Query 035100
Match_columns 73
No_of_seqs 113 out of 689
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 09:11:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035100.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035100hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03677 rpl7ae 50S ribosomal 99.8 8.8E-19 1.9E-23 110.8 8.2 69 1-71 48-116 (117)
2 KOG3167 Box H/ACA snoRNP compo 99.8 5.6E-19 1.2E-23 115.1 6.1 69 1-71 81-149 (153)
3 PRK04175 rpl7ae 50S ribosomal 99.8 2.1E-18 4.6E-23 109.9 8.3 69 1-71 52-120 (122)
4 PRK13600 putative ribosomal pr 99.7 5.8E-18 1.3E-22 102.3 5.6 49 1-50 35-83 (84)
5 COG1358 RPL8A Ribosomal protei 99.7 3.4E-17 7.3E-22 103.9 6.9 63 1-64 49-112 (116)
6 PTZ00222 60S ribosomal protein 99.7 2.7E-16 5.8E-21 110.8 8.1 65 1-66 154-221 (263)
7 PRK13602 putative ribosomal pr 99.6 5.5E-16 1.2E-20 92.9 5.7 49 1-50 33-81 (82)
8 PRK13601 putative L7Ae-like ri 99.6 6E-16 1.3E-20 93.0 5.7 51 1-52 30-80 (82)
9 PTZ00365 60S ribosomal protein 99.6 1.2E-15 2.6E-20 107.7 7.9 67 1-69 154-220 (266)
10 PRK06683 hypothetical protein; 99.6 6.7E-16 1.5E-20 92.6 5.5 50 1-51 33-82 (82)
11 KOG3387 60S ribosomal protein 99.6 1.2E-15 2.6E-20 98.0 6.5 73 1-73 56-131 (131)
12 PRK01018 50S ribosomal protein 99.6 1.8E-15 3.8E-20 93.3 6.1 56 1-57 38-94 (99)
13 PRK07714 hypothetical protein; 99.6 5.4E-15 1.2E-19 91.0 5.9 59 1-61 40-99 (100)
14 PRK07283 hypothetical protein; 99.6 8.4E-15 1.8E-19 90.0 5.7 57 1-60 40-97 (98)
15 PF01248 Ribosomal_L7Ae: Ribos 99.5 7.3E-15 1.6E-19 88.5 4.7 56 1-56 37-93 (95)
16 PTZ00106 60S ribosomal protein 99.5 1.4E-14 3.1E-19 90.7 5.9 55 1-56 47-102 (108)
17 PRK05583 ribosomal protein L7A 99.5 9.4E-14 2E-18 86.4 6.0 62 1-64 39-101 (104)
18 PRK09190 hypothetical protein; 99.2 1.1E-10 2.3E-15 80.9 6.7 63 1-65 133-202 (220)
19 KOG3406 40S ribosomal protein 98.3 2.3E-06 4.9E-11 55.4 6.2 53 1-53 56-119 (134)
20 COG1911 RPL30 Ribosomal protei 98.2 2.5E-06 5.5E-11 52.9 4.6 57 1-58 41-98 (100)
21 KOG3166 60S ribosomal protein 97.2 0.00041 9E-09 48.1 3.2 49 1-63 131-181 (209)
22 PF08228 RNase_P_pop3: RNase P 93.3 0.55 1.2E-05 31.3 6.5 59 3-63 82-146 (158)
23 PF15608 PELOTA_1: PELOTA RNA 91.3 0.53 1.2E-05 29.3 4.2 31 10-51 68-98 (100)
24 KOG2988 60S ribosomal protein 91.0 0.65 1.4E-05 29.5 4.5 39 23-61 69-108 (112)
25 PF11823 DUF3343: Protein of u 84.9 3.2 6.9E-05 23.5 4.5 48 11-63 14-61 (73)
26 PF13611 Peptidase_S76: Serine 82.2 1.7 3.7E-05 27.9 2.8 27 7-33 35-61 (121)
27 PF10087 DUF2325: Uncharacteri 79.7 4.5 9.8E-05 24.0 4.0 22 9-30 62-83 (97)
28 PLN02821 1-hydroxy-2-methyl-2- 78.6 6.3 0.00014 30.4 5.2 26 11-36 377-402 (460)
29 PF08032 SpoU_sub_bind: RNA 2' 76.1 6 0.00013 21.8 3.6 40 11-51 32-71 (76)
30 COG1648 CysG Siroheme synthase 75.7 13 0.00027 25.5 5.7 45 7-53 82-130 (210)
31 COG4422 Bacteriophage protein 74.9 2.5 5.4E-05 29.6 2.0 26 2-28 197-222 (250)
32 PRK05562 precorrin-2 dehydroge 66.3 27 0.00058 24.3 5.7 57 7-64 95-159 (223)
33 PF07997 DUF1694: Protein of u 66.0 13 0.00028 23.5 3.7 31 3-34 70-100 (120)
34 PF07505 Gp37_Gp68: Phage prot 65.9 8.1 0.00018 27.6 3.1 26 5-31 205-230 (261)
35 TIGR00216 ispH_lytB (E)-4-hydr 65.0 27 0.00058 25.2 5.6 56 11-69 223-278 (280)
36 PRK01045 ispH 4-hydroxy-3-meth 63.1 22 0.00048 25.8 5.0 54 11-68 225-279 (298)
37 PF03618 Kinase-PPPase: Kinase 62.9 31 0.00068 24.6 5.6 57 5-63 61-119 (255)
38 PRK12360 4-hydroxy-3-methylbut 62.1 22 0.00048 25.6 4.8 56 11-70 224-280 (281)
39 PRK13371 4-hydroxy-3-methylbut 61.8 29 0.00063 26.3 5.5 58 11-71 303-378 (387)
40 PF02401 LYTB: LytB protein; 61.0 53 0.0012 23.6 6.6 56 10-69 223-279 (281)
41 PF01976 DUF116: Protein of un 59.7 41 0.00089 22.1 5.4 51 11-63 75-125 (158)
42 PF05343 Peptidase_M42: M42 gl 59.2 17 0.00036 26.0 3.8 41 9-49 224-269 (292)
43 COG1535 EntB Isochorismate hyd 58.9 10 0.00023 26.4 2.5 20 10-29 59-78 (218)
44 KOG2486 Predicted GTPase [Gene 58.6 8.2 0.00018 28.5 2.1 25 10-34 236-260 (320)
45 PF13545 HTH_Crp_2: Crp-like h 58.5 7.3 0.00016 21.4 1.5 35 10-44 3-44 (76)
46 PF07498 Rho_N: Rho terminatio 58.4 4.9 0.00011 20.9 0.7 27 10-36 6-32 (43)
47 TIGR01470 cysG_Nterm siroheme 58.2 33 0.00072 23.1 4.9 43 10-53 82-127 (205)
48 cd04911 ACT_AKiii-YclM-BS_1 AC 57.4 37 0.0008 19.9 6.0 48 10-67 17-66 (76)
49 TIGR03697 NtcA_cyano global ni 56.4 9.7 0.00021 24.2 2.0 40 4-44 114-159 (193)
50 PLN03199 delta6-acyl-lipid des 54.9 7.7 0.00017 29.6 1.5 23 10-32 436-458 (485)
51 PRK12723 flagellar biosynthesi 54.4 46 0.001 24.9 5.5 49 3-52 214-262 (388)
52 PRK07377 hypothetical protein; 52.2 28 0.00061 23.9 3.7 34 8-41 93-128 (184)
53 TIGR03106 trio_M42_hydro hydro 51.8 40 0.00086 24.6 4.8 43 6-49 265-312 (343)
54 COG1419 FlhF Flagellar GTP-bin 51.7 46 0.001 25.4 5.2 63 4-66 242-305 (407)
55 PRK03980 flap endonuclease-1; 51.4 50 0.0011 23.7 5.1 35 4-39 79-115 (292)
56 PRK14725 pyruvate kinase; Prov 50.8 72 0.0016 25.7 6.3 58 10-68 523-593 (608)
57 TIGR03107 glu_aminopep glutamy 49.9 42 0.00092 24.7 4.7 43 6-49 264-310 (350)
58 KOG4201 Anthranilate synthase 49.5 43 0.00094 24.1 4.5 42 10-53 174-216 (289)
59 cd01483 E1_enzyme_family Super 49.3 30 0.00066 21.3 3.4 24 9-32 101-124 (143)
60 cd01485 E1-1_like Ubiquitin ac 49.2 15 0.00033 24.5 2.1 29 8-36 124-152 (198)
61 PF14367 DUF4411: Domain of un 49.2 3.3 7.1E-05 27.0 -1.1 21 11-31 134-154 (162)
62 PRK01889 GTPase RsgA; Reviewed 49.1 19 0.00041 26.3 2.7 31 4-35 125-155 (356)
63 PRK12423 LexA repressor; Provi 49.0 21 0.00046 23.9 2.8 30 9-42 10-40 (202)
64 PRK00087 4-hydroxy-3-methylbut 49.0 59 0.0013 25.7 5.6 41 11-53 221-261 (647)
65 COG1363 FrvX Cellulase M and r 48.7 15 0.00033 27.4 2.2 43 6-49 268-315 (355)
66 PRK10637 cysG siroheme synthas 48.3 49 0.0011 24.9 4.9 46 7-53 82-130 (457)
67 PF14370 Topo_C_assoc: C-termi 48.1 5 0.00011 23.5 -0.3 22 15-36 37-58 (71)
68 PF00899 ThiF: ThiF family; I 47.8 26 0.00057 21.5 2.9 25 8-32 103-127 (135)
69 TIGR00186 rRNA_methyl_3 rRNA m 47.4 66 0.0014 22.1 5.1 41 12-53 32-72 (237)
70 PF13848 Thioredoxin_6: Thiore 47.0 69 0.0015 19.9 5.5 41 10-51 63-103 (184)
71 TIGR01766 tspaseT_teng_C trans 46.8 26 0.00056 19.7 2.6 23 9-31 57-79 (82)
72 PF02603 Hpr_kinase_N: HPr Ser 46.4 20 0.00043 22.4 2.2 19 12-30 95-113 (127)
73 PF12651 RHH_3: Ribbon-helix-h 44.0 23 0.00051 18.4 1.9 19 7-25 10-28 (44)
74 cd01493 APPBP1_RUB Ubiquitin a 43.7 19 0.00042 27.2 2.1 28 10-37 125-152 (425)
75 PF01726 LexA_DNA_bind: LexA D 43.7 30 0.00065 19.4 2.5 29 9-41 10-38 (65)
76 TIGR00789 flhB_rel flhB C-term 43.4 32 0.00068 20.4 2.6 27 9-38 27-53 (82)
77 COG4359 Uncharacterized conser 43.1 71 0.0015 22.4 4.6 41 11-52 78-124 (220)
78 COG0160 GabT 4-aminobutyrate a 42.5 24 0.00053 27.1 2.5 23 5-27 239-261 (447)
79 PF07282 OrfB_Zn_ribbon: Putat 42.1 34 0.00075 18.7 2.6 23 10-32 4-26 (69)
80 PRK00124 hypothetical protein; 40.3 34 0.00074 22.6 2.7 26 3-30 7-32 (151)
81 PRK05339 PEP synthetase regula 40.2 1.1E+02 0.0023 22.1 5.3 58 5-64 67-126 (269)
82 PRK09864 putative peptidase; P 40.1 77 0.0017 23.5 4.8 21 6-27 263-283 (356)
83 PF10281 Ish1: Putative stress 40.0 23 0.0005 17.6 1.5 25 12-36 7-32 (38)
84 COG0800 Eda 2-keto-3-deoxy-6-p 39.6 15 0.00033 25.6 1.0 21 5-26 90-110 (211)
85 TIGR01182 eda Entner-Doudoroff 39.3 20 0.00043 24.6 1.5 44 5-51 85-129 (204)
86 PF13407 Peripla_BP_4: Peripla 39.2 1.1E+02 0.0024 20.0 5.8 21 11-31 69-89 (257)
87 PRK06718 precorrin-2 dehydroge 39.1 89 0.0019 20.9 4.6 42 10-53 83-127 (202)
88 PRK03892 ribonuclease P protei 39.1 56 0.0012 23.0 3.7 32 11-42 155-198 (216)
89 PRK06015 keto-hydroxyglutarate 39.0 21 0.00045 24.5 1.5 32 5-37 81-113 (201)
90 KOG0081 GTPase Rab27, small G 38.3 30 0.00065 23.9 2.2 16 13-28 146-161 (219)
91 PF00202 Aminotran_3: Aminotra 37.2 31 0.00067 24.7 2.3 26 7-32 196-221 (339)
92 PF10498 IFT57: Intra-flagella 37.0 20 0.00043 26.7 1.3 30 6-35 68-97 (359)
93 cd01491 Ube1_repeat1 Ubiquitin 36.4 22 0.00047 25.6 1.4 31 7-37 115-145 (286)
94 PRK08187 pyruvate kinase; Vali 36.3 1.9E+02 0.0042 22.5 6.5 58 10-68 406-476 (493)
95 PRK06552 keto-hydroxyglutarate 36.2 25 0.00053 24.1 1.6 44 5-51 93-137 (213)
96 cd02001 TPP_ComE_PpyrDC Thiami 35.9 54 0.0012 21.0 3.1 28 12-39 112-139 (157)
97 PLN03198 delta6-acyl-lipid des 35.8 23 0.00051 27.5 1.5 19 10-28 480-498 (526)
98 COG1671 Uncharacterized protei 35.6 48 0.001 22.0 2.8 29 3-33 8-36 (150)
99 PRK07114 keto-hydroxyglutarate 35.1 25 0.00055 24.4 1.5 32 5-37 96-128 (222)
100 PF01497 Peripla_BP_2: Peripla 34.7 49 0.0011 21.5 2.8 47 17-70 78-135 (238)
101 PF07905 PucR: Purine cataboli 34.5 47 0.001 20.4 2.5 27 10-36 87-113 (123)
102 cd01492 Aos1_SUMO Ubiquitin ac 34.2 43 0.00094 22.3 2.5 30 7-36 120-149 (197)
103 PRK07449 2-succinyl-5-enolpyru 33.2 1.5E+02 0.0033 22.6 5.5 57 13-71 507-567 (568)
104 smart00513 SAP Putative DNA-bi 33.2 50 0.0011 15.9 2.1 23 10-34 5-27 (35)
105 cd01143 YvrC Periplasmic bindi 33.0 1.3E+02 0.0028 18.9 5.2 28 14-41 74-111 (195)
106 cd04138 H_N_K_Ras_like H-Ras/N 32.9 38 0.00081 20.3 1.9 24 12-35 96-119 (162)
107 PF00462 Glutaredoxin: Glutare 32.8 54 0.0012 17.0 2.3 14 15-28 16-29 (60)
108 COG2047 Uncharacterized protei 32.6 1.2E+02 0.0025 21.9 4.5 35 8-42 102-136 (258)
109 COG1440 CelA Phosphotransferas 32.4 50 0.0011 20.6 2.3 27 10-37 61-87 (102)
110 PRK11889 flhF flagellar biosyn 32.3 2.2E+02 0.0048 22.1 6.2 65 3-68 277-346 (436)
111 PF02142 MGS: MGS-like domain 32.3 28 0.00061 20.3 1.2 16 11-26 79-94 (95)
112 cd01422 MGS Methylglyoxal synt 32.1 48 0.001 20.3 2.3 20 10-29 89-108 (115)
113 TIGR00853 pts-lac PTS system, 32.0 57 0.0012 19.4 2.6 20 11-30 64-83 (95)
114 cd01141 TroA_d Periplasmic bin 31.7 1.4E+02 0.003 18.9 4.8 26 14-39 84-119 (186)
115 PF13727 CoA_binding_3: CoA-bi 31.6 52 0.0011 20.2 2.4 23 6-28 152-174 (175)
116 PF01081 Aldolase: KDPG and KH 31.5 40 0.00087 23.0 2.0 46 5-53 85-131 (196)
117 PF14201 DUF4318: Domain of un 31.3 73 0.0016 18.6 2.8 26 7-32 17-42 (74)
118 PRK00098 GTPase RsgA; Reviewed 31.2 59 0.0013 23.0 2.9 26 10-35 99-124 (298)
119 smart00460 TGc Transglutaminas 31.2 72 0.0016 16.7 2.7 22 9-30 11-32 (68)
120 cd00568 TPP_enzymes Thiamine p 31.0 77 0.0017 19.6 3.2 26 13-38 127-152 (168)
121 TIGR02181 GRX_bact Glutaredoxi 30.9 74 0.0016 17.3 2.8 16 13-28 14-29 (79)
122 cd00532 MGS-like MGS-like doma 30.8 49 0.0011 19.9 2.1 18 11-28 88-105 (112)
123 cd05565 PTS_IIB_lactose PTS_II 30.6 55 0.0012 19.9 2.3 20 11-30 61-80 (99)
124 PRK14721 flhF flagellar biosyn 30.6 1.5E+02 0.0033 22.5 5.1 50 4-53 230-279 (420)
125 cd00755 YgdL_like Family of ac 30.5 76 0.0017 21.9 3.3 22 9-30 114-135 (231)
126 PRK14829 undecaprenyl pyrophos 30.2 62 0.0013 22.8 2.8 21 10-30 46-66 (243)
127 cd04141 Rit_Rin_Ric Rit/Rin/Ri 30.2 52 0.0011 20.7 2.3 23 13-35 98-120 (172)
128 PRK12288 GTPase RsgA; Reviewed 30.1 50 0.0011 24.2 2.4 30 5-35 134-163 (347)
129 cd02009 TPP_SHCHC_synthase Thi 29.9 70 0.0015 20.6 2.9 26 13-38 133-158 (175)
130 COG2257 Uncharacterized homolo 29.8 49 0.0011 20.3 1.9 28 9-39 32-59 (92)
131 PRK05965 hypothetical protein; 29.5 55 0.0012 24.6 2.6 25 5-29 232-256 (459)
132 PHA01623 hypothetical protein 29.3 60 0.0013 17.7 2.1 18 7-24 21-38 (56)
133 cd01879 FeoB Ferrous iron tran 29.2 77 0.0017 18.9 2.9 21 14-34 93-113 (158)
134 cd04795 SIS SIS domain. SIS (S 28.8 1E+02 0.0023 16.6 6.5 57 10-66 12-72 (87)
135 PF10881 DUF2726: Protein of u 28.7 64 0.0014 19.6 2.4 21 12-32 91-111 (126)
136 PF00391 PEP-utilizers: PEP-ut 28.7 42 0.00091 19.1 1.5 20 11-30 42-61 (80)
137 TIGR00157 ribosome small subun 28.5 62 0.0013 22.3 2.5 25 10-34 55-79 (245)
138 cd02004 TPP_BZL_OCoD_HPCL Thia 28.4 90 0.002 19.8 3.2 26 13-38 130-155 (172)
139 cd02015 TPP_AHAS Thiamine pyro 28.0 93 0.002 20.1 3.2 26 13-38 132-157 (186)
140 cd04103 Centaurin_gamma Centau 28.0 74 0.0016 19.9 2.7 25 12-36 89-113 (158)
141 PF10096 DUF2334: Uncharacteri 27.8 84 0.0018 21.7 3.1 25 3-27 7-34 (243)
142 cd01147 HemV-2 Metal binding p 27.8 1.9E+02 0.004 19.1 4.9 49 14-68 90-148 (262)
143 PF01297 TroA: Periplasmic sol 27.6 2E+02 0.0043 19.4 5.5 65 4-70 182-254 (256)
144 PF15496 DUF4646: Domain of un 27.6 51 0.0011 20.7 1.8 19 2-20 44-62 (123)
145 COG1162 Predicted GTPases [Gen 27.2 64 0.0014 23.7 2.5 31 4-35 93-123 (301)
146 PF02404 SCF: Stem cell factor 27.2 31 0.00067 25.1 0.9 30 11-40 41-70 (273)
147 PF06506 PrpR_N: Propionate ca 26.9 73 0.0016 20.6 2.6 24 14-37 135-159 (176)
148 PRK15116 sulfur acceptor prote 26.9 1E+02 0.0022 21.9 3.5 21 10-30 134-154 (268)
149 PRK14722 flhF flagellar biosyn 26.9 1.8E+02 0.0039 21.8 4.9 42 10-52 182-223 (374)
150 PRK11181 23S rRNA (guanosine-2 26.8 2.2E+02 0.0047 19.6 5.5 40 12-52 37-76 (244)
151 PTZ00217 flap endonuclease-1; 26.7 83 0.0018 23.6 3.1 35 4-39 134-170 (393)
152 PF01402 RHH_1: Ribbon-helix-h 26.6 54 0.0012 15.8 1.5 16 9-24 9-24 (39)
153 PF03931 Skp1_POZ: Skp1 family 26.5 45 0.00097 18.1 1.3 17 4-21 44-60 (62)
154 cd03372 TPP_ComE Thiamine pyro 26.4 1.9E+02 0.0041 18.8 4.6 41 13-53 114-157 (179)
155 PF03682 UPF0158: Uncharacteri 26.4 56 0.0012 21.5 2.0 21 10-30 126-146 (163)
156 PRK14723 flhF flagellar biosyn 26.2 1.7E+02 0.0037 24.2 4.9 50 2-52 222-271 (767)
157 PF03129 HGTP_anticodon: Antic 25.9 62 0.0013 18.3 1.9 21 15-35 45-65 (94)
158 PRK09590 celB cellobiose phosp 25.7 81 0.0018 19.2 2.5 20 11-30 64-83 (104)
159 PRK05718 keto-hydroxyglutarate 25.6 70 0.0015 21.9 2.4 45 6-53 93-138 (212)
160 KOG2518 5'-3' exonuclease [Rep 25.6 70 0.0015 25.5 2.6 31 2-33 122-152 (556)
161 COG2401 ABC-type ATPase fused 25.4 78 0.0017 25.1 2.8 32 10-41 546-577 (593)
162 smart00851 MGS MGS-like domain 25.4 60 0.0013 18.6 1.8 16 11-26 74-89 (90)
163 COG0484 DnaJ DnaJ-class molecu 25.3 61 0.0013 24.5 2.2 22 1-22 12-33 (371)
164 PRK11440 putative hydrolase; P 25.2 91 0.002 20.2 2.8 19 11-29 37-55 (188)
165 PF03460 NIR_SIR_ferr: Nitrite 25.1 35 0.00076 18.5 0.7 27 4-31 20-46 (69)
166 cd01863 Rab18 Rab18 subfamily. 24.8 55 0.0012 19.8 1.6 25 11-35 95-119 (161)
167 PF13241 NAD_binding_7: Putati 24.7 86 0.0019 18.5 2.4 23 9-31 72-94 (103)
168 PRK06943 adenosylmethionine--8 24.6 73 0.0016 23.9 2.5 24 6-29 240-263 (453)
169 TIGR02355 moeB molybdopterin s 24.5 1E+02 0.0022 21.3 3.0 28 9-36 126-153 (240)
170 cd00861 ProRS_anticodon_short 24.5 54 0.0012 18.4 1.5 19 16-34 48-66 (94)
171 TIGR00055 uppS undecaprenyl di 24.4 90 0.002 21.8 2.8 20 10-29 31-50 (226)
172 cd02002 TPP_BFDC Thiamine pyro 24.4 1.2E+02 0.0026 19.2 3.2 26 13-38 137-162 (178)
173 cd01424 MGS_CPS_II Methylglyox 24.2 72 0.0016 18.9 2.0 17 11-27 84-100 (110)
174 KOG3351 Predicted nucleotidylt 24.2 1.2E+02 0.0026 22.2 3.4 37 34-70 162-201 (293)
175 KOG0393 Ras-related small GTPa 24.1 52 0.0011 22.6 1.5 25 10-36 99-123 (198)
176 PF00586 AIRS: AIR synthase re 24.0 55 0.0012 18.8 1.5 17 10-26 76-92 (96)
177 PRK07027 cobalamin biosynthesi 23.9 92 0.002 19.5 2.5 23 13-36 51-73 (126)
178 PF02571 CbiJ: Precorrin-6x re 23.8 85 0.0018 22.0 2.6 23 9-31 80-102 (249)
179 COG0352 ThiE Thiamine monophos 23.8 81 0.0018 21.7 2.4 31 9-40 52-82 (211)
180 PRK07678 aminotransferase; Val 23.8 78 0.0017 23.7 2.5 23 6-28 231-253 (451)
181 PRK08742 adenosylmethionine--8 23.7 78 0.0017 24.0 2.5 24 6-29 255-278 (472)
182 PRK07482 hypothetical protein; 23.7 77 0.0017 23.9 2.5 23 6-28 238-260 (461)
183 PRK12289 GTPase RsgA; Reviewed 23.6 89 0.0019 23.0 2.7 26 10-35 108-133 (352)
184 cd01854 YjeQ_engC YjeQ/EngC. 23.6 86 0.0019 22.0 2.6 25 10-34 97-121 (287)
185 KOG4077 Cytochrome c oxidase, 23.5 72 0.0016 21.1 2.0 24 6-35 121-144 (149)
186 PRK07036 hypothetical protein; 23.4 81 0.0018 23.8 2.6 25 5-29 237-261 (466)
187 PF12687 DUF3801: Protein of u 23.4 2.5E+02 0.0054 19.1 6.6 50 10-66 43-92 (204)
188 PRK14839 undecaprenyl pyrophos 23.3 96 0.0021 22.0 2.7 20 10-29 41-60 (239)
189 cd01713 PAPS_reductase This do 23.2 1.1E+02 0.0024 18.4 2.8 26 8-33 41-66 (173)
190 TIGR01404 FlhB_rel_III type II 23.2 86 0.0019 23.1 2.6 22 9-30 288-309 (342)
191 PF04951 Peptidase_M55: D-amin 23.1 2.7E+02 0.0058 20.0 5.0 37 16-52 141-177 (265)
192 cd04176 Rap2 Rap2 subgroup. T 23.1 73 0.0016 19.3 2.0 15 20-34 104-118 (163)
193 TIGR03674 fen_arch flap struct 23.1 1.1E+02 0.0024 22.3 3.2 33 5-38 127-161 (338)
194 PRK09792 4-aminobutyrate trans 23.0 84 0.0018 23.2 2.5 30 6-35 216-245 (421)
195 PF02732 ERCC4: ERCC4 domain; 23.0 1.6E+02 0.0035 17.5 3.5 33 6-38 108-140 (143)
196 PRK12721 secretion system appa 23.0 89 0.0019 23.1 2.6 21 9-29 289-309 (349)
197 PRK02256 putative aminopeptida 23.0 84 0.0018 24.2 2.6 21 6-27 381-401 (462)
198 PRK02813 putative aminopeptida 22.9 1.5E+02 0.0032 22.5 3.8 26 8-33 348-373 (428)
199 TIGR02407 ectoine_ectB diamino 22.9 86 0.0019 23.1 2.6 26 6-31 212-237 (412)
200 PRK13918 CRP/FNR family transc 22.9 1.1E+02 0.0023 19.5 2.8 35 10-44 125-165 (202)
201 PRK09961 exoaminopeptidase; Pr 22.9 1.9E+02 0.0042 21.0 4.3 43 6-49 255-302 (344)
202 PF03851 UvdE: UV-endonuclease 22.9 60 0.0013 23.4 1.7 18 10-27 191-208 (275)
203 KOG2016 NEDD8-activating compl 22.8 79 0.0017 24.9 2.4 33 2-35 125-157 (523)
204 cd04165 GTPBP1_like GTPBP1-lik 22.8 82 0.0018 21.3 2.3 25 10-34 126-150 (224)
205 PF07085 DRTGG: DRTGG domain; 22.7 59 0.0013 19.1 1.4 21 10-30 73-93 (105)
206 PRK07480 putative aminotransfe 22.5 88 0.0019 23.5 2.6 24 5-28 236-259 (456)
207 PRK14831 undecaprenyl pyrophos 22.5 1E+02 0.0023 21.7 2.8 21 10-30 52-72 (249)
208 cd04117 Rab15 Rab15 subfamily. 22.5 88 0.0019 19.3 2.2 16 21-36 104-119 (161)
209 PTZ00371 aspartyl aminopeptida 22.4 1.4E+02 0.003 23.0 3.6 26 7-33 375-400 (465)
210 PRK08057 cobalt-precorrin-6x r 22.4 1E+02 0.0022 21.6 2.7 22 9-30 79-100 (248)
211 cd00738 HGTP_anticodon HGTP an 22.3 1.2E+02 0.0026 16.7 2.6 22 13-34 45-66 (94)
212 PRK06938 diaminobutyrate--2-ox 22.3 88 0.0019 23.6 2.5 22 6-27 249-270 (464)
213 TIGR00700 GABAtrnsam 4-aminobu 22.3 1E+02 0.0022 22.7 2.8 24 6-29 215-238 (420)
214 PF01171 ATP_bind_3: PP-loop f 22.2 96 0.0021 20.0 2.5 23 10-32 46-68 (182)
215 PRK05234 mgsA methylglyoxal sy 22.2 80 0.0017 20.3 2.0 20 11-30 95-114 (142)
216 KOG1602 Cis-prenyltransferase 22.1 67 0.0014 23.3 1.8 20 10-29 68-87 (271)
217 PF03808 Glyco_tran_WecB: Glyc 22.1 2.3E+02 0.005 18.3 5.3 64 3-66 29-99 (172)
218 PRK06298 type III secretion sy 22.1 94 0.002 23.1 2.6 27 9-38 290-316 (356)
219 cd02003 TPP_IolD Thiamine pyro 22.0 1.3E+02 0.0028 20.0 3.1 27 13-39 142-168 (205)
220 COG2877 KdsA 3-deoxy-D-manno-o 21.9 1.1E+02 0.0024 22.3 2.8 24 9-32 35-58 (279)
221 cd01019 ZnuA Zinc binding prot 21.9 2.9E+02 0.0062 19.3 6.3 63 4-69 211-283 (286)
222 PRK07481 hypothetical protein; 21.8 91 0.002 23.3 2.5 24 6-29 231-254 (449)
223 PRK13109 flhB flagellar biosyn 21.7 97 0.0021 23.0 2.6 22 9-30 298-319 (358)
224 cd04148 RGK RGK subfamily. Th 21.6 2.5E+02 0.0055 18.6 4.7 14 21-34 105-118 (221)
225 cd00475 CIS_IPPS Cis (Z)-Isopr 21.6 1.1E+02 0.0024 21.2 2.8 21 9-29 31-51 (221)
226 PRK08223 hypothetical protein; 21.6 1E+02 0.0022 22.3 2.7 21 9-29 131-151 (287)
227 PF00448 SRP54: SRP54-type pro 21.5 2E+02 0.0042 19.2 3.9 30 3-32 37-66 (196)
228 cd03418 GRX_GRXb_1_3_like Glut 21.5 1.5E+02 0.0031 15.7 2.8 18 12-29 14-31 (75)
229 PRK14837 undecaprenyl pyrophos 21.5 1.1E+02 0.0024 21.5 2.7 21 9-29 37-57 (230)
230 KOG1752 Glutaredoxin and relat 21.4 1.5E+02 0.0032 18.2 3.0 24 9-32 54-77 (104)
231 COG0803 LraI ABC-type metal io 21.4 1.3E+02 0.0028 21.4 3.2 38 3-41 223-266 (303)
232 cd02010 TPP_ALS Thiamine pyrop 21.3 1.4E+02 0.003 19.3 3.1 25 13-37 128-152 (177)
233 PRK09726 antitoxin HipB; Provi 21.2 1.1E+02 0.0025 17.5 2.4 33 6-44 9-41 (88)
234 TIGR03846 sulfopy_beta sulfopy 21.2 1.5E+02 0.0032 19.5 3.2 26 13-38 114-140 (181)
235 PRK06918 4-aminobutyrate amino 21.1 1.1E+02 0.0023 22.8 2.8 30 6-35 237-266 (451)
236 PF05889 SLA_LP_auto_ag: Solub 21.1 67 0.0015 24.4 1.7 18 10-27 173-190 (389)
237 cd02983 P5_C P5 family, C-term 21.0 2.2E+02 0.0048 17.7 4.9 28 24-52 3-30 (130)
238 KOG1401 Acetylornithine aminot 20.9 96 0.0021 24.0 2.5 24 5-29 224-247 (433)
239 TIGR00045 glycerate kinase. Th 20.9 2.8E+02 0.0061 20.9 4.9 25 11-35 304-328 (375)
240 TIGR01610 phage_O_Nterm phage 20.9 1.2E+02 0.0026 17.8 2.5 41 3-44 21-63 (95)
241 TIGR02356 adenyl_thiF thiazole 20.9 1.4E+02 0.0031 19.8 3.1 24 9-32 123-146 (202)
242 cd00757 ThiF_MoeB_HesA_family 20.8 1.5E+02 0.0032 20.0 3.3 27 10-36 124-150 (228)
243 cd00128 XPG Xeroderma pigmento 20.7 1.5E+02 0.0032 21.0 3.3 35 5-40 125-161 (316)
244 cd03420 SirA_RHOD_Pry_redox Si 20.7 1.3E+02 0.0029 16.5 2.6 22 7-29 36-57 (69)
245 TIGR00715 precor6x_red precorr 20.6 1.1E+02 0.0025 21.4 2.7 21 9-29 79-99 (256)
246 TIGR00699 GABAtrns_euk 4-amino 20.6 1E+02 0.0022 23.6 2.6 21 7-27 270-290 (464)
247 PRK10864 putative methyltransf 20.5 3.7E+02 0.0079 20.0 6.1 40 12-52 142-181 (346)
248 PF00009 GTP_EFTU: Elongation 20.5 82 0.0018 20.1 1.9 25 10-34 110-134 (188)
249 PRK06512 thiamine-phosphate py 20.5 2.9E+02 0.0063 18.8 4.7 55 11-67 153-211 (221)
250 cd01017 AdcA Metal binding pro 20.5 3E+02 0.0066 19.0 6.1 61 4-70 203-279 (282)
251 PF01890 CbiG_C: Cobalamin syn 20.5 89 0.0019 19.4 1.9 23 13-36 49-71 (121)
252 PRK14836 undecaprenyl pyrophos 20.4 1.1E+02 0.0023 21.8 2.5 20 10-29 46-65 (253)
253 PRK10240 undecaprenyl pyrophos 20.4 1.2E+02 0.0026 21.2 2.8 20 10-29 25-44 (229)
254 PRK05093 argD bifunctional N-s 20.4 1E+02 0.0023 22.2 2.6 20 7-26 203-222 (403)
255 PRK03244 argD acetylornithine 20.3 1.2E+02 0.0025 21.8 2.8 24 7-30 202-225 (398)
256 PRK06731 flhF flagellar biosyn 20.2 3.3E+02 0.0071 19.3 6.0 36 3-38 111-146 (270)
257 PRK14842 undecaprenyl pyrophos 20.2 1.2E+02 0.0026 21.4 2.8 20 10-29 40-59 (241)
258 PF12105 SpoU_methylas_C: SpoU 20.2 38 0.00082 18.9 0.2 16 14-29 31-46 (57)
259 PRK08156 type III secretion sy 20.2 1.1E+02 0.0023 22.9 2.6 27 9-38 284-310 (361)
260 cd04145 M_R_Ras_like M-Ras/R-R 20.2 1.1E+02 0.0023 18.4 2.2 23 13-35 98-120 (164)
261 COG4565 CitB Response regulato 20.1 76 0.0016 22.4 1.7 31 10-44 159-189 (224)
262 PF02037 SAP: SAP domain; Int 20.1 1.1E+02 0.0023 14.9 1.8 16 10-25 5-20 (35)
263 PRK06931 diaminobutyrate--2-ox 20.1 1E+02 0.0022 23.2 2.5 24 6-29 243-266 (459)
No 1
>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=99.78 E-value=8.8e-19 Score=110.84 Aligned_cols=69 Identities=33% Similarity=0.654 Sum_probs=59.9
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHHHHHHHHhh
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~~~ 71 (73)
||+|++|+++..+++.+|++++|||+++.||++||++||+++++++++|+|.| ....+++++..+|+.|
T Consensus 48 lA~D~s~~~~~~~i~~lc~~~~Ip~~~~~sk~eLG~a~Gk~~~~svvaI~d~g--~a~~~~~~~~~~i~~~ 116 (117)
T TIGR03677 48 IAEDVEPPEIVAHLPALCEEKGIPYVYVKKKEDLGAAAGLEVGAASAAIVDEG--KAEELLKEIIEKVEAL 116 (117)
T ss_pred EeCCCCcHHHHHHHHHHHHHcCCCEEEeCCHHHHHHHhCCCCCeEEEEEEchh--hhHHHHHHHHHHHHhc
Confidence 69999998789999999999999999999999999999998889999999998 4444555566666654
No 2
>KOG3167 consensus Box H/ACA snoRNP component, involved in ribosomal RNA pseudouridinylation [RNA processing and modification]
Probab=99.77 E-value=5.6e-19 Score=115.12 Aligned_cols=69 Identities=39% Similarity=0.739 Sum_probs=66.5
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHHHHHHHHhh
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~~~ 71 (73)
+|+|++|.|+.+|+|.+|+++||||+|++|++.||+|.|.+|+++++.+..++ ++++.++++.++++.|
T Consensus 81 lAgd~sPiDvi~HlP~lCEd~~vPYvy~psk~dlg~A~~~krpt~~v~v~p~~--eyke~ydev~eel~~l 149 (153)
T KOG3167|consen 81 LAGDTSPIDVITHLPALCEDRGVPYVYTPSKEDLGAAGGTKRPTCCVFVKPGG--EYKELYDEVLEELEAL 149 (153)
T ss_pred EecCCccHHHHhccchhhhccCCCccccccHHHHHHhcCCCCCceEEEEeeCh--hHHHHHHHHHHHHHhh
Confidence 68999999999999999999999999999999999999999999999999988 9999999999999876
No 3
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=99.77 E-value=2.1e-18 Score=109.87 Aligned_cols=69 Identities=38% Similarity=0.744 Sum_probs=59.4
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHHHHHHHHhh
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~~~ 71 (73)
||+|++|.++..+++.+|++++|||++++||++||++||+++++++++|+|.| ..+.+++++.+.|+.|
T Consensus 52 lA~D~s~~~i~~~~~~lc~~~~Vp~~~~~tk~eLG~a~Gk~~~~svvaI~d~g--~a~~~~~~~~~~i~~~ 120 (122)
T PRK04175 52 IAEDVDPEEIVAHLPLLCEEKKIPYVYVPSKKDLGKAAGLEVGAAAAAIVDAG--KAKELVEDIVEKVNEL 120 (122)
T ss_pred EeCCCChHHHHHHHHHHHHHcCCCEEEECCHHHHHHHhCCCCCeEEEEEechh--hhHHHHHHHHHHHHHh
Confidence 68999998789999999999999999999999999999999889999999998 4444555556665544
No 4
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=99.73 E-value=5.8e-18 Score=102.28 Aligned_cols=49 Identities=27% Similarity=0.447 Sum_probs=47.2
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEE
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVT 50 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~ 50 (73)
||.|++|. ++.|++.+|+++||||+|++||.+||++||+++++++++|+
T Consensus 35 iA~Da~~~-vv~~l~~lceek~Ip~v~V~s~~~LGkAcgi~V~aa~aai~ 83 (84)
T PRK13600 35 IAEDVEVY-LMTRVLSQINQKNIPVSFFKSKHALGKHVGINVNATIVALI 83 (84)
T ss_pred EeCCCCHH-HHHHHHHHHHHcCCCEEEECCHHHHHHHhCCCcCeEEEEEe
Confidence 68999999 99999999999999999999999999999999999999886
No 5
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=99.71 E-value=3.4e-17 Score=103.95 Aligned_cols=63 Identities=38% Similarity=0.668 Sum_probs=54.0
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-chHHHHHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQIQQL 64 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~~~~~ 64 (73)
||+|++|.+++.|+|.+|++++|||++++||.+||++||++. +.++++.+.+ +..+++++++.
T Consensus 49 iA~Dv~P~~~~~~l~~lc~~~~vpyv~V~sk~~LG~a~g~~~-~~vv~i~~~~~~~~~~~l~~~~ 112 (116)
T COG1358 49 IAEDVSPEELVKHLPALCEEKNVPYVYVGSKKELGKAVGKEV-RKVVAIVDKGFAKKLEDLVEKV 112 (116)
T ss_pred EecCCCHHHHHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCCc-ceeEEEeehhhhhHHHHHHHHh
Confidence 699999988999999999999999999999999999999994 4678999988 65555554443
No 6
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=99.67 E-value=2.7e-16 Score=110.77 Aligned_cols=65 Identities=26% Similarity=0.525 Sum_probs=54.6
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC---chHHHHHHHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE---ASQLKTQIQQLKD 66 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~---~~~~~~~~~~~~~ 66 (73)
||+|++|++++.+|+++|++++|||++++||++||+++|+++ +++++|+|.+ ...+.++++.++.
T Consensus 154 IA~DVsPie~vk~LpaLCrk~~VPY~iVktKaeLG~AIGkKt-ravVAItD~g~ed~~~l~~lv~~~~~ 221 (263)
T PTZ00222 154 IANNVDPVELVLWMPNLCRANKIPYAIVKDMARLGDAIGRKT-ATCVAITDVNAEDEAALKNLIRSVNA 221 (263)
T ss_pred EeCCCCHHHHHHHHHHHHHhcCCCEEEECCHHHHHHHHCCCC-CeEEEEeeCCcccHHHHHHHHHHHHH
Confidence 699999999999999999999999999999999999999874 5689999987 2445555544443
No 7
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=99.64 E-value=5.5e-16 Score=92.86 Aligned_cols=49 Identities=33% Similarity=0.545 Sum_probs=47.2
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEE
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVT 50 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~ 50 (73)
||+|++|+ +.++++.+|++++|||++++|+.+||+|||+++++++++|+
T Consensus 33 iA~D~~~~-~~~~i~~~c~~~~Vp~~~~~s~~eLG~a~G~~~~~a~~ai~ 81 (82)
T PRK13602 33 VAEDADPR-LTEKVEALANEKGVPVSKVDSMKKLGKACGIEVGAAAVAII 81 (82)
T ss_pred EECCCCHH-HHHHHHHHHHHcCCCEEEECCHHHHHHHHCCCcCEEEEEEe
Confidence 68999998 99999999999999999999999999999999999999886
No 8
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=99.63 E-value=6e-16 Score=93.00 Aligned_cols=51 Identities=24% Similarity=0.424 Sum_probs=48.4
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
||.|++|+ +.++|+++|++++|||.+++||.+||+|||+++++++++++-+
T Consensus 30 iA~Da~~~-~~k~i~~~c~~~~Vpv~~~~t~~eLG~A~G~~v~aa~~~~~~~ 80 (82)
T PRK13601 30 IAKDAEEH-VTKKIKELCEEKSIKIVYIDTMKELGVMCGIDVGAAAAADIIG 80 (82)
T ss_pred EeCCCCHH-HHHHHHHHHHhCCCCEEEeCCHHHHHHHHCCccCeeeEEEeec
Confidence 68999998 9999999999999999999999999999999999999988754
No 9
>PTZ00365 60S ribosomal protein L7Ae-like; Provisional
Probab=99.63 E-value=1.2e-15 Score=107.73 Aligned_cols=67 Identities=22% Similarity=0.468 Sum_probs=53.8
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHHHHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIE 69 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~ 69 (73)
||+|++|++++.++|++|++|+|||++++||++||+++|++ .+++++|++-. ++-+..++.+.+.|.
T Consensus 154 IA~DVsP~t~kk~LP~LC~k~~VPY~iv~sK~eLG~AIGkk-traVVAItdV~-~EDk~~l~~lv~~~~ 220 (266)
T PTZ00365 154 IAHDVDPIELVCFLPALCRKKEVPYCIIKGKSRLGKLVHQK-TAAVVAIDNVR-KEDQAEFDNLCKNFR 220 (266)
T ss_pred EeCCCCHHHHHHHHHHHHhccCCCEEEECCHHHHHHHhCCC-CceEEEecccC-HHHHHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999987 56789998875 233333444444443
No 10
>PRK06683 hypothetical protein; Provisional
Probab=99.63 E-value=6.7e-16 Score=92.64 Aligned_cols=50 Identities=24% Similarity=0.296 Sum_probs=47.8
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEe
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTS 51 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~ 51 (73)
||+|++|+ +.+.|.++|++++|||.+++|+.+||+|||+++++++++|..
T Consensus 33 iA~Da~~~-~~~~i~~~~~~~~Vpv~~~~t~~eLG~A~G~~~~~a~~ai~~ 82 (82)
T PRK06683 33 IAEDADMR-LTHVIIRTALQHNIPITKVESVRKLGKVAGIQVGASAIGIIS 82 (82)
T ss_pred EECCCCHH-HHHHHHHHHHhcCCCEEEECCHHHHHHHhCCcccEEEEEEeC
Confidence 69999999 999999999999999999999999999999999999999863
No 11
>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=99.62 E-value=1.2e-15 Score=98.02 Aligned_cols=73 Identities=78% Similarity=1.142 Sum_probs=68.1
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhC---CCCceEEEEEEeCCchHHHHHHHHHHHHHHhhcC
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACG---VTRPVVACSVTSNEASQLKTQIQQLKDAIEKLLI 73 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G---~~r~~~~vai~~~~~~~~~~~~~~~~~~~~~~~~ 73 (73)
+|.|+.|.++..|+|.+|+.+||||+||+|+..||.+|| ..|++.++.|...++.....++..++..++.|++
T Consensus 56 ~aaD~kP~eIt~HLp~LcedknVp~v~Vpsk~alG~~cg~~~~~r~~~a~~i~~~~~~~~~~~~q~l~~~~~~l~~ 131 (131)
T KOG3387|consen 56 MAADVKPLEITLHLPLLCEDKNVPYVFVPSKQALGLACGELVVLRPVIACSITTNEASIPLSQIQSLKRAIERLLI 131 (131)
T ss_pred EEccCCHHHHHHHhHHHhhccCCceEEeeccHHhhhhhhhHhhcCcceeEEEEeccccchhhHHHHhHHHHHHhcC
Confidence 589999999999999999999999999999999999999 8899999999998888888899999998888764
No 12
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=99.61 E-value=1.8e-15 Score=93.29 Aligned_cols=56 Identities=21% Similarity=0.246 Sum_probs=50.0
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEe-CChhhHhhHhCCCCceEEEEEEeCCchHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFV-PSKQALGRACGVTRPVVACSVTSNEASQL 57 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v-~sk~~LG~a~G~~r~~~~vai~~~~~~~~ 57 (73)
||+|++++ +.++++.+|++++||++.+ +|+++||+|||+++++++++|+|.|-.++
T Consensus 38 iA~D~~~~-~~~~i~~~c~~~~Ip~~~~~~tk~eLG~a~Gk~~~~~~vaI~D~G~a~~ 94 (99)
T PRK01018 38 VASNCPKD-IKEDIEYYAKLSGIPVYEYEGSSVELGTLCGKPFTVSALAIVDPGESDI 94 (99)
T ss_pred EeCCCCHH-HHHHHHHHHHHcCCCEEEECCCHHHHHHHhCCCCCEEEEEEecCCHHHH
Confidence 68999887 9999999999999998665 89999999999998788999999994443
No 13
>PRK07714 hypothetical protein; Provisional
Probab=99.57 E-value=5.4e-15 Score=90.97 Aligned_cols=59 Identities=24% Similarity=0.273 Sum_probs=53.2
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-chHHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQI 61 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~~ 61 (73)
+|+|++|+ +.++++.+|+.++|||++++|+++||++||++ ++++++|+|.| +..+.+++
T Consensus 40 iA~D~s~~-~~~ki~~~~~~~~vp~~~~~sk~eLG~a~Gk~-~~~~vai~d~g~a~~l~~~~ 99 (100)
T PRK07714 40 LSEDASVN-TTKKITDKCTYYNVPMRKVENRQQLGHAIGKD-ERVVVAVLDEGFAKKLRSML 99 (100)
T ss_pred EeCCCCHH-HHHHHHHHHHhcCCCEEEeCCHHHHHHHhCCC-cceEEEEeCchhHHHHHHHh
Confidence 58999999 99999999999999999999999999999998 45689999999 77666654
No 14
>PRK07283 hypothetical protein; Provisional
Probab=99.56 E-value=8.4e-15 Score=90.04 Aligned_cols=57 Identities=21% Similarity=0.200 Sum_probs=51.5
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-chHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQ 60 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~ 60 (73)
+|+|++|+ +.+++.+.|++++||++.++|+++||++||+++ ++++|+|.| ++.+.++
T Consensus 40 ~A~Das~~-~~kk~~~~~~~~~Vp~~~~~t~~eLG~a~Gk~~--~vvai~d~g~a~~l~~~ 97 (98)
T PRK07283 40 LANDAGPN-LTKKVTDKSNYYQVEVSTVFSTLELSAAVGKPR--KVLAVTDAGFSKKMRSL 97 (98)
T ss_pred EeCCCCHH-HHHHHHHHHHHcCCCEEEeCCHHHHHHHhCCCc--eEEEEeChhHHHHHHHh
Confidence 58999999 999999999999999999999999999999864 679999999 7766654
No 15
>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=99.55 E-value=7.3e-15 Score=88.52 Aligned_cols=56 Identities=54% Similarity=0.883 Sum_probs=50.8
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-chH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-ASQ 56 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~~ 56 (73)
+|+|++|.....+++.+|++++|||++++|+++||+++|++++++++++.|.| ++.
T Consensus 37 lA~d~~~~~~~~~l~~~c~~~~Ip~~~~~s~~eLG~~~g~~~~~~~~~i~d~~~a~~ 93 (95)
T PF01248_consen 37 LAEDCSPDSIKKHLPALCEEKNIPYVFVPSKEELGRACGKKRPVSALAIKDAGDAKI 93 (95)
T ss_dssp EETTSSSGHHHHHHHHHHHHTTEEEEEESHHHHHHHHTTSSSTSSEEEEEESTTHHH
T ss_pred EcCCCChhhhcccchhheeccceeEEEECCHHHHHHHHCCCCcEEEEEEECcccchh
Confidence 58999999666669999999999999999999999999999878899999998 443
No 16
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=99.54 E-value=1.4e-14 Score=90.73 Aligned_cols=55 Identities=20% Similarity=0.245 Sum_probs=50.1
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEE-eCChhhHhhHhCCCCceEEEEEEeCCchH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVF-VPSKQALGRACGVTRPVVACSVTSNEASQ 56 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~-v~sk~~LG~a~G~~r~~~~vai~~~~~~~ 56 (73)
||.|++++ +.+++..+|+.++||++. .+|+++||+|||+++++++++|+|.|.++
T Consensus 47 iA~D~~~~-~kkki~~~~~~~~Vpv~~~~~t~~eLG~A~Gk~~r~svvaI~D~G~a~ 102 (108)
T PTZ00106 47 ISNNCPPI-RRSEIEYYAMLSKTGVHHYAGNNNDLGTACGRHFRVSVMSITDAGDSD 102 (108)
T ss_pred EeCCCCHH-HHHHHHHHHhhcCCCEEEeCCCHHHHHHHhCCccCeEEEEEeCcchHH
Confidence 68999999 999999999999999985 69999999999999878899999999333
No 17
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=99.48 E-value=9.4e-14 Score=86.44 Aligned_cols=62 Identities=21% Similarity=0.236 Sum_probs=56.8
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-chHHHHHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQIQQL 64 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~~~~~ 64 (73)
+|+|++|+ ..+++..+|+.++||++...|+++||++||++. +++++|+|.+ +..+.+++++-
T Consensus 39 ~A~D~s~~-~kkki~~~~~~~~vp~~~~~t~~eLg~a~Gk~~-~~~iai~d~g~a~~l~~~~~~~ 101 (104)
T PRK05583 39 ISNDISEN-SKNKFKNYCNKYNIPYIEGYSKEELGNAIGRDE-IKILGVKDKNMAKKLLKLWNES 101 (104)
T ss_pred EeCCCCHh-HHHHHHHHHHHcCCCEEEecCHHHHHHHhCCCC-eEEEEEeChHHHHHHHHHHHhc
Confidence 58999999 999999999999999999999999999999984 7899999999 88888887653
No 18
>PRK09190 hypothetical protein; Provisional
Probab=99.16 E-value=1.1e-10 Score=80.91 Aligned_cols=63 Identities=19% Similarity=0.207 Sum_probs=56.0
Q ss_pred CCCCCCchhHHHhHHHHHhh------CCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-chHHHHHHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAED------KNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQIQQLK 65 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~------~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~~~~~~ 65 (73)
+|+|++++ ..++|..+|+. ++|||+..+|+++||+|+|++ ++++++|++.+ +..+.+.++.+.
T Consensus 133 ~A~DaS~~-t~kKl~~~~~~~~~~~~~~Vp~v~~~tk~eLg~AlGr~-~~~~vav~d~gfA~~l~~~~~rl~ 202 (220)
T PRK09190 133 HASDGAAD-GKRKLDQARRALVHETGREIPVIGLFTAAELGLAFGRE-NVIHAALLAGGAAERVVKRAQRLA 202 (220)
T ss_pred EeccCChh-HHHHHHHHHHhhcccccCCccEEEecCHHHHHHHhCCC-ceeEEEEcChHHHHHHHHHHHHHH
Confidence 58999999 99999999999 999999999999999999988 46789999999 777777766544
No 19
>KOG3406 consensus 40S ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=98.32 E-value=2.3e-06 Score=55.35 Aligned_cols=53 Identities=15% Similarity=0.234 Sum_probs=45.8
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCC-----------CceEEEEEEeCC
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVT-----------RPVVACSVTSNE 53 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~-----------r~~~~vai~~~~ 53 (73)
+|+|++....++-+.+||.+++||.+.+.+..+||+++|.. ++.+++++.|.|
T Consensus 56 Laencdep~yvKLVeALcaeh~iplikV~d~k~LGew~Glckid~eGnarKvvGcs~vvVkd~g 119 (134)
T KOG3406|consen 56 LAENCDEPMYVKLVEALCAEHQIPLIKVGDAKELGEWAGLCKIDSEGNARKVVGCSCVVVKDYG 119 (134)
T ss_pred EeccCCchHHHHHHHHHHhhcCCCeEEeccchhhhhhhceeeecCCCCeeEeecceEEEEeecc
Confidence 57886666699999999999999999999999999999864 256778888887
No 20
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=98.23 E-value=2.5e-06 Score=52.92 Aligned_cols=57 Identities=18% Similarity=0.278 Sum_probs=48.3
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEe-CChhhHhhHhCCCCceEEEEEEeCCchHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFV-PSKQALGRACGVTRPVVACSVTSNEASQLK 58 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v-~sk~~LG~a~G~~r~~~~vai~~~~~~~~~ 58 (73)
||+++.+. +.+.+.-++.=.+||+.+. .|..+||.+||+..+.++++|+|.|.+++.
T Consensus 41 iAsN~P~~-~k~~ieyYAkLs~ipV~~y~Gt~~eLG~~cgkpf~v~~laIiD~G~S~Il 98 (100)
T COG1911 41 IASNCPKE-LKEDIEYYAKLSDIPVYVYEGTSVELGTVCGKPFRVAALAIIDEGDSDIL 98 (100)
T ss_pred EecCCCHH-HHHHHHHHHHHcCCcEEEecCCceeHHhhhCCCceEEEEEEecCchhhhh
Confidence 47777666 9999999999999998766 467789999999999999999999966654
No 21
>KOG3166 consensus 60S ribosomal protein L7A [Translation, ribosomal structure and biogenesis]
Probab=97.17 E-value=0.00041 Score=48.06 Aligned_cols=49 Identities=24% Similarity=0.464 Sum_probs=32.8
Q ss_pred CCCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceE-EEEEEeCC-chHHHHHHHH
Q 035100 1 MAADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVV-ACSVTSNE-ASQLKTQIQQ 63 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~-~vai~~~~-~~~~~~~~~~ 63 (73)
+|+|+||.|++.++|++|..+ .+..+ .++++ ++++.+.. ...+..+++.
T Consensus 131 ~ahDvDPIELVvFLPaLC~km-----ivk~~---------~~kT~t~~a~v~~edk~~l~kl~e~ 181 (209)
T KOG3166|consen 131 TAHDVDPIELVVFLPALCRKM-----IVKGK---------HRKTCTTVAFVNSEDKGALAKLVEA 181 (209)
T ss_pred EecccCchhheeecHHhhhhh-----ccccc---------ccceeeeeeeechhhHHHHHHHHHH
Confidence 589999999999999999988 45555 33333 35554443 3445555443
No 22
>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=93.31 E-value=0.55 Score=31.29 Aligned_cols=59 Identities=31% Similarity=0.443 Sum_probs=44.8
Q ss_pred CCCCchhHHHhHHHHHhhCC--CCEEEeC--ChhhHhhHhCCCCceEEEEEEeCC--chHHHHHHHH
Q 035100 3 ADTEPLEILLHLPLLAEDKN--VPYVFVP--SKQALGRACGVTRPVVACSVTSNE--ASQLKTQIQQ 63 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~--IP~~~v~--sk~~LG~a~G~~r~~~~vai~~~~--~~~~~~~~~~ 63 (73)
.| .|.=+..|||.+|.-.+ |..+..+ +.++|+.++|..| +++++|..+. ++.+.+++++
T Consensus 82 ~D-~ps~L~~h~P~Lva~as~~vrLV~Lpkgs~~rLs~aLgi~r-~g~l~v~~~~~~~~~L~~~i~~ 146 (158)
T PF08228_consen 82 SD-QPSILTSHFPQLVATASKSVRLVQLPKGSEARLSEALGIPR-VGILAVRADAPGAKSLVDLIRS 146 (158)
T ss_pred CC-CcHHHHHHHHHHHHhccCcceEEeCChhHHHHHHHHhCCCC-ccEEEEecCCcccHHHHHHHHh
Confidence 35 34449999999999877 7777765 5677999999985 6678888764 6677777665
No 23
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=91.27 E-value=0.53 Score=29.28 Aligned_cols=31 Identities=45% Similarity=0.657 Sum_probs=25.1
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEe
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTS 51 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~ 51 (73)
=+.|+..||+++|||+..++++ +.+|++|+.
T Consensus 68 d~~Hl~~LA~ekgVpVe~~~d~-----------~Y~a~glIk 98 (100)
T PF15608_consen 68 DLAHLLLLAEEKGVPVEVYPDL-----------PYSACGLIK 98 (100)
T ss_pred cHHHHHHHHHHcCCcEEEeCCC-----------CeEEEEEee
Confidence 4789999999999999999885 345676654
No 24
>KOG2988 consensus 60S ribosomal protein L30 [Translation, ribosomal structure and biogenesis]
Probab=90.98 E-value=0.65 Score=29.47 Aligned_cols=39 Identities=23% Similarity=0.303 Sum_probs=29.2
Q ss_pred CCEE-EeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHH
Q 035100 23 VPYV-FVPSKQALGRACGVTRPVVACSVTSNEASQLKTQI 61 (73)
Q Consensus 23 IP~~-~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~ 61 (73)
.+|- +-....+||++||+--+.++..|+|.+++++...+
T Consensus 69 ~~v~~~sg~n~~lgt~~g~~fRv~v~~ivd~gds~~~~~l 108 (112)
T KOG2988|consen 69 TGVHHYSGNNVELGTACGKTFRVSVLSIVDLGDSDIIAAL 108 (112)
T ss_pred CceeeecCCcEeHHHHhcCeeEeeEEEEEeccchhhhhhc
Confidence 4444 44556789999999878899999999966665543
No 25
>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=84.92 E-value=3.2 Score=23.54 Aligned_cols=48 Identities=13% Similarity=0.441 Sum_probs=34.1
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHH
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQ 63 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~ 63 (73)
..+...+++++|+++..+++-.+++.-||.. +.+...+...+.+.+++
T Consensus 14 a~~~ek~lk~~gi~~~liP~P~~i~~~CG~a-----l~~~~~d~~~i~~~l~~ 61 (73)
T PF11823_consen 14 AMKAEKLLKKNGIPVRLIPTPREISAGCGLA-----LRFEPEDLEKIKEILEE 61 (73)
T ss_pred HHHHHHHHHHCCCcEEEeCCChhccCCCCEE-----EEEChhhHHHHHHHHHH
Confidence 3456788999999999999999999998832 44444334455555443
No 26
>PF13611 Peptidase_S76: Serine peptidase of plant viral polyprotein, P1
Probab=82.19 E-value=1.7 Score=27.94 Aligned_cols=27 Identities=7% Similarity=0.246 Sum_probs=23.5
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChhh
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQA 33 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~~ 33 (73)
-.|++..+.++|-+.|+|+.++.++..
T Consensus 35 i~dL~~~~~~ic~ergiPIe~I~~~k~ 61 (121)
T PF13611_consen 35 IDDLVREVTEICCERGIPIEIIDKKKR 61 (121)
T ss_pred HHHHHHHHHHHHHHcCCCEEEecCcce
Confidence 346899999999999999999998655
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=79.73 E-value=4.5 Score=23.95 Aligned_cols=22 Identities=14% Similarity=0.329 Sum_probs=19.7
Q ss_pred hHHHhHHHHHhhCCCCEEEeCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~s 30 (73)
+....+...|+++|+|+++..+
T Consensus 62 ~~~~~vk~~akk~~ip~~~~~~ 83 (97)
T PF10087_consen 62 NAMWKVKKAAKKYGIPIIYSRS 83 (97)
T ss_pred HHHHHHHHHHHHcCCcEEEECC
Confidence 4788899999999999999984
No 28
>PLN02821 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
Probab=78.58 E-value=6.3 Score=30.45 Aligned_cols=26 Identities=31% Similarity=0.553 Sum_probs=24.3
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
..||..+|+++|+|-.++.+.++|+.
T Consensus 377 T~~L~eIa~~~g~~sy~Ie~~~eI~~ 402 (460)
T PLN02821 377 TSHLQEIAEHKGIPSYWIDSEERIGP 402 (460)
T ss_pred HHHHHHHHHHhCCCEEEECCHHHcCc
Confidence 57899999999999999999999985
No 29
>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=76.09 E-value=6 Score=21.84 Aligned_cols=40 Identities=20% Similarity=0.245 Sum_probs=28.3
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEe
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTS 51 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~ 51 (73)
...+..+++.+|+|+..+. +..|.+.++...+-.++++..
T Consensus 32 ~~~i~~~~~~~~i~v~~v~-~~~l~~ls~~~~hQGv~a~v~ 71 (76)
T PF08032_consen 32 IKEILKLAKKKGIPVYEVS-KKVLDKLSDTENHQGVVAVVK 71 (76)
T ss_dssp THHHHHHHHHCT-EEEEE--HHHHHHCTTTSS-TTEEEEEE
T ss_pred HHHHHHHHHHcCCeEEEeC-HHHHHHHcCCCCCCeEEEEEe
Confidence 4578889999999999885 567999987665555566654
No 30
>COG1648 CysG Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme metabolism]
Probab=75.73 E-value=13 Score=25.55 Aligned_cols=45 Identities=9% Similarity=0.109 Sum_probs=33.2
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChhh----HhhHhCCCCceEEEEEEeCC
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQA----LGRACGVTRPVVACSVTSNE 53 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~~----LG~a~G~~r~~~~vai~~~~ 53 (73)
..++-..+-..|+++++|+..+...+. +...+. |+-..++|..+|
T Consensus 82 d~~ln~~i~~~a~~~~i~vNv~D~p~~~~f~~Pa~~~--r~~l~iaIsT~G 130 (210)
T COG1648 82 DEELNERIAKAARERRILVNVVDDPELCDFIFPAIVD--RGPLQIAISTGG 130 (210)
T ss_pred CHHHHHHHHHHHHHhCCceeccCCcccCceecceeec--cCCeEEEEECCC
Confidence 334888999999999999988877653 334433 444679999988
No 31
>COG4422 Bacteriophage protein gp37 [Function unknown]
Probab=74.86 E-value=2.5 Score=29.63 Aligned_cols=26 Identities=15% Similarity=0.298 Sum_probs=23.4
Q ss_pred CCCCCchhHHHhHHHHHhhCCCCEEEe
Q 035100 2 AADTEPLEILLHLPLLAEDKNVPYVFV 28 (73)
Q Consensus 2 A~D~~p~~~~~~l~~lc~~~~IP~~~v 28 (73)
|.+.+|. ++.+|.+.|...+.|+++-
T Consensus 197 aR~idp~-WvdeI~~~C~~~~~aFFFK 222 (250)
T COG4422 197 ARPIDPQ-WVDEIEDMCRDAGTAFFFK 222 (250)
T ss_pred CCCCCHH-HHHHHHHHHHhcCccchhH
Confidence 5688999 9999999999999999763
No 32
>PRK05562 precorrin-2 dehydrogenase; Provisional
Probab=66.32 E-value=27 Score=24.33 Aligned_cols=57 Identities=4% Similarity=-0.003 Sum_probs=37.7
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChhhHhhHhC---CCCceEEEEEEeCC-c----hHHHHHHHHH
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQALGRACG---VTRPVVACSVTSNE-A----SQLKTQIQQL 64 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G---~~r~~~~vai~~~~-~----~~~~~~~~~~ 64 (73)
..++-..+-..|+.+++++..+.+. ++|...- ..++--+++|..+| + ..+++.++++
T Consensus 95 D~~vN~~I~~~a~~~~~lvn~vd~p-~~~dFi~PAiv~rg~l~IaIST~G~sP~lar~lR~~ie~~ 159 (223)
T PRK05562 95 DEKLNNKIRKHCDRLYKLYIDCSDY-KKGLCIIPYQRSTKNFVFALNTKGGSPKTSVFIGEKVKNF 159 (223)
T ss_pred CHHHHHHHHHHHHHcCCeEEEcCCc-ccCeEEeeeEEecCCEEEEEECCCcCcHHHHHHHHHHHHH
Confidence 3348899999999999999988775 4453210 22444578898876 3 4455555543
No 33
>PF07997 DUF1694: Protein of unknown function (DUF1694); InterPro: IPR012543 This family contains many hypothetical proteins.; PDB: 2OHW_A.
Probab=65.99 E-value=13 Score=23.52 Aligned_cols=31 Identities=13% Similarity=0.192 Sum_probs=20.8
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCChhhH
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~L 34 (73)
++.+.. ...++..+|+++|+|+..|.+...=
T Consensus 70 g~l~~~-~~~~YiklA~~~~~~fTiv~~~~~~ 100 (120)
T PF07997_consen 70 GNLDYS-FQSKYIKLANKHGIPFTIVNDPEYH 100 (120)
T ss_dssp TTS-HH-HHHHHHHHHHHTT--EEEE---SS-
T ss_pred CCCCHH-HHHHHHHHHHHcCCCEEEeCCCCcc
Confidence 456666 8999999999999999999997653
No 34
>PF07505 Gp37_Gp68: Phage protein Gp37/Gp68; InterPro: IPR011101 This entry is represented by Burkholderia phage phiE125, Gp37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=65.87 E-value=8.1 Score=27.58 Aligned_cols=26 Identities=15% Similarity=0.186 Sum_probs=22.4
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeCCh
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~sk 31 (73)
.+|. ++..|.+.|.++|||+.+-..-
T Consensus 205 ~~~~-Wvr~irdqC~~~gvpFffKQwG 230 (261)
T PF07505_consen 205 MHPD-WVRSIRDQCAAAGVPFFFKQWG 230 (261)
T ss_pred CCHH-HHHHHHHHHHHcCCcEEEEeCC
Confidence 4565 9999999999999999987654
No 35
>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=64.98 E-value=27 Score=25.16 Aligned_cols=56 Identities=18% Similarity=0.173 Sum_probs=38.4
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHHHHHHHH
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIE 69 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~ 69 (73)
..+|-++|+++|.|-.++.+.++|...-=. +...++|+.+- +.=..+++++.+.++
T Consensus 223 T~rL~ei~~~~~~~t~~Ie~~~el~~~~l~--~~~~VGiTAGA-STP~~li~eVi~~l~ 278 (280)
T TIGR00216 223 TTRLYEIAEEHGPPSYLIETAEELPEEWLK--GVKVVGITAGA-STPDWIIEEVIRKIK 278 (280)
T ss_pred HHHHHHHHHHhCCCEEEECChHHCCHHHhC--CCCEEEEEecC-CCCHHHHHHHHHHHH
Confidence 578999999999999999999999843212 22348888653 444445555555443
No 36
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=63.08 E-value=22 Score=25.81 Aligned_cols=54 Identities=17% Similarity=0.155 Sum_probs=37.2
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhh-HhCCCCceEEEEEEeCCchHHHHHHHHHHHHH
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGR-ACGVTRPVVACSVTSNEASQLKTQIQQLKDAI 68 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~-a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~ 68 (73)
..+|-++|++++.|..++.+.++|-. ++ . +...++|+.+- +.=..+++++...+
T Consensus 225 T~kL~~i~~~~~~~t~~Ie~~~el~~~~l-~--~~~~VGitaGA-STP~~li~eV~~~l 279 (298)
T PRK01045 225 SNRLREVAEEAGAPAYLIDDASEIDPEWF-K--GVKTVGVTAGA-SAPEWLVQEVIARL 279 (298)
T ss_pred HHHHHHHHHHHCCCEEEECChHHCcHHHh-c--CCCEEEEEecC-CCCHHHHHHHHHHH
Confidence 57899999999999999999999974 33 1 23458888653 33334444444443
No 37
>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=62.87 E-value=31 Score=24.56 Aligned_cols=57 Identities=16% Similarity=0.189 Sum_probs=39.3
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeCCh--hhHhhHhCCCCceEEEEEEeCCchHHHHHHHH
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVPSK--QALGRACGVTRPVVACSVTSNEASQLKTQIQQ 63 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~sk--~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~ 63 (73)
++|. +...+...|+++|||++.+.+. ..|.+.+|.+ +....+....=+.+|-+.++-
T Consensus 61 v~~~-lr~~l~~~~~~~~i~~~Dll~~~l~~l~~~lg~~-p~~~pg~~~~ld~~Yf~RIeA 119 (255)
T PF03618_consen 61 VDPE-LREYLEEFCREHGIPCVDLLGPLLSALEEFLGQK-PSRKPGLQHQLDEDYFKRIEA 119 (255)
T ss_pred CCHH-HHHHHHHHHHhcCCCEEeccHHHHHHHHHHHCcC-cccccCccccchHHHHHHHHH
Confidence 4555 8999999999999999999875 4688888877 343344433323445555444
No 38
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=62.09 E-value=22 Score=25.59 Aligned_cols=56 Identities=14% Similarity=0.095 Sum_probs=39.6
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhh-HhCCCCceEEEEEEeCCchHHHHHHHHHHHHHHh
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGR-ACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEK 70 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~-a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~~ 70 (73)
..+|-++|++++.|-.++.+.++|-. ++- +...++|+.+ |+.=..+++++...++.
T Consensus 224 T~rL~eia~~~~~~t~~Ie~~~el~~~~~~---~~~~VGitaG-ASTP~~li~eV~~~l~~ 280 (281)
T PRK12360 224 TQKLVKICEKNCPNTFHIETADELDLEMLK---DYKIIGITAG-ASTPDWIIEEVIKKIKN 280 (281)
T ss_pred HHHHHHHHHHHCCCEEEECChHHCCHHHhC---CCCEEEEEcc-CCCCHHHHHHHHHHHHh
Confidence 57899999999999999999999963 332 2346888755 44555556666555543
No 39
>PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=61.81 E-value=29 Score=26.27 Aligned_cols=58 Identities=21% Similarity=0.214 Sum_probs=39.2
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhh------------------HhCCCCceEEEEEEeCCchHHHHHHHHHHHHHHhh
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGR------------------ACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~------------------a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~~~ 71 (73)
..+|-.+|++.+.|..++.+.++|-. ++-. ....|+|+.+ |+.=..+++++...+..+
T Consensus 303 T~rL~eia~~~g~~ty~Ie~~~eL~~~~~i~h~~~~~~~~~t~~wl~~--~~~~VGITAG-ASTP~~lI~eVi~~l~~l 378 (387)
T PRK13371 303 TTHLQEIAIERGIPSYHIDSPERILSGNSIEHKPLGKELVVTENWLPE--GPVTVGITSG-ASTPDKVVEDVIEKIFAL 378 (387)
T ss_pred HHHHHHHHHhcCCCEEEECCHHHcCCccccccccccchhhhhhhhhcc--CCCEEEEecC-CCCCHHHHHHHHHHHHHh
Confidence 57899999999999999999999964 4311 1235888755 344444555555554443
No 40
>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=61.02 E-value=53 Score=23.62 Aligned_cols=56 Identities=18% Similarity=0.171 Sum_probs=36.7
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhh-HhCCCCceEEEEEEeCCchHHHHHHHHHHHHHH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGR-ACGVTRPVVACSVTSNEASQLKTQIQQLKDAIE 69 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~-a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~ 69 (73)
-..+|-++|++++.|..++.+.++|=. ++.- ...++|+.+- +.=..+++++.+.++
T Consensus 223 NT~kL~eia~~~~~~t~~Ie~~~el~~~~l~~---~~~VGItaGA-STP~~ii~eVi~~l~ 279 (281)
T PF02401_consen 223 NTRKLAEIAKEHGKPTYHIETADELDPEWLKG---VKKVGITAGA-STPDWIIEEVIDRLE 279 (281)
T ss_dssp HHHHHHHHHHHCTTCEEEESSGGG--HHHHTT----SEEEEEE-T-TS-HHHHHHHHHHHH
T ss_pred cHHHHHHHHHHhCCCEEEeCCccccCHhHhCC---CCEEEEEccC-CCCHHHHHHHHHHHh
Confidence 367899999999999999999999963 4332 2258888764 444455555555544
No 41
>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=59.68 E-value=41 Score=22.11 Aligned_cols=51 Identities=20% Similarity=0.156 Sum_probs=40.2
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHH
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQ 63 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~ 63 (73)
+..+..+++++|+.+..+.+-.-+-+.+...++-+++|+--.- ++.+-+..
T Consensus 75 Ig~l~~lae~~g~~v~i~~Ggt~ar~~ik~~~p~~iigVAC~~--dL~~g~~~ 125 (158)
T PF01976_consen 75 IGDLKKLAEKYGYKVYIATGGTLARKIIKEYRPKAIIGVACER--DLISGIQD 125 (158)
T ss_pred hhHHHHHHHHcCCEEEEEcChHHHHHHHHHhCCCEEEEEechH--HHHHHHHH
Confidence 4567889999999999999999999988888888888886654 44444433
No 42
>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=59.21 E-value=17 Score=26.00 Aligned_cols=41 Identities=22% Similarity=0.336 Sum_probs=25.5
Q ss_pred hHHHhHHHHHhhCCCCEEE---eCChhhHhh--HhCCCCceEEEEE
Q 035100 9 EILLHLPLLAEDKNVPYVF---VPSKQALGR--ACGVTRPVVACSV 49 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~---v~sk~~LG~--a~G~~r~~~~vai 49 (73)
++..++.+.|++++|||=+ ..+-.+-+. ..|...++++++|
T Consensus 224 ~l~~~l~~~A~~~~Ip~Q~~~~~~ggTDa~~~~~~~~Gi~t~~i~i 269 (292)
T PF05343_consen 224 KLVDKLREIAEENGIPYQREVFSGGGTDAGAIQLSGGGIPTAVISI 269 (292)
T ss_dssp HHHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTSSEEEEEEE
T ss_pred HHHHHHHHHHHHcCCCeEEEecCCcccHHHHHHHcCCCCCEEEEec
Confidence 4999999999999999955 343455443 3333345655655
No 43
>COG1535 EntB Isochorismate hydrolase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=58.89 E-value=10 Score=26.39 Aligned_cols=20 Identities=15% Similarity=0.428 Sum_probs=17.0
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
-..++..+|++.|||++|.-
T Consensus 59 Ni~~Lr~~~~~~giPVvyTa 78 (218)
T COG1535 59 NIAKLRIWCKQAGIPVVYTA 78 (218)
T ss_pred HHHHHHHHHHHcCCcEEEEe
Confidence 35678999999999999874
No 44
>KOG2486 consensus Predicted GTPase [General function prediction only]
Probab=58.58 E-value=8.2 Score=28.51 Aligned_cols=25 Identities=20% Similarity=-0.040 Sum_probs=20.7
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~L 34 (73)
+--...+||.+++||+..|.||-+=
T Consensus 236 ~D~~~i~~~ge~~VP~t~vfTK~DK 260 (320)
T KOG2486|consen 236 TDNPEIAWLGENNVPMTSVFTKCDK 260 (320)
T ss_pred CChHHHHHHhhcCCCeEEeeehhhh
Confidence 4445678999999999999998763
No 45
>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=58.51 E-value=7.3 Score=21.44 Aligned_cols=35 Identities=20% Similarity=0.180 Sum_probs=26.8
Q ss_pred HHHhHHHHHhhCCC-------CEEEeCChhhHhhHhCCCCce
Q 035100 10 ILLHLPLLAEDKNV-------PYVFVPSKQALGRACGVTRPV 44 (73)
Q Consensus 10 ~~~~l~~lc~~~~I-------P~~~v~sk~~LG~a~G~~r~~ 44 (73)
+...+..+|+..+. .+..-.|.++|+..+|.+|.+
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~t 44 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRET 44 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHH
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHH
Confidence 45567777777665 467788999999999998644
No 46
>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=58.40 E-value=4.9 Score=20.86 Aligned_cols=27 Identities=22% Similarity=0.027 Sum_probs=19.1
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
.+..+..+|+++|||-..-..|.+|=.
T Consensus 6 ~~~eL~~iAk~lgI~~~~~~~K~eLI~ 32 (43)
T PF07498_consen 6 TLSELREIAKELGIEGYSKMRKQELIF 32 (43)
T ss_dssp -HHHHHHHHHCTT-TTGCCS-HHHHHH
T ss_pred CHHHHHHHHHHcCCCCCCcCCHHHHHH
Confidence 456788999999999877777777643
No 47
>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=58.23 E-value=33 Score=23.12 Aligned_cols=43 Identities=21% Similarity=0.217 Sum_probs=29.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHh-C--CCCceEEEEEEeCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRAC-G--VTRPVVACSVTSNE 53 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~-G--~~r~~~~vai~~~~ 53 (73)
+-..+...|+..++|+..+... +++... + ..++.-.++|..+|
T Consensus 82 ln~~i~~~a~~~~ilvn~~d~~-e~~~f~~pa~~~~g~l~iaisT~G 127 (205)
T TIGR01470 82 LNRRVAHAARARGVPVNVVDDP-ELCSFIFPSIVDRSPVVVAISSGG 127 (205)
T ss_pred HHHHHHHHHHHcCCEEEECCCc-ccCeEEEeeEEEcCCEEEEEECCC
Confidence 6788999999999999766554 444311 0 22445678898876
No 48
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=57.39 E-value=37 Score=19.86 Aligned_cols=48 Identities=19% Similarity=0.407 Sum_probs=31.1
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-ch-HHHHHHHHHHHH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-AS-QLKTQIQQLKDA 67 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~-~~~~~~~~~~~~ 67 (73)
...++...-+++||||..++| |++. -++.+.+.. .. .+.+.+.+++++
T Consensus 17 F~rk~L~I~E~~~is~Eh~PS--------GID~--~Siii~~~~~~~~~~~~i~~~i~~~ 66 (76)
T cd04911 17 FGRKLLSILEDNGISYEHMPS--------GIDD--ISIIIRDNQLTDEKEQKILAEIKEE 66 (76)
T ss_pred HHHHHHHHHHHcCCCEeeecC--------CCcc--EEEEEEccccchhhHHHHHHHHHHh
Confidence 445677788999999999998 4552 234444443 33 555556666654
No 49
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=56.43 E-value=9.7 Score=24.21 Aligned_cols=40 Identities=33% Similarity=0.341 Sum_probs=29.3
Q ss_pred CCCchhHHHhHHHHHhhCCCCE------EEeCChhhHhhHhCCCCce
Q 035100 4 DTEPLEILLHLPLLAEDKNVPY------VFVPSKQALGRACGVTRPV 44 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~------~~v~sk~~LG~a~G~~r~~ 44 (73)
++..+ +...+..+|+.+|.|. ..-.|.++|+..+|..|.+
T Consensus 114 ~~~~R-la~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tret 159 (193)
T TIGR03697 114 DMGSR-LVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVT 159 (193)
T ss_pred CHHHH-HHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHH
Confidence 44455 6777788898877552 3457999999999988744
No 50
>PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional
Probab=54.88 E-value=7.7 Score=29.63 Aligned_cols=23 Identities=9% Similarity=-0.032 Sum_probs=18.3
Q ss_pred HHHhHHHHHhhCCCCEEEeCChh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
+..-+.++|+++||||...+--+
T Consensus 436 i~piVk~~C~k~glpY~~~~~~~ 458 (485)
T PLN03199 436 CHALVESFCKEWGVKYHEADLVD 458 (485)
T ss_pred hhHHHHHHHHHhCCCccccCHHH
Confidence 66678899999999998766333
No 51
>PRK12723 flagellar biosynthesis regulator FlhF; Provisional
Probab=54.40 E-value=46 Score=24.93 Aligned_cols=49 Identities=8% Similarity=0.072 Sum_probs=34.7
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
.|..-..-...+..+|+..|+|+....+..++..++..-+.. -+.+.|.
T Consensus 214 ~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~~~~-DlVLIDT 262 (388)
T PRK12723 214 IDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQSKDF-DLVLVDT 262 (388)
T ss_pred ccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHhCCC-CEEEEcC
Confidence 344444456678999999999999999988888866544333 3555555
No 52
>PRK07377 hypothetical protein; Provisional
Probab=52.19 E-value=28 Score=23.87 Aligned_cols=34 Identities=21% Similarity=0.225 Sum_probs=29.0
Q ss_pred hhHHHhHHHHHhhCC--CCEEEeCChhhHhhHhCCC
Q 035100 8 LEILLHLPLLAEDKN--VPYVFVPSKQALGRACGVT 41 (73)
Q Consensus 8 ~~~~~~l~~lc~~~~--IP~~~v~sk~~LG~a~G~~ 41 (73)
..+...+..++++|+ +.++.+++.++|++|+-..
T Consensus 93 ~~l~~~l~~~~~~y~~rlElv~y~~~~~l~~aL~~~ 128 (184)
T PRK07377 93 DQLIDQLRTILDKYHLRLELVVYPDLQALEQALRDK 128 (184)
T ss_pred HHHHHHHHHHHHHhCceeeEEecCCHHHHHHHHhcC
Confidence 347888999999998 8888899999999997754
No 53
>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=51.84 E-value=40 Score=24.65 Aligned_cols=43 Identities=16% Similarity=0.101 Sum_probs=27.8
Q ss_pred CchhHHHhHHHHHhhCCCCEEE-eCC----hhhHhhHhCCCCceEEEEE
Q 035100 6 EPLEILLHLPLLAEDKNVPYVF-VPS----KQALGRACGVTRPVVACSV 49 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~-v~s----k~~LG~a~G~~r~~~~vai 49 (73)
.|. +...+..+|+++||||=+ +.+ -..--+..|...+++++++
T Consensus 265 ~~~-l~~~l~~~A~~~~Ip~Q~~~~~~~gtDa~~~~~~~~Gi~t~~i~i 312 (343)
T TIGR03106 265 DYH-LTRKLIRLCQDHGIPHRRDVFRYYRSDAASAVEAGHDIRTALVTF 312 (343)
T ss_pred CHH-HHHHHHHHHHHcCCCcEEEecCCCCChHHHHHHcCCCCCEEEeec
Confidence 355 899999999999999977 443 1111244444455555555
No 54
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=51.66 E-value=46 Score=25.41 Aligned_cols=63 Identities=25% Similarity=0.232 Sum_probs=41.3
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC-chHHHHHHHHHHH
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQIQQLKD 66 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~~~~~~~ 66 (73)
|..-.--+..+..+|+-.|+|+..+.+..+|-.++..=+..=+|.|-.-| +..=..+++++++
T Consensus 242 DtYRIGA~EQLk~Ya~im~vp~~vv~~~~el~~ai~~l~~~d~ILVDTaGrs~~D~~~i~el~~ 305 (407)
T COG1419 242 DTYRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEALRDCDVILVDTAGRSQYDKEKIEELKE 305 (407)
T ss_pred ccchhhHHHHHHHHHHHhCCceEEecCHHHHHHHHHHhhcCCEEEEeCCCCCccCHHHHHHHHH
Confidence 44444456788999999999999999999999887654433345554445 4333333444433
No 55
>PRK03980 flap endonuclease-1; Provisional
Probab=51.44 E-value=50 Score=23.71 Aligned_cols=35 Identities=20% Similarity=0.193 Sum_probs=28.0
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCCh--hhHhhHhC
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSK--QALGRACG 39 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk--~~LG~a~G 39 (73)
.+++. ....+..+++..||||+..++- ++++.++-
T Consensus 79 ~vt~~-~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~ 115 (292)
T PRK03980 79 RLTDE-IVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAK 115 (292)
T ss_pred cCCHH-HHHHHHHHHHHCCCCEEecCchHHHHHHHHHH
Confidence 34555 8888999999999999999986 45777764
No 56
>PRK14725 pyruvate kinase; Provisional
Probab=50.81 E-value=72 Score=25.66 Aligned_cols=58 Identities=12% Similarity=0.224 Sum_probs=36.2
Q ss_pred HHHhHHHHHhhCCCCEEE------------eCChhhHhhHhCCCCceEEEEEEeCC-chHHHHHHHHHHHHH
Q 035100 10 ILLHLPLLAEDKNVPYVF------------VPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQIQQLKDAI 68 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~------------v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~~~~~~~~~ 68 (73)
+.+.+..+|+.+|+|+++ .+|++|..-+..-- ++-|+.+..+. --+-.+.+.++...+
T Consensus 523 iQk~Ii~~c~~~~kPVI~ATQmLESM~~~p~PTRAEvtDVAnAv-gaD~VMLS~G~yPveAV~~l~~I~~r~ 593 (608)
T PRK14725 523 VQEEILWLCEAAHVPVIWATQVLESLAKKGLPSRAEITDAAMAL-RAECVMLNKGPHIVEAVRVLDDILRRM 593 (608)
T ss_pred HHHHHHHHHHHcCCCEEEEcchHhhhccCCCCCchhHHHHHhhh-cCCEEeecCCCCHHHHHHHHHHHHHHH
Confidence 788999999999999998 67778776432211 35566666332 233333344444443
No 57
>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=49.88 E-value=42 Score=24.67 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=29.1
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCCh--hhHh--hHhCCCCceEEEEE
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSK--QALG--RACGVTRPVVACSV 49 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk--~~LG--~a~G~~r~~~~vai 49 (73)
.|. +...+..+|+++||||-++.+. .+-+ +..+...++.++++
T Consensus 264 ~~~-l~~~l~~~A~~~~I~~Q~~~~~gGtDa~~~~~~~~Gvpt~~i~i 310 (350)
T TIGR03107 264 LPR-MKDFLLTTAEEAGIKYQYYVAKGGTDAGAAHLKNSGVPSTTIGV 310 (350)
T ss_pred CHH-HHHHHHHHHHHcCCCcEEecCCCCchHHHHHHhCCCCcEEEEcc
Confidence 344 8999999999999999986542 2222 44444456655655
No 58
>KOG4201 consensus Anthranilate synthase component II [Amino acid transport and metabolism]
Probab=49.48 E-value=43 Score=24.11 Aligned_cols=42 Identities=21% Similarity=0.316 Sum_probs=33.8
Q ss_pred HHHhHHHHHhhCCC-CEEEeCChhhHhhHhCCCCceEEEEEEeCC
Q 035100 10 ILLHLPLLAEDKNV-PYVFVPSKQALGRACGVTRPVVACSVTSNE 53 (73)
Q Consensus 10 ~~~~l~~lc~~~~I-P~~~v~sk~~LG~a~G~~r~~~~vai~~~~ 53 (73)
..+.+-..|+.-|. |.+.|.+++++++++++ ++-+++|-+.+
T Consensus 174 ~lk~l~k~~K~L~me~LVEVn~~eEm~ralei--GakvvGvNNRn 216 (289)
T KOG4201|consen 174 LLKELYKISKDLGMEPLVEVNDEEEMQRALEI--GAKVVGVNNRN 216 (289)
T ss_pred HHHHHHHHHHHcCCcceeeeccHHHHHHHHHh--CcEEEeecCCc
Confidence 56677788988775 89999999999999887 45668886654
No 59
>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=49.29 E-value=30 Score=21.32 Aligned_cols=24 Identities=8% Similarity=0.062 Sum_probs=20.6
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
+....+-.+|+++++|++...+..
T Consensus 101 ~~~~~l~~~~~~~~i~~i~~~~~g 124 (143)
T cd01483 101 AVRRALNRACKELGIPVIDAGGLG 124 (143)
T ss_pred HHHHHHHHHHHHcCCCEEEEcCCC
Confidence 367889999999999999988754
No 60
>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=49.21 E-value=15 Score=24.54 Aligned_cols=29 Identities=10% Similarity=0.259 Sum_probs=23.1
Q ss_pred hhHHHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 8 LEILLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 8 ~~~~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
.+....+-++|+++++|++...+..-.|.
T Consensus 124 ~~~~~~ln~~c~~~~ip~i~~~~~G~~G~ 152 (198)
T cd01485 124 YERTAKVNDVCRKHHIPFISCATYGLIGY 152 (198)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEeecCEEE
Confidence 44778899999999999999877555443
No 61
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=49.19 E-value=3.3 Score=27.03 Aligned_cols=21 Identities=19% Similarity=0.263 Sum_probs=17.3
Q ss_pred HHhHHHHHhhCCCCEEEeCCh
Q 035100 11 LLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk 31 (73)
..+||+.|+..||||+.....
T Consensus 134 ~~KIPdvC~~~gV~ci~~~~~ 154 (162)
T PF14367_consen 134 KIKIPDVCEHFGVPCINLFEF 154 (162)
T ss_pred CCCCChhHHhCCCcCCCHHHH
Confidence 467999999999999766554
No 62
>PRK01889 GTPase RsgA; Reviewed
Probab=49.08 E-value=19 Score=26.32 Aligned_cols=31 Identities=23% Similarity=0.079 Sum_probs=26.9
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
|.++. .+.++..+++..|+|.+.+.+|.+|-
T Consensus 125 ~~~~~-~ldr~L~~a~~~~i~piIVLNK~DL~ 155 (356)
T PRK01889 125 DFNLR-RIERYLALAWESGAEPVIVLTKADLC 155 (356)
T ss_pred CCChh-HHHHHHHHHHHcCCCEEEEEEChhcC
Confidence 45556 88899999999999999999999984
No 63
>PRK12423 LexA repressor; Provisional
Probab=48.98 E-value=21 Score=23.85 Aligned_cols=30 Identities=27% Similarity=0.408 Sum_probs=26.4
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhhHhCC-CC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGRACGV-TR 42 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~-~r 42 (73)
++...+.+.+.++|.| +|-.+|++++|. ++
T Consensus 10 ~il~~l~~~i~~~g~~----Ps~~eia~~~g~~s~ 40 (202)
T PRK12423 10 AILAFIRERIAQAGQP----PSLAEIAQAFGFASR 40 (202)
T ss_pred HHHHHHHHHHHHcCCC----CCHHHHHHHhCCCCh
Confidence 5788899999999999 999999999994 54
No 64
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=48.98 E-value=59 Score=25.70 Aligned_cols=41 Identities=12% Similarity=0.029 Sum_probs=31.1
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE 53 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~ 53 (73)
..+|-.+|+..|.|..++.+.++|-...=. +...++|+.+.
T Consensus 221 t~~L~~i~~~~~~~~~~ie~~~el~~~~~~--~~~~vgitaga 261 (647)
T PRK00087 221 TTKLYEICKSNCTNTIHIENAGELPEEWFK--GVKIIGVTAGA 261 (647)
T ss_pred HHHHHHHHHHHCCCEEEECChHHCCHHHhC--CCCEEEEEecc
Confidence 578999999999999999999999752211 22358887653
No 65
>COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism]
Probab=48.69 E-value=15 Score=27.36 Aligned_cols=43 Identities=28% Similarity=0.353 Sum_probs=29.1
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCCh---hhHh--hHhCCCCceEEEEE
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSK---QALG--RACGVTRPVVACSV 49 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk---~~LG--~a~G~~r~~~~vai 49 (73)
+|. +..++.++|+++||||-+--+. .+-| +.-|-..+++++++
T Consensus 268 ~~~-l~~~L~~~A~~~~Ip~Q~~v~~~ggTDA~a~~~~g~gvpta~Igi 315 (355)
T COG1363 268 HPK-LRKFLLELAEKNNIPYQVDVSPGGGTDAGAAHLTGGGVPTALIGI 315 (355)
T ss_pred CHH-HHHHHHHHHHHcCCCeEEEecCCCCccHHHHHHcCCCCceEEEec
Confidence 355 9999999999999999765444 2222 23333466766666
No 66
>PRK10637 cysG siroheme synthase; Provisional
Probab=48.33 E-value=49 Score=24.93 Aligned_cols=46 Identities=13% Similarity=0.076 Sum_probs=31.4
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChhhHhhHh-C--CCCceEEEEEEeCC
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQALGRAC-G--VTRPVVACSVTSNE 53 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~-G--~~r~~~~vai~~~~ 53 (73)
..++-..+-..|+..|+++..+... +++... + ..++--+++|..+|
T Consensus 82 d~~~n~~i~~~a~~~~~lvN~~d~~-~~~~f~~pa~~~~g~l~iaisT~G 130 (457)
T PRK10637 82 DDAVNQRVSEAAEARRIFCNVVDAP-KAASFIMPSIIDRSPLMVAVSSGG 130 (457)
T ss_pred CHHHhHHHHHHHHHcCcEEEECCCc-ccCeEEEeeEEecCCEEEEEECCC
Confidence 3458889999999999998777665 444210 0 22444678998887
No 67
>PF14370 Topo_C_assoc: C-terminal topoisomerase domain; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=48.07 E-value=5 Score=23.54 Aligned_cols=22 Identities=18% Similarity=0.116 Sum_probs=15.8
Q ss_pred HHHHhhCCCCEEEeCChhhHhh
Q 035100 15 PLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 15 ~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
.++|+.++||+.-+++|..+-+
T Consensus 37 vAWck~~~VPieKifsktlr~K 58 (71)
T PF14370_consen 37 VAWCKRHEVPIEKIFSKTLREK 58 (71)
T ss_dssp HHHHHHTT--GGGTS-HHHHHH
T ss_pred HHHHHHhCCcHHHHhhHHHHHh
Confidence 5899999999999999877653
No 68
>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=47.85 E-value=26 Score=21.46 Aligned_cols=25 Identities=16% Similarity=0.266 Sum_probs=19.2
Q ss_pred hhHHHhHHHHHhhCCCCEEEeCChh
Q 035100 8 LEILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 8 ~~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
.+....+..+|.++++|+++...-.
T Consensus 103 ~~~~~~l~~~~~~~~~p~i~~~~~g 127 (135)
T PF00899_consen 103 LAARLLLNEICREYGIPFIDAGVNG 127 (135)
T ss_dssp HHHHHHHHHHHHHTT-EEEEEEEET
T ss_pred HHHHHHHHHHHHHcCCCEEEEEeec
Confidence 4467788899999999999887643
No 69
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=47.44 E-value=66 Score=22.08 Aligned_cols=41 Identities=15% Similarity=0.064 Sum_probs=31.5
Q ss_pred HhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC
Q 035100 12 LHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE 53 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~ 53 (73)
..+..++++.++|+..+ +++.|-+.++...+-.++++.+..
T Consensus 32 ~~~~~~~~~~~~~~~~v-~~~~l~~l~~~~~~qGv~a~~~~~ 72 (237)
T TIGR00186 32 KKLIQLAKKQGINIQLV-DRQKLDQLTKGGNHQGIAAKVKPI 72 (237)
T ss_pred HHHHHHHHHcCCcEEEe-CHHHHHHHhCCCCCCeEEEEEecC
Confidence 45677888889999998 578999999876555667777653
No 70
>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=46.99 E-value=69 Score=19.90 Aligned_cols=41 Identities=12% Similarity=0.133 Sum_probs=31.9
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEe
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTS 51 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~ 51 (73)
....|..+-+.+..|.+...|.+.+.+..+.+++.. +.+..
T Consensus 63 ~~~~l~~fI~~~~~P~v~~~t~~n~~~~~~~~~~~~-~~~~~ 103 (184)
T PF13848_consen 63 TPEELKKFIKKNSFPLVPELTPENFEKLFSSPKPPV-LILFD 103 (184)
T ss_dssp SHHHHHHHHHHHSSTSCEEESTTHHHHHHSTSSEEE-EEEEE
T ss_pred CHHHHHHHHHHhccccccccchhhHHHHhcCCCceE-EEEEE
Confidence 456677888888999999999999999998876543 44444
No 71
>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=46.80 E-value=26 Score=19.71 Aligned_cols=23 Identities=13% Similarity=0.228 Sum_probs=19.4
Q ss_pred hHHHhHHHHHhhCCCCEEEeCCh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk 31 (73)
.+...+...|+.+||++..+...
T Consensus 57 ~~~~~l~yka~~~Gi~v~~v~~~ 79 (82)
T TIGR01766 57 KLISKIKYKAEEYGIEVIEVNPA 79 (82)
T ss_pred HHHHHHHHHHHHcCCeEEEeCcc
Confidence 46788899999999999998753
No 72
>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=46.43 E-value=20 Score=22.43 Aligned_cols=19 Identities=37% Similarity=0.417 Sum_probs=11.3
Q ss_pred HhHHHHHhhCCCCEEEeCC
Q 035100 12 LHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~s 30 (73)
..+..+|+++++|+....-
T Consensus 95 ~~l~e~a~~~~ipll~t~~ 113 (127)
T PF02603_consen 95 PELIELAEKYNIPLLRTPL 113 (127)
T ss_dssp HHHHHHHHHCT--EEEESS
T ss_pred HHHHHHHHHhCCcEEEcCC
Confidence 4566677777777766544
No 73
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=43.96 E-value=23 Score=18.35 Aligned_cols=19 Identities=26% Similarity=0.396 Sum_probs=15.7
Q ss_pred chhHHHhHHHHHhhCCCCE
Q 035100 7 PLEILLHLPLLAEDKNVPY 25 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~ 25 (73)
|.|+...+..++++.|||-
T Consensus 10 ~~el~~~L~~ls~~t~i~~ 28 (44)
T PF12651_consen 10 DKELYEKLKELSEETGIPK 28 (44)
T ss_pred CHHHHHHHHHHHHHHCCCH
Confidence 3458899999999999985
No 74
>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=43.70 E-value=19 Score=27.24 Aligned_cols=28 Identities=29% Similarity=0.364 Sum_probs=24.8
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRA 37 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a 37 (73)
...++-++|.+++||++.+.+.--.|..
T Consensus 125 ~~~~L~~~c~~~~iPlI~~~s~G~~G~v 152 (425)
T cd01493 125 TLLRLADVLWSANIPLLYVRSYGLYGYI 152 (425)
T ss_pred HHHHHHHHHHHcCCCEEEEecccCEEEE
Confidence 6677999999999999999999888854
No 75
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=43.68 E-value=30 Score=19.39 Aligned_cols=29 Identities=24% Similarity=0.485 Sum_probs=23.3
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGRACGVT 41 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~ 41 (73)
++..+|.+.-+++|.| +|-.++++++|.+
T Consensus 10 ~vL~~I~~~~~~~G~~----Pt~rEIa~~~g~~ 38 (65)
T PF01726_consen 10 EVLEFIREYIEENGYP----PTVREIAEALGLK 38 (65)
T ss_dssp HHHHHHHHHHHHHSS-------HHHHHHHHTSS
T ss_pred HHHHHHHHHHHHcCCC----CCHHHHHHHhCCC
Confidence 4788889999999999 6999999999987
No 76
>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=43.39 E-value=32 Score=20.36 Aligned_cols=27 Identities=19% Similarity=0.171 Sum_probs=20.6
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
++-.++...++++|||++.= ..|.+++
T Consensus 27 ~~A~~I~~~A~e~~VPi~~~---~~LAr~L 53 (82)
T TIGR00789 27 EVAERIIEIAKKHGIPIVED---PDLVDVL 53 (82)
T ss_pred HHHHHHHHHHHHcCCCEEeC---HHHHHHH
Confidence 46789999999999999643 4555554
No 77
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=43.11 E-value=71 Score=22.44 Aligned_cols=41 Identities=17% Similarity=0.370 Sum_probs=30.4
Q ss_pred HHhHHHHHhhCCCCEEEeCChhh------HhhHhCCCCceEEEEEEeC
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQA------LGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~------LG~a~G~~r~~~~vai~~~ 52 (73)
.+.+..+|++++||++.+.+-.. |-+.+|++| ..++-|..+
T Consensus 78 fKef~e~ike~di~fiVvSsGm~~fI~~lfe~ivgke~-i~~idi~sn 124 (220)
T COG4359 78 FKEFVEWIKEHDIPFIVVSSGMDPFIYPLFEGIVGKER-IYCIDIVSN 124 (220)
T ss_pred HHHHHHHHHHcCCCEEEEeCCCchHHHHHHHhhccccc-eeeeEEeec
Confidence 55678899999999999988543 668888885 445555443
No 78
>COG0160 GabT 4-aminobutyrate aminotransferase and related aminotransferases [Amino acid transport and metabolism]
Probab=42.52 E-value=24 Score=27.07 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=19.8
Q ss_pred CCchhHHHhHHHHHhhCCCCEEE
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~ 27 (73)
+-|.++...+.++|+++||+++.
T Consensus 239 v~p~~fl~~l~~~~~~~gillI~ 261 (447)
T COG0160 239 VPPKGFLKALRKLCREHGILLIA 261 (447)
T ss_pred CCCHHHHHHHHHHHHHcCCEEEE
Confidence 34667999999999999999975
No 79
>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=42.08 E-value=34 Score=18.70 Aligned_cols=23 Identities=22% Similarity=0.122 Sum_probs=20.4
Q ss_pred HHHhHHHHHhhCCCCEEEeCChh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
+...|...|+++|++++.|...-
T Consensus 4 ~~~~L~yka~~~G~~v~~v~~~~ 26 (69)
T PF07282_consen 4 FRQRLEYKAEEYGIQVVEVDEAY 26 (69)
T ss_pred HHHHHHHHHHHhCCEEEEECCCC
Confidence 67889999999999999998765
No 80
>PRK00124 hypothetical protein; Validated
Probab=40.30 E-value=34 Score=22.58 Aligned_cols=26 Identities=31% Similarity=0.400 Sum_probs=22.8
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCC
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~s 30 (73)
.|+-| ++..+...++++++|+++|.|
T Consensus 7 ADACP--Vk~~i~r~a~r~~i~v~~Vas 32 (151)
T PRK00124 7 ADACP--VKDIIIRVAERHGIPVTLVAS 32 (151)
T ss_pred CCCCc--HHHHHHHHHHHHCCeEEEEEe
Confidence 46777 788999999999999999985
No 81
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=40.17 E-value=1.1e+02 Score=22.12 Aligned_cols=58 Identities=14% Similarity=0.188 Sum_probs=37.4
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeCCh--hhHhhHhCCCCceEEEEEEeCCchHHHHHHHHH
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVPSK--QALGRACGVTRPVVACSVTSNEASQLKTQIQQL 64 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~sk--~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~ 64 (73)
++|. +...+...|+.+|||++.+.+- ..|.+.+|.+ +.-..+....=+.+|-+.++-+
T Consensus 67 v~~e-lr~~l~~~~~~~~i~~vdll~p~i~~le~~lg~~-p~~~pG~~~~ld~~Yf~RIeAi 126 (269)
T PRK05339 67 VDPE-LREILEERCAEFGIPCIDILGPLIAPLEQELGLK-PTPEPGRTHGLDEEYFKRIEAI 126 (269)
T ss_pred CCHH-HHHHHHHHHHHcCCCEEeccHHHHHHHHHHHCcC-CCCCCCcccCCcHHHHHHHHHH
Confidence 3455 8999999999999999999874 4577777776 2222232222134555555443
No 82
>PRK09864 putative peptidase; Provisional
Probab=40.10 E-value=77 Score=23.50 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=18.6
Q ss_pred CchhHHHhHHHHHhhCCCCEEE
Q 035100 6 EPLEILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~ 27 (73)
.|. +...+..+|+++||||=+
T Consensus 263 ~~~-l~~~l~~~A~~~~Ip~Q~ 283 (356)
T PRK09864 263 NQK-LVAALKSCAAHNDLPLQF 283 (356)
T ss_pred CHH-HHHHHHHHHHHcCCCceE
Confidence 455 899999999999999977
No 83
>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=39.96 E-value=23 Score=17.61 Aligned_cols=25 Identities=12% Similarity=0.157 Sum_probs=18.1
Q ss_pred HhHHHHHhhCCCCEEEeC-ChhhHhh
Q 035100 12 LHLPLLAEDKNVPYVFVP-SKQALGR 36 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~-sk~~LG~ 36 (73)
..+..+.+.+|||+-.-. ++++|=.
T Consensus 7 ~~L~~wL~~~gi~~~~~~~~rd~Ll~ 32 (38)
T PF10281_consen 7 SDLKSWLKSHGIPVPKSAKTRDELLK 32 (38)
T ss_pred HHHHHHHHHcCCCCCCCCCCHHHHHH
Confidence 456777888999987666 7777643
No 84
>COG0800 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]
Probab=39.60 E-value=15 Score=25.57 Aligned_cols=21 Identities=19% Similarity=0.366 Sum_probs=18.2
Q ss_pred CCchhHHHhHHHHHhhCCCCEE
Q 035100 5 TEPLEILLHLPLLAEDKNVPYV 26 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~ 26 (73)
++|+ +-..+...|..+++||+
T Consensus 90 VsP~-~~~ev~~~a~~~~ip~~ 110 (211)
T COG0800 90 VSPG-LNPEVAKAANRYGIPYI 110 (211)
T ss_pred ECCC-CCHHHHHHHHhCCCccc
Confidence 5777 88889999999999986
No 85
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=39.35 E-value=20 Score=24.58 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=27.9
Q ss_pred CCchhHHHhHHHHHhhCCCCEEE-eCChhhHhhHhCCCCceEEEEEEe
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVF-VPSKQALGRACGVTRPVVACSVTS 51 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~-v~sk~~LG~a~G~~r~~~~vai~~ 51 (73)
++|. +...+...|+++|+||+- +.|-.|+=+|.. .++..+=++.
T Consensus 85 vsP~-~~~~v~~~~~~~~i~~iPG~~TptEi~~A~~--~Ga~~vKlFP 129 (204)
T TIGR01182 85 VSPG-LTPELAKHAQDHGIPIIPGVATPSEIMLALE--LGITALKLFP 129 (204)
T ss_pred ECCC-CCHHHHHHHHHcCCcEECCCCCHHHHHHHHH--CCCCEEEECC
Confidence 4677 777888999999999874 345555555532 3333344444
No 86
>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=39.23 E-value=1.1e+02 Score=19.96 Aligned_cols=21 Identities=29% Similarity=0.256 Sum_probs=16.7
Q ss_pred HHhHHHHHhhCCCCEEEeCCh
Q 035100 11 LLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk 31 (73)
...+...|.++|||++.+.+-
T Consensus 69 ~~~~l~~~~~~gIpvv~~d~~ 89 (257)
T PF13407_consen 69 LAPFLEKAKAAGIPVVTVDSD 89 (257)
T ss_dssp THHHHHHHHHTTSEEEEESST
T ss_pred HHHHHHHHhhcCceEEEEecc
Confidence 345566788889999999887
No 87
>PRK06718 precorrin-2 dehydrogenase; Reviewed
Probab=39.14 E-value=89 Score=20.94 Aligned_cols=42 Identities=12% Similarity=0.115 Sum_probs=26.8
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhC---CCCceEEEEEEeCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACG---VTRPVVACSVTSNE 53 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G---~~r~~~~vai~~~~ 53 (73)
+-..+...| ..++++..+.. .++|...= .+++.-.++|..+|
T Consensus 83 lN~~i~~~a-~~~~lvn~~d~-~~~~~f~~Pa~~~~g~l~iaIsT~G 127 (202)
T PRK06718 83 VNEQVKEDL-PENALFNVITD-AESGNVVFPSALHRGKLTISVSTDG 127 (202)
T ss_pred HHHHHHHHH-HhCCcEEECCC-CccCeEEEeeEEEcCCeEEEEECCC
Confidence 777888899 45788766555 44563210 12455678998887
No 88
>PRK03892 ribonuclease P protein component 3; Provisional
Probab=39.10 E-value=56 Score=22.97 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=24.6
Q ss_pred HHhHHHHHhhCCCCEEEeCChh------------hHhhHhCCCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQ------------ALGRACGVTR 42 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~------------~LG~a~G~~r 42 (73)
...+..++++|++|++...+-+ .||..+|.+.
T Consensus 155 ~r~~l~L~rKYd~P~VISS~A~s~~~lRsPRdl~aL~~~iGme~ 198 (216)
T PRK03892 155 MMKAWQLVNKYKVPRFITSSAESKWEVRGPRDLMSLGINIGMEI 198 (216)
T ss_pred HHHHHHHHHHcCCCEEEecCcchhccCCCHHHHHHHHHHhCCCH
Confidence 4567789999999999887654 3777777763
No 89
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=39.03 E-value=21 Score=24.50 Aligned_cols=32 Identities=19% Similarity=0.178 Sum_probs=22.6
Q ss_pred CCchhHHHhHHHHHhhCCCCEEE-eCChhhHhhH
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVF-VPSKQALGRA 37 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~-v~sk~~LG~a 37 (73)
++|. +...+...|+++++||+- +.|-.|+=+|
T Consensus 81 vSP~-~~~~vi~~a~~~~i~~iPG~~TptEi~~A 113 (201)
T PRK06015 81 VSPG-TTQELLAAANDSDVPLLPGAATPSEVMAL 113 (201)
T ss_pred ECCC-CCHHHHHHHHHcCCCEeCCCCCHHHHHHH
Confidence 4677 778888999999999863 3444454444
No 90
>KOG0081 consensus GTPase Rab27, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.28 E-value=30 Score=23.91 Aligned_cols=16 Identities=25% Similarity=0.426 Sum_probs=13.4
Q ss_pred hHHHHHhhCCCCEEEe
Q 035100 13 HLPLLAEDKNVPYVFV 28 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v 28 (73)
...++|++||+||+..
T Consensus 146 qa~~La~kyglPYfET 161 (219)
T KOG0081|consen 146 QAAALADKYGLPYFET 161 (219)
T ss_pred HHHHHHHHhCCCeeee
Confidence 4678999999999764
No 91
>PF00202 Aminotran_3: Aminotransferase class-III; InterPro: IPR005814 Aminotransferases share certain mechanistic features with other pyridoxalphosphate-dependent enzymes, such as the covalent binding of the pyridoxalphosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [] into subfamilies. One of these, called class-III, includes acetylornithine aminotransferase (2.6.1.11 from EC), which catalyzes the transfer of an amino group from acetylornithine to alpha-ketoglutarate, yielding N-acetyl-glutamic-5-semi-aldehyde and glutamic acid; ornithine aminotransferase (2.6.1.13 from EC), which catalyzes the transfer of an amino group from ornithine to alpha-ketoglutarate, yielding glutamic-5-semi-aldehyde and glutamic acid; omega-amino acid--pyruvate aminotransferase (2.6.1.18 from EC), which catalyzes transamination between a variety of omega-amino acids, mono- and diamines, and pyruvate; 4-aminobutyrate aminotransferase (2.6.1.19 from EC) (GABA transaminase), which catalyzes the transfer of an amino group from GABA to alpha-ketoglutarate, yielding succinate semialdehyde and glutamic acid; DAPA aminotransferase (2.6.1.62 from EC), a bacterial enzyme (bioA), which catalyzes an intermediate step in the biosynthesis of biotin, the transamination of 7-keto-8-aminopelargonic acid to form 7,8-diaminopelargonic acid; 2,2-dialkylglycine decarboxylase (4.1.1.64 from EC), a Burkholderia cepacia (Pseudomonas cepacia) enzyme (dgdA) that catalyzes the decarboxylating amino transfer of 2,2-dialkylglycine and pyruvate to dialkyl ketone, alanine and carbon dioxide; glutamate-1-semialdehyde aminotransferase (5.4.3.8 from EC) (GSA); Bacillus subtilis aminotransferases yhxA and yodT; Haemophilus influenzae aminotransferase HI0949; and Caenorhabditis elegans aminotransferase T01B11.2.; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding; PDB: 2JJE_A 2CJH_A 2CIN_A 2JJH_A 2JJF_A 2JJG_A 2CJG_A 2CJD_A 3BS8_A 2YKX_C ....
Probab=37.24 E-value=31 Score=24.73 Aligned_cols=26 Identities=19% Similarity=0.232 Sum_probs=20.2
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChh
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
|.++...+..+|+++|++++.=.-..
T Consensus 196 ~~~~l~~l~~lc~~~gillI~DEV~t 221 (339)
T PF00202_consen 196 PPEYLRELRELCREHGILLIADEVQT 221 (339)
T ss_dssp -TTHHHHHHHHHHHTT-EEEEEETTT
T ss_pred ccchhhehcccccccccceecccccc
Confidence 45699999999999999998755555
No 92
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=37.03 E-value=20 Score=26.68 Aligned_cols=30 Identities=27% Similarity=0.318 Sum_probs=27.9
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
+|+.+...|...++..|+|.-|-++|-.-|
T Consensus 68 DPn~~~~~Il~~lr~~g~~~df~p~kLk~G 97 (359)
T PF10498_consen 68 DPNATISNILDELRKLGVPVDFPPSKLKQG 97 (359)
T ss_pred CHHHHHHHHHHHHHccCCCCCCChHHhhCC
Confidence 899999999999999999999999988766
No 93
>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=36.36 E-value=22 Score=25.58 Aligned_cols=31 Identities=13% Similarity=0.285 Sum_probs=25.6
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChhhHhhH
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQALGRA 37 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a 37 (73)
+.+...++-++|++++||++...+.--.|+.
T Consensus 115 ~~~~~~~in~~c~~~~ipfI~a~~~G~~G~v 145 (286)
T cd01491 115 SLEDQLKINEFCHSPGIKFISADTRGLFGSI 145 (286)
T ss_pred CHHHHHHHHHHHHHcCCEEEEEeccccEEEE
Confidence 3347788999999999999999887777753
No 94
>PRK08187 pyruvate kinase; Validated
Probab=36.27 E-value=1.9e+02 Score=22.53 Aligned_cols=58 Identities=16% Similarity=0.245 Sum_probs=37.9
Q ss_pred HHHhHHHHHhhCCCCEEE------------eCChhhHhhHhCCCCceEEEEEEeCC-chHHHHHHHHHHHHH
Q 035100 10 ILLHLPLLAEDKNVPYVF------------VPSKQALGRACGVTRPVVACSVTSNE-ASQLKTQIQQLKDAI 68 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~------------v~sk~~LG~a~G~~r~~~~vai~~~~-~~~~~~~~~~~~~~~ 68 (73)
+.+.+...|+.+|+|+++ .+|++|..-+..-. ++-|+.+..+. --+-.+.+..+...+
T Consensus 406 ~Qk~II~~craagkpvI~ATQmLESM~~~p~PTRAEvtDvAnad-gaDavMLs~G~ypveaV~~l~~I~~~~ 476 (493)
T PRK08187 406 MQEEILWLCEAAHVPVIWATQVLEGLVKKGLPSRAEMTDAAMAA-RAECVMLNKGPYLVEAVTFLDDLLARM 476 (493)
T ss_pred HHHHHHHHHHHhCCCeEEEchhhHhhccCCCCchHHHHHHHhhc-CCCEEeecCCCCHHHHHHHHHHHHHHH
Confidence 688999999999999986 68888888655444 45567776332 233333344443333
No 95
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=36.21 E-value=25 Score=24.12 Aligned_cols=44 Identities=9% Similarity=0.041 Sum_probs=27.6
Q ss_pred CCchhHHHhHHHHHhhCCCCEEE-eCChhhHhhHhCCCCceEEEEEEe
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVF-VPSKQALGRACGVTRPVVACSVTS 51 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~-v~sk~~LG~a~G~~r~~~~vai~~ 51 (73)
++|. +...+...|+++|+|++- +.|-.++=++.. .++..+.++.
T Consensus 93 vsP~-~~~~v~~~~~~~~i~~iPG~~T~~E~~~A~~--~Gad~vklFP 137 (213)
T PRK06552 93 VSPS-FNRETAKICNLYQIPYLPGCMTVTEIVTALE--AGSEIVKLFP 137 (213)
T ss_pred ECCC-CCHHHHHHHHHcCCCEECCcCCHHHHHHHHH--cCCCEEEECC
Confidence 4666 777888899999999863 444555555532 3344455543
No 96
>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=35.92 E-value=54 Score=20.97 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=22.4
Q ss_pred HhHHHHHhhCCCCEEEeCChhhHhhHhC
Q 035100 12 LHLPLLAEDKNVPYVFVPSKQALGRACG 39 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~sk~~LG~a~G 39 (73)
-.+..+++.+|+++..+.+.++|.+++.
T Consensus 112 ~d~~~lA~a~G~~~~~v~~~~el~~al~ 139 (157)
T cd02001 112 VNLEAWAAACGYLVLSAPLLGGLGSEFA 139 (157)
T ss_pred CCHHHHHHHCCCceEEcCCHHHHHHHHH
Confidence 3577888889999999999988886543
No 97
>PLN03198 delta6-acyl-lipid desaturase; Provisional
Probab=35.84 E-value=23 Score=27.52 Aligned_cols=19 Identities=16% Similarity=0.141 Sum_probs=16.4
Q ss_pred HHHhHHHHHhhCCCCEEEe
Q 035100 10 ILLHLPLLAEDKNVPYVFV 28 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v 28 (73)
+..-++++|+++|+||...
T Consensus 480 i~piVk~~C~k~GlpY~~~ 498 (526)
T PLN03198 480 IAPQVEAFCIKHGLVYEDV 498 (526)
T ss_pred HhHHHHHHHHHcCCCCCCC
Confidence 6667899999999999766
No 98
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.61 E-value=48 Score=22.02 Aligned_cols=29 Identities=24% Similarity=0.244 Sum_probs=24.8
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCChhh
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSKQA 33 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~ 33 (73)
.|+=| ++..+...++++|+|+.+|.+...
T Consensus 8 ADACP--Vk~~i~r~A~r~~~~v~~Van~~~ 36 (150)
T COG1671 8 ADACP--VKDEIYRVAERMGLKVTFVANFPH 36 (150)
T ss_pred CCCCc--hHHHHHHHHHHhCCeEEEEeCCCc
Confidence 35556 789999999999999999999765
No 99
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=35.14 E-value=25 Score=24.38 Aligned_cols=32 Identities=25% Similarity=0.394 Sum_probs=22.4
Q ss_pred CCchhHHHhHHHHHhhCCCCEEE-eCChhhHhhH
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVF-VPSKQALGRA 37 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~-v~sk~~LG~a 37 (73)
++|. +...+.+.|+++|+||+- +.|-.|+=+|
T Consensus 96 VsP~-~~~~v~~~~~~~~i~~iPG~~TpsEi~~A 128 (222)
T PRK07114 96 VTPL-FNPDIAKVCNRRKVPYSPGCGSLSEIGYA 128 (222)
T ss_pred ECCC-CCHHHHHHHHHcCCCEeCCCCCHHHHHHH
Confidence 4676 777888899999999863 4444555444
No 100
>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=34.73 E-value=49 Score=21.46 Aligned_cols=47 Identities=17% Similarity=0.372 Sum_probs=29.7
Q ss_pred HHhhCCCCEEEeCChh----------hHhhHhCCCCceEEEEEEeCC-chHHHHHHHHHHHHHHh
Q 035100 17 LAEDKNVPYVFVPSKQ----------ALGRACGVTRPVVACSVTSNE-ASQLKTQIQQLKDAIEK 70 (73)
Q Consensus 17 lc~~~~IP~~~v~sk~----------~LG~a~G~~r~~~~vai~~~~-~~~~~~~~~~~~~~~~~ 70 (73)
.-.+.++|++.+.+.. .||+++|++..+ .. ..++.+.++++++.+..
T Consensus 78 ~~~~~~ip~~~~~~~~~~~~~~~~i~~lg~~~g~~~~a-------~~~~~~~~~~~~~~~~~~~~ 135 (238)
T PF01497_consen 78 KLLEAGIPVVVFDSSSPFDDWKEQIRQLGKALGKEDQA-------EALIAEYDARLDEIRKRLAK 135 (238)
T ss_dssp HHHHTTSEEEEESSTTCSHHHHHHHHHHHHHHTSHHHH-------HHHHHHHHHHHHHHHHHHHH
T ss_pred HHhcccceEEEeecccchHHHHHHHHHHHHhcccHHHH-------HHHHHHHHHHHHHHHHhhhc
Confidence 3456799999999975 489999966211 00 24555556666665543
No 101
>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=34.51 E-value=47 Score=20.37 Aligned_cols=27 Identities=19% Similarity=0.309 Sum_probs=21.3
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
+-..+.++|++++.|++.++..-.+..
T Consensus 87 iP~~~i~~A~~~~lPli~ip~~~~f~~ 113 (123)
T PF07905_consen 87 IPEEIIELADELGLPLIEIPWEVPFSD 113 (123)
T ss_pred CCHHHHHHHHHcCCCEEEeCCCCCHHH
Confidence 556788999999999999988655443
No 102
>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=34.18 E-value=43 Score=22.33 Aligned_cols=30 Identities=13% Similarity=0.118 Sum_probs=23.5
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
+.+....+-++|.++++|++...+..-.|.
T Consensus 120 ~~~~~~~ln~~c~~~~ip~i~~~~~G~~G~ 149 (197)
T cd01492 120 SRAELVKINELCRKLGVKFYATGVHGLFGF 149 (197)
T ss_pred CHHHHHHHHHHHHHcCCCEEEEEecCCEEE
Confidence 345788899999999999988887555443
No 103
>PRK07449 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase; Validated
Probab=33.22 E-value=1.5e+02 Score=22.59 Aligned_cols=57 Identities=18% Similarity=0.050 Sum_probs=35.9
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhHh----CCCCceEEEEEEeCCchHHHHHHHHHHHHHHhh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRAC----GVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a~----G~~r~~~~vai~~~~~~~~~~~~~~~~~~~~~~ 71 (73)
.+..+++-+|+++..+.+.++|-.++ -.++++.+=..++.. +..+.++...+.++.|
T Consensus 507 df~~lA~a~G~~~~~V~~~~eL~~al~~a~~~~~p~lIev~id~~--~~~~~~~~~~~~~~~~ 567 (568)
T PRK07449 507 DFAHAAAMYGLEYHRPETWAELEEALADALPTPGLTVIEVKTNRS--QGAQLLQALLAQVSHL 567 (568)
T ss_pred CHHHHHHHcCCCccCCCCHHHHHHHHHHHhcCCCCEEEEEeCChh--hhHHHHHHHHHHhhcc
Confidence 57789999999999999999986543 333443322334433 4555555555555544
No 104
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=33.21 E-value=50 Score=15.94 Aligned_cols=23 Identities=13% Similarity=0.066 Sum_probs=15.9
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~L 34 (73)
.+..+.+.|+.+|+|. -.+|.+|
T Consensus 5 ~~~~Lk~~l~~~gl~~--~G~K~~L 27 (35)
T smart00513 5 KVSELKDELKKRGLST--SGTKAEL 27 (35)
T ss_pred cHHHHHHHHHHcCCCC--CCCHHHH
Confidence 3566788899988884 4555554
No 105
>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=32.96 E-value=1.3e+02 Score=18.90 Aligned_cols=28 Identities=25% Similarity=0.490 Sum_probs=20.2
Q ss_pred HHHHHhhCCCCEEEeCChh----------hHhhHhCCC
Q 035100 14 LPLLAEDKNVPYVFVPSKQ----------ALGRACGVT 41 (73)
Q Consensus 14 l~~lc~~~~IP~~~v~sk~----------~LG~a~G~~ 41 (73)
.....++.|+|++.+.... .||+++|++
T Consensus 74 ~~~~l~~~gi~v~~~~~~~~~~~~~~~~~~lg~~~g~~ 111 (195)
T cd01143 74 LLEKLKDAGIPVVVLPAASSLDEIYDQIELIGKITGAE 111 (195)
T ss_pred HHHHHHHcCCcEEEeCCCCCHHHHHHHHHHHHHHhCCh
Confidence 4456678899988776432 588998865
No 106
>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.
Probab=32.88 E-value=38 Score=20.26 Aligned_cols=24 Identities=25% Similarity=0.412 Sum_probs=17.7
Q ss_pred HhHHHHHhhCCCCEEEeCChhhHh
Q 035100 12 LHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
..+..++...++|++.+.+|.+|-
T Consensus 96 ~~i~~~~~~~~~piivv~nK~Dl~ 119 (162)
T cd04138 96 EQIKRVKDSDDVPMVLVGNKCDLA 119 (162)
T ss_pred HHHHHhcCCCCCCEEEEEECcccc
Confidence 444455556789999999998874
No 107
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=32.76 E-value=54 Score=17.03 Aligned_cols=14 Identities=29% Similarity=0.536 Sum_probs=7.1
Q ss_pred HHHHhhCCCCEEEe
Q 035100 15 PLLAEDKNVPYVFV 28 (73)
Q Consensus 15 ~~lc~~~~IP~~~v 28 (73)
..+.+++|+||.++
T Consensus 16 ~~~L~~~~i~y~~~ 29 (60)
T PF00462_consen 16 KEFLDEKGIPYEEV 29 (60)
T ss_dssp HHHHHHTTBEEEEE
T ss_pred HHHHHHcCCeeeEc
Confidence 34445555655544
No 108
>COG2047 Uncharacterized protein (ATP-grasp superfamily) [General function prediction only]
Probab=32.56 E-value=1.2e+02 Score=21.87 Aligned_cols=35 Identities=11% Similarity=0.183 Sum_probs=30.7
Q ss_pred hhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCC
Q 035100 8 LEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTR 42 (73)
Q Consensus 8 ~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r 42 (73)
.++...+.+.++++|.+.+|..+--.-|+.+..+|
T Consensus 102 yel~~~~Ld~a~e~g~~~IyTLGGy~vGkl~eep~ 136 (258)
T COG2047 102 YELTGKILDIAKEFGARMIYTLGGYGVGKLVEEPR 136 (258)
T ss_pred HHHHHHHHHHHHHcCCcEEEEecCcccCcccCCce
Confidence 46788999999999999999999999999987554
No 109
>COG1440 CelA Phosphotransferase system cellobiose-specific component IIB [Carbohydrate transport and metabolism]
Probab=32.36 E-value=50 Score=20.60 Aligned_cols=27 Identities=26% Similarity=0.346 Sum_probs=19.5
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRA 37 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a 37 (73)
....+...++.+|||+..+++. .-|..
T Consensus 61 ~~~~~~~~~~~~giPV~vI~~~-dYG~m 87 (102)
T COG1440 61 MLKQLKEAAEEKGIPVEVIDML-DYGMM 87 (102)
T ss_pred HHHHHHHHhcccCCCeEEeCHH-HccCc
Confidence 3467788899999999888763 33433
No 110
>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=32.30 E-value=2.2e+02 Score=22.05 Aligned_cols=65 Identities=11% Similarity=0.157 Sum_probs=39.3
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCC---ceEEEEEEeC-C-chHHHHHHHHHHHHH
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTR---PVVACSVTSN-E-ASQLKTQIQQLKDAI 68 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r---~~~~vai~~~-~-~~~~~~~~~~~~~~~ 68 (73)
.|.....-...+..+++..|+|+....+-..|.+++..-. .. -+.+.|. | +..-.++++++++.+
T Consensus 277 aDt~RiaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~~~-DvVLIDTaGRs~kd~~lm~EL~~~l 346 (436)
T PRK11889 277 TDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEARV-DYILIDTAGKNYRASETVEEMIETM 346 (436)
T ss_pred cCCcchHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhccCC-CEEEEeCccccCcCHHHHHHHHHHH
Confidence 3444334677788899999999998899888887763211 12 2445554 4 333334455554433
No 111
>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=32.25 E-value=28 Score=20.32 Aligned_cols=16 Identities=19% Similarity=0.218 Sum_probs=13.5
Q ss_pred HHhHHHHHhhCCCCEE
Q 035100 11 LLHLPLLAEDKNVPYV 26 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~ 26 (73)
...+..+|.+++||+.
T Consensus 79 g~~irr~a~~~~Ip~~ 94 (95)
T PF02142_consen 79 GYKIRRAAVEYNIPLF 94 (95)
T ss_dssp HHHHHHHHHHTTSHEE
T ss_pred cHHHHHHHHHcCCCCc
Confidence 4568899999999986
No 112
>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=32.06 E-value=48 Score=20.34 Aligned_cols=20 Identities=20% Similarity=0.104 Sum_probs=16.5
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
-...++..|-+++|||+...
T Consensus 89 dg~~iRr~a~~~~Ip~~Ttl 108 (115)
T cd01422 89 DVKALLRLCDVYNIPLATNR 108 (115)
T ss_pred cHHHHHHHHHHcCCCEEEcH
Confidence 35689999999999998654
No 113
>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=31.98 E-value=57 Score=19.38 Aligned_cols=20 Identities=20% Similarity=0.308 Sum_probs=16.3
Q ss_pred HHhHHHHHhhCCCCEEEeCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~s 30 (73)
...+...++++|+|+..++.
T Consensus 64 ~~~i~~~~~~~~ipv~~I~~ 83 (95)
T TIGR00853 64 LPDLKKETDKKGIPVEVING 83 (95)
T ss_pred HHHHHHHhhhcCCCEEEeCh
Confidence 45677888899999998876
No 114
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. 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 their ligands in the cleft between these domains.
Probab=31.70 E-value=1.4e+02 Score=18.89 Aligned_cols=26 Identities=15% Similarity=0.192 Sum_probs=17.9
Q ss_pred HHHHHhhCCCCEEEeCC----------hhhHhhHhC
Q 035100 14 LPLLAEDKNVPYVFVPS----------KQALGRACG 39 (73)
Q Consensus 14 l~~lc~~~~IP~~~v~s----------k~~LG~a~G 39 (73)
+...-++.|||++++.. -..+|+++|
T Consensus 84 ~~~~l~~~gIpvv~i~~~~~~~~~~~~i~~~g~~~g 119 (186)
T cd01141 84 ILDKLEQLGIPVLYVNEYPSPLGRAEWIKFAAAFYG 119 (186)
T ss_pred HHHHHHHcCCCEEEeCCCCChhhHHHHHHHHHHHcC
Confidence 45555788999988863 223777777
No 115
>PF13727 CoA_binding_3: CoA-binding domain; PDB: 3NKL_B.
Probab=31.58 E-value=52 Score=20.19 Aligned_cols=23 Identities=17% Similarity=0.046 Sum_probs=12.8
Q ss_pred CchhHHHhHHHHHhhCCCCEEEe
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFV 28 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v 28 (73)
++.+.+.++...|++.++.+..+
T Consensus 152 ~~~~~i~~ii~~~~~~~v~v~~v 174 (175)
T PF13727_consen 152 SEEEQIKRIIEELENHGVRVRVV 174 (175)
T ss_dssp S-HHHHHHHHHHHHTTT-EEEE-
T ss_pred cCHHHHHHHHHHHHhCCCEEEEe
Confidence 33446666777777777666554
No 116
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=31.53 E-value=40 Score=22.96 Aligned_cols=46 Identities=13% Similarity=0.093 Sum_probs=32.2
Q ss_pred CCchhHHHhHHHHHhhCCCCEEE-eCChhhHhhHhCCCCceEEEEEEeCC
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVF-VPSKQALGRACGVTRPVVACSVTSNE 53 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~-v~sk~~LG~a~G~~r~~~~vai~~~~ 53 (73)
++|. +-..+...|+++++||+- +.|-.|+=+|.. .+...+=++..+
T Consensus 85 vSP~-~~~~v~~~~~~~~i~~iPG~~TptEi~~A~~--~G~~~vK~FPA~ 131 (196)
T PF01081_consen 85 VSPG-FDPEVIEYAREYGIPYIPGVMTPTEIMQALE--AGADIVKLFPAG 131 (196)
T ss_dssp EESS---HHHHHHHHHHTSEEEEEESSHHHHHHHHH--TT-SEEEETTTT
T ss_pred ECCC-CCHHHHHHHHHcCCcccCCcCCHHHHHHHHH--CCCCEEEEecch
Confidence 4677 788899999999999998 889889877743 344445555543
No 117
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=31.35 E-value=73 Score=18.62 Aligned_cols=26 Identities=12% Similarity=0.101 Sum_probs=21.3
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChh
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
+.++...+...|.++|..+.++....
T Consensus 17 ~e~i~~aIE~YC~~~~~~l~Fisr~~ 42 (74)
T PF14201_consen 17 KEEICEAIEKYCIKNGESLEFISRDK 42 (74)
T ss_pred HHHHHHHHHHHHHHcCCceEEEecCC
Confidence 34578889999999999999987643
No 118
>PRK00098 GTPase RsgA; Reviewed
Probab=31.25 E-value=59 Score=22.97 Aligned_cols=26 Identities=27% Similarity=0.282 Sum_probs=21.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
...++...++..++|++.+.+|.+|-
T Consensus 99 ~idr~L~~~~~~~ip~iIVlNK~DL~ 124 (298)
T PRK00098 99 LLDRFLVLAEANGIKPIIVLNKIDLL 124 (298)
T ss_pred HHHHHHHHHHHCCCCEEEEEEhHHcC
Confidence 55666667888999999999999984
No 119
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=31.17 E-value=72 Score=16.69 Aligned_cols=22 Identities=18% Similarity=0.185 Sum_probs=17.9
Q ss_pred hHHHhHHHHHhhCCCCEEEeCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~s 30 (73)
+...-+..+|+..|||...+.+
T Consensus 11 ~~a~l~~~llr~~GIpar~v~g 32 (68)
T smart00460 11 EFAALFVALLRSLGIPARVVSG 32 (68)
T ss_pred HHHHHHHHHHHHCCCCeEEEee
Confidence 3566678899999999998875
No 120
>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=30.99 E-value=77 Score=19.56 Aligned_cols=26 Identities=27% Similarity=0.167 Sum_probs=20.1
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
.+..+++.+|+++..+.+.++|.+++
T Consensus 127 d~~~~a~~~G~~~~~v~~~~~l~~a~ 152 (168)
T cd00568 127 DFAALAEAYGAKGVRVEDPEDLEAAL 152 (168)
T ss_pred CHHHHHHHCCCeEEEECCHHHHHHHH
Confidence 46677888888888888888887654
No 121
>TIGR02181 GRX_bact Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides.
Probab=30.94 E-value=74 Score=17.35 Aligned_cols=16 Identities=19% Similarity=0.262 Sum_probs=11.2
Q ss_pred hHHHHHhhCCCCEEEe
Q 035100 13 HLPLLAEDKNVPYVFV 28 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v 28 (73)
....+.+++||||.++
T Consensus 14 ~a~~~L~~~~i~~~~~ 29 (79)
T TIGR02181 14 RAKALLSSKGVTFTEI 29 (79)
T ss_pred HHHHHHHHcCCCcEEE
Confidence 4456667788888776
No 122
>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=30.76 E-value=49 Score=19.89 Aligned_cols=18 Identities=22% Similarity=0.004 Sum_probs=15.1
Q ss_pred HHhHHHHHhhCCCCEEEe
Q 035100 11 LLHLPLLAEDKNVPYVFV 28 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v 28 (73)
...++..|-+++|||+.-
T Consensus 88 g~~iRR~A~~~~Ip~~T~ 105 (112)
T cd00532 88 GTALLRLARLYKIPVTTP 105 (112)
T ss_pred hHHHHHHHHHcCCCEEEC
Confidence 557889999999999764
No 123
>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=30.63 E-value=55 Score=19.90 Aligned_cols=20 Identities=10% Similarity=-0.011 Sum_probs=15.7
Q ss_pred HHhHHHHHhhCCCCEEEeCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~s 30 (73)
...+...+..+|||+..++.
T Consensus 61 ~~~i~~~~~~~~ipv~~I~~ 80 (99)
T cd05565 61 YDELKKDTDRLGIKLVTTTG 80 (99)
T ss_pred HHHHHHHhhhcCCCEEEeCH
Confidence 45677788899999987774
No 124
>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=30.63 E-value=1.5e+02 Score=22.54 Aligned_cols=50 Identities=10% Similarity=-0.071 Sum_probs=32.3
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCC
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNE 53 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~ 53 (73)
|....-....+..+|+-+|+|+..+.+..++-.+...-+..-.+.|-..|
T Consensus 230 d~~rigalEQL~~~a~ilGvp~~~v~~~~dl~~al~~l~~~d~VLIDTaG 279 (420)
T PRK14721 230 DSYRIGGHEQLRIYGKLLGVSVRSIKDIADLQLMLHELRGKHMVLIDTVG 279 (420)
T ss_pred CCcchhHHHHHHHHHHHcCCceecCCCHHHHHHHHHHhcCCCEEEecCCC
Confidence 33333456778899999999999999998887654432222234443334
No 125
>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=30.46 E-value=76 Score=21.93 Aligned_cols=22 Identities=9% Similarity=0.161 Sum_probs=18.5
Q ss_pred hHHHhHHHHHhhCCCCEEEeCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~s 30 (73)
+....+-.+|.++++|++...+
T Consensus 114 ~~k~~L~~~c~~~~ip~I~s~g 135 (231)
T cd00755 114 RAKVALIAYCRKRKIPVISSMG 135 (231)
T ss_pred HHHHHHHHHHHHhCCCEEEEeC
Confidence 3667799999999999999754
No 126
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=30.23 E-value=62 Score=22.78 Aligned_cols=21 Identities=24% Similarity=0.387 Sum_probs=18.3
Q ss_pred HHHhHHHHHhhCCCCEEEeCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~s 30 (73)
.+..+..+|.+.||+|+.++.
T Consensus 46 ~l~~iv~~c~~~gI~~vTvYa 66 (243)
T PRK14829 46 VLFDVVAGAIEAGVPYLSLYT 66 (243)
T ss_pred HHHHHHHHHHHcCCCEEEEee
Confidence 678899999999999987764
No 127
>cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign
Probab=30.17 E-value=52 Score=20.74 Aligned_cols=23 Identities=22% Similarity=0.349 Sum_probs=17.0
Q ss_pred hHHHHHhhCCCCEEEeCChhhHh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
.+.......++|++.+.+|.+|-
T Consensus 98 ~i~~~~~~~~~piilvgNK~Dl~ 120 (172)
T cd04141 98 LITRVRLTEDIPLVLVGNKVDLE 120 (172)
T ss_pred HHHHhcCCCCCCEEEEEEChhhh
Confidence 34444445689999999999873
No 128
>PRK12288 GTPase RsgA; Reviewed
Probab=30.08 E-value=50 Score=24.19 Aligned_cols=30 Identities=17% Similarity=0.031 Sum_probs=23.8
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
.++. .+..+..+++..++|.+.+.+|.+|-
T Consensus 134 ~s~~-~Ldr~L~~a~~~~i~~VIVlNK~DL~ 163 (347)
T PRK12288 134 LSLN-IIDRYLVACETLGIEPLIVLNKIDLL 163 (347)
T ss_pred CCHH-HHHHHHHHHHhcCCCEEEEEECccCC
Confidence 3444 66777778899999999999999983
No 129
>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=29.91 E-value=70 Score=20.62 Aligned_cols=26 Identities=27% Similarity=0.257 Sum_probs=20.0
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
.+..+++-+|+++..+.+.++|-.++
T Consensus 133 d~~~lA~a~G~~~~~v~~~~el~~al 158 (175)
T cd02009 133 DFEHLAKAYGLEYRRVSSLDELEQAL 158 (175)
T ss_pred CHHHHHHHcCCCeeeCCCHHHHHHHH
Confidence 46778888888888888888876543
No 130
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=29.79 E-value=49 Score=20.33 Aligned_cols=28 Identities=21% Similarity=0.060 Sum_probs=20.1
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhhHhC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGRACG 39 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G 39 (73)
++-.++...++++|||+.. -..|=+.+.
T Consensus 32 ~iAe~II~~Ake~~Vpi~e---dp~Lv~~L~ 59 (92)
T COG2257 32 EIAEKIIEKAKEHGVPIQE---DPLLVELLL 59 (92)
T ss_pred HHHHHHHHHHHHcCCCccc---CHHHHHHHH
Confidence 4678999999999999954 344444433
No 131
>PRK05965 hypothetical protein; Provisional
Probab=29.50 E-value=55 Score=24.61 Aligned_cols=25 Identities=12% Similarity=0.094 Sum_probs=20.5
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeC
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
.-|.+....+.++|+++|+.++.=.
T Consensus 232 ~p~~~yl~~lr~lc~~~gillI~DE 256 (459)
T PRK05965 232 VPPKGWLKAMREACRELGILFVADE 256 (459)
T ss_pred cCCHHHHHHHHHHHHHcCCEEEEec
Confidence 3456799999999999999987644
No 132
>PHA01623 hypothetical protein
Probab=29.32 E-value=60 Score=17.73 Aligned_cols=18 Identities=11% Similarity=0.230 Sum_probs=14.5
Q ss_pred chhHHHhHHHHHhhCCCC
Q 035100 7 PLEILLHLPLLAEDKNVP 24 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP 24 (73)
|.++...|..+|.++|++
T Consensus 21 deel~~~Ld~y~~~~g~~ 38 (56)
T PHA01623 21 DKDLKTRLKVYCAKNNLQ 38 (56)
T ss_pred CHHHHHHHHHHHHHcCCC
Confidence 345888999999999875
No 133
>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=29.18 E-value=77 Score=18.86 Aligned_cols=21 Identities=19% Similarity=0.123 Sum_probs=16.1
Q ss_pred HHHHHhhCCCCEEEeCChhhH
Q 035100 14 LPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 14 l~~lc~~~~IP~~~v~sk~~L 34 (73)
+...+.+.++|++.+.+|.+|
T Consensus 93 ~~~~~~~~~~~~iiv~NK~Dl 113 (158)
T cd01879 93 LTLQLLELGLPVVVALNMIDE 113 (158)
T ss_pred HHHHHHHcCCCEEEEEehhhh
Confidence 333455678999999999887
No 134
>cd04795 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=28.83 E-value=1e+02 Score=16.64 Aligned_cols=57 Identities=11% Similarity=0.074 Sum_probs=36.6
Q ss_pred HHHhHHHHHhhC-CCCEEEeCChhhH-hh-HhCCCCceEEEEEEeCC-chHHHHHHHHHHH
Q 035100 10 ILLHLPLLAEDK-NVPYVFVPSKQAL-GR-ACGVTRPVVACSVTSNE-ASQLKTQIQQLKD 66 (73)
Q Consensus 10 ~~~~l~~lc~~~-~IP~~~v~sk~~L-G~-a~G~~r~~~~vai~~~~-~~~~~~~~~~~~~ 66 (73)
+...+..+..+. ++|...+.+-... +. +...+....++++...| ..++.+.++.+++
T Consensus 12 ~a~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~i~iS~sg~t~~~~~~~~~a~~ 72 (87)
T cd04795 12 IAAYFALELLELTGIEVVALIATELEHASLLSLLRKGDVVIALSYSGRTEELLAALEIAKE 72 (87)
T ss_pred HHHHHHHHHhcccCCceEEeCCcHHHHHHHHhcCCCCCEEEEEECCCCCHHHHHHHHHHHH
Confidence 455566666677 8888877664432 22 33344455677887777 7778888777665
No 135
>PF10881 DUF2726: Protein of unknown function (DUF2726); InterPro: IPR024402 This domain found in bacterial proteins has no known function.
Probab=28.71 E-value=64 Score=19.62 Aligned_cols=21 Identities=10% Similarity=0.208 Sum_probs=16.4
Q ss_pred HhHHHHHhhCCCCEEEeCChh
Q 035100 12 LHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~sk~ 32 (73)
.....+|+..|||++.+.++.
T Consensus 91 ~~k~~~l~~agiplir~~~~~ 111 (126)
T PF10881_consen 91 EFKDRVLKKAGIPLIRISPKD 111 (126)
T ss_pred HHHHHHHHHCCCCEEEEeCCC
Confidence 456678899999999996643
No 136
>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=28.66 E-value=42 Score=19.12 Aligned_cols=20 Identities=20% Similarity=0.323 Sum_probs=15.9
Q ss_pred HHhHHHHHhhCCCCEEEeCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~s 30 (73)
.+|.--+|+++|||++.--+
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 47888999999999987664
No 137
>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=28.46 E-value=62 Score=22.26 Aligned_cols=25 Identities=28% Similarity=0.316 Sum_probs=19.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~L 34 (73)
.+..+..+++..++|++.+.+|.+|
T Consensus 55 ~l~r~l~~~~~~~i~~vIV~NK~DL 79 (245)
T TIGR00157 55 QLDRFLVVAEAQNIEPIIVLNKIDL 79 (245)
T ss_pred HHHHHHHHHHHCCCCEEEEEECccc
Confidence 4555566777788888888888887
No 138
>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=28.42 E-value=90 Score=19.81 Aligned_cols=26 Identities=23% Similarity=0.126 Sum_probs=17.9
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
.+..+++.+|+++..+.+.++|..++
T Consensus 130 d~~~la~a~G~~~~~v~~~~el~~al 155 (172)
T cd02004 130 RYDLVAEAFGGKGELVTTPEELKPAL 155 (172)
T ss_pred CHHHHHHHCCCeEEEECCHHHHHHHH
Confidence 35667777777777777777776543
No 139
>cd02015 TPP_AHAS Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate. 2-Acetolactate is the precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to form 2-aceto-2-hydroxybutyrate in isoleucine biosynthesis. In addition to requiring TPP and a divalent metal ion as cofactors, AHAS requires FAD.
Probab=28.00 E-value=93 Score=20.10 Aligned_cols=26 Identities=23% Similarity=0.146 Sum_probs=21.9
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
.+..+++-+|++...+.+.++|.+++
T Consensus 132 d~~~~a~a~G~~~~~v~~~~el~~al 157 (186)
T cd02015 132 DFVKLAEAYGIKGLRVEKPEELEAAL 157 (186)
T ss_pred CHHHHHHHCCCceEEeCCHHHHHHHH
Confidence 46778899999999999999987654
No 140
>cd04103 Centaurin_gamma Centaurin gamma. The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues.
Probab=27.99 E-value=74 Score=19.87 Aligned_cols=25 Identities=16% Similarity=0.356 Sum_probs=17.5
Q ss_pred HhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 12 LHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
..+...+.-.++|++.+.+|.+|+.
T Consensus 89 ~~i~~~~~~~~~piilvgnK~Dl~~ 113 (158)
T cd04103 89 HQLSSYRNISEIPLILVGTQDAISE 113 (158)
T ss_pred HHHHHhcCCCCCCEEEEeeHHHhhh
Confidence 3344443336799999999999864
No 141
>PF10096 DUF2334: Uncharacterized protein conserved in bacteria (DUF2334); InterPro: IPR018763 This group of proteins has no known function.
Probab=27.80 E-value=84 Score=21.71 Aligned_cols=25 Identities=24% Similarity=0.391 Sum_probs=18.3
Q ss_pred CCCCc---hhHHHhHHHHHhhCCCCEEE
Q 035100 3 ADTEP---LEILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 3 ~D~~p---~~~~~~l~~lc~~~~IP~~~ 27 (73)
+|++| .+....+.+...++|||+..
T Consensus 7 eDVsP~~~~~~l~~i~d~l~~~~ipf~v 34 (243)
T PF10096_consen 7 EDVSPFSDLEKLKEIADYLYKYGIPFSV 34 (243)
T ss_pred eCCCCCCCHHHHHHHHHHHHHCCCCEEE
Confidence 57777 23667788888899999653
No 142
>cd01147 HemV-2 Metal binding protein HemV-2. 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=27.76 E-value=1.9e+02 Score=19.14 Aligned_cols=49 Identities=14% Similarity=0.279 Sum_probs=27.9
Q ss_pred HHHHHhhCCCCEEEeCCh----------hhHhhHhCCCCceEEEEEEeCCchHHHHHHHHHHHHH
Q 035100 14 LPLLAEDKNVPYVFVPSK----------QALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAI 68 (73)
Q Consensus 14 l~~lc~~~~IP~~~v~sk----------~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~~~~~ 68 (73)
+..+.+..|+|++.+.+. ..||+++|++..+. .+ ..++++.++++++.+
T Consensus 90 ~~~l~~~~gipvv~~~~~~~~~~~~~~i~~lg~~~g~~~~a~--~~----~~~~~~~~~~i~~~~ 148 (262)
T cd01147 90 ADDLQKKTGIPVVVLDGGDSLEDTPEQIRLLGKVLGKEERAE--EL----ISFIESILADVEERT 148 (262)
T ss_pred HHHHHHhhCCCEEEEecCCchHhHHHHHHHHHHHhCCHHHHH--HH----HHHHHHHHHHHHHHh
Confidence 344445588999888764 34888888652110 00 234555555555554
No 143
>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=27.58 E-value=2e+02 Score=19.42 Aligned_cols=65 Identities=17% Similarity=0.194 Sum_probs=36.9
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCC--hhhHhhHhCCCCceEEEEEEeC-----C-chHHHHHHHHHHHHHHh
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPS--KQALGRACGVTRPVVACSVTSN-----E-ASQLKTQIQQLKDAIEK 70 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~s--k~~LG~a~G~~r~~~~vai~~~-----~-~~~~~~~~~~~~~~~~~ 70 (73)
+.+|. -+..+....++++|++++..+ ...+.+.+..+.++.+ ..++. . ..++.+.++..-+.+.+
T Consensus 182 ~ps~~-~l~~l~~~ik~~~v~~i~~e~~~~~~~~~~la~~~g~~v-v~ld~l~~~~~~~~~y~~~~~~n~~~l~~ 254 (256)
T PF01297_consen 182 EPSPK-DLAELIKLIKENKVKCIFTEPQFSSKLAEALAKETGVKV-VYLDPLGGGIPDGDSYLDMMEQNLDTLAE 254 (256)
T ss_dssp SS-HH-HHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHCCT-EE-EESSTTCSTTSSTTSHHHHHHHHHHHHHH
T ss_pred CCCHH-HHHHHHHHhhhcCCcEEEecCCCChHHHHHHHHHcCCcE-EEeCCCcCCCCCcCCHHHHHHHHHHHHHH
Confidence 45666 677788999999999999864 3334444433323333 33332 1 45777777766555543
No 144
>PF15496 DUF4646: Domain of unknown function (DUF4646)
Probab=27.57 E-value=51 Score=20.73 Aligned_cols=19 Identities=21% Similarity=0.120 Sum_probs=17.7
Q ss_pred CCCCCchhHHHhHHHHHhh
Q 035100 2 AADTEPLEILLHLPLLAED 20 (73)
Q Consensus 2 A~D~~p~~~~~~l~~lc~~ 20 (73)
++|+++.||..++.++.+.
T Consensus 44 ~~DVs~eDW~~F~~dl~~a 62 (123)
T PF15496_consen 44 SHDVSEEDWTRFLNDLSEA 62 (123)
T ss_pred hcCCCHHHHHHHHHHHHHH
Confidence 5899999999999999988
No 145
>COG1162 Predicted GTPases [General function prediction only]
Probab=27.23 E-value=64 Score=23.65 Aligned_cols=31 Identities=29% Similarity=0.205 Sum_probs=25.9
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
|.+++ ++.++..+|+..||.-+.+-+|.+|.
T Consensus 93 ~~~~~-~ldR~Lv~ae~~gi~pvIvlnK~DL~ 123 (301)
T COG1162 93 DFNTN-LLDRYLVLAEAGGIEPVIVLNKIDLL 123 (301)
T ss_pred CCCHH-HHHHHHHHHHHcCCcEEEEEEccccC
Confidence 55666 88888999999999988888888876
No 146
>PF02404 SCF: Stem cell factor; InterPro: IPR003452 Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. SCF stimulates the proliferation of mast cells and is able to augment the proliferation of both myeloid and lymphoid hematopoietic progenitors in bone marrow culture. It also mediates cell-cell adhesion and acts synergistically with other cytokines. SCF is a type I membrane protein, but is also found in a secretable, soluble form. The crystal structure of human SCF has been resolved and a potential receptor-binding site identified [].; GO: 0005173 stem cell factor receptor binding, 0007155 cell adhesion, 0016020 membrane; PDB: 1EXZ_A 1SCF_D 2E9W_C 2O26_A 2O27_A.
Probab=27.17 E-value=31 Score=25.05 Aligned_cols=30 Identities=20% Similarity=0.399 Sum_probs=18.2
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHhhHhCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALGRACGV 40 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~ 40 (73)
..-...+=.+|.||+-||+.++.||..|=.
T Consensus 41 ~~L~~NiP~DY~i~l~Yvp~~d~lp~~CWl 70 (273)
T PF02404_consen 41 SKLVANIPKDYKIPLKYVPKMDGLPGHCWL 70 (273)
T ss_dssp HHHHHTS-TT--EEEEE-TTTTTS-HHHCH
T ss_pred HHHHcCCCcccEeeeecccCCCCCCCceee
Confidence 333444557899999999999998876643
No 147
>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 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 a domain found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. In Salmonella enterica subsp. enterica serovar Typhimurium, PrpR acts as a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate []. ; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay); PDB: 2Q5C_A 2PJU_A.
Probab=26.94 E-value=73 Score=20.63 Aligned_cols=24 Identities=29% Similarity=0.426 Sum_probs=13.8
Q ss_pred HHHHHhhCCCCEEEeCC-hhhHhhH
Q 035100 14 LPLLAEDKNVPYVFVPS-KQALGRA 37 (73)
Q Consensus 14 l~~lc~~~~IP~~~v~s-k~~LG~a 37 (73)
...+|+++|+|++.+.| ++.+=+|
T Consensus 135 ~~~~A~~~gl~~v~i~sg~esi~~A 159 (176)
T PF06506_consen 135 VCRLARKLGLPGVLIESGEESIRRA 159 (176)
T ss_dssp HHHHHHHTTSEEEESS--HHHHHHH
T ss_pred HHHHHHHcCCcEEEEEecHHHHHHH
Confidence 35666777777777766 4444443
No 148
>PRK15116 sulfur acceptor protein CsdL; Provisional
Probab=26.93 E-value=1e+02 Score=21.91 Aligned_cols=21 Identities=14% Similarity=0.104 Sum_probs=17.8
Q ss_pred HHHhHHHHHhhCCCCEEEeCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~s 30 (73)
....+-++|.++++|++...+
T Consensus 134 ~k~~L~~~c~~~~ip~I~~gG 154 (268)
T PRK15116 134 PKAALIAYCRRNKIPLVTTGG 154 (268)
T ss_pred HHHHHHHHHHHcCCCEEEECC
Confidence 667899999999999998743
No 149
>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=26.87 E-value=1.8e+02 Score=21.78 Aligned_cols=42 Identities=17% Similarity=0.018 Sum_probs=29.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
-...+..+++.+|+|+..+.+..+|..++..-+..- +.++|.
T Consensus 182 a~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~~D-lVLIDT 223 (374)
T PRK14722 182 GHEQLRIFGKILGVPVHAVKDGGDLQLALAELRNKH-MVLIDT 223 (374)
T ss_pred HHHHHHHHHHHcCCceEecCCcccHHHHHHHhcCCC-EEEEcC
Confidence 356788899999999999999888876654322332 444444
No 150
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=26.77 E-value=2.2e+02 Score=19.65 Aligned_cols=40 Identities=13% Similarity=0.004 Sum_probs=30.9
Q ss_pred HhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 12 LHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
..+..+++++++|+..+ +++.|-+.++...+-.++++.+.
T Consensus 37 ~~~~~~~~~~~i~~~~v-~~~~l~~ls~~~~~qGv~a~~~~ 76 (244)
T PRK11181 37 LPLINELEAQGIVIQLA-NRQTLDEKAEGAVHQGIIARVKP 76 (244)
T ss_pred HHHHHHHHHcCCcEEEe-CHHHHhhhhcCCCCceEEEEEec
Confidence 55667888889998776 57889999987666666777765
No 151
>PTZ00217 flap endonuclease-1; Provisional
Probab=26.71 E-value=83 Score=23.59 Aligned_cols=35 Identities=9% Similarity=-0.019 Sum_probs=26.7
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCChh--hHhhHhC
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSKQ--ALGRACG 39 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk~--~LG~a~G 39 (73)
++++. ....+..+++..||||+..+.-+ +++.++-
T Consensus 134 ~vt~~-~~~~~~~lL~~~Gip~i~AP~EAdaq~A~L~~ 170 (393)
T PTZ00217 134 RVTKE-QNEDAKKLLRLMGIPVIEAPCEAEAQCAELVK 170 (393)
T ss_pred cCCHH-HHHHHHHHHHHcCCceEECCcCHHHHHHHHHH
Confidence 45555 77889999999999999988853 3666653
No 152
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=26.64 E-value=54 Score=15.76 Aligned_cols=16 Identities=25% Similarity=0.246 Sum_probs=12.2
Q ss_pred hHHHhHHHHHhhCCCC
Q 035100 9 EILLHLPLLAEDKNVP 24 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP 24 (73)
++...+..+|++.|.+
T Consensus 9 ~~~~~l~~~a~~~g~s 24 (39)
T PF01402_consen 9 ELYERLDELAKELGRS 24 (39)
T ss_dssp HHHHHHHHHHHHHTSS
T ss_pred HHHHHHHHHHHHHCcC
Confidence 4778888888887754
No 153
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=26.50 E-value=45 Score=18.12 Aligned_cols=17 Identities=18% Similarity=0.157 Sum_probs=13.3
Q ss_pred CCCchhHHHhHHHHHhhC
Q 035100 4 DTEPLEILLHLPLLAEDK 21 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~ 21 (73)
+++.. +..++.+||+.+
T Consensus 44 ~v~~~-~L~kViewc~~H 60 (62)
T PF03931_consen 44 NVSSR-ILKKVIEWCEHH 60 (62)
T ss_dssp TS-HH-HHHHHHHHHHHH
T ss_pred ccCHH-HHHHHHHHHHhc
Confidence 56677 899999999875
No 154
>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=26.40 E-value=1.9e+02 Score=18.79 Aligned_cols=41 Identities=17% Similarity=0.121 Sum_probs=28.9
Q ss_pred hHHHHHhhCCCCEEEeC-ChhhHhhHhCC--CCceEEEEEEeCC
Q 035100 13 HLPLLAEDKNVPYVFVP-SKQALGRACGV--TRPVVACSVTSNE 53 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~-sk~~LG~a~G~--~r~~~~vai~~~~ 53 (73)
.+..+++.+|+++..+. +.++|..++.. +.++.+-+.++.+
T Consensus 114 d~~~lA~a~G~~~~~v~~~~~el~~al~~a~~gp~lIev~~~~~ 157 (179)
T cd03372 114 DLEAVAKACGLDNVATVASEEAFEKAVEQALDGPSFIHVKIKPG 157 (179)
T ss_pred CHHHHHHHcCCCeEEecCCHHHHHHHHHHhcCCCEEEEEEEcCC
Confidence 46778999999999999 88888866543 3455444445443
No 155
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=26.35 E-value=56 Score=21.52 Aligned_cols=21 Identities=14% Similarity=0.088 Sum_probs=18.4
Q ss_pred HHHhHHHHHhhCCCCEEEeCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~s 30 (73)
+...+..||+++||+++.-.+
T Consensus 126 ~r~~a~eWleen~I~~~~~~~ 146 (163)
T PF03682_consen 126 LRERAIEWLEENGIEPVFEED 146 (163)
T ss_pred HHHHHHHHHHHcCCCcccccc
Confidence 567788999999999998886
No 156
>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=26.19 E-value=1.7e+02 Score=24.18 Aligned_cols=50 Identities=16% Similarity=0.076 Sum_probs=34.3
Q ss_pred CCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 2 AADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 2 A~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
+.|....-....+..+++..|+|+..+.+..++-.++..-... -+.++|.
T Consensus 222 t~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~~~~~-D~VLIDT 271 (767)
T PRK14723 222 TTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAALGDK-HLVLIDT 271 (767)
T ss_pred cCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHHhcCC-CEEEEeC
Confidence 3455444467788999999999999888888887776543333 2445554
No 157
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=25.85 E-value=62 Score=18.26 Aligned_cols=21 Identities=14% Similarity=0.412 Sum_probs=15.8
Q ss_pred HHHHhhCCCCEEEeCChhhHh
Q 035100 15 PLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 15 ~~lc~~~~IP~~~v~sk~~LG 35 (73)
...+...|+||+.+-+..++.
T Consensus 45 ~~~a~~~g~p~~iiiG~~e~~ 65 (94)
T PF03129_consen 45 IKYADKLGIPFIIIIGEKELE 65 (94)
T ss_dssp HHHHHHTTESEEEEEEHHHHH
T ss_pred HHHHhhcCCeEEEEECchhHh
Confidence 345667788888888888864
No 158
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=25.71 E-value=81 Score=19.24 Aligned_cols=20 Identities=15% Similarity=0.252 Sum_probs=15.7
Q ss_pred HHhHHHHHhhCCCCEEEeCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~s 30 (73)
...+...|+.+|+|+..++.
T Consensus 64 ~~~i~~~~~~~~ipv~~I~~ 83 (104)
T PRK09590 64 FKQFEEAGAKVGKPVVQIPP 83 (104)
T ss_pred HHHHHHHhhhcCCCEEEeCH
Confidence 45577788889999988765
No 159
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=25.62 E-value=70 Score=21.92 Aligned_cols=45 Identities=16% Similarity=0.097 Sum_probs=32.0
Q ss_pred CchhHHHhHHHHHhhCCCCEE-EeCChhhHhhHhCCCCceEEEEEEeCC
Q 035100 6 EPLEILLHLPLLAEDKNVPYV-FVPSKQALGRACGVTRPVVACSVTSNE 53 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~-~v~sk~~LG~a~G~~r~~~~vai~~~~ 53 (73)
+|. +-..+...|.+++||++ =+.|-.+.-++.. -++..+-+++.+
T Consensus 93 sP~-~~~~vi~~a~~~~i~~iPG~~TptEi~~a~~--~Ga~~vKlFPa~ 138 (212)
T PRK05718 93 SPG-LTPPLLKAAQEGPIPLIPGVSTPSELMLGME--LGLRTFKFFPAE 138 (212)
T ss_pred CCC-CCHHHHHHHHHcCCCEeCCCCCHHHHHHHHH--CCCCEEEEccch
Confidence 455 66678889999999999 7888888777743 334456666644
No 160
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=25.58 E-value=70 Score=25.46 Aligned_cols=31 Identities=23% Similarity=0.373 Sum_probs=26.6
Q ss_pred CCCCCchhHHHhHHHHHhhCCCCEEEeCChhh
Q 035100 2 AADTEPLEILLHLPLLAEDKNVPYVFVPSKQA 33 (73)
Q Consensus 2 A~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~ 33 (73)
+-|++|. +...+...|+..||+|+..+--+.
T Consensus 122 ~VdIT~~-ma~~lI~~~r~~nVe~IVAPyEAD 152 (556)
T KOG2518|consen 122 CVDITPE-MAHKLIQYLRSQNVEYIVAPYEAD 152 (556)
T ss_pred hccCcHH-HHHHHHHHHHHcCCceEecCcccc
Confidence 4588998 999999999999999998776544
No 161
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=25.40 E-value=78 Score=25.13 Aligned_cols=32 Identities=16% Similarity=0.306 Sum_probs=28.5
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhCCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACGVT 41 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~ 41 (73)
+..++..+|++.++|...+....++|.|+.-+
T Consensus 546 VArkiselaRe~giTlivvThrpEv~~AL~PD 577 (593)
T COG2401 546 VARKISELAREAGITLIVVTHRPEVGNALRPD 577 (593)
T ss_pred HHHHHHHHHHHhCCeEEEEecCHHHHhccCCc
Confidence 56789999999999999999999999997533
No 162
>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=25.40 E-value=60 Score=18.58 Aligned_cols=16 Identities=25% Similarity=0.158 Sum_probs=13.9
Q ss_pred HHhHHHHHhhCCCCEE
Q 035100 11 LLHLPLLAEDKNVPYV 26 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~ 26 (73)
...++..|.+++||+.
T Consensus 74 ~~~iRr~A~~~~Ip~~ 89 (90)
T smart00851 74 GKALRRAAENIDIPGA 89 (90)
T ss_pred cHHHHHHHHHcCCCee
Confidence 4578999999999986
No 163
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=25.31 E-value=61 Score=24.46 Aligned_cols=22 Identities=23% Similarity=0.173 Sum_probs=19.3
Q ss_pred CCCCCCchhHHHhHHHHHhhCC
Q 035100 1 MAADTEPLEILLHLPLLAEDKN 22 (73)
Q Consensus 1 iA~D~~p~~~~~~l~~lc~~~~ 22 (73)
|..|+++.|+++.+..|+.+|+
T Consensus 12 V~k~As~~EIKkAYRkLA~kyH 33 (371)
T COG0484 12 VSKDASEEEIKKAYRKLAKKYH 33 (371)
T ss_pred CCCCCCHHHHHHHHHHHHHHhC
Confidence 4578999999999999999986
No 164
>PRK11440 putative hydrolase; Provisional
Probab=25.19 E-value=91 Score=20.19 Aligned_cols=19 Identities=21% Similarity=0.193 Sum_probs=15.6
Q ss_pred HHhHHHHHhhCCCCEEEeC
Q 035100 11 LLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~ 29 (73)
+..+.+.++..|+|++++.
T Consensus 37 i~~l~~~ar~~g~pVi~~~ 55 (188)
T PRK11440 37 AARLAAKFRASGSPVVLVR 55 (188)
T ss_pred HHHHHHHHHHcCCcEEEEe
Confidence 4667788999999999874
No 165
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=25.10 E-value=35 Score=18.54 Aligned_cols=27 Identities=15% Similarity=0.049 Sum_probs=21.3
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCCh
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk 31 (73)
+.++. ....+-++++++|.+.+.+.+.
T Consensus 20 ~i~~~-~l~~la~ia~~yg~~~irlT~~ 46 (69)
T PF03460_consen 20 RISAE-QLRALAEIAEKYGDGEIRLTTR 46 (69)
T ss_dssp EEEHH-HHHHHHHHHHHHSTSEEEEETT
T ss_pred EECHH-HHHHHHHHHHHhCCCeEEECCC
Confidence 44555 7888999999999999887663
No 166
>cd01863 Rab18 Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. 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 mos
Probab=24.75 E-value=55 Score=19.76 Aligned_cols=25 Identities=16% Similarity=0.181 Sum_probs=18.5
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
...+...+...++|++.+.+|.++-
T Consensus 95 ~~~i~~~~~~~~~~~~iv~nK~D~~ 119 (161)
T cd01863 95 LNELETYSTNNDIVKMLVGNKIDKE 119 (161)
T ss_pred HHHHHHhCCCCCCcEEEEEECCccc
Confidence 3344455667889999999998875
No 167
>PF13241 NAD_binding_7: Putative NAD(P)-binding; PDB: 3DFZ_B 1PJT_A 1PJS_A 1PJQ_A 1KYQ_B.
Probab=24.68 E-value=86 Score=18.47 Aligned_cols=23 Identities=13% Similarity=0.004 Sum_probs=18.6
Q ss_pred hHHHhHHHHHhhCCCCEEEeCCh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk 31 (73)
++-..+...|+.+++|+..+...
T Consensus 72 ~~n~~i~~~a~~~~i~vn~~D~p 94 (103)
T PF13241_consen 72 ELNEAIYADARARGILVNVVDDP 94 (103)
T ss_dssp HHHHHHHHHHHHTTSEEEETT-C
T ss_pred HHHHHHHHHHhhCCEEEEECCCc
Confidence 47888999999999999877653
No 168
>PRK06943 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional
Probab=24.59 E-value=73 Score=23.95 Aligned_cols=24 Identities=17% Similarity=0.059 Sum_probs=20.0
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeC
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
-|.+....+..+|+++|+.++.=.
T Consensus 240 ~~~~yl~~lr~lc~~~gillI~DE 263 (453)
T PRK06943 240 HDPSYLRGLRALCDRYGVHLIADE 263 (453)
T ss_pred CCHHHHHHHHHHHHHcCCEEEeec
Confidence 456799999999999999997543
No 169
>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=24.54 E-value=1e+02 Score=21.27 Aligned_cols=28 Identities=21% Similarity=0.150 Sum_probs=20.8
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
+....+-++|.++++|+++-....--|+
T Consensus 126 ~~r~~ln~~~~~~~ip~v~~~~~g~~G~ 153 (240)
T TIGR02355 126 EVRNQLNRQCFAAKVPLVSGAAIRMEGQ 153 (240)
T ss_pred HHHHHHHHHHHHcCCCEEEEEecccEeE
Confidence 4777889999999999998654433343
No 170
>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=24.47 E-value=54 Score=18.36 Aligned_cols=19 Identities=26% Similarity=0.322 Sum_probs=12.0
Q ss_pred HHHhhCCCCEEEeCChhhH
Q 035100 16 LLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 16 ~lc~~~~IP~~~v~sk~~L 34 (73)
..++..|+||+.+-+..++
T Consensus 48 ~~a~~~g~~~~iiiG~~e~ 66 (94)
T cd00861 48 ADADLIGIPYRIVVGKKSA 66 (94)
T ss_pred hHHHhcCCCEEEEECCchh
Confidence 3456667777776666654
No 171
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=24.44 E-value=90 Score=21.81 Aligned_cols=20 Identities=10% Similarity=0.001 Sum_probs=17.6
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
.+..+..+|.+.||+++.++
T Consensus 31 ~~~~v~~~c~~~GI~~lT~y 50 (226)
T TIGR00055 31 SLRRILRWCANLGVECLTLY 50 (226)
T ss_pred HHHHHHHHHHHcCCCEEEEE
Confidence 67889999999999998775
No 172
>cd02002 TPP_BFDC Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This enzyme is dependent on TPP and a divalent metal cation as cofactors.
Probab=24.42 E-value=1.2e+02 Score=19.24 Aligned_cols=26 Identities=19% Similarity=0.146 Sum_probs=20.0
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
.+..+++-+|.++..+.+.++|..++
T Consensus 137 d~~~~a~a~G~~~~~v~~~~el~~al 162 (178)
T cd02002 137 DFAAIAKAFGVEAERVETPEELDEAL 162 (178)
T ss_pred CHHHHHHHcCCceEEeCCHHHHHHHH
Confidence 46678888888888888888877654
No 173
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=24.21 E-value=72 Score=18.88 Aligned_cols=17 Identities=24% Similarity=0.268 Sum_probs=14.2
Q ss_pred HHhHHHHHhhCCCCEEE
Q 035100 11 LLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~ 27 (73)
-..++..|-++|||++.
T Consensus 84 ~~~iRR~Av~~~ipl~T 100 (110)
T cd01424 84 GFSIRRAALEYKVPYFT 100 (110)
T ss_pred HHHHHHHHHHhCCCEEe
Confidence 35788999999999973
No 174
>KOG3351 consensus Predicted nucleotidyltransferase [General function prediction only]
Probab=24.16 E-value=1.2e+02 Score=22.19 Aligned_cols=37 Identities=24% Similarity=0.325 Sum_probs=25.1
Q ss_pred HhhHhCCCCceEEEEEEeCC---chHHHHHHHHHHHHHHh
Q 035100 34 LGRACGVTRPVVACSVTSNE---ASQLKTQIQQLKDAIEK 70 (73)
Q Consensus 34 LG~a~G~~r~~~~vai~~~~---~~~~~~~~~~~~~~~~~ 70 (73)
|..++=..+...+|+|+|++ .+.++++++-+.+.++.
T Consensus 162 Ls~aa~la~~~lVvGV~d~elL~kK~~~Eliepie~R~~~ 201 (293)
T KOG3351|consen 162 LSVAAELASDRLVVGVTDDELLKKKVLKELIEPIEERKEH 201 (293)
T ss_pred HHHHHHHhhceEEEEecChHHHHHhHHHHHhhhHHHHHHH
Confidence 33343333445789999997 67788888777777664
No 175
>KOG0393 consensus Ras-related small GTPase, Rho type [General function prediction only]
Probab=24.13 E-value=52 Score=22.63 Aligned_cols=25 Identities=24% Similarity=0.339 Sum_probs=18.5
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
|.-.+...| .++|++.|.+|.+|=.
T Consensus 99 W~pEi~~~c--p~vpiiLVGtk~DLr~ 123 (198)
T KOG0393|consen 99 WIPEIKHHC--PNVPIILVGTKADLRD 123 (198)
T ss_pred hhHHHHhhC--CCCCEEEEeehHHhhh
Confidence 444445555 5899999999999873
No 176
>PF00586 AIRS: AIR synthase related protein, N-terminal domain; InterPro: IPR000728 This family includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; GO: 0003824 catalytic activity; PDB: 3VIU_A 2Z1T_A 2Z1U_A 3C9U_B 3C9S_A 3C9R_A 1VQV_A 3C9T_B 3M84_A 3QTY_A ....
Probab=24.00 E-value=55 Score=18.84 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=12.8
Q ss_pred HHHhHHHHHhhCCCCEE
Q 035100 10 ILLHLPLLAEDKNVPYV 26 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~ 26 (73)
+++-+.+.|+++|+|++
T Consensus 76 ~~~Gi~~~~~~~g~~iv 92 (96)
T PF00586_consen 76 IVKGIAEACREFGIPIV 92 (96)
T ss_dssp HHHHHHHHHHHHT-EEE
T ss_pred HHHHHHHHHHHhCCcEe
Confidence 55667789999999985
No 177
>PRK07027 cobalamin biosynthesis protein CbiG; Provisional
Probab=23.90 E-value=92 Score=19.45 Aligned_cols=23 Identities=22% Similarity=0.153 Sum_probs=16.6
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
-+.++++++|+|+.++ +.++|-.
T Consensus 51 ~L~~~A~~lg~pl~~~-~~~eL~~ 73 (126)
T PRK07027 51 GLLALCARHGWPLRAF-SAAQLAA 73 (126)
T ss_pred HHHHHHHHhCCCeEEe-CHHHHHh
Confidence 4677888899998886 4456543
No 178
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=23.84 E-value=85 Score=21.98 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=18.0
Q ss_pred hHHHhHHHHHhhCCCCEEEeCCh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk 31 (73)
++.......|++.||||+.+.-.
T Consensus 80 ~is~na~~a~~~~~ipylR~eRp 102 (249)
T PF02571_consen 80 EISQNAIEACRELGIPYLRFERP 102 (249)
T ss_pred HHHHHHHHHHhhcCcceEEEEcC
Confidence 46677889999999999876443
No 179
>COG0352 ThiE Thiamine monophosphate synthase [Coenzyme metabolism]
Probab=23.84 E-value=81 Score=21.72 Aligned_cols=31 Identities=23% Similarity=0.382 Sum_probs=22.7
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhhHhCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGRACGV 40 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~ 40 (73)
+....+..+|.+|++|++ +.+.-+|-..+|-
T Consensus 52 ~~a~~~~~lc~~~~v~li-INd~~dlA~~~~A 82 (211)
T COG0352 52 ALAEKLRALCQKYGVPLI-INDRVDLALAVGA 82 (211)
T ss_pred HHHHHHHHHHHHhCCeEE-ecCcHHHHHhCCC
Confidence 466789999999999985 4555666555443
No 180
>PRK07678 aminotransferase; Validated
Probab=23.79 E-value=78 Score=23.70 Aligned_cols=23 Identities=4% Similarity=0.111 Sum_probs=19.3
Q ss_pred CchhHHHhHHHHHhhCCCCEEEe
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFV 28 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v 28 (73)
-|.+....+..+|+++|+.++.=
T Consensus 231 ~~~~fl~~lr~lc~~~g~llI~D 253 (451)
T PRK07678 231 PPQDYMKAVKEICQKHGALLISD 253 (451)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEe
Confidence 35568999999999999999753
No 181
>PRK08742 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional
Probab=23.71 E-value=78 Score=24.03 Aligned_cols=24 Identities=8% Similarity=-0.061 Sum_probs=19.9
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeC
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
-|.+....+.++|+++|+.++.=.
T Consensus 255 ~p~~fl~~lr~lc~~~gillI~DE 278 (472)
T PRK08742 255 HHPAYLRRARELCDAHGAFLIADE 278 (472)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEec
Confidence 356699999999999999997543
No 182
>PRK07482 hypothetical protein; Provisional
Probab=23.68 E-value=77 Score=23.85 Aligned_cols=23 Identities=4% Similarity=0.047 Sum_probs=19.3
Q ss_pred CchhHHHhHHHHHhhCCCCEEEe
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFV 28 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v 28 (73)
-|.+....+.++|+++|+.++.=
T Consensus 238 ~~~~yl~~lr~lc~~~giLlI~D 260 (461)
T PRK07482 238 PPAGYWPAIQAVLKKYDILLIAD 260 (461)
T ss_pred CCHHHHHHHHHHHHHhCCEEEEe
Confidence 35569999999999999998753
No 183
>PRK12289 GTPase RsgA; Reviewed
Probab=23.63 E-value=89 Score=23.02 Aligned_cols=26 Identities=23% Similarity=0.194 Sum_probs=21.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
.+..+...++..++|.+.+.+|.+|-
T Consensus 108 ~LdR~L~~a~~~~ip~ILVlNK~DLv 133 (352)
T PRK12289 108 QLSRFLVKAESTGLEIVLCLNKADLV 133 (352)
T ss_pred HHHHHHHHHHHCCCCEEEEEEchhcC
Confidence 44666677788899999999999983
No 184
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=23.60 E-value=86 Score=22.02 Aligned_cols=25 Identities=28% Similarity=0.276 Sum_probs=21.1
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~L 34 (73)
....+...++..++|.+.+.+|.+|
T Consensus 97 ~ldr~L~~~~~~~ip~iIVlNK~DL 121 (287)
T cd01854 97 LLDRYLVAAEAAGIEPVIVLTKADL 121 (287)
T ss_pred HHHHHHHHHHHcCCCEEEEEEHHHC
Confidence 5566777788899999999999998
No 185
>KOG4077 consensus Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion]
Probab=23.47 E-value=72 Score=21.14 Aligned_cols=24 Identities=21% Similarity=0.443 Sum_probs=19.8
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
.|. +++.+...|++-||| ++++||
T Consensus 121 Y~y-~v~elkpvl~ELGI~-----t~EeLg 144 (149)
T KOG4077|consen 121 YPY-YVKELKPVLNELGIP-----TPEELG 144 (149)
T ss_pred HHH-HHHHHHHHHHHhCCC-----CHHHhC
Confidence 456 788899999999987 588888
No 186
>PRK07036 hypothetical protein; Provisional
Probab=23.41 E-value=81 Score=23.80 Aligned_cols=25 Identities=8% Similarity=0.121 Sum_probs=20.3
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeC
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
..|.+....+..+|+++|++++.=.
T Consensus 237 ~p~~~yl~~lr~lc~~~g~llI~DE 261 (466)
T PRK07036 237 VPPPGYHARMREICRRYDILYISDE 261 (466)
T ss_pred cCCHHHHHHHHHHHHHcCCEEEEee
Confidence 3466789999999999999987543
No 187
>PF12687 DUF3801: Protein of unknown function (DUF3801); InterPro: IPR024234 This functionally uncharacterised protein family is found in bacteria. Proteins found in this family are typically between 158 and 187 amino acids in length and include the PcfB protein.
Probab=23.36 E-value=2.5e+02 Score=19.11 Aligned_cols=50 Identities=12% Similarity=0.102 Sum_probs=33.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeCCchHHHHHHHHHHH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKD 66 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~~~~~~~~~~~~~~~ 66 (73)
-+..|...++.|||.|+...++.. -+ +..-|...-.++..+...++++..
T Consensus 43 ~lk~F~k~AkKyGV~yav~kdk~~------~~-~~~~V~FkA~Da~~i~~af~~~~~ 92 (204)
T PF12687_consen 43 DLKEFKKEAKKYGVDYAVKKDKST------GP-GKYDVFFKAKDADVINRAFKEFSA 92 (204)
T ss_pred hHHHHHHHHHHcCCceEEeeccCC------CC-CcEEEEEEcCcHHHHHHHHHHHHH
Confidence 567788899999999999998764 22 232333333346677777766544
No 188
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=23.26 E-value=96 Score=21.96 Aligned_cols=20 Identities=10% Similarity=-0.011 Sum_probs=17.5
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
.+..+..+|.+.||+++.++
T Consensus 41 ~l~~i~~~c~~~GI~~lTvY 60 (239)
T PRK14839 41 AIRRVVEAAPDLGIGTLTLY 60 (239)
T ss_pred HHHHHHHHHHHcCCCEEEEE
Confidence 67889999999999998765
No 189
>cd01713 PAPS_reductase This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase acti
Probab=23.20 E-value=1.1e+02 Score=18.42 Aligned_cols=26 Identities=23% Similarity=0.254 Sum_probs=22.1
Q ss_pred hhHHHhHHHHHhhCCCCEEEeCChhh
Q 035100 8 LEILLHLPLLAEDKNVPYVFVPSKQA 33 (73)
Q Consensus 8 ~~~~~~l~~lc~~~~IP~~~v~sk~~ 33 (73)
.++..++..+|+++|+|+..+.....
T Consensus 41 ~~~~~~~~~~~~~~g~~~~~~~~~~~ 66 (173)
T cd01713 41 PETYEFVDRVAERYGLPLVVVRPPDS 66 (173)
T ss_pred HHHHHHHHHHHHHhCCCeEEECCCcc
Confidence 45889999999999999999877644
No 190
>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=23.17 E-value=86 Score=23.08 Aligned_cols=22 Identities=23% Similarity=0.202 Sum_probs=18.4
Q ss_pred hHHHhHHHHHhhCCCCEEEeCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~s 30 (73)
++-.++.+.++++|||++.-+.
T Consensus 288 ~~A~~Ir~iA~e~~VPiven~p 309 (342)
T TIGR01404 288 AQALAVRAYAEEAGIPVVRDIP 309 (342)
T ss_pred HHHHHHHHHHHHcCCCEeeCHH
Confidence 4778999999999999976543
No 191
>PF04951 Peptidase_M55: D-aminopeptidase; InterPro: IPR007035 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 M55 (DppA aminopeptidase family, clan MN). The type example is Bacillus subtilis DppA, which is a binuclear zinc-dependent, D-specific aminopeptidase. The structure reveals that DppA is a new example of a self-compartmentalising protease, a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organised in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterised by the SXDXEG key sequence []. The only known substrates are D-ala-D-ala and D-ala-gly-gly.; PDB: 1HI9_A.
Probab=23.11 E-value=2.7e+02 Score=19.95 Aligned_cols=37 Identities=24% Similarity=0.249 Sum_probs=20.6
Q ss_pred HHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 16 LLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 16 ~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
.+|-++|||++.+.+-+.|=+-.-.--|....+.++.
T Consensus 141 ~~Ag~~GVPV~lVsGD~~l~~ea~~~~P~~~tv~vK~ 177 (265)
T PF04951_consen 141 ALAGYYGVPVVLVSGDDALCEEAKELLPWIVTVAVKE 177 (265)
T ss_dssp HHHHHTT--EEEEEEEHHHHHHHHTTSTT-EEEEEEE
T ss_pred HHHhhcCCcEEEEeCcHHHHHHHHHhCCCceEEEEec
Confidence 5688899999999987776543322233333333333
No 192
>cd04176 Rap2 Rap2 subgroup. The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, incl
Probab=23.07 E-value=73 Score=19.29 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=12.9
Q ss_pred hCCCCEEEeCChhhH
Q 035100 20 DKNVPYVFVPSKQAL 34 (73)
Q Consensus 20 ~~~IP~~~v~sk~~L 34 (73)
..++|++.+.+|.+|
T Consensus 104 ~~~~piviv~nK~Dl 118 (163)
T cd04176 104 YEKVPIILVGNKVDL 118 (163)
T ss_pred CCCCCEEEEEECccc
Confidence 368999999999887
No 193
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=23.07 E-value=1.1e+02 Score=22.27 Aligned_cols=33 Identities=21% Similarity=0.216 Sum_probs=25.4
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeCChh--hHhhHh
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVPSKQ--ALGRAC 38 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~sk~--~LG~a~ 38 (73)
+++. ....+..+++..||||+..++-+ ++..++
T Consensus 127 ~~~~-~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~ 161 (338)
T TIGR03674 127 LTSE-IVESSKKLLDLMGIPYVQAPSEGEAQAAYMA 161 (338)
T ss_pred CCHH-HHHHHHHHHHHcCCeEEECCccHHHHHHHHH
Confidence 3444 78889999999999999999832 456555
No 194
>PRK09792 4-aminobutyrate transaminase; Provisional
Probab=23.03 E-value=84 Score=23.21 Aligned_cols=30 Identities=10% Similarity=0.274 Sum_probs=22.6
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
-|.+....+.++|+++|++++.=.-...+|
T Consensus 216 ~~~~~l~~l~~lc~~~g~llI~DEv~tg~g 245 (421)
T PRK09792 216 APKELVAAIRRLCDEHGIVMIADEVQSGFA 245 (421)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEeccccCCC
Confidence 356699999999999999997644444344
No 195
>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3.1.22 from EC) [], and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006259 DNA metabolic process; PDB: 2BHN_D 2BGW_B 1J22_A 1J25_A 1J24_A 1J23_A 2ZIU_A 2ZIW_A 2ZIV_A 2ZIX_A ....
Probab=22.99 E-value=1.6e+02 Score=17.54 Aligned_cols=33 Identities=18% Similarity=0.082 Sum_probs=26.4
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
+|.++...+..+--.+|+++.++.+.++....+
T Consensus 108 ~~~~i~~~L~~lq~~~~~~v~~~~~~~et~~~l 140 (143)
T PF02732_consen 108 SPSAIEEALVELQLRYGISVIFTESWEETADWL 140 (143)
T ss_dssp THHHHHHHHHHHHHCSS-EEEEESSHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHcCeEEEEECCHHHHHHHh
Confidence 455678888888888999999999999887653
No 196
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=22.97 E-value=89 Score=23.14 Aligned_cols=21 Identities=33% Similarity=0.335 Sum_probs=17.7
Q ss_pred hHHHhHHHHHhhCCCCEEEeC
Q 035100 9 EILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~ 29 (73)
++-.++.+.++++|||++.-+
T Consensus 289 ~~A~~Ir~iA~e~~VPiven~ 309 (349)
T PRK12721 289 AQALHIVKLAERNGIPVVENI 309 (349)
T ss_pred HHHHHHHHHHHHcCCCEEeCH
Confidence 467899999999999997543
No 197
>PRK02256 putative aminopeptidase 1; Provisional
Probab=22.96 E-value=84 Score=24.20 Aligned_cols=21 Identities=14% Similarity=0.129 Sum_probs=18.4
Q ss_pred CchhHHHhHHHHHhhCCCCEEE
Q 035100 6 EPLEILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~ 27 (73)
++. +...+..+|++.||||=.
T Consensus 381 ~~~-~~~~i~~iA~~~~Ip~Q~ 401 (462)
T PRK02256 381 NAE-FVAEVRNLFNKNNVVWQT 401 (462)
T ss_pred CHH-HHHHHHHHHHHcCCCEEE
Confidence 555 889999999999999877
No 198
>PRK02813 putative aminopeptidase 2; Provisional
Probab=22.93 E-value=1.5e+02 Score=22.50 Aligned_cols=26 Identities=27% Similarity=0.327 Sum_probs=20.5
Q ss_pred hhHHHhHHHHHhhCCCCEEEeCChhh
Q 035100 8 LEILLHLPLLAEDKNVPYVFVPSKQA 33 (73)
Q Consensus 8 ~~~~~~l~~lc~~~~IP~~~v~sk~~ 33 (73)
.+....+..+|++.+|||=+.-.+..
T Consensus 348 ~~~~a~~~~ia~~~~Ip~Q~~v~~~d 373 (428)
T PRK02813 348 AESAAVFKLLCEKAGVPYQEFVNRSD 373 (428)
T ss_pred HHHHHHHHHHHHHcCCCEEEEEecCC
Confidence 34888999999999999877555543
No 199
>TIGR02407 ectoine_ectB diaminobutyrate--2-oxoglutarate aminotransferase. Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (EC 2.6.1.76) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore or 1,3-diaminopropane biosynthesis. The family TIGR00709 previously included both groups but has now been revised to exclude the ectoine biosynthesis proteins of this family. Ectoine is a compatible solute particularly effective in conferring salt tolerance.
Probab=22.93 E-value=86 Score=23.07 Aligned_cols=26 Identities=15% Similarity=0.132 Sum_probs=20.5
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCCh
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSK 31 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk 31 (73)
-|.+....+..+|+++|++++.=.-.
T Consensus 212 ~~~~~l~~l~~lc~~~g~llI~DEV~ 237 (412)
T TIGR02407 212 ASDEWLQRLEKLCRRHDILLIVDDIQ 237 (412)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEechh
Confidence 35668999999999999998754433
No 200
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=22.89 E-value=1.1e+02 Score=19.54 Aligned_cols=35 Identities=20% Similarity=0.216 Sum_probs=24.8
Q ss_pred HHHhHHHHHhhCCC------CEEEeCChhhHhhHhCCCCce
Q 035100 10 ILLHLPLLAEDKNV------PYVFVPSKQALGRACGVTRPV 44 (73)
Q Consensus 10 ~~~~l~~lc~~~~I------P~~~v~sk~~LG~a~G~~r~~ 44 (73)
+...+..+++.++. .+..-.|.++|+..+|..|.+
T Consensus 125 la~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tret 165 (202)
T PRK13918 125 IAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRET 165 (202)
T ss_pred HHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHH
Confidence 66667777776532 344556999999999988744
No 201
>PRK09961 exoaminopeptidase; Provisional
Probab=22.87 E-value=1.9e+02 Score=21.00 Aligned_cols=43 Identities=19% Similarity=0.231 Sum_probs=27.3
Q ss_pred CchhHHHhHHHHHhhCCCCEEE-eCC--hhhHh--hHhCCCCceEEEEE
Q 035100 6 EPLEILLHLPLLAEDKNVPYVF-VPS--KQALG--RACGVTRPVVACSV 49 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~-v~s--k~~LG--~a~G~~r~~~~vai 49 (73)
+|. +...+...|++.+|||-+ +.+ -.+-+ +..+...+++.+++
T Consensus 255 ~~~-l~~~l~~~A~~~~Ip~Q~~~~~ggGTDa~~~~~~~~Giptv~ig~ 302 (344)
T PRK09961 255 PPK-LTAWIETVAAEIGIPLQADMFSNGGTDGGAVHLTGTGVPTVVMGP 302 (344)
T ss_pred CHH-HHHHHHHHHHHcCCCcEEEecCCCcchHHHHHHhCCCCCEEEech
Confidence 344 899999999999999988 222 23444 33333345555544
No 202
>PF03851 UvdE: UV-endonuclease UvdE; InterPro: IPR004601 Schizosaccharomyces pombe ultraviolet damage endonuclease (UVDE or Uve1p) performs the initial step in an alternative excision repair pathway for UV-induced DNA damage. This DNA repair pathway was originally thought to be specific for UV damage, however Uve1p also recognises UV-induced bipyrimidine photoadducts and other non-UV-induced DNA adducts []. The Deinococcus radiodurans UVSE protein has also shown to be a UV DNA damage endonuclease that catalyzes repair of UV-induced DNA damage by a similar mechanism [].; GO: 0004519 endonuclease activity, 0006289 nucleotide-excision repair, 0009411 response to UV; PDB: 3BZG_A 3BZJ_A 3C0L_A 3C0S_A 3C0Q_A.
Probab=22.86 E-value=60 Score=23.36 Aligned_cols=18 Identities=22% Similarity=0.420 Sum_probs=12.5
Q ss_pred HHHhHHHHHhhCCCCEEE
Q 035100 10 ILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~ 27 (73)
.+..+..+|++.|||+++
T Consensus 191 t~~d~L~ic~~~giP~Vf 208 (275)
T PF03851_consen 191 TVEDVLPICEKLGIPMVF 208 (275)
T ss_dssp -HHHHHHHHHHHT--EEE
T ss_pred CHHHHHHHHHHhCCCEEE
Confidence 455677899999999987
No 203
>KOG2016 consensus NEDD8-activating complex, APP-BP1/UBA5 component [Posttranslational modification, protein turnover, chaperones]
Probab=22.85 E-value=79 Score=24.92 Aligned_cols=33 Identities=27% Similarity=0.380 Sum_probs=25.9
Q ss_pred CCCCCchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 2 AADTEPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 2 A~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
|.+.-.. ...+++..|++.+||++...|---.|
T Consensus 125 atnl~E~-~~~kl~~~l~~~~vpll~~rs~Gl~G 157 (523)
T KOG2016|consen 125 ATNLNEQ-TLLKLAEILREANVPLLLTRSYGLAG 157 (523)
T ss_pred ccccchh-hhhhhHHHHHhcCCceEEEeeecceE
Confidence 4444444 77889999999999999998866555
No 204
>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=22.78 E-value=82 Score=21.33 Aligned_cols=25 Identities=28% Similarity=0.186 Sum_probs=17.8
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~L 34 (73)
....+..++.+.++|++.+-+|.++
T Consensus 126 ~d~~~l~~l~~~~ip~ivvvNK~D~ 150 (224)
T cd04165 126 MTKEHLGLALALNIPVFVVVTKIDL 150 (224)
T ss_pred HHHHHHHHHHHcCCCEEEEEECccc
Confidence 4455566777788888888777765
No 205
>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=22.68 E-value=59 Score=19.13 Aligned_cols=21 Identities=19% Similarity=0.221 Sum_probs=14.1
Q ss_pred HHHhHHHHHhhCCCCEEEeCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~s 30 (73)
.-..+..+|+++++|++.++.
T Consensus 73 ~~~~v~~la~~~~i~vi~t~~ 93 (105)
T PF07085_consen 73 PSEEVLELAKELGIPVISTPY 93 (105)
T ss_dssp --HHHHHHHHHHT-EEEE-SS
T ss_pred CCHHHHHHHHHCCCEEEEECC
Confidence 346678899999999988764
No 206
>PRK07480 putative aminotransferase; Validated
Probab=22.54 E-value=88 Score=23.54 Aligned_cols=24 Identities=8% Similarity=0.080 Sum_probs=19.8
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEe
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFV 28 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v 28 (73)
..|.+....+..+|+++|+.++.=
T Consensus 236 ~~~~~yl~~lr~lc~~~g~llI~D 259 (456)
T PRK07480 236 IPPATYWPEIQRICRKYDILLVAD 259 (456)
T ss_pred cCCHHHHHHHHHHHHHcCCEEEEe
Confidence 346678999999999999998653
No 207
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.48 E-value=1e+02 Score=21.74 Aligned_cols=21 Identities=14% Similarity=-0.001 Sum_probs=18.0
Q ss_pred HHHhHHHHHhhCCCCEEEeCC
Q 035100 10 ILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~s 30 (73)
.+..+..+|.+.||+++.++.
T Consensus 52 ~l~~i~~~c~~~GI~~vT~ya 72 (249)
T PRK14831 52 ALKDLLRCCKDWGIGALTAYA 72 (249)
T ss_pred HHHHHHHHHHHcCCCEEEEee
Confidence 678899999999999987753
No 208
>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=22.46 E-value=88 Score=19.25 Aligned_cols=16 Identities=13% Similarity=0.227 Sum_probs=13.7
Q ss_pred CCCCEEEeCChhhHhh
Q 035100 21 KNVPYVFVPSKQALGR 36 (73)
Q Consensus 21 ~~IP~~~v~sk~~LG~ 36 (73)
.++|++.+.+|.+|++
T Consensus 104 ~~~~iilvgnK~Dl~~ 119 (161)
T cd04117 104 EGVQKILIGNKADEEQ 119 (161)
T ss_pred CCCeEEEEEECccccc
Confidence 4799999999999864
No 209
>PTZ00371 aspartyl aminopeptidase; Provisional
Probab=22.42 E-value=1.4e+02 Score=22.97 Aligned_cols=26 Identities=19% Similarity=0.161 Sum_probs=21.0
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCChhh
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPSKQA 33 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~sk~~ 33 (73)
+. +...+..+|++.||||=..-.+..
T Consensus 375 ~~-~~a~i~~la~~~~Ip~Q~~~~~~d 400 (465)
T PTZ00371 375 GV-TASLLKAIAKKANIPIQEFVVKND 400 (465)
T ss_pred HH-HHHHHHHHHHHcCCCEEEEEecCC
Confidence 44 899999999999999877555544
No 210
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=22.39 E-value=1e+02 Score=21.64 Aligned_cols=22 Identities=14% Similarity=0.265 Sum_probs=18.3
Q ss_pred hHHHhHHHHHhhCCCCEEEeCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~s 30 (73)
++.....+.|++.||||+.+.-
T Consensus 79 ~is~~a~~ac~~~~ipyiR~eR 100 (248)
T PRK08057 79 QISANAAAACRALGIPYLRLER 100 (248)
T ss_pred HHHHHHHHHHHHhCCcEEEEeC
Confidence 4677888999999999987753
No 211
>cd00738 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b).
Probab=22.34 E-value=1.2e+02 Score=16.70 Aligned_cols=22 Identities=23% Similarity=0.279 Sum_probs=13.0
Q ss_pred hHHHHHhhCCCCEEEeCChhhH
Q 035100 13 HLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~L 34 (73)
+-...++..|+||+.+-+..++
T Consensus 45 k~~~~a~~~g~~~~iiig~~e~ 66 (94)
T cd00738 45 KKFREADLRGVPFAVVVGEDEL 66 (94)
T ss_pred HHHHHHHhCCCCEEEEECCChh
Confidence 3344556667776666666554
No 212
>PRK06938 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional
Probab=22.27 E-value=88 Score=23.64 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=18.9
Q ss_pred CchhHHHhHHHHHhhCCCCEEE
Q 035100 6 EPLEILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~ 27 (73)
-|.+....+..+|+++|+.++.
T Consensus 249 p~~~yl~~lr~lc~~~giLlI~ 270 (464)
T PRK06938 249 APIEWLRGLRRITEEAGIPLIV 270 (464)
T ss_pred CCHHHHHHHHHHHHHcCCEEEE
Confidence 3467999999999999999875
No 213
>TIGR00700 GABAtrnsam 4-aminobutyrate aminotransferase, prokaryotic type. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase.
Probab=22.26 E-value=1e+02 Score=22.67 Aligned_cols=24 Identities=4% Similarity=0.030 Sum_probs=19.3
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeC
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
.|.+....+.++|+++|++++.=.
T Consensus 215 ~~~~~l~~l~~lc~~~gillI~DE 238 (420)
T TIGR00700 215 PAKGFVPALLDWCREHGIVFIADE 238 (420)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEEe
Confidence 455679999999999999987533
No 214
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=22.23 E-value=96 Score=19.96 Aligned_cols=23 Identities=13% Similarity=0.166 Sum_probs=17.5
Q ss_pred HHHhHHHHHhhCCCCEEEeCChh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
-..++..+|++.|||+....-..
T Consensus 46 ~~~~v~~~~~~~~i~~~~~~~~~ 68 (182)
T PF01171_consen 46 EAEFVEEICEQLGIPLYIVRIDE 68 (182)
T ss_dssp HHHHHHHHHHHTT-EEEEEE--C
T ss_pred hHHHHHHHHHhcCCceEEEEeee
Confidence 56889999999999999887664
No 215
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=22.21 E-value=80 Score=20.26 Aligned_cols=20 Identities=25% Similarity=0.175 Sum_probs=16.1
Q ss_pred HHhHHHHHhhCCCCEEEeCC
Q 035100 11 LLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~s 30 (73)
...++..|-.++|||+.-..
T Consensus 95 ~~~IRR~Av~~~IP~~T~l~ 114 (142)
T PRK05234 95 VKALLRLADVWNIPVATNRA 114 (142)
T ss_pred HHHHHHHHHHcCCCEEcCHH
Confidence 45899999999999976443
No 216
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=22.13 E-value=67 Score=23.34 Aligned_cols=20 Identities=20% Similarity=0.110 Sum_probs=17.0
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
-+..+..+|.+.||+++.++
T Consensus 68 ~l~~ile~C~~lGI~~vT~f 87 (271)
T KOG1602|consen 68 ALKEILELCKELGIKEVTVF 87 (271)
T ss_pred HHHHHHHHHHHcCCcEEEEE
Confidence 56778999999999997764
No 217
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=22.12 E-value=2.3e+02 Score=18.28 Aligned_cols=64 Identities=8% Similarity=0.041 Sum_probs=41.3
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhh----HhCCCCce-EEEEEEeCC--chHHHHHHHHHHH
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGR----ACGVTRPV-VACSVTSNE--ASQLKTQIQQLKD 66 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~----a~G~~r~~-~~vai~~~~--~~~~~~~~~~~~~ 66 (73)
+.+++.|+...+...+++.+.++..+.++++... .+....|- .+++..+.. ..+..+.++.+++
T Consensus 29 ~rv~g~dl~~~l~~~~~~~~~~ifllG~~~~~~~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~~ 99 (172)
T PF03808_consen 29 ERVTGSDLFPDLLRRAEQRGKRIFLLGGSEEVLEKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRINA 99 (172)
T ss_pred cccCHHHHHHHHHHHHHHcCCeEEEEeCCHHHHHHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHHH
Confidence 3456778999999999999999999999998664 33333333 234444432 3455555555544
No 218
>PRK06298 type III secretion system protein; Validated
Probab=22.11 E-value=94 Score=23.09 Aligned_cols=27 Identities=19% Similarity=0.022 Sum_probs=20.6
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
++-.++.+.++++|||++.-.. |-|++
T Consensus 290 ~~A~~Ir~iA~e~~VPiven~p---LARaL 316 (356)
T PRK06298 290 LRAKRIIAEAEKYGVPIMRNVP---LAHQL 316 (356)
T ss_pred HHHHHHHHHHHHcCCCEEeCHH---HHHHH
Confidence 4678999999999999976543 44443
No 219
>cd02003 TPP_IolD Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism.
Probab=21.98 E-value=1.3e+02 Score=19.95 Aligned_cols=27 Identities=15% Similarity=0.010 Sum_probs=22.7
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhHhC
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRACG 39 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a~G 39 (73)
.+..+++.+|+++..+.+.++|..++.
T Consensus 142 d~~~~A~a~G~~~~~v~~~~el~~al~ 168 (205)
T cd02003 142 DFAANARSLGARVEKVKTIEELKAALA 168 (205)
T ss_pred CHHHHHHhCCCEEEEECCHHHHHHHHH
Confidence 577889999999999999999886653
No 220
>COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]
Probab=21.92 E-value=1.1e+02 Score=22.27 Aligned_cols=24 Identities=46% Similarity=0.620 Sum_probs=20.0
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
++-.++..+++..||||+|-.|=.
T Consensus 35 ~~a~~lk~~t~~lgi~~vfKsSfD 58 (279)
T COG2877 35 EIAEHLKELTEKLGIPYVFKSSFD 58 (279)
T ss_pred HHHHHHHHHHhccCCceEEecccc
Confidence 366789999999999999977644
No 221
>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=21.92 E-value=2.9e+02 Score=19.32 Aligned_cols=63 Identities=16% Similarity=0.227 Sum_probs=37.9
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCCh------hhHhhHhCCCCceEEEEEEeC----CchHHHHHHHHHHHHHH
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSK------QALGRACGVTRPVVACSVTSN----EASQLKTQIQQLKDAIE 69 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk------~~LG~a~G~~r~~~~vai~~~----~~~~~~~~~~~~~~~~~ 69 (73)
..+|. -+..+....++++|+++++.+. +.|-+..|.+ +..+-.+.. +..++.+.|++.-+.|.
T Consensus 211 eps~~-~l~~l~~~ik~~~v~~If~e~~~~~~~~~~ia~~~g~~--v~~l~~l~~~~~~~~~~Y~~~m~~n~~~i~ 283 (286)
T cd01019 211 DPGAK-RLAKIRKEIKEKGATCVFAEPQFHPKIAETLAEGTGAK--VGELDPLGGLIELGKNSYVNFLRNLADSLA 283 (286)
T ss_pred CCCHH-HHHHHHHHHHHcCCcEEEecCCCChHHHHHHHHhcCce--EEEecccccccccchhhHHHHHHHHHHHHH
Confidence 45666 6678889999999999998765 2344444432 211212221 13577777777655554
No 222
>PRK07481 hypothetical protein; Provisional
Probab=21.81 E-value=91 Score=23.33 Aligned_cols=24 Identities=4% Similarity=0.070 Sum_probs=19.6
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeC
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
-|.+....+..+|+++|+.++.=.
T Consensus 231 ~~~~fl~~lr~lc~~~g~llI~DE 254 (449)
T PRK07481 231 PPANFWPLVREVCDRHGILLIADE 254 (449)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEee
Confidence 355689999999999999987533
No 223
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=21.69 E-value=97 Score=23.04 Aligned_cols=22 Identities=23% Similarity=0.336 Sum_probs=18.4
Q ss_pred hHHHhHHHHHhhCCCCEEEeCC
Q 035100 9 EILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~s 30 (73)
++-.++.+.++++|||++.-+.
T Consensus 298 ~~A~~Ir~~A~e~~VPiven~p 319 (358)
T PRK13109 298 LIALKIREIAEENGIPVIEDKP 319 (358)
T ss_pred HHHHHHHHHHHHcCCCEEeCHH
Confidence 4678999999999999987544
No 224
>cd04148 RGK RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ra
Probab=21.63 E-value=2.5e+02 Score=18.56 Aligned_cols=14 Identities=29% Similarity=0.553 Sum_probs=12.7
Q ss_pred CCCCEEEeCChhhH
Q 035100 21 KNVPYVFVPSKQAL 34 (73)
Q Consensus 21 ~~IP~~~v~sk~~L 34 (73)
.++|++.+.+|.+|
T Consensus 105 ~~~piilV~NK~Dl 118 (221)
T cd04148 105 EDRPIILVGNKSDL 118 (221)
T ss_pred CCCCEEEEEEChhc
Confidence 57999999999987
No 225
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=21.63 E-value=1.1e+02 Score=21.20 Aligned_cols=21 Identities=19% Similarity=0.002 Sum_probs=18.3
Q ss_pred hHHHhHHHHHhhCCCCEEEeC
Q 035100 9 EILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~ 29 (73)
+.+..+..+|.+.||+++.++
T Consensus 31 ~~~~~i~~~~~~~gI~~lTvy 51 (221)
T cd00475 31 EKLRDILRWCLELGVKEVTLY 51 (221)
T ss_pred HHHHHHHHHHHHcCCCEEEEE
Confidence 367889999999999999887
No 226
>PRK08223 hypothetical protein; Validated
Probab=21.59 E-value=1e+02 Score=22.26 Aligned_cols=21 Identities=5% Similarity=0.096 Sum_probs=17.8
Q ss_pred hHHHhHHHHHhhCCCCEEEeC
Q 035100 9 EILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~ 29 (73)
+....+-+.|..+|+|+++-.
T Consensus 131 ~~r~~ln~~c~~~~iP~V~~~ 151 (287)
T PRK08223 131 DARRLVFAACQQRGIPALTAA 151 (287)
T ss_pred HHHHHHHHHHHHcCCCEEEEe
Confidence 477888999999999998853
No 227
>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=21.47 E-value=2e+02 Score=19.16 Aligned_cols=30 Identities=27% Similarity=0.304 Sum_probs=23.2
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCChh
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
.|.....-...+..+++..|||+....+..
T Consensus 37 ~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~ 66 (196)
T PF00448_consen 37 ADTYRIGAVEQLKTYAEILGVPFYVARTES 66 (196)
T ss_dssp ESTSSTHHHHHHHHHHHHHTEEEEESSTTS
T ss_pred CCCCCccHHHHHHHHHHHhccccchhhcch
Confidence 455555567889999999999998877553
No 228
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=21.47 E-value=1.5e+02 Score=15.73 Aligned_cols=18 Identities=22% Similarity=0.300 Sum_probs=12.8
Q ss_pred HhHHHHHhhCCCCEEEeC
Q 035100 12 LHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~ 29 (73)
.....+.+++||||.++.
T Consensus 14 ~~ak~~L~~~~i~~~~i~ 31 (75)
T cd03418 14 VRAKALLDKKGVDYEEID 31 (75)
T ss_pred HHHHHHHHHCCCcEEEEE
Confidence 345566678899998874
No 229
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=21.46 E-value=1.1e+02 Score=21.47 Aligned_cols=21 Identities=5% Similarity=-0.029 Sum_probs=17.8
Q ss_pred hHHHhHHHHHhhCCCCEEEeC
Q 035100 9 EILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~ 29 (73)
+.+..+..+|.+.||+++.++
T Consensus 37 ~~~~~i~~~c~~~GI~~lT~Y 57 (230)
T PRK14837 37 KRAKEIVKHSLKLGIKYLSLY 57 (230)
T ss_pred HHHHHHHHHHHHcCCCEEEEE
Confidence 367889999999999998765
No 230
>KOG1752 consensus Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=21.42 E-value=1.5e+02 Score=18.22 Aligned_cols=24 Identities=38% Similarity=0.484 Sum_probs=14.1
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
|+..-+..+.-+..+|++|+.++.
T Consensus 54 eiq~~l~~~tg~~tvP~vFI~Gk~ 77 (104)
T KOG1752|consen 54 EIQKALKKLTGQRTVPNVFIGGKF 77 (104)
T ss_pred HHHHHHHHhcCCCCCCEEEECCEE
Confidence 455555555555667777766543
No 231
>COG0803 LraI ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]
Probab=21.41 E-value=1.3e+02 Score=21.38 Aligned_cols=38 Identities=34% Similarity=0.492 Sum_probs=28.6
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCCh------hhHhhHhCCC
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSK------QALGRACGVT 41 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk------~~LG~a~G~~ 41 (73)
.+.+|. -+.++.++.++++|+++++.+- +.|-+-.|..
T Consensus 223 ~e~s~~-~l~~l~~~ik~~~i~~If~e~~~~~~~~~~la~e~g~~ 266 (303)
T COG0803 223 AEPSPK-DLAKLVDLIKKKNIKAIFVESNVSSKSAETLAKETGVK 266 (303)
T ss_pred cCCCHH-HHHHHHHHHHHcCCCEEEEeCCCChHHHHHHHHHhCCc
Confidence 466777 7788999999999999999653 3455666633
No 232
>cd02010 TPP_ALS Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2 molecules of pyruvate to acetolactate and carbon dioxide. ALS does not contain FAD, and requires TPP and a divalent metal cation for activity.
Probab=21.25 E-value=1.4e+02 Score=19.32 Aligned_cols=25 Identities=16% Similarity=-0.036 Sum_probs=19.8
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhhH
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGRA 37 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~a 37 (73)
.+..+++.+|+++..+.+.++|-.+
T Consensus 128 d~~~~a~a~G~~~~~v~~~~el~~a 152 (177)
T cd02010 128 DFVKYAESFGAKGYRIESADDLLPV 152 (177)
T ss_pred CHHHHHHHCCCEEEEECCHHHHHHH
Confidence 4667888889999999888887643
No 233
>PRK09726 antitoxin HipB; Provisional
Probab=21.23 E-value=1.1e+02 Score=17.48 Aligned_cols=33 Identities=12% Similarity=0.356 Sum_probs=25.0
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCce
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPV 44 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~ 44 (73)
+|..+...+..+.+..|+ |.++|++.+|.++++
T Consensus 9 ~~~~l~~~lk~~R~~~gl------tq~elA~~~gvs~~t 41 (88)
T PRK09726 9 SPTQLANAMKLVRQQNGW------TQSELAKKIGIKQAT 41 (88)
T ss_pred CHHHHHHHHHHHHHHcCC------CHHHHHHHHCcCHHH
Confidence 345577788888888885 679999999987533
No 234
>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=21.15 E-value=1.5e+02 Score=19.46 Aligned_cols=26 Identities=27% Similarity=0.309 Sum_probs=22.2
Q ss_pred hHHHHHhhCCCCEEE-eCChhhHhhHh
Q 035100 13 HLPLLAEDKNVPYVF-VPSKQALGRAC 38 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~-v~sk~~LG~a~ 38 (73)
.+..+++.+|+++.. +.+.++|-.++
T Consensus 114 d~~~lA~a~G~~~~~~v~~~~~l~~al 140 (181)
T TIGR03846 114 DLELVAKAAGIRNVEKVADEEELRDAL 140 (181)
T ss_pred CHHHHHHHCCCCeEEEeCCHHHHHHHH
Confidence 578899999999999 99999987654
No 235
>PRK06918 4-aminobutyrate aminotransferase; Reviewed
Probab=21.07 E-value=1.1e+02 Score=22.81 Aligned_cols=30 Identities=3% Similarity=0.135 Sum_probs=22.9
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
.|.+....+.++|+++|++++.=.-...+|
T Consensus 237 ~~~~~l~~l~~l~~~~gillI~DEV~tg~g 266 (451)
T PRK06918 237 PSKKFVQEVRNICSEHGILFVADEIQTGFA 266 (451)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEeccccCcC
Confidence 456689999999999999987655444454
No 236
>PF05889 SLA_LP_auto_ag: Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen); InterPro: IPR008829 This family consists of several eukaryotic and archaeal proteins which are related to the Homo sapiens soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis []. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway []. The archaeal sequences Q8TXK0 from SWISSPROT and Q8TYR3 from SWISSPROT are annotated as being pyridoxal phosphate-dependent enzymes.; GO: 0016740 transferase activity; PDB: 2E7J_B 2E7I_B 2Z67_C 3HL2_D 3BC8_A 3BCA_A 3BCB_A.
Probab=21.05 E-value=67 Score=24.40 Aligned_cols=18 Identities=6% Similarity=0.285 Sum_probs=12.9
Q ss_pred HHHhHHHHHhhCCCCEEE
Q 035100 10 ILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~ 27 (73)
-+..+-.+|++|+||.+.
T Consensus 173 ~i~~IakiC~~~~IPhlv 190 (389)
T PF05889_consen 173 DIEEIAKICKEYDIPHLV 190 (389)
T ss_dssp -HHHHHHHHHHHT--EEE
T ss_pred cHHHHHHHHHHcCCceEE
Confidence 356788999999999976
No 237
>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=21.02 E-value=2.2e+02 Score=17.66 Aligned_cols=28 Identities=7% Similarity=0.199 Sum_probs=21.8
Q ss_pred CEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 24 PYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 24 P~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
-++.+-+.+.|...|+-+ +.|++++.+.
T Consensus 3 ~~~~l~~~~~~~~~C~~~-~~C~i~~l~~ 30 (130)
T cd02983 3 EIIELTSEDVFEETCEEK-QLCIIAFLPH 30 (130)
T ss_pred ceEEecCHHHHHhhccCC-CeEEEEEcCc
Confidence 356777888889889875 6888888875
No 238
>KOG1401 consensus Acetylornithine aminotransferase [Amino acid transport and metabolism]
Probab=20.92 E-value=96 Score=23.99 Aligned_cols=24 Identities=25% Similarity=0.412 Sum_probs=19.5
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeC
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
++|. ...-++..|++++|++++=.
T Consensus 224 ~~pe-Fl~~L~k~C~~~~vl~I~DE 247 (433)
T KOG1401|consen 224 ADPE-FLIGLRKECDDNGVLLIFDE 247 (433)
T ss_pred CCHH-HHHHHHHHHhhcCceEEeeh
Confidence 4565 78889999999999998743
No 239
>TIGR00045 glycerate kinase. The only characterized member of this family so far is the glycerate kinase GlxK (EC 2.7.1.31) of E. coli. This enzyme acts after glyoxylate carboligase and 2-hydroxy-3-oxopropionate reductase (tartronate semialdehyde reductase) in the conversion of glyoxylate to 3-phosphoglycerate (the D-glycerate pathway) as a part of allantoin degradation.
Probab=20.92 E-value=2.8e+02 Score=20.86 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=19.9
Q ss_pred HHhHHHHHhhCCCCEEEeCChhhHh
Q 035100 11 LLHLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
...+-.+++.+++|++.+-+.-..+
T Consensus 304 p~~Va~~A~~~~vPviai~G~v~~~ 328 (375)
T TIGR00045 304 PVGVAKRAKKYGVPVIAIAGSLGDG 328 (375)
T ss_pred HHHHHHHHHHhCCeEEEEecccCCC
Confidence 3456778999999999998876555
No 240
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=20.90 E-value=1.2e+02 Score=17.83 Aligned_cols=41 Identities=12% Similarity=-0.038 Sum_probs=27.5
Q ss_pred CCCCchhHHHhHHHHHhh-CCCC-EEEeCChhhHhhHhCCCCce
Q 035100 3 ADTEPLEILLHLPLLAED-KNVP-YVFVPSKQALGRACGVTRPV 44 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~-~~IP-~~~v~sk~~LG~a~G~~r~~ 44 (73)
.|+.+. ...-+..+++. +|-+ ...-.|..+|+..+|.+|.+
T Consensus 21 ~~l~~r-~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~t 63 (95)
T TIGR01610 21 ADLSGR-EFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTH 63 (95)
T ss_pred CCCCHH-HHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHH
Confidence 467777 66777777763 2322 23346788999999998754
No 241
>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=20.88 E-value=1.4e+02 Score=19.78 Aligned_cols=24 Identities=4% Similarity=-0.092 Sum_probs=19.5
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQ 32 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~ 32 (73)
+....+-.+|.++++|++....-.
T Consensus 123 ~~r~~l~~~~~~~~ip~i~~~~~g 146 (202)
T TIGR02356 123 ATRYLINDACVALGTPLISAAVVG 146 (202)
T ss_pred HHHHHHHHHHHHcCCCEEEEEecc
Confidence 367778999999999999977543
No 242
>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=20.79 E-value=1.5e+02 Score=19.95 Aligned_cols=27 Identities=11% Similarity=-0.098 Sum_probs=21.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhh
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
....+-++|.++++|+++...-..-|+
T Consensus 124 ~r~~l~~~~~~~~ip~i~~g~~g~~g~ 150 (228)
T cd00757 124 TRYLINDACVKLGKPLVSGAVLGFEGQ 150 (228)
T ss_pred HHHHHHHHHHHcCCCEEEEEeccCEEE
Confidence 677899999999999999876544443
No 243
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=20.73 E-value=1.5e+02 Score=21.03 Aligned_cols=35 Identities=14% Similarity=0.234 Sum_probs=26.1
Q ss_pred CCchhHHHhHHHHHhhCCCCEEEeCChh--hHhhHhCC
Q 035100 5 TEPLEILLHLPLLAEDKNVPYVFVPSKQ--ALGRACGV 40 (73)
Q Consensus 5 ~~p~~~~~~l~~lc~~~~IP~~~v~sk~--~LG~a~G~ 40 (73)
+.+. ....+..+.+..||||+..+.-+ +++.++-.
T Consensus 125 ~~~~-~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~~ 161 (316)
T cd00128 125 VTPQ-MIEEAKELLRLMGIPYIVAPYEAEAQCAYLAKK 161 (316)
T ss_pred CCHH-HHHHHHHHHHHcCCCEEECCcCHHHHHHHHHhC
Confidence 4455 77889999999999999987653 36666543
No 244
>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=20.70 E-value=1.3e+02 Score=16.46 Aligned_cols=22 Identities=5% Similarity=0.004 Sum_probs=17.5
Q ss_pred chhHHHhHHHHHhhCCCCEEEeC
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
|. ....++.+|++.|-.+..+.
T Consensus 36 ~~-a~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 36 PG-FARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred cc-HHHHHHHHHHHcCCEEEEEE
Confidence 44 67889999999998887544
No 245
>TIGR00715 precor6x_red precorrin-6x reductase. This enzyme was found to be a monomer by gel filtration.
Probab=20.61 E-value=1.1e+02 Score=21.43 Aligned_cols=21 Identities=19% Similarity=0.395 Sum_probs=17.6
Q ss_pred hHHHhHHHHHhhCCCCEEEeC
Q 035100 9 EILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~ 29 (73)
++.......|++.||||+.+.
T Consensus 79 ~is~~a~~a~~~~~ipylR~e 99 (256)
T TIGR00715 79 QITTNATAVCKELGIPYVRFE 99 (256)
T ss_pred HHHHHHHHHHHHhCCcEEEEE
Confidence 366778899999999998874
No 246
>TIGR00699 GABAtrns_euk 4-aminobutyrate aminotransferase, eukaryotic type. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase.
Probab=20.57 E-value=1e+02 Score=23.57 Aligned_cols=21 Identities=14% Similarity=0.363 Sum_probs=18.4
Q ss_pred chhHHHhHHHHHhhCCCCEEE
Q 035100 7 PLEILLHLPLLAEDKNVPYVF 27 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~ 27 (73)
|.+....+.++|+++|+.++.
T Consensus 270 ~~~yl~~lr~lc~~~g~lLI~ 290 (464)
T TIGR00699 270 SPDFFRKLRDITKKHNVAFIV 290 (464)
T ss_pred CHHHHHHHHHHHHHcCCEEEE
Confidence 566899999999999999875
No 247
>PRK10864 putative methyltransferase; Provisional
Probab=20.54 E-value=3.7e+02 Score=19.99 Aligned_cols=40 Identities=15% Similarity=0.167 Sum_probs=29.4
Q ss_pred HhHHHHHhhCCCCEEEeCChhhHhhHhCCCCceEEEEEEeC
Q 035100 12 LHLPLLAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSN 52 (73)
Q Consensus 12 ~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~~~vai~~~ 52 (73)
..+..++..++++|..+ +.++|-++++...+-.++++...
T Consensus 142 ~~il~~~~~~~~~v~~V-~~~~l~kls~~~~hqGV~A~v~~ 181 (346)
T PRK10864 142 KEALRWMAANRKAYHVV-DEAELTKASGTEHHGGVCFLIKK 181 (346)
T ss_pred HHHHHHHHHcCCcEEEe-CHHHHHHHhCCCCCCeEEEEEeC
Confidence 44556777789997766 77889999988755666776654
No 248
>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=20.52 E-value=82 Score=20.13 Aligned_cols=25 Identities=16% Similarity=0.165 Sum_probs=17.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhH
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQAL 34 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~L 34 (73)
.......+|..+++|++.+-+|.++
T Consensus 110 ~~~~~l~~~~~~~~p~ivvlNK~D~ 134 (188)
T PF00009_consen 110 QTEEHLKILRELGIPIIVVLNKMDL 134 (188)
T ss_dssp HHHHHHHHHHHTT-SEEEEEETCTS
T ss_pred ccccccccccccccceEEeeeeccc
Confidence 4455666788888888888877653
No 249
>PRK06512 thiamine-phosphate pyrophosphorylase; Provisional
Probab=20.51 E-value=2.9e+02 Score=18.82 Aligned_cols=55 Identities=11% Similarity=0.047 Sum_probs=31.2
Q ss_pred HHhHHHHHhhCCCCEEEeC--ChhhHhhHhCCCCceEEEEEEeC--CchHHHHHHHHHHHH
Q 035100 11 LLHLPLLAEDKNVPYVFVP--SKQALGRACGVTRPVVACSVTSN--EASQLKTQIQQLKDA 67 (73)
Q Consensus 11 ~~~l~~lc~~~~IP~~~v~--sk~~LG~a~G~~r~~~~vai~~~--~~~~~~~~~~~~~~~ 67 (73)
...+..+|+.-++|++-+. +.+.+.++.. -++..+++.+. .+.+..+...++++.
T Consensus 153 l~~l~~~~~~~~iPvvAIGGI~~~n~~~~~~--~GA~giAvisai~~~~dp~~a~~~~~~~ 211 (221)
T PRK06512 153 LSLAEWWAEMIEIPCIVQAGSDLASAVEVAE--TGAEFVALERAVFDAHDPPLAVAQANAL 211 (221)
T ss_pred hHHHHHHHHhCCCCEEEEeCCCHHHHHHHHH--hCCCEEEEhHHhhCCCCHHHHHHHHHHH
Confidence 3455667888899999998 4666665533 23334555443 133444444444443
No 250
>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=20.49 E-value=3e+02 Score=19.01 Aligned_cols=61 Identities=15% Similarity=0.336 Sum_probs=37.4
Q ss_pred CCCchhHHHhHHHHHhhCCCCEEEeCChh------hHhhHhCCCCceEEEEEEeC----------CchHHHHHHHHHHHH
Q 035100 4 DTEPLEILLHLPLLAEDKNVPYVFVPSKQ------ALGRACGVTRPVVACSVTSN----------EASQLKTQIQQLKDA 67 (73)
Q Consensus 4 D~~p~~~~~~l~~lc~~~~IP~~~v~sk~------~LG~a~G~~r~~~~vai~~~----------~~~~~~~~~~~~~~~ 67 (73)
+.+|. -+..+..+.++++|+++++.... .|-+..|.+ ++ .++. ++.++.+.++..-+.
T Consensus 203 eps~~-~l~~l~~~ik~~~v~~if~e~~~~~~~~~~la~~~g~~----v~-~ld~l~~~~~~~~~~~~~y~~~m~~n~~~ 276 (282)
T cd01017 203 EPSPK-QLAELVEFVKKSDVKYIFFEENASSKIAETLAKETGAK----LL-VLNPLETLTKEEIDDGKDYFSLMKENLET 276 (282)
T ss_pred CCCHH-HHHHHHHHHHHcCCCEEEEeCCCChHHHHHHHHHcCCc----EE-EeccccccchhcccccCcHHHHHHHHHHH
Confidence 45666 67778889999999999986642 344454432 22 2221 124677777766555
Q ss_pred HHh
Q 035100 68 IEK 70 (73)
Q Consensus 68 ~~~ 70 (73)
+..
T Consensus 277 l~~ 279 (282)
T cd01017 277 LKR 279 (282)
T ss_pred HHH
Confidence 543
No 251
>PF01890 CbiG_C: Cobalamin synthesis G C-terminus; InterPro: IPR002750 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. CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6 []. CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit []. The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates []. This entry represents the core domain of CibG.; GO: 0009236 cobalamin biosynthetic process; PDB: 3BY5_A 2W6K_A 2W6L_A 3EEQ_B.
Probab=20.47 E-value=89 Score=19.39 Aligned_cols=23 Identities=30% Similarity=0.433 Sum_probs=17.0
Q ss_pred hHHHHHhhCCCCEEEeCChhhHhh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALGR 36 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG~ 36 (73)
-+.++++++|+|+.++. .++|-.
T Consensus 49 ~l~~~A~~l~~~~~~~~-~eeL~~ 71 (121)
T PF01890_consen 49 GLLELAEELGIPLRFFS-AEELNA 71 (121)
T ss_dssp HHHHHHHHCTSEEEEE--HHHHHC
T ss_pred HHHHHHHHhCCCeEEEC-HHHHhc
Confidence 57789999999998764 466654
No 252
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.44 E-value=1.1e+02 Score=21.76 Aligned_cols=20 Identities=5% Similarity=-0.019 Sum_probs=17.5
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
.+..+..+|.+.||+++.++
T Consensus 46 ~~~~iv~~c~~~gI~~lTvY 65 (253)
T PRK14836 46 AVRRTIEFCLEKGIEMLTLF 65 (253)
T ss_pred HHHHHHHHHHHcCCCEEehh
Confidence 67889999999999998765
No 253
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.42 E-value=1.2e+02 Score=21.17 Aligned_cols=20 Identities=5% Similarity=-0.001 Sum_probs=17.4
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
.+..+..+|.+.||+++.++
T Consensus 25 ~l~~i~~~c~~~GI~~lT~y 44 (229)
T PRK10240 25 SVRRAVSFAANNGIEALTLY 44 (229)
T ss_pred HHHHHHHHHHHcCCCEEEEE
Confidence 67889999999999998765
No 254
>PRK05093 argD bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein; Reviewed
Probab=20.41 E-value=1e+02 Score=22.21 Aligned_cols=20 Identities=25% Similarity=0.287 Sum_probs=17.4
Q ss_pred chhHHHhHHHHHhhCCCCEE
Q 035100 7 PLEILLHLPLLAEDKNVPYV 26 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~ 26 (73)
+.+....+.++|+++|++++
T Consensus 203 ~~~~l~~l~~l~~~~g~~lI 222 (403)
T PRK05093 203 TPEFLQGLRELCDQHNALLI 222 (403)
T ss_pred CHHHHHHHHHHHHHcCCEEE
Confidence 44589999999999999887
No 255
>PRK03244 argD acetylornithine aminotransferase; Provisional
Probab=20.33 E-value=1.2e+02 Score=21.75 Aligned_cols=24 Identities=13% Similarity=0.108 Sum_probs=18.3
Q ss_pred chhHHHhHHHHHhhCCCCEEEeCC
Q 035100 7 PLEILLHLPLLAEDKNVPYVFVPS 30 (73)
Q Consensus 7 p~~~~~~l~~lc~~~~IP~~~v~s 30 (73)
|.+....+.++|+++|++++.=.-
T Consensus 202 ~~~~l~~l~~l~~~~~~llI~DEv 225 (398)
T PRK03244 202 PAGYLAAAREITDRHGALLVLDEV 225 (398)
T ss_pred CHHHHHHHHHHHHHcCCEEEEecc
Confidence 445688999999999998765433
No 256
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=20.25 E-value=3.3e+02 Score=19.30 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=26.9
Q ss_pred CCCCchhHHHhHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 3 ADTEPLEILLHLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 3 ~D~~p~~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
.|-........+..+++..++|+....+...|..++
T Consensus 111 ~D~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l 146 (270)
T PRK06731 111 TDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRAL 146 (270)
T ss_pred cCCCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHH
Confidence 344444467778888999999999888887877664
No 257
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=20.23 E-value=1.2e+02 Score=21.38 Aligned_cols=20 Identities=5% Similarity=-0.112 Sum_probs=17.4
Q ss_pred HHHhHHHHHhhCCCCEEEeC
Q 035100 10 ILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~ 29 (73)
.+..+..+|.+.||+++.++
T Consensus 40 ~l~~i~~~c~~lgI~~vTvY 59 (241)
T PRK14842 40 AIDRLMDASLEYGLKNISLY 59 (241)
T ss_pred HHHHHHHHHHHcCCCEEEEE
Confidence 67788999999999998775
No 258
>PF12105 SpoU_methylas_C: SpoU, rRNA methylase, C-terminal; InterPro: IPR022724 This domain is found in bacteria and is about 60 amino acids in length. It is found in association with PF00588 from PFAM. This domain has a conserved LFE sequence motif. Some members of the Pfam family SpoU_methylase, PF00588 from PFAM, carry this very distinctive sequence at their extreme C terminus. The exact function of this domain is not known. ; GO: 0009020 tRNA (guanosine-2'-O-)-methyltransferase activity; PDB: 1ZJR_A.
Probab=20.22 E-value=38 Score=18.92 Aligned_cols=16 Identities=25% Similarity=0.385 Sum_probs=0.5
Q ss_pred HHHHHhhCCCCEEEeC
Q 035100 14 LPLLAEDKNVPYVFVP 29 (73)
Q Consensus 14 l~~lc~~~~IP~~~v~ 29 (73)
+-.+|+++|.||=.+.
T Consensus 31 lA~~cr~kg~pYP~Ld 46 (57)
T PF12105_consen 31 LAKWCRRKGLPYPPLD 46 (57)
T ss_dssp H---------------
T ss_pred HHhhcccccccccccc
Confidence 5578999999994443
No 259
>PRK08156 type III secretion system protein SpaS; Validated
Probab=20.18 E-value=1.1e+02 Score=22.93 Aligned_cols=27 Identities=30% Similarity=0.218 Sum_probs=20.6
Q ss_pred hHHHhHHHHHhhCCCCEEEeCChhhHhhHh
Q 035100 9 EILLHLPLLAEDKNVPYVFVPSKQALGRAC 38 (73)
Q Consensus 9 ~~~~~l~~lc~~~~IP~~~v~sk~~LG~a~ 38 (73)
++-.++.+.++++|||++.-+ -|-|++
T Consensus 284 ~~A~~IreiA~e~~VPiven~---pLARaL 310 (361)
T PRK08156 284 QRALAVRAYAEKVGVPVVRDI---KLARRL 310 (361)
T ss_pred HHHHHHHHHHHHCCCCEeeCH---HHHHHH
Confidence 477899999999999997654 355553
No 260
>cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily. This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali
Probab=20.16 E-value=1.1e+02 Score=18.42 Aligned_cols=23 Identities=17% Similarity=0.377 Sum_probs=16.3
Q ss_pred hHHHHHhhCCCCEEEeCChhhHh
Q 035100 13 HLPLLAEDKNVPYVFVPSKQALG 35 (73)
Q Consensus 13 ~l~~lc~~~~IP~~~v~sk~~LG 35 (73)
.+.......++|++.+.+|.+|-
T Consensus 98 ~~~~~~~~~~~piiiv~NK~Dl~ 120 (164)
T cd04145 98 QILRVKDRDEFPMILVGNKADLE 120 (164)
T ss_pred HHHHHhCCCCCCEEEEeeCcccc
Confidence 34444445689999999998764
No 261
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=20.07 E-value=76 Score=22.44 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=21.2
Q ss_pred HHHhHHHHHhhCCCCEEEeCChhhHhhHhCCCCce
Q 035100 10 ILLHLPLLAEDKNVPYVFVPSKQALGRACGVTRPV 44 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~~~v~sk~~LG~a~G~~r~~ 44 (73)
+...+..+-+.-+.| .|-++||+++|++|.+
T Consensus 159 Tl~~i~~~~~~~~~~----~Taeela~~~giSRvT 189 (224)
T COG4565 159 TLQKVREALKEPDQE----LTAEELAQALGISRVT 189 (224)
T ss_pred HHHHHHHHHhCcCCc----cCHHHHHHHhCccHHH
Confidence 455555555533344 5899999999999744
No 262
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=20.07 E-value=1.1e+02 Score=14.90 Aligned_cols=16 Identities=6% Similarity=0.092 Sum_probs=11.0
Q ss_pred HHHhHHHHHhhCCCCE
Q 035100 10 ILLHLPLLAEDKNVPY 25 (73)
Q Consensus 10 ~~~~l~~lc~~~~IP~ 25 (73)
.+..+...|++.|+|.
T Consensus 5 ~v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 5 TVAELKEELKERGLST 20 (35)
T ss_dssp HHHHHHHHHHHTTS-S
T ss_pred cHHHHHHHHHHCCCCC
Confidence 3566778888888875
No 263
>PRK06931 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional
Probab=20.07 E-value=1e+02 Score=23.18 Aligned_cols=24 Identities=13% Similarity=0.272 Sum_probs=20.0
Q ss_pred CchhHHHhHHHHHhhCCCCEEEeC
Q 035100 6 EPLEILLHLPLLAEDKNVPYVFVP 29 (73)
Q Consensus 6 ~p~~~~~~l~~lc~~~~IP~~~v~ 29 (73)
.|.+....+..+|+++|+.++.=.
T Consensus 243 ~~~~yl~~lr~lc~~~g~LlI~DE 266 (459)
T PRK06931 243 APVEWLQKIREVTQKHGILLIVDE 266 (459)
T ss_pred CCHHHHHHHHHHHHHcCCEEEEec
Confidence 456799999999999999987533
Done!