSLSVLDGAILVISAVEGVQAQTRILWRLLRKLNIPTIIFVNKIDRA 129 (237)
T ss_pred HHHHHHHHhCeEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECcccc
Confidence 45667777666666664433322234556667888999999998888765
No 187
>PRK05645 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=30.84 E-value=1.2e+02 Score=23.99 Aligned_cols=23 Identities=13% Similarity=0.085 Sum_probs=19.0
Q ss_pred eeecchhhhhcCCccEEEEeCCCCC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISP 39 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp 39 (117)
|+++.+++|++|. +|.|..|-++
T Consensus 171 ~~r~l~kaLk~g~--~v~il~Dq~~ 193 (295)
T PRK05645 171 GILSVIKEVRKGG--QVGIPADPEP 193 (295)
T ss_pred cHHHHHHHHhcCC--eEEEcCCCCC
Confidence 7888999999885 8888888775
No 188
>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=30.79 E-value=51 Score=28.41 Aligned_cols=43 Identities=12% Similarity=0.118 Sum_probs=30.9
Q ss_pred hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 21 LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
+.|.+-.+.+|+.+.++++. ..+ ++.++||-.+..-++++|.+
T Consensus 276 ~~i~~~g~~lvi~~~~I~~~--al~---~L~~~gI~~v~~v~~~~L~r 318 (519)
T TIGR02339 276 DKIADAGANVVFCQKGIDDL--AQH---YLAKAGILAVRRVKKSDIEK 318 (519)
T ss_pred HHHHhcCCcEEEECCCccHH--HHH---HHHHCCCEEEecCCHHHHHH
Confidence 46777778999999999973 333 44578887777767666553
No 189
>PRK13957 indole-3-glycerol-phosphate synthase; Provisional
Probab=30.72 E-value=1e+02 Score=24.74 Aligned_cols=64 Identities=9% Similarity=0.021 Sum_probs=49.4
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCC-CEEEECCHhHHHhhcCCCcceEEEEEe
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDI-PYIYVASKEDLANAGATKRPTCCVLVL 82 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~I-P~i~v~tK~eLG~A~G~~~~~svv~I~ 82 (117)
-.|...+-.-|---+++|+.-.++. -...+...|+..|. |.+.|.|.+||-+|.-.. +..++|-
T Consensus 114 ~~QI~ea~~~GADavLLI~~~L~~~-~l~~l~~~a~~lGle~LVEVh~~~El~~a~~~g--a~iiGIN 178 (247)
T PRK13957 114 EIQIREARAFGASAILLIVRILTPS-QIKSFLKHASSLGMDVLVEVHTEDEAKLALDCG--AEIIGIN 178 (247)
T ss_pred HHHHHHHHHcCCCEEEeEHhhCCHH-HHHHHHHHHHHcCCceEEEECCHHHHHHHHhCC--CCEEEEe
Confidence 3566777777776778888888874 47888899999998 788999999999887653 4456664
No 190
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=30.51 E-value=1.5e+02 Score=21.92 Aligned_cols=41 Identities=15% Similarity=0.045 Sum_probs=35.8
Q ss_pred heeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 43 ITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
+..+.++++++|+.+..+..-.-+-+.+...++-++++|..
T Consensus 75 Ig~l~~lae~~g~~v~i~~Ggt~ar~~ik~~~p~~iigVAC 115 (158)
T PF01976_consen 75 IGDLKKLAEKYGYKVYIATGGTLARKIIKEYRPKAIIGVAC 115 (158)
T ss_pred hhHHHHHHHHcCCEEEEEcChHHHHHHHHHhCCCEEEEEec
Confidence 55688899999999999998888888888888888999887
No 191
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=30.04 E-value=1.3e+02 Score=20.85 Aligned_cols=51 Identities=8% Similarity=0.021 Sum_probs=32.2
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhhcCCC
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANAGATK 73 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A~G~~ 73 (117)
+..+.++...+.++-|..|. ...+..+++++++++..+. ...+++++.|..
T Consensus 55 ~~~~~~~~~~v~vi~Is~d~-----~~~~~~~~~~~~~~~~~l~D~~~~~~~~~gv~ 106 (154)
T PRK09437 55 DNMDELKKAGVVVLGISTDK-----PEKLSRFAEKELLNFTLLSDEDHQVAEQFGVW 106 (154)
T ss_pred HHHHHHHHCCCEEEEEcCCC-----HHHHHHHHHHhCCCCeEEECCCchHHHHhCCC
Confidence 34444555556666666552 2445678888888777666 456788888853
No 192
>COG1493 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]
Probab=30.00 E-value=73 Score=26.63 Aligned_cols=42 Identities=7% Similarity=0.035 Sum_probs=34.7
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
++.++.|=+-+.-.+|+|.+..+ -..+.+.|++++||+....
T Consensus 71 ~~~i~~~~~~~~P~iI~sk~~~~---p~~l~~~a~~~~~pil~s~ 112 (308)
T COG1493 71 KKRIGKLFSLDTPALIVSKGLPI---PEELLDAAKKYNIPILTSK 112 (308)
T ss_pred HHHHHHHhCcCCCEEEEECCCCC---CHHHHHHHHHcCCceEEec
Confidence 45667777777889999999986 3567889999999998876
No 193
>PF05343 Peptidase_M42: M42 glutamyl aminopeptidase; InterPro: IPR008007 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M42 (glutamyl aminopeptidase family, clan MH). For members of this family and family M28 the predicted metal ligands occur in the same order in the sequence: H, D, E, D/E, H; and the active site residues occur in the motifs HXD and EE. ; PDB: 2WYR_C 2CF4_A 1VHO_A 3ISX_A 3KL9_G 1YLO_F 3CPX_C 1VHE_A 2GRE_F 1XFO_A ....
Probab=29.97 E-value=86 Score=25.31 Aligned_cols=55 Identities=18% Similarity=0.262 Sum_probs=34.6
Q ss_pred cEEEEeCCCCC---cchheeHHHHhhhCCCCEEE---ECCHhHHHhh--cCCCcceEEEEEee
Q 033552 29 RLCVIAGNISP---IDVITHVPILCEESDIPYIY---VASKEDLANA--GATKRPTCCVLVLT 83 (117)
Q Consensus 29 ~LViLA~Dasp---~~i~~~i~~lce~~~IP~i~---v~tK~eLG~A--~G~~~~~svv~I~~ 83 (117)
+-+|-..|.++ ..+..++.+.|++++|||-+ ..+--+-+.. .|...+++++.|-.
T Consensus 209 Gp~i~~~D~~~i~~~~l~~~l~~~A~~~~Ip~Q~~~~~~ggTDa~~~~~~~~Gi~t~~i~iP~ 271 (292)
T PF05343_consen 209 GPVIRVGDSSMIPNPKLVDKLREIAEENGIPYQREVFSGGGTDAGAIQLSGGGIPTAVISIPC 271 (292)
T ss_dssp -EEEEEEETTEESHHHHHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTSSEEEEEEEEE
T ss_pred CcEEEEccCCCCCCHHHHHHHHHHHHHcCCCeEEEecCCcccHHHHHHHcCCCCCEEEEeccc
Confidence 46777777764 37899999999999999966 3334555543 33344666666643
No 194
>KOG2016 consensus NEDD8-activating complex, APP-BP1/UBA5 component [Posttranslational modification, protein turnover, chaperones]
Probab=29.89 E-value=44 Score=29.64 Aligned_cols=37 Identities=19% Similarity=0.273 Sum_probs=30.5
Q ss_pred EEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 30 LCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 30 LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
=|++|+..-+.. ..++++.|.+.|||++.+.|---.|
T Consensus 121 tvViatnl~E~~-~~kl~~~l~~~~vpll~~rs~Gl~G 157 (523)
T KOG2016|consen 121 TVVIATNLNEQT-LLKLAEILREANVPLLLTRSYGLAG 157 (523)
T ss_pred eeeeccccchhh-hhhhHHHHHhcCCceEEEeeecceE
Confidence 478888888754 8899999999999999998765444
No 195
>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=29.88 E-value=53 Score=25.62 Aligned_cols=58 Identities=21% Similarity=0.319 Sum_probs=34.5
Q ss_pred CCCcchheeHHHHhhhCCCCEEEECCH------hHHHhhcCCCcceEEEEEeecCCCCccchHHHHhhHHHHHHHHHHH
Q 033552 37 ISPIDVITHVPILCEESDIPYIYVASK------EDLANAGATKRPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVEDV 109 (117)
Q Consensus 37 asp~~i~~~i~~lce~~~IP~i~v~tK------~eLG~A~G~~~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e~~~~~ 109 (117)
.+|.+ +..+..+.++++|+++++.+. +.|.+..|.+ ++.+. |. .++|-+++.+-.+.+
T Consensus 201 ps~~~-l~~l~~~ik~~~v~~if~e~~~~~~~~~~la~~~g~~----v~~ld--~~--------~~~y~~~m~~n~~~~ 264 (266)
T cd01018 201 PSPAD-LKRLIDLAKEKGVRVVFVQPQFSTKSAEAIAREIGAK----VVTID--PL--------AADWEENLLKVADAF 264 (266)
T ss_pred CCHHH-HHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHcCCe----EEEeC--Cc--------HHHHHHHHHHHHHHh
Confidence 33444 677888899999999998532 3455555542 23332 33 136777776665554
No 196
>cd01891 TypA_BipA TypA (tyrosine phosphorylated protein A)/BipA subfamily. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. co
Probab=29.76 E-value=50 Score=23.90 Aligned_cols=48 Identities=19% Similarity=0.099 Sum_probs=26.5
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
...++.-..-++++...-.+..-...+...+...++|++.+.+|.+|-
T Consensus 83 ~~~~~~~d~~ilV~d~~~~~~~~~~~~~~~~~~~~~p~iiv~NK~Dl~ 130 (194)
T cd01891 83 ERVLSMVDGVLLLVDASEGPMPQTRFVLKKALELGLKPIVVINKIDRP 130 (194)
T ss_pred HHHHHhcCEEEEEEECCCCccHHHHHHHHHHHHcCCCEEEEEECCCCC
Confidence 334444444344444322221222333445667899999999998873
No 197
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=29.67 E-value=41 Score=26.65 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=35.8
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+...-..-|+++...+||=|+=--...+.+.....|++.||||+-..
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 33455667788889999965554456788889999999999997654
No 198
>PF06684 AA_synth: Amino acid synthesis; InterPro: IPR009569 This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.; PDB: 3BYQ_A 2QTP_A.
Probab=29.58 E-value=55 Score=25.19 Aligned_cols=45 Identities=16% Similarity=0.083 Sum_probs=26.8
Q ss_pred CHhHHHhhcCCC-cceEEEEEeecCCCCccchHHHHhhHHHHHHHHH
Q 033552 62 SKEDLANAGATK-RPTCCVLVLTKPTKGELGQEEQDKLKADYTLVVE 107 (117)
Q Consensus 62 tK~eLG~A~G~~-~~~svv~I~~~~~~~~~~~~e~~~~~~~~~e~~~ 107 (117)
+..|.|.+.... +.++++++..||..+. -++|++.+.+.-.++=.
T Consensus 11 ~~~Egg~~~~~p~r~~a~aAVi~NP~AGr-~veDL~pl~~~~~~LG~ 56 (175)
T PF06684_consen 11 ILHEGGKPADPPLRRVAAAAVIKNPWAGR-YVEDLSPLMEIGPELGE 56 (175)
T ss_dssp EEECTTEEECCEEEEEEEEEEEE-TTTTS---S--HHHHHHHHHHHH
T ss_pred EeeeCCcCCCccceeEEEEEEEcCCCccc-chhhhHHHHHhhHHHHH
Confidence 444677766655 5678888889999997 66666666555554433
No 199
>cd07395 MPP_CSTP1 Homo sapiens CSTP1 and related proteins, metallophosphatase domain. CSTP1 (complete S-transactivated protein 1) is an uncharacterized Homo sapiens protein with a metallophosphatase domain, that is transactivated by the complete S protein of hepatitis B virus. CSTP1 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 th
Probab=29.41 E-value=77 Score=24.19 Aligned_cols=46 Identities=13% Similarity=0.126 Sum_probs=30.9
Q ss_pred eecchhhhhcC--CccEEEEeCCCCCcchh--------eeHHHHhhhC--CCCEEEEC
Q 033552 16 VVNDPLPLLFH--ECRLCVIAGNISPIDVI--------THVPILCEES--DIPYIYVA 61 (117)
Q Consensus 16 ~kqt~kaL~kg--~~~LViLA~Dasp~~i~--------~~i~~lce~~--~IP~i~v~ 61 (117)
+++.++.|++. +..+||+++|....... ..+...-+.. ++|+..+.
T Consensus 36 l~~~~~~i~~~~~~pd~ii~~GDl~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~~~i~ 93 (262)
T cd07395 36 TEQAVQAINKLNPKPKFVVVCGDLVNAMPGDELRERQVSDLKDVLSLLDPDIPLVCVC 93 (262)
T ss_pred HHHHHHHHHhcCCCCCEEEEeCCcCCCCcchhhHHHHHHHHHHHHhhccCCCcEEEeC
Confidence 47788888876 89999999999863211 1222333332 78998774
No 200
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=29.25 E-value=69 Score=27.74 Aligned_cols=60 Identities=13% Similarity=0.133 Sum_probs=45.0
Q ss_pred cceeeeecchhhhhcCCccEEEEeCCCCCc----------------------------------------chheeHHHHh
Q 033552 11 FNCVGVVNDPLPLLFHECRLCVIAGNISPI----------------------------------------DVITHVPILC 50 (117)
Q Consensus 11 ~~~vG~kqt~kaL~kg~~~LViLA~Dasp~----------------------------------------~i~~~i~~lc 50 (117)
..+-|..++.++|.-|.+..+++.+|-.-. +++..+...|
T Consensus 295 la~yG~~~vr~aL~~gaVd~llv~Edl~~~r~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~~~v~~~d~vd~l~e~a 374 (411)
T COG1503 295 LAVYGEEEVREALEMGAVDTLLVSEDLEKERVTYKCPTCGYENLKSKREFEQKRFRCPECGSEMEEVEVSDLVDELAELA 374 (411)
T ss_pred eeecchHHHHHHHHhcccceEEeeccccccceeecCCCcchhhhhcccccccccccCccccccccchhhhhHHHHHHHHH
Confidence 567899999999999999999999998831 2355566666
Q ss_pred hhCCCCEEEECCHhHHHhhc
Q 033552 51 EESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 51 e~~~IP~i~v~tK~eLG~A~ 70 (117)
++.|.-+.++.+..+-|.+.
T Consensus 375 ~~~Ga~ve~is~~~~eg~q~ 394 (411)
T COG1503 375 EESGAKVEIISDDTDEGAQL 394 (411)
T ss_pred HhcCCeEEEecCchHHHHHH
Confidence 67777777777666666554
No 201
>PRK05428 HPr kinase/phosphorylase; Provisional
Probab=29.20 E-value=82 Score=26.10 Aligned_cols=42 Identities=14% Similarity=0.166 Sum_probs=34.4
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
+.++.+-+.+.-++|++.+..|.. .+...|++++||+.....
T Consensus 73 ~~~~~l~~~~~P~iIvt~~~~~p~---~l~~~a~~~~ipll~t~~ 114 (308)
T PRK05428 73 ERLKKLFSLEPPCIIVTRGLEPPP---ELLEAAKEAGIPLLRTPL 114 (308)
T ss_pred HHHHHHhCCCCCEEEEECcCCCCH---HHHHHHHHcCCcEEEeCC
Confidence 456677778889999999998743 477899999999998774
No 202
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=29.07 E-value=17 Score=21.17 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=20.0
Q ss_pred heeHHHHhhhCCCCEEEECCHhHHHhh
Q 033552 43 ITHVPILCEESDIPYIYVASKEDLANA 69 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~tK~eLG~A 69 (117)
...+..+|++.|||-..-..|+||=.+
T Consensus 7 ~~eL~~iAk~lgI~~~~~~~K~eLI~~ 33 (43)
T PF07498_consen 7 LSELREIAKELGIEGYSKMRKQELIFA 33 (43)
T ss_dssp HHHHHHHHHCTT-TTGCCS-HHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCcCCHHHHHHH
Confidence 556888999999998888888887544
No 203
>cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts.
Probab=28.83 E-value=44 Score=26.36 Aligned_cols=48 Identities=19% Similarity=0.121 Sum_probs=31.2
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
+..+++.-.+-++++........-...+-..++.+++|++.+.+|-++
T Consensus 88 ~~~~l~~aD~~IlVvda~~g~~~~~~~i~~~~~~~~~P~iivvNK~D~ 135 (267)
T cd04169 88 TYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCRLRGIPIITFINKLDR 135 (267)
T ss_pred HHHHHHHCCEEEEEEECCCCccHHHHHHHHHHHhcCCCEEEEEECCcc
Confidence 566777666666666443222222345667788899999998888665
No 204
>PF04716 ETC_C1_NDUFA5: ETC complex I subunit conserved region; InterPro: IPR006806 This is a family of eukaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC) (1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N terminus of the member proteins [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022904 respiratory electron transport chain, 0005743 mitochondrial inner membrane
Probab=28.45 E-value=70 Score=20.00 Aligned_cols=21 Identities=14% Similarity=0.346 Sum_probs=18.5
Q ss_pred HHhhHHHHHHHHHHHHhhhcc
Q 033552 95 QDKLKADYTLVVEDVKELASS 115 (117)
Q Consensus 95 ~~~~~~~~~e~~~~~~~l~~~ 115 (117)
++.+..+|.+..+.|+++|..
T Consensus 4 r~~L~~lY~~~L~~L~~~P~~ 24 (57)
T PF04716_consen 4 REALISLYNKTLKALKKIPED 24 (57)
T ss_pred HHHHHHHHHHHHHHHHhCCCc
Confidence 578899999999999999864
No 205
>cd07393 MPP_DR1119 Deinococcus radiodurans DR1119 and related proteins, metallophosphatase domain. DR1119 is an uncharacterized Deinococcus radiodurans 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 coordinat
Probab=28.37 E-value=59 Score=24.77 Aligned_cols=49 Identities=12% Similarity=-0.004 Sum_probs=30.5
Q ss_pred eeee--ecchhhhhcC------CccEEEEeCCCCCcc---hheeHHHHhhhCCCCEEEEC
Q 033552 13 CVGV--VNDPLPLLFH------ECRLCVIAGNISPID---VITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 13 ~vG~--kqt~kaL~kg------~~~LViLA~Dasp~~---i~~~i~~lce~~~IP~i~v~ 61 (117)
..|- ++.+++|+.- ++-+|++|+|..... -......+.+....|+++|+
T Consensus 19 ~~g~~~~~~~~~i~~~~~~~~~~~D~viiaGDl~~~~~~~~~~~~l~~l~~l~~~v~~V~ 78 (232)
T cd07393 19 VFGPEWKNHTEKIKENWDNVVAPEDIVLIPGDISWAMKLEEAKLDLAWIDALPGTKVLLK 78 (232)
T ss_pred ccCccHHHHHHHHHHHHHhcCCCCCEEEEcCCCccCCChHHHHHHHHHHHhCCCCeEEEe
Confidence 5564 6777777776 899999999988311 01122234445555766664
No 206
>PRK06036 translation initiation factor IF-2B subunit alpha; Provisional
Probab=28.24 E-value=60 Score=27.15 Aligned_cols=40 Identities=13% Similarity=0.205 Sum_probs=28.5
Q ss_pred hhhcCCccEEEEeCCCCC-----cch-heeHHHHhhhCCCCEEEEC
Q 033552 22 PLLFHECRLCVIAGNISP-----IDV-ITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 22 aL~kg~~~LViLA~Dasp-----~~i-~~~i~~lce~~~IP~i~v~ 61 (117)
.|++|++..||++.|.=- +.+ ...+-.+|+++|||++.+.
T Consensus 221 ~M~~~~Vd~VivGAd~I~anGv~NKiGT~~lA~~Ak~~~vPfyV~a 266 (339)
T PRK06036 221 VMRQGMVDKVIVGADRITRDAVFNKIGTYTHSVLAKEHEIPFYVAA 266 (339)
T ss_pred HhccCCCCEEEECccchhhcCeehhhhHHHHHHHHHHhCCCEEEEe
Confidence 567789999999988632 111 1334667899999998764
No 207
>PLN02828 formyltetrahydrofolate deformylase
Probab=28.21 E-value=1.1e+02 Score=24.72 Aligned_cols=44 Identities=20% Similarity=0.176 Sum_probs=28.5
Q ss_pred cchhhhhcCC--ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 18 NDPLPLLFHE--CRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 18 qt~kaL~kg~--~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
..+.++++|+ +.++.+-+|-++.. ...+..+|+++|||+.+++.
T Consensus 86 ~ll~~~~~g~l~~eI~~ViSn~~~~~-~a~~~~~A~~~gIP~~~~~~ 131 (268)
T PLN02828 86 DLLHRWQDGRLPVDITCVISNHERGP-NTHVMRFLERHGIPYHYLPT 131 (268)
T ss_pred HHHHhhhcCCCCceEEEEEeCCCCCC-CchHHHHHHHcCCCEEEeCC
Confidence 3456677776 45665555543111 24667789999999997764
No 208
>PRK09864 putative peptidase; Provisional
Probab=28.19 E-value=1.6e+02 Score=24.68 Aligned_cols=20 Identities=10% Similarity=0.356 Sum_probs=18.0
Q ss_pred cchheeHHHHhhhCCCCEEE
Q 033552 40 IDVITHVPILCEESDIPYIY 59 (117)
Q Consensus 40 ~~i~~~i~~lce~~~IP~i~ 59 (117)
..+.+.+.++|+++||||-+
T Consensus 264 ~~l~~~l~~~A~~~~Ip~Q~ 283 (356)
T PRK09864 264 QKLVAALKSCAAHNDLPLQF 283 (356)
T ss_pred HHHHHHHHHHHHHcCCCceE
Confidence 36889999999999999988
No 209
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. 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=28.18 E-value=2.2e+02 Score=22.56 Aligned_cols=26 Identities=4% Similarity=0.129 Sum_probs=19.5
Q ss_pred CCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 37 ISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 37 asp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
.+|.+ +..+.+.+++++|+++++.+.
T Consensus 212 ps~~~-l~~l~~~ik~~~v~~If~e~~ 237 (286)
T cd01019 212 PGAKR-LAKIRKEIKEKGATCVFAEPQ 237 (286)
T ss_pred CCHHH-HHHHHHHHHHcCCcEEEecCC
Confidence 33443 667888999999999998643
No 210
>PRK08328 hypothetical protein; Provisional
Probab=28.11 E-value=60 Score=25.04 Aligned_cols=34 Identities=12% Similarity=0.008 Sum_probs=27.2
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
..+||-|.|-. +....+.+.|.++++|++...+-
T Consensus 119 ~D~Vid~~d~~--~~r~~l~~~~~~~~ip~i~g~~~ 152 (231)
T PRK08328 119 VDVIVDCLDNF--ETRYLLDDYAHKKGIPLVHGAVE 152 (231)
T ss_pred CCEEEECCCCH--HHHHHHHHHHHHcCCCEEEEeec
Confidence 67888898874 34677889999999999986554
No 211
>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=27.87 E-value=69 Score=27.69 Aligned_cols=44 Identities=9% Similarity=0.040 Sum_probs=32.4
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
-++.|.+-.+.+|+++.++++. ..+ ++.++||..+...++.+|-
T Consensus 279 ~v~~i~~~g~~lvi~~~~I~~~--al~---~L~~~~I~av~~v~~~~Le 322 (526)
T cd03339 279 MVEQVKDAGANLVICQWGFDDE--ANH---LLLQNGLPAVRWVGGVEIE 322 (526)
T ss_pred HHHHHHHCCCCEEEeCCCCCHH--HHH---HHHHCCCEEEEeCCHHHHH
Confidence 3666777778999999999973 333 6778888888776665544
No 212
>PHA02546 47 endonuclease subunit; Provisional
Probab=27.86 E-value=69 Score=26.11 Aligned_cols=46 Identities=13% Similarity=0.065 Sum_probs=30.1
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcc------hheeHH----HHhhhCCCCEEEEC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPID------VITHVP----ILCEESDIPYIYVA 61 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~------i~~~i~----~lce~~~IP~i~v~ 61 (117)
+.+.+..+++.++.+||+|+|.-... ....+. ..-.+.+||++.+.
T Consensus 28 l~~ii~~a~~~~vD~VliaGDlfD~~~~~~~~~~~~~~~~l~~~L~~~gi~v~~I~ 83 (340)
T PHA02546 28 IKQAIEYSKAHGITTWIQLGDTFDVRKAITQNTMNFVREKIFDLLKEAGITLHVLV 83 (340)
T ss_pred HHHHHHHHHHcCCCEEEECCcccCCCCCCCHHHHHHHHHHHHHHHHHCCCeEEEEc
Confidence 45566667888899999999997431 011121 22335689999885
No 213
>PRK03147 thiol-disulfide oxidoreductase; Provisional
Probab=27.83 E-value=1.5e+02 Score=20.64 Aligned_cols=57 Identities=5% Similarity=-0.004 Sum_probs=30.9
Q ss_pred hhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhhcCCCcceEEEEEe
Q 033552 22 PLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANAGATKRPTCCVLVL 82 (117)
Q Consensus 22 aL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A~G~~~~~svv~I~ 82 (117)
...+....++.+..|.++ ..+..+.+++++|+..+. ...++.++.|....-+.++|-
T Consensus 89 ~~~~~~~~vi~i~~d~~~----~~~~~~~~~~~~~~~~~~d~~~~~~~~~~v~~~P~~~lid 146 (173)
T PRK03147 89 KYKEKGVEIIAVNVDETE----LAVKNFVNRYGLTFPVAIDKGRQVIDAYGVGPLPTTFLID 146 (173)
T ss_pred HhhcCCeEEEEEEcCCCH----HHHHHHHHHhCCCceEEECCcchHHHHcCCCCcCeEEEEC
Confidence 334344556666555443 234445566677665544 346788888876322234443
No 214
>TIGR00829 FRU PTS system, fructose-specific, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters.
Probab=27.68 E-value=79 Score=20.96 Aligned_cols=44 Identities=9% Similarity=-0.082 Sum_probs=28.9
Q ss_pred eeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHh
Q 033552 14 VGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKE 64 (117)
Q Consensus 14 vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~ 64 (117)
.|+.+.+.+-.-..+.+||+|+|..+.+ .. +..|.|++.+...+
T Consensus 39 ~g~~~~lt~~~i~~Ad~viia~d~~~~~-~~------rf~gk~v~~~~~~~ 82 (85)
T TIGR00829 39 VGAQNALTAEDIAAADGVILAADREIDL-SR------RFAGKNVYETSTGD 82 (85)
T ss_pred cCccCCCCHHHHHhCCEEEEeccCCCch-hh------hcCCCeEEEecHHH
Confidence 4666666555566789999999988632 11 25667777765443
No 215
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=27.62 E-value=1.4e+02 Score=23.74 Aligned_cols=48 Identities=10% Similarity=0.149 Sum_probs=37.3
Q ss_pred CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCC
Q 033552 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATK 73 (117)
Q Consensus 26 g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~ 73 (117)
|..+..++..|..-..-...+..+++..++|+..+.+..+|..++..-
T Consensus 223 g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~ 270 (282)
T TIGR03499 223 GNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRL 270 (282)
T ss_pred CCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHc
Confidence 557888898887543346777888999999999888988888776643
No 216
>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=27.61 E-value=43 Score=26.55 Aligned_cols=49 Identities=14% Similarity=0.045 Sum_probs=36.7
Q ss_pred ceeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE
Q 033552 12 NCVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 12 ~~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v 60 (117)
+.=|..+-..-|+.+...+||=|+=-....+.......|++.||||+-+
T Consensus 51 ~lg~~~~l~~~l~~~~i~~vIDATHPfA~~is~na~~a~~~~~ipylR~ 99 (249)
T PF02571_consen 51 RLGDEEGLAEFLRENGIDAVIDATHPFAAEISQNAIEACRELGIPYLRF 99 (249)
T ss_pred CCCCHHHHHHHHHhCCCcEEEECCCchHHHHHHHHHHHHhhcCcceEEE
Confidence 3335566667788899999995555444667888999999999998754
No 217
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=27.37 E-value=72 Score=22.61 Aligned_cols=31 Identities=10% Similarity=0.007 Sum_probs=21.4
Q ss_pred CccEEEEeCCCCC--cchheeHHHHhhhCCCCE
Q 033552 27 ECRLCVIAGNISP--IDVITHVPILCEESDIPY 57 (117)
Q Consensus 27 ~~~LViLA~Dasp--~~i~~~i~~lce~~~IP~ 57 (117)
++..||+|.|++. ..|..++...|...+.|+
T Consensus 90 ~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~~~v 122 (142)
T cd01028 90 KADEIVLATDPDREGELIAWEILEVLKCDNKPV 122 (142)
T ss_pred cCCEEEEcCCCCcchHHHHHHHHHHhCCCCCCe
Confidence 3689999999995 446666777776533343
No 218
>PRK06628 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=27.34 E-value=1.2e+02 Score=23.93 Aligned_cols=46 Identities=13% Similarity=0.032 Sum_probs=30.6
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcc-h-----------heeHHHHhhhCCCCEEEECC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPID-V-----------ITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~-i-----------~~~i~~lce~~~IP~i~v~t 62 (117)
|+++.+++|++|. .|.+..|-++.+ + ..-...++...|.|++.+..
T Consensus 174 ~~r~l~k~Lk~g~--~v~il~Dq~~~~gv~v~FFG~~a~t~~~~a~LA~~~~apvv~~~~ 231 (290)
T PRK06628 174 GSRALVRAIKESE--SIVMLVDQKMNDGIEVPFLGHPAMTASAIAKIALQYKYPIIPCQI 231 (290)
T ss_pred hHHHHHHHHHcCC--eEEEEecccCCCCeeeecCCCccccchHHHHHHHHHCCCEEEEEE
Confidence 7889999999885 888888887521 1 11123466666776666664
No 219
>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=27.32 E-value=72 Score=21.20 Aligned_cols=44 Identities=27% Similarity=0.190 Sum_probs=28.6
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhc
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~ 70 (117)
.+.++++--|++...-......+....++|++.+.+|.++....
T Consensus 80 ~~~~~v~v~d~~~~~~~~~~~~~~~~~~~~vi~v~nK~D~~~~~ 123 (157)
T cd04164 80 EADLVLFVIDASRGLDEEDLEILELPADKPIIVVLNKSDLLPDS 123 (157)
T ss_pred hCCEEEEEEECCCCCCHHHHHHHHhhcCCCEEEEEEchhcCCcc
Confidence 35566666677632223334444446789999999999987544
No 220
>COG0218 Predicted GTPase [General function prediction only]
Probab=27.24 E-value=69 Score=25.08 Aligned_cols=38 Identities=26% Similarity=0.248 Sum_probs=26.9
Q ss_pred ccEEEEeCCC--CCcchheeHHHHhhhCCCCEEEECCHhH
Q 033552 28 CRLCVIAGNI--SPIDVITHVPILCEESDIPYIYVASKED 65 (117)
Q Consensus 28 ~~LViLA~Da--sp~~i~~~i~~lce~~~IP~i~v~tK~e 65 (117)
.+.||+=-|+ .|.+.=..+.++..+.++|++.+.||.+
T Consensus 107 L~~vvlliD~r~~~~~~D~em~~~l~~~~i~~~vv~tK~D 146 (200)
T COG0218 107 LKGVVLLIDARHPPKDLDREMIEFLLELGIPVIVVLTKAD 146 (200)
T ss_pred heEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEccc
Confidence 4444444444 4544455788899999999999998753
No 221
>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=27.23 E-value=62 Score=22.46 Aligned_cols=46 Identities=13% Similarity=0.102 Sum_probs=29.9
Q ss_pred eecchhhhhcCCccEEEEeCCCCC-------cchheeHHHHhhhCCCCEEEEC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISP-------IDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp-------~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+.+.++.+++..++++++.--..| ..+-..+..+|+++++|++...
T Consensus 90 l~~li~~~~~~~~~vil~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~d~~ 142 (177)
T cd01822 90 LRQMIETAQARGAPVLLVGMQAPPNYGPRYTRRFAAIYPELAEEYGVPLVPFF 142 (177)
T ss_pred HHHHHHHHHHCCCeEEEEecCCCCccchHHHHHHHHHHHHHHHHcCCcEechH
Confidence 455667777777887777532222 1234566778999999988643
No 222
>TIGR01766 tspaseT_teng_C transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam model pfam01385, and other proteins.
Probab=27.22 E-value=47 Score=21.07 Aligned_cols=23 Identities=26% Similarity=0.274 Sum_probs=18.9
Q ss_pred cchheeHHHHhhhCCCCEEEECC
Q 033552 40 IDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 40 ~~i~~~i~~lce~~~IP~i~v~t 62 (117)
..+...|...|+.+||+++.|.-
T Consensus 56 ~~~~~~l~yka~~~Gi~v~~v~~ 78 (82)
T TIGR01766 56 RKLISKIKYKAEEYGIEVIEVNP 78 (82)
T ss_pred HHHHHHHHHHHHHcCCeEEEeCc
Confidence 34677788899999999999864
No 223
>KOG2869 consensus Meiotic cell division protein Pelota/DOM34 [Translation, ribosomal structure and biogenesis]
Probab=27.09 E-value=33 Score=29.31 Aligned_cols=72 Identities=14% Similarity=0.071 Sum_probs=50.8
Q ss_pred ccceeeeecchhhhhcCCccEEEEe------CCCCCcchheeHHHHhh---hCCCCEEEECCHhHHHhhcCCCcceEEEE
Q 033552 10 SFNCVGVVNDPLPLLFHECRLCVIA------GNISPIDVITHVPILCE---ESDIPYIYVASKEDLANAGATKRPTCCVL 80 (117)
Q Consensus 10 ~~~~vG~kqt~kaL~kg~~~LViLA------~Dasp~~i~~~i~~lce---~~~IP~i~v~tK~eLG~A~G~~~~~svv~ 80 (117)
..-|.|.|++.+|.+.|..+-++|+ .|+.. .++...+|+ +.|-++.+..++...|.-+-.-.++| +
T Consensus 290 drA~yG~khV~~A~e~~AI~tLLitD~lfr~~DV~t---Rkkyv~lvesVk~~~gkv~Ifss~H~SGEqL~qltGia--A 364 (379)
T KOG2869|consen 290 DRACYGPKHVEKANEYGAIETLLITDELFRSQDVAT---RKKYVRLVESVKENNGKVFIFSSLHVSGEQLAQLTGIA--A 364 (379)
T ss_pred cccccCHHHHHHHHhhcchhheehhhhhcccccHHH---HHHHHHHHHHHHhcCCcEEEEehhhccHHHHHhhcCee--E
Confidence 3568999999999999998766664 44443 455566665 58999999999988887666543444 4
Q ss_pred EeecCC
Q 033552 81 VLTKPT 86 (117)
Q Consensus 81 I~~~~~ 86 (117)
|+.=|.
T Consensus 365 iLrfp~ 370 (379)
T KOG2869|consen 365 ILRFPL 370 (379)
T ss_pred EEecCC
Confidence 444343
No 224
>PRK08943 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase; Validated
Probab=27.07 E-value=1.6e+02 Score=23.47 Aligned_cols=23 Identities=4% Similarity=-0.246 Sum_probs=18.7
Q ss_pred eeecchhhhhcCCccEEEEeCCCCC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISP 39 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp 39 (117)
|+++.+++|++|. .|.+..|-++
T Consensus 190 ~~r~i~kaLk~g~--~v~il~Dq~~ 212 (314)
T PRK08943 190 GIKPFISSVRQGY--WGYYLPDEDH 212 (314)
T ss_pred hHHHHHHHHhCCC--eEEEeCCCCC
Confidence 6788899999885 7888888775
No 225
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=26.65 E-value=2.2e+02 Score=24.50 Aligned_cols=40 Identities=10% Similarity=0.119 Sum_probs=30.1
Q ss_pred hhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 22 PLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 22 aL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
.+++...+..+++.|+........+..+|+..++|+....
T Consensus 118 ~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~ 157 (437)
T PRK00771 118 YFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDP 157 (437)
T ss_pred HHHHcCCeEEEecCCCCCHHHHHHHHHHHHHcCCcEEecC
Confidence 3444446889999998744457788889999999987654
No 226
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.61 E-value=74 Score=24.80 Aligned_cols=45 Identities=11% Similarity=0.073 Sum_probs=28.0
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcch---------heeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDV---------ITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i---------~~~i~~lce~~~IP~i~v~ 61 (117)
.+.++.+++.++.+|++++|...... ...+..+.+...+|++.+.
T Consensus 29 ~~l~~~~~~~~~D~lli~GDi~d~~~p~~~~~~~~~~~l~~l~~~~~i~v~~i~ 82 (253)
T TIGR00619 29 DDLLEFAKAEQIDALLVAGDVFDTANPPAEAQELFNAFFRNLSDANPIPIVVIS 82 (253)
T ss_pred HHHHHHHHHcCCCEEEECCccCCCCCCCHHHHHHHHHHHHHHHhcCCceEEEEc
Confidence 34566667788999999999885221 1222333333339998774
No 227
>TIGR03598 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes.
Probab=26.48 E-value=59 Score=23.20 Aligned_cols=21 Identities=29% Similarity=0.325 Sum_probs=11.9
Q ss_pred HHHHhhhCCCCEEEECCHhHH
Q 033552 46 VPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 46 i~~lce~~~IP~i~v~tK~eL 66 (117)
+..++..+++|++.+.||-++
T Consensus 121 ~~~~~~~~~~pviiv~nK~D~ 141 (179)
T TIGR03598 121 MLEWLRERGIPVLIVLTKADK 141 (179)
T ss_pred HHHHHHHcCCCEEEEEECccc
Confidence 345566666666666655443
No 228
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=26.46 E-value=73 Score=27.46 Aligned_cols=44 Identities=11% Similarity=0.226 Sum_probs=35.0
Q ss_pred eeecchhhhhcCCccEEEEeCCCCC------cchheeHHHHhhhCCCCEE
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISP------IDVITHVPILCEESDIPYI 58 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp------~~i~~~i~~lce~~~IP~i 58 (117)
-+.+.-++++.+.+++.||.+==.| .+-..++.++|+.|||.+|
T Consensus 146 D~~~LE~~~~~~~vkl~iLCnPHNP~Grvwt~eeL~~i~elc~kh~v~VI 195 (388)
T COG1168 146 DFDALEKAFVDERVKLFILCNPHNPTGRVWTKEELRKIAELCLRHGVRVI 195 (388)
T ss_pred cHHHHHHHHhcCCccEEEEeCCCCCCCccccHHHHHHHHHHHHHcCCEEE
Confidence 3455667888999999999886665 3457889999999999776
No 229
>PF00218 IGPS: Indole-3-glycerol phosphate synthase; InterPro: IPR013798 Indole-3-glycerol phosphate synthase (4.1.1.48 from EC) (IGPS) catalyses the fourth step in the biosynthesis of tryptophan, the ring closure of 1-(2-carboxy-phenylamino)-1-deoxyribulose into indol-3-glycerol-phosphate. In some bacteria, IGPS is a single chain enzyme. In others, such as Escherichia coli, it is the N-terminal domain of a bifunctional enzyme that also catalyses N-(5'-phosphoribosyl)anthranilate isomerase (5.3.1.24 from EC) (PRAI) activity (see IPR001240 from INTERPRO), the third step of tryptophan biosynthesis. In fungi, IGPS is the central domain of a trifunctional enzyme that contains a PRAI C-terminal domain and a glutamine amidotransferase (2.4.2 from EC) (GATase) N-terminal domain (see IPR000991 from INTERPRO). A structure of the IGPS domain of the bifunctional enzyme from the mesophilic bacterium E. coli (eIGPS) has been compared with the monomeric indole-3-glycerol phosphate synthase from the hyperthermophilic archaeon Sulfolobus solfataricus (sIGPS). Both are single-domain (beta/alpha)8 barrel proteins, with one (eIGPS) or two (sIGPS) additional helices inserted before the first beta strand []. ; GO: 0004425 indole-3-glycerol-phosphate synthase activity; PDB: 1VC4_A 1PII_A 1JCM_P 1I4N_B 1J5T_A 3TSM_B 4FB7_A 3QJA_A 1JUL_A 2C3Z_A ....
Probab=26.45 E-value=80 Score=25.28 Aligned_cols=66 Identities=14% Similarity=0.031 Sum_probs=49.8
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCC-CEEEECCHhHHHhhcCCCcceEEEEEee
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDI-PYIYVASKEDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~I-P~i~v~tK~eLG~A~G~~~~~svv~I~~ 83 (117)
--.|...+-.-|---+++|++=.++ +....+...|++.|. |++.|.|.+||-+|... ++..++|-.
T Consensus 120 d~~QI~eA~~~GADaVLLI~~~L~~-~~l~~l~~~a~~lGle~lVEVh~~~El~~al~~--~a~iiGINn 186 (254)
T PF00218_consen 120 DPYQIYEARAAGADAVLLIAAILSD-DQLEELLELAHSLGLEALVEVHNEEELERALEA--GADIIGINN 186 (254)
T ss_dssp SHHHHHHHHHTT-SEEEEEGGGSGH-HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT--T-SEEEEES
T ss_pred CHHHHHHHHHcCCCEeehhHHhCCH-HHHHHHHHHHHHcCCCeEEEECCHHHHHHHHHc--CCCEEEEeC
Confidence 3457777778887778888888777 457899999999998 88999999999999754 355677643
No 230
>PRK14725 pyruvate kinase; Provisional
Probab=26.43 E-value=1.6e+02 Score=26.84 Aligned_cols=45 Identities=24% Similarity=0.573 Sum_probs=32.9
Q ss_pred chheeHHHHhhhCCCCEEE------------ECCHhHHHhhcCCCcceEEEEEeecCC
Q 033552 41 DVITHVPILCEESDIPYIY------------VASKEDLANAGATKRPTCCVLVLTKPT 86 (117)
Q Consensus 41 ~i~~~i~~lce~~~IP~i~------------v~tK~eLG~A~G~~~~~svv~I~~~~~ 86 (117)
.+.+.|..+|+.+++|+|+ .+|++|...+..-- ++-|+++..|+.
T Consensus 522 ~iQk~Ii~~c~~~~kPVI~ATQmLESM~~~p~PTRAEvtDVAnAv-gaD~VMLS~G~y 578 (608)
T PRK14725 522 EVQEEILWLCEAAHVPVIWATQVLESLAKKGLPSRAEITDAAMAL-RAECVMLNKGPH 578 (608)
T ss_pred HHHHHHHHHHHHcCCCEEEEcchHhhhccCCCCCchhHHHHHhhh-cCCEEeecCCCC
Confidence 4678888899999999998 67888888543322 466778764443
No 231
>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=26.43 E-value=1.2e+02 Score=20.48 Aligned_cols=45 Identities=9% Similarity=0.054 Sum_probs=30.0
Q ss_pred cEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCC
Q 033552 29 RLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATK 73 (117)
Q Consensus 29 ~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~ 73 (117)
.++|+.+-.....-.....+.|+++|+|++-+-+..+|...+...
T Consensus 45 dl~I~iS~SG~t~e~i~~~~~a~~~g~~iI~IT~~~~l~~~~~~~ 89 (119)
T cd05017 45 TLVIAVSYSGNTEETLSAVEQAKERGAKIVAITSGGKLLEMAREH 89 (119)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEeCCchHHHHHHHc
Confidence 455555444432235556668899999999887777888877643
No 232
>cd01484 E1-2_like Ubiquitin activating enzyme (E1), repeat 2-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. 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 homologou
Probab=26.33 E-value=57 Score=25.58 Aligned_cols=39 Identities=13% Similarity=-0.115 Sum_probs=31.5
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
...+||.|.|--+ ....+..+|..+++|++..++-.--|
T Consensus 91 ~~DvVi~a~Dn~~--aR~~ln~~c~~~~iplI~~g~~G~~G 129 (234)
T cd01484 91 QFHIIVNALDNII--ARRYVNGMLIFLIVPLIESGTEGFKG 129 (234)
T ss_pred CCCEEEECCCCHH--HHHHHHHHHHHcCCCEEEEcccCCce
Confidence 3678999988654 48889999999999999988854444
No 233
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=26.33 E-value=2.1e+02 Score=19.73 Aligned_cols=39 Identities=13% Similarity=0.017 Sum_probs=25.0
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhh
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANA 69 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A 69 (117)
++.++=.+..-+.+++.+.|+++|+++.... +-.++..-
T Consensus 6 lvCg~G~STSlla~k~k~~~~e~gi~~~i~a~~~~e~~~~ 45 (104)
T PRK09590 6 IICAAGMSSSMMAKKTTEYLKEQGKDIEVDAITATEGEKA 45 (104)
T ss_pred EECCCchHHHHHHHHHHHHHHHCCCceEEEEecHHHHHHh
Confidence 3333333333467889999999999986644 44455544
No 234
>COG1879 RbsB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=26.29 E-value=77 Score=24.69 Aligned_cols=42 Identities=12% Similarity=-0.002 Sum_probs=31.1
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
....|.+|--.+++.+.|... .....+.+.+.|||++.+.+.
T Consensus 84 i~~~ia~~~daIiv~~~d~~~---~~~~v~~a~~aGIpVv~~d~~ 125 (322)
T COG1879 84 IEDLIAQGVDAIIINPVDPDA---LTPAVKKAKAAGIPVVTVDSD 125 (322)
T ss_pred HHHHHHcCCCEEEEcCCChhh---hHHHHHHHHHCCCcEEEEecC
Confidence 344566777788888888664 566777888999999988764
No 235
>cd04170 EF-G_bact Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group
Probab=26.25 E-value=67 Score=24.82 Aligned_cols=51 Identities=18% Similarity=0.125 Sum_probs=31.2
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
.++..+++.-..-++++..+.....-...+-..++..++|.+.+.+|-++-
T Consensus 79 ~~~~~~l~~aD~~i~Vvd~~~g~~~~~~~~~~~~~~~~~p~iivvNK~D~~ 129 (268)
T cd04170 79 GETRAALRAADAALVVVSAQSGVEVGTEKLWEFADEAGIPRIIFINKMDRE 129 (268)
T ss_pred HHHHHHHHHCCEEEEEEeCCCCCCHHHHHHHHHHHHcCCCEEEEEECCccC
Confidence 346667766555555554443322223445557888999999998875533
No 236
>cd02001 TPP_ComE_PpyrDC Thiamine pyrophosphate (TPP) family, ComE and PpyrDC subfamily, TPP-binding module; composed of proteins similar to sulfopyruvate decarboxylase beta subunit (ComE) and phosphonopyruvate decarboxylase (Ppyr decarboxylase). Methanococcus jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits which, catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. Ppyr decarboxylase is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. Ppyr decarboxylase and ComDE require TPP and divalent metal cation cofactors.
Probab=26.23 E-value=82 Score=22.76 Aligned_cols=28 Identities=7% Similarity=-0.038 Sum_probs=22.3
Q ss_pred eeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 44 THVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 44 ~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
-.+..+++.+|++++.+.+.+||..++.
T Consensus 112 ~d~~~lA~a~G~~~~~v~~~~el~~al~ 139 (157)
T cd02001 112 VNLEAWAAACGYLVLSAPLLGGLGSEFA 139 (157)
T ss_pred CCHHHHHHHCCCceEEcCCHHHHHHHHH
Confidence 4577788888888888888888886654
No 237
>cd03018 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers.
Probab=26.05 E-value=1.9e+02 Score=19.60 Aligned_cols=49 Identities=10% Similarity=0.017 Sum_probs=30.9
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH---hHHHhhcCCC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK---EDLANAGATK 73 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK---~eLG~A~G~~ 73 (117)
.+.+++..+.++.|..|.. ..+..+.+++++++..+.+. .++++..|..
T Consensus 55 ~~~~~~~~v~vi~vs~d~~-----~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~g~~ 106 (149)
T cd03018 55 LELFEAAGAEVLGISVDSP-----FSLRAWAEENGLTFPLLSDFWPHGEVAKAYGVF 106 (149)
T ss_pred HHHHHhCCCEEEEecCCCH-----HHHHHHHHhcCCCceEecCCCchhHHHHHhCCc
Confidence 3444444566666666532 23556778888888777654 5778887764
No 238
>COG0182 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=25.96 E-value=88 Score=26.55 Aligned_cols=40 Identities=15% Similarity=0.245 Sum_probs=29.5
Q ss_pred hhcCCccEEEEeCCCCC--cchh-----eeHHHHhhhCCCCEEEECC
Q 033552 23 LLFHECRLCVIAGNISP--IDVI-----THVPILCEESDIPYIYVAS 62 (117)
Q Consensus 23 L~kg~~~LViLA~Dasp--~~i~-----~~i~~lce~~~IP~i~v~t 62 (117)
|++|.+..||+++|-=- .++. -.+-.+|+.+|||+....-
T Consensus 224 M~~g~Id~viVGADRI~~nGdvaNKIGTY~lAvlAk~~gIPFyVaAP 270 (346)
T COG0182 224 MQQGMIDAVIVGADRIAANGDVANKIGTYQLAVLAKHHGIPFYVAAP 270 (346)
T ss_pred HHhCCCcEEEEccceeecCCcchhhhhHHHHHHHHHHcCCCeEEEcc
Confidence 78999999999988431 1222 2356799999999988763
No 239
>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=25.84 E-value=45 Score=24.10 Aligned_cols=47 Identities=11% Similarity=0.021 Sum_probs=30.0
Q ss_pred ecchhhhhcCCccEEEEeC----CCC--------CcchheeHHHHhhhCCCCEEEECCH
Q 033552 17 VNDPLPLLFHECRLCVIAG----NIS--------PIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~----Das--------p~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
.+.++.+++..+.++++.- +.. -..+...+..+|+++|+|++...+.
T Consensus 97 ~~ii~~~~~~~~~~il~tp~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~vD~~~~ 155 (198)
T cd01821 97 RRYIAEARAKGATPILVTPVTRRTFDEGGKVEDTLGDYPAAMRELAAEEGVPLIDLNAA 155 (198)
T ss_pred HHHHHHHHHCCCeEEEECCccccccCCCCcccccchhHHHHHHHHHHHhCCCEEecHHH
Confidence 3455666766677666521 000 0123467888999999999998764
No 240
>PRK10427 putative PTS system fructose-like transporter subunit EIIB; Provisional
Probab=25.84 E-value=1.1e+02 Score=21.47 Aligned_cols=49 Identities=10% Similarity=0.046 Sum_probs=33.1
Q ss_pred eeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhh
Q 033552 14 VGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANA 69 (117)
Q Consensus 14 vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A 69 (117)
+|+.+.+.+-.-..+.+||+|+|....+ ..+..|.|++.+...+-|-.+
T Consensus 44 ~g~~~~lt~~~i~~Ad~VIia~d~~~~~-------~~rF~gk~v~~~s~~~ai~d~ 92 (114)
T PRK10427 44 LGTENRLTDEDIRRADVVLLITDIELAG-------AERFEHCRYVQCSIYAFLREP 92 (114)
T ss_pred cCcCCCCCHHHHHhCCEEEEEecCCCCc-------hhhhCCCeEEEecHHHHHHHH
Confidence 4666666556666789999999987312 335567788877766665543
No 241
>TIGR02740 TraF-like TraF-like protein. This protein is related to the F-type conjugation system pilus assembly proteins TraF (TIGR02739)and TrbB (TIGR02738) both of which exhibit a thioredoxin fold. The protein represented by this model has the same length and architecture as TraF, but lacks the CXXC-motif found in TrbB and believed to be responsible for the disulfide isomerase activity of that protein.
Probab=25.69 E-value=1.6e+02 Score=23.40 Aligned_cols=59 Identities=8% Similarity=-0.023 Sum_probs=39.3
Q ss_pred cchhhhhcCCccEEEEeCCCCC-cchheeHHHHhhhCCCCEEEECCH-------------hHHHhhcCCC-cce
Q 033552 18 NDPLPLLFHECRLCVIAGNISP-IDVITHVPILCEESDIPYIYVASK-------------EDLANAGATK-RPT 76 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp-~~i~~~i~~lce~~~IP~i~v~tK-------------~eLG~A~G~~-~~~ 76 (117)
++++.++..-+-+.|-|++|.+ ....-.|..+++++++.++.+..- ..+....|.. .|+
T Consensus 159 ~~l~~l~~k~~Lv~F~AswCp~C~~~~P~L~~la~~yg~~Vi~VsvD~~~~~~fp~~~~d~~la~~~gV~~vPt 232 (271)
T TIGR02740 159 RVMKDLAKKSGLFFFFKSDCPYCHQQAPILQAFEDRYGIEVLPVSVDGGPLPGFPNARPDAGQAQQLKIRTVPA 232 (271)
T ss_pred HHHHHhcCCeEEEEEECCCCccHHHHhHHHHHHHHHcCcEEEEEeCCCCccccCCcccCCHHHHHHcCCCcCCe
Confidence 5667776554556678888887 333456777899999888766532 2466777875 344
No 242
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=25.63 E-value=61 Score=24.07 Aligned_cols=42 Identities=12% Similarity=-0.039 Sum_probs=27.0
Q ss_pred eeecchhhhhc--CCccEEEEeCCCCC--cchheeHHHHhhhCCCC
Q 033552 15 GVVNDPLPLLF--HECRLCVIAGNISP--IDVITHVPILCEESDIP 56 (117)
Q Consensus 15 G~kqt~kaL~k--g~~~LViLA~Dasp--~~i~~~i~~lce~~~IP 56 (117)
+.+..++.|++ .++.-||||.|++- ..+..++.+.|...+.|
T Consensus 104 ~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~~~~ 149 (170)
T cd03361 104 DKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPYNKN 149 (170)
T ss_pred chHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhccCCCC
Confidence 34444555554 45889999999994 34566677777654433
No 243
>PF03494 Beta-APP: Beta-amyloid peptide (beta-APP); InterPro: IPR013803 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. This entry represents the amyloid-beta peptide (A-beta), which originates as a breakdown product from the cleavage of amyloid-beta precursor protein (APP, or A4), an integral, glycosylated membrane brain protein. More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein [].; GO: 0005488 binding, 0016021 integral to membrane; PDB: 2LMQ_F 3JTI_B 2LMO_B 3MOQ_D 2LNQ_E 2LMP_G 2BEG_B 1AMC_A 3OW9_B 3U0T_F ....
Probab=25.54 E-value=19 Score=21.09 Aligned_cols=13 Identities=15% Similarity=0.302 Sum_probs=10.8
Q ss_pred ccEEEEeCCCCCc
Q 033552 28 CRLCVIAGNISPI 40 (117)
Q Consensus 28 ~~LViLA~Dasp~ 40 (117)
.+++|+|+|.+.+
T Consensus 12 ~klvf~aEDvgSN 24 (39)
T PF03494_consen 12 KKLVFLAEDVGSN 24 (39)
T ss_dssp CCCCCCCCCCSSS
T ss_pred eEEEEEhhHcCCC
Confidence 4789999999874
No 244
>PRK08734 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=25.50 E-value=2.7e+02 Score=22.21 Aligned_cols=23 Identities=17% Similarity=-0.129 Sum_probs=18.9
Q ss_pred eeecchhhhhcCCccEEEEeCCCCC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISP 39 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp 39 (117)
|+++.+++|++|. +|.+..|-++
T Consensus 172 ~~r~li~~Lk~g~--~v~~l~Dq~~ 194 (305)
T PRK08734 172 AVRQLFKVLKDGG--AVGILPDQQP 194 (305)
T ss_pred hHHHHHHHHhcCC--eEEEeCCCCC
Confidence 5788899999885 8888888875
No 245
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=25.46 E-value=49 Score=29.60 Aligned_cols=34 Identities=24% Similarity=0.355 Sum_probs=30.4
Q ss_pred cchheeHHHHhhhCCCCEEEECCHhHHHhhcCCC
Q 033552 40 IDVITHVPILCEESDIPYIYVASKEDLANAGATK 73 (117)
Q Consensus 40 ~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~ 73 (117)
..+..+|..+|++.+||.+.+.+..|+|.|+.-+
T Consensus 544 ~rVArkiselaRe~giTlivvThrpEv~~AL~PD 577 (593)
T COG2401 544 VRVARKISELAREAGITLIVVTHRPEVGNALRPD 577 (593)
T ss_pred HHHHHHHHHHHHHhCCeEEEEecCHHHHhccCCc
Confidence 4467889999999999999999999999998755
No 246
>PRK08706 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=25.40 E-value=2.6e+02 Score=21.90 Aligned_cols=24 Identities=4% Similarity=-0.190 Sum_probs=16.7
Q ss_pred eeecchhhhhcCCccEEEEeCCCCC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISP 39 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp 39 (117)
|+++.+++|+++. ..|.+..|-++
T Consensus 165 ~~r~i~k~L~k~~-~~v~~l~Dq~~ 188 (289)
T PRK08706 165 GLRALVKQFRKSS-APFLYLPDQDF 188 (289)
T ss_pred hHHHHHHHHHhCC-ceEEEeCCCCC
Confidence 7889999997555 44444477764
No 247
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=25.31 E-value=44 Score=18.77 Aligned_cols=25 Identities=16% Similarity=0.279 Sum_probs=18.2
Q ss_pred eeHHHHhhhCCCCEEEEC-CHhHHHh
Q 033552 44 THVPILCEESDIPYIYVA-SKEDLAN 68 (117)
Q Consensus 44 ~~i~~lce~~~IP~i~v~-tK~eLG~ 68 (117)
..+..+.+.+|||+---. ++++|=.
T Consensus 7 ~~L~~wL~~~gi~~~~~~~~rd~Ll~ 32 (38)
T PF10281_consen 7 SDLKSWLKSHGIPVPKSAKTRDELLK 32 (38)
T ss_pred HHHHHHHHHcCCCCCCCCCCHHHHHH
Confidence 346678888999887666 7877744
No 248
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=25.12 E-value=2.6e+02 Score=24.89 Aligned_cols=47 Identities=15% Similarity=-0.020 Sum_probs=29.8
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCc--chh-----------eeHHHHhhhCCCCEEEECCH
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPI--DVI-----------THVPILCEESDIPYIYVASK 63 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~--~i~-----------~~i~~lce~~~IP~i~v~tK 63 (117)
|+++.+++|++| .+|.|..|-.+. .+. .-...++...++|+++++.+
T Consensus 534 ~~r~i~~aLk~g--~~v~il~Dq~~~~~~~~v~FfG~~a~~~~g~~~lA~~~~~pvv~~~~~ 593 (656)
T PRK15174 534 VVRACMQTLHSG--QSLVVAIDGALNLSAPTIDFFGQQITYSTFCSRLAWKMHLPTVFSVPI 593 (656)
T ss_pred HHHHHHHHHHcC--CeEEEEeCCCCCCCCceeccCCCccCcCcHHHHHHHHHCCCEEEeEEE
Confidence 577888899888 578888777742 111 11225666667777766663
No 249
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=24.87 E-value=66 Score=26.48 Aligned_cols=39 Identities=21% Similarity=0.225 Sum_probs=30.0
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
+.-+||.|.|-.. ....+.++|.++++|+++...-..-|
T Consensus 116 ~~DlVid~~D~~~--~r~~in~~~~~~~ip~i~~~~~g~~G 154 (338)
T PRK12475 116 EVDLIIDATDNFD--TRLLINDLSQKYNIPWIYGGCVGSYG 154 (338)
T ss_pred CCCEEEEcCCCHH--HHHHHHHHHHHcCCCEEEEEecccEE
Confidence 3779999998653 46778999999999999986544333
No 250
>COG1029 FwdB Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]
Probab=24.79 E-value=1.7e+02 Score=25.51 Aligned_cols=82 Identities=24% Similarity=0.198 Sum_probs=46.6
Q ss_pred hhhhcCCcc-EEEEeCCCCCcchheeHHHHhhhC--CCCEEEECCHhHHHhhcCCC-cceEEEEEee-------------
Q 033552 21 LPLLFHECR-LCVIAGNISPIDVITHVPILCEES--DIPYIYVASKEDLANAGATK-RPTCCVLVLT------------- 83 (117)
Q Consensus 21 kaL~kg~~~-LViLA~Dasp~~i~~~i~~lce~~--~IP~i~v~tK~eLG~A~G~~-~~~svv~I~~------------- 83 (117)
..|++.++- .+|||+| | ..|+|.-|-++ .||++-+.--.-.-..+..= .|.++.++-.
T Consensus 328 dlL~~k~vDAalvi~sD--p---~ah~P~~~~~~l~eIPvI~iDp~~~pTt~vadVviP~aI~gmE~~GTayRmD~V~v~ 402 (429)
T COG1029 328 DLLKRKEVDAALVIASD--P---GAHFPRDAVEHLAEIPVICIDPHPTPTTEVADVVIPSAIDGMEAEGTAYRMDGVPVR 402 (429)
T ss_pred HHHhccCCCeEEEEecC--c---cccChHHHHHHhhcCCEEEecCCCCcchhhcceecccceeeeeccceEEeecCceEe
Confidence 445555543 5667777 4 56899888874 79999887543333222111 1333333333
Q ss_pred -cCCCCccchHHHHhhHHHHHHHHH
Q 033552 84 -KPTKGELGQEEQDKLKADYTLVVE 107 (117)
Q Consensus 84 -~~~~~~~~~~e~~~~~~~~~e~~~ 107 (117)
.|...+....+++.++.+++++.+
T Consensus 403 ~k~~~es~~~sde~iLk~l~ekv~e 427 (429)
T COG1029 403 MKPVVESKTLSDEEILKKLLEKVKE 427 (429)
T ss_pred eEecccccccChHHHHHHHHHHHhh
Confidence 333333345677888888877653
No 251
>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=24.76 E-value=2.2e+02 Score=18.99 Aligned_cols=48 Identities=10% Similarity=0.084 Sum_probs=29.4
Q ss_pred hhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC-CHhHHHhhcCCCc
Q 033552 22 PLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA-SKEDLANAGATKR 74 (117)
Q Consensus 22 aL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~-tK~eLG~A~G~~~ 74 (117)
.++...+.+|.|+.|.. ..+..+++++++++..+. ....++++.|...
T Consensus 52 ~~~~~~~~vv~is~d~~-----~~~~~~~~~~~~~~~~l~D~~~~~~~~~gv~~ 100 (140)
T cd03017 52 EFKALGAVVIGVSPDSV-----ESHAKFAEKYGLPFPLLSDPDGKLAKAYGVWG 100 (140)
T ss_pred HHHHCCCEEEEEcCCCH-----HHHHHHHHHhCCCceEEECCccHHHHHhCCcc
Confidence 34444566777776622 234567777777665555 3457888888764
No 252
>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=24.68 E-value=92 Score=23.82 Aligned_cols=42 Identities=10% Similarity=0.125 Sum_probs=28.5
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
+..+.|+++++++||.-...++ .. ...++++.|+|++.+...
T Consensus 190 ~l~~~ik~~~v~~i~~e~~~~~-~~---~~~la~~~g~~vv~ld~l 231 (256)
T PF01297_consen 190 ELIKLIKENKVKCIFTEPQFSS-KL---AEALAKETGVKVVYLDPL 231 (256)
T ss_dssp HHHHHHHHTT-SEEEEETTS-T-HH---HHHHHHCCT-EEEESSTT
T ss_pred HHHHHhhhcCCcEEEecCCCCh-HH---HHHHHHHcCCcEEEeCCC
Confidence 4557778888888888766655 33 344689999999888776
No 253
>PF02347 GDC-P: Glycine cleavage system P-protein; InterPro: IPR020580 This family consists of glycine cleavage system P-proteins (1.4.4.2 from EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (2.1.2.10 from EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T []. The reaction catalysed by this protein is: Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 ; GO: 0004375 glycine dehydrogenase (decarboxylating) activity, 0055114 oxidation-reduction process; PDB: 1WYV_A 1WYT_C 1WYU_A.
Probab=24.61 E-value=1.4e+02 Score=25.81 Aligned_cols=62 Identities=16% Similarity=0.138 Sum_probs=38.2
Q ss_pred hcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCCc
Q 033552 24 LFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGE 89 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~~ 89 (117)
.+++.+-|++..++.|.. ..-+...|+-.++.++.++..+.-..- +..+++++|+...+-+.
T Consensus 150 ~~~~~~~vlv~~~~hP~~-~~v~~t~a~~~g~~iv~~~~~~~~~~d---~~~~a~v~vq~Pn~~G~ 211 (429)
T PF02347_consen 150 TKRKRNKVLVPESLHPQT-RAVLRTYAAPLGIEIVEVPLDEDGTTD---DDDTAAVMVQNPNTFGV 211 (429)
T ss_dssp HTT---EEEEETTS-CHH-HHHHHHHCCHCCEEEEEE-BBTTCSB----STTEEEEEEESS-TTSB
T ss_pred cccCCcEEEEcCCcChhh-HHHHHHhhhhCCeEEEEecccccCCcc---ccCeEEEEeecCCCCce
Confidence 344456899999999954 566777888899999999865432222 33577777765334553
No 254
>KOG3123 consensus Diphthine synthase [Translation, ribosomal structure and biogenesis]
Probab=24.57 E-value=2.7e+02 Score=22.64 Aligned_cols=75 Identities=9% Similarity=0.111 Sum_probs=46.7
Q ss_pred hcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh--hcCCC-----cceEEEEEeecCCCCccchHHHH
Q 033552 24 LFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN--AGATK-----RPTCCVLVLTKPTKGELGQEEQD 96 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~--A~G~~-----~~~svv~I~~~~~~~~~~~~e~~ 96 (117)
.+..+.++++..--.. +.-+.+.--+++.|||+..+.+-.-+-+ +||.. +.+|.+..+++=
T Consensus 74 d~~dVa~LVVGdPfgA-TTHsDlvlRAk~~~ipv~vIHNASimNavG~CGLqlY~fGetVSiv~ftd~w----------- 141 (272)
T KOG3123|consen 74 DKEDVAFLVVGDPFGA-TTHSDLVLRAKELGIPVEVIHNASIMNAVGCCGLQLYNFGETVSIVFFTDNW----------- 141 (272)
T ss_pred hhcceEEEEecCcccc-cchhhhheehhhcCCCeEEEechHHHhhhccceeeeeccCcEEEEEEEccCc-----------
Confidence 3444666666544443 4466777889999999999987655542 46653 245555555421
Q ss_pred hhHHHHHHHHHHHH
Q 033552 97 KLKADYTLVVEDVK 110 (117)
Q Consensus 97 ~~~~~~~e~~~~~~ 110 (117)
+=..+|+++.+.-+
T Consensus 142 rP~SfydkI~~Nr~ 155 (272)
T KOG3123|consen 142 RPESFYDKIKENRQ 155 (272)
T ss_pred CchhHHHHHHHhhh
Confidence 22358888876543
No 255
>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=24.55 E-value=68 Score=23.70 Aligned_cols=54 Identities=19% Similarity=0.130 Sum_probs=38.1
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCC
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGAT 72 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~ 72 (117)
+.+.+..++..+++.--|++..+--..+...-.+.++|++.+-+|.++-..-|.
T Consensus 70 ~~~~l~~~~~D~ii~VvDa~~l~r~l~l~~ql~e~g~P~vvvlN~~D~a~~~g~ 123 (156)
T PF02421_consen 70 ARDYLLSEKPDLIIVVVDATNLERNLYLTLQLLELGIPVVVVLNKMDEAERKGI 123 (156)
T ss_dssp HHHHHHHTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTE
T ss_pred HHHHHhhcCCCEEEEECCCCCHHHHHHHHHHHHHcCCCEEEEEeCHHHHHHcCC
Confidence 456777888999999999985221223444556789999999999777665443
No 256
>cd04117 Rab15 Rab15 subfamily. Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic 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 Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to
Probab=24.43 E-value=49 Score=23.08 Aligned_cols=41 Identities=15% Similarity=0.153 Sum_probs=24.3
Q ss_pred ccEEEEeCCCCCcchheeHHHHhh------hCCCCEEEECCHhHHHh
Q 033552 28 CRLCVIAGNISPIDVITHVPILCE------ESDIPYIYVASKEDLAN 68 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce------~~~IP~i~v~tK~eLG~ 68 (117)
+..+++.-|++..+-...+..+.+ ..++|++.+++|.+|+.
T Consensus 73 ~~~~i~v~d~~~~~sf~~~~~~~~~~~~~~~~~~~iilvgnK~Dl~~ 119 (161)
T cd04117 73 AQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQ 119 (161)
T ss_pred CcEEEEEEECCCHHHHHHHHHHHHHHHHhCCCCCeEEEEEECccccc
Confidence 345555556554333444443332 13689999999998864
No 257
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=24.38 E-value=75 Score=24.92 Aligned_cols=35 Identities=29% Similarity=0.349 Sum_probs=30.4
Q ss_pred CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE
Q 033552 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 26 g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v 60 (117)
-.++.++||+-.-...+...+..+-++++||++-.
T Consensus 140 pRv~iLVLAGslMGGkIteaVk~lr~~hgI~VISL 174 (218)
T COG1707 140 PRVGILVLAGSLMGGKITEAVKELREEHGIPVISL 174 (218)
T ss_pred ccceeEEEecccccchHHHHHHHHHHhcCCeEEEe
Confidence 34789999999887788999999999999999865
No 258
>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=24.28 E-value=69 Score=25.44 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=20.0
Q ss_pred heeHHHHhhhCCCCEEEECCHhHH
Q 033552 43 ITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
..++...++..++|.+.+.+|.+|
T Consensus 98 ldr~L~~~~~~~ip~iIVlNK~DL 121 (287)
T cd01854 98 LDRYLVAAEAAGIEPVIVLTKADL 121 (287)
T ss_pred HHHHHHHHHHcCCCEEEEEEHHHC
Confidence 455666778899999999999998
No 259
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=24.28 E-value=1.5e+02 Score=21.07 Aligned_cols=42 Identities=17% Similarity=0.132 Sum_probs=24.0
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
+.++.+.++.+.-+|+.....+ ... ....+.+.++|++.+.+
T Consensus 46 ~~~~~~~~~~~d~ii~~~~~~~-~~~--~~~~l~~~~ip~v~~~~ 87 (264)
T cd01537 46 SALENLIARGVDGIIIAPSDLT-APT--IVKLARKAGIPVVLVDR 87 (264)
T ss_pred HHHHHHHHcCCCEEEEecCCCc-chh--HHHHhhhcCCCEEEecc
Confidence 3444455555555555443222 222 45677889999988753
No 260
>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=24.17 E-value=97 Score=24.13 Aligned_cols=47 Identities=17% Similarity=0.140 Sum_probs=30.5
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcch----heeHHHHhhhCCCCEEEECC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPIDV----ITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~i----~~~i~~lce~~~IP~i~v~t 62 (117)
+...++.+++..+.+||+++|...... ...+.......++|+..+..
T Consensus 20 le~l~~~~~~~~~D~vv~~GDl~~~g~~~~~~~~~l~~l~~l~~pv~~V~G 70 (224)
T cd07388 20 LEKLVGLAPETGADAIVLIGNLLPKAAKSEDYAAFFRILGEAHLPTFYVPG 70 (224)
T ss_pred HHHHHHHHhhcCCCEEEECCCCCCCCCCHHHHHHHHHHHHhcCCceEEEcC
Confidence 344455556678999999999975220 22333444566789998873
No 261
>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=24.15 E-value=1.4e+02 Score=21.71 Aligned_cols=40 Identities=20% Similarity=0.361 Sum_probs=23.7
Q ss_pred cchhhhhcCCc-cEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 18 NDPLPLLFHEC-RLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 18 qt~kaL~kg~~-~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
+.++.+.++.+ ++++.+.|.++ . ....+.+.+||++.+.+
T Consensus 45 ~~i~~~~~~~vdgiii~~~~~~~-~----~~~~~~~~~ipvV~~~~ 85 (266)
T cd06278 45 AALRQLLQYRVDGVIVTSGTLSS-E----LAEECRRNGIPVVLINR 85 (266)
T ss_pred HHHHHHHHcCCCEEEEecCCCCH-H----HHHHHhhcCCCEEEECC
Confidence 34444444444 56665555332 2 24567778999999875
No 262
>PF10996 Beta-Casp: Beta-Casp domain; InterPro: IPR022712 The beta-CASP domain is found C-terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains []. ; PDB: 2YCB_B 2XR1_B 2I7T_A 2I7V_A 2I7X_A 3A4Y_A 3IE2_D 3IE1_B 3IE0_D 2DKF_D ....
Probab=24.09 E-value=1.2e+02 Score=20.30 Aligned_cols=54 Identities=17% Similarity=0.091 Sum_probs=35.2
Q ss_pred CCccceeeeecchhhhhcCCccEEEEeCCCCC--cchheeHHHHhhhCCCCEEEEC
Q 033552 8 LHSFNCVGVVNDPLPLLFHECRLCVIAGNISP--IDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 8 ~~~~~~vG~kqt~kaL~kg~~~LViLA~Dasp--~~i~~~i~~lce~~~IP~i~v~ 61 (117)
...++.+...+..+.|..-....||+|++..- ......+..+|.+.+--+++++
T Consensus 60 ~~~~~~~~~~~~~~~l~~~~~p~Vvias~gml~~G~s~~~l~~~~~d~~n~Ii~~g 115 (126)
T PF10996_consen 60 FDNFKFVKSVDESKELNALSGPKVVIASSGMLEGGRSRHYLKRLASDPRNTIIFTG 115 (126)
T ss_dssp TTTEEEEESHHHHHHHHHSCSSEEEEESSTTSSSSHHHHHHHHHTTSTTSEEEESS
T ss_pred CCCeEEecccccccccccCCCCeEEEeCCCCCCCCHHHHHHHHHcCCCCCeEEEec
Confidence 45667777777777776444668999988773 2345666667766555555554
No 263
>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=24.04 E-value=61 Score=25.19 Aligned_cols=24 Identities=29% Similarity=0.398 Sum_probs=18.7
Q ss_pred heeHHHHhhhCCCCEEEECCHhHH
Q 033552 43 ITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 43 ~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
...+...++..++|.+.+.+|.+|
T Consensus 56 l~r~l~~~~~~~i~~vIV~NK~DL 79 (245)
T TIGR00157 56 LDRFLVVAEAQNIEPIIVLNKIDL 79 (245)
T ss_pred HHHHHHHHHHCCCCEEEEEECccc
Confidence 444455677789999999999888
No 264
>cd03343 cpn60 cpn60 chaperonin family. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. Archaeal cpn60 (thermosome), together with TF55 from thermophilic bacteria and the eukaryotic cytosol chaperonin (CTT), belong to the type II group of chaperonins. Cpn60 consists of two stacked octameric rings, which are composed of one or two different subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis.
Probab=24.01 E-value=79 Score=27.14 Aligned_cols=44 Identities=11% Similarity=0.106 Sum_probs=31.1
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
++.|.+-.+.+|+.+.++++. ..+ ++.++||-++..-++++|-+
T Consensus 272 v~~i~~~g~~lvi~~~~I~~~--al~---~l~~~gI~~v~~v~~~~l~~ 315 (517)
T cd03343 272 VDKIADTGANVVFCQKGIDDL--AQH---YLAKAGILAVRRVKKSDMEK 315 (517)
T ss_pred HHHHHhcCCCEEEeCCCccHH--HHH---HHhHCCcEEEEeCCHHHHHH
Confidence 346777778999999999973 333 44578887777777666553
No 265
>cd00568 TPP_enzymes Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes.
Probab=23.97 E-value=1e+02 Score=21.42 Aligned_cols=27 Identities=30% Similarity=0.223 Sum_probs=19.8
Q ss_pred eHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 45 HVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 45 ~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
.+..+++.+|+++..+.+.++|.+++.
T Consensus 127 d~~~~a~~~G~~~~~v~~~~~l~~a~~ 153 (168)
T cd00568 127 DFAALAEAYGAKGVRVEDPEDLEAALA 153 (168)
T ss_pred CHHHHHHHCCCeEEEECCHHHHHHHHH
Confidence 466677778888888888877776543
No 266
>PF02472 ExbD: Biopolymer transport protein ExbD/TolR; InterPro: IPR003400 This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria []. The family consists of ExbD, and TolR which are involved in TonB-dependent transport of various receptor bound substrates including colicins [].; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2JWL_A 2JWK_A 2PFU_A.
Probab=23.97 E-value=72 Score=21.57 Aligned_cols=51 Identities=14% Similarity=0.112 Sum_probs=27.4
Q ss_pred eeecchhhhhcCCc---cEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhH
Q 033552 15 GVVNDPLPLLFHEC---RLCVIAGNISPIDVITHVPILCEESDIPYIYVASKED 65 (117)
Q Consensus 15 G~kqt~kaL~kg~~---~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~e 65 (117)
++.+.++.+..... .+++.|.+..+...+.++-+.|++.|+.-+.+-++.|
T Consensus 77 ~L~~~l~~~~~~~~~~~~v~i~aD~~~~y~~vv~vl~~l~~~g~~~v~l~t~~e 130 (130)
T PF02472_consen 77 ELEARLKELKQKNPDPVRVLIRADKDAPYQDVVDVLDALREAGFTKVSLATEKE 130 (130)
T ss_dssp CHHHHHHHHCCC-TTS--EEEEE-TTS-HHHHHHHHHHHHHTT---EE-TT---
T ss_pred HHHHHHHHhhccCCCcceEEEEeCCCCCHHHHHHHHHHHHHcCCCEEEEEEecC
Confidence 34444555544442 4666666666766788999999999999877776654
No 267
>TIGR03846 sulfopy_beta sulfopyruvate decarboxylase, beta subunit. Nearly every member of this protein family is the beta subunit, or else the C-terminal region, of sulfopyruvate decarboxylase, in an archaeal species capable of coenzyme M biosynthesis. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA (see PubMed:19581363).
Probab=23.92 E-value=3e+02 Score=20.31 Aligned_cols=27 Identities=22% Similarity=0.351 Sum_probs=23.3
Q ss_pred eHHHHhhhCCCCEEE-ECCHhHHHhhcC
Q 033552 45 HVPILCEESDIPYIY-VASKEDLANAGA 71 (117)
Q Consensus 45 ~i~~lce~~~IP~i~-v~tK~eLG~A~G 71 (117)
.+..+|+.+|+++.. +.+.++|-.++.
T Consensus 114 d~~~lA~a~G~~~~~~v~~~~~l~~al~ 141 (181)
T TIGR03846 114 DLELVAKAAGIRNVEKVADEEELRDALK 141 (181)
T ss_pred CHHHHHHHCCCCeEEEeCCHHHHHHHHH
Confidence 578899999999999 999999986653
No 268
>PF08862 DUF1829: Domain of unknown function DUF1829; InterPro: IPR014961 This short protein is usually associated with IPR014960 from INTERPRO.
Probab=23.87 E-value=1.2e+02 Score=20.28 Aligned_cols=39 Identities=10% Similarity=0.002 Sum_probs=30.9
Q ss_pred hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE
Q 033552 21 LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v 60 (117)
+.-++-+..+.+|..|..- .+...+....++++|..+-.
T Consensus 47 ~~~~~~~~~~~ii~ND~e~-~i~~~~~~a~~~y~I~~i~w 85 (88)
T PF08862_consen 47 KRNRKSNSKFYIILNDSEK-PISEDIINALEQYNIKPIPW 85 (88)
T ss_pred hhccCCCceEEEEECCCCC-ccCHHHHHHHHHCCCceecC
Confidence 4455666889999999874 57789999999999987654
No 269
>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=23.69 E-value=93 Score=24.41 Aligned_cols=68 Identities=19% Similarity=0.305 Sum_probs=37.0
Q ss_pred CCCCcchheeHHHHhhhCCCCEEEECCH------hHHHhhcCCCcceEEEEEeecCCCCccc--hHHHHhhHHHHHHHHH
Q 033552 36 NISPIDVITHVPILCEESDIPYIYVASK------EDLANAGATKRPTCCVLVLTKPTKGELG--QEEQDKLKADYTLVVE 107 (117)
Q Consensus 36 Dasp~~i~~~i~~lce~~~IP~i~v~tK------~eLG~A~G~~~~~svv~I~~~~~~~~~~--~~e~~~~~~~~~e~~~ 107 (117)
..+|.+ +..+..+.++++|+++++..- +.|.+..|.+ ++.+ + |...... .++...|-+++.+..+
T Consensus 203 eps~~~-l~~l~~~ik~~~v~~if~e~~~~~~~~~~la~~~g~~----v~~l-d-~l~~~~~~~~~~~~~y~~~m~~n~~ 275 (282)
T cd01017 203 EPSPKQ-LAELVEFVKKSDVKYIFFEENASSKIAETLAKETGAK----LLVL-N-PLETLTKEEIDDGKDYFSLMKENLE 275 (282)
T ss_pred CCCHHH-HHHHHHHHHHcCCCEEEEeCCCChHHHHHHHHHcCCc----EEEe-c-cccccchhcccccCcHHHHHHHHHH
Confidence 334444 677888899999999998533 3455555543 2222 2 2211100 0112467777776665
Q ss_pred HHH
Q 033552 108 DVK 110 (117)
Q Consensus 108 ~~~ 110 (117)
.+.
T Consensus 276 ~l~ 278 (282)
T cd01017 276 TLK 278 (282)
T ss_pred HHH
Confidence 554
No 270
>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=23.68 E-value=1.2e+02 Score=20.97 Aligned_cols=47 Identities=11% Similarity=0.047 Sum_probs=28.0
Q ss_pred hhhhhcCCccEEEEeCCCCC--cchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 20 PLPLLFHECRLCVIAGNISP--IDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp--~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
++.+.++ +.++++--|++. ...-..+.......+.|++.+.+|.+|-
T Consensus 6 ~~~i~~~-aD~vl~V~D~~~~~~~~~~~l~~~~~~~~~p~iiv~NK~Dl~ 54 (156)
T cd01859 6 VRRIIKE-SDVVLEVLDARDPELTRSRKLERYVLELGKKLLIVLNKADLV 54 (156)
T ss_pred HHHHHhh-CCEEEEEeeCCCCcccCCHHHHHHHHhCCCcEEEEEEhHHhC
Confidence 3444443 455555556642 1112234455566789999999999983
No 271
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=23.65 E-value=83 Score=27.63 Aligned_cols=41 Identities=15% Similarity=0.187 Sum_probs=34.2
Q ss_pred hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 21 LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+.+++...+..++|.|+.-..=+..+..++++.+||+.-..
T Consensus 122 ~~lkk~~~kvllVaaD~~RpAA~eQL~~La~q~~v~~f~~~ 162 (451)
T COG0541 122 KYLKKKGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSG 162 (451)
T ss_pred HHHHHcCCceEEEecccCChHHHHHHHHHHHHcCCceecCC
Confidence 35677778899999999843459999999999999998874
No 272
>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=23.56 E-value=1.2e+02 Score=23.73 Aligned_cols=43 Identities=9% Similarity=0.042 Sum_probs=27.5
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
.+.++.|+++.++.||.-.-.++. .. ..++++.|+|++.+...
T Consensus 210 ~~l~~~ik~~~v~~if~e~~~~~~-~~---~~la~~~g~~v~~ld~l 252 (282)
T cd01017 210 AELVEFVKKSDVKYIFFEENASSK-IA---ETLAKETGAKLLVLNPL 252 (282)
T ss_pred HHHHHHHHHcCCCEEEEeCCCChH-HH---HHHHHHcCCcEEEeccc
Confidence 344566777778877777666652 23 33677778887766543
No 273
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=23.55 E-value=2.9e+02 Score=19.99 Aligned_cols=64 Identities=9% Similarity=-0.048 Sum_probs=43.3
Q ss_pred hhhhcCCccEEEEeCCCCC----cchheeHHHHhhhCC---CCE--EEECCHhHHHhhcCCC-cceEEEEEeecC
Q 033552 21 LPLLFHECRLCVIAGNISP----IDVITHVPILCEESD---IPY--IYVASKEDLANAGATK-RPTCCVLVLTKP 85 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp----~~i~~~i~~lce~~~---IP~--i~v~tK~eLG~A~G~~-~~~svv~I~~~~ 85 (117)
..+..+...+||+++|... .++--=|++++++++ +-+ +.+..-.+|..-.|.. .|+ .++..+|.
T Consensus 29 ~~~~~~~~~vl~~~gdp~r~~E~~D~avvleELa~e~~~~~v~~akVDiD~~~~LA~~fgV~siPT-Ll~FkdGk 102 (132)
T PRK11509 29 DWLTQAPDGVVLLSSDPKRTPEVSDNPVMIGELLREFPDYTWQVAIADLEQSEAIGDRFGVFRFPA-TLVFTGGN 102 (132)
T ss_pred HHHhCCCcEEEEeCCCCCcCCccccHHHHHHHHHHHhcCCceEEEEEECCCCHHHHHHcCCccCCE-EEEEECCE
Confidence 3445666899999999763 456667888999975 334 4445778899999976 344 34444433
No 274
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=23.45 E-value=64 Score=27.00 Aligned_cols=36 Identities=25% Similarity=0.206 Sum_probs=24.6
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
+++|.=.+ .+-.+|.+.|+++|||++.-. -|.+++=
T Consensus 281 ~VvAKG~d--~~A~~Ir~iA~e~~VPiven~---pLARaLY 316 (349)
T PRK12721 281 RVLEKGKD--AQALHIVKLAERNGIPVVENI---PLARALF 316 (349)
T ss_pred EEEEEeCc--HHHHHHHHHHHHcCCCEEeCH---HHHHHHH
Confidence 34454444 367889999999999997643 4555544
No 275
>PRK08733 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=23.43 E-value=2.2e+02 Score=22.62 Aligned_cols=46 Identities=13% Similarity=-0.068 Sum_probs=30.4
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCc--c-hh-----------eeHHHHhhhCCCCEEEECC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPI--D-VI-----------THVPILCEESDIPYIYVAS 62 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~--~-i~-----------~~i~~lce~~~IP~i~v~t 62 (117)
|+++.+++|++|. +|.+..|-++. + +. .-...++...|.|++.+..
T Consensus 183 ~~r~~~kaLk~g~--~v~il~Dq~~~~~~gv~v~FfG~~a~t~~g~a~LA~~~~apvvp~~~ 242 (306)
T PRK08733 183 DLRATIKHLKRGG--FLWYAPDQDMRGKDTVFVPFFGHPASTITATHQLARLTGCAVVPYFH 242 (306)
T ss_pred cHHHHHHHHhCCC--eEEEeCCCCCCCCCcEEeCCCCCchhHHHHHHHHHHHhCCeEEEEEE
Confidence 6788889999884 78888886641 1 11 1123567777777776665
No 276
>PRK00093 GTP-binding protein Der; Reviewed
Probab=23.31 E-value=75 Score=26.23 Aligned_cols=48 Identities=21% Similarity=0.217 Sum_probs=29.8
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
+..+++.-.+-++++.........-..+..+.+..++|++.+.+|.++
T Consensus 74 ~~~~~~~ad~il~vvd~~~~~~~~~~~~~~~l~~~~~piilv~NK~D~ 121 (435)
T PRK00093 74 AELAIEEADVILFVVDGRAGLTPADEEIAKILRKSNKPVILVVNKVDG 121 (435)
T ss_pred HHHHHHhCCEEEEEEECCCCCCHHHHHHHHHHHHcCCcEEEEEECccC
Confidence 444555555444444443322222345667778889999999998875
No 277
>PRK05646 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=23.29 E-value=2.4e+02 Score=22.39 Aligned_cols=23 Identities=13% Similarity=-0.234 Sum_probs=18.8
Q ss_pred eeecchhhhhcCCccEEEEeCCCCC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISP 39 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp 39 (117)
|+++.+++|++|+ +|.+..|-++
T Consensus 182 ~~r~ilk~Lk~g~--~v~il~Dq~~ 204 (310)
T PRK05646 182 DVRGMLKLLRAGR--AIWYAPDQDY 204 (310)
T ss_pred hHHHHHHHHhCCC--eEEEeCCCCC
Confidence 7888999999885 7888888664
No 278
>COG0352 ThiE Thiamine monophosphate synthase [Coenzyme metabolism]
Probab=23.29 E-value=69 Score=24.99 Aligned_cols=56 Identities=18% Similarity=0.163 Sum_probs=42.0
Q ss_pred eecchhhhhcCCccEEEEeCCCCCc---chheeHHHHhhhCCCCEEEECCHhHHHhhcCC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPI---DVITHVPILCEESDIPYIYVASKEDLANAGAT 72 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~---~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~ 72 (117)
..+..++++.|-.-+.+-..|.+.. .....+..+|..+++|++. .+.-+|-.+.|-
T Consensus 24 ~~~ve~al~~Gv~~vQlR~K~~~~~~~~~~a~~~~~lc~~~~v~liI-Nd~~dlA~~~~A 82 (211)
T COG0352 24 LEWVEAALKGGVTAVQLREKDLSDEEYLALAEKLRALCQKYGVPLII-NDRVDLALAVGA 82 (211)
T ss_pred HHHHHHHHhCCCeEEEEecCCCChHHHHHHHHHHHHHHHHhCCeEEe-cCcHHHHHhCCC
Confidence 5777888999988888889998873 3456899999999999865 445555554443
No 279
>PRK12736 elongation factor Tu; Reviewed
Probab=23.28 E-value=63 Score=26.84 Aligned_cols=50 Identities=20% Similarity=0.248 Sum_probs=28.3
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCE-EEECCHhHH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPY-IYVASKEDL 66 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~-i~v~tK~eL 66 (117)
++++..+..-.+-++++..+-....-...+..++...++|. +.+-+|-++
T Consensus 90 ~~~~~~~~~~d~~llVvd~~~g~~~~t~~~~~~~~~~g~~~~IvviNK~D~ 140 (394)
T PRK12736 90 KNMITGAAQMDGAILVVAATDGPMPQTREHILLARQVGVPYLVVFLNKVDL 140 (394)
T ss_pred HHHHHHHhhCCEEEEEEECCCCCchhHHHHHHHHHHcCCCEEEEEEEecCC
Confidence 44555555555667777666432222333445788899995 454555443
No 280
>cd00861 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only.
Probab=23.18 E-value=1.2e+02 Score=19.06 Aligned_cols=45 Identities=16% Similarity=0.050 Sum_probs=27.2
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
...|++......+ |..+..+.+++. .|+..|+|++.+-..+|+..
T Consensus 24 a~~Lr~~g~~v~~---d~~~~~l~k~i~-~a~~~g~~~~iiiG~~e~~~ 68 (94)
T cd00861 24 YAELQAAGVDVLL---DDRNERPGVKFA-DADLIGIPYRIVVGKKSAAE 68 (94)
T ss_pred HHHHHHCCCEEEE---ECCCCCcccchh-HHHhcCCCEEEEECCchhhC
Confidence 3455554333333 333334444544 67899999999888888753
No 281
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=23.15 E-value=75 Score=20.46 Aligned_cols=45 Identities=9% Similarity=0.069 Sum_probs=31.1
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+...+..+......++++-+.+.. -.=.....+|++++||++..+
T Consensus 20 i~~~Ld~~~~~~~~~~lvhGga~~-GaD~iA~~wA~~~gv~~~~~~ 64 (71)
T PF10686_consen 20 IWAALDKVHARHPDMVLVHGGAPK-GADRIAARWARERGVPVIRFP 64 (71)
T ss_pred HHHHHHHHHHhCCCEEEEECCCCC-CHHHHHHHHHHHCCCeeEEeC
Confidence 345667777777888888888722 112445569999999998654
No 282
>PRK03980 flap endonuclease-1; Provisional
Probab=23.11 E-value=1.2e+02 Score=24.54 Aligned_cols=36 Identities=17% Similarity=0.331 Sum_probs=27.7
Q ss_pred CCCCCcchheeHHHHhhhCCCCEEEECCH--hHHHhhcC
Q 033552 35 GNISPIDVITHVPILCEESDIPYIYVASK--EDLANAGA 71 (117)
Q Consensus 35 ~Dasp~~i~~~i~~lce~~~IP~i~v~tK--~eLG~A~G 71 (117)
.++++ +.+..+..+++..||||+..+.- ++++..+-
T Consensus 78 ~~vt~-~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~ 115 (292)
T PRK03980 78 SRLTD-EIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAK 115 (292)
T ss_pred ccCCH-HHHHHHHHHHHHCCCCEEecCchHHHHHHHHHH
Confidence 34554 46888899999999999999986 46676663
No 283
>TIGR00461 gcvP glycine dehydrogenase (decarboxylating). This apparently ubiquitous enzyme is found in bacterial, mammalian and plant sources. The enzyme catalyzes the reaction: GLYCINE + LIPOYLPROTEIN = S-AMINOMETHYL-DIHYDROLIPOYLPROTEIN + CO2. It is part of the glycine decarboxylase multienzyme complex (GDC) consisting of four proteins P, H, L and T. Active site in E.coli is located as the (K) residues at position 713 of the SEED alignment.
Probab=23.09 E-value=3.3e+02 Score=26.15 Aligned_cols=59 Identities=17% Similarity=0.138 Sum_probs=40.0
Q ss_pred hcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCCCcceEEEEEeecCCCC
Q 033552 24 LFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKG 88 (117)
Q Consensus 24 ~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~~~~svv~I~~~~~~~ 88 (117)
.+++..-|+++.++.|. ...-+...++..|+.++.++ .++|-.++ .+++++++...+-+
T Consensus 149 ~~~~~~~vlv~~~~hP~-~~~v~~t~a~~~g~~v~~~~-~~~l~~~~----~~~~v~~q~Pn~~G 207 (939)
T TIGR00461 149 SKKKANKFFVAKDLHPQ-TKSVLHTRAKPFGIEVIVVD-CSDIKKAV----DVFGCLLQYPATDG 207 (939)
T ss_pred hcCCCCEEEECCCCCcc-hHHHHHHHHHhcCcEEEEEc-HHHHhhcC----CEEEEEEECCCCCe
Confidence 34455679999999995 46677778899999999885 45665554 24555554423344
No 284
>PRK08762 molybdopterin biosynthesis protein MoeB; Validated
Probab=23.06 E-value=68 Score=26.48 Aligned_cols=36 Identities=17% Similarity=0.179 Sum_probs=28.8
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHh
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKE 64 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~ 64 (117)
+..+||-|.|.-+ ....+.++|..++||+++.....
T Consensus 225 ~~D~Vv~~~d~~~--~r~~ln~~~~~~~ip~i~~~~~g 260 (376)
T PRK08762 225 DVDVVVDGADNFP--TRYLLNDACVKLGKPLVYGAVFR 260 (376)
T ss_pred CCCEEEECCCCHH--HHHHHHHHHHHcCCCEEEEEecc
Confidence 4778998988754 36678999999999999986543
No 285
>cd03010 TlpA_like_DsbE TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c.
Probab=23.06 E-value=1.7e+02 Score=19.45 Aligned_cols=28 Identities=7% Similarity=-0.002 Sum_probs=18.1
Q ss_pred HHHHhhhCCCCE--EEECCHhHHHhhcCCC
Q 033552 46 VPILCEESDIPY--IYVASKEDLANAGATK 73 (117)
Q Consensus 46 i~~lce~~~IP~--i~v~tK~eLG~A~G~~ 73 (117)
+..+++.+++|+ +......++.+..|..
T Consensus 70 ~~~~~~~~~~~~~~~~~D~~~~~~~~~~v~ 99 (127)
T cd03010 70 ALAWLARHGNPYAAVGFDPDGRVGIDLGVY 99 (127)
T ss_pred HHHHHHhcCCCCceEEECCcchHHHhcCCC
Confidence 344566677765 4456677788887765
No 286
>cd00636 TroA-like Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between two globular domains linked by a single helix. Many of these proteins also possess a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). The TroA-like proteins differ in their fold and ligand-binding mechanism from the PBPI and PBPII proteins, but are structurally similar, however, to the beta-subunit of the nitrogenase molybdenum-iron protein MoFe. Most TroA-like proteins are encoded by ABC-type operons and appear to function as periplasmic components of ABC transporters in metal ion uptake.
Probab=23.05 E-value=2.1e+02 Score=18.26 Aligned_cols=41 Identities=12% Similarity=-0.012 Sum_probs=26.9
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
-++..|.+-+.-+||...-..+ . .....++.++|++.+...
T Consensus 52 ~~~E~l~~l~pDlvi~~~~~~~-~----~~~~l~~~~i~~~~~~~~ 92 (148)
T cd00636 52 PNLEKIAALKPDLIIANGSGLE-A----WLDKLSKIAIPVVVVDEA 92 (148)
T ss_pred CCHHHHhccCCCEEEEecccch-h----HHHHHHHhCCCEEEECCC
Confidence 4566777778888887664332 2 444556777899887653
No 287
>TIGR02343 chap_CCT_epsi T-complex protein 1, epsilon 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 epsilon chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=23.00 E-value=76 Score=27.62 Aligned_cols=43 Identities=12% Similarity=0.096 Sum_probs=30.8
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
-++.|.+..+.+||++.++++. ..+ ++.++||..+...++.+|
T Consensus 283 ~l~~i~~~g~~lvi~~~~I~~~--al~---~L~~~~i~~v~~~~~~~l 325 (532)
T TIGR02343 283 MIDDIKKSGANIVICQWGFDDE--ANH---LLLQNDLPAVRWVGGHEL 325 (532)
T ss_pred HHHHHHHcCCCEEEeCCCccHH--HHH---HHHHCCcEEEEcCCHHHH
Confidence 3666777778999999999973 333 667778877776655444
No 288
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=22.92 E-value=1.1e+02 Score=20.74 Aligned_cols=34 Identities=12% Similarity=-0.018 Sum_probs=17.4
Q ss_pred ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 28 ~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
.+.+|+=+|..+..-.......+...+|++..+.
T Consensus 100 ~~~iv~iTDG~~~~~~~~~~~~~~~~~i~i~~v~ 133 (172)
T PF13519_consen 100 RRAIVLITDGEDNSSDIEAAKALKQQGITIYTVG 133 (172)
T ss_dssp EEEEEEEES-TTHCHHHHHHHHHHCTTEEEEEEE
T ss_pred ceEEEEecCCCCCcchhHHHHHHHHcCCeEEEEE
Confidence 4566666776653212223444556777765554
No 289
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=22.56 E-value=62 Score=22.25 Aligned_cols=19 Identities=21% Similarity=0.177 Sum_probs=8.3
Q ss_pred HhhhCCCCEEEECCHhHHH
Q 033552 49 LCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 49 lce~~~IP~i~v~tK~eLG 67 (117)
.++...+.++.+.+-+.||
T Consensus 60 ~~~~g~~~~ivv~~~~Rl~ 78 (148)
T smart00857 60 DLRAGDIDVLVVYKLDRLG 78 (148)
T ss_pred HHHcCCCCEEEEeccchhh
Confidence 3333444444444444444
No 290
>cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta
Probab=22.50 E-value=70 Score=25.31 Aligned_cols=51 Identities=14% Similarity=0.067 Sum_probs=34.8
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
.++.++++.-.+-++++...-....-...+-..+..+++|++.+-+|-++-
T Consensus 79 ~~~~~~l~~aD~ailVVDa~~g~~~~t~~~~~~~~~~~~p~ivviNK~D~~ 129 (270)
T cd01886 79 IEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQADRYNVPRIAFVNKMDRT 129 (270)
T ss_pred HHHHHHHHHcCEEEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECCCCC
Confidence 345667777777777775544433334566677888999999888777653
No 291
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs.
Probab=22.40 E-value=69 Score=26.67 Aligned_cols=37 Identities=22% Similarity=0.172 Sum_probs=25.8
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCC
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGAT 72 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~ 72 (117)
+++|.=++. +..+|.+.|+++|||++.-. -|.+++=.
T Consensus 280 ~VvAKG~d~--~A~~Ir~iA~e~~VPiven~---pLAR~Ly~ 316 (342)
T TIGR01404 280 LIICKGTDA--QALAVRAYAEEAGIPVVRDI---PLARQLYR 316 (342)
T ss_pred EEEEeeCcH--HHHHHHHHHHHcCCCEeeCH---HHHHHHHH
Confidence 445555553 67899999999999997654 45555543
No 292
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=22.28 E-value=1.7e+02 Score=20.96 Aligned_cols=41 Identities=17% Similarity=0.045 Sum_probs=23.5
Q ss_pred chhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 19 DPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
.++.+..+.+.-+++....++ ... ...+.+.+||++.+.+.
T Consensus 47 ~~~~~~~~~~d~iii~~~~~~-~~~---~~~~~~~~ipvv~~~~~ 87 (264)
T cd06267 47 ALELLLSRRVDGIILAPSRLD-DEL---LEELAALGIPVVLVDRP 87 (264)
T ss_pred HHHHHHHcCcCEEEEecCCcc-hHH---HHHHHHcCCCEEEeccc
Confidence 344455555555555443332 222 44678899999888654
No 293
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=22.01 E-value=60 Score=26.41 Aligned_cols=67 Identities=22% Similarity=0.184 Sum_probs=47.9
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEE---------------EECCHhHHHhhcCCCcceEEE
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYI---------------YVASKEDLANAGATKRPTCCV 79 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i---------------~v~tK~eLG~A~G~~~~~svv 79 (117)
|.-.-.+.|+...+.+||=|+--....+-......|++.||||+ .|.|.+|+.++.++--.+ |
T Consensus 54 ~~e~l~~~l~e~~i~llIDATHPyAa~iS~Na~~aake~gipy~r~eRP~~~~~gd~~~~V~d~~ea~~~~~~~~~r--V 131 (257)
T COG2099 54 GAEGLAAFLREEGIDLLIDATHPYAARISQNAARAAKETGIPYLRLERPPWAPNGDNWIEVADIEEAAEAAKQLGRR--V 131 (257)
T ss_pred CHHHHHHHHHHcCCCEEEECCChHHHHHHHHHHHHHHHhCCcEEEEECCccccCCCceEEecCHHHHHHHHhccCCc--E
Confidence 34455677889999999955543335677788899999999985 567888888887765333 3
Q ss_pred EEee
Q 033552 80 LVLT 83 (117)
Q Consensus 80 ~I~~ 83 (117)
+++.
T Consensus 132 flt~ 135 (257)
T COG2099 132 FLTT 135 (257)
T ss_pred EEec
Confidence 4444
No 294
>PRK06298 type III secretion system protein; Validated
Probab=21.98 E-value=68 Score=26.97 Aligned_cols=37 Identities=19% Similarity=0.146 Sum_probs=26.2
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCC
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGAT 72 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~ 72 (117)
+++|.=.+. +-.+|.+.|+++|||++.-. .|-+++=.
T Consensus 282 ~VvAKG~d~--~A~~Ir~iA~e~~VPiven~---pLARaLy~ 318 (356)
T PRK06298 282 WIIAMGINL--RAKRIIAEAEKYGVPIMRNV---PLAHQLLD 318 (356)
T ss_pred EEEEeeCcH--HHHHHHHHHHHcCCCEEeCH---HHHHHHHH
Confidence 445555553 67899999999999997643 56666543
No 295
>cd01885 EF2 EF2 (for archaea and eukarya). Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Seco
Probab=21.88 E-value=90 Score=24.04 Aligned_cols=49 Identities=14% Similarity=0.020 Sum_probs=30.9
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHH
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDL 66 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eL 66 (117)
++..+++...+-++++...-.+..-...+...+...++|.+.+.+|-++
T Consensus 89 ~~~~~l~~aD~~ilVvD~~~g~~~~t~~~l~~~~~~~~p~ilviNKiD~ 137 (222)
T cd01885 89 EVTAALRLCDGALVVVDAVEGVCVQTETVLRQALKERVKPVLVINKIDR 137 (222)
T ss_pred HHHHHHHhcCeeEEEEECCCCCCHHHHHHHHHHHHcCCCEEEEEECCCc
Confidence 5567777777777777555433222334445566677888888877765
No 296
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.87 E-value=1.1e+02 Score=22.69 Aligned_cols=44 Identities=11% Similarity=-0.041 Sum_probs=25.0
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
.+.++.+....+.-+|+.. +++.. .......+.++|||++.+.+
T Consensus 47 ~~~i~~l~~~~vdgiii~~-~~~~~-~~~~l~~~~~~~ipvV~~~~ 90 (271)
T cd06312 47 ARLIEAAIAAKPDGIVVTI-PDPDA-LDPAIKRAVAAGIPVISFNA 90 (271)
T ss_pred HHHHHHHHHhCCCEEEEeC-CChHH-hHHHHHHHHHCCCeEEEeCC
Confidence 3445555555666555544 22212 22344556788999999964
No 297
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=21.84 E-value=1.4e+02 Score=22.15 Aligned_cols=41 Identities=20% Similarity=0.279 Sum_probs=22.5
Q ss_pred chhhhhcCCccEEEEe-CCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 19 DPLPLLFHECRLCVIA-GNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 19 t~kaL~kg~~~LViLA-~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
.++.+....+.-+|+. .| +.. ...+...+.+++||++.+.+
T Consensus 47 ~i~~~~~~~~Dgiii~~~~--~~~-~~~~i~~~~~~~iPvV~~~~ 88 (282)
T cd06318 47 DVEDLLTRGVNVLIINPVD--PEG-LVPAVAAAKAAGVPVVVVDS 88 (282)
T ss_pred HHHHHHHcCCCEEEEecCC--ccc-hHHHHHHHHHCCCCEEEecC
Confidence 3455555555444554 33 222 22334456678888888764
No 298
>cd04102 RabL3 RabL3 (Rab-like3) subfamily. RabL3s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown.
Probab=21.73 E-value=56 Score=24.68 Aligned_cols=42 Identities=12% Similarity=0.197 Sum_probs=27.8
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhh-------------------------CCCCEEEECCHhHHHh
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEE-------------------------SDIPYIYVASKEDLAN 68 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~-------------------------~~IP~i~v~tK~eLG~ 68 (117)
.+..+|+--|++..+-...+..|.++ .++|++.|++|.+|-.
T Consensus 77 ~ad~iIlVyDvtn~~Sf~~l~~W~~ei~~~~~~~~~~~~~~~~~~~~~~~~~~~PiilVGnK~Dl~~ 143 (202)
T cd04102 77 QVNGIILVHDLTNRKSSQNLQRWSLEALNKDTFPTGLLVTNGDYDSEQFGGNQIPLLVIGTKLDQIP 143 (202)
T ss_pred cCCEEEEEEECcChHHHHHHHHHHHHHHHhhccccccccccccccccccCCCCceEEEEEECccchh
Confidence 36677777777643334445444222 4799999999999843
No 299
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=21.70 E-value=76 Score=25.19 Aligned_cols=41 Identities=22% Similarity=0.349 Sum_probs=28.6
Q ss_pred hheeHHHHhhhCCCCEEEECCH------hHHHhhcCCCcceEEEEEee
Q 033552 42 VITHVPILCEESDIPYIYVASK------EDLANAGATKRPTCCVLVLT 83 (117)
Q Consensus 42 i~~~i~~lce~~~IP~i~v~tK------~eLG~A~G~~~~~svv~I~~ 83 (117)
-.+.+..||++++||++.+.+- .-|-+..|+++ +.++=|.+
T Consensus 77 ~fKef~e~ike~di~fiVvSsGm~~fI~~lfe~ivgke~-i~~idi~s 123 (220)
T COG4359 77 GFKEFVEWIKEHDIPFIVVSSGMDPFIYPLFEGIVGKER-IYCIDIVS 123 (220)
T ss_pred cHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHhhccccc-eeeeEEee
Confidence 3677788999999999998763 34566677774 44444444
No 300
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=21.60 E-value=57 Score=22.71 Aligned_cols=40 Identities=13% Similarity=0.086 Sum_probs=25.8
Q ss_pred CCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 26 g~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
+++-.|+ |+-.. .+..+|...+++++||... -.+|=+.++
T Consensus 20 ~~AP~vv-A~G~G--~iAe~II~~Ake~~Vpi~e---dp~Lv~~L~ 59 (92)
T COG2257 20 DKAPKVV-ASGKG--EIAEKIIEKAKEHGVPIQE---DPLLVELLL 59 (92)
T ss_pred CCCCEEE-eecch--HHHHHHHHHHHHcCCCccc---CHHHHHHHH
Confidence 3444444 33333 3788999999999999954 445555544
No 301
>PLN02331 phosphoribosylglycinamide formyltransferase
Probab=21.56 E-value=1.7e+02 Score=22.52 Aligned_cols=43 Identities=14% Similarity=-0.011 Sum_probs=27.2
Q ss_pred ecchhhhhcCC--ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCH
Q 033552 17 VNDPLPLLFHE--CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASK 63 (117)
Q Consensus 17 kqt~kaL~kg~--~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK 63 (117)
...++++++|+ +.++++-+|-. ......+|+++|||+.....+
T Consensus 14 ~al~~~~~~~~l~~~i~~visn~~----~~~~~~~A~~~gIp~~~~~~~ 58 (207)
T PLN02331 14 RAIHDACLDGRVNGDVVVVVTNKP----GCGGAEYARENGIPVLVYPKT 58 (207)
T ss_pred HHHHHHHHcCCCCeEEEEEEEeCC----CChHHHHHHHhCCCEEEeccc
Confidence 34567778886 45555544432 123456999999999876543
No 302
>PF00362 Integrin_beta: Integrin, beta chain; InterPro: IPR002369 Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [, ]. The integrin receptors are composed of alpha and beta subunit heterodimers. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus. Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits []. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans []. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule []. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another. The structure of unliganded alphaV beta3 showed the molecule to be folded, with the head bent over towards the C termini of the legs which would normally be inserted into the membrane []. The head comprises a beta propeller domain at the end terminus of the alphaV subunit and an I/A domain inserted into a loop on the top of the hybrid domain in the beta subunit. The I/A domain consists of a Rossman fold with a core of beta parallel sheets surrounded by amphipathic alpha helices. Integrins are important therapeutic targets in conditions such as atherosclerosis, thrombosis, cancer and asthma []. At the N terminus of the beta subunit is a cysteine-containing domain reminiscent of that found in presenillins and semaphorins, which has hence been termed the PSI domain. C-terminal to the PSI domain is an A-domain, which has been predicted to adopt a Rossmann fold similar to that of the alpha subunit, but with additional loops between the second and third beta strands []. The murine gene Pactolus shares significant similarity with the beta subunit [], but lacks either one or both of the inserted loops. The C-terminal portion of the beta subunit extracellular domain contains an internally disulphide-bonded cysteine-rich region, while the intracellular tail contains putative sites of interaction with a variety of intracellular signalling and cytoskeletal proteins, such as focal adhesion kinase and alpha-actinin respectively []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first 20 amino acids of the beta-subunit cytoplasmic domain are also alpha helical, but the final 25 residues are disordered and, apart from a turn that follows a conserved NPxY motif, appear to lack defined structure, suggesting that this is adopted on effector binding. The two membrane-proximal helices mediate the link between the subunits via a series of hydrophobic and electrostatic contacts. This entry represents the N-terminal portion of the extracellular region of integrin beta subunits.; GO: 0005488 binding, 0007155 cell adhesion, 0007160 cell-matrix adhesion; PDB: 3VI4_B 3VI3_B 2VDQ_B 3IJE_B 1M1X_B 2VDR_B 3NIF_B 3NID_D 1TYE_F 2Q6W_F ....
Probab=21.55 E-value=58 Score=27.97 Aligned_cols=15 Identities=20% Similarity=0.142 Sum_probs=10.4
Q ss_pred hcCCccEEEEeCCCC
Q 033552 24 LFHECRLCVIAGNIS 38 (117)
Q Consensus 24 ~kg~~~LViLA~Das 38 (117)
|.+.-+|||++.|+.
T Consensus 229 r~~a~~llv~~TD~~ 243 (426)
T PF00362_consen 229 RNEARRLLVFSTDAG 243 (426)
T ss_dssp -STSEEEEEEEESS-
T ss_pred ccCceEEEEEEcCCc
Confidence 455678899988876
No 303
>PLN03126 Elongation factor Tu; Provisional
Probab=21.52 E-value=82 Score=27.34 Aligned_cols=50 Identities=16% Similarity=0.215 Sum_probs=30.7
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCC-EEEECCHhHH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIP-YIYVASKEDL 66 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP-~i~v~tK~eL 66 (117)
++++..+..-..-++++..+-.+..-......++...++| ++.+-+|-+|
T Consensus 159 ~~~~~g~~~aD~ailVVda~~G~~~qt~e~~~~~~~~gi~~iIvvvNK~Dl 209 (478)
T PLN03126 159 KNMITGAAQMDGAILVVSGADGPMPQTKEHILLAKQVGVPNMVVFLNKQDQ 209 (478)
T ss_pred HHHHHHHhhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCeEEEEEecccc
Confidence 4566667666677888876644322233444578899999 4454555443
No 304
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=21.51 E-value=1.2e+02 Score=21.68 Aligned_cols=33 Identities=12% Similarity=-0.129 Sum_probs=21.9
Q ss_pred chhhhhcCCccEEEEeCCCCC--cchheeHHHHhhh
Q 033552 19 DPLPLLFHECRLCVIAGNISP--IDVITHVPILCEE 52 (117)
Q Consensus 19 t~kaL~kg~~~LViLA~Dasp--~~i~~~i~~lce~ 52 (117)
.++.+.+ ++.-||+|.|++. ..|..++...|..
T Consensus 91 ~ik~l~~-~ad~ii~atD~DrEGE~I~~~i~~~~~~ 125 (151)
T cd03362 91 VLKKLAK-RADEIVIATDADREGELIGREILEYAKC 125 (151)
T ss_pred HHHHHHh-CCCeEEEccCCCccccHHHHHHHHHhCC
Confidence 3444444 3688999999995 3455566666664
No 305
>cd02004 TPP_BZL_OCoD_HPCL Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL cleaves the acyloin linkage of benzoin producing 2 molecules of benzaldehyde and enabling the Pseudomonas to grow on benzoin as the sole carbon and energy source. OCoD has a role in the detoxification of oxalate, catalyzing the decarboxylation of oxalyl-CoA to formate. 2-HPCL is a peroxisomal enzyme which plays a role in the alpha-oxidation of 3-methyl-branched fatty acids, catalyzing the cleavage of 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde. All these enzymes depend on Mg2+ and TPP for activity.
Probab=21.50 E-value=1.2e+02 Score=21.69 Aligned_cols=25 Identities=20% Similarity=0.060 Sum_probs=14.0
Q ss_pred HHHHhhhCCCCEEEECCHhHHHhhc
Q 033552 46 VPILCEESDIPYIYVASKEDLANAG 70 (117)
Q Consensus 46 i~~lce~~~IP~i~v~tK~eLG~A~ 70 (117)
+..+++.+|+++..+.+.++|..++
T Consensus 131 ~~~la~a~G~~~~~v~~~~el~~al 155 (172)
T cd02004 131 YDLVAEAFGGKGELVTTPEELKPAL 155 (172)
T ss_pred HHHHHHHCCCeEEEECCHHHHHHHH
Confidence 4445555666666666655555443
No 306
>cd05125 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
Probab=21.44 E-value=3e+02 Score=19.28 Aligned_cols=55 Identities=13% Similarity=0.110 Sum_probs=39.4
Q ss_pred CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhh---cCCCcceEEEEE
Q 033552 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANA---GATKRPTCCVLV 81 (117)
Q Consensus 27 ~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A---~G~~~~~svv~I 81 (117)
+..+|+|........+-..+....+++||.+....|.+....- .+-.|.+++++|
T Consensus 54 ~peiliiGtG~~~~~~~~~~~~~l~~~gi~vevm~T~~AcrtyN~L~~EgR~VaaaLi 111 (114)
T cd05125 54 RPEILVIGTGRKSRPLSPELRKYFKKLGIAVEVVDTRNACATFNFLAEEGRRVAAALI 111 (114)
T ss_pred CCCEEEEccCCCCCcCCHHHHHHHHHcCCEEEEECHHHHHHHHHHHHhCCCeEEEEEe
Confidence 5679999988875445556677888999999999998877733 333454555544
No 307
>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=21.32 E-value=58 Score=22.12 Aligned_cols=40 Identities=23% Similarity=0.331 Sum_probs=22.8
Q ss_pred cchhhhhcCCccEEEEeCCC-CCcchheeHHHHhhhCCCCEEEECCHhH
Q 033552 18 NDPLPLLFHECRLCVIAGNI-SPIDVITHVPILCEESDIPYIYVASKED 65 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Da-sp~~i~~~i~~lce~~~IP~i~v~tK~e 65 (117)
+.++.+ +++.+||+++|. ++.++...+..+ |+..+..=.+
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 556666 459999999999 443444443222 7777764333
No 308
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=21.21 E-value=71 Score=26.85 Aligned_cols=37 Identities=24% Similarity=0.208 Sum_probs=25.6
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCC
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGAT 72 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~ 72 (117)
+++|.=.+ .+-.+|.+.|+++|||++.-. .|-+++=.
T Consensus 290 ~VvAKG~d--~~A~~Ir~~A~e~~VPiven~---pLARaLy~ 326 (358)
T PRK13109 290 LVVAKGQD--LIALKIREIAEENGIPVIEDK---PLARSLYD 326 (358)
T ss_pred EEEEEeCc--HHHHHHHHHHHHcCCCEEeCH---HHHHHHHH
Confidence 34455444 367889999999999997654 45566544
No 309
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=21.17 E-value=1e+02 Score=26.11 Aligned_cols=45 Identities=11% Similarity=0.070 Sum_probs=28.3
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcch--------heeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDV--------ITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i--------~~~i~~lce~~~IP~i~v~ 61 (117)
.+.++.+++.++.+||||+|...... ...+...-.+.++|++.+.
T Consensus 29 ~~l~~~i~~~~~D~viIaGDifD~~~p~~~a~~~~~~~l~~L~~~~~~v~~I~ 81 (407)
T PRK10966 29 DWLLEQVQEHQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLVVLA 81 (407)
T ss_pred HHHHHHHHhcCCCEEEECCccccCCCCcHHHHHHHHHHHHHHHhcCCcEEEEc
Confidence 34566677889999999999984211 1111112234589998874
No 310
>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=21.15 E-value=1.1e+02 Score=20.69 Aligned_cols=40 Identities=13% Similarity=0.191 Sum_probs=24.1
Q ss_pred ccEEEEeCCCCCc--chheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 28 CRLCVIAGNISPI--DVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 28 ~~LViLA~Dasp~--~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
+.++++--|++.. .-......+++..++|++.+.+|.+|-
T Consensus 74 ~d~il~v~d~~~~~~~~~~~~~~~~~~~~~p~ivv~NK~Dl~ 115 (168)
T cd01887 74 TDIAILVVAADDGVMPQTIEAIKLAKAANVPFIVALNKIDKP 115 (168)
T ss_pred cCEEEEEEECCCCccHHHHHHHHHHHHcCCCEEEEEEceecc
Confidence 4455555555431 112223345677899999999988764
No 311
>PRK06553 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=21.14 E-value=3.9e+02 Score=21.23 Aligned_cols=51 Identities=8% Similarity=-0.238 Sum_probs=30.6
Q ss_pred eeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcCC
Q 033552 15 GVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGAT 72 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~ 72 (117)
|+++.+++|++|. .|.+..|-+|.+ -..+...|.|......-+.|.+.+|.
T Consensus 193 ~~r~l~r~Lk~g~--~v~il~DQ~~~~-----gv~v~FFG~~a~t~~~~a~LA~~~~a 243 (308)
T PRK06553 193 AAFALAGVLERGG--HVGMLVDQKFTR-----GVEVTFFGRPVKTNPLLAKLARQYDC 243 (308)
T ss_pred HHHHHHHHHHcCC--eEEEEecccCCC-----CceeccCCCcCCCCchHHHHHHHHCC
Confidence 5788899999885 888888887621 12234444444444444445554443
No 312
>PRK10444 UMP phosphatase; Provisional
Probab=21.00 E-value=78 Score=24.70 Aligned_cols=41 Identities=10% Similarity=0.003 Sum_probs=29.7
Q ss_pred eeeeecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCC
Q 033552 13 CVGVVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDI 55 (117)
Q Consensus 13 ~vG~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~I 55 (117)
+=|.++.++.|++....++|+.+..+. . ...+.+..+..|+
T Consensus 19 ~p~a~~~l~~L~~~g~~~~~~Tn~~~~-~-~~~~~~~l~~~G~ 59 (248)
T PRK10444 19 VPGAAEFLHRILDKGLPLVLLTNYPSQ-T-GQDLANRFATAGV 59 (248)
T ss_pred CccHHHHHHHHHHCCCeEEEEeCCCCC-C-HHHHHHHHHHcCC
Confidence 448889999999988999999999884 2 3344444455555
No 313
>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=20.97 E-value=73 Score=22.41 Aligned_cols=50 Identities=8% Similarity=-0.008 Sum_probs=32.3
Q ss_pred eeecchhhhhcCCccEEEEeC-CC---CC---------cchheeHHHHhhhCCCCEEEECCHh
Q 033552 15 GVVNDPLPLLFHECRLCVIAG-NI---SP---------IDVITHVPILCEESDIPYIYVASKE 64 (117)
Q Consensus 15 G~kqt~kaL~kg~~~LViLA~-Da---sp---------~~i~~~i~~lce~~~IP~i~v~tK~ 64 (117)
++++.++.++...+.++++.- +. +| ..+-..+..+|+++++|++...+..
T Consensus 93 ~~~~~i~~i~~~~~~vil~~~~~~~~~~~~~~~~~~~~~~~n~~l~~~a~~~~v~~vd~~~~~ 155 (185)
T cd01832 93 DLEEAVRRLRAAGARVVVFTIPDPAVLEPFRRRVRARLAAYNAVIRAVAARYGAVHVDLWEHP 155 (185)
T ss_pred HHHHHHHHHHhCCCEEEEecCCCccccchhHHHHHHHHHHHHHHHHHHHHHcCCEEEecccCc
Confidence 345677778765666666642 11 11 1134557888999999999987654
No 314
>cd02009 TPP_SHCHC_synthase Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting isochorismate and 2-oxoglutarate to SHCHC, pyruvate and carbon dioxide. The enzyme requires TPP and a divalent metal cation for activity.
Probab=20.88 E-value=1.1e+02 Score=22.30 Aligned_cols=24 Identities=25% Similarity=0.339 Sum_probs=15.5
Q ss_pred HHHHhhhCCCCEEEECCHhHHHhh
Q 033552 46 VPILCEESDIPYIYVASKEDLANA 69 (117)
Q Consensus 46 i~~lce~~~IP~i~v~tK~eLG~A 69 (117)
+..+|+.+|+++..+.+.+||-.+
T Consensus 134 ~~~lA~a~G~~~~~v~~~~el~~a 157 (175)
T cd02009 134 FEHLAKAYGLEYRRVSSLDELEQA 157 (175)
T ss_pred HHHHHHHcCCCeeeCCCHHHHHHH
Confidence 455666667777666666666544
No 315
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=20.87 E-value=72 Score=26.97 Aligned_cols=53 Identities=19% Similarity=0.102 Sum_probs=40.4
Q ss_pred CCccceeeeecc-----h----hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEE
Q 033552 8 LHSFNCVGVVND-----P----LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYV 60 (117)
Q Consensus 8 ~~~~~~vG~kqt-----~----kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v 60 (117)
.+.+=+||+.=+ + ..++++..+.++-|+|+--..=++.+..|++..|+|++--
T Consensus 139 p~Vil~vGVNG~GKTTTIaKLA~~l~~~g~~VllaA~DTFRAaAiEQL~~w~er~gv~vI~~ 200 (340)
T COG0552 139 PFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISG 200 (340)
T ss_pred cEEEEEEecCCCchHhHHHHHHHHHHHCCCeEEEEecchHHHHHHHHHHHHHHHhCCeEEcc
Confidence 455567777643 2 2346666889999999986555889999999999999984
No 316
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=20.78 E-value=3.7e+02 Score=22.31 Aligned_cols=47 Identities=21% Similarity=0.257 Sum_probs=36.7
Q ss_pred CccEEEEeCCCCC---cchheeHHHHhhhCCCCEEEECCHhHHHhhcCCC
Q 033552 27 ECRLCVIAGNISP---IDVITHVPILCEESDIPYIYVASKEDLANAGATK 73 (117)
Q Consensus 27 ~~~LViLA~Dasp---~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G~~ 73 (117)
+.-+|+||+-.-| .+.+..+...|+++++.++.=.|-+.|=+++--+
T Consensus 129 ~~d~VvlsGSlP~g~~~d~y~~li~~~~~~g~~vilD~Sg~~L~~~L~~~ 178 (310)
T COG1105 129 SDDIVVLSGSLPPGVPPDAYAELIRILRQQGAKVILDTSGEALLAALEAK 178 (310)
T ss_pred cCCEEEEeCCCCCCCCHHHHHHHHHHHHhcCCeEEEECChHHHHHHHccC
Confidence 3456999995442 4678999999999999998888888887776654
No 317
>PRK09108 type III secretion system protein HrcU; Validated
Probab=20.73 E-value=78 Score=26.55 Aligned_cols=36 Identities=19% Similarity=0.065 Sum_probs=26.1
Q ss_pred EEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHhhcC
Q 033552 31 CVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71 (117)
Q Consensus 31 ViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~A~G 71 (117)
+++|.=.+. +..+|.+.++++|||++.-. .|.+++-
T Consensus 283 ~VvAKG~d~--~A~~Ir~~A~e~~VPvven~---pLARaLy 318 (353)
T PRK09108 283 RVIAKGVDD--GALALRRHAHALGIPIVGNP---PVARALY 318 (353)
T ss_pred EEEEEeCcH--HHHHHHHHHHHcCCCEEeCH---HHHHHHh
Confidence 445555553 67899999999999997653 5666665
No 318
>TIGR00639 PurN phosphoribosylglycinamide formyltransferase, formyltetrahydrofolate-dependent. In phylogenetic analyses, the member from Saccharomyces cerevisiae shows a long branch length but membership in the family, while the formyltetrahydrofolate deformylases form a closely related outgroup.
Probab=20.60 E-value=1.4e+02 Score=22.52 Aligned_cols=41 Identities=7% Similarity=-0.074 Sum_probs=26.6
Q ss_pred ecchhhhhcCCc--cEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 17 VNDPLPLLFHEC--RLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 17 kqt~kaL~kg~~--~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+..+++++++.. .++++..|-.. .....+|+++|||+..+.
T Consensus 15 ~~ll~~~~~~~l~~~I~~vi~~~~~----~~~~~~A~~~gip~~~~~ 57 (190)
T TIGR00639 15 QAIIDACKEGKIPASVVLVISNKPD----AYGLERAAQAGIPTFVLS 57 (190)
T ss_pred HHHHHHHHcCCCCceEEEEEECCcc----chHHHHHHHcCCCEEEEC
Confidence 345677777763 55555455321 234678999999998755
No 319
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.57 E-value=73 Score=19.63 Aligned_cols=23 Identities=17% Similarity=0.089 Sum_probs=19.5
Q ss_pred hheeHHHHhhhCCCCEEEECCHh
Q 033552 42 VITHVPILCEESDIPYIYVASKE 64 (117)
Q Consensus 42 i~~~i~~lce~~~IP~i~v~tK~ 64 (117)
+...|..+|+++|++++.|....
T Consensus 4 ~~~~L~yka~~~G~~v~~v~~~~ 26 (69)
T PF07282_consen 4 FRQRLEYKAEEYGIQVVEVDEAY 26 (69)
T ss_pred HHHHHHHHHHHhCCEEEEECCCC
Confidence 46678889999999999998665
No 320
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=20.57 E-value=1e+02 Score=23.85 Aligned_cols=46 Identities=22% Similarity=0.382 Sum_probs=30.5
Q ss_pred cchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEE-ECCHhHHHhhc
Q 033552 18 NDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIY-VASKEDLANAG 70 (117)
Q Consensus 18 qt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~-v~tK~eLG~A~ 70 (117)
|.-++++-| +.+++ || .+-..+.+.|.+++||++= +.|-.|+=+|.
T Consensus 80 ~~~~a~~aG-A~Fiv-----sP-~~~~~v~~~~~~~~i~~iPG~~T~~E~~~A~ 126 (213)
T PRK06552 80 TARLAILAG-AQFIV-----SP-SFNRETAKICNLYQIPYLPGCMTVTEIVTAL 126 (213)
T ss_pred HHHHHHHcC-CCEEE-----CC-CCCHHHHHHHHHcCCCEECCcCCHHHHHHHH
Confidence 333444555 55555 67 3577788899999999873 44666666664
No 321
>cd06423 CESA_like CESA_like is the cellulose synthase superfamily. The cellulose synthase (CESA) superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains. The members include cellulose synthase catalytic subunit, chitin synthase, glucan biosynthesis protein and other families of CESA-like proteins. Cellulose synthase catalyzes the polymerization reaction of cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues in plants, most algae, some bacteria and fungi, and even some animals. In bacteria, algae and lower eukaryotes, there is a second unrelated type of cellulose synthase (Type II), which produces acylated cellulose, a derivative of cellulose. Chitin synthase catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin, which is a linear homopolymer of beta-(1,4)-linked GlcNAc residues and Glucan Biosynthesis protein catalyzes the
Probab=20.55 E-value=83 Score=20.49 Aligned_cols=52 Identities=17% Similarity=0.065 Sum_probs=28.5
Q ss_pred eecchhhhhcC---CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECCHhHHHh
Q 033552 16 VVNDPLPLLFH---ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLAN 68 (117)
Q Consensus 16 ~kqt~kaL~kg---~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~tK~eLG~ 68 (117)
+.+++++|.+. ...++|+. |.+.......+..........++++...+..|.
T Consensus 12 l~~~l~sl~~q~~~~~~iivvd-d~s~d~t~~~~~~~~~~~~~~~~~~~~~~~~g~ 66 (180)
T cd06423 12 IERTIESLLALDYPKLEVIVVD-DGSTDDTLEILEELAALYIRRVLVVRDKENGGK 66 (180)
T ss_pred HHHHHHHHHhCCCCceEEEEEe-CCCccchHHHHHHHhccccceEEEEEecccCCc
Confidence 45677788776 34555554 444434455555555544344555555555554
No 322
>PRK14869 putative manganese-dependent inorganic pyrophosphatase; Provisional
Probab=20.33 E-value=1.7e+02 Score=25.29 Aligned_cols=52 Identities=19% Similarity=0.160 Sum_probs=34.2
Q ss_pred hhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC-HhHHHhhcCCCcce
Q 033552 21 LPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS-KEDLANAGATKRPT 76 (117)
Q Consensus 21 kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t-K~eLG~A~G~~~~~ 76 (117)
.++++| +..+|+.++..|.+ .+.++|++.++|++.++. .-+-.+.+....++
T Consensus 196 ~ai~~~-~~~lIlt~g~~~~~---~v~~la~~~~i~ii~t~~dt~~t~~~l~~~~~V 248 (546)
T PRK14869 196 AAIEAG-VRLLIITGGAPVSE---DVLELAKENGVTVISTPYDTFTTARLINQSIPV 248 (546)
T ss_pred HHHHcC-CCEEEECCCCCCCH---HHHHHHHhCCCeEEEecccHHHHHHHhhcCCCH
Confidence 456666 67777777766533 477799999999998883 44444444444343
No 323
>COG0050 TufB GTPases - translation elongation factors [Translation, ribosomal structure and biogenesis]
Probab=20.27 E-value=1e+02 Score=26.39 Aligned_cols=47 Identities=23% Similarity=0.405 Sum_probs=30.8
Q ss_pred eeeeecchhhhhcCCc----cEEEEeCCCC--CcchheeHHHHhhhCCCCEEEEC
Q 033552 13 CVGVVNDPLPLLFHEC----RLCVIAGNIS--PIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 13 ~vG~kqt~kaL~kg~~----~LViLA~Das--p~~i~~~i~~lce~~~IP~i~v~ 61 (117)
|=|-..-+|.|--|.+ .++++|++-. |. ..+|+. ++++.|+||+.++
T Consensus 82 cPGHaDYvKNMItgAaqmDgAILVVsA~dGpmPq-TrEHiL-larqvGvp~ivvf 134 (394)
T COG0050 82 CPGHADYVKNMITGAAQMDGAILVVAATDGPMPQ-TREHIL-LARQVGVPYIVVF 134 (394)
T ss_pred CCChHHHHHHHhhhHHhcCccEEEEEcCCCCCCc-chhhhh-hhhhcCCcEEEEE
Confidence 4455555666655543 3455555545 44 478876 9999999999886
No 324
>TIGR00035 asp_race aspartate racemase.
Probab=20.16 E-value=88 Score=23.84 Aligned_cols=47 Identities=13% Similarity=0.181 Sum_probs=33.7
Q ss_pred eecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC--HhHH
Q 033552 16 VVNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS--KEDL 66 (117)
Q Consensus 16 ~kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t--K~eL 66 (117)
+.+.++.|++..+.+++||.++.. .. +..+-+..+||++.+.. .+.+
T Consensus 64 l~~~~~~L~~~g~d~iviaCNTah-~~---~~~l~~~~~iPii~i~~~~~~~~ 112 (229)
T TIGR00035 64 LIDIAVKLENAGADFIIMPCNTAH-KF---AEDIQKAIGIPLISMIEETAEAV 112 (229)
T ss_pred HHHHHHHHHHcCCCEEEECCccHH-HH---HHHHHHhCCCCEechHHHHHHHH
Confidence 455677777888999999999875 22 45566677899988543 4444
No 325
>PRK10867 signal recognition particle protein; Provisional
Probab=20.16 E-value=3.3e+02 Score=23.47 Aligned_cols=39 Identities=15% Similarity=0.227 Sum_probs=29.6
Q ss_pred hhcC-CccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 23 LLFH-ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 23 L~kg-~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
+++. ..+.++++.|..-..-...+..+++..+||++...
T Consensus 124 l~~~~G~kV~lV~~D~~R~aa~eQL~~~a~~~gv~v~~~~ 163 (433)
T PRK10867 124 LKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGVPVFPSG 163 (433)
T ss_pred HHHhcCCcEEEEEccccchHHHHHHHHHHhhcCCeEEecC
Confidence 3433 46788999998754446788889999999988664
No 326
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=20.16 E-value=1.7e+02 Score=23.49 Aligned_cols=38 Identities=18% Similarity=0.179 Sum_probs=24.1
Q ss_pred cchhhhhcCC--ccEEEEeCCCCCcchheeHHHHhhhCCCCEEEEC
Q 033552 18 NDPLPLLFHE--CRLCVIAGNISPIDVITHVPILCEESDIPYIYVA 61 (117)
Q Consensus 18 qt~kaL~kg~--~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~ 61 (117)
..+++++.|. +.++.+-+|-. .+..+|+++|||+..+.
T Consensus 105 al~~~~~~~~~~~~i~~visn~~------~~~~lA~~~gIp~~~~~ 144 (286)
T PRK06027 105 DLLWRWRSGELPVEIAAVISNHD------DLRSLVERFGIPFHHVP 144 (286)
T ss_pred HHHHHHHcCCCCcEEEEEEEcCh------hHHHHHHHhCCCEEEec
Confidence 3445556654 56666666643 23446999999998865
No 327
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=20.10 E-value=1.8e+02 Score=21.21 Aligned_cols=39 Identities=13% Similarity=0.066 Sum_probs=21.3
Q ss_pred hhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCCEEEECC
Q 033552 20 PLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVAS 62 (117)
Q Consensus 20 ~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP~i~v~t 62 (117)
++.+..+.+.=+|+........ ....+.+++||++.+.+
T Consensus 48 ~~~l~~~~vdgiIi~~~~~~~~----~~~~l~~~~ipvV~~~~ 86 (265)
T cd06299 48 LDNLLSQRVDGIIVVPHEQSAE----QLEDLLKRGIPVVFVDR 86 (265)
T ss_pred HHHHHhcCCCEEEEcCCCCChH----HHHHHHhCCCCEEEEec
Confidence 4555666665555554322111 23455667888877754
No 328
>CHL00071 tufA elongation factor Tu
Probab=20.09 E-value=85 Score=26.22 Aligned_cols=50 Identities=16% Similarity=0.184 Sum_probs=29.5
Q ss_pred ecchhhhhcCCccEEEEeCCCCCcchheeHHHHhhhCCCC-EEEECCHhHH
Q 033552 17 VNDPLPLLFHECRLCVIAGNISPIDVITHVPILCEESDIP-YIYVASKEDL 66 (117)
Q Consensus 17 kqt~kaL~kg~~~LViLA~Dasp~~i~~~i~~lce~~~IP-~i~v~tK~eL 66 (117)
+++++++..-.+-++++..+-.+..-...+..++...++| ++.+-+|-++
T Consensus 90 ~~~~~~~~~~D~~ilVvda~~g~~~qt~~~~~~~~~~g~~~iIvvvNK~D~ 140 (409)
T CHL00071 90 KNMITGAAQMDGAILVVSAADGPMPQTKEHILLAKQVGVPNIVVFLNKEDQ 140 (409)
T ss_pred HHHHHHHHhCCEEEEEEECCCCCcHHHHHHHHHHHHcCCCEEEEEEEccCC
Confidence 4455666655566666665543323344455688899999 5455555444
No 329
>PRK09331 Sep-tRNA:Cys-tRNA synthetase; Provisional
Probab=20.01 E-value=1.2e+02 Score=24.73 Aligned_cols=39 Identities=15% Similarity=0.230 Sum_probs=25.1
Q ss_pred CccEEEEeCCCC----CcchheeHHHHhhhCCCCEEEECCHhHHH
Q 033552 27 ECRLCVIAGNIS----PIDVITHVPILCEESDIPYIYVASKEDLA 67 (117)
Q Consensus 27 ~~~LViLA~Das----p~~i~~~i~~lce~~~IP~i~v~tK~eLG 67 (117)
+.++|++.+=.+ ..+ ...|.++|+++|++++ ++.-..+|
T Consensus 158 ~~~lV~l~~~~~~tG~~~~-l~~I~~la~~~g~~li-vD~a~~~g 200 (387)
T PRK09331 158 PPALALLTHVDGNYGNLAD-AKKVAKVAHEYGIPFL-LNGAYTVG 200 (387)
T ss_pred CCEEEEEECCCCCCccccc-HHHHHHHHHHcCCEEE-EECCcccC
Confidence 578888865222 233 6678889999999765 44333333
Done!